Multiple sequence alignment - TraesCS4B01G123500

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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 TraesCS4B01G123500 chr4B 100.000 4811 0 0 1 4811 147332057 147327247 0.000000e+00 8885.0
1 TraesCS4B01G123500 chr4B 82.677 635 37 38 1 603 625354958 625355551 3.340000e-136 496.0
2 TraesCS4B01G123500 chr4B 92.500 80 5 1 4637 4715 334214530 334214451 3.940000e-21 113.0
3 TraesCS4B01G123500 chr4B 85.859 99 12 2 2085 2183 652878850 652878754 2.370000e-18 104.0
4 TraesCS4B01G123500 chr4A 95.276 1651 58 6 636 2283 472193933 472195566 0.000000e+00 2599.0
5 TraesCS4B01G123500 chr4A 93.370 1448 74 8 2675 4104 472196620 472198063 0.000000e+00 2122.0
6 TraesCS4B01G123500 chr4A 91.216 592 42 6 1 588 744381360 744381945 0.000000e+00 797.0
7 TraesCS4B01G123500 chr4A 84.520 646 46 19 1 602 621469607 621470242 1.490000e-164 590.0
8 TraesCS4B01G123500 chr4A 97.778 90 2 0 4121 4210 254283635 254283724 6.450000e-34 156.0
9 TraesCS4B01G123500 chr4D 95.668 1616 63 5 638 2253 102875213 102873605 0.000000e+00 2590.0
10 TraesCS4B01G123500 chr4D 95.970 1191 33 7 2916 4091 102872615 102871425 0.000000e+00 1919.0
11 TraesCS4B01G123500 chr4D 88.806 402 35 3 2495 2895 102873436 102873044 7.240000e-133 484.0
12 TraesCS4B01G123500 chr4D 96.226 106 3 1 490 594 502967735 502967630 6.400000e-39 172.0
13 TraesCS4B01G123500 chr4D 86.598 97 11 2 2085 2181 483809481 483809575 6.590000e-19 106.0
14 TraesCS4B01G123500 chr4D 88.750 80 8 1 4637 4715 478731381 478731460 3.960000e-16 97.1
15 TraesCS4B01G123500 chr3B 96.840 538 12 2 4159 4696 796994109 796994641 0.000000e+00 894.0
16 TraesCS4B01G123500 chr3B 100.000 175 0 0 4637 4811 796994641 796994815 1.670000e-84 324.0
17 TraesCS4B01G123500 chr3B 83.660 153 19 6 1632 1781 264009158 264009307 6.490000e-29 139.0
18 TraesCS4B01G123500 chr2B 91.883 616 37 8 1 603 439694336 439693721 0.000000e+00 848.0
19 TraesCS4B01G123500 chr2B 89.263 624 35 6 1 592 664366154 664365531 0.000000e+00 752.0
20 TraesCS4B01G123500 chr2B 89.137 626 37 11 1 597 508655278 508654655 0.000000e+00 750.0
21 TraesCS4B01G123500 chr2B 93.387 499 30 3 1 496 772679278 772678780 0.000000e+00 736.0
22 TraesCS4B01G123500 chr2B 91.225 547 32 7 1 531 694775121 694774575 0.000000e+00 730.0
23 TraesCS4B01G123500 chr2B 92.886 492 34 1 1 491 694746415 694745924 0.000000e+00 713.0
24 TraesCS4B01G123500 chr5A 92.361 576 39 5 4123 4696 457253534 457254106 0.000000e+00 815.0
25 TraesCS4B01G123500 chr5A 95.946 148 5 1 4637 4784 457254106 457254252 6.220000e-59 239.0
26 TraesCS4B01G123500 chr5A 96.667 90 3 0 4121 4210 59029021 59029110 3.000000e-32 150.0
27 TraesCS4B01G123500 chr3A 92.014 576 37 5 4123 4696 531733762 531734330 0.000000e+00 800.0
28 TraesCS4B01G123500 chr3A 96.622 148 4 1 4637 4784 531734383 531734529 1.340000e-60 244.0
29 TraesCS4B01G123500 chr3A 83.444 151 23 2 1632 1781 244351925 244352074 6.490000e-29 139.0
30 TraesCS4B01G123500 chr1A 91.840 576 38 5 4123 4696 77795666 77795098 0.000000e+00 795.0
31 TraesCS4B01G123500 chr1A 96.947 131 4 0 4637 4767 77795098 77794968 2.250000e-53 220.0
32 TraesCS4B01G123500 chr7B 90.312 609 47 9 1 607 682899269 682898671 0.000000e+00 787.0
33 TraesCS4B01G123500 chr7B 88.748 631 39 7 1 602 147731085 147731712 0.000000e+00 743.0
34 TraesCS4B01G123500 chr7B 84.261 629 48 16 1 600 73484195 73483589 2.510000e-157 566.0
35 TraesCS4B01G123500 chr7B 96.667 90 3 0 4121 4210 263933002 263932913 3.000000e-32 150.0
36 TraesCS4B01G123500 chrUn 88.013 634 43 10 1 601 46198143 46198776 0.000000e+00 719.0
37 TraesCS4B01G123500 chrUn 86.735 98 11 2 2085 2182 24270037 24270132 1.830000e-19 108.0
38 TraesCS4B01G123500 chrUn 86.598 97 11 2 2085 2181 92970965 92970871 6.590000e-19 106.0
39 TraesCS4B01G123500 chr7A 86.991 638 49 18 1 616 712079551 712080176 0.000000e+00 688.0
40 TraesCS4B01G123500 chr7A 91.165 498 39 4 4123 4616 585847658 585847162 0.000000e+00 671.0
41 TraesCS4B01G123500 chr5D 86.888 633 50 10 1 601 547449082 547448451 0.000000e+00 678.0
42 TraesCS4B01G123500 chr5D 86.735 98 11 2 2085 2182 485912416 485912321 1.830000e-19 108.0
43 TraesCS4B01G123500 chr5B 84.127 630 48 12 1 600 366025126 366024519 3.250000e-156 562.0
44 TraesCS4B01G123500 chr5B 91.731 387 20 2 4123 4508 711178277 711178652 1.190000e-145 527.0
45 TraesCS4B01G123500 chr5B 91.915 235 13 4 4436 4666 711178654 711178886 1.670000e-84 324.0
46 TraesCS4B01G123500 chr6B 83.797 611 61 21 1 597 94142559 94143145 3.270000e-151 545.0
47 TraesCS4B01G123500 chr6B 83.621 464 31 13 182 600 673360180 673360643 1.260000e-105 394.0
48 TraesCS4B01G123500 chr6B 85.818 275 22 9 4532 4790 240543962 240543689 4.740000e-70 276.0
49 TraesCS4B01G123500 chr6B 92.308 117 8 1 487 602 88373144 88373260 1.070000e-36 165.0
50 TraesCS4B01G123500 chr2D 95.455 110 4 1 487 595 305947139 305947248 1.780000e-39 174.0
51 TraesCS4B01G123500 chr2D 86.735 98 11 2 2085 2182 647763266 647763361 1.830000e-19 108.0
52 TraesCS4B01G123500 chr2D 88.750 80 8 1 4637 4715 43459623 43459702 3.960000e-16 97.1
53 TraesCS4B01G123500 chr1D 92.920 113 7 1 490 601 472353373 472353261 3.850000e-36 163.0
54 TraesCS4B01G123500 chr7D 86.598 97 11 2 2085 2181 541328922 541329016 6.590000e-19 106.0
55 TraesCS4B01G123500 chr6A 100.000 39 0 0 2968 3006 592819188 592819150 6.680000e-09 73.1
56 TraesCS4B01G123500 chr6A 93.182 44 3 0 4643 4686 599982334 599982291 1.120000e-06 65.8


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 TraesCS4B01G123500 chr4B 147327247 147332057 4810 True 8885.000000 8885 100.000000 1 4811 1 chr4B.!!$R1 4810
1 TraesCS4B01G123500 chr4B 625354958 625355551 593 False 496.000000 496 82.677000 1 603 1 chr4B.!!$F1 602
2 TraesCS4B01G123500 chr4A 472193933 472198063 4130 False 2360.500000 2599 94.323000 636 4104 2 chr4A.!!$F4 3468
3 TraesCS4B01G123500 chr4A 744381360 744381945 585 False 797.000000 797 91.216000 1 588 1 chr4A.!!$F3 587
4 TraesCS4B01G123500 chr4A 621469607 621470242 635 False 590.000000 590 84.520000 1 602 1 chr4A.!!$F2 601
5 TraesCS4B01G123500 chr4D 102871425 102875213 3788 True 1664.333333 2590 93.481333 638 4091 3 chr4D.!!$R2 3453
6 TraesCS4B01G123500 chr3B 796994109 796994815 706 False 609.000000 894 98.420000 4159 4811 2 chr3B.!!$F2 652
7 TraesCS4B01G123500 chr2B 439693721 439694336 615 True 848.000000 848 91.883000 1 603 1 chr2B.!!$R1 602
8 TraesCS4B01G123500 chr2B 664365531 664366154 623 True 752.000000 752 89.263000 1 592 1 chr2B.!!$R3 591
9 TraesCS4B01G123500 chr2B 508654655 508655278 623 True 750.000000 750 89.137000 1 597 1 chr2B.!!$R2 596
10 TraesCS4B01G123500 chr2B 694774575 694775121 546 True 730.000000 730 91.225000 1 531 1 chr2B.!!$R5 530
11 TraesCS4B01G123500 chr5A 457253534 457254252 718 False 527.000000 815 94.153500 4123 4784 2 chr5A.!!$F2 661
12 TraesCS4B01G123500 chr3A 531733762 531734529 767 False 522.000000 800 94.318000 4123 4784 2 chr3A.!!$F2 661
13 TraesCS4B01G123500 chr1A 77794968 77795666 698 True 507.500000 795 94.393500 4123 4767 2 chr1A.!!$R1 644
14 TraesCS4B01G123500 chr7B 682898671 682899269 598 True 787.000000 787 90.312000 1 607 1 chr7B.!!$R3 606
15 TraesCS4B01G123500 chr7B 147731085 147731712 627 False 743.000000 743 88.748000 1 602 1 chr7B.!!$F1 601
16 TraesCS4B01G123500 chr7B 73483589 73484195 606 True 566.000000 566 84.261000 1 600 1 chr7B.!!$R1 599
17 TraesCS4B01G123500 chrUn 46198143 46198776 633 False 719.000000 719 88.013000 1 601 1 chrUn.!!$F2 600
18 TraesCS4B01G123500 chr7A 712079551 712080176 625 False 688.000000 688 86.991000 1 616 1 chr7A.!!$F1 615
19 TraesCS4B01G123500 chr5D 547448451 547449082 631 True 678.000000 678 86.888000 1 601 1 chr5D.!!$R2 600
20 TraesCS4B01G123500 chr5B 366024519 366025126 607 True 562.000000 562 84.127000 1 600 1 chr5B.!!$R1 599
21 TraesCS4B01G123500 chr5B 711178277 711178886 609 False 425.500000 527 91.823000 4123 4666 2 chr5B.!!$F1 543
22 TraesCS4B01G123500 chr6B 94142559 94143145 586 False 545.000000 545 83.797000 1 597 1 chr6B.!!$F2 596

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
28 29 0.248539 GGAACGACGAAGATAGCGCT 60.249 55.0 17.26 17.26 0.00 5.92 F
629 696 0.248990 TTTATGCTACCCCGCGTACG 60.249 55.0 11.84 11.84 39.67 3.67 F
2288 2358 0.179004 ACGGTTGTCTTCCCATGCAA 60.179 50.0 0.00 0.00 0.00 4.08 F
2645 3609 0.106868 CAGATTGAGGAGCATGCCCA 60.107 55.0 22.33 10.78 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1144 1211 0.184933 CACCCTCCCTTTGGAACACA 59.815 55.0 0.00 0.0 41.17 3.72 R
2351 3020 0.038166 GGTTGGAGAAGGGACATGCA 59.962 55.0 0.00 0.0 0.00 3.96 R
3423 4799 0.729690 GGAAGTCATTCTTGCTCGCC 59.270 55.0 0.00 0.0 40.56 5.54 R
4335 5726 0.038892 ACGTAAACGCACGACCAGAT 60.039 50.0 11.19 0.0 44.69 2.90 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
28 29 0.248539 GGAACGACGAAGATAGCGCT 60.249 55.000 17.26 17.26 0.00 5.92
97 98 1.555533 AGTTCGAAGGGATCCAACTCC 59.444 52.381 15.23 0.00 34.31 3.85
151 152 3.160585 CAGAACCCTGGAGCACCA 58.839 61.111 1.91 1.91 44.76 4.17
620 687 5.311844 AGGAGATCCCTTTTTATGCTACC 57.688 43.478 0.00 0.00 44.85 3.18
621 688 4.104897 AGGAGATCCCTTTTTATGCTACCC 59.895 45.833 0.00 0.00 44.85 3.69
622 689 4.399219 GAGATCCCTTTTTATGCTACCCC 58.601 47.826 0.00 0.00 0.00 4.95
623 690 2.721425 TCCCTTTTTATGCTACCCCG 57.279 50.000 0.00 0.00 0.00 5.73
624 691 1.029681 CCCTTTTTATGCTACCCCGC 58.970 55.000 0.00 0.00 0.00 6.13
625 692 0.661020 CCTTTTTATGCTACCCCGCG 59.339 55.000 0.00 0.00 0.00 6.46
626 693 1.375551 CTTTTTATGCTACCCCGCGT 58.624 50.000 4.92 0.00 0.00 6.01
627 694 2.553086 CTTTTTATGCTACCCCGCGTA 58.447 47.619 4.92 0.00 0.00 4.42
628 695 1.938625 TTTTATGCTACCCCGCGTAC 58.061 50.000 4.92 0.00 31.55 3.67
629 696 0.248990 TTTATGCTACCCCGCGTACG 60.249 55.000 11.84 11.84 39.67 3.67
630 697 1.383456 TTATGCTACCCCGCGTACGT 61.383 55.000 17.90 0.00 37.70 3.57
631 698 2.062361 TATGCTACCCCGCGTACGTG 62.062 60.000 21.58 21.58 37.70 4.49
632 699 4.120331 GCTACCCCGCGTACGTGT 62.120 66.667 25.62 15.46 37.70 4.49
633 700 2.568090 CTACCCCGCGTACGTGTT 59.432 61.111 25.62 12.95 37.70 3.32
634 701 1.514873 CTACCCCGCGTACGTGTTC 60.515 63.158 25.62 4.34 37.70 3.18
635 702 2.872337 CTACCCCGCGTACGTGTTCC 62.872 65.000 25.62 3.95 37.70 3.62
636 703 4.060038 CCCCGCGTACGTGTTCCT 62.060 66.667 25.62 0.00 37.70 3.36
729 796 1.961793 TTTTGAGTGGGACGAACTGG 58.038 50.000 0.00 0.00 0.00 4.00
772 839 2.224314 GCTTTGGAACAGAAAGTCTCGG 59.776 50.000 0.00 0.00 42.39 4.63
790 857 8.095937 AGTCTCGGTTTTGTTCTATTTTTAGG 57.904 34.615 0.00 0.00 0.00 2.69
880 947 7.475015 CACACAATGTCTCAAGAGAAAAGAAA 58.525 34.615 0.57 0.00 39.48 2.52
1128 1195 4.478317 AGGGGAAGGAATGTATGTCAATGA 59.522 41.667 0.00 0.00 0.00 2.57
1466 1533 5.006358 GCAACATTGACCGATCGTTAAGTAT 59.994 40.000 15.09 0.00 0.00 2.12
1467 1534 6.199531 GCAACATTGACCGATCGTTAAGTATA 59.800 38.462 15.09 0.00 0.00 1.47
1568 1635 0.688087 GGATCCCGAAGACCTCCAGT 60.688 60.000 0.00 0.00 0.00 4.00
1577 1644 2.526873 ACCTCCAGTTGGACGGCT 60.527 61.111 13.33 3.11 39.78 5.52
1813 1880 2.623889 CCACCTCGTAGCAGCTAGTATT 59.376 50.000 1.02 0.00 0.00 1.89
1814 1881 3.819337 CCACCTCGTAGCAGCTAGTATTA 59.181 47.826 1.02 0.00 0.00 0.98
1815 1882 4.459685 CCACCTCGTAGCAGCTAGTATTAT 59.540 45.833 1.02 0.00 0.00 1.28
1816 1883 5.646793 CCACCTCGTAGCAGCTAGTATTATA 59.353 44.000 1.02 0.00 0.00 0.98
1817 1884 6.319152 CCACCTCGTAGCAGCTAGTATTATAT 59.681 42.308 1.02 0.00 0.00 0.86
1818 1885 7.498239 CCACCTCGTAGCAGCTAGTATTATATA 59.502 40.741 1.02 0.00 0.00 0.86
1819 1886 9.058174 CACCTCGTAGCAGCTAGTATTATATAT 57.942 37.037 1.02 0.00 0.00 0.86
1929 1999 3.377172 CCAACAGTCGTCCTTGTTTCTTT 59.623 43.478 0.00 0.00 35.46 2.52
1995 2065 3.804193 CCTTTCCTTGAGCGGCGC 61.804 66.667 26.86 26.86 0.00 6.53
2024 2094 3.971702 ACTGCACCCTCCTTGCCC 61.972 66.667 0.00 0.00 39.39 5.36
2065 2135 5.189180 AGCAGGAATATGAGGTTTGACTTC 58.811 41.667 0.00 0.00 0.00 3.01
2073 2143 9.399403 GAATATGAGGTTTGACTTCTCAAAAAC 57.601 33.333 0.00 0.00 45.89 2.43
2080 2150 5.576447 TTGACTTCTCAAAAACTTGGTCC 57.424 39.130 0.00 0.00 33.20 4.46
2098 2168 8.749354 ACTTGGTCCAAGGATGTAAAAATATTC 58.251 33.333 30.76 0.00 44.81 1.75
2157 2227 9.766277 GACTTTTCAAAATAGAACTAGATGCAG 57.234 33.333 0.00 0.00 0.00 4.41
2159 2229 9.552114 CTTTTCAAAATAGAACTAGATGCAGTG 57.448 33.333 0.00 0.00 0.00 3.66
2280 2350 4.143179 CCTTCAATTACGACGGTTGTCTTC 60.143 45.833 3.84 0.00 43.21 2.87
2281 2351 3.319755 TCAATTACGACGGTTGTCTTCC 58.680 45.455 3.84 0.00 43.21 3.46
2282 2352 2.375173 ATTACGACGGTTGTCTTCCC 57.625 50.000 3.84 0.00 43.21 3.97
2283 2353 1.039068 TTACGACGGTTGTCTTCCCA 58.961 50.000 3.84 0.00 43.21 4.37
2284 2354 1.259609 TACGACGGTTGTCTTCCCAT 58.740 50.000 3.84 0.00 43.21 4.00
2286 2356 1.635663 CGACGGTTGTCTTCCCATGC 61.636 60.000 0.00 0.00 43.21 4.06
2287 2357 0.605319 GACGGTTGTCTTCCCATGCA 60.605 55.000 0.00 0.00 42.08 3.96
2288 2358 0.179004 ACGGTTGTCTTCCCATGCAA 60.179 50.000 0.00 0.00 0.00 4.08
2289 2359 0.240945 CGGTTGTCTTCCCATGCAAC 59.759 55.000 0.00 3.77 40.08 4.17
2291 2361 0.603065 GTTGTCTTCCCATGCAACCC 59.397 55.000 0.00 0.00 36.25 4.11
2292 2362 0.893270 TTGTCTTCCCATGCAACCCG 60.893 55.000 0.00 0.00 0.00 5.28
2293 2363 1.303317 GTCTTCCCATGCAACCCGT 60.303 57.895 0.00 0.00 0.00 5.28
2294 2364 1.303236 TCTTCCCATGCAACCCGTG 60.303 57.895 0.00 0.00 0.00 4.94
2298 2368 4.406533 CCATGCAACCCGTGGTAA 57.593 55.556 0.00 0.00 44.22 2.85
2311 2381 1.201414 CGTGGTAATCCCTTTGTTGGC 59.799 52.381 0.00 0.00 0.00 4.52
2348 3017 6.208644 CACAAAACTCTTAATGTTCTGGTGG 58.791 40.000 0.00 0.00 0.00 4.61
2351 3020 7.724061 ACAAAACTCTTAATGTTCTGGTGGTAT 59.276 33.333 1.66 0.00 0.00 2.73
2376 3045 1.423921 GTCCCTTCTCCAACCCTTTGA 59.576 52.381 0.00 0.00 34.24 2.69
2381 3050 2.762535 TCTCCAACCCTTTGATCGTC 57.237 50.000 0.00 0.00 34.24 4.20
2385 3054 1.076332 CAACCCTTTGATCGTCGGTC 58.924 55.000 0.00 0.00 34.24 4.79
2396 3065 0.526211 TCGTCGGTCCAAGTCTCATG 59.474 55.000 0.00 0.00 0.00 3.07
2413 3082 7.564793 AGTCTCATGTAACTTGTGGCATATTA 58.435 34.615 0.00 0.00 0.00 0.98
2414 3083 8.046708 AGTCTCATGTAACTTGTGGCATATTAA 58.953 33.333 0.00 0.00 0.00 1.40
2453 3417 9.364989 GGATCCAAGATTATCTCTAGAAATTCG 57.635 37.037 6.95 0.00 32.41 3.34
2457 3421 6.613153 AGATTATCTCTAGAAATTCGGGGG 57.387 41.667 0.00 0.00 30.26 5.40
2459 3423 1.129058 TCTCTAGAAATTCGGGGGCC 58.871 55.000 0.00 0.00 0.00 5.80
2460 3424 1.132500 CTCTAGAAATTCGGGGGCCT 58.868 55.000 0.84 0.00 0.00 5.19
2463 3427 2.047830 CTAGAAATTCGGGGGCCTAGT 58.952 52.381 0.84 0.00 0.00 2.57
2464 3428 0.546598 AGAAATTCGGGGGCCTAGTG 59.453 55.000 0.84 0.00 0.00 2.74
2465 3429 1.076995 AAATTCGGGGGCCTAGTGC 60.077 57.895 0.84 0.00 40.16 4.40
2466 3430 2.886730 AAATTCGGGGGCCTAGTGCG 62.887 60.000 0.84 0.00 42.61 5.34
2469 3433 4.090588 CGGGGGCCTAGTGCGAAA 62.091 66.667 0.84 0.00 42.61 3.46
2470 3434 2.595655 GGGGGCCTAGTGCGAAAT 59.404 61.111 0.84 0.00 42.61 2.17
2471 3435 1.834301 GGGGGCCTAGTGCGAAATA 59.166 57.895 0.84 0.00 42.61 1.40
2472 3436 0.534427 GGGGGCCTAGTGCGAAATAC 60.534 60.000 0.84 0.00 42.61 1.89
2473 3437 0.534427 GGGGCCTAGTGCGAAATACC 60.534 60.000 0.84 0.00 42.61 2.73
2474 3438 0.534427 GGGCCTAGTGCGAAATACCC 60.534 60.000 0.84 0.00 42.61 3.69
2475 3439 0.179468 GGCCTAGTGCGAAATACCCA 59.821 55.000 0.00 0.00 42.61 4.51
2476 3440 1.407712 GGCCTAGTGCGAAATACCCAA 60.408 52.381 0.00 0.00 42.61 4.12
2477 3441 2.572290 GCCTAGTGCGAAATACCCAAT 58.428 47.619 0.00 0.00 0.00 3.16
2478 3442 2.290641 GCCTAGTGCGAAATACCCAATG 59.709 50.000 0.00 0.00 0.00 2.82
2479 3443 2.878406 CCTAGTGCGAAATACCCAATGG 59.122 50.000 0.00 0.00 37.80 3.16
2489 3453 4.373551 CCCAATGGGCCCCTAAAC 57.626 61.111 22.27 0.00 35.35 2.01
2490 3454 1.756561 CCCAATGGGCCCCTAAACG 60.757 63.158 22.27 1.00 35.35 3.60
2491 3455 1.756561 CCAATGGGCCCCTAAACGG 60.757 63.158 22.27 7.39 0.00 4.44
2492 3456 1.000145 CAATGGGCCCCTAAACGGT 60.000 57.895 22.27 0.00 0.00 4.83
2493 3457 0.613572 CAATGGGCCCCTAAACGGTT 60.614 55.000 22.27 0.00 0.00 4.44
2534 3498 4.336889 TCGTCTCCATGAGTGTCTTTTT 57.663 40.909 0.00 0.00 0.00 1.94
2535 3499 4.058124 TCGTCTCCATGAGTGTCTTTTTG 58.942 43.478 0.00 0.00 0.00 2.44
2584 3548 2.381752 TGAGGGGCTAGATCGAATCA 57.618 50.000 0.00 0.00 0.00 2.57
2610 3574 2.118313 TGTGTCGATCGGGACTAGAA 57.882 50.000 16.41 0.00 37.81 2.10
2640 3604 2.499289 AGTTCGACAGATTGAGGAGCAT 59.501 45.455 0.00 0.00 0.00 3.79
2645 3609 0.106868 CAGATTGAGGAGCATGCCCA 60.107 55.000 22.33 10.78 0.00 5.36
2646 3610 0.627451 AGATTGAGGAGCATGCCCAA 59.373 50.000 22.33 17.42 0.00 4.12
2649 3613 0.991146 TTGAGGAGCATGCCCAACTA 59.009 50.000 22.33 12.41 0.00 2.24
2681 3645 0.249911 GACCAGCTAACCGGGCATAG 60.250 60.000 6.32 6.62 31.13 2.23
2811 3775 2.446848 CCATGGACGGCCCTGATCT 61.447 63.158 15.07 0.00 32.08 2.75
2825 3789 3.455910 CCCTGATCTGATTAGGTTGGTGA 59.544 47.826 22.52 0.00 34.40 4.02
2829 3793 5.674525 TGATCTGATTAGGTTGGTGATGTC 58.325 41.667 0.00 0.00 0.00 3.06
2844 3808 4.927425 GGTGATGTCGCAAAAAGACTACTA 59.073 41.667 0.00 0.00 39.24 1.82
2878 3896 3.135712 ACATCATATCCAGGTTGGCGTTA 59.864 43.478 0.00 0.00 37.47 3.18
2883 3901 1.136565 CCAGGTTGGCGTTATTGCG 59.863 57.895 0.00 0.00 35.06 4.85
2895 3913 2.443416 GTTATTGCGGAAAGACCCCTT 58.557 47.619 0.00 0.00 34.64 3.95
3044 4420 3.569701 ACCAATGACGCATTTCACTCTTT 59.430 39.130 2.86 0.00 31.05 2.52
3056 4432 7.504818 GCATTTCACTCTTTACTTGATTTTGC 58.495 34.615 0.00 0.00 0.00 3.68
3327 4703 1.898574 CAGCACCAACCAGACCACC 60.899 63.158 0.00 0.00 0.00 4.61
3423 4799 3.774959 CTTCCTGTCGCCGATCCCG 62.775 68.421 0.00 0.00 0.00 5.14
3680 5056 3.576356 CGGTGATGGCGTGGATGC 61.576 66.667 0.00 0.00 0.00 3.91
3716 5092 2.202349 GCGGCACAACATCTTCGC 60.202 61.111 0.00 0.00 36.51 4.70
3938 5328 1.395805 GCGGCGCGAGTTTGAAATTC 61.396 55.000 19.09 0.00 0.00 2.17
4048 5438 3.618594 CAGATGTGATCGATGGACGTTTT 59.381 43.478 0.54 0.00 43.13 2.43
4091 5481 4.257267 TGACTGTAGTGAAGGTGATGTG 57.743 45.455 0.00 0.00 0.00 3.21
4093 5483 3.990469 GACTGTAGTGAAGGTGATGTGTG 59.010 47.826 0.00 0.00 0.00 3.82
4095 5485 3.727726 TGTAGTGAAGGTGATGTGTGTG 58.272 45.455 0.00 0.00 0.00 3.82
4100 5490 6.299805 AGTGAAGGTGATGTGTGTGTATAT 57.700 37.500 0.00 0.00 0.00 0.86
4104 5494 9.929180 GTGAAGGTGATGTGTGTGTATATATAT 57.071 33.333 0.00 0.00 0.00 0.86
4134 5524 5.544562 CCCTCTTCCCTCCCTACTAATAAAG 59.455 48.000 0.00 0.00 0.00 1.85
4141 5531 4.299978 CTCCCTACTAATAAAGCAGCGAC 58.700 47.826 0.00 0.00 0.00 5.19
4234 5624 8.507249 CACTCCCTTTTCAAGTTGTTATCTAAG 58.493 37.037 2.11 0.00 0.00 2.18
4335 5726 1.067693 CATCACGCACGCAAACTCTA 58.932 50.000 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.202932 CGGTGGCAGCGCTATCTT 60.203 61.111 26.78 0.00 30.39 2.40
351 353 2.666190 CTGGTGTGCGTGGGAGTG 60.666 66.667 0.00 0.00 0.00 3.51
589 654 1.467432 GGGATCTCCTCCTCCCGAT 59.533 63.158 0.00 0.00 44.28 4.18
616 683 1.514873 GAACACGTACGCGGGGTAG 60.515 63.158 16.72 0.00 44.17 3.18
617 684 2.566010 GAACACGTACGCGGGGTA 59.434 61.111 16.72 0.19 44.17 3.69
621 688 0.918619 CAATAGGAACACGTACGCGG 59.081 55.000 16.72 10.71 43.45 6.46
622 689 1.898938 TCAATAGGAACACGTACGCG 58.101 50.000 16.72 8.78 44.93 6.01
623 690 3.504863 TCTTCAATAGGAACACGTACGC 58.495 45.455 16.72 0.00 0.00 4.42
624 691 6.493116 AGTATCTTCAATAGGAACACGTACG 58.507 40.000 15.01 15.01 0.00 3.67
625 692 7.911362 GAGTATCTTCAATAGGAACACGTAC 57.089 40.000 0.00 0.00 0.00 3.67
710 777 1.487142 TCCAGTTCGTCCCACTCAAAA 59.513 47.619 0.00 0.00 0.00 2.44
729 796 3.627732 TCTTGAGTCGACTGTGTCTTC 57.372 47.619 25.58 7.32 0.00 2.87
772 839 7.598493 TGAGCATGCCTAAAAATAGAACAAAAC 59.402 33.333 15.66 0.00 0.00 2.43
790 857 2.292845 GGAAAAGGATAGCTGAGCATGC 59.707 50.000 10.51 10.51 0.00 4.06
880 947 7.112452 AGGTCAACAATACAAAGCTTTTCTT 57.888 32.000 9.53 0.34 36.34 2.52
1128 1195 7.943079 TGGAACACATGAACTAATCAATGAT 57.057 32.000 0.00 0.00 42.54 2.45
1143 1210 1.158007 ACCCTCCCTTTGGAACACAT 58.842 50.000 0.00 0.00 41.17 3.21
1144 1211 0.184933 CACCCTCCCTTTGGAACACA 59.815 55.000 0.00 0.00 41.17 3.72
1466 1533 7.874528 CACTATAAGATCCTGCACATCACATTA 59.125 37.037 4.15 0.00 0.00 1.90
1467 1534 6.709397 CACTATAAGATCCTGCACATCACATT 59.291 38.462 4.15 0.00 0.00 2.71
1814 1881 9.823647 GCATGTGTGCCTTAGAACTATATATAT 57.176 33.333 0.00 0.00 45.76 0.86
1929 1999 7.317722 ACTAAAGGAAGAAAGCTAGAGGAAA 57.682 36.000 0.00 0.00 0.00 3.13
2024 2094 1.772182 CTCTAATTAGACAGCGCCCG 58.228 55.000 11.24 0.00 0.00 6.13
2065 2135 4.342092 ACATCCTTGGACCAAGTTTTTGAG 59.658 41.667 28.45 14.11 39.58 3.02
2073 2143 8.197439 GGAATATTTTTACATCCTTGGACCAAG 58.803 37.037 25.05 25.05 40.75 3.61
2098 2168 4.718940 ACTTTGACCAAGTTTGTGAAGG 57.281 40.909 5.38 0.00 43.89 3.46
2157 2227 4.718961 ACTCCCTATGTTCCATAATGCAC 58.281 43.478 0.00 0.00 0.00 4.57
2159 2229 8.409358 AAAATACTCCCTATGTTCCATAATGC 57.591 34.615 0.00 0.00 0.00 3.56
2253 2323 2.706890 ACCGTCGTAATTGAAGGCAAT 58.293 42.857 0.00 0.00 46.35 3.56
2254 2324 2.172851 ACCGTCGTAATTGAAGGCAA 57.827 45.000 0.00 0.00 40.67 4.52
2280 2350 0.682855 ATTACCACGGGTTGCATGGG 60.683 55.000 8.12 0.00 37.86 4.00
2281 2351 0.738389 GATTACCACGGGTTGCATGG 59.262 55.000 1.63 1.63 37.09 3.66
2282 2352 0.738389 GGATTACCACGGGTTGCATG 59.262 55.000 0.72 0.00 37.09 4.06
2283 2353 0.395173 GGGATTACCACGGGTTGCAT 60.395 55.000 0.72 0.00 39.85 3.96
2284 2354 1.001887 GGGATTACCACGGGTTGCA 60.002 57.895 0.72 0.00 39.85 4.08
2286 2356 1.816224 CAAAGGGATTACCACGGGTTG 59.184 52.381 0.72 0.00 43.89 3.77
2287 2357 1.426215 ACAAAGGGATTACCACGGGTT 59.574 47.619 0.72 0.00 43.89 4.11
2288 2358 1.069775 ACAAAGGGATTACCACGGGT 58.930 50.000 1.14 1.14 43.89 5.28
2289 2359 1.816224 CAACAAAGGGATTACCACGGG 59.184 52.381 0.00 0.00 43.89 5.28
2290 2360 1.816224 CCAACAAAGGGATTACCACGG 59.184 52.381 0.00 0.00 43.89 4.94
2291 2361 1.201414 GCCAACAAAGGGATTACCACG 59.799 52.381 0.00 0.00 43.89 4.94
2292 2362 2.231235 CAGCCAACAAAGGGATTACCAC 59.769 50.000 0.00 0.00 43.89 4.16
2293 2363 2.524306 CAGCCAACAAAGGGATTACCA 58.476 47.619 0.00 0.00 43.89 3.25
2294 2364 1.204704 GCAGCCAACAAAGGGATTACC 59.795 52.381 0.00 0.00 40.67 2.85
2295 2365 1.892474 TGCAGCCAACAAAGGGATTAC 59.108 47.619 0.00 0.00 0.00 1.89
2296 2366 2.300956 TGCAGCCAACAAAGGGATTA 57.699 45.000 0.00 0.00 0.00 1.75
2297 2367 1.551883 GATGCAGCCAACAAAGGGATT 59.448 47.619 0.00 0.00 0.00 3.01
2298 2368 1.188863 GATGCAGCCAACAAAGGGAT 58.811 50.000 0.00 0.00 0.00 3.85
2348 3017 2.945668 GTTGGAGAAGGGACATGCATAC 59.054 50.000 0.00 0.00 0.00 2.39
2351 3020 0.038166 GGTTGGAGAAGGGACATGCA 59.962 55.000 0.00 0.00 0.00 3.96
2376 3045 1.135139 CATGAGACTTGGACCGACGAT 59.865 52.381 0.00 0.00 0.00 3.73
2381 3050 3.594603 AGTTACATGAGACTTGGACCG 57.405 47.619 0.00 0.00 0.00 4.79
2423 3387 9.755122 TTTCTAGAGATAATCTTGGATCCGATA 57.245 33.333 7.39 0.00 39.64 2.92
2437 3401 3.326880 GGCCCCCGAATTTCTAGAGATAA 59.673 47.826 0.00 0.00 0.00 1.75
2438 3402 2.904434 GGCCCCCGAATTTCTAGAGATA 59.096 50.000 0.00 0.00 0.00 1.98
2453 3417 0.534427 GTATTTCGCACTAGGCCCCC 60.534 60.000 0.00 0.00 40.31 5.40
2457 3421 2.032680 TTGGGTATTTCGCACTAGGC 57.967 50.000 0.00 0.00 38.70 3.93
2459 3423 2.878406 CCCATTGGGTATTTCGCACTAG 59.122 50.000 14.10 0.00 38.25 2.57
2460 3424 2.925724 CCCATTGGGTATTTCGCACTA 58.074 47.619 14.10 0.00 38.25 2.74
2463 3427 1.040339 GGCCCATTGGGTATTTCGCA 61.040 55.000 22.82 0.00 46.51 5.10
2464 3428 1.739667 GGCCCATTGGGTATTTCGC 59.260 57.895 22.82 6.45 46.51 4.70
2465 3429 1.112916 GGGGCCCATTGGGTATTTCG 61.113 60.000 26.86 0.00 46.51 3.46
2466 3430 0.264657 AGGGGCCCATTGGGTATTTC 59.735 55.000 27.72 5.70 46.51 2.17
2467 3431 1.626621 TAGGGGCCCATTGGGTATTT 58.373 50.000 27.72 9.43 46.51 1.40
2468 3432 1.626621 TTAGGGGCCCATTGGGTATT 58.373 50.000 27.72 2.27 46.51 1.89
2469 3433 1.219469 GTTTAGGGGCCCATTGGGTAT 59.781 52.381 27.72 3.14 46.51 2.73
2470 3434 0.632294 GTTTAGGGGCCCATTGGGTA 59.368 55.000 27.72 3.69 46.51 3.69
2471 3435 1.390525 GTTTAGGGGCCCATTGGGT 59.609 57.895 27.72 4.91 46.51 4.51
2473 3437 1.756561 CCGTTTAGGGGCCCATTGG 60.757 63.158 27.72 14.96 35.97 3.16
2474 3438 0.613572 AACCGTTTAGGGGCCCATTG 60.614 55.000 27.72 9.37 46.96 2.82
2475 3439 0.613572 CAACCGTTTAGGGGCCCATT 60.614 55.000 27.72 14.21 46.96 3.16
2476 3440 1.000145 CAACCGTTTAGGGGCCCAT 60.000 57.895 27.72 21.79 46.96 4.00
2477 3441 2.437002 CAACCGTTTAGGGGCCCA 59.563 61.111 27.72 8.13 46.96 5.36
2478 3442 1.974875 CACAACCGTTTAGGGGCCC 60.975 63.158 17.12 17.12 46.96 5.80
2479 3443 2.632544 GCACAACCGTTTAGGGGCC 61.633 63.158 0.00 0.00 46.96 5.80
2480 3444 2.632544 GGCACAACCGTTTAGGGGC 61.633 63.158 0.00 0.00 46.96 5.80
2481 3445 3.676216 GGCACAACCGTTTAGGGG 58.324 61.111 0.00 0.00 46.96 4.79
2490 3454 4.025401 CGGAAGTGCGGCACAACC 62.025 66.667 32.29 29.14 36.74 3.77
2491 3455 3.276846 ACGGAAGTGCGGCACAAC 61.277 61.111 32.29 23.85 46.97 3.32
2510 3474 1.546476 AGACACTCATGGAGACGAACC 59.454 52.381 0.00 0.00 33.32 3.62
2512 3476 4.336889 AAAAGACACTCATGGAGACGAA 57.663 40.909 0.00 0.00 33.32 3.85
2534 3498 0.323360 CGAAAGGATTCCCCAAGGCA 60.323 55.000 0.00 0.00 37.41 4.75
2535 3499 1.667154 GCGAAAGGATTCCCCAAGGC 61.667 60.000 0.00 0.00 37.41 4.35
2584 3548 0.320421 CCCGATCGACACAACCTGTT 60.320 55.000 18.66 0.00 31.03 3.16
2610 3574 6.204882 CCTCAATCTGTCGAACTAAGGTTTTT 59.795 38.462 0.00 0.00 35.58 1.94
2615 3579 4.677584 CTCCTCAATCTGTCGAACTAAGG 58.322 47.826 0.00 0.00 0.00 2.69
2626 3590 0.106868 TGGGCATGCTCCTCAATCTG 60.107 55.000 16.70 0.00 0.00 2.90
2640 3604 0.840288 TGGCTCTCCTTAGTTGGGCA 60.840 55.000 0.00 0.00 0.00 5.36
2645 3609 1.909986 GGTCCTTGGCTCTCCTTAGTT 59.090 52.381 0.00 0.00 0.00 2.24
2646 3610 1.203313 TGGTCCTTGGCTCTCCTTAGT 60.203 52.381 0.00 0.00 0.00 2.24
2649 3613 1.846712 GCTGGTCCTTGGCTCTCCTT 61.847 60.000 0.00 0.00 0.00 3.36
2681 3645 3.726291 TTTTCAGGCCTAGCACAAAAC 57.274 42.857 3.98 0.00 0.00 2.43
2721 3685 9.519191 CCCCTGATTTTGATGTGATGTATATAA 57.481 33.333 0.00 0.00 0.00 0.98
2811 3775 2.027653 TGCGACATCACCAACCTAATCA 60.028 45.455 0.00 0.00 0.00 2.57
2825 3789 8.718102 ACATTATAGTAGTCTTTTTGCGACAT 57.282 30.769 0.00 0.00 33.89 3.06
2856 3820 1.490490 ACGCCAACCTGGATATGATGT 59.510 47.619 0.00 0.00 40.96 3.06
2857 3821 2.260844 ACGCCAACCTGGATATGATG 57.739 50.000 0.00 0.00 40.96 3.07
2860 3824 3.304659 GCAATAACGCCAACCTGGATATG 60.305 47.826 0.00 0.00 40.96 1.78
2861 3825 2.884639 GCAATAACGCCAACCTGGATAT 59.115 45.455 0.00 0.00 40.96 1.63
2862 3826 2.294074 GCAATAACGCCAACCTGGATA 58.706 47.619 0.00 0.00 40.96 2.59
2864 3828 1.302383 CGCAATAACGCCAACCTGGA 61.302 55.000 0.00 0.00 40.96 3.86
2865 3829 1.136565 CGCAATAACGCCAACCTGG 59.863 57.895 0.00 0.00 41.55 4.45
2883 3901 8.304596 CAACTAATTCTTAAAAGGGGTCTTTCC 58.695 37.037 0.00 0.00 41.92 3.13
2914 3932 1.838077 AGCCTACCTTTGACCGCTAAT 59.162 47.619 0.00 0.00 0.00 1.73
2967 4342 9.950680 TTGATCAAATAAGGCTAAAATCGATTC 57.049 29.630 11.83 0.00 0.00 2.52
3007 4382 3.124921 GGTCCATGAACACGGCCG 61.125 66.667 26.86 26.86 0.00 6.13
3044 4420 5.933187 ACACACATACGCAAAATCAAGTA 57.067 34.783 0.00 0.00 0.00 2.24
3056 4432 5.215239 TGTTGCATCAATACACACATACG 57.785 39.130 0.00 0.00 0.00 3.06
3327 4703 1.063174 CGGTACCGGAAGTTCTCGTAG 59.937 57.143 27.00 0.00 35.56 3.51
3423 4799 0.729690 GGAAGTCATTCTTGCTCGCC 59.270 55.000 0.00 0.00 40.56 5.54
3468 4844 2.047560 GGGCCGTACAAGAGCGTT 60.048 61.111 0.00 0.00 0.00 4.84
3716 5092 2.045926 CCTGAAACCTCCCGCCAG 60.046 66.667 0.00 0.00 0.00 4.85
3799 5175 3.640407 ATGTGGTCAGCCGGCAGT 61.640 61.111 31.54 5.56 37.67 4.40
3800 5176 3.129502 CATGTGGTCAGCCGGCAG 61.130 66.667 31.54 22.82 37.67 4.85
3813 5189 0.978146 CCTCGAACTCCCTCCCATGT 60.978 60.000 0.00 0.00 0.00 3.21
3960 5350 2.671619 CGGCCGGTCCAACACAAT 60.672 61.111 20.10 0.00 34.01 2.71
3986 5376 2.468831 GAAGCTGAGATCAAGCTACCG 58.531 52.381 19.74 0.00 38.01 4.02
4100 5490 5.809252 AGGGAGGGAAGAGGGAAGATATATA 59.191 44.000 0.00 0.00 0.00 0.86
4104 5494 2.236851 AGGGAGGGAAGAGGGAAGATA 58.763 52.381 0.00 0.00 0.00 1.98
4105 5495 1.031112 AGGGAGGGAAGAGGGAAGAT 58.969 55.000 0.00 0.00 0.00 2.40
4106 5496 1.291335 GTAGGGAGGGAAGAGGGAAGA 59.709 57.143 0.00 0.00 0.00 2.87
4107 5497 1.292546 AGTAGGGAGGGAAGAGGGAAG 59.707 57.143 0.00 0.00 0.00 3.46
4108 5498 1.405243 AGTAGGGAGGGAAGAGGGAA 58.595 55.000 0.00 0.00 0.00 3.97
4109 5499 2.315503 TAGTAGGGAGGGAAGAGGGA 57.684 55.000 0.00 0.00 0.00 4.20
4110 5500 3.639625 ATTAGTAGGGAGGGAAGAGGG 57.360 52.381 0.00 0.00 0.00 4.30
4111 5501 5.012251 GCTTTATTAGTAGGGAGGGAAGAGG 59.988 48.000 0.00 0.00 0.00 3.69
4112 5502 5.602978 TGCTTTATTAGTAGGGAGGGAAGAG 59.397 44.000 0.00 0.00 0.00 2.85
4113 5503 5.535029 TGCTTTATTAGTAGGGAGGGAAGA 58.465 41.667 0.00 0.00 0.00 2.87
4114 5504 5.743422 GCTGCTTTATTAGTAGGGAGGGAAG 60.743 48.000 0.00 0.00 37.11 3.46
4115 5505 4.102681 GCTGCTTTATTAGTAGGGAGGGAA 59.897 45.833 0.00 0.00 37.11 3.97
4116 5506 3.646637 GCTGCTTTATTAGTAGGGAGGGA 59.353 47.826 0.00 0.00 37.11 4.20
4117 5507 4.009370 GCTGCTTTATTAGTAGGGAGGG 57.991 50.000 0.00 0.00 37.11 4.30
4121 5511 4.051922 CAGTCGCTGCTTTATTAGTAGGG 58.948 47.826 0.00 0.00 46.42 3.53
4141 5531 1.513586 GACGTACGACCGGAAGCAG 60.514 63.158 24.41 0.00 0.00 4.24
4234 5624 6.166276 CGTTTTGTAAAACTGAAGCGTTTTC 58.834 36.000 15.72 0.00 43.73 2.29
4335 5726 0.038892 ACGTAAACGCACGACCAGAT 60.039 50.000 11.19 0.00 44.69 2.90


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

AutoCloner maintained by Alex Coulton.