Multiple sequence alignment - TraesCS2A01G129400

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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 TraesCS2A01G129400 chr2A 100.000 2787 0 0 1 2787 77336850 77339636 0.000000e+00 5147
1 TraesCS2A01G129400 chr2B 92.822 2424 91 26 1 2410 118324235 118326589 0.000000e+00 3435
2 TraesCS2A01G129400 chr2B 90.972 144 2 2 2545 2679 118326945 118327086 1.700000e-42 183
3 TraesCS2A01G129400 chr2B 94.783 115 6 0 2673 2787 118327820 118327934 2.210000e-41 180
4 TraesCS2A01G129400 chr7B 75.482 1607 307 59 1 1548 750247590 750249168 0.000000e+00 704
5 TraesCS2A01G129400 chr7B 73.592 799 160 39 621 1386 692889640 692890420 2.750000e-65 259
6 TraesCS2A01G129400 chr7B 79.464 224 39 5 3 225 750197720 750197937 4.810000e-33 152
7 TraesCS2A01G129400 chr7A 75.096 1570 308 57 33 1543 732922100 732920555 0.000000e+00 656
8 TraesCS2A01G129400 chr7A 75.129 969 196 26 606 1544 732934634 732933681 2.000000e-111 412
9 TraesCS2A01G129400 chr7A 73.298 955 216 27 611 1544 732803544 732802608 5.790000e-82 315
10 TraesCS2A01G129400 chr6B 78.544 261 42 13 1207 1460 708071670 708071417 2.870000e-35 159


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 TraesCS2A01G129400 chr2A 77336850 77339636 2786 False 5147 5147 100.000 1 2787 1 chr2A.!!$F1 2786
1 TraesCS2A01G129400 chr2B 118324235 118327934 3699 False 1266 3435 92.859 1 2787 3 chr2B.!!$F1 2786
2 TraesCS2A01G129400 chr7B 750247590 750249168 1578 False 704 704 75.482 1 1548 1 chr7B.!!$F3 1547
3 TraesCS2A01G129400 chr7B 692889640 692890420 780 False 259 259 73.592 621 1386 1 chr7B.!!$F1 765
4 TraesCS2A01G129400 chr7A 732920555 732922100 1545 True 656 656 75.096 33 1543 1 chr7A.!!$R2 1510
5 TraesCS2A01G129400 chr7A 732933681 732934634 953 True 412 412 75.129 606 1544 1 chr7A.!!$R3 938
6 TraesCS2A01G129400 chr7A 732802608 732803544 936 True 315 315 73.298 611 1544 1 chr7A.!!$R1 933

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
974 1019 0.953727 TGGTTGACTTGTGCATCTGC 59.046 50.0 0.0 0.0 42.5 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2434 2498 0.108804 TACTGTTGCTACTGCTCCGC 60.109 55.0 5.16 0.0 40.48 5.54 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
111 112 1.608109 TCGCAGTTACAACGACCTACA 59.392 47.619 0.00 0.00 0.00 2.74
115 116 3.427863 GCAGTTACAACGACCTACAAGAC 59.572 47.826 0.00 0.00 0.00 3.01
202 203 7.116948 GTGTCGGATCTTATTGAGTTATGGATG 59.883 40.741 0.00 0.00 0.00 3.51
231 232 3.758023 TGCTTCATTCCACATACACCAAG 59.242 43.478 0.00 0.00 0.00 3.61
400 401 3.033368 AGAGAAGACGGCTTTCTTGAC 57.967 47.619 4.21 0.00 35.90 3.18
449 459 5.931724 GCTTCCTCTCTCTTTTCATATAGCC 59.068 44.000 0.00 0.00 0.00 3.93
498 512 3.815401 AGTATGGTGTTTCTTGCTGACAC 59.185 43.478 0.00 0.00 42.14 3.67
710 734 1.618837 TGAAAACTCAGACCTCGAGGG 59.381 52.381 34.04 18.71 40.27 4.30
974 1019 0.953727 TGGTTGACTTGTGCATCTGC 59.046 50.000 0.00 0.00 42.50 4.26
1007 1058 3.817709 TCGCTATCATGACATGGTGAA 57.182 42.857 15.37 0.00 0.00 3.18
1008 1059 4.135747 TCGCTATCATGACATGGTGAAA 57.864 40.909 15.37 0.00 0.00 2.69
1009 1060 4.512484 TCGCTATCATGACATGGTGAAAA 58.488 39.130 15.37 0.00 0.00 2.29
1014 1065 7.043854 CGCTATCATGACATGGTGAAAATTTTC 60.044 37.037 21.60 21.60 37.69 2.29
1210 1264 8.699130 TCTATCTAGAAGCTGATGTCATTGAAA 58.301 33.333 0.00 0.00 0.00 2.69
1290 1344 3.800506 GGTATAAAGGTCGAACCATGTCG 59.199 47.826 0.00 0.00 41.95 4.35
1314 1368 3.062466 GCCCAAGGGTTTCCTCGC 61.062 66.667 7.05 0.00 44.07 5.03
1317 1371 1.559065 CCCAAGGGTTTCCTCGCCTA 61.559 60.000 0.00 0.00 44.07 3.93
1337 1391 8.038944 TCGCCTACAAGAGTTAAAACTTGATAT 58.961 33.333 21.64 8.70 43.98 1.63
1431 1485 2.040278 CAAGGAGATGTGGAAGTTCCCA 59.960 50.000 19.42 16.03 35.03 4.37
1433 1487 2.307098 AGGAGATGTGGAAGTTCCCAAG 59.693 50.000 19.42 0.00 38.06 3.61
1476 1530 7.977853 CCATCCCTCAAGAATTTGAAACTAATG 59.022 37.037 0.00 0.00 42.48 1.90
1487 1541 9.232473 GAATTTGAAACTAATGAGTAAGTCCCT 57.768 33.333 0.00 0.00 33.58 4.20
1545 1599 1.202463 CGGAGAGGATGCAAGGTACTG 60.202 57.143 0.00 0.00 40.86 2.74
1546 1600 1.834263 GGAGAGGATGCAAGGTACTGT 59.166 52.381 0.00 0.00 40.86 3.55
1547 1601 3.031736 GGAGAGGATGCAAGGTACTGTA 58.968 50.000 0.00 0.00 40.86 2.74
1567 1621 4.408921 TGTAGCTTACTATGCCCTCATGTT 59.591 41.667 0.00 0.00 34.22 2.71
1571 1625 4.513318 GCTTACTATGCCCTCATGTTCTTC 59.487 45.833 0.00 0.00 34.22 2.87
1572 1626 5.686124 GCTTACTATGCCCTCATGTTCTTCT 60.686 44.000 0.00 0.00 34.22 2.85
1573 1627 4.851639 ACTATGCCCTCATGTTCTTCTT 57.148 40.909 0.00 0.00 34.22 2.52
1576 1630 6.721318 ACTATGCCCTCATGTTCTTCTTTAA 58.279 36.000 0.00 0.00 34.22 1.52
1612 1666 5.779529 TTACGGTCAGATATTACAGTCCC 57.220 43.478 0.00 0.00 0.00 4.46
1630 1686 6.070653 ACAGTCCCCGTATATTTTCAGTACAA 60.071 38.462 0.00 0.00 0.00 2.41
1631 1687 6.479001 CAGTCCCCGTATATTTTCAGTACAAG 59.521 42.308 0.00 0.00 0.00 3.16
1632 1688 5.756833 GTCCCCGTATATTTTCAGTACAAGG 59.243 44.000 0.00 0.00 0.00 3.61
1633 1689 5.662208 TCCCCGTATATTTTCAGTACAAGGA 59.338 40.000 0.00 0.00 0.00 3.36
1634 1690 5.756833 CCCCGTATATTTTCAGTACAAGGAC 59.243 44.000 0.00 0.00 0.00 3.85
1635 1691 5.756833 CCCGTATATTTTCAGTACAAGGACC 59.243 44.000 0.00 0.00 0.00 4.46
1636 1692 5.461078 CCGTATATTTTCAGTACAAGGACCG 59.539 44.000 0.00 0.00 0.00 4.79
1637 1693 6.267817 CGTATATTTTCAGTACAAGGACCGA 58.732 40.000 0.00 0.00 0.00 4.69
1638 1694 6.417044 CGTATATTTTCAGTACAAGGACCGAG 59.583 42.308 0.00 0.00 0.00 4.63
1639 1695 4.884668 ATTTTCAGTACAAGGACCGAGA 57.115 40.909 0.00 0.00 0.00 4.04
1640 1696 4.884668 TTTTCAGTACAAGGACCGAGAT 57.115 40.909 0.00 0.00 0.00 2.75
1641 1697 5.988310 TTTTCAGTACAAGGACCGAGATA 57.012 39.130 0.00 0.00 0.00 1.98
1642 1698 4.978083 TTCAGTACAAGGACCGAGATAC 57.022 45.455 0.00 0.00 0.00 2.24
1643 1699 4.232188 TCAGTACAAGGACCGAGATACT 57.768 45.455 0.00 0.00 0.00 2.12
1644 1700 4.197750 TCAGTACAAGGACCGAGATACTC 58.802 47.826 0.00 0.00 0.00 2.59
1645 1701 3.945921 CAGTACAAGGACCGAGATACTCA 59.054 47.826 0.00 0.00 0.00 3.41
1646 1702 4.580995 CAGTACAAGGACCGAGATACTCAT 59.419 45.833 0.00 0.00 0.00 2.90
1647 1703 5.763698 CAGTACAAGGACCGAGATACTCATA 59.236 44.000 0.00 0.00 0.00 2.15
1648 1704 6.262496 CAGTACAAGGACCGAGATACTCATAA 59.738 42.308 0.00 0.00 0.00 1.90
1649 1705 7.005296 AGTACAAGGACCGAGATACTCATAAT 58.995 38.462 0.00 0.00 0.00 1.28
1650 1706 8.162085 AGTACAAGGACCGAGATACTCATAATA 58.838 37.037 0.00 0.00 0.00 0.98
1651 1707 7.834881 ACAAGGACCGAGATACTCATAATAA 57.165 36.000 0.00 0.00 0.00 1.40
1686 1742 4.464069 ACTTATCTGTGACTTGCTCTCC 57.536 45.455 0.00 0.00 0.00 3.71
1724 1780 5.782047 TGCTTGTTTGGAATGATGGTTTAG 58.218 37.500 0.00 0.00 0.00 1.85
1728 1784 7.147915 GCTTGTTTGGAATGATGGTTTAGGATA 60.148 37.037 0.00 0.00 0.00 2.59
1734 1790 7.410174 TGGAATGATGGTTTAGGATAAACAGT 58.590 34.615 12.91 2.72 32.04 3.55
1741 1797 4.320641 GGTTTAGGATAAACAGTTTGCGCA 60.321 41.667 5.66 5.66 32.04 6.09
1750 1806 2.285083 ACAGTTTGCGCACTCAAGTTA 58.715 42.857 11.12 0.00 0.00 2.24
1787 1844 3.904717 TCCTTGCAGGTGGAACTTTAAA 58.095 40.909 0.00 0.00 36.53 1.52
1801 1858 6.017687 TGGAACTTTAAAGAAGGTTTACGAGC 60.018 38.462 21.92 0.00 35.19 5.03
1802 1859 6.204301 GGAACTTTAAAGAAGGTTTACGAGCT 59.796 38.462 21.92 0.00 35.19 4.09
1827 1884 4.431416 TGCTGGTGGAACTTTAAGAAGA 57.569 40.909 0.00 0.00 36.69 2.87
1845 1902 1.480954 AGATTTACGAGTGGCGGACAT 59.519 47.619 0.00 0.00 46.49 3.06
1861 1918 7.115947 GTGGCGGACATGTCTAAGTATTATTAC 59.884 40.741 24.50 3.09 0.00 1.89
1862 1919 7.014905 TGGCGGACATGTCTAAGTATTATTACT 59.985 37.037 24.50 0.00 40.48 2.24
1863 1920 8.517878 GGCGGACATGTCTAAGTATTATTACTA 58.482 37.037 24.50 0.00 37.70 1.82
1864 1921 9.339492 GCGGACATGTCTAAGTATTATTACTAC 57.661 37.037 24.50 1.68 37.70 2.73
1905 1967 3.494254 TCCCCTTGTTGCGGTGGT 61.494 61.111 0.00 0.00 0.00 4.16
1920 1982 2.546795 CGGTGGTATGAGAGAAGGATGC 60.547 54.545 0.00 0.00 0.00 3.91
1942 2004 7.707624 TGCATCCTTTCTGAATGTATCTTTT 57.292 32.000 0.00 0.00 0.00 2.27
1948 2010 5.560966 TTCTGAATGTATCTTTTTCGCCC 57.439 39.130 0.00 0.00 0.00 6.13
1949 2011 4.843728 TCTGAATGTATCTTTTTCGCCCT 58.156 39.130 0.00 0.00 0.00 5.19
1950 2012 5.253330 TCTGAATGTATCTTTTTCGCCCTT 58.747 37.500 0.00 0.00 0.00 3.95
1951 2013 5.354234 TCTGAATGTATCTTTTTCGCCCTTC 59.646 40.000 0.00 0.00 0.00 3.46
1952 2014 4.398044 TGAATGTATCTTTTTCGCCCTTCC 59.602 41.667 0.00 0.00 0.00 3.46
1953 2015 3.713826 TGTATCTTTTTCGCCCTTCCT 57.286 42.857 0.00 0.00 0.00 3.36
1954 2016 3.606687 TGTATCTTTTTCGCCCTTCCTC 58.393 45.455 0.00 0.00 0.00 3.71
1967 2029 3.385755 GCCCTTCCTCAAATTATGTGCAT 59.614 43.478 0.00 0.00 0.00 3.96
1968 2030 4.584325 GCCCTTCCTCAAATTATGTGCATA 59.416 41.667 0.00 0.00 0.00 3.14
1969 2031 5.244626 GCCCTTCCTCAAATTATGTGCATAT 59.755 40.000 0.31 0.31 0.00 1.78
2030 2094 1.067354 ACGTCTAACCACCGGTGAATC 60.067 52.381 36.07 16.92 35.34 2.52
2038 2102 3.309296 ACCACCGGTGAATCTAGATGAT 58.691 45.455 36.07 3.88 32.98 2.45
2039 2103 3.070159 ACCACCGGTGAATCTAGATGATG 59.930 47.826 36.07 15.97 32.60 3.07
2040 2104 3.321968 CCACCGGTGAATCTAGATGATGA 59.678 47.826 36.07 0.00 35.21 2.92
2045 2109 4.388165 CGGTGAATCTAGATGATGATGTGC 59.612 45.833 5.86 0.00 35.21 4.57
2103 2167 5.667539 TTGATTCCCACAAACAAAACTGA 57.332 34.783 0.00 0.00 0.00 3.41
2113 2177 7.279758 CCCACAAACAAAACTGATGTGTTATTT 59.720 33.333 0.00 0.00 39.70 1.40
2114 2178 9.307121 CCACAAACAAAACTGATGTGTTATTTA 57.693 29.630 0.00 0.00 39.70 1.40
2194 2258 4.261741 GCAATGTCAGTCAGTTTGGTTCAT 60.262 41.667 0.00 0.00 0.00 2.57
2247 2311 1.481242 CCCAGGTTCTGCTTCCCTTTT 60.481 52.381 0.00 0.00 0.00 2.27
2252 2316 1.618837 GTTCTGCTTCCCTTTTTCCCC 59.381 52.381 0.00 0.00 0.00 4.81
2309 2373 0.798776 GTTGTATTCTGCACGCAGCT 59.201 50.000 14.25 6.66 45.94 4.24
2313 2377 1.999735 GTATTCTGCACGCAGCTACAA 59.000 47.619 14.25 3.88 45.94 2.41
2314 2378 1.522668 ATTCTGCACGCAGCTACAAA 58.477 45.000 14.25 3.51 45.94 2.83
2315 2379 0.586319 TTCTGCACGCAGCTACAAAC 59.414 50.000 14.25 0.00 45.94 2.93
2316 2380 0.249868 TCTGCACGCAGCTACAAACT 60.250 50.000 14.25 0.00 45.94 2.66
2318 2382 2.002586 CTGCACGCAGCTACAAACTAT 58.997 47.619 6.03 0.00 45.94 2.12
2319 2383 3.119280 TCTGCACGCAGCTACAAACTATA 60.119 43.478 14.25 0.00 45.94 1.31
2320 2384 2.927477 TGCACGCAGCTACAAACTATAC 59.073 45.455 2.02 0.00 45.94 1.47
2322 2386 3.369756 GCACGCAGCTACAAACTATACAA 59.630 43.478 0.00 0.00 41.15 2.41
2325 2389 3.855379 CGCAGCTACAAACTATACAACGA 59.145 43.478 0.00 0.00 0.00 3.85
2326 2390 4.259292 CGCAGCTACAAACTATACAACGAC 60.259 45.833 0.00 0.00 0.00 4.34
2327 2391 4.624024 GCAGCTACAAACTATACAACGACA 59.376 41.667 0.00 0.00 0.00 4.35
2328 2392 5.220228 GCAGCTACAAACTATACAACGACAG 60.220 44.000 0.00 0.00 0.00 3.51
2329 2393 4.863131 AGCTACAAACTATACAACGACAGC 59.137 41.667 0.00 0.00 0.00 4.40
2330 2394 4.624024 GCTACAAACTATACAACGACAGCA 59.376 41.667 0.00 0.00 0.00 4.41
2331 2395 5.119588 GCTACAAACTATACAACGACAGCAA 59.880 40.000 0.00 0.00 0.00 3.91
2332 2396 5.994887 ACAAACTATACAACGACAGCAAA 57.005 34.783 0.00 0.00 0.00 3.68
2333 2397 6.366315 ACAAACTATACAACGACAGCAAAA 57.634 33.333 0.00 0.00 0.00 2.44
2334 2398 6.787225 ACAAACTATACAACGACAGCAAAAA 58.213 32.000 0.00 0.00 0.00 1.94
2376 2440 8.081633 TCCACAGTCAACTAATTTTAAGCATTG 58.918 33.333 0.00 0.00 0.00 2.82
2377 2441 7.867403 CCACAGTCAACTAATTTTAAGCATTGT 59.133 33.333 0.00 0.00 0.00 2.71
2393 2457 9.865321 TTAAGCATTGTACTACTCGTAGATTTT 57.135 29.630 10.83 0.00 36.97 1.82
2417 2481 2.879826 GTGTAACATTGCAGGGATTGC 58.120 47.619 0.00 0.00 45.53 3.56
2426 2490 1.530771 CAGGGATTGCAGAGGAGGG 59.469 63.158 0.00 0.00 0.00 4.30
2427 2491 1.695597 AGGGATTGCAGAGGAGGGG 60.696 63.158 0.00 0.00 0.00 4.79
2428 2492 2.761465 GGGATTGCAGAGGAGGGGG 61.761 68.421 0.00 0.00 0.00 5.40
2452 2516 4.996976 CGGAGCAGTAGCAACAGT 57.003 55.556 0.00 0.00 45.49 3.55
2454 2518 2.363788 CGGAGCAGTAGCAACAGTAA 57.636 50.000 0.00 0.00 45.49 2.24
2455 2519 2.263077 CGGAGCAGTAGCAACAGTAAG 58.737 52.381 0.00 0.00 45.49 2.34
2456 2520 2.352814 CGGAGCAGTAGCAACAGTAAGT 60.353 50.000 0.00 0.00 45.49 2.24
2457 2521 3.119602 CGGAGCAGTAGCAACAGTAAGTA 60.120 47.826 0.00 0.00 45.49 2.24
2458 2522 4.425520 GGAGCAGTAGCAACAGTAAGTAG 58.574 47.826 0.00 0.00 45.49 2.57
2459 2523 4.082136 GGAGCAGTAGCAACAGTAAGTAGT 60.082 45.833 0.00 0.00 45.49 2.73
2460 2524 5.125097 GGAGCAGTAGCAACAGTAAGTAGTA 59.875 44.000 0.00 0.00 45.49 1.82
2461 2525 5.952033 AGCAGTAGCAACAGTAAGTAGTAC 58.048 41.667 0.00 0.00 45.49 2.73
2462 2526 5.100943 GCAGTAGCAACAGTAAGTAGTACC 58.899 45.833 0.00 0.00 41.58 3.34
2463 2527 5.330295 CAGTAGCAACAGTAAGTAGTACCG 58.670 45.833 0.00 0.00 32.58 4.02
2464 2528 5.122869 CAGTAGCAACAGTAAGTAGTACCGA 59.877 44.000 0.00 0.00 32.58 4.69
2465 2529 4.431661 AGCAACAGTAAGTAGTACCGAC 57.568 45.455 0.00 0.00 32.58 4.79
2466 2530 4.077822 AGCAACAGTAAGTAGTACCGACT 58.922 43.478 0.00 0.00 39.92 4.18
2467 2531 5.248640 AGCAACAGTAAGTAGTACCGACTA 58.751 41.667 4.76 0.00 37.10 2.59
2479 2543 2.799371 CGACTACCGGGAGCTCAC 59.201 66.667 15.67 11.90 33.91 3.51
2480 2544 2.044555 CGACTACCGGGAGCTCACA 61.045 63.158 15.67 0.00 33.91 3.58
2481 2545 1.810532 GACTACCGGGAGCTCACAG 59.189 63.158 15.67 7.33 0.00 3.66
2482 2546 2.286127 GACTACCGGGAGCTCACAGC 62.286 65.000 15.67 0.00 42.84 4.40
2491 2555 2.047844 GCTCACAGCTTCCGCAGA 60.048 61.111 0.00 0.00 38.45 4.26
2492 2556 1.449246 GCTCACAGCTTCCGCAGAT 60.449 57.895 0.00 0.00 38.45 2.90
2493 2557 1.427592 GCTCACAGCTTCCGCAGATC 61.428 60.000 0.00 0.00 38.45 2.75
2494 2558 0.108472 CTCACAGCTTCCGCAGATCA 60.108 55.000 0.00 0.00 39.10 2.92
2495 2559 0.321346 TCACAGCTTCCGCAGATCAA 59.679 50.000 0.00 0.00 39.10 2.57
2496 2560 1.159285 CACAGCTTCCGCAGATCAAA 58.841 50.000 0.00 0.00 39.10 2.69
2497 2561 1.741706 CACAGCTTCCGCAGATCAAAT 59.258 47.619 0.00 0.00 39.10 2.32
2498 2562 2.938451 CACAGCTTCCGCAGATCAAATA 59.062 45.455 0.00 0.00 39.10 1.40
2499 2563 2.939103 ACAGCTTCCGCAGATCAAATAC 59.061 45.455 0.00 0.00 39.10 1.89
2500 2564 2.033407 CAGCTTCCGCAGATCAAATACG 60.033 50.000 0.00 0.00 39.10 3.06
2501 2565 1.933853 GCTTCCGCAGATCAAATACGT 59.066 47.619 0.00 0.00 35.78 3.57
2502 2566 2.033662 GCTTCCGCAGATCAAATACGTC 60.034 50.000 0.00 0.00 35.78 4.34
2503 2567 1.835121 TCCGCAGATCAAATACGTCG 58.165 50.000 0.00 0.00 0.00 5.12
2504 2568 0.852777 CCGCAGATCAAATACGTCGG 59.147 55.000 0.00 0.00 0.00 4.79
2505 2569 0.229753 CGCAGATCAAATACGTCGGC 59.770 55.000 0.00 0.00 0.00 5.54
2506 2570 0.229753 GCAGATCAAATACGTCGGCG 59.770 55.000 8.42 8.42 44.93 6.46
2572 2869 1.712977 CGGCCAGCATCTTCAAGCTC 61.713 60.000 2.24 0.00 39.50 4.09
2573 2870 0.394080 GGCCAGCATCTTCAAGCTCT 60.394 55.000 0.00 0.00 39.50 4.09
2653 2959 3.904339 GGATACAAATAGAGGGAGAGGCA 59.096 47.826 0.00 0.00 0.00 4.75
2696 3742 1.141234 GGGACTTTACGAGCTCGGG 59.859 63.158 36.93 24.86 44.95 5.14
2698 3744 1.098050 GGACTTTACGAGCTCGGGTA 58.902 55.000 36.93 20.42 44.95 3.69
2699 3745 1.202234 GGACTTTACGAGCTCGGGTAC 60.202 57.143 36.93 25.14 44.95 3.34
2763 3809 0.387202 CTCTATGGCTGTCGGAGGTG 59.613 60.000 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 8.717717 TCAAGAGTATATCAATCCATGTTTCCT 58.282 33.333 0.00 0.00 0.00 3.36
19 20 8.908786 TCAAGAGTATATCAATCCATGTTTCC 57.091 34.615 0.00 0.00 0.00 3.13
231 232 5.005779 CGTGCTATTTCTTCCAGTGTATGTC 59.994 44.000 0.00 0.00 0.00 3.06
400 401 5.224135 TGACATGCAGTTTTGTCAATCATG 58.776 37.500 16.48 0.00 46.75 3.07
476 486 3.815401 GTGTCAGCAAGAAACACCATACT 59.185 43.478 0.00 0.00 37.84 2.12
498 512 4.550577 TGCATTATAAAGTGCATCCACG 57.449 40.909 9.22 0.00 45.60 4.94
974 1019 6.311445 GTCATGATAGCGATATTTGGTACCAG 59.689 42.308 15.65 3.28 0.00 4.00
1014 1065 7.707104 AGGTTGTTAGTTGTCTCATTTTTCTG 58.293 34.615 0.00 0.00 0.00 3.02
1210 1264 0.251832 AGGATCGGCATCGGGTCTAT 60.252 55.000 0.00 0.00 36.95 1.98
1290 1344 1.248486 GAAACCCTTGGGCAGAGAAC 58.752 55.000 5.46 0.00 0.00 3.01
1433 1487 2.486966 GAAGGTGCAGCAATCCGC 59.513 61.111 19.63 0.00 42.91 5.54
1476 1530 4.712337 TCTCCAGAAATCAGGGACTTACTC 59.288 45.833 0.00 0.00 34.60 2.59
1487 1541 3.008266 TGTGCTGTCATCTCCAGAAATCA 59.992 43.478 0.00 0.00 31.38 2.57
1544 1598 3.967326 ACATGAGGGCATAGTAAGCTACA 59.033 43.478 0.00 0.00 32.27 2.74
1545 1599 4.608948 ACATGAGGGCATAGTAAGCTAC 57.391 45.455 0.00 0.00 32.27 3.58
1546 1600 4.901849 AGAACATGAGGGCATAGTAAGCTA 59.098 41.667 0.00 0.00 32.27 3.32
1547 1601 3.713764 AGAACATGAGGGCATAGTAAGCT 59.286 43.478 0.00 0.00 32.27 3.74
1571 1625 9.698617 GACCGTAAACAGCAGTAAATATTAAAG 57.301 33.333 0.00 0.00 0.00 1.85
1572 1626 9.217278 TGACCGTAAACAGCAGTAAATATTAAA 57.783 29.630 0.00 0.00 0.00 1.52
1573 1627 8.774890 TGACCGTAAACAGCAGTAAATATTAA 57.225 30.769 0.00 0.00 0.00 1.40
1576 1630 6.636705 TCTGACCGTAAACAGCAGTAAATAT 58.363 36.000 0.00 0.00 34.57 1.28
1585 1639 6.040878 ACTGTAATATCTGACCGTAAACAGC 58.959 40.000 0.00 0.00 36.21 4.40
1594 1648 3.662247 CGGGGACTGTAATATCTGACC 57.338 52.381 0.00 0.00 0.00 4.02
1612 1666 5.461078 CGGTCCTTGTACTGAAAATATACGG 59.539 44.000 0.00 0.00 0.00 4.02
1630 1686 8.480133 AACTTTATTATGAGTATCTCGGTCCT 57.520 34.615 0.00 0.00 34.92 3.85
1631 1687 8.578151 AGAACTTTATTATGAGTATCTCGGTCC 58.422 37.037 0.00 0.00 34.92 4.46
1632 1688 9.400638 CAGAACTTTATTATGAGTATCTCGGTC 57.599 37.037 0.00 0.00 34.92 4.79
1633 1689 8.915036 ACAGAACTTTATTATGAGTATCTCGGT 58.085 33.333 0.00 0.00 34.92 4.69
1634 1690 9.751542 AACAGAACTTTATTATGAGTATCTCGG 57.248 33.333 0.00 0.00 34.92 4.63
1686 1742 0.324091 AAGCAAGGCAGGGAAGGATG 60.324 55.000 0.00 0.00 0.00 3.51
1724 1780 2.225491 TGAGTGCGCAAACTGTTTATCC 59.775 45.455 14.00 0.00 0.00 2.59
1728 1784 1.472480 ACTTGAGTGCGCAAACTGTTT 59.528 42.857 14.00 0.00 0.00 2.83
1734 1790 4.975502 CAGAAAATAACTTGAGTGCGCAAA 59.024 37.500 14.00 1.19 0.00 3.68
1787 1844 3.067833 GCAAGAAGCTCGTAAACCTTCT 58.932 45.455 0.00 0.00 45.17 2.85
1801 1858 4.821805 TCTTAAAGTTCCACCAGCAAGAAG 59.178 41.667 0.00 0.00 0.00 2.85
1802 1859 4.787551 TCTTAAAGTTCCACCAGCAAGAA 58.212 39.130 0.00 0.00 0.00 2.52
1803 1860 4.431416 TCTTAAAGTTCCACCAGCAAGA 57.569 40.909 0.00 0.00 0.00 3.02
1804 1861 4.821805 TCTTCTTAAAGTTCCACCAGCAAG 59.178 41.667 0.00 0.00 33.95 4.01
1805 1862 4.787551 TCTTCTTAAAGTTCCACCAGCAA 58.212 39.130 0.00 0.00 33.95 3.91
1806 1863 4.431416 TCTTCTTAAAGTTCCACCAGCA 57.569 40.909 0.00 0.00 33.95 4.41
1807 1864 5.966742 AATCTTCTTAAAGTTCCACCAGC 57.033 39.130 0.00 0.00 33.95 4.85
1808 1865 7.386848 TCGTAAATCTTCTTAAAGTTCCACCAG 59.613 37.037 0.00 0.00 33.95 4.00
1809 1866 7.218614 TCGTAAATCTTCTTAAAGTTCCACCA 58.781 34.615 0.00 0.00 33.95 4.17
1810 1867 7.387122 ACTCGTAAATCTTCTTAAAGTTCCACC 59.613 37.037 0.00 0.00 33.95 4.61
1811 1868 8.221766 CACTCGTAAATCTTCTTAAAGTTCCAC 58.778 37.037 0.00 0.00 33.95 4.02
1827 1884 1.066430 ACATGTCCGCCACTCGTAAAT 60.066 47.619 0.00 0.00 36.19 1.40
1863 1920 9.606631 GACAAAGACATCTGAATTAGGAATAGT 57.393 33.333 0.00 0.00 0.00 2.12
1864 1921 9.050601 GGACAAAGACATCTGAATTAGGAATAG 57.949 37.037 0.00 0.00 0.00 1.73
1865 1922 7.993183 GGGACAAAGACATCTGAATTAGGAATA 59.007 37.037 0.00 0.00 0.00 1.75
1866 1923 6.830838 GGGACAAAGACATCTGAATTAGGAAT 59.169 38.462 0.00 0.00 0.00 3.01
1920 1982 7.430502 GCGAAAAAGATACATTCAGAAAGGATG 59.569 37.037 0.00 0.00 0.00 3.51
1927 1989 4.843728 AGGGCGAAAAAGATACATTCAGA 58.156 39.130 0.00 0.00 0.00 3.27
1931 1993 4.600062 AGGAAGGGCGAAAAAGATACATT 58.400 39.130 0.00 0.00 0.00 2.71
1942 2004 3.694072 CACATAATTTGAGGAAGGGCGAA 59.306 43.478 0.00 0.00 0.00 4.70
1950 2012 9.353431 ACATACAATATGCACATAATTTGAGGA 57.647 29.630 9.76 0.00 0.00 3.71
1951 2013 9.970395 AACATACAATATGCACATAATTTGAGG 57.030 29.630 9.76 3.59 0.00 3.86
2038 2102 9.710900 AAATCAGAAATATAGATACGCACATCA 57.289 29.630 0.00 0.00 0.00 3.07
2039 2103 9.964253 CAAATCAGAAATATAGATACGCACATC 57.036 33.333 0.00 0.00 0.00 3.06
2040 2104 9.710900 TCAAATCAGAAATATAGATACGCACAT 57.289 29.630 0.00 0.00 0.00 3.21
2045 2109 9.193133 ACGGTTCAAATCAGAAATATAGATACG 57.807 33.333 0.00 0.00 0.00 3.06
2121 2185 9.918630 CCATGTCAAGAGAGAAAAATACATTTT 57.081 29.630 0.00 0.00 43.85 1.82
2123 2187 8.517878 CACCATGTCAAGAGAGAAAAATACATT 58.482 33.333 0.00 0.00 0.00 2.71
2124 2188 7.884877 TCACCATGTCAAGAGAGAAAAATACAT 59.115 33.333 0.00 0.00 0.00 2.29
2126 2190 7.625185 GCTCACCATGTCAAGAGAGAAAAATAC 60.625 40.741 0.00 0.00 0.00 1.89
2194 2258 5.470098 GTCTAGAACTTGGCATTCAGTGAAA 59.530 40.000 10.14 0.00 0.00 2.69
2247 2311 1.145571 AGGTGTAGCACAAAGGGGAA 58.854 50.000 1.61 0.00 35.86 3.97
2252 2316 1.148310 CCGTCAGGTGTAGCACAAAG 58.852 55.000 1.61 0.00 35.86 2.77
2309 2373 7.479897 TTTTGCTGTCGTTGTATAGTTTGTA 57.520 32.000 0.00 0.00 0.00 2.41
2333 2397 7.069331 TGACTGTGGATGGTGTTTAAGATTTTT 59.931 33.333 0.00 0.00 0.00 1.94
2334 2398 6.549364 TGACTGTGGATGGTGTTTAAGATTTT 59.451 34.615 0.00 0.00 0.00 1.82
2335 2399 6.068010 TGACTGTGGATGGTGTTTAAGATTT 58.932 36.000 0.00 0.00 0.00 2.17
2336 2400 5.630121 TGACTGTGGATGGTGTTTAAGATT 58.370 37.500 0.00 0.00 0.00 2.40
2337 2401 5.241403 TGACTGTGGATGGTGTTTAAGAT 57.759 39.130 0.00 0.00 0.00 2.40
2338 2402 4.698201 TGACTGTGGATGGTGTTTAAGA 57.302 40.909 0.00 0.00 0.00 2.10
2339 2403 4.821805 AGTTGACTGTGGATGGTGTTTAAG 59.178 41.667 0.00 0.00 0.00 1.85
2340 2404 4.787551 AGTTGACTGTGGATGGTGTTTAA 58.212 39.130 0.00 0.00 0.00 1.52
2341 2405 4.431416 AGTTGACTGTGGATGGTGTTTA 57.569 40.909 0.00 0.00 0.00 2.01
2393 2457 5.295950 CAATCCCTGCAATGTTACACAAAA 58.704 37.500 0.00 0.00 0.00 2.44
2410 2474 2.761465 CCCCCTCCTCTGCAATCCC 61.761 68.421 0.00 0.00 0.00 3.85
2411 2475 2.922234 CCCCCTCCTCTGCAATCC 59.078 66.667 0.00 0.00 0.00 3.01
2427 2491 3.665675 CTACTGCTCCGCCACACCC 62.666 68.421 0.00 0.00 0.00 4.61
2428 2492 2.125512 CTACTGCTCCGCCACACC 60.126 66.667 0.00 0.00 0.00 4.16
2429 2493 2.815647 GCTACTGCTCCGCCACAC 60.816 66.667 0.00 0.00 36.03 3.82
2430 2494 2.878089 TTGCTACTGCTCCGCCACA 61.878 57.895 0.00 0.00 40.48 4.17
2431 2495 2.047274 TTGCTACTGCTCCGCCAC 60.047 61.111 0.00 0.00 40.48 5.01
2432 2496 2.047274 GTTGCTACTGCTCCGCCA 60.047 61.111 0.00 0.00 40.48 5.69
2433 2497 2.047274 TGTTGCTACTGCTCCGCC 60.047 61.111 0.00 0.00 40.48 6.13
2434 2498 0.108804 TACTGTTGCTACTGCTCCGC 60.109 55.000 5.16 0.00 40.48 5.54
2435 2499 2.263077 CTTACTGTTGCTACTGCTCCG 58.737 52.381 5.16 0.00 40.48 4.63
2436 2500 3.320673 ACTTACTGTTGCTACTGCTCC 57.679 47.619 5.16 0.00 40.48 4.70
2437 2501 5.061920 ACTACTTACTGTTGCTACTGCTC 57.938 43.478 5.16 0.00 40.48 4.26
2438 2502 5.105837 GGTACTACTTACTGTTGCTACTGCT 60.106 44.000 5.16 0.00 40.48 4.24
2439 2503 5.100943 GGTACTACTTACTGTTGCTACTGC 58.899 45.833 5.16 0.00 40.20 4.40
2440 2504 5.122869 TCGGTACTACTTACTGTTGCTACTG 59.877 44.000 3.77 3.77 38.16 2.74
2441 2505 5.123027 GTCGGTACTACTTACTGTTGCTACT 59.877 44.000 0.00 0.00 38.16 2.57
2442 2506 5.123027 AGTCGGTACTACTTACTGTTGCTAC 59.877 44.000 0.00 0.00 38.16 3.58
2443 2507 5.248640 AGTCGGTACTACTTACTGTTGCTA 58.751 41.667 0.00 0.00 38.16 3.49
2444 2508 4.077822 AGTCGGTACTACTTACTGTTGCT 58.922 43.478 0.00 0.00 38.16 3.91
2445 2509 4.431661 AGTCGGTACTACTTACTGTTGC 57.568 45.455 0.00 0.00 38.16 4.17
2462 2526 1.994507 CTGTGAGCTCCCGGTAGTCG 61.995 65.000 12.15 0.00 38.88 4.18
2463 2527 1.810532 CTGTGAGCTCCCGGTAGTC 59.189 63.158 12.15 0.00 0.00 2.59
2464 2528 2.352032 GCTGTGAGCTCCCGGTAGT 61.352 63.158 12.15 0.00 38.45 2.73
2465 2529 2.496817 GCTGTGAGCTCCCGGTAG 59.503 66.667 12.15 0.00 38.45 3.18
2482 2546 2.216488 CGACGTATTTGATCTGCGGAAG 59.784 50.000 0.00 0.00 0.00 3.46
2483 2547 2.190161 CGACGTATTTGATCTGCGGAA 58.810 47.619 0.00 0.00 0.00 4.30
2484 2548 1.535226 CCGACGTATTTGATCTGCGGA 60.535 52.381 0.00 0.00 39.85 5.54
2485 2549 0.852777 CCGACGTATTTGATCTGCGG 59.147 55.000 0.00 0.00 0.00 5.69
2486 2550 0.229753 GCCGACGTATTTGATCTGCG 59.770 55.000 0.00 0.00 0.00 5.18
2487 2551 0.229753 CGCCGACGTATTTGATCTGC 59.770 55.000 0.00 0.00 33.53 4.26
2488 2552 1.781429 CTCGCCGACGTATTTGATCTG 59.219 52.381 0.00 0.00 41.18 2.90
2489 2553 1.269102 CCTCGCCGACGTATTTGATCT 60.269 52.381 0.00 0.00 41.18 2.75
2490 2554 1.129326 CCTCGCCGACGTATTTGATC 58.871 55.000 0.00 0.00 41.18 2.92
2491 2555 0.874607 GCCTCGCCGACGTATTTGAT 60.875 55.000 0.00 0.00 41.18 2.57
2492 2556 1.517694 GCCTCGCCGACGTATTTGA 60.518 57.895 0.00 0.00 41.18 2.69
2493 2557 1.355796 TTGCCTCGCCGACGTATTTG 61.356 55.000 0.00 0.00 41.18 2.32
2494 2558 0.671163 TTTGCCTCGCCGACGTATTT 60.671 50.000 0.00 0.00 41.18 1.40
2495 2559 1.079681 TTTGCCTCGCCGACGTATT 60.080 52.632 0.00 0.00 41.18 1.89
2496 2560 1.518572 CTTTGCCTCGCCGACGTAT 60.519 57.895 0.00 0.00 41.18 3.06
2497 2561 2.126228 CTTTGCCTCGCCGACGTA 60.126 61.111 0.00 0.00 41.18 3.57
2499 2563 4.735132 TCCTTTGCCTCGCCGACG 62.735 66.667 0.00 0.00 42.01 5.12
2500 2564 2.125106 ATCCTTTGCCTCGCCGAC 60.125 61.111 0.00 0.00 0.00 4.79
2501 2565 2.125147 CATCCTTTGCCTCGCCGA 60.125 61.111 0.00 0.00 0.00 5.54
2502 2566 3.204827 CCATCCTTTGCCTCGCCG 61.205 66.667 0.00 0.00 0.00 6.46
2503 2567 3.521796 GCCATCCTTTGCCTCGCC 61.522 66.667 0.00 0.00 0.00 5.54
2504 2568 3.521796 GGCCATCCTTTGCCTCGC 61.522 66.667 0.00 0.00 44.46 5.03
2505 2569 3.204827 CGGCCATCCTTTGCCTCG 61.205 66.667 2.24 0.00 45.71 4.63
2506 2570 2.830370 CCGGCCATCCTTTGCCTC 60.830 66.667 2.24 0.00 45.71 4.70
2533 2830 2.593468 TAACGCAGGCAGGAGGATGC 62.593 60.000 0.00 0.00 45.74 3.91
2534 2831 0.811616 GTAACGCAGGCAGGAGGATG 60.812 60.000 0.00 0.00 0.00 3.51
2535 2832 1.522569 GTAACGCAGGCAGGAGGAT 59.477 57.895 0.00 0.00 0.00 3.24
2536 2833 2.978824 GTAACGCAGGCAGGAGGA 59.021 61.111 0.00 0.00 0.00 3.71
2537 2834 2.509336 CGTAACGCAGGCAGGAGG 60.509 66.667 0.00 0.00 0.00 4.30
2538 2835 2.509336 CCGTAACGCAGGCAGGAG 60.509 66.667 0.00 0.00 0.00 3.69
2653 2959 2.074922 TTCCTTTCTCCCCAATCCCT 57.925 50.000 0.00 0.00 0.00 4.20
2696 3742 2.361610 TCGTGACCCTCCCCGTAC 60.362 66.667 0.00 0.00 0.00 3.67
2730 3776 0.179078 ATAGAGAGCAGCAGCAGCAC 60.179 55.000 12.92 5.78 45.49 4.40


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

AutoCloner maintained by Alex Coulton.