Multiple sequence alignment - TraesCS3D01G301100

Loading Multiple Alignment...

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 TraesCS3D01G301100 chr3D 100.000 3301 0 0 1 3301 415648543 415645243 0.000000e+00 6096.0
1 TraesCS3D01G301100 chr3D 93.548 589 28 5 2713 3301 536145349 536145927 0.000000e+00 869.0
2 TraesCS3D01G301100 chr3D 77.805 829 130 36 1498 2288 573907440 573908252 2.320000e-126 462.0
3 TraesCS3D01G301100 chr3D 76.593 816 146 29 1498 2279 573845154 573845958 1.100000e-109 407.0
4 TraesCS3D01G301100 chr3D 80.435 414 64 13 999 1407 573906971 573907372 1.930000e-77 300.0
5 TraesCS3D01G301100 chr3D 82.996 247 15 18 2543 2777 455553404 455553173 7.230000e-47 198.0
6 TraesCS3D01G301100 chr3D 78.061 196 34 8 2067 2254 575627421 575627227 7.490000e-22 115.0
7 TraesCS3D01G301100 chr3A 91.173 1824 102 35 734 2543 534534489 534536267 0.000000e+00 2422.0
8 TraesCS3D01G301100 chr3A 76.650 818 147 27 1498 2279 708905898 708906707 2.370000e-111 412.0
9 TraesCS3D01G301100 chr3A 76.783 603 92 33 1498 2062 709061760 709062352 8.960000e-76 294.0
10 TraesCS3D01G301100 chr3A 77.568 477 82 14 1832 2288 708920483 708920954 7.020000e-67 265.0
11 TraesCS3D01G301100 chr3A 86.239 109 13 2 2181 2288 709062457 709062564 2.080000e-22 117.0
12 TraesCS3D01G301100 chr3B 92.684 1613 61 31 909 2507 542135099 542133530 0.000000e+00 2272.0
13 TraesCS3D01G301100 chr3B 76.464 837 132 46 1504 2288 763236635 763235812 8.590000e-106 394.0
14 TraesCS3D01G301100 chr3B 78.304 401 75 10 1003 1397 763269810 763269416 7.070000e-62 248.0
15 TraesCS3D01G301100 chr3B 87.500 112 6 1 765 876 542135203 542135100 4.470000e-24 122.0
16 TraesCS3D01G301100 chr3B 76.087 230 40 11 2067 2288 766192713 766192935 4.510000e-19 106.0
17 TraesCS3D01G301100 chr3B 75.536 233 44 11 2067 2292 766587608 766587382 5.830000e-18 102.0
18 TraesCS3D01G301100 chr3B 88.732 71 8 0 2541 2611 43097040 43096970 1.630000e-13 87.9
19 TraesCS3D01G301100 chr7D 98.432 1084 5 2 1216 2299 6136955 6135884 0.000000e+00 1897.0
20 TraesCS3D01G301100 chr7D 95.833 528 22 0 2774 3301 528157180 528156653 0.000000e+00 854.0
21 TraesCS3D01G301100 chr7D 94.139 563 21 2 1 558 6137510 6136955 0.000000e+00 846.0
22 TraesCS3D01G301100 chr7D 88.142 253 18 2 2541 2782 71621356 71621105 1.160000e-74 291.0
23 TraesCS3D01G301100 chr1D 91.074 773 47 7 2540 3301 37965171 37965932 0.000000e+00 1026.0
24 TraesCS3D01G301100 chr1D 93.423 593 30 6 2708 3300 277088634 277089217 0.000000e+00 870.0
25 TraesCS3D01G301100 chr1D 95.076 528 24 1 2774 3301 433297597 433298122 0.000000e+00 830.0
26 TraesCS3D01G301100 chr1D 88.583 254 17 6 2540 2782 419462263 419462011 6.920000e-77 298.0
27 TraesCS3D01G301100 chr2D 95.186 644 15 2 1 635 390601033 390601669 0.000000e+00 1003.0
28 TraesCS3D01G301100 chr2D 87.747 253 20 1 2541 2782 627586104 627585852 5.390000e-73 285.0
29 TraesCS3D01G301100 chr2D 90.789 76 7 0 2544 2619 549023261 549023336 5.830000e-18 102.0
30 TraesCS3D01G301100 chr5D 90.141 781 56 16 2540 3301 396426042 396426820 0.000000e+00 996.0
31 TraesCS3D01G301100 chr6D 93.603 594 27 6 2708 3301 6552430 6551848 0.000000e+00 876.0
32 TraesCS3D01G301100 chr2A 92.761 594 31 3 2708 3301 186360530 186361111 0.000000e+00 848.0
33 TraesCS3D01G301100 chr5A 92.724 591 32 7 2712 3301 698732052 698731472 0.000000e+00 843.0
34 TraesCS3D01G301100 chr5A 91.429 70 6 0 2542 2611 584710676 584710607 2.710000e-16 97.1
35 TraesCS3D01G301100 chr6A 88.164 659 46 16 1 635 64663732 64664382 0.000000e+00 756.0
36 TraesCS3D01G301100 chr6A 88.845 251 16 4 2543 2782 153514617 153514368 6.920000e-77 298.0
37 TraesCS3D01G301100 chr6A 87.755 245 18 2 2543 2775 551869033 551868789 3.240000e-70 276.0
38 TraesCS3D01G301100 chr6A 83.534 249 33 5 2541 2782 71059899 71059652 3.310000e-55 226.0
39 TraesCS3D01G301100 chr7B 94.344 442 15 2 1 433 537544030 537543590 0.000000e+00 669.0
40 TraesCS3D01G301100 chr7B 89.767 215 14 2 422 635 537538710 537538503 5.430000e-68 268.0
41 TraesCS3D01G301100 chr4D 90.157 254 13 2 2540 2782 396622110 396622362 1.480000e-83 320.0
42 TraesCS3D01G301100 chr4D 89.024 246 17 1 2541 2776 22556634 22556879 2.490000e-76 296.0
43 TraesCS3D01G301100 chr4D 82.857 245 11 13 2543 2775 310478275 310478050 1.210000e-44 191.0
44 TraesCS3D01G301100 chr7A 85.950 242 29 4 2543 2782 535595345 535595107 1.520000e-63 254.0
45 TraesCS3D01G301100 chrUn 86.842 76 10 0 2543 2618 122326413 122326338 5.870000e-13 86.1
46 TraesCS3D01G301100 chr2B 92.000 50 4 0 1824 1873 726130920 726130969 1.640000e-08 71.3


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 TraesCS3D01G301100 chr3D 415645243 415648543 3300 True 6096.0 6096 100.0000 1 3301 1 chr3D.!!$R1 3300
1 TraesCS3D01G301100 chr3D 536145349 536145927 578 False 869.0 869 93.5480 2713 3301 1 chr3D.!!$F1 588
2 TraesCS3D01G301100 chr3D 573845154 573845958 804 False 407.0 407 76.5930 1498 2279 1 chr3D.!!$F2 781
3 TraesCS3D01G301100 chr3D 573906971 573908252 1281 False 381.0 462 79.1200 999 2288 2 chr3D.!!$F3 1289
4 TraesCS3D01G301100 chr3A 534534489 534536267 1778 False 2422.0 2422 91.1730 734 2543 1 chr3A.!!$F1 1809
5 TraesCS3D01G301100 chr3A 708905898 708906707 809 False 412.0 412 76.6500 1498 2279 1 chr3A.!!$F2 781
6 TraesCS3D01G301100 chr3A 709061760 709062564 804 False 205.5 294 81.5110 1498 2288 2 chr3A.!!$F4 790
7 TraesCS3D01G301100 chr3B 542133530 542135203 1673 True 1197.0 2272 90.0920 765 2507 2 chr3B.!!$R5 1742
8 TraesCS3D01G301100 chr3B 763235812 763236635 823 True 394.0 394 76.4640 1504 2288 1 chr3B.!!$R2 784
9 TraesCS3D01G301100 chr7D 6135884 6137510 1626 True 1371.5 1897 96.2855 1 2299 2 chr7D.!!$R3 2298
10 TraesCS3D01G301100 chr7D 528156653 528157180 527 True 854.0 854 95.8330 2774 3301 1 chr7D.!!$R2 527
11 TraesCS3D01G301100 chr1D 37965171 37965932 761 False 1026.0 1026 91.0740 2540 3301 1 chr1D.!!$F1 761
12 TraesCS3D01G301100 chr1D 277088634 277089217 583 False 870.0 870 93.4230 2708 3300 1 chr1D.!!$F2 592
13 TraesCS3D01G301100 chr1D 433297597 433298122 525 False 830.0 830 95.0760 2774 3301 1 chr1D.!!$F3 527
14 TraesCS3D01G301100 chr2D 390601033 390601669 636 False 1003.0 1003 95.1860 1 635 1 chr2D.!!$F1 634
15 TraesCS3D01G301100 chr5D 396426042 396426820 778 False 996.0 996 90.1410 2540 3301 1 chr5D.!!$F1 761
16 TraesCS3D01G301100 chr6D 6551848 6552430 582 True 876.0 876 93.6030 2708 3301 1 chr6D.!!$R1 593
17 TraesCS3D01G301100 chr2A 186360530 186361111 581 False 848.0 848 92.7610 2708 3301 1 chr2A.!!$F1 593
18 TraesCS3D01G301100 chr5A 698731472 698732052 580 True 843.0 843 92.7240 2712 3301 1 chr5A.!!$R2 589
19 TraesCS3D01G301100 chr6A 64663732 64664382 650 False 756.0 756 88.1640 1 635 1 chr6A.!!$F1 634

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
804 846 0.601576 CCATCAACGTGGAACCGTCA 60.602 55.0 0.0 0.0 42.02 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2769 2974 0.584541 TTTTTATAACGAGCGCGCGC 60.585 50.0 45.1 45.1 42.48 6.86 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
44 45 3.582998 ATATTCTGCAAGCTTGGCCTA 57.417 42.857 27.10 8.07 0.00 3.93
227 228 1.808945 CTCGAAGAAATTGCACAGGCT 59.191 47.619 0.00 0.00 37.12 4.58
435 476 1.149101 AGGCCCAGAAACAAAGAGGA 58.851 50.000 0.00 0.00 0.00 3.71
455 496 2.372690 CCGTCTCGCGTTGTTCTGG 61.373 63.158 5.77 0.00 39.32 3.86
456 497 1.371267 CGTCTCGCGTTGTTCTGGA 60.371 57.895 5.77 0.00 35.54 3.86
457 498 1.606350 CGTCTCGCGTTGTTCTGGAC 61.606 60.000 5.77 2.62 35.54 4.02
458 499 1.371267 TCTCGCGTTGTTCTGGACG 60.371 57.895 5.77 0.00 41.89 4.79
459 500 2.355363 TCGCGTTGTTCTGGACGG 60.355 61.111 5.77 0.00 39.52 4.79
460 501 3.411351 CGCGTTGTTCTGGACGGG 61.411 66.667 0.00 0.00 43.81 5.28
461 502 3.723348 GCGTTGTTCTGGACGGGC 61.723 66.667 0.00 0.00 39.52 6.13
510 551 3.326946 TGTATTAAATGCATGGGCCCT 57.673 42.857 25.70 5.48 40.13 5.19
523 565 1.854939 TGGGCCCTGATCAGATTTCAT 59.145 47.619 25.70 0.00 0.00 2.57
598 640 6.634035 CGAAATGAATGAATGCACGTGATAAT 59.366 34.615 22.23 6.35 0.00 1.28
635 677 2.813754 CGGGCTCAGAAATGAGTTTTCA 59.186 45.455 7.07 0.00 45.19 2.69
636 678 3.253188 CGGGCTCAGAAATGAGTTTTCAA 59.747 43.478 7.07 0.00 45.19 2.69
637 679 4.550422 GGGCTCAGAAATGAGTTTTCAAC 58.450 43.478 7.07 0.00 45.19 3.18
638 680 4.037923 GGGCTCAGAAATGAGTTTTCAACA 59.962 41.667 7.07 0.00 45.19 3.33
639 681 5.451798 GGGCTCAGAAATGAGTTTTCAACAA 60.452 40.000 7.07 0.00 45.19 2.83
640 682 6.042143 GGCTCAGAAATGAGTTTTCAACAAA 58.958 36.000 7.07 0.00 45.19 2.83
641 683 6.703165 GGCTCAGAAATGAGTTTTCAACAAAT 59.297 34.615 7.07 0.00 45.19 2.32
642 684 7.306983 GGCTCAGAAATGAGTTTTCAACAAATG 60.307 37.037 7.07 0.00 45.19 2.32
643 685 7.223387 GCTCAGAAATGAGTTTTCAACAAATGT 59.777 33.333 7.07 0.00 45.19 2.71
644 686 8.410030 TCAGAAATGAGTTTTCAACAAATGTG 57.590 30.769 1.41 0.00 45.19 3.21
645 687 8.034215 TCAGAAATGAGTTTTCAACAAATGTGT 58.966 29.630 1.41 0.00 45.19 3.72
646 688 8.323140 CAGAAATGAGTTTTCAACAAATGTGTC 58.677 33.333 0.00 0.00 45.19 3.67
647 689 6.810888 AATGAGTTTTCAACAAATGTGTCG 57.189 33.333 0.00 0.00 36.80 4.35
648 690 4.101942 TGAGTTTTCAACAAATGTGTCGC 58.898 39.130 0.00 0.00 36.80 5.19
649 691 4.101942 GAGTTTTCAACAAATGTGTCGCA 58.898 39.130 0.00 0.00 36.80 5.10
650 692 4.681744 AGTTTTCAACAAATGTGTCGCAT 58.318 34.783 0.00 0.00 36.80 4.73
651 693 8.371462 ATGAGTTTTCAACAAATGTGTCGCATT 61.371 33.333 5.77 5.77 42.09 3.56
652 694 6.269315 AGTTTTCAACAAATGTGTCGCATTA 58.731 32.000 11.91 0.00 46.29 1.90
653 695 6.417635 AGTTTTCAACAAATGTGTCGCATTAG 59.582 34.615 11.91 3.84 46.29 1.73
654 696 5.681337 TTCAACAAATGTGTCGCATTAGA 57.319 34.783 11.91 5.89 46.29 2.10
655 697 5.281693 TCAACAAATGTGTCGCATTAGAG 57.718 39.130 11.91 7.99 46.29 2.43
656 698 4.154015 TCAACAAATGTGTCGCATTAGAGG 59.846 41.667 11.91 5.51 46.29 3.69
657 699 3.937814 ACAAATGTGTCGCATTAGAGGA 58.062 40.909 11.91 0.00 46.29 3.71
658 700 4.323417 ACAAATGTGTCGCATTAGAGGAA 58.677 39.130 11.91 0.00 46.29 3.36
659 701 4.393062 ACAAATGTGTCGCATTAGAGGAAG 59.607 41.667 11.91 0.71 46.29 3.46
660 702 2.672961 TGTGTCGCATTAGAGGAAGG 57.327 50.000 0.00 0.00 0.00 3.46
661 703 1.899814 TGTGTCGCATTAGAGGAAGGT 59.100 47.619 0.00 0.00 0.00 3.50
662 704 2.301870 TGTGTCGCATTAGAGGAAGGTT 59.698 45.455 0.00 0.00 0.00 3.50
663 705 3.244422 TGTGTCGCATTAGAGGAAGGTTT 60.244 43.478 0.00 0.00 0.00 3.27
664 706 4.020928 TGTGTCGCATTAGAGGAAGGTTTA 60.021 41.667 0.00 0.00 0.00 2.01
665 707 4.933400 GTGTCGCATTAGAGGAAGGTTTAA 59.067 41.667 0.00 0.00 0.00 1.52
666 708 5.410439 GTGTCGCATTAGAGGAAGGTTTAAA 59.590 40.000 0.00 0.00 0.00 1.52
667 709 6.093633 GTGTCGCATTAGAGGAAGGTTTAAAT 59.906 38.462 0.00 0.00 0.00 1.40
668 710 7.279313 GTGTCGCATTAGAGGAAGGTTTAAATA 59.721 37.037 0.00 0.00 0.00 1.40
669 711 7.494625 TGTCGCATTAGAGGAAGGTTTAAATAG 59.505 37.037 0.00 0.00 0.00 1.73
670 712 7.709613 GTCGCATTAGAGGAAGGTTTAAATAGA 59.290 37.037 0.00 0.00 0.00 1.98
671 713 8.262227 TCGCATTAGAGGAAGGTTTAAATAGAA 58.738 33.333 0.00 0.00 0.00 2.10
672 714 8.889717 CGCATTAGAGGAAGGTTTAAATAGAAA 58.110 33.333 0.00 0.00 0.00 2.52
677 719 8.220898 AGAGGAAGGTTTAAATAGAAAGAGGT 57.779 34.615 0.00 0.00 0.00 3.85
678 720 8.322828 AGAGGAAGGTTTAAATAGAAAGAGGTC 58.677 37.037 0.00 0.00 0.00 3.85
679 721 7.403671 AGGAAGGTTTAAATAGAAAGAGGTCC 58.596 38.462 0.00 0.00 0.00 4.46
680 722 7.018249 AGGAAGGTTTAAATAGAAAGAGGTCCA 59.982 37.037 0.00 0.00 0.00 4.02
681 723 7.834681 GGAAGGTTTAAATAGAAAGAGGTCCAT 59.165 37.037 0.00 0.00 0.00 3.41
682 724 9.244292 GAAGGTTTAAATAGAAAGAGGTCCATT 57.756 33.333 0.00 0.00 0.00 3.16
683 725 9.601810 AAGGTTTAAATAGAAAGAGGTCCATTT 57.398 29.630 0.00 0.00 0.00 2.32
684 726 9.244292 AGGTTTAAATAGAAAGAGGTCCATTTC 57.756 33.333 10.26 10.26 35.99 2.17
685 727 9.244292 GGTTTAAATAGAAAGAGGTCCATTTCT 57.756 33.333 20.04 20.04 45.33 2.52
688 730 9.901172 TTAAATAGAAAGAGGTCCATTTCTACC 57.099 33.333 22.22 0.00 45.73 3.18
689 731 7.510675 AATAGAAAGAGGTCCATTTCTACCA 57.489 36.000 22.22 10.35 45.73 3.25
690 732 5.843019 AGAAAGAGGTCCATTTCTACCAA 57.157 39.130 16.54 0.00 42.47 3.67
691 733 6.200878 AGAAAGAGGTCCATTTCTACCAAA 57.799 37.500 16.54 0.00 42.47 3.28
692 734 6.241645 AGAAAGAGGTCCATTTCTACCAAAG 58.758 40.000 16.54 0.00 42.47 2.77
693 735 5.584551 AAGAGGTCCATTTCTACCAAAGT 57.415 39.130 0.00 0.00 38.30 2.66
694 736 6.697641 AAGAGGTCCATTTCTACCAAAGTA 57.302 37.500 0.00 0.00 38.30 2.24
695 737 6.051179 AGAGGTCCATTTCTACCAAAGTAC 57.949 41.667 0.00 0.00 38.30 2.73
696 738 5.785940 AGAGGTCCATTTCTACCAAAGTACT 59.214 40.000 0.00 0.00 38.30 2.73
697 739 6.051179 AGGTCCATTTCTACCAAAGTACTC 57.949 41.667 0.00 0.00 38.30 2.59
698 740 5.045797 AGGTCCATTTCTACCAAAGTACTCC 60.046 44.000 0.00 0.00 38.30 3.85
699 741 4.868734 GTCCATTTCTACCAAAGTACTCCG 59.131 45.833 0.00 0.00 0.00 4.63
700 742 4.529377 TCCATTTCTACCAAAGTACTCCGT 59.471 41.667 0.00 0.00 0.00 4.69
701 743 5.716228 TCCATTTCTACCAAAGTACTCCGTA 59.284 40.000 0.00 0.00 0.00 4.02
702 744 6.381994 TCCATTTCTACCAAAGTACTCCGTAT 59.618 38.462 0.00 0.00 0.00 3.06
703 745 7.560991 TCCATTTCTACCAAAGTACTCCGTATA 59.439 37.037 0.00 0.00 0.00 1.47
704 746 8.199449 CCATTTCTACCAAAGTACTCCGTATAA 58.801 37.037 0.00 0.00 0.00 0.98
705 747 9.245962 CATTTCTACCAAAGTACTCCGTATAAG 57.754 37.037 0.00 0.00 0.00 1.73
706 748 7.944729 TTCTACCAAAGTACTCCGTATAAGT 57.055 36.000 0.00 0.00 0.00 2.24
707 749 7.559590 TCTACCAAAGTACTCCGTATAAGTC 57.440 40.000 0.00 0.00 0.00 3.01
708 750 7.112122 TCTACCAAAGTACTCCGTATAAGTCA 58.888 38.462 0.00 0.00 0.00 3.41
709 751 6.594788 ACCAAAGTACTCCGTATAAGTCAA 57.405 37.500 0.00 0.00 0.00 3.18
710 752 6.996509 ACCAAAGTACTCCGTATAAGTCAAA 58.003 36.000 0.00 0.00 0.00 2.69
711 753 7.618137 ACCAAAGTACTCCGTATAAGTCAAAT 58.382 34.615 0.00 0.00 0.00 2.32
712 754 8.098912 ACCAAAGTACTCCGTATAAGTCAAATT 58.901 33.333 0.00 0.00 0.00 1.82
713 755 8.943002 CCAAAGTACTCCGTATAAGTCAAATTT 58.057 33.333 0.00 0.00 0.00 1.82
714 756 9.968743 CAAAGTACTCCGTATAAGTCAAATTTC 57.031 33.333 0.00 0.00 0.00 2.17
715 757 9.939802 AAAGTACTCCGTATAAGTCAAATTTCT 57.060 29.630 0.00 0.00 0.00 2.52
716 758 8.928270 AGTACTCCGTATAAGTCAAATTTCTG 57.072 34.615 0.00 0.00 0.00 3.02
717 759 8.746530 AGTACTCCGTATAAGTCAAATTTCTGA 58.253 33.333 0.00 0.00 0.00 3.27
718 760 7.829378 ACTCCGTATAAGTCAAATTTCTGAC 57.171 36.000 2.57 2.57 45.10 3.51
719 761 6.817140 ACTCCGTATAAGTCAAATTTCTGACC 59.183 38.462 6.65 0.00 45.77 4.02
720 762 6.110707 TCCGTATAAGTCAAATTTCTGACCC 58.889 40.000 6.65 0.00 45.77 4.46
721 763 5.006358 CCGTATAAGTCAAATTTCTGACCCG 59.994 44.000 6.65 3.16 45.77 5.28
722 764 4.965119 ATAAGTCAAATTTCTGACCCGC 57.035 40.909 6.65 0.00 45.77 6.13
723 765 2.270352 AGTCAAATTTCTGACCCGCA 57.730 45.000 6.65 0.00 45.77 5.69
724 766 2.582052 AGTCAAATTTCTGACCCGCAA 58.418 42.857 6.65 0.00 45.77 4.85
725 767 2.955660 AGTCAAATTTCTGACCCGCAAA 59.044 40.909 6.65 0.00 45.77 3.68
726 768 3.383185 AGTCAAATTTCTGACCCGCAAAA 59.617 39.130 6.65 0.00 45.77 2.44
727 769 4.116238 GTCAAATTTCTGACCCGCAAAAA 58.884 39.130 0.00 0.00 39.93 1.94
801 843 0.887387 AACCCATCAACGTGGAACCG 60.887 55.000 0.00 0.00 42.02 4.44
802 844 1.302192 CCCATCAACGTGGAACCGT 60.302 57.895 0.00 0.00 42.02 4.83
803 845 1.296056 CCCATCAACGTGGAACCGTC 61.296 60.000 0.00 0.00 42.02 4.79
804 846 0.601576 CCATCAACGTGGAACCGTCA 60.602 55.000 0.00 0.00 42.02 4.35
805 847 1.222300 CATCAACGTGGAACCGTCAA 58.778 50.000 0.00 0.00 40.85 3.18
806 848 1.070175 CATCAACGTGGAACCGTCAAC 60.070 52.381 0.00 0.00 40.85 3.18
807 849 0.810823 TCAACGTGGAACCGTCAACC 60.811 55.000 0.00 0.00 40.85 3.77
821 871 2.030562 AACCGTGTGGAAGGCTCG 59.969 61.111 0.00 0.00 39.21 5.03
851 902 1.818363 GGAAATCCGAAGCGTCCCC 60.818 63.158 0.00 0.00 0.00 4.81
857 908 2.742372 CGAAGCGTCCCCACCAAG 60.742 66.667 0.00 0.00 0.00 3.61
885 936 1.885388 CACAACACCTCGCGTCCAA 60.885 57.895 5.77 0.00 0.00 3.53
969 1020 1.066752 GTCGCAACCAAAACCCACC 59.933 57.895 0.00 0.00 0.00 4.61
974 1025 1.074850 AACCAAAACCCACCCCCAG 60.075 57.895 0.00 0.00 0.00 4.45
2365 2517 8.592105 TTTGAGCTTTCTGGATGTTATTTTTG 57.408 30.769 0.00 0.00 0.00 2.44
2366 2518 7.288810 TGAGCTTTCTGGATGTTATTTTTGT 57.711 32.000 0.00 0.00 0.00 2.83
2374 2528 8.755696 TCTGGATGTTATTTTTGTTAATGTGC 57.244 30.769 0.00 0.00 0.00 4.57
2407 2572 4.646492 AGTGAACTTTTCTGCCTGTTGATT 59.354 37.500 0.00 0.00 0.00 2.57
2408 2573 4.741676 GTGAACTTTTCTGCCTGTTGATTG 59.258 41.667 0.00 0.00 0.00 2.67
2409 2574 4.402155 TGAACTTTTCTGCCTGTTGATTGT 59.598 37.500 0.00 0.00 0.00 2.71
2410 2575 5.105392 TGAACTTTTCTGCCTGTTGATTGTT 60.105 36.000 0.00 0.00 0.00 2.83
2411 2576 5.343307 ACTTTTCTGCCTGTTGATTGTTT 57.657 34.783 0.00 0.00 0.00 2.83
2412 2577 5.351458 ACTTTTCTGCCTGTTGATTGTTTC 58.649 37.500 0.00 0.00 0.00 2.78
2413 2578 4.998671 TTTCTGCCTGTTGATTGTTTCA 57.001 36.364 0.00 0.00 0.00 2.69
2414 2579 4.572985 TTCTGCCTGTTGATTGTTTCAG 57.427 40.909 0.00 0.00 35.27 3.02
2415 2580 3.819368 TCTGCCTGTTGATTGTTTCAGA 58.181 40.909 0.00 0.00 35.27 3.27
2416 2581 4.206375 TCTGCCTGTTGATTGTTTCAGAA 58.794 39.130 0.00 0.00 35.27 3.02
2417 2582 4.644234 TCTGCCTGTTGATTGTTTCAGAAA 59.356 37.500 0.00 0.00 35.27 2.52
2418 2583 5.302568 TCTGCCTGTTGATTGTTTCAGAAAT 59.697 36.000 0.00 0.00 35.27 2.17
2419 2584 5.916318 TGCCTGTTGATTGTTTCAGAAATT 58.084 33.333 0.00 0.00 35.27 1.82
2420 2585 5.984926 TGCCTGTTGATTGTTTCAGAAATTC 59.015 36.000 0.00 0.00 35.27 2.17
2421 2586 6.183360 TGCCTGTTGATTGTTTCAGAAATTCT 60.183 34.615 0.00 0.00 35.27 2.40
2422 2587 6.145048 GCCTGTTGATTGTTTCAGAAATTCTG 59.855 38.462 16.39 16.39 45.59 3.02
2460 2625 6.263168 CCTTTTCAAAGATGTGTCCAGTACTT 59.737 38.462 0.00 0.00 38.28 2.24
2490 2656 1.070289 CGGGGGAGTACTATCTTTGGC 59.930 57.143 0.00 0.00 0.00 4.52
2492 2658 2.158798 GGGGGAGTACTATCTTTGGCAC 60.159 54.545 0.00 0.00 0.00 5.01
2513 2679 3.513912 ACGTGGATCCAAGATACACTTCA 59.486 43.478 31.07 0.00 36.61 3.02
2538 2704 2.087646 GGACACCAGAAATGAAGGAGC 58.912 52.381 0.00 0.00 0.00 4.70
2556 2722 3.604582 GAGCATAAGAGCAACTCCAACT 58.395 45.455 0.00 0.00 36.85 3.16
2558 2724 3.077359 GCATAAGAGCAACTCCAACTGT 58.923 45.455 0.00 0.00 0.00 3.55
2583 2749 1.261089 CTCAAACGGACGGCGTTTTTA 59.739 47.619 16.19 1.49 37.45 1.52
2588 2765 1.061411 GGACGGCGTTTTTATCCGC 59.939 57.895 16.19 0.00 46.49 5.54
2596 2773 4.288132 GCGTTTTTATCCGCTTTTTGTC 57.712 40.909 0.00 0.00 46.08 3.18
2597 2774 3.120616 GCGTTTTTATCCGCTTTTTGTCC 59.879 43.478 0.00 0.00 46.08 4.02
2598 2775 3.359580 CGTTTTTATCCGCTTTTTGTCCG 59.640 43.478 0.00 0.00 0.00 4.79
2599 2776 4.292599 GTTTTTATCCGCTTTTTGTCCGT 58.707 39.130 0.00 0.00 0.00 4.69
2600 2777 4.571372 TTTTATCCGCTTTTTGTCCGTT 57.429 36.364 0.00 0.00 0.00 4.44
2601 2778 4.571372 TTTATCCGCTTTTTGTCCGTTT 57.429 36.364 0.00 0.00 0.00 3.60
2602 2779 2.415697 ATCCGCTTTTTGTCCGTTTG 57.584 45.000 0.00 0.00 0.00 2.93
2603 2780 0.382515 TCCGCTTTTTGTCCGTTTGG 59.617 50.000 0.00 0.00 0.00 3.28
2605 2782 0.101579 CGCTTTTTGTCCGTTTGGGT 59.898 50.000 0.00 0.00 37.00 4.51
2656 2833 3.307906 AGTGCGTCTAACGGGCCA 61.308 61.111 4.39 0.00 42.82 5.36
2691 2868 1.255635 GCGCGCGTTTTAGATCATGC 61.256 55.000 32.35 5.38 0.00 4.06
2703 2880 0.816825 GATCATGCCAGCGTCCATGT 60.817 55.000 11.44 2.61 39.74 3.21
2770 2975 4.877619 GGGGGAAAGCGGCCTAGC 62.878 72.222 0.00 0.00 37.41 3.42
2856 3062 2.594882 CTAGCCTCGCCGCCTCTA 60.595 66.667 0.00 0.00 0.00 2.43
3113 3319 4.257654 TCCCGCGGCTTTTCACCA 62.258 61.111 22.85 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 7.443259 TGATGATGATTTGACGCATATCAAT 57.557 32.000 13.53 6.93 38.37 2.57
180 181 5.187967 CCAGGACAAGTATCTTCTAACCTGT 59.812 44.000 0.00 0.00 40.16 4.00
227 228 2.472029 CTTCTCCCTTTCTCTAGGCCA 58.528 52.381 5.01 0.00 33.73 5.36
461 502 4.680237 TTGCAGCCGTCCCAGTCG 62.680 66.667 0.00 0.00 0.00 4.18
510 551 5.367302 TGCGTATTGGATGAAATCTGATCA 58.633 37.500 0.00 0.00 44.71 2.92
523 565 6.859508 CGTCTGTATACTTTATGCGTATTGGA 59.140 38.462 4.17 0.00 0.00 3.53
598 640 0.830648 CCCGAGCTCAAATGGTCCTA 59.169 55.000 15.40 0.00 0.00 2.94
640 682 2.501723 ACCTTCCTCTAATGCGACACAT 59.498 45.455 0.00 0.00 42.30 3.21
641 683 1.899814 ACCTTCCTCTAATGCGACACA 59.100 47.619 0.00 0.00 0.00 3.72
642 684 2.674796 ACCTTCCTCTAATGCGACAC 57.325 50.000 0.00 0.00 0.00 3.67
643 685 3.695830 AAACCTTCCTCTAATGCGACA 57.304 42.857 0.00 0.00 0.00 4.35
644 686 6.679327 ATTTAAACCTTCCTCTAATGCGAC 57.321 37.500 0.00 0.00 0.00 5.19
645 687 7.788026 TCTATTTAAACCTTCCTCTAATGCGA 58.212 34.615 0.00 0.00 0.00 5.10
646 688 8.433421 TTCTATTTAAACCTTCCTCTAATGCG 57.567 34.615 0.00 0.00 0.00 4.73
651 693 9.335211 ACCTCTTTCTATTTAAACCTTCCTCTA 57.665 33.333 0.00 0.00 0.00 2.43
652 694 8.220898 ACCTCTTTCTATTTAAACCTTCCTCT 57.779 34.615 0.00 0.00 0.00 3.69
653 695 7.553402 GGACCTCTTTCTATTTAAACCTTCCTC 59.447 40.741 0.00 0.00 0.00 3.71
654 696 7.018249 TGGACCTCTTTCTATTTAAACCTTCCT 59.982 37.037 0.00 0.00 0.00 3.36
655 697 7.173032 TGGACCTCTTTCTATTTAAACCTTCC 58.827 38.462 0.00 0.00 0.00 3.46
656 698 8.809468 ATGGACCTCTTTCTATTTAAACCTTC 57.191 34.615 0.00 0.00 0.00 3.46
657 699 9.601810 AAATGGACCTCTTTCTATTTAAACCTT 57.398 29.630 0.00 0.00 35.55 3.50
658 700 9.244292 GAAATGGACCTCTTTCTATTTAAACCT 57.756 33.333 10.94 0.00 36.95 3.50
659 701 9.244292 AGAAATGGACCTCTTTCTATTTAAACC 57.756 33.333 16.43 0.00 39.34 3.27
662 704 9.901172 GGTAGAAATGGACCTCTTTCTATTTAA 57.099 33.333 22.13 8.31 42.67 1.52
663 705 9.053472 TGGTAGAAATGGACCTCTTTCTATTTA 57.947 33.333 22.13 13.98 42.67 1.40
664 706 7.928873 TGGTAGAAATGGACCTCTTTCTATTT 58.071 34.615 22.13 7.83 42.67 1.40
665 707 7.510675 TGGTAGAAATGGACCTCTTTCTATT 57.489 36.000 22.13 8.34 42.67 1.73
666 708 7.510675 TTGGTAGAAATGGACCTCTTTCTAT 57.489 36.000 22.13 8.82 42.67 1.98
667 709 6.945636 TTGGTAGAAATGGACCTCTTTCTA 57.054 37.500 18.36 18.36 40.96 2.10
668 710 5.843019 TTGGTAGAAATGGACCTCTTTCT 57.157 39.130 19.80 19.80 42.66 2.52
669 711 6.004574 ACTTTGGTAGAAATGGACCTCTTTC 58.995 40.000 10.46 10.46 0.00 2.62
670 712 5.953571 ACTTTGGTAGAAATGGACCTCTTT 58.046 37.500 0.00 0.00 0.00 2.52
671 713 5.584551 ACTTTGGTAGAAATGGACCTCTT 57.415 39.130 0.00 0.00 0.00 2.85
672 714 5.785940 AGTACTTTGGTAGAAATGGACCTCT 59.214 40.000 0.00 0.00 0.00 3.69
673 715 6.051179 AGTACTTTGGTAGAAATGGACCTC 57.949 41.667 0.00 0.00 0.00 3.85
674 716 5.045797 GGAGTACTTTGGTAGAAATGGACCT 60.046 44.000 0.00 0.00 0.00 3.85
675 717 5.183969 GGAGTACTTTGGTAGAAATGGACC 58.816 45.833 0.00 0.00 0.00 4.46
676 718 4.868734 CGGAGTACTTTGGTAGAAATGGAC 59.131 45.833 0.00 0.00 0.00 4.02
677 719 4.529377 ACGGAGTACTTTGGTAGAAATGGA 59.471 41.667 0.00 0.00 41.94 3.41
678 720 4.828829 ACGGAGTACTTTGGTAGAAATGG 58.171 43.478 0.00 0.00 41.94 3.16
692 734 8.805688 GTCAGAAATTTGACTTATACGGAGTAC 58.194 37.037 0.00 0.00 44.19 2.73
693 735 7.977853 GGTCAGAAATTTGACTTATACGGAGTA 59.022 37.037 9.54 0.00 46.18 2.59
694 736 6.817140 GGTCAGAAATTTGACTTATACGGAGT 59.183 38.462 9.54 0.00 45.32 3.85
695 737 6.258068 GGGTCAGAAATTTGACTTATACGGAG 59.742 42.308 9.54 0.00 45.32 4.63
696 738 6.110707 GGGTCAGAAATTTGACTTATACGGA 58.889 40.000 9.54 0.00 45.32 4.69
697 739 5.006358 CGGGTCAGAAATTTGACTTATACGG 59.994 44.000 9.54 0.00 45.32 4.02
698 740 5.501897 GCGGGTCAGAAATTTGACTTATACG 60.502 44.000 9.54 8.10 45.32 3.06
699 741 5.353123 TGCGGGTCAGAAATTTGACTTATAC 59.647 40.000 9.54 0.00 45.32 1.47
700 742 5.492895 TGCGGGTCAGAAATTTGACTTATA 58.507 37.500 9.54 0.00 45.32 0.98
701 743 4.331968 TGCGGGTCAGAAATTTGACTTAT 58.668 39.130 9.54 0.00 45.32 1.73
702 744 3.745799 TGCGGGTCAGAAATTTGACTTA 58.254 40.909 9.54 0.00 45.32 2.24
703 745 2.582052 TGCGGGTCAGAAATTTGACTT 58.418 42.857 9.54 0.00 45.32 3.01
704 746 2.270352 TGCGGGTCAGAAATTTGACT 57.730 45.000 9.54 0.00 45.32 3.41
705 747 3.363341 TTTGCGGGTCAGAAATTTGAC 57.637 42.857 0.00 0.00 45.28 3.18
706 748 4.392921 TTTTTGCGGGTCAGAAATTTGA 57.607 36.364 0.00 0.00 0.00 2.69
801 843 1.227853 AGCCTTCCACACGGTTGAC 60.228 57.895 0.00 0.00 0.00 3.18
802 844 1.070786 GAGCCTTCCACACGGTTGA 59.929 57.895 0.00 0.00 0.00 3.18
803 845 2.317609 CGAGCCTTCCACACGGTTG 61.318 63.158 0.00 0.00 0.00 3.77
804 846 2.030562 CGAGCCTTCCACACGGTT 59.969 61.111 0.00 0.00 0.00 4.44
805 847 3.222354 GACGAGCCTTCCACACGGT 62.222 63.158 0.00 0.00 0.00 4.83
806 848 2.432628 GACGAGCCTTCCACACGG 60.433 66.667 0.00 0.00 0.00 4.94
807 849 1.734477 CAGACGAGCCTTCCACACG 60.734 63.158 0.00 0.00 0.00 4.49
821 871 1.756430 GGATTTCCCTTCTGCCAGAC 58.244 55.000 0.00 0.00 0.00 3.51
902 953 1.509644 TTGAAGCTCCGTGCAGCAAG 61.510 55.000 0.00 0.00 45.94 4.01
2365 2517 8.270026 GTTCACTAAAAGAACTGCACATTAAC 57.730 34.615 0.00 0.00 41.56 2.01
2412 2577 8.218338 AGGCAAGTAATGTATCAGAATTTCTG 57.782 34.615 18.49 18.49 45.59 3.02
2413 2578 8.814038 AAGGCAAGTAATGTATCAGAATTTCT 57.186 30.769 0.00 0.00 0.00 2.52
2414 2579 9.860898 AAAAGGCAAGTAATGTATCAGAATTTC 57.139 29.630 0.00 0.00 0.00 2.17
2415 2580 9.860898 GAAAAGGCAAGTAATGTATCAGAATTT 57.139 29.630 0.00 0.00 0.00 1.82
2416 2581 9.023962 TGAAAAGGCAAGTAATGTATCAGAATT 57.976 29.630 0.00 0.00 0.00 2.17
2417 2582 8.579850 TGAAAAGGCAAGTAATGTATCAGAAT 57.420 30.769 0.00 0.00 0.00 2.40
2418 2583 7.994425 TGAAAAGGCAAGTAATGTATCAGAA 57.006 32.000 0.00 0.00 0.00 3.02
2419 2584 7.994425 TTGAAAAGGCAAGTAATGTATCAGA 57.006 32.000 0.00 0.00 0.00 3.27
2420 2585 8.514594 TCTTTGAAAAGGCAAGTAATGTATCAG 58.485 33.333 3.08 0.00 36.67 2.90
2421 2586 8.402798 TCTTTGAAAAGGCAAGTAATGTATCA 57.597 30.769 3.08 0.00 36.67 2.15
2422 2587 9.294030 CATCTTTGAAAAGGCAAGTAATGTATC 57.706 33.333 3.08 0.00 36.67 2.24
2423 2588 8.806146 ACATCTTTGAAAAGGCAAGTAATGTAT 58.194 29.630 3.08 0.00 36.67 2.29
2424 2589 8.081633 CACATCTTTGAAAAGGCAAGTAATGTA 58.918 33.333 3.08 0.00 36.67 2.29
2460 2625 4.127918 AGTACTCCCCCGATCATATTGA 57.872 45.455 0.00 0.00 0.00 2.57
2490 2656 3.526931 AGTGTATCTTGGATCCACGTG 57.473 47.619 15.91 9.08 0.00 4.49
2492 2658 4.123497 TGAAGTGTATCTTGGATCCACG 57.877 45.455 15.91 13.74 36.40 4.94
2513 2679 3.897505 CCTTCATTTCTGGTGTCCCTTTT 59.102 43.478 0.00 0.00 0.00 2.27
2538 2704 3.686726 GGACAGTTGGAGTTGCTCTTATG 59.313 47.826 0.00 0.00 0.00 1.90
2583 2749 1.000717 CCAAACGGACAAAAAGCGGAT 60.001 47.619 0.00 0.00 0.00 4.18
2588 2765 1.268845 CGGACCCAAACGGACAAAAAG 60.269 52.381 0.00 0.00 34.64 2.27
2591 2768 2.188161 GCGGACCCAAACGGACAAA 61.188 57.895 0.00 0.00 34.64 2.83
2592 2769 2.592287 GCGGACCCAAACGGACAA 60.592 61.111 0.00 0.00 34.64 3.18
2593 2770 4.629523 GGCGGACCCAAACGGACA 62.630 66.667 0.00 0.00 34.64 4.02
2656 2833 1.933115 GCGCGGTCATGAAATGGGTT 61.933 55.000 8.83 0.00 46.73 4.11
2691 2868 2.880879 CGACGACATGGACGCTGG 60.881 66.667 12.98 1.57 0.00 4.85
2703 2880 2.281208 CCAAAACCAGGGCGACGA 60.281 61.111 0.00 0.00 0.00 4.20
2769 2974 0.584541 TTTTTATAACGAGCGCGCGC 60.585 50.000 45.10 45.10 42.48 6.86
2770 2975 1.363264 CTTTTTATAACGAGCGCGCG 58.637 50.000 31.62 31.62 42.48 6.86
2771 2976 1.726659 CCTTTTTATAACGAGCGCGC 58.273 50.000 26.66 26.66 42.48 6.86
2772 2977 1.726659 GCCTTTTTATAACGAGCGCG 58.273 50.000 8.75 8.75 44.79 6.86
2856 3062 1.359117 CGGATCGACATGGTAGCGT 59.641 57.895 0.00 0.00 0.00 5.07
2860 3066 2.725641 CGGCGGATCGACATGGTA 59.274 61.111 0.00 0.00 32.52 3.25
3223 3429 0.670546 GCTTGTAGAACTGGCGCTCA 60.671 55.000 7.64 2.39 0.00 4.26


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

AutoCloner maintained by Alex Coulton.