diff test-data/MADE1.hmm @ 5:750269125dc9 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
author iuc
date Tue, 16 Jun 2020 05:38:16 -0400
parents d0875d3f6544
children dc8860ba75d1
line wrap: on
line diff
--- a/test-data/MADE1.hmm	Mon Jun 11 15:52:17 2018 -0400
+++ b/test-data/MADE1.hmm	Tue Jun 16 05:38:16 2020 -0400
@@ -1,268 +1,268 @@
-HMMER3/f [3.2 | June 2018]
+HMMER3/f [3.3 | Nov 2019]
 NAME  MADE1
 ACC   DF0000629.2
 DESC  MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon
 LENG  80
-MAXL  369
+MAXL  190
 ALPH  DNA
 RF    yes
 MM    no
 CONS  yes
 CS    no
 MAP   yes
-DATE  Fri Jun  8 12:16:29 2018
+DATE  Thu May 14 18:28:16 2020
 NSEQ  1997
-EFFN  3.911818
+EFFN  4.772646
 CKSUM 3015610723
 GA    15.98
 TC    32.00
 NC    15.90
-STATS LOCAL MSV       -8.5408  0.71858
-STATS LOCAL VITERBI   -9.6095  0.71858
-STATS LOCAL FORWARD   -3.4185  0.71858
+STATS LOCAL MSV       -8.5015  0.71857
+STATS LOCAL VITERBI   -9.4437  0.71857
+STATS LOCAL FORWARD   -3.3601  0.71857
 HMM          A        C        G        T   
             m->m     m->i     m->d     i->m     i->i     d->m     d->d
-  COMPO   1.24273  1.59618  1.63103  1.16152
+  COMPO   1.26505  1.57847  1.62734  1.15507
           1.38629  1.38629  1.38629  1.38629
-          0.03960  3.94183  3.94183  1.46634  0.26236  0.00000        *
-      1   2.69765  2.44396  2.81521  0.24089      1 t x - -
+          0.03610  4.03273  4.03273  1.46634  0.26236  0.00000        *
+      1   2.88347  2.59729  3.00766  0.19823      1 t x - -
           1.38629  1.38629  1.38629  1.38629
-          0.03960  3.94183  3.94183  1.46634  0.26236  1.09861  0.40547
-      2   2.72939  2.37873  2.85832  0.24244      2 t x - -
+          0.03610  4.03273  4.03273  1.46634  0.26236  1.09861  0.40547
+      2   2.84764  2.33775  2.99223  0.22904      2 t x - -
           1.38629  1.38629  1.38629  1.38629
-          0.03725  4.00179  4.00179  1.46634  0.26236  1.09861  0.40547
-      3   0.16099  3.16370  2.87328  2.99734      3 a x - -
+          0.03318  4.11545  4.11545  1.46634  0.26236  1.09861  0.40547
+      3   0.23331  2.81609  2.55800  2.64795      3 a x - -
           1.38629  1.38629  1.38629  1.38629
-          0.03604  4.03416  4.03416  1.46634  0.26236  1.09861  0.40547
-      4   1.98862  2.42132  0.42649  2.10770      4 g x - -
+          0.03194  4.15297  4.15297  1.46634  0.26236  1.09861  0.40547
+      4   2.10142  2.78158  0.31096  2.48849      4 g x - -
           1.38629  1.38629  1.38629  1.38629
-          0.03539  4.05203  4.05203  1.46634  0.26236  1.09861  0.40547
-      5   1.96369  2.69532  0.36534  2.32099      5 g x - -
+          0.03116  4.17730  4.17730  1.46634  0.26236  1.09861  0.40547
+      5   2.03766  2.72525  0.33174  2.44801      5 g x - -
           1.38629  1.38629  1.38629  1.38629
-          0.03764  4.06427  3.92372  1.46634  0.26236  1.09861  0.40547
-      6   2.56994  2.11239  2.71946  0.30571      6 t x - -
-          1.37159  1.41129  1.39124  1.37159
-          0.03806  3.89715  4.07214  1.48830  0.25587  1.07889  0.41548
-      7   2.58388  2.10353  2.64646  0.31253     12 t x - -
-          1.38764  1.38524  1.38764  1.38465
-          0.03494  4.03864  4.09125  1.43264  0.27270  1.09736  0.40609
-      8   2.18552  2.70201  0.28821  2.64645     14 g x - -
+          0.03089  4.19229  4.17979  1.46634  0.26236  1.09861  0.40547
+      6   2.50266  2.06695  2.58843  0.33348      6 t x - -
+          1.38538  1.38782  1.38660  1.38538
+          0.03244  4.19073  4.08723  1.46789  0.26190  1.09694  0.40630
+      7   2.60375  2.25725  2.67883  0.28406     12 t x - -
+          1.38907  1.38673  1.38907  1.38033
+          0.03193  4.10189  4.20735  1.39886  0.28353  1.08252  0.41361
+      8   2.19186  2.93555  0.26232  2.71924     14 g x - -
           1.38629  1.38629  1.38629  1.38629
-          0.03628  4.09157  3.96779  1.46634  0.26236  1.09861  0.40547
-      9   2.16916  2.82142  0.28427  2.60854     15 g x - -
-          1.38091  1.39033  1.38365  1.39033
-          0.03566  4.00237  4.08886  1.42105  0.27636  1.08174  0.41401
-     10   2.45517  2.15232  2.42886  0.34277     18 t x - -
-          1.39065  1.39065  1.39065  1.37335
-          0.03536  4.01212  4.09576  1.42916  0.27379  1.09844  0.40555
-     11   2.10260  2.95484  0.28160  2.64222     21 g x - -
-          1.36740  1.40555  1.40555  1.36740
-          0.03843  3.92069  4.02468  1.45555  0.26562  1.09860  0.40547
-     12   2.54740  0.30185  2.61355  2.21647     26 c x - -
-          1.38748  1.38276  1.38748  1.38748
-          0.03457  4.05446  4.09623  1.43672  0.27142  1.08954  0.41003
-     13   0.28443  2.72003  2.32214  2.48149     28 a x - -
-          1.38740  1.38740  1.38298  1.38740
-          0.03441  4.05976  4.10001  1.43856  0.27085  1.09845  0.40555
-     14   0.29412  2.55413  2.49679  2.35701     30 a x - -
-          1.38194  1.39067  1.38194  1.39067
-          0.03505  4.02482  4.10005  1.42899  0.27385  1.09875  0.40540
-     15   0.18837  2.99710  2.82270  2.77556     33 a x - -
-          1.39015  1.39472  1.37503  1.38539
-          0.03725  3.97815  4.02618  1.41936  0.27690  1.09910  0.40522
-     16   0.50816  2.05151  2.22111  1.82407     37 a x - -
-          1.36727  1.38730  1.39683  1.39405
-          0.04830  3.89881  3.61610  1.36783  0.29391  1.08909  0.41026
-     17   2.11260  2.73141  0.29747  2.64152     41 g x - -
-          1.36913  1.40376  1.40376  1.36913
-          0.03705  3.93681  4.08299  1.45644  0.26535  1.09300  0.40828
-     18   2.24459  1.90539  2.34054  0.43234     46 t x - -
-          1.33632  1.42493  1.39937  1.38665
-          0.04427  3.64574  4.06297  1.63077  0.21788  1.12291  0.39354
-     19   0.44322  2.17202  2.18055  2.03175     57 a x - -
-          1.41047  1.41471  1.36338  1.35797
-          0.03970  3.81957  4.07540  1.58572  0.22916  1.12604  0.39203
-     20   0.33340  2.42691  2.40824  2.25160     66 a x - -
-          1.29389  1.44615  1.37917  1.43324
-          0.04223  3.70146  4.09459  1.52224  0.24619  1.08955  0.41003
-     21   2.50563  1.98543  2.69600  0.33746     74 t x - -
-          1.39462  1.39462  1.42862  1.32990
-          0.04184  3.80216  3.98177  1.68754  0.20454  1.07729  0.41630
-     22   2.54484  1.97505  2.66483  0.33806     84 t x - -
-          1.39134  1.39489  1.38662  1.37246
-          0.03877  3.97504  3.95038  1.41745  0.27751  1.10706  0.40127
-     23   2.10159  2.83856  0.29282  2.61635     88 g x - -
-          1.39682  1.39682  1.35536  1.39682
-          0.05046  3.75402  3.65808  1.24245  0.34063  1.10542  0.40208
-     24   2.25298  0.61854  2.50691  1.29221     90 c x - -
-          1.35803  1.49605  1.46737  1.24379
-          0.06091  3.28322  3.83564  1.80825  0.17906  1.14129  0.38479
-     25   1.27819  2.23285  0.76242  1.91259    106 g x - -
-          1.29024  1.67349  1.68279  1.04597
-          0.05752  3.44263  3.73311  2.37512  0.09762  1.13899  0.38587
-     26   1.86925  2.58352  0.39466  2.33986    131 g x - -
-          1.31084  1.49412  1.46666  1.29002
-          0.04698  3.54257  4.07715  2.06694  0.13533  1.02968  0.44180
-     27   2.38297  1.93394  2.39162  0.39800    151 t x - -
-          1.33582  1.47359  1.44163  1.30411
-          0.04951  3.48445  4.03783  2.00196  0.14511  1.12431  0.39286
-     28   2.41717  2.17810  2.62774  0.32113    170 t x - -
-          1.36805  1.48060  1.37439  1.32840
-          0.04849  3.50958  4.05014  2.35966  0.09922  1.12592  0.39208
-     29   2.57764  2.35132  2.56552  0.28512    194 t x - -
-          1.43829  1.43458  1.24787  1.43829
-          0.04667  3.56670  4.05428  2.27140  0.10889  1.12876  0.39073
-     30   2.47248  2.07688  2.62257  0.33172    215 t x - -
-          1.25120  1.52623  1.70635  1.15531
-          0.08932  3.31524  3.01336  2.61336  0.07611  1.12714  0.39150
-     31   2.25937  2.13157  2.02027  0.43957    248 t x - -
-          1.18172  1.43522  1.72841  1.28150
-          0.07936  2.93117  3.77395  2.34189  0.10109  0.91545  0.51138
-     32   2.04508  2.84981  0.30490  2.58263    280 g x - -
-          1.17665  1.66785  1.66218  1.16056
-          0.05998  3.23615  3.96853  2.64545  0.07362  1.07884  0.41550
-     33   2.45103  0.38098  2.56776  1.87147    317 c x - -
-          1.24153  1.52524  1.60663  1.22783
-          0.05538  3.39046  3.90294  2.52486  0.08346  1.11838  0.39573
-     34   2.22082  0.36258  2.75077  2.02704    347 c x - -
-          1.15008  1.62014  1.86511  1.10673
-          0.06086  3.18178  4.04341  2.75736  0.06556  1.13451  0.38799
-     35   0.27033  2.66664  2.52541  2.43767    388 a x - -
-          1.24951  1.47565  1.41392  1.42074
-          0.07123  3.00373  3.95552  2.97118  0.05260  1.13905  0.38584
-     36   2.83107  2.41670  2.97197  0.22235    439 t x - -
-          1.37071  1.57683  1.38637  1.23972
-          0.05293  3.45216  3.91807  2.33621  0.10169  1.11003  0.39980
-     37   2.52322  2.25084  2.45909  0.31611    465 t x - -
-          1.26335  1.55077  1.59008  1.19965
-          0.07504  3.13329  3.55006  2.90286  0.05643  1.10636  0.40161
-     38   0.45807  2.30687  1.98940  2.03143    512 a x - -
-          1.15472  1.67511  1.53797  1.26320
-          0.09820  3.13076  2.99876  2.62156  0.07547  1.16981  0.37168
-     39   2.37471  0.42180  2.44763  1.80427    550 c x - -
-          1.23785  1.49058  1.48364  1.35502
-          0.06081  3.19472  4.01643  2.26388  0.10975  1.04403  0.43391
-     40   2.32826  1.95481  2.36781  0.40458    578 t x - -
-          1.36586  1.46001  1.43000  1.29720
-          0.05257  3.39673  4.03256  1.75730  0.18936  1.17882  0.36765
-     41   2.68669  2.13935  2.81520  0.28200    592 t x - -
-          1.34965  1.42793  1.45781  1.31633
-          0.04735  3.57826  3.99988  1.93109  0.15664  1.13176  0.38929
-     42   2.55904  2.16444  2.70859  0.29952    609 t x - -
-          1.12072  1.61936  1.63578  1.26895
-          0.07346  3.25910  3.42962  2.65714  0.07273  1.16768  0.37264
-     43   1.99923  1.61027  2.26343  0.57851    646 t x - -
-          1.32290  1.58747  1.61095  1.11018
-          0.06656  3.08568  3.97944  2.30872  0.10468  0.98144  0.46964
-     44   0.23887  2.79899  2.55209  2.60783    675 a x - -
-          1.18557  1.50323  1.59070  1.31590
-          0.05597  3.38637  3.88222  2.28298  0.10756  1.13989  0.38545
-     45   0.29593  2.53488  2.53903  2.32335    701 a x - -
-          1.08710  1.54222  1.59276  1.40430
-          0.07539  2.94521  3.91062  1.84934  0.17119  1.12860  0.39080
-     46   2.58352  2.40524  2.76700  0.25955    725 t x - -
-          1.19685  1.58503  1.74852  1.14293
-          0.06124  3.18279  4.02089  2.64816  0.07341  1.08734  0.41115
-     47   2.13251  2.88788  0.29508  2.50964    764 g x - -
-          1.20891  1.55463  1.68206  1.19000
-          0.06526  3.12574  3.94910  2.27651  0.10830  1.09988  0.40483
-     48   2.23841  2.99164  0.25118  2.72900    792 g x - -
-          1.26330  1.55339  1.52606  1.24355
-          0.05464  3.34968  4.01313  2.57858  0.07891  1.11066  0.39949
-     49   2.57533  0.32900  2.64632  2.01501    824 c x - -
-          1.35118  1.39828  1.40141  1.39516
-          0.04340  3.79297  3.91506  1.54788  0.23914  1.12122  0.39435
-     50   0.46433  2.04127  2.23437  2.00605    833 a x - -
-          1.23062  1.36903  1.62282  1.36182
-          0.05764  3.31530  3.92762  2.13660  0.12563  1.09396  0.40780
-     51   0.27513  2.77017  2.28518  2.57549    853 a x - -
-          1.27958  1.58726  1.46109  1.25394
-          0.05750  3.30072  3.96214  2.42368  0.09277  1.13333  0.38855
-     52   0.20149  2.86434  2.84551  2.69770    883 a x - -
-          1.23645  1.62259  1.71174  1.10368
-          0.05756  3.26729  4.02702  2.37267  0.09787  1.13770  0.38648
-     53   0.26982  2.65833  2.50477  2.46835    911 a x - -
-          1.36005  1.50358  1.48100  1.22550
-          0.06921  3.37553  3.42118  2.19529  0.11802  1.13826  0.38622
-     54   0.40022  2.19284  2.22687  2.20396    934 a x - -
-          1.12070  1.60472  1.53213  1.35895
-          0.05523  3.36752  3.94966  2.24890  0.11151  1.02145  0.44640
-     55   2.11356  0.46400  2.46442  1.79955    960 c x - -
-          1.23932  1.35913  1.50478  1.46331
-          0.05187  3.47055  3.94022  2.17140  0.12106  1.10399  0.40279
-     56   1.85868  0.79440  2.22069  1.25971    983 c x - -
-          1.21951  1.50212  1.51138  1.34185
-          0.06404  3.29054  3.69705  1.69351  0.20318  1.11833  0.39575
-     57   1.33272  2.32720  0.71452  1.90215    999 g x - -
-          1.12229  1.49343  1.56653  1.42255
-          0.04920  3.46654  4.08749  2.02027  0.14228  1.15003  0.38072
-     58   2.48337  0.43652  2.46331  1.68683   1017 c x - -
-          1.34704  1.55461  1.38112  1.28222
-          0.04823  3.61532  3.90311  2.01908  0.14246  1.07530  0.41733
-     59   0.41659  2.44509  1.93972  2.20507   1034 a x - -
-          1.38198  1.38198  1.39194  1.38932
-          0.03641  3.98130  4.06929  1.40885  0.28028  1.14581  0.38268
-     60   0.41612  2.39160  1.97116  2.21075   1037 a x - -
-          1.03649  1.46430  1.57421  1.57557
-          0.04769  3.52580  4.06641  2.13225  0.12621  1.03124  0.44093
-     61   2.66264  2.12302  2.82746  0.28581   1056 t x - -
-          1.36925  1.39635  1.38930  1.39048
-          0.04097  3.97400  3.84718  1.42709  0.27444  1.10349  0.40304
-     62   2.26510  2.13196  2.42551  0.37231   1060 t x - -
-          1.37965  1.39147  1.39147  1.38264
-          0.04082  3.91610  3.90805  1.34598  0.30149  1.06394  0.42326
-     63   0.41244  2.25761  2.16787  2.12907   1062 a x - -
-          1.34515  1.41203  1.41203  1.37753
-          0.04054  3.77835  4.08203  1.36896  0.29353  1.10284  0.40336
-     64   2.51464  0.37905  2.62296  1.82008   1068 c x - -
-          1.39543  1.38753  1.39233  1.37008
-          0.03854  3.90584  4.03535  1.40940  0.28010  1.10667  0.40146
-     65   2.16380  2.11332  2.18714  0.42765   1073 t x - -
-          1.38764  1.38471  1.38519  1.38764
-          0.03575  4.05376  4.03073  1.43270  0.27268  1.08530  0.41219
-     66   2.79349  2.39141  2.87271  0.23478   1075 t x - -
-          1.37227  1.39101  1.39101  1.39101
-          0.03597  4.01447  4.05827  1.42619  0.27473  1.09128  0.40915
-     67   2.82488  2.47749  2.93179  0.21887   1078 t x - -
-          1.38141  1.39112  1.38915  1.38353
-          0.03661  3.99477  4.04370  1.40962  0.28003  1.10594  0.40182
-     68   2.77679  2.30433  2.90694  0.24425   1081 t x - -
-          1.37593  1.38989  1.45520  1.32825
-          0.04447  3.68736  3.99242  1.66809  0.20900  1.07378  0.41811
-     69   2.47698  3.17398  0.19595  2.95437   1093 g x - -
-          1.38264  1.38264  1.39734  1.38264
-          0.05358  3.96553  3.40487  1.43194  0.27292  1.08430  0.41270
-     70   2.84327  0.27906  2.97336  2.00890   1097 c x - -
+          0.03142  4.21107  4.12859  1.46634  0.26236  1.09861  0.40547
+      9   2.07901  2.78051  0.30613  2.56850     15 g x - -
+          1.38350  1.38805  1.38560  1.38805
+          0.03149  4.16813  4.16598  1.44243  0.26965  1.09240  0.40859
+     10   2.57980  2.23058  2.70339  0.28799     18 t x - -
+          1.38730  1.38730  1.38730  1.38328
+          0.03029  4.19523  4.21518  1.45741  0.26506  1.09679  0.40638
+     11   2.09819  2.95912  0.27277  2.74586     21 g x - -
+          1.38506  1.38753  1.38753  1.38506
+          0.03438  4.20499  3.96976  1.46555  0.26260  1.09847  0.40554
+     12   2.73996  0.25202  2.91136  2.26531     26 c x - -
+          1.38701  1.38416  1.38701  1.38701
+          0.03125  4.18883  4.16044  1.44829  0.26784  1.07539  0.41728
+     13   0.27970  2.57147  2.50665  2.45312     28 a x - -
+          1.38695  1.38695  1.38433  1.38695
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           1.38629  1.38629  1.38629  1.38629
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-     74   0.27014  2.61416  2.53262  2.47636   1106 a x - -
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           1.38629  1.38629  1.38629  1.38629
-          0.03426  4.08396  4.08396  1.46634  0.26236  1.09364  0.40796
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           1.38629  1.38629  1.38629  1.38629
-          0.03466  4.07266  4.07266  1.46634  0.26236  1.09861  0.40547
-     77   2.20588  0.45134  2.35553  1.84373   1109 c x - -
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           1.38629  1.38629  1.38629  1.38629
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+     78   2.61838  2.21121  2.70403  0.28691   1110 t x - -
           1.38629  1.38629  1.38629  1.38629
-          0.03711  4.00561  4.00561  1.46634  0.26236  1.09861  0.40547
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           1.38629  1.38629  1.38629  1.38629
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-     80   0.17484  3.04770  2.86638  2.88183   1112 a x - -
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+     80   0.12738  3.34162  3.14941  3.18577   1112 a x - -
           1.38629  1.38629  1.38629  1.38629
-          0.02045  3.90014        *  1.46634  0.26236  0.00000        *
+          0.01820  4.01567        *  1.46634  0.26236  0.00000        *
 //