comparison databases/lastal_params @ 0:1d1b9e1b2e2f draft

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0:1d1b9e1b2e2f

# lastal version: 956
# maximum percent identity: 100
# scale of score parameters: 4.5512
# scale used while training: 91.024

# lastal -j7 -S1 -P8 -r5 -q5 -a15 -b3 ps_tail_near /tmp/tmpLzO6pN

# aligned letter pairs: 645322.5
# deletes: 53030.076
# inserts: 52961.894
# delOpens: 27321.807
# insOpens: 27522.598
# alignments: 1715
# mean delete size: 1.94094
# mean insert size: 1.92431
# delOpenProb: 0.0389264
# insOpenProb: 0.0392125
# delExtendProb: 0.484787
# insExtendProb: 0.480332

# delExistCost: 290
# insExistCost: 288
# delExtendCost: 66
# insExtendCost: 67

# substitution percent identity: 80.7124

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 167864.68      8440.25411     14824.7457     10778.6026    
# C 8305.6793      92568.78       5527.30401     14593.1965    
# G 14303.26163    5657.737106    91602.82       8233.2595     
# T 10559.8569     14962.3325     8284.02998     168830.9      

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.260119       0.0130788      0.0229721      0.0167023     
# C 0.0128703      0.143442       0.00856498     0.0226133     
# G 0.022164       0.0087671      0.141946       0.0127581     
# T 0.0163633      0.0231853      0.0128367      0.261616      

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     89   -137    -85   -161
# C   -138    128   -128    -87
# G    -87   -126    129   -138
# T   -163    -85   -138     89

# lastal -j7 -S1 -P8 -p- ps_tail_near /tmp/tmpLzO6pN

# aligned letter pairs: 657515.8
# deletes: 54576.405
# inserts: 54467.682
# delOpens: 29338.269
# insOpens: 29782.167
# alignments: 1810
# mean delete size: 1.86025
# mean insert size: 1.82887
# delOpenProb: 0.0408357
# insOpenProb: 0.0414535
# delExtendProb: 0.462437
# insExtendProb: 0.453214

# delExistCost: 277
# insExistCost: 273
# delExtendCost: 70
# insExtendCost: 72

# substitution percent identity: 82.8127

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 172119.6       6326.08979     16347.823382   7375.214      
# C 6451.841992    99738.42       4226.312847    16076.55299   
# G 15766.519333   4374.698921    99296.38       6396.707638   
# T 7212.54884     16138.520254   6316.90954     173353.79     

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.261772       0.00962117     0.0248629      0.0112167     
# C 0.00981242     0.151689       0.00642768     0.0244504     
# G 0.0239788      0.00665335     0.151017       0.00972857    
# T 0.0109694      0.0245446      0.0096072      0.263649      

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     93   -165    -79   -194
# C   -163    128   -159    -81
# G    -81   -156    129   -164
# T   -196    -81   -166     93

# lastal -j7 -S1 -P8 -p- ps_tail_near /tmp/tmpLzO6pN

# aligned letter pairs: 668948.5
# deletes: 57981.575
# inserts: 58221.335
# delOpens: 31807.825
# insOpens: 32507.3002
# alignments: 1869
# mean delete size: 1.82287
# mean insert size: 1.79102
# delOpenProb: 0.0432681
# insOpenProb: 0.0442196
# delExtendProb: 0.451415
# insExtendProb: 0.44166

# delExistCost: 268
# insExistCost: 263
# delExtendCost: 72
# insExtendCost: 74

# substitution percent identity: 83.6608

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 177183.17      5504.869925    17286.571547   6133.25055    
# C 5702.212901    102462.3342    3582.471673    16864.00328   
# G 16580.481274   3711.7686366   101712.376     5579.04028    
# T 6057.34017     16811.744918   5490.65923     178306.52     

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.26486        0.00822889     0.0258406      0.00916822    
# C 0.00852388     0.153165       0.00535521     0.025209      
# G 0.0247851      0.00554849     0.152044       0.00833976    
# T 0.00905474     0.0251308      0.00820765     0.266539      

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     94   -180    -75   -213
# C   -176    129   -175    -78
# G    -78   -172    130   -178
# T   -214    -78   -180     93

# lastal -j7 -S1 -P8 -p- ps_tail_near /tmp/tmpLzO6pN

# aligned letter pairs: 668279.1
# deletes: 59484.735
# inserts: 59870.687
# delOpens: 32991.303
# insOpens: 33795.3266
# alignments: 1880
# mean delete size: 1.80304
# mean insert size: 1.77157
# delOpenProb: 0.0447676
# insOpenProb: 0.0458586
# delExtendProb: 0.445382
# insExtendProb: 0.435528

# delExistCost: 263
# insExistCost: 257
# delExtendCost: 74
# insExtendCost: 76

# substitution percent identity: 84.0864

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 177957.15      4999.54926     17535.51502    5493.75775    
# C 5256.33764     102819.702     3231.546315    17061.52644   
# G 16831.203718   3359.0874106   102142.74      5159.982219   
# T 5414.11539     16979.044906   5031.32483     179044.28     

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.266277       0.00748081     0.0262383      0.00822029    
# C 0.00786504     0.153849       0.00483535     0.0255291     
# G 0.0251845      0.00502619     0.152836       0.00772086    
# T 0.00810112     0.0254057      0.00752835     0.267903      

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     94   -188    -74   -223
# C   -184    130   -185    -77
# G    -77   -181    130   -185
# T   -224    -77   -188     94

# lastal -j7 -S1 -P8 -p- ps_tail_near /tmp/tmpLzO6pN

# aligned letter pairs: 673098.9
# deletes: 60509.124
# inserts: 60931.728
# delOpens: 33889.837
# insOpens: 34772.3604
# alignments: 1904
# mean delete size: 1.78547
# mean insert size: 1.7523
# delOpenProb: 0.0455713
# insOpenProb: 0.046758
# delExtendProb: 0.439922
# insExtendProb: 0.429323

# delExistCost: 259
# insExistCost: 253
# delExtendCost: 75
# insExtendCost: 77

# substitution percent identity: 84.2455

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 179372.81      4809.447538    17825.281852   5240.02635    
# C 5095.922788    103957.344     3086.126043    17363.08133   
# G 17133.73643    3204.862713    103068.961     5016.900182   
# T 5166.54604     17246.079885   4855.804638    180660.07     

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.266486       0.00714519     0.0264822      0.00778488    
# C 0.00757079     0.154445       0.00458492     0.0257956     
# G 0.0254549      0.00476133     0.153125       0.00745339    
# T 0.00767571     0.0256218      0.00721406     0.268399      

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     94   -192    -73   -228
# C   -187    130   -190    -76
# G    -76   -186    130   -188
# T   -229    -76   -191     94

# lastal -j7 -S1 -P8 -p- ps_tail_near /tmp/tmpLzO6pN

# aligned letter pairs: 671420
# deletes: 60847.457
# inserts: 61216.623
# delOpens: 34223.687
# insOpens: 35105.5057
# alignments: 1905
# mean delete size: 1.77793
# mean insert size: 1.74379
# delOpenProb: 0.0460829
# insOpenProb: 0.0472703
# delExtendProb: 0.437549
# insExtendProb: 0.426536

# delExistCost: 257
# insExistCost: 251
# delExtendCost: 75
# insExtendCost: 78

# substitution percent identity: 84.3547

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 179262.53      4683.13191     17831.725501   5066.33631    
# C 4991.393335    103798.9414    2969.9483841   17350.46316   
# G 17164.537784   3080.0882855   102891.659     4902.7599     
# T 5005.67514     17264.047033   4734.516842    180415.41     

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.266993       0.00697504     0.0265585      0.00754578    
# C 0.00743416     0.154598       0.00442343     0.0258417     
# G 0.0255648      0.00458747     0.153246       0.00730215    
# T 0.00745543     0.025713       0.00705157     0.26871       

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     94   -195    -73   -231
# C   -189    130   -193    -76
# G    -76   -189    131   -190
# T   -232    -76   -194     94

# lastal -j7 -S1 -P8 -p- ps_tail_near /tmp/tmpLzO6pN

# aligned letter pairs: 667385.9
# deletes: 60863.037
# inserts: 61068.724
# delOpens: 34293.856
# insOpens: 35128.4285
# alignments: 1897
# mean delete size: 1.77475
# mean insert size: 1.73844
# delOpenProb: 0.0464242
# insOpenProb: 0.047554
# delExtendProb: 0.436541
# insExtendProb: 0.424772

# delExistCost: 256
# insExistCost: 250
# delExtendCost: 75
# insExtendCost: 78

# substitution percent identity: 84.4482

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 178271.09      4572.202785    17691.13197    4943.68897    
# C 4898.898701    103247.5099    2897.9008978   17271.5722    
# G 17034.463563   2999.2086819   102377.98      4810.85091    
# T 4878.05409     17171.526982   4621.916292    179704.11     

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.267116       0.00685085     0.0265079      0.00740747    
# C 0.00734036     0.154703       0.00434213     0.0258792     
# G 0.0255239      0.00449392     0.1534         0.00720843    
# T 0.00730913     0.0257293      0.00692534     0.269263      

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     94   -196    -73   -233
# C   -190    131   -194    -76
# G    -76   -191    131   -191
# T   -233    -76   -195     94

# lastal -j7 -S1 -P8 -p- ps_tail_near /tmp/tmpLzO6pN

# aligned letter pairs: 666793.9
# deletes: 61173.009
# inserts: 61424.737
# delOpens: 34485.443
# insOpens: 35339.5034
# alignments: 1894
# mean delete size: 1.77388
# mean insert size: 1.73813
# delOpenProb: 0.0466957
# insOpenProb: 0.0478522
# delExtendProb: 0.436264
# insExtendProb: 0.42467

# delExistCost: 256
# insExistCost: 249
# delExtendCost: 76
# insExtendCost: 78

# substitution percent identity: 84.4957

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 178068.02      4536.310792    17696.513353   4890.10953    
# C 4868.64896     103333.5423    2873.6084247   17235.19293   
# G 17046.992851   2960.6778678   102434.344     4775.391737   
# T 4821.6702      17094.342963   4580.523287    179565.01     

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.267056       0.0068033      0.0265402      0.00733391    
# C 0.00730172     0.154974       0.00430967     0.0258484     
# G 0.0255661      0.00444026     0.153625       0.00716186    
# T 0.00723127     0.0256371      0.00686961     0.269301      

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     95   -197    -73   -233
# C   -190    131   -195    -76
# G    -76   -192    131   -192
# T   -234    -76   -196     94

# lastal -j7 -S1 -P8 -p- ps_tail_near /tmp/tmpLzO6pN

# aligned letter pairs: 668372.5
# deletes: 61372.74
# inserts: 61752.015
# delOpens: 34634.079
# insOpens: 35602.1868
# alignments: 1894
# mean delete size: 1.77203
# mean insert size: 1.7345
# delOpenProb: 0.046771
# insOpenProb: 0.0480783
# delExtendProb: 0.435677
# insExtendProb: 0.423465

# delExistCost: 255
# insExistCost: 248
# delExtendCost: 76
# insExtendCost: 78

# substitution percent identity: 84.4884

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 178606.63      4528.388304    17729.296579   4898.0761     
# C 4885.271035    103599.7129    2872.5313126   17312.05326   
# G 17066.490557   2960.3238425   102604.038     4769.454259   
# T 4821.57531     17246.644431   4582.143026    179869.01     

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.267235       0.00677546     0.0265269      0.00732859    
# C 0.00730943     0.155008       0.00429793     0.0259026     
# G 0.0255352      0.00442929     0.153518       0.00713615    
# T 0.00721413     0.0258047      0.00685589     0.269123      

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     95   -197    -73   -233
# C   -190    130   -195    -76
# G    -76   -192    131   -192
# T   -235    -76   -196     94

# lastal -j7 -S1 -P8 -p- ps_tail_near /tmp/tmpLzO6pN

# aligned letter pairs: 665455.3
# deletes: 61135.865
# inserts: 61504.017
# delOpens: 34525.4
# insOpens: 35494.9299
# alignments: 1886
# mean delete size: 1.77075
# mean insert size: 1.73275
# delOpenProb: 0.0468228
# insOpenProb: 0.0481377
# delExtendProb: 0.435268
# insExtendProb: 0.422884

# delExistCost: 255
# insExistCost: 248
# delExtendCost: 76
# insExtendCost: 78

# substitution percent identity: 84.5159

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 177989.73      4503.762429    17609.060952   4856.77481    
# C 4849.472712    103109.4119    2852.8739936   17229.83623   
# G 16964.556937   2940.9623514   102150.05      4736.10198    
# T 4758.08398     17182.445961   4551.911074    179145.32     

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.267481       0.0067682      0.0264627      0.0072987     
# C 0.00728772     0.154951       0.00428726     0.0258928     
# G 0.0254941      0.00441964     0.15351        0.00711735    
# T 0.00715039     0.0258216      0.00684055     0.269217      

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     95   -197    -73   -234
# C   -191    131   -196    -76
# G    -76   -192    131   -192
# T   -235    -76   -196     94

# lastal -j7 -S1 -P8 -p- ps_tail_near /tmp/tmpLzO6pN

# aligned letter pairs: 667215.5
# deletes: 61476.418
# inserts: 61879.205
# delOpens: 34711.673
# insOpens: 35697.4767
# alignments: 1892
# mean delete size: 1.77106
# mean insert size: 1.73343
# delOpenProb: 0.0469383
# insOpenProb: 0.0482713
# delExtendProb: 0.435366
# insExtendProb: 0.42311

# delExistCost: 255
# insExistCost: 248
# delExtendCost: 76
# insExtendCost: 78

# substitution percent identity: 84.5201

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 178292.03      4511.809138    17670.490922   4851.35066    
# C 4842.564675    103502.2645    2843.789638    17283.582     
# G 17031.671871   2952.5211926   102467.621     4751.735375   
# T 4777.82579     17198.105981   4567.418934    179660.81     

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.267222       0.00676225     0.0264843      0.00727115    
# C 0.00725798     0.155128       0.00426224     0.0259044     
# G 0.0255269      0.0044252      0.153577       0.00712185    
# T 0.00716095     0.0257763      0.00684559     0.269274      

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     95   -197    -73   -234
# C   -191    130   -196    -76
# G    -76   -192    131   -192
# T   -235    -76   -196     94

# lastal -j7 -S1 -P8 -p- ps_tail_near /tmp/tmpLzO6pN

# aligned letter pairs: 665601.7
# deletes: 61110.454
# inserts: 61539.036
# delOpens: 34519.822
# insOpens: 35512.5895
# alignments: 1890
# mean delete size: 1.7703
# mean insert size: 1.73288
# delOpenProb: 0.0468049
# insOpenProb: 0.048151
# delExtendProb: 0.435124
# insExtendProb: 0.422926

# delExistCost: 255
# insExistCost: 248
# delExtendCost: 76
# insExtendCost: 78

# substitution percent identity: 84.5287

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 178045.53      4503.713821    17604.443539   4828.70278    
# C 4826.541757    103105.4814    2834.2139601   17243.04778   
# G 16969.584056   2940.3365692   102106.499     4732.997971   
# T 4762.93067     17171.077328   4556.037659    179345.31     

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.267506       0.00676664     0.0264499      0.00725492    
# C 0.00725167     0.154912       0.00425828     0.0259069     
# G 0.0254961      0.00441773     0.153411       0.00711113    
# T 0.0071561      0.0257988      0.00684525     0.269459      

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     95   -197    -73   -235
# C   -191    131   -196    -76
# G    -76   -192    131   -193
# T   -235    -76   -196     94

# lastal -j7 -S1 -P8 -p- ps_tail_near /tmp/tmpLzO6pN

# aligned letter pairs: 667867
# deletes: 61545.493
# inserts: 61947.098
# delOpens: 34751.308
# insOpens: 35738.0794
# alignments: 1897
# mean delete size: 1.77103
# mean insert size: 1.73336
# delOpenProb: 0.0469451
# insOpenProb: 0.0482781
# delExtendProb: 0.435356
# insExtendProb: 0.423087

# delExistCost: 255
# insExistCost: 248
# delExtendCost: 76
# insExtendCost: 78

# substitution percent identity: 84.5213

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 178479.93      4519.435975    17696.250205   4834.79514    
# C 4852.489573    103558.824     2845.7910385   17318.78409   
# G 17063.13382    2956.1887816   102498.451     4733.342314   
# T 4784.65867     17197.72566    4572.985914    179943.91     

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.267243       0.00676707     0.0264971      0.00723927    
# C 0.00726576     0.155061       0.00426108     0.0259319     
# G 0.0255491      0.00442638     0.153474       0.00708736    
# T 0.0071642      0.0257506      0.00684726     0.269435      

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     95   -197    -73   -235
# C   -191    131   -196    -76
# G    -75   -192    131   -193
# T   -235    -76   -196     94

# lastal -j7 -S1 -P8 -p- ps_tail_near /tmp/tmpLzO6pN

# aligned letter pairs: 667848.4
# deletes: 61567.479
# inserts: 62006.567
# delOpens: 34755.709
# insOpens: 35753.0592
# alignments: 1895
# mean delete size: 1.77143
# mean insert size: 1.7343
# delOpenProb: 0.0469511
# insOpenProb: 0.0482984
# delExtendProb: 0.435486
# insExtendProb: 0.423399

# delExistCost: 255
# insExistCost: 248
# delExtendCost: 76
# insExtendCost: 78

# substitution percent identity: 84.5102

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 178498.03      4524.992357    17712.490447   4841.2626     
# C 4848.343909    103538.1147    2846.8428447   17309.54422   
# G 17107.155533   2955.1213614   102468.661     4729.73675    
# T 4786.48956     17208.555606   4576.294121    179887.61     

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.267277       0.00677557     0.0265221      0.00724914    
# C 0.00725975     0.155034       0.00426277     0.0259187     
# G 0.0256157      0.0044249      0.153433       0.00708215    
# T 0.00716713     0.0257675      0.00685239     0.269358      

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     95   -197    -72   -234
# C   -191    131   -196    -76
# G    -75   -192    131   -193
# T   -235    -76   -196     94

# lastal -j7 -S1 -P8 -p- ps_tail_near /tmp/tmpLzO6pN

# aligned letter pairs: 667329.4
# deletes: 61526.981
# inserts: 61935.551
# delOpens: 34736.121
# insOpens: 35715.1049
# alignments: 1891
# mean delete size: 1.77127
# mean insert size: 1.73416
# delOpenProb: 0.0469615
# insOpenProb: 0.048285
# delExtendProb: 0.435433
# insExtendProb: 0.42335

# delExistCost: 255
# insExistCost: 248
# delExtendCost: 76
# insExtendCost: 78

# substitution percent identity: 84.5031

# count matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 178304.73      4517.257925    17741.252681   4858.77123    
# C 4843.594396    103456.2463    2845.5696656   17298.79994   
# G 17092.716475   2952.0734537   102484.764     4727.692877   
# T 4781.83456     17183.48844    4570.956339    179662.41     

# probability matrix (query letters = columns, reference letters = rows):
#   A              C              G              T             
# A 0.267194       0.00676923     0.0265857      0.007281      
# C 0.00725826     0.155032       0.00426416     0.0259227     
# G 0.0256139      0.00442376     0.153576       0.00708457    
# T 0.00716571     0.0257499      0.0068497      0.269229      

# score matrix (query letters = columns, reference letters = rows):
#        A      C      G      T
# A     95   -197    -72   -234
# C   -191    131   -196    -76
# G    -75   -192    131   -193
# T   -235    -76   -196     94

#last -a 13
#last -A 12
#last -b 4
#last -B 4
#last -S 1
# score matrix (query letters = columns, reference letters = rows):
       A      C      G      T
A      5    -10     -4    -12
C    -10      7    -10     -4
G     -4    -10      7    -10
T    -12     -4    -10      5