Multiple sequence alignment - TraesCS3B01G147200

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3B01G147200 chr3B 100.000 3158 0 0 1 3158 137605300 137602143 0.000000e+00 5832
1 TraesCS3B01G147200 chr3B 98.611 144 2 0 384 527 43177104 43176961 4.040000e-64 255
2 TraesCS3B01G147200 chr3B 97.973 148 2 1 380 527 237604212 237604358 4.040000e-64 255
3 TraesCS3B01G147200 chr3A 95.988 2293 67 12 607 2892 104559198 104556924 0.000000e+00 3701
4 TraesCS3B01G147200 chr3A 92.513 374 15 5 1 373 104559557 104559196 1.000000e-144 523
5 TraesCS3B01G147200 chr3A 83.902 205 19 9 2897 3087 104556864 104556660 1.930000e-42 183
6 TraesCS3B01G147200 chr3D 96.838 2024 63 1 579 2601 88094111 88092088 0.000000e+00 3382
7 TraesCS3B01G147200 chr3D 97.211 502 12 1 2586 3087 88092071 88091572 0.000000e+00 848
8 TraesCS3B01G147200 chr3D 93.050 259 15 3 128 385 88094690 88094434 2.970000e-100 375
9 TraesCS3B01G147200 chr5B 98.026 152 2 1 380 531 447183709 447183859 2.420000e-66 263
10 TraesCS3B01G147200 chr5B 100.000 139 0 0 385 523 578136783 578136645 1.120000e-64 257
11 TraesCS3B01G147200 chr7B 97.987 149 2 1 379 526 581889432 581889580 1.120000e-64 257
12 TraesCS3B01G147200 chr6B 95.652 161 5 2 378 538 121791715 121791557 1.120000e-64 257
13 TraesCS3B01G147200 chr6B 95.570 158 5 2 378 534 125024815 125024971 5.230000e-63 252
14 TraesCS3B01G147200 chr6B 97.297 148 2 2 380 527 647570329 647570184 1.880000e-62 250
15 TraesCS3B01G147200 chrUn 97.297 148 3 1 379 526 39189563 39189417 1.880000e-62 250


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G147200 chr3B 137602143 137605300 3157 True 5832 5832 100.000000 1 3158 1 chr3B.!!$R2 3157
1 TraesCS3B01G147200 chr3A 104556660 104559557 2897 True 1469 3701 90.801000 1 3087 3 chr3A.!!$R1 3086
2 TraesCS3B01G147200 chr3D 88091572 88094690 3118 True 1535 3382 95.699667 128 3087 3 chr3D.!!$R1 2959

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
442 444 0.033109 GGGGATTGGGGAGGTTTGAG 60.033 60.0 0.0 0.0 0.00 3.02 F
562 564 0.038599 ATGTGCTCACTGCCCATGAA 59.961 50.0 0.0 0.0 38.32 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1783 2055 0.387929 TCTCCATCGGCGAACATACC 59.612 55.0 15.93 0.0 0.0 2.73 R
2556 2836 2.533266 ATAACAAGCTCGCGGATCAT 57.467 45.0 6.13 0.0 0.0 2.45 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 8.359892 AGGGATATACTGGGTATATTATGTGGT 58.640 37.037 10.35 0.00 40.47 4.16
70 71 0.737367 CGATTCAAGGTGCGAGCTGA 60.737 55.000 0.00 0.00 0.00 4.26
79 80 4.479993 GCGAGCTGATGGGGCAGT 62.480 66.667 0.00 0.00 38.17 4.40
80 81 2.513204 CGAGCTGATGGGGCAGTG 60.513 66.667 0.00 0.00 38.17 3.66
81 82 2.827642 GAGCTGATGGGGCAGTGC 60.828 66.667 6.55 6.55 38.17 4.40
279 280 1.199789 GCCGAAGCACATTCAACATCA 59.800 47.619 0.00 0.00 37.83 3.07
298 299 8.667463 CAACATCAAAGTTTCTCCATTTGTTTT 58.333 29.630 0.00 0.00 35.80 2.43
325 327 6.846325 AAAAAGTTCTCTGTAAAGGAGTCG 57.154 37.500 0.00 0.00 33.06 4.18
382 384 0.685097 TCTTCGGTTCCTTGACCCTG 59.315 55.000 0.00 0.00 36.28 4.45
383 385 0.396811 CTTCGGTTCCTTGACCCTGT 59.603 55.000 0.00 0.00 36.28 4.00
384 386 1.621814 CTTCGGTTCCTTGACCCTGTA 59.378 52.381 0.00 0.00 36.28 2.74
385 387 1.263356 TCGGTTCCTTGACCCTGTAG 58.737 55.000 0.00 0.00 36.28 2.74
386 388 0.249398 CGGTTCCTTGACCCTGTAGG 59.751 60.000 0.00 0.00 43.78 3.18
387 389 0.035343 GGTTCCTTGACCCTGTAGGC 60.035 60.000 0.00 0.00 40.58 3.93
388 390 0.035343 GTTCCTTGACCCTGTAGGCC 60.035 60.000 0.00 0.00 40.58 5.19
389 391 0.474854 TTCCTTGACCCTGTAGGCCA 60.475 55.000 5.01 0.00 40.58 5.36
390 392 0.253160 TCCTTGACCCTGTAGGCCAT 60.253 55.000 5.01 0.00 40.58 4.40
391 393 0.107017 CCTTGACCCTGTAGGCCATG 60.107 60.000 5.01 0.00 40.58 3.66
392 394 0.620556 CTTGACCCTGTAGGCCATGT 59.379 55.000 5.01 0.00 40.58 3.21
393 395 1.004745 CTTGACCCTGTAGGCCATGTT 59.995 52.381 5.01 0.00 40.58 2.71
394 396 0.618458 TGACCCTGTAGGCCATGTTC 59.382 55.000 5.01 0.00 40.58 3.18
395 397 0.462047 GACCCTGTAGGCCATGTTCG 60.462 60.000 5.01 0.00 40.58 3.95
396 398 1.153168 CCCTGTAGGCCATGTTCGG 60.153 63.158 5.01 0.00 0.00 4.30
397 399 1.602237 CCTGTAGGCCATGTTCGGT 59.398 57.895 5.01 0.00 0.00 4.69
398 400 0.035439 CCTGTAGGCCATGTTCGGTT 60.035 55.000 5.01 0.00 0.00 4.44
399 401 1.208535 CCTGTAGGCCATGTTCGGTTA 59.791 52.381 5.01 0.00 0.00 2.85
400 402 2.355310 CCTGTAGGCCATGTTCGGTTAA 60.355 50.000 5.01 0.00 0.00 2.01
401 403 3.541632 CTGTAGGCCATGTTCGGTTAAT 58.458 45.455 5.01 0.00 0.00 1.40
402 404 3.537580 TGTAGGCCATGTTCGGTTAATC 58.462 45.455 5.01 0.00 0.00 1.75
403 405 2.052782 AGGCCATGTTCGGTTAATCC 57.947 50.000 5.01 0.00 0.00 3.01
404 406 1.029681 GGCCATGTTCGGTTAATCCC 58.970 55.000 0.00 0.00 0.00 3.85
405 407 1.029681 GCCATGTTCGGTTAATCCCC 58.970 55.000 0.00 0.00 0.00 4.81
406 408 1.409661 GCCATGTTCGGTTAATCCCCT 60.410 52.381 0.00 0.00 0.00 4.79
407 409 2.948600 GCCATGTTCGGTTAATCCCCTT 60.949 50.000 0.00 0.00 0.00 3.95
408 410 2.687935 CCATGTTCGGTTAATCCCCTTG 59.312 50.000 0.00 0.00 0.00 3.61
409 411 1.828979 TGTTCGGTTAATCCCCTTGC 58.171 50.000 0.00 0.00 0.00 4.01
410 412 1.100510 GTTCGGTTAATCCCCTTGCC 58.899 55.000 0.00 0.00 0.00 4.52
411 413 0.699399 TTCGGTTAATCCCCTTGCCA 59.301 50.000 0.00 0.00 0.00 4.92
412 414 0.034863 TCGGTTAATCCCCTTGCCAC 60.035 55.000 0.00 0.00 0.00 5.01
413 415 0.322997 CGGTTAATCCCCTTGCCACA 60.323 55.000 0.00 0.00 0.00 4.17
414 416 1.474330 GGTTAATCCCCTTGCCACAG 58.526 55.000 0.00 0.00 0.00 3.66
415 417 1.474330 GTTAATCCCCTTGCCACAGG 58.526 55.000 0.00 0.00 0.00 4.00
422 424 3.362040 CCTTGCCACAGGGATTGAA 57.638 52.632 0.00 0.00 31.89 2.69
423 425 1.180029 CCTTGCCACAGGGATTGAAG 58.820 55.000 0.00 0.00 31.89 3.02
424 426 1.180029 CTTGCCACAGGGATTGAAGG 58.820 55.000 0.00 0.00 35.59 3.46
425 427 0.251742 TTGCCACAGGGATTGAAGGG 60.252 55.000 0.00 0.00 35.59 3.95
426 428 1.380380 GCCACAGGGATTGAAGGGG 60.380 63.158 0.00 0.00 35.59 4.79
427 429 1.863155 GCCACAGGGATTGAAGGGGA 61.863 60.000 0.00 0.00 35.59 4.81
428 430 0.929244 CCACAGGGATTGAAGGGGAT 59.071 55.000 0.00 0.00 35.59 3.85
429 431 1.288932 CCACAGGGATTGAAGGGGATT 59.711 52.381 0.00 0.00 35.59 3.01
430 432 2.381911 CACAGGGATTGAAGGGGATTG 58.618 52.381 0.00 0.00 0.00 2.67
431 433 1.288932 ACAGGGATTGAAGGGGATTGG 59.711 52.381 0.00 0.00 0.00 3.16
432 434 0.936691 AGGGATTGAAGGGGATTGGG 59.063 55.000 0.00 0.00 0.00 4.12
433 435 0.105504 GGGATTGAAGGGGATTGGGG 60.106 60.000 0.00 0.00 0.00 4.96
434 436 0.933700 GGATTGAAGGGGATTGGGGA 59.066 55.000 0.00 0.00 0.00 4.81
435 437 1.133356 GGATTGAAGGGGATTGGGGAG 60.133 57.143 0.00 0.00 0.00 4.30
436 438 0.936691 ATTGAAGGGGATTGGGGAGG 59.063 55.000 0.00 0.00 0.00 4.30
437 439 0.479589 TTGAAGGGGATTGGGGAGGT 60.480 55.000 0.00 0.00 0.00 3.85
438 440 0.479589 TGAAGGGGATTGGGGAGGTT 60.480 55.000 0.00 0.00 0.00 3.50
439 441 0.710588 GAAGGGGATTGGGGAGGTTT 59.289 55.000 0.00 0.00 0.00 3.27
440 442 0.413434 AAGGGGATTGGGGAGGTTTG 59.587 55.000 0.00 0.00 0.00 2.93
441 443 0.479589 AGGGGATTGGGGAGGTTTGA 60.480 55.000 0.00 0.00 0.00 2.69
442 444 0.033109 GGGGATTGGGGAGGTTTGAG 60.033 60.000 0.00 0.00 0.00 3.02
443 445 0.999712 GGGATTGGGGAGGTTTGAGA 59.000 55.000 0.00 0.00 0.00 3.27
444 446 1.357761 GGGATTGGGGAGGTTTGAGAA 59.642 52.381 0.00 0.00 0.00 2.87
445 447 2.621668 GGGATTGGGGAGGTTTGAGAAG 60.622 54.545 0.00 0.00 0.00 2.85
446 448 2.621668 GGATTGGGGAGGTTTGAGAAGG 60.622 54.545 0.00 0.00 0.00 3.46
447 449 1.827792 TTGGGGAGGTTTGAGAAGGA 58.172 50.000 0.00 0.00 0.00 3.36
448 450 2.059756 TGGGGAGGTTTGAGAAGGAT 57.940 50.000 0.00 0.00 0.00 3.24
449 451 2.358258 TGGGGAGGTTTGAGAAGGATT 58.642 47.619 0.00 0.00 0.00 3.01
450 452 2.721906 TGGGGAGGTTTGAGAAGGATTT 59.278 45.455 0.00 0.00 0.00 2.17
451 453 3.142028 TGGGGAGGTTTGAGAAGGATTTT 59.858 43.478 0.00 0.00 0.00 1.82
452 454 3.511540 GGGGAGGTTTGAGAAGGATTTTG 59.488 47.826 0.00 0.00 0.00 2.44
453 455 4.407365 GGGAGGTTTGAGAAGGATTTTGA 58.593 43.478 0.00 0.00 0.00 2.69
454 456 4.218635 GGGAGGTTTGAGAAGGATTTTGAC 59.781 45.833 0.00 0.00 0.00 3.18
455 457 5.073428 GGAGGTTTGAGAAGGATTTTGACT 58.927 41.667 0.00 0.00 0.00 3.41
456 458 5.536538 GGAGGTTTGAGAAGGATTTTGACTT 59.463 40.000 0.00 0.00 0.00 3.01
457 459 6.396829 AGGTTTGAGAAGGATTTTGACTTG 57.603 37.500 0.00 0.00 0.00 3.16
458 460 4.984785 GGTTTGAGAAGGATTTTGACTTGC 59.015 41.667 0.00 0.00 0.00 4.01
459 461 5.451798 GGTTTGAGAAGGATTTTGACTTGCA 60.452 40.000 0.00 0.00 0.00 4.08
460 462 5.850557 TTGAGAAGGATTTTGACTTGCAA 57.149 34.783 0.00 0.00 33.88 4.08
461 463 5.443185 TGAGAAGGATTTTGACTTGCAAG 57.557 39.130 24.84 24.84 37.87 4.01
462 464 4.279169 TGAGAAGGATTTTGACTTGCAAGG 59.721 41.667 29.18 12.28 37.87 3.61
463 465 3.575687 AGAAGGATTTTGACTTGCAAGGG 59.424 43.478 29.18 7.81 37.87 3.95
464 466 3.243359 AGGATTTTGACTTGCAAGGGA 57.757 42.857 29.18 13.09 37.87 4.20
465 467 3.782992 AGGATTTTGACTTGCAAGGGAT 58.217 40.909 29.18 14.92 37.87 3.85
466 468 4.162651 AGGATTTTGACTTGCAAGGGATT 58.837 39.130 29.18 9.27 37.87 3.01
467 469 4.594491 AGGATTTTGACTTGCAAGGGATTT 59.406 37.500 29.18 8.87 37.87 2.17
468 470 5.779771 AGGATTTTGACTTGCAAGGGATTTA 59.220 36.000 29.18 11.01 37.87 1.40
469 471 6.269769 AGGATTTTGACTTGCAAGGGATTTAA 59.730 34.615 29.18 15.31 37.87 1.52
470 472 7.038088 AGGATTTTGACTTGCAAGGGATTTAAT 60.038 33.333 29.18 18.73 37.87 1.40
471 473 7.278646 GGATTTTGACTTGCAAGGGATTTAATC 59.721 37.037 29.18 23.91 37.87 1.75
472 474 6.036577 TTTGACTTGCAAGGGATTTAATCC 57.963 37.500 29.18 15.22 39.39 3.01
484 486 5.079998 GGATTTAATCCCCTTCAATCCCT 57.920 43.478 12.74 0.00 43.88 4.20
485 487 5.467738 GGATTTAATCCCCTTCAATCCCTT 58.532 41.667 12.74 0.00 43.88 3.95
486 488 5.905331 GGATTTAATCCCCTTCAATCCCTTT 59.095 40.000 12.74 0.00 43.88 3.11
487 489 6.042093 GGATTTAATCCCCTTCAATCCCTTTC 59.958 42.308 12.74 0.00 43.88 2.62
488 490 5.544441 TTAATCCCCTTCAATCCCTTTCA 57.456 39.130 0.00 0.00 0.00 2.69
489 491 4.418395 AATCCCCTTCAATCCCTTTCAA 57.582 40.909 0.00 0.00 0.00 2.69
490 492 3.913370 TCCCCTTCAATCCCTTTCAAA 57.087 42.857 0.00 0.00 0.00 2.69
491 493 3.506398 TCCCCTTCAATCCCTTTCAAAC 58.494 45.455 0.00 0.00 0.00 2.93
492 494 2.567169 CCCCTTCAATCCCTTTCAAACC 59.433 50.000 0.00 0.00 0.00 3.27
493 495 3.510459 CCCTTCAATCCCTTTCAAACCT 58.490 45.455 0.00 0.00 0.00 3.50
494 496 3.511540 CCCTTCAATCCCTTTCAAACCTC 59.488 47.826 0.00 0.00 0.00 3.85
495 497 4.411013 CCTTCAATCCCTTTCAAACCTCT 58.589 43.478 0.00 0.00 0.00 3.69
496 498 4.835056 CCTTCAATCCCTTTCAAACCTCTT 59.165 41.667 0.00 0.00 0.00 2.85
497 499 5.047731 CCTTCAATCCCTTTCAAACCTCTTC 60.048 44.000 0.00 0.00 0.00 2.87
498 500 5.060427 TCAATCCCTTTCAAACCTCTTCA 57.940 39.130 0.00 0.00 0.00 3.02
499 501 5.454062 TCAATCCCTTTCAAACCTCTTCAA 58.546 37.500 0.00 0.00 0.00 2.69
500 502 5.896678 TCAATCCCTTTCAAACCTCTTCAAA 59.103 36.000 0.00 0.00 0.00 2.69
501 503 5.791336 ATCCCTTTCAAACCTCTTCAAAC 57.209 39.130 0.00 0.00 0.00 2.93
502 504 3.958147 TCCCTTTCAAACCTCTTCAAACC 59.042 43.478 0.00 0.00 0.00 3.27
503 505 3.069586 CCCTTTCAAACCTCTTCAAACCC 59.930 47.826 0.00 0.00 0.00 4.11
504 506 3.960755 CCTTTCAAACCTCTTCAAACCCT 59.039 43.478 0.00 0.00 0.00 4.34
505 507 4.038042 CCTTTCAAACCTCTTCAAACCCTC 59.962 45.833 0.00 0.00 0.00 4.30
506 508 3.223674 TCAAACCTCTTCAAACCCTCC 57.776 47.619 0.00 0.00 0.00 4.30
507 509 2.158519 TCAAACCTCTTCAAACCCTCCC 60.159 50.000 0.00 0.00 0.00 4.30
508 510 1.529744 AACCTCTTCAAACCCTCCCA 58.470 50.000 0.00 0.00 0.00 4.37
509 511 1.529744 ACCTCTTCAAACCCTCCCAA 58.470 50.000 0.00 0.00 0.00 4.12
510 512 1.856920 ACCTCTTCAAACCCTCCCAAA 59.143 47.619 0.00 0.00 0.00 3.28
511 513 2.239400 CCTCTTCAAACCCTCCCAAAC 58.761 52.381 0.00 0.00 0.00 2.93
512 514 2.239400 CTCTTCAAACCCTCCCAAACC 58.761 52.381 0.00 0.00 0.00 3.27
513 515 0.958822 CTTCAAACCCTCCCAAACCG 59.041 55.000 0.00 0.00 0.00 4.44
514 516 0.551879 TTCAAACCCTCCCAAACCGA 59.448 50.000 0.00 0.00 0.00 4.69
515 517 0.551879 TCAAACCCTCCCAAACCGAA 59.448 50.000 0.00 0.00 0.00 4.30
516 518 0.671796 CAAACCCTCCCAAACCGAAC 59.328 55.000 0.00 0.00 0.00 3.95
517 519 0.259356 AAACCCTCCCAAACCGAACA 59.741 50.000 0.00 0.00 0.00 3.18
518 520 0.259356 AACCCTCCCAAACCGAACAA 59.741 50.000 0.00 0.00 0.00 2.83
519 521 0.179001 ACCCTCCCAAACCGAACAAG 60.179 55.000 0.00 0.00 0.00 3.16
520 522 0.893727 CCCTCCCAAACCGAACAAGG 60.894 60.000 0.00 0.00 37.30 3.61
521 523 1.524008 CCTCCCAAACCGAACAAGGC 61.524 60.000 0.00 0.00 33.69 4.35
522 524 1.524008 CTCCCAAACCGAACAAGGCC 61.524 60.000 0.00 0.00 33.69 5.19
539 541 2.039879 AGGCCGTAATGAGTTTGGACTT 59.960 45.455 0.00 0.00 33.01 3.01
540 542 3.262405 AGGCCGTAATGAGTTTGGACTTA 59.738 43.478 0.00 0.00 33.01 2.24
541 543 3.621715 GGCCGTAATGAGTTTGGACTTAG 59.378 47.826 0.00 0.00 35.88 2.18
542 544 3.621715 GCCGTAATGAGTTTGGACTTAGG 59.378 47.826 0.00 0.00 35.88 2.69
543 545 4.622220 GCCGTAATGAGTTTGGACTTAGGA 60.622 45.833 0.00 0.00 35.88 2.94
544 546 5.671493 CCGTAATGAGTTTGGACTTAGGAT 58.329 41.667 0.00 0.00 35.88 3.24
545 547 5.523916 CCGTAATGAGTTTGGACTTAGGATG 59.476 44.000 0.00 0.00 35.88 3.51
546 548 6.106673 CGTAATGAGTTTGGACTTAGGATGT 58.893 40.000 0.00 0.00 35.88 3.06
547 549 6.036083 CGTAATGAGTTTGGACTTAGGATGTG 59.964 42.308 0.00 0.00 35.88 3.21
548 550 3.674997 TGAGTTTGGACTTAGGATGTGC 58.325 45.455 0.00 0.00 35.88 4.57
549 551 3.327757 TGAGTTTGGACTTAGGATGTGCT 59.672 43.478 0.00 0.00 35.88 4.40
550 552 3.935828 GAGTTTGGACTTAGGATGTGCTC 59.064 47.826 0.00 0.00 35.88 4.26
551 553 3.327757 AGTTTGGACTTAGGATGTGCTCA 59.672 43.478 0.00 0.00 29.87 4.26
552 554 3.334583 TTGGACTTAGGATGTGCTCAC 57.665 47.619 0.00 0.00 0.00 3.51
553 555 2.540383 TGGACTTAGGATGTGCTCACT 58.460 47.619 1.47 0.00 0.00 3.41
554 556 2.234661 TGGACTTAGGATGTGCTCACTG 59.765 50.000 1.47 0.00 0.00 3.66
555 557 2.275318 GACTTAGGATGTGCTCACTGC 58.725 52.381 1.47 0.00 43.25 4.40
556 558 1.065854 ACTTAGGATGTGCTCACTGCC 60.066 52.381 1.47 3.14 42.00 4.85
557 559 0.253044 TTAGGATGTGCTCACTGCCC 59.747 55.000 1.47 0.74 42.00 5.36
558 560 0.909133 TAGGATGTGCTCACTGCCCA 60.909 55.000 1.47 0.00 42.00 5.36
559 561 1.077212 GGATGTGCTCACTGCCCAT 60.077 57.895 1.47 0.00 42.31 4.00
560 562 1.381928 GGATGTGCTCACTGCCCATG 61.382 60.000 1.47 0.00 39.79 3.66
561 563 0.393402 GATGTGCTCACTGCCCATGA 60.393 55.000 0.00 0.00 39.79 3.07
562 564 0.038599 ATGTGCTCACTGCCCATGAA 59.961 50.000 0.00 0.00 38.32 2.57
563 565 0.607217 TGTGCTCACTGCCCATGAAG 60.607 55.000 0.00 0.00 42.00 3.02
564 566 1.676635 TGCTCACTGCCCATGAAGC 60.677 57.895 0.00 0.00 42.00 3.86
565 567 2.413142 GCTCACTGCCCATGAAGCC 61.413 63.158 0.00 0.00 35.15 4.35
566 568 1.751927 CTCACTGCCCATGAAGCCC 60.752 63.158 0.00 0.00 0.00 5.19
567 569 2.757099 CACTGCCCATGAAGCCCC 60.757 66.667 0.00 0.00 0.00 5.80
568 570 4.066139 ACTGCCCATGAAGCCCCC 62.066 66.667 0.00 0.00 0.00 5.40
591 863 2.028658 GCTGATGTGAGTCACTCCTTGA 60.029 50.000 23.29 2.99 35.11 3.02
597 869 3.244665 TGTGAGTCACTCCTTGATGCAAT 60.245 43.478 23.29 0.00 36.32 3.56
615 887 5.718146 TGCAATGTTTGAGTTTCTTGTTGA 58.282 33.333 0.00 0.00 0.00 3.18
622 894 7.546358 TGTTTGAGTTTCTTGTTGATGTGAAT 58.454 30.769 0.00 0.00 0.00 2.57
718 990 4.159693 TCCGCTAAGTCTAGAAAAGCATCA 59.840 41.667 17.57 3.30 32.69 3.07
724 996 5.946942 AGTCTAGAAAAGCATCAGATCCA 57.053 39.130 0.00 0.00 0.00 3.41
753 1025 3.324207 GGACCACTTCCCAACACTC 57.676 57.895 0.00 0.00 38.70 3.51
825 1097 7.044314 GCAATACCATAACTTTGTCGTATTTGC 60.044 37.037 0.00 0.00 0.00 3.68
868 1140 5.582665 CCTTACTGAATCTGTTGCTAGAACC 59.417 44.000 0.00 0.00 0.00 3.62
951 1223 7.838079 AAATGCTGGCCATAATTCAATACTA 57.162 32.000 5.51 0.00 32.67 1.82
961 1233 8.783093 GCCATAATTCAATACTACAAGTATGCA 58.217 33.333 0.51 0.00 40.32 3.96
1136 1408 5.215069 AGGTAGGTCATCTTCATCTGATGT 58.785 41.667 16.66 0.00 41.30 3.06
1371 1643 5.538067 AAGAAGCTTATGCGAAAGAGAAC 57.462 39.130 0.00 0.00 45.42 3.01
1452 1724 1.134907 CCAGCAAACAAGCATCCATCC 60.135 52.381 0.00 0.00 36.85 3.51
1635 1907 1.172812 ACCCTTCAGCAAAACCTCGC 61.173 55.000 0.00 0.00 0.00 5.03
1767 2039 7.361438 TGGGGGATTATGTACTTGAATTGAAT 58.639 34.615 0.00 0.00 0.00 2.57
1783 2055 0.664166 GAATGGTGGCAGCAACAACG 60.664 55.000 24.45 0.00 0.00 4.10
1815 2087 4.497006 GCCGATGGAGATGAATTTGACTTG 60.497 45.833 0.00 0.00 0.00 3.16
1816 2088 4.036027 CCGATGGAGATGAATTTGACTTGG 59.964 45.833 0.00 0.00 0.00 3.61
1817 2089 4.877823 CGATGGAGATGAATTTGACTTGGA 59.122 41.667 0.00 0.00 0.00 3.53
1827 2102 5.072329 TGAATTTGACTTGGAGGAGAGACTT 59.928 40.000 0.00 0.00 0.00 3.01
1998 2273 0.178921 ACAGAAGGCACAGGGAGAGA 60.179 55.000 0.00 0.00 0.00 3.10
2198 2474 3.435601 GGGCCTGTTCATTCTATCCATGT 60.436 47.826 0.84 0.00 0.00 3.21
2287 2563 2.424246 TCCCTTTTCGCTTTGTTTCGTT 59.576 40.909 0.00 0.00 0.00 3.85
2421 2701 2.074230 TTTTCCTGTGCTGCCTTGCG 62.074 55.000 0.00 0.00 35.36 4.85
2540 2820 0.109458 TGTATCGCTGCGACGAACTT 60.109 50.000 28.41 12.91 46.59 2.66
2556 2836 4.754618 ACGAACTTGATTGTGCAGTTGATA 59.245 37.500 0.00 0.00 0.00 2.15
2602 2914 5.253330 TGTGTGGATCTTCTTTATGGTTCC 58.747 41.667 0.00 0.00 0.00 3.62
2770 3084 1.949847 ATCCTCAGTTGCCGAGTCCG 61.950 60.000 0.00 0.00 0.00 4.79
2854 3168 0.961019 GCATTGGAGTTGGAGTTGCA 59.039 50.000 0.00 0.00 0.00 4.08
2876 3190 4.798907 CACTTATCGCGTGTAAATCTCTGT 59.201 41.667 5.77 0.00 0.00 3.41
2877 3191 4.798907 ACTTATCGCGTGTAAATCTCTGTG 59.201 41.667 5.77 0.00 0.00 3.66
2925 3295 6.676990 ATTCATACCTGACATAGAGCATGA 57.323 37.500 0.00 0.00 38.10 3.07
3000 3380 6.040166 GTCATCCAGAGTCATTATTGGCAAAT 59.960 38.462 3.01 0.00 0.00 2.32
3089 3472 9.657419 ATCCTTTTCTTAATTGCATTTACTTGG 57.343 29.630 0.59 0.18 0.00 3.61
3090 3473 8.093927 TCCTTTTCTTAATTGCATTTACTTGGG 58.906 33.333 0.59 1.05 0.00 4.12
3091 3474 7.148423 CCTTTTCTTAATTGCATTTACTTGGGC 60.148 37.037 0.59 0.00 0.00 5.36
3092 3475 5.991933 TCTTAATTGCATTTACTTGGGCA 57.008 34.783 0.59 0.00 0.00 5.36
3093 3476 6.543430 TCTTAATTGCATTTACTTGGGCAT 57.457 33.333 0.59 0.00 35.98 4.40
3094 3477 6.339730 TCTTAATTGCATTTACTTGGGCATG 58.660 36.000 0.59 0.00 35.98 4.06
3095 3478 4.822685 AATTGCATTTACTTGGGCATGA 57.177 36.364 0.00 0.00 35.98 3.07
3096 3479 3.872511 TTGCATTTACTTGGGCATGAG 57.127 42.857 0.00 0.00 35.98 2.90
3097 3480 3.084536 TGCATTTACTTGGGCATGAGA 57.915 42.857 0.00 0.00 0.00 3.27
3098 3481 3.429492 TGCATTTACTTGGGCATGAGAA 58.571 40.909 0.00 0.00 0.00 2.87
3099 3482 3.193267 TGCATTTACTTGGGCATGAGAAC 59.807 43.478 0.00 0.00 0.00 3.01
3100 3483 3.731867 GCATTTACTTGGGCATGAGAACG 60.732 47.826 0.00 0.00 0.00 3.95
3101 3484 2.107950 TTACTTGGGCATGAGAACGG 57.892 50.000 0.00 0.00 0.00 4.44
3102 3485 0.251916 TACTTGGGCATGAGAACGGG 59.748 55.000 0.00 0.00 0.00 5.28
3103 3486 1.299648 CTTGGGCATGAGAACGGGA 59.700 57.895 0.00 0.00 0.00 5.14
3104 3487 0.745845 CTTGGGCATGAGAACGGGAG 60.746 60.000 0.00 0.00 0.00 4.30
3116 3499 3.569873 ACGGGAGTTTGCATTAGGG 57.430 52.632 0.00 0.00 43.33 3.53
3117 3500 0.696501 ACGGGAGTTTGCATTAGGGT 59.303 50.000 0.00 0.00 43.33 4.34
3118 3501 1.094785 CGGGAGTTTGCATTAGGGTG 58.905 55.000 0.00 0.00 0.00 4.61
3119 3502 1.613255 CGGGAGTTTGCATTAGGGTGT 60.613 52.381 0.00 0.00 0.00 4.16
3120 3503 2.525368 GGGAGTTTGCATTAGGGTGTT 58.475 47.619 0.00 0.00 0.00 3.32
3121 3504 2.897326 GGGAGTTTGCATTAGGGTGTTT 59.103 45.455 0.00 0.00 0.00 2.83
3122 3505 4.083565 GGGAGTTTGCATTAGGGTGTTTA 58.916 43.478 0.00 0.00 0.00 2.01
3123 3506 4.709886 GGGAGTTTGCATTAGGGTGTTTAT 59.290 41.667 0.00 0.00 0.00 1.40
3124 3507 5.394115 GGGAGTTTGCATTAGGGTGTTTATG 60.394 44.000 0.00 0.00 0.00 1.90
3125 3508 5.394115 GGAGTTTGCATTAGGGTGTTTATGG 60.394 44.000 0.00 0.00 0.00 2.74
3126 3509 5.329399 AGTTTGCATTAGGGTGTTTATGGA 58.671 37.500 0.00 0.00 0.00 3.41
3127 3510 5.957774 AGTTTGCATTAGGGTGTTTATGGAT 59.042 36.000 0.00 0.00 0.00 3.41
3128 3511 7.122715 AGTTTGCATTAGGGTGTTTATGGATA 58.877 34.615 0.00 0.00 0.00 2.59
3129 3512 7.285401 AGTTTGCATTAGGGTGTTTATGGATAG 59.715 37.037 0.00 0.00 0.00 2.08
3130 3513 6.508030 TGCATTAGGGTGTTTATGGATAGA 57.492 37.500 0.00 0.00 0.00 1.98
3131 3514 7.090319 TGCATTAGGGTGTTTATGGATAGAT 57.910 36.000 0.00 0.00 0.00 1.98
3132 3515 6.942005 TGCATTAGGGTGTTTATGGATAGATG 59.058 38.462 0.00 0.00 0.00 2.90
3133 3516 6.375455 GCATTAGGGTGTTTATGGATAGATGG 59.625 42.308 0.00 0.00 0.00 3.51
3134 3517 6.448369 TTAGGGTGTTTATGGATAGATGGG 57.552 41.667 0.00 0.00 0.00 4.00
3135 3518 4.577096 AGGGTGTTTATGGATAGATGGGA 58.423 43.478 0.00 0.00 0.00 4.37
3136 3519 4.981647 AGGGTGTTTATGGATAGATGGGAA 59.018 41.667 0.00 0.00 0.00 3.97
3137 3520 5.616986 AGGGTGTTTATGGATAGATGGGAAT 59.383 40.000 0.00 0.00 0.00 3.01
3138 3521 6.104691 AGGGTGTTTATGGATAGATGGGAATT 59.895 38.462 0.00 0.00 0.00 2.17
3139 3522 6.209391 GGGTGTTTATGGATAGATGGGAATTG 59.791 42.308 0.00 0.00 0.00 2.32
3140 3523 7.004086 GGTGTTTATGGATAGATGGGAATTGA 58.996 38.462 0.00 0.00 0.00 2.57
3141 3524 7.040409 GGTGTTTATGGATAGATGGGAATTGAC 60.040 40.741 0.00 0.00 0.00 3.18
3142 3525 7.721399 GTGTTTATGGATAGATGGGAATTGACT 59.279 37.037 0.00 0.00 0.00 3.41
3143 3526 8.281531 TGTTTATGGATAGATGGGAATTGACTT 58.718 33.333 0.00 0.00 0.00 3.01
3144 3527 8.787852 GTTTATGGATAGATGGGAATTGACTTC 58.212 37.037 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 8.648693 GGGACCACATAATATACCCAGTATATC 58.351 40.741 7.53 0.00 39.78 1.63
28 29 0.621571 AGAGGTATGCCAAGCAGGGA 60.622 55.000 1.54 0.00 43.65 4.20
51 52 0.737367 TCAGCTCGCACCTTGAATCG 60.737 55.000 0.00 0.00 0.00 3.34
80 81 4.779733 TCCTCTCCAGTCCCCGGC 62.780 72.222 0.00 0.00 0.00 6.13
81 82 2.136878 CATCCTCTCCAGTCCCCGG 61.137 68.421 0.00 0.00 0.00 5.73
82 83 1.075970 TCATCCTCTCCAGTCCCCG 60.076 63.158 0.00 0.00 0.00 5.73
83 84 0.263172 TCTCATCCTCTCCAGTCCCC 59.737 60.000 0.00 0.00 0.00 4.81
84 85 1.063266 ACTCTCATCCTCTCCAGTCCC 60.063 57.143 0.00 0.00 0.00 4.46
85 86 2.031120 CACTCTCATCCTCTCCAGTCC 58.969 57.143 0.00 0.00 0.00 3.85
86 87 1.408702 GCACTCTCATCCTCTCCAGTC 59.591 57.143 0.00 0.00 0.00 3.51
87 88 1.272928 TGCACTCTCATCCTCTCCAGT 60.273 52.381 0.00 0.00 0.00 4.00
88 89 1.482954 TGCACTCTCATCCTCTCCAG 58.517 55.000 0.00 0.00 0.00 3.86
89 90 1.761198 CATGCACTCTCATCCTCTCCA 59.239 52.381 0.00 0.00 0.00 3.86
90 91 1.070445 CCATGCACTCTCATCCTCTCC 59.930 57.143 0.00 0.00 0.00 3.71
120 121 6.943718 CAGACCCAAAACCCAACTAAATACTA 59.056 38.462 0.00 0.00 0.00 1.82
304 306 5.786264 TCGACTCCTTTACAGAGAACTTT 57.214 39.130 0.00 0.00 35.27 2.66
325 327 7.550551 TCTTTACTGATGAATCATGGTCTGTTC 59.449 37.037 0.00 0.00 36.02 3.18
382 384 2.876550 GGATTAACCGAACATGGCCTAC 59.123 50.000 3.32 0.00 0.00 3.18
383 385 2.158726 GGGATTAACCGAACATGGCCTA 60.159 50.000 3.32 0.00 40.11 3.93
384 386 1.409661 GGGATTAACCGAACATGGCCT 60.410 52.381 3.32 0.00 40.11 5.19
385 387 1.029681 GGGATTAACCGAACATGGCC 58.970 55.000 0.00 0.00 40.11 5.36
386 388 1.029681 GGGGATTAACCGAACATGGC 58.970 55.000 0.00 0.00 40.11 4.40
387 389 2.687935 CAAGGGGATTAACCGAACATGG 59.312 50.000 0.00 0.00 40.11 3.66
388 390 2.099098 GCAAGGGGATTAACCGAACATG 59.901 50.000 0.00 0.00 40.11 3.21
389 391 2.375146 GCAAGGGGATTAACCGAACAT 58.625 47.619 0.00 0.00 40.11 2.71
390 392 1.614850 GGCAAGGGGATTAACCGAACA 60.615 52.381 0.00 0.00 40.11 3.18
391 393 1.100510 GGCAAGGGGATTAACCGAAC 58.899 55.000 0.00 0.00 40.11 3.95
392 394 0.699399 TGGCAAGGGGATTAACCGAA 59.301 50.000 0.00 0.00 40.11 4.30
393 395 0.034863 GTGGCAAGGGGATTAACCGA 60.035 55.000 0.00 0.00 40.11 4.69
394 396 0.322997 TGTGGCAAGGGGATTAACCG 60.323 55.000 0.00 0.00 40.11 4.44
395 397 1.474330 CTGTGGCAAGGGGATTAACC 58.526 55.000 0.00 0.00 38.08 2.85
396 398 1.474330 CCTGTGGCAAGGGGATTAAC 58.526 55.000 7.57 0.00 33.28 2.01
397 399 3.998560 CCTGTGGCAAGGGGATTAA 57.001 52.632 7.57 0.00 33.28 1.40
404 406 1.180029 CTTCAATCCCTGTGGCAAGG 58.820 55.000 8.28 8.28 37.05 3.61
405 407 1.180029 CCTTCAATCCCTGTGGCAAG 58.820 55.000 0.00 0.00 0.00 4.01
406 408 0.251742 CCCTTCAATCCCTGTGGCAA 60.252 55.000 0.00 0.00 0.00 4.52
407 409 1.383799 CCCTTCAATCCCTGTGGCA 59.616 57.895 0.00 0.00 0.00 4.92
408 410 1.380380 CCCCTTCAATCCCTGTGGC 60.380 63.158 0.00 0.00 0.00 5.01
409 411 0.929244 ATCCCCTTCAATCCCTGTGG 59.071 55.000 0.00 0.00 0.00 4.17
410 412 2.381911 CAATCCCCTTCAATCCCTGTG 58.618 52.381 0.00 0.00 0.00 3.66
411 413 1.288932 CCAATCCCCTTCAATCCCTGT 59.711 52.381 0.00 0.00 0.00 4.00
412 414 1.412074 CCCAATCCCCTTCAATCCCTG 60.412 57.143 0.00 0.00 0.00 4.45
413 415 0.936691 CCCAATCCCCTTCAATCCCT 59.063 55.000 0.00 0.00 0.00 4.20
414 416 0.105504 CCCCAATCCCCTTCAATCCC 60.106 60.000 0.00 0.00 0.00 3.85
415 417 0.933700 TCCCCAATCCCCTTCAATCC 59.066 55.000 0.00 0.00 0.00 3.01
416 418 1.133356 CCTCCCCAATCCCCTTCAATC 60.133 57.143 0.00 0.00 0.00 2.67
417 419 0.936691 CCTCCCCAATCCCCTTCAAT 59.063 55.000 0.00 0.00 0.00 2.57
418 420 0.479589 ACCTCCCCAATCCCCTTCAA 60.480 55.000 0.00 0.00 0.00 2.69
419 421 0.479589 AACCTCCCCAATCCCCTTCA 60.480 55.000 0.00 0.00 0.00 3.02
420 422 0.710588 AAACCTCCCCAATCCCCTTC 59.289 55.000 0.00 0.00 0.00 3.46
421 423 0.413434 CAAACCTCCCCAATCCCCTT 59.587 55.000 0.00 0.00 0.00 3.95
422 424 0.479589 TCAAACCTCCCCAATCCCCT 60.480 55.000 0.00 0.00 0.00 4.79
423 425 0.033109 CTCAAACCTCCCCAATCCCC 60.033 60.000 0.00 0.00 0.00 4.81
424 426 0.999712 TCTCAAACCTCCCCAATCCC 59.000 55.000 0.00 0.00 0.00 3.85
425 427 2.621668 CCTTCTCAAACCTCCCCAATCC 60.622 54.545 0.00 0.00 0.00 3.01
426 428 2.308866 TCCTTCTCAAACCTCCCCAATC 59.691 50.000 0.00 0.00 0.00 2.67
427 429 2.358258 TCCTTCTCAAACCTCCCCAAT 58.642 47.619 0.00 0.00 0.00 3.16
428 430 1.827792 TCCTTCTCAAACCTCCCCAA 58.172 50.000 0.00 0.00 0.00 4.12
429 431 2.059756 ATCCTTCTCAAACCTCCCCA 57.940 50.000 0.00 0.00 0.00 4.96
430 432 3.458044 AAATCCTTCTCAAACCTCCCC 57.542 47.619 0.00 0.00 0.00 4.81
431 433 4.218635 GTCAAAATCCTTCTCAAACCTCCC 59.781 45.833 0.00 0.00 0.00 4.30
432 434 5.073428 AGTCAAAATCCTTCTCAAACCTCC 58.927 41.667 0.00 0.00 0.00 4.30
433 435 6.442112 CAAGTCAAAATCCTTCTCAAACCTC 58.558 40.000 0.00 0.00 0.00 3.85
434 436 5.221322 GCAAGTCAAAATCCTTCTCAAACCT 60.221 40.000 0.00 0.00 0.00 3.50
435 437 4.984785 GCAAGTCAAAATCCTTCTCAAACC 59.015 41.667 0.00 0.00 0.00 3.27
436 438 5.591099 TGCAAGTCAAAATCCTTCTCAAAC 58.409 37.500 0.00 0.00 0.00 2.93
437 439 5.850557 TGCAAGTCAAAATCCTTCTCAAA 57.149 34.783 0.00 0.00 0.00 2.69
438 440 5.221303 CCTTGCAAGTCAAAATCCTTCTCAA 60.221 40.000 24.35 0.00 33.65 3.02
439 441 4.279169 CCTTGCAAGTCAAAATCCTTCTCA 59.721 41.667 24.35 0.00 33.65 3.27
440 442 4.321527 CCCTTGCAAGTCAAAATCCTTCTC 60.322 45.833 24.35 0.00 33.65 2.87
441 443 3.575687 CCCTTGCAAGTCAAAATCCTTCT 59.424 43.478 24.35 0.00 33.65 2.85
442 444 3.573967 TCCCTTGCAAGTCAAAATCCTTC 59.426 43.478 24.35 0.00 33.65 3.46
443 445 3.575805 TCCCTTGCAAGTCAAAATCCTT 58.424 40.909 24.35 0.00 33.65 3.36
444 446 3.243359 TCCCTTGCAAGTCAAAATCCT 57.757 42.857 24.35 0.00 33.65 3.24
445 447 4.541973 AATCCCTTGCAAGTCAAAATCC 57.458 40.909 24.35 0.00 33.65 3.01
446 448 7.278646 GGATTAAATCCCTTGCAAGTCAAAATC 59.721 37.037 24.35 20.70 43.88 2.17
447 449 7.105588 GGATTAAATCCCTTGCAAGTCAAAAT 58.894 34.615 24.35 14.96 43.88 1.82
448 450 6.463360 GGATTAAATCCCTTGCAAGTCAAAA 58.537 36.000 24.35 11.23 43.88 2.44
449 451 6.036577 GGATTAAATCCCTTGCAAGTCAAA 57.963 37.500 24.35 10.27 43.88 2.69
450 452 5.659440 GGATTAAATCCCTTGCAAGTCAA 57.341 39.130 24.35 10.08 43.88 3.18
463 465 6.611236 TGAAAGGGATTGAAGGGGATTAAATC 59.389 38.462 0.00 0.00 37.85 2.17
464 466 6.511208 TGAAAGGGATTGAAGGGGATTAAAT 58.489 36.000 0.00 0.00 0.00 1.40
465 467 5.909760 TGAAAGGGATTGAAGGGGATTAAA 58.090 37.500 0.00 0.00 0.00 1.52
466 468 5.544441 TGAAAGGGATTGAAGGGGATTAA 57.456 39.130 0.00 0.00 0.00 1.40
467 469 5.544441 TTGAAAGGGATTGAAGGGGATTA 57.456 39.130 0.00 0.00 0.00 1.75
468 470 4.418395 TTGAAAGGGATTGAAGGGGATT 57.582 40.909 0.00 0.00 0.00 3.01
469 471 4.096681 GTTTGAAAGGGATTGAAGGGGAT 58.903 43.478 0.00 0.00 0.00 3.85
470 472 3.506398 GTTTGAAAGGGATTGAAGGGGA 58.494 45.455 0.00 0.00 0.00 4.81
471 473 2.567169 GGTTTGAAAGGGATTGAAGGGG 59.433 50.000 0.00 0.00 0.00 4.79
472 474 3.510459 AGGTTTGAAAGGGATTGAAGGG 58.490 45.455 0.00 0.00 0.00 3.95
473 475 4.411013 AGAGGTTTGAAAGGGATTGAAGG 58.589 43.478 0.00 0.00 0.00 3.46
474 476 5.536161 TGAAGAGGTTTGAAAGGGATTGAAG 59.464 40.000 0.00 0.00 0.00 3.02
475 477 5.454062 TGAAGAGGTTTGAAAGGGATTGAA 58.546 37.500 0.00 0.00 0.00 2.69
476 478 5.060427 TGAAGAGGTTTGAAAGGGATTGA 57.940 39.130 0.00 0.00 0.00 2.57
477 479 5.789643 TTGAAGAGGTTTGAAAGGGATTG 57.210 39.130 0.00 0.00 0.00 2.67
478 480 5.070446 GGTTTGAAGAGGTTTGAAAGGGATT 59.930 40.000 0.00 0.00 0.00 3.01
479 481 4.588951 GGTTTGAAGAGGTTTGAAAGGGAT 59.411 41.667 0.00 0.00 0.00 3.85
480 482 3.958147 GGTTTGAAGAGGTTTGAAAGGGA 59.042 43.478 0.00 0.00 0.00 4.20
481 483 3.069586 GGGTTTGAAGAGGTTTGAAAGGG 59.930 47.826 0.00 0.00 0.00 3.95
482 484 3.960755 AGGGTTTGAAGAGGTTTGAAAGG 59.039 43.478 0.00 0.00 0.00 3.11
483 485 4.038042 GGAGGGTTTGAAGAGGTTTGAAAG 59.962 45.833 0.00 0.00 0.00 2.62
484 486 3.958147 GGAGGGTTTGAAGAGGTTTGAAA 59.042 43.478 0.00 0.00 0.00 2.69
485 487 3.562182 GGAGGGTTTGAAGAGGTTTGAA 58.438 45.455 0.00 0.00 0.00 2.69
486 488 2.158519 GGGAGGGTTTGAAGAGGTTTGA 60.159 50.000 0.00 0.00 0.00 2.69
487 489 2.239400 GGGAGGGTTTGAAGAGGTTTG 58.761 52.381 0.00 0.00 0.00 2.93
488 490 1.856920 TGGGAGGGTTTGAAGAGGTTT 59.143 47.619 0.00 0.00 0.00 3.27
489 491 1.529744 TGGGAGGGTTTGAAGAGGTT 58.470 50.000 0.00 0.00 0.00 3.50
490 492 1.529744 TTGGGAGGGTTTGAAGAGGT 58.470 50.000 0.00 0.00 0.00 3.85
491 493 2.239400 GTTTGGGAGGGTTTGAAGAGG 58.761 52.381 0.00 0.00 0.00 3.69
492 494 2.239400 GGTTTGGGAGGGTTTGAAGAG 58.761 52.381 0.00 0.00 0.00 2.85
493 495 1.477923 CGGTTTGGGAGGGTTTGAAGA 60.478 52.381 0.00 0.00 0.00 2.87
494 496 0.958822 CGGTTTGGGAGGGTTTGAAG 59.041 55.000 0.00 0.00 0.00 3.02
495 497 0.551879 TCGGTTTGGGAGGGTTTGAA 59.448 50.000 0.00 0.00 0.00 2.69
496 498 0.551879 TTCGGTTTGGGAGGGTTTGA 59.448 50.000 0.00 0.00 0.00 2.69
497 499 0.671796 GTTCGGTTTGGGAGGGTTTG 59.328 55.000 0.00 0.00 0.00 2.93
498 500 0.259356 TGTTCGGTTTGGGAGGGTTT 59.741 50.000 0.00 0.00 0.00 3.27
499 501 0.259356 TTGTTCGGTTTGGGAGGGTT 59.741 50.000 0.00 0.00 0.00 4.11
500 502 0.179001 CTTGTTCGGTTTGGGAGGGT 60.179 55.000 0.00 0.00 0.00 4.34
501 503 0.893727 CCTTGTTCGGTTTGGGAGGG 60.894 60.000 0.00 0.00 0.00 4.30
502 504 1.524008 GCCTTGTTCGGTTTGGGAGG 61.524 60.000 0.00 0.00 0.00 4.30
503 505 1.524008 GGCCTTGTTCGGTTTGGGAG 61.524 60.000 0.00 0.00 0.00 4.30
504 506 1.529713 GGCCTTGTTCGGTTTGGGA 60.530 57.895 0.00 0.00 0.00 4.37
505 507 2.914908 CGGCCTTGTTCGGTTTGGG 61.915 63.158 0.00 0.00 0.00 4.12
506 508 0.885596 TACGGCCTTGTTCGGTTTGG 60.886 55.000 0.00 0.00 0.00 3.28
507 509 0.945813 TTACGGCCTTGTTCGGTTTG 59.054 50.000 0.00 0.00 0.00 2.93
508 510 1.538075 CATTACGGCCTTGTTCGGTTT 59.462 47.619 0.00 0.00 0.00 3.27
509 511 1.161843 CATTACGGCCTTGTTCGGTT 58.838 50.000 0.00 0.00 0.00 4.44
510 512 0.322322 TCATTACGGCCTTGTTCGGT 59.678 50.000 0.00 0.00 0.00 4.69
511 513 1.006832 CTCATTACGGCCTTGTTCGG 58.993 55.000 0.00 0.00 0.00 4.30
512 514 1.722011 ACTCATTACGGCCTTGTTCG 58.278 50.000 0.00 0.00 0.00 3.95
513 515 3.365969 CCAAACTCATTACGGCCTTGTTC 60.366 47.826 0.00 0.00 0.00 3.18
514 516 2.556622 CCAAACTCATTACGGCCTTGTT 59.443 45.455 0.00 0.00 0.00 2.83
515 517 2.159382 CCAAACTCATTACGGCCTTGT 58.841 47.619 0.00 0.00 0.00 3.16
516 518 2.161609 GTCCAAACTCATTACGGCCTTG 59.838 50.000 0.00 0.00 0.00 3.61
517 519 2.039879 AGTCCAAACTCATTACGGCCTT 59.960 45.455 0.00 0.00 0.00 4.35
518 520 1.628846 AGTCCAAACTCATTACGGCCT 59.371 47.619 0.00 0.00 0.00 5.19
519 521 2.109425 AGTCCAAACTCATTACGGCC 57.891 50.000 0.00 0.00 0.00 6.13
520 522 3.621715 CCTAAGTCCAAACTCATTACGGC 59.378 47.826 0.00 0.00 33.48 5.68
521 523 5.080969 TCCTAAGTCCAAACTCATTACGG 57.919 43.478 0.00 0.00 33.48 4.02
522 524 6.036083 CACATCCTAAGTCCAAACTCATTACG 59.964 42.308 0.00 0.00 33.48 3.18
547 549 2.413142 GGCTTCATGGGCAGTGAGC 61.413 63.158 12.21 0.00 44.65 4.26
548 550 1.751927 GGGCTTCATGGGCAGTGAG 60.752 63.158 12.21 0.00 0.00 3.51
549 551 2.356278 GGGCTTCATGGGCAGTGA 59.644 61.111 12.21 0.00 0.00 3.41
550 552 2.757099 GGGGCTTCATGGGCAGTG 60.757 66.667 12.21 0.00 0.00 3.66
551 553 4.066139 GGGGGCTTCATGGGCAGT 62.066 66.667 12.21 0.00 0.00 4.40
565 567 2.187946 GACTCACATCAGCGGGGG 59.812 66.667 0.00 0.00 0.00 5.40
566 568 1.448540 GTGACTCACATCAGCGGGG 60.449 63.158 4.17 0.00 34.08 5.73
567 569 0.459237 GAGTGACTCACATCAGCGGG 60.459 60.000 7.90 0.00 36.74 6.13
568 570 0.459237 GGAGTGACTCACATCAGCGG 60.459 60.000 15.33 0.00 36.74 5.52
569 571 0.529833 AGGAGTGACTCACATCAGCG 59.470 55.000 15.33 0.00 36.74 5.18
570 572 2.028658 TCAAGGAGTGACTCACATCAGC 60.029 50.000 15.33 0.00 36.74 4.26
571 573 3.949842 TCAAGGAGTGACTCACATCAG 57.050 47.619 15.33 0.00 36.74 2.90
572 574 3.618263 GCATCAAGGAGTGACTCACATCA 60.618 47.826 15.33 0.00 39.72 3.07
573 575 2.935201 GCATCAAGGAGTGACTCACATC 59.065 50.000 15.33 6.12 39.72 3.06
574 576 2.303890 TGCATCAAGGAGTGACTCACAT 59.696 45.455 15.33 0.00 39.72 3.21
575 577 1.693606 TGCATCAAGGAGTGACTCACA 59.306 47.619 15.33 0.00 39.72 3.58
576 578 2.462456 TGCATCAAGGAGTGACTCAC 57.538 50.000 15.33 0.38 39.72 3.51
577 579 3.244665 ACATTGCATCAAGGAGTGACTCA 60.245 43.478 15.33 0.00 39.72 3.41
591 863 6.339730 TCAACAAGAAACTCAAACATTGCAT 58.660 32.000 0.00 0.00 0.00 3.96
597 869 6.507958 TCACATCAACAAGAAACTCAAACA 57.492 33.333 0.00 0.00 0.00 2.83
615 887 3.071874 TGGGAAGCTCGAAATTCACAT 57.928 42.857 9.53 0.00 33.99 3.21
622 894 0.457853 CGTCGATGGGAAGCTCGAAA 60.458 55.000 0.00 0.00 44.63 3.46
643 915 2.226330 CCAACGGGAAACATGAACTCA 58.774 47.619 0.00 0.00 35.59 3.41
718 990 0.716591 TCCCCACACTACCTGGATCT 59.283 55.000 0.00 0.00 0.00 2.75
753 1025 4.815269 TGGAAATTTGTCCCAATAAAGCG 58.185 39.130 0.00 0.00 36.80 4.68
799 1071 7.044314 GCAAATACGACAAAGTTATGGTATTGC 60.044 37.037 7.69 0.00 32.62 3.56
806 1078 8.958175 TTAAAGGCAAATACGACAAAGTTATG 57.042 30.769 0.00 0.00 0.00 1.90
932 1204 7.807977 ACTTGTAGTATTGAATTATGGCCAG 57.192 36.000 13.05 0.00 0.00 4.85
951 1223 9.690913 ATGGCAATATTATAGATGCATACTTGT 57.309 29.630 0.00 0.00 40.51 3.16
1257 1529 2.650322 AGAAGTACAGAGGAGGAGGACA 59.350 50.000 0.00 0.00 0.00 4.02
1371 1643 1.180029 CAGAATCACCAAGGGCCAAG 58.820 55.000 6.18 0.00 0.00 3.61
1452 1724 1.673626 GGGCATGCAAGTTCCATTGTG 60.674 52.381 21.36 0.00 32.56 3.33
1767 2039 2.610532 TACCGTTGTTGCTGCCACCA 62.611 55.000 1.07 0.00 0.00 4.17
1783 2055 0.387929 TCTCCATCGGCGAACATACC 59.612 55.000 15.93 0.00 0.00 2.73
1815 2087 5.479027 AGTGAAGAAGTTAAGTCTCTCCTCC 59.521 44.000 0.00 0.00 0.00 4.30
1816 2088 6.584185 AGTGAAGAAGTTAAGTCTCTCCTC 57.416 41.667 0.00 0.00 0.00 3.71
1817 2089 6.014925 GGAAGTGAAGAAGTTAAGTCTCTCCT 60.015 42.308 0.00 0.00 0.00 3.69
1827 2102 5.419542 CGATCCATGGAAGTGAAGAAGTTA 58.580 41.667 20.67 0.00 0.00 2.24
2198 2474 3.668491 GCGTTATTTTTGCCTAACTCGCA 60.668 43.478 0.00 0.00 39.72 5.10
2421 2701 3.524541 GGGCATTCACATCAAAATCCAC 58.475 45.455 0.00 0.00 0.00 4.02
2540 2820 4.512571 CGGATCATATCAACTGCACAATCA 59.487 41.667 0.00 0.00 0.00 2.57
2556 2836 2.533266 ATAACAAGCTCGCGGATCAT 57.467 45.000 6.13 0.00 0.00 2.45
2770 3084 6.564328 CCAAGAATAGACAGGCCAAATTTAC 58.436 40.000 5.01 0.00 0.00 2.01
2854 3168 4.798907 CACAGAGATTTACACGCGATAAGT 59.201 41.667 15.93 7.90 0.00 2.24
2876 3190 5.684184 CGCAAGTACGTATCAGTTAATAGCA 59.316 40.000 0.00 0.00 0.00 3.49
2877 3191 6.125079 CGCAAGTACGTATCAGTTAATAGC 57.875 41.667 0.00 0.00 0.00 2.97
3000 3380 9.990868 TCTTATAGCCAATCCATAGTATGAGTA 57.009 33.333 11.91 0.00 0.00 2.59
3074 3457 4.467082 TCTCATGCCCAAGTAAATGCAATT 59.533 37.500 0.00 0.00 38.98 2.32
3087 3470 1.488705 AACTCCCGTTCTCATGCCCA 61.489 55.000 0.00 0.00 0.00 5.36
3088 3471 0.322546 AAACTCCCGTTCTCATGCCC 60.323 55.000 0.00 0.00 31.66 5.36
3089 3472 0.804989 CAAACTCCCGTTCTCATGCC 59.195 55.000 0.00 0.00 31.66 4.40
3090 3473 0.169009 GCAAACTCCCGTTCTCATGC 59.831 55.000 0.00 0.00 31.66 4.06
3091 3474 1.522668 TGCAAACTCCCGTTCTCATG 58.477 50.000 0.00 0.00 31.66 3.07
3092 3475 2.496899 ATGCAAACTCCCGTTCTCAT 57.503 45.000 0.00 0.00 31.66 2.90
3093 3476 2.270352 AATGCAAACTCCCGTTCTCA 57.730 45.000 0.00 0.00 31.66 3.27
3094 3477 2.678336 CCTAATGCAAACTCCCGTTCTC 59.322 50.000 0.00 0.00 31.66 2.87
3095 3478 2.618045 CCCTAATGCAAACTCCCGTTCT 60.618 50.000 0.00 0.00 31.66 3.01
3096 3479 1.743394 CCCTAATGCAAACTCCCGTTC 59.257 52.381 0.00 0.00 31.66 3.95
3097 3480 1.074889 ACCCTAATGCAAACTCCCGTT 59.925 47.619 0.00 0.00 34.03 4.44
3098 3481 0.696501 ACCCTAATGCAAACTCCCGT 59.303 50.000 0.00 0.00 0.00 5.28
3099 3482 1.094785 CACCCTAATGCAAACTCCCG 58.905 55.000 0.00 0.00 0.00 5.14
3100 3483 2.215942 ACACCCTAATGCAAACTCCC 57.784 50.000 0.00 0.00 0.00 4.30
3101 3484 5.394115 CCATAAACACCCTAATGCAAACTCC 60.394 44.000 0.00 0.00 0.00 3.85
3102 3485 5.417580 TCCATAAACACCCTAATGCAAACTC 59.582 40.000 0.00 0.00 0.00 3.01
3103 3486 5.329399 TCCATAAACACCCTAATGCAAACT 58.671 37.500 0.00 0.00 0.00 2.66
3104 3487 5.652994 TCCATAAACACCCTAATGCAAAC 57.347 39.130 0.00 0.00 0.00 2.93
3105 3488 7.350382 TCTATCCATAAACACCCTAATGCAAA 58.650 34.615 0.00 0.00 0.00 3.68
3106 3489 6.905736 TCTATCCATAAACACCCTAATGCAA 58.094 36.000 0.00 0.00 0.00 4.08
3107 3490 6.508030 TCTATCCATAAACACCCTAATGCA 57.492 37.500 0.00 0.00 0.00 3.96
3108 3491 6.375455 CCATCTATCCATAAACACCCTAATGC 59.625 42.308 0.00 0.00 0.00 3.56
3109 3492 6.886459 CCCATCTATCCATAAACACCCTAATG 59.114 42.308 0.00 0.00 0.00 1.90
3110 3493 6.797540 TCCCATCTATCCATAAACACCCTAAT 59.202 38.462 0.00 0.00 0.00 1.73
3111 3494 6.154645 TCCCATCTATCCATAAACACCCTAA 58.845 40.000 0.00 0.00 0.00 2.69
3112 3495 5.733000 TCCCATCTATCCATAAACACCCTA 58.267 41.667 0.00 0.00 0.00 3.53
3113 3496 4.577096 TCCCATCTATCCATAAACACCCT 58.423 43.478 0.00 0.00 0.00 4.34
3114 3497 4.993705 TCCCATCTATCCATAAACACCC 57.006 45.455 0.00 0.00 0.00 4.61
3115 3498 7.004086 TCAATTCCCATCTATCCATAAACACC 58.996 38.462 0.00 0.00 0.00 4.16
3116 3499 7.721399 AGTCAATTCCCATCTATCCATAAACAC 59.279 37.037 0.00 0.00 0.00 3.32
3117 3500 7.815383 AGTCAATTCCCATCTATCCATAAACA 58.185 34.615 0.00 0.00 0.00 2.83
3118 3501 8.697507 AAGTCAATTCCCATCTATCCATAAAC 57.302 34.615 0.00 0.00 0.00 2.01
3119 3502 8.924511 GAAGTCAATTCCCATCTATCCATAAA 57.075 34.615 0.00 0.00 31.14 1.40


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.