Multiple sequence alignment - TraesCS5A01G266300

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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 TraesCS5A01G266300 chr5A 100.000 2647 0 0 1 2647 477819976 477817330 0.000000e+00 4889
1 TraesCS5A01G266300 chr5A 99.155 592 5 0 1 592 477826861 477826270 0.000000e+00 1066
2 TraesCS5A01G266300 chr5A 98.477 591 3 1 1 591 465340477 465339893 0.000000e+00 1037
3 TraesCS5A01G266300 chr5A 97.804 592 7 1 1 592 465347307 465346722 0.000000e+00 1016
4 TraesCS5A01G266300 chr5A 97.635 592 8 1 1 592 51935251 51935836 0.000000e+00 1011
5 TraesCS5A01G266300 chr5A 97.306 594 14 1 1 592 625933026 625933619 0.000000e+00 1007
6 TraesCS5A01G266300 chr5A 82.090 201 31 4 1246 1442 677950906 677951105 1.630000e-37 167
7 TraesCS5A01G266300 chr5A 80.892 157 28 2 1289 1444 528270439 528270594 3.580000e-24 122
8 TraesCS5A01G266300 chr5B 96.327 980 30 2 655 1634 450620284 450619311 0.000000e+00 1605
9 TraesCS5A01G266300 chr5B 89.865 148 15 0 1298 1445 448274401 448274254 9.670000e-45 191
10 TraesCS5A01G266300 chr5B 95.833 72 1 2 1690 1760 450619311 450619241 5.990000e-22 115
11 TraesCS5A01G266300 chr2A 97.746 843 18 1 1806 2647 766143552 766142710 0.000000e+00 1450
12 TraesCS5A01G266300 chr1A 96.564 844 29 0 1804 2647 428207139 428207982 0.000000e+00 1399
13 TraesCS5A01G266300 chr1A 95.952 840 34 0 1808 2647 563763486 563762647 0.000000e+00 1363
14 TraesCS5A01G266300 chr7A 95.482 841 37 1 1807 2647 518693267 518692428 0.000000e+00 1341
15 TraesCS5A01G266300 chr4D 94.749 838 43 1 1810 2647 379696332 379695496 0.000000e+00 1303
16 TraesCS5A01G266300 chr4D 81.592 201 32 4 1246 1442 497647931 497648130 7.580000e-36 161
17 TraesCS5A01G266300 chr4D 80.882 204 34 4 1246 1445 497668823 497668621 3.530000e-34 156
18 TraesCS5A01G266300 chr3D 93.698 841 53 0 1807 2647 551078068 551077228 0.000000e+00 1260
19 TraesCS5A01G266300 chr6B 93.698 841 46 3 1807 2647 513857188 513858021 0.000000e+00 1253
20 TraesCS5A01G266300 chr6B 93.470 827 47 4 1822 2647 159951185 159950365 0.000000e+00 1221
21 TraesCS5A01G266300 chr4B 92.299 844 60 2 1805 2647 440586707 440585868 0.000000e+00 1194
22 TraesCS5A01G266300 chrUn 97.808 593 6 2 1 592 409905357 409905943 0.000000e+00 1016
23 TraesCS5A01G266300 chrUn 97.647 595 9 4 1 592 413133182 413132590 0.000000e+00 1016
24 TraesCS5A01G266300 chrUn 97.639 593 7 3 1 592 422011848 422011262 0.000000e+00 1011
25 TraesCS5A01G266300 chr4A 97.639 593 7 3 1 592 624235464 624236050 0.000000e+00 1011
26 TraesCS5A01G266300 chr5D 87.116 846 96 9 655 1499 377312896 377312063 0.000000e+00 946
27 TraesCS5A01G266300 chr5D 89.726 146 15 0 1300 1445 375407501 375407356 1.250000e-43 187
28 TraesCS5A01G266300 chr1B 83.212 137 23 0 1304 1440 594009978 594009842 2.770000e-25 126


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 TraesCS5A01G266300 chr5A 477817330 477819976 2646 True 4889 4889 100.000 1 2647 1 chr5A.!!$R3 2646
1 TraesCS5A01G266300 chr5A 477826270 477826861 591 True 1066 1066 99.155 1 592 1 chr5A.!!$R4 591
2 TraesCS5A01G266300 chr5A 465339893 465340477 584 True 1037 1037 98.477 1 591 1 chr5A.!!$R1 590
3 TraesCS5A01G266300 chr5A 465346722 465347307 585 True 1016 1016 97.804 1 592 1 chr5A.!!$R2 591
4 TraesCS5A01G266300 chr5A 51935251 51935836 585 False 1011 1011 97.635 1 592 1 chr5A.!!$F1 591
5 TraesCS5A01G266300 chr5A 625933026 625933619 593 False 1007 1007 97.306 1 592 1 chr5A.!!$F3 591
6 TraesCS5A01G266300 chr5B 450619241 450620284 1043 True 860 1605 96.080 655 1760 2 chr5B.!!$R2 1105
7 TraesCS5A01G266300 chr2A 766142710 766143552 842 True 1450 1450 97.746 1806 2647 1 chr2A.!!$R1 841
8 TraesCS5A01G266300 chr1A 428207139 428207982 843 False 1399 1399 96.564 1804 2647 1 chr1A.!!$F1 843
9 TraesCS5A01G266300 chr1A 563762647 563763486 839 True 1363 1363 95.952 1808 2647 1 chr1A.!!$R1 839
10 TraesCS5A01G266300 chr7A 518692428 518693267 839 True 1341 1341 95.482 1807 2647 1 chr7A.!!$R1 840
11 TraesCS5A01G266300 chr4D 379695496 379696332 836 True 1303 1303 94.749 1810 2647 1 chr4D.!!$R1 837
12 TraesCS5A01G266300 chr3D 551077228 551078068 840 True 1260 1260 93.698 1807 2647 1 chr3D.!!$R1 840
13 TraesCS5A01G266300 chr6B 513857188 513858021 833 False 1253 1253 93.698 1807 2647 1 chr6B.!!$F1 840
14 TraesCS5A01G266300 chr6B 159950365 159951185 820 True 1221 1221 93.470 1822 2647 1 chr6B.!!$R1 825
15 TraesCS5A01G266300 chr4B 440585868 440586707 839 True 1194 1194 92.299 1805 2647 1 chr4B.!!$R1 842
16 TraesCS5A01G266300 chrUn 409905357 409905943 586 False 1016 1016 97.808 1 592 1 chrUn.!!$F1 591
17 TraesCS5A01G266300 chrUn 413132590 413133182 592 True 1016 1016 97.647 1 592 1 chrUn.!!$R1 591
18 TraesCS5A01G266300 chrUn 422011262 422011848 586 True 1011 1011 97.639 1 592 1 chrUn.!!$R2 591
19 TraesCS5A01G266300 chr4A 624235464 624236050 586 False 1011 1011 97.639 1 592 1 chr4A.!!$F1 591
20 TraesCS5A01G266300 chr5D 377312063 377312896 833 True 946 946 87.116 655 1499 1 chr5D.!!$R2 844

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
649 659 0.46546 TCTGACCGCAAGTGCCTTTT 60.465 50.0 0.0 0.0 37.91 2.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1652 1662 0.239347 CTATAGCTTTGCATGGCCGC 59.761 55.0 0.0 0.0 0.0 6.53 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
304 307 2.787994 CTGCTGTTGGATGGAGTCTTT 58.212 47.619 0.00 0.00 0.00 2.52
592 602 1.298859 CTGCTACGTTCCCCAACAGC 61.299 60.000 0.00 0.00 33.86 4.40
593 603 1.302192 GCTACGTTCCCCAACAGCA 60.302 57.895 0.00 0.00 33.60 4.41
594 604 0.887387 GCTACGTTCCCCAACAGCAA 60.887 55.000 0.00 0.00 33.60 3.91
595 605 1.156736 CTACGTTCCCCAACAGCAAG 58.843 55.000 0.00 0.00 32.14 4.01
596 606 0.470766 TACGTTCCCCAACAGCAAGT 59.529 50.000 0.00 0.00 32.14 3.16
597 607 0.470766 ACGTTCCCCAACAGCAAGTA 59.529 50.000 0.00 0.00 32.14 2.24
598 608 1.156736 CGTTCCCCAACAGCAAGTAG 58.843 55.000 0.00 0.00 32.14 2.57
599 609 1.542547 CGTTCCCCAACAGCAAGTAGT 60.543 52.381 0.00 0.00 32.14 2.73
600 610 1.880027 GTTCCCCAACAGCAAGTAGTG 59.120 52.381 0.00 0.00 32.14 2.74
601 611 1.136828 TCCCCAACAGCAAGTAGTGT 58.863 50.000 0.00 0.00 0.00 3.55
602 612 1.202758 TCCCCAACAGCAAGTAGTGTG 60.203 52.381 0.00 0.00 0.00 3.82
603 613 1.202758 CCCCAACAGCAAGTAGTGTGA 60.203 52.381 0.00 0.00 0.00 3.58
604 614 1.873591 CCCAACAGCAAGTAGTGTGAC 59.126 52.381 0.00 0.00 0.00 3.67
605 615 2.485479 CCCAACAGCAAGTAGTGTGACT 60.485 50.000 0.00 0.00 0.00 3.41
606 616 3.206150 CCAACAGCAAGTAGTGTGACTT 58.794 45.455 0.00 0.00 40.35 3.01
607 617 4.377021 CCAACAGCAAGTAGTGTGACTTA 58.623 43.478 0.00 0.00 37.57 2.24
608 618 4.814234 CCAACAGCAAGTAGTGTGACTTAA 59.186 41.667 0.00 0.00 37.57 1.85
609 619 5.050091 CCAACAGCAAGTAGTGTGACTTAAG 60.050 44.000 0.00 0.00 37.57 1.85
610 620 5.277857 ACAGCAAGTAGTGTGACTTAAGT 57.722 39.130 8.13 8.13 37.57 2.24
611 621 5.671493 ACAGCAAGTAGTGTGACTTAAGTT 58.329 37.500 10.02 0.00 37.57 2.66
612 622 5.753921 ACAGCAAGTAGTGTGACTTAAGTTC 59.246 40.000 10.02 7.14 37.57 3.01
613 623 5.753438 CAGCAAGTAGTGTGACTTAAGTTCA 59.247 40.000 10.02 9.63 37.57 3.18
614 624 5.753921 AGCAAGTAGTGTGACTTAAGTTCAC 59.246 40.000 24.51 24.51 37.57 3.18
615 625 5.050295 GCAAGTAGTGTGACTTAAGTTCACC 60.050 44.000 26.44 19.36 37.57 4.02
616 626 5.211174 AGTAGTGTGACTTAAGTTCACCC 57.789 43.478 26.44 20.88 35.45 4.61
617 627 3.107642 AGTGTGACTTAAGTTCACCCG 57.892 47.619 26.44 0.00 35.45 5.28
618 628 2.696707 AGTGTGACTTAAGTTCACCCGA 59.303 45.455 26.44 12.94 35.45 5.14
619 629 3.133362 AGTGTGACTTAAGTTCACCCGAA 59.867 43.478 26.44 12.71 35.45 4.30
620 630 4.062991 GTGTGACTTAAGTTCACCCGAAT 58.937 43.478 23.55 0.00 32.61 3.34
621 631 4.062293 TGTGACTTAAGTTCACCCGAATG 58.938 43.478 23.55 0.00 32.61 2.67
622 632 4.202274 TGTGACTTAAGTTCACCCGAATGA 60.202 41.667 23.55 9.86 32.61 2.57
623 633 4.151867 GTGACTTAAGTTCACCCGAATGAC 59.848 45.833 19.29 2.38 32.61 3.06
624 634 4.202274 TGACTTAAGTTCACCCGAATGACA 60.202 41.667 10.02 0.00 32.61 3.58
625 635 4.710324 ACTTAAGTTCACCCGAATGACAA 58.290 39.130 1.12 0.00 32.61 3.18
626 636 4.755123 ACTTAAGTTCACCCGAATGACAAG 59.245 41.667 1.12 0.00 32.61 3.16
627 637 2.930826 AGTTCACCCGAATGACAAGT 57.069 45.000 0.00 0.00 32.61 3.16
628 638 3.208747 AGTTCACCCGAATGACAAGTT 57.791 42.857 0.00 0.00 32.61 2.66
629 639 3.139077 AGTTCACCCGAATGACAAGTTC 58.861 45.455 0.00 0.00 32.61 3.01
630 640 3.139077 GTTCACCCGAATGACAAGTTCT 58.861 45.455 0.00 0.00 32.61 3.01
631 641 3.040147 TCACCCGAATGACAAGTTCTC 57.960 47.619 0.00 0.00 0.00 2.87
632 642 2.632996 TCACCCGAATGACAAGTTCTCT 59.367 45.455 0.00 0.00 0.00 3.10
633 643 2.738846 CACCCGAATGACAAGTTCTCTG 59.261 50.000 0.00 0.00 0.00 3.35
634 644 2.632996 ACCCGAATGACAAGTTCTCTGA 59.367 45.455 0.00 0.00 0.00 3.27
635 645 2.996621 CCCGAATGACAAGTTCTCTGAC 59.003 50.000 0.00 0.00 0.00 3.51
636 646 2.996621 CCGAATGACAAGTTCTCTGACC 59.003 50.000 0.00 0.00 0.00 4.02
637 647 2.663602 CGAATGACAAGTTCTCTGACCG 59.336 50.000 0.00 0.00 0.00 4.79
638 648 2.086054 ATGACAAGTTCTCTGACCGC 57.914 50.000 0.00 0.00 0.00 5.68
639 649 0.750249 TGACAAGTTCTCTGACCGCA 59.250 50.000 0.00 0.00 0.00 5.69
640 650 1.138069 TGACAAGTTCTCTGACCGCAA 59.862 47.619 0.00 0.00 0.00 4.85
641 651 1.795286 GACAAGTTCTCTGACCGCAAG 59.205 52.381 0.00 0.00 0.00 4.01
642 652 1.139058 ACAAGTTCTCTGACCGCAAGT 59.861 47.619 0.00 0.00 0.00 3.16
643 653 1.528586 CAAGTTCTCTGACCGCAAGTG 59.471 52.381 0.00 0.00 0.00 3.16
644 654 0.601311 AGTTCTCTGACCGCAAGTGC 60.601 55.000 0.00 0.00 37.78 4.40
645 655 1.301716 TTCTCTGACCGCAAGTGCC 60.302 57.895 0.00 0.00 37.91 5.01
646 656 1.758440 TTCTCTGACCGCAAGTGCCT 61.758 55.000 0.00 0.00 37.91 4.75
647 657 1.302033 CTCTGACCGCAAGTGCCTT 60.302 57.895 0.00 0.00 37.91 4.35
648 658 0.886490 CTCTGACCGCAAGTGCCTTT 60.886 55.000 0.00 0.00 37.91 3.11
649 659 0.465460 TCTGACCGCAAGTGCCTTTT 60.465 50.000 0.00 0.00 37.91 2.27
650 660 1.202710 TCTGACCGCAAGTGCCTTTTA 60.203 47.619 0.00 0.00 37.91 1.52
651 661 0.948678 TGACCGCAAGTGCCTTTTAC 59.051 50.000 0.00 0.00 37.91 2.01
652 662 1.235724 GACCGCAAGTGCCTTTTACT 58.764 50.000 0.00 0.00 37.91 2.24
653 663 1.197036 GACCGCAAGTGCCTTTTACTC 59.803 52.381 0.00 0.00 37.91 2.59
900 910 3.272574 AGCATTCATTCGACTGGTGAT 57.727 42.857 2.65 0.00 32.00 3.06
904 914 4.260375 GCATTCATTCGACTGGTGATGTAC 60.260 45.833 2.65 0.00 0.00 2.90
963 973 6.086896 CGATGTCATTGCTATAACAGTACTCG 59.913 42.308 0.00 0.00 0.00 4.18
1064 1074 5.523188 TCAAACATTTGGACATTTGTCTTGC 59.477 36.000 10.32 0.00 44.20 4.01
1071 1081 2.490903 GGACATTTGTCTTGCTGCTGAT 59.509 45.455 10.32 0.00 44.20 2.90
1077 1087 1.012841 GTCTTGCTGCTGATAGTGGC 58.987 55.000 0.00 0.00 0.00 5.01
1078 1088 0.614812 TCTTGCTGCTGATAGTGGCA 59.385 50.000 0.00 0.00 36.94 4.92
1079 1089 1.211212 TCTTGCTGCTGATAGTGGCAT 59.789 47.619 0.00 0.00 37.83 4.40
1108 1118 6.014012 TCCCCAAACTCCGATTATTTTTCTT 58.986 36.000 0.00 0.00 0.00 2.52
1146 1156 3.051940 TGCCTGTCCTATCTTGGAGAT 57.948 47.619 0.00 0.00 38.70 2.75
1155 1165 4.140536 CCTATCTTGGAGATTTTCAGGCC 58.859 47.826 0.00 0.00 36.20 5.19
1298 1308 5.466728 TGTTTCAGTTCTTCAAGATTCCTCG 59.533 40.000 0.00 0.00 0.00 4.63
1499 1509 6.283694 TGCTTATAGGCTGAATAGACACAAG 58.716 40.000 8.44 0.00 32.87 3.16
1506 1516 4.491676 GCTGAATAGACACAAGTTCGGTA 58.508 43.478 0.00 0.00 31.28 4.02
1507 1517 4.927425 GCTGAATAGACACAAGTTCGGTAA 59.073 41.667 0.00 0.00 31.28 2.85
1517 1527 3.058224 ACAAGTTCGGTAAATGCTTCAGC 60.058 43.478 0.00 0.00 42.50 4.26
1533 1543 3.818787 GCGAAGGCAGGCACATGG 61.819 66.667 0.00 0.00 39.62 3.66
1566 1576 0.652592 CAAAGCGGTCTTGGCTATCG 59.347 55.000 0.00 0.00 40.53 2.92
1610 1620 3.146847 CCCCTCCACTGTCAAGTTAAAC 58.853 50.000 0.00 0.00 32.98 2.01
1642 1652 3.041701 CAGCCGTTGCCATGTTGT 58.958 55.556 0.00 0.00 38.69 3.32
1643 1653 1.363443 CAGCCGTTGCCATGTTGTT 59.637 52.632 0.00 0.00 38.69 2.83
1644 1654 0.249405 CAGCCGTTGCCATGTTGTTT 60.249 50.000 0.00 0.00 38.69 2.83
1645 1655 1.000827 CAGCCGTTGCCATGTTGTTTA 60.001 47.619 0.00 0.00 38.69 2.01
1646 1656 1.683917 AGCCGTTGCCATGTTGTTTAA 59.316 42.857 0.00 0.00 38.69 1.52
1647 1657 1.790043 GCCGTTGCCATGTTGTTTAAC 59.210 47.619 0.00 0.00 37.32 2.01
1648 1658 2.047769 CCGTTGCCATGTTGTTTAACG 58.952 47.619 0.00 0.00 39.71 3.18
1649 1659 2.287069 CCGTTGCCATGTTGTTTAACGA 60.287 45.455 8.64 0.00 42.23 3.85
1650 1660 2.717011 CGTTGCCATGTTGTTTAACGAC 59.283 45.455 8.45 8.45 42.23 4.34
1651 1661 2.672188 TGCCATGTTGTTTAACGACG 57.328 45.000 10.48 0.00 39.71 5.12
1652 1662 1.264557 TGCCATGTTGTTTAACGACGG 59.735 47.619 10.48 7.76 39.71 4.79
1653 1663 1.958417 CCATGTTGTTTAACGACGGC 58.042 50.000 10.48 0.00 39.71 5.68
1654 1664 1.586908 CATGTTGTTTAACGACGGCG 58.413 50.000 10.39 10.39 39.71 6.46
1655 1665 0.513820 ATGTTGTTTAACGACGGCGG 59.486 50.000 18.49 0.00 43.17 6.13
1656 1666 1.439201 GTTGTTTAACGACGGCGGC 60.439 57.895 18.49 7.52 43.17 6.53
1657 1667 2.606030 TTGTTTAACGACGGCGGCC 61.606 57.895 18.49 9.54 43.17 6.13
1658 1668 3.043121 GTTTAACGACGGCGGCCA 61.043 61.111 18.49 0.00 43.17 5.36
1659 1669 2.047083 TTTAACGACGGCGGCCAT 60.047 55.556 18.49 2.38 43.17 4.40
1660 1670 2.392181 TTTAACGACGGCGGCCATG 61.392 57.895 18.49 10.16 43.17 3.66
1665 1675 4.481112 GACGGCGGCCATGCAAAG 62.481 66.667 20.71 2.83 36.28 2.77
1668 1678 3.140141 GGCGGCCATGCAAAGCTA 61.140 61.111 15.62 0.00 36.28 3.32
1669 1679 2.492773 GGCGGCCATGCAAAGCTAT 61.493 57.895 15.62 0.00 36.28 2.97
1670 1680 1.172180 GGCGGCCATGCAAAGCTATA 61.172 55.000 15.62 0.00 36.28 1.31
1671 1681 0.239347 GCGGCCATGCAAAGCTATAG 59.761 55.000 2.24 0.00 34.15 1.31
1672 1682 0.239347 CGGCCATGCAAAGCTATAGC 59.761 55.000 17.33 17.33 42.49 2.97
1673 1683 1.321474 GGCCATGCAAAGCTATAGCA 58.679 50.000 26.07 6.78 45.16 3.49
1674 1684 1.682854 GGCCATGCAAAGCTATAGCAA 59.317 47.619 26.07 6.98 45.16 3.91
1675 1685 2.544486 GGCCATGCAAAGCTATAGCAAC 60.544 50.000 26.07 12.46 45.16 4.17
1676 1686 2.544486 GCCATGCAAAGCTATAGCAACC 60.544 50.000 26.07 11.71 45.16 3.77
1677 1687 2.689471 CCATGCAAAGCTATAGCAACCA 59.311 45.455 26.07 16.47 45.16 3.67
1678 1688 3.319972 CCATGCAAAGCTATAGCAACCAT 59.680 43.478 26.07 17.80 45.16 3.55
1679 1689 4.543692 CATGCAAAGCTATAGCAACCATC 58.456 43.478 26.07 10.38 45.16 3.51
1680 1690 3.889815 TGCAAAGCTATAGCAACCATCT 58.110 40.909 26.07 0.78 45.16 2.90
1681 1691 5.034852 TGCAAAGCTATAGCAACCATCTA 57.965 39.130 26.07 2.59 45.16 1.98
1682 1692 5.059161 TGCAAAGCTATAGCAACCATCTAG 58.941 41.667 26.07 6.76 45.16 2.43
1683 1693 5.059833 GCAAAGCTATAGCAACCATCTAGT 58.940 41.667 26.07 0.00 45.16 2.57
1684 1694 5.049818 GCAAAGCTATAGCAACCATCTAGTG 60.050 44.000 26.07 9.33 45.16 2.74
1685 1695 5.878406 AAGCTATAGCAACCATCTAGTGT 57.122 39.130 26.07 0.00 45.16 3.55
1686 1696 5.878406 AGCTATAGCAACCATCTAGTGTT 57.122 39.130 26.07 0.00 45.16 3.32
1687 1697 6.240549 AGCTATAGCAACCATCTAGTGTTT 57.759 37.500 26.07 0.00 45.16 2.83
1688 1698 7.361457 AGCTATAGCAACCATCTAGTGTTTA 57.639 36.000 26.07 0.00 45.16 2.01
1689 1699 7.437748 AGCTATAGCAACCATCTAGTGTTTAG 58.562 38.462 26.07 0.00 45.16 1.85
1690 1700 7.070074 AGCTATAGCAACCATCTAGTGTTTAGT 59.930 37.037 26.07 0.00 45.16 2.24
1691 1701 7.711339 GCTATAGCAACCATCTAGTGTTTAGTT 59.289 37.037 20.01 0.00 41.59 2.24
1693 1703 8.943909 ATAGCAACCATCTAGTGTTTAGTTAC 57.056 34.615 0.00 0.00 0.00 2.50
1694 1704 6.171213 AGCAACCATCTAGTGTTTAGTTACC 58.829 40.000 0.00 0.00 0.00 2.85
1695 1705 5.935789 GCAACCATCTAGTGTTTAGTTACCA 59.064 40.000 0.00 0.00 0.00 3.25
1696 1706 6.428771 GCAACCATCTAGTGTTTAGTTACCAA 59.571 38.462 0.00 0.00 0.00 3.67
1753 1763 6.105333 TGCAAAATTATATGGGCTGTGTTTC 58.895 36.000 0.00 0.00 0.00 2.78
1754 1764 6.070881 TGCAAAATTATATGGGCTGTGTTTCT 60.071 34.615 0.00 0.00 0.00 2.52
1757 1767 8.872845 CAAAATTATATGGGCTGTGTTTCTTTC 58.127 33.333 0.00 0.00 0.00 2.62
1758 1768 7.961326 AATTATATGGGCTGTGTTTCTTTCT 57.039 32.000 0.00 0.00 0.00 2.52
1760 1770 5.649782 ATATGGGCTGTGTTTCTTTCTTG 57.350 39.130 0.00 0.00 0.00 3.02
1761 1771 3.011566 TGGGCTGTGTTTCTTTCTTGA 57.988 42.857 0.00 0.00 0.00 3.02
1762 1772 3.360867 TGGGCTGTGTTTCTTTCTTGAA 58.639 40.909 0.00 0.00 0.00 2.69
1763 1773 3.130340 TGGGCTGTGTTTCTTTCTTGAAC 59.870 43.478 0.00 0.00 0.00 3.18
1764 1774 3.381590 GGGCTGTGTTTCTTTCTTGAACT 59.618 43.478 0.00 0.00 0.00 3.01
1765 1775 4.578928 GGGCTGTGTTTCTTTCTTGAACTA 59.421 41.667 0.00 0.00 0.00 2.24
1766 1776 5.278022 GGGCTGTGTTTCTTTCTTGAACTAG 60.278 44.000 0.00 0.00 0.00 2.57
1767 1777 5.208503 GCTGTGTTTCTTTCTTGAACTAGC 58.791 41.667 0.00 0.00 0.00 3.42
1768 1778 5.220854 GCTGTGTTTCTTTCTTGAACTAGCA 60.221 40.000 0.00 0.00 0.00 3.49
1769 1779 6.363577 TGTGTTTCTTTCTTGAACTAGCAG 57.636 37.500 0.00 0.00 0.00 4.24
1770 1780 6.112734 TGTGTTTCTTTCTTGAACTAGCAGA 58.887 36.000 0.00 0.00 0.00 4.26
1771 1781 6.597672 TGTGTTTCTTTCTTGAACTAGCAGAA 59.402 34.615 0.00 0.00 0.00 3.02
1772 1782 6.907748 GTGTTTCTTTCTTGAACTAGCAGAAC 59.092 38.462 0.00 0.00 0.00 3.01
1773 1783 6.823689 TGTTTCTTTCTTGAACTAGCAGAACT 59.176 34.615 0.00 0.00 0.00 3.01
1774 1784 6.851222 TTCTTTCTTGAACTAGCAGAACTG 57.149 37.500 0.00 0.00 0.00 3.16
1775 1785 5.918608 TCTTTCTTGAACTAGCAGAACTGT 58.081 37.500 3.77 0.00 0.00 3.55
1776 1786 5.755375 TCTTTCTTGAACTAGCAGAACTGTG 59.245 40.000 3.77 0.00 0.00 3.66
1777 1787 3.393800 TCTTGAACTAGCAGAACTGTGC 58.606 45.455 3.77 0.00 44.35 4.57
1778 1788 2.908688 TGAACTAGCAGAACTGTGCA 57.091 45.000 1.37 0.00 46.60 4.57
1779 1789 2.759191 TGAACTAGCAGAACTGTGCAG 58.241 47.619 1.37 0.00 46.60 4.41
1780 1790 2.103094 TGAACTAGCAGAACTGTGCAGT 59.897 45.455 1.37 0.00 46.60 4.40
1790 1800 2.634982 ACTGTGCAGTTTGTTGTGTG 57.365 45.000 0.00 0.00 38.83 3.82
1791 1801 2.158559 ACTGTGCAGTTTGTTGTGTGA 58.841 42.857 0.00 0.00 38.83 3.58
1792 1802 2.754552 ACTGTGCAGTTTGTTGTGTGAT 59.245 40.909 0.00 0.00 38.83 3.06
1793 1803 3.944650 ACTGTGCAGTTTGTTGTGTGATA 59.055 39.130 0.00 0.00 38.83 2.15
1794 1804 4.035558 ACTGTGCAGTTTGTTGTGTGATAG 59.964 41.667 0.00 0.00 38.83 2.08
1795 1805 3.944650 TGTGCAGTTTGTTGTGTGATAGT 59.055 39.130 0.00 0.00 0.00 2.12
1796 1806 5.119694 TGTGCAGTTTGTTGTGTGATAGTA 58.880 37.500 0.00 0.00 0.00 1.82
1797 1807 5.007234 TGTGCAGTTTGTTGTGTGATAGTAC 59.993 40.000 0.00 0.00 0.00 2.73
1798 1808 5.007234 GTGCAGTTTGTTGTGTGATAGTACA 59.993 40.000 0.00 0.00 0.00 2.90
1799 1809 5.586643 TGCAGTTTGTTGTGTGATAGTACAA 59.413 36.000 0.00 0.00 34.66 2.41
1800 1810 6.262049 TGCAGTTTGTTGTGTGATAGTACAAT 59.738 34.615 0.00 0.00 38.84 2.71
1801 1811 6.797033 GCAGTTTGTTGTGTGATAGTACAATC 59.203 38.462 0.00 0.00 38.84 2.67
1802 1812 7.519809 GCAGTTTGTTGTGTGATAGTACAATCA 60.520 37.037 0.00 0.00 38.84 2.57
2017 2027 5.010314 CACAAACCCTGACACTACTACTACA 59.990 44.000 0.00 0.00 0.00 2.74
2060 2071 4.713553 ACACCACAACACAAGACATCATA 58.286 39.130 0.00 0.00 0.00 2.15
2098 2109 0.038526 GACAAGCCGAGAGACCGAAA 60.039 55.000 0.00 0.00 0.00 3.46
2100 2111 1.202604 ACAAGCCGAGAGACCGAAAAA 60.203 47.619 0.00 0.00 0.00 1.94
2151 2162 2.086054 ATGACGTCACTCTTGCCTTC 57.914 50.000 22.71 0.00 0.00 3.46
2416 2427 1.483424 GCTCGATGACTAACGCCTGC 61.483 60.000 0.00 0.00 0.00 4.85
2625 2636 1.134521 GGGCATGATCTGTAACACCGA 60.135 52.381 0.00 0.00 0.00 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
304 307 1.286553 GGAGAGAGGGAGAGGTTGAGA 59.713 57.143 0.00 0.00 0.00 3.27
592 602 5.465724 GGGTGAACTTAAGTCACACTACTTG 59.534 44.000 28.32 0.00 39.95 3.16
593 603 5.608449 GGGTGAACTTAAGTCACACTACTT 58.392 41.667 28.32 7.76 42.31 2.24
594 604 4.261909 CGGGTGAACTTAAGTCACACTACT 60.262 45.833 28.32 8.35 35.79 2.57
595 605 3.985925 CGGGTGAACTTAAGTCACACTAC 59.014 47.826 28.32 23.15 35.79 2.73
596 606 3.890756 TCGGGTGAACTTAAGTCACACTA 59.109 43.478 28.32 19.55 35.79 2.74
597 607 2.696707 TCGGGTGAACTTAAGTCACACT 59.303 45.455 28.32 10.13 35.79 3.55
598 608 3.102052 TCGGGTGAACTTAAGTCACAC 57.898 47.619 25.75 25.34 36.21 3.82
599 609 3.823281 TTCGGGTGAACTTAAGTCACA 57.177 42.857 25.75 19.06 36.21 3.58
600 610 4.151867 GTCATTCGGGTGAACTTAAGTCAC 59.848 45.833 20.73 20.73 36.81 3.67
601 611 4.202274 TGTCATTCGGGTGAACTTAAGTCA 60.202 41.667 8.95 6.15 36.81 3.41
602 612 4.312443 TGTCATTCGGGTGAACTTAAGTC 58.688 43.478 8.95 3.51 36.81 3.01
603 613 4.345859 TGTCATTCGGGTGAACTTAAGT 57.654 40.909 1.12 1.12 36.81 2.24
604 614 4.755123 ACTTGTCATTCGGGTGAACTTAAG 59.245 41.667 0.00 0.00 36.81 1.85
605 615 4.710324 ACTTGTCATTCGGGTGAACTTAA 58.290 39.130 0.00 0.00 36.81 1.85
606 616 4.345859 ACTTGTCATTCGGGTGAACTTA 57.654 40.909 0.00 0.00 36.81 2.24
607 617 3.208747 ACTTGTCATTCGGGTGAACTT 57.791 42.857 0.00 0.00 36.81 2.66
608 618 2.930826 ACTTGTCATTCGGGTGAACT 57.069 45.000 0.00 0.00 36.81 3.01
609 619 3.139077 AGAACTTGTCATTCGGGTGAAC 58.861 45.455 0.00 0.00 36.81 3.18
610 620 3.071023 AGAGAACTTGTCATTCGGGTGAA 59.929 43.478 0.00 0.00 38.76 3.18
611 621 2.632996 AGAGAACTTGTCATTCGGGTGA 59.367 45.455 0.00 0.00 0.00 4.02
612 622 2.738846 CAGAGAACTTGTCATTCGGGTG 59.261 50.000 0.00 0.00 0.00 4.61
613 623 2.632996 TCAGAGAACTTGTCATTCGGGT 59.367 45.455 0.00 0.00 0.00 5.28
614 624 2.996621 GTCAGAGAACTTGTCATTCGGG 59.003 50.000 0.00 0.00 0.00 5.14
615 625 2.996621 GGTCAGAGAACTTGTCATTCGG 59.003 50.000 0.00 0.00 0.00 4.30
616 626 2.663602 CGGTCAGAGAACTTGTCATTCG 59.336 50.000 0.00 0.00 0.00 3.34
617 627 2.413453 GCGGTCAGAGAACTTGTCATTC 59.587 50.000 0.00 0.00 0.00 2.67
618 628 2.224281 TGCGGTCAGAGAACTTGTCATT 60.224 45.455 0.00 0.00 0.00 2.57
619 629 1.344438 TGCGGTCAGAGAACTTGTCAT 59.656 47.619 0.00 0.00 0.00 3.06
620 630 0.750249 TGCGGTCAGAGAACTTGTCA 59.250 50.000 0.00 0.00 0.00 3.58
621 631 1.795286 CTTGCGGTCAGAGAACTTGTC 59.205 52.381 0.00 0.00 0.00 3.18
622 632 1.139058 ACTTGCGGTCAGAGAACTTGT 59.861 47.619 0.00 0.00 0.00 3.16
623 633 1.528586 CACTTGCGGTCAGAGAACTTG 59.471 52.381 0.00 0.00 0.00 3.16
624 634 1.871080 CACTTGCGGTCAGAGAACTT 58.129 50.000 0.00 0.00 0.00 2.66
625 635 0.601311 GCACTTGCGGTCAGAGAACT 60.601 55.000 0.00 0.00 0.00 3.01
626 636 1.569479 GGCACTTGCGGTCAGAGAAC 61.569 60.000 0.00 0.00 43.26 3.01
627 637 1.301716 GGCACTTGCGGTCAGAGAA 60.302 57.895 0.00 0.00 43.26 2.87
628 638 2.210013 AGGCACTTGCGGTCAGAGA 61.210 57.895 0.00 0.00 43.26 3.10
629 639 2.345244 AGGCACTTGCGGTCAGAG 59.655 61.111 0.00 0.00 43.26 3.35
644 654 0.744771 GCTGAGCCGGGAGTAAAAGG 60.745 60.000 2.18 0.00 0.00 3.11
645 655 0.036388 TGCTGAGCCGGGAGTAAAAG 60.036 55.000 2.18 0.00 0.00 2.27
646 656 0.398696 TTGCTGAGCCGGGAGTAAAA 59.601 50.000 2.18 0.00 0.00 1.52
647 657 0.036388 CTTGCTGAGCCGGGAGTAAA 60.036 55.000 2.18 0.00 0.00 2.01
648 658 1.596934 CTTGCTGAGCCGGGAGTAA 59.403 57.895 2.18 0.00 0.00 2.24
649 659 3.019003 GCTTGCTGAGCCGGGAGTA 62.019 63.158 2.18 0.00 46.01 2.59
650 660 4.400961 GCTTGCTGAGCCGGGAGT 62.401 66.667 2.18 0.00 46.01 3.85
900 910 7.227711 TGAAATCAAGAAGTTTCGGAATGTACA 59.772 33.333 0.00 0.00 37.19 2.90
904 914 6.467047 CGATGAAATCAAGAAGTTTCGGAATG 59.533 38.462 0.00 0.00 45.97 2.67
940 950 6.697455 CACGAGTACTGTTATAGCAATGACAT 59.303 38.462 0.00 0.00 31.81 3.06
1064 1074 4.217118 GGGAAAATATGCCACTATCAGCAG 59.783 45.833 0.00 0.00 43.38 4.24
1071 1081 4.941713 AGTTTGGGGAAAATATGCCACTA 58.058 39.130 0.00 0.00 42.44 2.74
1077 1087 5.852282 AATCGGAGTTTGGGGAAAATATG 57.148 39.130 0.00 0.00 0.00 1.78
1078 1088 8.547481 AAATAATCGGAGTTTGGGGAAAATAT 57.453 30.769 0.00 0.00 0.00 1.28
1079 1089 7.964666 AAATAATCGGAGTTTGGGGAAAATA 57.035 32.000 0.00 0.00 0.00 1.40
1146 1156 3.562557 GTGACTTACTTTCGGCCTGAAAA 59.437 43.478 18.79 8.77 45.59 2.29
1182 1192 4.093743 TCTGTGCACCATAGGTAAGAGAA 58.906 43.478 15.69 0.00 32.11 2.87
1186 1196 4.207891 AGTTCTGTGCACCATAGGTAAG 57.792 45.455 15.69 1.99 32.11 2.34
1499 1509 1.730064 TCGCTGAAGCATTTACCGAAC 59.270 47.619 2.79 0.00 42.21 3.95
1506 1516 0.524862 CTGCCTTCGCTGAAGCATTT 59.475 50.000 11.33 0.00 42.21 2.32
1507 1517 1.310933 CCTGCCTTCGCTGAAGCATT 61.311 55.000 11.33 0.00 42.21 3.56
1517 1527 2.360350 ACCATGTGCCTGCCTTCG 60.360 61.111 0.00 0.00 0.00 3.79
1566 1576 5.333875 GGACTTTCACCATAACGTGTCTTTC 60.334 44.000 0.00 0.00 35.18 2.62
1610 1620 1.718757 GGCTGCAGGGCTTGATAACG 61.719 60.000 17.12 0.00 37.53 3.18
1634 1644 1.723384 CGCCGTCGTTAAACAACATGG 60.723 52.381 0.00 0.00 0.00 3.66
1635 1645 1.586908 CGCCGTCGTTAAACAACATG 58.413 50.000 0.00 0.00 0.00 3.21
1637 1647 1.933005 CCGCCGTCGTTAAACAACA 59.067 52.632 0.00 0.00 0.00 3.33
1638 1648 1.439201 GCCGCCGTCGTTAAACAAC 60.439 57.895 0.00 0.00 0.00 3.32
1639 1649 2.606030 GGCCGCCGTCGTTAAACAA 61.606 57.895 0.00 0.00 0.00 2.83
1640 1650 3.043121 GGCCGCCGTCGTTAAACA 61.043 61.111 0.00 0.00 0.00 2.83
1641 1651 2.392974 ATGGCCGCCGTCGTTAAAC 61.393 57.895 4.58 0.00 0.00 2.01
1642 1652 2.047083 ATGGCCGCCGTCGTTAAA 60.047 55.556 4.58 0.00 0.00 1.52
1643 1653 2.816083 CATGGCCGCCGTCGTTAA 60.816 61.111 0.00 0.00 0.00 2.01
1648 1658 4.481112 CTTTGCATGGCCGCCGTC 62.481 66.667 0.00 0.00 0.00 4.79
1651 1661 1.172180 TATAGCTTTGCATGGCCGCC 61.172 55.000 1.04 1.04 0.00 6.13
1652 1662 0.239347 CTATAGCTTTGCATGGCCGC 59.761 55.000 0.00 0.00 0.00 6.53
1653 1663 0.239347 GCTATAGCTTTGCATGGCCG 59.761 55.000 17.75 0.00 38.21 6.13
1654 1664 1.321474 TGCTATAGCTTTGCATGGCC 58.679 50.000 24.61 0.00 42.66 5.36
1655 1665 2.544486 GGTTGCTATAGCTTTGCATGGC 60.544 50.000 24.61 2.70 42.66 4.40
1656 1666 2.689471 TGGTTGCTATAGCTTTGCATGG 59.311 45.455 24.61 0.00 42.66 3.66
1657 1667 4.277672 AGATGGTTGCTATAGCTTTGCATG 59.722 41.667 24.61 0.00 42.66 4.06
1658 1668 4.467769 AGATGGTTGCTATAGCTTTGCAT 58.532 39.130 24.61 3.95 42.66 3.96
1659 1669 3.889815 AGATGGTTGCTATAGCTTTGCA 58.110 40.909 24.61 2.77 42.66 4.08
1660 1670 5.049818 CACTAGATGGTTGCTATAGCTTTGC 60.050 44.000 24.61 11.87 42.66 3.68
1661 1671 6.051717 ACACTAGATGGTTGCTATAGCTTTG 58.948 40.000 24.61 9.28 42.66 2.77
1662 1672 6.240549 ACACTAGATGGTTGCTATAGCTTT 57.759 37.500 24.61 5.82 42.66 3.51
1663 1673 5.878406 ACACTAGATGGTTGCTATAGCTT 57.122 39.130 24.61 5.49 42.66 3.74
1664 1674 5.878406 AACACTAGATGGTTGCTATAGCT 57.122 39.130 24.61 4.64 42.66 3.32
1665 1675 7.210873 ACTAAACACTAGATGGTTGCTATAGC 58.789 38.462 18.18 18.18 39.17 2.97
1668 1678 7.985752 GGTAACTAAACACTAGATGGTTGCTAT 59.014 37.037 0.00 0.00 39.17 2.97
1669 1679 7.038870 TGGTAACTAAACACTAGATGGTTGCTA 60.039 37.037 0.00 0.00 39.17 3.49
1670 1680 6.171213 GGTAACTAAACACTAGATGGTTGCT 58.829 40.000 0.00 0.00 39.17 3.91
1671 1681 5.935789 TGGTAACTAAACACTAGATGGTTGC 59.064 40.000 0.00 0.00 39.17 4.17
1672 1682 7.972832 TTGGTAACTAAACACTAGATGGTTG 57.027 36.000 0.00 0.00 39.17 3.77
1673 1683 7.664318 CCTTTGGTAACTAAACACTAGATGGTT 59.336 37.037 0.00 0.00 42.47 3.67
1674 1684 7.016858 TCCTTTGGTAACTAAACACTAGATGGT 59.983 37.037 0.00 0.00 37.61 3.55
1675 1685 7.391620 TCCTTTGGTAACTAAACACTAGATGG 58.608 38.462 0.00 0.00 37.61 3.51
1676 1686 8.842358 TTCCTTTGGTAACTAAACACTAGATG 57.158 34.615 0.00 0.00 37.61 2.90
1677 1687 9.856162 TTTTCCTTTGGTAACTAAACACTAGAT 57.144 29.630 0.00 0.00 37.61 1.98
1678 1688 9.683870 TTTTTCCTTTGGTAACTAAACACTAGA 57.316 29.630 0.00 0.00 37.61 2.43
1692 1702 9.588096 ACTTGATAGTTCTATTTTTCCTTTGGT 57.412 29.630 0.00 0.00 0.00 3.67
1693 1703 9.846248 CACTTGATAGTTCTATTTTTCCTTTGG 57.154 33.333 0.00 0.00 30.26 3.28
1753 1763 5.559799 GCACAGTTCTGCTAGTTCAAGAAAG 60.560 44.000 0.00 0.00 34.06 2.62
1754 1764 4.273480 GCACAGTTCTGCTAGTTCAAGAAA 59.727 41.667 0.00 0.00 34.06 2.52
1757 1767 3.133691 TGCACAGTTCTGCTAGTTCAAG 58.866 45.455 0.00 0.00 38.07 3.02
1758 1768 3.133691 CTGCACAGTTCTGCTAGTTCAA 58.866 45.455 0.00 0.00 38.07 2.69
1760 1770 2.760374 ACTGCACAGTTCTGCTAGTTC 58.240 47.619 0.00 0.00 38.83 3.01
1761 1771 2.918712 ACTGCACAGTTCTGCTAGTT 57.081 45.000 0.00 0.00 38.83 2.24
1771 1781 2.158559 TCACACAACAAACTGCACAGT 58.841 42.857 0.00 0.00 44.94 3.55
1772 1782 2.917701 TCACACAACAAACTGCACAG 57.082 45.000 0.00 0.00 0.00 3.66
1773 1783 3.944650 ACTATCACACAACAAACTGCACA 59.055 39.130 0.00 0.00 0.00 4.57
1774 1784 4.552166 ACTATCACACAACAAACTGCAC 57.448 40.909 0.00 0.00 0.00 4.57
1775 1785 5.119694 TGTACTATCACACAACAAACTGCA 58.880 37.500 0.00 0.00 0.00 4.41
1776 1786 5.666969 TGTACTATCACACAACAAACTGC 57.333 39.130 0.00 0.00 0.00 4.40
1777 1787 7.860613 TGATTGTACTATCACACAACAAACTG 58.139 34.615 14.83 0.00 37.47 3.16
1818 1828 2.225348 GCAAAACTTTTGCCTCCGC 58.775 52.632 23.40 2.73 39.38 5.54
2017 2027 3.593442 TCTTGTTGGGATTCACTTGGT 57.407 42.857 0.00 0.00 0.00 3.67
2060 2071 0.995024 CCTCTTGGATTGGGAGGTGT 59.005 55.000 0.00 0.00 41.04 4.16
2098 2109 3.499338 TCTGGTTGCTTGATGGATGTTT 58.501 40.909 0.00 0.00 0.00 2.83
2100 2111 2.306805 TCTCTGGTTGCTTGATGGATGT 59.693 45.455 0.00 0.00 0.00 3.06
2151 2162 2.061028 GCAAACAAAAGAAGATGGGCG 58.939 47.619 0.00 0.00 0.00 6.13
2625 2636 4.836125 GACAATGATGTGGTTGTGACTT 57.164 40.909 0.00 0.00 40.74 3.01


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

AutoCloner maintained by Alex Coulton.