Multiple sequence alignment - TraesCS5A01G418400

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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 TraesCS5A01G418400 chr5A 100.000 2762 0 0 1 2762 606305993 606308754 0.000000e+00 5101.0
1 TraesCS5A01G418400 chr5A 78.131 503 77 19 994 1493 606526291 606526763 3.480000e-74 289.0
2 TraesCS5A01G418400 chr5A 87.295 244 21 6 1236 1473 606307130 606307369 1.260000e-68 270.0
3 TraesCS5A01G418400 chr5A 87.295 244 21 6 1138 1377 606307228 606307465 1.260000e-68 270.0
4 TraesCS5A01G418400 chr5A 84.783 138 12 4 1637 1765 606461312 606461449 2.230000e-26 130.0
5 TraesCS5A01G418400 chr5A 77.340 203 32 10 748 943 606526012 606526207 1.050000e-19 108.0
6 TraesCS5A01G418400 chr5D 90.386 2174 111 40 647 2762 484973662 484975795 0.000000e+00 2767.0
7 TraesCS5A01G418400 chr5D 76.683 609 97 19 994 1590 485294476 485295051 2.080000e-76 296.0
8 TraesCS5A01G418400 chr5D 86.385 213 25 3 1138 1346 484974252 484974464 2.140000e-56 230.0
9 TraesCS5A01G418400 chr5D 83.628 226 27 6 1236 1455 484974154 484974375 1.300000e-48 204.0
10 TraesCS5A01G418400 chr5D 86.538 156 11 6 89 234 484972229 484972384 2.200000e-36 163.0
11 TraesCS5A01G418400 chr5D 87.143 140 9 4 1637 1767 485294957 485295096 1.710000e-32 150.0
12 TraesCS5A01G418400 chr5D 89.474 76 8 0 1169 1244 484974389 484974464 2.260000e-16 97.1
13 TraesCS5A01G418400 chr5B 87.424 2131 156 57 646 2758 596439408 596437372 0.000000e+00 2348.0
14 TraesCS5A01G418400 chr5B 83.918 485 54 8 1262 1731 596438899 596438424 2.520000e-120 442.0
15 TraesCS5A01G418400 chr5B 94.500 200 9 2 89 286 596439881 596439682 9.610000e-80 307.0
16 TraesCS5A01G418400 chr5B 89.844 128 10 1 379 506 596439572 596439448 7.920000e-36 161.0
17 TraesCS5A01G418400 chr5B 85.612 139 11 4 1638 1767 596904758 596904896 1.330000e-28 137.0
18 TraesCS5A01G418400 chr5B 83.621 116 13 2 1364 1473 596438899 596438784 1.350000e-18 104.0
19 TraesCS5A01G418400 chr5B 87.342 79 8 2 305 382 596439683 596439606 3.790000e-14 89.8
20 TraesCS5A01G418400 chr6D 86.667 120 12 1 529 648 63720133 63720248 2.230000e-26 130.0
21 TraesCS5A01G418400 chr6A 86.667 120 12 1 533 652 14134075 14133960 2.230000e-26 130.0
22 TraesCS5A01G418400 chr6A 87.500 112 10 1 536 647 17939146 17939253 2.890000e-25 126.0
23 TraesCS5A01G418400 chr1B 87.719 114 10 1 535 648 492329963 492329854 2.230000e-26 130.0
24 TraesCS5A01G418400 chr4A 86.325 117 12 1 531 647 622170734 622170846 1.040000e-24 124.0
25 TraesCS5A01G418400 chr4A 86.726 113 11 1 537 649 613542645 613542537 3.740000e-24 122.0
26 TraesCS5A01G418400 chr2B 86.325 117 12 1 532 648 63171619 63171731 1.040000e-24 124.0
27 TraesCS5A01G418400 chr3A 87.273 110 10 1 537 646 601362060 601362165 3.740000e-24 122.0
28 TraesCS5A01G418400 chr2D 86.607 112 11 1 537 648 343104445 343104552 1.340000e-23 121.0


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 TraesCS5A01G418400 chr5A 606305993 606308754 2761 False 1880.333333 5101 91.530000 1 2762 3 chr5A.!!$F2 2761
1 TraesCS5A01G418400 chr5D 484972229 484975795 3566 False 692.220000 2767 87.282200 89 2762 5 chr5D.!!$F1 2673
2 TraesCS5A01G418400 chr5D 485294476 485295096 620 False 223.000000 296 81.913000 994 1767 2 chr5D.!!$F2 773
3 TraesCS5A01G418400 chr5B 596437372 596439881 2509 True 575.300000 2348 87.774833 89 2758 6 chr5B.!!$R1 2669

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
84 85 0.109964 CGCCTTTGGAATTCGCGAAA 60.11 50.0 27.23 6.19 45.41 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1796 2886 0.179192 GCACGGTCATGACGTACGTA 60.179 55.0 22.87 10.32 43.58 3.57 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
21 22 4.422073 TGATCTGAACCAAACACACTCT 57.578 40.909 0.00 0.00 0.00 3.24
22 23 4.780815 TGATCTGAACCAAACACACTCTT 58.219 39.130 0.00 0.00 0.00 2.85
23 24 5.924356 TGATCTGAACCAAACACACTCTTA 58.076 37.500 0.00 0.00 0.00 2.10
24 25 6.353323 TGATCTGAACCAAACACACTCTTAA 58.647 36.000 0.00 0.00 0.00 1.85
25 26 6.826231 TGATCTGAACCAAACACACTCTTAAA 59.174 34.615 0.00 0.00 0.00 1.52
26 27 6.677781 TCTGAACCAAACACACTCTTAAAG 57.322 37.500 0.00 0.00 0.00 1.85
27 28 5.588648 TCTGAACCAAACACACTCTTAAAGG 59.411 40.000 0.00 0.00 0.00 3.11
28 29 4.097286 TGAACCAAACACACTCTTAAAGGC 59.903 41.667 0.00 0.00 0.00 4.35
29 30 3.898482 ACCAAACACACTCTTAAAGGCT 58.102 40.909 0.00 0.00 0.00 4.58
30 31 5.043737 ACCAAACACACTCTTAAAGGCTA 57.956 39.130 0.00 0.00 0.00 3.93
31 32 4.820173 ACCAAACACACTCTTAAAGGCTAC 59.180 41.667 0.00 0.00 0.00 3.58
32 33 4.819630 CCAAACACACTCTTAAAGGCTACA 59.180 41.667 0.00 0.00 0.00 2.74
33 34 5.298276 CCAAACACACTCTTAAAGGCTACAA 59.702 40.000 0.00 0.00 0.00 2.41
34 35 6.430451 CAAACACACTCTTAAAGGCTACAAG 58.570 40.000 0.00 0.00 0.00 3.16
35 36 4.065789 ACACACTCTTAAAGGCTACAAGC 58.934 43.478 0.00 0.00 41.46 4.01
36 37 4.065088 CACACTCTTAAAGGCTACAAGCA 58.935 43.478 0.78 0.00 44.75 3.91
37 38 4.153117 CACACTCTTAAAGGCTACAAGCAG 59.847 45.833 0.78 0.00 44.75 4.24
38 39 4.040461 ACACTCTTAAAGGCTACAAGCAGA 59.960 41.667 0.78 0.00 44.75 4.26
39 40 4.390297 CACTCTTAAAGGCTACAAGCAGAC 59.610 45.833 0.78 0.00 44.75 3.51
40 41 4.040461 ACTCTTAAAGGCTACAAGCAGACA 59.960 41.667 0.78 0.00 44.75 3.41
41 42 5.165961 TCTTAAAGGCTACAAGCAGACAT 57.834 39.130 0.78 0.00 44.75 3.06
42 43 5.178797 TCTTAAAGGCTACAAGCAGACATC 58.821 41.667 0.78 0.00 44.75 3.06
43 44 3.710209 AAAGGCTACAAGCAGACATCT 57.290 42.857 0.78 0.00 44.75 2.90
44 45 2.977772 AGGCTACAAGCAGACATCTC 57.022 50.000 0.78 0.00 44.75 2.75
45 46 2.182827 AGGCTACAAGCAGACATCTCA 58.817 47.619 0.78 0.00 44.75 3.27
46 47 2.168106 AGGCTACAAGCAGACATCTCAG 59.832 50.000 0.78 0.00 44.75 3.35
47 48 1.932511 GCTACAAGCAGACATCTCAGC 59.067 52.381 0.00 0.00 41.89 4.26
48 49 2.548875 CTACAAGCAGACATCTCAGCC 58.451 52.381 0.00 0.00 29.08 4.85
49 50 0.982704 ACAAGCAGACATCTCAGCCT 59.017 50.000 0.00 0.00 29.08 4.58
50 51 2.182827 ACAAGCAGACATCTCAGCCTA 58.817 47.619 0.00 0.00 29.08 3.93
51 52 2.568956 ACAAGCAGACATCTCAGCCTAA 59.431 45.455 0.00 0.00 29.08 2.69
52 53 2.935201 CAAGCAGACATCTCAGCCTAAC 59.065 50.000 0.00 0.00 29.08 2.34
53 54 1.135915 AGCAGACATCTCAGCCTAACG 59.864 52.381 0.00 0.00 29.08 3.18
54 55 1.134965 GCAGACATCTCAGCCTAACGT 60.135 52.381 0.00 0.00 0.00 3.99
55 56 2.534298 CAGACATCTCAGCCTAACGTG 58.466 52.381 0.00 0.00 0.00 4.49
56 57 1.478510 AGACATCTCAGCCTAACGTGG 59.521 52.381 0.00 0.00 0.00 4.94
64 65 4.770874 CCTAACGTGGCCCACCCG 62.771 72.222 8.62 0.00 35.87 5.28
76 77 3.061848 CACCCGCGCCTTTGGAAT 61.062 61.111 0.00 0.00 0.00 3.01
77 78 2.282887 ACCCGCGCCTTTGGAATT 60.283 55.556 0.00 0.00 0.00 2.17
78 79 2.340328 ACCCGCGCCTTTGGAATTC 61.340 57.895 0.00 0.00 0.00 2.17
79 80 2.100216 CCGCGCCTTTGGAATTCG 59.900 61.111 0.00 0.00 0.00 3.34
80 81 2.576847 CGCGCCTTTGGAATTCGC 60.577 61.111 0.00 0.00 42.05 4.70
81 82 2.576847 GCGCCTTTGGAATTCGCG 60.577 61.111 17.01 17.01 45.35 5.87
82 83 3.034370 GCGCCTTTGGAATTCGCGA 62.034 57.895 23.09 3.71 45.41 5.87
83 84 1.499949 CGCCTTTGGAATTCGCGAA 59.500 52.632 25.66 25.66 45.41 4.70
84 85 0.109964 CGCCTTTGGAATTCGCGAAA 60.110 50.000 27.23 6.19 45.41 3.46
85 86 1.664588 CGCCTTTGGAATTCGCGAAAA 60.665 47.619 27.23 12.80 45.41 2.29
86 87 2.399448 GCCTTTGGAATTCGCGAAAAA 58.601 42.857 27.23 19.38 0.00 1.94
196 206 2.092049 AGAAGAAACCCAAAACGTCCCT 60.092 45.455 0.00 0.00 0.00 4.20
208 219 3.696782 CGTCCCTTCACGTCACTAG 57.303 57.895 0.00 0.00 34.95 2.57
234 245 1.507141 CGGACACTTGGTTGGACAGC 61.507 60.000 0.00 0.00 0.00 4.40
286 327 1.137479 CCAGCCATTCCGAATTGCAAT 59.863 47.619 17.02 5.99 32.34 3.56
287 328 2.466846 CAGCCATTCCGAATTGCAATC 58.533 47.619 13.38 5.66 32.34 2.67
288 329 1.410153 AGCCATTCCGAATTGCAATCC 59.590 47.619 13.38 0.00 32.34 3.01
289 330 1.136695 GCCATTCCGAATTGCAATCCA 59.863 47.619 13.38 0.00 30.45 3.41
290 331 2.418471 GCCATTCCGAATTGCAATCCAA 60.418 45.455 13.38 3.75 37.94 3.53
291 332 3.859443 CCATTCCGAATTGCAATCCAAA 58.141 40.909 13.38 5.75 36.92 3.28
292 333 3.618150 CCATTCCGAATTGCAATCCAAAC 59.382 43.478 13.38 1.94 36.92 2.93
293 334 4.497300 CATTCCGAATTGCAATCCAAACT 58.503 39.130 13.38 0.00 36.92 2.66
294 335 3.848272 TCCGAATTGCAATCCAAACTC 57.152 42.857 13.38 4.42 36.92 3.01
295 336 3.153130 TCCGAATTGCAATCCAAACTCA 58.847 40.909 13.38 0.00 36.92 3.41
296 337 3.571828 TCCGAATTGCAATCCAAACTCAA 59.428 39.130 13.38 0.00 36.92 3.02
297 338 4.038522 TCCGAATTGCAATCCAAACTCAAA 59.961 37.500 13.38 0.00 36.92 2.69
298 339 4.749099 CCGAATTGCAATCCAAACTCAAAA 59.251 37.500 13.38 0.00 36.92 2.44
299 340 5.236047 CCGAATTGCAATCCAAACTCAAAAA 59.764 36.000 13.38 0.00 36.92 1.94
374 428 5.615289 CTTCAGGAAGAGAAAGAAACCTCA 58.385 41.667 2.88 0.00 40.79 3.86
377 431 7.502060 TCAGGAAGAGAAAGAAACCTCATAT 57.498 36.000 0.00 0.00 32.07 1.78
410 505 2.660670 TCTCCTACTCCCTCCGATTC 57.339 55.000 0.00 0.00 0.00 2.52
446 541 6.670902 TGGCTCCCTTAGTACAACTTTAGTAT 59.329 38.462 0.00 0.00 0.00 2.12
448 543 8.358895 GGCTCCCTTAGTACAACTTTAGTATAG 58.641 40.741 0.00 0.00 0.00 1.31
499 594 7.007456 GCTTTAGTACAGAATTTCGCATTTGAC 59.993 37.037 0.00 0.00 0.00 3.18
508 603 0.389817 TCGCATTTGACGACCTCTGG 60.390 55.000 0.00 0.00 33.96 3.86
509 604 1.796796 GCATTTGACGACCTCTGGC 59.203 57.895 0.00 0.00 0.00 4.85
510 605 1.648467 GCATTTGACGACCTCTGGCC 61.648 60.000 0.00 0.00 0.00 5.36
514 609 3.138798 GACGACCTCTGGCCGCTA 61.139 66.667 0.00 0.00 0.00 4.26
515 610 3.412879 GACGACCTCTGGCCGCTAC 62.413 68.421 0.00 0.00 0.00 3.58
537 641 5.871834 ACCACCATGTAGTTAAAGCAAGTA 58.128 37.500 0.00 0.00 0.00 2.24
538 642 5.704053 ACCACCATGTAGTTAAAGCAAGTAC 59.296 40.000 0.00 0.00 41.60 2.73
539 643 5.938125 CCACCATGTAGTTAAAGCAAGTACT 59.062 40.000 0.00 0.00 41.72 2.73
540 644 6.092259 CCACCATGTAGTTAAAGCAAGTACTC 59.908 42.308 0.00 0.00 41.72 2.59
541 645 6.092259 CACCATGTAGTTAAAGCAAGTACTCC 59.908 42.308 0.00 0.00 41.72 3.85
548 670 6.127101 AGTTAAAGCAAGTACTCCCTTTGTT 58.873 36.000 21.70 3.71 0.00 2.83
549 671 4.918810 AAAGCAAGTACTCCCTTTGTTG 57.081 40.909 15.82 2.15 0.00 3.33
551 673 1.953686 GCAAGTACTCCCTTTGTTGCA 59.046 47.619 0.00 0.00 40.01 4.08
552 674 2.360801 GCAAGTACTCCCTTTGTTGCAA 59.639 45.455 0.00 0.00 40.01 4.08
556 678 6.737346 GCAAGTACTCCCTTTGTTGCAAATTA 60.737 38.462 0.00 0.00 40.01 1.40
557 679 6.327279 AGTACTCCCTTTGTTGCAAATTAC 57.673 37.500 0.00 0.00 0.00 1.89
561 683 3.886505 TCCCTTTGTTGCAAATTACTCGT 59.113 39.130 0.00 0.00 0.00 4.18
562 684 4.339814 TCCCTTTGTTGCAAATTACTCGTT 59.660 37.500 0.00 0.00 0.00 3.85
564 686 5.627780 CCCTTTGTTGCAAATTACTCGTTAC 59.372 40.000 0.00 0.00 0.00 2.50
566 688 6.359617 CCTTTGTTGCAAATTACTCGTTACAG 59.640 38.462 0.00 0.00 0.00 2.74
573 695 7.866729 TGCAAATTACTCGTTACAGAAATGAA 58.133 30.769 0.00 0.00 32.68 2.57
574 696 8.511321 TGCAAATTACTCGTTACAGAAATGAAT 58.489 29.630 0.00 0.00 32.68 2.57
575 697 8.788813 GCAAATTACTCGTTACAGAAATGAATG 58.211 33.333 0.00 0.00 32.68 2.67
580 702 9.647797 TTACTCGTTACAGAAATGAATGTATGT 57.352 29.630 0.00 0.00 32.68 2.29
583 705 9.516314 CTCGTTACAGAAATGAATGTATGTAGA 57.484 33.333 0.00 0.00 32.68 2.59
585 707 9.901724 CGTTACAGAAATGAATGTATGTAGAAC 57.098 33.333 0.00 0.00 32.24 3.01
623 745 9.971922 CATCTAGATATATCCATATTTGCGACA 57.028 33.333 4.54 0.00 0.00 4.35
626 748 9.809096 CTAGATATATCCATATTTGCGACAAGT 57.191 33.333 9.18 0.00 0.00 3.16
632 754 6.043327 TCCATATTTGCGACAAGTAATTCG 57.957 37.500 0.00 0.00 38.31 3.34
633 755 5.007234 TCCATATTTGCGACAAGTAATTCGG 59.993 40.000 0.00 0.00 35.73 4.30
634 756 5.007234 CCATATTTGCGACAAGTAATTCGGA 59.993 40.000 0.00 0.00 35.73 4.55
635 757 6.457663 CCATATTTGCGACAAGTAATTCGGAA 60.458 38.462 0.00 0.00 42.78 4.30
636 758 3.799137 TTGCGACAAGTAATTCGGAAC 57.201 42.857 0.00 0.00 40.13 3.62
652 1642 2.377073 GGAACGAAGGGAGTAGCTAGT 58.623 52.381 0.00 0.00 0.00 2.57
738 1728 3.689161 CGTCCATACCACACATTGTTGAT 59.311 43.478 0.00 0.00 0.00 2.57
804 1794 1.103398 AATGCGACCCATGCTAAGCC 61.103 55.000 0.00 0.00 33.49 4.35
884 1875 4.012374 CCCTTGCAGAAATTTAGAGCTGA 58.988 43.478 8.40 0.00 0.00 4.26
930 1921 2.045926 GACATGCAGGGCTCCGTT 60.046 61.111 2.31 0.00 0.00 4.44
961 1952 1.007524 CACGCAAAGCAACGAAACAAC 60.008 47.619 0.00 0.00 0.00 3.32
990 1981 2.420722 AGAGAGCAACTGAGTACGTAGC 59.579 50.000 0.00 0.00 0.00 3.58
1317 2323 2.746277 CCGCTGCCAACAGTACCC 60.746 66.667 0.00 0.00 46.30 3.69
1421 2433 3.431725 GCTGCCAACAGTACCCGC 61.432 66.667 0.00 0.00 46.30 6.13
1440 2452 4.077184 GTGCCGACCATCCCGACA 62.077 66.667 0.00 0.00 0.00 4.35
1447 2459 2.186903 CCATCCCGACAGTTCCCG 59.813 66.667 0.00 0.00 0.00 5.14
1600 2681 1.748879 CCAGTGCCATTACCACCGG 60.749 63.158 0.00 0.00 33.75 5.28
1725 2806 0.597637 CTGGCGTGCCTAAGATACCG 60.598 60.000 12.84 0.00 36.94 4.02
1792 2882 1.595466 CCGACGCACTAGAGGAGTAT 58.405 55.000 0.00 0.00 35.64 2.12
1794 2884 3.336468 CCGACGCACTAGAGGAGTATAT 58.664 50.000 0.00 0.00 35.64 0.86
1795 2885 4.502016 CCGACGCACTAGAGGAGTATATA 58.498 47.826 0.00 0.00 35.64 0.86
1796 2886 5.117584 CCGACGCACTAGAGGAGTATATAT 58.882 45.833 0.00 0.00 35.64 0.86
1797 2887 6.279123 CCGACGCACTAGAGGAGTATATATA 58.721 44.000 0.00 0.00 35.64 0.86
1798 2888 6.200665 CCGACGCACTAGAGGAGTATATATAC 59.799 46.154 14.05 14.05 35.64 1.47
1882 2972 9.136952 ACGAGTGTAATATAACTTTGACTTGAC 57.863 33.333 0.00 0.00 0.00 3.18
1915 3006 5.208463 TGAGCACTACATGTACAAGTCAA 57.792 39.130 7.07 0.00 0.00 3.18
1916 3007 5.606505 TGAGCACTACATGTACAAGTCAAA 58.393 37.500 7.07 0.00 0.00 2.69
1928 3019 3.527533 ACAAGTCAAAGTACGTGCAAGA 58.472 40.909 6.65 0.00 32.86 3.02
1929 3020 3.555956 ACAAGTCAAAGTACGTGCAAGAG 59.444 43.478 6.65 0.00 32.86 2.85
1930 3021 3.728076 AGTCAAAGTACGTGCAAGAGA 57.272 42.857 6.65 0.00 0.00 3.10
1931 3022 3.643763 AGTCAAAGTACGTGCAAGAGAG 58.356 45.455 6.65 0.00 0.00 3.20
1932 3023 3.318275 AGTCAAAGTACGTGCAAGAGAGA 59.682 43.478 6.65 0.00 0.00 3.10
1933 3024 3.670991 GTCAAAGTACGTGCAAGAGAGAG 59.329 47.826 6.65 0.00 0.00 3.20
1935 3026 1.178276 AGTACGTGCAAGAGAGAGGG 58.822 55.000 6.65 0.00 0.00 4.30
2035 3127 7.147707 ACCTGTCTATACTTGTCCCTTTATGTC 60.148 40.741 0.00 0.00 0.00 3.06
2036 3128 7.147724 CCTGTCTATACTTGTCCCTTTATGTCA 60.148 40.741 0.00 0.00 0.00 3.58
2037 3129 8.319057 TGTCTATACTTGTCCCTTTATGTCAT 57.681 34.615 0.00 0.00 0.00 3.06
2038 3130 8.768397 TGTCTATACTTGTCCCTTTATGTCATT 58.232 33.333 0.00 0.00 0.00 2.57
2256 3363 2.622942 TGTCATGGTTGCCTTTGTTCTC 59.377 45.455 0.00 0.00 0.00 2.87
2337 3444 5.847265 AGGGGGCTTTAACCTCATTTAAAAA 59.153 36.000 0.00 0.00 31.98 1.94
2374 3481 6.660521 TGTCAAATTCAAGAGCTTACATGGAT 59.339 34.615 0.00 0.00 0.00 3.41
2388 3495 2.291800 ACATGGATCCAGAGGGTTTTGG 60.292 50.000 21.33 2.03 35.74 3.28
2416 3523 3.994392 GTGACTCTTATCTGCGTTTGGAA 59.006 43.478 0.00 0.00 0.00 3.53
2417 3524 3.994392 TGACTCTTATCTGCGTTTGGAAC 59.006 43.478 0.00 0.00 0.00 3.62
2572 3697 5.923733 AACACTCACATACTAAGGAGGAG 57.076 43.478 0.00 0.00 0.00 3.69
2582 3707 7.776030 CACATACTAAGGAGGAGTTAAGAGAGA 59.224 40.741 0.00 0.00 0.00 3.10
2584 3709 9.362151 CATACTAAGGAGGAGTTAAGAGAGATT 57.638 37.037 0.00 0.00 0.00 2.40
2591 3716 9.374711 AGGAGGAGTTAAGAGAGATTATTTAGG 57.625 37.037 0.00 0.00 0.00 2.69
2615 3740 3.117587 TCCATGCAATCCCATCACATGTA 60.118 43.478 0.00 0.00 37.10 2.29
2633 3758 6.309009 CACATGTAGCTATAGATGCGTAAAGG 59.691 42.308 3.21 0.00 36.39 3.11
2657 3782 7.074237 AGGGTCTCAATCTATGAATTTATGGGT 59.926 37.037 0.00 0.00 37.67 4.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.422073 AGAGTGTGTTTGGTTCAGATCA 57.578 40.909 0.00 0.00 0.00 2.92
1 2 6.861065 TTAAGAGTGTGTTTGGTTCAGATC 57.139 37.500 0.00 0.00 0.00 2.75
2 3 6.263168 CCTTTAAGAGTGTGTTTGGTTCAGAT 59.737 38.462 0.00 0.00 0.00 2.90
3 4 5.588648 CCTTTAAGAGTGTGTTTGGTTCAGA 59.411 40.000 0.00 0.00 0.00 3.27
4 5 5.733373 GCCTTTAAGAGTGTGTTTGGTTCAG 60.733 44.000 0.00 0.00 0.00 3.02
5 6 4.097286 GCCTTTAAGAGTGTGTTTGGTTCA 59.903 41.667 0.00 0.00 0.00 3.18
6 7 4.338400 AGCCTTTAAGAGTGTGTTTGGTTC 59.662 41.667 0.00 0.00 0.00 3.62
7 8 4.278310 AGCCTTTAAGAGTGTGTTTGGTT 58.722 39.130 0.00 0.00 0.00 3.67
8 9 3.898482 AGCCTTTAAGAGTGTGTTTGGT 58.102 40.909 0.00 0.00 0.00 3.67
9 10 4.819630 TGTAGCCTTTAAGAGTGTGTTTGG 59.180 41.667 0.00 0.00 0.00 3.28
10 11 6.371809 TTGTAGCCTTTAAGAGTGTGTTTG 57.628 37.500 0.00 0.00 0.00 2.93
11 12 5.008712 GCTTGTAGCCTTTAAGAGTGTGTTT 59.991 40.000 0.00 0.00 34.48 2.83
12 13 4.515567 GCTTGTAGCCTTTAAGAGTGTGTT 59.484 41.667 0.00 0.00 34.48 3.32
13 14 4.065789 GCTTGTAGCCTTTAAGAGTGTGT 58.934 43.478 0.00 0.00 34.48 3.72
14 15 4.065088 TGCTTGTAGCCTTTAAGAGTGTG 58.935 43.478 0.00 0.00 41.51 3.82
15 16 4.040461 TCTGCTTGTAGCCTTTAAGAGTGT 59.960 41.667 0.00 0.00 41.51 3.55
16 17 4.390297 GTCTGCTTGTAGCCTTTAAGAGTG 59.610 45.833 0.00 0.00 41.51 3.51
17 18 4.040461 TGTCTGCTTGTAGCCTTTAAGAGT 59.960 41.667 0.00 0.00 41.51 3.24
18 19 4.569943 TGTCTGCTTGTAGCCTTTAAGAG 58.430 43.478 0.00 0.00 41.51 2.85
19 20 4.617253 TGTCTGCTTGTAGCCTTTAAGA 57.383 40.909 0.00 0.00 41.51 2.10
20 21 5.181748 AGATGTCTGCTTGTAGCCTTTAAG 58.818 41.667 0.00 0.00 41.51 1.85
21 22 5.165961 AGATGTCTGCTTGTAGCCTTTAA 57.834 39.130 0.00 0.00 41.51 1.52
22 23 4.222810 TGAGATGTCTGCTTGTAGCCTTTA 59.777 41.667 0.00 0.00 41.51 1.85
23 24 3.008375 TGAGATGTCTGCTTGTAGCCTTT 59.992 43.478 0.00 0.00 41.51 3.11
24 25 2.568956 TGAGATGTCTGCTTGTAGCCTT 59.431 45.455 0.00 0.00 41.51 4.35
25 26 2.168106 CTGAGATGTCTGCTTGTAGCCT 59.832 50.000 0.00 0.00 41.51 4.58
26 27 2.548875 CTGAGATGTCTGCTTGTAGCC 58.451 52.381 0.00 0.00 41.51 3.93
27 28 1.932511 GCTGAGATGTCTGCTTGTAGC 59.067 52.381 13.58 0.00 42.75 3.58
28 29 2.168106 AGGCTGAGATGTCTGCTTGTAG 59.832 50.000 18.95 0.00 44.81 2.74
29 30 2.182827 AGGCTGAGATGTCTGCTTGTA 58.817 47.619 18.95 0.00 44.81 2.41
30 31 0.982704 AGGCTGAGATGTCTGCTTGT 59.017 50.000 18.95 4.35 44.81 3.16
31 32 2.935201 GTTAGGCTGAGATGTCTGCTTG 59.065 50.000 18.95 0.00 44.81 4.01
32 33 2.417924 CGTTAGGCTGAGATGTCTGCTT 60.418 50.000 18.95 14.97 44.81 3.91
33 34 1.135915 CGTTAGGCTGAGATGTCTGCT 59.864 52.381 18.95 9.42 44.81 4.24
34 35 1.134965 ACGTTAGGCTGAGATGTCTGC 60.135 52.381 12.62 12.62 44.73 4.26
35 36 2.534298 CACGTTAGGCTGAGATGTCTG 58.466 52.381 0.00 0.00 0.00 3.51
36 37 1.478510 CCACGTTAGGCTGAGATGTCT 59.521 52.381 0.00 0.00 0.00 3.41
37 38 1.927895 CCACGTTAGGCTGAGATGTC 58.072 55.000 0.00 0.00 0.00 3.06
47 48 4.770874 CGGGTGGGCCACGTTAGG 62.771 72.222 29.18 12.81 34.83 2.69
59 60 2.542211 GAATTCCAAAGGCGCGGGTG 62.542 60.000 8.83 0.00 0.00 4.61
60 61 2.282887 AATTCCAAAGGCGCGGGT 60.283 55.556 8.83 0.00 0.00 5.28
61 62 2.489751 GAATTCCAAAGGCGCGGG 59.510 61.111 8.83 0.00 0.00 6.13
62 63 2.100216 CGAATTCCAAAGGCGCGG 59.900 61.111 8.83 0.00 0.00 6.46
63 64 2.576847 GCGAATTCCAAAGGCGCG 60.577 61.111 0.00 0.00 38.24 6.86
64 65 2.521733 TTCGCGAATTCCAAAGGCGC 62.522 55.000 19.38 0.00 45.85 6.53
66 67 2.058913 TTTTCGCGAATTCCAAAGGC 57.941 45.000 24.05 0.00 0.00 4.35
85 86 2.549926 CTTTCCAAAGGCGCAGTTTTT 58.450 42.857 10.83 0.79 32.40 1.94
86 87 1.806247 GCTTTCCAAAGGCGCAGTTTT 60.806 47.619 10.83 3.62 36.53 2.43
87 88 0.249447 GCTTTCCAAAGGCGCAGTTT 60.249 50.000 10.83 5.30 36.53 2.66
119 120 2.368439 TCGAATTCTGATTTGGGCCTG 58.632 47.619 4.53 0.00 0.00 4.85
183 192 1.946267 CGTGAAGGGACGTTTTGGG 59.054 57.895 0.00 0.00 34.56 4.12
196 206 1.403647 CGCCCAATCTAGTGACGTGAA 60.404 52.381 0.00 0.00 0.00 3.18
205 215 1.656652 CAAGTGTCCGCCCAATCTAG 58.343 55.000 0.00 0.00 0.00 2.43
208 219 0.893727 AACCAAGTGTCCGCCCAATC 60.894 55.000 0.00 0.00 0.00 2.67
234 245 1.142748 GGAGGACATGTCTCCTGCG 59.857 63.158 24.50 0.00 45.46 5.18
377 431 6.154706 GGGAGTAGGAGAATTTTAGTCAGACA 59.845 42.308 2.66 0.00 0.00 3.41
410 505 8.375506 TGTACTAAGGGAGCCAGAATTAATATG 58.624 37.037 0.00 0.00 0.00 1.78
471 566 5.779806 TGCGAAATTCTGTACTAAAGCTC 57.220 39.130 0.00 0.00 0.00 4.09
473 568 7.007456 GTCAAATGCGAAATTCTGTACTAAAGC 59.993 37.037 0.00 0.00 0.00 3.51
474 569 7.214449 CGTCAAATGCGAAATTCTGTACTAAAG 59.786 37.037 0.00 0.00 0.00 1.85
475 570 7.012943 CGTCAAATGCGAAATTCTGTACTAAA 58.987 34.615 0.00 0.00 0.00 1.85
476 571 6.366604 TCGTCAAATGCGAAATTCTGTACTAA 59.633 34.615 0.00 0.00 35.28 2.24
508 603 0.107848 AACTACATGGTGGTAGCGGC 60.108 55.000 0.00 0.00 43.61 6.53
509 604 3.530265 TTAACTACATGGTGGTAGCGG 57.470 47.619 0.00 0.00 43.61 5.52
510 605 3.308866 GCTTTAACTACATGGTGGTAGCG 59.691 47.826 0.00 0.00 43.61 4.26
514 609 4.725490 ACTTGCTTTAACTACATGGTGGT 58.275 39.130 0.00 0.00 0.00 4.16
515 610 5.938125 AGTACTTGCTTTAACTACATGGTGG 59.062 40.000 0.00 0.00 0.00 4.61
537 641 4.023193 CGAGTAATTTGCAACAAAGGGAGT 60.023 41.667 0.00 0.00 0.00 3.85
538 642 4.023193 ACGAGTAATTTGCAACAAAGGGAG 60.023 41.667 0.00 0.00 0.00 4.30
539 643 3.886505 ACGAGTAATTTGCAACAAAGGGA 59.113 39.130 0.00 0.00 0.00 4.20
540 644 4.237349 ACGAGTAATTTGCAACAAAGGG 57.763 40.909 0.00 0.00 0.00 3.95
541 645 6.202937 TGTAACGAGTAATTTGCAACAAAGG 58.797 36.000 0.00 0.00 0.00 3.11
548 670 7.428282 TCATTTCTGTAACGAGTAATTTGCA 57.572 32.000 0.00 0.00 0.00 4.08
549 671 8.788813 CATTCATTTCTGTAACGAGTAATTTGC 58.211 33.333 0.00 0.00 0.00 3.68
556 678 9.302345 CTACATACATTCATTTCTGTAACGAGT 57.698 33.333 0.00 0.00 32.02 4.18
557 679 9.516314 TCTACATACATTCATTTCTGTAACGAG 57.484 33.333 0.00 0.00 32.02 4.18
596 718 9.973450 GTCGCAAATATGGATATATCTAGATGT 57.027 33.333 15.79 11.37 0.00 3.06
597 719 9.971922 TGTCGCAAATATGGATATATCTAGATG 57.028 33.333 15.79 1.93 0.00 2.90
600 722 9.809096 ACTTGTCGCAAATATGGATATATCTAG 57.191 33.333 12.42 0.00 0.00 2.43
607 729 7.095397 CCGAATTACTTGTCGCAAATATGGATA 60.095 37.037 0.00 0.00 35.93 2.59
610 732 5.007234 TCCGAATTACTTGTCGCAAATATGG 59.993 40.000 0.00 0.00 35.93 2.74
611 733 6.043327 TCCGAATTACTTGTCGCAAATATG 57.957 37.500 0.00 0.00 35.93 1.78
612 734 6.483687 GTTCCGAATTACTTGTCGCAAATAT 58.516 36.000 0.00 0.00 35.93 1.28
614 736 4.668177 CGTTCCGAATTACTTGTCGCAAAT 60.668 41.667 0.00 0.00 35.93 2.32
619 741 3.060363 CCTTCGTTCCGAATTACTTGTCG 59.940 47.826 0.00 0.00 44.85 4.35
621 743 3.007182 TCCCTTCGTTCCGAATTACTTGT 59.993 43.478 0.00 0.00 44.85 3.16
623 745 3.260128 ACTCCCTTCGTTCCGAATTACTT 59.740 43.478 0.00 0.00 44.85 2.24
624 746 2.830321 ACTCCCTTCGTTCCGAATTACT 59.170 45.455 0.00 0.00 44.85 2.24
626 748 3.181483 GCTACTCCCTTCGTTCCGAATTA 60.181 47.826 0.00 0.00 44.85 1.40
627 749 2.418334 GCTACTCCCTTCGTTCCGAATT 60.418 50.000 0.00 0.00 44.85 2.17
628 750 1.136500 GCTACTCCCTTCGTTCCGAAT 59.864 52.381 0.00 0.00 44.85 3.34
630 752 0.323178 AGCTACTCCCTTCGTTCCGA 60.323 55.000 0.00 0.00 0.00 4.55
631 753 1.334243 CTAGCTACTCCCTTCGTTCCG 59.666 57.143 0.00 0.00 0.00 4.30
632 754 2.377073 ACTAGCTACTCCCTTCGTTCC 58.623 52.381 0.00 0.00 0.00 3.62
633 755 4.082354 TGAAACTAGCTACTCCCTTCGTTC 60.082 45.833 0.00 0.00 0.00 3.95
634 756 3.830755 TGAAACTAGCTACTCCCTTCGTT 59.169 43.478 0.00 0.00 0.00 3.85
635 757 3.428532 TGAAACTAGCTACTCCCTTCGT 58.571 45.455 0.00 0.00 0.00 3.85
636 758 3.735514 GCTGAAACTAGCTACTCCCTTCG 60.736 52.174 0.00 0.00 40.52 3.79
637 759 3.787785 GCTGAAACTAGCTACTCCCTTC 58.212 50.000 0.00 0.00 40.52 3.46
638 760 3.897141 GCTGAAACTAGCTACTCCCTT 57.103 47.619 0.00 0.00 40.52 3.95
652 1642 4.553330 CCTCACCTAGGTTTAGCTGAAA 57.447 45.455 13.15 0.00 40.94 2.69
665 1655 0.847373 TTTTGTGGCCACCTCACCTA 59.153 50.000 32.62 9.77 34.46 3.08
738 1728 0.821711 CGAAGGGGTGCTGGAACAAA 60.822 55.000 0.00 0.00 38.70 2.83
804 1794 2.983592 GGTTGTTGGCCACCCGAG 60.984 66.667 3.88 0.00 0.00 4.63
898 1889 4.825422 TGCATGTCCATCTTATAGCTAGC 58.175 43.478 6.62 6.62 0.00 3.42
899 1890 5.417811 CCTGCATGTCCATCTTATAGCTAG 58.582 45.833 0.00 0.00 0.00 3.42
900 1891 4.223700 CCCTGCATGTCCATCTTATAGCTA 59.776 45.833 0.00 0.00 0.00 3.32
901 1892 3.008813 CCCTGCATGTCCATCTTATAGCT 59.991 47.826 0.00 0.00 0.00 3.32
930 1921 3.833304 TTGCGTGTGGTGCAATGA 58.167 50.000 0.00 0.00 46.62 2.57
961 1952 3.509575 ACTCAGTTGCTCTCTTGGACTAG 59.490 47.826 0.00 0.00 0.00 2.57
1120 2117 4.660938 AACGACCAGGGGCAAGGC 62.661 66.667 0.00 0.00 0.00 4.35
1130 2127 3.618750 GGACCGTGGGAACGACCA 61.619 66.667 0.00 0.00 41.20 4.02
1577 2658 1.003812 GTGGTAATGGCACTGGTACCA 59.996 52.381 15.39 15.39 42.87 3.25
1651 2732 4.452733 GTCGGGAAGGGACGGCAG 62.453 72.222 0.00 0.00 34.37 4.85
1792 2882 4.377328 GCACGGTCATGACGTACGTATATA 60.377 45.833 22.87 8.69 43.58 0.86
1794 2884 2.286359 GCACGGTCATGACGTACGTATA 60.286 50.000 22.87 14.05 43.58 1.47
1795 2885 1.532505 GCACGGTCATGACGTACGTAT 60.533 52.381 22.87 12.19 43.58 3.06
1796 2886 0.179192 GCACGGTCATGACGTACGTA 60.179 55.000 22.87 10.32 43.58 3.57
1797 2887 1.443194 GCACGGTCATGACGTACGT 60.443 57.895 23.04 23.04 43.58 3.57
1798 2888 0.800683 ATGCACGGTCATGACGTACG 60.801 55.000 19.33 18.47 43.58 3.67
1882 2972 4.227512 TGTAGTGCTCAAACAAATGCTG 57.772 40.909 0.00 0.00 0.00 4.41
1915 3006 1.546476 CCCTCTCTCTTGCACGTACTT 59.454 52.381 0.00 0.00 0.00 2.24
1916 3007 1.178276 CCCTCTCTCTTGCACGTACT 58.822 55.000 0.00 0.00 0.00 2.73
1945 3037 2.726760 CACGCACACAAGAGAGTACTTC 59.273 50.000 0.00 0.00 0.00 3.01
2035 3127 5.256474 ACAAAGAATGACTCCCACCTAATG 58.744 41.667 0.00 0.00 0.00 1.90
2036 3128 5.520748 ACAAAGAATGACTCCCACCTAAT 57.479 39.130 0.00 0.00 0.00 1.73
2037 3129 4.993705 ACAAAGAATGACTCCCACCTAA 57.006 40.909 0.00 0.00 0.00 2.69
2038 3130 6.326583 CCTATACAAAGAATGACTCCCACCTA 59.673 42.308 0.00 0.00 0.00 3.08
2039 3131 5.131142 CCTATACAAAGAATGACTCCCACCT 59.869 44.000 0.00 0.00 0.00 4.00
2147 3246 7.315890 GCAAGCTTTTGAAACTTATGATACCT 58.684 34.615 0.00 0.00 0.00 3.08
2337 3444 9.146984 CTCTTGAATTTGACATGCATACATTTT 57.853 29.630 0.00 0.45 32.87 1.82
2347 3454 6.750501 CCATGTAAGCTCTTGAATTTGACATG 59.249 38.462 10.29 10.29 40.69 3.21
2374 3481 4.290985 TCACATAATCCAAAACCCTCTGGA 59.709 41.667 0.00 0.00 45.65 3.86
2388 3495 7.340699 CAAACGCAGATAAGAGTCACATAATC 58.659 38.462 0.00 0.00 0.00 1.75
2553 3678 7.411808 TCTTAACTCCTCCTTAGTATGTGAGT 58.588 38.462 0.00 0.00 33.30 3.41
2557 3682 7.874252 TCTCTCTTAACTCCTCCTTAGTATGT 58.126 38.462 0.00 0.00 0.00 2.29
2572 3697 9.495572 CATGGACCCTAAATAATCTCTCTTAAC 57.504 37.037 0.00 0.00 0.00 2.01
2582 3707 5.086621 GGGATTGCATGGACCCTAAATAAT 58.913 41.667 5.72 0.00 39.28 1.28
2584 3709 3.465210 TGGGATTGCATGGACCCTAAATA 59.535 43.478 13.19 0.00 42.49 1.40
2591 3716 1.035139 GTGATGGGATTGCATGGACC 58.965 55.000 0.00 0.00 0.00 4.46
2615 3740 4.153411 AGACCCTTTACGCATCTATAGCT 58.847 43.478 0.00 0.00 0.00 3.32
2633 3758 7.721399 ACACCCATAAATTCATAGATTGAGACC 59.279 37.037 0.00 0.00 35.27 3.85


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

AutoCloner maintained by Alex Coulton.