annotate test-data/last_train.txt @ 0:9a7e91fc6562 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"

# lastal version: 1021
# 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 ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB

# 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- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB

# 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: 70.0105

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 3158           583.4          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 0.21341        0.0394248      0.0290516      0.0264634     
# C 0.0398032      0.207126       0.0105962      0.0523051     
# G 0.0170431      0.00599008     0.106165       0.00462637    
# T 0.0231521      0.0425807      0.00885876     0.173404      

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

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     75    -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 -t90.8564 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB

# aligned letter pairs: 14881
# deletes: 258.8
# inserts: 446.1
# delOpens: 112.91
# insOpens: 168
# alignments: 2
# mean delete size: 2.29209
# mean insert size: 2.65536
# matchProb: 0.981278
# delOpenProb: 0.00744548
# insOpenProb: 0.0110782
# delExtendProb: 0.563717
# insExtendProb: 0.623403

# substitution percent identity: 68.9366

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 3126           618.3          445            406.6         
# C 622.8          3041           159.4          805.4         
# G 265.2          91.16          1560           68.22         
# T 357.3          660            133.33         2554          

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.209606       0.0414585      0.0298383      0.0272635     
# C 0.0417602      0.203906       0.0106882      0.054004      
# G 0.0177823      0.0061125      0.104602       0.00457431    
# T 0.0239578      0.0442546      0.0089401      0.171252      

# delExistCost: 470
# insExistCost: 457
# delExtendCost: 52
# insExtendCost: 42

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

# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.1831 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB

# aligned letter pairs: 14981
# deletes: 214.8
# inserts: 402.9
# delOpens: 82.32
# insOpens: 131.98
# alignments: 2
# mean delete size: 2.60933
# mean insert size: 3.05274
# matchProb: 0.985702
# delOpenProb: 0.0054164
# insOpenProb: 0.00868387
# delExtendProb: 0.61676
# insExtendProb: 0.672425

# substitution percent identity: 68.4035

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 3114           635.9          450            416.3         
# C 640.1          3019           164.9          816.3         
# G 270.6          93.43          1560           69.38         
# T 365.7          670            135.53         2543          

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.208097       0.0424949      0.0300719      0.0278198     
# C 0.0427756      0.201749       0.0110197      0.0545504     
# G 0.0180832      0.00624359     0.104249       0.00463642    
# T 0.0244384      0.0447737      0.00905699     0.16994       

# delExistCost: 518
# insExistCost: 498
# delExtendCost: 44
# insExtendCost: 36

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     74    -71    -43    -97
# C    -70     71   -135    -36
# G    -71   -169    146   -183
# T   -101    -46   -133     88

# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t90.7211 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB

# aligned letter pairs: 14981
# deletes: 197.5
# inserts: 386.4
# delOpens: 68.51
# insOpens: 115.71
# alignments: 2
# mean delete size: 2.88279
# mean insert size: 3.33938
# matchProb: 0.987657
# delOpenProb: 0.00451668
# insOpenProb: 0.00762845
# delExtendProb: 0.653114
# insExtendProb: 0.700543

# substitution percent identity: 68.1501

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 3103           643.6          451.1          422.5         
# C 649.8          3008           167            819.5         
# G 272.7          94.59          1560           70.43         
# T 369.8          675.4          136.61         2542          

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.20706        0.0429467      0.0301014      0.0281929     
# C 0.0433604      0.20072        0.0111437      0.0546843     
# G 0.0181969      0.00631188     0.104097       0.00469971    
# T 0.0246763      0.0450686      0.00911582     0.169625      

# delExistCost: 549
# insExistCost: 522
# delExtendCost: 39
# insExtendCost: 32

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     74    -69    -43    -95
# C    -68     70   -134    -35
# G    -71   -168    146   -182
# T   -100    -45   -132     88

# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t90.7441 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB

# aligned letter pairs: 14981
# deletes: 192.1
# inserts: 380.9
# delOpens: 62.34
# insOpens: 108.21
# alignments: 2
# mean delete size: 3.08149
# mean insert size: 3.52001
# matchProb: 0.988548
# delOpenProb: 0.00411362
# insOpenProb: 0.00714043
# delExtendProb: 0.675482
# insExtendProb: 0.71591

# substitution percent identity: 67.9883

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 3093           648            451.1          425.7         
# C 654.2          3008           169            821.5         
# G 272.8          95.26          1550           71.05         
# T 371.8          677.5          136.66         2532          

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.206509       0.0432647      0.0301184      0.0284225     
# C 0.0436786      0.200834       0.0112835      0.0548487     
# G 0.0182139      0.00636018     0.103488       0.00474376    
# T 0.0248238      0.0452343      0.00912431     0.169053      

# delExistCost: 566
# insExistCost: 534
# delExtendCost: 36
# insExtendCost: 30

# 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 -t91.2473 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB

# aligned letter pairs: 14981
# deletes: 194.5
# inserts: 383.3
# delOpens: 60.42
# insOpens: 106.36
# alignments: 2
# mean delete size: 3.21913
# mean insert size: 3.6038
# matchProb: 0.988794
# delOpenProb: 0.00398791
# insOpenProb: 0.0070201
# delExtendProb: 0.689357
# insExtendProb: 0.722515

# substitution percent identity: 67.9593

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 3093           648.9          451.2          426.7         
# C 655.2          3008           169            821.4         
# G 273.8          95.46          1550           71.26         
# T 372.8          678.6          136.64         2532          

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.206421       0.0433063      0.0301122      0.0284771     
# C 0.0437268      0.200748       0.0112787      0.0548186     
# G 0.0182729      0.00637081     0.103444       0.00475575    
# T 0.0248799      0.0452884      0.00911908     0.168981      

# 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   -132    -35
# G    -70   -167    147   -180
# T    -99    -45   -131     88

# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.2311 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB

# aligned letter pairs: 14981
# deletes: 196.9
# inserts: 385.7
# delOpens: 59.47
# insOpens: 105.68
# alignments: 2
# mean delete size: 3.31091
# mean insert size: 3.6497
# matchProb: 0.9889
# delOpenProb: 0.00392563
# insOpenProb: 0.00697597
# delExtendProb: 0.697969
# insExtendProb: 0.726005

# substitution percent identity: 67.9572

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 3093           648.8          451.2          426.6         
# C 655.1          3008           169.9          821.4         
# G 273.8          95.45          1550           71.26         
# T 372.7          678.6          136.63         2532          

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.206414       0.0432982      0.0301112      0.0284695     
# C 0.0437187      0.200742       0.0113384      0.0548169     
# G 0.0182723      0.00636994     0.103441       0.0047556     
# T 0.0248725      0.045287       0.00911813     0.168975      

# 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   -132    -35
# G    -70   -167    147   -180
# T    -99    -45   -131     88

# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.1656 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB

# 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: 67.9308

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 3093           648.8          451.2          426.6         
# C 656            2998           169.9          821.4         
# G 273.8          95.55          1550           71.36         
# T 372.7          678.6          136.62         2532          

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.206537       0.043324       0.0301292      0.0284865     
# C 0.0438048      0.200193       0.0113452      0.0548495     
# G 0.0182832      0.00638041     0.103502       0.00476511    
# T 0.0248873      0.0453139      0.00912288     0.169076      

# 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   -132     88

# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t90.815 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB

# 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: 67.93

# 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

# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.0834 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB

# 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