Multiple sequence alignment - TraesCS6A01G329300

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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 TraesCS6A01G329300 chr6A 100.000 2915 0 0 1 2915 562682169 562685083 0.000000e+00 5384.0
1 TraesCS6A01G329300 chr6A 92.058 617 36 6 1 616 562672675 562673279 0.000000e+00 856.0
2 TraesCS6A01G329300 chr6A 76.403 606 106 19 1 584 80642691 80643281 2.840000e-75 292.0
3 TraesCS6A01G329300 chr6A 78.475 223 44 4 304 525 21707995 21707776 3.030000e-30 143.0
4 TraesCS6A01G329300 chr6B 94.081 1588 53 14 576 2134 632176371 632177946 0.000000e+00 2374.0
5 TraesCS6A01G329300 chr6B 88.457 823 57 17 2115 2910 632177972 632178783 0.000000e+00 959.0
6 TraesCS6A01G329300 chr6B 76.038 530 100 15 1 504 687539881 687540409 1.730000e-62 250.0
7 TraesCS6A01G329300 chr6B 75.785 223 44 6 225 446 488845921 488846134 1.430000e-18 104.0
8 TraesCS6A01G329300 chr6D 95.096 1509 47 11 637 2134 419262880 419264372 0.000000e+00 2351.0
9 TraesCS6A01G329300 chr6D 91.925 805 50 8 2117 2915 419264400 419265195 0.000000e+00 1112.0
10 TraesCS6A01G329300 chr3D 82.617 512 67 12 3 499 84968210 84968714 1.600000e-117 433.0
11 TraesCS6A01G329300 chr5D 78.819 491 70 10 1 460 276703919 276704406 1.700000e-77 300.0
12 TraesCS6A01G329300 chr5D 82.110 218 36 2 308 525 222901063 222900849 1.780000e-42 183.0
13 TraesCS6A01G329300 chr5D 80.769 208 31 6 1 199 222901399 222901192 1.400000e-33 154.0
14 TraesCS6A01G329300 chr5B 76.136 616 104 16 1 584 371392408 371391804 1.710000e-72 283.0
15 TraesCS6A01G329300 chr5B 83.333 204 28 4 302 503 648728082 648728281 1.780000e-42 183.0
16 TraesCS6A01G329300 chr1B 75.985 533 102 15 1 510 666183818 666184347 4.820000e-63 252.0
17 TraesCS6A01G329300 chr2D 76.716 408 79 14 111 508 500663711 500663310 2.280000e-51 213.0
18 TraesCS6A01G329300 chr2D 79.167 216 43 2 307 522 78009414 78009201 6.510000e-32 148.0
19 TraesCS6A01G329300 chr4A 79.848 263 36 14 1 246 602867792 602867530 2.990000e-40 176.0
20 TraesCS6A01G329300 chr7A 78.761 226 42 6 301 525 646109031 646108811 2.340000e-31 147.0
21 TraesCS6A01G329300 chr2A 89.908 109 10 1 1 109 764390239 764390346 3.920000e-29 139.0
22 TraesCS6A01G329300 chr2A 88.991 109 11 1 1 109 764439646 764439753 1.820000e-27 134.0
23 TraesCS6A01G329300 chr2A 88.991 109 11 1 1 109 764456984 764457091 1.820000e-27 134.0
24 TraesCS6A01G329300 chr4D 74.706 170 30 6 105 262 81914546 81914714 2.430000e-06 63.9


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 TraesCS6A01G329300 chr6A 562682169 562685083 2914 False 5384.0 5384 100.0000 1 2915 1 chr6A.!!$F3 2914
1 TraesCS6A01G329300 chr6A 562672675 562673279 604 False 856.0 856 92.0580 1 616 1 chr6A.!!$F2 615
2 TraesCS6A01G329300 chr6A 80642691 80643281 590 False 292.0 292 76.4030 1 584 1 chr6A.!!$F1 583
3 TraesCS6A01G329300 chr6B 632176371 632178783 2412 False 1666.5 2374 91.2690 576 2910 2 chr6B.!!$F3 2334
4 TraesCS6A01G329300 chr6B 687539881 687540409 528 False 250.0 250 76.0380 1 504 1 chr6B.!!$F2 503
5 TraesCS6A01G329300 chr6D 419262880 419265195 2315 False 1731.5 2351 93.5105 637 2915 2 chr6D.!!$F1 2278
6 TraesCS6A01G329300 chr3D 84968210 84968714 504 False 433.0 433 82.6170 3 499 1 chr3D.!!$F1 496
7 TraesCS6A01G329300 chr5B 371391804 371392408 604 True 283.0 283 76.1360 1 584 1 chr5B.!!$R1 583
8 TraesCS6A01G329300 chr1B 666183818 666184347 529 False 252.0 252 75.9850 1 510 1 chr1B.!!$F1 509

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
548 591 0.036199 TTATCCCCAAACGGACACGG 60.036 55.0 0.0 0.0 46.48 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1936 2023 0.179156 GACCAGATGCAACATTGGCG 60.179 55.0 2.57 0.0 33.98 5.69 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
343 386 2.747686 GAGGGAAAGTGTGGGCGA 59.252 61.111 0.00 0.00 0.00 5.54
449 492 1.895131 CCAAAGTTGGGTCAGGAATGG 59.105 52.381 1.83 0.00 44.70 3.16
450 493 2.490718 CCAAAGTTGGGTCAGGAATGGA 60.491 50.000 1.83 0.00 44.70 3.41
451 494 3.434309 CAAAGTTGGGTCAGGAATGGAT 58.566 45.455 0.00 0.00 0.00 3.41
452 495 3.372440 AAGTTGGGTCAGGAATGGATC 57.628 47.619 0.00 0.00 0.00 3.36
453 496 1.210478 AGTTGGGTCAGGAATGGATCG 59.790 52.381 0.00 0.00 0.00 3.69
454 497 1.209504 GTTGGGTCAGGAATGGATCGA 59.790 52.381 0.00 0.00 0.00 3.59
455 498 1.578897 TGGGTCAGGAATGGATCGAA 58.421 50.000 0.00 0.00 0.00 3.71
456 499 1.912731 TGGGTCAGGAATGGATCGAAA 59.087 47.619 0.00 0.00 0.00 3.46
457 500 2.092968 TGGGTCAGGAATGGATCGAAAG 60.093 50.000 0.00 0.00 0.00 2.62
458 501 1.943340 GGTCAGGAATGGATCGAAAGC 59.057 52.381 0.00 0.00 0.00 3.51
459 502 1.594862 GTCAGGAATGGATCGAAAGCG 59.405 52.381 0.00 0.00 39.35 4.68
470 513 2.766970 TCGAAAGCGAACCAAAAAGG 57.233 45.000 0.00 0.00 44.78 3.11
471 514 1.128513 CGAAAGCGAACCAAAAAGGC 58.871 50.000 0.00 0.00 39.90 4.35
472 515 1.535015 CGAAAGCGAACCAAAAAGGCA 60.535 47.619 0.00 0.00 39.90 4.75
473 516 1.858458 GAAAGCGAACCAAAAAGGCAC 59.142 47.619 0.00 0.00 43.14 5.01
474 517 0.820871 AAGCGAACCAAAAAGGCACA 59.179 45.000 0.00 0.00 43.14 4.57
475 518 0.820871 AGCGAACCAAAAAGGCACAA 59.179 45.000 0.00 0.00 43.14 3.33
476 519 0.927537 GCGAACCAAAAAGGCACAAC 59.072 50.000 0.00 0.00 43.14 3.32
477 520 1.196200 CGAACCAAAAAGGCACAACG 58.804 50.000 0.00 0.00 43.14 4.10
478 521 1.566404 GAACCAAAAAGGCACAACGG 58.434 50.000 0.00 0.00 43.14 4.44
479 522 0.899019 AACCAAAAAGGCACAACGGT 59.101 45.000 0.00 0.00 43.14 4.83
480 523 0.458260 ACCAAAAAGGCACAACGGTC 59.542 50.000 0.00 0.00 43.14 4.79
481 524 0.744281 CCAAAAAGGCACAACGGTCT 59.256 50.000 0.00 0.00 0.00 3.85
482 525 1.535860 CCAAAAAGGCACAACGGTCTG 60.536 52.381 0.00 0.00 0.00 3.51
483 526 1.134175 CAAAAAGGCACAACGGTCTGT 59.866 47.619 0.00 0.00 0.00 3.41
484 527 1.470051 AAAAGGCACAACGGTCTGTT 58.530 45.000 0.00 0.00 43.09 3.16
485 528 1.470051 AAAGGCACAACGGTCTGTTT 58.530 45.000 0.00 0.00 39.29 2.83
486 529 0.738389 AAGGCACAACGGTCTGTTTG 59.262 50.000 0.00 0.00 39.29 2.93
487 530 1.299089 GGCACAACGGTCTGTTTGC 60.299 57.895 16.83 16.83 39.29 3.68
488 531 1.724582 GGCACAACGGTCTGTTTGCT 61.725 55.000 20.96 0.00 40.87 3.91
489 532 0.317020 GCACAACGGTCTGTTTGCTC 60.317 55.000 17.40 0.00 39.29 4.26
490 533 1.299541 CACAACGGTCTGTTTGCTCT 58.700 50.000 0.00 0.00 39.29 4.09
491 534 1.261619 CACAACGGTCTGTTTGCTCTC 59.738 52.381 0.00 0.00 39.29 3.20
492 535 0.508641 CAACGGTCTGTTTGCTCTCG 59.491 55.000 0.00 0.00 39.29 4.04
493 536 1.222115 AACGGTCTGTTTGCTCTCGC 61.222 55.000 0.00 0.00 37.59 5.03
494 537 2.720758 CGGTCTGTTTGCTCTCGCG 61.721 63.158 0.00 0.00 39.65 5.87
495 538 2.472049 GTCTGTTTGCTCTCGCGC 59.528 61.111 0.00 0.00 39.65 6.86
496 539 3.105782 TCTGTTTGCTCTCGCGCG 61.106 61.111 26.76 26.76 39.65 6.86
497 540 3.406361 CTGTTTGCTCTCGCGCGT 61.406 61.111 30.98 0.00 39.65 6.01
498 541 2.943345 CTGTTTGCTCTCGCGCGTT 61.943 57.895 30.98 0.00 39.65 4.84
499 542 2.497628 GTTTGCTCTCGCGCGTTG 60.498 61.111 30.98 22.78 39.65 4.10
500 543 3.711842 TTTGCTCTCGCGCGTTGG 61.712 61.111 30.98 20.13 39.65 3.77
511 554 2.125269 GCGTTGGGCGGTCTGTAT 60.125 61.111 0.00 0.00 41.69 2.29
512 555 1.743995 GCGTTGGGCGGTCTGTATT 60.744 57.895 0.00 0.00 41.69 1.89
513 556 0.460635 GCGTTGGGCGGTCTGTATTA 60.461 55.000 0.00 0.00 41.69 0.98
514 557 1.808891 GCGTTGGGCGGTCTGTATTAT 60.809 52.381 0.00 0.00 41.69 1.28
515 558 2.132762 CGTTGGGCGGTCTGTATTATC 58.867 52.381 0.00 0.00 36.85 1.75
516 559 2.223971 CGTTGGGCGGTCTGTATTATCT 60.224 50.000 0.00 0.00 36.85 1.98
517 560 3.131396 GTTGGGCGGTCTGTATTATCTG 58.869 50.000 0.00 0.00 0.00 2.90
518 561 2.394632 TGGGCGGTCTGTATTATCTGT 58.605 47.619 0.00 0.00 0.00 3.41
519 562 2.769663 TGGGCGGTCTGTATTATCTGTT 59.230 45.455 0.00 0.00 0.00 3.16
520 563 3.199071 TGGGCGGTCTGTATTATCTGTTT 59.801 43.478 0.00 0.00 0.00 2.83
521 564 4.406326 TGGGCGGTCTGTATTATCTGTTTA 59.594 41.667 0.00 0.00 0.00 2.01
522 565 5.071250 TGGGCGGTCTGTATTATCTGTTTAT 59.929 40.000 0.00 0.00 0.00 1.40
523 566 5.638234 GGGCGGTCTGTATTATCTGTTTATC 59.362 44.000 0.00 0.00 0.00 1.75
524 567 5.638234 GGCGGTCTGTATTATCTGTTTATCC 59.362 44.000 0.00 0.00 0.00 2.59
525 568 6.456501 GCGGTCTGTATTATCTGTTTATCCT 58.543 40.000 0.00 0.00 0.00 3.24
526 569 6.929606 GCGGTCTGTATTATCTGTTTATCCTT 59.070 38.462 0.00 0.00 0.00 3.36
527 570 7.441458 GCGGTCTGTATTATCTGTTTATCCTTT 59.559 37.037 0.00 0.00 0.00 3.11
528 571 9.976511 CGGTCTGTATTATCTGTTTATCCTTTA 57.023 33.333 0.00 0.00 0.00 1.85
540 583 9.416284 TCTGTTTATCCTTTATTATCCCCAAAC 57.584 33.333 0.00 0.00 0.00 2.93
541 584 8.228035 TGTTTATCCTTTATTATCCCCAAACG 57.772 34.615 0.00 0.00 0.00 3.60
542 585 7.285858 TGTTTATCCTTTATTATCCCCAAACGG 59.714 37.037 0.00 0.00 0.00 4.44
543 586 5.656549 ATCCTTTATTATCCCCAAACGGA 57.343 39.130 0.00 0.00 36.02 4.69
544 587 4.784177 TCCTTTATTATCCCCAAACGGAC 58.216 43.478 0.00 0.00 33.77 4.79
545 588 4.227754 TCCTTTATTATCCCCAAACGGACA 59.772 41.667 0.00 0.00 33.77 4.02
546 589 4.337274 CCTTTATTATCCCCAAACGGACAC 59.663 45.833 0.00 0.00 33.77 3.67
548 591 0.036199 TTATCCCCAAACGGACACGG 60.036 55.000 0.00 0.00 46.48 4.94
549 592 0.903924 TATCCCCAAACGGACACGGA 60.904 55.000 0.00 0.00 46.48 4.69
550 593 2.459202 ATCCCCAAACGGACACGGAC 62.459 60.000 0.00 0.00 46.48 4.79
551 594 2.424302 CCCAAACGGACACGGACT 59.576 61.111 0.00 0.00 46.48 3.85
552 595 1.959226 CCCAAACGGACACGGACTG 60.959 63.158 0.00 0.00 46.48 3.51
553 596 1.959226 CCAAACGGACACGGACTGG 60.959 63.158 0.00 0.00 46.48 4.00
554 597 1.227438 CAAACGGACACGGACTGGT 60.227 57.895 0.00 0.00 46.48 4.00
555 598 1.068585 AAACGGACACGGACTGGTC 59.931 57.895 0.00 0.00 46.48 4.02
556 599 1.678598 AAACGGACACGGACTGGTCA 61.679 55.000 3.10 0.00 46.48 4.02
557 600 1.469335 AACGGACACGGACTGGTCAT 61.469 55.000 3.10 0.00 46.48 3.06
558 601 1.292223 CGGACACGGACTGGTCATT 59.708 57.895 3.10 0.00 35.74 2.57
559 602 0.320421 CGGACACGGACTGGTCATTT 60.320 55.000 3.10 0.00 35.74 2.32
560 603 1.067425 CGGACACGGACTGGTCATTTA 60.067 52.381 3.10 0.00 35.74 1.40
561 604 2.618053 GGACACGGACTGGTCATTTAG 58.382 52.381 3.10 0.00 35.74 1.85
562 605 2.028385 GGACACGGACTGGTCATTTAGT 60.028 50.000 3.10 0.00 35.74 2.24
563 606 2.993899 GACACGGACTGGTCATTTAGTG 59.006 50.000 3.10 6.92 34.22 2.74
564 607 2.367567 ACACGGACTGGTCATTTAGTGT 59.632 45.455 3.10 7.43 36.85 3.55
565 608 2.993899 CACGGACTGGTCATTTAGTGTC 59.006 50.000 3.10 0.00 0.00 3.67
566 609 2.259618 CGGACTGGTCATTTAGTGTCG 58.740 52.381 3.10 0.00 0.00 4.35
567 610 2.352421 CGGACTGGTCATTTAGTGTCGT 60.352 50.000 3.10 0.00 0.00 4.34
568 611 2.993899 GGACTGGTCATTTAGTGTCGTG 59.006 50.000 3.10 0.00 0.00 4.35
569 612 2.412089 GACTGGTCATTTAGTGTCGTGC 59.588 50.000 0.00 0.00 0.00 5.34
570 613 1.390123 CTGGTCATTTAGTGTCGTGCG 59.610 52.381 0.00 0.00 0.00 5.34
571 614 0.719465 GGTCATTTAGTGTCGTGCGG 59.281 55.000 0.00 0.00 0.00 5.69
572 615 1.425412 GTCATTTAGTGTCGTGCGGT 58.575 50.000 0.00 0.00 0.00 5.68
573 616 1.126113 GTCATTTAGTGTCGTGCGGTG 59.874 52.381 0.00 0.00 0.00 4.94
574 617 0.442310 CATTTAGTGTCGTGCGGTGG 59.558 55.000 0.00 0.00 0.00 4.61
577 620 1.457823 TTAGTGTCGTGCGGTGGAGT 61.458 55.000 0.00 0.00 0.00 3.85
581 624 4.980805 TCGTGCGGTGGAGTTGCC 62.981 66.667 0.00 0.00 37.10 4.52
596 639 0.766131 TTGCCCTTACGAACCAGGAA 59.234 50.000 0.00 0.00 30.81 3.36
597 640 0.766131 TGCCCTTACGAACCAGGAAA 59.234 50.000 0.00 0.00 30.81 3.13
613 656 2.700897 AGGAAAGGTGACCGATCCTATG 59.299 50.000 23.92 0.00 40.12 2.23
627 670 0.108186 CCTATGCTTGCACCAGTCGA 60.108 55.000 0.00 0.00 0.00 4.20
630 673 3.414700 GCTTGCACCAGTCGACCG 61.415 66.667 13.01 0.70 0.00 4.79
632 675 2.022129 CTTGCACCAGTCGACCGAC 61.022 63.158 13.01 14.03 44.86 4.79
665 708 6.567769 ACGTTGACAATTTTCAAATCACAC 57.432 33.333 8.56 0.00 37.24 3.82
669 712 4.739228 TGACAATTTTCAAATCACACTGCG 59.261 37.500 0.00 0.00 0.00 5.18
672 715 2.772568 TTTCAAATCACACTGCGTGG 57.227 45.000 12.18 3.32 46.36 4.94
731 774 4.442073 GCAAGTTTACACAAAGTGCATCAG 59.558 41.667 0.00 0.00 36.52 2.90
750 793 0.652592 GCATCCGCGGCATATATGAC 59.347 55.000 23.51 13.03 0.00 3.06
758 801 3.495193 GCGGCATATATGACAGCAAATG 58.505 45.455 22.40 6.73 34.77 2.32
1605 1689 3.431725 CTGCCCGCCGAAAAGGAC 61.432 66.667 0.00 0.00 45.00 3.85
1725 1809 0.172803 ATGCGTACTGGAAGACGGAC 59.827 55.000 0.00 0.00 39.51 4.79
1936 2023 1.906574 TCTGGTATGACTGTCAACCCC 59.093 52.381 25.48 20.13 31.20 4.95
1937 2024 0.611200 TGGTATGACTGTCAACCCCG 59.389 55.000 25.48 0.00 31.20 5.73
1939 2026 0.743345 GTATGACTGTCAACCCCGCC 60.743 60.000 15.31 0.00 0.00 6.13
1940 2027 1.195442 TATGACTGTCAACCCCGCCA 61.195 55.000 15.31 0.00 0.00 5.69
2029 2119 4.224147 TGGGTAATCAGCTTACAGTTGCTA 59.776 41.667 1.08 0.00 41.35 3.49
2145 2280 7.182817 TCTTGTTATGTAGTGTCTGGCTATT 57.817 36.000 0.00 0.00 0.00 1.73
2147 2282 8.195436 TCTTGTTATGTAGTGTCTGGCTATTAC 58.805 37.037 0.00 0.00 0.00 1.89
2148 2283 7.655521 TGTTATGTAGTGTCTGGCTATTACT 57.344 36.000 0.00 0.00 0.00 2.24
2149 2284 8.756486 TGTTATGTAGTGTCTGGCTATTACTA 57.244 34.615 0.00 0.00 0.00 1.82
2150 2285 8.627403 TGTTATGTAGTGTCTGGCTATTACTAC 58.373 37.037 0.00 0.00 42.34 2.73
2201 2337 4.801891 TGTGTGGTAGTATGACTTCGTTC 58.198 43.478 0.00 0.00 0.00 3.95
2214 2350 4.819630 TGACTTCGTTCCACAAAATTAGCT 59.180 37.500 0.00 0.00 0.00 3.32
2254 2390 5.278071 CCCGTCAGCTAGAAGATACTGTTAG 60.278 48.000 0.00 0.00 0.00 2.34
2263 2399 7.923344 GCTAGAAGATACTGTTAGATTCTGCAA 59.077 37.037 0.00 0.00 0.00 4.08
2299 2438 3.805422 TGCGAACGAAGTAACATCTTGTT 59.195 39.130 0.00 0.00 45.00 2.83
2300 2439 4.271533 TGCGAACGAAGTAACATCTTGTTT 59.728 37.500 0.00 0.00 45.00 2.83
2301 2440 5.202640 GCGAACGAAGTAACATCTTGTTTT 58.797 37.500 0.00 0.00 45.00 2.43
2320 2459 6.096036 TGTTTTGAAAAACTGCGAAAGATCA 58.904 32.000 17.08 0.00 46.37 2.92
2370 2509 6.036300 TGGTTTCAGTTTGTTTACACGACTAG 59.964 38.462 0.00 0.00 0.00 2.57
2481 2620 5.126779 ACTCCTCAGTTCTTTGTTTTCCTC 58.873 41.667 0.00 0.00 0.00 3.71
2509 2648 9.322769 ACTGTAACCCTTAATTCGATATATCCT 57.677 33.333 7.15 0.00 0.00 3.24
2512 2651 9.379791 GTAACCCTTAATTCGATATATCCTTGG 57.620 37.037 7.15 1.10 0.00 3.61
2514 2653 7.852263 ACCCTTAATTCGATATATCCTTGGAG 58.148 38.462 7.15 0.00 0.00 3.86
2536 2675 9.117183 TGGAGATCTGATTCTCAAATACAAATG 57.883 33.333 0.00 0.00 43.28 2.32
2540 2679 9.395707 GATCTGATTCTCAAATACAAATGCATC 57.604 33.333 0.00 0.00 0.00 3.91
2565 2704 4.910195 ACTTCAGCCATCTATTCAACACA 58.090 39.130 0.00 0.00 0.00 3.72
2571 2710 7.112122 TCAGCCATCTATTCAACACATTACTT 58.888 34.615 0.00 0.00 0.00 2.24
2607 2749 4.310769 CAGGCATAGTTACTGATACAGCC 58.689 47.826 0.00 0.00 39.82 4.85
2615 2757 0.254178 ACTGATACAGCCAAGGCAGG 59.746 55.000 14.40 7.52 44.88 4.85
2657 2799 7.042456 ACTGTGCTTCTTCTATGCAATAATACG 60.042 37.037 0.00 0.00 39.71 3.06
2703 2853 4.508405 CCCTACCCCACTTGAAATCTTTCA 60.508 45.833 1.28 1.28 44.78 2.69
2825 2975 5.529060 GGTTTCATATTCCTTAGAGCACCTG 59.471 44.000 0.00 0.00 0.00 4.00
2826 2976 5.957771 TTCATATTCCTTAGAGCACCTGT 57.042 39.130 0.00 0.00 0.00 4.00
2903 3068 6.479990 TCCTGAATATCTACATTGCAAAGTCG 59.520 38.462 11.12 5.24 0.00 4.18
2910 3075 6.887376 TCTACATTGCAAAGTCGATACTTC 57.113 37.500 11.12 0.00 45.37 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
161 178 1.048724 ATCCCGAATCGGCCAAGAGA 61.049 55.000 17.50 7.37 46.86 3.10
178 195 1.808133 CGGAGGTAGCCAAGCTTGATC 60.808 57.143 28.05 17.76 40.44 2.92
440 483 1.480545 TCGCTTTCGATCCATTCCTGA 59.519 47.619 0.00 0.00 40.21 3.86
449 492 3.234386 CCTTTTTGGTTCGCTTTCGATC 58.766 45.455 0.00 0.00 45.04 3.69
450 493 2.607038 GCCTTTTTGGTTCGCTTTCGAT 60.607 45.455 0.00 0.00 39.43 3.59
451 494 1.268845 GCCTTTTTGGTTCGCTTTCGA 60.269 47.619 0.00 0.00 39.31 3.71
452 495 1.128513 GCCTTTTTGGTTCGCTTTCG 58.871 50.000 0.00 0.00 38.35 3.46
453 496 1.858458 GTGCCTTTTTGGTTCGCTTTC 59.142 47.619 0.00 0.00 38.35 2.62
454 497 1.205893 TGTGCCTTTTTGGTTCGCTTT 59.794 42.857 0.00 0.00 38.35 3.51
455 498 0.820871 TGTGCCTTTTTGGTTCGCTT 59.179 45.000 0.00 0.00 38.35 4.68
456 499 0.820871 TTGTGCCTTTTTGGTTCGCT 59.179 45.000 0.00 0.00 38.35 4.93
457 500 0.927537 GTTGTGCCTTTTTGGTTCGC 59.072 50.000 0.00 0.00 38.35 4.70
458 501 1.196200 CGTTGTGCCTTTTTGGTTCG 58.804 50.000 0.00 0.00 38.35 3.95
459 502 1.134936 ACCGTTGTGCCTTTTTGGTTC 60.135 47.619 0.00 0.00 38.35 3.62
460 503 0.899019 ACCGTTGTGCCTTTTTGGTT 59.101 45.000 0.00 0.00 38.35 3.67
461 504 0.458260 GACCGTTGTGCCTTTTTGGT 59.542 50.000 0.00 0.00 38.35 3.67
462 505 0.744281 AGACCGTTGTGCCTTTTTGG 59.256 50.000 0.00 0.00 39.35 3.28
463 506 1.134175 ACAGACCGTTGTGCCTTTTTG 59.866 47.619 0.00 0.00 0.00 2.44
464 507 1.470051 ACAGACCGTTGTGCCTTTTT 58.530 45.000 0.00 0.00 0.00 1.94
465 508 1.470051 AACAGACCGTTGTGCCTTTT 58.530 45.000 0.00 0.00 36.12 2.27
466 509 1.134175 CAAACAGACCGTTGTGCCTTT 59.866 47.619 0.00 0.00 38.07 3.11
467 510 0.738389 CAAACAGACCGTTGTGCCTT 59.262 50.000 0.00 0.00 38.07 4.35
468 511 1.724582 GCAAACAGACCGTTGTGCCT 61.725 55.000 0.00 0.00 38.07 4.75
469 512 1.299089 GCAAACAGACCGTTGTGCC 60.299 57.895 0.00 0.00 38.07 5.01
470 513 0.317020 GAGCAAACAGACCGTTGTGC 60.317 55.000 0.00 0.00 39.69 4.57
471 514 1.261619 GAGAGCAAACAGACCGTTGTG 59.738 52.381 0.00 0.00 38.07 3.33
472 515 1.583054 GAGAGCAAACAGACCGTTGT 58.417 50.000 0.00 0.00 38.07 3.32
473 516 0.508641 CGAGAGCAAACAGACCGTTG 59.491 55.000 0.00 0.00 38.07 4.10
474 517 2.900528 CGAGAGCAAACAGACCGTT 58.099 52.632 0.00 0.00 40.50 4.44
475 518 4.655527 CGAGAGCAAACAGACCGT 57.344 55.556 0.00 0.00 0.00 4.83
494 537 0.460635 TAATACAGACCGCCCAACGC 60.461 55.000 0.00 0.00 41.76 4.84
495 538 2.132762 GATAATACAGACCGCCCAACG 58.867 52.381 0.00 0.00 43.15 4.10
496 539 3.131396 CAGATAATACAGACCGCCCAAC 58.869 50.000 0.00 0.00 0.00 3.77
497 540 2.769663 ACAGATAATACAGACCGCCCAA 59.230 45.455 0.00 0.00 0.00 4.12
498 541 2.394632 ACAGATAATACAGACCGCCCA 58.605 47.619 0.00 0.00 0.00 5.36
499 542 3.470645 AACAGATAATACAGACCGCCC 57.529 47.619 0.00 0.00 0.00 6.13
500 543 5.638234 GGATAAACAGATAATACAGACCGCC 59.362 44.000 0.00 0.00 0.00 6.13
501 544 6.456501 AGGATAAACAGATAATACAGACCGC 58.543 40.000 0.00 0.00 0.00 5.68
502 545 8.888579 AAAGGATAAACAGATAATACAGACCG 57.111 34.615 0.00 0.00 0.00 4.79
514 557 9.416284 GTTTGGGGATAATAAAGGATAAACAGA 57.584 33.333 0.00 0.00 0.00 3.41
515 558 8.349983 CGTTTGGGGATAATAAAGGATAAACAG 58.650 37.037 0.00 0.00 0.00 3.16
516 559 7.285858 CCGTTTGGGGATAATAAAGGATAAACA 59.714 37.037 0.00 0.00 0.00 2.83
517 560 7.503230 TCCGTTTGGGGATAATAAAGGATAAAC 59.497 37.037 0.00 0.00 36.01 2.01
518 561 7.503230 GTCCGTTTGGGGATAATAAAGGATAAA 59.497 37.037 0.00 0.00 38.61 1.40
519 562 6.999871 GTCCGTTTGGGGATAATAAAGGATAA 59.000 38.462 0.00 0.00 38.61 1.75
520 563 6.101442 TGTCCGTTTGGGGATAATAAAGGATA 59.899 38.462 0.00 0.00 38.61 2.59
521 564 5.103855 TGTCCGTTTGGGGATAATAAAGGAT 60.104 40.000 0.00 0.00 38.61 3.24
522 565 4.227754 TGTCCGTTTGGGGATAATAAAGGA 59.772 41.667 0.00 0.00 38.61 3.36
523 566 4.337274 GTGTCCGTTTGGGGATAATAAAGG 59.663 45.833 0.00 0.00 38.61 3.11
524 567 4.034742 CGTGTCCGTTTGGGGATAATAAAG 59.965 45.833 0.00 0.00 38.61 1.85
525 568 3.940221 CGTGTCCGTTTGGGGATAATAAA 59.060 43.478 0.00 0.00 38.61 1.40
526 569 3.533547 CGTGTCCGTTTGGGGATAATAA 58.466 45.455 0.00 0.00 38.61 1.40
527 570 2.158928 CCGTGTCCGTTTGGGGATAATA 60.159 50.000 0.00 0.00 38.61 0.98
528 571 1.407712 CCGTGTCCGTTTGGGGATAAT 60.408 52.381 0.00 0.00 38.61 1.28
529 572 0.036199 CCGTGTCCGTTTGGGGATAA 60.036 55.000 0.00 0.00 38.61 1.75
530 573 0.903924 TCCGTGTCCGTTTGGGGATA 60.904 55.000 0.00 0.00 38.61 2.59
531 574 2.218454 TCCGTGTCCGTTTGGGGAT 61.218 57.895 0.00 0.00 38.61 3.85
532 575 2.843411 TCCGTGTCCGTTTGGGGA 60.843 61.111 0.00 0.00 36.01 4.81
533 576 2.667199 GTCCGTGTCCGTTTGGGG 60.667 66.667 0.00 0.00 36.01 4.96
534 577 1.959226 CAGTCCGTGTCCGTTTGGG 60.959 63.158 0.00 0.00 35.24 4.12
535 578 1.959226 CCAGTCCGTGTCCGTTTGG 60.959 63.158 0.00 0.00 0.00 3.28
536 579 1.219522 GACCAGTCCGTGTCCGTTTG 61.220 60.000 0.00 0.00 0.00 2.93
537 580 1.068585 GACCAGTCCGTGTCCGTTT 59.931 57.895 0.00 0.00 0.00 3.60
538 581 1.469335 ATGACCAGTCCGTGTCCGTT 61.469 55.000 0.00 0.00 0.00 4.44
539 582 1.469335 AATGACCAGTCCGTGTCCGT 61.469 55.000 0.00 0.00 0.00 4.69
540 583 0.320421 AAATGACCAGTCCGTGTCCG 60.320 55.000 0.00 0.00 0.00 4.79
541 584 2.028385 ACTAAATGACCAGTCCGTGTCC 60.028 50.000 0.00 0.00 0.00 4.02
542 585 2.993899 CACTAAATGACCAGTCCGTGTC 59.006 50.000 0.00 0.00 0.00 3.67
543 586 2.367567 ACACTAAATGACCAGTCCGTGT 59.632 45.455 0.00 0.00 0.00 4.49
544 587 2.993899 GACACTAAATGACCAGTCCGTG 59.006 50.000 0.00 0.00 0.00 4.94
545 588 2.352421 CGACACTAAATGACCAGTCCGT 60.352 50.000 0.00 0.00 0.00 4.69
546 589 2.259618 CGACACTAAATGACCAGTCCG 58.740 52.381 0.00 0.00 0.00 4.79
547 590 2.993899 CACGACACTAAATGACCAGTCC 59.006 50.000 0.00 0.00 0.00 3.85
548 591 2.412089 GCACGACACTAAATGACCAGTC 59.588 50.000 0.00 0.00 0.00 3.51
549 592 2.413837 GCACGACACTAAATGACCAGT 58.586 47.619 0.00 0.00 0.00 4.00
550 593 1.390123 CGCACGACACTAAATGACCAG 59.610 52.381 0.00 0.00 0.00 4.00
551 594 1.424403 CGCACGACACTAAATGACCA 58.576 50.000 0.00 0.00 0.00 4.02
552 595 0.719465 CCGCACGACACTAAATGACC 59.281 55.000 0.00 0.00 0.00 4.02
553 596 1.126113 CACCGCACGACACTAAATGAC 59.874 52.381 0.00 0.00 0.00 3.06
554 597 1.424403 CACCGCACGACACTAAATGA 58.576 50.000 0.00 0.00 0.00 2.57
555 598 0.442310 CCACCGCACGACACTAAATG 59.558 55.000 0.00 0.00 0.00 2.32
556 599 0.319083 TCCACCGCACGACACTAAAT 59.681 50.000 0.00 0.00 0.00 1.40
557 600 0.319211 CTCCACCGCACGACACTAAA 60.319 55.000 0.00 0.00 0.00 1.85
558 601 1.287815 CTCCACCGCACGACACTAA 59.712 57.895 0.00 0.00 0.00 2.24
559 602 1.457823 AACTCCACCGCACGACACTA 61.458 55.000 0.00 0.00 0.00 2.74
560 603 2.792947 AACTCCACCGCACGACACT 61.793 57.895 0.00 0.00 0.00 3.55
561 604 2.279918 AACTCCACCGCACGACAC 60.280 61.111 0.00 0.00 0.00 3.67
562 605 2.279851 CAACTCCACCGCACGACA 60.280 61.111 0.00 0.00 0.00 4.35
563 606 3.712881 GCAACTCCACCGCACGAC 61.713 66.667 0.00 0.00 0.00 4.34
564 607 4.980805 GGCAACTCCACCGCACGA 62.981 66.667 0.00 0.00 34.01 4.35
566 609 2.741486 TAAGGGCAACTCCACCGCAC 62.741 60.000 0.00 0.00 36.21 5.34
567 610 2.521451 TAAGGGCAACTCCACCGCA 61.521 57.895 0.00 0.00 36.21 5.69
568 611 2.038837 GTAAGGGCAACTCCACCGC 61.039 63.158 0.00 0.00 36.21 5.68
569 612 1.740296 CGTAAGGGCAACTCCACCG 60.740 63.158 0.00 0.00 36.21 4.94
570 613 0.035739 TTCGTAAGGGCAACTCCACC 59.964 55.000 0.00 0.00 36.21 4.61
571 614 1.154197 GTTCGTAAGGGCAACTCCAC 58.846 55.000 0.00 0.00 36.21 4.02
572 615 0.035739 GGTTCGTAAGGGCAACTCCA 59.964 55.000 0.00 0.00 36.21 3.86
573 616 0.035739 TGGTTCGTAAGGGCAACTCC 59.964 55.000 0.00 0.00 38.47 3.85
574 617 1.439679 CTGGTTCGTAAGGGCAACTC 58.560 55.000 0.00 0.00 38.47 3.01
577 620 0.766131 TTCCTGGTTCGTAAGGGCAA 59.234 50.000 0.00 0.00 34.08 4.52
581 624 2.038033 TCACCTTTCCTGGTTCGTAAGG 59.962 50.000 0.00 0.00 38.45 2.69
596 639 1.794714 AGCATAGGATCGGTCACCTT 58.205 50.000 0.00 0.00 37.68 3.50
597 640 1.414181 CAAGCATAGGATCGGTCACCT 59.586 52.381 0.00 0.00 39.95 4.00
613 656 3.414700 CGGTCGACTGGTGCAAGC 61.415 66.667 16.99 0.00 0.00 4.01
665 708 4.451096 ACTTATGACAAAACTACCACGCAG 59.549 41.667 0.00 0.00 0.00 5.18
669 712 8.784043 AGATTTGACTTATGACAAAACTACCAC 58.216 33.333 12.03 0.00 38.39 4.16
731 774 0.652592 GTCATATATGCCGCGGATGC 59.347 55.000 33.48 15.01 37.91 3.91
758 801 2.954753 CTGACACACCGCGGAAAGC 61.955 63.158 35.90 16.90 43.95 3.51
963 1029 4.738998 TGGCTTGGATGGCGTGGG 62.739 66.667 0.00 0.00 35.06 4.61
964 1030 3.136123 CTGGCTTGGATGGCGTGG 61.136 66.667 0.00 0.00 35.06 4.94
965 1031 3.818787 GCTGGCTTGGATGGCGTG 61.819 66.667 0.00 0.00 35.06 5.34
1086 1152 2.918276 GGGCTAGGGTAGGGCTCG 60.918 72.222 0.00 0.00 0.00 5.03
1623 1707 1.820481 CTCCTCCTCGTCGTCCTCC 60.820 68.421 0.00 0.00 0.00 4.30
1629 1713 3.578272 CGCTCCTCCTCCTCGTCG 61.578 72.222 0.00 0.00 0.00 5.12
1936 2023 0.179156 GACCAGATGCAACATTGGCG 60.179 55.000 2.57 0.00 33.98 5.69
1937 2024 1.180029 AGACCAGATGCAACATTGGC 58.820 50.000 2.57 0.00 33.98 4.52
1939 2026 3.754850 TCTGAAGACCAGATGCAACATTG 59.245 43.478 0.00 0.00 46.38 2.82
1940 2027 4.025040 TCTGAAGACCAGATGCAACATT 57.975 40.909 0.00 0.00 46.38 2.71
2149 2284 8.257306 GGGTTACCATTGATGACAAAATATTGT 58.743 33.333 2.98 0.00 44.03 2.71
2150 2285 8.477256 AGGGTTACCATTGATGACAAAATATTG 58.523 33.333 2.98 0.00 39.54 1.90
2164 2299 2.819608 CCACACAAGAGGGTTACCATTG 59.180 50.000 2.98 7.63 39.97 2.82
2201 2337 6.017400 ACAGTTGATGAGCTAATTTTGTGG 57.983 37.500 0.00 0.00 0.00 4.17
2263 2399 2.604914 CGTTCGCACTGAAGAGCATAAT 59.395 45.455 0.78 0.00 37.23 1.28
2299 2438 6.130298 TCTGATCTTTCGCAGTTTTTCAAA 57.870 33.333 0.00 0.00 33.90 2.69
2300 2439 5.749596 TCTGATCTTTCGCAGTTTTTCAA 57.250 34.783 0.00 0.00 33.90 2.69
2301 2440 5.296780 AGTTCTGATCTTTCGCAGTTTTTCA 59.703 36.000 0.00 0.00 33.90 2.69
2320 2459 2.433868 TTTTAGCACGCTCGAGTTCT 57.566 45.000 15.13 8.46 0.00 3.01
2352 2491 3.396560 GGCCTAGTCGTGTAAACAAACT 58.603 45.455 0.00 5.16 0.00 2.66
2370 2509 4.262164 CCAAGTTATGCAATTATCTGGGCC 60.262 45.833 0.00 0.00 0.00 5.80
2536 2675 2.926778 AGATGGCTGAAGTAGGATGC 57.073 50.000 0.00 0.00 0.00 3.91
2540 2679 5.525378 GTGTTGAATAGATGGCTGAAGTAGG 59.475 44.000 0.00 0.00 0.00 3.18
2565 2704 5.823045 GCCTGGCTTATCAGTTACAAGTAAT 59.177 40.000 12.43 0.00 33.14 1.89
2571 2710 3.931907 ATGCCTGGCTTATCAGTTACA 57.068 42.857 21.03 0.00 33.14 2.41
2580 2722 5.600898 TGTATCAGTAACTATGCCTGGCTTA 59.399 40.000 21.03 16.60 0.00 3.09
2607 2749 3.525268 AACAAAACTGTTCCTGCCTTG 57.475 42.857 0.00 0.00 0.00 3.61
2657 2799 6.037098 GGACATAGATTGCATAGATCGTACC 58.963 44.000 0.00 0.00 0.00 3.34
2703 2853 6.710597 ATCATTGCATAGAAGAAGCACATT 57.289 33.333 0.00 0.00 38.11 2.71
2825 2975 8.489990 TGTCTACTATGGCGTCTAGATAATAC 57.510 38.462 0.00 0.00 0.00 1.89
2826 2976 9.327628 GATGTCTACTATGGCGTCTAGATAATA 57.672 37.037 0.00 0.00 0.00 0.98


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

AutoCloner maintained by Alex Coulton.