/fh/fast/matsen_e/dralph/code/partis-dev/bin/partis cache-parameters --infname /fh/fast/matsen_e/data/chaim-iarc/08248_partis.yaml --print-git-commit --locus igh --parameter-dir /fh/fast/matsen_e/processed-data/partis/chaim-iarc/v1/08248 --sw-cachefname /fh/fast/matsen_e/processed-data/partis/chaim-iarc/v1/08248/sw-cache.yaml --plotdir /fh/fast/matsen_e/processed-data/partis/chaim-iarc/v1/08248/plots --debug-allele-finding --n-procs 15
  commit: a04abc73925f14fcd0125aa6ad6687154c39f590
     tag: v0.15.0  (well, 133 commits ahead of)
  note: running on a lot of sequences (238759) without setting --outfname. Which is ok, but there will be no persistent record of the results (except the parameter directory).
caching parameters
  vsearch: 186601 / 238759 v annotations (52158 failed) with 174 v genes in 15.2 sec
  removing least likely genes with total counts 186601.0
   [94mv[0m groups separated by 6 snps  (-: same group as previous kept gene)
     genes to keep              counts         removed genes (snps counts) 
        [95mh[0m[91mv[0m[95m4[0m[95m-39[0m[93m07[0m                34680           (3 174) (2  65) (4  50) (4 2.5)  [95mh[0m[91mv[0m[95m4[0m[95m-39[0m[93m01[0m [95mh[0m[91mv[0m[95m4[0m[95m-39[0m[93m06[0m [95mh[0m[91mv[0m[95m4[0m[95m-39[0m[93m02[0m [95mh[0m[91mv[0m[95m4[0m[95m-39[0m[93m05[0m       
        [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01[0m                16325           (1 573) (1 213) (2 100) (1 1.0)  [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m02[0m [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m12[0m [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m04[0m [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m08[0m       
        [95mh[0m[91mv[0m[95m4[0m[95m-38-2[0m[93m02[0m              12901           (1 314)  [95mh[0m[91mv[0m[95m4[0m[95m-38-2[0m[93m01[0m                                                        
        [95mh[0m[91mv[0m[95m1[0m[95m-2[0m[93m02[0m                 11034           (1  86) (2  74) (4 2.2)  [95mh[0m[91mv[0m[95m1[0m[95m-2[0m[93m04[0m [95mh[0m[91mv[0m[95m1[0m[95m-2[0m[93m05[0m [95mh[0m[91mv[0m[95m1[0m[95m-2[0m[93m01[0m                           
        [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01[0m                11029           (2 562) (1 138) (1  22) (1  10) (5  10) (5 0.3)  [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m08[0m [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m02[0m [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m03[0m [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m07[0m [95mh[0m[91mv[0m[95m4[0m[95m-4[0m[93m08[0m [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m04[0m     
        [95mh[0m[91mv[0m[95m4[0m[95m-61[0m[93m02[0m                 8758                                                                                      
        [95mh[0m[91mv[0m[95m3[0m[95m-23[0m[93m04[0m                 6778           (1 3962) (3  22)  [95mh[0m[91mv[0m[95m3[0m[95m-23[0m[93m01[0m [95mh[0m[91mv[0m[95m3[0m[95m-23[0m[93m02[0m                                        
        [95mh[0m[91mv[0m[95m1[0m[95m-69[0m[93m13[0m                 5838           (3 1243) (2  23) (2  13) (1 3.5) (2 2.5) (5 1.3) (3 1.0) (3 0.3)  [95mh[0m[91mv[0m[95m1[0m[95m-69[0m[93m10[0m [95mh[0m[91mv[0m[95m1[0m[95m-69[0m[93m14[0m [95mh[0m[91mv[0m[95m1[0m[95m-69[0m[93m01[0m [95mh[0m[91mv[0m[95m1[0m[95m-69[0m[93m12[0m [95mh[0m[91mv[0m[95m1[0m[95m-69[0m[93m05[0m [95mh[0m[91mv[0m[95m1[0m[95m-69[0m[93m04[0m [95mh[0m[91mv[0m[95m1[0m[95m-69[0m[93m06[0m [95mh[0m[91mv[0m[95m1[0m[95m-69[0m[93m09[0m     
        [95mh[0m[91mv[0m[95m3[0m[95m-7[0m[93m01[0m                  5239           (1  80) (1  50)  [95mh[0m[91mv[0m[95m3[0m[95m-7[0m[93m03[0m [95mh[0m[91mv[0m[95m3[0m[95m-7[0m[93m02[0m                                           
        [95mh[0m[91mv[0m[95m3[0m[95m-48[0m[93m03[0m                 4807                                                                                      
        [95mh[0m[91mv[0m[95m3[0m[95m-53[0m[93m01[0m                 4068           (5 1963) (5 397) (5  39) (2  18) (1 4.5) (3 3.0) (3 2.0)  [95mh[0m[91mv[0m[95m3[0m[95m-66[0m[93m01[0m [95mh[0m[91mv[0m[95m3[0m[95m-66[0m[93m04[0m [95mh[0m[91mv[0m[95m3[0m[95m-66[0m[93m02[0m [95mh[0m[91mv[0m[95m3[0m[95m-53[0m[93m03[0m [95mh[0m[91mv[0m[95m3[0m[95m-53[0m[93m02[0m [95mh[0m[91mv[0m[95m3[0m[95m-53[0m[93m04[0m [95mh[0m[91mv[0m[95m3[0m[95m-66[0m[93m03[0m     
        [95mh[0m[91mv[0m[95m3[0m[95m-30[0m[93m04[0m                 3571           (3 3144) (4 3124) (3 478) (4 254) (5 202) (1 122) (3 115) (1  67) (1  49) (2  43) (4  34) (2  34) (2  23) (5  19) (2  12) (4  12) (2  10) (2 8.5) (1 7.2) (2 6.0) (4 1.0) (4 0.5) (5 0.5) (2 0.3)  [95mh[0m[91mv[0m[95m3[0m[95m-30[0m[93m18[0m [95mh[0m[91mv[0m[95m3[0m[95m-33[0m[93m01[0m [95mh[0m[91mv[0m[95m3[0m[95m-30[0m[93m03[0m [95mh[0m[91mv[0m[95m3[0m[95m-33[0m[93m06[0m [95mh[0m[91mv[0m[95m3[0m[95m-33[0m[93m05[0m [95mh[0m[91mv[0m[95m3[0m[95m-30[0m[93m14[0m [95mh[0m[91mv[0m[95m3[0m[95m-30[0m[93m19[0m [95mh[0m[91mv[0m[95m3[0m[95m-30-3[0m[93m01[0m [95mh[0m[91mv[0m[95m3[0m[95m-30[0m[93m09[0m [95mh[0m[91mv[0m[95m3[0m[95m-30[0m[93m10[0m [95mh[0m[91mv[0m[95m3[0m[95m-30[0m[93m13[0m [95mh[0m[91mv[0m[95m3[0m[95m-30[0m[93m15[0m [95mh[0m[91mv[0m[95m3[0m[95m-33[0m[93m04[0m [95mh[0m[91mv[0m[95m3[0m[95m-33[0m[93m03[0m [95mh[0m[91mv[0m[95m3[0m[95m-30[0m[93m16[0m [95mh[0m[91mv[0m[95m3[0m[95m-30[0m[93m06[0m [95mh[0m[91mv[0m[95m3[0m[95m-30-3[0m[93m02[0m [95mh[0m[91mv[0m[95m3[0m[95m-30[0m[93m07[0m [95mh[0m[91mv[0m[95m3[0m[95m-30[0m[93m01[0m [95mh[0m[91mv[0m[95m3[0m[95m-30[0m[93m17[0m [95mh[0m[91mv[0m[95m3[0m[95m-30[0m[93m02[0m [95mh[0m[91mv[0m[95m3[0m[95m-30[0m[93m05[0m [95mh[0m[91mv[0m[95m3[0m[95m-30[0m[93m12[0m [95mh[0m[91mv[0m[95m3[0m[95m-30[0m[93m11[0m     
        [95mh[0m[91mv[0m[95m1[0m[95m-8[0m[93m02[0m                  3496           (1 254)  [95mh[0m[91mv[0m[95m1[0m[95m-8[0m[93m01[0m                                                           
        [95mh[0m[91mv[0m[95m3[0m[95m-21[0m[93m01[0m                 3321           (1 253) (1  35) (1 3.8)  [95mh[0m[91mv[0m[95m3[0m[95m-21[0m[93m02[0m [95mh[0m[91mv[0m[95m3[0m[95m-21[0m[93m04[0m [95mh[0m[91mv[0m[95m3[0m[95m-21[0m[93m03[0m                        
        [95mh[0m[91mv[0m[95m1[0m[95m-18[0m[93m01[0m                 2892           (1  17) (1  16)  [95mh[0m[91mv[0m[95m1[0m[95m-18[0m[93m04[0m [95mh[0m[91mv[0m[95m1[0m[95m-18[0m[93m03[0m                                         
        [95mh[0m[91mv[0m[95m1[0m[95m-46[0m[93m01[0m                 2865           (1 203) (0  88)  [95mh[0m[91mv[0m[95m1[0m[95m-46[0m[93m02[0m [95mh[0m[91mv[0m[95m1[0m[95m-46[0m[93m03[0m                                         
        [95mh[0m[91mv[0m[95m4[0m[95m-4[0m[93m02[0m                  2709           (2 3.7)  [95mh[0m[91mv[0m[95m4[0m[95m-4[0m[93m01[0m                                                           
        [95mh[0m[91mv[0m[95m3[0m[95m-74[0m[93m01[0m                 2472           (2 754) (1  11)  [95mh[0m[91mv[0m[95m3[0m[95m-74[0m[93m03[0m [95mh[0m[91mv[0m[95m3[0m[95m-74[0m[93m02[0m                                         
        [95mh[0m[91mv[0m[95m4[0m[95m-30-2[0m[93m01[0m               2443           (1  61) (4 1.8) (1 1.5)  [95mh[0m[91mv[0m[95m4[0m[95m-30-2[0m[93m06[0m [95mh[0m[91mv[0m[95m4[0m[95m-30-2[0m[93m05[0m [95mh[0m[91mv[0m[95m4[0m[95m-30-2[0m[93m02[0m                  
        [95mh[0m[91mv[0m[95m5[0m[95m-51[0m[93m03[0m                 2231           (1 2162) (1 9.7) (3 3.2)  [95mh[0m[91mv[0m[95m5[0m[95m-51[0m[93m01[0m [95mh[0m[91mv[0m[95m5[0m[95m-51[0m[93m04[0m [95mh[0m[91mv[0m[95m5[0m[95m-51[0m[93m02[0m                       
        [95mh[0m[91mv[0m[95m6[0m[95m-1[0m[93m01[0m                  2215           (1 6.0)  [95mh[0m[91mv[0m[95m6[0m[95m-1[0m[93m02[0m                                                           
        [95mh[0m[91mv[0m[95m1[0m[95m-24[0m[93m01[0m                 1984                                                                                      
        [95mh[0m[91mv[0m[95m2[0m[95m-5[0m[93m01[0m                  1849           (1  41) (1  12) (2 4.2) (3 1.0) (3 1.0)  [95mh[0m[91mv[0m[95m2[0m[95m-5[0m[93m02[0m [95mh[0m[91mv[0m[95m2[0m[95m-5[0m[93m04[0m [95mh[0m[91mv[0m[95m2[0m[95m-5[0m[93m05[0m [95mh[0m[91mv[0m[95m2[0m[95m-5[0m[93m09[0m [95mh[0m[91mv[0m[95m2[0m[95m-5[0m[93m06[0m     
        [95mh[0m[91mv[0m[95m4[0m[95m-31[0m[93m03[0m                 1414           (1 2.0) (5 1.8) (1 1.5)  [95mh[0m[91mv[0m[95m4[0m[95m-31[0m[93m01[0m [95mh[0m[91mv[0m[95m4[0m[95m-30-4[0m[93m01[0m [95mh[0m[91mv[0m[95m4[0m[95m-31[0m[93m02[0m                      
        [95mh[0m[91mv[0m[95m4[0m[95m-30-4[0m[93m07[0m               1210                                                                                      
        [95mh[0m[91mv[0m[95m3[0m[95m-15[0m[93m01[0m                 1047           (1  35) (2  31) (1  21) (1  11) (3 6.7)  [95mh[0m[91mv[0m[95m3[0m[95m-15[0m[93m02[0m [95mh[0m[91mv[0m[95m3[0m[95m-15[0m[93m06[0m [95mh[0m[91mv[0m[95m3[0m[95m-15[0m[93m05[0m [95mh[0m[91mv[0m[95m3[0m[95m-15[0m[93m04[0m [95mh[0m[91mv[0m[95m3[0m[95m-15[0m[93m07[0m     
        [95mh[0m[91mv[0m[95m3[0m[95m-9[0m[93m03[0m                   967           (1  82)  [95mh[0m[91mv[0m[95m3[0m[95m-9[0m[93m01[0m                                                           
        [95mh[0m[91mv[0m[95m3[0m[95m-49[0m[93m04[0m                  826           (1 3.5) (2 2.0) (4 1.0)  [95mh[0m[91mv[0m[95m3[0m[95m-49[0m[93m03[0m [95mh[0m[91mv[0m[95m3[0m[95m-49[0m[93m05[0m [95mh[0m[91mv[0m[95m3[0m[95m-49[0m[93m02[0m                        
        [95mh[0m[91mv[0m[95m1[0m[95m-69-2[0m[93m01[0m                702                                                                                      
        [95mh[0m[91mv[0m[95m3[0m[95m-64[0m[93m01[0m                  498           (2 6.5)  [95mh[0m[91mv[0m[95m3[0m[95m-64[0m[93m02[0m                                                          
        [95mh[0m[91mv[0m[95m4[0m[95m-61[0m[93m08[0m                  467           (1 280) (2 123)  [95mh[0m[91mv[0m[95m4[0m[95m-61[0m[93m01[0m [95mh[0m[91mv[0m[95m4[0m[95m-61[0m[93m03[0m                                         
        [95mh[0m[91mv[0m[95m3[0m[95m-43[0m[93m01[0m                  464           (4 3.0)  [95mh[0m[91mv[0m[95m3[0m[95m-43[0m[93m02[0m                                                          
        [95mh[0m[91mv[0m[95m2[0m[95m-26[0m[93m01[0m                  384                                                                                      
        [95mh[0m[91mv[0m[95m3[0m[95m-73[0m[93m02[0m                  320           (1 5.5)  [95mh[0m[91mv[0m[95m3[0m[95m-73[0m[93m01[0m                                                          
        [95mh[0m[91mv[0m[95m3[0m[95m-72[0m[93m01[0m                  313                                                                                      
        [95mh[0m[91mv[0m[95m3[0m[95m-11[0m[93m04[0m                  295           (1 4.0)  [95mh[0m[91mv[0m[95m3[0m[95m-11[0m[93m01[0m                                                          
        [95mh[0m[91mv[0m[95m2[0m[95m-70[0m[93m10[0m                  283           (4 260) (4 253) (5  22) (5 1.5)  [95mh[0m[91mv[0m[95m2[0m[95m-70[0m[93m11[0m [95mh[0m[91mv[0m[95m2[0m[95m-70[0m[93m01[0m [95mh[0m[91mv[0m[95m2[0m[95m-70[0m[93m13[0m [95mh[0m[91mv[0m[95m2[0m[95m-70[0m[93m12[0m       
        [95mh[0m[91mv[0m[95m1[0m[95m-58[0m[93m02[0m                  220           (1 9.0)  [95mh[0m[91mv[0m[95m1[0m[95m-58[0m[93m01[0m                                                          
        [95mh[0m[91mv[0m[95m3[0m[95m-20[0m[93m01[0m                  194                                                                                      
        [94mnone[0m                        -               (0  65) (1 2.8) (1 0.8)  [95mh[0m[91mv[0m[95m4[0m[95m-28[0m[93m07[0m [95mh[0m[91mv[0m[95m4[0m[95m-28[0m[93m01[0m [95mh[0m[91mv[0m[95m4[0m[95m-28[0m[93m03[0m                        
        [94mnone[0m                        -               (0  64) (2  24) (3 0.3)  [95mh[0m[91mv[0m[95m3[0m[95m-13[0m[93m03[0m [95mh[0m[91mv[0m[95m3[0m[95m-13[0m[93m01[0m [95mh[0m[91mv[0m[95m3[0m[95m-13[0m[93m04[0m                        
        [94mnone[0m                        -               (0  56) (1 6.0) (1 0.5)  [95mh[0m[91mv[0m[95m7[0m[95m-4-1[0m[93m02[0m [95mh[0m[91mv[0m[95m7[0m[95m-4-1[0m[93m01[0m [95mh[0m[91mv[0m[95m7[0m[95m-4-1[0m[93m04[0m                     
        [94mnone[0m                        -               (0  55)  [95mh[0m[91mv[0m[95m1[0m[95m-3[0m[93m02[0m                                                           
        [94mnone[0m                        -               (0  24)  [95mh[0m[91mv[0m[95m4[0m[95m-61[0m[93m05[0m                                                          
        [94mnone[0m                        -               (0  23)  [95mh[0m[91mv[0m[95m4[0m[95m-4[0m[93m07[0m                                                           
        [94mnone[0m                        -               (0  15) (3 3.7)  [95mh[0m[91mv[0m[95m3[0m[95m-23[0m[93m05[0m [95mh[0m[91mv[0m[95m3[0m[95m-23[0m[93m03[0m                                         
        [94mnone[0m                        -               (0  10)  [95mh[0m[91mv[0m[95m1[0m[95m-45[0m[93m02[0m                                                          
        [94mnone[0m                        -               (0 9.7)  [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m10[0m                                                          
        [94mnone[0m                        -               (0 5.8) (2 4.3) (1 3.3)  [95mh[0m[91mv[0m[95m3[0m[95m-48[0m[93m04[0m [95mh[0m[91mv[0m[95m3[0m[95m-48[0m[93m02[0m [95mh[0m[91mv[0m[95m3[0m[95m-48[0m[93m01[0m                        
        [94mnone[0m                        -               (0 4.5)  [95mh[0m[91mv[0m[95m3[0m[95m-11[0m[93m06[0m                                                          
        [94mnone[0m                        -               (0 3.6)  [95mh[0m[91mv[0m[95m4[0m[95m-30-4[0m[93m02[0m                                                        
        [94mnone[0m                        -               (0 3.3)  [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m11[0m                                                          
        [94mnone[0m                        -               (0 3.2)  [95mh[0m[91mv[0m[95m4[0m[95m-30-2[0m[93m03[0m                                                        
        [94mnone[0m                        -               (0 3.1)  [95mh[0m[91mv[0m[95m4[0m[95m-31[0m[93m05[0m                                                          
        [94mnone[0m                        -               (0 3.0)  [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m10[0m                                                          
        [94mnone[0m                        -               (0 1.7)  [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m09[0m                                                          
        [94mnone[0m                        -               (0 1.0)  [95mh[0m[91mv[0m[95m3[0m[95m-NL1[0m[93m01[0m                                                         
        [94mnone[0m                        -               (0 1.0)  [95mh[0m[91mv[0m[95m3[0m[95m-15[0m[93m03[0m                                                          
    keeping 39 / 204 v genes
smith-waterman  (new-allele fitting)
  vsearch: 186583 / 238759 v annotations (52176 failed) with 39 v genes in 49.2 sec
    running 15 procs for 238759 seqs
    running 18 procs for 95331 seqs
      info for 181692 / 238759 = 0.761   (57067 failed)
  [91mwarning[0m smith-waterman step failed to find alignments for a large fraction of input sequences (see previous line)   [91mnote:[0m maybe need to take reverse complement? (partis only searches in forward direction)
      kept 89351 (0.374) unproductive
      removed 4324 / 181692 = 0.02 duplicate sequences after trimming framework insertions (leaving 177368)
    water time: 724.7  (ig-sw 240.6  processing 147.2)
allele finding
    excluding 19 / 39 genes whose reads are too short (adjust with --min-allele-finding-gene-length) 
                        total   clones    representatives
      [95mh[0m[91mv[0m[95m1[0m[95m-46[0m[93m01[0m          2698    1815      2034
      [95mh[0m[91mv[0m[95m1[0m[95m-69[0m[93m13[0m          5096    3776      4326
      [95mh[0m[91mv[0m[95m1[0m[95m-8[0m[93m02[0m           2397    1842      1842
      [95mh[0m[91mv[0m[95m2[0m[95m-5[0m[93m01[0m           1878     974      1533
      [95mh[0m[91mv[0m[95m2[0m[95m-70[0m[93m10[0m           704     357       357
      [95mh[0m[91mv[0m[95m3[0m[95m-21[0m[93m01[0m          3228    1796      2470
      [95mh[0m[91mv[0m[95m3[0m[95m-23[0m[93m04[0m          9642    4942      5994
      [95mh[0m[91mv[0m[95m3[0m[95m-48[0m[93m03[0m          4399    2491      3025
      [95mh[0m[91mv[0m[95m3[0m[95m-49[0m[93m04[0m           808     392       549
      [95mh[0m[91mv[0m[95m3[0m[95m-53[0m[93m01[0m          5893    3038      3582
      [95mh[0m[91mv[0m[95m3[0m[95m-7[0m[93m01[0m           4849    2921      3345
      [95mh[0m[91mv[0m[95m3[0m[95m-74[0m[93m01[0m          2826    1439      1509
      [95mh[0m[91mv[0m[95m4[0m[95m-30-2[0m[93m01[0m        2428    1360      2045
      [95mh[0m[91mv[0m[95m4[0m[95m-31[0m[93m03[0m          1384     760      1099
      [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01[0m         16563    6846     12038
      [95mh[0m[91mv[0m[95m4[0m[95m-39[0m[93m07[0m         32812   14423     21224
      [95mh[0m[91mv[0m[95m4[0m[95m-4[0m[93m02[0m           2487    1071      1629
      [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01[0m         11752    5290      7564
      [95mh[0m[91mv[0m[95m4[0m[95m-61[0m[93m02[0m          8367    4055      5587
      [95mh[0m[91mv[0m[95m5[0m[95m-51[0m[93m03[0m          4278    2703      2937
    84689 seqs chosen to represent 62291 clones with 124489 total seqs
   v mutations:
                    0      1      2      3      4      5      6      7      8      9     10     11     12     13     14     15     16     17     18     19     20     21     22     23
                  772    184     36     87     50     72    179    119     57     33     54     35     53     34     61     18     26     30      8      5     82     30      5      4     [95mh[0m[91mv[0m[95m1[0m[95m-46[0m[93m01[0m
                 1892   1269    177    444     66     32     34     77     40     18     74     71     28     21     15      9      2     13     16     11      8      5      3      1     [95mh[0m[91mv[0m[95m1[0m[95m-69[0m[93m13[0m
                    0   1077    180     37     55     44     34     39     33     21     17     34     35     84     22     21     10     30     36      5      8     10      7      3     [95mh[0m[91mv[0m[95m1[0m[95m-8[0m[93m02[0m
                  950    250     38     39     25     31     34     17     49     14     17     10     10     10      9     15      3      3      0      2      0      3      3      1     [95mh[0m[91mv[0m[95m2[0m[95m-5[0m[93m01[0m
                    0      0    111     43     24     38     24     27     24      9     11      9     11      7      8      2      3      2      1      2      1      0      0      0     [95mh[0m[91mv[0m[95m2[0m[95m-70[0m[93m10[0m
                 1199    338     65     77     59     72     41     71     60     71     73     57     37     36     41     32     73     18     10      9     15      5      3      8     [95mh[0m[91mv[0m[95m3[0m[95m-21[0m[93m01[0m
                 1714   1288    161    106    106    140    152    143    208    186    161    169    184    200    180    115    120    121    103    102    104     88     77     66     [95mh[0m[91mv[0m[95m3[0m[95m-23[0m[93m04[0m
                 1156    301     97    128    126    147    108     83     91    110    113    119     62     70     26     50     62     18     29     67     14     22      3     23     [95mh[0m[91mv[0m[95m3[0m[95m-48[0m[93m03[0m
                  277     43     21     20     19      5     20     22     15     15     12     23      7      1     12     10      5     15      2      0      1      1      0      3     [95mh[0m[91mv[0m[95m3[0m[95m-49[0m[93m04[0m
                  981    298     84     41    136    450    203    123     90     98     98     78    101    109    172     69    109     67     74     70     40     25     53     13     [95mh[0m[91mv[0m[95m3[0m[95m-53[0m[93m01[0m
                 1037    221    145    121    160    116    189    165    176    216    157    117    119     61     96     87     31     39     20     13      8     25     17      9     [95mh[0m[91mv[0m[95m3[0m[95m-7[0m[93m01[0m
                  256     59     43     51     47     71     62     36    100    113     61     52     68     92     89     50     74     72     37     20     21     18      8      9     [95mh[0m[91mv[0m[95m3[0m[95m-74[0m[93m01[0m
                 1331    336     68     37     30     22     25     27     20     15     15     16     22     20     10      7     10      6      5      3     11      3      5      1     [95mh[0m[91mv[0m[95m4[0m[95m-30-2[0m[93m01[0m
                  736    115     26     23     24     15     35     22      4     13     14     12      2      8      7     13      6      5      7      8      0      1      3      0     [95mh[0m[91mv[0m[95m4[0m[95m-31[0m[93m03[0m
                 6954   2269    510    305    378    296    250    166    134     86    134     95     86     64     61     46     49     53     32     14     13     14     13     16     [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01[0m
                11461   3072    631    387    437    398    380    333    392    388    390    454    357    265    276    388    194    231    163    183    156     89     96    103     [95mh[0m[91mv[0m[95m4[0m[95m-39[0m[93m07[0m
                  955    214     39     33     34     38     23     18     23     54     20     27     23     10     14     15     11     11     16     25     15      1      9      1     [95mh[0m[91mv[0m[95m4[0m[95m-4[0m[93m02[0m
                 3948   1427    180     83    142    115    112    121    117    113    125    124    139    134    122     95     62    107    103     60     48     25     40     22     [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01[0m
                 2908    774    165    127    168    110    108    165    159    103     93     87    105     80     99     81     49     33     34     48     31     23     24     13     [95mh[0m[91mv[0m[95m4[0m[95m-61[0m[93m02[0m
                  671    567    178    174    149    232    162    162    154     94     78     66     48     77     39      9     27     17      9     13      4      1      3      3     [95mh[0m[91mv[0m[95m5[0m[95m-51[0m[93m03[0m
   sequence counts:
                 excluded             excluded                 excluded             included                       actually
              >23 mutations       5p del (>N bases)        3p del (>N bases)       total seqs        clones          used
                    49                8    (0)                27  (39)               2698             1815           2034      [95mh[0m[91mv[0m[95m1[0m[95m-46[0m[93m01[0m
                    55                9    (0)                42   (8)               5096             3776           4326      [95mh[0m[91mv[0m[95m1[0m[95m-69[0m[93m13[0m
                   177                7    (0)                21  (27)               2397             1842           1842      [95mh[0m[91mv[0m[95m1[0m[95m-8[0m[93m02[0m
                    34                4   (37)                17  (36)               1878              974           1533      [95mh[0m[91mv[0m[95m2[0m[95m-5[0m[93m01[0m
                    25                7   (21)                 7  (71)                704              357            357      [95mh[0m[91mv[0m[95m2[0m[95m-70[0m[93m10[0m
                    97               10    (0)                13   (7)               3228             1796           2470      [95mh[0m[91mv[0m[95m3[0m[95m-21[0m[93m01[0m
                   848               13    (0)                84   (8)               9642             4942           5994      [95mh[0m[91mv[0m[95m3[0m[95m-23[0m[93m04[0m
                   130               44    (8)                 2  (101)               4399             2491           3025      [95mh[0m[91mv[0m[95m3[0m[95m-48[0m[93m03[0m
                    22                2   (39)                 8  (37)                808              392            549      [95mh[0m[91mv[0m[95m3[0m[95m-49[0m[93m04[0m
                   352                3    (0)                57  (10)               5893             3038           3582      [95mh[0m[91mv[0m[95m3[0m[95m-53[0m[93m01[0m
                   224               18    (0)                40  (99)               4849             2921           3345      [95mh[0m[91mv[0m[95m3[0m[95m-7[0m[93m01[0m
                   325                9    (0)                12  (59)               2826             1439           1509      [95mh[0m[91mv[0m[95m3[0m[95m-74[0m[93m01[0m
                    19                0    (0)                21   (8)               2428             1360           2045      [95mh[0m[91mv[0m[95m4[0m[95m-30-2[0m[93m01[0m
                    21                9   (82)                 8  (23)               1384              760           1099      [95mh[0m[91mv[0m[95m4[0m[95m-31[0m[93m03[0m
                   318                2    (0)               154   (6)              16563             6846          12038      [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01[0m
                  1424               12    (0)               320   (7)              32812            14423          21224      [95mh[0m[91mv[0m[95m4[0m[95m-39[0m[93m07[0m
                   220                3    (0)                27  (39)               2487             1071           1629      [95mh[0m[91mv[0m[95m4[0m[95m-4[0m[93m02[0m
                   466                3    (0)               110   (6)              11752             5290           7564      [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01[0m
                   249                5    (0)                65   (6)               8367             4055           5587      [95mh[0m[91mv[0m[95m4[0m[95m-61[0m[93m02[0m
                    77               25   (29)                44  (65)               4278             2703           2937      [95mh[0m[91mv[0m[95m5[0m[95m-51[0m[93m03[0m
[94mtry 0[0m: looking for new alleles among 20 genes (0 genes didn't have enough counts)
 [95mh[0m[91mv[0m[95m1[0m[95m-46[0m[93m01[0m              2034 counts
             position   ratio       (one piece / two pieces)              0          1          2          3          4          5          6          7          8          9         10         11         12         13         14         15         16         17         18         19         20         21         22         23
    6 snps
                 [93m101[0m     3.61              10. / 2.84                   0 / 772    2 / 184    2 / 36     4 / 87     0 / 50    10 / 72    79 / 179   54 / 119   26 / 57    11 / 33    16 / 54     8 / 35    27 / 53     9 / 34    32 / 61     3 / 18                                                                                          
                 [93m196[0m     2.91             5.27 / 1.81                   0 / 772    4 / 184    0 / 36     1 / 87     0 / 50     0 / 72    33 / 179   29 / 119    4 / 57     4 / 33     9 / 54     6 / 35     3 / 53     0 / 34     3 / 61     1 / 18                                                                                          
                  99     1.86             2.70 / 1.45                   0 / 772    0 / 184    0 / 36     0 / 87     0 / 50     3 / 72    27 / 179   12 / 119   10 / 57     0 / 33     4 / 54     4 / 35     3 / 53     1 / 34     8 / 61     2 / 18                                                                                          
                 251     1.05             3.49 / 3.33                   0 / 772    0 / 184    0 / 36     0 / 87     3 / 50     0 / 72    30 / 179    6 / 119    0 / 57     0 / 33     0 / 54     0 / 35     1 / 53     9 / 34     4 / 61     0 / 18                                                                                          
                 207     0.93             3.81 / 4.10                   0 / 772    0 / 184    0 / 36     0 / 87     0 / 50     0 / 72    13 / 179    5 / 119    0 / 57     0 / 33     0 / 54     0 / 35     0 / 53     0 / 34    25 / 61     1 / 18                                                                                          
                  38     0.90             3.36 / 3.72                   0 / 772    0 / 184    0 / 36     0 / 87     0 / 50     1 / 72    16 / 179    2 / 119    0 / 57     0 / 33     0 / 54     0 / 35     0 / 53     0 / 34    22 / 61     0 / 18                                                                                          
   snps       min ratio
    6          0.90     min snp ratio 0.90 too small (less than 2.25) 
 [95mh[0m[91mv[0m[95m1[0m[95m-69[0m[93m13[0m              4326 counts
             position   ratio       (one piece / two pieces)              0          1          2          3          4          5          6          7          8          9         10         11         12         13         14         15         16         17         18         19         20         21         22         23
    3 snps
                 [93m169[0m      26.             459. / 18.                    0 / 1892   2 / 1269   6 / 177  411 / 444   42 / 66     5 / 32     8 / 34    44 / 77    31 / 40     6 / 18    27 / 74    32 / 71     3 / 28                                                                                                                           
                 [93m219[0m      24.             425. / 18.                    0 / 1892   3 / 1269   1 / 177  409 / 444   48 / 66     6 / 32     7 / 34    44 / 77    11 / 40     3 / 18    26 / 74    43 / 71     4 / 28                                                                                                                           
                 [93m162[0m      20.             478. / 24.                    0 / 1892   0 / 1269   9 / 177  411 / 444   42 / 66     5 / 32     6 / 34    43 / 77    10 / 40     1 / 18    24 / 74    41 / 71     4 / 28                                                                                                                           
    7 snps
                 [93m155[0m     2.32             2.74 / 1.18                   0 / 1892   1 / 1269   0 / 177    0 / 444    0 / 66     2 / 32     0 / 34    14 / 77     3 / 40     0 / 18     5 / 74    14 / 71     2 / 28     0 / 21     0 / 15     0 / 9      0 / 2                                                                                
                 206     1.46             3.89 / 2.66                   0 / 1892   1 / 1269   3 / 177    0 / 444    0 / 66     0 / 32     0 / 34    11 / 77     2 / 40     1 / 18     7 / 74     3 / 71     1 / 28    10 / 21     7 / 15     2 / 9      0 / 2                                                                                
                 224     1.32             2.57 / 1.94                   0 / 1892   0 / 1269   0 / 177    0 / 444    0 / 66     0 / 32     0 / 34    23 / 77     2 / 40     2 / 18     0 / 74     2 / 71     0 / 28     0 / 21     0 / 15     1 / 9      0 / 2                                                                                
                 159     1.19             2.81 / 2.35                   0 / 1892   0 / 1269   0 / 177    0 / 444    0 / 66     0 / 32     0 / 34    14 / 77     3 / 40     0 / 18     3 / 74     0 / 71     3 / 28     7 / 21     1 / 15     2 / 9      1 / 2                                                                                
                 166     1.02             2.96 / 2.91                   0 / 1892   0 / 1269   0 / 177    0 / 444    0 / 66     0 / 32     0 / 34    23 / 77     0 / 40     2 / 18     0 / 74     1 / 71     0 / 28     0 / 21     5 / 15     1 / 9      0 / 2                                                                                
                 149     1.01             2.80 / 2.77                   0 / 1892   3 / 1269   1 / 177    0 / 444    0 / 66     0 / 32     0 / 34    12 / 77     2 / 40     0 / 18     0 / 74     3 / 71     7 / 28     2 / 21     7 / 15     1 / 9      0 / 2                                                                                
                 201     0.99             2.82 / 2.85                   0 / 1892   4 / 1269   1 / 177    0 / 444    1 / 66     0 / 32     0 / 34    14 / 77     4 / 40     0 / 18     1 / 74     0 / 71     2 / 28     0 / 21     7 / 15     1 / 9      1 / 2                                                                                
   snps       min ratio
    3           20.     candidate 
    7          0.99     min snp ratio 0.99 too small (less than 2.25) 
        exact sequence in glfo under name [95mh[0m[91mv[0m[95m1[0m[95m-69[0m[93m10[0m
  [91mnew[0m [95mh[0m[91mv[0m[95m1[0m[95m-69[0m[93m10[0m separated from [95mh[0m[91mv[0m[95m1[0m[95m-69[0m[93m13[0m by 3 snps at:   162 (T --> C)  169 (C --> T)  219 (G --> A)
 [95mh[0m[91mv[0m[95m1[0m[95m-8[0m[93m02[0m               1842 counts
             position   ratio       (one piece / two pieces)              0          1          2          3          4          5          6          7          8          9         10         11         12         13         14         15         16         17         18         19         20         21         22         23
    1 snp
                 [93m209[0m    2e+05            6e+04 / 0.31                   0 / 0   1077 / 1077 180 / 180   37 / 37    55 / 55    43 / 44    32 / 34    39 / 39    33 / 33    21 / 21    17 / 17                                                                                                                                                 
   snps       min ratio
    1         2e+05     candidate 
        no equivalent gene for [95mh[0m[91mv[0m[95m1[0m[95m-8[0m[93m02+G209T[0m       nearest is [95mh[0m[91mv[0m[95m1[0m[95m-8[0m[93m02[0m (1 snp, 0 indels):
            CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCAGCTATGATATCAACTGGGTGCGACAGGCCACTGGACAAGGGCTTGAGTGGATGGGATGGATGAACCCTAACAGTGGTAACACAGGCTATGCACAGAAGTTCCAGGGCAGAGTCACCAT[91mG[0mACCAGGAACACCTCCATAAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGG [95mh[0m[91mv[0m[95m1[0m[95m-8[0m[93m02+G209T[0m
            CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCAGCTATGATATCAACTGGGTGCGACAGGCCACTGGACAAGGGCTTGAGTGGATGGGATGGATGAACCCTAACAGTGGTAACACAGGCTATGCACAGAAGTTCCAGGGCAGAGTCACCATTACCAGGAACACCTCCATAAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGG [95mh[0m[91mv[0m[95m1[0m[95m-8[0m[93m02[0m
  [91mnew[0m [95mh[0m[91mv[0m[95m1[0m[95m-8[0m[93m02+G209T[0m separated from [95mh[0m[91mv[0m[95m1[0m[95m-8[0m[93m02[0m by 1 snp at:   209 (G --> T)
 [95mh[0m[91mv[0m[95m2[0m[95m-5[0m[93m01[0m               1533 counts
 [95mh[0m[91mv[0m[95m2[0m[95m-70[0m[93m10[0m              357 counts
             position   ratio       (one piece / two pieces)              0          1          2          3          4          5          6          7          8          9         10         11         12         13         14         15         16         17         18         19         20         21         22         23
    2 snps
                 [93m147[0m    2e+04             576. / 0.03                   0 / 0      0 / 0    110 / 111   43 / 43    24 / 24    38 / 38    24 / 24    27 / 27    24 / 24     9 / 9     11 / 11     9 / 9                                                                                                                                       
                 [93m102[0m      15.              13. / 0.86                   0 / 0      0 / 0     74 / 111   22 / 43    17 / 24    25 / 38    16 / 24    22 / 27    19 / 24     8 / 9      8 / 11     8 / 9                                                                                                                                       
   snps       min ratio
    2           15.     candidate 
        [94mequivalent[0m gene [95mh[0m[91mv[0m[95m2[0m[95m-70[0m[93m11[0m with same cpos in glfo for [95mh[0m[91mv[0m[95m2[0m[95m-70[0m[93m10+C102T.A147C[0m (blue bases are not considered):
            [94mCAGGTCACCTTGAAGGAGTCT[0mGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACGCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTAC[7mTGT[0m[94mAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC[0m   [95mh[0m[91mv[0m[95m2[0m[95m-70[0m[93m10+C102T.A147C[0m
            [94mCGGGTCACCTTGAGGGAGTCT[0mGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACGCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTAC[7mTGT[0m[94mAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC[0m   [95mh[0m[91mv[0m[95m2[0m[95m-70[0m[93m11[0m
  [91mnew[0m [95mh[0m[91mv[0m[95m2[0m[95m-70[0m[93m11[0m separated from [95mh[0m[91mv[0m[95m2[0m[95m-70[0m[93m10[0m by 2 snps at:   102 (C --> T)  147 (A --> C)
 [95mh[0m[91mv[0m[95m3[0m[95m-21[0m[93m01[0m              2470 counts
 [95mh[0m[91mv[0m[95m3[0m[95m-23[0m[93m04[0m              5994 counts
             position   ratio       (one piece / two pieces)              0          1          2          3          4          5          6          7          8          9         10         11         12         13         14         15         16         17         18         19         20         21         22         23
    1 snp
                 [93m 12[0m      21.             175. / 8.13                   0 / 1714 733 / 1288  86 / 161   23 / 106   42 / 106   58 / 140   42 / 152   43 / 143   76 / 208   54 / 186   47 / 161                                                                                                                                                
    3 snps
                 [93m148[0m      37.              76. / 2.08                   0 / 1714   0 / 1288   7 / 161   30 / 106   43 / 106   49 / 140   66 / 152   63 / 143  105 / 208   82 / 186   68 / 161   80 / 169   81 / 184                                                                                                                          
                 [93m234[0m     3.41             6.07 / 1.78                   0 / 1714   0 / 1288   0 / 161   11 / 106    3 / 106    5 / 140    9 / 152   22 / 143   12 / 208   17 / 186   15 / 161   14 / 169   19 / 184                                                                                                                          
                 152     2.24             2.56 / 1.14                   0 / 1714   0 / 1288   0 / 161    9 / 106    2 / 106    4 / 140    8 / 152    4 / 143    7 / 208    5 / 186    7 / 161   14 / 169    9 / 184                                                                                                                          
   snps       min ratio
    1           21.     candidate 
    3          2.24     min snp ratio 2.24 too small (less than 2.25) 
        exact sequence in glfo under name [95mh[0m[91mv[0m[95m3[0m[95m-23[0m[93m01[0m
  [91mnew[0m [95mh[0m[91mv[0m[95m3[0m[95m-23[0m[93m01[0m separated from [95mh[0m[91mv[0m[95m3[0m[95m-23[0m[93m04[0m by 1 snp at:   12 (G --> T)
 [95mh[0m[91mv[0m[95m3[0m[95m-48[0m[93m03[0m              3025 counts
             position   ratio       (one piece / two pieces)              0          1          2          3          4          5          6          7          8          9         10         11         12         13         14         15         16         17         18         19         20         21         22         23
    4 snps
                 [93m172[0m     2.66             4.06 / 1.53                   0 / 1156   0 / 301    0 / 97     4 / 128   17 / 126   14 / 147   14 / 108   11 / 83    18 / 91    22 / 110   27 / 113   24 / 119   13 / 62    31 / 70                                                                                                                
                  90     1.11             4.50 / 4.04                   0 / 1156   0 / 301    3 / 97     4 / 128   22 / 126   19 / 147    4 / 108   12 / 83    16 / 91     6 / 110    8 / 113   12 / 119    4 / 62    19 / 70                                                                                                                
                  83     1.02             2.17 / 2.13                   0 / 1156   2 / 301    1 / 97     2 / 128   15 / 126   11 / 147    3 / 108   10 / 83     7 / 91     9 / 110   13 / 113   19 / 119   17 / 62    13 / 70                                                                                                                
                  17     0.87             3.38 / 3.90                   0 / 1156   2 / 301    0 / 97     1 / 128   16 / 126    2 / 147    0 / 108    5 / 83     2 / 91     0 / 110    7 / 113   11 / 119    8 / 62     0 / 70                                                                                                                
   snps       min ratio
    4          0.87     min snp ratio 0.87 too small (less than 2.25) 
 [95mh[0m[91mv[0m[95m3[0m[95m-49[0m[93m04[0m              549 counts
 [95mh[0m[91mv[0m[95m3[0m[95m-53[0m[93m01[0m              3582 counts
             position   ratio       (one piece / two pieces)              0          1          2          3          4          5          6          7          8          9         10         11         12         13         14         15         16         17         18         19         20         21         22         23
    5 snps
                 [93m 23[0m     5.66             162. / 29.                    0 / 981    2 / 298    0 / 84     0 / 41     3 / 136  395 / 450   90 / 203   34 / 123   29 / 90    40 / 98    44 / 98    17 / 78    41 / 101   44 / 109   71 / 172                                                                                                    
                 [93m 77[0m     5.51             142. / 26.                    0 / 981    0 / 298    2 / 84     2 / 41     8 / 136  394 / 450   93 / 203   41 / 123   33 / 90    43 / 98    46 / 98    20 / 78    63 / 101   62 / 109   91 / 172                                                                                                    
                 [93m 33[0m     5.47             159. / 29.                    0 / 981    0 / 298    0 / 84     0 / 41     7 / 136  395 / 450   92 / 203   32 / 123   28 / 90    43 / 98    44 / 98    19 / 78    42 / 101   41 / 109   74 / 172                                                                                                    
                 [93m272[0m     5.43             159. / 29.                    0 / 981    0 / 298    1 / 84     0 / 41     5 / 136  394 / 450   92 / 203   32 / 123   26 / 90    41 / 98    44 / 98    18 / 78    41 / 101   44 / 109   69 / 172                                                                                                    
                 [93m195[0m     5.17             151. / 29.                    0 / 981    3 / 298    0 / 84     0 / 41     6 / 136  394 / 450   92 / 203   32 / 123   27 / 90    41 / 98    44 / 98    17 / 78    41 / 101   44 / 109   69 / 172                                                                                                    
   snps       min ratio
    5          5.17     candidate 
        exact sequence in glfo under name [95mh[0m[91mv[0m[95m3[0m[95m-66[0m[93m01[0m
  [91mnew[0m [95mh[0m[91mv[0m[95m3[0m[95m-66[0m[93m01[0m separated from [95mh[0m[91mv[0m[95m3[0m[95m-53[0m[93m01[0m by 5 snps at:   23 (A --> G)  33 (A --> G)  77 (G --> A)  195 (C --> A)  272 (C --> T)
 [95mh[0m[91mv[0m[95m3[0m[95m-7[0m[93m01[0m               3345 counts
             position   ratio       (one piece / two pieces)              0          1          2          3          4          5          6          7          8          9         10         11         12         13         14         15         16         17         18         19         20         21         22         23
    1 snp
                   9     1.04             3.72 / 3.59                   0 / 1037  10 / 221   15 / 145    8 / 121   12 / 160   11 / 116    7 / 189   25 / 165   27 / 176   34 / 216   19 / 157                                                                                                                                                
    3 snps
                  92     1.72             7.28 / 4.24                   0 / 1037   6 / 221    3 / 145   25 / 121   43 / 160   22 / 116   60 / 189   57 / 165   80 / 176   65 / 216   70 / 157   66 / 117   40 / 119                                                                                                                          
                  82     1.38             2.73 / 1.98                   0 / 1037   3 / 221    0 / 145    9 / 121    8 / 160   16 / 116   26 / 189   23 / 165   25 / 176   20 / 216   32 / 157   20 / 117   21 / 119                                                                                                                          
                 173     1.22             3.55 / 2.92                   0 / 1037   0 / 221    1 / 145   13 / 121   15 / 160   17 / 116    9 / 189   12 / 165   29 / 176   24 / 216   17 / 157   26 / 117   22 / 119                                                                                                                          
   snps       min ratio
    1          1.04     min snp ratio 1.04 too small (less than 2.25) 
    3          1.22     min snp ratio 1.22 too small (less than 2.25) 
 [95mh[0m[91mv[0m[95m3[0m[95m-74[0m[93m01[0m              1509 counts
 [95mh[0m[91mv[0m[95m4[0m[95m-30-2[0m[93m01[0m            2045 counts
 [95mh[0m[91mv[0m[95m4[0m[95m-31[0m[93m03[0m              1099 counts
 [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01[0m              12038 counts
             position   ratio       (one piece / two pieces)              0          1          2          3          4          5          6          7          8          9         10         11         12         13         14         15         16         17         18         19         20         21         22         23
    1 snp
                 [93m270[0m     4.45             5.65 / 1.27                   0 / 6954  50 / 2269   6 / 510    3 / 305    3 / 378    1 / 296    5 / 250    0 / 166    1 / 134    0 / 86     2 / 134                                                                                                                                                
    1 snp
                 [93m116[0m     3.49             2.58 / 0.74                   0 / 6954  20 / 2269   8 / 510    4 / 305    6 / 378    6 / 296    4 / 250    3 / 166    0 / 134    1 / 86     1 / 134                                                                                                                                                
    4 snps
                 [93m227[0m     3.37              14. / 4.01                   0 / 6954   4 / 2269  15 / 510   20 / 305   52 / 378   31 / 296   27 / 250   26 / 166   28 / 134   10 / 86    29 / 134   18 / 95    11 / 86     8 / 64                                                                                                                
                 [93m131[0m     3.33              12. / 3.73                   0 / 6954  18 / 2269  13 / 510    3 / 305   89 / 378   63 / 296   30 / 250   19 / 166    8 / 134   11 / 86    16 / 134    8 / 95    10 / 86    11 / 64                                                                                                                
                 117     1.23             3.41 / 2.78                   0 / 6954  26 / 2269  13 / 510    6 / 305   24 / 378   12 / 296   18 / 250    2 / 166    6 / 134    4 / 86     7 / 134   12 / 95     3 / 86     8 / 64                                                                                                                
                 230     1.18             2.55 / 2.17                   0 / 6954  11 / 2269   6 / 510    3 / 305   23 / 378   14 / 296   11 / 250    5 / 166    5 / 134    1 / 86     9 / 134    7 / 95    16 / 86     3 / 64                                                                                                                
    5 snps
                 104     1.58             4.25 / 2.69                   0 / 6954  26 / 2269   5 / 510   14 / 305   13 / 378   43 / 296   27 / 250   26 / 166    8 / 134   18 / 86    13 / 134    9 / 95    13 / 86     5 / 64    14 / 61                                                                                                     
                  62     1.57             3.97 / 2.53                   0 / 6954   8 / 2269  13 / 510   12 / 305    7 / 378   38 / 296   18 / 250    8 / 166    7 / 134    5 / 86     5 / 134    2 / 95     6 / 86     8 / 64     4 / 61                                                                                                     
                 180     1.28             3.51 / 2.75                   0 / 6954  12 / 2269  10 / 510    2 / 305    6 / 378   23 / 296    6 / 250    2 / 166   17 / 134    3 / 86     5 / 134    1 / 95     3 / 86     0 / 64     1 / 61                                                                                                     
                 280     1.18             4.32 / 3.65                   0 / 6954   2 / 2269  14 / 510    6 / 305    4 / 378   19 / 296    6 / 250   18 / 166    4 / 134    3 / 86     4 / 134   12 / 95     5 / 86     1 / 64     7 / 61                                                                                                     
                 215     1.15             2.63 / 2.28                   0 / 6954   8 / 2269   3 / 510    2 / 305    4 / 378   22 / 296    5 / 250    0 / 166    0 / 134    0 / 86     0 / 134    2 / 95     5 / 86     1 / 64     0 / 61                                                                                                     
    6 snps
                 [93m201[0m     2.38             5.59 / 2.35                   0 / 6954   3 / 2269   1 / 510    6 / 305    1 / 378    2 / 296   25 / 250   12 / 166   19 / 134    6 / 86     6 / 134    4 / 95     6 / 86     2 / 64     7 / 61    13 / 46                                                                                          
                  90     1.60             3.43 / 2.14                   0 / 6954   7 / 2269   2 / 510   10 / 305    2 / 378    5 / 296   23 / 250   15 / 166    4 / 134    6 / 86     5 / 134   13 / 95    10 / 86     6 / 64     6 / 61     3 / 46                                                                                          
                   8     1.60             4.85 / 3.04                   0 / 6954  13 / 2269  10 / 510    4 / 305    2 / 378    9 / 296   26 / 250   20 / 166    6 / 134    4 / 86    25 / 134   14 / 95    10 / 86     6 / 64    11 / 61     3 / 46                                                                                          
                   9     1.14             4.25 / 3.72                   0 / 6953   5 / 2269   3 / 510    0 / 305    3 / 378    6 / 296   33 / 250    9 / 166    3 / 134    1 / 86    22 / 134    2 / 95     2 / 86     3 / 64     6 / 61     2 / 46                                                                                          
                  96     1.09             3.17 / 2.90                   0 / 6954   7 / 2269   6 / 510    0 / 305   12 / 378    2 / 296   18 / 250    5 / 166    8 / 134    9 / 86     0 / 134    4 / 95     6 / 86     2 / 64     1 / 61     2 / 46                                                                                          
                 146     0.90             3.27 / 3.64                   0 / 6954  36 / 2269  10 / 510   12 / 305   40 / 378   10 / 296   25 / 250   18 / 166    9 / 134    7 / 86    28 / 134   15 / 95    26 / 86    16 / 64     8 / 61    11 / 46                                                                                          
    8 snps
                 [93m156[0m     2.35             4.20 / 1.79                   0 / 6954   6 / 2269   2 / 510    2 / 305    9 / 378    9 / 296    5 / 250    4 / 166   18 / 134   11 / 86    12 / 134   18 / 95    16 / 86     9 / 64     9 / 61     9 / 46     1 / 49     5 / 53                                                                    
                 202     1.57             3.67 / 2.34                   0 / 6954  14 / 2269   4 / 510   11 / 305   14 / 378    4 / 296    9 / 250    9 / 166   25 / 134    4 / 86    12 / 134    3 / 95     7 / 86     1 / 64     7 / 61     2 / 46     0 / 49     1 / 53                                                                    
                 149     1.52             4.93 / 3.24                   0 / 6954   0 / 2269   0 / 510   17 / 305    6 / 378    1 / 296    2 / 250    4 / 166   17 / 134    5 / 86     5 / 134   11 / 95     4 / 86    13 / 64     6 / 61     3 / 46     4 / 49     1 / 53                                                                    
                  14     1.40             2.64 / 1.89                   0 / 6954  11 / 2269   5 / 510    9 / 305    8 / 378   16 / 296    9 / 250    9 / 166   22 / 134    6 / 86    15 / 134    8 / 95    11 / 86     8 / 64    13 / 61     4 / 46     1 / 49     9 / 53                                                                    
                  71     1.24             4.07 / 3.30                   0 / 6954   9 / 2269   1 / 510    2 / 305    6 / 378    4 / 296    2 / 250    2 / 166   23 / 134    8 / 86     6 / 134   12 / 95     2 / 86    11 / 64     3 / 61     1 / 46    13 / 49     8 / 53                                                                    
                 211     1.10             3.58 / 3.25                   0 / 6954   0 / 2269   0 / 510    4 / 305    1 / 378    5 / 296    7 / 250    5 / 166   24 / 134    0 / 86     5 / 134    7 / 95     6 / 86     2 / 64     4 / 61     1 / 46     0 / 49     0 / 53                                                                    
                 135     1.02             2.52 / 2.47                   0 / 6954   6 / 2269   0 / 510    0 / 305    1 / 378    3 / 296    2 / 250    8 / 166   22 / 134    3 / 86     2 / 134    1 / 95     6 / 86     3 / 64     1 / 61     2 / 46     3 / 49     0 / 53                                                                    
                 134     0.97             2.74 / 2.82                   0 / 6954  10 / 2269   1 / 510    0 / 305    0 / 378    0 / 296    1 / 250    0 / 166   23 / 134    2 / 86     1 / 134    0 / 95     2 / 86     4 / 64     4 / 61     2 / 46     2 / 49     0 / 53                                                                    
   snps       min ratio
    1          4.45     candidate 
    1          3.49     candidate 
    4          1.18     min snp ratio 1.18 too small (less than 2.25) 
    5          1.15     min snp ratio 1.15 too small (less than 2.25) 
    6          0.90     min snp ratio 0.90 too small (less than 2.25) 
    8          0.97     min snp ratio 0.97 too small (less than 2.25) 
        no equivalent gene for [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01+G116A[0m       nearest is [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01[0m (1 snp, 0 indels):
            CAGGTGCAGCTACAGCAGTGGGGCGCAGGACTGTTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTATGGTGGGTCCTTCAGTGGTTACTACTGGAGCTGGATCCGCCA[91mG[0mCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCAATCATAGTGGAAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCTGTGTATTACTGTGCGAGAGG [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01+G116A[0m
            CAGGTGCAGCTACAGCAGTGGGGCGCAGGACTGTTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTATGGTGGGTCCTTCAGTGGTTACTACTGGAGCTGGATCCGCCAACCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCAATCATAGTGGAAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCTGTGTATTACTGTGCGAGAGG [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01[0m
  [91mnew[0m [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01+G116A[0m separated from [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01[0m by 1 snp at:   116 (G --> A)
        no equivalent gene for [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01+G270A[0m       nearest is [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01[0m (1 snp, 0 indels):
            CAGGTGCAGCTACAGCAGTGGGGCGCAGGACTGTTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTATGGTGGGTCCTTCAGTGGTTACTACTGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCAATCATAGTGGAAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACG[91mG[0mCTGTGTATTACTGTGCGAGAGG [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01+G270A[0m
            CAGGTGCAGCTACAGCAGTGGGGCGCAGGACTGTTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTATGGTGGGTCCTTCAGTGGTTACTACTGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCAATCATAGTGGAAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGACTGTGTATTACTGTGCGAGAGG [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01[0m
  [91mnew[0m [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01+G270A[0m separated from [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01[0m by 1 snp at:   270 (G --> A)
 [95mh[0m[91mv[0m[95m4[0m[95m-39[0m[93m07[0m              21224 counts
             position   ratio       (one piece / two pieces)              0          1          2          3          4          5          6          7          8          9         10         11         12         13         14         15         16         17         18         19         20         21         22         23
    1 snp
                 [93m 19[0m     4.78             2.82 / 0.59                   0 / 11461  23 / 3072   4 / 631    1 / 387    1 / 437    3 / 398    3 / 380    2 / 333    1 / 392    0 / 388    2 / 390                                                                                                                                                
    3 snps
                 236     1.98             8.32 / 4.21                   0 / 11461  17 / 3072   4 / 631   17 / 387   40 / 437   48 / 398   55 / 380   27 / 333   29 / 392   27 / 388   43 / 390   32 / 454   43 / 357                                                                                                                          
                 [93m 84[0m     3.47              11. / 3.26                   0 / 11461   0 / 3072   2 / 631   10 / 387   30 / 437   11 / 398    9 / 380   17 / 333   16 / 392   14 / 388   21 / 390   50 / 454   24 / 357                                                                                                                          
                 [93m 99[0m     2.68             6.65 / 2.48                   0 / 11461   7 / 3072   0 / 631    8 / 387   28 / 437   19 / 398   11 / 380   19 / 333   36 / 392   18 / 388   30 / 390   31 / 454   29 / 357                                                                                                                          
    3 snps
                 [93m216[0m     4.35             9.93 / 2.28                   0 / 11461  20 / 3072   9 / 631   40 / 387   39 / 437   38 / 398   61 / 380   65 / 333   53 / 392   63 / 388   79 / 390  106 / 454   68 / 357                                                                                                                          
                 [93m 92[0m     4.66             9.95 / 2.13                   0 / 11461   1 / 3072   2 / 631    9 / 387   17 / 437   12 / 398   15 / 380   12 / 333   34 / 392   17 / 388   39 / 390   25 / 454   19 / 357                                                                                                                          
                 [93m177[0m     3.11             3.25 / 1.05                   0 / 11461   7 / 3072   2 / 631   12 / 387   14 / 437   25 / 398   11 / 380   18 / 333   18 / 392   18 / 388   28 / 390   22 / 454   19 / 357                                                                                                                          
    4 snps
                 [93m185[0m     2.43              11. / 4.47                   0 / 11461   5 / 3072   8 / 631    0 / 387   28 / 437    8 / 398   20 / 380   31 / 333   27 / 392   43 / 388   39 / 390   65 / 454   29 / 357   25 / 265                                                                                                               
                 [93m281[0m     3.99              17. / 4.26                   0 / 11461  17 / 3072  12 / 631   12 / 387   44 / 437   34 / 398   78 / 380   63 / 333   73 / 392   77 / 388  116 / 390  130 / 454  103 / 356   94 / 265                                                                                                               
                 [93m 84[0m     2.54              10. / 4.11                   0 / 11461   0 / 3072   2 / 631   10 / 387   30 / 437   11 / 398    9 / 380   17 / 333   16 / 392   14 / 388   21 / 390   50 / 454   24 / 357   12 / 265                                                                                                               
                 140     1.35             5.56 / 4.11                   0 / 11461   4 / 3072  19 / 631    2 / 387   26 / 437    6 / 398    8 / 380    2 / 333    9 / 392    4 / 388   12 / 389    4 / 454    0 / 357    4 / 265                                                                                                               
    4 snps
                  91     1.87             7.60 / 4.07                   0 / 11461   9 / 3072   1 / 631    2 / 387   17 / 437    5 / 398   41 / 380   23 / 333   28 / 392   25 / 388   28 / 390   39 / 454   30 / 357   35 / 265                                                                                                               
                 275     1.20             4.64 / 3.85                   0 / 11461  28 / 3072   2 / 631    2 / 387   21 / 437    0 / 398    1 / 380    6 / 333    0 / 392    2 / 388    0 / 390    2 / 454    0 / 357    0 / 265                                                                                                               
                 [93m236[0m     2.27             7.69 / 3.39                   0 / 11461  17 / 3072   4 / 631   17 / 387   40 / 437   48 / 398   55 / 380   27 / 333   29 / 392   27 / 388   43 / 390   32 / 454   43 / 357   33 / 265                                                                                                               
                 138     1.74             5.57 / 3.20                   0 / 11461  17 / 3072   3 / 631    2 / 387   36 / 437    5 / 398    6 / 380    2 / 333    5 / 392    1 / 388    4 / 390    2 / 454    0 / 357    0 / 265                                                                                                               
    4 snps
                 215     1.01             2.62 / 2.59                   0 / 11460   6 / 3072   1 / 631    7 / 387   26 / 437    7 / 398    6 / 380   10 / 333    4 / 392   11 / 388   11 / 390   13 / 454   10 / 357   13 / 265                                                                                                               
                 131     1.08             2.32 / 2.15                   0 / 11461   8 / 3072   2 / 631    5 / 387   25 / 437    9 / 398    8 / 380    6 / 333    7 / 392    5 / 388    8 / 390   10 / 454   16 / 357   13 / 265                                                                                                               
                 225     1.57             2.86 / 1.82                   0 / 11461   4 / 3072   0 / 631    2 / 387   25 / 437    5 / 398    5 / 380    6 / 333    5 / 392    4 / 388    3 / 390    2 / 454    3 / 357    6 / 265                                                                                                               
                 [93m134[0m     2.43             4.29 / 1.77                   0 / 11461  17 / 3072   4 / 631    5 / 387   22 / 437    5 / 398    7 / 380    2 / 333    7 / 392    5 / 388    6 / 390    2 / 454    1 / 357    4 / 265                                                                                                               
    5 snps
                 [93m166[0m     6.01              18. / 2.99                   0 / 11461   2 / 3072   1 / 631    3 / 387    4 / 437   21 / 398   32 / 380   20 / 333   20 / 392   33 / 388   41 / 390   57 / 454   63 / 357   58 / 265   36 / 276                                                                                                    
                 [93m253[0m     4.45              40. / 8.98                   0 / 11461  13 / 3072  16 / 631   31 / 387   56 / 437  108 / 398  106 / 380   87 / 333   99 / 392  108 / 388  137 / 390  182 / 454  143 / 357  110 / 265  146 / 276                                                                                                    
                 160     1.91             3.80 / 1.99                   0 / 11461  34 / 3072  21 / 631   15 / 387   10 / 437   49 / 398   45 / 380   30 / 333   48 / 392   41 / 388   41 / 390   67 / 454   57 / 357   42 / 265   31 / 276                                                                                                    
                 258     1.09             4.84 / 4.45                   0 / 11461  11 / 3072   0 / 631    8 / 387    1 / 437   18 / 398    6 / 380    9 / 333   10 / 392   11 / 388   13 / 390   10 / 454   14 / 357   36 / 265   26 / 276                                                                                                    
                 170     1.01             3.94 / 3.89                   0 / 11461  15 / 3072   2 / 631    5 / 387    2 / 437   18 / 398    8 / 380   15 / 333   17 / 392    8 / 388   11 / 390    5 / 454   10 / 357   13 / 265   27 / 276                                                                                                    
    6 snps
                 [93m 91[0m     3.20             6.71 / 2.10                   0 / 11461   9 / 3072   1 / 631    2 / 387   17 / 437    5 / 398   41 / 380   23 / 333   28 / 392   25 / 388   28 / 390   39 / 454   30 / 357   35 / 265   28 / 276   31 / 388                                                                                         
                 147     2.14             3.69 / 1.72                   0 / 11461   3 / 3072   5 / 631    1 / 387    6 / 437    3 / 398   21 / 380   14 / 333   13 / 392   19 / 388   24 / 390   12 / 454    9 / 357    3 / 265   10 / 276   14 / 388                                                                                         
                 165     1.62             4.01 / 2.47                   0 / 11461  12 / 3072   5 / 631    0 / 387    3 / 437    7 / 398   29 / 380   12 / 333   13 / 392   21 / 388   28 / 390   31 / 454   24 / 357   18 / 265   12 / 276   43 / 388                                                                                         
                 287     1.43             5.86 / 4.11                   0 / 11461  19 / 3072  12 / 631    9 / 387    6 / 437   13 / 398   38 / 380   33 / 333   27 / 392   25 / 388   62 / 390   66 / 454   36 / 357   35 / 265   65 / 276   77 / 388                                                                                         
                 206     0.97             2.59 / 2.66                   0 / 11461   7 / 3072   0 / 631    0 / 387    0 / 437    4 / 398   22 / 380    2 / 333    0 / 392    1 / 388    0 / 390    2 / 454    1 / 357    0 / 265    5 / 276    0 / 388                                                                                         
                  29     0.90             3.85 / 4.26                   0 / 11461   2 / 3072   1 / 631    3 / 387    0 / 437    1 / 398   34 / 380    4 / 333    5 / 392    0 / 388    5 / 390   13 / 454    4 / 357    2 / 265   10 / 276    5 / 388                                                                                         
   snps       min ratio
    1          4.78     candidate 
    3          1.98     min snp ratio 1.98 too small (less than 2.25) 
    3          3.11     positions 216 and 92 have inconsistent discontinuities

    4          1.35     min snp ratio 1.35 too small (less than 2.25) 
    4          1.20     min snp ratio 1.20 too small (less than 2.25) 
    4          1.01     min snp ratio 1.01 too small (less than 2.25) 
    5          1.01     min snp ratio 1.01 too small (less than 2.25) 
    6          0.90     min snp ratio 0.90 too small (less than 2.25) 
        no equivalent gene for [95mh[0m[91mv[0m[95m4[0m[95m-39[0m[93m07+C19T[0m       nearest is [95mh[0m[91mv[0m[95m4[0m[95m-39[0m[93m07[0m (1 snp, 0 indels):
            CAGCTGCAGCTGCAGGAGT[91mC[0mGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA [95mh[0m[91mv[0m[95m4[0m[95m-39[0m[93m07+C19T[0m
            CAGCTGCAGCTGCAGGAGTTGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA [95mh[0m[91mv[0m[95m4[0m[95m-39[0m[93m07[0m
  [91mnew[0m [95mh[0m[91mv[0m[95m4[0m[95m-39[0m[93m07+C19T[0m separated from [95mh[0m[91mv[0m[95m4[0m[95m-39[0m[93m07[0m by 1 snp at:   19 (C --> T)
 [95mh[0m[91mv[0m[95m4[0m[95m-4[0m[93m02[0m               1629 counts
 [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01[0m              7564 counts
             position   ratio       (one piece / two pieces)              0          1          2          3          4          5          6          7          8          9         10         11         12         13         14         15         16         17         18         19         20         21         22         23
    1 snp
                 [93m260[0m      10.              89. / 8.67                   0 / 3948 506 / 1427  55 / 180   20 / 83    34 / 142   24 / 115   23 / 112   28 / 121    5 / 117   32 / 113   31 / 125                                                                                                                                                
    1 snp
                 [93m114[0m      18.             2.72 / 0.15                   0 / 3948  25 / 1426   3 / 180    1 / 83     1 / 142    1 / 115    1 / 112    2 / 121    1 / 117    1 / 113    0 / 125                                                                                                                                                
   snps       min ratio
    1           10.     candidate 
    1           18.     candidate 
        no equivalent gene for [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01+C114T[0m       nearest is [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01[0m (1 snp, 0 indels):
            CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGG[91mC[0mAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01+C114T[0m
            CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGTAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01[0m
  [91mnew[0m [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01+C114T[0m separated from [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01[0m by 1 snp at:   114 (C --> T)
        no equivalent gene for [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01+T260C[0m       nearest is [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01[0m (1 snp, 0 indels):
            CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGC[91mT[0mGCGGACACGGCCGTGTATTACTGTGCGAGAGA [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01+T260C[0m
            CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01[0m
  [91mnew[0m [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01+T260C[0m separated from [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01[0m by 1 snp at:   260 (T --> C)
 [95mh[0m[91mv[0m[95m4[0m[95m-61[0m[93m02[0m              5587 counts
             position   ratio       (one piece / two pieces)              0          1          2          3          4          5          6          7          8          9         10         11         12         13         14         15         16         17         18         19         20         21         22         23
    3 snps
                 [93m253[0m     3.77              12. / 3.31                   0 / 2908   3 / 774    2 / 165   17 / 127   10 / 168   20 / 110   34 / 108   38 / 165   44 / 159   26 / 103   40 / 93    32 / 87    43 / 105                                                                                                                          
                 172     1.50             2.49 / 1.66                   0 / 2905   6 / 774    3 / 165   12 / 127    9 / 168    7 / 110   17 / 107   32 / 165   24 / 157   22 / 103   23 / 92    16 / 87    21 / 105                                                                                                                          
                 166     1.47             4.81 / 3.27                   0 / 2908   1 / 774    1 / 165   13 / 127   11 / 168    7 / 110   15 / 108   10 / 165    4 / 159   18 / 103   12 / 93     8 / 87    12 / 105                                                                                                                          
   snps       min ratio
    3          1.47     min snp ratio 1.47 too small (less than 2.25) 
 [95mh[0m[91mv[0m[95m5[0m[95m-51[0m[93m03[0m              2937 counts
             position   ratio       (one piece / two pieces)              0          1          2          3          4          5          6          7          8          9         10         11         12         13         14         15         16         17         18         19         20         21         22         23
    1 snp
                 [93m203[0m     6.69             158. / 24.                    0 / 671  419 / 567   88 / 178   74 / 174   42 / 149   70 / 232   63 / 162   65 / 162   59 / 154   46 / 94    48 / 78                                                                                                                                                 
    5 snps
                 205     1.94             4.97 / 2.55                   0 / 671    0 / 567    0 / 178    3 / 174    5 / 149   28 / 232   15 / 162   16 / 162    9 / 154   14 / 94    21 / 78    10 / 66     2 / 48     5 / 77     3 / 39                                                                                                     
                 214     1.58             5.82 / 3.68                   0 / 671    3 / 567    6 / 178    9 / 174    5 / 149   36 / 232   42 / 162   24 / 162   22 / 154   22 / 94    13 / 78    22 / 66     3 / 48    23 / 77    13 / 39                                                                                                     
                  34     1.51             6.57 / 4.35                   0 / 671    0 / 567    0 / 178    0 / 174    0 / 149   20 / 232    9 / 162    7 / 162   42 / 154    2 / 94     9 / 78     1 / 66     0 / 48     1 / 77     2 / 39                                                                                                     
                 175     1.48             5.25 / 3.56                   0 / 671    1 / 567    7 / 178    2 / 174   13 / 149   45 / 232   16 / 162   13 / 162   12 / 154   14 / 94    11 / 78     4 / 66     4 / 48    18 / 77     4 / 39                                                                                                     
                 179     1.36             3.96 / 2.91                   0 / 671    2 / 567    6 / 178   14 / 174    0 / 149   14 / 232   19 / 162   19 / 162   10 / 154    5 / 94    10 / 78     9 / 66     7 / 48    17 / 77     9 / 39                                                                                                     
    8 snps
                  99     1.87             2.29 / 1.23                   0 / 671    0 / 567    1 / 178    0 / 174    2 / 149    1 / 232    1 / 162    0 / 162   20 / 154    6 / 94     7 / 78     1 / 66     0 / 48     7 / 77     1 / 39     0 / 9      1 / 27     0 / 17                                                                    
                 182     1.75             4.32 / 2.47                   0 / 671    3 / 567    3 / 178   10 / 174   11 / 149   16 / 232   10 / 162   20 / 162   44 / 154   21 / 94    11 / 78    22 / 66    20 / 48    26 / 77    14 / 39     4 / 9      4 / 27     4 / 17                                                                    
                 156     1.28             4.82 / 3.77                   0 / 671    0 / 567    0 / 178    0 / 174    0 / 149    5 / 232    1 / 162    0 / 162   20 / 154    1 / 94     5 / 78     3 / 66     1 / 48    10 / 77     5 / 39     0 / 9     10 / 27    10 / 17                                                                    
                 137     1.26             2.84 / 2.25                   0 / 671    0 / 567    0 / 178    0 / 174    0 / 149    1 / 232    0 / 162    4 / 162   21 / 154    7 / 94     0 / 78     3 / 66     5 / 48     6 / 77     1 / 39     2 / 9      5 / 27     2 / 17                                                                    
                 170     1.26             5.61 / 4.45                   0 / 671    0 / 567    0 / 178    5 / 174    6 / 149   27 / 232    7 / 162   15 / 162   33 / 154    7 / 94    19 / 78    24 / 66    11 / 48    15 / 77     4 / 39     2 / 9      5 / 27     3 / 17                                                                    
                  89     1.05             3.17 / 3.01                   0 / 671    1 / 567    1 / 178    4 / 174    0 / 149    5 / 232   18 / 162    3 / 162   19 / 154    2 / 94    15 / 78     7 / 66     7 / 48     9 / 77     2 / 39     1 / 9      3 / 27     1 / 17                                                                    
                  39     1.05             2.64 / 2.52                   0 / 671    3 / 567    5 / 178    2 / 174   11 / 149   10 / 232    1 / 162    4 / 162   20 / 154    3 / 94     6 / 78     1 / 66     3 / 48     1 / 77     1 / 39     2 / 9      2 / 27     2 / 17                                                                    
                 220     0.98             2.67 / 2.74                   0 / 671    1 / 567    3 / 178    1 / 174    1 / 149    7 / 232    0 / 162    2 / 162   19 / 154    1 / 94     2 / 78     1 / 66     2 / 48    14 / 77     7 / 39     1 / 9      1 / 27     2 / 17                                                                    
   snps       min ratio
    1          6.69     candidate 
    5          1.36     min snp ratio 1.36 too small (less than 2.25) 
    8          0.98     min snp ratio 0.98 too small (less than 2.25) 
        no equivalent gene for [95mh[0m[91mv[0m[95m5[0m[95m-51[0m[93m03+C203T[0m       nearest is [95mh[0m[91mv[0m[95m5[0m[95m-51[0m[93m03[0m (1 snp, 0 indels):
            GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCGGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGT[91mC[0mACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGA [95mh[0m[91mv[0m[95m5[0m[95m-51[0m[93m03+C203T[0m
            GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCGGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTTACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGA [95mh[0m[91mv[0m[95m5[0m[95m-51[0m[93m03[0m
  [91mnew[0m [95mh[0m[91mv[0m[95m5[0m[95m-51[0m[93m03+C203T[0m separated from [95mh[0m[91mv[0m[95m5[0m[95m-51[0m[93m03[0m by 1 snp at:   203 (C --> T)
  found 11 new alleles: [95mh[0m[91mv[0m[95m1[0m[95m-69[0m[93m10[0m [95mh[0m[91mv[0m[95m1[0m[95m-8[0m[93m02+G209T[0m [95mh[0m[91mv[0m[95m2[0m[95m-70[0m[93m11[0m [95mh[0m[91mv[0m[95m3[0m[95m-23[0m[93m01[0m [95mh[0m[91mv[0m[95m3[0m[95m-66[0m[93m01[0m [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01+G116A[0m [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01+G270A[0m [95mh[0m[91mv[0m[95m4[0m[95m-39[0m[93m07+C19T[0m [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01+C114T[0m [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01+T260C[0m [95mh[0m[91mv[0m[95m5[0m[95m-51[0m[93m03+C203T[0m
  allele finding: 1323 fits in 36.0 sec
    plotting allele finding (14.5 sec)
    adding new allele to glfo: 
      template CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAGGGATCATCCCTATCTTTGGTACAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACGAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGA   [95mh[0m[91mv[0m[95m1[0m[95m-69[0m[93m13[0m
           new CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAGGGATCATCCCTATC[91mC[0mTTGGTA[91mT[0mAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGAC[91mA[0mAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGA   [95mh[0m[91mv[0m[95m1[0m[95m-69[0m[93m10[0m
    adding new allele to glfo: 
      template CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCAGCTATGATATCAACTGGGTGCGACAGGCCACTGGACAAGGGCTTGAGTGGATGGGATGGATGAACCCTAACAGTGGTAACACAGGCTATGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGAACACCTCCATAAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGG   [95mh[0m[91mv[0m[95m1[0m[95m-8[0m[93m02[0m
           new CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCAGCTATGATATCAACTGGGTGCGACAGGCCACTGGACAAGGGCTTGAGTGGATGGGATGGATGAACCCTAACAGTGGTAACACAGGCTATGCACAGAAGTTCCAGGGCAGAGTCACCAT[91mT[0mACCAGGAACACCTCCATAAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGG   [95mh[0m[91mv[0m[95m1[0m[95m-8[0m[93m02+G209T[0m
    [91mremoving[0m template gene [95mh[0m[91mv[0m[95m1[0m[95m-8[0m[93m02[0m
    adding new allele to glfo: 
      template CAGGTCACCTTGAAGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGCGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGATTGCACGCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC   [95mh[0m[91mv[0m[95m2[0m[95m-70[0m[93m10[0m
           new C[91mG[0mGGTCACCTTGA[91mG[0mGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATG[91mT[0mGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGG[91mC[0mTTGCACGCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC   [95mh[0m[91mv[0m[95m2[0m[95m-70[0m[93m11[0m
    adding new allele to glfo: 
      template GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA   [95mh[0m[91mv[0m[95m3[0m[95m-23[0m[93m04[0m
           new GAGGTGCAGCTG[91mT[0mTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA   [95mh[0m[91mv[0m[95m3[0m[95m-23[0m[93m01[0m
    adding new allele to glfo: 
      template GAGGTGCAGCTGGTGGAGTCTGGAGGAGGCTTGATCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGGTTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA   [95mh[0m[91mv[0m[95m3[0m[95m-53[0m[93m01[0m
           new GAGGTGCAGCTGGTGGAGTCTGG[91mG[0mGGAGGCTTG[91mG[0mTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGG[91mA[0mTTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGC[91mA[0mGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCCGAGGACACGGC[91mT[0mGTGTATTACTGTGCGAGAGA   [95mh[0m[91mv[0m[95m3[0m[95m-66[0m[93m01[0m
    adding new allele to glfo: 
      template CAGGTGCAGCTACAGCAGTGGGGCGCAGGACTGTTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTATGGTGGGTCCTTCAGTGGTTACTACTGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCAATCATAGTGGAAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCTGTGTATTACTGTGCGAGAGG   [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01[0m
           new CAGGTGCAGCTACAGCAGTGGGGCGCAGGACTGTTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTATGGTGGGTCCTTCAGTGGTTACTACTGGAGCTGGATCCGCCA[91mA[0mCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCAATCATAGTGGAAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCTGTGTATTACTGTGCGAGAGG   [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01+G116A[0m
    adding new allele to glfo: 
      template CAGGTGCAGCTACAGCAGTGGGGCGCAGGACTGTTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTATGGTGGGTCCTTCAGTGGTTACTACTGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCAATCATAGTGGAAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCTGTGTATTACTGTGCGAGAGG   [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01[0m
           new CAGGTGCAGCTACAGCAGTGGGGCGCAGGACTGTTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTATGGTGGGTCCTTCAGTGGTTACTACTGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCAATCATAGTGGAAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACG[91mA[0mCTGTGTATTACTGTGCGAGAGG   [95mh[0m[91mv[0m[95m4[0m[95m-34[0m[93m01+G270A[0m
    adding new allele to glfo: 
      template CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA   [95mh[0m[91mv[0m[95m4[0m[95m-39[0m[93m07[0m
           new CAGCTGCAGCTGCAGGAGT[91mT[0mGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA   [95mh[0m[91mv[0m[95m4[0m[95m-39[0m[93m07+C19T[0m
    adding new allele to glfo: 
      template CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA   [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01[0m
           new CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGG[91mT[0mAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA   [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01+C114T[0m
    adding new allele to glfo: 
      template CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA   [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01[0m
           new CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGC[91mC[0mGCGGACACGGCCGTGTATTACTGTGCGAGAGA   [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01+T260C[0m
    adding new allele to glfo: 
      template GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCGGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGA   [95mh[0m[91mv[0m[95m5[0m[95m-51[0m[93m03[0m
           new GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCGGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGT[91mT[0mACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGA   [95mh[0m[91mv[0m[95m5[0m[95m-51[0m[93m03+C203T[0m
smith-waterman  (writing parameters)
  vsearch: 186583 / 238759 v annotations (52176 failed) with 49 v genes in 57.0 sec
    running 15 procs for 181692 seqs
    running 18 procs for 38817 seqs
      info for 181137 / 238759 = 0.759   (57622 failed)
  [91mwarning[0m smith-waterman step failed to find alignments for a large fraction of input sequences (see previous line)   [91mnote:[0m maybe need to take reverse complement? (partis only searches in forward direction)
      kept 88799 (0.372) unproductive
      removed 4043 / 181137 = 0.02 duplicate sequences after trimming framework insertions (leaving 177094)
        writing sw results to /fh/fast/matsen_e/processed-data/partis/chaim-iarc/v1/08248/sw-cache.yaml
  plotting parameters in /fh/fast/matsen_e/processed-data/partis/chaim-iarc/v1/08248/plots/sw (16.3 sec)
    writing parameters to /fh/fast/matsen_e/processed-data/partis/chaim-iarc/v1/08248/sw (1.7 sec)
    water time: 808.5  (ig-sw 352.6  processing 143.4)
  writing hmms (12.7 sec)
hmm
    skipping matches from 2 genes without enough counts: [95mh[0m[91mv[0m[95m4[0m[95m-39[0m[93m07+C19T[0m [95mh[0m[91mv[0m[95m4[0m[95m-59[0m[93m01+C114T[0m
    prepare_for_hmm: (18.3 sec)
    running 15 procs
                    calcd:         vtb 177094        fwd      0
             min-max time:  546.7 - 685.5 sec
    read output
  plotting parameters in /fh/fast/matsen_e/processed-data/partis/chaim-iarc/v1/08248/plots/hmm (14.8 sec)
    writing parameters to /fh/fast/matsen_e/processed-data/partis/chaim-iarc/v1/08248/hmm (1.8 sec)
        processed 177094 hmm output lines with 173650 sequences in 173650 events  (3444 failures)
            [91mwarning[0m skipped 3444 invalid events
         infra time: 420.1
      hmm step time: 1108.5
  writing hmms (17.9 sec)
      total time: 2895.3
