Multiple sequence alignment - TraesCS1A01G083200

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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 TraesCS1A01G083200 chr1A 100.000 2411 0 0 1 2411 66996226 66998636 0.000000e+00 4453.0
1 TraesCS1A01G083200 chr1A 90.638 737 42 2 1 731 67036239 67036954 0.000000e+00 953.0
2 TraesCS1A01G083200 chr5B 99.323 1626 11 0 786 2411 641826630 641828255 0.000000e+00 2942.0
3 TraesCS1A01G083200 chr5B 99.139 1626 14 0 786 2411 45830648 45832273 0.000000e+00 2926.0
4 TraesCS1A01G083200 chr5B 98.831 1626 19 0 786 2411 471412861 471414486 0.000000e+00 2898.0
5 TraesCS1A01G083200 chr5B 100.000 43 0 0 734 776 677669984 677669942 1.990000e-11 80.5
6 TraesCS1A01G083200 chr7A 99.139 1626 14 0 786 2411 626411702 626410077 0.000000e+00 2926.0
7 TraesCS1A01G083200 chr7A 99.077 1626 15 0 786 2411 499579583 499577958 0.000000e+00 2920.0
8 TraesCS1A01G083200 chr7B 99.016 1626 15 1 786 2411 640732852 640731228 0.000000e+00 2913.0
9 TraesCS1A01G083200 chr7B 83.446 296 31 10 322 616 290257360 290257638 2.380000e-65 259.0
10 TraesCS1A01G083200 chr6B 98.954 1626 17 0 786 2411 180933847 180932222 0.000000e+00 2909.0
11 TraesCS1A01G083200 chr1B 98.893 1626 18 0 786 2411 117196709 117195084 0.000000e+00 2904.0
12 TraesCS1A01G083200 chr6A 98.831 1626 15 1 786 2411 85281680 85280059 0.000000e+00 2894.0
13 TraesCS1A01G083200 chr2A 91.228 741 56 4 1 734 189193463 189192725 0.000000e+00 1000.0
14 TraesCS1A01G083200 chr2A 89.747 751 69 4 1 744 189200860 189200111 0.000000e+00 953.0
15 TraesCS1A01G083200 chr2A 89.069 741 73 5 1 734 189201689 189200950 0.000000e+00 913.0
16 TraesCS1A01G083200 chr2A 86.235 494 67 1 106 598 190433709 190434202 3.530000e-148 534.0
17 TraesCS1A01G083200 chr2A 82.815 547 81 7 75 611 190426235 190426778 6.030000e-131 477.0
18 TraesCS1A01G083200 chr3A 89.069 741 73 6 1 734 419272747 419272008 0.000000e+00 913.0
19 TraesCS1A01G083200 chr3A 88.874 737 74 3 5 734 419280051 419279316 0.000000e+00 900.0
20 TraesCS1A01G083200 chr2D 85.965 456 53 9 163 616 334861366 334861812 6.030000e-131 477.0


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 TraesCS1A01G083200 chr1A 66996226 66998636 2410 False 4453 4453 100.000 1 2411 1 chr1A.!!$F1 2410
1 TraesCS1A01G083200 chr1A 67036239 67036954 715 False 953 953 90.638 1 731 1 chr1A.!!$F2 730
2 TraesCS1A01G083200 chr5B 641826630 641828255 1625 False 2942 2942 99.323 786 2411 1 chr5B.!!$F3 1625
3 TraesCS1A01G083200 chr5B 45830648 45832273 1625 False 2926 2926 99.139 786 2411 1 chr5B.!!$F1 1625
4 TraesCS1A01G083200 chr5B 471412861 471414486 1625 False 2898 2898 98.831 786 2411 1 chr5B.!!$F2 1625
5 TraesCS1A01G083200 chr7A 626410077 626411702 1625 True 2926 2926 99.139 786 2411 1 chr7A.!!$R2 1625
6 TraesCS1A01G083200 chr7A 499577958 499579583 1625 True 2920 2920 99.077 786 2411 1 chr7A.!!$R1 1625
7 TraesCS1A01G083200 chr7B 640731228 640732852 1624 True 2913 2913 99.016 786 2411 1 chr7B.!!$R1 1625
8 TraesCS1A01G083200 chr6B 180932222 180933847 1625 True 2909 2909 98.954 786 2411 1 chr6B.!!$R1 1625
9 TraesCS1A01G083200 chr1B 117195084 117196709 1625 True 2904 2904 98.893 786 2411 1 chr1B.!!$R1 1625
10 TraesCS1A01G083200 chr6A 85280059 85281680 1621 True 2894 2894 98.831 786 2411 1 chr6A.!!$R1 1625
11 TraesCS1A01G083200 chr2A 189192725 189193463 738 True 1000 1000 91.228 1 734 1 chr2A.!!$R1 733
12 TraesCS1A01G083200 chr2A 189200111 189201689 1578 True 933 953 89.408 1 744 2 chr2A.!!$R2 743
13 TraesCS1A01G083200 chr2A 190426235 190426778 543 False 477 477 82.815 75 611 1 chr2A.!!$F1 536
14 TraesCS1A01G083200 chr3A 419272008 419272747 739 True 913 913 89.069 1 734 1 chr3A.!!$R1 733
15 TraesCS1A01G083200 chr3A 419279316 419280051 735 True 900 900 88.874 5 734 1 chr3A.!!$R2 729

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
435 1292 0.034059 CCCTCTGTTCGTTGCTCTGT 59.966 55.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1410 2272 1.400494 GGTAAACGATGGATTTGCGCT 59.6 47.619 9.73 0.0 0.0 5.92 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
70 900 2.017559 GCCGCCTACAAGACGATCCT 62.018 60.000 0.00 0.00 0.00 3.24
117 951 0.863220 TTCCCTCCCCCTCCCTCTTA 60.863 60.000 0.00 0.00 0.00 2.10
157 991 2.032528 CCAACTGAAGCTCCGCCA 59.967 61.111 0.00 0.00 0.00 5.69
337 1171 4.708968 GCCCCGCGCTCGATCTAG 62.709 72.222 5.56 0.00 38.10 2.43
434 1291 0.671781 CCCCTCTGTTCGTTGCTCTG 60.672 60.000 0.00 0.00 0.00 3.35
435 1292 0.034059 CCCTCTGTTCGTTGCTCTGT 59.966 55.000 0.00 0.00 0.00 3.41
436 1293 1.541233 CCCTCTGTTCGTTGCTCTGTT 60.541 52.381 0.00 0.00 0.00 3.16
437 1294 1.528586 CCTCTGTTCGTTGCTCTGTTG 59.471 52.381 0.00 0.00 0.00 3.33
438 1295 0.937304 TCTGTTCGTTGCTCTGTTGC 59.063 50.000 0.00 0.00 0.00 4.17
439 1296 0.383491 CTGTTCGTTGCTCTGTTGCG 60.383 55.000 0.00 0.00 35.36 4.85
440 1297 1.722507 GTTCGTTGCTCTGTTGCGC 60.723 57.895 0.00 0.00 35.36 6.09
441 1298 2.892334 TTCGTTGCTCTGTTGCGCC 61.892 57.895 4.18 0.00 35.36 6.53
442 1299 4.724697 CGTTGCTCTGTTGCGCCG 62.725 66.667 4.18 0.00 35.36 6.46
456 1313 3.723348 GCCGCCCAAGTGTCGAAC 61.723 66.667 0.00 0.00 0.00 3.95
457 1314 3.411351 CCGCCCAAGTGTCGAACG 61.411 66.667 0.00 0.00 0.00 3.95
458 1315 2.355363 CGCCCAAGTGTCGAACGA 60.355 61.111 0.00 0.00 0.00 3.85
459 1316 1.736645 CGCCCAAGTGTCGAACGAT 60.737 57.895 0.00 0.00 0.00 3.73
460 1317 1.787847 GCCCAAGTGTCGAACGATG 59.212 57.895 0.00 0.00 0.00 3.84
461 1318 1.635663 GCCCAAGTGTCGAACGATGG 61.636 60.000 0.00 4.11 39.22 3.51
462 1319 1.635663 CCCAAGTGTCGAACGATGGC 61.636 60.000 8.48 0.16 38.58 4.40
463 1320 1.635663 CCAAGTGTCGAACGATGGCC 61.636 60.000 0.00 0.00 34.98 5.36
464 1321 1.736645 AAGTGTCGAACGATGGCCG 60.737 57.895 0.00 0.00 45.44 6.13
465 1322 3.849953 GTGTCGAACGATGGCCGC 61.850 66.667 0.00 0.00 43.32 6.53
482 1339 4.735132 CGGCGACCGTGACCATGT 62.735 66.667 0.00 0.00 42.73 3.21
483 1340 2.813908 GGCGACCGTGACCATGTC 60.814 66.667 0.00 0.00 0.00 3.06
484 1341 2.048597 GCGACCGTGACCATGTCA 60.049 61.111 0.00 0.00 40.50 3.58
491 1348 2.031919 TGACCATGTCACGCCCAC 59.968 61.111 0.00 0.00 37.67 4.61
492 1349 2.746277 GACCATGTCACGCCCACC 60.746 66.667 0.00 0.00 32.09 4.61
493 1350 4.697756 ACCATGTCACGCCCACCG 62.698 66.667 0.00 0.00 44.21 4.94
523 1380 3.225798 TGGCTGCCCAGTTTGTGC 61.226 61.111 17.53 0.00 35.79 4.57
524 1381 3.994853 GGCTGCCCAGTTTGTGCC 61.995 66.667 7.66 0.00 0.00 5.01
525 1382 3.994853 GCTGCCCAGTTTGTGCCC 61.995 66.667 0.00 0.00 0.00 5.36
526 1383 2.203538 CTGCCCAGTTTGTGCCCT 60.204 61.111 0.00 0.00 0.00 5.19
527 1384 2.521465 TGCCCAGTTTGTGCCCTG 60.521 61.111 0.00 0.00 0.00 4.45
528 1385 3.305516 GCCCAGTTTGTGCCCTGG 61.306 66.667 0.00 0.00 46.43 4.45
529 1386 3.305516 CCCAGTTTGTGCCCTGGC 61.306 66.667 0.00 0.00 45.68 4.85
530 1387 3.305516 CCAGTTTGTGCCCTGGCC 61.306 66.667 5.57 0.00 41.65 5.36
531 1388 3.673484 CAGTTTGTGCCCTGGCCG 61.673 66.667 5.57 0.00 41.09 6.13
545 1402 4.424566 GCCGCACCCACATGCAAG 62.425 66.667 0.00 0.00 46.47 4.01
546 1403 4.424566 CCGCACCCACATGCAAGC 62.425 66.667 0.00 0.00 46.47 4.01
547 1404 4.764336 CGCACCCACATGCAAGCG 62.764 66.667 0.00 0.00 46.47 4.68
549 1406 3.367743 CACCCACATGCAAGCGCT 61.368 61.111 2.64 2.64 39.64 5.92
550 1407 2.598394 ACCCACATGCAAGCGCTT 60.598 55.556 18.98 18.98 39.64 4.68
551 1408 2.126228 CCCACATGCAAGCGCTTG 60.126 61.111 39.20 39.20 46.12 4.01
552 1409 2.126228 CCACATGCAAGCGCTTGG 60.126 61.111 41.83 30.47 45.23 3.61
553 1410 2.807895 CACATGCAAGCGCTTGGC 60.808 61.111 41.83 33.82 45.23 4.52
554 1411 4.060038 ACATGCAAGCGCTTGGCC 62.060 61.111 41.83 29.80 45.23 5.36
586 1443 4.971125 GCATCCGCCGTAGCTCCC 62.971 72.222 0.00 0.00 36.60 4.30
587 1444 3.227276 CATCCGCCGTAGCTCCCT 61.227 66.667 0.00 0.00 36.60 4.20
588 1445 3.227276 ATCCGCCGTAGCTCCCTG 61.227 66.667 0.00 0.00 36.60 4.45
611 1468 3.015145 GCCCCCACTTGCCTCCTA 61.015 66.667 0.00 0.00 0.00 2.94
612 1469 2.998949 CCCCCACTTGCCTCCTAC 59.001 66.667 0.00 0.00 0.00 3.18
613 1470 1.616628 CCCCCACTTGCCTCCTACT 60.617 63.158 0.00 0.00 0.00 2.57
614 1471 1.604378 CCCCACTTGCCTCCTACTG 59.396 63.158 0.00 0.00 0.00 2.74
615 1472 1.078143 CCCACTTGCCTCCTACTGC 60.078 63.158 0.00 0.00 0.00 4.40
616 1473 1.078143 CCACTTGCCTCCTACTGCC 60.078 63.158 0.00 0.00 0.00 4.85
617 1474 1.557269 CCACTTGCCTCCTACTGCCT 61.557 60.000 0.00 0.00 0.00 4.75
618 1475 0.326264 CACTTGCCTCCTACTGCCTT 59.674 55.000 0.00 0.00 0.00 4.35
619 1476 0.326264 ACTTGCCTCCTACTGCCTTG 59.674 55.000 0.00 0.00 0.00 3.61
620 1477 0.393537 CTTGCCTCCTACTGCCTTGG 60.394 60.000 0.00 0.00 0.00 3.61
621 1478 2.124529 GCCTCCTACTGCCTTGGC 60.125 66.667 4.43 4.43 0.00 4.52
622 1479 2.592308 CCTCCTACTGCCTTGGCC 59.408 66.667 9.35 0.00 0.00 5.36
623 1480 2.592308 CTCCTACTGCCTTGGCCC 59.408 66.667 9.35 0.00 0.00 5.80
624 1481 3.015145 TCCTACTGCCTTGGCCCC 61.015 66.667 9.35 0.00 0.00 5.80
625 1482 3.017581 CCTACTGCCTTGGCCCCT 61.018 66.667 9.35 0.00 0.00 4.79
626 1483 2.592308 CTACTGCCTTGGCCCCTC 59.408 66.667 9.35 0.00 0.00 4.30
627 1484 3.391665 CTACTGCCTTGGCCCCTCG 62.392 68.421 9.35 0.00 0.00 4.63
678 1535 3.745803 GCTGCTGCTTCCTGCCAC 61.746 66.667 8.53 0.00 42.00 5.01
679 1536 2.033757 CTGCTGCTTCCTGCCACT 59.966 61.111 0.00 0.00 42.00 4.00
680 1537 2.281970 TGCTGCTTCCTGCCACTG 60.282 61.111 0.00 0.00 42.00 3.66
681 1538 3.745803 GCTGCTTCCTGCCACTGC 61.746 66.667 0.00 0.00 42.00 4.40
682 1539 3.429141 CTGCTTCCTGCCACTGCG 61.429 66.667 0.00 0.00 41.78 5.18
683 1540 4.254709 TGCTTCCTGCCACTGCGT 62.255 61.111 0.00 0.00 41.78 5.24
684 1541 2.980233 GCTTCCTGCCACTGCGTT 60.980 61.111 0.00 0.00 41.78 4.84
685 1542 2.970974 GCTTCCTGCCACTGCGTTC 61.971 63.158 0.00 0.00 41.78 3.95
686 1543 1.302033 CTTCCTGCCACTGCGTTCT 60.302 57.895 0.00 0.00 41.78 3.01
687 1544 0.037326 CTTCCTGCCACTGCGTTCTA 60.037 55.000 0.00 0.00 41.78 2.10
688 1545 0.613260 TTCCTGCCACTGCGTTCTAT 59.387 50.000 0.00 0.00 41.78 1.98
689 1546 1.480789 TCCTGCCACTGCGTTCTATA 58.519 50.000 0.00 0.00 41.78 1.31
690 1547 1.409064 TCCTGCCACTGCGTTCTATAG 59.591 52.381 0.00 0.00 41.78 1.31
691 1548 1.137086 CCTGCCACTGCGTTCTATAGT 59.863 52.381 0.00 0.00 41.78 2.12
692 1549 2.418746 CCTGCCACTGCGTTCTATAGTT 60.419 50.000 0.00 0.00 41.78 2.24
693 1550 2.604914 CTGCCACTGCGTTCTATAGTTG 59.395 50.000 0.00 0.00 41.78 3.16
694 1551 2.028476 TGCCACTGCGTTCTATAGTTGT 60.028 45.455 0.00 0.00 41.78 3.32
695 1552 3.000727 GCCACTGCGTTCTATAGTTGTT 58.999 45.455 0.00 0.00 0.00 2.83
696 1553 3.181520 GCCACTGCGTTCTATAGTTGTTG 60.182 47.826 0.00 0.00 0.00 3.33
697 1554 3.994392 CCACTGCGTTCTATAGTTGTTGT 59.006 43.478 0.00 0.00 0.00 3.32
698 1555 4.143115 CCACTGCGTTCTATAGTTGTTGTG 60.143 45.833 0.00 4.15 0.00 3.33
699 1556 3.432252 ACTGCGTTCTATAGTTGTTGTGC 59.568 43.478 0.00 0.00 0.00 4.57
700 1557 3.659786 TGCGTTCTATAGTTGTTGTGCT 58.340 40.909 0.00 0.00 0.00 4.40
701 1558 3.431912 TGCGTTCTATAGTTGTTGTGCTG 59.568 43.478 0.00 0.00 0.00 4.41
702 1559 3.725010 GCGTTCTATAGTTGTTGTGCTGC 60.725 47.826 0.00 0.00 0.00 5.25
703 1560 3.679980 CGTTCTATAGTTGTTGTGCTGCT 59.320 43.478 0.00 0.00 0.00 4.24
704 1561 4.201628 CGTTCTATAGTTGTTGTGCTGCTC 60.202 45.833 0.00 0.00 0.00 4.26
705 1562 4.808414 TCTATAGTTGTTGTGCTGCTCT 57.192 40.909 0.00 0.00 0.00 4.09
706 1563 4.498241 TCTATAGTTGTTGTGCTGCTCTG 58.502 43.478 0.00 0.00 0.00 3.35
707 1564 1.229428 TAGTTGTTGTGCTGCTCTGC 58.771 50.000 0.00 0.00 0.00 4.26
708 1565 0.465097 AGTTGTTGTGCTGCTCTGCT 60.465 50.000 0.00 0.00 0.00 4.24
709 1566 0.383231 GTTGTTGTGCTGCTCTGCTT 59.617 50.000 0.00 0.00 0.00 3.91
710 1567 0.382873 TTGTTGTGCTGCTCTGCTTG 59.617 50.000 0.00 0.00 0.00 4.01
711 1568 1.371389 GTTGTGCTGCTCTGCTTGC 60.371 57.895 0.00 0.00 0.00 4.01
712 1569 1.527611 TTGTGCTGCTCTGCTTGCT 60.528 52.632 0.00 0.00 32.36 3.91
713 1570 0.250424 TTGTGCTGCTCTGCTTGCTA 60.250 50.000 0.00 0.00 32.36 3.49
714 1571 0.952497 TGTGCTGCTCTGCTTGCTAC 60.952 55.000 0.00 0.00 32.36 3.58
715 1572 1.376424 TGCTGCTCTGCTTGCTACC 60.376 57.895 0.00 0.00 32.36 3.18
716 1573 1.376424 GCTGCTCTGCTTGCTACCA 60.376 57.895 0.00 0.00 0.00 3.25
717 1574 0.747283 GCTGCTCTGCTTGCTACCAT 60.747 55.000 0.00 0.00 0.00 3.55
718 1575 1.297664 CTGCTCTGCTTGCTACCATC 58.702 55.000 0.00 0.00 0.00 3.51
719 1576 0.907486 TGCTCTGCTTGCTACCATCT 59.093 50.000 0.00 0.00 0.00 2.90
720 1577 2.102084 CTGCTCTGCTTGCTACCATCTA 59.898 50.000 0.00 0.00 0.00 1.98
721 1578 2.702478 TGCTCTGCTTGCTACCATCTAT 59.298 45.455 0.00 0.00 0.00 1.98
722 1579 3.065655 GCTCTGCTTGCTACCATCTATG 58.934 50.000 0.00 0.00 0.00 2.23
723 1580 3.494048 GCTCTGCTTGCTACCATCTATGT 60.494 47.826 0.00 0.00 0.00 2.29
724 1581 4.701765 CTCTGCTTGCTACCATCTATGTT 58.298 43.478 0.00 0.00 0.00 2.71
725 1582 4.445453 TCTGCTTGCTACCATCTATGTTG 58.555 43.478 0.00 0.00 0.00 3.33
726 1583 4.162131 TCTGCTTGCTACCATCTATGTTGA 59.838 41.667 0.00 0.00 0.00 3.18
727 1584 5.039920 TGCTTGCTACCATCTATGTTGAT 57.960 39.130 0.00 0.00 0.00 2.57
728 1585 4.818005 TGCTTGCTACCATCTATGTTGATG 59.182 41.667 0.00 0.00 42.38 3.07
729 1586 4.320057 GCTTGCTACCATCTATGTTGATGC 60.320 45.833 0.00 0.00 41.65 3.91
730 1587 4.694760 TGCTACCATCTATGTTGATGCT 57.305 40.909 0.00 0.00 41.65 3.79
731 1588 5.806654 TGCTACCATCTATGTTGATGCTA 57.193 39.130 0.00 0.00 41.65 3.49
732 1589 5.541845 TGCTACCATCTATGTTGATGCTAC 58.458 41.667 0.00 0.00 41.65 3.58
733 1590 5.305386 TGCTACCATCTATGTTGATGCTACT 59.695 40.000 0.00 0.00 41.65 2.57
734 1591 5.866633 GCTACCATCTATGTTGATGCTACTC 59.133 44.000 0.00 0.00 41.65 2.59
735 1592 6.295011 GCTACCATCTATGTTGATGCTACTCT 60.295 42.308 0.00 0.00 41.65 3.24
736 1593 7.094162 GCTACCATCTATGTTGATGCTACTCTA 60.094 40.741 0.00 0.00 41.65 2.43
737 1594 7.225784 ACCATCTATGTTGATGCTACTCTAG 57.774 40.000 0.00 0.00 41.65 2.43
738 1595 6.210385 ACCATCTATGTTGATGCTACTCTAGG 59.790 42.308 0.00 0.00 41.65 3.02
739 1596 6.350864 CCATCTATGTTGATGCTACTCTAGGG 60.351 46.154 0.00 0.00 41.65 3.53
740 1597 5.706447 TCTATGTTGATGCTACTCTAGGGT 58.294 41.667 0.00 0.00 0.00 4.34
741 1598 4.679373 ATGTTGATGCTACTCTAGGGTG 57.321 45.455 5.20 0.00 0.00 4.61
742 1599 2.168521 TGTTGATGCTACTCTAGGGTGC 59.831 50.000 5.20 7.84 0.00 5.01
743 1600 2.432510 GTTGATGCTACTCTAGGGTGCT 59.567 50.000 5.20 0.00 0.00 4.40
744 1601 2.752030 TGATGCTACTCTAGGGTGCTT 58.248 47.619 5.20 5.46 0.00 3.91
745 1602 2.432146 TGATGCTACTCTAGGGTGCTTG 59.568 50.000 5.20 0.00 0.00 4.01
746 1603 0.537188 TGCTACTCTAGGGTGCTTGC 59.463 55.000 5.20 5.29 0.00 4.01
747 1604 0.537188 GCTACTCTAGGGTGCTTGCA 59.463 55.000 5.20 0.00 0.00 4.08
748 1605 1.740718 GCTACTCTAGGGTGCTTGCAC 60.741 57.143 16.50 16.50 0.00 4.57
749 1606 0.530744 TACTCTAGGGTGCTTGCACG 59.469 55.000 17.87 7.01 0.00 5.34
750 1607 2.047274 TCTAGGGTGCTTGCACGC 60.047 61.111 27.69 27.69 38.16 5.34
752 1609 2.358615 TAGGGTGCTTGCACGCTG 60.359 61.111 37.75 0.00 45.86 5.18
762 1619 3.240203 GCACGCTGCGTTTCTACA 58.760 55.556 26.77 0.00 38.32 2.74
763 1620 1.787847 GCACGCTGCGTTTCTACAT 59.212 52.632 26.77 0.00 38.32 2.29
764 1621 0.996462 GCACGCTGCGTTTCTACATA 59.004 50.000 26.77 0.00 38.32 2.29
765 1622 1.392168 GCACGCTGCGTTTCTACATAA 59.608 47.619 26.77 0.00 38.32 1.90
766 1623 2.783316 GCACGCTGCGTTTCTACATAAC 60.783 50.000 26.77 1.27 38.32 1.89
767 1624 2.410392 CACGCTGCGTTTCTACATAACA 59.590 45.455 26.77 0.00 38.32 2.41
768 1625 2.666508 ACGCTGCGTTTCTACATAACAG 59.333 45.455 23.57 0.00 36.35 3.16
769 1626 2.921121 CGCTGCGTTTCTACATAACAGA 59.079 45.455 14.93 0.00 0.00 3.41
770 1627 3.000674 CGCTGCGTTTCTACATAACAGAG 60.001 47.826 14.93 0.00 0.00 3.35
771 1628 3.242123 GCTGCGTTTCTACATAACAGAGC 60.242 47.826 0.00 0.00 0.00 4.09
772 1629 3.920446 TGCGTTTCTACATAACAGAGCA 58.080 40.909 0.00 0.00 0.00 4.26
773 1630 4.503910 TGCGTTTCTACATAACAGAGCAT 58.496 39.130 0.00 0.00 0.00 3.79
774 1631 5.656480 TGCGTTTCTACATAACAGAGCATA 58.344 37.500 0.00 0.00 0.00 3.14
775 1632 6.280643 TGCGTTTCTACATAACAGAGCATAT 58.719 36.000 0.00 0.00 0.00 1.78
776 1633 6.200854 TGCGTTTCTACATAACAGAGCATATG 59.799 38.462 0.00 0.00 35.97 1.78
777 1634 6.584954 CGTTTCTACATAACAGAGCATATGC 58.415 40.000 20.36 20.36 42.49 3.14
778 1635 6.200854 CGTTTCTACATAACAGAGCATATGCA 59.799 38.462 28.62 8.05 45.16 3.96
779 1636 7.095481 CGTTTCTACATAACAGAGCATATGCAT 60.095 37.037 28.62 14.54 45.16 3.96
780 1637 9.208022 GTTTCTACATAACAGAGCATATGCATA 57.792 33.333 28.62 9.27 45.16 3.14
781 1638 8.992835 TTCTACATAACAGAGCATATGCATAG 57.007 34.615 28.62 18.71 45.16 2.23
782 1639 7.038048 TCTACATAACAGAGCATATGCATAGC 58.962 38.462 28.62 14.69 45.16 2.97
783 1640 5.802465 ACATAACAGAGCATATGCATAGCT 58.198 37.500 28.62 22.56 45.16 3.32
784 1641 6.236409 ACATAACAGAGCATATGCATAGCTT 58.764 36.000 28.62 14.69 45.16 3.74
972 1829 3.199946 TGGCAGATCGATCTAGGGTTTTT 59.800 43.478 26.87 0.00 34.85 1.94
1289 2146 3.118408 ACAGTGCAGTTTGGTTGTCTAGA 60.118 43.478 0.00 0.00 0.00 2.43
1410 2272 4.469657 AGTTGGATAAGTTGGCAGTTTGA 58.530 39.130 0.00 0.00 0.00 2.69
2062 2924 4.141937 CGGATAAGAACCATCCAGAGACAA 60.142 45.833 2.54 0.00 41.87 3.18
2286 3148 0.321671 CAGATGGAGTGGAACGTGGT 59.678 55.000 0.00 0.00 45.86 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
117 951 1.460689 TGTGGGAGAGGGAAACGGT 60.461 57.895 0.00 0.00 0.00 4.83
157 991 1.843368 CAACAAGGTCATCCATGGCT 58.157 50.000 6.96 0.00 36.82 4.75
369 1224 3.787001 CAGGGGAAGGCGGAGGAC 61.787 72.222 0.00 0.00 0.00 3.85
370 1225 4.332543 ACAGGGGAAGGCGGAGGA 62.333 66.667 0.00 0.00 0.00 3.71
371 1226 4.101448 CACAGGGGAAGGCGGAGG 62.101 72.222 0.00 0.00 0.00 4.30
372 1227 3.003173 TCACAGGGGAAGGCGGAG 61.003 66.667 0.00 0.00 0.00 4.63
373 1228 3.003173 CTCACAGGGGAAGGCGGA 61.003 66.667 0.00 0.00 0.00 5.54
374 1229 4.785453 GCTCACAGGGGAAGGCGG 62.785 72.222 0.00 0.00 0.00 6.13
439 1296 3.723348 GTTCGACACTTGGGCGGC 61.723 66.667 0.00 0.00 0.00 6.53
440 1297 3.411351 CGTTCGACACTTGGGCGG 61.411 66.667 0.00 0.00 0.00 6.13
441 1298 1.736645 ATCGTTCGACACTTGGGCG 60.737 57.895 0.00 0.00 0.00 6.13
442 1299 1.635663 CCATCGTTCGACACTTGGGC 61.636 60.000 0.00 0.00 0.00 5.36
443 1300 1.635663 GCCATCGTTCGACACTTGGG 61.636 60.000 12.39 3.76 30.43 4.12
444 1301 1.635663 GGCCATCGTTCGACACTTGG 61.636 60.000 0.00 7.83 32.09 3.61
445 1302 1.787847 GGCCATCGTTCGACACTTG 59.212 57.895 0.00 0.00 0.00 3.16
446 1303 1.736645 CGGCCATCGTTCGACACTT 60.737 57.895 2.24 0.00 0.00 3.16
447 1304 2.126071 CGGCCATCGTTCGACACT 60.126 61.111 2.24 0.00 0.00 3.55
448 1305 3.849953 GCGGCCATCGTTCGACAC 61.850 66.667 2.24 0.00 41.72 3.67
466 1323 2.813908 GACATGGTCACGGTCGCC 60.814 66.667 0.00 0.00 32.09 5.54
467 1324 2.048597 TGACATGGTCACGGTCGC 60.049 61.111 0.00 0.00 37.67 5.19
474 1331 2.031919 GTGGGCGTGACATGGTCA 59.968 61.111 0.00 0.00 40.50 4.02
475 1332 2.746277 GGTGGGCGTGACATGGTC 60.746 66.667 0.00 0.00 0.00 4.02
476 1333 4.697756 CGGTGGGCGTGACATGGT 62.698 66.667 0.00 0.00 0.00 3.55
501 1358 3.850098 AAACTGGGCAGCCAGGACG 62.850 63.158 15.19 0.00 41.67 4.79
502 1359 2.116125 AAACTGGGCAGCCAGGAC 59.884 61.111 15.19 0.00 41.67 3.85
503 1360 2.115910 CAAACTGGGCAGCCAGGA 59.884 61.111 15.19 0.00 41.67 3.86
504 1361 2.203538 ACAAACTGGGCAGCCAGG 60.204 61.111 15.19 7.59 41.67 4.45
505 1362 3.045142 CACAAACTGGGCAGCCAG 58.955 61.111 15.19 11.38 42.90 4.85
514 1371 3.673484 CGGCCAGGGCACAAACTG 61.673 66.667 14.59 0.00 44.11 3.16
532 1389 2.922950 AAGCGCTTGCATGTGGGTG 61.923 57.895 24.40 0.00 42.66 4.61
533 1390 2.598394 AAGCGCTTGCATGTGGGT 60.598 55.556 24.40 0.00 42.66 4.51
534 1391 2.126228 CAAGCGCTTGCATGTGGG 60.126 61.111 34.84 11.28 42.66 4.61
535 1392 2.126228 CCAAGCGCTTGCATGTGG 60.126 61.111 38.53 24.73 42.66 4.17
536 1393 2.807895 GCCAAGCGCTTGCATGTG 60.808 61.111 38.53 26.86 42.66 3.21
537 1394 4.060038 GGCCAAGCGCTTGCATGT 62.060 61.111 38.53 8.06 42.66 3.21
569 1426 4.971125 GGGAGCTACGGCGGATGC 62.971 72.222 13.24 12.39 44.37 3.91
570 1427 3.227276 AGGGAGCTACGGCGGATG 61.227 66.667 13.24 1.29 44.37 3.51
571 1428 3.227276 CAGGGAGCTACGGCGGAT 61.227 66.667 13.24 0.00 44.37 4.18
594 1451 3.015145 TAGGAGGCAAGTGGGGGC 61.015 66.667 0.00 0.00 0.00 5.80
595 1452 1.616628 AGTAGGAGGCAAGTGGGGG 60.617 63.158 0.00 0.00 0.00 5.40
596 1453 1.604378 CAGTAGGAGGCAAGTGGGG 59.396 63.158 0.00 0.00 0.00 4.96
597 1454 1.078143 GCAGTAGGAGGCAAGTGGG 60.078 63.158 0.00 0.00 0.00 4.61
598 1455 1.078143 GGCAGTAGGAGGCAAGTGG 60.078 63.158 0.00 0.00 0.00 4.00
599 1456 0.326264 AAGGCAGTAGGAGGCAAGTG 59.674 55.000 0.00 0.00 0.00 3.16
600 1457 0.326264 CAAGGCAGTAGGAGGCAAGT 59.674 55.000 0.00 0.00 0.00 3.16
601 1458 0.393537 CCAAGGCAGTAGGAGGCAAG 60.394 60.000 0.00 0.00 0.00 4.01
602 1459 1.685224 CCAAGGCAGTAGGAGGCAA 59.315 57.895 0.00 0.00 0.00 4.52
603 1460 2.971598 GCCAAGGCAGTAGGAGGCA 61.972 63.158 6.14 0.00 41.63 4.75
604 1461 2.124529 GCCAAGGCAGTAGGAGGC 60.125 66.667 6.14 0.00 41.49 4.70
605 1462 2.592308 GGCCAAGGCAGTAGGAGG 59.408 66.667 13.87 0.00 44.11 4.30
606 1463 2.592308 GGGCCAAGGCAGTAGGAG 59.408 66.667 13.87 0.00 44.11 3.69
607 1464 3.015145 GGGGCCAAGGCAGTAGGA 61.015 66.667 13.87 0.00 44.11 2.94
608 1465 3.017581 AGGGGCCAAGGCAGTAGG 61.018 66.667 13.87 0.00 44.11 3.18
609 1466 2.592308 GAGGGGCCAAGGCAGTAG 59.408 66.667 13.87 0.00 44.11 2.57
610 1467 3.399181 CGAGGGGCCAAGGCAGTA 61.399 66.667 13.87 0.00 44.11 2.74
666 1523 3.772853 AACGCAGTGGCAGGAAGCA 62.773 57.895 0.00 0.00 45.00 3.91
667 1524 2.970974 GAACGCAGTGGCAGGAAGC 61.971 63.158 0.00 0.00 45.00 3.86
668 1525 0.037326 TAGAACGCAGTGGCAGGAAG 60.037 55.000 0.00 0.00 45.00 3.46
669 1526 0.613260 ATAGAACGCAGTGGCAGGAA 59.387 50.000 0.00 0.00 45.00 3.36
670 1527 1.409064 CTATAGAACGCAGTGGCAGGA 59.591 52.381 0.00 0.00 45.00 3.86
671 1528 1.137086 ACTATAGAACGCAGTGGCAGG 59.863 52.381 6.78 0.00 45.00 4.85
672 1529 2.586258 ACTATAGAACGCAGTGGCAG 57.414 50.000 6.78 0.00 45.00 4.85
673 1530 2.028476 ACAACTATAGAACGCAGTGGCA 60.028 45.455 6.78 0.00 45.00 4.92
674 1531 2.618053 ACAACTATAGAACGCAGTGGC 58.382 47.619 6.78 0.00 45.00 5.01
675 1532 3.994392 ACAACAACTATAGAACGCAGTGG 59.006 43.478 6.78 0.00 45.00 4.00
676 1533 4.666655 GCACAACAACTATAGAACGCAGTG 60.667 45.833 6.78 8.76 45.00 3.66
678 1535 3.679980 AGCACAACAACTATAGAACGCAG 59.320 43.478 6.78 0.00 0.00 5.18
679 1536 3.431912 CAGCACAACAACTATAGAACGCA 59.568 43.478 6.78 0.00 0.00 5.24
680 1537 3.725010 GCAGCACAACAACTATAGAACGC 60.725 47.826 6.78 0.00 0.00 4.84
681 1538 3.679980 AGCAGCACAACAACTATAGAACG 59.320 43.478 6.78 0.00 0.00 3.95
682 1539 4.932200 AGAGCAGCACAACAACTATAGAAC 59.068 41.667 6.78 0.00 0.00 3.01
683 1540 4.931601 CAGAGCAGCACAACAACTATAGAA 59.068 41.667 6.78 0.00 0.00 2.10
684 1541 4.498241 CAGAGCAGCACAACAACTATAGA 58.502 43.478 6.78 0.00 0.00 1.98
685 1542 3.063180 GCAGAGCAGCACAACAACTATAG 59.937 47.826 0.00 0.00 0.00 1.31
686 1543 3.002791 GCAGAGCAGCACAACAACTATA 58.997 45.455 0.00 0.00 0.00 1.31
687 1544 1.808945 GCAGAGCAGCACAACAACTAT 59.191 47.619 0.00 0.00 0.00 2.12
688 1545 1.202687 AGCAGAGCAGCACAACAACTA 60.203 47.619 0.00 0.00 36.85 2.24
689 1546 0.465097 AGCAGAGCAGCACAACAACT 60.465 50.000 0.00 0.00 36.85 3.16
690 1547 0.383231 AAGCAGAGCAGCACAACAAC 59.617 50.000 0.00 0.00 36.85 3.32
691 1548 0.382873 CAAGCAGAGCAGCACAACAA 59.617 50.000 0.00 0.00 36.85 2.83
692 1549 2.027325 CAAGCAGAGCAGCACAACA 58.973 52.632 0.00 0.00 36.85 3.33
693 1550 1.371389 GCAAGCAGAGCAGCACAAC 60.371 57.895 0.00 0.00 36.85 3.32
694 1551 0.250424 TAGCAAGCAGAGCAGCACAA 60.250 50.000 0.00 0.00 35.04 3.33
695 1552 0.952497 GTAGCAAGCAGAGCAGCACA 60.952 55.000 0.00 0.00 35.04 4.57
696 1553 1.642952 GGTAGCAAGCAGAGCAGCAC 61.643 60.000 0.00 0.00 35.04 4.40
697 1554 1.376424 GGTAGCAAGCAGAGCAGCA 60.376 57.895 0.00 0.00 35.04 4.41
698 1555 0.747283 ATGGTAGCAAGCAGAGCAGC 60.747 55.000 0.00 0.00 36.36 5.25
699 1556 1.134461 AGATGGTAGCAAGCAGAGCAG 60.134 52.381 0.00 0.00 36.36 4.24
700 1557 0.907486 AGATGGTAGCAAGCAGAGCA 59.093 50.000 0.00 0.00 36.36 4.26
701 1558 2.898729 TAGATGGTAGCAAGCAGAGC 57.101 50.000 0.00 0.00 36.36 4.09
702 1559 4.333913 ACATAGATGGTAGCAAGCAGAG 57.666 45.455 0.00 0.00 36.36 3.35
703 1560 4.162131 TCAACATAGATGGTAGCAAGCAGA 59.838 41.667 0.00 0.00 36.36 4.26
704 1561 4.445453 TCAACATAGATGGTAGCAAGCAG 58.555 43.478 0.00 0.00 36.36 4.24
705 1562 4.486125 TCAACATAGATGGTAGCAAGCA 57.514 40.909 0.00 0.00 37.55 3.91
706 1563 4.320057 GCATCAACATAGATGGTAGCAAGC 60.320 45.833 0.00 0.00 44.33 4.01
707 1564 5.354054 GCATCAACATAGATGGTAGCAAG 57.646 43.478 0.00 0.00 44.33 4.01
714 1571 6.350864 CCCTAGAGTAGCATCAACATAGATGG 60.351 46.154 6.13 0.00 44.33 3.51
715 1572 6.210385 ACCCTAGAGTAGCATCAACATAGATG 59.790 42.308 0.00 0.00 46.36 2.90
716 1573 6.210385 CACCCTAGAGTAGCATCAACATAGAT 59.790 42.308 0.00 0.00 0.00 1.98
717 1574 5.536538 CACCCTAGAGTAGCATCAACATAGA 59.463 44.000 0.00 0.00 0.00 1.98
718 1575 5.777802 CACCCTAGAGTAGCATCAACATAG 58.222 45.833 0.00 0.00 0.00 2.23
719 1576 4.039245 GCACCCTAGAGTAGCATCAACATA 59.961 45.833 0.00 0.00 0.00 2.29
720 1577 3.181461 GCACCCTAGAGTAGCATCAACAT 60.181 47.826 0.00 0.00 0.00 2.71
721 1578 2.168521 GCACCCTAGAGTAGCATCAACA 59.831 50.000 0.00 0.00 0.00 3.33
722 1579 2.432510 AGCACCCTAGAGTAGCATCAAC 59.567 50.000 0.00 0.00 0.00 3.18
723 1580 2.752030 AGCACCCTAGAGTAGCATCAA 58.248 47.619 0.00 0.00 0.00 2.57
724 1581 2.432146 CAAGCACCCTAGAGTAGCATCA 59.568 50.000 0.00 0.00 0.00 3.07
725 1582 2.804933 GCAAGCACCCTAGAGTAGCATC 60.805 54.545 0.00 0.00 0.00 3.91
726 1583 1.139853 GCAAGCACCCTAGAGTAGCAT 59.860 52.381 0.00 0.00 0.00 3.79
727 1584 0.537188 GCAAGCACCCTAGAGTAGCA 59.463 55.000 0.00 0.00 0.00 3.49
728 1585 0.537188 TGCAAGCACCCTAGAGTAGC 59.463 55.000 0.00 0.00 0.00 3.58
729 1586 1.469940 CGTGCAAGCACCCTAGAGTAG 60.470 57.143 18.54 0.00 43.49 2.57
730 1587 0.530744 CGTGCAAGCACCCTAGAGTA 59.469 55.000 18.54 0.00 43.49 2.59
731 1588 1.293498 CGTGCAAGCACCCTAGAGT 59.707 57.895 18.54 0.00 43.49 3.24
732 1589 2.103042 GCGTGCAAGCACCCTAGAG 61.103 63.158 20.14 5.50 43.49 2.43
733 1590 2.047274 GCGTGCAAGCACCCTAGA 60.047 61.111 20.14 0.00 43.49 2.43
734 1591 2.046892 AGCGTGCAAGCACCCTAG 60.047 61.111 26.30 6.53 43.49 3.02
735 1592 2.358615 CAGCGTGCAAGCACCCTA 60.359 61.111 26.30 0.00 43.49 3.53
739 1596 4.612536 AACGCAGCGTGCAAGCAC 62.613 61.111 23.78 16.33 45.36 4.40
740 1597 3.805385 GAAACGCAGCGTGCAAGCA 62.805 57.895 23.78 0.00 45.36 3.91
741 1598 2.170260 TAGAAACGCAGCGTGCAAGC 62.170 55.000 23.78 17.43 45.36 4.01
742 1599 0.451135 GTAGAAACGCAGCGTGCAAG 60.451 55.000 23.78 0.00 45.36 4.01
743 1600 1.154814 TGTAGAAACGCAGCGTGCAA 61.155 50.000 23.78 4.72 45.36 4.08
744 1601 0.948623 ATGTAGAAACGCAGCGTGCA 60.949 50.000 23.78 15.40 45.36 4.57
745 1602 0.996462 TATGTAGAAACGCAGCGTGC 59.004 50.000 23.78 16.88 39.99 5.34
746 1603 2.410392 TGTTATGTAGAAACGCAGCGTG 59.590 45.455 23.78 0.00 39.99 5.34
747 1604 2.666508 CTGTTATGTAGAAACGCAGCGT 59.333 45.455 16.61 16.61 43.97 5.07
748 1605 2.921121 TCTGTTATGTAGAAACGCAGCG 59.079 45.455 14.82 14.82 0.00 5.18
749 1606 3.242123 GCTCTGTTATGTAGAAACGCAGC 60.242 47.826 0.00 0.00 31.16 5.25
750 1607 3.926527 TGCTCTGTTATGTAGAAACGCAG 59.073 43.478 0.00 0.00 0.00 5.18
751 1608 3.920446 TGCTCTGTTATGTAGAAACGCA 58.080 40.909 0.00 0.00 0.00 5.24
752 1609 6.584954 CATATGCTCTGTTATGTAGAAACGC 58.415 40.000 0.00 0.00 0.00 4.84
753 1610 6.200854 TGCATATGCTCTGTTATGTAGAAACG 59.799 38.462 27.13 0.00 42.66 3.60
754 1611 7.482654 TGCATATGCTCTGTTATGTAGAAAC 57.517 36.000 27.13 0.00 42.66 2.78
755 1612 9.428097 CTATGCATATGCTCTGTTATGTAGAAA 57.572 33.333 27.13 2.56 42.66 2.52
756 1613 7.547019 GCTATGCATATGCTCTGTTATGTAGAA 59.453 37.037 27.13 3.22 42.66 2.10
757 1614 7.038048 GCTATGCATATGCTCTGTTATGTAGA 58.962 38.462 27.13 3.67 42.66 2.59
758 1615 7.040494 AGCTATGCATATGCTCTGTTATGTAG 58.960 38.462 27.13 14.71 42.66 2.74
759 1616 6.939622 AGCTATGCATATGCTCTGTTATGTA 58.060 36.000 27.13 4.41 42.66 2.29
760 1617 5.802465 AGCTATGCATATGCTCTGTTATGT 58.198 37.500 27.13 5.97 42.66 2.29
761 1618 6.738832 AAGCTATGCATATGCTCTGTTATG 57.261 37.500 27.13 10.40 42.66 1.90
762 1619 7.756395 AAAAGCTATGCATATGCTCTGTTAT 57.244 32.000 27.13 14.11 42.66 1.89
763 1620 7.572523 AAAAAGCTATGCATATGCTCTGTTA 57.427 32.000 27.13 7.43 42.66 2.41
764 1621 6.461110 AAAAAGCTATGCATATGCTCTGTT 57.539 33.333 27.13 16.25 42.66 3.16
784 1641 1.004200 GCCGTCGGGGAGAGAAAAA 60.004 57.895 14.38 0.00 38.47 1.94
972 1829 2.260434 GTCTAGTCGCCGCCAACA 59.740 61.111 0.00 0.00 0.00 3.33
1289 2146 2.178544 AGCATGGCCTTATTCCAATCCT 59.821 45.455 3.32 0.00 37.13 3.24
1410 2272 1.400494 GGTAAACGATGGATTTGCGCT 59.600 47.619 9.73 0.00 0.00 5.92
2062 2924 1.683385 TCCATCATCGCTCGACTGAAT 59.317 47.619 0.00 0.00 0.00 2.57
2286 3148 3.832490 CCGATCCATCATACTGGTCCTTA 59.168 47.826 0.00 0.00 37.57 2.69


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

AutoCloner maintained by Alex Coulton.