Multiple sequence alignment - TraesCS5B01G027300

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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 TraesCS5B01G027300 chr5B 100.000 3723 0 0 1 3723 26448080 26444358 0.000000e+00 6876.0
1 TraesCS5B01G027300 chr5B 90.441 136 13 0 2582 2717 35289745 35289880 2.950000e-41 180.0
2 TraesCS5B01G027300 chr5B 88.652 141 12 2 1564 1700 248763405 248763545 6.390000e-38 169.0
3 TraesCS5B01G027300 chr5B 90.909 121 11 0 1197 1317 35288864 35288984 2.980000e-36 163.0
4 TraesCS5B01G027300 chr5D 93.823 939 51 3 609 1540 35181471 35180533 0.000000e+00 1406.0
5 TraesCS5B01G027300 chr5D 94.364 763 37 4 2909 3670 35178809 35178052 0.000000e+00 1166.0
6 TraesCS5B01G027300 chr5D 97.267 439 12 0 2329 2767 35180165 35179727 0.000000e+00 745.0
7 TraesCS5B01G027300 chr5D 81.119 286 37 10 2441 2717 41297805 41298082 2.910000e-51 213.0
8 TraesCS5B01G027300 chr5D 89.344 122 13 0 1196 1317 41297068 41297189 1.790000e-33 154.0
9 TraesCS5B01G027300 chr5D 89.655 58 5 1 3666 3723 35169346 35169290 5.160000e-09 73.1
10 TraesCS5B01G027300 chr5D 97.143 35 1 0 2188 2222 209318221 209318255 4.020000e-05 60.2
11 TraesCS5B01G027300 chr5A 93.848 829 29 6 2910 3721 23823243 23822420 0.000000e+00 1229.0
12 TraesCS5B01G027300 chr5A 90.979 909 59 12 612 1498 23853738 23852831 0.000000e+00 1203.0
13 TraesCS5B01G027300 chr5A 91.014 868 52 11 1758 2609 23852768 23851911 0.000000e+00 1147.0
14 TraesCS5B01G027300 chr5A 97.204 608 15 2 1 607 589367936 589368542 0.000000e+00 1027.0
15 TraesCS5B01G027300 chr5A 91.877 357 9 6 2579 2917 23823669 23823315 7.230000e-132 481.0
16 TraesCS5B01G027300 chr5A 82.230 287 31 12 2441 2717 29627597 29627873 2.890000e-56 230.0
17 TraesCS5B01G027300 chr5A 89.344 122 13 0 1196 1317 29626824 29626945 1.790000e-33 154.0
18 TraesCS5B01G027300 chr1B 98.033 610 11 1 1 609 463563656 463563047 0.000000e+00 1059.0
19 TraesCS5B01G027300 chr3B 97.712 612 11 3 1 610 817253528 817254138 0.000000e+00 1050.0
20 TraesCS5B01G027300 chr3B 97.222 612 15 2 1 611 22080116 22079506 0.000000e+00 1035.0
21 TraesCS5B01G027300 chr3B 80.556 180 10 11 1537 1694 770117109 770117285 8.450000e-22 115.0
22 TraesCS5B01G027300 chr3A 97.858 607 12 1 1 606 177883704 177884310 0.000000e+00 1048.0
23 TraesCS5B01G027300 chr3A 98.164 599 9 2 1 597 708011732 708012330 0.000000e+00 1044.0
24 TraesCS5B01G027300 chr6B 97.537 609 14 1 1 608 247047329 247047937 0.000000e+00 1040.0
25 TraesCS5B01G027300 chr6B 90.441 136 8 2 1541 1672 714327294 714327160 1.370000e-39 174.0
26 TraesCS5B01G027300 chr6A 97.830 599 11 2 1 598 560643987 560644584 0.000000e+00 1033.0
27 TraesCS5B01G027300 chr6A 94.872 39 2 0 2441 2479 1482348 1482386 1.120000e-05 62.1
28 TraesCS5B01G027300 chr2B 97.377 610 9 4 1 603 224844058 224843449 0.000000e+00 1031.0
29 TraesCS5B01G027300 chr2B 83.951 162 9 6 1527 1673 619959386 619959545 5.010000e-29 139.0
30 TraesCS5B01G027300 chr2B 81.579 152 9 7 1539 1673 697572257 697572406 1.410000e-19 108.0
31 TraesCS5B01G027300 chr4A 82.637 311 34 15 2577 2883 687317203 687317497 1.330000e-64 257.0
32 TraesCS5B01G027300 chr4A 78.788 330 50 15 997 1315 687315815 687316135 1.750000e-48 204.0
33 TraesCS5B01G027300 chr2A 82.315 311 35 17 2576 2883 720384510 720384803 6.170000e-63 252.0
34 TraesCS5B01G027300 chr2A 79.635 329 50 16 997 1315 720383160 720383481 1.740000e-53 220.0
35 TraesCS5B01G027300 chr2A 84.247 146 8 4 1541 1672 62232867 62232723 1.090000e-25 128.0
36 TraesCS5B01G027300 chr3D 81.646 316 34 17 2576 2884 25523430 25523728 1.340000e-59 241.0
37 TraesCS5B01G027300 chr3D 91.597 119 10 0 1197 1315 25522326 25522444 8.270000e-37 165.0
38 TraesCS5B01G027300 chr7D 80.696 316 37 17 2576 2884 37663105 37662807 1.350000e-54 224.0
39 TraesCS5B01G027300 chr7D 78.313 332 58 12 997 1315 37664422 37664092 6.300000e-48 202.0
40 TraesCS5B01G027300 chr7D 88.757 169 11 7 1541 1703 594159880 594159714 2.270000e-47 200.0
41 TraesCS5B01G027300 chr4B 86.982 169 14 7 1538 1699 52579433 52579600 2.280000e-42 183.0
42 TraesCS5B01G027300 chr4B 88.571 140 12 2 1564 1699 98709523 98709662 2.300000e-37 167.0
43 TraesCS5B01G027300 chr4B 88.571 140 12 2 1564 1699 98711503 98711642 2.300000e-37 167.0
44 TraesCS5B01G027300 chr7B 91.667 132 8 2 1543 1672 484623100 484622970 2.950000e-41 180.0
45 TraesCS5B01G027300 chr7A 89.286 140 11 2 1564 1699 499894718 499894579 4.940000e-39 172.0
46 TraesCS5B01G027300 chr7A 77.901 181 16 12 1538 1695 6766237 6766416 1.420000e-14 91.6
47 TraesCS5B01G027300 chr1D 88.652 141 11 4 1564 1699 4229796 4229656 2.300000e-37 167.0
48 TraesCS5B01G027300 chrUn 80.412 194 19 12 2441 2624 290597479 290597295 3.020000e-26 130.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G027300 chr5B 26444358 26448080 3722 True 6876.000000 6876 100.000000 1 3723 1 chr5B.!!$R1 3722
1 TraesCS5B01G027300 chr5D 35178052 35181471 3419 True 1105.666667 1406 95.151333 609 3670 3 chr5D.!!$R2 3061
2 TraesCS5B01G027300 chr5A 23851911 23853738 1827 True 1175.000000 1203 90.996500 612 2609 2 chr5A.!!$R2 1997
3 TraesCS5B01G027300 chr5A 589367936 589368542 606 False 1027.000000 1027 97.204000 1 607 1 chr5A.!!$F1 606
4 TraesCS5B01G027300 chr5A 23822420 23823669 1249 True 855.000000 1229 92.862500 2579 3721 2 chr5A.!!$R1 1142
5 TraesCS5B01G027300 chr1B 463563047 463563656 609 True 1059.000000 1059 98.033000 1 609 1 chr1B.!!$R1 608
6 TraesCS5B01G027300 chr3B 817253528 817254138 610 False 1050.000000 1050 97.712000 1 610 1 chr3B.!!$F2 609
7 TraesCS5B01G027300 chr3B 22079506 22080116 610 True 1035.000000 1035 97.222000 1 611 1 chr3B.!!$R1 610
8 TraesCS5B01G027300 chr3A 177883704 177884310 606 False 1048.000000 1048 97.858000 1 606 1 chr3A.!!$F1 605
9 TraesCS5B01G027300 chr3A 708011732 708012330 598 False 1044.000000 1044 98.164000 1 597 1 chr3A.!!$F2 596
10 TraesCS5B01G027300 chr6B 247047329 247047937 608 False 1040.000000 1040 97.537000 1 608 1 chr6B.!!$F1 607
11 TraesCS5B01G027300 chr6A 560643987 560644584 597 False 1033.000000 1033 97.830000 1 598 1 chr6A.!!$F2 597
12 TraesCS5B01G027300 chr2B 224843449 224844058 609 True 1031.000000 1031 97.377000 1 603 1 chr2B.!!$R1 602
13 TraesCS5B01G027300 chr4A 687315815 687317497 1682 False 230.500000 257 80.712500 997 2883 2 chr4A.!!$F1 1886
14 TraesCS5B01G027300 chr2A 720383160 720384803 1643 False 236.000000 252 80.975000 997 2883 2 chr2A.!!$F1 1886
15 TraesCS5B01G027300 chr3D 25522326 25523728 1402 False 203.000000 241 86.621500 1197 2884 2 chr3D.!!$F1 1687
16 TraesCS5B01G027300 chr7D 37662807 37664422 1615 True 213.000000 224 79.504500 997 2884 2 chr7D.!!$R2 1887

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
829 845 1.227002 GGACCGAGCTCCAATCGAC 60.227 63.158 8.47 0.0 42.76 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2726 3004 0.341961 TGGTAGGGTAGCATGAGGGT 59.658 55.0 0.0 0.0 0.0 4.34 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
234 238 4.521292 GGGGGCGCCATCAATCCA 62.521 66.667 30.85 0.00 0.00 3.41
352 362 5.399596 GCGCTTGGTAAAAAGAAAGAGAAAG 59.600 40.000 0.00 0.00 0.00 2.62
387 397 1.411216 GGATCGAACCCTGGTCTCCTA 60.411 57.143 0.00 0.00 0.00 2.94
586 596 2.419574 GGACGGGCAGAAGCACTATTTA 60.420 50.000 0.00 0.00 43.86 1.40
628 638 8.719560 AGATAAGGGAGAATTCGTCTAAAAAC 57.280 34.615 0.00 0.00 36.41 2.43
828 844 2.423898 GGGACCGAGCTCCAATCGA 61.424 63.158 8.47 0.00 42.76 3.59
829 845 1.227002 GGACCGAGCTCCAATCGAC 60.227 63.158 8.47 0.00 42.76 4.20
833 849 2.893398 GAGCTCCAATCGACCGGT 59.107 61.111 6.92 6.92 0.00 5.28
870 886 2.044946 GATCCAACGGCTGCCCTT 60.045 61.111 14.12 4.93 0.00 3.95
929 945 3.017139 CCTCCCTCTCCTACCGGT 58.983 66.667 13.98 13.98 0.00 5.28
956 972 5.453648 CGAAATCTAGATAGCTAGCAACGT 58.546 41.667 18.83 0.00 43.13 3.99
957 973 5.915758 CGAAATCTAGATAGCTAGCAACGTT 59.084 40.000 18.83 0.00 43.13 3.99
1046 1064 1.436983 CCGATAAAGTCCGGCAAGGC 61.437 60.000 0.00 0.00 39.22 4.35
1103 1121 1.524482 GCATCACCCTCTCCTCCAC 59.476 63.158 0.00 0.00 0.00 4.02
1117 1135 0.318699 CTCCACGAGCGTCAAGAACA 60.319 55.000 0.00 0.00 0.00 3.18
1136 1154 2.100916 ACATCGAGAAGGGTATGAACGG 59.899 50.000 0.00 0.00 0.00 4.44
1209 1259 1.400142 CAACAAACAGTGTGCTCCGAA 59.600 47.619 0.00 0.00 40.60 4.30
1297 1347 2.038952 CTCAACATCACCACCAGGAAGA 59.961 50.000 0.00 0.00 38.69 2.87
1325 1375 5.152623 TGTGGAGAAGGTGATTACTCTTG 57.847 43.478 0.00 0.00 0.00 3.02
1326 1376 3.935828 GTGGAGAAGGTGATTACTCTTGC 59.064 47.826 0.00 0.00 0.00 4.01
1333 1383 2.673368 GGTGATTACTCTTGCGGTCTTG 59.327 50.000 0.00 0.00 0.00 3.02
1336 1386 0.394938 TTACTCTTGCGGTCTTGCCA 59.605 50.000 0.00 0.00 36.97 4.92
1367 1418 4.199310 TCTGCTGTATCCCATTTGCTTAC 58.801 43.478 0.00 0.00 0.00 2.34
1512 1569 2.876550 GTGATGATAGCATGCTGAGCAA 59.123 45.455 30.42 10.30 43.62 3.91
1540 1597 4.278419 GGCAAAACATTTAGACCACTGAGT 59.722 41.667 0.00 0.00 0.00 3.41
1541 1598 5.215160 GCAAAACATTTAGACCACTGAGTG 58.785 41.667 5.42 5.42 0.00 3.51
1542 1599 5.221048 GCAAAACATTTAGACCACTGAGTGT 60.221 40.000 12.15 0.00 34.99 3.55
1543 1600 6.680378 GCAAAACATTTAGACCACTGAGTGTT 60.680 38.462 12.15 0.00 41.53 3.32
1545 1602 7.730364 AAACATTTAGACCACTGAGTGTTAG 57.270 36.000 12.15 0.00 39.94 2.34
1546 1603 6.665992 ACATTTAGACCACTGAGTGTTAGA 57.334 37.500 12.15 0.00 30.91 2.10
1547 1604 7.062749 ACATTTAGACCACTGAGTGTTAGAA 57.937 36.000 12.15 0.49 30.91 2.10
1548 1605 7.155328 ACATTTAGACCACTGAGTGTTAGAAG 58.845 38.462 12.15 0.00 30.91 2.85
1549 1606 6.726490 TTTAGACCACTGAGTGTTAGAAGT 57.274 37.500 12.15 0.50 0.00 3.01
1550 1607 7.828508 TTTAGACCACTGAGTGTTAGAAGTA 57.171 36.000 12.15 0.00 0.00 2.24
1551 1608 8.418597 TTTAGACCACTGAGTGTTAGAAGTAT 57.581 34.615 12.15 1.08 0.00 2.12
1552 1609 9.524496 TTTAGACCACTGAGTGTTAGAAGTATA 57.476 33.333 12.15 0.13 0.00 1.47
1553 1610 9.524496 TTAGACCACTGAGTGTTAGAAGTATAA 57.476 33.333 12.15 6.19 0.00 0.98
1554 1611 8.596781 AGACCACTGAGTGTTAGAAGTATAAT 57.403 34.615 12.15 0.00 0.00 1.28
1555 1612 9.036980 AGACCACTGAGTGTTAGAAGTATAATT 57.963 33.333 12.15 0.00 0.00 1.40
1605 1662 7.632721 GTTTAAACCATGTACGACTTCTTTCA 58.367 34.615 7.12 0.00 0.00 2.69
1606 1663 7.972832 TTAAACCATGTACGACTTCTTTCAT 57.027 32.000 0.00 0.00 0.00 2.57
1607 1664 9.491675 TTTAAACCATGTACGACTTCTTTCATA 57.508 29.630 0.00 0.00 0.00 2.15
1608 1665 6.963049 AACCATGTACGACTTCTTTCATAC 57.037 37.500 0.00 0.00 0.00 2.39
1609 1666 6.032956 ACCATGTACGACTTCTTTCATACA 57.967 37.500 0.00 0.00 0.00 2.29
1610 1667 5.867716 ACCATGTACGACTTCTTTCATACAC 59.132 40.000 0.00 0.00 0.00 2.90
1611 1668 5.291128 CCATGTACGACTTCTTTCATACACC 59.709 44.000 0.00 0.00 0.00 4.16
1612 1669 5.456548 TGTACGACTTCTTTCATACACCA 57.543 39.130 0.00 0.00 0.00 4.17
1613 1670 5.845103 TGTACGACTTCTTTCATACACCAA 58.155 37.500 0.00 0.00 0.00 3.67
1614 1671 5.924254 TGTACGACTTCTTTCATACACCAAG 59.076 40.000 0.00 0.00 0.00 3.61
1615 1672 4.957296 ACGACTTCTTTCATACACCAAGT 58.043 39.130 0.00 0.00 0.00 3.16
1616 1673 4.989168 ACGACTTCTTTCATACACCAAGTC 59.011 41.667 0.00 0.00 37.47 3.01
1617 1674 5.221461 ACGACTTCTTTCATACACCAAGTCT 60.221 40.000 7.75 0.00 38.29 3.24
1618 1675 5.346281 CGACTTCTTTCATACACCAAGTCTC 59.654 44.000 7.75 0.00 38.29 3.36
1619 1676 6.426646 ACTTCTTTCATACACCAAGTCTCT 57.573 37.500 0.00 0.00 0.00 3.10
1620 1677 6.459923 ACTTCTTTCATACACCAAGTCTCTC 58.540 40.000 0.00 0.00 0.00 3.20
1621 1678 6.268847 ACTTCTTTCATACACCAAGTCTCTCT 59.731 38.462 0.00 0.00 0.00 3.10
1622 1679 6.274157 TCTTTCATACACCAAGTCTCTCTC 57.726 41.667 0.00 0.00 0.00 3.20
1623 1680 5.775195 TCTTTCATACACCAAGTCTCTCTCA 59.225 40.000 0.00 0.00 0.00 3.27
1624 1681 6.438741 TCTTTCATACACCAAGTCTCTCTCAT 59.561 38.462 0.00 0.00 0.00 2.90
1625 1682 7.615757 TCTTTCATACACCAAGTCTCTCTCATA 59.384 37.037 0.00 0.00 0.00 2.15
1626 1683 7.904558 TTCATACACCAAGTCTCTCTCATAT 57.095 36.000 0.00 0.00 0.00 1.78
1627 1684 7.904558 TCATACACCAAGTCTCTCTCATATT 57.095 36.000 0.00 0.00 0.00 1.28
1628 1685 7.720442 TCATACACCAAGTCTCTCTCATATTG 58.280 38.462 0.00 0.00 0.00 1.90
1629 1686 7.343057 TCATACACCAAGTCTCTCTCATATTGT 59.657 37.037 0.00 0.00 0.00 2.71
1630 1687 8.633561 CATACACCAAGTCTCTCTCATATTGTA 58.366 37.037 0.00 0.00 0.00 2.41
1631 1688 6.868622 ACACCAAGTCTCTCTCATATTGTAC 58.131 40.000 0.00 0.00 0.00 2.90
1632 1689 6.665680 ACACCAAGTCTCTCTCATATTGTACT 59.334 38.462 0.00 0.00 0.00 2.73
1633 1690 7.147983 ACACCAAGTCTCTCTCATATTGTACTC 60.148 40.741 0.00 0.00 0.00 2.59
1634 1691 7.068103 CACCAAGTCTCTCTCATATTGTACTCT 59.932 40.741 0.00 0.00 0.00 3.24
1635 1692 8.275758 ACCAAGTCTCTCTCATATTGTACTCTA 58.724 37.037 0.00 0.00 0.00 2.43
1636 1693 9.295825 CCAAGTCTCTCTCATATTGTACTCTAT 57.704 37.037 0.00 0.00 0.00 1.98
1652 1709 9.475620 TTGTACTCTATATATATCCCACACCTG 57.524 37.037 0.00 0.00 0.00 4.00
1653 1710 8.059461 TGTACTCTATATATATCCCACACCTGG 58.941 40.741 0.00 0.00 37.29 4.45
1662 1719 2.376063 CCACACCTGGGTCAGATCA 58.624 57.895 0.00 0.00 33.23 2.92
1663 1720 0.692476 CCACACCTGGGTCAGATCAA 59.308 55.000 0.00 0.00 33.23 2.57
1664 1721 1.283029 CCACACCTGGGTCAGATCAAT 59.717 52.381 0.00 0.00 33.23 2.57
1665 1722 2.505407 CCACACCTGGGTCAGATCAATA 59.495 50.000 0.00 0.00 33.23 1.90
1666 1723 3.054434 CCACACCTGGGTCAGATCAATAA 60.054 47.826 0.00 0.00 33.23 1.40
1667 1724 3.941483 CACACCTGGGTCAGATCAATAAC 59.059 47.826 0.00 0.00 32.44 1.89
1668 1725 3.587061 ACACCTGGGTCAGATCAATAACA 59.413 43.478 0.00 0.00 32.44 2.41
1669 1726 4.042809 ACACCTGGGTCAGATCAATAACAA 59.957 41.667 0.00 0.00 32.44 2.83
1670 1727 4.396166 CACCTGGGTCAGATCAATAACAAC 59.604 45.833 0.00 0.00 32.44 3.32
1671 1728 4.042809 ACCTGGGTCAGATCAATAACAACA 59.957 41.667 0.00 0.00 32.44 3.33
1672 1729 5.009631 CCTGGGTCAGATCAATAACAACAA 58.990 41.667 0.00 0.00 32.44 2.83
1673 1730 5.653769 CCTGGGTCAGATCAATAACAACAAT 59.346 40.000 0.00 0.00 32.44 2.71
1674 1731 6.828273 CCTGGGTCAGATCAATAACAACAATA 59.172 38.462 0.00 0.00 32.44 1.90
1675 1732 7.503566 CCTGGGTCAGATCAATAACAACAATAT 59.496 37.037 0.00 0.00 32.44 1.28
1676 1733 8.821686 TGGGTCAGATCAATAACAACAATATT 57.178 30.769 0.00 0.00 0.00 1.28
1677 1734 8.902806 TGGGTCAGATCAATAACAACAATATTC 58.097 33.333 0.00 0.00 0.00 1.75
1678 1735 8.902806 GGGTCAGATCAATAACAACAATATTCA 58.097 33.333 0.00 0.00 0.00 2.57
1686 1743 9.418839 TCAATAACAACAATATTCATCCATCCA 57.581 29.630 0.00 0.00 0.00 3.41
1700 1757 9.872684 ATTCATCCATCCAATATTTTCTACACT 57.127 29.630 0.00 0.00 0.00 3.55
1701 1758 8.681486 TCATCCATCCAATATTTTCTACACTG 57.319 34.615 0.00 0.00 0.00 3.66
1702 1759 8.493607 TCATCCATCCAATATTTTCTACACTGA 58.506 33.333 0.00 0.00 0.00 3.41
1703 1760 8.781196 CATCCATCCAATATTTTCTACACTGAG 58.219 37.037 0.00 0.00 0.00 3.35
1704 1761 8.089625 TCCATCCAATATTTTCTACACTGAGA 57.910 34.615 0.00 0.00 0.00 3.27
1705 1762 8.717717 TCCATCCAATATTTTCTACACTGAGAT 58.282 33.333 0.00 0.00 0.00 2.75
1733 1791 9.231297 CTTTGGGTCTTTGATGTCTCTAAATTA 57.769 33.333 0.00 0.00 0.00 1.40
1763 1821 2.519377 AATTGATGATTGGCATGCCG 57.481 45.000 30.87 0.00 37.34 5.69
1767 1825 0.029834 GATGATTGGCATGCCGTCAC 59.970 55.000 33.86 25.62 37.34 3.67
1768 1826 1.386525 ATGATTGGCATGCCGTCACC 61.387 55.000 33.86 21.32 36.59 4.02
1769 1827 3.112126 GATTGGCATGCCGTCACCG 62.112 63.158 30.87 0.00 39.42 4.94
1770 1828 3.918253 ATTGGCATGCCGTCACCGT 62.918 57.895 30.87 9.11 39.42 4.83
1778 1839 0.869068 TGCCGTCACCGTAATTGTTG 59.131 50.000 0.00 0.00 0.00 3.33
1786 1847 5.786574 CGTCACCGTAATTGTTGTGTTATTC 59.213 40.000 0.00 0.00 0.00 1.75
1826 1887 3.631686 ACATGCTTAGTTCTGTTTGTGCA 59.368 39.130 0.00 0.00 0.00 4.57
1836 1898 7.133891 AGTTCTGTTTGTGCAGTGTAATATC 57.866 36.000 0.00 0.00 37.70 1.63
1841 1913 7.875554 TCTGTTTGTGCAGTGTAATATCAAGTA 59.124 33.333 0.00 0.00 37.70 2.24
1844 1916 7.971183 TTGTGCAGTGTAATATCAAGTACAA 57.029 32.000 0.00 0.00 37.86 2.41
1849 1921 7.279981 TGCAGTGTAATATCAAGTACAATGGAC 59.720 37.037 13.10 0.00 46.55 4.02
1936 2016 3.978352 GCTTTTTAAAAGCTGATGCCG 57.022 42.857 28.63 0.00 40.01 5.69
1960 2040 4.626172 GGTTTGTCTAGTGCTGCTAGTAAC 59.374 45.833 13.07 13.85 45.65 2.50
2010 2103 2.775890 GTCCTACGTAGGGATCATCGA 58.224 52.381 35.39 15.43 43.79 3.59
2016 2109 3.728845 ACGTAGGGATCATCGATTTTGG 58.271 45.455 0.00 0.00 0.00 3.28
2025 2118 1.068402 CATCGATTTTGGCTGTGTGCA 60.068 47.619 0.00 0.00 45.15 4.57
2026 2119 0.310543 TCGATTTTGGCTGTGTGCAC 59.689 50.000 10.75 10.75 45.15 4.57
2029 2122 1.391157 ATTTTGGCTGTGTGCACCGT 61.391 50.000 15.69 0.00 45.15 4.83
2031 2124 1.440938 TTTGGCTGTGTGCACCGTAC 61.441 55.000 15.69 6.62 45.15 3.67
2036 2129 1.955529 CTGTGTGCACCGTACGATGC 61.956 60.000 27.85 27.85 42.40 3.91
2043 2136 1.743995 ACCGTACGATGCAAAGGCC 60.744 57.895 18.76 0.00 40.13 5.19
2047 2140 2.661066 TACGATGCAAAGGCCGGGA 61.661 57.895 2.18 0.00 40.13 5.14
2106 2201 6.544928 TCAGTTAGAACTCATCATAGCCAA 57.455 37.500 0.00 0.00 37.08 4.52
2114 2209 6.944862 AGAACTCATCATAGCCAAATTATCCC 59.055 38.462 0.00 0.00 0.00 3.85
2181 2297 3.117550 TGCTTAATGATGGGCTGGTACAT 60.118 43.478 0.00 0.00 38.20 2.29
2182 2298 3.503748 GCTTAATGATGGGCTGGTACATC 59.496 47.826 0.00 0.00 42.86 3.06
2327 2473 3.850752 TCTTCCAAACATTTGCCCCTTA 58.149 40.909 0.00 0.00 36.86 2.69
2351 2497 1.831580 AGAAAGAGCCATTGAGGTGC 58.168 50.000 0.00 0.00 40.61 5.01
2664 2942 0.178767 TCCCCAGACATCATCAAGCG 59.821 55.000 0.00 0.00 0.00 4.68
2726 3004 2.028112 GTGACCATCAGCCAGTAGTCAA 60.028 50.000 0.00 0.00 36.13 3.18
2823 3592 6.072119 ACCAAGACGTTTTCTTTGAGACTTTT 60.072 34.615 0.00 0.00 42.37 2.27
2917 3987 6.877611 AAGTTATCGTCTTGGATTTTGTGT 57.122 33.333 0.00 0.00 0.00 3.72
2956 4026 3.243877 CGTCGTTATTTCAGCATCTCCAG 59.756 47.826 0.00 0.00 0.00 3.86
2986 4056 2.290641 AGCGTTCTTGTTTGGATGTCAC 59.709 45.455 0.00 0.00 0.00 3.67
3138 4208 8.992073 GCTGTTCAATTAACATCCAAAGAAAAT 58.008 29.630 0.00 0.00 46.81 1.82
3360 4446 3.932710 AGTAACTTCATGTACACGCATGG 59.067 43.478 0.00 0.00 44.54 3.66
3433 4519 3.064324 CCGAGCAAGGCAAAGGGG 61.064 66.667 0.00 0.00 0.00 4.79
3438 4524 0.189822 AGCAAGGCAAAGGGGGTAAA 59.810 50.000 0.00 0.00 0.00 2.01
3445 4531 2.536066 GCAAAGGGGGTAAAGGACAAT 58.464 47.619 0.00 0.00 0.00 2.71
3468 4554 3.315470 AGAAACGCAGAGCATCGACTATA 59.685 43.478 0.00 0.00 42.67 1.31
3469 4555 3.924918 AACGCAGAGCATCGACTATAT 57.075 42.857 0.00 0.00 42.67 0.86
3474 4560 5.802451 ACGCAGAGCATCGACTATATTAATG 59.198 40.000 0.00 0.00 42.67 1.90
3486 4572 9.203421 TCGACTATATTAATGCACAAAGTATGG 57.797 33.333 0.00 0.00 0.00 2.74
3608 4694 3.517296 TGGCACAACAAATTCTCCCTA 57.483 42.857 0.00 0.00 31.92 3.53
3685 4771 3.733077 GCATTGCATAGGTCAAAGACAGC 60.733 47.826 3.15 0.00 33.68 4.40
3686 4772 2.113860 TGCATAGGTCAAAGACAGCC 57.886 50.000 0.00 0.00 33.68 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
121 124 9.340695 CAAAATATCAAACAATTGCGAGTTCTA 57.659 29.630 5.05 0.00 36.45 2.10
352 362 0.179097 GATCCCTGGTTCTCACGCTC 60.179 60.000 0.00 0.00 0.00 5.03
840 856 4.201122 GGATCTGCTGGCCTGGGG 62.201 72.222 12.06 0.00 0.00 4.96
920 936 2.894240 GATTTCGCGCACCGGTAGGA 62.894 60.000 6.87 0.00 41.02 2.94
929 945 3.670895 GCTAGCTATCTAGATTTCGCGCA 60.671 47.826 11.25 0.00 43.95 6.09
956 972 2.284331 TACTGGAGGAGGCCGCAA 60.284 61.111 9.31 0.00 0.00 4.85
957 973 3.075005 GTACTGGAGGAGGCCGCA 61.075 66.667 9.31 0.00 0.00 5.69
1021 1039 1.518572 CGGACTTTATCGGCAGCGT 60.519 57.895 0.00 0.00 0.00 5.07
1068 1086 4.624364 CGGACCCTGTGCAGCACA 62.624 66.667 26.63 26.63 42.45 4.57
1103 1121 0.910513 CTCGATGTTCTTGACGCTCG 59.089 55.000 0.00 0.00 37.37 5.03
1117 1135 2.623889 CTCCGTTCATACCCTTCTCGAT 59.376 50.000 0.00 0.00 0.00 3.59
1136 1154 3.772572 AGAGAAGGAAGGAAGTAAGCCTC 59.227 47.826 0.00 0.00 33.76 4.70
1209 1259 4.927782 TTGGCGCGCTTCACCAGT 62.928 61.111 32.29 0.00 34.28 4.00
1297 1347 1.847968 CACCTTCTCCACAGGGGGT 60.848 63.158 0.00 0.00 35.50 4.95
1326 1376 1.374758 GACCAGAGTGGCAAGACCG 60.375 63.158 0.00 0.00 42.67 4.79
1333 1383 1.079266 CAGCAGAGACCAGAGTGGC 60.079 63.158 0.00 0.00 42.67 5.01
1336 1386 2.383855 GGATACAGCAGAGACCAGAGT 58.616 52.381 0.00 0.00 0.00 3.24
1367 1418 7.923888 AGAGCATATATACAACACAAAGCAAG 58.076 34.615 0.00 0.00 0.00 4.01
1502 1559 1.552578 TTGCCTCATTTGCTCAGCAT 58.447 45.000 0.00 0.00 38.76 3.79
1512 1569 5.539955 AGTGGTCTAAATGTTTTGCCTCATT 59.460 36.000 0.00 0.00 36.07 2.57
1580 1637 7.632721 TGAAAGAAGTCGTACATGGTTTAAAC 58.367 34.615 9.98 9.98 0.00 2.01
1581 1638 7.789273 TGAAAGAAGTCGTACATGGTTTAAA 57.211 32.000 0.00 0.00 0.00 1.52
1582 1639 7.972832 ATGAAAGAAGTCGTACATGGTTTAA 57.027 32.000 0.00 0.00 0.00 1.52
1583 1640 8.089597 TGTATGAAAGAAGTCGTACATGGTTTA 58.910 33.333 0.00 0.00 42.42 2.01
1584 1641 6.932400 TGTATGAAAGAAGTCGTACATGGTTT 59.068 34.615 0.00 0.00 42.42 3.27
1585 1642 6.367969 GTGTATGAAAGAAGTCGTACATGGTT 59.632 38.462 9.73 0.00 46.47 3.67
1586 1643 5.867716 GTGTATGAAAGAAGTCGTACATGGT 59.132 40.000 9.73 0.00 46.47 3.55
1587 1644 5.291128 GGTGTATGAAAGAAGTCGTACATGG 59.709 44.000 9.73 0.00 46.47 3.66
1588 1645 5.867174 TGGTGTATGAAAGAAGTCGTACATG 59.133 40.000 9.73 0.00 46.47 3.21
1589 1646 6.032956 TGGTGTATGAAAGAAGTCGTACAT 57.967 37.500 9.73 0.00 46.47 2.29
1590 1647 5.456548 TGGTGTATGAAAGAAGTCGTACA 57.543 39.130 3.68 3.68 44.15 2.90
1591 1648 5.924825 ACTTGGTGTATGAAAGAAGTCGTAC 59.075 40.000 0.00 0.00 39.49 3.67
1592 1649 6.015688 AGACTTGGTGTATGAAAGAAGTCGTA 60.016 38.462 0.00 0.00 42.60 3.43
1593 1650 4.957296 ACTTGGTGTATGAAAGAAGTCGT 58.043 39.130 0.00 0.00 0.00 4.34
1594 1651 5.230942 AGACTTGGTGTATGAAAGAAGTCG 58.769 41.667 0.00 0.00 42.60 4.18
1595 1652 6.459923 AGAGACTTGGTGTATGAAAGAAGTC 58.540 40.000 0.00 0.00 39.62 3.01
1596 1653 6.268847 AGAGAGACTTGGTGTATGAAAGAAGT 59.731 38.462 0.00 0.00 0.00 3.01
1597 1654 6.696411 AGAGAGACTTGGTGTATGAAAGAAG 58.304 40.000 0.00 0.00 0.00 2.85
1598 1655 6.267699 TGAGAGAGACTTGGTGTATGAAAGAA 59.732 38.462 0.00 0.00 0.00 2.52
1599 1656 5.775195 TGAGAGAGACTTGGTGTATGAAAGA 59.225 40.000 0.00 0.00 0.00 2.52
1600 1657 6.030548 TGAGAGAGACTTGGTGTATGAAAG 57.969 41.667 0.00 0.00 0.00 2.62
1601 1658 6.611613 ATGAGAGAGACTTGGTGTATGAAA 57.388 37.500 0.00 0.00 0.00 2.69
1602 1659 7.904558 ATATGAGAGAGACTTGGTGTATGAA 57.095 36.000 0.00 0.00 0.00 2.57
1603 1660 7.343057 ACAATATGAGAGAGACTTGGTGTATGA 59.657 37.037 0.00 0.00 0.00 2.15
1604 1661 7.495901 ACAATATGAGAGAGACTTGGTGTATG 58.504 38.462 0.00 0.00 0.00 2.39
1605 1662 7.667575 ACAATATGAGAGAGACTTGGTGTAT 57.332 36.000 0.00 0.00 0.00 2.29
1606 1663 7.834681 AGTACAATATGAGAGAGACTTGGTGTA 59.165 37.037 0.00 0.00 0.00 2.90
1607 1664 6.665680 AGTACAATATGAGAGAGACTTGGTGT 59.334 38.462 0.00 0.00 0.00 4.16
1608 1665 7.068103 AGAGTACAATATGAGAGAGACTTGGTG 59.932 40.741 0.00 0.00 0.00 4.17
1609 1666 7.122715 AGAGTACAATATGAGAGAGACTTGGT 58.877 38.462 0.00 0.00 0.00 3.67
1610 1667 7.581213 AGAGTACAATATGAGAGAGACTTGG 57.419 40.000 0.00 0.00 0.00 3.61
1626 1683 9.475620 CAGGTGTGGGATATATATAGAGTACAA 57.524 37.037 0.00 0.00 0.00 2.41
1627 1684 8.059461 CCAGGTGTGGGATATATATAGAGTACA 58.941 40.741 0.00 0.00 40.67 2.90
1628 1685 8.466617 CCAGGTGTGGGATATATATAGAGTAC 57.533 42.308 0.00 0.00 40.67 2.73
1644 1701 0.692476 TTGATCTGACCCAGGTGTGG 59.308 55.000 0.00 0.00 44.56 4.17
1645 1702 2.795231 ATTGATCTGACCCAGGTGTG 57.205 50.000 0.00 0.00 31.51 3.82
1646 1703 3.587061 TGTTATTGATCTGACCCAGGTGT 59.413 43.478 0.00 0.00 31.51 4.16
1647 1704 4.220693 TGTTATTGATCTGACCCAGGTG 57.779 45.455 0.00 0.00 31.51 4.00
1648 1705 4.042809 TGTTGTTATTGATCTGACCCAGGT 59.957 41.667 0.00 0.00 31.51 4.00
1649 1706 4.588899 TGTTGTTATTGATCTGACCCAGG 58.411 43.478 0.00 0.00 31.51 4.45
1650 1707 6.764308 ATTGTTGTTATTGATCTGACCCAG 57.236 37.500 0.00 0.00 0.00 4.45
1651 1708 8.821686 AATATTGTTGTTATTGATCTGACCCA 57.178 30.769 0.00 0.00 0.00 4.51
1652 1709 8.902806 TGAATATTGTTGTTATTGATCTGACCC 58.097 33.333 0.00 0.00 0.00 4.46
1660 1717 9.418839 TGGATGGATGAATATTGTTGTTATTGA 57.581 29.630 0.00 0.00 0.00 2.57
1674 1731 9.872684 AGTGTAGAAAATATTGGATGGATGAAT 57.127 29.630 0.00 0.00 0.00 2.57
1675 1732 9.123902 CAGTGTAGAAAATATTGGATGGATGAA 57.876 33.333 0.00 0.00 0.00 2.57
1676 1733 8.493607 TCAGTGTAGAAAATATTGGATGGATGA 58.506 33.333 0.00 0.00 0.00 2.92
1677 1734 8.681486 TCAGTGTAGAAAATATTGGATGGATG 57.319 34.615 0.00 0.00 0.00 3.51
1678 1735 8.717717 TCTCAGTGTAGAAAATATTGGATGGAT 58.282 33.333 0.00 0.00 0.00 3.41
1679 1736 8.089625 TCTCAGTGTAGAAAATATTGGATGGA 57.910 34.615 0.00 0.00 0.00 3.41
1680 1737 8.915057 ATCTCAGTGTAGAAAATATTGGATGG 57.085 34.615 0.00 0.00 0.00 3.51
1687 1744 9.838339 CCCAAAGTATCTCAGTGTAGAAAATAT 57.162 33.333 0.00 0.00 0.00 1.28
1688 1745 8.822805 ACCCAAAGTATCTCAGTGTAGAAAATA 58.177 33.333 0.00 0.00 0.00 1.40
1689 1746 7.690256 ACCCAAAGTATCTCAGTGTAGAAAAT 58.310 34.615 0.00 0.00 0.00 1.82
1690 1747 7.016268 AGACCCAAAGTATCTCAGTGTAGAAAA 59.984 37.037 0.00 0.00 0.00 2.29
1691 1748 6.497259 AGACCCAAAGTATCTCAGTGTAGAAA 59.503 38.462 0.00 0.00 0.00 2.52
1692 1749 6.017192 AGACCCAAAGTATCTCAGTGTAGAA 58.983 40.000 0.00 0.00 0.00 2.10
1693 1750 5.580998 AGACCCAAAGTATCTCAGTGTAGA 58.419 41.667 0.00 0.00 0.00 2.59
1694 1751 5.923733 AGACCCAAAGTATCTCAGTGTAG 57.076 43.478 0.00 0.00 0.00 2.74
1695 1752 6.269077 TCAAAGACCCAAAGTATCTCAGTGTA 59.731 38.462 0.00 0.00 0.00 2.90
1696 1753 5.071788 TCAAAGACCCAAAGTATCTCAGTGT 59.928 40.000 0.00 0.00 0.00 3.55
1697 1754 5.551233 TCAAAGACCCAAAGTATCTCAGTG 58.449 41.667 0.00 0.00 0.00 3.66
1698 1755 5.825593 TCAAAGACCCAAAGTATCTCAGT 57.174 39.130 0.00 0.00 0.00 3.41
1699 1756 6.176183 ACATCAAAGACCCAAAGTATCTCAG 58.824 40.000 0.00 0.00 0.00 3.35
1700 1757 6.013379 AGACATCAAAGACCCAAAGTATCTCA 60.013 38.462 0.00 0.00 0.00 3.27
1701 1758 6.410540 AGACATCAAAGACCCAAAGTATCTC 58.589 40.000 0.00 0.00 0.00 2.75
1702 1759 6.214412 AGAGACATCAAAGACCCAAAGTATCT 59.786 38.462 0.00 0.00 0.00 1.98
1703 1760 6.410540 AGAGACATCAAAGACCCAAAGTATC 58.589 40.000 0.00 0.00 0.00 2.24
1704 1761 6.380079 AGAGACATCAAAGACCCAAAGTAT 57.620 37.500 0.00 0.00 0.00 2.12
1705 1762 5.825593 AGAGACATCAAAGACCCAAAGTA 57.174 39.130 0.00 0.00 0.00 2.24
1706 1763 4.713792 AGAGACATCAAAGACCCAAAGT 57.286 40.909 0.00 0.00 0.00 2.66
1707 1764 7.693969 ATTTAGAGACATCAAAGACCCAAAG 57.306 36.000 0.00 0.00 0.00 2.77
1733 1791 6.935771 TGCCAATCATCAATTACAAAAAGCTT 59.064 30.769 0.00 0.00 0.00 3.74
1743 1801 2.957680 ACGGCATGCCAATCATCAATTA 59.042 40.909 34.93 0.00 35.37 1.40
1746 1804 0.740149 GACGGCATGCCAATCATCAA 59.260 50.000 34.93 0.00 35.37 2.57
1763 1821 6.795114 CAGAATAACACAACAATTACGGTGAC 59.205 38.462 8.89 0.00 35.33 3.67
1767 1825 8.879759 AGATACAGAATAACACAACAATTACGG 58.120 33.333 0.00 0.00 0.00 4.02
1814 1875 7.228507 ACTTGATATTACACTGCACAAACAGAA 59.771 33.333 0.00 0.00 40.25 3.02
1826 1887 9.959721 AAAGTCCATTGTACTTGATATTACACT 57.040 29.630 0.00 0.00 37.26 3.55
1836 1898 4.062293 TCCGACAAAGTCCATTGTACTTG 58.938 43.478 0.00 0.00 43.31 3.16
1841 1913 3.338249 CTCATCCGACAAAGTCCATTGT 58.662 45.455 0.00 0.00 45.82 2.71
1844 1916 1.278985 TGCTCATCCGACAAAGTCCAT 59.721 47.619 0.00 0.00 0.00 3.41
1849 1921 4.212847 CCTTCATATGCTCATCCGACAAAG 59.787 45.833 0.00 0.00 0.00 2.77
1927 2007 0.392461 TAGACAAACCCGGCATCAGC 60.392 55.000 0.00 0.00 41.10 4.26
1936 2016 2.762535 TAGCAGCACTAGACAAACCC 57.237 50.000 0.00 0.00 0.00 4.11
2010 2103 1.363443 CGGTGCACACAGCCAAAAT 59.637 52.632 20.43 0.00 44.83 1.82
2016 2109 1.736645 ATCGTACGGTGCACACAGC 60.737 57.895 20.43 4.94 45.96 4.40
2025 2118 1.743995 GGCCTTTGCATCGTACGGT 60.744 57.895 16.52 4.91 40.13 4.83
2026 2119 2.808958 CGGCCTTTGCATCGTACGG 61.809 63.158 16.52 0.69 40.13 4.02
2029 2122 1.978455 ATCCCGGCCTTTGCATCGTA 61.978 55.000 0.00 0.00 40.13 3.43
2031 2124 1.227823 TATCCCGGCCTTTGCATCG 60.228 57.895 0.00 0.00 40.13 3.84
2089 2184 6.944862 GGGATAATTTGGCTATGATGAGTTCT 59.055 38.462 0.00 0.00 0.00 3.01
2181 2297 0.550914 AAGCTCCCACACAACAAGGA 59.449 50.000 0.00 0.00 0.00 3.36
2182 2298 1.338020 GAAAGCTCCCACACAACAAGG 59.662 52.381 0.00 0.00 0.00 3.61
2327 2473 5.686124 GCACCTCAATGGCTCTTTCTACTAT 60.686 44.000 0.00 0.00 40.22 2.12
2351 2497 6.879276 ATAAACATGCATCCAGAGATTGAG 57.121 37.500 0.00 0.00 0.00 3.02
2726 3004 0.341961 TGGTAGGGTAGCATGAGGGT 59.658 55.000 0.00 0.00 0.00 4.34
2898 3689 7.201574 CGGAAATACACAAAATCCAAGACGATA 60.202 37.037 0.00 0.00 0.00 2.92
2914 3705 2.597305 CGTGCACTCTACGGAAATACAC 59.403 50.000 16.19 0.00 37.86 2.90
2917 3987 2.476686 CGACGTGCACTCTACGGAAATA 60.477 50.000 16.19 0.00 45.24 1.40
2956 4026 4.679654 CCAAACAAGAACGCTACCAAATTC 59.320 41.667 0.00 0.00 0.00 2.17
3226 4296 5.122396 GGCCATTATAAGAGGAAGTAATGCG 59.878 44.000 0.00 0.00 34.68 4.73
3360 4446 1.391787 GCAACAAAAGGTTACGTCGC 58.608 50.000 0.00 0.00 37.72 5.19
3409 4495 1.444119 TTGCCTTGCTCGGTGTCAAC 61.444 55.000 0.00 0.00 0.00 3.18
3413 4499 1.898574 CCTTTGCCTTGCTCGGTGT 60.899 57.895 0.00 0.00 0.00 4.16
3433 4519 4.933400 TCTGCGTTTCTATTGTCCTTTACC 59.067 41.667 0.00 0.00 0.00 2.85
3438 4524 2.028112 TGCTCTGCGTTTCTATTGTCCT 60.028 45.455 0.00 0.00 0.00 3.85
3445 4531 1.472878 AGTCGATGCTCTGCGTTTCTA 59.527 47.619 0.00 0.00 0.00 2.10
3468 4554 6.610830 TGGGAATCCATACTTTGTGCATTAAT 59.389 34.615 0.09 0.00 38.32 1.40
3469 4555 5.954752 TGGGAATCCATACTTTGTGCATTAA 59.045 36.000 0.09 0.00 38.32 1.40
3485 4571 6.209391 TCTCAAAACAGAGAAAATGGGAATCC 59.791 38.462 0.00 0.00 41.45 3.01
3486 4572 7.219484 TCTCAAAACAGAGAAAATGGGAATC 57.781 36.000 0.00 0.00 41.45 2.52
3608 4694 7.230849 TGAAGATTTGCCTTGACATTACATT 57.769 32.000 0.00 0.00 0.00 2.71
3685 4771 2.094390 TGTCAGGATACGTTTCCTTCGG 60.094 50.000 23.11 13.39 43.88 4.30
3686 4772 3.226346 TGTCAGGATACGTTTCCTTCG 57.774 47.619 23.11 14.04 43.88 3.79


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

AutoCloner maintained by Alex Coulton.