Multiple sequence alignment - TraesCS7A01G556200

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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 TraesCS7A01G556200 chr7A 100.000 3020 0 0 1 3020 727720711 727723730 0.000000e+00 5578
1 TraesCS7A01G556200 chr7A 90.390 999 68 13 1926 2908 727607229 727608215 0.000000e+00 1288
2 TraesCS7A01G556200 chr7A 95.288 573 26 1 1 572 727606628 727607200 0.000000e+00 907
3 TraesCS7A01G556200 chr7A 75.889 647 105 32 1078 1694 727692353 727692978 1.770000e-72 283
4 TraesCS7A01G556200 chr7A 75.517 629 115 27 1203 1824 727710462 727711058 3.840000e-69 272
5 TraesCS7A01G556200 chr7A 91.724 145 12 0 593 737 54981210 54981354 5.110000e-48 202
6 TraesCS7A01G556200 chr7A 93.701 127 7 1 2894 3020 727608552 727608677 3.970000e-44 189
7 TraesCS7A01G556200 chr7B 88.889 1062 63 18 737 1767 734379072 734380109 0.000000e+00 1256
8 TraesCS7A01G556200 chr7B 81.443 970 135 30 737 1684 734407389 734408335 0.000000e+00 752
9 TraesCS7A01G556200 chr7B 89.691 388 35 5 2405 2788 734380587 734380973 9.730000e-135 490
10 TraesCS7A01G556200 chr7B 98.113 106 2 0 2910 3015 734381107 734381212 5.140000e-43 185
11 TraesCS7A01G556200 chr7B 92.941 85 6 0 396 480 734378892 734378976 1.140000e-24 124
12 TraesCS7A01G556200 chr7D 89.840 876 80 5 839 1713 638331335 638330468 0.000000e+00 1116
13 TraesCS7A01G556200 chr7D 92.399 592 45 0 1 592 638332371 638331780 0.000000e+00 845
14 TraesCS7A01G556200 chr7D 91.115 619 49 6 2405 3020 638329930 638329315 0.000000e+00 833
15 TraesCS7A01G556200 chr7D 82.473 639 96 11 1082 1712 638296963 638296333 2.050000e-151 545
16 TraesCS7A01G556200 chr7D 81.745 619 102 8 1071 1684 638288525 638287913 9.660000e-140 507
17 TraesCS7A01G556200 chr7D 90.096 313 29 2 1710 2022 638330228 638329918 3.630000e-109 405
18 TraesCS7A01G556200 chr7D 93.525 139 9 0 597 735 38730163 38730025 1.100000e-49 207
19 TraesCS7A01G556200 chr2B 78.886 341 64 8 1 339 481120258 481119924 1.090000e-54 224
20 TraesCS7A01G556200 chr2B 93.878 147 8 1 594 740 154722643 154722498 1.410000e-53 220
21 TraesCS7A01G556200 chr1D 93.151 146 10 0 595 740 241230776 241230921 6.560000e-52 215
22 TraesCS7A01G556200 chr2D 90.066 151 15 0 595 745 636425162 636425012 2.380000e-46 196
23 TraesCS7A01G556200 chr6A 90.278 144 14 0 597 740 19884868 19884725 3.970000e-44 189
24 TraesCS7A01G556200 chr6A 84.138 145 22 1 594 737 28665191 28665335 4.060000e-29 139
25 TraesCS7A01G556200 chr3D 80.816 245 44 3 13 257 606386011 606386252 3.970000e-44 189
26 TraesCS7A01G556200 chr5A 88.816 152 17 0 593 744 559089390 559089239 1.430000e-43 187
27 TraesCS7A01G556200 chr3A 79.675 246 47 3 13 257 737665574 737665331 1.110000e-39 174
28 TraesCS7A01G556200 chr4D 86.111 144 20 0 597 740 266784402 266784259 4.030000e-34 156
29 TraesCS7A01G556200 chr4D 78.509 228 34 8 1 213 466831856 466831629 5.250000e-28 135


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 TraesCS7A01G556200 chr7A 727720711 727723730 3019 False 5578.000000 5578 100.000000 1 3020 1 chr7A.!!$F4 3019
1 TraesCS7A01G556200 chr7A 727606628 727608677 2049 False 794.666667 1288 93.126333 1 3020 3 chr7A.!!$F5 3019
2 TraesCS7A01G556200 chr7A 727692353 727692978 625 False 283.000000 283 75.889000 1078 1694 1 chr7A.!!$F2 616
3 TraesCS7A01G556200 chr7A 727710462 727711058 596 False 272.000000 272 75.517000 1203 1824 1 chr7A.!!$F3 621
4 TraesCS7A01G556200 chr7B 734407389 734408335 946 False 752.000000 752 81.443000 737 1684 1 chr7B.!!$F1 947
5 TraesCS7A01G556200 chr7B 734378892 734381212 2320 False 513.750000 1256 92.408500 396 3015 4 chr7B.!!$F2 2619
6 TraesCS7A01G556200 chr7D 638329315 638332371 3056 True 799.750000 1116 90.862500 1 3020 4 chr7D.!!$R4 3019
7 TraesCS7A01G556200 chr7D 638296333 638296963 630 True 545.000000 545 82.473000 1082 1712 1 chr7D.!!$R3 630
8 TraesCS7A01G556200 chr7D 638287913 638288525 612 True 507.000000 507 81.745000 1071 1684 1 chr7D.!!$R2 613

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
676 683 0.036765 TTGCCGCTCTCCGTATTTGT 60.037 50.0 0.0 0.0 34.38 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2272 3232 0.035725 CCCTGCTCATTGCTCAGTGA 60.036 55.0 0.0 0.0 43.37 3.41 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
50 51 2.939640 GCATCTCTGGGCGGTTAAAGAA 60.940 50.000 0.00 0.00 0.00 2.52
217 218 2.866065 GCTTGCGGGCTTTAAAACACAT 60.866 45.455 0.00 0.00 0.00 3.21
221 222 3.821600 TGCGGGCTTTAAAACACATAGAA 59.178 39.130 0.00 0.00 0.00 2.10
260 261 3.950794 TTGGATGGTCGGCTCACGC 62.951 63.158 0.00 0.00 43.86 5.34
272 273 1.269621 GGCTCACGCATTAGTATCCGT 60.270 52.381 0.00 0.00 38.10 4.69
294 295 2.042095 TGGTCCCCATCGGTCCAT 59.958 61.111 0.00 0.00 44.02 3.41
311 312 0.385751 CATAGACGGATGCGGTGTCT 59.614 55.000 12.44 7.53 44.63 3.41
319 320 1.234821 GATGCGGTGTCTGGTTTGAA 58.765 50.000 0.00 0.00 0.00 2.69
484 485 2.038557 ACGAAATGAGTTGGCACTACCT 59.961 45.455 0.00 0.00 40.22 3.08
584 591 3.737850 GCATGGATGGTCTCTAGGAAAG 58.262 50.000 0.00 0.00 0.00 2.62
586 593 3.121929 TGGATGGTCTCTAGGAAAGCT 57.878 47.619 0.00 0.00 0.00 3.74
592 599 4.610333 TGGTCTCTAGGAAAGCTGACATA 58.390 43.478 0.00 0.00 33.12 2.29
593 600 5.211973 TGGTCTCTAGGAAAGCTGACATAT 58.788 41.667 0.00 0.00 33.12 1.78
594 601 5.663106 TGGTCTCTAGGAAAGCTGACATATT 59.337 40.000 0.00 0.00 33.12 1.28
595 602 6.156949 TGGTCTCTAGGAAAGCTGACATATTT 59.843 38.462 0.00 0.00 33.12 1.40
596 603 7.344612 TGGTCTCTAGGAAAGCTGACATATTTA 59.655 37.037 0.00 0.00 33.12 1.40
597 604 7.870445 GGTCTCTAGGAAAGCTGACATATTTAG 59.130 40.741 0.00 0.00 33.12 1.85
598 605 7.870445 GTCTCTAGGAAAGCTGACATATTTAGG 59.130 40.741 0.00 0.00 32.33 2.69
599 606 6.525629 TCTAGGAAAGCTGACATATTTAGGC 58.474 40.000 0.00 0.00 0.00 3.93
600 607 5.379706 AGGAAAGCTGACATATTTAGGCT 57.620 39.130 0.00 0.00 0.00 4.58
601 608 5.128919 AGGAAAGCTGACATATTTAGGCTG 58.871 41.667 0.00 0.00 0.00 4.85
602 609 4.884164 GGAAAGCTGACATATTTAGGCTGT 59.116 41.667 0.00 0.00 0.00 4.40
603 610 5.220931 GGAAAGCTGACATATTTAGGCTGTG 60.221 44.000 0.00 0.00 0.00 3.66
604 611 4.494091 AGCTGACATATTTAGGCTGTGT 57.506 40.909 0.00 0.00 0.00 3.72
605 612 4.848357 AGCTGACATATTTAGGCTGTGTT 58.152 39.130 0.00 0.00 0.00 3.32
606 613 4.878397 AGCTGACATATTTAGGCTGTGTTC 59.122 41.667 0.00 0.00 0.00 3.18
607 614 4.260375 GCTGACATATTTAGGCTGTGTTCG 60.260 45.833 0.00 0.00 0.00 3.95
608 615 4.188462 TGACATATTTAGGCTGTGTTCGG 58.812 43.478 0.00 0.00 0.00 4.30
609 616 2.943033 ACATATTTAGGCTGTGTTCGGC 59.057 45.455 0.00 0.00 44.51 5.54
610 617 2.772077 TATTTAGGCTGTGTTCGGCA 57.228 45.000 0.00 0.00 46.81 5.69
611 618 1.453155 ATTTAGGCTGTGTTCGGCAG 58.547 50.000 0.00 0.00 46.81 4.85
612 619 0.107831 TTTAGGCTGTGTTCGGCAGT 59.892 50.000 0.00 0.00 46.81 4.40
613 620 0.320421 TTAGGCTGTGTTCGGCAGTC 60.320 55.000 0.00 0.00 46.81 3.51
614 621 2.167398 TAGGCTGTGTTCGGCAGTCC 62.167 60.000 0.00 0.00 46.81 3.85
615 622 2.280797 GCTGTGTTCGGCAGTCCA 60.281 61.111 0.00 0.00 44.61 4.02
616 623 2.607892 GCTGTGTTCGGCAGTCCAC 61.608 63.158 0.00 0.00 44.61 4.02
617 624 1.961277 CTGTGTTCGGCAGTCCACC 60.961 63.158 6.30 0.00 0.00 4.61
626 633 3.680786 CAGTCCACCGCTCCGTCA 61.681 66.667 0.00 0.00 0.00 4.35
627 634 3.681835 AGTCCACCGCTCCGTCAC 61.682 66.667 0.00 0.00 0.00 3.67
628 635 4.736896 GTCCACCGCTCCGTCACC 62.737 72.222 0.00 0.00 0.00 4.02
630 637 4.742201 CCACCGCTCCGTCACCAG 62.742 72.222 0.00 0.00 0.00 4.00
631 638 3.680786 CACCGCTCCGTCACCAGA 61.681 66.667 0.00 0.00 0.00 3.86
632 639 2.915659 ACCGCTCCGTCACCAGAA 60.916 61.111 0.00 0.00 0.00 3.02
633 640 2.342279 CCGCTCCGTCACCAGAAA 59.658 61.111 0.00 0.00 0.00 2.52
634 641 1.738099 CCGCTCCGTCACCAGAAAG 60.738 63.158 0.00 0.00 0.00 2.62
635 642 2.383527 CGCTCCGTCACCAGAAAGC 61.384 63.158 0.00 0.00 0.00 3.51
636 643 2.383527 GCTCCGTCACCAGAAAGCG 61.384 63.158 0.00 0.00 0.00 4.68
637 644 1.738099 CTCCGTCACCAGAAAGCGG 60.738 63.158 0.00 0.00 43.32 5.52
638 645 2.342279 CCGTCACCAGAAAGCGGA 59.658 61.111 0.00 0.00 44.57 5.54
639 646 1.738099 CCGTCACCAGAAAGCGGAG 60.738 63.158 0.00 0.00 44.57 4.63
661 668 2.182537 CGGAGCAGCCAATTTGCC 59.817 61.111 0.00 0.00 42.48 4.52
662 669 2.182537 GGAGCAGCCAATTTGCCG 59.817 61.111 0.00 0.00 42.48 5.69
663 670 2.507769 GAGCAGCCAATTTGCCGC 60.508 61.111 1.55 1.55 42.48 6.53
664 671 2.993264 AGCAGCCAATTTGCCGCT 60.993 55.556 6.42 6.42 42.48 5.52
665 672 2.507769 GCAGCCAATTTGCCGCTC 60.508 61.111 2.59 0.00 35.54 5.03
666 673 2.998279 GCAGCCAATTTGCCGCTCT 61.998 57.895 2.59 0.00 35.54 4.09
667 674 1.138247 CAGCCAATTTGCCGCTCTC 59.862 57.895 0.00 0.00 0.00 3.20
668 675 2.048603 AGCCAATTTGCCGCTCTCC 61.049 57.895 0.00 0.00 0.00 3.71
669 676 2.793946 CCAATTTGCCGCTCTCCG 59.206 61.111 0.00 0.00 0.00 4.63
670 677 2.040544 CCAATTTGCCGCTCTCCGT 61.041 57.895 0.00 0.00 34.38 4.69
671 678 0.742990 CCAATTTGCCGCTCTCCGTA 60.743 55.000 0.00 0.00 34.38 4.02
672 679 1.299541 CAATTTGCCGCTCTCCGTAT 58.700 50.000 0.00 0.00 34.38 3.06
673 680 1.670811 CAATTTGCCGCTCTCCGTATT 59.329 47.619 0.00 0.00 34.38 1.89
674 681 2.038387 ATTTGCCGCTCTCCGTATTT 57.962 45.000 0.00 0.00 34.38 1.40
675 682 1.083489 TTTGCCGCTCTCCGTATTTG 58.917 50.000 0.00 0.00 34.38 2.32
676 683 0.036765 TTGCCGCTCTCCGTATTTGT 60.037 50.000 0.00 0.00 34.38 2.83
677 684 0.818938 TGCCGCTCTCCGTATTTGTA 59.181 50.000 0.00 0.00 34.38 2.41
678 685 1.411246 TGCCGCTCTCCGTATTTGTAT 59.589 47.619 0.00 0.00 34.38 2.29
679 686 2.159014 TGCCGCTCTCCGTATTTGTATT 60.159 45.455 0.00 0.00 34.38 1.89
680 687 2.221055 GCCGCTCTCCGTATTTGTATTG 59.779 50.000 0.00 0.00 34.38 1.90
681 688 3.454375 CCGCTCTCCGTATTTGTATTGT 58.546 45.455 0.00 0.00 34.38 2.71
682 689 4.613944 CCGCTCTCCGTATTTGTATTGTA 58.386 43.478 0.00 0.00 34.38 2.41
683 690 5.227908 CCGCTCTCCGTATTTGTATTGTAT 58.772 41.667 0.00 0.00 34.38 2.29
684 691 5.118664 CCGCTCTCCGTATTTGTATTGTATG 59.881 44.000 0.00 0.00 34.38 2.39
685 692 5.388475 CGCTCTCCGTATTTGTATTGTATGC 60.388 44.000 0.00 0.00 0.00 3.14
686 693 5.107065 GCTCTCCGTATTTGTATTGTATGCC 60.107 44.000 0.00 0.00 0.00 4.40
687 694 4.986034 TCTCCGTATTTGTATTGTATGCCG 59.014 41.667 0.00 0.00 0.00 5.69
688 695 3.495377 TCCGTATTTGTATTGTATGCCGC 59.505 43.478 0.00 0.00 0.00 6.53
689 696 3.496884 CCGTATTTGTATTGTATGCCGCT 59.503 43.478 0.00 0.00 0.00 5.52
690 697 4.377022 CCGTATTTGTATTGTATGCCGCTC 60.377 45.833 0.00 0.00 0.00 5.03
691 698 4.377022 CGTATTTGTATTGTATGCCGCTCC 60.377 45.833 0.00 0.00 0.00 4.70
692 699 1.577468 TTGTATTGTATGCCGCTCCG 58.423 50.000 0.00 0.00 0.00 4.63
693 700 0.878523 TGTATTGTATGCCGCTCCGC 60.879 55.000 0.00 0.00 0.00 5.54
694 701 0.600255 GTATTGTATGCCGCTCCGCT 60.600 55.000 0.00 0.00 0.00 5.52
695 702 0.319555 TATTGTATGCCGCTCCGCTC 60.320 55.000 0.00 0.00 0.00 5.03
696 703 2.996168 ATTGTATGCCGCTCCGCTCC 62.996 60.000 0.00 0.00 0.00 4.70
713 720 2.579787 CGCAGCGGAGTTACGGAG 60.580 66.667 7.00 0.00 0.00 4.63
714 721 2.886124 GCAGCGGAGTTACGGAGC 60.886 66.667 0.00 0.00 0.00 4.70
715 722 2.579787 CAGCGGAGTTACGGAGCG 60.580 66.667 0.00 0.00 0.00 5.03
716 723 3.823330 AGCGGAGTTACGGAGCGG 61.823 66.667 0.00 0.00 0.00 5.52
717 724 3.818787 GCGGAGTTACGGAGCGGA 61.819 66.667 0.00 0.00 0.00 5.54
718 725 2.408022 CGGAGTTACGGAGCGGAG 59.592 66.667 0.00 0.00 0.00 4.63
719 726 2.806237 GGAGTTACGGAGCGGAGG 59.194 66.667 0.00 0.00 0.00 4.30
720 727 2.783288 GGAGTTACGGAGCGGAGGG 61.783 68.421 0.00 0.00 0.00 4.30
721 728 1.751927 GAGTTACGGAGCGGAGGGA 60.752 63.158 0.00 0.00 0.00 4.20
722 729 1.076192 AGTTACGGAGCGGAGGGAT 60.076 57.895 0.00 0.00 0.00 3.85
723 730 0.686769 AGTTACGGAGCGGAGGGATT 60.687 55.000 0.00 0.00 0.00 3.01
724 731 0.249363 GTTACGGAGCGGAGGGATTC 60.249 60.000 0.00 0.00 0.00 2.52
725 732 1.397390 TTACGGAGCGGAGGGATTCC 61.397 60.000 0.00 0.00 43.04 3.01
732 739 3.625099 GGAGGGATTCCGAACGGA 58.375 61.111 12.04 12.04 43.52 4.69
733 740 1.442148 GGAGGGATTCCGAACGGAG 59.558 63.158 15.34 0.00 46.06 4.63
734 741 1.227292 GAGGGATTCCGAACGGAGC 60.227 63.158 15.34 11.67 46.06 4.70
735 742 2.203029 GGGATTCCGAACGGAGCC 60.203 66.667 20.76 20.76 46.06 4.70
752 759 1.946745 GCCTTAGCTGCTAACTCCAG 58.053 55.000 17.67 8.04 35.50 3.86
772 789 2.893489 AGCACTGATCACTAGTGTCACA 59.107 45.455 21.99 17.50 45.60 3.58
853 1212 2.283145 AGCATGCAGGAAGAAACACT 57.717 45.000 21.98 0.00 0.00 3.55
906 1278 2.344872 GTCCCGGCGTTACCTGTT 59.655 61.111 6.01 0.00 35.61 3.16
972 1353 1.578583 CCTCCACGCTATAAAACCCG 58.421 55.000 0.00 0.00 0.00 5.28
1049 1431 1.133325 ACAGAGTCCACAGTCCAGACT 60.133 52.381 0.00 0.00 43.42 3.24
1065 1447 1.958579 AGACTATACGGCGCACCATAA 59.041 47.619 10.83 0.00 34.57 1.90
1066 1448 2.056577 GACTATACGGCGCACCATAAC 58.943 52.381 10.83 0.00 34.57 1.89
1271 1662 4.070552 GTCTGCGTCCTCGGCCTT 62.071 66.667 0.00 0.00 37.56 4.35
1373 1769 1.447838 GAAGAAGGCCATCGACGCA 60.448 57.895 5.01 0.00 0.00 5.24
1380 1776 2.885644 CCATCGACGCACTTCCCG 60.886 66.667 0.00 0.00 0.00 5.14
1566 1980 4.431131 CATGCCCCTCCTGCCGTT 62.431 66.667 0.00 0.00 0.00 4.44
1642 2059 0.596082 GTAGTGGCGGCAAACAACAT 59.404 50.000 15.50 0.00 0.00 2.71
1703 2120 2.094182 TGAAGATAGCACCACGGTCTTC 60.094 50.000 7.37 7.37 40.81 2.87
1713 2373 3.937079 CACCACGGTCTTCCCTTAATTAC 59.063 47.826 0.00 0.00 0.00 1.89
1773 2718 7.766219 TTTGCTAGTTAGGCTAAGTAATTCG 57.234 36.000 19.52 11.02 0.00 3.34
1777 2722 8.636213 TGCTAGTTAGGCTAAGTAATTCGTTAT 58.364 33.333 19.52 0.00 0.00 1.89
1842 2788 9.733556 ATTAATTATTCAGGTCTGTTGTACACA 57.266 29.630 0.00 0.00 0.00 3.72
1867 2813 8.534778 CAGTTCTTGAGCTTCATTTTGTTTTAC 58.465 33.333 0.00 0.00 0.00 2.01
1888 2834 4.781934 ACTTCTTCTGCTGTTTTGGTAGT 58.218 39.130 0.00 0.00 0.00 2.73
1891 2837 6.260271 ACTTCTTCTGCTGTTTTGGTAGTTAC 59.740 38.462 0.00 0.00 0.00 2.50
1944 2890 6.095440 GGAATAGCTCAATTTTGTAGCTTGGA 59.905 38.462 16.70 5.81 40.03 3.53
2032 2979 6.152154 TGTTCTAAATAAAAAGGTGCTAGGCC 59.848 38.462 0.00 0.00 0.00 5.19
2035 2982 0.694196 TAAAAAGGTGCTAGGCCGGT 59.306 50.000 1.90 0.00 0.00 5.28
2037 2984 2.064242 AAAAGGTGCTAGGCCGGTGT 62.064 55.000 1.90 0.00 0.00 4.16
2038 2985 2.465055 AAAGGTGCTAGGCCGGTGTC 62.465 60.000 1.90 0.00 0.00 3.67
2083 3030 2.434884 CATTGAGCCACCGAGCGT 60.435 61.111 0.00 0.00 38.01 5.07
2092 3039 0.108329 CCACCGAGCGTCACCTTTAT 60.108 55.000 0.00 0.00 0.00 1.40
2106 3053 5.048782 GTCACCTTTATCATTGCAACACAGA 60.049 40.000 0.00 0.00 0.00 3.41
2122 3069 7.697352 CAACACAGATTGTATTGCAGAAAAA 57.303 32.000 0.00 0.00 37.51 1.94
2217 3164 7.994425 TTCTGCAATAGAGGTTTCATTGTAA 57.006 32.000 0.00 0.00 36.61 2.41
2272 3232 6.506538 AGAGACCTTGCCATATAAACTCAT 57.493 37.500 0.00 0.00 0.00 2.90
2275 3235 6.058183 AGACCTTGCCATATAAACTCATCAC 58.942 40.000 0.00 0.00 0.00 3.06
2296 3256 3.455469 GCAATGAGCAGGGGCCAC 61.455 66.667 4.39 0.00 44.79 5.01
2400 3360 1.228644 AGCCAGTTGATGCCAAGCA 60.229 52.632 0.00 0.00 44.86 3.91
2440 3400 5.401079 CCAAAGCGTGTAGGTGTAAATTTTG 59.599 40.000 0.00 0.00 0.00 2.44
2461 3421 0.583438 CTTTATGCGACAGCCATCCG 59.417 55.000 0.00 0.00 44.33 4.18
2719 3682 7.282675 AGCTTTTAGTCTCCATCAGAATCAATG 59.717 37.037 0.00 0.00 30.18 2.82
2855 3818 2.004017 AGTCTTTGTCGCGTGTCAAAA 58.996 42.857 19.10 9.87 33.75 2.44
2880 3843 2.516930 CCTAGCCGGCAATGTGGG 60.517 66.667 31.54 15.84 0.00 4.61
2895 3858 2.481441 TGTGGGTGCCATCTCTATCTT 58.519 47.619 0.00 0.00 35.28 2.40
2968 4366 1.613630 ATCCGCCAGACCAGGAGTT 60.614 57.895 0.00 0.00 37.49 3.01
3016 4414 1.301716 CTCGGTGTTGACCAGGTGG 60.302 63.158 0.00 0.00 43.33 4.61
3017 4415 1.754380 CTCGGTGTTGACCAGGTGGA 61.754 60.000 0.00 0.00 43.33 4.02
3019 4417 1.228154 GGTGTTGACCAGGTGGACC 60.228 63.158 0.00 0.00 42.59 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 1.307097 GCCCAGAGATGCTCAATCAC 58.693 55.000 0.00 0.00 37.81 3.06
184 185 1.667724 CCCGCAAGCTCAAGATAACTG 59.332 52.381 0.00 0.00 0.00 3.16
191 192 0.881118 TTAAAGCCCGCAAGCTCAAG 59.119 50.000 0.00 0.00 44.11 3.02
217 218 6.519679 TCTAGCTGTAAACATCCGTTTCTA 57.480 37.500 0.00 0.00 44.27 2.10
221 222 5.354234 CCAAATCTAGCTGTAAACATCCGTT 59.646 40.000 0.00 0.00 36.73 4.44
234 235 1.202698 GCCGACCATCCAAATCTAGCT 60.203 52.381 0.00 0.00 0.00 3.32
260 261 3.978687 GACCAGTCCACGGATACTAATG 58.021 50.000 0.00 0.00 0.00 1.90
294 295 1.663379 CCAGACACCGCATCCGTCTA 61.663 60.000 0.00 0.00 37.92 2.59
311 312 1.962807 CCAAGGCTGACATTCAAACCA 59.037 47.619 0.00 0.00 0.00 3.67
319 320 2.203584 AGGAATCTCCAAGGCTGACAT 58.796 47.619 0.00 0.00 39.61 3.06
484 485 5.071788 TGCTCCCTAGAAGAAGAAGAAAACA 59.928 40.000 0.00 0.00 0.00 2.83
584 591 4.260375 CGAACACAGCCTAAATATGTCAGC 60.260 45.833 0.00 0.00 0.00 4.26
586 593 4.188462 CCGAACACAGCCTAAATATGTCA 58.812 43.478 0.00 0.00 0.00 3.58
592 599 1.271379 ACTGCCGAACACAGCCTAAAT 60.271 47.619 0.00 0.00 38.79 1.40
593 600 0.107831 ACTGCCGAACACAGCCTAAA 59.892 50.000 0.00 0.00 38.79 1.85
594 601 0.320421 GACTGCCGAACACAGCCTAA 60.320 55.000 0.00 0.00 38.79 2.69
595 602 1.292223 GACTGCCGAACACAGCCTA 59.708 57.895 0.00 0.00 38.79 3.93
596 603 2.031163 GACTGCCGAACACAGCCT 59.969 61.111 0.00 0.00 38.79 4.58
597 604 3.050275 GGACTGCCGAACACAGCC 61.050 66.667 0.00 0.00 38.79 4.85
598 605 2.280797 TGGACTGCCGAACACAGC 60.281 61.111 0.00 0.00 38.79 4.40
599 606 1.961277 GGTGGACTGCCGAACACAG 60.961 63.158 8.53 0.00 41.08 3.66
600 607 2.110213 GGTGGACTGCCGAACACA 59.890 61.111 8.53 0.00 36.79 3.72
609 616 3.680786 TGACGGAGCGGTGGACTG 61.681 66.667 0.00 0.00 0.00 3.51
610 617 3.681835 GTGACGGAGCGGTGGACT 61.682 66.667 0.00 0.00 0.00 3.85
611 618 4.736896 GGTGACGGAGCGGTGGAC 62.737 72.222 0.00 0.00 0.00 4.02
613 620 4.742201 CTGGTGACGGAGCGGTGG 62.742 72.222 0.00 0.00 39.98 4.61
614 621 3.680786 TCTGGTGACGGAGCGGTG 61.681 66.667 0.00 0.00 42.04 4.94
620 627 2.342279 CCGCTTTCTGGTGACGGA 59.658 61.111 0.00 0.00 46.71 4.69
621 628 1.738099 CTCCGCTTTCTGGTGACGG 60.738 63.158 0.00 0.00 45.15 4.79
622 629 2.383527 GCTCCGCTTTCTGGTGACG 61.384 63.158 0.00 0.00 0.00 4.35
623 630 2.383527 CGCTCCGCTTTCTGGTGAC 61.384 63.158 0.00 0.00 0.00 3.67
624 631 2.048222 CGCTCCGCTTTCTGGTGA 60.048 61.111 0.00 0.00 0.00 4.02
641 648 4.120331 AAATTGGCTGCTCCGCGC 62.120 61.111 0.00 0.00 37.80 6.86
642 649 2.202518 CAAATTGGCTGCTCCGCG 60.203 61.111 0.00 0.00 37.80 6.46
643 650 2.507769 GCAAATTGGCTGCTCCGC 60.508 61.111 0.00 0.00 36.84 5.54
644 651 2.182537 GGCAAATTGGCTGCTCCG 59.817 61.111 12.54 0.00 40.14 4.63
645 652 2.182537 CGGCAAATTGGCTGCTCC 59.817 61.111 17.34 0.00 41.25 4.70
649 656 1.138247 GAGAGCGGCAAATTGGCTG 59.862 57.895 17.34 9.49 41.25 4.85
650 657 2.048603 GGAGAGCGGCAAATTGGCT 61.049 57.895 17.34 7.19 41.25 4.75
651 658 2.491621 GGAGAGCGGCAAATTGGC 59.508 61.111 9.68 9.68 39.85 4.52
652 659 0.742990 TACGGAGAGCGGCAAATTGG 60.743 55.000 1.45 0.00 0.00 3.16
653 660 1.299541 ATACGGAGAGCGGCAAATTG 58.700 50.000 1.45 0.00 0.00 2.32
654 661 2.038387 AATACGGAGAGCGGCAAATT 57.962 45.000 1.45 0.00 0.00 1.82
655 662 1.670811 CAAATACGGAGAGCGGCAAAT 59.329 47.619 1.45 0.00 0.00 2.32
656 663 1.083489 CAAATACGGAGAGCGGCAAA 58.917 50.000 1.45 0.00 0.00 3.68
657 664 0.036765 ACAAATACGGAGAGCGGCAA 60.037 50.000 1.45 0.00 0.00 4.52
658 665 0.818938 TACAAATACGGAGAGCGGCA 59.181 50.000 1.45 0.00 0.00 5.69
659 666 2.150397 ATACAAATACGGAGAGCGGC 57.850 50.000 0.00 0.00 0.00 6.53
660 667 3.454375 ACAATACAAATACGGAGAGCGG 58.546 45.455 0.00 0.00 0.00 5.52
661 668 5.388475 GCATACAATACAAATACGGAGAGCG 60.388 44.000 0.00 0.00 0.00 5.03
662 669 5.107065 GGCATACAATACAAATACGGAGAGC 60.107 44.000 0.00 0.00 0.00 4.09
663 670 5.118664 CGGCATACAATACAAATACGGAGAG 59.881 44.000 0.00 0.00 0.00 3.20
664 671 4.986034 CGGCATACAATACAAATACGGAGA 59.014 41.667 0.00 0.00 0.00 3.71
665 672 4.377022 GCGGCATACAATACAAATACGGAG 60.377 45.833 0.00 0.00 0.00 4.63
666 673 3.495377 GCGGCATACAATACAAATACGGA 59.505 43.478 0.00 0.00 0.00 4.69
667 674 3.496884 AGCGGCATACAATACAAATACGG 59.503 43.478 1.45 0.00 0.00 4.02
668 675 4.377022 GGAGCGGCATACAATACAAATACG 60.377 45.833 1.45 0.00 0.00 3.06
669 676 4.377022 CGGAGCGGCATACAATACAAATAC 60.377 45.833 1.45 0.00 0.00 1.89
670 677 3.743911 CGGAGCGGCATACAATACAAATA 59.256 43.478 1.45 0.00 0.00 1.40
671 678 2.548057 CGGAGCGGCATACAATACAAAT 59.452 45.455 1.45 0.00 0.00 2.32
672 679 1.937223 CGGAGCGGCATACAATACAAA 59.063 47.619 1.45 0.00 0.00 2.83
673 680 1.577468 CGGAGCGGCATACAATACAA 58.423 50.000 1.45 0.00 0.00 2.41
674 681 3.282557 CGGAGCGGCATACAATACA 57.717 52.632 1.45 0.00 0.00 2.29
696 703 2.579787 CTCCGTAACTCCGCTGCG 60.580 66.667 16.34 16.34 0.00 5.18
697 704 2.886124 GCTCCGTAACTCCGCTGC 60.886 66.667 0.00 0.00 0.00 5.25
698 705 2.579787 CGCTCCGTAACTCCGCTG 60.580 66.667 0.00 0.00 0.00 5.18
699 706 3.823330 CCGCTCCGTAACTCCGCT 61.823 66.667 0.00 0.00 0.00 5.52
700 707 3.753070 CTCCGCTCCGTAACTCCGC 62.753 68.421 0.00 0.00 0.00 5.54
701 708 2.408022 CTCCGCTCCGTAACTCCG 59.592 66.667 0.00 0.00 0.00 4.63
702 709 2.783288 CCCTCCGCTCCGTAACTCC 61.783 68.421 0.00 0.00 0.00 3.85
703 710 1.108132 ATCCCTCCGCTCCGTAACTC 61.108 60.000 0.00 0.00 0.00 3.01
704 711 0.686769 AATCCCTCCGCTCCGTAACT 60.687 55.000 0.00 0.00 0.00 2.24
705 712 0.249363 GAATCCCTCCGCTCCGTAAC 60.249 60.000 0.00 0.00 0.00 2.50
706 713 1.397390 GGAATCCCTCCGCTCCGTAA 61.397 60.000 0.00 0.00 33.37 3.18
707 714 1.831286 GGAATCCCTCCGCTCCGTA 60.831 63.158 0.00 0.00 33.37 4.02
708 715 3.155167 GGAATCCCTCCGCTCCGT 61.155 66.667 0.00 0.00 33.37 4.69
715 722 1.442148 CTCCGTTCGGAATCCCTCC 59.558 63.158 14.79 0.00 41.40 4.30
716 723 1.227292 GCTCCGTTCGGAATCCCTC 60.227 63.158 14.79 0.00 33.41 4.30
717 724 2.732619 GGCTCCGTTCGGAATCCCT 61.733 63.158 14.79 0.00 33.41 4.20
718 725 2.203029 GGCTCCGTTCGGAATCCC 60.203 66.667 14.79 11.27 33.41 3.85
719 726 0.462789 TAAGGCTCCGTTCGGAATCC 59.537 55.000 14.79 16.73 33.41 3.01
720 727 1.854227 CTAAGGCTCCGTTCGGAATC 58.146 55.000 14.79 9.70 33.41 2.52
721 728 0.179081 GCTAAGGCTCCGTTCGGAAT 60.179 55.000 14.79 4.94 33.41 3.01
722 729 1.217244 GCTAAGGCTCCGTTCGGAA 59.783 57.895 14.79 0.00 33.41 4.30
723 730 2.890371 GCTAAGGCTCCGTTCGGA 59.110 61.111 13.34 13.34 35.22 4.55
733 740 1.946745 CTGGAGTTAGCAGCTAAGGC 58.053 55.000 15.55 9.96 39.06 4.35
734 741 1.946745 GCTGGAGTTAGCAGCTAAGG 58.053 55.000 15.55 5.17 43.17 2.69
752 759 3.303881 TGTGACACTAGTGATCAGTGC 57.696 47.619 29.30 15.54 45.96 4.40
772 789 7.151308 TCGTGGAAATTAAGCAAATCATTGTT 58.849 30.769 0.00 0.00 38.85 2.83
808 826 4.870991 GCTCCTTTTAGCTTACTACCAGTG 59.129 45.833 0.00 0.00 39.50 3.66
816 836 3.081804 TGCTTGGCTCCTTTTAGCTTAC 58.918 45.455 0.00 0.00 42.37 2.34
853 1212 1.006337 GCGCAAATGCCACTTTGGA 60.006 52.632 0.30 0.00 40.96 3.53
866 1225 2.822255 GATTAGTGGCGGGCGCAA 60.822 61.111 17.69 9.68 44.11 4.85
867 1226 4.849310 GGATTAGTGGCGGGCGCA 62.849 66.667 17.69 0.00 44.11 6.09
972 1353 1.423056 GTGTGCGATGCTCTGCTTC 59.577 57.895 0.00 0.00 0.00 3.86
1049 1431 0.751452 TGGTTATGGTGCGCCGTATA 59.249 50.000 18.76 5.66 36.24 1.47
1065 1447 2.358003 GTCGCTTCTGCTGCTGGT 60.358 61.111 6.69 0.00 36.97 4.00
1066 1448 2.357881 TGTCGCTTCTGCTGCTGG 60.358 61.111 6.69 0.00 36.97 4.85
1196 1587 2.100631 CGAGTTCACCGCCATCACC 61.101 63.158 0.00 0.00 0.00 4.02
1310 1701 2.038813 TGGTCGGAGGATGAGGCA 59.961 61.111 0.00 0.00 0.00 4.75
1373 1769 2.603776 AAGGAGACGGCGGGAAGT 60.604 61.111 13.24 0.00 0.00 3.01
1417 1828 4.803426 CAGAGGACGAGCACGCCC 62.803 72.222 2.62 1.03 42.21 6.13
1457 1871 2.990479 CCCTCCCCTTCCGTGAAG 59.010 66.667 6.66 6.66 39.17 3.02
1566 1980 0.107214 GCAGAAACGATGATGGGGGA 60.107 55.000 0.00 0.00 0.00 4.81
1727 2387 9.949174 GCAAAACAAAAGGAAATGAAACATAAT 57.051 25.926 0.00 0.00 0.00 1.28
1737 2398 6.929049 GCCTAACTAGCAAAACAAAAGGAAAT 59.071 34.615 0.00 0.00 0.00 2.17
1741 2402 5.453567 AGCCTAACTAGCAAAACAAAAGG 57.546 39.130 0.00 0.00 0.00 3.11
1773 2718 7.864307 ACACAACTAACTAAGACGTCATAAC 57.136 36.000 19.50 0.00 0.00 1.89
1832 2778 4.137116 AGCTCAAGAACTGTGTACAACA 57.863 40.909 0.00 0.00 37.22 3.33
1842 2788 8.470002 AGTAAAACAAAATGAAGCTCAAGAACT 58.530 29.630 0.00 0.00 0.00 3.01
1846 2792 8.862550 AGAAGTAAAACAAAATGAAGCTCAAG 57.137 30.769 0.00 0.00 0.00 3.02
1850 2796 7.436376 GCAGAAGAAGTAAAACAAAATGAAGCT 59.564 33.333 0.00 0.00 0.00 3.74
1867 2813 5.757850 AACTACCAAAACAGCAGAAGAAG 57.242 39.130 0.00 0.00 0.00 2.85
1888 2834 1.155889 TCGACGAACAGGCTACGTAA 58.844 50.000 12.07 3.60 40.29 3.18
1891 2837 0.591741 GGATCGACGAACAGGCTACG 60.592 60.000 0.00 6.42 0.00 3.51
2065 3012 3.869272 CGCTCGGTGGCTCAATGC 61.869 66.667 0.00 0.00 41.94 3.56
2074 3021 1.278238 GATAAAGGTGACGCTCGGTG 58.722 55.000 0.00 0.00 0.00 4.94
2083 3030 5.069318 TCTGTGTTGCAATGATAAAGGTGA 58.931 37.500 0.59 0.00 0.00 4.02
2087 3034 9.577110 AATACAATCTGTGTTGCAATGATAAAG 57.423 29.630 0.59 0.00 41.98 1.85
2122 3069 4.973396 CAACATGATACGTGTTGCAGAAT 58.027 39.130 19.03 0.00 46.64 2.40
2233 3181 7.373493 CAAGGTCTCTATTGCAAAATCTTTGT 58.627 34.615 1.71 0.00 0.00 2.83
2272 3232 0.035725 CCCTGCTCATTGCTCAGTGA 60.036 55.000 0.00 0.00 43.37 3.41
2275 3235 2.119655 GCCCCTGCTCATTGCTCAG 61.120 63.158 0.00 0.00 43.37 3.35
2283 3243 4.641645 CAACGTGGCCCCTGCTCA 62.642 66.667 0.00 0.00 37.74 4.26
2296 3256 3.936902 TGTTCTTTCTTTCGGTCAACG 57.063 42.857 0.00 0.00 46.11 4.10
2330 3290 2.733593 GACGCGTGTCCAGACCAC 60.734 66.667 20.70 0.00 39.30 4.16
2348 3308 1.810606 ATCCGCCGGCTCACTCATAG 61.811 60.000 26.68 4.88 0.00 2.23
2400 3360 8.454894 ACACGCTTTGGTTTTTATTTGAAAAAT 58.545 25.926 0.00 0.00 32.55 1.82
2440 3400 0.308993 GATGGCTGTCGCATAAAGGC 59.691 55.000 0.00 0.00 38.10 4.35
2545 3507 5.512942 TGATTTGTTCCATACTTCCTCCA 57.487 39.130 0.00 0.00 0.00 3.86
2551 3513 7.959658 TCATCCAATGATTTGTTCCATACTT 57.040 32.000 0.00 0.00 33.59 2.24
2572 3534 7.212976 AGCTATTGTCACACTCGATTTATCAT 58.787 34.615 0.00 0.00 0.00 2.45
2573 3535 6.573434 AGCTATTGTCACACTCGATTTATCA 58.427 36.000 0.00 0.00 0.00 2.15
2574 3536 7.470289 AAGCTATTGTCACACTCGATTTATC 57.530 36.000 0.00 0.00 0.00 1.75
2719 3682 0.903942 TTGCTTCAATCAATGGGGGC 59.096 50.000 0.00 0.00 0.00 5.80
2816 3779 7.736447 AAGACTATTCTTTCAGGAACAACAG 57.264 36.000 0.00 0.00 39.17 3.16
2844 3807 2.095768 AGGACATGAATTTTGACACGCG 60.096 45.455 3.53 3.53 0.00 6.01
2847 3810 4.437390 CGGCTAGGACATGAATTTTGACAC 60.437 45.833 0.00 0.00 0.00 3.67
2855 3818 0.546122 TTGCCGGCTAGGACATGAAT 59.454 50.000 29.70 0.00 45.00 2.57
2880 3843 2.748605 CCACGAAGATAGAGATGGCAC 58.251 52.381 0.00 0.00 0.00 5.01
2895 3858 6.649141 CCAAAGTATATATAAAGCTGCCACGA 59.351 38.462 0.00 0.00 0.00 4.35
2968 4366 1.801242 TCAACTCTTGGGGACTGACA 58.199 50.000 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.