annotate test-data/last_train_E.txt @ 5:f5a5a2b39ff2 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 4568799de240022f4058ec1602e08f536916e2af"

# lastal version: 1205
# maximum percent identity: 100
# scale of score parameters: 4.5512
# scale used while training: 91.024

# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -r5 -q5 -a15 -b3 -A15 -B3 /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpw04gddt3

# aligned letter pairs: 14901
# deletes: 694
# inserts: 834
# delOpens: 350
# insOpens: 402
# alignments: 1
# mean delete size: 1.98286
# mean insert size: 2.07463
# matchProb: 0.951836
# delOpenProb: 0.0223571
# insOpenProb: 0.0256787
# delExtendProb: 0.495677
# insExtendProb: 0.517986

# substitution percent identity: 71.9408

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 3291           532            387            390           
# C 552            3221           180            685           
# G 235            102            1561           84.7          
# T 335            554            146            2651          

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.220773       0.0356887      0.0259615      0.0261627     
# C 0.0370303      0.216077       0.0120751      0.0459525     
# G 0.0157647      0.00684256     0.104718       0.00568201    
# T 0.0224731      0.0371645      0.00979425     0.177839      

# delExistCost: 346
# insExistCost: 342
# delExtendCost: 62
# insExtendCost: 58

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     76    -90    -59   -105
# C    -87     73   -129    -54
# G    -88   -164    145   -167
# T   -112    -66   -127     90

# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.4322 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpw04gddt3

# aligned letter pairs: 14771
# deletes: 379.3
# inserts: 567.1
# delOpens: 185.2
# insOpens: 246.1
# alignments: 2
# mean delete size: 2.04806
# mean insert size: 2.30435
# matchProb: 0.971438
# delOpenProb: 0.01218
# insOpenProb: 0.0161851
# delExtendProb: 0.511732
# insExtendProb: 0.566038

# substitution percent identity: 70.0152

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 3158           582.4          429.9          391.6         
# C 589            3065           156.8          774           
# G 252.2          88.64          1571           68.46         
# T 342.6          630.1          131.09         2566          

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.213425       0.0393599      0.0290536      0.0264652     
# C 0.0398059      0.20714        0.0105969      0.0523086     
# G 0.0170442      0.00599049     0.106172       0.00462668    
# T 0.0231537      0.0425836      0.00885935     0.173416      

# delExistCost: 406
# insExistCost: 400
# delExtendCost: 60
# insExtendCost: 51

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     76    -79    -48   -102
# C    -78     72   -140    -41
# G    -79   -174    146   -185
# T   -107    -52   -136     89

# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.6863 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpw04gddt3

# aligned letter pairs: 14881
# deletes: 264.3
# inserts: 451.9
# delOpens: 116.18
# insOpens: 171.3
# alignments: 2
# mean delete size: 2.27492
# mean insert size: 2.63806
# matchProb: 0.980854
# delOpenProb: 0.00765779
# insOpenProb: 0.0112909
# delExtendProb: 0.560424
# insExtendProb: 0.620934

# substitution percent identity: 68.9602

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 3126           617.2          445            406.6         
# C 621.9          3041           159.4          804.4         
# G 264.2          91.07          1560           68.32         
# T 357.3          658.9          133.32         2554          

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.209677       0.0413989      0.0298485      0.0272728     
# C 0.0417142      0.203976       0.0106918      0.0539554     
# G 0.0177213      0.00610855     0.104638       0.00458259    
# T 0.023966       0.0441959      0.00894248     0.17131       

# delExistCost: 466
# insExistCost: 453
# delExtendCost: 52
# insExtendCost: 43

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     75    -74    -44    -99
# C    -73     71   -138    -37
# G    -74   -171    147   -185
# T   -103    -48   -134     88

# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.1379 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpw04gddt3

# aligned letter pairs: 14981
# deletes: 217
# inserts: 405.1
# delOpens: 83.75
# insOpens: 134.12
# alignments: 2
# mean delete size: 2.59104
# mean insert size: 3.02043
# matchProb: 0.985471
# delOpenProb: 0.00550919
# insOpenProb: 0.0088226
# delExtendProb: 0.614055
# insExtendProb: 0.668921

# substitution percent identity: 68.4369

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 3114           634.8          449.1          416.3         
# C 639            3019           163.9          815.3         
# G 269.6          93.35          1560           69.28         
# T 364.7          670            135.51         2543          

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.208199       0.0424421      0.0300264      0.0278334     
# C 0.0427229      0.201847       0.0109582      0.0545102     
# G 0.0180252      0.00624129     0.1043         0.00463199    
# T 0.0243835      0.0447956      0.00906007     0.170023      

# delExistCost: 516
# insExistCost: 495
# delExtendCost: 44
# insExtendCost: 36

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     75    -71    -43    -97
# C    -70     71   -135    -36
# G    -72   -169    147   -183
# T   -101    -46   -133     88

# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.7798 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpw04gddt3

# aligned letter pairs: 14981
# deletes: 204.2
# inserts: 393.3
# delOpens: 71.01
# insOpens: 119.07
# alignments: 2
# mean delete size: 2.87565
# mean insert size: 3.3031
# matchProb: 0.987276
# delOpenProb: 0.00467969
# insOpenProb: 0.00784693
# delExtendProb: 0.652253
# insExtendProb: 0.697254

# substitution percent identity: 68.1926

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 3104           642.4          451.1          421.4         
# C 647.7          3009           167            819.4         
# G 271.7          94.39          1560           70.33         
# T 368.8          674.3          136.58         2543          

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.207194       0.0428807      0.0301113      0.0281288     
# C 0.0432345      0.200853       0.0111474      0.0546956     
# G 0.0181362      0.00630061     0.104131       0.00469458    
# T 0.0246177      0.04501        0.00911682     0.169747      

# delExistCost: 545
# insExistCost: 517
# delExtendCost: 39
# insExtendCost: 33

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     74    -70    -43    -96
# C    -69     70   -134    -35
# G    -71   -168    146   -182
# T   -100    -46   -132     88

# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t90.3541 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpw04gddt3

# aligned letter pairs: 14981
# deletes: 194.4
# inserts: 382.1
# delOpens: 63.11
# insOpens: 109.31
# alignments: 2
# mean delete size: 3.08034
# mean insert size: 3.49556
# matchProb: 0.988426
# delOpenProb: 0.00416391
# insOpenProb: 0.00721213
# delExtendProb: 0.67536
# insExtendProb: 0.713923

# substitution percent identity: 68.0193

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 3093           646.9          451.1          424.6         
# C 652.9          3008           168            821.5         
# G 272.7          95.16          1550           70.95         
# T 370.8          676.5          136.64         2532          

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.206603       0.0432109      0.0301321      0.028362      
# C 0.0436117      0.200925       0.0112219      0.0548737     
# G 0.0182155      0.00635639     0.103535       0.00473924    
# T 0.0247683      0.0451881      0.00912713     0.16913       

# delExistCost: 565
# insExistCost: 533
# delExtendCost: 36
# insExtendCost: 30

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     74    -69    -42    -95
# C    -68     70   -133    -35
# G    -70   -167    147   -181
# T    -99    -45   -131     88

# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.1953 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpw04gddt3

# aligned letter pairs: 14981
# deletes: 195.6
# inserts: 384.5
# delOpens: 60.75
# insOpens: 106.8
# alignments: 2
# mean delete size: 3.21975
# mean insert size: 3.60019
# matchProb: 0.988744
# delOpenProb: 0.00400949
# insOpenProb: 0.00704878
# delExtendProb: 0.689417
# insExtendProb: 0.722237

# substitution percent identity: 67.9748

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 3093           648.9          451.2          425.6         
# C 655.1          3008           169            821.4         
# G 272.8          95.36          1550           71.16         
# T 372.8          677.6          136.64         2532          

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.206468       0.0433161      0.030119       0.0284102     
# C 0.04373        0.200794       0.0112813      0.0548311     
# G 0.0182103      0.00636558     0.103467       0.00475016    
# T 0.0248856      0.045232       0.00912115     0.169019      

# delExistCost: 575
# insExistCost: 539
# delExtendCost: 34
# insExtendCost: 29

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     74    -69    -42    -94
# C    -68     70   -133    -35
# G    -70   -167    147   -181
# T    -99    -45   -131     88

# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.1816 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpw04gddt3

# aligned letter pairs: 14981
# deletes: 196.9
# inserts: 385.7
# delOpens: 59.46
# insOpens: 105.67
# alignments: 2
# mean delete size: 3.31147
# mean insert size: 3.65004
# matchProb: 0.988902
# delOpenProb: 0.00392498
# insOpenProb: 0.00697532
# delExtendProb: 0.698019
# insExtendProb: 0.726031

# substitution percent identity: 67.9622

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 3093           648.8          451.2          426.6         
# C 655            3008           168.9          821.4         
# G 273.8          95.45          1550           71.26         
# T 372.7          678.6          136.62         2532          

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.206429       0.0433015      0.0301135      0.0284716     
# C 0.0437152      0.200756       0.0112725      0.0548209     
# G 0.0182736      0.00637041     0.103448       0.00475595    
# T 0.0248743      0.0452903      0.00911813     0.168988      

# delExistCost: 580
# insExistCost: 541
# delExtendCost: 33
# insExtendCost: 29

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     74    -69    -42    -94
# C    -68     70   -133    -35
# G    -70   -167    147   -180
# T    -99    -45   -131     88

# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.131 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpw04gddt3

# aligned letter pairs: 14981
# deletes: 197
# inserts: 385.7
# delOpens: 58.72
# insOpens: 105.14
# alignments: 2
# mean delete size: 3.3549
# mean insert size: 3.66844
# matchProb: 0.988985
# delOpenProb: 0.00387646
# insOpenProb: 0.00694091
# delExtendProb: 0.701929
# insExtendProb: 0.727405

# substitution percent identity: 67.9358

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 3093           648.8          451.2          426.6         
# C 656            2998           168.9          821.4         
# G 273.8          95.45          1550           71.36         
# T 372.7          678.6          136.62         2532          

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.206552       0.0433272      0.0301314      0.0284886     
# C 0.043808       0.200208       0.0112792      0.0548535     
# G 0.0182845      0.0063742      0.10351        0.00476546    
# T 0.0248891      0.0453173      0.00912355     0.169088      

# delExistCost: 584
# insExistCost: 542
# delExtendCost: 32
# insExtendCost: 29

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     74    -69    -42    -94
# C    -68     70   -132    -35
# G    -70   -166    146   -180
# T    -99    -45   -131     88

# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t90.8423 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpw04gddt3

# aligned letter pairs: 14981
# deletes: 197
# inserts: 384.7
# delOpens: 57.97
# insOpens: 104.51
# alignments: 2
# mean delete size: 3.39831
# mean insert size: 3.68099
# matchProb: 0.989075
# delOpenProb: 0.00382729
# insOpenProb: 0.00689995
# delExtendProb: 0.705736
# insExtendProb: 0.728334

# substitution percent identity: 67.9254

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 3093           648.8          451.2          427.6         
# C 656            2998           169.9          821.4         
# G 273.8          95.75          1550           71.36         
# T 372.7          678.6          136.62         2532          

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.20652        0.0433205      0.0301267      0.028551      
# C 0.0438013      0.200177       0.0113443      0.0548451     
# G 0.0182817      0.00639325     0.103494       0.00476473    
# T 0.0248853      0.0453103      0.00912215     0.169062      

# delExistCost: 586
# insExistCost: 543
# delExtendCost: 32
# insExtendCost: 29

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     74    -69    -43    -94
# C    -68     70   -132    -35
# G    -70   -166    146   -180
# T    -99    -45   -132     88

# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t90.682 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpw04gddt3

# aligned letter pairs: 14981
# deletes: 194.8
# inserts: 383.5
# delOpens: 57.43
# insOpens: 103.95
# alignments: 2
# mean delete size: 3.39196
# mean insert size: 3.68927
# matchProb: 0.989147
# delOpenProb: 0.00379192
# insOpenProb: 0.00686348
# delExtendProb: 0.705185
# insExtendProb: 0.728944

# substitution percent identity: 67.9249

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 3093           649.9          451.1          427.6         
# C 656            2998           169.9          821.4         
# G 273.8          95.75          1550           71.46         
# T 372.7          678.6          135.62         2532          

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.206519       0.0433937      0.0301199      0.0285508     
# C 0.043801       0.200176       0.0113442      0.0548447     
# G 0.0182816      0.00639321     0.103493       0.00477137    
# T 0.0248851      0.04531        0.00905532     0.169061      

# delExistCost: 587
# insExistCost: 543
# delExtendCost: 32
# insExtendCost: 29

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     74    -68    -42    -94
# C    -68     70   -132    -35
# G    -70   -166    147   -180
# T    -99    -45   -132     88

# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.2049 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpw04gddt3

# aligned letter pairs: 14981
# deletes: 195.9
# inserts: 384.7
# delOpens: 57.66
# insOpens: 104.5
# alignments: 2
# mean delete size: 3.3975
# mean insert size: 3.68134
# matchProb: 0.989096
# delOpenProb: 0.00380691
# insOpenProb: 0.00689944
# delExtendProb: 0.705666
# insExtendProb: 0.72836

# substitution percent identity: 67.9195

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 3093           649.9          451.2          427.6         
# C 656.1          2998           169.9          821.4         
# G 273.8          95.74          1550           71.46         
# T 373.7          678.6          135.62         2532          

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.206503       0.0433902      0.0301241      0.0285485     
# C 0.0438042      0.20016        0.0113433      0.0548404     
# G 0.0182801      0.00639203     0.103485       0.00477099    
# T 0.0249499      0.0453064      0.0090546      0.169048      

# delExistCost: 586
# insExistCost: 543
# delExtendCost: 32
# insExtendCost: 29

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     74    -68    -42    -94
# C    -68     70   -132    -35
# G    -70   -166    147   -180
# T    -99    -45   -132     88

# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.2167 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpw04gddt3

# aligned letter pairs: 14981
# deletes: 196
# inserts: 384.7
# delOpens: 57.87
# insOpens: 104.51
# alignments: 2
# mean delete size: 3.3869
# mean insert size: 3.68099
# matchProb: 0.989081
# delOpenProb: 0.00382071
# insOpenProb: 0.0069
# delExtendProb: 0.704745
# insExtendProb: 0.728334

# substitution percent identity: 67.9245

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 3093           649.9          451.2          427.6         
# C 656.1          2998           169.9          821.4         
# G 273.8          95.64          1550           71.46         
# T 372.7          678.6          135.62         2532          

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.206518       0.0433934      0.0301264      0.0285506     
# C 0.0438074      0.200175       0.0113441      0.0548444     
# G 0.0182815      0.00638583     0.103493       0.00477134    
# T 0.024885       0.0453097      0.00905527     0.16906       

# delExistCost: 586
# insExistCost: 543
# delExtendCost: 32
# insExtendCost: 29

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     74    -69    -42    -94
# C    -68     70   -132    -35
# G    -70   -166    147   -180
# T    -99    -45   -132     88

# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.0834 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpw04gddt3

# aligned letter pairs: 14981
# deletes: 196
# inserts: 384.7
# delOpens: 57.87
# insOpens: 104.51
# alignments: 2
# mean delete size: 3.3869
# mean insert size: 3.68099
# matchProb: 0.989081
# delOpenProb: 0.00382071
# insOpenProb: 0.0069
# delExtendProb: 0.704745
# insExtendProb: 0.728334

# substitution percent identity: 67.93

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 3093           648.8          451.2          427.6         
# C 656            2998           169.9          821.4         
# G 273.8          95.75          1550           71.36         
# T 372.7          678.6          135.61         2532          

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.206534       0.0433235      0.0301288      0.0285529     
# C 0.0438042      0.200191       0.011345       0.0548488     
# G 0.0182829      0.00639368     0.103501       0.00476505    
# T 0.024887       0.0453133      0.00905532     0.169074      

# delExistCost: 586
# insExistCost: 543
# delExtendCost: 32
# insExtendCost: 29

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     74    -69    -42    -94
# C    -68     70   -132    -35
# G    -70   -166    147   -180
# T    -99    -45   -132     88

#last -X 0
#last -Q 0
#last -t4.80115
#last -a 29
#last -A 28
#last -b 2
#last -B 1
#last -s 1
#last -S 1
# score matrix (query letters = columns, reference letters = rows):
       A      C      G      T
A      4     -3     -2     -5
C     -3      4     -7     -2
G     -3     -8      7     -9
T     -5     -2     -7      4