Multiple sequence alignment - TraesCS2A01G471900

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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 TraesCS2A01G471900 chr2A 100.000 2339 0 0 1 2339 713914027 713916365 0.000000e+00 4320.0
1 TraesCS2A01G471900 chr2A 94.933 1046 48 5 320 1362 742308988 742307945 0.000000e+00 1633.0
2 TraesCS2A01G471900 chr7D 96.842 1045 31 2 320 1363 232925266 232926309 0.000000e+00 1746.0
3 TraesCS2A01G471900 chr7D 96.743 1044 33 1 320 1362 497912164 497911121 0.000000e+00 1738.0
4 TraesCS2A01G471900 chr7D 96.648 1044 34 1 320 1362 149106659 149105616 0.000000e+00 1733.0
5 TraesCS2A01G471900 chr2D 96.555 1045 34 2 320 1362 273018230 273019274 0.000000e+00 1729.0
6 TraesCS2A01G471900 chr2D 90.705 312 28 1 1364 1675 575759485 575759795 4.650000e-112 414.0
7 TraesCS2A01G471900 chr2D 86.850 327 25 8 8 319 575759163 575759486 1.330000e-92 350.0
8 TraesCS2A01G471900 chr2D 90.574 244 20 3 2095 2336 575690327 575690569 1.040000e-83 320.0
9 TraesCS2A01G471900 chr2D 88.163 245 20 5 2095 2336 575760155 575760393 1.370000e-72 283.0
10 TraesCS2A01G471900 chr2D 84.472 161 17 4 169 323 575759795 575759953 4.030000e-33 152.0
11 TraesCS2A01G471900 chr2D 75.401 374 36 21 5 323 575689464 575689836 1.890000e-26 130.0
12 TraesCS2A01G471900 chr2D 88.235 68 2 2 262 323 575690060 575690127 2.490000e-10 76.8
13 TraesCS2A01G471900 chr3D 96.077 1045 39 2 320 1363 87390355 87391398 0.000000e+00 1701.0
14 TraesCS2A01G471900 chr5A 95.881 1044 41 2 320 1362 635794214 635793172 0.000000e+00 1688.0
15 TraesCS2A01G471900 chr6A 94.556 1047 50 5 318 1362 35542769 35543810 0.000000e+00 1611.0
16 TraesCS2A01G471900 chr6D 94.163 1045 59 2 320 1362 413277146 413278190 0.000000e+00 1591.0
17 TraesCS2A01G471900 chr2B 93.750 240 11 2 2097 2336 691776907 691777142 7.950000e-95 357.0
18 TraesCS2A01G471900 chr7A 97.059 34 1 0 1530 1563 127083459 127083492 9.030000e-05 58.4


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 TraesCS2A01G471900 chr2A 713914027 713916365 2338 False 4320.00 4320 100.0000 1 2339 1 chr2A.!!$F1 2338
1 TraesCS2A01G471900 chr2A 742307945 742308988 1043 True 1633.00 1633 94.9330 320 1362 1 chr2A.!!$R1 1042
2 TraesCS2A01G471900 chr7D 232925266 232926309 1043 False 1746.00 1746 96.8420 320 1363 1 chr7D.!!$F1 1043
3 TraesCS2A01G471900 chr7D 497911121 497912164 1043 True 1738.00 1738 96.7430 320 1362 1 chr7D.!!$R2 1042
4 TraesCS2A01G471900 chr7D 149105616 149106659 1043 True 1733.00 1733 96.6480 320 1362 1 chr7D.!!$R1 1042
5 TraesCS2A01G471900 chr2D 273018230 273019274 1044 False 1729.00 1729 96.5550 320 1362 1 chr2D.!!$F1 1042
6 TraesCS2A01G471900 chr2D 575759163 575760393 1230 False 299.75 414 87.5475 8 2336 4 chr2D.!!$F3 2328
7 TraesCS2A01G471900 chr3D 87390355 87391398 1043 False 1701.00 1701 96.0770 320 1363 1 chr3D.!!$F1 1043
8 TraesCS2A01G471900 chr5A 635793172 635794214 1042 True 1688.00 1688 95.8810 320 1362 1 chr5A.!!$R1 1042
9 TraesCS2A01G471900 chr6A 35542769 35543810 1041 False 1611.00 1611 94.5560 318 1362 1 chr6A.!!$F1 1044
10 TraesCS2A01G471900 chr6D 413277146 413278190 1044 False 1591.00 1591 94.1630 320 1362 1 chr6D.!!$F1 1042


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
940 961 1.204146 GGGGGCAGTATTGAGAGACA 58.796 55.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1749 1772 0.03779 AGCCGAAGAAGCACTCAGAC 60.038 55.0 0.0 0.0 0.0 3.51 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
20 22 1.370437 CATGCTGATCTCCCTCGGG 59.630 63.158 0.00 0.00 0.00 5.14
22 24 3.157252 GCTGATCTCCCTCGGGCA 61.157 66.667 0.00 0.00 34.68 5.36
23 25 3.136750 CTGATCTCCCTCGGGCAG 58.863 66.667 0.00 0.00 34.68 4.85
34 36 2.249413 CTCGGGCAGCTCTGGTGAAT 62.249 60.000 0.66 0.00 32.22 2.57
40 42 2.559440 GCAGCTCTGGTGAATCTAAGG 58.441 52.381 0.66 0.00 32.22 2.69
53 55 5.411669 GTGAATCTAAGGGTCGTTGTTTGAT 59.588 40.000 0.00 0.00 0.00 2.57
55 57 6.148811 TGAATCTAAGGGTCGTTGTTTGATTC 59.851 38.462 0.00 0.00 40.15 2.52
57 59 2.951229 AGGGTCGTTGTTTGATTCCT 57.049 45.000 0.00 0.00 0.00 3.36
58 60 4.360951 AAGGGTCGTTGTTTGATTCCTA 57.639 40.909 0.00 0.00 0.00 2.94
59 61 3.671716 AGGGTCGTTGTTTGATTCCTAC 58.328 45.455 0.00 0.00 0.00 3.18
60 62 2.414138 GGGTCGTTGTTTGATTCCTACG 59.586 50.000 0.00 0.00 0.00 3.51
62 64 3.930848 GGTCGTTGTTTGATTCCTACGAT 59.069 43.478 0.00 0.00 39.73 3.73
63 65 5.104374 GGTCGTTGTTTGATTCCTACGATA 58.896 41.667 0.00 0.00 39.73 2.92
64 66 5.577945 GGTCGTTGTTTGATTCCTACGATAA 59.422 40.000 0.00 0.00 39.73 1.75
81 83 9.916397 CCTACGATAAACTGCTATTTACTTTTG 57.084 33.333 0.00 0.00 0.00 2.44
90 92 7.488322 ACTGCTATTTACTTTTGCTTTTGTCA 58.512 30.769 0.00 0.00 0.00 3.58
94 96 6.833342 ATTTACTTTTGCTTTTGTCAGCTG 57.167 33.333 7.63 7.63 40.79 4.24
95 97 2.543641 ACTTTTGCTTTTGTCAGCTGC 58.456 42.857 9.47 4.92 40.79 5.25
138 140 7.036220 GCTTGAGCTCAACTACTCTTGTATTA 58.964 38.462 25.16 0.00 38.21 0.98
142 144 5.958987 AGCTCAACTACTCTTGTATTAGGGT 59.041 40.000 0.00 0.00 32.47 4.34
187 190 6.477033 CCGTAAGCCATCTATATGCATCTTAC 59.523 42.308 0.19 11.05 36.63 2.34
193 196 8.105197 AGCCATCTATATGCATCTTACATGAAA 58.895 33.333 0.19 0.00 0.00 2.69
195 198 8.671921 CCATCTATATGCATCTTACATGAAACC 58.328 37.037 0.19 0.00 0.00 3.27
207 210 6.759827 TCTTACATGAAACCGTAGCTAATTCC 59.240 38.462 0.00 0.00 0.00 3.01
263 271 7.857569 TGCATATTTAATAGCACGGTAAGTTC 58.142 34.615 5.46 0.00 31.05 3.01
284 292 8.747538 AGTTCAGTTAAACTCCAAACTTGTAT 57.252 30.769 0.00 0.00 34.37 2.29
289 303 7.012894 CAGTTAAACTCCAAACTTGTATGGACA 59.987 37.037 0.00 0.00 40.74 4.02
310 324 1.680735 GAGTGTTGAATGGTGGCACAA 59.319 47.619 20.82 9.03 44.16 3.33
322 336 4.148079 TGGTGGCACAATACTTCATTTCA 58.852 39.130 20.82 0.00 44.16 2.69
384 398 8.200792 GTGTCAGATATGGAAGTTATCTTGTCT 58.799 37.037 0.00 0.00 34.85 3.41
398 412 5.948992 ATCTTGTCTGGCTAAAGTCAAAC 57.051 39.130 0.00 0.00 0.00 2.93
497 512 2.532250 TGTCCTACATGCTCTCAGGA 57.468 50.000 0.00 0.00 34.79 3.86
653 669 5.878406 TTACTCCTTCCAGATCAAGATCC 57.122 43.478 6.45 0.00 38.58 3.36
700 716 5.950758 TCGAGAAATGGTAGCTATCTCTC 57.049 43.478 15.78 13.16 35.50 3.20
886 906 5.101628 GCTTTGTGAAACTCAATGTTGACA 58.898 37.500 0.00 0.00 39.13 3.58
925 946 2.041301 TGGAGGGTACGATGGGGG 60.041 66.667 0.00 0.00 0.00 5.40
940 961 1.204146 GGGGGCAGTATTGAGAGACA 58.796 55.000 0.00 0.00 0.00 3.41
965 986 5.222048 ACAAAGGTAGGTTTATTGCAGGAGA 60.222 40.000 0.00 0.00 0.00 3.71
1009 1030 1.215647 GACGTTCTCATGGCGGAGT 59.784 57.895 5.98 0.00 36.30 3.85
1050 1071 2.288666 CTAGATTTAGCGCAAAGGGCA 58.711 47.619 11.47 0.00 44.06 5.36
1203 1224 9.988350 ATCATGACTAAATTCGAACATTGTAAC 57.012 29.630 0.00 0.00 0.00 2.50
1283 1305 2.644676 GGATTGGTTTGAGGAGCCTAC 58.355 52.381 0.00 0.00 0.00 3.18
1393 1416 9.343539 CTCCTTATAAAGTTCTTTATGGAAGGG 57.656 37.037 26.31 19.65 35.41 3.95
1418 1441 4.520492 TCCTCTGCAATTCTTTGAACTTCC 59.480 41.667 0.00 0.00 34.60 3.46
1424 1447 4.676924 GCAATTCTTTGAACTTCCACTTCG 59.323 41.667 0.00 0.00 34.60 3.79
1431 1454 4.139420 CTTCCACTTCGCGCGCTG 62.139 66.667 30.48 22.06 0.00 5.18
1501 1524 5.481105 TGCTAGGCAAATCAAGGAAATTTG 58.519 37.500 0.00 4.61 43.69 2.32
1502 1525 5.011943 TGCTAGGCAAATCAAGGAAATTTGT 59.988 36.000 0.00 0.00 43.09 2.83
1516 1539 4.039124 GGAAATTTGTCTTCAAGCCCAAGA 59.961 41.667 0.00 0.00 34.88 3.02
1522 1545 3.632145 TGTCTTCAAGCCCAAGAAAGAAC 59.368 43.478 0.00 0.00 31.60 3.01
1524 1547 1.604604 TCAAGCCCAAGAAAGAACGG 58.395 50.000 0.00 0.00 0.00 4.44
1525 1548 0.598065 CAAGCCCAAGAAAGAACGGG 59.402 55.000 0.00 0.00 42.03 5.28
1565 1588 7.946207 AGAAAAGGAAGGAAAGAGAATTTCAC 58.054 34.615 0.00 0.00 0.00 3.18
1588 1611 3.875727 CCAGAAGACATGCTTACATCAGG 59.124 47.826 0.00 0.00 36.83 3.86
1613 1636 4.201812 CGCAACCCTACAAACATGAGTATG 60.202 45.833 0.00 0.00 40.24 2.39
1623 1646 1.340017 ACATGAGTATGCACCACCACC 60.340 52.381 0.00 0.00 37.85 4.61
1626 1649 0.324943 GAGTATGCACCACCACCTGT 59.675 55.000 0.00 0.00 0.00 4.00
1629 1652 2.081462 GTATGCACCACCACCTGTAAC 58.919 52.381 0.00 0.00 0.00 2.50
1643 1666 6.102663 CCACCTGTAACTTCACTCTAGATTG 58.897 44.000 3.74 3.74 0.00 2.67
1650 1673 8.570488 TGTAACTTCACTCTAGATTGTACGAAA 58.430 33.333 9.66 0.00 0.00 3.46
1652 1675 7.216973 ACTTCACTCTAGATTGTACGAAACT 57.783 36.000 9.66 0.00 0.00 2.66
1653 1676 7.085116 ACTTCACTCTAGATTGTACGAAACTG 58.915 38.462 9.66 0.00 0.00 3.16
1675 1698 2.280524 TGTCCTTGAACGCGTGGG 60.281 61.111 14.98 13.38 0.00 4.61
1678 1701 3.283684 CCTTGAACGCGTGGGCAA 61.284 61.111 14.98 16.75 39.92 4.52
1680 1703 2.824489 TTGAACGCGTGGGCAACA 60.824 55.556 14.98 3.93 39.92 3.33
1681 1704 2.128853 CTTGAACGCGTGGGCAACAT 62.129 55.000 14.98 0.00 39.92 2.71
1682 1705 2.126888 GAACGCGTGGGCAACATG 60.127 61.111 14.98 0.00 39.92 3.21
1683 1706 3.609214 GAACGCGTGGGCAACATGG 62.609 63.158 14.98 0.00 39.92 3.66
1686 1709 3.762247 GCGTGGGCAACATGGCAT 61.762 61.111 6.25 0.00 45.76 4.40
1687 1710 2.972267 CGTGGGCAACATGGCATT 59.028 55.556 0.00 0.00 45.76 3.56
1690 1713 0.391528 GTGGGCAACATGGCATTTCC 60.392 55.000 0.00 0.00 45.76 3.13
1693 1716 2.041701 GGGCAACATGGCATTTCCTAT 58.958 47.619 0.00 0.00 45.76 2.57
1694 1717 2.036346 GGGCAACATGGCATTTCCTATC 59.964 50.000 0.00 0.00 45.76 2.08
1696 1719 4.144297 GGCAACATGGCATTTCCTATCTA 58.856 43.478 0.00 0.00 43.14 1.98
1697 1720 4.217118 GGCAACATGGCATTTCCTATCTAG 59.783 45.833 0.00 0.00 43.14 2.43
1698 1721 4.823989 GCAACATGGCATTTCCTATCTAGT 59.176 41.667 0.00 0.00 35.26 2.57
1700 1723 6.486657 GCAACATGGCATTTCCTATCTAGTAA 59.513 38.462 0.00 0.00 35.26 2.24
1702 1725 6.223852 ACATGGCATTTCCTATCTAGTAACG 58.776 40.000 0.00 0.00 35.26 3.18
1703 1726 4.628074 TGGCATTTCCTATCTAGTAACGC 58.372 43.478 0.00 0.00 35.26 4.84
1705 1728 4.448060 GGCATTTCCTATCTAGTAACGCAC 59.552 45.833 0.00 0.00 0.00 5.34
1706 1729 5.047847 GCATTTCCTATCTAGTAACGCACA 58.952 41.667 0.00 0.00 0.00 4.57
1708 1731 6.346919 GCATTTCCTATCTAGTAACGCACATG 60.347 42.308 0.00 0.00 0.00 3.21
1710 1733 5.690997 TCCTATCTAGTAACGCACATGAG 57.309 43.478 0.00 0.00 0.00 2.90
1723 1746 3.818961 CACATGAGTGCTAACTGTTGG 57.181 47.619 0.00 0.69 39.21 3.77
1726 1749 0.472044 TGAGTGCTAACTGTTGGGCA 59.528 50.000 15.38 15.38 36.52 5.36
1742 1765 1.228657 GGCAGTCCCAGTTCGACAAC 61.229 60.000 0.00 0.00 32.41 3.32
1743 1766 0.249911 GCAGTCCCAGTTCGACAACT 60.250 55.000 0.00 0.00 44.26 3.16
1745 1768 1.341531 CAGTCCCAGTTCGACAACTCT 59.658 52.381 0.00 0.00 41.24 3.24
1746 1769 1.341531 AGTCCCAGTTCGACAACTCTG 59.658 52.381 0.00 0.00 41.24 3.35
1747 1770 1.068741 GTCCCAGTTCGACAACTCTGT 59.931 52.381 0.00 0.00 41.24 3.41
1749 1772 1.867233 CCCAGTTCGACAACTCTGTTG 59.133 52.381 8.66 8.66 41.24 3.33
1750 1773 2.550978 CCAGTTCGACAACTCTGTTGT 58.449 47.619 14.80 14.80 41.24 3.32
1751 1774 2.540101 CCAGTTCGACAACTCTGTTGTC 59.460 50.000 25.02 25.02 41.24 3.18
1752 1775 3.448686 CAGTTCGACAACTCTGTTGTCT 58.551 45.455 28.91 15.51 44.79 3.41
1753 1776 3.243877 CAGTTCGACAACTCTGTTGTCTG 59.756 47.826 28.91 23.71 44.79 3.51
1757 1780 2.791560 CGACAACTCTGTTGTCTGAGTG 59.208 50.000 28.91 16.41 46.80 3.51
1758 1781 2.541762 GACAACTCTGTTGTCTGAGTGC 59.458 50.000 26.60 7.92 46.80 4.40
1760 1783 3.201290 CAACTCTGTTGTCTGAGTGCTT 58.799 45.455 8.13 0.00 46.80 3.91
1761 1784 3.104843 ACTCTGTTGTCTGAGTGCTTC 57.895 47.619 6.90 0.00 46.12 3.86
1762 1785 2.697751 ACTCTGTTGTCTGAGTGCTTCT 59.302 45.455 6.90 0.00 46.12 2.85
1763 1786 3.133721 ACTCTGTTGTCTGAGTGCTTCTT 59.866 43.478 6.90 0.00 46.12 2.52
1764 1787 3.722147 TCTGTTGTCTGAGTGCTTCTTC 58.278 45.455 0.00 0.00 0.00 2.87
1765 1788 2.473816 TGTTGTCTGAGTGCTTCTTCG 58.526 47.619 0.00 0.00 0.00 3.79
1766 1789 1.795286 GTTGTCTGAGTGCTTCTTCGG 59.205 52.381 0.00 0.00 0.00 4.30
1768 1791 0.037790 GTCTGAGTGCTTCTTCGGCT 60.038 55.000 0.00 0.00 0.00 5.52
1769 1792 0.681733 TCTGAGTGCTTCTTCGGCTT 59.318 50.000 0.00 0.00 0.00 4.35
1770 1793 1.070758 TCTGAGTGCTTCTTCGGCTTT 59.929 47.619 0.00 0.00 0.00 3.51
1771 1794 1.196354 CTGAGTGCTTCTTCGGCTTTG 59.804 52.381 0.00 0.00 0.00 2.77
1773 1796 1.462670 GAGTGCTTCTTCGGCTTTGAG 59.537 52.381 0.00 0.00 0.00 3.02
1774 1797 0.110010 GTGCTTCTTCGGCTTTGAGC 60.110 55.000 0.00 0.00 41.46 4.26
1775 1798 0.250467 TGCTTCTTCGGCTTTGAGCT 60.250 50.000 0.00 0.00 41.99 4.09
1776 1799 1.001974 TGCTTCTTCGGCTTTGAGCTA 59.998 47.619 0.00 0.00 41.99 3.32
1777 1800 2.284190 GCTTCTTCGGCTTTGAGCTAT 58.716 47.619 0.00 0.00 41.99 2.97
1778 1801 2.680339 GCTTCTTCGGCTTTGAGCTATT 59.320 45.455 0.00 0.00 41.99 1.73
1779 1802 3.127721 GCTTCTTCGGCTTTGAGCTATTT 59.872 43.478 0.00 0.00 41.99 1.40
1780 1803 4.379918 GCTTCTTCGGCTTTGAGCTATTTT 60.380 41.667 0.00 0.00 41.99 1.82
1781 1804 5.703876 CTTCTTCGGCTTTGAGCTATTTTT 58.296 37.500 0.00 0.00 41.99 1.94
1782 1805 6.622896 GCTTCTTCGGCTTTGAGCTATTTTTA 60.623 38.462 0.00 0.00 41.99 1.52
1785 1808 7.826690 TCTTCGGCTTTGAGCTATTTTTATTT 58.173 30.769 0.00 0.00 41.99 1.40
1786 1809 7.968405 TCTTCGGCTTTGAGCTATTTTTATTTC 59.032 33.333 0.00 0.00 41.99 2.17
1787 1810 7.391148 TCGGCTTTGAGCTATTTTTATTTCT 57.609 32.000 0.00 0.00 41.99 2.52
1790 1921 8.925700 CGGCTTTGAGCTATTTTTATTTCTTTT 58.074 29.630 0.00 0.00 41.99 2.27
1931 2082 9.567776 TGACAAACATTTTTAGATACCTTCTGA 57.432 29.630 0.00 0.00 35.79 3.27
2029 2180 8.568732 AAATACATGTTTTCGTGAAAATTCGT 57.431 26.923 2.30 9.99 41.64 3.85
2030 2181 9.666626 AAATACATGTTTTCGTGAAAATTCGTA 57.333 25.926 2.30 11.47 41.64 3.43
2031 2182 9.666626 AATACATGTTTTCGTGAAAATTCGTAA 57.333 25.926 2.30 0.00 41.64 3.18
2032 2183 9.834628 ATACATGTTTTCGTGAAAATTCGTAAT 57.165 25.926 2.30 0.34 41.64 1.89
2033 2184 8.568732 ACATGTTTTCGTGAAAATTCGTAATT 57.431 26.923 10.64 0.00 41.64 1.40
2034 2185 9.026074 ACATGTTTTCGTGAAAATTCGTAATTT 57.974 25.926 10.64 0.00 41.64 1.82
2127 2278 2.330924 ATCTAAGCTCCTTGGGCCGC 62.331 60.000 0.00 0.00 0.00 6.53
2149 2300 2.436115 GTGACCGGCCCAGTTAGC 60.436 66.667 0.00 0.00 0.00 3.09
2177 2328 2.358737 CTCCCAGGCCACACGTTC 60.359 66.667 5.01 0.00 0.00 3.95
2178 2329 2.847234 TCCCAGGCCACACGTTCT 60.847 61.111 5.01 0.00 0.00 3.01
2179 2330 1.534476 TCCCAGGCCACACGTTCTA 60.534 57.895 5.01 0.00 0.00 2.10
2180 2331 1.079127 CCCAGGCCACACGTTCTAG 60.079 63.158 5.01 0.00 0.00 2.43
2181 2332 1.079127 CCAGGCCACACGTTCTAGG 60.079 63.158 5.01 0.00 0.00 3.02
2222 2373 2.601562 GTGGGCGACGATTCCATAC 58.398 57.895 0.00 0.00 32.71 2.39
2228 2379 0.462375 CGACGATTCCATACCCACCA 59.538 55.000 0.00 0.00 0.00 4.17
2243 2394 1.384525 CACCAACGGTTTTCCACTCA 58.615 50.000 0.00 0.00 40.70 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.370437 CGAGGGAGATCAGCATGGG 59.630 63.158 0.00 0.00 36.16 4.00
1 2 1.370437 CCGAGGGAGATCAGCATGG 59.630 63.158 0.00 0.00 36.16 3.66
2 3 1.370437 CCCGAGGGAGATCAGCATG 59.630 63.158 0.84 0.00 37.50 4.06
3 4 2.515071 GCCCGAGGGAGATCAGCAT 61.515 63.158 13.28 0.00 37.50 3.79
4 5 3.157252 GCCCGAGGGAGATCAGCA 61.157 66.667 13.28 0.00 37.50 4.41
5 6 3.157252 TGCCCGAGGGAGATCAGC 61.157 66.667 13.28 0.00 37.50 4.26
6 7 3.136750 CTGCCCGAGGGAGATCAG 58.863 66.667 13.28 5.76 44.17 2.90
20 22 2.559440 CCTTAGATTCACCAGAGCTGC 58.441 52.381 0.00 0.00 0.00 5.25
22 24 2.769095 GACCCTTAGATTCACCAGAGCT 59.231 50.000 0.00 0.00 0.00 4.09
23 25 2.482142 CGACCCTTAGATTCACCAGAGC 60.482 54.545 0.00 0.00 0.00 4.09
29 31 4.753107 TCAAACAACGACCCTTAGATTCAC 59.247 41.667 0.00 0.00 0.00 3.18
34 36 4.041198 AGGAATCAAACAACGACCCTTAGA 59.959 41.667 0.00 0.00 0.00 2.10
40 42 3.319755 TCGTAGGAATCAAACAACGACC 58.680 45.455 0.00 0.00 34.74 4.79
53 55 9.880157 AAAGTAAATAGCAGTTTATCGTAGGAA 57.120 29.630 0.00 0.00 0.00 3.36
55 57 9.916397 CAAAAGTAAATAGCAGTTTATCGTAGG 57.084 33.333 0.00 0.00 0.00 3.18
57 59 9.158233 AGCAAAAGTAAATAGCAGTTTATCGTA 57.842 29.630 0.00 0.00 0.00 3.43
58 60 8.040716 AGCAAAAGTAAATAGCAGTTTATCGT 57.959 30.769 0.00 0.00 0.00 3.73
59 61 8.895932 AAGCAAAAGTAAATAGCAGTTTATCG 57.104 30.769 0.00 0.00 0.00 2.92
62 64 9.810545 ACAAAAGCAAAAGTAAATAGCAGTTTA 57.189 25.926 0.00 0.00 0.00 2.01
63 65 8.716646 ACAAAAGCAAAAGTAAATAGCAGTTT 57.283 26.923 0.00 0.00 0.00 2.66
64 66 7.978975 TGACAAAAGCAAAAGTAAATAGCAGTT 59.021 29.630 0.00 0.00 0.00 3.16
81 83 1.605710 TCTCTTGCAGCTGACAAAAGC 59.394 47.619 20.43 0.00 43.88 3.51
90 92 2.753452 CCAATTCATGTCTCTTGCAGCT 59.247 45.455 0.00 0.00 0.00 4.24
94 96 3.015327 AGCTCCAATTCATGTCTCTTGC 58.985 45.455 0.00 0.00 0.00 4.01
95 97 4.698780 TCAAGCTCCAATTCATGTCTCTTG 59.301 41.667 0.00 0.00 32.46 3.02
142 144 2.299867 GGAACACGACAACTAGGGGTAA 59.700 50.000 0.00 0.00 0.00 2.85
155 157 8.925039 GCATATAGATGGCTTACGGAACACGA 62.925 46.154 0.00 0.00 38.64 4.35
187 190 3.564225 GGGGAATTAGCTACGGTTTCATG 59.436 47.826 0.00 0.00 0.00 3.07
193 196 1.343681 TGGAGGGGAATTAGCTACGGT 60.344 52.381 0.00 0.00 0.00 4.83
195 198 3.118371 ACTTTGGAGGGGAATTAGCTACG 60.118 47.826 0.00 0.00 0.00 3.51
254 262 6.259387 AGTTTGGAGTTTAACTGAACTTACCG 59.741 38.462 0.93 0.00 39.84 4.02
255 263 7.563888 AGTTTGGAGTTTAACTGAACTTACC 57.436 36.000 0.93 0.00 39.84 2.85
263 271 7.012894 TGTCCATACAAGTTTGGAGTTTAACTG 59.987 37.037 11.84 0.00 40.50 3.16
284 292 2.487086 CCACCATTCAACACTCTGTCCA 60.487 50.000 0.00 0.00 0.00 4.02
289 303 1.133823 TGTGCCACCATTCAACACTCT 60.134 47.619 0.00 0.00 32.49 3.24
310 324 4.644685 CCCATCCCGTTTGAAATGAAGTAT 59.355 41.667 0.00 0.00 0.00 2.12
322 336 2.987125 CTCCGTCCCATCCCGTTT 59.013 61.111 0.00 0.00 0.00 3.60
497 512 4.806247 GCAAGTGCTTCGTATCTTCTACAT 59.194 41.667 0.00 0.00 38.21 2.29
653 669 1.018148 TTTGTACCCCATAATGCGCG 58.982 50.000 0.00 0.00 0.00 6.86
700 716 4.412199 TCTTTCCCACCATAGATACCAAGG 59.588 45.833 0.00 0.00 0.00 3.61
842 862 1.408822 CCCTAGGAGGACATTGCCAAC 60.409 57.143 11.48 0.00 37.67 3.77
886 906 2.887152 GCAAGTCATGGTCAAAAGAGGT 59.113 45.455 0.00 0.00 0.00 3.85
925 946 4.757149 ACCTTTGTTGTCTCTCAATACTGC 59.243 41.667 0.00 0.00 38.38 4.40
940 961 5.390387 TCCTGCAATAAACCTACCTTTGTT 58.610 37.500 0.00 0.00 0.00 2.83
965 986 6.155221 TGCACAGTAGTCTATCTTTCCATTCT 59.845 38.462 0.00 0.00 0.00 2.40
1009 1030 3.010584 AGGCCAAATTTGAGAGCTAAGGA 59.989 43.478 19.86 0.00 0.00 3.36
1050 1071 5.745312 TGATGATTAGGCGATTACATCCT 57.255 39.130 0.00 0.00 34.97 3.24
1203 1224 4.937620 TGTGCTACTTTATTTGCCTCTCTG 59.062 41.667 0.00 0.00 0.00 3.35
1387 1410 2.174424 AGAATTGCAGAGGATCCCTTCC 59.826 50.000 8.55 0.00 45.85 3.46
1393 1416 5.893897 AGTTCAAAGAATTGCAGAGGATC 57.106 39.130 0.00 0.00 36.45 3.36
1400 1423 5.591099 GAAGTGGAAGTTCAAAGAATTGCA 58.409 37.500 5.01 0.00 45.59 4.08
1401 1424 4.676924 CGAAGTGGAAGTTCAAAGAATTGC 59.323 41.667 5.01 0.00 46.63 3.56
1405 1428 2.286833 CGCGAAGTGGAAGTTCAAAGAA 59.713 45.455 0.00 0.00 46.63 2.52
1431 1454 0.871722 TGTAGTTCACATGCGTTGCC 59.128 50.000 0.00 0.00 30.04 4.52
1501 1524 3.304057 CGTTCTTTCTTGGGCTTGAAGAC 60.304 47.826 0.00 0.00 0.00 3.01
1502 1525 2.878406 CGTTCTTTCTTGGGCTTGAAGA 59.122 45.455 0.00 0.00 0.00 2.87
1516 1539 4.546829 TTAGCATAGTGTCCCGTTCTTT 57.453 40.909 0.00 0.00 0.00 2.52
1522 1545 6.202954 CCTTTTCTTATTAGCATAGTGTCCCG 59.797 42.308 0.00 0.00 0.00 5.14
1524 1547 8.732746 TTCCTTTTCTTATTAGCATAGTGTCC 57.267 34.615 0.00 0.00 0.00 4.02
1525 1548 8.831550 CCTTCCTTTTCTTATTAGCATAGTGTC 58.168 37.037 0.00 0.00 0.00 3.67
1565 1588 3.875727 CTGATGTAAGCATGTCTTCTGGG 59.124 47.826 5.78 0.00 36.25 4.45
1588 1611 0.109319 CATGTTTGTAGGGTTGCGGC 60.109 55.000 0.00 0.00 0.00 6.53
1613 1636 1.235724 GAAGTTACAGGTGGTGGTGC 58.764 55.000 0.00 0.00 0.00 5.01
1623 1646 7.749808 TCGTACAATCTAGAGTGAAGTTACAG 58.250 38.462 25.87 13.07 0.00 2.74
1626 1649 8.790718 AGTTTCGTACAATCTAGAGTGAAGTTA 58.209 33.333 25.87 5.72 0.00 2.24
1629 1652 7.085116 ACAGTTTCGTACAATCTAGAGTGAAG 58.915 38.462 25.87 15.40 0.00 3.02
1643 1666 3.366440 AGGACACAGACAGTTTCGTAC 57.634 47.619 0.00 0.00 0.00 3.67
1650 1673 1.806623 GCGTTCAAGGACACAGACAGT 60.807 52.381 0.00 0.00 0.00 3.55
1652 1675 0.874175 CGCGTTCAAGGACACAGACA 60.874 55.000 0.00 0.00 0.00 3.41
1653 1676 0.874607 ACGCGTTCAAGGACACAGAC 60.875 55.000 5.58 0.00 0.00 3.51
1675 1698 4.823989 ACTAGATAGGAAATGCCATGTTGC 59.176 41.667 0.00 0.00 40.02 4.17
1678 1701 6.223852 CGTTACTAGATAGGAAATGCCATGT 58.776 40.000 0.00 0.00 40.02 3.21
1680 1703 5.221641 TGCGTTACTAGATAGGAAATGCCAT 60.222 40.000 0.00 0.00 40.02 4.40
1681 1704 4.100344 TGCGTTACTAGATAGGAAATGCCA 59.900 41.667 0.00 5.19 40.02 4.92
1682 1705 4.448060 GTGCGTTACTAGATAGGAAATGCC 59.552 45.833 0.00 0.00 35.88 4.40
1683 1706 5.047847 TGTGCGTTACTAGATAGGAAATGC 58.952 41.667 0.00 11.53 36.59 3.56
1685 1708 7.050970 TCATGTGCGTTACTAGATAGGAAAT 57.949 36.000 0.00 0.00 0.00 2.17
1686 1709 6.096423 ACTCATGTGCGTTACTAGATAGGAAA 59.904 38.462 0.00 0.00 0.00 3.13
1687 1710 5.593095 ACTCATGTGCGTTACTAGATAGGAA 59.407 40.000 0.00 0.00 0.00 3.36
1703 1726 2.485426 CCCAACAGTTAGCACTCATGTG 59.515 50.000 0.00 0.00 46.37 3.21
1705 1728 1.470098 GCCCAACAGTTAGCACTCATG 59.530 52.381 3.16 0.00 0.00 3.07
1706 1729 1.073763 TGCCCAACAGTTAGCACTCAT 59.926 47.619 6.15 0.00 0.00 2.90
1708 1731 1.160137 CTGCCCAACAGTTAGCACTC 58.840 55.000 6.15 0.00 41.86 3.51
1723 1746 1.070786 TTGTCGAACTGGGACTGCC 59.929 57.895 0.00 0.00 35.45 4.85
1726 1749 1.341531 CAGAGTTGTCGAACTGGGACT 59.658 52.381 0.00 0.00 42.80 3.85
1727 1750 1.068741 ACAGAGTTGTCGAACTGGGAC 59.931 52.381 0.00 0.00 42.80 4.46
1729 1752 1.867233 CAACAGAGTTGTCGAACTGGG 59.133 52.381 0.00 0.00 42.80 4.45
1730 1753 2.540101 GACAACAGAGTTGTCGAACTGG 59.460 50.000 22.41 0.00 42.80 4.00
1731 1754 3.843426 GACAACAGAGTTGTCGAACTG 57.157 47.619 22.41 0.00 42.80 3.16
1737 1760 2.541762 GCACTCAGACAACAGAGTTGTC 59.458 50.000 26.94 26.94 46.71 3.18
1738 1761 2.169352 AGCACTCAGACAACAGAGTTGT 59.831 45.455 14.68 14.68 40.09 3.32
1739 1762 2.831333 AGCACTCAGACAACAGAGTTG 58.169 47.619 8.24 8.24 40.09 3.16
1742 1765 3.383620 AGAAGCACTCAGACAACAGAG 57.616 47.619 0.00 0.00 36.06 3.35
1743 1766 3.722147 GAAGAAGCACTCAGACAACAGA 58.278 45.455 0.00 0.00 0.00 3.41
1745 1768 2.473816 CGAAGAAGCACTCAGACAACA 58.526 47.619 0.00 0.00 0.00 3.33
1746 1769 1.795286 CCGAAGAAGCACTCAGACAAC 59.205 52.381 0.00 0.00 0.00 3.32
1747 1770 1.873903 GCCGAAGAAGCACTCAGACAA 60.874 52.381 0.00 0.00 0.00 3.18
1749 1772 0.037790 AGCCGAAGAAGCACTCAGAC 60.038 55.000 0.00 0.00 0.00 3.51
1750 1773 0.681733 AAGCCGAAGAAGCACTCAGA 59.318 50.000 0.00 0.00 0.00 3.27
1751 1774 1.196354 CAAAGCCGAAGAAGCACTCAG 59.804 52.381 0.00 0.00 0.00 3.35
1752 1775 1.202639 TCAAAGCCGAAGAAGCACTCA 60.203 47.619 0.00 0.00 0.00 3.41
1753 1776 1.462670 CTCAAAGCCGAAGAAGCACTC 59.537 52.381 0.00 0.00 0.00 3.51
1756 1779 0.250467 AGCTCAAAGCCGAAGAAGCA 60.250 50.000 0.00 0.00 43.77 3.91
1757 1780 1.726853 TAGCTCAAAGCCGAAGAAGC 58.273 50.000 0.00 0.00 43.77 3.86
1758 1781 4.954092 AAATAGCTCAAAGCCGAAGAAG 57.046 40.909 0.00 0.00 43.77 2.85
1760 1783 7.391148 AATAAAAATAGCTCAAAGCCGAAGA 57.609 32.000 0.00 0.00 43.77 2.87
1761 1784 7.970614 AGAAATAAAAATAGCTCAAAGCCGAAG 59.029 33.333 0.00 0.00 43.77 3.79
1762 1785 7.826690 AGAAATAAAAATAGCTCAAAGCCGAA 58.173 30.769 0.00 0.00 43.77 4.30
1763 1786 7.391148 AGAAATAAAAATAGCTCAAAGCCGA 57.609 32.000 0.00 0.00 43.77 5.54
1764 1787 8.466086 AAAGAAATAAAAATAGCTCAAAGCCG 57.534 30.769 0.00 0.00 43.77 5.52
1905 2056 9.567776 TCAGAAGGTATCTAAAAATGTTTGTCA 57.432 29.630 0.00 0.00 36.32 3.58
2003 2154 9.666626 ACGAATTTTCACGAAAACATGTATTTA 57.333 25.926 7.09 0.00 42.32 1.40
2004 2155 8.568732 ACGAATTTTCACGAAAACATGTATTT 57.431 26.923 7.09 2.16 42.32 1.40
2005 2156 9.666626 TTACGAATTTTCACGAAAACATGTATT 57.333 25.926 7.09 0.00 42.32 1.89
2006 2157 9.834628 ATTACGAATTTTCACGAAAACATGTAT 57.165 25.926 7.09 0.00 42.32 2.29
2007 2158 9.666626 AATTACGAATTTTCACGAAAACATGTA 57.333 25.926 7.09 7.40 42.32 2.29
2008 2159 8.568732 AATTACGAATTTTCACGAAAACATGT 57.431 26.923 7.09 0.00 42.32 3.21
2009 2160 9.842444 AAAATTACGAATTTTCACGAAAACATG 57.158 25.926 7.09 0.00 45.32 3.21
2104 2255 3.099905 GGCCCAAGGAGCTTAGATTTTT 58.900 45.455 0.00 0.00 0.00 1.94
2105 2256 2.739943 GGCCCAAGGAGCTTAGATTTT 58.260 47.619 0.00 0.00 0.00 1.82
2106 2257 1.408822 CGGCCCAAGGAGCTTAGATTT 60.409 52.381 0.00 0.00 0.00 2.17
2107 2258 0.181350 CGGCCCAAGGAGCTTAGATT 59.819 55.000 0.00 0.00 0.00 2.40
2108 2259 1.832912 CGGCCCAAGGAGCTTAGAT 59.167 57.895 0.00 0.00 0.00 1.98
2110 2261 2.514824 GCGGCCCAAGGAGCTTAG 60.515 66.667 0.00 0.00 0.00 2.18
2130 2281 1.079127 CTAACTGGGCCGGTCACAG 60.079 63.158 20.44 21.80 38.19 3.66
2135 2286 2.928396 AGTGCTAACTGGGCCGGT 60.928 61.111 13.59 13.59 34.48 5.28
2165 2316 2.955881 GCCCTAGAACGTGTGGCCT 61.956 63.158 3.32 0.00 36.07 5.19
2181 2332 3.697439 TAACGCTCATGGGCCAGCC 62.697 63.158 13.12 0.00 31.37 4.85
2222 2373 0.753848 AGTGGAAAACCGTTGGTGGG 60.754 55.000 0.00 0.00 35.34 4.61
2228 2379 0.256464 TGGGTGAGTGGAAAACCGTT 59.744 50.000 0.00 0.00 34.62 4.44



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

AutoCloner maintained by Alex Coulton.