Multiple sequence alignment - TraesCS1B01G240800

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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 TraesCS1B01G240800 chr1B 100.000 2376 0 0 1 2376 428615071 428617446 0.000000e+00 4388
1 TraesCS1B01G240800 chr1B 96.418 670 8 3 1 656 134724831 134724164 0.000000e+00 1090
2 TraesCS1B01G240800 chr1B 93.388 121 4 2 1505 1621 428638205 428638325 2.430000e-40 176
3 TraesCS1B01G240800 chr1A 96.379 856 24 4 645 1493 397083959 397084814 0.000000e+00 1402
4 TraesCS1B01G240800 chr1A 92.117 647 46 4 1 643 290209511 290210156 0.000000e+00 907
5 TraesCS1B01G240800 chr4A 98.765 648 8 0 1 648 742720343 742719696 0.000000e+00 1153
6 TraesCS1B01G240800 chr7B 98.605 645 9 0 1 645 337363980 337363336 0.000000e+00 1142
7 TraesCS1B01G240800 chr7B 91.489 705 54 4 1673 2376 705324839 705324140 0.000000e+00 965
8 TraesCS1B01G240800 chrUn 98.140 645 12 0 1 645 36768806 36768162 0.000000e+00 1125
9 TraesCS1B01G240800 chrUn 96.206 659 9 2 1 645 41158076 41158732 0.000000e+00 1064
10 TraesCS1B01G240800 chr3B 96.067 661 10 4 1 646 52348140 52348799 0.000000e+00 1062
11 TraesCS1B01G240800 chr3B 92.827 711 42 4 1667 2376 739218010 739218712 0.000000e+00 1022
12 TraesCS1B01G240800 chr3B 92.308 715 53 2 1664 2376 605290838 605291552 0.000000e+00 1014
13 TraesCS1B01G240800 chr5D 93.036 718 42 2 1667 2376 199004065 199004782 0.000000e+00 1042
14 TraesCS1B01G240800 chr5D 91.271 653 51 5 1 648 432163590 432162939 0.000000e+00 885
15 TraesCS1B01G240800 chr6B 93.099 710 40 4 1668 2376 712054338 712053637 0.000000e+00 1031
16 TraesCS1B01G240800 chr3D 92.618 718 45 2 1667 2376 179917902 179918619 0.000000e+00 1026
17 TraesCS1B01G240800 chr3D 91.185 658 49 8 1 651 550600514 550599859 0.000000e+00 885
18 TraesCS1B01G240800 chr3A 92.587 715 39 6 1664 2376 489307550 489306848 0.000000e+00 1014
19 TraesCS1B01G240800 chr7A 92.405 711 45 5 1667 2376 33528009 33527307 0.000000e+00 1005
20 TraesCS1B01G240800 chr2D 90.153 721 40 13 1663 2376 591386425 591387121 0.000000e+00 909
21 TraesCS1B01G240800 chr1D 94.326 564 16 3 647 1210 316236201 316236748 0.000000e+00 850
22 TraesCS1B01G240800 chr1D 96.928 293 8 1 1202 1493 316243969 316244261 7.630000e-135 490
23 TraesCS1B01G240800 chr1D 92.727 165 4 1 1505 1661 316602276 316602440 5.110000e-57 231
24 TraesCS1B01G240800 chr2A 91.791 402 29 2 1976 2376 385354907 385354509 7.420000e-155 556


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 TraesCS1B01G240800 chr1B 428615071 428617446 2375 False 4388 4388 100.000 1 2376 1 chr1B.!!$F1 2375
1 TraesCS1B01G240800 chr1B 134724164 134724831 667 True 1090 1090 96.418 1 656 1 chr1B.!!$R1 655
2 TraesCS1B01G240800 chr1A 397083959 397084814 855 False 1402 1402 96.379 645 1493 1 chr1A.!!$F2 848
3 TraesCS1B01G240800 chr1A 290209511 290210156 645 False 907 907 92.117 1 643 1 chr1A.!!$F1 642
4 TraesCS1B01G240800 chr4A 742719696 742720343 647 True 1153 1153 98.765 1 648 1 chr4A.!!$R1 647
5 TraesCS1B01G240800 chr7B 337363336 337363980 644 True 1142 1142 98.605 1 645 1 chr7B.!!$R1 644
6 TraesCS1B01G240800 chr7B 705324140 705324839 699 True 965 965 91.489 1673 2376 1 chr7B.!!$R2 703
7 TraesCS1B01G240800 chrUn 36768162 36768806 644 True 1125 1125 98.140 1 645 1 chrUn.!!$R1 644
8 TraesCS1B01G240800 chrUn 41158076 41158732 656 False 1064 1064 96.206 1 645 1 chrUn.!!$F1 644
9 TraesCS1B01G240800 chr3B 52348140 52348799 659 False 1062 1062 96.067 1 646 1 chr3B.!!$F1 645
10 TraesCS1B01G240800 chr3B 739218010 739218712 702 False 1022 1022 92.827 1667 2376 1 chr3B.!!$F3 709
11 TraesCS1B01G240800 chr3B 605290838 605291552 714 False 1014 1014 92.308 1664 2376 1 chr3B.!!$F2 712
12 TraesCS1B01G240800 chr5D 199004065 199004782 717 False 1042 1042 93.036 1667 2376 1 chr5D.!!$F1 709
13 TraesCS1B01G240800 chr5D 432162939 432163590 651 True 885 885 91.271 1 648 1 chr5D.!!$R1 647
14 TraesCS1B01G240800 chr6B 712053637 712054338 701 True 1031 1031 93.099 1668 2376 1 chr6B.!!$R1 708
15 TraesCS1B01G240800 chr3D 179917902 179918619 717 False 1026 1026 92.618 1667 2376 1 chr3D.!!$F1 709
16 TraesCS1B01G240800 chr3D 550599859 550600514 655 True 885 885 91.185 1 651 1 chr3D.!!$R1 650
17 TraesCS1B01G240800 chr3A 489306848 489307550 702 True 1014 1014 92.587 1664 2376 1 chr3A.!!$R1 712
18 TraesCS1B01G240800 chr7A 33527307 33528009 702 True 1005 1005 92.405 1667 2376 1 chr7A.!!$R1 709
19 TraesCS1B01G240800 chr2D 591386425 591387121 696 False 909 909 90.153 1663 2376 1 chr2D.!!$F1 713
20 TraesCS1B01G240800 chr1D 316236201 316236748 547 False 850 850 94.326 647 1210 1 chr1D.!!$F1 563

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
77 79 0.461135 GTAAGCGTAATGGACCCGGA 59.539 55.0 0.73 0.0 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1627 1653 0.036388 GTCGCCTGAGGATTTGTCCA 60.036 55.0 0.65 0.0 0.0 4.02 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
77 79 0.461135 GTAAGCGTAATGGACCCGGA 59.539 55.000 0.73 0.00 0.00 5.14
687 707 4.293662 AGGCGATCTTCTTCTTCCTTTT 57.706 40.909 0.00 0.00 0.00 2.27
690 710 4.216472 GGCGATCTTCTTCTTCCTTTTGTT 59.784 41.667 0.00 0.00 0.00 2.83
716 736 2.334946 GCGAGGCAATCAGGTGCAA 61.335 57.895 0.00 0.00 46.81 4.08
722 742 1.603678 GGCAATCAGGTGCAACTGTTG 60.604 52.381 30.13 28.92 46.81 3.33
921 941 3.462678 GGCGAGAGGGGGAGTCAC 61.463 72.222 0.00 0.00 0.00 3.67
922 942 2.680352 GCGAGAGGGGGAGTCACA 60.680 66.667 0.00 0.00 0.00 3.58
1060 1080 7.107542 TCTTATGGTTGGACAATGTAAGTACC 58.892 38.462 0.00 0.00 0.00 3.34
1147 1173 6.946229 ATTATCAATGTAATAGGTCGTCGC 57.054 37.500 0.00 0.00 0.00 5.19
1249 1275 5.617252 ACCGTGAAATTTTGTCTTCCTAGA 58.383 37.500 0.00 0.00 0.00 2.43
1267 1293 9.892130 CTTCCTAGAAATTGTACATCTAAAGGT 57.108 33.333 11.19 0.00 0.00 3.50
1309 1335 1.743252 GTGCTACTGCTGCCTCACC 60.743 63.158 0.00 0.00 40.48 4.02
1510 1536 3.895232 TGAAATGGACTCAGTAGCTCC 57.105 47.619 0.00 0.00 0.00 4.70
1511 1537 3.173151 TGAAATGGACTCAGTAGCTCCA 58.827 45.455 0.00 0.00 37.34 3.86
1512 1538 3.776969 TGAAATGGACTCAGTAGCTCCAT 59.223 43.478 0.00 0.00 41.47 3.41
1513 1539 4.225942 TGAAATGGACTCAGTAGCTCCATT 59.774 41.667 8.01 8.01 45.48 3.16
1514 1540 4.851639 AATGGACTCAGTAGCTCCATTT 57.148 40.909 8.01 0.00 43.52 2.32
1515 1541 3.895232 TGGACTCAGTAGCTCCATTTC 57.105 47.619 0.00 0.00 31.81 2.17
1516 1542 3.173151 TGGACTCAGTAGCTCCATTTCA 58.827 45.455 0.00 0.00 31.81 2.69
1517 1543 3.055819 TGGACTCAGTAGCTCCATTTCAC 60.056 47.826 0.00 0.00 31.81 3.18
1518 1544 3.196685 GGACTCAGTAGCTCCATTTCACT 59.803 47.826 0.00 0.00 0.00 3.41
1519 1545 4.323104 GGACTCAGTAGCTCCATTTCACTT 60.323 45.833 0.00 0.00 0.00 3.16
1520 1546 4.826556 ACTCAGTAGCTCCATTTCACTTC 58.173 43.478 0.00 0.00 0.00 3.01
1521 1547 4.187694 CTCAGTAGCTCCATTTCACTTCC 58.812 47.826 0.00 0.00 0.00 3.46
1522 1548 3.582647 TCAGTAGCTCCATTTCACTTCCA 59.417 43.478 0.00 0.00 0.00 3.53
1523 1549 3.937706 CAGTAGCTCCATTTCACTTCCAG 59.062 47.826 0.00 0.00 0.00 3.86
1524 1550 3.584848 AGTAGCTCCATTTCACTTCCAGT 59.415 43.478 0.00 0.00 0.00 4.00
1526 1552 2.107204 AGCTCCATTTCACTTCCAGTGT 59.893 45.455 3.87 0.00 46.03 3.55
1527 1553 2.485814 GCTCCATTTCACTTCCAGTGTC 59.514 50.000 3.87 0.00 46.03 3.67
1528 1554 3.077359 CTCCATTTCACTTCCAGTGTCC 58.923 50.000 3.87 0.00 46.03 4.02
1529 1555 2.162681 CCATTTCACTTCCAGTGTCCC 58.837 52.381 3.87 0.00 46.03 4.46
1530 1556 2.488891 CCATTTCACTTCCAGTGTCCCA 60.489 50.000 3.87 0.00 46.03 4.37
1531 1557 2.341846 TTTCACTTCCAGTGTCCCAC 57.658 50.000 3.87 0.00 46.03 4.61
1532 1558 0.105964 TTCACTTCCAGTGTCCCACG 59.894 55.000 3.87 0.00 46.03 4.94
1533 1559 1.961277 CACTTCCAGTGTCCCACGC 60.961 63.158 0.00 0.00 41.19 5.34
1534 1560 2.738521 CTTCCAGTGTCCCACGCG 60.739 66.667 3.53 3.53 39.64 6.01
1535 1561 4.980805 TTCCAGTGTCCCACGCGC 62.981 66.667 5.73 0.00 39.64 6.86
1538 1564 4.710695 CAGTGTCCCACGCGCGTA 62.711 66.667 37.24 18.77 39.64 4.42
1539 1565 4.712425 AGTGTCCCACGCGCGTAC 62.712 66.667 37.24 29.47 39.64 3.67
1540 1566 4.712425 GTGTCCCACGCGCGTACT 62.712 66.667 37.24 11.15 0.00 2.73
1541 1567 3.980989 TGTCCCACGCGCGTACTT 61.981 61.111 37.24 10.68 0.00 2.24
1542 1568 3.475774 GTCCCACGCGCGTACTTG 61.476 66.667 37.24 23.02 0.00 3.16
1543 1569 4.728102 TCCCACGCGCGTACTTGG 62.728 66.667 37.24 30.42 0.00 3.61
1544 1570 4.728102 CCCACGCGCGTACTTGGA 62.728 66.667 37.24 0.00 0.00 3.53
1545 1571 3.475774 CCACGCGCGTACTTGGAC 61.476 66.667 37.24 0.00 0.00 4.02
1546 1572 3.823421 CACGCGCGTACTTGGACG 61.823 66.667 37.24 17.08 45.70 4.79
1547 1573 4.332637 ACGCGCGTACTTGGACGT 62.333 61.111 37.08 4.68 44.74 4.34
1548 1574 2.202336 CGCGCGTACTTGGACGTA 60.202 61.111 24.19 0.00 44.74 3.57
1549 1575 2.491271 CGCGCGTACTTGGACGTAC 61.491 63.158 24.19 0.00 44.74 3.67
1550 1576 1.442520 GCGCGTACTTGGACGTACA 60.443 57.895 8.43 0.00 44.74 2.90
1551 1577 1.668253 GCGCGTACTTGGACGTACAC 61.668 60.000 8.43 0.00 44.74 2.90
1552 1578 0.110056 CGCGTACTTGGACGTACACT 60.110 55.000 0.00 0.00 44.74 3.55
1553 1579 1.334054 GCGTACTTGGACGTACACTG 58.666 55.000 0.00 0.00 44.74 3.66
1554 1580 1.334054 CGTACTTGGACGTACACTGC 58.666 55.000 0.00 0.00 39.71 4.40
1555 1581 1.068748 CGTACTTGGACGTACACTGCT 60.069 52.381 0.00 0.00 39.71 4.24
1556 1582 2.325761 GTACTTGGACGTACACTGCTG 58.674 52.381 0.00 0.00 39.56 4.41
1557 1583 0.600255 ACTTGGACGTACACTGCTGC 60.600 55.000 0.00 0.00 0.00 5.25
1558 1584 0.319900 CTTGGACGTACACTGCTGCT 60.320 55.000 0.00 0.00 0.00 4.24
1559 1585 0.105964 TTGGACGTACACTGCTGCTT 59.894 50.000 0.00 0.00 0.00 3.91
1560 1586 0.319555 TGGACGTACACTGCTGCTTC 60.320 55.000 0.00 0.00 0.00 3.86
1561 1587 0.319555 GGACGTACACTGCTGCTTCA 60.320 55.000 0.00 0.00 0.00 3.02
1562 1588 1.497991 GACGTACACTGCTGCTTCAA 58.502 50.000 0.00 0.00 0.00 2.69
1563 1589 1.192534 GACGTACACTGCTGCTTCAAC 59.807 52.381 0.00 0.00 0.00 3.18
1564 1590 0.512952 CGTACACTGCTGCTTCAACC 59.487 55.000 0.00 0.00 0.00 3.77
1565 1591 0.512952 GTACACTGCTGCTTCAACCG 59.487 55.000 0.00 0.00 0.00 4.44
1566 1592 1.227999 TACACTGCTGCTTCAACCGC 61.228 55.000 0.00 0.00 0.00 5.68
1567 1593 3.349006 ACTGCTGCTTCAACCGCG 61.349 61.111 0.00 0.00 0.00 6.46
1568 1594 3.349006 CTGCTGCTTCAACCGCGT 61.349 61.111 4.92 0.00 0.00 6.01
1569 1595 3.584250 CTGCTGCTTCAACCGCGTG 62.584 63.158 4.92 0.00 0.00 5.34
1571 1597 3.648982 CTGCTTCAACCGCGTGCA 61.649 61.111 4.92 4.76 0.00 4.57
1572 1598 2.969806 CTGCTTCAACCGCGTGCAT 61.970 57.895 4.92 0.00 33.02 3.96
1573 1599 2.502510 GCTTCAACCGCGTGCATG 60.503 61.111 4.92 0.09 0.00 4.06
1574 1600 2.502510 CTTCAACCGCGTGCATGC 60.503 61.111 21.27 21.27 0.00 4.06
1575 1601 3.252665 CTTCAACCGCGTGCATGCA 62.253 57.895 29.23 18.46 34.15 3.96
1576 1602 2.531927 CTTCAACCGCGTGCATGCAT 62.532 55.000 29.23 14.85 34.15 3.96
1577 1603 2.799488 TTCAACCGCGTGCATGCATG 62.799 55.000 31.36 31.36 36.13 4.06
1593 1619 2.109609 CATGCATGCATTGGTACGAC 57.890 50.000 30.32 0.00 33.90 4.34
1594 1620 0.657312 ATGCATGCATTGGTACGACG 59.343 50.000 27.46 0.00 31.82 5.12
1595 1621 0.672091 TGCATGCATTGGTACGACGT 60.672 50.000 18.46 5.52 0.00 4.34
1596 1622 0.247655 GCATGCATTGGTACGACGTG 60.248 55.000 14.21 0.00 0.00 4.49
1597 1623 1.355005 CATGCATTGGTACGACGTGA 58.645 50.000 11.56 0.00 0.00 4.35
1598 1624 1.324435 CATGCATTGGTACGACGTGAG 59.676 52.381 11.56 0.00 0.00 3.51
1599 1625 1.011968 TGCATTGGTACGACGTGAGC 61.012 55.000 11.56 6.03 0.00 4.26
1600 1626 1.011968 GCATTGGTACGACGTGAGCA 61.012 55.000 11.56 7.88 0.00 4.26
1601 1627 1.640428 CATTGGTACGACGTGAGCAT 58.360 50.000 11.56 0.00 0.00 3.79
1602 1628 1.324435 CATTGGTACGACGTGAGCATG 59.676 52.381 11.56 4.37 0.00 4.06
1603 1629 1.011968 TTGGTACGACGTGAGCATGC 61.012 55.000 10.51 10.51 0.00 4.06
1604 1630 2.165301 GGTACGACGTGAGCATGCC 61.165 63.158 15.66 6.65 0.00 4.40
1605 1631 1.445410 GTACGACGTGAGCATGCCA 60.445 57.895 15.66 9.53 0.00 4.92
1606 1632 1.153842 TACGACGTGAGCATGCCAG 60.154 57.895 15.66 5.90 0.00 4.85
1607 1633 3.857854 CGACGTGAGCATGCCAGC 61.858 66.667 15.66 4.86 0.00 4.85
1608 1634 2.743538 GACGTGAGCATGCCAGCA 60.744 61.111 15.66 7.79 36.85 4.41
1609 1635 2.045634 ACGTGAGCATGCCAGCAT 60.046 55.556 15.66 0.00 36.85 3.79
1629 1655 1.565759 TGGGACAAATCCTCCTCATGG 59.434 52.381 0.00 0.00 45.46 3.66
1630 1656 1.846439 GGGACAAATCCTCCTCATGGA 59.154 52.381 0.00 0.00 45.46 3.41
1631 1657 2.422093 GGGACAAATCCTCCTCATGGAC 60.422 54.545 0.00 0.00 45.46 4.02
1632 1658 2.239654 GGACAAATCCTCCTCATGGACA 59.760 50.000 0.00 0.00 42.45 4.02
1633 1659 3.308402 GGACAAATCCTCCTCATGGACAA 60.308 47.826 0.00 0.00 42.45 3.18
1634 1660 4.335416 GACAAATCCTCCTCATGGACAAA 58.665 43.478 0.00 0.00 37.46 2.83
1635 1661 4.939255 ACAAATCCTCCTCATGGACAAAT 58.061 39.130 0.00 0.00 37.46 2.32
1636 1662 4.952335 ACAAATCCTCCTCATGGACAAATC 59.048 41.667 0.00 0.00 37.46 2.17
1637 1663 3.872459 ATCCTCCTCATGGACAAATCC 57.128 47.619 0.00 0.00 46.48 3.01
1638 1664 2.850833 TCCTCCTCATGGACAAATCCT 58.149 47.619 0.00 0.00 46.43 3.24
1639 1665 2.774234 TCCTCCTCATGGACAAATCCTC 59.226 50.000 0.00 0.00 46.43 3.71
1640 1666 2.507058 CCTCCTCATGGACAAATCCTCA 59.493 50.000 0.00 0.00 46.43 3.86
1641 1667 3.433314 CCTCCTCATGGACAAATCCTCAG 60.433 52.174 0.00 0.00 46.43 3.35
1642 1668 2.507058 TCCTCATGGACAAATCCTCAGG 59.493 50.000 0.00 0.00 46.43 3.86
1643 1669 2.295885 CTCATGGACAAATCCTCAGGC 58.704 52.381 0.00 0.00 46.43 4.85
1644 1670 1.019673 CATGGACAAATCCTCAGGCG 58.980 55.000 0.00 0.00 46.43 5.52
1645 1671 0.911769 ATGGACAAATCCTCAGGCGA 59.088 50.000 0.00 0.00 46.43 5.54
1646 1672 0.036388 TGGACAAATCCTCAGGCGAC 60.036 55.000 0.00 0.00 46.43 5.19
1647 1673 0.036388 GGACAAATCCTCAGGCGACA 60.036 55.000 0.00 0.00 42.45 4.35
1648 1674 1.407437 GGACAAATCCTCAGGCGACAT 60.407 52.381 0.00 0.00 42.45 3.06
1649 1675 2.359900 GACAAATCCTCAGGCGACATT 58.640 47.619 0.00 0.00 0.00 2.71
1650 1676 2.352960 GACAAATCCTCAGGCGACATTC 59.647 50.000 0.00 0.00 0.00 2.67
1651 1677 1.328680 CAAATCCTCAGGCGACATTCG 59.671 52.381 0.00 0.00 43.89 3.34
1652 1678 0.537188 AATCCTCAGGCGACATTCGT 59.463 50.000 0.00 0.00 42.81 3.85
1653 1679 1.399714 ATCCTCAGGCGACATTCGTA 58.600 50.000 0.00 0.00 42.81 3.43
1654 1680 0.454600 TCCTCAGGCGACATTCGTAC 59.545 55.000 0.00 0.00 42.81 3.67
1655 1681 0.866061 CCTCAGGCGACATTCGTACG 60.866 60.000 9.53 9.53 42.81 3.67
1656 1682 0.098200 CTCAGGCGACATTCGTACGA 59.902 55.000 15.28 15.28 42.81 3.43
1657 1683 0.179181 TCAGGCGACATTCGTACGAC 60.179 55.000 19.36 5.43 42.81 4.34
1658 1684 1.226211 AGGCGACATTCGTACGACG 60.226 57.895 19.36 18.72 42.81 5.12
1659 1685 1.512734 GGCGACATTCGTACGACGT 60.513 57.895 19.36 17.98 42.81 4.34
1660 1686 1.617179 GCGACATTCGTACGACGTG 59.383 57.895 19.36 20.85 42.81 4.49
1661 1687 0.790495 GCGACATTCGTACGACGTGA 60.790 55.000 27.22 12.35 42.81 4.35
1662 1688 1.169408 CGACATTCGTACGACGTGAG 58.831 55.000 27.22 18.97 43.14 3.51
1663 1689 1.531912 GACATTCGTACGACGTGAGG 58.468 55.000 27.22 15.08 43.14 3.86
1664 1690 0.877071 ACATTCGTACGACGTGAGGT 59.123 50.000 27.22 15.65 43.14 3.85
1665 1691 2.076100 ACATTCGTACGACGTGAGGTA 58.924 47.619 27.22 10.04 43.14 3.08
1675 1701 3.066814 GTGAGGTACCCCGCGTCT 61.067 66.667 8.74 0.00 35.12 4.18
1719 1745 0.996583 ATTAGGTTTTCCCCCGAGCA 59.003 50.000 0.00 0.00 41.86 4.26
1815 1841 3.141488 CACCTCCTCCTCCGTCCG 61.141 72.222 0.00 0.00 0.00 4.79
1819 1845 3.336568 TCCTCCTCCGTCCGTCCT 61.337 66.667 0.00 0.00 0.00 3.85
1822 1848 3.972971 CTCCTCCGTCCGTCCTCGT 62.973 68.421 0.00 0.00 35.01 4.18
1835 1861 2.526046 CCTCGTGTTGGTCCCCCTT 61.526 63.158 0.00 0.00 0.00 3.95
2005 2041 1.656587 TGGGCTTCTTCCTCTGCTTA 58.343 50.000 0.00 0.00 0.00 3.09
2042 2079 0.184692 TCATGGTGTTGGGTGCTTGA 59.815 50.000 0.00 0.00 0.00 3.02
2080 2117 2.753029 GGCCTCAGAGTGGTGCTT 59.247 61.111 0.00 0.00 0.00 3.91
2222 2259 3.591835 CGTTGGTGCTGGCCGTTT 61.592 61.111 0.00 0.00 0.00 3.60
2235 2272 4.097863 CGTTTTTCCTCGGCCGCC 62.098 66.667 23.51 0.00 0.00 6.13
2324 2361 1.867363 AGGCCTCCGTCTACTTCAAT 58.133 50.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 79 0.112412 AAATGGGGCAAAGACCGTCT 59.888 50.000 0.00 0.00 0.00 4.18
687 707 2.125673 GCCTCGCTTCGGCTAACA 60.126 61.111 0.00 0.00 44.17 2.41
716 736 2.441750 TCCCTTTAGCAGGTTCAACAGT 59.558 45.455 0.00 0.00 42.02 3.55
722 742 3.751518 TGTTCTTCCCTTTAGCAGGTTC 58.248 45.455 0.00 0.00 42.02 3.62
1099 1121 1.300266 TGCATGGATGTCAGTGCACG 61.300 55.000 12.01 6.78 42.13 5.34
1147 1173 1.049855 AGATGCTCTCAGGCTCAGGG 61.050 60.000 0.00 0.00 0.00 4.45
1258 1284 3.529319 AGCCCCAGAATTCACCTTTAGAT 59.471 43.478 8.44 0.00 0.00 1.98
1267 1293 0.552848 GATCCCAGCCCCAGAATTCA 59.447 55.000 8.44 0.00 0.00 2.57
1444 1470 3.893720 ACACTCGTGAAAAGGTACTACG 58.106 45.455 3.74 0.00 38.49 3.51
1488 1514 4.125703 GGAGCTACTGAGTCCATTTCATG 58.874 47.826 0.00 0.00 0.00 3.07
1489 1515 3.776969 TGGAGCTACTGAGTCCATTTCAT 59.223 43.478 0.00 0.00 35.36 2.57
1490 1516 3.173151 TGGAGCTACTGAGTCCATTTCA 58.827 45.455 0.00 0.00 35.36 2.69
1491 1517 3.895232 TGGAGCTACTGAGTCCATTTC 57.105 47.619 0.00 0.00 35.36 2.17
1495 1521 3.055819 GTGAAATGGAGCTACTGAGTCCA 60.056 47.826 0.00 0.00 44.48 4.02
1496 1522 3.196685 AGTGAAATGGAGCTACTGAGTCC 59.803 47.826 0.00 0.00 0.00 3.85
1497 1523 4.464069 AGTGAAATGGAGCTACTGAGTC 57.536 45.455 0.00 0.00 0.00 3.36
1498 1524 4.323104 GGAAGTGAAATGGAGCTACTGAGT 60.323 45.833 0.00 0.00 0.00 3.41
1499 1525 4.187694 GGAAGTGAAATGGAGCTACTGAG 58.812 47.826 0.00 0.00 0.00 3.35
1500 1526 3.582647 TGGAAGTGAAATGGAGCTACTGA 59.417 43.478 0.00 0.00 0.00 3.41
1501 1527 3.937706 CTGGAAGTGAAATGGAGCTACTG 59.062 47.826 0.00 0.00 0.00 2.74
1502 1528 4.213564 CTGGAAGTGAAATGGAGCTACT 57.786 45.455 0.00 0.00 0.00 2.57
1524 1550 3.980989 AAGTACGCGCGTGGGACA 61.981 61.111 42.78 22.45 0.00 4.02
1525 1551 3.475774 CAAGTACGCGCGTGGGAC 61.476 66.667 42.78 32.43 0.00 4.46
1526 1552 4.728102 CCAAGTACGCGCGTGGGA 62.728 66.667 42.78 23.29 34.97 4.37
1527 1553 4.728102 TCCAAGTACGCGCGTGGG 62.728 66.667 42.78 33.92 38.32 4.61
1528 1554 3.475774 GTCCAAGTACGCGCGTGG 61.476 66.667 42.78 33.85 38.97 4.94
1529 1555 3.823421 CGTCCAAGTACGCGCGTG 61.823 66.667 42.78 26.78 35.87 5.34
1530 1556 2.965147 TACGTCCAAGTACGCGCGT 61.965 57.895 39.05 39.05 46.71 6.01
1531 1557 2.202336 TACGTCCAAGTACGCGCG 60.202 61.111 30.96 30.96 46.71 6.86
1532 1558 3.366997 GTACGTCCAAGTACGCGC 58.633 61.111 5.73 0.00 46.71 6.86
1536 1562 2.325761 CAGCAGTGTACGTCCAAGTAC 58.674 52.381 0.00 0.78 45.22 2.73
1537 1563 1.336517 GCAGCAGTGTACGTCCAAGTA 60.337 52.381 0.00 0.00 0.00 2.24
1538 1564 0.600255 GCAGCAGTGTACGTCCAAGT 60.600 55.000 0.00 0.00 0.00 3.16
1539 1565 0.319900 AGCAGCAGTGTACGTCCAAG 60.320 55.000 0.00 0.00 0.00 3.61
1540 1566 0.105964 AAGCAGCAGTGTACGTCCAA 59.894 50.000 0.00 0.00 0.00 3.53
1541 1567 0.319555 GAAGCAGCAGTGTACGTCCA 60.320 55.000 0.00 0.00 0.00 4.02
1542 1568 0.319555 TGAAGCAGCAGTGTACGTCC 60.320 55.000 0.00 0.00 0.00 4.79
1543 1569 1.192534 GTTGAAGCAGCAGTGTACGTC 59.807 52.381 0.00 0.00 0.00 4.34
1544 1570 1.217882 GTTGAAGCAGCAGTGTACGT 58.782 50.000 0.00 0.00 0.00 3.57
1545 1571 0.512952 GGTTGAAGCAGCAGTGTACG 59.487 55.000 0.00 0.00 0.00 3.67
1546 1572 0.512952 CGGTTGAAGCAGCAGTGTAC 59.487 55.000 0.00 0.00 0.00 2.90
1547 1573 1.227999 GCGGTTGAAGCAGCAGTGTA 61.228 55.000 0.00 0.00 34.19 2.90
1548 1574 2.546494 GCGGTTGAAGCAGCAGTGT 61.546 57.895 0.00 0.00 34.19 3.55
1549 1575 2.253452 GCGGTTGAAGCAGCAGTG 59.747 61.111 0.00 0.00 34.19 3.66
1550 1576 3.349006 CGCGGTTGAAGCAGCAGT 61.349 61.111 0.00 0.00 34.19 4.40
1551 1577 3.349006 ACGCGGTTGAAGCAGCAG 61.349 61.111 12.47 6.71 34.19 4.24
1552 1578 3.648982 CACGCGGTTGAAGCAGCA 61.649 61.111 12.47 0.00 34.19 4.41
1554 1580 2.969806 ATGCACGCGGTTGAAGCAG 61.970 57.895 12.47 0.00 38.75 4.24
1555 1581 2.977456 ATGCACGCGGTTGAAGCA 60.977 55.556 12.47 10.95 39.79 3.91
1556 1582 2.502510 CATGCACGCGGTTGAAGC 60.503 61.111 12.47 4.99 0.00 3.86
1557 1583 2.502510 GCATGCACGCGGTTGAAG 60.503 61.111 14.21 0.00 0.00 3.02
1558 1584 2.624868 ATGCATGCACGCGGTTGAA 61.625 52.632 25.37 0.00 33.35 2.69
1559 1585 3.055110 ATGCATGCACGCGGTTGA 61.055 55.556 25.37 0.00 33.35 3.18
1560 1586 2.877113 CATGCATGCACGCGGTTG 60.877 61.111 25.37 12.71 33.35 3.77
1574 1600 1.595246 CGTCGTACCAATGCATGCATG 60.595 52.381 32.79 23.00 36.68 4.06
1575 1601 0.657312 CGTCGTACCAATGCATGCAT 59.343 50.000 27.46 27.46 38.46 3.96
1576 1602 0.672091 ACGTCGTACCAATGCATGCA 60.672 50.000 25.04 25.04 0.00 3.96
1577 1603 0.247655 CACGTCGTACCAATGCATGC 60.248 55.000 11.82 11.82 0.00 4.06
1578 1604 1.324435 CTCACGTCGTACCAATGCATG 59.676 52.381 0.00 0.00 0.00 4.06
1579 1605 1.640428 CTCACGTCGTACCAATGCAT 58.360 50.000 0.00 0.00 0.00 3.96
1580 1606 1.011968 GCTCACGTCGTACCAATGCA 61.012 55.000 0.00 0.00 0.00 3.96
1581 1607 1.011968 TGCTCACGTCGTACCAATGC 61.012 55.000 0.00 0.00 0.00 3.56
1582 1608 1.324435 CATGCTCACGTCGTACCAATG 59.676 52.381 0.00 0.00 0.00 2.82
1583 1609 1.640428 CATGCTCACGTCGTACCAAT 58.360 50.000 0.00 0.00 0.00 3.16
1584 1610 1.011968 GCATGCTCACGTCGTACCAA 61.012 55.000 11.37 0.00 0.00 3.67
1585 1611 1.445410 GCATGCTCACGTCGTACCA 60.445 57.895 11.37 0.00 0.00 3.25
1586 1612 2.165301 GGCATGCTCACGTCGTACC 61.165 63.158 18.92 0.00 0.00 3.34
1587 1613 1.413767 CTGGCATGCTCACGTCGTAC 61.414 60.000 18.92 0.00 0.00 3.67
1588 1614 1.153842 CTGGCATGCTCACGTCGTA 60.154 57.895 18.92 0.00 0.00 3.43
1589 1615 2.433145 CTGGCATGCTCACGTCGT 60.433 61.111 18.92 0.00 0.00 4.34
1590 1616 3.857854 GCTGGCATGCTCACGTCG 61.858 66.667 18.92 3.53 0.00 5.12
1591 1617 2.110967 ATGCTGGCATGCTCACGTC 61.111 57.895 18.92 0.00 35.03 4.34
1592 1618 2.045634 ATGCTGGCATGCTCACGT 60.046 55.556 18.92 5.48 35.03 4.49
1593 1619 2.407616 CATGCTGGCATGCTCACG 59.592 61.111 18.92 8.92 45.71 4.35
1600 1626 1.117150 GATTTGTCCCATGCTGGCAT 58.883 50.000 1.86 1.86 35.79 4.40
1601 1627 0.971959 GGATTTGTCCCATGCTGGCA 60.972 55.000 0.00 0.00 35.79 4.92
1602 1628 0.685458 AGGATTTGTCCCATGCTGGC 60.685 55.000 0.00 0.00 35.79 4.85
1603 1629 1.396653 GAGGATTTGTCCCATGCTGG 58.603 55.000 0.00 0.00 37.25 4.85
1604 1630 1.064166 AGGAGGATTTGTCCCATGCTG 60.064 52.381 0.00 0.00 34.21 4.41
1605 1631 1.213926 GAGGAGGATTTGTCCCATGCT 59.786 52.381 0.00 0.00 34.21 3.79
1606 1632 1.064463 TGAGGAGGATTTGTCCCATGC 60.064 52.381 0.00 0.00 34.21 4.06
1607 1633 3.220110 CATGAGGAGGATTTGTCCCATG 58.780 50.000 0.00 0.00 36.89 3.66
1608 1634 2.176364 CCATGAGGAGGATTTGTCCCAT 59.824 50.000 0.00 0.00 36.89 4.00
1609 1635 1.565759 CCATGAGGAGGATTTGTCCCA 59.434 52.381 0.00 0.00 36.89 4.37
1610 1636 1.846439 TCCATGAGGAGGATTTGTCCC 59.154 52.381 0.00 0.00 39.61 4.46
1611 1637 2.239654 TGTCCATGAGGAGGATTTGTCC 59.760 50.000 0.00 0.00 46.92 4.02
1612 1638 3.634397 TGTCCATGAGGAGGATTTGTC 57.366 47.619 0.00 0.00 46.92 3.18
1613 1639 4.387026 TTTGTCCATGAGGAGGATTTGT 57.613 40.909 0.00 0.00 46.92 2.83
1614 1640 4.340381 GGATTTGTCCATGAGGAGGATTTG 59.660 45.833 0.00 0.00 46.92 2.32
1615 1641 4.231426 AGGATTTGTCCATGAGGAGGATTT 59.769 41.667 0.00 0.00 46.92 2.17
1616 1642 3.790408 AGGATTTGTCCATGAGGAGGATT 59.210 43.478 0.00 0.00 46.92 3.01
1617 1643 3.393941 GAGGATTTGTCCATGAGGAGGAT 59.606 47.826 0.00 0.00 46.92 3.24
1618 1644 2.774234 GAGGATTTGTCCATGAGGAGGA 59.226 50.000 0.00 0.00 46.92 3.71
1619 1645 2.507058 TGAGGATTTGTCCATGAGGAGG 59.493 50.000 0.00 0.00 46.92 4.30
1620 1646 3.433314 CCTGAGGATTTGTCCATGAGGAG 60.433 52.174 0.00 0.00 46.92 3.69
1621 1647 2.507058 CCTGAGGATTTGTCCATGAGGA 59.493 50.000 0.00 0.00 43.21 3.71
1622 1648 2.928334 CCTGAGGATTTGTCCATGAGG 58.072 52.381 0.00 0.00 0.00 3.86
1623 1649 2.295885 GCCTGAGGATTTGTCCATGAG 58.704 52.381 0.65 0.00 0.00 2.90
1624 1650 1.407299 CGCCTGAGGATTTGTCCATGA 60.407 52.381 0.65 0.00 0.00 3.07
1625 1651 1.019673 CGCCTGAGGATTTGTCCATG 58.980 55.000 0.65 0.00 0.00 3.66
1626 1652 0.911769 TCGCCTGAGGATTTGTCCAT 59.088 50.000 0.65 0.00 0.00 3.41
1627 1653 0.036388 GTCGCCTGAGGATTTGTCCA 60.036 55.000 0.65 0.00 0.00 4.02
1628 1654 0.036388 TGTCGCCTGAGGATTTGTCC 60.036 55.000 0.65 0.00 0.00 4.02
1629 1655 2.029838 ATGTCGCCTGAGGATTTGTC 57.970 50.000 0.65 0.00 0.00 3.18
1630 1656 2.359900 GAATGTCGCCTGAGGATTTGT 58.640 47.619 0.65 0.00 0.00 2.83
1631 1657 1.328680 CGAATGTCGCCTGAGGATTTG 59.671 52.381 0.65 0.00 31.14 2.32
1632 1658 1.066143 ACGAATGTCGCCTGAGGATTT 60.066 47.619 0.65 0.00 45.12 2.17
1633 1659 0.537188 ACGAATGTCGCCTGAGGATT 59.463 50.000 0.65 0.00 45.12 3.01
1634 1660 1.067212 GTACGAATGTCGCCTGAGGAT 59.933 52.381 0.65 0.00 45.12 3.24
1635 1661 0.454600 GTACGAATGTCGCCTGAGGA 59.545 55.000 0.65 0.00 45.12 3.71
1636 1662 0.866061 CGTACGAATGTCGCCTGAGG 60.866 60.000 10.44 0.00 45.12 3.86
1637 1663 0.098200 TCGTACGAATGTCGCCTGAG 59.902 55.000 17.11 0.00 45.12 3.35
1638 1664 0.179181 GTCGTACGAATGTCGCCTGA 60.179 55.000 21.39 0.00 45.12 3.86
1639 1665 1.461317 CGTCGTACGAATGTCGCCTG 61.461 60.000 21.39 0.00 46.05 4.85
1640 1666 1.226211 CGTCGTACGAATGTCGCCT 60.226 57.895 21.39 0.00 46.05 5.52
1641 1667 1.512734 ACGTCGTACGAATGTCGCC 60.513 57.895 21.39 4.55 46.05 5.54
1642 1668 0.790495 TCACGTCGTACGAATGTCGC 60.790 55.000 21.39 5.33 46.05 5.19
1643 1669 1.169408 CTCACGTCGTACGAATGTCG 58.831 55.000 21.39 20.69 46.05 4.35
1644 1670 1.135859 ACCTCACGTCGTACGAATGTC 60.136 52.381 21.39 6.53 46.05 3.06
1645 1671 0.877071 ACCTCACGTCGTACGAATGT 59.123 50.000 21.39 18.35 46.05 2.71
1646 1672 2.434761 GTACCTCACGTCGTACGAATG 58.565 52.381 21.39 20.40 46.05 2.67
1647 1673 1.398390 GGTACCTCACGTCGTACGAAT 59.602 52.381 21.39 8.62 46.05 3.34
1648 1674 0.796312 GGTACCTCACGTCGTACGAA 59.204 55.000 21.39 3.01 46.05 3.85
1649 1675 2.456000 GGTACCTCACGTCGTACGA 58.544 57.895 15.28 15.28 46.05 3.43
1663 1689 2.101770 CGAGAAGACGCGGGGTAC 59.898 66.667 12.47 0.00 35.82 3.34
1698 1724 1.064979 GCTCGGGGGAAAACCTAATCA 60.065 52.381 0.00 0.00 40.03 2.57
1861 1887 3.865929 CTCCACACAGCCTCGCGTT 62.866 63.158 5.77 0.00 0.00 4.84
1862 1888 4.363990 CTCCACACAGCCTCGCGT 62.364 66.667 5.77 0.00 0.00 6.01
2042 2079 3.268647 ATCCCAGACCGACCCCCTT 62.269 63.158 0.00 0.00 0.00 3.95
2291 2328 1.347378 GAGGCCTTCAGATCTGGATCC 59.653 57.143 22.42 16.77 38.58 3.36
2324 2361 3.473647 CATCGGAGGCAGCCCTGA 61.474 66.667 8.22 10.84 43.12 3.86


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

AutoCloner maintained by Alex Coulton.