------------------------------------------------------------- Wise2 - database searching mode Program: estwisedb version: $Name: wise2-2-0 $ released: unreleased This program is freely distributed under a Gnu Public License. See -version for more info on copyright Bugs and credits to Ewan Birney ------------------------------------------------------------- Algorithm type: EstWise Search algorithm: 333 Implementation: Single Threaded processor (serial) Search mode: Single protein vs cdna db Protein info from: rrm.HMM Dna info from: dna.db Start/End local Codon Table: codon.table Subs error: 0.01 Indel error: 0.01 Null model: synchronous Protein Insertion: modelled Alignment Alg 333 [Warning: Can't fit histogram to a db smaller than 1,000] #High Score list #Protein ID DNA Str ID Bits Evalue -------------------------------------------------------------------------- Protein SEED DNA [+] MMD728 84.99 Protein SEED DNA [+] MMD729 84.99 Protein SEED DNA [+] MMFLI2X 84.99 Protein SEED DNA [+] SAHNRNPH 69.54 #Alignments ----------------------------------------------------------------------- >Results for SEED vs MMD728 (forward) [1] estwisedb output Score 84.99 bits over entire alignment. This will be different from per-alignment scores. See manual for details For computer parsable output, try estwisedb -help or read the manual Scores as bits over a synchronous coding model Alignment 1 Score 85.04 (Bits) SEED 1 LFVGNLPPDVTEEDLKDLFSKFGPIVSIKIVRDIIEKPKETGKSKGFAF FVG++ +D+ E+ L+D+F+++G+I+ I+I++D + GK +GFAF IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTD-----RGSGKKRGFAF MMD728 343 atgggaaggaggccccgttgctgaaggagaaag agagaaagtgt tttggtaaacaaaatgaataaagatattattca ggggaaggtct ctttttaactaatcaatttggtggtagaatgtc actgaggcttt SEED 50 VEFESEEDAEKALEALNGKELGGRKLRV V+F+++++ +K + ++++G++++V VTFDDHDSVDKIVI-QKYHTVNGHNCEV MMD728 475 gatggcgtggaaga catcagagcatgg tctaaaactaattt aaaactagaagat tcttctctgtgttt gacttgtccctaa // -9.59 [-1:0 "MATCH_STATE" -3324],[341:344 "CODON" -3324] 3.14 [0:1 "MATCH_STATE" 1088],[344:347 "CODON" 1088] 3.05 [1:2 "MATCH_STATE" 1058],[347:350 "CODON" 1058] 2.39 [2:3 "MATCH_STATE" 827],[350:353 "CODON" 827] 1.72 [3:4 "MATCH_STATE" 596],[353:356 "CODON" 596] 0.58 [4:5 "MATCH_STATE" 202],[356:359 "CODON" 202] -0.64 [5:6 "MATCH_STATE" -221],[359:362 "CODON" -221] 0.56 [6:7 "MATCH_STATE" 193],[362:365 "CODON" 193] 2.33 [7:8 "MATCH_STATE" 807],[365:368 "CODON" 807] 1.65 [8:9 "MATCH_STATE" 572],[368:371 "CODON" 572] -1.23 [9:10 "MATCH_STATE" -428],[371:374 "CODON" -428] 2.40 [10:11 "MATCH_STATE" 833],[374:377 "CODON" 833] 0.44 [11:12 "MATCH_STATE" 154],[377:380 "CODON" 154] -0.91 [12:13 "MATCH_STATE" -314],[380:383 "CODON" -314] 2.74 [13:14 "MATCH_STATE" 951],[383:386 "CODON" 951] 1.71 [14:15 "MATCH_STATE" 593],[386:389 "CODON" 593] 2.05 [15:16 "MATCH_STATE" 710],[389:392 "CODON" 710] 1.12 [16:17 "MATCH_STATE" 387],[392:395 "CODON" 387] 4.13 [17:18 "MATCH_STATE" 1430],[395:398 "CODON" 1430] 0.90 [18:19 "MATCH_STATE" 311],[398:401 "CODON" 311] 1.64 [19:20 "MATCH_STATE" 568],[401:404 "CODON" 568] 2.74 [20:21 "MATCH_STATE" 949],[404:407 "CODON" 949] 3.43 [21:22 "MATCH_STATE" 1188],[407:410 "CODON" 1188] 1.26 [22:23 "MATCH_STATE" 436],[410:413 "CODON" 436] 2.63 [23:24 "MATCH_STATE" 913],[413:416 "CODON" 913] 1.12 [24:25 "MATCH_STATE" 388],[416:419 "CODON" 388] -2.39 [25:26 "MATCH_STATE" -827],[419:422 "CODON" -827] 2.14 [26:27 "MATCH_STATE" 742],[422:425 "CODON" 742] 0.45 [27:28 "MATCH_STATE" 156],[425:428 "CODON" 156] 2.09 [28:29 "MATCH_STATE" 724],[428:431 "CODON" 724] 1.87 [29:30 "MATCH_STATE" 647],[431:434 "CODON" 647] 0.71 [30:31 "MATCH_STATE" 245],[434:437 "CODON" 245] 2.89 [31:32 "MATCH_STATE" 1001],[437:440 "CODON" 1001] -0.11 [32:33 "DELETE_STATE" -38],[440:440 "INSERT" -38] -0.07 [33:34 "DELETE_STATE" -24],[440:440 "INSERT" -24] -0.05 [34:35 "DELETE_STATE" -18],[440:440 "INSERT" -18] -0.05 [35:36 "DELETE_STATE" -18],[440:440 "INSERT" -18] -0.05 [36:37 "DELETE_STATE" -19],[440:440 "INSERT" -19] 0.65 [37:38 "MATCH_STATE" 226],[440:443 "CODON" 226] -0.69 [38:39 "MATCH_STATE" -240],[443:446 "CODON" -240] -0.09 [39:40 "MATCH_STATE" -31],[446:449 "CODON" -31] 2.43 [40:41 "MATCH_STATE" 843],[449:452 "CODON" 843] 1.87 [41:42 "MATCH_STATE" 648],[452:455 "CODON" 648] -0.52 [42:43 "MATCH_STATE" -181],[455:458 "CODON" -181] 2.18 [43:44 "MATCH_STATE" 756],[458:461 "CODON" 756] 3.16 [44:45 "MATCH_STATE" 1095],[461:464 "CODON" 1095] 2.99 [45:46 "MATCH_STATE" 1035],[464:467 "CODON" 1035] 2.44 [46:47 "MATCH_STATE" 846],[467:470 "CODON" 846] 3.94 [47:48 "MATCH_STATE" 1367],[470:473 "CODON" 1367] 3.22 [48:49 "MATCH_STATE" 1115],[473:476 "CODON" 1115] 1.24 [49:50 "MATCH_STATE" 429],[476:479 "CODON" 429] 3.92 [50:51 "MATCH_STATE" 1359],[479:482 "CODON" 1359] 1.09 [51:52 "MATCH_STATE" 379],[482:485 "CODON" 379] 1.85 [52:53 "MATCH_STATE" 640],[485:488 "CODON" 640] 1.41 [53:54 "MATCH_STATE" 489],[488:491 "CODON" 489] 1.56 [54:55 "MATCH_STATE" 539],[491:494 "CODON" 539] 1.20 [55:56 "MATCH_STATE" 416],[494:497 "CODON" 416] -0.02 [56:57 "MATCH_STATE" -6],[497:500 "CODON" -6] 0.94 [57:58 "MATCH_STATE" 325],[500:503 "CODON" 325] 2.25 [58:59 "MATCH_STATE" 781],[503:506 "CODON" 781] -0.21 [59:60 "MATCH_STATE" -73],[506:509 "CODON" -73] 1.52 [60:61 "MATCH_STATE" 526],[509:512 "CODON" 526] -0.86 [61:62 "MATCH_STATE" -297],[512:515 "CODON" -297] -2.45 [62:63 "DELETE_STATE" -848],[515:515 "INSERT" -848] -0.46 [63:64 "MATCH_STATE" -159],[515:518 "CODON" -159] -0.37 [64:65 "MATCH_STATE" -127],[518:521 "CODON" -127] -0.68 [65:66 "MATCH_STATE" -236],[521:524 "CODON" -236] 0.88 [66:67 "MATCH_STATE" 304],[524:527 "CODON" 304] 0.64 [67:68 "MATCH_STATE" 223],[527:530 "CODON" 223] 1.19 [68:69 "MATCH_STATE" 412],[530:533 "CODON" 412] 1.63 [69:70 "MATCH_STATE" 565],[533:536 "CODON" 565] 2.67 [70:71 "MATCH_STATE" 925],[536:539 "CODON" 925] 1.82 [71:72 "MATCH_STATE" 630],[539:542 "CODON" 630] 0.16 [72:73 "MATCH_STATE" 55],[542:545 "CODON" 55] 0.81 [73:74 "MATCH_STATE" 282],[545:548 "CODON" 282] 0.28 [74:75 "MATCH_STATE" 98],[548:551 "CODON" 98] 2.67 [75:76 "MATCH_STATE" 926],[551:554 "CODON" 926] -0.06 [76:0 "END" -20],[554:554 "END" -20] // >Results for SEED vs MMD729 (forward) [2] estwisedb output Score 84.99 bits over entire alignment. This will be different from per-alignment scores. See manual for details For computer parsable output, try estwisedb -help or read the manual Scores as bits over a synchronous coding model Alignment 1 Score 85.04 (Bits) SEED 1 LFVGNLPPDVTEEDLKDLFSKFGPIVSIKIVRDIIEKPKETGKSKGFAF FVG++ +D+ E+ L+D+F+++G+I+ I+I++D + GK +GFAF IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTD-----RGSGKKRGFAF MMD729 343 atgggaaggaggccccgttgctgaaggagaaag agagaaagtgt tttggtaaacaaaatgaataaagatattattca ggggaaggtct ctttttaactaatcaatttggtggtagaatgtc actgaggcttt SEED 50 VEFESEEDAEKALEALNGKELGGRKLRV V+F+++++ +K + ++++G++++V VTFDDHDSVDKIVI-QKYHTVNGHNCEV MMD729 475 gatggcgtggaaga catcagagcatgg tctaaaactaattt aaaactagaagat tcttctctgtgttt gacttgtccctaa // -9.59 [-1:0 "MATCH_STATE" -3324],[341:344 "CODON" -3324] 3.14 [0:1 "MATCH_STATE" 1088],[344:347 "CODON" 1088] 3.05 [1:2 "MATCH_STATE" 1058],[347:350 "CODON" 1058] 2.39 [2:3 "MATCH_STATE" 827],[350:353 "CODON" 827] 1.72 [3:4 "MATCH_STATE" 596],[353:356 "CODON" 596] 0.58 [4:5 "MATCH_STATE" 202],[356:359 "CODON" 202] -0.64 [5:6 "MATCH_STATE" -221],[359:362 "CODON" -221] 0.56 [6:7 "MATCH_STATE" 193],[362:365 "CODON" 193] 2.33 [7:8 "MATCH_STATE" 807],[365:368 "CODON" 807] 1.65 [8:9 "MATCH_STATE" 572],[368:371 "CODON" 572] -1.23 [9:10 "MATCH_STATE" -428],[371:374 "CODON" -428] 2.40 [10:11 "MATCH_STATE" 833],[374:377 "CODON" 833] 0.44 [11:12 "MATCH_STATE" 154],[377:380 "CODON" 154] -0.91 [12:13 "MATCH_STATE" -314],[380:383 "CODON" -314] 2.74 [13:14 "MATCH_STATE" 951],[383:386 "CODON" 951] 1.71 [14:15 "MATCH_STATE" 593],[386:389 "CODON" 593] 2.05 [15:16 "MATCH_STATE" 710],[389:392 "CODON" 710] 1.12 [16:17 "MATCH_STATE" 387],[392:395 "CODON" 387] 4.13 [17:18 "MATCH_STATE" 1430],[395:398 "CODON" 1430] 0.90 [18:19 "MATCH_STATE" 311],[398:401 "CODON" 311] 1.64 [19:20 "MATCH_STATE" 568],[401:404 "CODON" 568] 2.74 [20:21 "MATCH_STATE" 949],[404:407 "CODON" 949] 3.43 [21:22 "MATCH_STATE" 1188],[407:410 "CODON" 1188] 1.26 [22:23 "MATCH_STATE" 436],[410:413 "CODON" 436] 2.63 [23:24 "MATCH_STATE" 913],[413:416 "CODON" 913] 1.12 [24:25 "MATCH_STATE" 388],[416:419 "CODON" 388] -2.39 [25:26 "MATCH_STATE" -827],[419:422 "CODON" -827] 2.14 [26:27 "MATCH_STATE" 742],[422:425 "CODON" 742] 0.45 [27:28 "MATCH_STATE" 156],[425:428 "CODON" 156] 2.09 [28:29 "MATCH_STATE" 724],[428:431 "CODON" 724] 1.87 [29:30 "MATCH_STATE" 647],[431:434 "CODON" 647] 0.71 [30:31 "MATCH_STATE" 245],[434:437 "CODON" 245] 2.89 [31:32 "MATCH_STATE" 1001],[437:440 "CODON" 1001] -0.11 [32:33 "DELETE_STATE" -38],[440:440 "INSERT" -38] -0.07 [33:34 "DELETE_STATE" -24],[440:440 "INSERT" -24] -0.05 [34:35 "DELETE_STATE" -18],[440:440 "INSERT" -18] -0.05 [35:36 "DELETE_STATE" -18],[440:440 "INSERT" -18] -0.05 [36:37 "DELETE_STATE" -19],[440:440 "INSERT" -19] 0.65 [37:38 "MATCH_STATE" 226],[440:443 "CODON" 226] -0.69 [38:39 "MATCH_STATE" -240],[443:446 "CODON" -240] -0.09 [39:40 "MATCH_STATE" -31],[446:449 "CODON" -31] 2.43 [40:41 "MATCH_STATE" 843],[449:452 "CODON" 843] 1.87 [41:42 "MATCH_STATE" 648],[452:455 "CODON" 648] -0.52 [42:43 "MATCH_STATE" -181],[455:458 "CODON" -181] 2.18 [43:44 "MATCH_STATE" 756],[458:461 "CODON" 756] 3.16 [44:45 "MATCH_STATE" 1095],[461:464 "CODON" 1095] 2.99 [45:46 "MATCH_STATE" 1035],[464:467 "CODON" 1035] 2.44 [46:47 "MATCH_STATE" 846],[467:470 "CODON" 846] 3.94 [47:48 "MATCH_STATE" 1367],[470:473 "CODON" 1367] 3.22 [48:49 "MATCH_STATE" 1115],[473:476 "CODON" 1115] 1.24 [49:50 "MATCH_STATE" 429],[476:479 "CODON" 429] 3.92 [50:51 "MATCH_STATE" 1359],[479:482 "CODON" 1359] 1.09 [51:52 "MATCH_STATE" 379],[482:485 "CODON" 379] 1.85 [52:53 "MATCH_STATE" 640],[485:488 "CODON" 640] 1.41 [53:54 "MATCH_STATE" 489],[488:491 "CODON" 489] 1.56 [54:55 "MATCH_STATE" 539],[491:494 "CODON" 539] 1.20 [55:56 "MATCH_STATE" 416],[494:497 "CODON" 416] -0.02 [56:57 "MATCH_STATE" -6],[497:500 "CODON" -6] 0.94 [57:58 "MATCH_STATE" 325],[500:503 "CODON" 325] 2.25 [58:59 "MATCH_STATE" 781],[503:506 "CODON" 781] -0.21 [59:60 "MATCH_STATE" -73],[506:509 "CODON" -73] 1.52 [60:61 "MATCH_STATE" 526],[509:512 "CODON" 526] -0.86 [61:62 "MATCH_STATE" -297],[512:515 "CODON" -297] -2.45 [62:63 "DELETE_STATE" -848],[515:515 "INSERT" -848] -0.46 [63:64 "MATCH_STATE" -159],[515:518 "CODON" -159] -0.37 [64:65 "MATCH_STATE" -127],[518:521 "CODON" -127] -0.68 [65:66 "MATCH_STATE" -236],[521:524 "CODON" -236] 0.88 [66:67 "MATCH_STATE" 304],[524:527 "CODON" 304] 0.64 [67:68 "MATCH_STATE" 223],[527:530 "CODON" 223] 1.19 [68:69 "MATCH_STATE" 412],[530:533 "CODON" 412] 1.63 [69:70 "MATCH_STATE" 565],[533:536 "CODON" 565] 2.67 [70:71 "MATCH_STATE" 925],[536:539 "CODON" 925] 1.82 [71:72 "MATCH_STATE" 630],[539:542 "CODON" 630] 0.16 [72:73 "MATCH_STATE" 55],[542:545 "CODON" 55] 0.81 [73:74 "MATCH_STATE" 282],[545:548 "CODON" 282] 0.28 [74:75 "MATCH_STATE" 98],[548:551 "CODON" 98] 2.67 [75:76 "MATCH_STATE" 926],[551:554 "CODON" 926] -0.06 [76:0 "END" -20],[554:554 "END" -20] // >Results for SEED vs MMFLI2X (forward) [3] estwisedb output Score 84.99 bits over entire alignment. This will be different from per-alignment scores. See manual for details For computer parsable output, try estwisedb -help or read the manual Scores as bits over a synchronous coding model Alignment 1 Score 85.04 (Bits) SEED 1 LFVGNLPPDVTEEDLKDLFSKFGPIVSIKIVRDIIEKPKETGKSKGFAF FVG++ +D+ E+ L+D+F+++G+I+ I+I++D + GK +GFAF IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTD-----RGSGKKRGFAF MMFLI2X 378 atgggaaggaggccccgttgctgaaggagaaag agagaaagtgt tttggtaaacaaaatgaataaagatattattca ggggaaggtct ctttttaactaatcaatttggtggtagaatgtc actgaggcttt SEED 50 VEFESEEDAEKALEALNGKELGGRKLRV V+F+++++ +K + ++++G++++V VTFDDHDSVDKIVI-QKYHTVNGHNCEV MMFLI2X 510 gatggcgtggaaga catcagagcatgg tctaaaactaattt aaaactagaagat tcttctctgtgttt gacttgtccctaa // -9.59 [-1:0 "MATCH_STATE" -3324],[376:379 "CODON" -3324] 3.14 [0:1 "MATCH_STATE" 1088],[379:382 "CODON" 1088] 3.05 [1:2 "MATCH_STATE" 1058],[382:385 "CODON" 1058] 2.39 [2:3 "MATCH_STATE" 827],[385:388 "CODON" 827] 1.72 [3:4 "MATCH_STATE" 596],[388:391 "CODON" 596] 0.58 [4:5 "MATCH_STATE" 202],[391:394 "CODON" 202] -0.64 [5:6 "MATCH_STATE" -221],[394:397 "CODON" -221] 0.56 [6:7 "MATCH_STATE" 193],[397:400 "CODON" 193] 2.33 [7:8 "MATCH_STATE" 807],[400:403 "CODON" 807] 1.65 [8:9 "MATCH_STATE" 572],[403:406 "CODON" 572] -1.23 [9:10 "MATCH_STATE" -428],[406:409 "CODON" -428] 2.40 [10:11 "MATCH_STATE" 833],[409:412 "CODON" 833] 0.44 [11:12 "MATCH_STATE" 154],[412:415 "CODON" 154] -0.91 [12:13 "MATCH_STATE" -314],[415:418 "CODON" -314] 2.74 [13:14 "MATCH_STATE" 951],[418:421 "CODON" 951] 1.71 [14:15 "MATCH_STATE" 593],[421:424 "CODON" 593] 2.05 [15:16 "MATCH_STATE" 710],[424:427 "CODON" 710] 1.12 [16:17 "MATCH_STATE" 387],[427:430 "CODON" 387] 4.13 [17:18 "MATCH_STATE" 1430],[430:433 "CODON" 1430] 0.90 [18:19 "MATCH_STATE" 311],[433:436 "CODON" 311] 1.64 [19:20 "MATCH_STATE" 568],[436:439 "CODON" 568] 2.74 [20:21 "MATCH_STATE" 949],[439:442 "CODON" 949] 3.43 [21:22 "MATCH_STATE" 1188],[442:445 "CODON" 1188] 1.26 [22:23 "MATCH_STATE" 436],[445:448 "CODON" 436] 2.63 [23:24 "MATCH_STATE" 913],[448:451 "CODON" 913] 1.12 [24:25 "MATCH_STATE" 388],[451:454 "CODON" 388] -2.39 [25:26 "MATCH_STATE" -827],[454:457 "CODON" -827] 2.14 [26:27 "MATCH_STATE" 742],[457:460 "CODON" 742] 0.45 [27:28 "MATCH_STATE" 156],[460:463 "CODON" 156] 2.09 [28:29 "MATCH_STATE" 724],[463:466 "CODON" 724] 1.87 [29:30 "MATCH_STATE" 647],[466:469 "CODON" 647] 0.71 [30:31 "MATCH_STATE" 245],[469:472 "CODON" 245] 2.89 [31:32 "MATCH_STATE" 1001],[472:475 "CODON" 1001] -0.11 [32:33 "DELETE_STATE" -38],[475:475 "INSERT" -38] -0.07 [33:34 "DELETE_STATE" -24],[475:475 "INSERT" -24] -0.05 [34:35 "DELETE_STATE" -18],[475:475 "INSERT" -18] -0.05 [35:36 "DELETE_STATE" -18],[475:475 "INSERT" -18] -0.05 [36:37 "DELETE_STATE" -19],[475:475 "INSERT" -19] 0.65 [37:38 "MATCH_STATE" 226],[475:478 "CODON" 226] -0.69 [38:39 "MATCH_STATE" -240],[478:481 "CODON" -240] -0.09 [39:40 "MATCH_STATE" -31],[481:484 "CODON" -31] 2.43 [40:41 "MATCH_STATE" 843],[484:487 "CODON" 843] 1.87 [41:42 "MATCH_STATE" 648],[487:490 "CODON" 648] -0.52 [42:43 "MATCH_STATE" -181],[490:493 "CODON" -181] 2.18 [43:44 "MATCH_STATE" 756],[493:496 "CODON" 756] 3.16 [44:45 "MATCH_STATE" 1095],[496:499 "CODON" 1095] 2.99 [45:46 "MATCH_STATE" 1035],[499:502 "CODON" 1035] 2.44 [46:47 "MATCH_STATE" 846],[502:505 "CODON" 846] 3.94 [47:48 "MATCH_STATE" 1367],[505:508 "CODON" 1367] 3.22 [48:49 "MATCH_STATE" 1115],[508:511 "CODON" 1115] 1.24 [49:50 "MATCH_STATE" 429],[511:514 "CODON" 429] 3.92 [50:51 "MATCH_STATE" 1359],[514:517 "CODON" 1359] 1.09 [51:52 "MATCH_STATE" 379],[517:520 "CODON" 379] 1.85 [52:53 "MATCH_STATE" 640],[520:523 "CODON" 640] 1.41 [53:54 "MATCH_STATE" 489],[523:526 "CODON" 489] 1.56 [54:55 "MATCH_STATE" 539],[526:529 "CODON" 539] 1.20 [55:56 "MATCH_STATE" 416],[529:532 "CODON" 416] -0.02 [56:57 "MATCH_STATE" -6],[532:535 "CODON" -6] 0.94 [57:58 "MATCH_STATE" 325],[535:538 "CODON" 325] 2.25 [58:59 "MATCH_STATE" 781],[538:541 "CODON" 781] -0.21 [59:60 "MATCH_STATE" -73],[541:544 "CODON" -73] 1.52 [60:61 "MATCH_STATE" 526],[544:547 "CODON" 526] -0.86 [61:62 "MATCH_STATE" -297],[547:550 "CODON" -297] -2.45 [62:63 "DELETE_STATE" -848],[550:550 "INSERT" -848] -0.46 [63:64 "MATCH_STATE" -159],[550:553 "CODON" -159] -0.37 [64:65 "MATCH_STATE" -127],[553:556 "CODON" -127] -0.68 [65:66 "MATCH_STATE" -236],[556:559 "CODON" -236] 0.88 [66:67 "MATCH_STATE" 304],[559:562 "CODON" 304] 0.64 [67:68 "MATCH_STATE" 223],[562:565 "CODON" 223] 1.19 [68:69 "MATCH_STATE" 412],[565:568 "CODON" 412] 1.63 [69:70 "MATCH_STATE" 565],[568:571 "CODON" 565] 2.67 [70:71 "MATCH_STATE" 925],[571:574 "CODON" 925] 1.82 [71:72 "MATCH_STATE" 630],[574:577 "CODON" 630] 0.16 [72:73 "MATCH_STATE" 55],[577:580 "CODON" 55] 0.81 [73:74 "MATCH_STATE" 282],[580:583 "CODON" 282] 0.28 [74:75 "MATCH_STATE" 98],[583:586 "CODON" 98] 2.67 [75:76 "MATCH_STATE" 926],[586:589 "CODON" 926] -0.06 [76:0 "END" -20],[589:589 "END" -20] // >Results for SEED vs SAHNRNPH (forward) [4] estwisedb output Score 69.54 bits over entire alignment. This will be different from per-alignment scores. See manual for details For computer parsable output, try estwisedb -help or read the manual Scores as bits over a synchronous coding model Alignment 1 Score 69.60 (Bits) SEED 1 LFVGNLPPDVTEEDLKDLFSKFGPIVSIKIVRDIIEKPKETGKSKGFAF LF+G+L + +T+E LK++F++ G+IV++ +++D ++T++S+GF+F LFIGGLDYRTTDESLKQHFEQWGEIVDVVVMKD-----PKTKRSRGFGF SAHNRNPH 148 ctaggtgtaaaggtcacctgctggagggggaag caaaatagtgt tttggtaagccaactaaataaggattattttaa cacagcggtgt atttagctaatcgcagattaagtaattggtggc taggggagtgc SEED 50 VEFESEEDAEKALEALNGKELGGRKLRV +++ ++A + ++++GR+++ ITYSRAHMVDDAQN-ARPHKVDGRVVEP SAHNRNPH 280 aattagcaggggca gcccagggcgggc tcacgcattaacaa cgcaataggttac atccaatggtttgt tcacatttttggg // -9.89 [-1:0 "MATCH_STATE" -3429],[146:149 "CODON" -3429] 3.14 [0:1 "MATCH_STATE" 1088],[149:152 "CODON" 1088] 2.22 [1:2 "MATCH_STATE" 769],[152:155 "CODON" 769] 2.39 [2:3 "MATCH_STATE" 827],[155:158 "CODON" 827] 1.72 [3:4 "MATCH_STATE" 595],[158:161 "CODON" 595] 2.86 [4:5 "MATCH_STATE" 992],[161:164 "CODON" 992] -0.47 [5:6 "MATCH_STATE" -162],[164:167 "CODON" -162] 1.89 [6:7 "MATCH_STATE" 654],[167:170 "CODON" 654] -1.86 [7:8 "MATCH_STATE" -643],[170:173 "CODON" -643] 1.65 [8:9 "MATCH_STATE" 572],[173:176 "CODON" 572] 2.86 [9:10 "MATCH_STATE" 992],[176:179 "CODON" 992] 1.02 [10:11 "MATCH_STATE" 355],[179:182 "CODON" 355] 1.97 [11:12 "MATCH_STATE" 683],[182:185 "CODON" 683] -0.26 [12:13 "MATCH_STATE" -90],[185:188 "CODON" -90] 2.74 [13:14 "MATCH_STATE" 951],[188:191 "CODON" 951] 1.70 [14:15 "MATCH_STATE" 589],[191:194 "CODON" 589] 1.43 [15:16 "MATCH_STATE" 494],[194:197 "CODON" 494] 0.82 [16:17 "MATCH_STATE" 284],[197:200 "CODON" 284] 4.13 [17:18 "MATCH_STATE" 1430],[200:203 "CODON" 1430] 0.90 [18:19 "MATCH_STATE" 311],[203:206 "CODON" 311] 1.64 [19:20 "MATCH_STATE" 568],[206:209 "CODON" 568] -0.35 [20:21 "MATCH_STATE" -121],[209:212 "CODON" -121] 3.43 [21:22 "MATCH_STATE" 1188],[212:215 "CODON" 1188] 0.83 [22:23 "MATCH_STATE" 288],[215:218 "CODON" 288] 2.63 [23:24 "MATCH_STATE" 913],[218:221 "CODON" 913] 1.20 [24:25 "MATCH_STATE" 417],[221:224 "CODON" 417] 1.10 [25:26 "MATCH_STATE" 382],[224:227 "CODON" 382] 1.47 [26:27 "MATCH_STATE" 509],[227:230 "CODON" 509] -0.13 [27:28 "MATCH_STATE" -45],[230:233 "CODON" -45] 1.87 [28:29 "MATCH_STATE" 649],[233:236 "CODON" 649] 1.87 [29:30 "MATCH_STATE" 647],[236:239 "CODON" 647] 0.93 [30:31 "MATCH_STATE" 324],[239:242 "CODON" 324] 2.89 [31:32 "MATCH_STATE" 1001],[242:245 "CODON" 1001] -0.11 [32:33 "DELETE_STATE" -38],[245:245 "INSERT" -38] -0.07 [33:34 "DELETE_STATE" -24],[245:245 "INSERT" -24] -0.05 [34:35 "DELETE_STATE" -18],[245:245 "INSERT" -18] -0.05 [35:36 "DELETE_STATE" -18],[245:245 "INSERT" -18] -0.05 [36:37 "DELETE_STATE" -19],[245:245 "INSERT" -19] 0.25 [37:38 "MATCH_STATE" 85],[245:248 "CODON" 85] 0.03 [38:39 "MATCH_STATE" 12],[248:251 "CODON" 12] 2.90 [39:40 "MATCH_STATE" 1005],[251:254 "CODON" 1005] 1.30 [40:41 "MATCH_STATE" 450],[254:257 "CODON" 450] 1.93 [41:42 "MATCH_STATE" 669],[257:260 "CODON" 669] 2.19 [42:43 "MATCH_STATE" 758],[260:263 "CODON" 758] 2.18 [43:44 "MATCH_STATE" 757],[263:266 "CODON" 757] 3.16 [44:45 "MATCH_STATE" 1094],[266:269 "CODON" 1094] 2.99 [45:46 "MATCH_STATE" 1035],[269:272 "CODON" 1035] 2.26 [46:47 "MATCH_STATE" 784],[272:275 "CODON" 784] 3.94 [47:48 "MATCH_STATE" 1367],[275:278 "CODON" 1367] 1.77 [48:49 "MATCH_STATE" 613],[278:281 "CODON" 613] 1.24 [49:50 "MATCH_STATE" 429],[281:284 "CODON" 429] 2.82 [50:51 "MATCH_STATE" 977],[284:287 "CODON" 977] -0.68 [51:52 "MATCH_STATE" -236],[287:290 "CODON" -236] -0.07 [52:53 "MATCH_STATE" -23],[290:293 "CODON" -23] -1.03 [53:54 "MATCH_STATE" -358],[293:296 "CODON" -358] -0.88 [54:55 "MATCH_STATE" -305],[296:299 "CODON" -305] -1.13 [55:56 "MATCH_STATE" -390],[299:302 "CODON" -390] -0.02 [56:57 "MATCH_STATE" -6],[302:305 "CODON" -6] 0.94 [57:58 "MATCH_STATE" 325],[305:308 "CODON" 325] 0.48 [58:59 "MATCH_STATE" 168],[308:311 "CODON" 168] 3.17 [59:60 "MATCH_STATE" 1099],[311:314 "CODON" 1099] -0.93 [60:61 "MATCH_STATE" -322],[314:317 "CODON" -322] 0.06 [61:62 "MATCH_STATE" 22],[317:320 "CODON" 22] -2.45 [62:63 "DELETE_STATE" -848],[320:320 "INSERT" -848] -0.51 [63:64 "MATCH_STATE" -177],[320:323 "CODON" -177] -0.99 [64:65 "MATCH_STATE" -344],[323:326 "CODON" -344] -4.60 [65:66 "MATCH_STATE" -1593],[326:329 "CODON" -1593] 0.88 [66:67 "MATCH_STATE" 304],[329:332 "CODON" 304] 0.94 [67:68 "MATCH_STATE" 327],[332:335 "CODON" 327] 1.20 [68:69 "MATCH_STATE" 416],[335:338 "CODON" 416] 0.84 [69:70 "MATCH_STATE" 292],[338:341 "CODON" 292] 2.67 [70:71 "MATCH_STATE" 925],[341:344 "CODON" 925] 2.40 [71:72 "MATCH_STATE" 833],[344:347 "CODON" 833] 0.35 [72:73 "MATCH_STATE" 123],[347:350 "CODON" 123] 1.10 [73:74 "MATCH_STATE" 382],[350:353 "CODON" 382] 0.28 [74:75 "MATCH_STATE" 98],[353:356 "CODON" 98] -1.42 [75:76 "MATCH_STATE" -492],[356:359 "CODON" -492] -0.06 [76:0 "END" -20],[359:359 "END" -20] //