diff test-data/MADE1.hmm @ 0:dca536c5cca5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
author iuc
date Sat, 25 Jun 2016 15:05:21 -0400
parents
children f92edeb5e4c4
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/MADE1.hmm	Sat Jun 25 15:05:21 2016 -0400
@@ -0,0 +1,265 @@
+HMMER3/f [3.1b2 | February 2015]
+NAME  MADE1
+ACC   DF0000629.2
+DESC  MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon
+LENG  80
+MAXL  425
+ALPH  DNA
+RF    yes
+MM    no
+CONS  yes
+CS    no
+MAP   yes
+DATE  Sat Jun 25 17:24:24 2016
+NSEQ  1997
+EFFN  3.911818
+CKSUM 3015610723
+STATS LOCAL MSV       -8.5408  0.71858
+STATS LOCAL VITERBI   -9.6224  0.71858
+STATS LOCAL FORWARD   -3.4150  0.71858
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.24533  1.59094  1.62722  1.16493
+          1.38629  1.38629  1.38629  1.38629
+          0.21058  4.11281  1.75146  1.46634  0.26236  0.00000        *
+      1   2.69765  2.44396  2.81521  0.24089      1 t x - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03960  3.94183  3.94183  1.46634  0.26236  1.10301  0.40327
+      2   2.72939  2.37873  2.85832  0.24244      2 t x - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03725  4.00179  4.00179  1.46634  0.26236  1.21367  0.35255
+      3   0.16099  3.16370  2.87328  2.99734      3 a x - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03604  4.03416  4.03416  1.46634  0.26236  1.32877  0.30762
+      4   1.98862  2.42132  0.42649  2.10770      4 g x - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03539  4.05203  4.05203  1.46634  0.26236  1.35213  0.29933
+      5   1.96369  2.69532  0.36534  2.32099      5 g x - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03764  4.06427  3.92372  1.46634  0.26236  1.00259  0.45717
+      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  1.50442  0.25122  1.12269  0.39364
+      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  1.40070  0.28293  1.44046  0.27026
+      8   2.18552  2.70201  0.28821  2.64645     14 g x - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03628  4.09157  3.96779  1.46634  0.26236  1.26997  0.32967
+      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  1.38021  0.28972  1.26961  0.32981
+     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  1.39554  0.28462  1.25024  0.33748
+     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  1.44733  0.26814  1.15789  0.37709
+     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  1.40847  0.28040  1.17686  0.36852
+     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  1.41198  0.27926  0.97690  0.47237
+     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  1.39522  0.28473  1.16906  0.37202
+     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  1.37955  0.28994  1.16870  0.37218
+     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  1.29026  0.32186  1.08301  0.41336
+     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  1.44872  0.26771  1.09472  0.40742
+     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  1.70501  0.20061  1.19872  0.35894
+     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  1.65588  0.21186  1.24390  0.34004
+     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  1.55158  0.23815  1.01872  0.44794
+     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  1.80466  0.17976  1.00279  0.45705
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+          1.39134  1.39489  1.38662  1.37246
+          0.03877  3.97504  3.95038  1.37620  0.29107  1.13932  0.38572
+     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  1.08330  0.41321  1.13019  0.39004
+     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  1.89752  0.16245  1.28788  0.32276
+     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  2.58671  0.07825  1.26818  0.33037
+     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  2.25245  0.11109  0.86163  0.54900
+     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  2.15951  0.12260  1.21681  0.35122
+     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  2.58370  0.07850  1.22399  0.34822
+     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  2.49706  0.08591  1.23744  0.34267
+     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  2.81842  0.06156  1.22909  0.34610
+     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  2.46269  0.08906  0.60457  0.79034
+     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  2.83684  0.06040  1.01952  0.44749
+     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  2.73920  0.06680  1.18729  0.36391
+     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  2.94504  0.05403  1.25991  0.33363
+     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  3.13655  0.04440  1.28173  0.32512
+     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  2.54402  0.08181  1.14651  0.38235
+     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  3.08962  0.04659  1.13108  0.38962
+     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  2.79197  0.06326  1.39915  0.28343
+     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  2.41851  0.09327  0.94671  0.49105
+     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  1.84862  0.17133  1.40979  0.27997
+     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  2.09424  0.13144  1.22129  0.34934
+     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  2.85641  0.05919  1.38363  0.28857
+     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  2.44774  0.09046  0.75593  0.63407
+     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  2.46900  0.08847  1.27945  0.32599
+     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  1.91623  0.15918  1.22327  0.34852
+     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  2.82961  0.06085  1.05474  0.42814
+     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  2.41448  0.09367  1.10396  0.40280
+     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  2.78872  0.06347  1.15133  0.38012
+     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  1.59549  0.22666  1.20075  0.35806
+     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  2.28791  0.10700  1.07910  0.41536
+     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  2.60776  0.07656  1.25708  0.33475
+     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  2.54508  0.08172  1.27391  0.32814
+     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  2.36646  0.09851  1.27560  0.32748
+     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  2.42917  0.09224  0.84774  0.55928
+     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  2.35854  0.09933  1.12102  0.39445
+     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  1.75742  0.18933  1.18410  0.36532
+     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  2.17995  0.11996  1.31769  0.31164
+     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  2.20911  0.11631  1.00864  0.45368
+     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  1.35873  0.29704  1.31330  0.31325
+     60   0.41612  2.39160  1.97116  2.21075   1037 a x - -
+          1.03649  1.46430  1.57421  1.57557
+          0.04787  3.52599  4.05584  2.32461  0.10294  0.84329  0.56263
+     61   2.66264  2.12302  2.82746  0.28581   1056 t x - -
+          1.36925  1.39635  1.38930  1.39048
+          0.04103  3.97406  3.84419  1.39433  0.28502  1.12555  0.39227
+     62   2.26510  2.13196  2.42551  0.37231   1060 t x - -
+          1.37965  1.39147  1.39147  1.38264
+          0.04136  3.91664  3.88204  1.24613  0.33914  0.95630  0.48501
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+          1.34515  1.41203  1.41203  1.37753
+          0.04086  3.77867  4.06371  1.30483  0.31638  1.13245  0.38897
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+          1.39543  1.38753  1.39233  1.37008
+          0.03884  3.90614  4.01884  1.36573  0.29463  1.15716  0.37743
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+          1.38764  1.38471  1.38519  1.38764
+          0.03603  4.05405  4.01529  1.40080  0.28289  1.06383  0.42332
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+          1.37227  1.39101  1.39101  1.39101
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+          1.38141  1.39112  1.38915  1.38353
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+          1.37593  1.38989  1.45520  1.32825
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+          1.38536  1.38781  1.38781  1.38421
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+          1.38629  1.38629  1.38629  1.38629
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+          1.38629  1.38629  1.38629  1.38629
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+     75   0.52873  2.16549  1.91736  1.90409   1107 a x - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04237  4.09207  3.69758  1.46634  0.26236  1.41112  0.27954
+     76   2.33134  0.38082  2.65861  1.90055   1108 c x - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04659  4.08459  3.55121  1.46634  0.26236  1.54765  0.23921
+     77   2.20588  0.45134  2.35553  1.84373   1109 c x - -
+          1.38629  1.38629  1.38629  1.38629
+          0.05904  4.07266  3.21140  1.46634  0.26236  1.68734  0.20458
+     78   2.69018  2.22054  2.82311  0.26898   1110 t x - -
+          1.38629  1.38629  1.38629  1.38629
+          0.08061  4.04912  2.81320  1.46634  0.26236  1.91269  0.15980
+     79   0.16248  3.15867  2.86159  2.98963   1111 a x - -
+          1.38629  1.38629  1.38629  1.38629
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+     80   0.17484  3.04770  2.86638  2.88183   1112 a x - -
+          1.38629  1.38629  1.38629  1.38629
+          0.02045  3.90014        *  1.46634  0.26236  0.00000        *
+//