Multiple sequence alignment - TraesCS5A01G169900

Loading Multiple Alignment...

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 TraesCS5A01G169900 chr5A 100.000 2469 0 0 1 2469 362416235 362413767 0.000000e+00 4560
1 TraesCS5A01G169900 chr5A 97.740 177 4 0 1511 1687 71460381 71460205 3.080000e-79 305
2 TraesCS5A01G169900 chr5A 97.191 178 4 1 1511 1687 29678155 29678332 1.440000e-77 300
3 TraesCS5A01G169900 chr5A 96.089 179 5 2 1511 1689 101083279 101083455 8.640000e-75 291
4 TraesCS5A01G169900 chr5B 91.342 1513 82 27 17 1507 308924018 308922533 0.000000e+00 2023
5 TraesCS5A01G169900 chr5B 87.710 773 93 1 1697 2469 688808226 688807456 0.000000e+00 900
6 TraesCS5A01G169900 chr5B 92.271 207 11 3 1498 1700 92234882 92234677 3.110000e-74 289
7 TraesCS5A01G169900 chr5D 90.654 1530 70 29 17 1509 273115791 273114298 0.000000e+00 1965
8 TraesCS5A01G169900 chr1D 93.445 778 49 2 1693 2469 487966893 487966117 0.000000e+00 1153
9 TraesCS5A01G169900 chr2D 92.674 778 56 1 1693 2469 14856016 14855239 0.000000e+00 1120
10 TraesCS5A01G169900 chr2D 93.617 188 9 2 1511 1697 101884241 101884056 6.720000e-71 278
11 TraesCS5A01G169900 chrUn 91.062 772 68 1 1698 2469 259896789 259897559 0.000000e+00 1042
12 TraesCS5A01G169900 chr1B 91.062 772 68 1 1698 2469 666343486 666342716 0.000000e+00 1042
13 TraesCS5A01G169900 chr1B 90.231 778 75 1 1693 2469 14253140 14253917 0.000000e+00 1014
14 TraesCS5A01G169900 chr4B 89.119 772 84 0 1698 2469 574680127 574679356 0.000000e+00 961
15 TraesCS5A01G169900 chr7D 87.179 780 96 4 1693 2469 627284672 627283894 0.000000e+00 883
16 TraesCS5A01G169900 chr1A 87.035 779 98 3 1693 2469 510689344 510690121 0.000000e+00 876
17 TraesCS5A01G169900 chr6A 96.610 177 6 0 1511 1687 494463103 494463279 6.680000e-76 294
18 TraesCS5A01G169900 chr6A 95.000 180 9 0 1511 1690 537876440 537876261 1.450000e-72 283
19 TraesCS5A01G169900 chr7A 96.111 180 6 1 1511 1689 509467300 509467121 2.400000e-75 292
20 TraesCS5A01G169900 chr4A 95.028 181 7 2 1511 1690 100636537 100636358 1.450000e-72 283


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 TraesCS5A01G169900 chr5A 362413767 362416235 2468 True 4560 4560 100.000 1 2469 1 chr5A.!!$R2 2468
1 TraesCS5A01G169900 chr5B 308922533 308924018 1485 True 2023 2023 91.342 17 1507 1 chr5B.!!$R2 1490
2 TraesCS5A01G169900 chr5B 688807456 688808226 770 True 900 900 87.710 1697 2469 1 chr5B.!!$R3 772
3 TraesCS5A01G169900 chr5D 273114298 273115791 1493 True 1965 1965 90.654 17 1509 1 chr5D.!!$R1 1492
4 TraesCS5A01G169900 chr1D 487966117 487966893 776 True 1153 1153 93.445 1693 2469 1 chr1D.!!$R1 776
5 TraesCS5A01G169900 chr2D 14855239 14856016 777 True 1120 1120 92.674 1693 2469 1 chr2D.!!$R1 776
6 TraesCS5A01G169900 chrUn 259896789 259897559 770 False 1042 1042 91.062 1698 2469 1 chrUn.!!$F1 771
7 TraesCS5A01G169900 chr1B 666342716 666343486 770 True 1042 1042 91.062 1698 2469 1 chr1B.!!$R1 771
8 TraesCS5A01G169900 chr1B 14253140 14253917 777 False 1014 1014 90.231 1693 2469 1 chr1B.!!$F1 776
9 TraesCS5A01G169900 chr4B 574679356 574680127 771 True 961 961 89.119 1698 2469 1 chr4B.!!$R1 771
10 TraesCS5A01G169900 chr7D 627283894 627284672 778 True 883 883 87.179 1693 2469 1 chr7D.!!$R1 776
11 TraesCS5A01G169900 chr1A 510689344 510690121 777 False 876 876 87.035 1693 2469 1 chr1A.!!$F1 776

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
64 66 0.112218 ACCCACTGTATTTGCTGGCA 59.888 50.0 0.00 0.0 0.00 4.92 F
382 384 0.465705 GCAGGATCACCATCGAAGGA 59.534 55.0 14.76 0.0 38.94 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1085 1124 0.674895 AAGAAAGCTCGCCGCAAGAT 60.675 50.000 0.00 0.0 42.61 2.40 R
1774 1825 1.140375 GCAAGCATTAGCAGTGCCC 59.860 57.895 12.58 0.0 43.97 5.36 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 3.964411 CCATCCAGCCATGATACATGAT 58.036 45.455 12.46 0.00 0.00 2.45
25 26 4.898320 TCCAGCCATGATACATGATACAC 58.102 43.478 12.46 0.00 0.00 2.90
42 44 3.678056 ACACTGGCGAGTTTCTGATTA 57.322 42.857 0.00 0.00 0.00 1.75
48 50 3.504520 TGGCGAGTTTCTGATTAAAACCC 59.495 43.478 0.00 0.00 37.33 4.11
64 66 0.112218 ACCCACTGTATTTGCTGGCA 59.888 50.000 0.00 0.00 0.00 4.92
67 69 2.159198 CCCACTGTATTTGCTGGCAATC 60.159 50.000 8.86 4.30 35.70 2.67
68 70 2.478370 CCACTGTATTTGCTGGCAATCG 60.478 50.000 8.86 0.00 35.70 3.34
127 129 1.916777 GAGGGAAGGGTCCGGTTCA 60.917 63.158 0.00 0.00 46.04 3.18
130 132 2.046217 GAAGGGTCCGGTTCAGGC 60.046 66.667 0.00 0.00 0.00 4.85
382 384 0.465705 GCAGGATCACCATCGAAGGA 59.534 55.000 14.76 0.00 38.94 3.36
420 422 2.028658 TCCTGCTCATATCCAAGATCGC 60.029 50.000 0.00 0.00 0.00 4.58
432 434 1.600957 CAAGATCGCCATGGATGTGAC 59.399 52.381 18.40 0.82 0.00 3.67
555 557 1.305219 GCATTGTAACCGCTGGCTGA 61.305 55.000 0.00 0.00 0.00 4.26
565 567 1.499502 GCTGGCTGAAAAGCTCGAC 59.500 57.895 0.00 0.00 36.47 4.20
589 596 4.020543 AGGATCATATCGGTAGAGGAAGC 58.979 47.826 0.00 0.00 0.00 3.86
590 597 3.764434 GGATCATATCGGTAGAGGAAGCA 59.236 47.826 0.00 0.00 0.00 3.91
591 598 4.142271 GGATCATATCGGTAGAGGAAGCAG 60.142 50.000 0.00 0.00 0.00 4.24
592 599 2.558795 TCATATCGGTAGAGGAAGCAGC 59.441 50.000 0.00 0.00 0.00 5.25
593 600 2.067365 TATCGGTAGAGGAAGCAGCA 57.933 50.000 0.00 0.00 0.00 4.41
594 601 0.749649 ATCGGTAGAGGAAGCAGCAG 59.250 55.000 0.00 0.00 0.00 4.24
603 610 4.601084 AGAGGAAGCAGCAGTAGTAGTAA 58.399 43.478 0.00 0.00 0.00 2.24
607 614 6.130569 AGGAAGCAGCAGTAGTAGTAATAGT 58.869 40.000 0.00 0.00 0.00 2.12
610 617 7.229106 GGAAGCAGCAGTAGTAGTAATAGTAGT 59.771 40.741 0.00 0.00 0.00 2.73
613 620 8.431222 AGCAGCAGTAGTAGTAATAGTAGTAGT 58.569 37.037 0.00 0.00 0.00 2.73
661 668 3.120304 TGAGTCTGTATCGTGTTGTCGAG 60.120 47.826 0.00 0.00 43.00 4.04
727 739 5.118510 CCATTTGCGTTTTACTGTTTCCATC 59.881 40.000 0.00 0.00 0.00 3.51
728 740 3.907894 TGCGTTTTACTGTTTCCATCC 57.092 42.857 0.00 0.00 0.00 3.51
729 741 3.215151 TGCGTTTTACTGTTTCCATCCA 58.785 40.909 0.00 0.00 0.00 3.41
730 742 3.823873 TGCGTTTTACTGTTTCCATCCAT 59.176 39.130 0.00 0.00 0.00 3.41
780 792 1.487976 CCCAGACATGAGTAGCACCAT 59.512 52.381 0.00 0.00 0.00 3.55
858 870 4.012374 CCTCTGATGTTGCAACTGGTATT 58.988 43.478 28.61 8.06 0.00 1.89
859 871 5.185454 CCTCTGATGTTGCAACTGGTATTA 58.815 41.667 28.61 10.86 0.00 0.98
860 872 5.065218 CCTCTGATGTTGCAACTGGTATTAC 59.935 44.000 28.61 11.89 0.00 1.89
924 952 3.047796 GTTTCAACTTGCATGCACTGAG 58.952 45.455 22.58 18.06 0.00 3.35
927 955 0.870393 AACTTGCATGCACTGAGTCG 59.130 50.000 22.58 5.48 0.00 4.18
959 987 1.209019 AGCACTGATAACTGCTCCCTG 59.791 52.381 0.00 0.00 39.66 4.45
975 1003 3.906846 CTCCCTGCCTCCATAAATAGACT 59.093 47.826 0.00 0.00 0.00 3.24
1043 1082 2.224523 TGTGTCACCTTCCATTCACCTC 60.225 50.000 0.00 0.00 0.00 3.85
1045 1084 2.224523 TGTCACCTTCCATTCACCTCAC 60.225 50.000 0.00 0.00 0.00 3.51
1050 1089 2.240667 CCTTCCATTCACCTCACCTCAT 59.759 50.000 0.00 0.00 0.00 2.90
1116 1155 1.876156 AGCTTTCTTTCACCAGAAGCG 59.124 47.619 0.00 0.00 34.22 4.68
1151 1190 0.875908 CGATGGCGATCATGACGGTT 60.876 55.000 9.52 0.00 40.82 4.44
1358 1398 6.524101 ACAGAAAGAGAGAGATAGGTGTTC 57.476 41.667 0.00 0.00 0.00 3.18
1382 1426 4.072839 CTGTGGATGGATGGATGATTGAG 58.927 47.826 0.00 0.00 0.00 3.02
1509 1560 7.305763 GCTTGTACAAACAAATTACGGAAACAG 60.306 37.037 10.03 0.00 44.79 3.16
1510 1561 7.086230 TGTACAAACAAATTACGGAAACAGT 57.914 32.000 0.00 0.00 30.91 3.55
1511 1562 6.967767 TGTACAAACAAATTACGGAAACAGTG 59.032 34.615 0.00 0.00 30.91 3.66
1512 1563 5.956642 ACAAACAAATTACGGAAACAGTGT 58.043 33.333 0.00 0.00 0.00 3.55
1513 1564 6.031471 ACAAACAAATTACGGAAACAGTGTC 58.969 36.000 0.00 0.00 0.00 3.67
1514 1565 6.127842 ACAAACAAATTACGGAAACAGTGTCT 60.128 34.615 0.00 0.00 0.00 3.41
1515 1566 7.066043 ACAAACAAATTACGGAAACAGTGTCTA 59.934 33.333 0.00 0.00 0.00 2.59
1516 1567 7.556733 AACAAATTACGGAAACAGTGTCTAA 57.443 32.000 0.00 0.00 0.00 2.10
1517 1568 7.739498 ACAAATTACGGAAACAGTGTCTAAT 57.261 32.000 0.00 0.00 0.00 1.73
1518 1569 8.161699 ACAAATTACGGAAACAGTGTCTAATT 57.838 30.769 0.00 0.00 0.00 1.40
1519 1570 8.287503 ACAAATTACGGAAACAGTGTCTAATTC 58.712 33.333 0.00 0.00 0.00 2.17
1520 1571 7.972832 AATTACGGAAACAGTGTCTAATTCA 57.027 32.000 0.00 0.00 0.00 2.57
1521 1572 6.774354 TTACGGAAACAGTGTCTAATTCAC 57.226 37.500 0.00 0.00 36.22 3.18
1522 1573 4.699637 ACGGAAACAGTGTCTAATTCACA 58.300 39.130 0.00 0.00 38.16 3.58
1523 1574 5.305585 ACGGAAACAGTGTCTAATTCACAT 58.694 37.500 0.00 0.00 38.16 3.21
1524 1575 5.408604 ACGGAAACAGTGTCTAATTCACATC 59.591 40.000 0.00 0.00 38.16 3.06
1525 1576 5.639506 CGGAAACAGTGTCTAATTCACATCT 59.360 40.000 0.00 0.00 38.16 2.90
1526 1577 6.811665 CGGAAACAGTGTCTAATTCACATCTA 59.188 38.462 0.00 0.00 38.16 1.98
1527 1578 7.009631 CGGAAACAGTGTCTAATTCACATCTAG 59.990 40.741 0.00 0.00 38.16 2.43
1528 1579 8.035394 GGAAACAGTGTCTAATTCACATCTAGA 58.965 37.037 0.00 0.00 38.16 2.43
1529 1580 9.593134 GAAACAGTGTCTAATTCACATCTAGAT 57.407 33.333 0.00 0.00 38.16 1.98
1530 1581 8.939201 AACAGTGTCTAATTCACATCTAGATG 57.061 34.615 27.63 27.63 44.15 2.90
1557 1608 8.934023 TTTTTAAGGATGTCACATCTAACCTT 57.066 30.769 17.46 14.42 39.21 3.50
1558 1609 8.561738 TTTTAAGGATGTCACATCTAACCTTC 57.438 34.615 17.46 0.00 37.44 3.46
1559 1610 4.762289 AGGATGTCACATCTAACCTTCC 57.238 45.455 17.46 0.00 0.00 3.46
1560 1611 4.104086 AGGATGTCACATCTAACCTTCCA 58.896 43.478 17.46 0.00 0.00 3.53
1561 1612 4.080863 AGGATGTCACATCTAACCTTCCAC 60.081 45.833 17.46 0.00 0.00 4.02
1562 1613 4.323485 GGATGTCACATCTAACCTTCCACA 60.323 45.833 17.46 0.00 0.00 4.17
1563 1614 4.698201 TGTCACATCTAACCTTCCACAA 57.302 40.909 0.00 0.00 0.00 3.33
1564 1615 4.641396 TGTCACATCTAACCTTCCACAAG 58.359 43.478 0.00 0.00 0.00 3.16
1565 1616 4.102524 TGTCACATCTAACCTTCCACAAGT 59.897 41.667 0.00 0.00 0.00 3.16
1566 1617 5.305902 TGTCACATCTAACCTTCCACAAGTA 59.694 40.000 0.00 0.00 0.00 2.24
1567 1618 6.013725 TGTCACATCTAACCTTCCACAAGTAT 60.014 38.462 0.00 0.00 0.00 2.12
1568 1619 7.179516 TGTCACATCTAACCTTCCACAAGTATA 59.820 37.037 0.00 0.00 0.00 1.47
1569 1620 8.204836 GTCACATCTAACCTTCCACAAGTATAT 58.795 37.037 0.00 0.00 0.00 0.86
1570 1621 9.429109 TCACATCTAACCTTCCACAAGTATATA 57.571 33.333 0.00 0.00 0.00 0.86
1574 1625 9.726438 ATCTAACCTTCCACAAGTATATAATGC 57.274 33.333 0.00 0.00 0.00 3.56
1575 1626 8.710239 TCTAACCTTCCACAAGTATATAATGCA 58.290 33.333 0.00 0.00 0.00 3.96
1576 1627 9.507329 CTAACCTTCCACAAGTATATAATGCAT 57.493 33.333 0.00 0.00 0.00 3.96
1577 1628 7.986085 ACCTTCCACAAGTATATAATGCATC 57.014 36.000 0.00 0.00 0.00 3.91
1578 1629 7.517320 ACCTTCCACAAGTATATAATGCATCA 58.483 34.615 0.00 0.00 0.00 3.07
1579 1630 7.998383 ACCTTCCACAAGTATATAATGCATCAA 59.002 33.333 0.00 0.00 0.00 2.57
1580 1631 8.292448 CCTTCCACAAGTATATAATGCATCAAC 58.708 37.037 0.00 0.00 0.00 3.18
1581 1632 8.744568 TTCCACAAGTATATAATGCATCAACA 57.255 30.769 0.00 0.00 0.00 3.33
1582 1633 8.744568 TCCACAAGTATATAATGCATCAACAA 57.255 30.769 0.00 0.00 0.00 2.83
1583 1634 8.839343 TCCACAAGTATATAATGCATCAACAAG 58.161 33.333 0.00 0.00 0.00 3.16
1584 1635 8.839343 CCACAAGTATATAATGCATCAACAAGA 58.161 33.333 0.00 0.00 0.00 3.02
1630 1681 7.639113 AAAAATAGACCACAAACAGAGTGAA 57.361 32.000 0.00 0.00 39.30 3.18
1631 1682 7.639113 AAAATAGACCACAAACAGAGTGAAA 57.361 32.000 0.00 0.00 39.30 2.69
1632 1683 7.639113 AAATAGACCACAAACAGAGTGAAAA 57.361 32.000 0.00 0.00 39.30 2.29
1633 1684 7.823745 AATAGACCACAAACAGAGTGAAAAT 57.176 32.000 0.00 0.00 39.30 1.82
1634 1685 5.757850 AGACCACAAACAGAGTGAAAATC 57.242 39.130 0.00 0.00 39.30 2.17
1635 1686 5.192927 AGACCACAAACAGAGTGAAAATCA 58.807 37.500 0.00 0.00 39.30 2.57
1636 1687 5.297776 AGACCACAAACAGAGTGAAAATCAG 59.702 40.000 0.00 0.00 39.30 2.90
1637 1688 4.949856 ACCACAAACAGAGTGAAAATCAGT 59.050 37.500 0.00 0.00 39.30 3.41
1638 1689 5.418840 ACCACAAACAGAGTGAAAATCAGTT 59.581 36.000 0.00 0.00 42.40 3.16
1640 1691 7.122055 ACCACAAACAGAGTGAAAATCAGTTTA 59.878 33.333 0.00 0.00 46.29 2.01
1641 1692 7.645340 CCACAAACAGAGTGAAAATCAGTTTAG 59.355 37.037 0.00 0.00 46.29 1.85
1642 1693 8.397906 CACAAACAGAGTGAAAATCAGTTTAGA 58.602 33.333 0.00 0.00 46.29 2.10
1643 1694 9.125026 ACAAACAGAGTGAAAATCAGTTTAGAT 57.875 29.630 0.00 0.00 46.29 1.98
1644 1695 9.390795 CAAACAGAGTGAAAATCAGTTTAGATG 57.609 33.333 0.00 0.00 46.29 2.90
1645 1696 8.682936 AACAGAGTGAAAATCAGTTTAGATGT 57.317 30.769 0.00 0.00 37.35 3.06
1646 1697 8.092521 ACAGAGTGAAAATCAGTTTAGATGTG 57.907 34.615 0.00 0.00 30.01 3.21
1647 1698 7.173907 ACAGAGTGAAAATCAGTTTAGATGTGG 59.826 37.037 0.00 0.00 30.01 4.17
1648 1699 6.150140 AGAGTGAAAATCAGTTTAGATGTGGC 59.850 38.462 0.00 0.00 30.01 5.01
1649 1700 5.769662 AGTGAAAATCAGTTTAGATGTGGCA 59.230 36.000 0.00 0.00 0.00 4.92
1650 1701 6.435277 AGTGAAAATCAGTTTAGATGTGGCAT 59.565 34.615 0.00 0.00 0.00 4.40
1651 1702 7.611467 AGTGAAAATCAGTTTAGATGTGGCATA 59.389 33.333 0.00 0.00 0.00 3.14
1652 1703 8.243426 GTGAAAATCAGTTTAGATGTGGCATAA 58.757 33.333 0.00 0.00 0.00 1.90
1653 1704 8.243426 TGAAAATCAGTTTAGATGTGGCATAAC 58.757 33.333 0.00 0.00 0.00 1.89
1654 1705 7.944729 AAATCAGTTTAGATGTGGCATAACT 57.055 32.000 0.00 0.00 0.00 2.24
1655 1706 9.461312 AAAATCAGTTTAGATGTGGCATAACTA 57.539 29.630 0.00 0.00 0.00 2.24
1656 1707 9.632638 AAATCAGTTTAGATGTGGCATAACTAT 57.367 29.630 2.25 0.00 0.00 2.12
1657 1708 8.613060 ATCAGTTTAGATGTGGCATAACTATG 57.387 34.615 2.25 0.00 36.78 2.23
1658 1709 7.564793 TCAGTTTAGATGTGGCATAACTATGT 58.435 34.615 2.25 0.00 36.11 2.29
1659 1710 7.710907 TCAGTTTAGATGTGGCATAACTATGTC 59.289 37.037 2.25 0.00 38.72 3.06
1660 1711 7.495606 CAGTTTAGATGTGGCATAACTATGTCA 59.504 37.037 2.25 0.00 45.17 3.58
1671 1722 8.815912 TGGCATAACTATGTCACATCTATATGT 58.184 33.333 0.00 0.00 42.78 2.29
1672 1723 9.091784 GGCATAACTATGTCACATCTATATGTG 57.908 37.037 13.60 13.60 46.15 3.21
1673 1724 9.645059 GCATAACTATGTCACATCTATATGTGT 57.355 33.333 17.81 5.02 45.68 3.72
1684 1735 7.753309 ACATCTATATGTGTCCTAGACAGAC 57.247 40.000 0.00 0.00 44.79 3.51
1685 1736 6.717540 ACATCTATATGTGTCCTAGACAGACC 59.282 42.308 0.00 0.00 44.79 3.85
1686 1737 5.632118 TCTATATGTGTCCTAGACAGACCC 58.368 45.833 0.00 0.00 43.57 4.46
1687 1738 2.930109 ATGTGTCCTAGACAGACCCT 57.070 50.000 0.00 0.00 43.57 4.34
1688 1739 2.696526 TGTGTCCTAGACAGACCCTT 57.303 50.000 0.00 0.00 43.57 3.95
1689 1740 3.820195 TGTGTCCTAGACAGACCCTTA 57.180 47.619 0.00 0.00 43.57 2.69
1690 1741 3.428532 TGTGTCCTAGACAGACCCTTAC 58.571 50.000 0.00 0.00 43.57 2.34
1691 1742 2.422832 GTGTCCTAGACAGACCCTTACG 59.577 54.545 0.00 0.00 43.57 3.18
1692 1743 2.022934 GTCCTAGACAGACCCTTACGG 58.977 57.143 0.00 0.00 32.87 4.02
1693 1744 1.918262 TCCTAGACAGACCCTTACGGA 59.082 52.381 0.00 0.00 34.64 4.69
1694 1745 2.309755 TCCTAGACAGACCCTTACGGAA 59.690 50.000 0.00 0.00 34.64 4.30
1695 1746 3.094572 CCTAGACAGACCCTTACGGAAA 58.905 50.000 0.00 0.00 34.64 3.13
1723 1774 5.363292 TCTCCCTGAGAATCTTGATCTTGAG 59.637 44.000 0.00 0.00 35.59 3.02
1774 1825 3.058639 GTGCTTCTTTCTGTAAGCCAGTG 60.059 47.826 4.75 0.00 46.01 3.66
1807 1858 0.954452 CTTGCAGAAGAACACCCACC 59.046 55.000 0.00 0.00 0.00 4.61
1813 1864 1.343465 AGAAGAACACCCACCGTACTG 59.657 52.381 0.00 0.00 0.00 2.74
1826 1877 1.822990 CCGTACTGACTAAGGCCAAGA 59.177 52.381 5.01 0.00 0.00 3.02
1848 1899 3.274288 CTTGTGGCTTATCTCACCCTTC 58.726 50.000 0.00 0.00 33.29 3.46
1942 1994 6.039270 GTGCCTATGTGATACTATTGCCAAAA 59.961 38.462 0.00 0.00 0.00 2.44
1983 2036 6.428295 TGGGTTCCAAGAAACTAAAAGAGAA 58.572 36.000 0.00 0.00 0.00 2.87
2002 2055 5.013599 AGAGAAGTTATTGCTGAGGGTTTCT 59.986 40.000 0.00 0.00 0.00 2.52
2046 2099 6.588719 AATGACTATGCTTGGCACTTTTTA 57.411 33.333 0.00 0.00 43.04 1.52
2088 2141 3.580895 GTGGGATCCTTTTGGGCTTTAAA 59.419 43.478 12.58 0.00 40.87 1.52
2328 2382 2.754186 AACTGAGAAAAGCAGTGGGCAT 60.754 45.455 0.00 0.00 45.27 4.40
2329 2383 4.866858 AACTGAGAAAAGCAGTGGGCATG 61.867 47.826 0.00 0.00 45.27 4.06
2400 2454 5.600069 GGCCCTGATGGAAATTTCTATTTCT 59.400 40.000 17.05 0.00 45.81 2.52
2451 2505 3.505293 AGAGCTCTCCAATTTTTGCTGTC 59.495 43.478 11.45 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.428413 TCATGTATCATGGCTGGATGG 57.572 47.619 9.39 0.00 0.00 3.51
1 2 5.353400 GTGTATCATGTATCATGGCTGGATG 59.647 44.000 9.39 0.00 0.00 3.51
3 4 4.594491 AGTGTATCATGTATCATGGCTGGA 59.406 41.667 9.39 0.00 0.00 3.86
4 5 4.694037 CAGTGTATCATGTATCATGGCTGG 59.306 45.833 9.39 0.00 0.00 4.85
5 6 4.694037 CCAGTGTATCATGTATCATGGCTG 59.306 45.833 9.39 9.48 0.00 4.85
6 7 4.805272 GCCAGTGTATCATGTATCATGGCT 60.805 45.833 17.35 1.81 45.60 4.75
7 8 3.438087 GCCAGTGTATCATGTATCATGGC 59.562 47.826 12.36 12.36 43.33 4.40
8 9 3.681417 CGCCAGTGTATCATGTATCATGG 59.319 47.826 9.39 0.00 0.00 3.66
9 10 4.559153 TCGCCAGTGTATCATGTATCATG 58.441 43.478 3.65 3.65 0.00 3.07
10 11 4.281941 ACTCGCCAGTGTATCATGTATCAT 59.718 41.667 0.00 0.00 0.00 2.45
11 12 3.636764 ACTCGCCAGTGTATCATGTATCA 59.363 43.478 0.00 0.00 0.00 2.15
12 13 4.244425 ACTCGCCAGTGTATCATGTATC 57.756 45.455 0.00 0.00 0.00 2.24
13 14 4.672587 AACTCGCCAGTGTATCATGTAT 57.327 40.909 0.00 0.00 31.06 2.29
14 15 4.159693 AGAAACTCGCCAGTGTATCATGTA 59.840 41.667 0.00 0.00 31.06 2.29
15 16 3.055819 AGAAACTCGCCAGTGTATCATGT 60.056 43.478 0.00 0.00 31.06 3.21
21 22 3.678056 AATCAGAAACTCGCCAGTGTA 57.322 42.857 0.00 0.00 31.06 2.90
25 26 4.379499 GGGTTTTAATCAGAAACTCGCCAG 60.379 45.833 0.00 0.00 37.22 4.85
42 44 2.037121 GCCAGCAAATACAGTGGGTTTT 59.963 45.455 0.00 0.00 0.00 2.43
48 50 2.789208 CGATTGCCAGCAAATACAGTG 58.211 47.619 9.44 0.00 39.55 3.66
64 66 0.178068 AGTCCATAACCTGCGCGATT 59.822 50.000 12.10 0.00 0.00 3.34
67 69 1.206745 CGTAGTCCATAACCTGCGCG 61.207 60.000 0.00 0.00 0.00 6.86
68 70 1.488261 GCGTAGTCCATAACCTGCGC 61.488 60.000 0.00 0.00 36.28 6.09
127 129 1.994507 CTTCATCCGACGACGAGCCT 61.995 60.000 9.28 0.00 42.66 4.58
130 132 0.586748 CGACTTCATCCGACGACGAG 60.587 60.000 9.28 0.00 42.66 4.18
286 288 1.767681 GTCTCCATGATCTTGGCCTCT 59.232 52.381 20.32 0.00 36.66 3.69
391 393 9.678260 ATCTTGGATATGAGCAGGAAATAATAC 57.322 33.333 0.00 0.00 0.00 1.89
392 394 9.896645 GATCTTGGATATGAGCAGGAAATAATA 57.103 33.333 0.00 0.00 0.00 0.98
393 395 7.551974 CGATCTTGGATATGAGCAGGAAATAAT 59.448 37.037 0.00 0.00 0.00 1.28
432 434 0.604780 GGCACTCCGATCATCATGGG 60.605 60.000 0.00 0.00 0.00 4.00
555 557 5.336055 CCGATATGATCCTAGTCGAGCTTTT 60.336 44.000 8.02 0.00 34.46 2.27
565 567 5.298276 GCTTCCTCTACCGATATGATCCTAG 59.702 48.000 0.00 0.00 0.00 3.02
610 617 9.086336 CGGTTATTAGAATCCGTTGTTTTACTA 57.914 33.333 0.00 0.00 38.45 1.82
613 620 7.818930 ACTCGGTTATTAGAATCCGTTGTTTTA 59.181 33.333 0.00 0.00 42.95 1.52
620 627 4.643784 ACTCACTCGGTTATTAGAATCCGT 59.356 41.667 0.00 0.00 42.95 4.69
713 725 8.235092 ATGAGAAGCATGGATGGAAACAGTAAA 61.235 37.037 0.00 0.00 39.05 2.01
729 741 0.627451 TTCCCTGCCATGAGAAGCAT 59.373 50.000 0.00 0.00 38.56 3.79
730 742 0.405198 TTTCCCTGCCATGAGAAGCA 59.595 50.000 0.00 0.00 37.46 3.91
780 792 9.454859 ACTGATGATTGATACGATACATAGAGA 57.545 33.333 0.00 0.00 0.00 3.10
858 870 9.179909 CAGGTAAACACCAAATACATAATGGTA 57.820 33.333 0.00 0.00 45.45 3.25
860 872 8.287439 TCAGGTAAACACCAAATACATAATGG 57.713 34.615 0.00 0.00 40.16 3.16
874 886 6.638468 CAGCAGATTCTTTTTCAGGTAAACAC 59.362 38.462 0.00 0.00 0.00 3.32
879 896 5.702670 CAGACAGCAGATTCTTTTTCAGGTA 59.297 40.000 0.00 0.00 0.00 3.08
880 897 4.518211 CAGACAGCAGATTCTTTTTCAGGT 59.482 41.667 0.00 0.00 0.00 4.00
882 899 5.686159 ACAGACAGCAGATTCTTTTTCAG 57.314 39.130 0.00 0.00 0.00 3.02
883 900 6.095300 TGAAACAGACAGCAGATTCTTTTTCA 59.905 34.615 8.23 8.23 42.27 2.69
884 901 6.498304 TGAAACAGACAGCAGATTCTTTTTC 58.502 36.000 0.00 0.00 38.32 2.29
889 917 4.712476 AGTTGAAACAGACAGCAGATTCT 58.288 39.130 0.00 0.00 0.00 2.40
890 918 5.210715 CAAGTTGAAACAGACAGCAGATTC 58.789 41.667 0.00 0.00 0.00 2.52
924 952 1.377202 TGCTTGGCCAAGATCCGAC 60.377 57.895 42.96 26.33 40.79 4.79
927 955 0.322816 TCAGTGCTTGGCCAAGATCC 60.323 55.000 42.96 28.97 40.79 3.36
1043 1082 2.295909 GCTAGCTAGGTGAGATGAGGTG 59.704 54.545 22.10 0.00 0.00 4.00
1045 1084 2.591923 TGCTAGCTAGGTGAGATGAGG 58.408 52.381 22.10 0.00 0.00 3.86
1050 1089 3.020274 CTCTGTTGCTAGCTAGGTGAGA 58.980 50.000 22.10 7.61 0.00 3.27
1085 1124 0.674895 AAGAAAGCTCGCCGCAAGAT 60.675 50.000 0.00 0.00 42.61 2.40
1097 1136 1.068954 CCGCTTCTGGTGAAAGAAAGC 60.069 52.381 0.00 0.00 35.79 3.51
1358 1398 3.503800 ATCATCCATCCATCCACAGTG 57.496 47.619 0.00 0.00 0.00 3.66
1382 1426 3.428870 GTCACGTACATACTGCATATGGC 59.571 47.826 4.56 0.00 44.51 4.40
1468 1519 9.765795 GTTTGTACAAGCTGATAGTAGGAATAT 57.234 33.333 14.51 0.00 0.00 1.28
1479 1530 6.205853 TCCGTAATTTGTTTGTACAAGCTGAT 59.794 34.615 21.06 12.76 44.56 2.90
1483 1534 6.472808 TGTTTCCGTAATTTGTTTGTACAAGC 59.527 34.615 14.87 14.87 44.56 4.01
1489 1540 5.956642 ACACTGTTTCCGTAATTTGTTTGT 58.043 33.333 0.00 0.00 0.00 2.83
1532 1583 8.934023 AAGGTTAGATGTGACATCCTTAAAAA 57.066 30.769 21.05 4.81 32.96 1.94
1533 1584 7.610305 GGAAGGTTAGATGTGACATCCTTAAAA 59.390 37.037 21.05 6.42 34.55 1.52
1534 1585 7.110155 GGAAGGTTAGATGTGACATCCTTAAA 58.890 38.462 21.05 8.69 34.55 1.52
1535 1586 6.214615 TGGAAGGTTAGATGTGACATCCTTAA 59.785 38.462 21.05 11.73 34.55 1.85
1536 1587 5.724370 TGGAAGGTTAGATGTGACATCCTTA 59.276 40.000 21.05 6.22 34.55 2.69
1537 1588 4.536090 TGGAAGGTTAGATGTGACATCCTT 59.464 41.667 21.05 17.24 36.67 3.36
1538 1589 4.080863 GTGGAAGGTTAGATGTGACATCCT 60.081 45.833 21.05 9.66 0.00 3.24
1539 1590 4.192317 GTGGAAGGTTAGATGTGACATCC 58.808 47.826 21.05 7.40 0.00 3.51
1540 1591 4.832248 TGTGGAAGGTTAGATGTGACATC 58.168 43.478 17.46 17.46 0.00 3.06
1541 1592 4.908601 TGTGGAAGGTTAGATGTGACAT 57.091 40.909 0.00 0.00 0.00 3.06
1542 1593 4.102524 ACTTGTGGAAGGTTAGATGTGACA 59.897 41.667 0.00 0.00 32.95 3.58
1543 1594 4.642429 ACTTGTGGAAGGTTAGATGTGAC 58.358 43.478 0.00 0.00 32.95 3.67
1544 1595 4.974645 ACTTGTGGAAGGTTAGATGTGA 57.025 40.909 0.00 0.00 32.95 3.58
1548 1599 9.726438 GCATTATATACTTGTGGAAGGTTAGAT 57.274 33.333 0.00 0.00 32.95 1.98
1549 1600 8.710239 TGCATTATATACTTGTGGAAGGTTAGA 58.290 33.333 0.00 0.00 32.95 2.10
1550 1601 8.902540 TGCATTATATACTTGTGGAAGGTTAG 57.097 34.615 0.00 0.00 32.95 2.34
1551 1602 9.502091 GATGCATTATATACTTGTGGAAGGTTA 57.498 33.333 0.00 0.00 32.95 2.85
1552 1603 7.998383 TGATGCATTATATACTTGTGGAAGGTT 59.002 33.333 0.00 0.00 32.95 3.50
1553 1604 7.517320 TGATGCATTATATACTTGTGGAAGGT 58.483 34.615 0.00 0.00 32.95 3.50
1554 1605 7.984422 TGATGCATTATATACTTGTGGAAGG 57.016 36.000 0.00 0.00 32.95 3.46
1555 1606 8.839343 TGTTGATGCATTATATACTTGTGGAAG 58.161 33.333 0.00 0.00 35.07 3.46
1556 1607 8.744568 TGTTGATGCATTATATACTTGTGGAA 57.255 30.769 0.00 0.00 0.00 3.53
1557 1608 8.744568 TTGTTGATGCATTATATACTTGTGGA 57.255 30.769 0.00 0.00 0.00 4.02
1558 1609 8.839343 TCTTGTTGATGCATTATATACTTGTGG 58.161 33.333 0.00 0.00 0.00 4.17
1606 1657 7.639113 TTCACTCTGTTTGTGGTCTATTTTT 57.361 32.000 0.00 0.00 36.21 1.94
1607 1658 7.639113 TTTCACTCTGTTTGTGGTCTATTTT 57.361 32.000 0.00 0.00 36.21 1.82
1608 1659 7.639113 TTTTCACTCTGTTTGTGGTCTATTT 57.361 32.000 0.00 0.00 36.21 1.40
1609 1660 7.502226 TGATTTTCACTCTGTTTGTGGTCTATT 59.498 33.333 0.00 0.00 36.21 1.73
1610 1661 6.998074 TGATTTTCACTCTGTTTGTGGTCTAT 59.002 34.615 0.00 0.00 36.21 1.98
1611 1662 6.353323 TGATTTTCACTCTGTTTGTGGTCTA 58.647 36.000 0.00 0.00 36.21 2.59
1612 1663 5.192927 TGATTTTCACTCTGTTTGTGGTCT 58.807 37.500 0.00 0.00 36.21 3.85
1613 1664 5.066505 ACTGATTTTCACTCTGTTTGTGGTC 59.933 40.000 0.00 0.00 36.21 4.02
1614 1665 4.949856 ACTGATTTTCACTCTGTTTGTGGT 59.050 37.500 0.00 0.00 36.21 4.16
1615 1666 5.505173 ACTGATTTTCACTCTGTTTGTGG 57.495 39.130 0.00 0.00 36.21 4.17
1616 1667 8.397906 TCTAAACTGATTTTCACTCTGTTTGTG 58.602 33.333 14.59 9.55 41.71 3.33
1617 1668 8.506168 TCTAAACTGATTTTCACTCTGTTTGT 57.494 30.769 14.59 0.00 41.71 2.83
1618 1669 9.390795 CATCTAAACTGATTTTCACTCTGTTTG 57.609 33.333 14.59 7.92 41.71 2.93
1619 1670 9.125026 ACATCTAAACTGATTTTCACTCTGTTT 57.875 29.630 11.33 11.33 43.11 2.83
1620 1671 8.562892 CACATCTAAACTGATTTTCACTCTGTT 58.437 33.333 0.00 0.00 36.66 3.16
1621 1672 7.173907 CCACATCTAAACTGATTTTCACTCTGT 59.826 37.037 0.00 0.00 0.00 3.41
1622 1673 7.524912 CCACATCTAAACTGATTTTCACTCTG 58.475 38.462 0.00 0.00 0.00 3.35
1623 1674 6.150140 GCCACATCTAAACTGATTTTCACTCT 59.850 38.462 0.00 0.00 0.00 3.24
1624 1675 6.072508 TGCCACATCTAAACTGATTTTCACTC 60.073 38.462 0.00 0.00 0.00 3.51
1625 1676 5.769662 TGCCACATCTAAACTGATTTTCACT 59.230 36.000 0.00 0.00 0.00 3.41
1626 1677 6.012658 TGCCACATCTAAACTGATTTTCAC 57.987 37.500 0.00 0.00 0.00 3.18
1627 1678 6.839124 ATGCCACATCTAAACTGATTTTCA 57.161 33.333 0.00 0.00 0.00 2.69
1628 1679 8.462016 AGTTATGCCACATCTAAACTGATTTTC 58.538 33.333 0.00 0.00 0.00 2.29
1629 1680 8.353423 AGTTATGCCACATCTAAACTGATTTT 57.647 30.769 0.00 0.00 0.00 1.82
1630 1681 7.944729 AGTTATGCCACATCTAAACTGATTT 57.055 32.000 0.00 0.00 0.00 2.17
1631 1682 9.060347 CATAGTTATGCCACATCTAAACTGATT 57.940 33.333 5.05 0.00 0.00 2.57
1632 1683 8.213679 ACATAGTTATGCCACATCTAAACTGAT 58.786 33.333 0.00 0.00 37.19 2.90
1633 1684 7.564793 ACATAGTTATGCCACATCTAAACTGA 58.435 34.615 0.00 0.00 37.19 3.41
1634 1685 7.495606 TGACATAGTTATGCCACATCTAAACTG 59.504 37.037 0.00 0.00 37.19 3.16
1635 1686 7.495934 GTGACATAGTTATGCCACATCTAAACT 59.504 37.037 12.00 0.00 43.64 2.66
1636 1687 7.279981 TGTGACATAGTTATGCCACATCTAAAC 59.720 37.037 14.64 0.00 46.98 2.01
1637 1688 7.334858 TGTGACATAGTTATGCCACATCTAAA 58.665 34.615 14.64 0.00 46.98 1.85
1638 1689 6.883744 TGTGACATAGTTATGCCACATCTAA 58.116 36.000 14.64 0.00 46.98 2.10
1639 1690 6.478512 TGTGACATAGTTATGCCACATCTA 57.521 37.500 14.64 0.00 46.98 1.98
1640 1691 5.357742 TGTGACATAGTTATGCCACATCT 57.642 39.130 14.64 0.00 46.98 2.90
1644 1695 9.091784 CATATAGATGTGACATAGTTATGCCAC 57.908 37.037 10.49 10.49 44.20 5.01
1645 1696 8.815912 ACATATAGATGTGACATAGTTATGCCA 58.184 33.333 1.31 0.00 44.90 4.92
1661 1712 6.151985 GGGTCTGTCTAGGACACATATAGATG 59.848 46.154 0.00 0.00 37.67 2.90
1662 1713 6.046168 AGGGTCTGTCTAGGACACATATAGAT 59.954 42.308 3.18 0.00 39.36 1.98
1663 1714 5.372959 AGGGTCTGTCTAGGACACATATAGA 59.627 44.000 3.18 0.00 39.36 1.98
1664 1715 5.636123 AGGGTCTGTCTAGGACACATATAG 58.364 45.833 3.18 0.00 39.36 1.31
1665 1716 5.664815 AGGGTCTGTCTAGGACACATATA 57.335 43.478 3.18 0.00 39.36 0.86
1666 1717 4.544564 AGGGTCTGTCTAGGACACATAT 57.455 45.455 3.18 0.00 39.36 1.78
1667 1718 4.332683 AAGGGTCTGTCTAGGACACATA 57.667 45.455 3.18 0.00 39.36 2.29
1668 1719 2.930109 AGGGTCTGTCTAGGACACAT 57.070 50.000 3.18 0.00 39.36 3.21
1669 1720 2.696526 AAGGGTCTGTCTAGGACACA 57.303 50.000 3.18 0.00 39.36 3.72
1670 1721 2.422832 CGTAAGGGTCTGTCTAGGACAC 59.577 54.545 0.00 0.00 37.67 3.67
1671 1722 2.719739 CGTAAGGGTCTGTCTAGGACA 58.280 52.381 0.43 0.43 40.50 4.02
1686 1737 4.081642 TCTCAGGGAGAACATTTCCGTAAG 60.082 45.833 0.00 0.00 35.59 2.34
1687 1738 3.835978 TCTCAGGGAGAACATTTCCGTAA 59.164 43.478 0.00 0.00 35.59 3.18
1688 1739 3.437213 TCTCAGGGAGAACATTTCCGTA 58.563 45.455 0.00 0.00 35.59 4.02
1689 1740 2.257207 TCTCAGGGAGAACATTTCCGT 58.743 47.619 0.00 0.00 35.59 4.69
1690 1741 3.334583 TTCTCAGGGAGAACATTTCCG 57.665 47.619 4.64 0.00 42.78 4.30
1723 1774 7.120726 ACAGGTGTGCTAACTAAATCATTAACC 59.879 37.037 0.00 0.00 0.00 2.85
1774 1825 1.140375 GCAAGCATTAGCAGTGCCC 59.860 57.895 12.58 0.00 43.97 5.36
1784 1835 1.615392 GGGTGTTCTTCTGCAAGCATT 59.385 47.619 0.00 0.00 0.00 3.56
1807 1858 2.492484 AGTCTTGGCCTTAGTCAGTACG 59.508 50.000 3.32 0.00 0.00 3.67
1813 1864 2.427506 CCACAAGTCTTGGCCTTAGTC 58.572 52.381 16.85 0.00 34.12 2.59
1826 1877 2.269940 AGGGTGAGATAAGCCACAAGT 58.730 47.619 0.00 0.00 40.33 3.16
1875 1927 4.907269 CCAAGGCCCCTAATATTCCAAATT 59.093 41.667 0.00 0.00 0.00 1.82
1983 2036 4.985538 TGAAGAAACCCTCAGCAATAACT 58.014 39.130 0.00 0.00 0.00 2.24
2028 2081 4.737054 CAGGTAAAAAGTGCCAAGCATAG 58.263 43.478 0.00 0.00 41.91 2.23
2046 2099 2.774234 ACCAGCAGTATTATCAGCAGGT 59.226 45.455 0.00 0.00 41.29 4.00
2139 2193 9.553064 CCATCAGTCTTATTTTTGATAGTAGCT 57.447 33.333 0.00 0.00 0.00 3.32
2235 2289 5.865552 AGCAACATTCAAAGTATCATGCAAC 59.134 36.000 0.00 0.00 33.89 4.17
2277 2331 6.661805 TCCTAACTAAATTGAAATCCCCACAC 59.338 38.462 0.00 0.00 0.00 3.82
2328 2382 7.514721 AGAGGAAGGTAGTTTGTTGATTAACA 58.485 34.615 0.00 0.00 44.66 2.41
2329 2383 7.981102 AGAGGAAGGTAGTTTGTTGATTAAC 57.019 36.000 0.00 0.00 37.32 2.01
2334 2388 8.215050 TCATTAAAGAGGAAGGTAGTTTGTTGA 58.785 33.333 0.00 0.00 0.00 3.18
2400 2454 9.931698 TTATTAGACCAGGTGAAGACTCTATTA 57.068 33.333 0.00 0.00 0.00 0.98


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

AutoCloner maintained by Alex Coulton.