comparison test-data/last_train.txt @ 3:3de2195f32c0 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 72dc050116d14e7a1342e7f9a2f7e095033d9a3a"

2:bf30030e5265

# 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

3:3de2195f32c0

# lastal version: 1021
# maximum percent identity: 100
# scale of score parameters: 4.5512
# scale used while training: 91.024

# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -r5 -q5 -a15 -b3 -A15 -B3 /home/rdallet/galaxy/tools/last/test-data/humdb /tmp/tmpow095T/tmp/tmpmqx0kk84

# aligned letter pairs: 14938.3
# deletes: 664.27
# inserts: 839.49
# delOpens: 344.82
# insOpens: 404.93
# alignments: 3
# mean delete size: 1.92643
# mean insert size: 2.07317
# matchProb: 0.951966
# delOpenProb: 0.0219742
# insOpenProb: 0.0258048
# delExtendProb: 0.480904
# insExtendProb: 0.517648

# substitution percent identity: 71.9318

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 3296.3         533.237        387.81         392.24        
# C 553.59         3241.5         182.39         686.22        
# G 232.54         102.399        1565.4         84.91         
# T 335.173        558.68         147.16         2651          

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.22048        0.0356667      0.0259395      0.0262358     
# C 0.0370281      0.216815       0.0121996      0.0458993     
# G 0.0155539      0.00684918     0.104705       0.00567939    
# T 0.0224188      0.0373685      0.00984312     0.177318      

# delExistCost: 343
# insExistCost: 341
# delExtendCost: 64
# insExtendCost: 58

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     76    -90    -59   -104
# C    -87     73   -128    -55
# G    -89   -164    145   -167
# T   -112    -66   -127     90

# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.3148 -p- /home/rdallet/galaxy/tools/last/test-data/humdb /tmp/tmpow095T/tmp/tmpmqx0kk84

# aligned letter pairs: 14338.3
# deletes: 327.44
# inserts: 474.13
# delOpens: 166.73
# insOpens: 216.45
# alignments: 10
# mean delete size: 1.96389
# mean insert size: 2.19048
# matchProb: 0.973244
# delOpenProb: 0.0113172
# insOpenProb: 0.014692
# delExtendProb: 0.490807
# insExtendProb: 0.54348

# substitution percent identity: 70.6019

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 3076.4         546.106        412.41         369.93        
# C 561.42         2983.2         149.401        735.35        
# G 245.82         80.868         1562.07        66.655        
# T 326.724        603.44         120.838        2510.5        

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.214366       0.0380532      0.0287371      0.0257771     
# C 0.0391203      0.207872       0.0104104      0.0512399     
# G 0.017129       0.00563496     0.108846       0.00464458    
# T 0.0227664      0.0420483      0.0084201      0.174934      

# delExistCost: 405
# insExistCost: 402
# delExtendCost: 64
# insExtendCost: 54

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     77    -81    -49   -104
# C    -79     73   -142    -42
# G    -80   -181    146   -186
# T   -108    -52   -142     90

# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.4973 -p- /home/rdallet/galaxy/tools/last/test-data/humdb /tmp/tmpow095T/tmp/tmpmqx0kk84

# aligned letter pairs: 14657.7
# deletes: 218.21
# inserts: 385.36
# delOpens: 102.2
# insOpens: 152.161
# alignments: 10
# mean delete size: 2.13513
# mean insert size: 2.53258
# matchProb: 0.982218
# delOpenProb: 0.00684846
# insOpenProb: 0.0101964
# delExtendProb: 0.531644
# insExtendProb: 0.605146

# substitution percent identity: 69.4007

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 3091.6         591.394        434.35         391.72        
# C 605.8          2996.8         154.6091       779.75        
# G 260.46         83.802         1568.22        67.9713       
# T 351.852        646.07         124.676        2532.5        

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.210577       0.0402814      0.0295847      0.0266811     
# C 0.0412626      0.20412        0.0105308      0.0531108     
# G 0.0177406      0.00570797     0.106816       0.0046297     
# T 0.0239655      0.0440055      0.008492       0.172495      

# delExistCost: 466
# insExistCost: 457
# delExtendCost: 57
# insExtendCost: 45

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     76    -75    -45   -100
# C    -73     72   -140    -38
# G    -75   -178    147   -185
# T   -103    -48   -140     89

# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.5154 -p- /home/rdallet/galaxy/tools/last/test-data/humdb /tmp/tmpow095T/tmp/tmpmqx0kk84

# aligned letter pairs: 14615.5
# deletes: 176.132
# inserts: 337.667
# delOpens: 73.361
# insOpens: 117.993
# alignments: 8
# mean delete size: 2.40089
# mean insert size: 2.86175
# matchProb: 0.986477
# delOpenProb: 0.00495152
# insOpenProb: 0.00796397
# delExtendProb: 0.583489
# insExtendProb: 0.650564

# substitution percent identity: 68.8798

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 3057.2         603.516        434.56         399.47        
# C 620.42         2962.4         159.336        789.74        
# G 264.31         86.899         1557.17        68.449        
# T 353.847        650            125.897        2508.2        

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.208805       0.0412198      0.0296802      0.0272836     
# C 0.0423743      0.20233        0.0108826      0.0539388     
# G 0.0180522      0.00593515     0.106354       0.00467503    
# T 0.0241675      0.0443946      0.00859869     0.171309      

# delExistCost: 514
# insExistCost: 497
# delExtendCost: 49
# insExtendCost: 39

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     75    -72    -44    -98
# C    -71     72   -137    -37
# G    -73   -174    146   -184
# T   -102    -46   -138     89

# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.0742 -p- /home/rdallet/galaxy/tools/last/test-data/humdb /tmp/tmpow095T/tmp/tmpmqx0kk84

# aligned letter pairs: 14806.2
# deletes: 167.925
# inserts: 326.866
# delOpens: 62.871
# insOpens: 105.559
# alignments: 7
# mean delete size: 2.67095
# mean insert size: 3.09652
# matchProb: 0.988224
# delOpenProb: 0.00419626
# insOpenProb: 0.00704543
# delExtendProb: 0.625601
# insExtendProb: 0.677057

# substitution percent identity: 68.3956

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 3074.6         626.457        444.21         418.05        
# C 637.55         2977.3         164.69         809.88        
# G 269.41         92.415         1559.3         69.29         
# T 359.136        664.2          129.482        2527.2        

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.207419       0.042262       0.0299673      0.0282025     
# C 0.0430104      0.200854       0.0111103      0.0546361     
# G 0.0181749      0.0062345      0.105193       0.00467444    
# T 0.024228       0.0448082      0.00873511     0.17049       

# delExistCost: 546
# insExistCost: 519
# delExtendCost: 42
# insExtendCost: 35

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     75    -70    -43    -95
# C    -69     71   -134    -36
# G    -71   -169    146   -183
# T   -101    -45   -136     88

# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.1177 -p- /home/rdallet/galaxy/tools/last/test-data/humdb /tmp/tmpow095T/tmp/tmpmqx0kk84

# aligned letter pairs: 14896.9
# deletes: 177.451
# inserts: 344.879
# delOpens: 59.29
# insOpens: 103.311
# alignments: 5
# mean delete size: 2.99293
# mean insert size: 3.33826
# matchProb: 0.988809
# delOpenProb: 0.00393548
# insOpenProb: 0.00685746
# delExtendProb: 0.66588
# insExtendProb: 0.700443

# substitution percent identity: 68.1858

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 3084.6         635.337        445.51         422.24        
# C 649.18         2997.2         169.11         816.24        
# G 273.53         93.848         1562.4         71.64         
# T 365.354        674.15         132.032        2532.3        

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.206678       0.0425696      0.0298506      0.0282914     
# C 0.0434971      0.200822       0.0113309      0.0546907     
# G 0.0183274      0.00628811     0.104686       0.00480011    
# T 0.0244799      0.0451702      0.00884656     0.169672      

# delExistCost: 567
# insExistCost: 531
# delExtendCost: 37
# insExtendCost: 32

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     75    -70    -43    -95
# C    -68     71   -132    -35
# G    -70   -168    146   -181
# T   -100    -45   -135     88

# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.5512 -p- /home/rdallet/galaxy/tools/last/test-data/humdb /tmp/tmpow095T/tmp/tmpmqx0kk84

# aligned letter pairs: 14897.4
# deletes: 183.45
# inserts: 350.682
# delOpens: 57.728
# insOpens: 101.786
# alignments: 5
# mean delete size: 3.17783
# mean insert size: 3.44529
# matchProb: 0.989012
# delOpenProb: 0.00383246
# insOpenProb: 0.00675739
# delExtendProb: 0.68532
# insExtendProb: 0.709748

# substitution percent identity: 68.1676

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 3083.6         635.04         445.71         423.87        
# C 650.27         2996.2         169.49         816.21        
# G 272.96         94.054         1562.4         71.81         
# T 365.777        674.06         132.018        2532.4        

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.206594       0.0425463      0.0298616      0.0283983     
# C 0.0435666      0.200739       0.0113555      0.0546843     
# G 0.0182877      0.00630141     0.104677       0.00481111    
# T 0.0245062      0.0451605      0.00884491     0.169665      

# delExistCost: 578
# insExistCost: 536
# delExtendCost: 34
# insExtendCost: 31

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     75    -70    -43    -94
# C    -68     71   -132    -36
# G    -71   -168    146   -180
# T   -100    -45   -135     88

# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.3765 -p- /home/rdallet/galaxy/tools/last/test-data/humdb /tmp/tmpow095T/tmp/tmpmqx0kk84

# aligned letter pairs: 14897.3
# deletes: 186.949
# inserts: 354.265
# delOpens: 56.756
# insOpens: 101.214
# alignments: 5
# mean delete size: 3.29391
# mean insert size: 3.50016
# matchProb: 0.989113
# delOpenProb: 0.00376834
# insOpenProb: 0.00672015
# delExtendProb: 0.696409
# insExtendProb: 0.714299

# substitution percent identity: 68.1476

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 3081.6         633.831        445.71         424.07        
# C 650.26         2986.2         169.38         816.09        
# G 272.84         94.051         1561.4         71.9          
# T 365.569        674.07         131.791        2532.4        

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.206664       0.0425072      0.029891       0.0284398     
# C 0.0436089      0.200266       0.0113593      0.0547301     
# G 0.0182977      0.00630742     0.104714       0.00482189    
# T 0.0245165      0.0452057      0.00883841     0.169833      

# delExistCost: 584
# insExistCost: 539
# delExtendCost: 33
# insExtendCost: 30

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     75    -70    -43    -94
# C    -68     71   -132    -35
# G    -71   -168    146   -180
# T   -100    -45   -135     88

# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.5205 -p- /home/rdallet/galaxy/tools/last/test-data/humdb /tmp/tmpow095T/tmp/tmpmqx0kk84

# aligned letter pairs: 14897.4
# deletes: 188.951
# inserts: 357.176
# delOpens: 56.362
# insOpens: 100.973
# alignments: 5
# mean delete size: 3.35245
# mean insert size: 3.53734
# matchProb: 0.989155
# delOpenProb: 0.00374231
# insOpenProb: 0.00670439
# delExtendProb: 0.701711
# insExtendProb: 0.717302

# substitution percent identity: 68.1403

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 3081.6         634.732        445.81         423.98        
# C 650.18         2986.2         169.39         816.1         
# G 273.05         94.134         1561.4         71.9          
# T 365.574        674.07         131.782        2531.4        

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.206662       0.0425672      0.0298975      0.0284335     
# C 0.0436032      0.200264       0.0113598      0.0547303     
# G 0.0183116      0.00631293     0.104713       0.00482185    
# T 0.0245166      0.0452053      0.00883773     0.169764      

# delExistCost: 587
# insExistCost: 541
# delExtendCost: 32
# insExtendCost: 30

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     75    -70    -43    -94
# C    -68     71   -132    -35
# G    -71   -168    146   -180
# T   -100    -45   -135     88

# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.4821 -p- /home/rdallet/galaxy/tools/last/test-data/humdb /tmp/tmpow095T/tmp/tmpmqx0kk84

# aligned letter pairs: 14897.4
# deletes: 189.355
# inserts: 357.265
# delOpens: 56.08
# insOpens: 100.658
# alignments: 5
# mean delete size: 3.37652
# mean insert size: 3.5493
# matchProb: 0.989194
# delOpenProb: 0.00372374
# insOpenProb: 0.00668374
# delExtendProb: 0.703837
# insExtendProb: 0.718254

# substitution percent identity: 68.1453

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 3081.6         633.731        445.81         423.98        
# C 650.08         2986.2         169.39         816.1         
# G 273.05         94.136         1561.4         71.9          
# T 365.674        674.07         131.672        2531.4        

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.206677       0.0425032      0.0298997      0.0284356     
# C 0.0435997      0.200279       0.0113607      0.0547344     
# G 0.018313       0.00631353     0.10472        0.0048222     
# T 0.0245251      0.0452087      0.00883101     0.169776      

# delExistCost: 588
# insExistCost: 541
# delExtendCost: 32
# insExtendCost: 30

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     75    -70    -43    -94
# C    -68     71   -132    -35
# G    -71   -168    146   -180
# T   -100    -45   -135     88

# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.4704 -p- /home/rdallet/galaxy/tools/last/test-data/humdb /tmp/tmpow095T/tmp/tmpmqx0kk84

# aligned letter pairs: 14897.4
# deletes: 188.951
# inserts: 356.964
# delOpens: 55.8286
# insOpens: 100.647
# alignments: 5
# mean delete size: 3.38448
# mean insert size: 3.54669
# matchProb: 0.989211
# delOpenProb: 0.00370711
# insOpenProb: 0.00668312
# delExtendProb: 0.704534
# insExtendProb: 0.718047

# substitution percent identity: 68.1409

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 3081.6         633.731        445.81         424.08        
# C 650.28         2986.2         169.49         816.1         
# G 273.05         94.136         1561.4         71.9          
# T 365.673        674.17         131.672        2530.4        

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.206684       0.0425046      0.0299007      0.0284432     
# C 0.0436146      0.200286       0.0113678      0.0547362     
# G 0.0183136      0.00631375     0.104724       0.00482237    
# T 0.0245259      0.0452169      0.0088313      0.169715      

# delExistCost: 588
# insExistCost: 541
# delExtendCost: 32
# insExtendCost: 30

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     75    -70    -43    -94
# C    -68     71   -132    -35
# G    -71   -168    146   -180
# T   -100    -45   -135     88

#last -X 0
#last -Q 0
#last -t4.72795
#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     -4     -8      7     -9
T     -5     -2     -7      4