Multiple sequence alignment - TraesCS4A01G291400

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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 TraesCS4A01G291400 chr4A 100.000 2456 0 0 1 2456 594461773 594459318 0.000000e+00 4536.0
1 TraesCS4A01G291400 chr4A 92.593 54 4 0 2375 2428 598724607 598724554 7.280000e-11 78.7
2 TraesCS4A01G291400 chr4A 89.655 58 5 1 2367 2424 514080171 514080115 3.390000e-09 73.1
3 TraesCS4A01G291400 chr4D 89.215 1363 84 21 442 1767 8816928 8818264 0.000000e+00 1644.0
4 TraesCS4A01G291400 chr4D 89.723 613 51 11 1843 2447 8818327 8818935 0.000000e+00 773.0
5 TraesCS4A01G291400 chr4D 90.152 396 24 6 1 388 8816544 8816932 3.650000e-138 501.0
6 TraesCS4A01G291400 chr4D 90.769 65 6 0 1971 2035 8819405 8819469 1.210000e-13 87.9
7 TraesCS4A01G291400 chr4B 84.004 1044 88 37 796 1768 16502813 16503848 0.000000e+00 929.0
8 TraesCS4A01G291400 chr4B 88.418 613 59 8 1843 2449 16797363 16797969 0.000000e+00 728.0
9 TraesCS4A01G291400 chr4B 87.581 620 55 16 1843 2456 16503908 16504511 0.000000e+00 699.0
10 TraesCS4A01G291400 chr4B 85.915 639 45 23 1139 1737 16796644 16797277 7.410000e-180 640.0
11 TraesCS4A01G291400 chr4B 86.395 441 33 10 1 428 16795524 16795950 8.000000e-125 457.0
12 TraesCS4A01G291400 chr4B 86.889 389 25 9 50 428 16502061 16502433 1.760000e-111 412.0
13 TraesCS4A01G291400 chr4B 86.731 309 26 7 796 1090 16796342 16796649 1.820000e-86 329.0
14 TraesCS4A01G291400 chr4B 79.853 273 17 15 495 756 16502571 16502816 5.430000e-37 165.0
15 TraesCS4A01G291400 chr4B 77.323 269 39 15 497 756 16796090 16796345 3.290000e-29 139.0
16 TraesCS4A01G291400 chr4B 92.593 54 4 0 2375 2428 613321823 613321876 7.280000e-11 78.7
17 TraesCS4A01G291400 chr2D 92.857 56 3 1 2367 2422 13653173 13653119 2.020000e-11 80.5
18 TraesCS4A01G291400 chr1D 92.857 56 3 1 2374 2428 447468451 447468506 2.020000e-11 80.5
19 TraesCS4A01G291400 chr6D 86.154 65 8 1 2369 2432 303059847 303059911 4.380000e-08 69.4
20 TraesCS4A01G291400 chr2B 100.000 29 0 0 2428 2456 152501312 152501340 1.000000e-03 54.7


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 TraesCS4A01G291400 chr4A 594459318 594461773 2455 True 4536.000 4536 100.00000 1 2456 1 chr4A.!!$R2 2455
1 TraesCS4A01G291400 chr4D 8816544 8819469 2925 False 751.475 1644 89.96475 1 2447 4 chr4D.!!$F1 2446
2 TraesCS4A01G291400 chr4B 16502061 16504511 2450 False 551.250 929 84.58175 50 2456 4 chr4B.!!$F2 2406
3 TraesCS4A01G291400 chr4B 16795524 16797969 2445 False 458.600 728 84.95640 1 2449 5 chr4B.!!$F3 2448

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
637 740 0.179067 ACCGAACGCAGAAAAGGACA 60.179 50.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1751 2006 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.0 0.0 0.0 0.0 3.82 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
27 28 2.271800 CGAGACTTCCCAACAGTATGC 58.728 52.381 0.00 0.00 42.53 3.14
30 31 4.434520 GAGACTTCCCAACAGTATGCTAC 58.565 47.826 0.00 0.00 42.53 3.58
36 42 7.048512 ACTTCCCAACAGTATGCTACTTATTC 58.951 38.462 0.00 0.00 42.53 1.75
102 108 5.873179 TCGTTCTTCCATGTATCCAAAAC 57.127 39.130 0.00 0.00 0.00 2.43
243 262 2.425312 TGATTTGTCTCGGCTCTCTCTC 59.575 50.000 0.00 0.00 0.00 3.20
244 263 2.208132 TTTGTCTCGGCTCTCTCTCT 57.792 50.000 0.00 0.00 0.00 3.10
256 275 3.393970 CTCTCTGGCGGCTCCCAA 61.394 66.667 11.43 0.00 33.73 4.12
257 276 3.382803 CTCTCTGGCGGCTCCCAAG 62.383 68.421 11.43 0.00 33.73 3.61
268 287 2.084610 GCTCCCAAGCCAACATTTTC 57.915 50.000 0.00 0.00 43.10 2.29
269 288 1.620323 GCTCCCAAGCCAACATTTTCT 59.380 47.619 0.00 0.00 43.10 2.52
287 311 8.932791 ACATTTTCTACATTTTCTACAGGTACG 58.067 33.333 0.00 0.00 0.00 3.67
288 312 6.956299 TTTCTACATTTTCTACAGGTACGC 57.044 37.500 0.00 0.00 0.00 4.42
290 314 3.308438 ACATTTTCTACAGGTACGCGT 57.692 42.857 19.17 19.17 0.00 6.01
297 327 3.864686 CAGGTACGCGTGCATGGC 61.865 66.667 29.96 13.03 0.00 4.40
375 405 1.464023 CGGTAGCATTGTCACGCAAAG 60.464 52.381 0.00 0.00 40.91 2.77
398 428 4.538283 CGAGATCCGCGTGCTCGT 62.538 66.667 24.77 0.00 44.59 4.18
419 450 1.200252 TGACGAGCAAGCAGAGTAGAC 59.800 52.381 0.00 0.00 0.00 2.59
428 459 1.886585 CAGAGTAGACTGCTGCGGT 59.113 57.895 15.10 15.10 0.00 5.68
430 461 1.096416 AGAGTAGACTGCTGCGGTAC 58.904 55.000 15.16 10.22 0.00 3.34
476 562 2.979676 CAACCTCGCTGCAGGCAA 60.980 61.111 17.12 0.00 41.91 4.52
574 677 0.407139 AGTTCTGCTTTGGGCTCCAT 59.593 50.000 0.00 0.00 42.39 3.41
576 679 1.252904 TTCTGCTTTGGGCTCCATGC 61.253 55.000 10.54 10.54 42.39 4.06
577 680 1.980232 CTGCTTTGGGCTCCATGCA 60.980 57.895 15.80 15.80 45.15 3.96
578 681 1.305465 TGCTTTGGGCTCCATGCAT 60.305 52.632 13.97 0.00 45.15 3.96
579 682 1.143183 GCTTTGGGCTCCATGCATG 59.857 57.895 20.19 20.19 45.15 4.06
580 683 1.324740 GCTTTGGGCTCCATGCATGA 61.325 55.000 28.31 12.81 45.15 3.07
581 684 1.410004 CTTTGGGCTCCATGCATGAT 58.590 50.000 28.31 0.00 45.15 2.45
582 685 1.340248 CTTTGGGCTCCATGCATGATC 59.660 52.381 28.31 14.99 45.15 2.92
583 686 0.468585 TTGGGCTCCATGCATGATCC 60.469 55.000 28.31 22.08 45.15 3.36
584 687 1.358051 TGGGCTCCATGCATGATCCT 61.358 55.000 28.31 0.00 45.15 3.24
585 688 0.694771 GGGCTCCATGCATGATCCTA 59.305 55.000 28.31 6.84 45.15 2.94
586 689 1.284198 GGGCTCCATGCATGATCCTAT 59.716 52.381 28.31 0.00 45.15 2.57
587 690 2.641305 GGCTCCATGCATGATCCTATC 58.359 52.381 28.31 8.96 45.15 2.08
588 691 2.277969 GCTCCATGCATGATCCTATCG 58.722 52.381 28.31 8.56 42.31 2.92
589 692 2.354503 GCTCCATGCATGATCCTATCGT 60.355 50.000 28.31 0.00 42.31 3.73
590 693 3.519579 CTCCATGCATGATCCTATCGTC 58.480 50.000 28.31 0.00 0.00 4.20
591 694 2.094545 TCCATGCATGATCCTATCGTCG 60.095 50.000 28.31 6.55 0.00 5.12
592 695 2.353109 CCATGCATGATCCTATCGTCGT 60.353 50.000 28.31 0.00 0.00 4.34
593 696 2.706555 TGCATGATCCTATCGTCGTC 57.293 50.000 0.00 0.00 0.00 4.20
594 697 1.269723 TGCATGATCCTATCGTCGTCC 59.730 52.381 0.00 0.00 0.00 4.79
607 710 4.838152 CGTCCCTCCCACATGCCG 62.838 72.222 0.00 0.00 0.00 5.69
637 740 0.179067 ACCGAACGCAGAAAAGGACA 60.179 50.000 0.00 0.00 0.00 4.02
667 797 2.588314 GGCTGAGCTGCTGATCGG 60.588 66.667 7.01 12.84 37.97 4.18
668 798 2.186384 GCTGAGCTGCTGATCGGT 59.814 61.111 17.51 0.00 37.31 4.69
694 825 4.794439 CGTCACATCGGCCGAGCA 62.794 66.667 33.87 11.36 0.00 4.26
734 865 0.884704 CCCTGTTTGCGCCGCTATAT 60.885 55.000 11.67 0.00 0.00 0.86
745 876 1.207329 GCCGCTATATAACCTCCAGGG 59.793 57.143 0.00 0.00 40.27 4.45
762 893 4.256813 GAACCCGTCACGTTCCTC 57.743 61.111 0.00 0.00 34.75 3.71
763 894 1.731969 GAACCCGTCACGTTCCTCG 60.732 63.158 0.00 0.00 46.00 4.63
764 895 3.853597 AACCCGTCACGTTCCTCGC 62.854 63.158 0.00 0.00 44.19 5.03
772 903 3.912907 CGTTCCTCGCCGGCCTAT 61.913 66.667 23.46 0.00 0.00 2.57
773 904 2.280186 GTTCCTCGCCGGCCTATG 60.280 66.667 23.46 6.82 0.00 2.23
774 905 2.762459 TTCCTCGCCGGCCTATGT 60.762 61.111 23.46 0.00 0.00 2.29
775 906 1.456145 TTCCTCGCCGGCCTATGTA 60.456 57.895 23.46 0.00 0.00 2.29
776 907 0.830444 TTCCTCGCCGGCCTATGTAT 60.830 55.000 23.46 0.00 0.00 2.29
777 908 1.079819 CCTCGCCGGCCTATGTATG 60.080 63.158 23.46 3.72 0.00 2.39
778 909 1.666011 CTCGCCGGCCTATGTATGT 59.334 57.895 23.46 0.00 0.00 2.29
779 910 0.885879 CTCGCCGGCCTATGTATGTA 59.114 55.000 23.46 0.00 0.00 2.29
780 911 0.885879 TCGCCGGCCTATGTATGTAG 59.114 55.000 23.46 1.37 0.00 2.74
781 912 0.601558 CGCCGGCCTATGTATGTAGT 59.398 55.000 23.46 0.00 0.00 2.73
782 913 1.814394 CGCCGGCCTATGTATGTAGTA 59.186 52.381 23.46 0.00 0.00 1.82
783 914 2.426024 CGCCGGCCTATGTATGTAGTAT 59.574 50.000 23.46 0.00 0.00 2.12
784 915 3.628942 CGCCGGCCTATGTATGTAGTATA 59.371 47.826 23.46 0.00 0.00 1.47
785 916 4.261072 CGCCGGCCTATGTATGTAGTATAG 60.261 50.000 23.46 0.00 0.00 1.31
786 917 4.499357 GCCGGCCTATGTATGTAGTATAGC 60.499 50.000 18.11 0.00 0.00 2.97
787 918 4.888239 CCGGCCTATGTATGTAGTATAGCT 59.112 45.833 0.00 0.00 0.00 3.32
788 919 6.060136 CCGGCCTATGTATGTAGTATAGCTA 58.940 44.000 0.00 0.00 0.00 3.32
919 1098 2.183679 GGCTCTTCTTCTTCCTCCTCA 58.816 52.381 0.00 0.00 0.00 3.86
953 1132 2.484651 TCTTCGTCTTCTTCGTCTCAGG 59.515 50.000 0.00 0.00 0.00 3.86
957 1136 1.542030 GTCTTCTTCGTCTCAGGCAGA 59.458 52.381 0.00 0.00 0.00 4.26
959 1138 2.828520 TCTTCTTCGTCTCAGGCAGATT 59.171 45.455 0.00 0.00 32.08 2.40
961 1140 1.478510 TCTTCGTCTCAGGCAGATTCC 59.521 52.381 0.00 0.00 32.08 3.01
962 1141 1.205655 CTTCGTCTCAGGCAGATTCCA 59.794 52.381 0.00 0.00 32.08 3.53
963 1142 0.532573 TCGTCTCAGGCAGATTCCAC 59.467 55.000 0.00 0.00 32.08 4.02
964 1143 0.534412 CGTCTCAGGCAGATTCCACT 59.466 55.000 0.00 0.00 32.08 4.00
965 1144 1.738365 CGTCTCAGGCAGATTCCACTG 60.738 57.143 0.00 0.00 40.43 3.66
974 1167 2.392662 CAGATTCCACTGGGAGCTAGA 58.607 52.381 0.00 0.00 46.01 2.43
987 1180 3.181480 GGGAGCTAGAGTGATTCACTGAC 60.181 52.174 23.57 10.38 45.44 3.51
992 1185 4.439974 GCTAGAGTGATTCACTGACCTCTG 60.440 50.000 23.57 11.56 45.44 3.35
1251 1464 2.970974 GAGCAGGTCCAGCAAACGC 61.971 63.158 9.19 0.00 0.00 4.84
1437 1650 1.021920 CAGAGGAGAGCGTCGTCAGA 61.022 60.000 12.47 0.00 41.74 3.27
1576 1828 8.154203 TCATGTTTGTTAGTGGATGAGAAGTAA 58.846 33.333 0.00 0.00 0.00 2.24
1577 1829 7.962964 TGTTTGTTAGTGGATGAGAAGTAAG 57.037 36.000 0.00 0.00 0.00 2.34
1578 1830 7.506114 TGTTTGTTAGTGGATGAGAAGTAAGT 58.494 34.615 0.00 0.00 0.00 2.24
1579 1831 7.441157 TGTTTGTTAGTGGATGAGAAGTAAGTG 59.559 37.037 0.00 0.00 0.00 3.16
1604 1856 3.834231 ACCAAACAAATCAGAATCCTGGG 59.166 43.478 0.00 0.00 40.76 4.45
1633 1888 7.648142 TGGAGTTTTAAATTCACTCACATGTC 58.352 34.615 16.53 3.42 39.02 3.06
1703 1958 3.321682 CCCATGAACATGTGACCAACTTT 59.678 43.478 0.00 0.00 37.11 2.66
1707 1962 3.631686 TGAACATGTGACCAACTTTCTGG 59.368 43.478 0.00 0.00 42.68 3.86
1717 1972 2.362077 CCAACTTTCTGGACTTTGGTGG 59.638 50.000 0.00 0.00 38.96 4.61
1733 1988 1.265905 GGTGGCAAAACTTGTCTACGG 59.734 52.381 0.00 0.00 35.94 4.02
1744 1999 0.530744 TGTCTACGGATGCCACAGAC 59.469 55.000 0.00 0.00 35.68 3.51
1750 2005 0.246360 CGGATGCCACAGACTACACA 59.754 55.000 0.00 0.00 0.00 3.72
1751 2006 1.726853 GGATGCCACAGACTACACAC 58.273 55.000 0.00 0.00 0.00 3.82
1753 2008 2.069273 GATGCCACAGACTACACACAC 58.931 52.381 0.00 0.00 0.00 3.82
1755 2010 1.217882 GCCACAGACTACACACACAC 58.782 55.000 0.00 0.00 0.00 3.82
1756 2011 1.472552 GCCACAGACTACACACACACA 60.473 52.381 0.00 0.00 0.00 3.72
1757 2012 2.201732 CCACAGACTACACACACACAC 58.798 52.381 0.00 0.00 0.00 3.82
1758 2013 2.418060 CCACAGACTACACACACACACA 60.418 50.000 0.00 0.00 0.00 3.72
1759 2014 2.603110 CACAGACTACACACACACACAC 59.397 50.000 0.00 0.00 0.00 3.82
1760 2015 2.232696 ACAGACTACACACACACACACA 59.767 45.455 0.00 0.00 0.00 3.72
1761 2016 2.603110 CAGACTACACACACACACACAC 59.397 50.000 0.00 0.00 0.00 3.82
1762 2017 2.232696 AGACTACACACACACACACACA 59.767 45.455 0.00 0.00 0.00 3.72
1763 2018 2.343101 ACTACACACACACACACACAC 58.657 47.619 0.00 0.00 0.00 3.82
1764 2019 2.289133 ACTACACACACACACACACACA 60.289 45.455 0.00 0.00 0.00 3.72
1765 2020 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1766 2021 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1767 2022 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1768 2023 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1769 2024 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1770 2025 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1771 2026 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1772 2027 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1773 2028 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1774 2029 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1775 2030 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1776 2031 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1777 2032 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1778 2033 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1779 2034 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1780 2035 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1781 2036 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1782 2037 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1783 2038 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1784 2039 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1785 2040 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1786 2041 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1787 2042 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1788 2043 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1789 2044 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1790 2045 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1791 2046 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1792 2047 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1793 2048 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1794 2049 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1795 2050 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1796 2051 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1797 2052 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1798 2053 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1799 2054 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1800 2055 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1801 2056 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1815 2072 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1840 2097 7.882791 ACAGTTGTGTAAATATGGACATCAGAA 59.117 33.333 0.00 0.00 34.05 3.02
1845 2138 9.112725 TGTGTAAATATGGACATCAGAATTCAG 57.887 33.333 8.44 0.00 0.00 3.02
1854 2147 7.223584 TGGACATCAGAATTCAGTCTTAACAA 58.776 34.615 8.44 0.00 0.00 2.83
1932 2226 5.534278 TGAAGTTTGGTTGTATGAGCAATGA 59.466 36.000 0.00 0.00 36.95 2.57
1948 2242 9.956720 ATGAGCAATGAAAGTATTATTTGTAGC 57.043 29.630 0.00 0.00 0.00 3.58
1993 2287 3.504863 ACATGAGCATTTCATTTGACGC 58.495 40.909 0.00 0.00 44.14 5.19
2023 2317 9.494271 TGAATGAATGCCTTATCTAACTCATAC 57.506 33.333 0.00 0.00 0.00 2.39
2025 2319 6.455647 TGAATGCCTTATCTAACTCATACGG 58.544 40.000 0.00 0.00 0.00 4.02
2035 2329 5.396484 TCTAACTCATACGGACGTTTTCTG 58.604 41.667 1.57 0.00 36.55 3.02
2063 2357 6.380095 TGACGGGGCACATATTTATTAAAC 57.620 37.500 0.00 0.00 0.00 2.01
2161 2461 9.761504 TTTTCATCAGTTTCAAGAAATATGCAA 57.238 25.926 0.00 0.00 32.36 4.08
2192 2492 4.341806 TGAGACCGGCGTCCTAAAAATATA 59.658 41.667 6.01 0.00 40.12 0.86
2441 2742 2.814919 TCGGTTGTGTGTTTGTTCACTT 59.185 40.909 0.00 0.00 38.90 3.16
2452 2753 6.544197 TGTGTTTGTTCACTTATTTCAGCCTA 59.456 34.615 0.00 0.00 38.90 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 52 9.114952 TGACATTTCTTTTGTAATGTAGTGACA 57.885 29.630 0.00 0.00 45.89 3.58
102 108 2.132089 TTTGTAGGGTCCAAGCCGGG 62.132 60.000 2.18 0.00 41.56 5.73
140 159 2.736721 GCAATGGCTATTCTAATCGCGA 59.263 45.455 13.09 13.09 36.96 5.87
256 275 8.177119 TGTAGAAAATGTAGAAAATGTTGGCT 57.823 30.769 0.00 0.00 0.00 4.75
257 276 7.542130 CCTGTAGAAAATGTAGAAAATGTTGGC 59.458 37.037 0.00 0.00 0.00 4.52
258 277 8.576442 ACCTGTAGAAAATGTAGAAAATGTTGG 58.424 33.333 0.00 0.00 0.00 3.77
261 280 8.932791 CGTACCTGTAGAAAATGTAGAAAATGT 58.067 33.333 0.00 0.00 0.00 2.71
262 281 7.903431 GCGTACCTGTAGAAAATGTAGAAAATG 59.097 37.037 0.00 0.00 0.00 2.32
263 282 7.201496 CGCGTACCTGTAGAAAATGTAGAAAAT 60.201 37.037 0.00 0.00 0.00 1.82
264 283 6.089820 CGCGTACCTGTAGAAAATGTAGAAAA 59.910 38.462 0.00 0.00 0.00 2.29
265 284 5.574055 CGCGTACCTGTAGAAAATGTAGAAA 59.426 40.000 0.00 0.00 0.00 2.52
266 285 5.097529 CGCGTACCTGTAGAAAATGTAGAA 58.902 41.667 0.00 0.00 0.00 2.10
267 286 4.156556 ACGCGTACCTGTAGAAAATGTAGA 59.843 41.667 11.67 0.00 0.00 2.59
268 287 4.264614 CACGCGTACCTGTAGAAAATGTAG 59.735 45.833 13.44 0.00 0.00 2.74
269 288 4.168014 CACGCGTACCTGTAGAAAATGTA 58.832 43.478 13.44 0.00 0.00 2.29
287 311 4.450122 CACGACTGCCATGCACGC 62.450 66.667 0.00 0.00 32.60 5.34
288 312 3.792047 CCACGACTGCCATGCACG 61.792 66.667 0.00 0.00 34.90 5.34
290 314 2.358615 GACCACGACTGCCATGCA 60.359 61.111 0.00 0.00 36.92 3.96
297 327 2.430921 GGACGCAGACCACGACTG 60.431 66.667 0.00 0.00 43.12 3.51
398 428 1.886542 TCTACTCTGCTTGCTCGTCAA 59.113 47.619 0.00 0.00 0.00 3.18
433 475 1.958205 GATCTTGATCTGGGCGGCG 60.958 63.158 0.51 0.51 0.00 6.46
436 478 2.835580 ATCTGATCTTGATCTGGGCG 57.164 50.000 14.51 0.00 0.00 6.13
476 562 2.093973 AGATTTGATCGACCTCGCACTT 60.094 45.455 0.00 0.00 39.60 3.16
562 665 1.340248 GATCATGCATGGAGCCCAAAG 59.660 52.381 25.97 0.00 44.83 2.77
574 677 1.269723 GGACGACGATAGGATCATGCA 59.730 52.381 0.00 0.00 43.77 3.96
576 679 2.162608 GAGGGACGACGATAGGATCATG 59.837 54.545 0.00 0.00 43.77 3.07
577 680 2.438411 GAGGGACGACGATAGGATCAT 58.562 52.381 0.00 0.00 43.77 2.45
578 681 1.544982 GGAGGGACGACGATAGGATCA 60.545 57.143 0.00 0.00 43.77 2.92
579 682 1.166989 GGAGGGACGACGATAGGATC 58.833 60.000 0.00 0.00 43.77 3.36
580 683 0.251253 GGGAGGGACGACGATAGGAT 60.251 60.000 0.00 0.00 43.77 3.24
581 684 1.150081 GGGAGGGACGACGATAGGA 59.850 63.158 0.00 0.00 43.77 2.94
582 685 1.152819 TGGGAGGGACGACGATAGG 60.153 63.158 0.00 0.00 43.77 2.57
583 686 0.750546 TGTGGGAGGGACGACGATAG 60.751 60.000 0.00 0.00 46.19 2.08
584 687 0.106369 ATGTGGGAGGGACGACGATA 60.106 55.000 0.00 0.00 0.00 2.92
585 688 1.381327 ATGTGGGAGGGACGACGAT 60.381 57.895 0.00 0.00 0.00 3.73
586 689 2.036731 ATGTGGGAGGGACGACGA 59.963 61.111 0.00 0.00 0.00 4.20
587 690 2.184322 CATGTGGGAGGGACGACG 59.816 66.667 0.00 0.00 0.00 5.12
588 691 2.125106 GCATGTGGGAGGGACGAC 60.125 66.667 0.00 0.00 0.00 4.34
589 692 3.399181 GGCATGTGGGAGGGACGA 61.399 66.667 0.00 0.00 0.00 4.20
590 693 4.838152 CGGCATGTGGGAGGGACG 62.838 72.222 0.00 0.00 0.00 4.79
593 696 4.738998 TTGCGGCATGTGGGAGGG 62.739 66.667 2.28 0.00 0.00 4.30
594 697 2.676121 TTTGCGGCATGTGGGAGG 60.676 61.111 2.28 0.00 0.00 4.30
607 710 1.724581 CGTTCGGTTTCGCCTTTGC 60.725 57.895 0.00 0.00 36.13 3.68
627 730 2.668550 GCCGGCGTGTCCTTTTCT 60.669 61.111 12.58 0.00 0.00 2.52
667 797 3.728279 GATGTGACGGCCGGGGTAC 62.728 68.421 31.76 21.28 0.00 3.34
668 798 3.463585 GATGTGACGGCCGGGGTA 61.464 66.667 31.76 13.65 0.00 3.69
686 817 0.109132 CAAGGTTTGATTGCTCGGCC 60.109 55.000 0.00 0.00 0.00 6.13
694 825 3.254903 GGTTAGTTCGGCAAGGTTTGATT 59.745 43.478 0.00 0.00 0.00 2.57
734 865 0.906282 GACGGGTTCCCTGGAGGTTA 60.906 60.000 6.31 0.00 36.75 2.85
745 876 1.731969 CGAGGAACGTGACGGGTTC 60.732 63.158 10.66 4.78 42.32 3.62
755 886 3.912907 ATAGGCCGGCGAGGAACG 61.913 66.667 22.54 0.00 45.00 3.95
756 887 1.741327 TACATAGGCCGGCGAGGAAC 61.741 60.000 22.54 4.96 45.00 3.62
757 888 0.830444 ATACATAGGCCGGCGAGGAA 60.830 55.000 22.54 4.21 45.00 3.36
758 889 1.228769 ATACATAGGCCGGCGAGGA 60.229 57.895 22.54 6.91 45.00 3.71
759 890 1.079819 CATACATAGGCCGGCGAGG 60.080 63.158 22.54 15.41 44.97 4.63
760 891 0.885879 TACATACATAGGCCGGCGAG 59.114 55.000 22.54 12.42 0.00 5.03
761 892 0.885879 CTACATACATAGGCCGGCGA 59.114 55.000 22.54 11.84 0.00 5.54
762 893 0.601558 ACTACATACATAGGCCGGCG 59.398 55.000 22.54 9.21 0.00 6.46
763 894 4.499357 GCTATACTACATACATAGGCCGGC 60.499 50.000 21.18 21.18 0.00 6.13
764 895 4.888239 AGCTATACTACATACATAGGCCGG 59.112 45.833 0.00 0.00 0.00 6.13
786 917 0.523546 CGACGTGGTGCTAGCTGTAG 60.524 60.000 17.23 6.28 0.00 2.74
787 918 1.239296 ACGACGTGGTGCTAGCTGTA 61.239 55.000 17.23 0.00 0.00 2.74
788 919 1.239296 TACGACGTGGTGCTAGCTGT 61.239 55.000 17.23 6.56 0.00 4.40
789 920 0.797249 GTACGACGTGGTGCTAGCTG 60.797 60.000 17.23 3.28 0.00 4.24
790 921 1.505353 GTACGACGTGGTGCTAGCT 59.495 57.895 17.23 0.00 0.00 3.32
791 922 1.515736 GGTACGACGTGGTGCTAGC 60.516 63.158 17.31 8.10 0.00 3.42
792 923 1.138247 GGGTACGACGTGGTGCTAG 59.862 63.158 17.31 0.00 0.00 3.42
793 924 2.689785 CGGGTACGACGTGGTGCTA 61.690 63.158 17.31 0.00 44.60 3.49
794 925 4.047059 CGGGTACGACGTGGTGCT 62.047 66.667 17.31 0.00 44.60 4.40
813 984 1.652563 GTTCTTGGTTCGGTGGTGC 59.347 57.895 0.00 0.00 0.00 5.01
814 985 0.464735 TGGTTCTTGGTTCGGTGGTG 60.465 55.000 0.00 0.00 0.00 4.17
953 1132 0.833287 TAGCTCCCAGTGGAATCTGC 59.167 55.000 11.95 7.19 41.17 4.26
957 1136 2.114616 CACTCTAGCTCCCAGTGGAAT 58.885 52.381 11.95 0.00 41.17 3.01
959 1138 0.704664 TCACTCTAGCTCCCAGTGGA 59.295 55.000 11.95 0.00 38.48 4.02
961 1140 2.762887 TGAATCACTCTAGCTCCCAGTG 59.237 50.000 11.65 11.65 39.18 3.66
962 1141 2.763448 GTGAATCACTCTAGCTCCCAGT 59.237 50.000 6.07 0.00 0.00 4.00
963 1142 3.030291 AGTGAATCACTCTAGCTCCCAG 58.970 50.000 10.56 0.00 41.21 4.45
964 1143 2.762887 CAGTGAATCACTCTAGCTCCCA 59.237 50.000 13.72 0.00 43.43 4.37
965 1144 3.027412 TCAGTGAATCACTCTAGCTCCC 58.973 50.000 13.72 0.00 43.43 4.30
974 1167 1.277557 GCCAGAGGTCAGTGAATCACT 59.722 52.381 10.56 10.56 46.51 3.41
987 1180 0.399091 TACCCATCTCCAGCCAGAGG 60.399 60.000 1.05 0.00 34.46 3.69
992 1185 0.615850 GCCTATACCCATCTCCAGCC 59.384 60.000 0.00 0.00 0.00 4.85
1042 1243 3.322466 CCAGGAGAAGGCCACCGT 61.322 66.667 5.01 0.00 0.00 4.83
1136 1340 2.270205 CCTCCTTGGCGCTGTCAT 59.730 61.111 7.64 0.00 0.00 3.06
1329 1542 1.672356 CTTCTGGGCCTCGTTGTGG 60.672 63.158 4.53 0.00 0.00 4.17
1334 1547 1.965754 GAGCATCTTCTGGGCCTCGT 61.966 60.000 4.53 0.00 0.00 4.18
1459 1672 8.799367 CAGAGAGAGTCAATCTAATGATCATCT 58.201 37.037 9.06 0.00 38.84 2.90
1557 1809 5.542635 ACCACTTACTTCTCATCCACTAACA 59.457 40.000 0.00 0.00 0.00 2.41
1576 1828 5.476945 GGATTCTGATTTGTTTGGTACCACT 59.523 40.000 16.04 0.00 0.00 4.00
1577 1829 5.476945 AGGATTCTGATTTGTTTGGTACCAC 59.523 40.000 16.04 4.60 0.00 4.16
1578 1830 5.476599 CAGGATTCTGATTTGTTTGGTACCA 59.523 40.000 11.60 11.60 43.49 3.25
1579 1831 5.105756 CCAGGATTCTGATTTGTTTGGTACC 60.106 44.000 4.43 4.43 43.49 3.34
1604 1856 6.017109 TGTGAGTGAATTTAAAACTCCAGAGC 60.017 38.462 13.44 3.36 39.69 4.09
1661 1916 2.937149 GGTCCTCGCCTTTTTAGCTTAG 59.063 50.000 0.00 0.00 0.00 2.18
1663 1918 1.613520 GGGTCCTCGCCTTTTTAGCTT 60.614 52.381 0.00 0.00 0.00 3.74
1703 1958 1.754226 GTTTTGCCACCAAAGTCCAGA 59.246 47.619 0.00 0.00 41.58 3.86
1707 1962 3.119137 AGACAAGTTTTGCCACCAAAGTC 60.119 43.478 0.00 0.00 41.58 3.01
1717 1972 2.414161 GGCATCCGTAGACAAGTTTTGC 60.414 50.000 0.00 0.00 0.00 3.68
1733 1988 2.069273 GTGTGTGTAGTCTGTGGCATC 58.931 52.381 0.00 0.00 0.00 3.91
1744 1999 2.093625 GTGTGTGTGTGTGTGTGTGTAG 59.906 50.000 0.00 0.00 0.00 2.74
1750 2005 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1751 2006 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1753 2008 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1755 2010 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1756 2011 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1757 2012 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1758 2013 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1759 2014 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1760 2015 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1761 2016 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1762 2017 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1763 2018 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1764 2019 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1765 2020 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1766 2021 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1767 2022 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1768 2023 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1769 2024 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1770 2025 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1771 2026 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1772 2027 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1773 2028 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1774 2029 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1775 2030 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1776 2031 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1777 2032 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1778 2033 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1779 2034 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1780 2035 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1781 2036 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1782 2037 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1783 2038 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1784 2039 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1785 2040 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1786 2041 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1787 2042 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1788 2043 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1789 2044 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1790 2045 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1791 2046 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1792 2047 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1793 2048 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1794 2049 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1795 2050 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1796 2051 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1797 2052 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1798 2053 1.155889 CTGTGTGTGTGTGTGTGTGT 58.844 50.000 0.00 0.00 0.00 3.72
1799 2054 1.155889 ACTGTGTGTGTGTGTGTGTG 58.844 50.000 0.00 0.00 0.00 3.82
1800 2055 1.535028 CAACTGTGTGTGTGTGTGTGT 59.465 47.619 0.00 0.00 0.00 3.72
1801 2056 1.535028 ACAACTGTGTGTGTGTGTGTG 59.465 47.619 0.00 0.00 36.31 3.82
1815 2072 7.848223 TCTGATGTCCATATTTACACAACTG 57.152 36.000 0.00 0.00 0.00 3.16
1840 2097 4.447138 TGGTGGGTTGTTAAGACTGAAT 57.553 40.909 0.00 0.00 0.00 2.57
1845 2138 3.146847 CCTCTTGGTGGGTTGTTAAGAC 58.853 50.000 0.00 0.00 0.00 3.01
1873 2166 1.717194 ACGTATGTTGTACCGCCAAG 58.283 50.000 0.00 0.00 0.00 3.61
1963 2257 9.104965 CAAATGAAATGCTCATGTAATTTCCAT 57.895 29.630 18.82 13.11 44.43 3.41
1978 2272 3.307674 TCAAGTGCGTCAAATGAAATGC 58.692 40.909 0.00 0.00 0.00 3.56
1993 2287 8.218338 AGTTAGATAAGGCATTCATTCAAGTG 57.782 34.615 0.00 0.00 0.00 3.16
2023 2317 3.484649 CCGTCATATACAGAAAACGTCCG 59.515 47.826 0.00 0.00 0.00 4.79
2025 2319 3.800506 CCCCGTCATATACAGAAAACGTC 59.199 47.826 0.00 0.00 0.00 4.34
2035 2329 7.859325 AATAAATATGTGCCCCGTCATATAC 57.141 36.000 0.00 0.00 36.59 1.47
2155 2455 4.515191 GCCGGTCTCAAATTCTATTGCATA 59.485 41.667 1.90 0.00 0.00 3.14
2161 2461 2.483188 GGACGCCGGTCTCAAATTCTAT 60.483 50.000 1.90 0.00 42.97 1.98
2332 2633 3.336509 AGGTATGGATGTAGGTGAGCT 57.663 47.619 0.00 0.00 0.00 4.09
2340 2641 7.070629 TGTAGATGTGGTAAGGTATGGATGTA 58.929 38.462 0.00 0.00 0.00 2.29
2378 2679 9.396022 GAACATCTTATATTTGTGAAAGGAGGA 57.604 33.333 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.