Multiple sequence alignment - TraesCS5B01G192500

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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 TraesCS5B01G192500 chr5B 100.000 2489 0 0 1 2489 347676510 347678998 0.000000e+00 4597
1 TraesCS5B01G192500 chr5B 99.610 769 3 0 1721 2489 306213152 306213920 0.000000e+00 1404
2 TraesCS5B01G192500 chr5B 99.352 772 5 0 1718 2489 393967933 393968704 0.000000e+00 1399
3 TraesCS5B01G192500 chr5B 99.226 775 6 0 1715 2489 430701488 430702262 0.000000e+00 1399
4 TraesCS5B01G192500 chr5B 85.075 402 45 11 1103 1489 347928228 347928629 1.790000e-106 396
5 TraesCS5B01G192500 chr5A 90.429 1306 68 24 317 1593 395063781 395062504 0.000000e+00 1666
6 TraesCS5B01G192500 chr5A 98.473 786 10 2 1704 2489 214038397 214039180 0.000000e+00 1384
7 TraesCS5B01G192500 chr5A 84.270 445 46 11 1060 1489 395001420 395000985 1.780000e-111 412
8 TraesCS5B01G192500 chr5A 90.374 187 14 4 84 269 395063981 395063798 2.470000e-60 243
9 TraesCS5B01G192500 chr5A 92.481 133 5 3 1591 1719 71452778 71452909 4.230000e-43 185
10 TraesCS5B01G192500 chr4A 99.741 771 2 0 1719 2489 422951764 422952534 0.000000e+00 1413
11 TraesCS5B01G192500 chr4A 99.740 769 2 0 1721 2489 422958788 422959556 0.000000e+00 1410
12 TraesCS5B01G192500 chr7A 99.610 769 3 0 1721 2489 183683476 183682708 0.000000e+00 1404
13 TraesCS5B01G192500 chr6B 99.481 770 4 0 1720 2489 21474816 21474047 0.000000e+00 1400
14 TraesCS5B01G192500 chr1B 99.480 769 4 0 1721 2489 172822866 172822098 0.000000e+00 1399
15 TraesCS5B01G192500 chr5D 90.011 951 35 26 37 951 302875565 302876491 0.000000e+00 1175
16 TraesCS5B01G192500 chr5D 91.547 698 40 5 915 1593 302876491 302877188 0.000000e+00 944
17 TraesCS5B01G192500 chr5D 83.700 454 50 11 1051 1489 302895639 302896083 8.290000e-110 407
18 TraesCS5B01G192500 chr5D 93.701 127 8 0 1594 1720 555039261 555039135 9.090000e-45 191
19 TraesCS5B01G192500 chr5D 93.077 130 5 3 1594 1720 288133467 288133339 1.180000e-43 187
20 TraesCS5B01G192500 chr2B 93.130 131 8 1 1590 1720 798332446 798332575 9.090000e-45 191
21 TraesCS5B01G192500 chr6A 93.750 128 5 2 1594 1720 554780637 554780762 3.270000e-44 189
22 TraesCS5B01G192500 chr6A 91.852 135 10 1 1586 1720 593696916 593697049 1.180000e-43 187
23 TraesCS5B01G192500 chr1D 93.701 127 7 1 1594 1720 191375451 191375576 3.270000e-44 189
24 TraesCS5B01G192500 chr7B 93.023 129 7 2 1594 1720 4094918 4095046 1.180000e-43 187
25 TraesCS5B01G192500 chrUn 92.969 128 8 1 1594 1720 8089843 8089970 4.230000e-43 185


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 TraesCS5B01G192500 chr5B 347676510 347678998 2488 False 4597.0 4597 100.0000 1 2489 1 chr5B.!!$F2 2488
1 TraesCS5B01G192500 chr5B 306213152 306213920 768 False 1404.0 1404 99.6100 1721 2489 1 chr5B.!!$F1 768
2 TraesCS5B01G192500 chr5B 393967933 393968704 771 False 1399.0 1399 99.3520 1718 2489 1 chr5B.!!$F4 771
3 TraesCS5B01G192500 chr5B 430701488 430702262 774 False 1399.0 1399 99.2260 1715 2489 1 chr5B.!!$F5 774
4 TraesCS5B01G192500 chr5A 214038397 214039180 783 False 1384.0 1384 98.4730 1704 2489 1 chr5A.!!$F2 785
5 TraesCS5B01G192500 chr5A 395062504 395063981 1477 True 954.5 1666 90.4015 84 1593 2 chr5A.!!$R2 1509
6 TraesCS5B01G192500 chr4A 422951764 422952534 770 False 1413.0 1413 99.7410 1719 2489 1 chr4A.!!$F1 770
7 TraesCS5B01G192500 chr4A 422958788 422959556 768 False 1410.0 1410 99.7400 1721 2489 1 chr4A.!!$F2 768
8 TraesCS5B01G192500 chr7A 183682708 183683476 768 True 1404.0 1404 99.6100 1721 2489 1 chr7A.!!$R1 768
9 TraesCS5B01G192500 chr6B 21474047 21474816 769 True 1400.0 1400 99.4810 1720 2489 1 chr6B.!!$R1 769
10 TraesCS5B01G192500 chr1B 172822098 172822866 768 True 1399.0 1399 99.4800 1721 2489 1 chr1B.!!$R1 768
11 TraesCS5B01G192500 chr5D 302875565 302877188 1623 False 1059.5 1175 90.7790 37 1593 2 chr5D.!!$F2 1556

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
291 294 0.031616 TCCCAACAAAACAAGGGGCT 60.032 50.0 0.0 0.0 41.77 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1670 1771 0.338467 ATTTTTAGGGAGGGTGGGCC 59.662 55.0 0.0 0.0 0.0 5.8 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
18 19 2.227737 ACGAACACCCTTCCCAAGT 58.772 52.632 0.00 0.00 0.00 3.16
19 20 0.108019 ACGAACACCCTTCCCAAGTC 59.892 55.000 0.00 0.00 0.00 3.01
20 21 0.605589 CGAACACCCTTCCCAAGTCC 60.606 60.000 0.00 0.00 0.00 3.85
21 22 0.476771 GAACACCCTTCCCAAGTCCA 59.523 55.000 0.00 0.00 0.00 4.02
22 23 0.930726 AACACCCTTCCCAAGTCCAA 59.069 50.000 0.00 0.00 0.00 3.53
23 24 0.478507 ACACCCTTCCCAAGTCCAAG 59.521 55.000 0.00 0.00 0.00 3.61
24 25 0.771127 CACCCTTCCCAAGTCCAAGA 59.229 55.000 0.00 0.00 0.00 3.02
25 26 0.771755 ACCCTTCCCAAGTCCAAGAC 59.228 55.000 0.00 0.00 0.00 3.01
26 27 0.321653 CCCTTCCCAAGTCCAAGACG 60.322 60.000 0.00 0.00 37.67 4.18
27 28 0.685097 CCTTCCCAAGTCCAAGACGA 59.315 55.000 0.00 0.00 37.67 4.20
28 29 1.071699 CCTTCCCAAGTCCAAGACGAA 59.928 52.381 0.00 0.00 37.67 3.85
29 30 2.143925 CTTCCCAAGTCCAAGACGAAC 58.856 52.381 0.00 0.00 37.67 3.95
30 31 1.124780 TCCCAAGTCCAAGACGAACA 58.875 50.000 0.00 0.00 37.67 3.18
31 32 1.487142 TCCCAAGTCCAAGACGAACAA 59.513 47.619 0.00 0.00 37.67 2.83
32 33 1.873591 CCCAAGTCCAAGACGAACAAG 59.126 52.381 0.00 0.00 37.67 3.16
33 34 1.264288 CCAAGTCCAAGACGAACAAGC 59.736 52.381 0.00 0.00 37.67 4.01
34 35 1.939934 CAAGTCCAAGACGAACAAGCA 59.060 47.619 0.00 0.00 37.67 3.91
35 36 2.325583 AGTCCAAGACGAACAAGCAA 57.674 45.000 0.00 0.00 37.67 3.91
36 37 2.639065 AGTCCAAGACGAACAAGCAAA 58.361 42.857 0.00 0.00 37.67 3.68
37 38 3.214328 AGTCCAAGACGAACAAGCAAAT 58.786 40.909 0.00 0.00 37.67 2.32
38 39 3.251004 AGTCCAAGACGAACAAGCAAATC 59.749 43.478 0.00 0.00 37.67 2.17
39 40 3.003275 GTCCAAGACGAACAAGCAAATCA 59.997 43.478 0.00 0.00 0.00 2.57
40 41 3.820467 TCCAAGACGAACAAGCAAATCAT 59.180 39.130 0.00 0.00 0.00 2.45
41 42 4.278170 TCCAAGACGAACAAGCAAATCATT 59.722 37.500 0.00 0.00 0.00 2.57
70 71 6.202331 TCCCTTCTAGGATACAAGTCATCAA 58.798 40.000 0.00 0.00 37.67 2.57
71 72 6.098409 TCCCTTCTAGGATACAAGTCATCAAC 59.902 42.308 0.00 0.00 37.67 3.18
72 73 6.098982 CCCTTCTAGGATACAAGTCATCAACT 59.901 42.308 0.00 0.00 37.67 3.16
73 74 7.206687 CCTTCTAGGATACAAGTCATCAACTC 58.793 42.308 0.00 0.00 37.67 3.01
74 75 7.147828 CCTTCTAGGATACAAGTCATCAACTCA 60.148 40.741 0.00 0.00 37.67 3.41
75 76 7.904558 TCTAGGATACAAGTCATCAACTCAT 57.095 36.000 0.00 0.00 37.17 2.90
76 77 7.946207 TCTAGGATACAAGTCATCAACTCATC 58.054 38.462 0.00 0.00 37.17 2.92
77 78 6.550938 AGGATACAAGTCATCAACTCATCA 57.449 37.500 0.00 0.00 37.17 3.07
78 79 7.134362 AGGATACAAGTCATCAACTCATCAT 57.866 36.000 0.00 0.00 37.17 2.45
79 80 6.990939 AGGATACAAGTCATCAACTCATCATG 59.009 38.462 0.00 0.00 37.17 3.07
80 81 6.204301 GGATACAAGTCATCAACTCATCATGG 59.796 42.308 0.00 0.00 37.17 3.66
90 91 6.298441 TCAACTCATCATGGACAGATTACA 57.702 37.500 0.00 0.00 0.00 2.41
222 225 1.272490 TGAAAGCGGTCGACTGAAGAT 59.728 47.619 28.38 10.13 0.00 2.40
223 226 1.656095 GAAAGCGGTCGACTGAAGATG 59.344 52.381 28.38 4.65 0.00 2.90
291 294 0.031616 TCCCAACAAAACAAGGGGCT 60.032 50.000 0.00 0.00 41.77 5.19
298 301 4.621087 AACAAGGGGCTGGGGTGC 62.621 66.667 0.00 0.00 0.00 5.01
336 348 4.346127 TGATTATACTGCCATCTCACAGCT 59.654 41.667 0.00 0.00 37.42 4.24
340 352 1.480137 ACTGCCATCTCACAGCTAGTC 59.520 52.381 0.00 0.00 37.42 2.59
442 455 2.671963 GCGGAGGTTGGGGTGAAC 60.672 66.667 0.00 0.00 0.00 3.18
527 542 0.329596 AGCCTCAGCCCACCTTAAAG 59.670 55.000 0.00 0.00 41.25 1.85
539 554 2.752903 CACCTTAAAGTATGGGTGGTGC 59.247 50.000 0.00 0.00 43.69 5.01
540 555 2.377193 ACCTTAAAGTATGGGTGGTGCA 59.623 45.455 0.00 0.00 0.00 4.57
629 657 3.746492 CGAACTTTCCCGAAGAAACTGAT 59.254 43.478 0.00 0.00 39.60 2.90
632 660 4.714632 ACTTTCCCGAAGAAACTGATTCA 58.285 39.130 0.44 0.00 39.60 2.57
643 671 5.003804 AGAAACTGATTCATAAACAGCGGT 58.996 37.500 0.44 0.00 40.72 5.68
676 704 7.728847 AGAATTAACGTTTAAACCTTACCGT 57.271 32.000 5.91 3.26 0.00 4.83
849 877 0.108615 CGCCTCGTTTGTCTCATCCT 60.109 55.000 0.00 0.00 0.00 3.24
857 885 1.763968 TTGTCTCATCCTCGATCGGT 58.236 50.000 16.41 0.00 0.00 4.69
893 939 8.512956 CCTATATATTATGGGTATCTCCGTTCG 58.487 40.741 0.00 0.00 37.00 3.95
906 952 0.713883 CCGTTCGTTCTCCAACATCG 59.286 55.000 0.00 0.00 32.14 3.84
959 1041 0.617413 ATCACCTGACCAGCAAGAGG 59.383 55.000 0.00 0.00 0.00 3.69
970 1054 2.816672 CCAGCAAGAGGTTTCTTCTTCC 59.183 50.000 0.00 0.00 41.71 3.46
977 1064 1.903183 AGGTTTCTTCTTCCTCCTCCG 59.097 52.381 0.00 0.00 0.00 4.63
988 1075 0.250234 CCTCCTCCGCTGTTTCATCA 59.750 55.000 0.00 0.00 0.00 3.07
1248 1335 4.697756 GCGCTGCAGTACCACCCA 62.698 66.667 16.64 0.00 0.00 4.51
1260 1347 3.941188 CACCCAGACGTGTGCCCT 61.941 66.667 7.28 0.00 0.00 5.19
1364 1451 0.794981 CAGTACGACGCTCAGCTGAC 60.795 60.000 13.74 9.19 0.00 3.51
1365 1452 1.514443 GTACGACGCTCAGCTGACC 60.514 63.158 13.74 5.48 0.00 4.02
1398 1494 4.115199 AGGCCAGATGGGTTCGCC 62.115 66.667 5.01 0.00 39.65 5.54
1407 1503 3.384532 GGGTTCGCCAGGGACGTA 61.385 66.667 0.00 0.00 39.65 3.57
1413 1509 2.727392 CGCCAGGGACGTATGGGAA 61.727 63.158 13.95 0.00 37.05 3.97
1416 1512 1.146263 CAGGGACGTATGGGAAGCC 59.854 63.158 0.00 0.00 0.00 4.35
1461 1557 2.435938 GAACGGCGGCAGAATGGA 60.436 61.111 13.24 0.00 35.86 3.41
1464 1560 3.204827 CGGCGGCAGAATGGAAGG 61.205 66.667 10.53 0.00 35.86 3.46
1490 1586 2.101770 CGGCCGACGGTTCTAGAC 59.898 66.667 24.07 0.00 39.42 2.59
1497 1598 2.240040 CGACGGTTCTAGACTTGAACG 58.760 52.381 19.15 16.68 43.21 3.95
1573 1674 3.569873 CCAGTCTGGGGCGTTAAAT 57.430 52.632 11.46 0.00 32.67 1.40
1574 1675 2.702592 CCAGTCTGGGGCGTTAAATA 57.297 50.000 11.46 0.00 32.67 1.40
1600 1701 9.955208 ATTGTGTATGCATGTTTATGAGTAATG 57.045 29.630 10.16 0.00 36.36 1.90
1601 1702 7.416817 TGTGTATGCATGTTTATGAGTAATGC 58.583 34.615 10.16 0.00 36.36 3.56
1602 1703 7.282901 TGTGTATGCATGTTTATGAGTAATGCT 59.717 33.333 10.16 0.00 36.36 3.79
1603 1704 8.773645 GTGTATGCATGTTTATGAGTAATGCTA 58.226 33.333 10.16 0.00 36.36 3.49
1604 1705 8.773645 TGTATGCATGTTTATGAGTAATGCTAC 58.226 33.333 10.16 7.62 36.36 3.58
1605 1706 7.806409 ATGCATGTTTATGAGTAATGCTACA 57.194 32.000 0.00 0.00 36.36 2.74
1606 1707 7.015226 TGCATGTTTATGAGTAATGCTACAC 57.985 36.000 7.38 0.00 36.36 2.90
1607 1708 6.129393 GCATGTTTATGAGTAATGCTACACG 58.871 40.000 0.00 0.00 36.36 4.49
1608 1709 6.238103 GCATGTTTATGAGTAATGCTACACGT 60.238 38.462 0.00 0.00 36.36 4.49
1609 1710 7.042992 GCATGTTTATGAGTAATGCTACACGTA 60.043 37.037 0.00 0.00 36.36 3.57
1610 1711 7.745022 TGTTTATGAGTAATGCTACACGTAC 57.255 36.000 0.00 0.00 0.00 3.67
1611 1712 7.314393 TGTTTATGAGTAATGCTACACGTACA 58.686 34.615 0.00 0.00 0.00 2.90
1612 1713 7.813627 TGTTTATGAGTAATGCTACACGTACAA 59.186 33.333 0.00 0.00 0.00 2.41
1613 1714 8.649841 GTTTATGAGTAATGCTACACGTACAAA 58.350 33.333 0.00 0.00 0.00 2.83
1614 1715 6.642683 ATGAGTAATGCTACACGTACAAAC 57.357 37.500 0.00 0.00 0.00 2.93
1632 1733 6.740411 ACAAACGAGTTACAAGGTTTTACA 57.260 33.333 0.00 0.00 30.73 2.41
1633 1734 7.143514 ACAAACGAGTTACAAGGTTTTACAA 57.856 32.000 0.00 0.00 30.73 2.41
1634 1735 7.592051 ACAAACGAGTTACAAGGTTTTACAAA 58.408 30.769 0.00 0.00 30.73 2.83
1635 1736 7.538334 ACAAACGAGTTACAAGGTTTTACAAAC 59.462 33.333 0.00 0.00 30.73 2.93
1636 1737 6.740411 ACGAGTTACAAGGTTTTACAAACA 57.260 33.333 0.00 0.00 0.00 2.83
1637 1738 6.778108 ACGAGTTACAAGGTTTTACAAACAG 58.222 36.000 0.00 0.00 0.00 3.16
1638 1739 6.183360 ACGAGTTACAAGGTTTTACAAACAGG 60.183 38.462 0.00 0.00 0.00 4.00
1639 1740 6.459670 AGTTACAAGGTTTTACAAACAGGG 57.540 37.500 2.00 0.00 0.00 4.45
1640 1741 5.953548 AGTTACAAGGTTTTACAAACAGGGT 59.046 36.000 2.00 0.00 0.00 4.34
1641 1742 6.438108 AGTTACAAGGTTTTACAAACAGGGTT 59.562 34.615 2.00 0.00 0.00 4.11
1642 1743 7.614974 AGTTACAAGGTTTTACAAACAGGGTTA 59.385 33.333 2.00 0.00 0.00 2.85
1643 1744 6.854091 ACAAGGTTTTACAAACAGGGTTAA 57.146 33.333 2.00 0.00 0.00 2.01
1644 1745 7.426606 ACAAGGTTTTACAAACAGGGTTAAT 57.573 32.000 2.00 0.00 0.00 1.40
1645 1746 7.853299 ACAAGGTTTTACAAACAGGGTTAATT 58.147 30.769 2.00 0.00 0.00 1.40
1646 1747 8.322828 ACAAGGTTTTACAAACAGGGTTAATTT 58.677 29.630 2.00 0.00 0.00 1.82
1647 1748 8.608317 CAAGGTTTTACAAACAGGGTTAATTTG 58.392 33.333 2.00 0.00 38.89 2.32
1648 1749 8.080363 AGGTTTTACAAACAGGGTTAATTTGA 57.920 30.769 5.68 0.00 36.91 2.69
1649 1750 8.710239 AGGTTTTACAAACAGGGTTAATTTGAT 58.290 29.630 5.68 0.00 36.91 2.57
1650 1751 9.332502 GGTTTTACAAACAGGGTTAATTTGATT 57.667 29.630 5.68 0.00 36.91 2.57
1652 1753 8.894768 TTTACAAACAGGGTTAATTTGATTGG 57.105 30.769 5.68 0.00 36.91 3.16
1653 1754 6.493189 ACAAACAGGGTTAATTTGATTGGT 57.507 33.333 5.68 0.00 36.91 3.67
1654 1755 6.521162 ACAAACAGGGTTAATTTGATTGGTC 58.479 36.000 5.68 0.00 36.91 4.02
1655 1756 6.098982 ACAAACAGGGTTAATTTGATTGGTCA 59.901 34.615 5.68 0.00 36.91 4.02
1656 1757 6.739331 AACAGGGTTAATTTGATTGGTCAA 57.261 33.333 0.00 0.00 42.41 3.18
1657 1758 6.933514 ACAGGGTTAATTTGATTGGTCAAT 57.066 33.333 0.00 0.00 43.49 2.57
1658 1759 8.429237 AACAGGGTTAATTTGATTGGTCAATA 57.571 30.769 0.00 0.00 43.49 1.90
1659 1760 7.836842 ACAGGGTTAATTTGATTGGTCAATAC 58.163 34.615 0.00 0.00 43.49 1.89
1660 1761 7.453126 ACAGGGTTAATTTGATTGGTCAATACA 59.547 33.333 0.00 0.00 43.49 2.29
1661 1762 8.477256 CAGGGTTAATTTGATTGGTCAATACAT 58.523 33.333 0.00 0.00 43.49 2.29
1662 1763 8.477256 AGGGTTAATTTGATTGGTCAATACATG 58.523 33.333 0.00 0.00 43.49 3.21
1663 1764 7.710475 GGGTTAATTTGATTGGTCAATACATGG 59.290 37.037 0.00 0.00 43.49 3.66
1664 1765 7.710475 GGTTAATTTGATTGGTCAATACATGGG 59.290 37.037 0.00 0.00 43.49 4.00
1665 1766 5.874897 ATTTGATTGGTCAATACATGGGG 57.125 39.130 0.00 0.00 43.49 4.96
1666 1767 4.599720 TTGATTGGTCAATACATGGGGA 57.400 40.909 0.00 0.00 39.36 4.81
1667 1768 4.169059 TGATTGGTCAATACATGGGGAG 57.831 45.455 0.00 0.00 0.00 4.30
1668 1769 3.117550 TGATTGGTCAATACATGGGGAGG 60.118 47.826 0.00 0.00 0.00 4.30
1669 1770 0.550914 TGGTCAATACATGGGGAGGC 59.449 55.000 0.00 0.00 0.00 4.70
1670 1771 0.535102 GGTCAATACATGGGGAGGCG 60.535 60.000 0.00 0.00 0.00 5.52
1671 1772 0.535102 GTCAATACATGGGGAGGCGG 60.535 60.000 0.00 0.00 0.00 6.13
1672 1773 1.898574 CAATACATGGGGAGGCGGC 60.899 63.158 0.00 0.00 0.00 6.53
1673 1774 3.133365 AATACATGGGGAGGCGGCC 62.133 63.158 12.11 12.11 0.00 6.13
1686 1787 3.012722 CGGCCCACCCTCCCTAAA 61.013 66.667 0.00 0.00 0.00 1.85
1687 1788 2.608550 CGGCCCACCCTCCCTAAAA 61.609 63.158 0.00 0.00 0.00 1.52
1688 1789 1.778309 GGCCCACCCTCCCTAAAAA 59.222 57.895 0.00 0.00 0.00 1.94
1689 1790 0.338467 GGCCCACCCTCCCTAAAAAT 59.662 55.000 0.00 0.00 0.00 1.82
1690 1791 1.688311 GGCCCACCCTCCCTAAAAATC 60.688 57.143 0.00 0.00 0.00 2.17
1691 1792 1.006639 GCCCACCCTCCCTAAAAATCA 59.993 52.381 0.00 0.00 0.00 2.57
1692 1793 2.950418 GCCCACCCTCCCTAAAAATCAG 60.950 54.545 0.00 0.00 0.00 2.90
1693 1794 2.358195 CCCACCCTCCCTAAAAATCAGG 60.358 54.545 0.00 0.00 0.00 3.86
1702 1803 3.701664 CCTAAAAATCAGGGGAGCAAGT 58.298 45.455 0.00 0.00 0.00 3.16
1703 1804 4.089361 CCTAAAAATCAGGGGAGCAAGTT 58.911 43.478 0.00 0.00 0.00 2.66
1704 1805 4.528206 CCTAAAAATCAGGGGAGCAAGTTT 59.472 41.667 0.00 0.00 0.00 2.66
1705 1806 4.341366 AAAAATCAGGGGAGCAAGTTTG 57.659 40.909 0.00 0.00 0.00 2.93
1706 1807 2.683211 AATCAGGGGAGCAAGTTTGT 57.317 45.000 0.00 0.00 0.00 2.83
1707 1808 1.915141 ATCAGGGGAGCAAGTTTGTG 58.085 50.000 0.00 0.00 0.00 3.33
1708 1809 0.843309 TCAGGGGAGCAAGTTTGTGA 59.157 50.000 0.00 0.00 0.00 3.58
1709 1810 1.425066 TCAGGGGAGCAAGTTTGTGAT 59.575 47.619 0.00 0.00 0.00 3.06
1710 1811 2.158475 TCAGGGGAGCAAGTTTGTGATT 60.158 45.455 0.00 0.00 0.00 2.57
1711 1812 2.029649 CAGGGGAGCAAGTTTGTGATTG 60.030 50.000 0.00 0.00 0.00 2.67
1712 1813 1.273327 GGGGAGCAAGTTTGTGATTGG 59.727 52.381 0.00 0.00 0.00 3.16
1713 1814 1.963515 GGGAGCAAGTTTGTGATTGGT 59.036 47.619 0.00 0.00 39.67 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.605589 GGACTTGGGAAGGGTGTTCG 60.606 60.000 0.00 0.00 0.00 3.95
2 3 0.476771 TGGACTTGGGAAGGGTGTTC 59.523 55.000 0.00 0.00 0.00 3.18
4 5 0.478507 CTTGGACTTGGGAAGGGTGT 59.521 55.000 0.00 0.00 0.00 4.16
5 6 0.771127 TCTTGGACTTGGGAAGGGTG 59.229 55.000 0.00 0.00 0.00 4.61
6 7 0.771755 GTCTTGGACTTGGGAAGGGT 59.228 55.000 0.00 0.00 0.00 4.34
7 8 0.321653 CGTCTTGGACTTGGGAAGGG 60.322 60.000 0.00 0.00 0.00 3.95
8 9 0.685097 TCGTCTTGGACTTGGGAAGG 59.315 55.000 0.00 0.00 0.00 3.46
9 10 2.143925 GTTCGTCTTGGACTTGGGAAG 58.856 52.381 0.00 0.00 0.00 3.46
11 12 1.124780 TGTTCGTCTTGGACTTGGGA 58.875 50.000 0.00 0.00 0.00 4.37
12 13 1.873591 CTTGTTCGTCTTGGACTTGGG 59.126 52.381 0.00 0.00 0.00 4.12
13 14 1.264288 GCTTGTTCGTCTTGGACTTGG 59.736 52.381 0.00 0.00 0.00 3.61
14 15 1.939934 TGCTTGTTCGTCTTGGACTTG 59.060 47.619 0.00 0.00 0.00 3.16
15 16 2.325583 TGCTTGTTCGTCTTGGACTT 57.674 45.000 0.00 0.00 0.00 3.01
16 17 2.325583 TTGCTTGTTCGTCTTGGACT 57.674 45.000 0.00 0.00 0.00 3.85
17 18 3.003275 TGATTTGCTTGTTCGTCTTGGAC 59.997 43.478 0.00 0.00 0.00 4.02
18 19 3.210227 TGATTTGCTTGTTCGTCTTGGA 58.790 40.909 0.00 0.00 0.00 3.53
19 20 3.624326 TGATTTGCTTGTTCGTCTTGG 57.376 42.857 0.00 0.00 0.00 3.61
20 21 6.515043 AAAATGATTTGCTTGTTCGTCTTG 57.485 33.333 0.00 0.00 0.00 3.02
56 57 6.988580 TCCATGATGAGTTGATGACTTGTATC 59.011 38.462 0.00 0.00 39.19 2.24
70 71 6.305272 ACTTGTAATCTGTCCATGATGAGT 57.695 37.500 0.00 0.00 0.00 3.41
71 72 7.621428 AAACTTGTAATCTGTCCATGATGAG 57.379 36.000 0.00 0.00 0.00 2.90
72 73 7.448161 ACAAAACTTGTAATCTGTCCATGATGA 59.552 33.333 0.00 0.00 43.27 2.92
73 74 7.539710 CACAAAACTTGTAATCTGTCCATGATG 59.460 37.037 0.00 0.00 43.23 3.07
74 75 7.596494 CACAAAACTTGTAATCTGTCCATGAT 58.404 34.615 0.00 0.00 43.23 2.45
75 76 6.514870 GCACAAAACTTGTAATCTGTCCATGA 60.515 38.462 0.00 0.00 43.23 3.07
76 77 5.630680 GCACAAAACTTGTAATCTGTCCATG 59.369 40.000 0.00 0.00 43.23 3.66
77 78 5.278957 GGCACAAAACTTGTAATCTGTCCAT 60.279 40.000 0.00 0.00 43.23 3.41
78 79 4.037446 GGCACAAAACTTGTAATCTGTCCA 59.963 41.667 0.00 0.00 43.23 4.02
79 80 4.278419 AGGCACAAAACTTGTAATCTGTCC 59.722 41.667 0.00 0.00 43.23 4.02
80 81 5.215160 CAGGCACAAAACTTGTAATCTGTC 58.785 41.667 0.00 0.00 43.23 3.51
90 91 3.552068 GCGAATTACCAGGCACAAAACTT 60.552 43.478 0.00 0.00 0.00 2.66
184 186 8.216453 CCGCTTTCAGAAAAAGAAAATGTATTG 58.784 33.333 0.00 0.00 34.84 1.90
185 187 7.926018 ACCGCTTTCAGAAAAAGAAAATGTATT 59.074 29.630 0.00 0.00 34.84 1.89
207 210 0.388649 ACACATCTTCAGTCGACCGC 60.389 55.000 13.01 0.00 0.00 5.68
222 225 3.353029 CATGGCGCGGTGAACACA 61.353 61.111 8.83 0.00 0.00 3.72
223 226 3.353836 ACATGGCGCGGTGAACAC 61.354 61.111 16.23 0.00 0.00 3.32
298 301 7.143340 CAGTATAATCAGCCAATGTCAAATGG 58.857 38.462 4.10 4.10 39.80 3.16
313 316 4.346127 AGCTGTGAGATGGCAGTATAATCA 59.654 41.667 0.00 0.00 35.33 2.57
336 348 7.604927 ACCAATGCAACTCTAATAAAACGACTA 59.395 33.333 0.00 0.00 0.00 2.59
340 352 6.027749 GGACCAATGCAACTCTAATAAAACG 58.972 40.000 0.00 0.00 0.00 3.60
376 389 0.096281 TGATTTTTCATCGTCGCCGC 59.904 50.000 0.00 0.00 0.00 6.53
438 451 2.189833 CCCTCGTCTCGATGGTTCA 58.810 57.895 5.55 0.00 37.01 3.18
442 455 0.179026 TCCTACCCTCGTCTCGATGG 60.179 60.000 10.81 10.81 44.85 3.51
527 542 0.964860 TGTGCATGCACCACCCATAC 60.965 55.000 40.01 18.49 45.63 2.39
629 657 5.759506 TTTTTCAGACCGCTGTTTATGAA 57.240 34.783 0.00 2.04 42.84 2.57
713 741 2.032071 GGTGGTGGACCGGTGAAG 59.968 66.667 14.63 0.00 39.43 3.02
857 885 7.867921 ACCCATAATATATAGGCGATTGGAAA 58.132 34.615 0.00 0.00 0.00 3.13
893 939 1.017387 GGATGGCGATGTTGGAGAAC 58.983 55.000 0.00 0.00 0.00 3.01
906 952 2.981560 CTGTGTTGTGGCGGATGGC 61.982 63.158 0.00 0.00 42.51 4.40
959 1041 1.276705 AGCGGAGGAGGAAGAAGAAAC 59.723 52.381 0.00 0.00 0.00 2.78
970 1054 1.649664 CTGATGAAACAGCGGAGGAG 58.350 55.000 0.00 0.00 0.00 3.69
988 1075 0.108138 GTGTTCATGGACGGCTAGCT 60.108 55.000 15.72 0.00 0.00 3.32
996 1083 2.690778 GCTGGCGGTGTTCATGGAC 61.691 63.158 0.00 0.00 0.00 4.02
1398 1494 1.146263 GGCTTCCCATACGTCCCTG 59.854 63.158 0.00 0.00 0.00 4.45
1416 1512 3.716006 CGCAGCACGGACAACTGG 61.716 66.667 0.00 0.00 38.44 4.00
1479 1575 2.228343 CTCCGTTCAAGTCTAGAACCGT 59.772 50.000 0.00 0.00 41.72 4.83
1490 1586 3.000727 GGGTATGTTCACTCCGTTCAAG 58.999 50.000 0.00 0.00 0.00 3.02
1497 1598 2.093447 CAGACTGGGGTATGTTCACTCC 60.093 54.545 0.00 0.00 39.77 3.85
1574 1675 9.955208 CATTACTCATAAACATGCATACACAAT 57.045 29.630 0.00 0.00 0.00 2.71
1593 1694 5.109815 CGTTTGTACGTGTAGCATTACTC 57.890 43.478 0.00 0.00 42.72 2.59
1607 1708 7.683746 TGTAAAACCTTGTAACTCGTTTGTAC 58.316 34.615 0.00 0.00 0.00 2.90
1608 1709 7.840342 TGTAAAACCTTGTAACTCGTTTGTA 57.160 32.000 0.00 0.00 0.00 2.41
1609 1710 6.740411 TGTAAAACCTTGTAACTCGTTTGT 57.260 33.333 0.00 0.00 0.00 2.83
1610 1711 7.537991 TGTTTGTAAAACCTTGTAACTCGTTTG 59.462 33.333 0.71 0.00 0.00 2.93
1611 1712 7.592051 TGTTTGTAAAACCTTGTAACTCGTTT 58.408 30.769 0.71 0.00 0.00 3.60
1612 1713 7.143514 TGTTTGTAAAACCTTGTAACTCGTT 57.856 32.000 0.71 0.00 0.00 3.85
1613 1714 6.183360 CCTGTTTGTAAAACCTTGTAACTCGT 60.183 38.462 0.71 0.00 0.00 4.18
1614 1715 6.196571 CCTGTTTGTAAAACCTTGTAACTCG 58.803 40.000 0.71 0.00 0.00 4.18
1615 1716 6.095860 ACCCTGTTTGTAAAACCTTGTAACTC 59.904 38.462 0.71 0.00 0.00 3.01
1616 1717 5.953548 ACCCTGTTTGTAAAACCTTGTAACT 59.046 36.000 0.71 0.00 0.00 2.24
1617 1718 6.211587 ACCCTGTTTGTAAAACCTTGTAAC 57.788 37.500 0.71 0.00 0.00 2.50
1618 1719 6.854091 AACCCTGTTTGTAAAACCTTGTAA 57.146 33.333 0.71 0.00 0.00 2.41
1619 1720 7.951347 TTAACCCTGTTTGTAAAACCTTGTA 57.049 32.000 0.71 0.00 0.00 2.41
1620 1721 6.854091 TTAACCCTGTTTGTAAAACCTTGT 57.146 33.333 0.71 0.00 0.00 3.16
1621 1722 8.608317 CAAATTAACCCTGTTTGTAAAACCTTG 58.392 33.333 0.71 0.00 0.00 3.61
1622 1723 8.541234 TCAAATTAACCCTGTTTGTAAAACCTT 58.459 29.630 0.71 0.00 35.09 3.50
1623 1724 8.080363 TCAAATTAACCCTGTTTGTAAAACCT 57.920 30.769 0.71 0.00 35.09 3.50
1624 1725 8.896320 ATCAAATTAACCCTGTTTGTAAAACC 57.104 30.769 0.71 0.00 35.09 3.27
1626 1727 9.331282 CCAATCAAATTAACCCTGTTTGTAAAA 57.669 29.630 0.00 0.00 35.09 1.52
1627 1728 8.487028 ACCAATCAAATTAACCCTGTTTGTAAA 58.513 29.630 0.00 0.00 35.09 2.01
1628 1729 8.024145 ACCAATCAAATTAACCCTGTTTGTAA 57.976 30.769 0.00 0.00 35.09 2.41
1629 1730 7.287927 TGACCAATCAAATTAACCCTGTTTGTA 59.712 33.333 0.00 0.00 35.09 2.41
1630 1731 6.098982 TGACCAATCAAATTAACCCTGTTTGT 59.901 34.615 0.00 0.00 35.09 2.83
1631 1732 6.520272 TGACCAATCAAATTAACCCTGTTTG 58.480 36.000 0.00 0.00 34.90 2.93
1632 1733 6.739331 TGACCAATCAAATTAACCCTGTTT 57.261 33.333 0.00 0.00 0.00 2.83
1633 1734 6.739331 TTGACCAATCAAATTAACCCTGTT 57.261 33.333 0.00 0.00 41.99 3.16
1646 1747 3.117550 CCTCCCCATGTATTGACCAATCA 60.118 47.826 0.00 0.00 32.50 2.57
1647 1748 3.490348 CCTCCCCATGTATTGACCAATC 58.510 50.000 0.00 0.00 32.50 2.67
1648 1749 2.424812 GCCTCCCCATGTATTGACCAAT 60.425 50.000 0.64 0.64 34.93 3.16
1649 1750 1.064017 GCCTCCCCATGTATTGACCAA 60.064 52.381 0.00 0.00 0.00 3.67
1650 1751 0.550914 GCCTCCCCATGTATTGACCA 59.449 55.000 0.00 0.00 0.00 4.02
1651 1752 0.535102 CGCCTCCCCATGTATTGACC 60.535 60.000 0.00 0.00 0.00 4.02
1652 1753 0.535102 CCGCCTCCCCATGTATTGAC 60.535 60.000 0.00 0.00 0.00 3.18
1653 1754 1.836391 CCGCCTCCCCATGTATTGA 59.164 57.895 0.00 0.00 0.00 2.57
1654 1755 1.898574 GCCGCCTCCCCATGTATTG 60.899 63.158 0.00 0.00 0.00 1.90
1655 1756 2.515901 GCCGCCTCCCCATGTATT 59.484 61.111 0.00 0.00 0.00 1.89
1656 1757 3.570212 GGCCGCCTCCCCATGTAT 61.570 66.667 0.71 0.00 0.00 2.29
1669 1770 2.144859 TTTTTAGGGAGGGTGGGCCG 62.145 60.000 0.00 0.00 34.97 6.13
1670 1771 0.338467 ATTTTTAGGGAGGGTGGGCC 59.662 55.000 0.00 0.00 0.00 5.80
1671 1772 1.006639 TGATTTTTAGGGAGGGTGGGC 59.993 52.381 0.00 0.00 0.00 5.36
1672 1773 2.358195 CCTGATTTTTAGGGAGGGTGGG 60.358 54.545 0.00 0.00 0.00 4.61
1673 1774 3.018423 CCTGATTTTTAGGGAGGGTGG 57.982 52.381 0.00 0.00 0.00 4.61
1681 1782 3.701664 ACTTGCTCCCCTGATTTTTAGG 58.298 45.455 0.00 0.00 35.01 2.69
1682 1783 5.011023 ACAAACTTGCTCCCCTGATTTTTAG 59.989 40.000 0.00 0.00 0.00 1.85
1683 1784 4.898861 ACAAACTTGCTCCCCTGATTTTTA 59.101 37.500 0.00 0.00 0.00 1.52
1684 1785 3.711190 ACAAACTTGCTCCCCTGATTTTT 59.289 39.130 0.00 0.00 0.00 1.94
1685 1786 3.070015 CACAAACTTGCTCCCCTGATTTT 59.930 43.478 0.00 0.00 0.00 1.82
1686 1787 2.629617 CACAAACTTGCTCCCCTGATTT 59.370 45.455 0.00 0.00 0.00 2.17
1687 1788 2.158475 TCACAAACTTGCTCCCCTGATT 60.158 45.455 0.00 0.00 0.00 2.57
1688 1789 1.425066 TCACAAACTTGCTCCCCTGAT 59.575 47.619 0.00 0.00 0.00 2.90
1689 1790 0.843309 TCACAAACTTGCTCCCCTGA 59.157 50.000 0.00 0.00 0.00 3.86
1690 1791 1.915141 ATCACAAACTTGCTCCCCTG 58.085 50.000 0.00 0.00 0.00 4.45
1691 1792 2.242043 CAATCACAAACTTGCTCCCCT 58.758 47.619 0.00 0.00 0.00 4.79
1692 1793 1.273327 CCAATCACAAACTTGCTCCCC 59.727 52.381 0.00 0.00 0.00 4.81
1693 1794 1.963515 ACCAATCACAAACTTGCTCCC 59.036 47.619 0.00 0.00 0.00 4.30
1694 1795 3.733443 AACCAATCACAAACTTGCTCC 57.267 42.857 0.00 0.00 0.00 4.70
1695 1796 5.438761 ACTAACCAATCACAAACTTGCTC 57.561 39.130 0.00 0.00 0.00 4.26
1696 1797 6.017109 CACTACTAACCAATCACAAACTTGCT 60.017 38.462 0.00 0.00 0.00 3.91
1697 1798 6.142817 CACTACTAACCAATCACAAACTTGC 58.857 40.000 0.00 0.00 0.00 4.01
1698 1799 7.259290 ACACTACTAACCAATCACAAACTTG 57.741 36.000 0.00 0.00 0.00 3.16
1699 1800 7.201785 CCAACACTACTAACCAATCACAAACTT 60.202 37.037 0.00 0.00 0.00 2.66
1700 1801 6.262273 CCAACACTACTAACCAATCACAAACT 59.738 38.462 0.00 0.00 0.00 2.66
1701 1802 6.261381 TCCAACACTACTAACCAATCACAAAC 59.739 38.462 0.00 0.00 0.00 2.93
1702 1803 6.358178 TCCAACACTACTAACCAATCACAAA 58.642 36.000 0.00 0.00 0.00 2.83
1703 1804 5.931294 TCCAACACTACTAACCAATCACAA 58.069 37.500 0.00 0.00 0.00 3.33
1704 1805 5.554437 TCCAACACTACTAACCAATCACA 57.446 39.130 0.00 0.00 0.00 3.58
1705 1806 6.870971 TTTCCAACACTACTAACCAATCAC 57.129 37.500 0.00 0.00 0.00 3.06
1706 1807 9.173021 CATATTTCCAACACTACTAACCAATCA 57.827 33.333 0.00 0.00 0.00 2.57
1707 1808 8.129211 GCATATTTCCAACACTACTAACCAATC 58.871 37.037 0.00 0.00 0.00 2.67
1708 1809 7.068226 GGCATATTTCCAACACTACTAACCAAT 59.932 37.037 0.00 0.00 0.00 3.16
1709 1810 6.376018 GGCATATTTCCAACACTACTAACCAA 59.624 38.462 0.00 0.00 0.00 3.67
1710 1811 5.883673 GGCATATTTCCAACACTACTAACCA 59.116 40.000 0.00 0.00 0.00 3.67
1711 1812 5.298527 GGGCATATTTCCAACACTACTAACC 59.701 44.000 0.00 0.00 0.00 2.85
1712 1813 6.120220 AGGGCATATTTCCAACACTACTAAC 58.880 40.000 0.00 0.00 0.00 2.34
1713 1814 6.321821 AGGGCATATTTCCAACACTACTAA 57.678 37.500 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.