Multiple sequence alignment - TraesCS7D01G245200

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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 TraesCS7D01G245200 chr7D 100.000 5863 0 0 1 5863 213791938 213786076 0.000000e+00 10828.0
1 TraesCS7D01G245200 chr7D 89.076 119 13 0 2181 2299 401073555 401073437 1.320000e-31 148.0
2 TraesCS7D01G245200 chr7B 96.543 2777 74 7 3094 5863 187779554 187782315 0.000000e+00 4577.0
3 TraesCS7D01G245200 chr7B 87.194 2163 87 71 1 2114 187776558 187778579 0.000000e+00 2285.0
4 TraesCS7D01G245200 chr7B 91.304 920 68 11 2141 3051 187778638 187779554 0.000000e+00 1245.0
5 TraesCS7D01G245200 chr7A 91.727 2635 137 33 3271 5844 225633428 225630814 0.000000e+00 3583.0
6 TraesCS7D01G245200 chr7A 87.599 1137 67 33 562 1651 225636568 225635459 0.000000e+00 1251.0
7 TraesCS7D01G245200 chr7A 93.866 538 19 8 1 536 225637228 225636703 0.000000e+00 798.0
8 TraesCS7D01G245200 chr7A 92.927 410 20 2 2298 2707 225634776 225634376 6.540000e-164 588.0
9 TraesCS7D01G245200 chr7A 88.553 463 36 6 2800 3256 225634373 225633922 4.000000e-151 545.0
10 TraesCS7D01G245200 chr7A 94.721 341 10 6 1666 1999 225635475 225635136 1.870000e-144 523.0
11 TraesCS7D01G245200 chr7A 78.710 155 31 2 1219 1372 685230148 685229995 1.040000e-17 102.0
12 TraesCS7D01G245200 chr1B 79.755 326 41 14 2723 3034 668003712 668003398 4.600000e-51 213.0
13 TraesCS7D01G245200 chr5A 78.481 316 47 19 2810 3107 510011560 510011248 2.790000e-43 187.0
14 TraesCS7D01G245200 chr5A 88.312 154 15 3 1222 1374 477587136 477586985 1.300000e-41 182.0
15 TraesCS7D01G245200 chr5A 85.714 98 10 3 4453 4549 477584952 477584858 3.740000e-17 100.0
16 TraesCS7D01G245200 chr5B 88.235 153 18 0 1218 1370 450107990 450107838 3.610000e-42 183.0
17 TraesCS7D01G245200 chr5B 90.083 121 12 0 2178 2298 636985892 636986012 2.190000e-34 158.0
18 TraesCS7D01G245200 chr5B 85.714 98 10 3 4453 4549 450105736 450105642 3.740000e-17 100.0
19 TraesCS7D01G245200 chr5D 87.037 162 17 4 1216 1375 376939827 376939668 4.670000e-41 180.0
20 TraesCS7D01G245200 chr5D 87.200 125 15 1 2178 2302 433503128 433503251 2.200000e-29 141.0
21 TraesCS7D01G245200 chr5D 85.714 98 10 3 4453 4549 376937555 376937461 3.740000e-17 100.0
22 TraesCS7D01G245200 chr6D 90.678 118 10 1 2181 2298 60497048 60496932 7.870000e-34 156.0
23 TraesCS7D01G245200 chr4B 90.517 116 9 2 2185 2299 589029033 589029147 1.020000e-32 152.0
24 TraesCS7D01G245200 chr4B 100.000 28 0 0 348 375 12144213 12144186 1.100000e-02 52.8
25 TraesCS7D01G245200 chr6A 89.256 121 9 3 2181 2299 150961280 150961162 1.320000e-31 148.0
26 TraesCS7D01G245200 chr1D 89.076 119 13 0 2181 2299 314570928 314570810 1.320000e-31 148.0
27 TraesCS7D01G245200 chr2A 80.628 191 34 2 2112 2299 655281275 655281085 1.700000e-30 145.0
28 TraesCS7D01G245200 chr3B 81.553 103 16 3 1274 1374 713321538 713321639 1.350000e-11 82.4
29 TraesCS7D01G245200 chr3B 85.246 61 9 0 2975 3035 715256293 715256353 4.900000e-06 63.9
30 TraesCS7D01G245200 chr3A 81.553 103 16 3 1274 1374 673899284 673899385 1.350000e-11 82.4
31 TraesCS7D01G245200 chr3D 81.633 98 16 2 1274 1370 538401370 538401466 4.870000e-11 80.5


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 TraesCS7D01G245200 chr7D 213786076 213791938 5862 True 10828.000000 10828 100.000000 1 5863 1 chr7D.!!$R1 5862
1 TraesCS7D01G245200 chr7B 187776558 187782315 5757 False 2702.333333 4577 91.680333 1 5863 3 chr7B.!!$F1 5862
2 TraesCS7D01G245200 chr7A 225630814 225637228 6414 True 1214.666667 3583 91.565500 1 5844 6 chr7A.!!$R2 5843

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
920 1077 0.039708 GCAAGCAAGAGCAGTGTTCC 60.040 55.0 3.01 0.0 45.49 3.62 F
2250 2628 0.038166 TGACTTGAATCCTGGTGGGC 59.962 55.0 0.00 0.0 34.39 5.36 F
3099 3489 0.923358 ACACCCAGGAACCAAAGTGA 59.077 50.0 11.88 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2659 3038 0.320771 CTCCTTCCCGGTGTTCACAG 60.321 60.0 0.0 0.92 0.00 3.66 R
4105 5014 0.109597 GTTGCTCACCAAAGGATGCG 60.110 55.0 0.0 0.00 34.68 4.73 R
4913 5828 0.547712 AGGCAGGGGCTTCTTCAGTA 60.548 55.0 0.0 0.00 40.87 2.74 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
28 30 2.355132 GCTCGCTCAAGTAGTAGTAGCA 59.645 50.000 0.00 0.00 32.69 3.49
29 31 3.547214 GCTCGCTCAAGTAGTAGTAGCAG 60.547 52.174 0.00 0.00 32.69 4.24
30 32 2.355132 TCGCTCAAGTAGTAGTAGCAGC 59.645 50.000 0.00 0.00 32.69 5.25
178 181 0.461961 CAGGTCTACTGGGTAGCAGC 59.538 60.000 0.00 0.00 43.70 5.25
180 183 0.461961 GGTCTACTGGGTAGCAGCAG 59.538 60.000 0.00 0.00 36.22 4.24
181 184 0.179097 GTCTACTGGGTAGCAGCAGC 60.179 60.000 0.00 0.00 36.22 5.25
263 273 3.609853 TCATGGGAAACATCTACTGTGC 58.390 45.455 0.00 0.00 37.84 4.57
266 276 0.727398 GGAAACATCTACTGTGCGGC 59.273 55.000 0.00 0.00 38.39 6.53
409 419 2.438614 TCTCACCTCCTCTCGGCG 60.439 66.667 0.00 0.00 0.00 6.46
534 544 4.880899 GCACGGGCATACAAAACC 57.119 55.556 3.77 0.00 40.72 3.27
535 545 1.214325 GCACGGGCATACAAAACCC 59.786 57.895 3.77 0.00 40.72 4.11
720 850 4.462132 CCATGACAAGTTGAGAGAGAGAGA 59.538 45.833 10.54 0.00 0.00 3.10
721 851 5.393352 CCATGACAAGTTGAGAGAGAGAGAG 60.393 48.000 10.54 0.00 0.00 3.20
722 852 4.979335 TGACAAGTTGAGAGAGAGAGAGA 58.021 43.478 10.54 0.00 0.00 3.10
723 853 5.003160 TGACAAGTTGAGAGAGAGAGAGAG 58.997 45.833 10.54 0.00 0.00 3.20
724 854 5.221823 TGACAAGTTGAGAGAGAGAGAGAGA 60.222 44.000 10.54 0.00 0.00 3.10
725 855 5.248640 ACAAGTTGAGAGAGAGAGAGAGAG 58.751 45.833 10.54 0.00 0.00 3.20
726 856 5.013079 ACAAGTTGAGAGAGAGAGAGAGAGA 59.987 44.000 10.54 0.00 0.00 3.10
727 857 5.350504 AGTTGAGAGAGAGAGAGAGAGAG 57.649 47.826 0.00 0.00 0.00 3.20
728 858 5.026121 AGTTGAGAGAGAGAGAGAGAGAGA 58.974 45.833 0.00 0.00 0.00 3.10
729 859 5.128499 AGTTGAGAGAGAGAGAGAGAGAGAG 59.872 48.000 0.00 0.00 0.00 3.20
730 860 4.871822 TGAGAGAGAGAGAGAGAGAGAGA 58.128 47.826 0.00 0.00 0.00 3.10
731 861 4.892345 TGAGAGAGAGAGAGAGAGAGAGAG 59.108 50.000 0.00 0.00 0.00 3.20
732 862 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
733 863 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
734 864 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
765 895 1.005037 CTAGGCTGTCGCACCAACA 60.005 57.895 0.00 0.00 38.10 3.33
769 899 1.301401 GCTGTCGCACCAACAGGTA 60.301 57.895 5.51 0.00 43.50 3.08
775 905 0.320374 CGCACCAACAGGTAAGGAGA 59.680 55.000 0.00 0.00 33.30 3.71
779 909 3.165875 CACCAACAGGTAAGGAGAGAGA 58.834 50.000 0.00 0.00 33.30 3.10
780 910 3.772025 CACCAACAGGTAAGGAGAGAGAT 59.228 47.826 0.00 0.00 33.30 2.75
785 932 1.221781 AGGTAAGGAGAGAGATGGGGG 59.778 57.143 0.00 0.00 0.00 5.40
812 959 1.376037 GAAGGGTGAAGCCTGGTCG 60.376 63.158 0.96 0.00 37.43 4.79
827 974 2.959599 TCGCTCGTGTGTGTGTGC 60.960 61.111 0.00 0.00 0.00 4.57
831 978 2.125872 TCGTGTGTGTGTGCGTGT 60.126 55.556 0.00 0.00 0.00 4.49
834 981 1.499949 GTGTGTGTGTGCGTGTGTT 59.500 52.632 0.00 0.00 0.00 3.32
842 995 0.108774 TGTGCGTGTGTTTCCCCATA 59.891 50.000 0.00 0.00 0.00 2.74
919 1076 0.950116 AGCAAGCAAGAGCAGTGTTC 59.050 50.000 0.00 0.00 45.49 3.18
920 1077 0.039708 GCAAGCAAGAGCAGTGTTCC 60.040 55.000 3.01 0.00 45.49 3.62
921 1078 1.311859 CAAGCAAGAGCAGTGTTCCA 58.688 50.000 3.01 0.00 45.49 3.53
922 1079 1.002033 CAAGCAAGAGCAGTGTTCCAC 60.002 52.381 3.01 0.00 45.49 4.02
923 1080 0.181114 AGCAAGAGCAGTGTTCCACA 59.819 50.000 3.01 0.00 45.49 4.17
924 1081 0.590195 GCAAGAGCAGTGTTCCACAG 59.410 55.000 3.01 0.00 41.58 3.66
951 1108 2.187946 CCTCCACGACCAGCATCC 59.812 66.667 0.00 0.00 0.00 3.51
957 1114 3.790437 CGACCAGCATCCCCAGCT 61.790 66.667 0.00 0.00 44.62 4.24
962 1119 3.790437 AGCATCCCCAGCTCACCG 61.790 66.667 0.00 0.00 38.01 4.94
964 1121 4.100084 CATCCCCAGCTCACCGCA 62.100 66.667 0.00 0.00 42.61 5.69
965 1122 4.101448 ATCCCCAGCTCACCGCAC 62.101 66.667 0.00 0.00 42.61 5.34
1011 1168 1.819208 CGCCGCAATGGAGATTGGA 60.819 57.895 0.00 0.00 40.56 3.53
1148 1323 3.118454 CGGCGTCAATGCGTCCTT 61.118 61.111 0.00 0.00 35.06 3.36
1385 1560 0.548682 AGGTCACCATTGCTCCTCCT 60.549 55.000 0.00 0.00 0.00 3.69
1397 1572 2.522193 CCTCCTACCTCCGCCTCC 60.522 72.222 0.00 0.00 0.00 4.30
1398 1573 2.604152 CTCCTACCTCCGCCTCCT 59.396 66.667 0.00 0.00 0.00 3.69
1421 1596 0.388649 TCTCGCTGCGTTTCTCTTCC 60.389 55.000 22.48 0.00 0.00 3.46
1424 1606 1.678269 CGCTGCGTTTCTCTTCCTCG 61.678 60.000 14.93 0.00 0.00 4.63
1452 1634 6.312918 GCCAATTTCTTGACGTATTCTGTAGA 59.687 38.462 0.00 0.00 34.04 2.59
1453 1635 7.464710 GCCAATTTCTTGACGTATTCTGTAGAG 60.465 40.741 0.00 0.00 34.04 2.43
1454 1636 7.545965 CCAATTTCTTGACGTATTCTGTAGAGT 59.454 37.037 0.00 0.00 34.04 3.24
1455 1637 9.569167 CAATTTCTTGACGTATTCTGTAGAGTA 57.431 33.333 0.00 0.00 34.04 2.59
1456 1638 9.570488 AATTTCTTGACGTATTCTGTAGAGTAC 57.430 33.333 0.00 4.91 34.94 2.73
1559 1749 5.123979 GCCCAAGCATTAATAGGTATAGCAC 59.876 44.000 4.48 0.00 39.53 4.40
1596 1797 1.077429 CTTAGCTTGGTGGGGCCTC 60.077 63.158 0.84 0.00 38.35 4.70
1624 1825 3.501828 TGTGTCAATTGCTTTGCGTCTAT 59.498 39.130 0.00 0.00 35.16 1.98
1625 1826 4.693095 TGTGTCAATTGCTTTGCGTCTATA 59.307 37.500 0.00 0.00 35.16 1.31
1626 1827 5.180304 TGTGTCAATTGCTTTGCGTCTATAA 59.820 36.000 0.00 0.00 35.16 0.98
1627 1828 6.128035 TGTGTCAATTGCTTTGCGTCTATAAT 60.128 34.615 0.00 0.00 35.16 1.28
1628 1829 6.747280 GTGTCAATTGCTTTGCGTCTATAATT 59.253 34.615 0.00 0.00 35.16 1.40
1629 1830 7.908082 GTGTCAATTGCTTTGCGTCTATAATTA 59.092 33.333 0.00 0.00 35.16 1.40
1630 1831 8.122330 TGTCAATTGCTTTGCGTCTATAATTAG 58.878 33.333 0.00 0.00 35.16 1.73
1632 1833 8.673711 TCAATTGCTTTGCGTCTATAATTAGTT 58.326 29.630 0.00 0.00 35.16 2.24
1633 1834 9.289303 CAATTGCTTTGCGTCTATAATTAGTTT 57.711 29.630 0.00 0.00 0.00 2.66
1634 1835 9.503427 AATTGCTTTGCGTCTATAATTAGTTTC 57.497 29.630 0.00 0.00 0.00 2.78
1635 1836 7.603963 TGCTTTGCGTCTATAATTAGTTTCA 57.396 32.000 0.00 0.00 0.00 2.69
1636 1837 7.461107 TGCTTTGCGTCTATAATTAGTTTCAC 58.539 34.615 0.00 0.00 0.00 3.18
1637 1838 7.118535 TGCTTTGCGTCTATAATTAGTTTCACA 59.881 33.333 0.00 0.00 0.00 3.58
1638 1839 7.960738 GCTTTGCGTCTATAATTAGTTTCACAA 59.039 33.333 0.00 0.00 0.00 3.33
1639 1840 9.478019 CTTTGCGTCTATAATTAGTTTCACAAG 57.522 33.333 0.00 0.00 0.00 3.16
1640 1841 7.000575 TGCGTCTATAATTAGTTTCACAAGC 57.999 36.000 0.00 0.00 0.00 4.01
1641 1842 6.816640 TGCGTCTATAATTAGTTTCACAAGCT 59.183 34.615 0.00 0.00 0.00 3.74
1642 1843 7.333423 TGCGTCTATAATTAGTTTCACAAGCTT 59.667 33.333 0.00 0.00 0.00 3.74
1643 1844 7.846592 GCGTCTATAATTAGTTTCACAAGCTTC 59.153 37.037 0.00 0.00 0.00 3.86
1644 1845 9.088512 CGTCTATAATTAGTTTCACAAGCTTCT 57.911 33.333 0.00 0.00 0.00 2.85
1651 1852 9.822185 AATTAGTTTCACAAGCTTCTTTCATTT 57.178 25.926 0.00 0.00 0.00 2.32
1652 1853 9.822185 ATTAGTTTCACAAGCTTCTTTCATTTT 57.178 25.926 0.00 0.00 0.00 1.82
1653 1854 9.651913 TTAGTTTCACAAGCTTCTTTCATTTTT 57.348 25.926 0.00 0.00 0.00 1.94
1687 1897 4.892934 ACACAAGCTTCTTTCATTGGGTTA 59.107 37.500 0.00 0.00 35.85 2.85
1704 1914 4.040217 TGGGTTAGGTGTTAGCGACTTTTA 59.960 41.667 0.00 0.00 0.00 1.52
1708 1918 7.334171 GGGTTAGGTGTTAGCGACTTTTATTTA 59.666 37.037 0.00 0.00 0.00 1.40
1749 1963 7.180748 GCTTGTAGCAGCTTAATACTTTGTAC 58.819 38.462 0.00 0.00 41.89 2.90
1809 2025 7.770801 TGGTAGACTGATTGATATGTTTTCG 57.229 36.000 0.00 0.00 0.00 3.46
2034 2377 6.094603 TCGTCATAGGTTGGTAGTCTTAAGTC 59.905 42.308 1.63 0.00 0.00 3.01
2048 2393 5.414144 AGTCTTAAGTCTGGTAAGTCCGTAC 59.586 44.000 1.63 0.00 39.52 3.67
2097 2443 1.223211 GAGGGGCAAGCTTCTCTCC 59.777 63.158 0.00 0.20 0.00 3.71
2131 2502 7.579589 TTTAACATACGCGTATACACTTGTT 57.420 32.000 29.79 28.13 0.00 2.83
2134 2505 4.796830 ACATACGCGTATACACTTGTTCTG 59.203 41.667 29.79 17.26 0.00 3.02
2151 2529 2.085677 TGTGAACACACACGCACAG 58.914 52.632 3.39 0.00 42.86 3.66
2170 2548 0.886490 GCCAATCCCTATGAGCACCG 60.886 60.000 0.00 0.00 0.00 4.94
2172 2550 1.134098 CCAATCCCTATGAGCACCGTT 60.134 52.381 0.00 0.00 0.00 4.44
2183 2561 0.679505 AGCACCGTTTAGAGACTGCA 59.320 50.000 0.00 0.00 0.00 4.41
2188 2566 2.299013 ACCGTTTAGAGACTGCACATCA 59.701 45.455 0.00 0.00 0.00 3.07
2192 2570 1.834188 TAGAGACTGCACATCACCGA 58.166 50.000 0.00 0.00 0.00 4.69
2194 2572 1.344438 AGAGACTGCACATCACCGAAA 59.656 47.619 0.00 0.00 0.00 3.46
2198 2576 3.189287 AGACTGCACATCACCGAAAATTC 59.811 43.478 0.00 0.00 0.00 2.17
2236 2614 1.538047 AAATGCGAGCACCATGACTT 58.462 45.000 0.00 0.00 0.00 3.01
2241 2619 1.063174 GCGAGCACCATGACTTGAATC 59.937 52.381 0.00 0.00 0.00 2.52
2245 2623 1.747355 GCACCATGACTTGAATCCTGG 59.253 52.381 0.00 0.00 39.56 4.45
2249 2627 2.372264 CATGACTTGAATCCTGGTGGG 58.628 52.381 0.00 0.00 0.00 4.61
2250 2628 0.038166 TGACTTGAATCCTGGTGGGC 59.962 55.000 0.00 0.00 34.39 5.36
2253 2631 1.992557 ACTTGAATCCTGGTGGGCTAA 59.007 47.619 0.00 0.00 34.39 3.09
2255 2633 3.181423 ACTTGAATCCTGGTGGGCTAAAA 60.181 43.478 0.00 0.00 34.39 1.52
2275 2653 4.838904 AAATACCAGTGTCCTCCTAACC 57.161 45.455 0.00 0.00 0.00 2.85
2279 2657 1.486726 CCAGTGTCCTCCTAACCATCC 59.513 57.143 0.00 0.00 0.00 3.51
2328 2706 8.405418 TCTCTTTAGTTAGCTGACTTTCTACA 57.595 34.615 17.16 0.00 0.00 2.74
2444 2822 8.936864 GGGTTACAGATGTTTATATGTGCTATC 58.063 37.037 0.00 0.00 39.01 2.08
2597 2975 9.868277 CACATTGCTTACCTATTTTGGATTTTA 57.132 29.630 0.00 0.00 0.00 1.52
2659 3038 1.226491 GATGTTGGTGCGCTCATGC 60.226 57.895 9.73 4.47 0.00 4.06
2685 3064 2.444895 CCGGGAAGGAGGGGAGAG 60.445 72.222 0.00 0.00 45.00 3.20
2737 3116 4.847512 TGTGAGGGGAACTTTTGGTCTATA 59.152 41.667 0.00 0.00 36.15 1.31
2744 3123 6.346896 GGGAACTTTTGGTCTATAGGTGTAG 58.653 44.000 0.00 0.00 36.15 2.74
2745 3124 6.070366 GGGAACTTTTGGTCTATAGGTGTAGT 60.070 42.308 0.00 0.00 36.15 2.73
2746 3125 7.124750 GGGAACTTTTGGTCTATAGGTGTAGTA 59.875 40.741 0.00 0.00 36.15 1.82
2747 3126 7.978414 GGAACTTTTGGTCTATAGGTGTAGTAC 59.022 40.741 0.00 0.00 36.15 2.73
2748 3127 8.426569 AACTTTTGGTCTATAGGTGTAGTACA 57.573 34.615 0.00 0.00 0.00 2.90
2918 3306 6.183360 CGGCCAAAATAGTGTGAATAGTGATT 60.183 38.462 2.24 0.00 0.00 2.57
2959 3348 1.439679 CCCTTTAGTCAACGCTGGTC 58.560 55.000 0.00 0.00 0.00 4.02
2964 3353 4.319549 CCTTTAGTCAACGCTGGTCTTTTC 60.320 45.833 0.00 0.00 0.00 2.29
2995 3384 9.906660 TGAAAATTTACATACTAGTGCAAAAGG 57.093 29.630 5.39 0.00 0.00 3.11
3023 3413 9.668497 AGTCAAGTTTACTCTAAAAACACTTCT 57.332 29.630 2.00 0.00 38.92 2.85
3099 3489 0.923358 ACACCCAGGAACCAAAGTGA 59.077 50.000 11.88 0.00 0.00 3.41
3191 3581 2.031037 TCAATTTGCGAGTTTGCGAC 57.969 45.000 0.00 0.00 37.81 5.19
3530 4408 1.202830 ACATGTACGGTTCCTTTGCCA 60.203 47.619 0.00 0.00 0.00 4.92
3562 4440 2.225496 TGGGGCCAGTTTTTCCATGTAT 60.225 45.455 4.39 0.00 0.00 2.29
3682 4560 1.110442 TGACCAGGCCTGTTGTTTTG 58.890 50.000 30.63 15.99 0.00 2.44
3768 4650 9.950680 GCAGCTTGCTATATCTTTGTTAAATTA 57.049 29.630 0.00 0.00 40.96 1.40
3823 4707 6.017605 CGTTAGTAGTACCCATCTCGTATTGT 60.018 42.308 0.00 0.00 0.00 2.71
3915 4800 9.632969 CATAACTTTTATTCGGTCATTAACTCG 57.367 33.333 0.00 0.00 0.00 4.18
4003 4912 2.365293 GTTCCACCAGTTGCCTGAATTT 59.635 45.455 0.00 0.00 41.50 1.82
4160 5072 2.423892 TCTTGCTCTCACCGATCACTAC 59.576 50.000 0.00 0.00 0.00 2.73
4171 5083 2.527100 CGATCACTACCGGTCAAGTTC 58.473 52.381 12.40 4.68 0.00 3.01
4406 5318 2.436646 GCATACAGCAGCCACGGT 60.437 61.111 0.00 0.00 44.79 4.83
4437 5349 3.011517 GCCCAGAGCTCCCTCCAA 61.012 66.667 10.93 0.00 38.96 3.53
4913 5828 4.349503 TGCGCAGGGAAGCATGGT 62.350 61.111 5.66 0.00 38.59 3.55
4945 5860 1.173043 CCTGCCTGCCGTTCATTTTA 58.827 50.000 0.00 0.00 0.00 1.52
5068 5988 6.535865 CCCATGTGATGTAAACCATGAATTTG 59.464 38.462 0.00 0.00 37.47 2.32
5270 6192 1.743958 AGTGAGATCAAGCAATGCAGC 59.256 47.619 8.35 0.00 0.00 5.25
5384 6311 3.763897 ACTGCCAAGAATAATGTGTTCCC 59.236 43.478 0.00 0.00 0.00 3.97
5755 6685 2.160417 GGCTGGAACAAAGAGATGAACG 59.840 50.000 0.00 0.00 38.70 3.95
5793 6724 3.391049 ACTCTAACTTCAACTGTTCGGC 58.609 45.455 0.00 0.00 0.00 5.54
5794 6725 2.737252 CTCTAACTTCAACTGTTCGGCC 59.263 50.000 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 30 2.669240 GAAACAGGGCTACGGGCT 59.331 61.111 2.91 0.00 41.46 5.19
29 31 2.437895 GGAAACAGGGCTACGGGC 60.438 66.667 0.00 0.00 40.90 6.13
30 32 2.271173 GGGAAACAGGGCTACGGG 59.729 66.667 0.00 0.00 0.00 5.28
178 181 0.179134 GGACCTGTACGCTGTAGCTG 60.179 60.000 0.00 0.00 39.32 4.24
180 183 1.226603 CGGACCTGTACGCTGTAGC 60.227 63.158 0.00 0.00 37.78 3.58
181 184 1.310933 ACCGGACCTGTACGCTGTAG 61.311 60.000 9.46 0.00 35.10 2.74
182 185 1.303561 ACCGGACCTGTACGCTGTA 60.304 57.895 9.46 0.00 35.10 2.74
183 186 2.599578 ACCGGACCTGTACGCTGT 60.600 61.111 9.46 0.00 35.10 4.40
184 187 2.126071 CACCGGACCTGTACGCTG 60.126 66.667 9.46 0.00 35.10 5.18
185 188 0.895100 TAACACCGGACCTGTACGCT 60.895 55.000 9.46 0.00 35.10 5.07
186 189 0.038343 TTAACACCGGACCTGTACGC 60.038 55.000 9.46 0.00 35.10 4.42
187 190 2.331194 CTTTAACACCGGACCTGTACG 58.669 52.381 9.46 0.00 36.49 3.67
242 252 3.609853 GCACAGTAGATGTTTCCCATGA 58.390 45.455 0.00 0.00 41.41 3.07
409 419 2.677836 TCCACTTATCAAATCACGCAGC 59.322 45.455 0.00 0.00 0.00 5.25
479 489 1.135689 CGTATGGTGAAAAGGCTGTGC 60.136 52.381 0.00 0.00 0.00 4.57
531 541 2.785776 GGAGGGGTTGGGTTGGGTT 61.786 63.158 0.00 0.00 0.00 4.11
532 542 3.190391 GGAGGGGTTGGGTTGGGT 61.190 66.667 0.00 0.00 0.00 4.51
533 543 3.992641 GGGAGGGGTTGGGTTGGG 61.993 72.222 0.00 0.00 0.00 4.12
534 544 4.360405 CGGGAGGGGTTGGGTTGG 62.360 72.222 0.00 0.00 0.00 3.77
720 850 3.964031 GGTCTCTCTCTCTCTCTCTCTCT 59.036 52.174 0.00 0.00 0.00 3.10
721 851 3.070302 GGGTCTCTCTCTCTCTCTCTCTC 59.930 56.522 0.00 0.00 0.00 3.20
722 852 3.041946 GGGTCTCTCTCTCTCTCTCTCT 58.958 54.545 0.00 0.00 0.00 3.10
723 853 2.771943 TGGGTCTCTCTCTCTCTCTCTC 59.228 54.545 0.00 0.00 0.00 3.20
724 854 2.505819 GTGGGTCTCTCTCTCTCTCTCT 59.494 54.545 0.00 0.00 0.00 3.10
725 855 2.238646 TGTGGGTCTCTCTCTCTCTCTC 59.761 54.545 0.00 0.00 0.00 3.20
726 856 2.026262 GTGTGGGTCTCTCTCTCTCTCT 60.026 54.545 0.00 0.00 0.00 3.10
727 857 2.026262 AGTGTGGGTCTCTCTCTCTCTC 60.026 54.545 0.00 0.00 0.00 3.20
728 858 1.992557 AGTGTGGGTCTCTCTCTCTCT 59.007 52.381 0.00 0.00 0.00 3.10
729 859 2.507407 AGTGTGGGTCTCTCTCTCTC 57.493 55.000 0.00 0.00 0.00 3.20
730 860 2.241176 CCTAGTGTGGGTCTCTCTCTCT 59.759 54.545 0.00 0.00 0.00 3.10
731 861 2.650322 CCTAGTGTGGGTCTCTCTCTC 58.350 57.143 0.00 0.00 0.00 3.20
732 862 1.341581 GCCTAGTGTGGGTCTCTCTCT 60.342 57.143 0.00 0.00 0.00 3.10
733 863 1.107945 GCCTAGTGTGGGTCTCTCTC 58.892 60.000 0.00 0.00 0.00 3.20
734 864 0.707616 AGCCTAGTGTGGGTCTCTCT 59.292 55.000 0.00 0.00 31.32 3.10
765 895 1.221781 CCCCCATCTCTCTCCTTACCT 59.778 57.143 0.00 0.00 0.00 3.08
769 899 2.367947 AAACCCCCATCTCTCTCCTT 57.632 50.000 0.00 0.00 0.00 3.36
775 905 5.272402 CCTTCAAATTAAACCCCCATCTCT 58.728 41.667 0.00 0.00 0.00 3.10
779 909 3.843619 CACCCTTCAAATTAAACCCCCAT 59.156 43.478 0.00 0.00 0.00 4.00
780 910 3.116707 TCACCCTTCAAATTAAACCCCCA 60.117 43.478 0.00 0.00 0.00 4.96
785 932 5.230182 CAGGCTTCACCCTTCAAATTAAAC 58.770 41.667 0.00 0.00 40.58 2.01
812 959 3.261951 ACGCACACACACACGAGC 61.262 61.111 0.00 0.00 0.00 5.03
831 978 2.304761 GAGTGGTGACTATGGGGAAACA 59.695 50.000 0.00 0.00 30.16 2.83
834 981 2.467880 GAGAGTGGTGACTATGGGGAA 58.532 52.381 0.00 0.00 30.16 3.97
842 995 2.252714 GAAAGAGGGAGAGTGGTGACT 58.747 52.381 0.00 0.00 33.98 3.41
919 1076 3.252284 AGGTGGAGGTGGCTGTGG 61.252 66.667 0.00 0.00 0.00 4.17
920 1077 2.348998 GAGGTGGAGGTGGCTGTG 59.651 66.667 0.00 0.00 0.00 3.66
921 1078 2.930562 GGAGGTGGAGGTGGCTGT 60.931 66.667 0.00 0.00 0.00 4.40
922 1079 2.930019 TGGAGGTGGAGGTGGCTG 60.930 66.667 0.00 0.00 0.00 4.85
923 1080 2.930562 GTGGAGGTGGAGGTGGCT 60.931 66.667 0.00 0.00 0.00 4.75
924 1081 4.394712 CGTGGAGGTGGAGGTGGC 62.395 72.222 0.00 0.00 0.00 5.01
957 1114 2.920384 TAGCTGGTGGTGCGGTGA 60.920 61.111 0.00 0.00 35.28 4.02
962 1119 1.144936 CCTAGCTAGCTGGTGGTGC 59.855 63.158 27.68 0.00 0.00 5.01
964 1121 0.688087 GGTCCTAGCTAGCTGGTGGT 60.688 60.000 27.68 1.87 0.00 4.16
965 1122 1.739338 CGGTCCTAGCTAGCTGGTGG 61.739 65.000 27.68 23.35 0.00 4.61
966 1123 0.752009 TCGGTCCTAGCTAGCTGGTG 60.752 60.000 27.68 17.25 0.00 4.17
967 1124 0.752376 GTCGGTCCTAGCTAGCTGGT 60.752 60.000 27.68 3.54 0.00 4.00
968 1125 1.787057 CGTCGGTCCTAGCTAGCTGG 61.787 65.000 27.68 23.99 0.00 4.85
969 1126 0.814410 TCGTCGGTCCTAGCTAGCTG 60.814 60.000 27.68 16.13 0.00 4.24
1124 1299 4.465512 CATTGACGCCGCCACTGC 62.466 66.667 0.00 0.00 0.00 4.40
1125 1300 4.465512 GCATTGACGCCGCCACTG 62.466 66.667 0.00 0.00 0.00 3.66
1168 1343 2.689034 CTTCCCCTTCCTCCCGCT 60.689 66.667 0.00 0.00 0.00 5.52
1385 1560 0.989212 AGAGAGAGGAGGCGGAGGTA 60.989 60.000 0.00 0.00 0.00 3.08
1397 1572 0.170116 AGAAACGCAGCGAGAGAGAG 59.830 55.000 24.65 0.00 0.00 3.20
1398 1573 0.169230 GAGAAACGCAGCGAGAGAGA 59.831 55.000 24.65 0.00 0.00 3.10
1421 1596 0.179189 GTCAAGAAATTGGCGGCGAG 60.179 55.000 12.98 0.00 0.00 5.03
1424 1606 4.458164 CGTCAAGAAATTGGCGGC 57.542 55.556 0.00 0.00 45.28 6.53
1452 1634 6.040616 GCTAGGAATACACCATGTACTGTACT 59.959 42.308 17.98 2.36 35.42 2.73
1453 1635 6.214399 GCTAGGAATACACCATGTACTGTAC 58.786 44.000 10.98 10.98 35.42 2.90
1454 1636 5.303589 GGCTAGGAATACACCATGTACTGTA 59.696 44.000 0.00 0.00 35.42 2.74
1455 1637 4.101119 GGCTAGGAATACACCATGTACTGT 59.899 45.833 0.00 0.00 35.42 3.55
1456 1638 4.100963 TGGCTAGGAATACACCATGTACTG 59.899 45.833 0.00 0.00 35.42 2.74
1596 1797 2.507339 AAGCAATTGACACAAACGGG 57.493 45.000 10.34 0.00 0.00 5.28
1625 1826 9.822185 AAATGAAAGAAGCTTGTGAAACTAATT 57.178 25.926 2.10 0.00 38.04 1.40
1626 1827 9.822185 AAAATGAAAGAAGCTTGTGAAACTAAT 57.178 25.926 2.10 0.00 38.04 1.73
1627 1828 9.651913 AAAAATGAAAGAAGCTTGTGAAACTAA 57.348 25.926 2.10 0.00 38.04 2.24
1654 1855 3.020984 AGAAGCTTGTGTTCCCGAAAAA 58.979 40.909 2.10 0.00 0.00 1.94
1655 1856 2.650322 AGAAGCTTGTGTTCCCGAAAA 58.350 42.857 2.10 0.00 0.00 2.29
1656 1857 2.341846 AGAAGCTTGTGTTCCCGAAA 57.658 45.000 2.10 0.00 0.00 3.46
1657 1858 2.341846 AAGAAGCTTGTGTTCCCGAA 57.658 45.000 2.10 0.00 0.00 4.30
1658 1859 2.218603 GAAAGAAGCTTGTGTTCCCGA 58.781 47.619 2.10 0.00 0.00 5.14
1659 1860 1.946768 TGAAAGAAGCTTGTGTTCCCG 59.053 47.619 2.10 0.00 0.00 5.14
1660 1861 4.301628 CAATGAAAGAAGCTTGTGTTCCC 58.698 43.478 2.10 0.00 0.00 3.97
1661 1862 4.301628 CCAATGAAAGAAGCTTGTGTTCC 58.698 43.478 2.10 0.00 0.00 3.62
1662 1863 4.202151 ACCCAATGAAAGAAGCTTGTGTTC 60.202 41.667 2.10 7.55 0.00 3.18
1663 1864 3.706086 ACCCAATGAAAGAAGCTTGTGTT 59.294 39.130 2.10 0.00 0.00 3.32
1664 1865 3.299503 ACCCAATGAAAGAAGCTTGTGT 58.700 40.909 2.10 0.00 0.00 3.72
1704 1914 8.033178 ACAAGCAATGGCCCTAATAAATAAAT 57.967 30.769 0.00 0.00 42.56 1.40
1708 1918 5.011023 GCTACAAGCAATGGCCCTAATAAAT 59.989 40.000 0.00 0.00 41.89 1.40
1809 2025 0.749454 GGCAGGGATGTCACATCACC 60.749 60.000 16.91 15.47 0.00 4.02
2048 2393 0.739112 GGAGCTTGAGTTGAGCCGAG 60.739 60.000 0.00 0.00 41.03 4.63
2053 2398 5.764487 AAAGAAAAGGAGCTTGAGTTGAG 57.236 39.130 0.00 0.00 0.00 3.02
2120 2491 6.838198 GTGTGTTCACAGAACAAGTGTATA 57.162 37.500 13.53 0.00 43.37 1.47
2134 2505 1.297598 GCTGTGCGTGTGTGTTCAC 60.298 57.895 0.00 0.00 44.08 3.18
2151 2529 0.886490 CGGTGCTCATAGGGATTGGC 60.886 60.000 0.00 0.00 0.00 4.52
2170 2548 2.668457 CGGTGATGTGCAGTCTCTAAAC 59.332 50.000 0.00 0.00 0.00 2.01
2172 2550 2.167662 TCGGTGATGTGCAGTCTCTAA 58.832 47.619 0.00 0.00 0.00 2.10
2183 2561 9.573133 GATTTATTTCAGAATTTTCGGTGATGT 57.427 29.630 0.00 0.00 0.00 3.06
2188 2566 8.348285 TCTGGATTTATTTCAGAATTTTCGGT 57.652 30.769 0.00 0.00 34.97 4.69
2198 2576 9.734620 TCGCATTTATTTCTGGATTTATTTCAG 57.265 29.630 0.00 0.00 0.00 3.02
2236 2614 3.534357 TTTTTAGCCCACCAGGATTCA 57.466 42.857 0.00 0.00 38.24 2.57
2241 2619 3.094484 TGGTATTTTTAGCCCACCAGG 57.906 47.619 0.00 0.00 34.40 4.45
2245 2623 3.442625 GGACACTGGTATTTTTAGCCCAC 59.557 47.826 0.00 0.00 0.00 4.61
2249 2627 4.844884 AGGAGGACACTGGTATTTTTAGC 58.155 43.478 0.00 0.00 0.00 3.09
2250 2628 6.822170 GGTTAGGAGGACACTGGTATTTTTAG 59.178 42.308 0.00 0.00 0.00 1.85
2253 2631 4.600111 TGGTTAGGAGGACACTGGTATTTT 59.400 41.667 0.00 0.00 0.00 1.82
2255 2633 3.798515 TGGTTAGGAGGACACTGGTATT 58.201 45.455 0.00 0.00 0.00 1.89
2262 2640 2.355818 GGTTGGATGGTTAGGAGGACAC 60.356 54.545 0.00 0.00 0.00 3.67
2296 2674 5.575218 GTCAGCTAACTAAAGAGAGAAGTGC 59.425 44.000 0.00 0.00 0.00 4.40
2328 2706 9.485206 AATAGTTTACAGAAAGTTACATGACGT 57.515 29.630 0.00 0.00 30.63 4.34
2444 2822 7.978975 TCAACAAAGGAAATACAAAGAAGTTGG 59.021 33.333 0.00 0.00 41.97 3.77
2632 3010 1.996786 GCACCAACATCCCGAGCATG 61.997 60.000 0.00 0.00 0.00 4.06
2659 3038 0.320771 CTCCTTCCCGGTGTTCACAG 60.321 60.000 0.00 0.92 0.00 3.66
2716 3095 4.473559 CCTATAGACCAAAAGTTCCCCTCA 59.526 45.833 0.00 0.00 0.00 3.86
2805 3186 8.970691 ATGGAAGATCAAGTTTATTTCAAACG 57.029 30.769 0.00 0.00 35.42 3.60
2887 3272 3.829601 TCACACTATTTTGGCCGGAATTT 59.170 39.130 5.05 0.00 0.00 1.82
2944 3333 4.067972 AGAAAAGACCAGCGTTGACTAA 57.932 40.909 0.00 0.00 0.00 2.24
2945 3334 3.746045 AGAAAAGACCAGCGTTGACTA 57.254 42.857 0.00 0.00 0.00 2.59
2964 3353 8.440059 TGCACTAGTATGTAAATTTTCACGAAG 58.560 33.333 0.00 0.00 0.00 3.79
3099 3489 8.557304 ACATTTCTCATCAATATGGGGAAATT 57.443 30.769 12.72 0.00 40.12 1.82
3156 3546 5.570589 GCAAATTGAAATCTAGTGTGCTGTC 59.429 40.000 0.00 0.00 0.00 3.51
3161 3551 5.931532 ACTCGCAAATTGAAATCTAGTGTG 58.068 37.500 0.00 0.00 0.00 3.82
3165 3555 5.002840 CGCAAACTCGCAAATTGAAATCTAG 59.997 40.000 0.00 0.00 0.00 2.43
3191 3581 3.826157 TGATTGGTAACTGCCCTTTCAAG 59.174 43.478 0.00 0.00 37.61 3.02
3530 4408 1.217942 ACTGGCCCCAGAAAAGAAAGT 59.782 47.619 20.59 0.00 46.30 2.66
3562 4440 1.064017 GGCCTTCATAATCACACCCCA 60.064 52.381 0.00 0.00 0.00 4.96
3682 4560 3.924144 TGGGAACAAACAAGCATAATGC 58.076 40.909 0.00 0.00 40.27 3.56
3858 4742 8.739039 CAAATCTCACAGGGTTTCATTGTATAA 58.261 33.333 0.00 0.00 0.00 0.98
3915 4800 6.109359 ACTGAATTTAGCAGTGAGGTATGAC 58.891 40.000 0.00 0.00 44.39 3.06
4003 4912 1.536766 CAGCTGCGTTTTCCTTGATCA 59.463 47.619 0.00 0.00 0.00 2.92
4105 5014 0.109597 GTTGCTCACCAAAGGATGCG 60.110 55.000 0.00 0.00 34.68 4.73
4130 5042 1.803555 GTGAGAGCAAGAGAGGCAAAC 59.196 52.381 0.00 0.00 0.00 2.93
4160 5072 1.068333 CAGCAAATGGAACTTGACCGG 60.068 52.381 0.00 0.00 0.00 5.28
4166 5078 4.282703 AGAGCAAATCAGCAAATGGAACTT 59.717 37.500 0.00 0.00 36.85 2.66
4171 5083 3.678072 CACAAGAGCAAATCAGCAAATGG 59.322 43.478 0.00 0.00 36.85 3.16
4289 5201 4.554363 CGGTAGCCTGGTCGAGCG 62.554 72.222 10.46 4.87 0.00 5.03
4437 5349 3.314331 CCCTGCGAGACACCCACT 61.314 66.667 0.00 0.00 0.00 4.00
4760 5672 3.650950 GGCCTGTTCCCCTGCAGA 61.651 66.667 17.39 0.00 34.87 4.26
4913 5828 0.547712 AGGCAGGGGCTTCTTCAGTA 60.548 55.000 0.00 0.00 40.87 2.74
5068 5988 3.961182 TCGACAAGCATACCGATACTTC 58.039 45.455 0.00 0.00 0.00 3.01
5270 6192 0.801251 CTTTCGGAGCAAAGGAGCTG 59.199 55.000 0.00 0.00 46.75 4.24
5353 6279 2.827800 TTCTTGGCAGTCTCTGTCAG 57.172 50.000 4.33 0.00 46.93 3.51
5411 6338 0.743097 GGATCAGCATCCCAGCAAAC 59.257 55.000 0.00 0.00 42.91 2.93
5755 6685 4.329545 TCGTGGGAAGGCTGCACC 62.330 66.667 0.50 1.45 39.61 5.01
5793 6724 5.157940 AGGGACTATTCATCAATCATCGG 57.842 43.478 0.00 0.00 36.02 4.18
5794 6725 4.861462 CGAGGGACTATTCATCAATCATCG 59.139 45.833 0.00 0.00 41.55 3.84


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

AutoCloner maintained by Alex Coulton.