Multiple sequence alignment - TraesCS1D01G128500

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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 TraesCS1D01G128500 chr1D 100.000 4991 0 0 1872 6862 141710459 141705469 0.000000e+00 9217.0
1 TraesCS1D01G128500 chr1D 100.000 1578 0 0 1 1578 141712330 141710753 0.000000e+00 2915.0
2 TraesCS1D01G128500 chr1D 100.000 452 0 0 7229 7680 141705102 141704651 0.000000e+00 835.0
3 TraesCS1D01G128500 chr1D 91.981 212 17 0 156 367 453231701 453231912 1.620000e-76 298.0
4 TraesCS1D01G128500 chr1D 91.667 72 3 3 6192 6262 440050456 440050387 6.340000e-16 97.1
5 TraesCS1D01G128500 chr1B 98.091 4976 61 11 1872 6840 195595665 195590717 0.000000e+00 8632.0
6 TraesCS1D01G128500 chr1B 97.098 896 14 7 691 1578 195596583 195595692 0.000000e+00 1500.0
7 TraesCS1D01G128500 chr1B 95.796 333 10 1 7352 7680 195590456 195590124 1.130000e-147 534.0
8 TraesCS1D01G128500 chr1A 95.960 4381 128 21 1872 6211 148954499 148958871 0.000000e+00 7064.0
9 TraesCS1D01G128500 chr1A 96.633 891 17 7 700 1578 148953551 148954440 0.000000e+00 1467.0
10 TraesCS1D01G128500 chr1A 97.822 597 13 0 6266 6862 148958885 148959481 0.000000e+00 1031.0
11 TraesCS1D01G128500 chr1A 91.960 398 22 7 7290 7680 148959827 148960221 4.050000e-152 549.0
12 TraesCS1D01G128500 chr1A 84.848 198 21 2 232 420 584838800 584838997 2.830000e-44 191.0
13 TraesCS1D01G128500 chr1A 84.146 164 17 3 145 299 581293978 581293815 4.800000e-32 150.0
14 TraesCS1D01G128500 chr1A 82.031 128 20 2 340 465 144563314 144563440 1.050000e-18 106.0
15 TraesCS1D01G128500 chr2D 96.110 617 17 2 1 616 516394617 516395227 0.000000e+00 1000.0
16 TraesCS1D01G128500 chr2D 96.852 540 10 2 1 539 305943181 305943714 0.000000e+00 896.0
17 TraesCS1D01G128500 chr7B 90.123 648 43 8 1 636 614225092 614224454 0.000000e+00 822.0
18 TraesCS1D01G128500 chr7B 96.923 65 2 0 6199 6263 661996385 661996449 8.150000e-20 110.0
19 TraesCS1D01G128500 chr4A 92.632 475 26 4 1 475 419970915 419970450 0.000000e+00 675.0
20 TraesCS1D01G128500 chr4A 91.789 475 30 3 1 475 46438041 46438506 0.000000e+00 652.0
21 TraesCS1D01G128500 chr4B 84.431 501 50 11 157 630 349116662 349117161 1.170000e-127 468.0
22 TraesCS1D01G128500 chr4B 81.124 498 57 9 157 621 42544322 42544815 1.570000e-96 364.0
23 TraesCS1D01G128500 chr4B 92.405 79 6 0 4388 4466 16428892 16428970 6.300000e-21 113.0
24 TraesCS1D01G128500 chr4B 92.405 79 6 0 4388 4466 229683064 229682986 6.300000e-21 113.0
25 TraesCS1D01G128500 chr4B 100.000 28 0 0 601 628 467924108 467924081 1.400000e-02 52.8
26 TraesCS1D01G128500 chr2B 84.000 500 53 10 156 629 651323350 651323848 9.090000e-124 455.0
27 TraesCS1D01G128500 chr2B 83.832 501 52 12 156 629 480011294 480010796 4.230000e-122 449.0
28 TraesCS1D01G128500 chr6B 83.806 494 52 11 156 622 480658749 480658257 1.970000e-120 444.0
29 TraesCS1D01G128500 chr6B 83.537 492 53 11 157 621 95581595 95581105 1.180000e-117 435.0
30 TraesCS1D01G128500 chr6B 94.318 88 5 0 6271 6358 278674697 278674610 1.340000e-27 135.0
31 TraesCS1D01G128500 chr6B 89.888 89 8 1 4379 4466 66015852 66015764 6.300000e-21 113.0
32 TraesCS1D01G128500 chr6B 91.667 72 5 1 6192 6263 6187699 6187629 1.760000e-16 99.0
33 TraesCS1D01G128500 chr4D 88.398 362 29 6 156 505 48514592 48514952 2.560000e-114 424.0
34 TraesCS1D01G128500 chr4D 89.773 88 9 0 6276 6363 231221874 231221787 6.300000e-21 113.0
35 TraesCS1D01G128500 chr5B 83.505 485 36 17 158 618 384517432 384517896 5.550000e-111 412.0
36 TraesCS1D01G128500 chr5B 86.207 116 16 0 350 465 617238980 617239095 8.090000e-25 126.0
37 TraesCS1D01G128500 chr5B 92.405 79 6 0 4388 4466 581597360 581597438 6.300000e-21 113.0
38 TraesCS1D01G128500 chr5B 92.857 70 4 1 6194 6263 546085305 546085373 4.900000e-17 100.0
39 TraesCS1D01G128500 chr5B 100.000 29 0 0 603 631 536581976 536582004 4.000000e-03 54.7
40 TraesCS1D01G128500 chr5A 81.299 508 60 18 156 628 622982986 622983493 5.620000e-101 379.0
41 TraesCS1D01G128500 chr6D 93.478 92 6 0 6271 6362 155602045 155601954 3.740000e-28 137.0
42 TraesCS1D01G128500 chr6D 95.000 80 4 0 6271 6350 13067041 13067120 8.090000e-25 126.0
43 TraesCS1D01G128500 chr6D 96.774 62 2 0 6202 6263 185090705 185090766 3.790000e-18 104.0
44 TraesCS1D01G128500 chr6A 93.478 92 6 0 6271 6362 209391425 209391334 3.740000e-28 137.0
45 TraesCS1D01G128500 chr3D 87.963 108 11 2 6266 6372 108916257 108916363 8.090000e-25 126.0
46 TraesCS1D01G128500 chr3D 92.222 90 6 1 6266 6355 523157382 523157470 8.090000e-25 126.0
47 TraesCS1D01G128500 chrUn 93.671 79 5 0 4388 4466 434714136 434714214 1.350000e-22 119.0
48 TraesCS1D01G128500 chrUn 92.405 79 6 0 4388 4466 392729878 392729956 6.300000e-21 113.0
49 TraesCS1D01G128500 chrUn 92.405 79 6 0 4388 4466 420601279 420601201 6.300000e-21 113.0
50 TraesCS1D01G128500 chr3B 96.923 65 0 2 6201 6263 802705159 802705095 2.930000e-19 108.0
51 TraesCS1D01G128500 chr3B 98.276 58 1 0 6206 6263 132527384 132527327 1.360000e-17 102.0
52 TraesCS1D01G128500 chr7D 88.462 78 8 1 6189 6266 575717784 575717708 8.210000e-15 93.5
53 TraesCS1D01G128500 chr2A 100.000 29 0 0 601 629 153035173 153035201 4.000000e-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 TraesCS1D01G128500 chr1D 141704651 141712330 7679 True 4322.333333 9217 100.00000 1 7680 3 chr1D.!!$R2 7679
1 TraesCS1D01G128500 chr1B 195590124 195596583 6459 True 3555.333333 8632 96.99500 691 7680 3 chr1B.!!$R1 6989
2 TraesCS1D01G128500 chr1A 148953551 148960221 6670 False 2527.750000 7064 95.59375 700 7680 4 chr1A.!!$F3 6980
3 TraesCS1D01G128500 chr2D 516394617 516395227 610 False 1000.000000 1000 96.11000 1 616 1 chr2D.!!$F2 615
4 TraesCS1D01G128500 chr2D 305943181 305943714 533 False 896.000000 896 96.85200 1 539 1 chr2D.!!$F1 538
5 TraesCS1D01G128500 chr7B 614224454 614225092 638 True 822.000000 822 90.12300 1 636 1 chr7B.!!$R1 635
6 TraesCS1D01G128500 chr5A 622982986 622983493 507 False 379.000000 379 81.29900 156 628 1 chr5A.!!$F1 472

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
664 709 0.034477 GGTGGACGATTTGGATGGGT 60.034 55.000 0.0 0.0 0.00 4.51 F
669 714 0.038166 ACGATTTGGATGGGTGCAGT 59.962 50.000 0.0 0.0 0.00 4.40 F
673 718 0.187117 TTTGGATGGGTGCAGTTGGA 59.813 50.000 0.0 0.0 0.00 3.53 F
683 728 0.321346 TGCAGTTGGATTCGCTCTCA 59.679 50.000 0.0 0.0 0.00 3.27 F
1017 1070 0.531200 GAATGGAGGACTCGAACGGT 59.469 55.000 0.0 0.0 0.00 4.83 F
2094 2153 0.884704 TGTGCTTTTCCGTCAGAGCC 60.885 55.000 0.0 0.0 34.30 4.70 F
2101 2160 2.529780 TTCCGTCAGAGCCGTTTTAA 57.470 45.000 0.0 0.0 0.00 1.52 F
2105 2164 2.739913 CCGTCAGAGCCGTTTTAATGAA 59.260 45.455 0.0 0.0 0.00 2.57 F
3575 3640 0.980231 AGAGTCTGGAGTGGGATGGC 60.980 60.000 0.0 0.0 0.00 4.40 F
4750 4839 4.972440 GGCTGATTCGTCAAATTATTCTGC 59.028 41.667 0.0 0.0 0.00 4.26 F
5538 5627 6.022163 AGAAATGTCAAGCTCAAAATGGAG 57.978 37.500 0.0 0.0 37.97 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2111 2170 0.599558 GGCAGCTGCACAGATTGAAA 59.400 50.000 37.63 0.00 44.36 2.69 R
2115 2174 0.677098 CTCTGGCAGCTGCACAGATT 60.677 55.000 37.65 0.00 42.78 2.40 R
2121 2180 0.958876 CAATGACTCTGGCAGCTGCA 60.959 55.000 37.63 23.01 44.36 4.41 R
2122 2181 0.959372 ACAATGACTCTGGCAGCTGC 60.959 55.000 30.88 30.88 41.14 5.25 R
2517 2576 1.831736 GCTGGTAGACTAAGGCTGGAA 59.168 52.381 0.00 0.00 0.00 3.53 R
2927 2987 1.923899 TGTGTGCATGCACTTTGTTG 58.076 45.000 41.43 0.00 46.30 3.33 R
3575 3640 2.690653 ATCCCCAACACACACCACCG 62.691 60.000 0.00 0.00 0.00 4.94 R
4059 4128 4.524802 TGGAAATATGGCTGTGGAATCT 57.475 40.909 0.00 0.00 0.00 2.40 R
4674 4763 7.175641 GGATAACTTGGCTGCATGATTAATACT 59.824 37.037 0.50 0.00 0.00 2.12 R
5925 6015 1.214424 AGTAAGCCACCCAACAAGTGT 59.786 47.619 0.00 0.00 33.20 3.55 R
6706 6805 3.216187 TCTTTGAATCCGTTGGTCCAA 57.784 42.857 0.00 0.00 0.00 3.53 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
426 448 1.457643 CGGAGGCTGGGTGGATCTA 60.458 63.158 0.00 0.00 0.00 1.98
504 526 3.882444 TCGGGAGAGAAAGAAGTATCGA 58.118 45.455 0.00 0.00 0.00 3.59
520 565 3.662759 ATCGAGGCCCAAAAATTAGGA 57.337 42.857 0.00 0.00 0.00 2.94
565 610 1.388837 GGTTGTTTCCCTTGTGCGGT 61.389 55.000 0.00 0.00 0.00 5.68
592 637 2.356673 GCCCGAGTTTTCGTCCGT 60.357 61.111 0.00 0.00 45.28 4.69
637 682 8.545229 TTAATAGTAGTGTAGATACGGAGAGC 57.455 38.462 0.00 0.00 0.00 4.09
638 683 3.391965 AGTAGTGTAGATACGGAGAGCG 58.608 50.000 0.00 0.00 0.00 5.03
639 684 1.595466 AGTGTAGATACGGAGAGCGG 58.405 55.000 0.00 0.00 0.00 5.52
640 685 1.140452 AGTGTAGATACGGAGAGCGGA 59.860 52.381 0.00 0.00 0.00 5.54
641 686 1.263752 GTGTAGATACGGAGAGCGGAC 59.736 57.143 0.00 0.00 0.00 4.79
642 687 0.512085 GTAGATACGGAGAGCGGACG 59.488 60.000 0.00 0.00 0.00 4.79
643 688 1.226686 TAGATACGGAGAGCGGACGC 61.227 60.000 8.91 8.91 42.33 5.19
655 700 4.446413 GGACGCGGGTGGACGATT 62.446 66.667 10.96 0.00 35.47 3.34
656 701 2.433664 GACGCGGGTGGACGATTT 60.434 61.111 10.96 0.00 35.47 2.17
657 702 2.736682 GACGCGGGTGGACGATTTG 61.737 63.158 10.96 0.00 35.47 2.32
658 703 3.496131 CGCGGGTGGACGATTTGG 61.496 66.667 0.00 0.00 35.47 3.28
659 704 2.046700 GCGGGTGGACGATTTGGA 60.047 61.111 0.00 0.00 35.47 3.53
660 705 1.451387 GCGGGTGGACGATTTGGAT 60.451 57.895 0.00 0.00 35.47 3.41
661 706 1.714899 GCGGGTGGACGATTTGGATG 61.715 60.000 0.00 0.00 35.47 3.51
662 707 1.095228 CGGGTGGACGATTTGGATGG 61.095 60.000 0.00 0.00 35.47 3.51
663 708 0.751643 GGGTGGACGATTTGGATGGG 60.752 60.000 0.00 0.00 0.00 4.00
664 709 0.034477 GGTGGACGATTTGGATGGGT 60.034 55.000 0.00 0.00 0.00 4.51
665 710 1.094785 GTGGACGATTTGGATGGGTG 58.905 55.000 0.00 0.00 0.00 4.61
666 711 0.679640 TGGACGATTTGGATGGGTGC 60.680 55.000 0.00 0.00 0.00 5.01
667 712 0.679640 GGACGATTTGGATGGGTGCA 60.680 55.000 0.00 0.00 0.00 4.57
668 713 0.734889 GACGATTTGGATGGGTGCAG 59.265 55.000 0.00 0.00 0.00 4.41
669 714 0.038166 ACGATTTGGATGGGTGCAGT 59.962 50.000 0.00 0.00 0.00 4.40
670 715 1.176527 CGATTTGGATGGGTGCAGTT 58.823 50.000 0.00 0.00 0.00 3.16
671 716 1.135315 CGATTTGGATGGGTGCAGTTG 60.135 52.381 0.00 0.00 0.00 3.16
672 717 1.205417 GATTTGGATGGGTGCAGTTGG 59.795 52.381 0.00 0.00 0.00 3.77
673 718 0.187117 TTTGGATGGGTGCAGTTGGA 59.813 50.000 0.00 0.00 0.00 3.53
674 719 0.409092 TTGGATGGGTGCAGTTGGAT 59.591 50.000 0.00 0.00 0.00 3.41
675 720 0.409092 TGGATGGGTGCAGTTGGATT 59.591 50.000 0.00 0.00 0.00 3.01
676 721 1.106285 GGATGGGTGCAGTTGGATTC 58.894 55.000 0.00 0.00 0.00 2.52
677 722 0.734889 GATGGGTGCAGTTGGATTCG 59.265 55.000 0.00 0.00 0.00 3.34
678 723 1.315257 ATGGGTGCAGTTGGATTCGC 61.315 55.000 0.00 0.00 0.00 4.70
679 724 1.675641 GGGTGCAGTTGGATTCGCT 60.676 57.895 0.00 0.00 0.00 4.93
680 725 1.648467 GGGTGCAGTTGGATTCGCTC 61.648 60.000 0.00 0.00 0.00 5.03
681 726 0.674895 GGTGCAGTTGGATTCGCTCT 60.675 55.000 0.00 0.00 0.00 4.09
682 727 0.723981 GTGCAGTTGGATTCGCTCTC 59.276 55.000 0.00 0.00 0.00 3.20
683 728 0.321346 TGCAGTTGGATTCGCTCTCA 59.679 50.000 0.00 0.00 0.00 3.27
684 729 1.270785 TGCAGTTGGATTCGCTCTCAA 60.271 47.619 0.00 0.00 0.00 3.02
685 730 2.012673 GCAGTTGGATTCGCTCTCAAT 58.987 47.619 0.00 0.00 0.00 2.57
686 731 2.421424 GCAGTTGGATTCGCTCTCAATT 59.579 45.455 0.00 0.00 0.00 2.32
687 732 3.623060 GCAGTTGGATTCGCTCTCAATTA 59.377 43.478 0.00 0.00 0.00 1.40
688 733 4.494855 GCAGTTGGATTCGCTCTCAATTAC 60.495 45.833 0.00 0.00 0.00 1.89
689 734 4.631377 CAGTTGGATTCGCTCTCAATTACA 59.369 41.667 0.00 0.00 0.00 2.41
697 742 3.192633 TCGCTCTCAATTACAGTGCAGTA 59.807 43.478 0.00 0.00 31.89 2.74
698 743 4.115516 CGCTCTCAATTACAGTGCAGTAT 58.884 43.478 0.00 0.00 31.89 2.12
774 821 3.476552 GAACAACAGACACATTCCCTGA 58.523 45.455 0.00 0.00 0.00 3.86
1017 1070 0.531200 GAATGGAGGACTCGAACGGT 59.469 55.000 0.00 0.00 0.00 4.83
1388 1441 4.384868 CCCCCATTTCGTTAACAGACCTAT 60.385 45.833 6.39 0.00 0.00 2.57
1390 1443 4.814771 CCCATTTCGTTAACAGACCTATCC 59.185 45.833 6.39 0.00 0.00 2.59
1402 1460 6.295719 ACAGACCTATCCTCGTTTAAATGT 57.704 37.500 7.28 0.00 0.00 2.71
1524 1582 3.120165 GCTCTTTTGGGTCGAAATCTGAC 60.120 47.826 0.00 0.00 35.60 3.51
2094 2153 0.884704 TGTGCTTTTCCGTCAGAGCC 60.885 55.000 0.00 0.00 34.30 4.70
2101 2160 2.529780 TTCCGTCAGAGCCGTTTTAA 57.470 45.000 0.00 0.00 0.00 1.52
2102 2161 2.754946 TCCGTCAGAGCCGTTTTAAT 57.245 45.000 0.00 0.00 0.00 1.40
2105 2164 2.739913 CCGTCAGAGCCGTTTTAATGAA 59.260 45.455 0.00 0.00 0.00 2.57
2113 2172 3.659786 GCCGTTTTAATGAAGGCCTTTT 58.340 40.909 21.54 13.67 41.81 2.27
2114 2173 3.678072 GCCGTTTTAATGAAGGCCTTTTC 59.322 43.478 21.54 8.70 41.81 2.29
2115 2174 4.797933 GCCGTTTTAATGAAGGCCTTTTCA 60.798 41.667 21.54 15.09 41.81 2.69
2116 2175 5.293560 CCGTTTTAATGAAGGCCTTTTCAA 58.706 37.500 21.54 5.94 40.21 2.69
2117 2176 5.931724 CCGTTTTAATGAAGGCCTTTTCAAT 59.068 36.000 21.54 9.93 40.21 2.57
2118 2177 6.090763 CCGTTTTAATGAAGGCCTTTTCAATC 59.909 38.462 21.54 6.14 40.21 2.67
2119 2178 6.868339 CGTTTTAATGAAGGCCTTTTCAATCT 59.132 34.615 21.54 5.93 40.21 2.40
2120 2179 7.148755 CGTTTTAATGAAGGCCTTTTCAATCTG 60.149 37.037 21.54 2.40 40.21 2.90
2121 2180 6.916360 TTAATGAAGGCCTTTTCAATCTGT 57.084 33.333 21.54 0.00 40.21 3.41
2122 2181 4.796038 ATGAAGGCCTTTTCAATCTGTG 57.204 40.909 21.54 0.00 40.21 3.66
2627 2686 7.183460 AGCCGGGACTCTCTTAACTATATATT 58.817 38.462 2.18 0.00 0.00 1.28
2812 2871 7.600752 GCTACCTGTCTTCATATCATTCTTACC 59.399 40.741 0.00 0.00 0.00 2.85
2927 2987 3.201290 CCAGAATGTCACATAGAGGCAC 58.799 50.000 0.00 0.00 0.00 5.01
3492 3557 8.072480 AGTATTGGATTACCCCTCTTTACTAGT 58.928 37.037 0.00 0.00 34.81 2.57
3575 3640 0.980231 AGAGTCTGGAGTGGGATGGC 60.980 60.000 0.00 0.00 0.00 4.40
4750 4839 4.972440 GGCTGATTCGTCAAATTATTCTGC 59.028 41.667 0.00 0.00 0.00 4.26
5472 5561 7.251704 ACAATATCTGTACATAAGCTTGCAC 57.748 36.000 9.86 2.05 36.10 4.57
5538 5627 6.022163 AGAAATGTCAAGCTCAAAATGGAG 57.978 37.500 0.00 0.00 37.97 3.86
5918 6008 6.862090 ACTAATTATCTAGCGCTCTTTAACCG 59.138 38.462 16.34 0.00 0.00 4.44
5925 6015 1.069500 GCGCTCTTTAACCGCTTTTGA 60.069 47.619 0.00 0.00 43.95 2.69
5960 6059 4.202010 TGGCTTACTTTGTTCTCTGTTTGC 60.202 41.667 0.00 0.00 0.00 3.68
6121 6220 6.822170 TGCCAAAATTTATTGCTGCATCATAA 59.178 30.769 1.84 2.75 0.00 1.90
6220 6319 2.237643 GTATTCTACTCCCTCCGTCCC 58.762 57.143 0.00 0.00 0.00 4.46
6705 6804 5.760131 CCCCATCTTCTTTCTTATTCCACT 58.240 41.667 0.00 0.00 0.00 4.00
6706 6805 6.190587 CCCCATCTTCTTTCTTATTCCACTT 58.809 40.000 0.00 0.00 0.00 3.16
6745 6846 9.767684 TTCAAAGAAGCAATAATATGTACAACG 57.232 29.630 0.00 0.00 0.00 4.10
6769 6870 5.798434 GTGAAACCGCATAATTTCTTACACC 59.202 40.000 0.00 0.00 36.09 4.16
7278 7379 9.846248 GATTAATTCAACTGCTATCTGTTTTGT 57.154 29.630 0.00 0.00 32.96 2.83
7279 7380 9.630098 ATTAATTCAACTGCTATCTGTTTTGTG 57.370 29.630 0.00 0.00 32.96 3.33
7280 7381 6.639632 ATTCAACTGCTATCTGTTTTGTGT 57.360 33.333 0.00 0.00 32.96 3.72
7281 7382 5.422666 TCAACTGCTATCTGTTTTGTGTG 57.577 39.130 0.00 0.00 32.96 3.82
7282 7383 5.122519 TCAACTGCTATCTGTTTTGTGTGA 58.877 37.500 0.00 0.00 32.96 3.58
7283 7384 5.588246 TCAACTGCTATCTGTTTTGTGTGAA 59.412 36.000 0.00 0.00 32.96 3.18
7284 7385 6.262944 TCAACTGCTATCTGTTTTGTGTGAAT 59.737 34.615 0.00 0.00 32.96 2.57
7285 7386 6.639632 ACTGCTATCTGTTTTGTGTGAATT 57.360 33.333 0.00 0.00 0.00 2.17
7286 7387 7.042797 ACTGCTATCTGTTTTGTGTGAATTT 57.957 32.000 0.00 0.00 0.00 1.82
7287 7388 8.165239 ACTGCTATCTGTTTTGTGTGAATTTA 57.835 30.769 0.00 0.00 0.00 1.40
7288 7389 8.796475 ACTGCTATCTGTTTTGTGTGAATTTAT 58.204 29.630 0.00 0.00 0.00 1.40
7350 7451 5.020795 GGAACAACCCCCAAACTGTTATAT 58.979 41.667 0.00 0.00 32.31 0.86
7495 7598 6.959361 ACTACAAAAAGCATCAACAGTACAG 58.041 36.000 0.00 0.00 0.00 2.74
7545 7653 6.839124 CTCATAGAGCTCTCCATTCATAGT 57.161 41.667 22.17 0.00 0.00 2.12
7575 7683 1.692519 ACAAAGCTCACTACGGGACTT 59.307 47.619 0.00 0.00 0.00 3.01
7636 7744 3.957508 AGGAGGACCCTAACTCTAGAC 57.042 52.381 0.00 0.00 45.48 2.59
7671 7779 3.137544 TCAGGTCCAAAAAGCAACTCCTA 59.862 43.478 0.00 0.00 0.00 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
214 216 1.002134 CGTGGAAGCCATTGGAGGT 60.002 57.895 6.95 0.00 35.28 3.85
415 426 0.722676 ACTTCCCCTAGATCCACCCA 59.277 55.000 0.00 0.00 0.00 4.51
426 448 2.227036 CCTCCTGTGCACTTCCCCT 61.227 63.158 19.41 0.00 0.00 4.79
504 526 2.833943 CAGCTTCCTAATTTTTGGGCCT 59.166 45.455 4.53 0.00 0.00 5.19
520 565 1.748122 CAGATTCCGCTGGCAGCTT 60.748 57.895 34.17 17.78 39.60 3.74
565 610 0.244450 AAACTCGGGCGTTCGTATGA 59.756 50.000 0.00 0.00 0.00 2.15
578 623 1.762419 TTCTGACGGACGAAAACTCG 58.238 50.000 0.00 0.00 39.31 4.18
638 683 3.945304 AAATCGTCCACCCGCGTCC 62.945 63.158 4.92 0.00 0.00 4.79
639 684 2.433664 AAATCGTCCACCCGCGTC 60.434 61.111 4.92 0.00 0.00 5.19
640 685 2.740826 CAAATCGTCCACCCGCGT 60.741 61.111 4.92 0.00 0.00 6.01
641 686 3.496131 CCAAATCGTCCACCCGCG 61.496 66.667 0.00 0.00 0.00 6.46
642 687 1.451387 ATCCAAATCGTCCACCCGC 60.451 57.895 0.00 0.00 0.00 6.13
643 688 1.095228 CCATCCAAATCGTCCACCCG 61.095 60.000 0.00 0.00 0.00 5.28
644 689 0.751643 CCCATCCAAATCGTCCACCC 60.752 60.000 0.00 0.00 0.00 4.61
645 690 0.034477 ACCCATCCAAATCGTCCACC 60.034 55.000 0.00 0.00 0.00 4.61
646 691 1.094785 CACCCATCCAAATCGTCCAC 58.905 55.000 0.00 0.00 0.00 4.02
647 692 0.679640 GCACCCATCCAAATCGTCCA 60.680 55.000 0.00 0.00 0.00 4.02
648 693 0.679640 TGCACCCATCCAAATCGTCC 60.680 55.000 0.00 0.00 0.00 4.79
649 694 0.734889 CTGCACCCATCCAAATCGTC 59.265 55.000 0.00 0.00 0.00 4.20
650 695 0.038166 ACTGCACCCATCCAAATCGT 59.962 50.000 0.00 0.00 0.00 3.73
651 696 1.135315 CAACTGCACCCATCCAAATCG 60.135 52.381 0.00 0.00 0.00 3.34
652 697 1.205417 CCAACTGCACCCATCCAAATC 59.795 52.381 0.00 0.00 0.00 2.17
653 698 1.203162 TCCAACTGCACCCATCCAAAT 60.203 47.619 0.00 0.00 0.00 2.32
654 699 0.187117 TCCAACTGCACCCATCCAAA 59.813 50.000 0.00 0.00 0.00 3.28
655 700 0.409092 ATCCAACTGCACCCATCCAA 59.591 50.000 0.00 0.00 0.00 3.53
656 701 0.409092 AATCCAACTGCACCCATCCA 59.591 50.000 0.00 0.00 0.00 3.41
657 702 1.106285 GAATCCAACTGCACCCATCC 58.894 55.000 0.00 0.00 0.00 3.51
658 703 0.734889 CGAATCCAACTGCACCCATC 59.265 55.000 0.00 0.00 0.00 3.51
659 704 1.315257 GCGAATCCAACTGCACCCAT 61.315 55.000 0.00 0.00 0.00 4.00
660 705 1.971167 GCGAATCCAACTGCACCCA 60.971 57.895 0.00 0.00 0.00 4.51
661 706 1.648467 GAGCGAATCCAACTGCACCC 61.648 60.000 0.00 0.00 0.00 4.61
662 707 0.674895 AGAGCGAATCCAACTGCACC 60.675 55.000 0.00 0.00 0.00 5.01
663 708 0.723981 GAGAGCGAATCCAACTGCAC 59.276 55.000 0.00 0.00 0.00 4.57
664 709 0.321346 TGAGAGCGAATCCAACTGCA 59.679 50.000 0.00 0.00 0.00 4.41
665 710 1.442769 TTGAGAGCGAATCCAACTGC 58.557 50.000 0.00 0.00 0.00 4.40
666 711 4.631377 TGTAATTGAGAGCGAATCCAACTG 59.369 41.667 0.00 0.00 0.00 3.16
667 712 4.832248 TGTAATTGAGAGCGAATCCAACT 58.168 39.130 0.00 0.00 0.00 3.16
668 713 4.631813 ACTGTAATTGAGAGCGAATCCAAC 59.368 41.667 0.00 0.00 0.00 3.77
669 714 4.631377 CACTGTAATTGAGAGCGAATCCAA 59.369 41.667 0.00 0.00 0.00 3.53
670 715 4.183865 CACTGTAATTGAGAGCGAATCCA 58.816 43.478 0.00 0.00 0.00 3.41
671 716 3.001736 GCACTGTAATTGAGAGCGAATCC 59.998 47.826 0.00 0.00 0.00 3.01
672 717 3.618594 TGCACTGTAATTGAGAGCGAATC 59.381 43.478 0.00 0.00 30.42 2.52
673 718 3.599343 TGCACTGTAATTGAGAGCGAAT 58.401 40.909 0.00 0.00 30.42 3.34
674 719 2.995939 CTGCACTGTAATTGAGAGCGAA 59.004 45.455 0.00 0.00 30.42 4.70
675 720 2.029020 ACTGCACTGTAATTGAGAGCGA 60.029 45.455 0.00 0.00 30.42 4.93
676 721 2.341257 ACTGCACTGTAATTGAGAGCG 58.659 47.619 0.00 0.00 30.42 5.03
677 722 5.111989 TCATACTGCACTGTAATTGAGAGC 58.888 41.667 0.00 0.00 0.00 4.09
678 723 7.306457 CGAATCATACTGCACTGTAATTGAGAG 60.306 40.741 0.00 0.00 0.00 3.20
679 724 6.476706 CGAATCATACTGCACTGTAATTGAGA 59.523 38.462 0.00 0.00 0.00 3.27
680 725 6.643845 CGAATCATACTGCACTGTAATTGAG 58.356 40.000 0.00 0.00 0.00 3.02
681 726 5.006649 GCGAATCATACTGCACTGTAATTGA 59.993 40.000 0.00 0.00 0.00 2.57
682 727 5.007039 AGCGAATCATACTGCACTGTAATTG 59.993 40.000 0.00 0.00 0.00 2.32
683 728 5.118990 AGCGAATCATACTGCACTGTAATT 58.881 37.500 0.00 0.00 0.00 1.40
684 729 4.697514 AGCGAATCATACTGCACTGTAAT 58.302 39.130 0.00 0.00 0.00 1.89
685 730 4.112634 GAGCGAATCATACTGCACTGTAA 58.887 43.478 0.00 0.00 0.00 2.41
686 731 3.381590 AGAGCGAATCATACTGCACTGTA 59.618 43.478 0.00 0.00 0.00 2.74
687 732 2.167281 AGAGCGAATCATACTGCACTGT 59.833 45.455 0.00 0.00 0.00 3.55
688 733 2.793790 GAGAGCGAATCATACTGCACTG 59.206 50.000 0.00 0.00 0.00 3.66
689 734 2.428530 TGAGAGCGAATCATACTGCACT 59.571 45.455 0.00 0.00 0.00 4.40
753 800 3.476552 TCAGGGAATGTGTCTGTTGTTC 58.523 45.455 0.00 0.00 0.00 3.18
1388 1441 6.228258 ACAGAGCTAAACATTTAAACGAGGA 58.772 36.000 0.00 0.00 0.00 3.71
1390 1443 6.234213 CGACAGAGCTAAACATTTAAACGAG 58.766 40.000 0.00 0.00 0.00 4.18
1402 1460 1.343142 TGAGCAACCGACAGAGCTAAA 59.657 47.619 0.00 0.00 37.48 1.85
1524 1582 5.228635 GCACGCATCAAAAACATATCTTCTG 59.771 40.000 0.00 0.00 0.00 3.02
2094 2153 6.868339 AGATTGAAAAGGCCTTCATTAAAACG 59.132 34.615 20.79 0.00 35.31 3.60
2101 2160 3.056322 GCACAGATTGAAAAGGCCTTCAT 60.056 43.478 20.79 11.30 35.31 2.57
2102 2161 2.297033 GCACAGATTGAAAAGGCCTTCA 59.703 45.455 20.79 11.27 33.48 3.02
2105 2164 1.891150 CTGCACAGATTGAAAAGGCCT 59.109 47.619 0.00 0.00 0.00 5.19
2109 2168 2.325761 GCAGCTGCACAGATTGAAAAG 58.674 47.619 33.36 0.00 41.59 2.27
2111 2170 0.599558 GGCAGCTGCACAGATTGAAA 59.400 50.000 37.63 0.00 44.36 2.69
2113 2172 0.958876 CTGGCAGCTGCACAGATTGA 60.959 55.000 35.00 13.88 44.36 2.57
2114 2173 0.958876 TCTGGCAGCTGCACAGATTG 60.959 55.000 35.92 22.53 40.67 2.67
2115 2174 0.677098 CTCTGGCAGCTGCACAGATT 60.677 55.000 37.65 0.00 42.78 2.40
2116 2175 1.078356 CTCTGGCAGCTGCACAGAT 60.078 57.895 37.65 0.00 42.78 2.90
2117 2176 2.346365 CTCTGGCAGCTGCACAGA 59.654 61.111 36.31 36.31 42.10 3.41
2118 2177 2.032223 ACTCTGGCAGCTGCACAG 59.968 61.111 37.63 35.27 44.36 3.66
2119 2178 2.031616 GACTCTGGCAGCTGCACA 59.968 61.111 37.63 29.43 44.36 4.57
2120 2179 0.959372 AATGACTCTGGCAGCTGCAC 60.959 55.000 37.63 26.73 44.36 4.57
2121 2180 0.958876 CAATGACTCTGGCAGCTGCA 60.959 55.000 37.63 23.01 44.36 4.41
2122 2181 0.959372 ACAATGACTCTGGCAGCTGC 60.959 55.000 30.88 30.88 41.14 5.25
2517 2576 1.831736 GCTGGTAGACTAAGGCTGGAA 59.168 52.381 0.00 0.00 0.00 3.53
2812 2871 6.722301 CACTGGATATACAATTTCAGCTGTG 58.278 40.000 14.67 7.08 0.00 3.66
2927 2987 1.923899 TGTGTGCATGCACTTTGTTG 58.076 45.000 41.43 0.00 46.30 3.33
3492 3557 8.328758 ACAAATCATCCAAGAGTAATAAGTGGA 58.671 33.333 0.00 0.00 42.38 4.02
3575 3640 2.690653 ATCCCCAACACACACCACCG 62.691 60.000 0.00 0.00 0.00 4.94
4059 4128 4.524802 TGGAAATATGGCTGTGGAATCT 57.475 40.909 0.00 0.00 0.00 2.40
4674 4763 7.175641 GGATAACTTGGCTGCATGATTAATACT 59.824 37.037 0.50 0.00 0.00 2.12
4750 4839 9.396022 ACCTTGAATACCTGTAAATATCAAGTG 57.604 33.333 10.59 5.97 32.65 3.16
5398 5487 7.617041 AATAGCATGGTTGAGAAAAGACTAC 57.383 36.000 1.12 0.00 0.00 2.73
5621 5711 9.199982 CATCATCCATATTAAAACCATGAAAGC 57.800 33.333 0.00 0.00 0.00 3.51
5918 6008 2.539476 CACCCAACAAGTGTCAAAAGC 58.461 47.619 0.00 0.00 0.00 3.51
5925 6015 1.214424 AGTAAGCCACCCAACAAGTGT 59.786 47.619 0.00 0.00 33.20 3.55
5960 6059 6.709643 CCGAGATGCTACTTTTATTGAACAG 58.290 40.000 0.00 0.00 0.00 3.16
6399 6498 7.530426 AAAGGAGATGATGTAAGCAAAGTTT 57.470 32.000 0.00 0.00 33.49 2.66
6705 6804 3.556999 TCTTTGAATCCGTTGGTCCAAA 58.443 40.909 5.69 0.00 0.00 3.28
6706 6805 3.216187 TCTTTGAATCCGTTGGTCCAA 57.784 42.857 0.00 0.00 0.00 3.53
6745 6846 5.798434 GGTGTAAGAAATTATGCGGTTTCAC 59.202 40.000 0.00 0.00 36.92 3.18
6769 6870 5.922544 AGATTTTCCAAGAAAGATTGTTGCG 59.077 36.000 0.00 0.00 33.01 4.85
7306 7407 7.505585 TGTTCCAACCAGATCTCTTGTAAAAAT 59.494 33.333 0.00 0.00 0.00 1.82
7307 7408 6.831353 TGTTCCAACCAGATCTCTTGTAAAAA 59.169 34.615 0.00 0.00 0.00 1.94
7308 7409 6.361433 TGTTCCAACCAGATCTCTTGTAAAA 58.639 36.000 0.00 0.00 0.00 1.52
7350 7451 8.668353 CAATCTAAGAGCAAATACAGCAGTTAA 58.332 33.333 0.00 0.00 0.00 2.01
7387 7488 5.694006 GCTTGCTCTAACATGATTCGATAGT 59.306 40.000 0.00 0.00 37.40 2.12
7545 7653 4.623932 AGTGAGCTTTGTATCTTCACCA 57.376 40.909 0.00 0.00 0.00 4.17
7636 7744 5.840243 TTGGACCTGATTGCAATCTTATG 57.160 39.130 33.23 22.22 36.39 1.90


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

AutoCloner maintained by Alex Coulton.