Multiple sequence alignment - TraesCS7A01G565300

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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 TraesCS7A01G565300 chr7A 100.000 2393 0 0 1 2393 734916981 734919373 0.000000e+00 4420.0
1 TraesCS7A01G565300 chr7A 88.402 1026 95 8 1365 2375 734906688 734907704 0.000000e+00 1214.0
2 TraesCS7A01G565300 chr7A 80.769 78 13 2 88 164 360610092 360610168 2.570000e-05 60.2
3 TraesCS7A01G565300 chr7D 95.256 1602 67 5 797 2393 632834120 632835717 0.000000e+00 2529.0
4 TraesCS7A01G565300 chr7D 77.419 124 20 4 68 189 84345919 84346036 1.540000e-07 67.6
5 TraesCS7A01G565300 chr7D 81.429 70 11 2 122 189 104530116 104530185 3.320000e-04 56.5
6 TraesCS7A01G565300 chr7B 90.870 1391 94 19 806 2187 748343239 748341873 0.000000e+00 1834.0
7 TraesCS7A01G565300 chr7B 77.797 1180 217 29 1032 2189 749162803 749161647 0.000000e+00 686.0
8 TraesCS7A01G565300 chr7B 79.714 350 54 10 1473 1813 746414946 746414605 1.110000e-58 237.0
9 TraesCS7A01G565300 chr2D 90.682 601 53 3 26 623 551837371 551837971 0.000000e+00 797.0
10 TraesCS7A01G565300 chr2D 79.261 352 58 10 282 623 466718261 466717915 5.140000e-57 231.0
11 TraesCS7A01G565300 chr2D 76.923 455 60 28 207 624 179937377 179936931 1.440000e-52 217.0
12 TraesCS7A01G565300 chr2D 76.786 448 50 29 212 625 569954227 569953800 4.030000e-48 202.0
13 TraesCS7A01G565300 chr2D 77.165 127 21 4 68 192 629573172 629573052 1.540000e-07 67.6
14 TraesCS7A01G565300 chr5B 88.475 590 35 7 1 588 648610305 648610863 0.000000e+00 682.0
15 TraesCS7A01G565300 chr6A 78.131 1102 210 19 1025 2107 540829521 540828432 0.000000e+00 671.0
16 TraesCS7A01G565300 chr6A 76.744 516 81 32 114 623 318661720 318662202 3.950000e-63 252.0
17 TraesCS7A01G565300 chr6A 92.500 40 2 1 240 279 61210723 61210761 3.320000e-04 56.5
18 TraesCS7A01G565300 chr4D 76.430 437 67 22 202 618 421642014 421641594 1.120000e-48 204.0
19 TraesCS7A01G565300 chr2B 75.336 446 73 21 196 632 11178549 11178132 1.890000e-41 180.0
20 TraesCS7A01G565300 chr5D 84.756 164 21 4 195 356 270250718 270250879 6.850000e-36 161.0
21 TraesCS7A01G565300 chr5D 83.186 113 17 2 75 186 476040289 476040178 4.210000e-18 102.0
22 TraesCS7A01G565300 chr5D 77.852 149 23 5 26 172 550185183 550185323 1.520000e-12 84.2
23 TraesCS7A01G565300 chr1B 85.315 143 18 2 478 617 461300331 461300189 6.890000e-31 145.0
24 TraesCS7A01G565300 chr3D 93.220 59 4 0 559 617 28247524 28247466 1.180000e-13 87.9
25 TraesCS7A01G565300 chr1A 82.418 91 11 4 528 615 516170893 516170981 9.170000e-10 75.0
26 TraesCS7A01G565300 chr1A 92.500 40 2 1 240 279 9208579 9208541 3.320000e-04 56.5
27 TraesCS7A01G565300 chrUn 77.419 124 20 4 68 189 27019164 27019281 1.540000e-07 67.6
28 TraesCS7A01G565300 chr1D 82.609 69 10 2 212 279 70603492 70603425 2.570000e-05 60.2
29 TraesCS7A01G565300 chr1D 100.000 29 0 0 240 268 153810507 153810479 1.000000e-03 54.7


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 TraesCS7A01G565300 chr7A 734916981 734919373 2392 False 4420 4420 100.000 1 2393 1 chr7A.!!$F3 2392
1 TraesCS7A01G565300 chr7A 734906688 734907704 1016 False 1214 1214 88.402 1365 2375 1 chr7A.!!$F2 1010
2 TraesCS7A01G565300 chr7D 632834120 632835717 1597 False 2529 2529 95.256 797 2393 1 chr7D.!!$F3 1596
3 TraesCS7A01G565300 chr7B 748341873 748343239 1366 True 1834 1834 90.870 806 2187 1 chr7B.!!$R2 1381
4 TraesCS7A01G565300 chr7B 749161647 749162803 1156 True 686 686 77.797 1032 2189 1 chr7B.!!$R3 1157
5 TraesCS7A01G565300 chr2D 551837371 551837971 600 False 797 797 90.682 26 623 1 chr2D.!!$F1 597
6 TraesCS7A01G565300 chr5B 648610305 648610863 558 False 682 682 88.475 1 588 1 chr5B.!!$F1 587
7 TraesCS7A01G565300 chr6A 540828432 540829521 1089 True 671 671 78.131 1025 2107 1 chr6A.!!$R1 1082

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
32 33 0.542702 ACAAACTGGGGCCATTGGAG 60.543 55.0 6.95 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1400 1447 0.035739 TGTAACGCCCCTTGAACTCC 59.964 55.0 0.0 0.0 0.0 3.85 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
17 18 3.447040 GCTGCAAGGGAGCACAAA 58.553 55.556 4.80 0.00 40.11 2.83
18 19 1.006922 GCTGCAAGGGAGCACAAAC 60.007 57.895 4.80 0.00 40.11 2.93
19 20 1.458639 GCTGCAAGGGAGCACAAACT 61.459 55.000 4.80 0.00 40.11 2.66
23 24 1.153756 AAGGGAGCACAAACTGGGG 59.846 57.895 0.00 0.00 0.00 4.96
25 26 2.991540 GGAGCACAAACTGGGGCC 60.992 66.667 0.00 0.00 0.00 5.80
26 27 2.203480 GAGCACAAACTGGGGCCA 60.203 61.111 4.39 0.00 0.00 5.36
28 29 1.152269 AGCACAAACTGGGGCCATT 60.152 52.632 4.39 0.00 0.00 3.16
29 30 1.004679 GCACAAACTGGGGCCATTG 60.005 57.895 4.39 7.44 0.00 2.82
30 31 1.672898 CACAAACTGGGGCCATTGG 59.327 57.895 4.39 0.00 0.00 3.16
31 32 0.831288 CACAAACTGGGGCCATTGGA 60.831 55.000 6.95 0.00 0.00 3.53
32 33 0.542702 ACAAACTGGGGCCATTGGAG 60.543 55.000 6.95 0.00 0.00 3.86
33 34 1.610379 AAACTGGGGCCATTGGAGC 60.610 57.895 6.95 0.00 0.00 4.70
34 35 2.097978 AAACTGGGGCCATTGGAGCT 62.098 55.000 6.95 0.00 0.00 4.09
37 38 4.883354 GGGGCCATTGGAGCTCCG 62.883 72.222 27.43 14.31 42.12 4.63
40 41 4.802051 GCCATTGGAGCTCCGCCA 62.802 66.667 27.43 14.57 39.43 5.69
41 42 2.045045 CCATTGGAGCTCCGCCAA 60.045 61.111 27.43 17.45 46.28 4.52
43 44 2.117156 CATTGGAGCTCCGCCAAGG 61.117 63.158 27.43 14.98 45.53 3.61
45 46 2.142292 ATTGGAGCTCCGCCAAGGTT 62.142 55.000 27.43 0.00 45.53 3.50
46 47 2.747855 GGAGCTCCGCCAAGGTTG 60.748 66.667 19.06 0.00 41.99 3.77
47 48 3.435186 GAGCTCCGCCAAGGTTGC 61.435 66.667 0.87 0.00 41.99 4.17
49 50 3.294493 GCTCCGCCAAGGTTGCAA 61.294 61.111 0.00 0.00 41.99 4.08
50 51 2.639327 GCTCCGCCAAGGTTGCAAT 61.639 57.895 0.59 0.00 41.99 3.56
51 52 1.213537 CTCCGCCAAGGTTGCAATG 59.786 57.895 0.59 0.00 41.99 2.82
73 74 1.285641 CTCCACCGCGTTTGCAATT 59.714 52.632 4.92 0.00 42.97 2.32
85 108 1.588824 TTGCAATTGAGCTCCGCCTG 61.589 55.000 12.15 4.61 34.99 4.85
124 148 3.009140 CAGCTACAATGGAGCGCG 58.991 61.111 12.36 0.00 44.98 6.86
125 149 2.892425 AGCTACAATGGAGCGCGC 60.892 61.111 26.66 26.66 44.98 6.86
127 151 2.202932 CTACAATGGAGCGCGCCT 60.203 61.111 30.49 15.76 0.00 5.52
138 162 2.203056 CGCGCCTGGGATCATTGA 60.203 61.111 0.00 0.00 0.00 2.57
144 168 1.978454 CCTGGGATCATTGAAGCTCC 58.022 55.000 0.00 0.00 0.00 4.70
173 197 4.537433 AATGGAGCTCCGCCTCGC 62.537 66.667 27.43 2.45 39.43 5.03
207 231 1.977854 TCACCACAGCTACAATGGAGT 59.022 47.619 11.36 0.00 36.94 3.85
229 253 3.043999 GCCGGGGCTGTAATGGAGT 62.044 63.158 2.18 0.00 38.26 3.85
230 254 1.607612 CCGGGGCTGTAATGGAGTT 59.392 57.895 0.00 0.00 0.00 3.01
233 257 0.919710 GGGGCTGTAATGGAGTTCCT 59.080 55.000 0.00 0.00 36.82 3.36
371 396 1.451207 CCCCGACGATGCAATGGAA 60.451 57.895 0.00 0.00 0.00 3.53
377 402 1.663643 GACGATGCAATGGAACGCTAA 59.336 47.619 4.16 0.00 0.00 3.09
476 502 1.077212 ACAGATGTGCCATGGAGCC 60.077 57.895 18.40 1.96 0.00 4.70
525 552 0.968393 AGGAAGACGTGAGAGGGCTC 60.968 60.000 0.00 0.00 41.67 4.70
552 579 2.592287 GACGAACGGCCACCCAAA 60.592 61.111 2.24 0.00 0.00 3.28
555 582 2.597510 GAACGGCCACCCAAAGCT 60.598 61.111 2.24 0.00 0.00 3.74
623 650 2.009042 GCTGATTTGTAGCAGTCGCCT 61.009 52.381 0.00 0.00 39.95 5.52
624 651 2.350522 CTGATTTGTAGCAGTCGCCTT 58.649 47.619 0.00 0.00 39.83 4.35
625 652 2.076100 TGATTTGTAGCAGTCGCCTTG 58.924 47.619 0.00 0.00 39.83 3.61
626 653 2.076863 GATTTGTAGCAGTCGCCTTGT 58.923 47.619 0.00 0.00 39.83 3.16
627 654 1.961793 TTTGTAGCAGTCGCCTTGTT 58.038 45.000 0.00 0.00 39.83 2.83
628 655 2.823924 TTGTAGCAGTCGCCTTGTTA 57.176 45.000 0.00 0.00 39.83 2.41
629 656 3.328382 TTGTAGCAGTCGCCTTGTTAT 57.672 42.857 0.00 0.00 39.83 1.89
630 657 3.328382 TGTAGCAGTCGCCTTGTTATT 57.672 42.857 0.00 0.00 39.83 1.40
631 658 4.459390 TGTAGCAGTCGCCTTGTTATTA 57.541 40.909 0.00 0.00 39.83 0.98
632 659 5.018539 TGTAGCAGTCGCCTTGTTATTAT 57.981 39.130 0.00 0.00 39.83 1.28
633 660 4.808895 TGTAGCAGTCGCCTTGTTATTATG 59.191 41.667 0.00 0.00 39.83 1.90
634 661 3.206150 AGCAGTCGCCTTGTTATTATGG 58.794 45.455 0.00 0.00 39.83 2.74
635 662 2.943033 GCAGTCGCCTTGTTATTATGGT 59.057 45.455 0.00 0.00 0.00 3.55
636 663 3.377172 GCAGTCGCCTTGTTATTATGGTT 59.623 43.478 0.00 0.00 0.00 3.67
637 664 4.495844 GCAGTCGCCTTGTTATTATGGTTC 60.496 45.833 0.00 0.00 0.00 3.62
638 665 4.634004 CAGTCGCCTTGTTATTATGGTTCA 59.366 41.667 0.00 0.00 0.00 3.18
639 666 5.123186 CAGTCGCCTTGTTATTATGGTTCAA 59.877 40.000 0.00 0.00 0.00 2.69
640 667 5.123344 AGTCGCCTTGTTATTATGGTTCAAC 59.877 40.000 0.00 0.00 0.00 3.18
641 668 5.004448 TCGCCTTGTTATTATGGTTCAACA 58.996 37.500 0.00 0.00 0.00 3.33
642 669 5.123186 TCGCCTTGTTATTATGGTTCAACAG 59.877 40.000 0.00 0.00 32.86 3.16
643 670 5.123186 CGCCTTGTTATTATGGTTCAACAGA 59.877 40.000 0.00 0.00 32.86 3.41
644 671 6.348950 CGCCTTGTTATTATGGTTCAACAGAA 60.349 38.462 0.00 0.00 32.86 3.02
645 672 6.806739 GCCTTGTTATTATGGTTCAACAGAAC 59.193 38.462 0.00 0.00 40.68 3.01
646 673 7.523052 GCCTTGTTATTATGGTTCAACAGAACA 60.523 37.037 10.16 0.00 42.66 3.18
647 674 8.023128 CCTTGTTATTATGGTTCAACAGAACAG 58.977 37.037 10.16 0.00 42.66 3.16
648 675 6.908825 TGTTATTATGGTTCAACAGAACAGC 58.091 36.000 10.16 0.00 42.66 4.40
649 676 6.714810 TGTTATTATGGTTCAACAGAACAGCT 59.285 34.615 10.16 0.00 42.66 4.24
650 677 7.880713 TGTTATTATGGTTCAACAGAACAGCTA 59.119 33.333 10.16 0.00 42.66 3.32
651 678 8.893727 GTTATTATGGTTCAACAGAACAGCTAT 58.106 33.333 10.16 2.62 42.66 2.97
652 679 6.985188 TTATGGTTCAACAGAACAGCTATC 57.015 37.500 10.16 0.00 42.66 2.08
653 680 4.623932 TGGTTCAACAGAACAGCTATCT 57.376 40.909 10.16 0.00 42.66 1.98
654 681 5.738619 TGGTTCAACAGAACAGCTATCTA 57.261 39.130 10.16 0.00 42.66 1.98
655 682 5.724328 TGGTTCAACAGAACAGCTATCTAG 58.276 41.667 10.16 0.00 42.66 2.43
656 683 4.568760 GGTTCAACAGAACAGCTATCTAGC 59.431 45.833 10.16 0.81 42.66 3.42
705 732 7.916914 TGAGATATATGCATGGTGAAATCAG 57.083 36.000 10.16 0.00 0.00 2.90
706 733 7.682628 TGAGATATATGCATGGTGAAATCAGA 58.317 34.615 10.16 0.00 0.00 3.27
707 734 8.158789 TGAGATATATGCATGGTGAAATCAGAA 58.841 33.333 10.16 0.00 0.00 3.02
708 735 8.563123 AGATATATGCATGGTGAAATCAGAAG 57.437 34.615 10.16 0.00 0.00 2.85
709 736 8.380867 AGATATATGCATGGTGAAATCAGAAGA 58.619 33.333 10.16 0.00 0.00 2.87
710 737 9.175312 GATATATGCATGGTGAAATCAGAAGAT 57.825 33.333 10.16 0.00 35.53 2.40
711 738 7.834881 ATATGCATGGTGAAATCAGAAGATT 57.165 32.000 10.16 0.00 46.20 2.40
712 739 8.929260 ATATGCATGGTGAAATCAGAAGATTA 57.071 30.769 10.16 0.00 43.52 1.75
713 740 7.649533 ATGCATGGTGAAATCAGAAGATTAA 57.350 32.000 0.00 0.00 43.52 1.40
714 741 7.649533 TGCATGGTGAAATCAGAAGATTAAT 57.350 32.000 0.00 0.00 43.52 1.40
715 742 8.070034 TGCATGGTGAAATCAGAAGATTAATT 57.930 30.769 0.00 0.00 43.52 1.40
716 743 7.977293 TGCATGGTGAAATCAGAAGATTAATTG 59.023 33.333 0.00 0.00 43.52 2.32
717 744 7.042925 GCATGGTGAAATCAGAAGATTAATTGC 60.043 37.037 0.00 0.00 43.52 3.56
718 745 6.866480 TGGTGAAATCAGAAGATTAATTGCC 58.134 36.000 0.00 0.00 43.52 4.52
719 746 6.436847 TGGTGAAATCAGAAGATTAATTGCCA 59.563 34.615 0.00 0.00 43.52 4.92
720 747 7.124599 TGGTGAAATCAGAAGATTAATTGCCAT 59.875 33.333 0.00 0.00 43.52 4.40
721 748 8.632679 GGTGAAATCAGAAGATTAATTGCCATA 58.367 33.333 0.00 0.00 43.52 2.74
722 749 9.455847 GTGAAATCAGAAGATTAATTGCCATAC 57.544 33.333 0.00 0.00 43.52 2.39
723 750 9.187996 TGAAATCAGAAGATTAATTGCCATACA 57.812 29.630 0.00 0.00 43.52 2.29
736 763 4.357325 TTGCCATACAATACCAAATGGGT 58.643 39.130 4.17 0.00 43.17 4.51
737 764 4.161189 TTGCCATACAATACCAAATGGGTG 59.839 41.667 4.17 1.86 41.53 4.61
738 765 7.365462 TTGCCATACAATACCAAATGGGTGC 62.365 44.000 4.17 0.00 41.53 5.01
750 777 6.814506 CCAAATGGGTGCAATTTTATTTCA 57.185 33.333 0.00 0.00 0.00 2.69
751 778 7.393841 CCAAATGGGTGCAATTTTATTTCAT 57.606 32.000 0.00 0.00 0.00 2.57
752 779 7.474190 CCAAATGGGTGCAATTTTATTTCATC 58.526 34.615 0.00 0.00 0.00 2.92
753 780 7.337436 CCAAATGGGTGCAATTTTATTTCATCT 59.663 33.333 0.00 0.00 0.00 2.90
754 781 8.392612 CAAATGGGTGCAATTTTATTTCATCTC 58.607 33.333 0.00 0.00 0.00 2.75
755 782 5.976458 TGGGTGCAATTTTATTTCATCTCC 58.024 37.500 0.00 0.00 0.00 3.71
756 783 5.483231 TGGGTGCAATTTTATTTCATCTCCA 59.517 36.000 0.00 0.00 0.00 3.86
757 784 6.013898 TGGGTGCAATTTTATTTCATCTCCAA 60.014 34.615 0.00 0.00 0.00 3.53
758 785 7.049754 GGGTGCAATTTTATTTCATCTCCAAT 58.950 34.615 0.00 0.00 0.00 3.16
759 786 7.553760 GGGTGCAATTTTATTTCATCTCCAATT 59.446 33.333 0.00 0.00 0.00 2.32
760 787 8.949177 GGTGCAATTTTATTTCATCTCCAATTT 58.051 29.630 0.00 0.00 0.00 1.82
761 788 9.763465 GTGCAATTTTATTTCATCTCCAATTTG 57.237 29.630 0.00 0.00 0.00 2.32
762 789 9.504708 TGCAATTTTATTTCATCTCCAATTTGT 57.495 25.926 0.00 0.00 0.00 2.83
763 790 9.763465 GCAATTTTATTTCATCTCCAATTTGTG 57.237 29.630 0.00 0.00 0.00 3.33
767 794 7.887996 TTATTTCATCTCCAATTTGTGTTGC 57.112 32.000 0.00 0.00 0.00 4.17
768 795 4.933505 TTCATCTCCAATTTGTGTTGCA 57.066 36.364 0.00 0.00 0.00 4.08
769 796 4.933505 TCATCTCCAATTTGTGTTGCAA 57.066 36.364 0.00 0.00 34.87 4.08
770 797 5.471556 TCATCTCCAATTTGTGTTGCAAT 57.528 34.783 0.59 0.00 36.89 3.56
771 798 5.472148 TCATCTCCAATTTGTGTTGCAATC 58.528 37.500 0.59 0.00 36.89 2.67
772 799 5.244402 TCATCTCCAATTTGTGTTGCAATCT 59.756 36.000 0.59 0.00 36.89 2.40
773 800 5.534207 TCTCCAATTTGTGTTGCAATCTT 57.466 34.783 0.59 0.00 36.89 2.40
774 801 6.647334 TCTCCAATTTGTGTTGCAATCTTA 57.353 33.333 0.59 0.00 36.89 2.10
775 802 7.230849 TCTCCAATTTGTGTTGCAATCTTAT 57.769 32.000 0.59 0.00 36.89 1.73
776 803 7.669427 TCTCCAATTTGTGTTGCAATCTTATT 58.331 30.769 0.59 0.00 36.89 1.40
777 804 8.149647 TCTCCAATTTGTGTTGCAATCTTATTT 58.850 29.630 0.59 0.00 36.89 1.40
778 805 8.309163 TCCAATTTGTGTTGCAATCTTATTTC 57.691 30.769 0.59 0.00 36.89 2.17
779 806 7.387397 TCCAATTTGTGTTGCAATCTTATTTCC 59.613 33.333 0.59 0.00 36.89 3.13
780 807 7.172875 CCAATTTGTGTTGCAATCTTATTTCCA 59.827 33.333 0.59 0.00 36.89 3.53
781 808 8.723311 CAATTTGTGTTGCAATCTTATTTCCAT 58.277 29.630 0.59 0.00 36.89 3.41
782 809 8.851541 ATTTGTGTTGCAATCTTATTTCCATT 57.148 26.923 0.59 0.00 36.89 3.16
783 810 7.655236 TTGTGTTGCAATCTTATTTCCATTG 57.345 32.000 0.59 0.00 31.07 2.82
784 811 6.757237 TGTGTTGCAATCTTATTTCCATTGT 58.243 32.000 0.59 0.00 31.29 2.71
785 812 7.215789 TGTGTTGCAATCTTATTTCCATTGTT 58.784 30.769 0.59 0.00 31.29 2.83
786 813 7.714377 TGTGTTGCAATCTTATTTCCATTGTTT 59.286 29.630 0.59 0.00 31.29 2.83
787 814 8.558700 GTGTTGCAATCTTATTTCCATTGTTTT 58.441 29.630 0.59 0.00 31.29 2.43
788 815 9.118300 TGTTGCAATCTTATTTCCATTGTTTTT 57.882 25.926 0.59 0.00 31.29 1.94
791 818 9.434420 TGCAATCTTATTTCCATTGTTTTTAGG 57.566 29.630 0.00 0.00 31.29 2.69
792 819 8.882736 GCAATCTTATTTCCATTGTTTTTAGGG 58.117 33.333 0.00 0.00 31.29 3.53
793 820 9.382275 CAATCTTATTTCCATTGTTTTTAGGGG 57.618 33.333 0.00 0.00 0.00 4.79
794 821 8.679344 ATCTTATTTCCATTGTTTTTAGGGGT 57.321 30.769 0.00 0.00 0.00 4.95
795 822 9.777008 ATCTTATTTCCATTGTTTTTAGGGGTA 57.223 29.630 0.00 0.00 0.00 3.69
803 830 7.459444 TCCATTGTTTTTAGGGGTATTTCCATT 59.541 33.333 0.00 0.00 38.11 3.16
804 831 7.552330 CCATTGTTTTTAGGGGTATTTCCATTG 59.448 37.037 0.00 0.00 38.11 2.82
830 857 2.671963 GCAGGGGACGAACCAACC 60.672 66.667 0.00 0.00 41.20 3.77
855 885 1.595093 GGTCCGTGAAGGCCCAAATG 61.595 60.000 0.00 0.00 38.12 2.32
856 886 1.976474 TCCGTGAAGGCCCAAATGC 60.976 57.895 0.00 0.00 40.77 3.56
860 890 2.285024 TGAAGGCCCAAATGCTGCC 61.285 57.895 0.00 4.54 45.70 4.85
863 893 4.440127 GGCCCAAATGCTGCCGTG 62.440 66.667 0.00 0.00 35.08 4.94
893 923 1.610886 GCGTAGGAGCAAAGGAAACCT 60.611 52.381 0.00 0.00 37.05 3.50
901 931 3.400255 AGCAAAGGAAACCTACTTCGAC 58.600 45.455 0.00 0.00 31.13 4.20
953 983 2.031163 GATCCGCCTCCAATCCCG 59.969 66.667 0.00 0.00 0.00 5.14
961 991 1.301244 CTCCAATCCCGGATCAGCG 60.301 63.158 0.73 0.00 33.56 5.18
978 1008 2.190578 GCCTCCTTCCCCACATCG 59.809 66.667 0.00 0.00 0.00 3.84
1007 1037 1.091771 CGGCCGTGAGCAATGATTCT 61.092 55.000 19.50 0.00 46.50 2.40
1217 1247 1.230324 GCCTTCTTACATCATCCCGC 58.770 55.000 0.00 0.00 0.00 6.13
1400 1447 3.051606 CATCGTTTGCTAATTCCACCG 57.948 47.619 0.00 0.00 0.00 4.94
1517 1564 1.031029 TCTTGCTGCTTGTGTGTGCA 61.031 50.000 0.00 0.00 37.63 4.57
1778 1825 4.847278 ATCCAGGCAGAGGATGGT 57.153 55.556 5.50 0.00 44.04 3.55
1931 1978 0.037232 CTCGGGTCAAGGGACAGAAC 60.037 60.000 0.00 0.00 46.17 3.01
1950 1997 7.156876 CAGAACACCTGGCTGAAATTTATAA 57.843 36.000 0.00 0.00 39.23 0.98
2108 2162 4.130118 GTTTCTATGCACCAGGTGATAGG 58.870 47.826 24.96 9.92 35.23 2.57
2159 2220 9.679661 TGGTCTAATCTTGCTATATTTTGTTCA 57.320 29.630 0.00 0.00 0.00 3.18
2366 2431 9.645059 TGTTGTTGTTCAGAAATTGTTTAATCA 57.355 25.926 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.943265 AGCTCCAATGGCCCCAGT 60.943 61.111 0.00 0.00 0.00 4.00
18 19 2.123982 GAGCTCCAATGGCCCCAG 60.124 66.667 0.87 0.00 0.00 4.45
19 20 3.743017 GGAGCTCCAATGGCCCCA 61.743 66.667 28.43 0.00 35.64 4.96
33 34 1.213537 CATTGCAACCTTGGCGGAG 59.786 57.895 0.00 0.00 36.31 4.63
34 35 2.274645 CCATTGCAACCTTGGCGGA 61.275 57.895 0.00 0.00 36.31 5.54
36 37 1.213537 CTCCATTGCAACCTTGGCG 59.786 57.895 11.96 3.21 0.00 5.69
37 38 1.079612 GCTCCATTGCAACCTTGGC 60.080 57.895 11.96 5.32 0.00 4.52
39 40 0.529378 GGAGCTCCATTGCAACCTTG 59.471 55.000 28.43 0.00 35.64 3.61
40 41 0.112995 TGGAGCTCCATTGCAACCTT 59.887 50.000 32.00 0.00 42.01 3.50
41 42 1.769665 TGGAGCTCCATTGCAACCT 59.230 52.632 32.00 0.00 42.01 3.50
50 51 3.936203 AAACGCGGTGGAGCTCCA 61.936 61.111 32.00 32.00 45.30 3.86
51 52 3.423154 CAAACGCGGTGGAGCTCC 61.423 66.667 26.78 26.78 34.40 4.70
85 108 0.244721 GTGAAGCTCCATTGCAACCC 59.755 55.000 0.00 0.00 34.99 4.11
124 148 1.316651 GAGCTTCAATGATCCCAGGC 58.683 55.000 0.00 0.00 0.00 4.85
125 149 1.813092 CGGAGCTTCAATGATCCCAGG 60.813 57.143 0.00 0.00 39.17 4.45
127 151 3.786656 CGGAGCTTCAATGATCCCA 57.213 52.632 0.00 0.00 39.17 4.37
173 197 1.068055 GTGGTGAAGCTCCATTGCAAG 60.068 52.381 4.94 0.00 37.30 4.01
229 253 0.250684 TCATTGCAGCCACGAAGGAA 60.251 50.000 2.86 0.00 41.22 3.36
230 254 0.250684 TTCATTGCAGCCACGAAGGA 60.251 50.000 2.86 0.00 41.22 3.36
233 257 0.890542 AGCTTCATTGCAGCCACGAA 60.891 50.000 4.61 0.00 38.09 3.85
352 376 2.124736 CCATTGCATCGTCGGGGT 60.125 61.111 0.00 0.00 0.00 4.95
371 396 2.186903 CTGCATCCCCGTTAGCGT 59.813 61.111 0.00 0.00 36.15 5.07
476 502 1.370414 CTTCCACCAAAGCAACGCG 60.370 57.895 3.53 3.53 0.00 6.01
525 552 1.569493 CCGTTCGTCCAAGCAACAG 59.431 57.895 0.00 0.00 0.00 3.16
552 579 0.030369 CGTAGCCGTCCGATTTAGCT 59.970 55.000 0.00 0.00 37.58 3.32
630 657 7.898710 GCTAGATAGCTGTTCTGTTGAACCATA 60.899 40.741 10.39 0.00 43.96 2.74
631 658 7.128120 GCTAGATAGCTGTTCTGTTGAACCAT 61.128 42.308 10.39 0.00 43.96 3.55
632 659 5.854745 GCTAGATAGCTGTTCTGTTGAACCA 60.855 44.000 10.39 0.00 43.96 3.67
633 660 4.568760 GCTAGATAGCTGTTCTGTTGAACC 59.431 45.833 10.39 0.00 43.96 3.62
634 661 5.710613 GCTAGATAGCTGTTCTGTTGAAC 57.289 43.478 10.39 2.35 45.62 3.18
679 706 9.609346 CTGATTTCACCATGCATATATCTCATA 57.391 33.333 0.00 0.00 0.00 2.15
680 707 8.326529 TCTGATTTCACCATGCATATATCTCAT 58.673 33.333 0.00 0.00 0.00 2.90
681 708 7.682628 TCTGATTTCACCATGCATATATCTCA 58.317 34.615 0.00 0.00 0.00 3.27
682 709 8.557592 TTCTGATTTCACCATGCATATATCTC 57.442 34.615 0.00 0.00 0.00 2.75
683 710 8.380867 TCTTCTGATTTCACCATGCATATATCT 58.619 33.333 0.00 0.00 0.00 1.98
684 711 8.557592 TCTTCTGATTTCACCATGCATATATC 57.442 34.615 0.00 0.00 0.00 1.63
685 712 9.529823 AATCTTCTGATTTCACCATGCATATAT 57.470 29.630 0.00 0.00 39.68 0.86
686 713 8.929260 AATCTTCTGATTTCACCATGCATATA 57.071 30.769 0.00 0.00 39.68 0.86
687 714 7.834881 AATCTTCTGATTTCACCATGCATAT 57.165 32.000 0.00 0.00 39.68 1.78
688 715 8.750515 TTAATCTTCTGATTTCACCATGCATA 57.249 30.769 0.00 0.00 42.37 3.14
689 716 7.649533 TTAATCTTCTGATTTCACCATGCAT 57.350 32.000 0.00 0.00 42.37 3.96
690 717 7.649533 ATTAATCTTCTGATTTCACCATGCA 57.350 32.000 0.00 0.00 42.37 3.96
691 718 7.042925 GCAATTAATCTTCTGATTTCACCATGC 60.043 37.037 0.00 0.00 42.37 4.06
692 719 7.437267 GGCAATTAATCTTCTGATTTCACCATG 59.563 37.037 0.00 0.00 42.37 3.66
693 720 7.124599 TGGCAATTAATCTTCTGATTTCACCAT 59.875 33.333 0.00 0.00 42.37 3.55
694 721 6.436847 TGGCAATTAATCTTCTGATTTCACCA 59.563 34.615 0.00 0.00 42.37 4.17
695 722 6.866480 TGGCAATTAATCTTCTGATTTCACC 58.134 36.000 0.00 0.00 42.37 4.02
696 723 9.455847 GTATGGCAATTAATCTTCTGATTTCAC 57.544 33.333 0.00 0.00 42.37 3.18
697 724 9.187996 TGTATGGCAATTAATCTTCTGATTTCA 57.812 29.630 0.00 0.00 42.37 2.69
702 729 9.066892 GGTATTGTATGGCAATTAATCTTCTGA 57.933 33.333 0.00 0.00 44.82 3.27
703 730 8.849168 TGGTATTGTATGGCAATTAATCTTCTG 58.151 33.333 0.00 0.00 44.82 3.02
704 731 8.995027 TGGTATTGTATGGCAATTAATCTTCT 57.005 30.769 0.00 0.00 44.82 2.85
707 734 9.985730 CATTTGGTATTGTATGGCAATTAATCT 57.014 29.630 0.00 0.00 44.82 2.40
708 735 9.206870 CCATTTGGTATTGTATGGCAATTAATC 57.793 33.333 0.00 0.00 44.82 1.75
709 736 8.156165 CCCATTTGGTATTGTATGGCAATTAAT 58.844 33.333 0.00 0.00 44.82 1.40
710 737 7.504403 CCCATTTGGTATTGTATGGCAATTAA 58.496 34.615 0.00 0.00 44.82 1.40
711 738 7.060383 CCCATTTGGTATTGTATGGCAATTA 57.940 36.000 0.00 0.00 44.82 1.40
712 739 5.927819 CCCATTTGGTATTGTATGGCAATT 58.072 37.500 0.00 0.00 44.82 2.32
727 754 6.814506 TGAAATAAAATTGCACCCATTTGG 57.185 33.333 0.00 0.00 41.37 3.28
728 755 8.271312 AGATGAAATAAAATTGCACCCATTTG 57.729 30.769 0.00 0.00 0.00 2.32
729 756 7.553760 GGAGATGAAATAAAATTGCACCCATTT 59.446 33.333 0.00 0.00 0.00 2.32
730 757 7.049754 GGAGATGAAATAAAATTGCACCCATT 58.950 34.615 0.00 0.00 0.00 3.16
731 758 6.156602 TGGAGATGAAATAAAATTGCACCCAT 59.843 34.615 0.00 0.00 0.00 4.00
732 759 5.483231 TGGAGATGAAATAAAATTGCACCCA 59.517 36.000 0.00 0.00 0.00 4.51
733 760 5.976458 TGGAGATGAAATAAAATTGCACCC 58.024 37.500 0.00 0.00 0.00 4.61
734 761 8.496707 AATTGGAGATGAAATAAAATTGCACC 57.503 30.769 0.00 0.00 0.00 5.01
735 762 9.763465 CAAATTGGAGATGAAATAAAATTGCAC 57.237 29.630 0.00 0.00 0.00 4.57
736 763 9.504708 ACAAATTGGAGATGAAATAAAATTGCA 57.495 25.926 0.00 0.00 0.00 4.08
737 764 9.763465 CACAAATTGGAGATGAAATAAAATTGC 57.237 29.630 0.00 0.00 0.00 3.56
741 768 8.772705 GCAACACAAATTGGAGATGAAATAAAA 58.227 29.630 0.00 0.00 0.00 1.52
742 769 7.930325 TGCAACACAAATTGGAGATGAAATAAA 59.070 29.630 0.00 0.00 0.00 1.40
743 770 7.440198 TGCAACACAAATTGGAGATGAAATAA 58.560 30.769 0.00 0.00 0.00 1.40
744 771 6.990798 TGCAACACAAATTGGAGATGAAATA 58.009 32.000 0.00 0.00 0.00 1.40
745 772 5.856156 TGCAACACAAATTGGAGATGAAAT 58.144 33.333 0.00 0.00 0.00 2.17
746 773 5.273674 TGCAACACAAATTGGAGATGAAA 57.726 34.783 0.00 0.00 0.00 2.69
747 774 4.933505 TGCAACACAAATTGGAGATGAA 57.066 36.364 0.00 0.00 0.00 2.57
748 775 4.933505 TTGCAACACAAATTGGAGATGA 57.066 36.364 0.00 0.00 34.56 2.92
749 776 5.475719 AGATTGCAACACAAATTGGAGATG 58.524 37.500 0.00 0.00 42.86 2.90
750 777 5.733620 AGATTGCAACACAAATTGGAGAT 57.266 34.783 0.00 0.00 42.86 2.75
751 778 5.534207 AAGATTGCAACACAAATTGGAGA 57.466 34.783 0.00 0.00 42.86 3.71
752 779 7.894376 AATAAGATTGCAACACAAATTGGAG 57.106 32.000 0.00 0.00 42.86 3.86
753 780 7.387397 GGAAATAAGATTGCAACACAAATTGGA 59.613 33.333 0.00 0.00 42.86 3.53
754 781 7.172875 TGGAAATAAGATTGCAACACAAATTGG 59.827 33.333 0.00 0.00 42.86 3.16
755 782 8.085720 TGGAAATAAGATTGCAACACAAATTG 57.914 30.769 0.00 0.00 42.86 2.32
756 783 8.851541 ATGGAAATAAGATTGCAACACAAATT 57.148 26.923 0.00 0.97 42.86 1.82
757 784 8.723311 CAATGGAAATAAGATTGCAACACAAAT 58.277 29.630 0.00 0.00 42.86 2.32
758 785 7.714377 ACAATGGAAATAAGATTGCAACACAAA 59.286 29.630 0.00 0.00 42.86 2.83
759 786 7.215789 ACAATGGAAATAAGATTGCAACACAA 58.784 30.769 0.00 0.00 44.01 3.33
760 787 6.757237 ACAATGGAAATAAGATTGCAACACA 58.243 32.000 0.00 0.00 34.21 3.72
761 788 7.656707 AACAATGGAAATAAGATTGCAACAC 57.343 32.000 0.00 0.00 34.21 3.32
762 789 8.674263 AAAACAATGGAAATAAGATTGCAACA 57.326 26.923 0.00 0.00 34.21 3.33
765 792 9.434420 CCTAAAAACAATGGAAATAAGATTGCA 57.566 29.630 0.00 0.00 35.04 4.08
766 793 8.882736 CCCTAAAAACAATGGAAATAAGATTGC 58.117 33.333 0.00 0.00 31.45 3.56
767 794 9.382275 CCCCTAAAAACAATGGAAATAAGATTG 57.618 33.333 0.00 0.00 33.99 2.67
768 795 9.111519 ACCCCTAAAAACAATGGAAATAAGATT 57.888 29.630 0.00 0.00 0.00 2.40
769 796 8.679344 ACCCCTAAAAACAATGGAAATAAGAT 57.321 30.769 0.00 0.00 0.00 2.40
770 797 9.777008 ATACCCCTAAAAACAATGGAAATAAGA 57.223 29.630 0.00 0.00 0.00 2.10
774 801 8.325787 GGAAATACCCCTAAAAACAATGGAAAT 58.674 33.333 0.00 0.00 0.00 2.17
775 802 7.292591 TGGAAATACCCCTAAAAACAATGGAAA 59.707 33.333 0.00 0.00 38.00 3.13
776 803 6.787957 TGGAAATACCCCTAAAAACAATGGAA 59.212 34.615 0.00 0.00 38.00 3.53
777 804 6.323737 TGGAAATACCCCTAAAAACAATGGA 58.676 36.000 0.00 0.00 38.00 3.41
778 805 6.613153 TGGAAATACCCCTAAAAACAATGG 57.387 37.500 0.00 0.00 38.00 3.16
779 806 8.100164 ACAATGGAAATACCCCTAAAAACAATG 58.900 33.333 0.00 0.00 38.00 2.82
780 807 8.213489 ACAATGGAAATACCCCTAAAAACAAT 57.787 30.769 0.00 0.00 38.00 2.71
781 808 7.619512 ACAATGGAAATACCCCTAAAAACAA 57.380 32.000 0.00 0.00 38.00 2.83
782 809 7.619512 AACAATGGAAATACCCCTAAAAACA 57.380 32.000 0.00 0.00 38.00 2.83
783 810 9.647797 CTTAACAATGGAAATACCCCTAAAAAC 57.352 33.333 0.00 0.00 38.00 2.43
784 811 8.315482 GCTTAACAATGGAAATACCCCTAAAAA 58.685 33.333 0.00 0.00 38.00 1.94
785 812 7.093245 GGCTTAACAATGGAAATACCCCTAAAA 60.093 37.037 0.00 0.00 38.00 1.52
786 813 6.381707 GGCTTAACAATGGAAATACCCCTAAA 59.618 38.462 0.00 0.00 38.00 1.85
787 814 5.894964 GGCTTAACAATGGAAATACCCCTAA 59.105 40.000 0.00 0.00 38.00 2.69
788 815 5.044030 TGGCTTAACAATGGAAATACCCCTA 60.044 40.000 0.00 0.00 38.00 3.53
789 816 4.264623 TGGCTTAACAATGGAAATACCCCT 60.265 41.667 0.00 0.00 38.00 4.79
790 817 4.027437 TGGCTTAACAATGGAAATACCCC 58.973 43.478 0.00 0.00 38.00 4.95
791 818 4.441495 GCTGGCTTAACAATGGAAATACCC 60.441 45.833 0.00 0.00 38.00 3.69
792 819 4.159506 TGCTGGCTTAACAATGGAAATACC 59.840 41.667 0.00 0.00 39.54 2.73
793 820 5.323371 TGCTGGCTTAACAATGGAAATAC 57.677 39.130 0.00 0.00 0.00 1.89
794 821 4.402155 CCTGCTGGCTTAACAATGGAAATA 59.598 41.667 0.00 0.00 0.00 1.40
795 822 3.196254 CCTGCTGGCTTAACAATGGAAAT 59.804 43.478 0.00 0.00 0.00 2.17
803 830 1.378762 GTCCCCTGCTGGCTTAACA 59.621 57.895 3.63 0.00 0.00 2.41
804 831 1.745489 CGTCCCCTGCTGGCTTAAC 60.745 63.158 3.63 0.00 0.00 2.01
843 870 2.580815 GGCAGCATTTGGGCCTTC 59.419 61.111 4.53 0.00 44.32 3.46
863 893 2.512286 TCCTACGCATGCAGCAGC 60.512 61.111 19.57 3.97 46.13 5.25
864 894 2.532256 GCTCCTACGCATGCAGCAG 61.532 63.158 19.57 10.64 46.13 4.24
877 907 3.557264 CGAAGTAGGTTTCCTTTGCTCCT 60.557 47.826 0.00 0.00 34.61 3.69
878 908 2.742589 CGAAGTAGGTTTCCTTTGCTCC 59.257 50.000 0.00 0.00 34.61 4.70
893 923 2.681064 CGGGGGTGGGTCGAAGTA 60.681 66.667 0.00 0.00 0.00 2.24
953 983 2.110006 GGAAGGAGGCGCTGATCC 59.890 66.667 7.64 13.00 35.71 3.36
961 991 2.190578 CGATGTGGGGAAGGAGGC 59.809 66.667 0.00 0.00 0.00 4.70
967 997 2.047655 GTGCGTCGATGTGGGGAA 60.048 61.111 6.48 0.00 0.00 3.97
986 1016 2.819984 AATCATTGCTCACGGCCGGT 62.820 55.000 31.76 12.63 40.92 5.28
1217 1247 7.870445 GGATAGGAGTAAACTTGAGCTTATCAG 59.130 40.741 0.00 0.00 39.68 2.90
1316 1361 3.708631 CTCCCTGTGTATGATGAGGAAGT 59.291 47.826 0.00 0.00 0.00 3.01
1400 1447 0.035739 TGTAACGCCCCTTGAACTCC 59.964 55.000 0.00 0.00 0.00 3.85
1920 1967 1.062488 AGCCAGGTGTTCTGTCCCTT 61.062 55.000 0.00 0.00 41.83 3.95
1931 1978 8.641498 ATCCTATTATAAATTTCAGCCAGGTG 57.359 34.615 0.00 0.00 0.00 4.00
1950 1997 6.325028 CCATCGGTATCCTCAACATATCCTAT 59.675 42.308 0.00 0.00 0.00 2.57
2108 2162 6.672266 TCCTACAATATGAGGAGGAATGAC 57.328 41.667 6.88 0.00 36.92 3.06
2159 2220 5.041191 AGCAAAGGTATTCGAGAATCCAT 57.959 39.130 1.11 0.00 32.50 3.41
2366 2431 7.172532 TCAAAGTATTTTCACACATTAGCGAGT 59.827 33.333 0.00 0.00 35.03 4.18


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

AutoCloner maintained by Alex Coulton.