Multiple sequence alignment - TraesCS4B01G086200

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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 TraesCS4B01G086200 chr4B 100.000 3197 0 0 1 3197 86133031 86129835 0.000000e+00 5904.0
1 TraesCS4B01G086200 chr4B 90.915 1431 89 26 866 2280 520298347 520296942 0.000000e+00 1884.0
2 TraesCS4B01G086200 chr4B 87.240 1395 137 27 866 2245 522669333 522670701 0.000000e+00 1552.0
3 TraesCS4B01G086200 chr4B 86.340 1369 140 27 895 2238 527644877 527643531 0.000000e+00 1448.0
4 TraesCS4B01G086200 chr4B 87.202 672 70 7 2 661 618630109 618630776 0.000000e+00 750.0
5 TraesCS4B01G086200 chr4B 87.054 672 71 7 2 661 618636882 618637549 0.000000e+00 745.0
6 TraesCS4B01G086200 chr4B 91.745 424 11 8 2263 2666 86097269 86096850 4.630000e-158 568.0
7 TraesCS4B01G086200 chr4B 88.889 180 15 2 2491 2666 520296793 520296615 1.930000e-52 217.0
8 TraesCS4B01G086200 chr4B 89.286 56 3 3 2437 2489 520296403 520296348 2.060000e-07 67.6
9 TraesCS4B01G086200 chr4D 91.484 1914 95 19 789 2649 57840490 57842388 0.000000e+00 2569.0
10 TraesCS4B01G086200 chr4D 89.145 1824 128 38 866 2666 423989894 423988118 0.000000e+00 2207.0
11 TraesCS4B01G086200 chr4D 90.186 1559 106 40 819 2354 424169697 424168163 0.000000e+00 1988.0
12 TraesCS4B01G086200 chr4D 89.783 1566 103 42 819 2351 424110683 424109142 0.000000e+00 1953.0
13 TraesCS4B01G086200 chr4D 88.591 1455 121 21 866 2303 424322783 424321357 0.000000e+00 1725.0
14 TraesCS4B01G086200 chr4D 89.011 1365 113 22 866 2217 426870181 426871521 0.000000e+00 1655.0
15 TraesCS4B01G086200 chr4D 91.518 896 53 13 1468 2351 424196575 424195691 0.000000e+00 1212.0
16 TraesCS4B01G086200 chr4D 94.906 530 27 0 2668 3197 468259939 468259410 0.000000e+00 830.0
17 TraesCS4B01G086200 chr4D 83.471 726 99 18 1486 2195 426901241 426901961 0.000000e+00 656.0
18 TraesCS4B01G086200 chr4D 91.244 217 15 1 2454 2666 424109075 424108859 3.120000e-75 292.0
19 TraesCS4B01G086200 chr4D 90.783 217 16 1 2454 2666 424195624 424195408 1.450000e-73 287.0
20 TraesCS4B01G086200 chr4D 89.444 180 14 2 2491 2666 424168069 424167891 4.150000e-54 222.0
21 TraesCS4B01G086200 chr4D 89.326 178 16 2 2491 2666 424309016 424308840 1.490000e-53 220.0
22 TraesCS4B01G086200 chr4A 87.182 1888 134 61 819 2663 40260693 40262515 0.000000e+00 2047.0
23 TraesCS4B01G086200 chr4A 85.326 1397 142 33 823 2203 38682939 38681590 0.000000e+00 1386.0
24 TraesCS4B01G086200 chr4A 88.401 569 39 9 2113 2663 539140504 539141063 0.000000e+00 660.0
25 TraesCS4B01G086200 chr4A 87.805 82 7 2 978 1059 40258132 40258210 3.400000e-15 93.5
26 TraesCS4B01G086200 chr1B 95.113 532 25 1 2666 3197 646488820 646489350 0.000000e+00 837.0
27 TraesCS4B01G086200 chr1B 87.349 664 67 11 3 654 379627267 379627925 0.000000e+00 745.0
28 TraesCS4B01G086200 chr1B 86.846 669 68 14 3 660 671544046 671544705 0.000000e+00 730.0
29 TraesCS4B01G086200 chr3A 94.776 536 28 0 2662 3197 699422558 699422023 0.000000e+00 835.0
30 TraesCS4B01G086200 chr3A 85.373 670 84 7 2 660 550470565 550471231 0.000000e+00 682.0
31 TraesCS4B01G086200 chr2A 94.361 532 29 1 2666 3197 768629741 768630271 0.000000e+00 815.0
32 TraesCS4B01G086200 chr2A 83.721 645 88 8 2 630 189166912 189167555 7.640000e-166 593.0
33 TraesCS4B01G086200 chr7B 94.361 532 27 2 2666 3197 158378261 158377733 0.000000e+00 813.0
34 TraesCS4B01G086200 chr2D 94.184 533 30 1 2666 3197 287895183 287894651 0.000000e+00 811.0
35 TraesCS4B01G086200 chr2D 85.993 614 65 11 2 598 176560705 176561314 3.480000e-179 638.0
36 TraesCS4B01G086200 chr2D 84.129 649 69 20 2 624 626641275 626640635 5.900000e-167 597.0
37 TraesCS4B01G086200 chr5D 93.482 537 34 1 2661 3197 77588699 77589234 0.000000e+00 797.0
38 TraesCS4B01G086200 chr6B 93.774 530 31 2 2666 3194 292768220 292767692 0.000000e+00 795.0
39 TraesCS4B01G086200 chr7A 93.433 533 35 0 2665 3197 651183549 651183017 0.000000e+00 791.0
40 TraesCS4B01G086200 chr7A 84.461 547 74 7 124 659 637613383 637612837 2.180000e-146 529.0
41 TraesCS4B01G086200 chr6A 87.126 668 74 6 2 659 451602354 451601689 0.000000e+00 747.0
42 TraesCS4B01G086200 chrUn 87.054 672 71 7 2 661 332621977 332622644 0.000000e+00 745.0
43 TraesCS4B01G086200 chrUn 83.600 250 25 9 866 1115 60140501 60140268 1.490000e-53 220.0
44 TraesCS4B01G086200 chrUn 83.600 250 25 9 866 1115 235654848 235654615 1.490000e-53 220.0
45 TraesCS4B01G086200 chr1A 86.333 600 69 6 2 589 13969728 13970326 2.690000e-180 641.0
46 TraesCS4B01G086200 chr1A 85.859 198 28 0 462 659 57121601 57121404 8.990000e-51 211.0
47 TraesCS4B01G086200 chr5A 85.039 635 78 14 2 622 24413608 24412977 5.820000e-177 630.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4B01G086200 chr4B 86129835 86133031 3196 True 5904.000000 5904 100.000000 1 3197 1 chr4B.!!$R2 3196
1 TraesCS4B01G086200 chr4B 522669333 522670701 1368 False 1552.000000 1552 87.240000 866 2245 1 chr4B.!!$F1 1379
2 TraesCS4B01G086200 chr4B 527643531 527644877 1346 True 1448.000000 1448 86.340000 895 2238 1 chr4B.!!$R3 1343
3 TraesCS4B01G086200 chr4B 618630109 618630776 667 False 750.000000 750 87.202000 2 661 1 chr4B.!!$F2 659
4 TraesCS4B01G086200 chr4B 618636882 618637549 667 False 745.000000 745 87.054000 2 661 1 chr4B.!!$F3 659
5 TraesCS4B01G086200 chr4B 520296348 520298347 1999 True 722.866667 1884 89.696667 866 2666 3 chr4B.!!$R4 1800
6 TraesCS4B01G086200 chr4D 57840490 57842388 1898 False 2569.000000 2569 91.484000 789 2649 1 chr4D.!!$F1 1860
7 TraesCS4B01G086200 chr4D 423988118 423989894 1776 True 2207.000000 2207 89.145000 866 2666 1 chr4D.!!$R1 1800
8 TraesCS4B01G086200 chr4D 424321357 424322783 1426 True 1725.000000 1725 88.591000 866 2303 1 chr4D.!!$R3 1437
9 TraesCS4B01G086200 chr4D 426870181 426871521 1340 False 1655.000000 1655 89.011000 866 2217 1 chr4D.!!$F2 1351
10 TraesCS4B01G086200 chr4D 424108859 424110683 1824 True 1122.500000 1953 90.513500 819 2666 2 chr4D.!!$R5 1847
11 TraesCS4B01G086200 chr4D 424167891 424169697 1806 True 1105.000000 1988 89.815000 819 2666 2 chr4D.!!$R6 1847
12 TraesCS4B01G086200 chr4D 468259410 468259939 529 True 830.000000 830 94.906000 2668 3197 1 chr4D.!!$R4 529
13 TraesCS4B01G086200 chr4D 424195408 424196575 1167 True 749.500000 1212 91.150500 1468 2666 2 chr4D.!!$R7 1198
14 TraesCS4B01G086200 chr4D 426901241 426901961 720 False 656.000000 656 83.471000 1486 2195 1 chr4D.!!$F3 709
15 TraesCS4B01G086200 chr4A 38681590 38682939 1349 True 1386.000000 1386 85.326000 823 2203 1 chr4A.!!$R1 1380
16 TraesCS4B01G086200 chr4A 40258132 40262515 4383 False 1070.250000 2047 87.493500 819 2663 2 chr4A.!!$F2 1844
17 TraesCS4B01G086200 chr4A 539140504 539141063 559 False 660.000000 660 88.401000 2113 2663 1 chr4A.!!$F1 550
18 TraesCS4B01G086200 chr1B 646488820 646489350 530 False 837.000000 837 95.113000 2666 3197 1 chr1B.!!$F2 531
19 TraesCS4B01G086200 chr1B 379627267 379627925 658 False 745.000000 745 87.349000 3 654 1 chr1B.!!$F1 651
20 TraesCS4B01G086200 chr1B 671544046 671544705 659 False 730.000000 730 86.846000 3 660 1 chr1B.!!$F3 657
21 TraesCS4B01G086200 chr3A 699422023 699422558 535 True 835.000000 835 94.776000 2662 3197 1 chr3A.!!$R1 535
22 TraesCS4B01G086200 chr3A 550470565 550471231 666 False 682.000000 682 85.373000 2 660 1 chr3A.!!$F1 658
23 TraesCS4B01G086200 chr2A 768629741 768630271 530 False 815.000000 815 94.361000 2666 3197 1 chr2A.!!$F2 531
24 TraesCS4B01G086200 chr2A 189166912 189167555 643 False 593.000000 593 83.721000 2 630 1 chr2A.!!$F1 628
25 TraesCS4B01G086200 chr7B 158377733 158378261 528 True 813.000000 813 94.361000 2666 3197 1 chr7B.!!$R1 531
26 TraesCS4B01G086200 chr2D 287894651 287895183 532 True 811.000000 811 94.184000 2666 3197 1 chr2D.!!$R1 531
27 TraesCS4B01G086200 chr2D 176560705 176561314 609 False 638.000000 638 85.993000 2 598 1 chr2D.!!$F1 596
28 TraesCS4B01G086200 chr2D 626640635 626641275 640 True 597.000000 597 84.129000 2 624 1 chr2D.!!$R2 622
29 TraesCS4B01G086200 chr5D 77588699 77589234 535 False 797.000000 797 93.482000 2661 3197 1 chr5D.!!$F1 536
30 TraesCS4B01G086200 chr6B 292767692 292768220 528 True 795.000000 795 93.774000 2666 3194 1 chr6B.!!$R1 528
31 TraesCS4B01G086200 chr7A 651183017 651183549 532 True 791.000000 791 93.433000 2665 3197 1 chr7A.!!$R2 532
32 TraesCS4B01G086200 chr7A 637612837 637613383 546 True 529.000000 529 84.461000 124 659 1 chr7A.!!$R1 535
33 TraesCS4B01G086200 chr6A 451601689 451602354 665 True 747.000000 747 87.126000 2 659 1 chr6A.!!$R1 657
34 TraesCS4B01G086200 chrUn 332621977 332622644 667 False 745.000000 745 87.054000 2 661 1 chrUn.!!$F1 659
35 TraesCS4B01G086200 chr1A 13969728 13970326 598 False 641.000000 641 86.333000 2 589 1 chr1A.!!$F1 587
36 TraesCS4B01G086200 chr5A 24412977 24413608 631 True 630.000000 630 85.039000 2 622 1 chr5A.!!$R1 620

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
672 718 0.248702 GTTCCCTTTTCGCAACGCAA 60.249 50.0 0.0 0.0 0.0 4.85 F
673 719 0.248702 TTCCCTTTTCGCAACGCAAC 60.249 50.0 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1547 3372 0.446616 GATTTTGACGAGTTCCCCGC 59.553 55.0 0.00 0.0 0.00 6.13 R
2330 4214 1.030457 TGTGCACAATGACACATGCA 58.970 45.0 19.28 6.1 45.45 3.96 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
113 117 5.659079 TGTAACTGGGGTCTTGTTTCAAAAT 59.341 36.000 0.00 0.00 0.00 1.82
117 121 6.993079 ACTGGGGTCTTGTTTCAAAATATTC 58.007 36.000 0.00 0.00 0.00 1.75
120 124 7.242359 TGGGGTCTTGTTTCAAAATATTCCTA 58.758 34.615 0.00 0.00 0.00 2.94
180 192 3.131046 AGTTGTGAAGGGCTTTTTCTGTG 59.869 43.478 0.00 0.00 0.00 3.66
196 208 3.278574 TCTGTGACAAGGGTCTTGTTTG 58.721 45.455 13.56 6.06 44.61 2.93
247 260 0.752009 AGCGCCCGACATTAGAGAGA 60.752 55.000 2.29 0.00 0.00 3.10
469 499 3.625082 GATTTTGTGGTGGCGCCGG 62.625 63.158 23.90 0.00 41.21 6.13
601 647 1.974543 TCAGAGCGCTGATCCAACA 59.025 52.632 18.48 0.00 45.88 3.33
611 657 3.739209 CGCTGATCCAACAGAGCTTCATA 60.739 47.826 0.00 0.00 39.94 2.15
630 676 7.499321 TTCATACGGCGGATGTTTTTAATAT 57.501 32.000 29.63 2.27 0.00 1.28
631 677 6.893759 TCATACGGCGGATGTTTTTAATATG 58.106 36.000 29.63 14.26 0.00 1.78
664 710 2.075761 CGTAGCGGTTCCCTTTTCG 58.924 57.895 0.00 0.00 0.00 3.46
667 713 3.035727 GCGGTTCCCTTTTCGCAA 58.964 55.556 0.00 0.00 46.33 4.85
668 714 1.371267 GCGGTTCCCTTTTCGCAAC 60.371 57.895 0.00 0.00 46.33 4.17
670 716 1.371267 GGTTCCCTTTTCGCAACGC 60.371 57.895 0.00 0.00 0.00 4.84
672 718 0.248702 GTTCCCTTTTCGCAACGCAA 60.249 50.000 0.00 0.00 0.00 4.85
673 719 0.248702 TTCCCTTTTCGCAACGCAAC 60.249 50.000 0.00 0.00 0.00 4.17
674 720 1.660264 CCCTTTTCGCAACGCAACC 60.660 57.895 0.00 0.00 0.00 3.77
676 722 2.635305 CTTTTCGCAACGCAACCGC 61.635 57.895 0.00 0.00 38.22 5.68
677 723 4.615834 TTTCGCAACGCAACCGCC 62.616 61.111 0.00 0.00 38.22 6.13
681 727 4.036804 GCAACGCAACCGCCATGA 62.037 61.111 0.00 0.00 38.22 3.07
682 728 2.642129 CAACGCAACCGCCATGAA 59.358 55.556 0.00 0.00 38.22 2.57
683 729 1.007964 CAACGCAACCGCCATGAAA 60.008 52.632 0.00 0.00 38.22 2.69
684 730 1.003262 CAACGCAACCGCCATGAAAG 61.003 55.000 0.00 0.00 38.22 2.62
685 731 1.169661 AACGCAACCGCCATGAAAGA 61.170 50.000 0.00 0.00 38.22 2.52
686 732 1.169661 ACGCAACCGCCATGAAAGAA 61.170 50.000 0.00 0.00 38.22 2.52
688 734 1.701704 GCAACCGCCATGAAAGAAAG 58.298 50.000 0.00 0.00 0.00 2.62
689 735 1.269448 GCAACCGCCATGAAAGAAAGA 59.731 47.619 0.00 0.00 0.00 2.52
690 736 2.288152 GCAACCGCCATGAAAGAAAGAA 60.288 45.455 0.00 0.00 0.00 2.52
691 737 3.798548 GCAACCGCCATGAAAGAAAGAAA 60.799 43.478 0.00 0.00 0.00 2.52
693 739 4.664150 ACCGCCATGAAAGAAAGAAAAA 57.336 36.364 0.00 0.00 0.00 1.94
716 762 2.672996 CCGTCAGGCCCCAAACAG 60.673 66.667 0.00 0.00 0.00 3.16
717 763 3.365265 CGTCAGGCCCCAAACAGC 61.365 66.667 0.00 0.00 0.00 4.40
719 765 3.884774 TCAGGCCCCAAACAGCGT 61.885 61.111 0.00 0.00 0.00 5.07
720 766 2.912025 CAGGCCCCAAACAGCGTT 60.912 61.111 0.00 0.00 0.00 4.84
721 767 2.912025 AGGCCCCAAACAGCGTTG 60.912 61.111 0.00 0.00 0.00 4.10
722 768 3.989787 GGCCCCAAACAGCGTTGG 61.990 66.667 3.74 9.24 46.57 3.77
724 770 4.341502 CCCCAAACAGCGTTGGCG 62.342 66.667 3.74 0.40 45.80 5.69
725 771 3.591835 CCCAAACAGCGTTGGCGT 61.592 61.111 3.74 0.00 45.80 5.68
726 772 2.411290 CCAAACAGCGTTGGCGTT 59.589 55.556 3.74 0.00 46.35 4.84
728 774 0.804156 CCAAACAGCGTTGGCGTTTT 60.804 50.000 3.74 0.00 46.35 2.43
730 776 0.804156 AAACAGCGTTGGCGTTTTGG 60.804 50.000 3.74 0.00 46.35 3.28
731 777 1.658686 AACAGCGTTGGCGTTTTGGA 61.659 50.000 3.74 0.00 46.35 3.53
732 778 1.064946 CAGCGTTGGCGTTTTGGAA 59.935 52.632 0.00 0.00 46.35 3.53
734 780 0.526739 AGCGTTGGCGTTTTGGAAAC 60.527 50.000 0.00 0.00 46.35 2.78
740 786 2.728015 CGTTTTGGAAACGCGGGC 60.728 61.111 12.47 0.00 36.82 6.13
741 787 2.728015 GTTTTGGAAACGCGGGCG 60.728 61.111 12.47 12.04 46.03 6.13
742 788 3.967335 TTTTGGAAACGCGGGCGG 61.967 61.111 18.03 0.00 44.69 6.13
756 802 2.356194 GCGGCAAGCCAACCAAAG 60.356 61.111 12.19 0.00 40.81 2.77
758 804 1.441311 CGGCAAGCCAACCAAAGTT 59.559 52.632 12.19 0.00 36.33 2.66
759 805 0.597377 CGGCAAGCCAACCAAAGTTC 60.597 55.000 12.19 0.00 32.45 3.01
760 806 0.597377 GGCAAGCCAACCAAAGTTCG 60.597 55.000 6.14 0.00 32.45 3.95
762 808 0.934436 CAAGCCAACCAAAGTTCGCG 60.934 55.000 0.00 0.00 43.93 5.87
763 809 2.050442 GCCAACCAAAGTTCGCGG 60.050 61.111 6.13 0.00 30.33 6.46
765 811 2.050442 CAACCAAAGTTCGCGGCC 60.050 61.111 6.13 0.00 32.45 6.13
766 812 2.203294 AACCAAAGTTCGCGGCCT 60.203 55.556 6.13 0.00 0.00 5.19
767 813 1.826487 AACCAAAGTTCGCGGCCTT 60.826 52.632 6.13 5.75 0.00 4.35
768 814 2.070654 AACCAAAGTTCGCGGCCTTG 62.071 55.000 6.13 6.13 0.00 3.61
769 815 2.429069 CAAAGTTCGCGGCCTTGC 60.429 61.111 6.13 0.00 0.00 4.01
844 2588 5.252547 TGAATTTGAATCCGACTCCAATCA 58.747 37.500 0.00 0.00 0.00 2.57
933 2718 1.153568 CGCTTCCATCTTCCTCGCA 60.154 57.895 0.00 0.00 0.00 5.10
966 2758 2.356667 CCCCTTCTCCAGCAACCC 59.643 66.667 0.00 0.00 0.00 4.11
1116 2919 1.143684 ACCAACAACATCAGGAGCACT 59.856 47.619 0.00 0.00 0.00 4.40
1149 2960 2.419198 GAGACATGCCTCGGCGAT 59.581 61.111 11.27 0.00 45.51 4.58
1399 3211 4.821589 CGCCGACCCTCCAGAAGC 62.822 72.222 0.00 0.00 0.00 3.86
1411 3223 1.079543 CAGAAGCTCCTGTGGGACG 60.080 63.158 0.00 0.00 36.57 4.79
1547 3372 2.202932 CATCCTCGTCGGCCAAGG 60.203 66.667 2.24 3.63 0.00 3.61
2034 3898 1.080569 CAAGCACCGATGGTTTGCC 60.081 57.895 0.00 0.00 44.10 4.52
2036 3900 3.053291 GCACCGATGGTTTGCCGA 61.053 61.111 0.00 0.00 37.67 5.54
2159 4033 7.413438 CCACAGAAGAATCTACTCAAAATTCCG 60.413 40.741 0.00 0.00 33.50 4.30
2251 4129 6.605849 CCATCTATGTAAATTGCTTCGATGG 58.394 40.000 12.90 12.90 39.33 3.51
2272 4150 3.273434 GCCATCAAGCAGTAGTTGATCA 58.727 45.455 0.00 0.00 41.69 2.92
2300 4179 2.663188 GATCGCCAGATCGCCCAC 60.663 66.667 0.00 0.00 43.17 4.61
2301 4180 3.157217 GATCGCCAGATCGCCCACT 62.157 63.158 0.00 0.00 43.17 4.00
2302 4181 1.806461 GATCGCCAGATCGCCCACTA 61.806 60.000 0.00 0.00 43.17 2.74
2330 4214 2.560105 GTTGGCCTGCTTCTCTGAATTT 59.440 45.455 3.32 0.00 0.00 1.82
2392 4290 6.183360 CGTAGTGTTGAGAGATCCATTAGACA 60.183 42.308 0.00 0.00 0.00 3.41
2393 4291 6.805016 AGTGTTGAGAGATCCATTAGACAT 57.195 37.500 0.00 0.00 0.00 3.06
2435 4334 6.541086 CAGATGCTCTGTTGTTATTGAGTTC 58.459 40.000 5.34 0.00 39.58 3.01
2471 4376 2.962421 TGCGGTTTTTCCAAAATCCTCT 59.038 40.909 9.27 0.00 36.21 3.69
2541 4452 3.553715 CCGAGTGATGGATGAATCGATGT 60.554 47.826 0.00 0.00 32.13 3.06
2543 4454 4.149571 CGAGTGATGGATGAATCGATGTTC 59.850 45.833 0.00 0.00 32.13 3.18
2576 4487 2.355132 GCTGGTGCAGATTTCATGAGAG 59.645 50.000 0.00 0.00 39.41 3.20
2652 4568 8.342634 GTTCATGTAGTTCAGTGTATGTGTTTT 58.657 33.333 0.00 0.00 0.00 2.43
2673 4589 5.828299 TTCACCATCTTTGTCGAAAAAGT 57.172 34.783 24.03 11.46 38.16 2.66
2734 4835 1.065998 ACACCCAGTACAAACACACGT 60.066 47.619 0.00 0.00 0.00 4.49
2801 4903 1.228429 GCAGCAACACCACCCCTAA 60.228 57.895 0.00 0.00 0.00 2.69
3179 5281 2.881403 GCATCCAAGACCTTGACACCAT 60.881 50.000 11.06 0.00 42.93 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 89 3.771577 AACAAGACCCCAGTTACAGAG 57.228 47.619 0.00 0.00 0.00 3.35
91 95 8.485578 AATATTTTGAAACAAGACCCCAGTTA 57.514 30.769 0.00 0.00 0.00 2.24
180 192 5.474825 TGTTTTTCAAACAAGACCCTTGTC 58.525 37.500 12.10 0.00 42.09 3.18
196 208 4.723248 CTTCAACTCGGGCTATGTTTTTC 58.277 43.478 0.00 0.00 0.00 2.29
247 260 4.011966 TGTTGCAATGTCTGATCACTCT 57.988 40.909 0.59 0.00 0.00 3.24
476 506 2.341543 CGTCCTGACACAGCTGCT 59.658 61.111 15.27 0.00 0.00 4.24
601 647 0.032678 CATCCGCCGTATGAAGCTCT 59.967 55.000 0.00 0.00 0.00 4.09
611 657 4.035909 GGACATATTAAAAACATCCGCCGT 59.964 41.667 0.00 0.00 0.00 5.68
664 710 3.550339 TTCATGGCGGTTGCGTTGC 62.550 57.895 0.00 0.00 44.10 4.17
665 711 1.003262 CTTTCATGGCGGTTGCGTTG 61.003 55.000 0.00 0.00 44.10 4.10
666 712 1.169661 TCTTTCATGGCGGTTGCGTT 61.170 50.000 0.00 0.00 44.10 4.84
667 713 1.169661 TTCTTTCATGGCGGTTGCGT 61.170 50.000 0.00 0.00 44.10 5.24
668 714 0.039617 TTTCTTTCATGGCGGTTGCG 60.040 50.000 0.00 0.00 44.10 4.85
670 716 3.641437 TTCTTTCTTTCATGGCGGTTG 57.359 42.857 0.00 0.00 0.00 3.77
672 718 4.664150 TTTTTCTTTCTTTCATGGCGGT 57.336 36.364 0.00 0.00 0.00 5.68
700 746 3.365265 GCTGTTTGGGGCCTGACG 61.365 66.667 0.84 0.00 0.00 4.35
701 747 3.365265 CGCTGTTTGGGGCCTGAC 61.365 66.667 0.84 0.09 0.00 3.51
702 748 3.429372 AACGCTGTTTGGGGCCTGA 62.429 57.895 0.84 0.00 0.00 3.86
703 749 2.912025 AACGCTGTTTGGGGCCTG 60.912 61.111 0.84 0.00 0.00 4.85
704 750 2.912025 CAACGCTGTTTGGGGCCT 60.912 61.111 0.84 0.00 0.00 5.19
706 752 4.662961 GCCAACGCTGTTTGGGGC 62.663 66.667 9.82 7.72 45.55 5.80
708 754 2.621371 AAACGCCAACGCTGTTTGGG 62.621 55.000 9.82 8.62 45.55 4.12
711 757 0.804156 CCAAAACGCCAACGCTGTTT 60.804 50.000 0.00 0.00 45.53 2.83
712 758 1.226831 CCAAAACGCCAACGCTGTT 60.227 52.632 0.00 0.00 45.53 3.16
713 759 1.658686 TTCCAAAACGCCAACGCTGT 61.659 50.000 0.00 0.00 45.53 4.40
714 760 0.526524 TTTCCAAAACGCCAACGCTG 60.527 50.000 0.00 0.00 45.53 5.18
715 761 0.526739 GTTTCCAAAACGCCAACGCT 60.527 50.000 0.00 0.00 45.53 5.07
716 762 1.803286 CGTTTCCAAAACGCCAACGC 61.803 55.000 11.45 0.00 45.53 4.84
724 770 2.728015 CGCCCGCGTTTCCAAAAC 60.728 61.111 4.92 0.00 34.35 2.43
725 771 3.967335 CCGCCCGCGTTTCCAAAA 61.967 61.111 4.92 0.00 37.81 2.44
739 785 2.356194 CTTTGGTTGGCTTGCCGC 60.356 61.111 7.18 2.58 38.13 6.53
740 786 0.597377 GAACTTTGGTTGGCTTGCCG 60.597 55.000 7.18 0.00 35.58 5.69
741 787 0.597377 CGAACTTTGGTTGGCTTGCC 60.597 55.000 4.43 4.43 35.58 4.52
742 788 2.885502 CGAACTTTGGTTGGCTTGC 58.114 52.632 0.00 0.00 35.58 4.01
747 793 2.050442 GCCGCGAACTTTGGTTGG 60.050 61.111 8.23 0.00 35.58 3.77
748 794 2.050442 GGCCGCGAACTTTGGTTG 60.050 61.111 8.23 0.00 35.58 3.77
749 795 1.826487 AAGGCCGCGAACTTTGGTT 60.826 52.632 8.23 0.00 38.52 3.67
750 796 2.203294 AAGGCCGCGAACTTTGGT 60.203 55.556 8.23 0.00 0.00 3.67
752 798 2.429069 GCAAGGCCGCGAACTTTG 60.429 61.111 8.23 13.52 0.00 2.77
776 822 3.121030 CTAGGCACAGCACACGCC 61.121 66.667 0.00 0.00 46.62 5.68
777 823 3.121030 CCTAGGCACAGCACACGC 61.121 66.667 0.00 0.00 38.99 5.34
778 824 3.121030 GCCTAGGCACAGCACACG 61.121 66.667 29.33 0.00 41.49 4.49
779 825 1.899437 TAGGCCTAGGCACAGCACAC 61.899 60.000 34.09 14.74 44.11 3.82
780 826 1.612146 TAGGCCTAGGCACAGCACA 60.612 57.895 34.09 8.41 44.11 4.57
783 829 2.825264 CCTAGGCCTAGGCACAGC 59.175 66.667 39.72 17.37 45.36 4.40
953 2745 1.846261 AGCTTGGGTTGCTGGAGAA 59.154 52.632 0.00 0.00 39.56 2.87
966 2758 3.147294 CGACGGACGAACAGCTTG 58.853 61.111 0.00 0.00 45.77 4.01
1116 2919 1.451567 CTCCTCCTCGTACTCCGCA 60.452 63.158 0.00 0.00 36.19 5.69
1395 3207 2.266055 CCGTCCCACAGGAGCTTC 59.734 66.667 0.00 0.00 45.21 3.86
1453 3271 0.723981 GCGAAGAGCTTCCACATGAC 59.276 55.000 0.00 0.00 44.04 3.06
1547 3372 0.446616 GATTTTGACGAGTTCCCCGC 59.553 55.000 0.00 0.00 0.00 6.13
2251 4129 3.273434 TGATCAACTACTGCTTGATGGC 58.727 45.455 3.11 0.00 38.27 4.40
2299 4178 3.721087 AGCAGGCCAACACTAATTAGT 57.279 42.857 12.50 12.50 36.90 2.24
2300 4179 4.265073 AGAAGCAGGCCAACACTAATTAG 58.735 43.478 11.05 11.05 0.00 1.73
2301 4180 4.019321 AGAGAAGCAGGCCAACACTAATTA 60.019 41.667 5.01 0.00 0.00 1.40
2302 4181 3.084786 GAGAAGCAGGCCAACACTAATT 58.915 45.455 5.01 0.00 0.00 1.40
2330 4214 1.030457 TGTGCACAATGACACATGCA 58.970 45.000 19.28 6.10 45.45 3.96
2392 4290 7.031372 GCATCTGTAAACAACATGTCATCAAT 58.969 34.615 0.00 0.00 37.50 2.57
2393 4291 6.207221 AGCATCTGTAAACAACATGTCATCAA 59.793 34.615 0.00 0.00 37.50 2.57
2519 4430 2.800881 TCGATTCATCCATCACTCGG 57.199 50.000 0.00 0.00 0.00 4.63
2520 4431 3.646946 ACATCGATTCATCCATCACTCG 58.353 45.455 0.00 0.00 0.00 4.18
2541 4452 2.224018 GCACCAGCAGGACATTTTTGAA 60.224 45.455 0.35 0.00 41.58 2.69
2543 4454 1.787012 GCACCAGCAGGACATTTTTG 58.213 50.000 0.35 0.00 41.58 2.44
2652 4568 5.123227 AGACTTTTTCGACAAAGATGGTGA 58.877 37.500 26.39 0.00 37.24 4.02
2673 4589 2.922740 ATATAAAGCGGGGCGAAAGA 57.077 45.000 0.00 0.00 0.00 2.52
2734 4835 3.568743 GTGCGTGTGTTGCGGTGA 61.569 61.111 0.00 0.00 34.24 4.02
2754 4855 2.551071 GCCTATGTATCTTGTCCTGGGC 60.551 54.545 0.00 0.00 0.00 5.36
2801 4903 1.991121 TCTCTTCGTGGTGGTAGTGT 58.009 50.000 0.00 0.00 0.00 3.55
2890 4992 2.671070 CTTGGATCGGGCAGTGGT 59.329 61.111 0.00 0.00 0.00 4.16
2895 4997 0.690744 TCTGATCCTTGGATCGGGCA 60.691 55.000 28.36 14.38 38.24 5.36
3070 5172 1.377072 CATCATGGTCGTGTGGGCA 60.377 57.895 0.00 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.