Multiple sequence alignment - TraesCS7A01G142900

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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 TraesCS7A01G142900 chr7A 100.000 2388 0 0 1 2388 94385399 94383012 0.000000e+00 4410.0
1 TraesCS7A01G142900 chr7A 83.858 1208 98 44 567 1722 94400730 94399568 0.000000e+00 1061.0
2 TraesCS7A01G142900 chr7A 88.083 579 61 6 2 576 731747980 731747406 0.000000e+00 680.0
3 TraesCS7A01G142900 chr7A 97.297 74 2 0 1788 1861 94383539 94383612 2.490000e-25 126.0
4 TraesCS7A01G142900 chr7A 91.398 93 5 2 2294 2383 1840483 1840391 8.960000e-25 124.0
5 TraesCS7A01G142900 chr7B 93.070 1443 80 15 333 1766 44259315 44257884 0.000000e+00 2093.0
6 TraesCS7A01G142900 chr7B 86.448 1188 112 21 576 1722 44272422 44271243 0.000000e+00 1256.0
7 TraesCS7A01G142900 chr7B 83.213 1251 129 50 567 1762 44294034 44292810 0.000000e+00 1072.0
8 TraesCS7A01G142900 chr7B 86.038 530 32 15 1858 2383 44257842 44257351 4.520000e-147 531.0
9 TraesCS7A01G142900 chr7B 89.286 84 8 1 1783 1865 680190557 680190640 1.170000e-18 104.0
10 TraesCS7A01G142900 chr7D 88.356 584 60 3 1 576 417938810 417939393 0.000000e+00 695.0
11 TraesCS7A01G142900 chr7D 88.356 584 60 3 1 576 418076030 418076613 0.000000e+00 695.0
12 TraesCS7A01G142900 chr7D 88.376 585 59 4 1 576 418627715 418628299 0.000000e+00 695.0
13 TraesCS7A01G142900 chr7D 85.446 639 58 17 567 1179 92238471 92237842 1.200000e-177 632.0
14 TraesCS7A01G142900 chr7D 87.659 551 54 11 1226 1766 92229913 92229367 1.560000e-176 628.0
15 TraesCS7A01G142900 chr7D 84.242 679 49 24 576 1234 92235509 92234869 2.030000e-170 608.0
16 TraesCS7A01G142900 chr7D 84.000 650 68 12 668 1281 92230561 92229912 2.040000e-165 592.0
17 TraesCS7A01G142900 chr7D 84.182 550 53 20 1229 1766 92237734 92237207 9.850000e-139 503.0
18 TraesCS7A01G142900 chr7D 84.526 517 27 15 1868 2383 92229089 92228625 1.670000e-126 462.0
19 TraesCS7A01G142900 chr7D 79.481 385 61 10 1885 2262 92237120 92236747 8.470000e-65 257.0
20 TraesCS7A01G142900 chr7D 85.401 137 17 1 1230 1366 92234685 92234552 3.200000e-29 139.0
21 TraesCS7A01G142900 chr1D 88.325 197 20 1 2 195 21910437 21910633 1.430000e-57 233.0
22 TraesCS7A01G142900 chr1D 87.879 198 22 2 2 197 21913539 21913342 5.130000e-57 231.0
23 TraesCS7A01G142900 chr1D 91.398 93 5 2 2294 2383 461624619 461624711 8.960000e-25 124.0
24 TraesCS7A01G142900 chr1B 87.940 199 21 3 2 197 37322188 37321990 5.130000e-57 231.0
25 TraesCS7A01G142900 chr2D 84.810 158 17 5 2 158 29682031 29682182 4.110000e-33 152.0
26 TraesCS7A01G142900 chr2D 89.655 87 8 1 1788 1873 642198791 642198705 2.510000e-20 110.0
27 TraesCS7A01G142900 chr2D 90.244 82 5 3 1783 1861 642198710 642198791 1.170000e-18 104.0
28 TraesCS7A01G142900 chr5D 91.398 93 5 2 2294 2383 80121808 80121900 8.960000e-25 124.0
29 TraesCS7A01G142900 chr5D 90.909 77 6 1 1783 1858 332506252 332506328 4.200000e-18 102.0
30 TraesCS7A01G142900 chr4D 91.398 93 5 2 2294 2383 123306959 123307051 8.960000e-25 124.0
31 TraesCS7A01G142900 chr4D 91.398 93 5 2 2294 2383 123461470 123461378 8.960000e-25 124.0
32 TraesCS7A01G142900 chr4D 91.398 93 5 2 2294 2383 123647390 123647482 8.960000e-25 124.0
33 TraesCS7A01G142900 chr3D 91.398 93 5 2 2294 2383 414539585 414539493 8.960000e-25 124.0
34 TraesCS7A01G142900 chr2A 91.398 93 5 2 2294 2383 30195451 30195359 8.960000e-25 124.0
35 TraesCS7A01G142900 chr2A 93.939 66 4 0 1 66 747258468 747258403 1.510000e-17 100.0
36 TraesCS7A01G142900 chrUn 90.323 93 6 2 2294 2383 455454061 455453969 4.170000e-23 119.0
37 TraesCS7A01G142900 chr3A 92.208 77 5 1 1785 1861 586897374 586897449 9.030000e-20 108.0
38 TraesCS7A01G142900 chr2B 90.123 81 6 1 1788 1866 514348528 514348608 1.170000e-18 104.0
39 TraesCS7A01G142900 chr5A 88.506 87 6 2 1783 1866 638032985 638032900 4.200000e-18 102.0
40 TraesCS7A01G142900 chr4A 88.750 80 6 3 1784 1861 598725655 598725733 7.030000e-16 95.3


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 TraesCS7A01G142900 chr7A 94383012 94385399 2387 True 4410.000 4410 100.000000 1 2388 1 chr7A.!!$R2 2387
1 TraesCS7A01G142900 chr7A 94399568 94400730 1162 True 1061.000 1061 83.858000 567 1722 1 chr7A.!!$R3 1155
2 TraesCS7A01G142900 chr7A 731747406 731747980 574 True 680.000 680 88.083000 2 576 1 chr7A.!!$R4 574
3 TraesCS7A01G142900 chr7B 44257351 44259315 1964 True 1312.000 2093 89.554000 333 2383 2 chr7B.!!$R3 2050
4 TraesCS7A01G142900 chr7B 44271243 44272422 1179 True 1256.000 1256 86.448000 576 1722 1 chr7B.!!$R1 1146
5 TraesCS7A01G142900 chr7B 44292810 44294034 1224 True 1072.000 1072 83.213000 567 1762 1 chr7B.!!$R2 1195
6 TraesCS7A01G142900 chr7D 417938810 417939393 583 False 695.000 695 88.356000 1 576 1 chr7D.!!$F1 575
7 TraesCS7A01G142900 chr7D 418076030 418076613 583 False 695.000 695 88.356000 1 576 1 chr7D.!!$F2 575
8 TraesCS7A01G142900 chr7D 418627715 418628299 584 False 695.000 695 88.376000 1 576 1 chr7D.!!$F3 575
9 TraesCS7A01G142900 chr7D 92228625 92238471 9846 True 477.625 632 84.367125 567 2383 8 chr7D.!!$R1 1816

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
270 272 0.391528 GGCCGCCTTGCATTCAAAAT 60.392 50.0 0.71 0.0 0.00 1.82 F
1238 9180 1.207791 ATCCGCAGAGAAAGGGATGT 58.792 50.0 0.00 0.0 37.86 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1267 9209 0.250234 CCTCCACTTCATCGCCTGAA 59.750 55.000 1.17 1.17 41.61 3.02 R
2165 10364 1.431036 GGAGTCGTAGCCGTGGTAC 59.569 63.158 3.94 3.94 33.76 3.34 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
37 38 3.631686 TGCCATATTAATTTGAGCAGCGT 59.368 39.130 13.76 0.00 0.00 5.07
162 164 1.165907 TTGCTCTGGAAGGCACAACG 61.166 55.000 0.00 0.00 39.31 4.10
185 187 2.238521 TGCTCCAAAATCACTTCACCC 58.761 47.619 0.00 0.00 0.00 4.61
206 208 1.080772 CCTGTCGACTAGCAACGCA 60.081 57.895 17.92 0.00 0.00 5.24
250 252 1.376649 AGGAGCTTCCAAACCTCCAT 58.623 50.000 8.45 0.00 45.99 3.41
269 271 1.005156 GGCCGCCTTGCATTCAAAA 60.005 52.632 0.71 0.00 0.00 2.44
270 272 0.391528 GGCCGCCTTGCATTCAAAAT 60.392 50.000 0.71 0.00 0.00 1.82
307 309 1.678970 CCAGGCCCAAGTTACAGGC 60.679 63.158 0.00 3.00 46.37 4.85
376 382 2.037251 GACAGGGAATAGCGCTATGGAA 59.963 50.000 29.62 4.73 37.76 3.53
440 446 3.650942 AGTTCCAAACTGAGTCCCACATA 59.349 43.478 0.00 0.00 41.01 2.29
445 451 4.080919 CCAAACTGAGTCCCACATATCTGA 60.081 45.833 0.00 0.00 0.00 3.27
457 463 4.840680 CCACATATCTGATGGGTTAGAGGA 59.159 45.833 0.00 0.00 0.00 3.71
493 499 3.070018 CCAGCTTATGGCCGAATTAGAG 58.930 50.000 0.00 0.00 43.83 2.43
523 532 1.230635 GCATGATAGGCCGAACGCAT 61.231 55.000 0.00 0.00 40.31 4.73
871 8713 2.744202 CTCAGGGTCAAATGGTTCTTCG 59.256 50.000 0.00 0.00 0.00 3.79
927 8781 1.815003 CTGTTCCATTCCAACTCAGCC 59.185 52.381 0.00 0.00 0.00 4.85
1161 9021 1.347320 GTCTCCGGTGTTTCGATGTC 58.653 55.000 0.00 0.00 0.00 3.06
1225 9113 1.546923 TCTCGGTTACAGAAATCCGCA 59.453 47.619 0.00 0.00 42.28 5.69
1235 9123 1.909302 AGAAATCCGCAGAGAAAGGGA 59.091 47.619 0.00 0.00 0.00 4.20
1238 9180 1.207791 ATCCGCAGAGAAAGGGATGT 58.792 50.000 0.00 0.00 37.86 3.06
1320 9262 2.264120 GAGAAAGAGAGGGCAGGGGC 62.264 65.000 0.00 0.00 40.13 5.80
1421 9365 4.382362 CCCTGCATTCTCCATTCTTTTTCC 60.382 45.833 0.00 0.00 0.00 3.13
1431 9379 6.717084 TCTCCATTCTTTTTCCCTTTCTTCTC 59.283 38.462 0.00 0.00 0.00 2.87
1444 9392 6.269538 TCCCTTTCTTCTCTAGATGATCATGG 59.730 42.308 14.30 2.76 31.54 3.66
1453 9401 1.202782 AGATGATCATGGTGAGGCAGC 60.203 52.381 14.30 0.00 0.00 5.25
1474 9425 3.211865 CATGCTGCTGGTATGACAAGAT 58.788 45.455 0.00 0.00 39.83 2.40
1480 9431 5.363562 TGCTGGTATGACAAGATCAAGAT 57.636 39.130 0.00 0.00 41.93 2.40
1657 9610 2.713967 ATGGCCGGAAATGCTGCAC 61.714 57.895 5.05 0.00 0.00 4.57
1703 9656 4.582701 TTGTGTCTGGGCTACAAAATTG 57.417 40.909 0.00 0.00 31.95 2.32
1722 9675 9.528018 CAAAATTGTTGAAACTACTACACCAAT 57.472 29.630 0.00 0.00 30.39 3.16
1766 9722 6.757897 TTTGCAGGGACATCAAAATAGTAG 57.242 37.500 0.00 0.00 31.24 2.57
1794 9963 7.989947 TTTTGAGTCTGGTATTATACTCCCT 57.010 36.000 2.21 0.00 38.04 4.20
1795 9964 7.598759 TTTGAGTCTGGTATTATACTCCCTC 57.401 40.000 2.21 4.30 38.04 4.30
1796 9965 5.642165 TGAGTCTGGTATTATACTCCCTCC 58.358 45.833 2.21 0.00 38.04 4.30
1797 9966 4.664392 AGTCTGGTATTATACTCCCTCCG 58.336 47.826 2.21 0.00 0.00 4.63
1798 9967 4.106019 AGTCTGGTATTATACTCCCTCCGT 59.894 45.833 2.21 0.00 0.00 4.69
1799 9968 4.458642 GTCTGGTATTATACTCCCTCCGTC 59.541 50.000 2.21 0.00 0.00 4.79
1800 9969 3.762823 CTGGTATTATACTCCCTCCGTCC 59.237 52.174 2.21 0.00 0.00 4.79
1801 9970 3.095332 GGTATTATACTCCCTCCGTCCC 58.905 54.545 2.21 0.00 0.00 4.46
1802 9971 3.501019 GGTATTATACTCCCTCCGTCCCA 60.501 52.174 2.21 0.00 0.00 4.37
1803 9972 2.852714 TTATACTCCCTCCGTCCCAA 57.147 50.000 0.00 0.00 0.00 4.12
1804 9973 2.852714 TATACTCCCTCCGTCCCAAA 57.147 50.000 0.00 0.00 0.00 3.28
1805 9974 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
1806 9975 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
1807 9976 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
1808 9977 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
1809 9978 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
1810 9979 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
1811 9980 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
1812 9981 2.026636 CCCTCCGTCCCAAAATAAGTGA 60.027 50.000 0.00 0.00 0.00 3.41
1813 9982 3.007635 CCTCCGTCCCAAAATAAGTGAC 58.992 50.000 0.00 0.00 0.00 3.67
1814 9983 3.307480 CCTCCGTCCCAAAATAAGTGACT 60.307 47.826 0.00 0.00 0.00 3.41
1815 9984 3.933332 CTCCGTCCCAAAATAAGTGACTC 59.067 47.826 0.00 0.00 0.00 3.36
1816 9985 2.671396 CCGTCCCAAAATAAGTGACTCG 59.329 50.000 0.00 0.00 0.00 4.18
1817 9986 3.581755 CGTCCCAAAATAAGTGACTCGA 58.418 45.455 0.00 0.00 0.00 4.04
1818 9987 3.612860 CGTCCCAAAATAAGTGACTCGAG 59.387 47.826 11.84 11.84 0.00 4.04
1819 9988 4.566987 GTCCCAAAATAAGTGACTCGAGT 58.433 43.478 20.18 20.18 0.00 4.18
1820 9989 4.995487 GTCCCAAAATAAGTGACTCGAGTT 59.005 41.667 21.08 6.08 0.00 3.01
1821 9990 5.469084 GTCCCAAAATAAGTGACTCGAGTTT 59.531 40.000 21.08 12.75 0.00 2.66
1822 9991 5.468746 TCCCAAAATAAGTGACTCGAGTTTG 59.531 40.000 21.08 16.23 0.00 2.93
1823 9992 5.238650 CCCAAAATAAGTGACTCGAGTTTGT 59.761 40.000 21.08 5.70 0.00 2.83
1824 9993 6.425721 CCCAAAATAAGTGACTCGAGTTTGTA 59.574 38.462 21.08 10.21 0.00 2.41
1825 9994 7.288672 CCAAAATAAGTGACTCGAGTTTGTAC 58.711 38.462 21.08 15.71 0.00 2.90
1826 9995 7.042321 CCAAAATAAGTGACTCGAGTTTGTACA 60.042 37.037 21.08 9.76 0.00 2.90
1827 9996 8.332464 CAAAATAAGTGACTCGAGTTTGTACAA 58.668 33.333 21.08 3.59 0.00 2.41
1828 9997 8.428186 AAATAAGTGACTCGAGTTTGTACAAA 57.572 30.769 21.08 17.01 0.00 2.83
1840 10009 5.713822 GTTTGTACAAACTCGAGTCACTT 57.286 39.130 33.99 6.87 45.26 3.16
1841 10010 6.817270 GTTTGTACAAACTCGAGTCACTTA 57.183 37.500 33.99 5.34 45.26 2.24
1842 10011 7.404139 GTTTGTACAAACTCGAGTCACTTAT 57.596 36.000 33.99 1.04 45.26 1.73
1843 10012 7.848491 GTTTGTACAAACTCGAGTCACTTATT 58.152 34.615 33.99 5.22 45.26 1.40
1844 10013 8.333186 GTTTGTACAAACTCGAGTCACTTATTT 58.667 33.333 33.99 4.41 45.26 1.40
1845 10014 8.428186 TTGTACAAACTCGAGTCACTTATTTT 57.572 30.769 20.33 3.59 0.00 1.82
1846 10015 7.847487 TGTACAAACTCGAGTCACTTATTTTG 58.153 34.615 20.33 18.12 0.00 2.44
1847 10016 6.300354 ACAAACTCGAGTCACTTATTTTGG 57.700 37.500 20.33 0.00 0.00 3.28
1848 10017 5.238650 ACAAACTCGAGTCACTTATTTTGGG 59.761 40.000 20.33 0.00 0.00 4.12
1849 10018 4.884668 ACTCGAGTCACTTATTTTGGGA 57.115 40.909 13.58 0.00 0.00 4.37
1850 10019 4.566987 ACTCGAGTCACTTATTTTGGGAC 58.433 43.478 13.58 0.00 0.00 4.46
1851 10020 4.283722 ACTCGAGTCACTTATTTTGGGACT 59.716 41.667 13.58 0.00 41.22 3.85
1852 10021 4.566004 TCGAGTCACTTATTTTGGGACTG 58.434 43.478 3.22 0.00 38.82 3.51
1853 10022 4.282449 TCGAGTCACTTATTTTGGGACTGA 59.718 41.667 3.22 0.00 38.82 3.41
1854 10023 4.627467 CGAGTCACTTATTTTGGGACTGAG 59.373 45.833 3.22 0.00 38.82 3.35
1855 10024 4.911390 AGTCACTTATTTTGGGACTGAGG 58.089 43.478 0.00 0.00 37.43 3.86
1856 10025 4.010349 GTCACTTATTTTGGGACTGAGGG 58.990 47.826 0.00 0.00 0.00 4.30
1864 10033 4.348020 TTTGGGACTGAGGGAGTAGTAT 57.652 45.455 0.00 0.00 33.83 2.12
1874 10072 7.929959 ACTGAGGGAGTAGTATGCAGTATATA 58.070 38.462 0.00 0.00 33.78 0.86
1921 10120 3.181507 GCAAAATCGAACTAGCATCAGCA 60.182 43.478 0.00 0.00 45.49 4.41
1952 10151 3.623510 GCTGGTTCCAGTAGCTATTTGAC 59.376 47.826 18.42 0.00 36.52 3.18
1957 10156 7.573710 TGGTTCCAGTAGCTATTTGACATAAT 58.426 34.615 0.00 0.00 0.00 1.28
1958 10157 7.715249 TGGTTCCAGTAGCTATTTGACATAATC 59.285 37.037 0.00 0.00 0.00 1.75
1963 10162 8.501580 CCAGTAGCTATTTGACATAATCACATG 58.498 37.037 0.00 0.00 36.92 3.21
2008 10207 1.342819 AGTTGCAGAGACCAGTCTGAC 59.657 52.381 4.74 0.00 46.02 3.51
2023 10222 5.181811 CCAGTCTGACATGCTAACAAAATGA 59.818 40.000 10.88 0.00 0.00 2.57
2033 10232 6.899393 TGCTAACAAAATGACTGAAGGAAT 57.101 33.333 0.00 0.00 0.00 3.01
2034 10233 7.994425 TGCTAACAAAATGACTGAAGGAATA 57.006 32.000 0.00 0.00 0.00 1.75
2035 10234 7.816640 TGCTAACAAAATGACTGAAGGAATAC 58.183 34.615 0.00 0.00 0.00 1.89
2036 10235 6.961554 GCTAACAAAATGACTGAAGGAATACG 59.038 38.462 0.00 0.00 0.00 3.06
2037 10236 7.148474 GCTAACAAAATGACTGAAGGAATACGA 60.148 37.037 0.00 0.00 0.00 3.43
2038 10237 6.727824 ACAAAATGACTGAAGGAATACGAG 57.272 37.500 0.00 0.00 0.00 4.18
2039 10238 5.122396 ACAAAATGACTGAAGGAATACGAGC 59.878 40.000 0.00 0.00 0.00 5.03
2040 10239 4.744795 AATGACTGAAGGAATACGAGCT 57.255 40.909 0.00 0.00 0.00 4.09
2041 10240 4.744795 ATGACTGAAGGAATACGAGCTT 57.255 40.909 0.00 0.00 0.00 3.74
2042 10241 3.849911 TGACTGAAGGAATACGAGCTTG 58.150 45.455 0.00 0.00 0.00 4.01
2043 10242 3.509967 TGACTGAAGGAATACGAGCTTGA 59.490 43.478 8.31 0.00 0.00 3.02
2044 10243 3.851098 ACTGAAGGAATACGAGCTTGAC 58.149 45.455 8.31 0.00 0.00 3.18
2045 10244 3.258372 ACTGAAGGAATACGAGCTTGACA 59.742 43.478 8.31 0.00 0.00 3.58
2046 10245 4.245660 CTGAAGGAATACGAGCTTGACAA 58.754 43.478 8.31 0.00 0.00 3.18
2047 10246 4.832248 TGAAGGAATACGAGCTTGACAAT 58.168 39.130 8.31 0.00 0.00 2.71
2048 10247 5.245531 TGAAGGAATACGAGCTTGACAATT 58.754 37.500 8.31 4.42 0.00 2.32
2049 10248 5.705441 TGAAGGAATACGAGCTTGACAATTT 59.295 36.000 8.31 0.00 0.00 1.82
2050 10249 6.206634 TGAAGGAATACGAGCTTGACAATTTT 59.793 34.615 8.31 0.00 0.00 1.82
2051 10250 5.942872 AGGAATACGAGCTTGACAATTTTG 58.057 37.500 8.31 0.00 0.00 2.44
2052 10251 5.473504 AGGAATACGAGCTTGACAATTTTGT 59.526 36.000 8.31 0.00 45.65 2.83
2055 10254 3.952535 ACGAGCTTGACAATTTTGTGAC 58.047 40.909 8.31 0.00 42.43 3.67
2076 10275 6.260936 GTGACCATATCTTCCATTGGTTACTG 59.739 42.308 1.86 0.00 42.38 2.74
2077 10276 6.157820 TGACCATATCTTCCATTGGTTACTGA 59.842 38.462 1.86 0.00 42.41 3.41
2104 10303 6.650427 AGTACAGTCTGATAAGTCACACAA 57.350 37.500 6.91 0.00 0.00 3.33
2165 10364 7.043656 CCAACTTAAAACTGACGCTTAAAAAGG 60.044 37.037 0.00 0.00 0.00 3.11
2172 10371 2.801679 TGACGCTTAAAAAGGTACCACG 59.198 45.455 15.94 6.84 0.00 4.94
2192 10391 2.231478 CGGCTACGACTCCCATATCAAT 59.769 50.000 0.00 0.00 44.60 2.57
2200 10399 5.780282 ACGACTCCCATATCAATCATAGGAA 59.220 40.000 0.00 0.00 0.00 3.36
2207 10406 8.727149 TCCCATATCAATCATAGGAAAAGACTT 58.273 33.333 0.00 0.00 0.00 3.01
2258 10457 9.748708 TTAAAACTGAACTTCCATTCTTCAATG 57.251 29.630 0.00 0.00 39.45 2.82
2287 10486 1.603802 CTGGCACGTGATTCAAACTGT 59.396 47.619 22.23 0.00 0.00 3.55
2306 10505 3.440127 TGTCACATCCACCAGTGATCTA 58.560 45.455 0.00 0.00 45.46 1.98
2307 10506 3.837731 TGTCACATCCACCAGTGATCTAA 59.162 43.478 0.00 0.00 45.46 2.10
2309 10508 5.221823 TGTCACATCCACCAGTGATCTAAAA 60.222 40.000 0.00 0.00 45.46 1.52
2310 10509 5.352569 GTCACATCCACCAGTGATCTAAAAG 59.647 44.000 0.00 0.00 45.46 2.27
2311 10510 5.013079 TCACATCCACCAGTGATCTAAAAGT 59.987 40.000 0.00 0.00 39.65 2.66
2312 10511 5.122869 CACATCCACCAGTGATCTAAAAGTG 59.877 44.000 0.00 0.00 37.97 3.16
2313 10512 5.013079 ACATCCACCAGTGATCTAAAAGTGA 59.987 40.000 0.00 0.00 0.00 3.41
2314 10513 5.762179 TCCACCAGTGATCTAAAAGTGAT 57.238 39.130 0.00 0.00 0.00 3.06
2384 10583 5.861727 AGGCCCACTTTACTATATAAACGG 58.138 41.667 0.00 0.00 0.00 4.44
2385 10584 4.453478 GGCCCACTTTACTATATAAACGGC 59.547 45.833 0.00 0.00 0.00 5.68
2386 10585 5.303165 GCCCACTTTACTATATAAACGGCT 58.697 41.667 0.00 0.00 0.00 5.52
2387 10586 5.761726 GCCCACTTTACTATATAAACGGCTT 59.238 40.000 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 3.754323 ACACACGGAGAAGAAACACAAAA 59.246 39.130 0.00 0.00 0.00 2.44
69 70 0.882927 TGGTACTTGTGGTTGAGCGC 60.883 55.000 0.00 0.00 0.00 5.92
105 107 6.445357 TGGTCTACCAAAGTTGAAAGAAAC 57.555 37.500 0.00 0.00 44.35 2.78
185 187 1.805945 GTTGCTAGTCGACAGGGCG 60.806 63.158 19.50 1.88 0.00 6.13
250 252 1.752358 TTTTGAATGCAAGGCGGCCA 61.752 50.000 23.09 0.00 35.04 5.36
269 271 5.544176 CCTGGATACCATAAGACACCTACAT 59.456 44.000 0.00 0.00 30.82 2.29
270 272 4.899457 CCTGGATACCATAAGACACCTACA 59.101 45.833 0.00 0.00 30.82 2.74
307 309 1.017387 GATAAACCCGAGCTGCCTTG 58.983 55.000 0.00 0.00 0.00 3.61
309 311 0.912486 AAGATAAACCCGAGCTGCCT 59.088 50.000 0.00 0.00 0.00 4.75
376 382 6.872585 TTAAAATCTTCATTTGGAGGGCAT 57.127 33.333 0.00 0.00 32.18 4.40
404 410 3.788227 TGGAACTTAACATGTCCAGCT 57.212 42.857 0.00 0.00 0.00 4.24
440 446 4.140591 TCAGGATCCTCTAACCCATCAGAT 60.141 45.833 12.69 0.00 0.00 2.90
445 451 2.320781 CGTCAGGATCCTCTAACCCAT 58.679 52.381 12.69 0.00 0.00 4.00
457 463 1.064314 AGCTGGAGACTACGTCAGGAT 60.064 52.381 0.00 0.00 34.60 3.24
490 496 1.210538 TCATGCAGAATGGGAGCTCT 58.789 50.000 14.64 0.00 36.86 4.09
493 499 2.434428 CCTATCATGCAGAATGGGAGC 58.566 52.381 7.50 0.00 36.86 4.70
871 8713 0.326264 AGATGTGGACTCTGTTGCCC 59.674 55.000 0.00 0.00 0.00 5.36
927 8781 0.318441 TCCTGCTCCAAGTGAACTCG 59.682 55.000 0.00 0.00 0.00 4.18
939 8797 1.481772 AGCTGAGAGACAATCCTGCTC 59.518 52.381 0.00 0.00 32.10 4.26
1036 8896 1.064906 CACCATCAGGAGCAGAACCAT 60.065 52.381 0.00 0.00 38.69 3.55
1065 8925 4.119363 TCCAGCCTGATGCCCTGC 62.119 66.667 0.00 0.00 42.71 4.85
1102 8962 2.281484 GAGCACAGGGTTGCCGAA 60.281 61.111 0.00 0.00 44.14 4.30
1161 9021 1.011904 CCGATCATCGCGCAACAAG 60.012 57.895 8.75 0.00 38.82 3.16
1225 9113 4.401925 CCTTGTTCAACATCCCTTTCTCT 58.598 43.478 0.00 0.00 0.00 3.10
1235 9123 2.559668 CACCATCAGCCTTGTTCAACAT 59.440 45.455 0.00 0.00 0.00 2.71
1238 9180 2.655090 TCACCATCAGCCTTGTTCAA 57.345 45.000 0.00 0.00 0.00 2.69
1267 9209 0.250234 CCTCCACTTCATCGCCTGAA 59.750 55.000 1.17 1.17 41.61 3.02
1273 9215 1.144936 GGCCTCCTCCACTTCATCG 59.855 63.158 0.00 0.00 0.00 3.84
1421 9365 6.930164 CACCATGATCATCTAGAGAAGAAAGG 59.070 42.308 4.86 1.81 37.89 3.11
1431 9379 3.865302 GCTGCCTCACCATGATCATCTAG 60.865 52.174 4.86 0.14 0.00 2.43
1453 9401 2.635714 TCTTGTCATACCAGCAGCATG 58.364 47.619 0.00 0.00 40.87 4.06
1463 9411 7.714377 ACATCTTGGATCTTGATCTTGTCATAC 59.286 37.037 10.03 0.00 36.54 2.39
1468 9419 6.058553 TCACATCTTGGATCTTGATCTTGT 57.941 37.500 10.03 4.91 0.00 3.16
1474 9425 5.705397 AGGAATCACATCTTGGATCTTGA 57.295 39.130 0.00 0.00 0.00 3.02
1657 9610 3.503748 CAGAGTACTTGGCCAGGAAAAAG 59.496 47.826 23.57 10.34 0.00 2.27
1703 9656 8.601476 GTGCTATATTGGTGTAGTAGTTTCAAC 58.399 37.037 0.00 0.00 0.00 3.18
1722 9675 8.589338 TGCAAAAGGAAAAATAAAGGTGCTATA 58.411 29.630 0.00 0.00 0.00 1.31
1725 9678 5.679601 TGCAAAAGGAAAAATAAAGGTGCT 58.320 33.333 0.00 0.00 0.00 4.40
1775 9944 4.106019 ACGGAGGGAGTATAATACCAGACT 59.894 45.833 3.85 0.00 0.00 3.24
1780 9949 3.095332 GGGACGGAGGGAGTATAATACC 58.905 54.545 0.00 0.00 0.00 2.73
1789 9958 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
1791 9960 2.026636 TCACTTATTTTGGGACGGAGGG 60.027 50.000 0.00 0.00 0.00 4.30
1792 9961 3.007635 GTCACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
1793 9962 3.933332 GAGTCACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 33.84 4.63
1794 9963 3.615592 CGAGTCACTTATTTTGGGACGGA 60.616 47.826 0.00 0.00 33.84 4.69
1795 9964 2.671396 CGAGTCACTTATTTTGGGACGG 59.329 50.000 0.00 0.00 33.84 4.79
1796 9965 3.581755 TCGAGTCACTTATTTTGGGACG 58.418 45.455 0.00 0.00 33.84 4.79
1797 9966 4.566987 ACTCGAGTCACTTATTTTGGGAC 58.433 43.478 13.58 0.00 0.00 4.46
1798 9967 4.884668 ACTCGAGTCACTTATTTTGGGA 57.115 40.909 13.58 0.00 0.00 4.37
1799 9968 5.238650 ACAAACTCGAGTCACTTATTTTGGG 59.761 40.000 20.33 0.00 0.00 4.12
1800 9969 6.300354 ACAAACTCGAGTCACTTATTTTGG 57.700 37.500 20.33 0.00 0.00 3.28
1801 9970 7.847487 TGTACAAACTCGAGTCACTTATTTTG 58.153 34.615 20.33 18.12 0.00 2.44
1802 9971 8.428186 TTGTACAAACTCGAGTCACTTATTTT 57.572 30.769 20.33 3.59 0.00 1.82
1803 9972 8.333186 GTTTGTACAAACTCGAGTCACTTATTT 58.667 33.333 33.99 4.41 45.26 1.40
1804 9973 7.848491 GTTTGTACAAACTCGAGTCACTTATT 58.152 34.615 33.99 5.22 45.26 1.40
1805 9974 7.404139 GTTTGTACAAACTCGAGTCACTTAT 57.596 36.000 33.99 1.04 45.26 1.73
1806 9975 6.817270 GTTTGTACAAACTCGAGTCACTTA 57.183 37.500 33.99 5.34 45.26 2.24
1807 9976 5.713822 GTTTGTACAAACTCGAGTCACTT 57.286 39.130 33.99 6.87 45.26 3.16
1819 9988 8.428186 AAATAAGTGACTCGAGTTTGTACAAA 57.572 30.769 21.08 17.01 0.00 2.83
1820 9989 8.332464 CAAAATAAGTGACTCGAGTTTGTACAA 58.668 33.333 21.08 3.59 0.00 2.41
1821 9990 7.042321 CCAAAATAAGTGACTCGAGTTTGTACA 60.042 37.037 21.08 9.76 0.00 2.90
1822 9991 7.288672 CCAAAATAAGTGACTCGAGTTTGTAC 58.711 38.462 21.08 15.71 0.00 2.90
1823 9992 6.425721 CCCAAAATAAGTGACTCGAGTTTGTA 59.574 38.462 21.08 10.21 0.00 2.41
1824 9993 5.238650 CCCAAAATAAGTGACTCGAGTTTGT 59.761 40.000 21.08 5.70 0.00 2.83
1825 9994 5.468746 TCCCAAAATAAGTGACTCGAGTTTG 59.531 40.000 21.08 16.23 0.00 2.93
1826 9995 5.469084 GTCCCAAAATAAGTGACTCGAGTTT 59.531 40.000 21.08 12.75 0.00 2.66
1827 9996 4.995487 GTCCCAAAATAAGTGACTCGAGTT 59.005 41.667 21.08 6.08 0.00 3.01
1828 9997 4.283722 AGTCCCAAAATAAGTGACTCGAGT 59.716 41.667 20.18 20.18 30.81 4.18
1829 9998 4.627467 CAGTCCCAAAATAAGTGACTCGAG 59.373 45.833 11.84 11.84 34.21 4.04
1830 9999 4.282449 TCAGTCCCAAAATAAGTGACTCGA 59.718 41.667 0.00 0.00 34.21 4.04
1831 10000 4.566004 TCAGTCCCAAAATAAGTGACTCG 58.434 43.478 0.00 0.00 34.21 4.18
1832 10001 4.938226 CCTCAGTCCCAAAATAAGTGACTC 59.062 45.833 0.00 0.00 34.21 3.36
1833 10002 4.263506 CCCTCAGTCCCAAAATAAGTGACT 60.264 45.833 0.00 0.00 36.77 3.41
1834 10003 4.010349 CCCTCAGTCCCAAAATAAGTGAC 58.990 47.826 0.00 0.00 0.00 3.67
1835 10004 3.913799 TCCCTCAGTCCCAAAATAAGTGA 59.086 43.478 0.00 0.00 0.00 3.41
1836 10005 4.263506 ACTCCCTCAGTCCCAAAATAAGTG 60.264 45.833 0.00 0.00 0.00 3.16
1837 10006 3.916989 ACTCCCTCAGTCCCAAAATAAGT 59.083 43.478 0.00 0.00 0.00 2.24
1838 10007 4.576330 ACTCCCTCAGTCCCAAAATAAG 57.424 45.455 0.00 0.00 0.00 1.73
1839 10008 5.098663 ACTACTCCCTCAGTCCCAAAATAA 58.901 41.667 0.00 0.00 36.43 1.40
1840 10009 4.695606 ACTACTCCCTCAGTCCCAAAATA 58.304 43.478 0.00 0.00 36.43 1.40
1841 10010 3.532102 ACTACTCCCTCAGTCCCAAAAT 58.468 45.455 0.00 0.00 36.43 1.82
1842 10011 2.986050 ACTACTCCCTCAGTCCCAAAA 58.014 47.619 0.00 0.00 36.43 2.44
1843 10012 2.715763 ACTACTCCCTCAGTCCCAAA 57.284 50.000 0.00 0.00 36.43 3.28
1844 10013 3.643237 CATACTACTCCCTCAGTCCCAA 58.357 50.000 0.00 0.00 36.43 4.12
1845 10014 2.690026 GCATACTACTCCCTCAGTCCCA 60.690 54.545 0.00 0.00 36.43 4.37
1846 10015 1.964933 GCATACTACTCCCTCAGTCCC 59.035 57.143 0.00 0.00 36.43 4.46
1847 10016 2.625790 CTGCATACTACTCCCTCAGTCC 59.374 54.545 0.00 0.00 36.43 3.85
1848 10017 3.292460 ACTGCATACTACTCCCTCAGTC 58.708 50.000 0.00 0.00 36.43 3.51
1849 10018 3.390175 ACTGCATACTACTCCCTCAGT 57.610 47.619 0.00 0.00 39.41 3.41
1850 10019 8.809468 TTATATACTGCATACTACTCCCTCAG 57.191 38.462 0.00 0.00 0.00 3.35
1851 10020 9.021807 GTTTATATACTGCATACTACTCCCTCA 57.978 37.037 0.00 0.00 0.00 3.86
1852 10021 9.245481 AGTTTATATACTGCATACTACTCCCTC 57.755 37.037 0.00 0.00 0.00 4.30
1853 10022 9.026121 CAGTTTATATACTGCATACTACTCCCT 57.974 37.037 9.93 0.00 39.12 4.20
1874 10072 8.893727 GCTGGAACATAAACTATGATACAGTTT 58.106 33.333 14.24 5.84 46.12 2.66
1882 10080 7.335673 TCGATTTTGCTGGAACATAAACTATGA 59.664 33.333 0.75 0.00 38.20 2.15
1952 10151 5.235616 GCAAAATGCTTCCCATGTGATTATG 59.764 40.000 0.00 0.00 40.96 1.90
1957 10156 1.275856 GGCAAAATGCTTCCCATGTGA 59.724 47.619 2.00 0.00 44.28 3.58
1958 10157 1.276989 AGGCAAAATGCTTCCCATGTG 59.723 47.619 2.00 0.00 44.28 3.21
1963 10162 1.078918 GCCAGGCAAAATGCTTCCC 60.079 57.895 6.55 0.00 44.28 3.97
2008 10207 6.258230 TCCTTCAGTCATTTTGTTAGCATG 57.742 37.500 0.00 0.00 0.00 4.06
2023 10222 3.258372 TGTCAAGCTCGTATTCCTTCAGT 59.742 43.478 0.00 0.00 0.00 3.41
2033 10232 4.024387 GGTCACAAAATTGTCAAGCTCGTA 60.024 41.667 0.00 0.00 39.91 3.43
2034 10233 3.243068 GGTCACAAAATTGTCAAGCTCGT 60.243 43.478 0.00 0.00 39.91 4.18
2035 10234 3.243035 TGGTCACAAAATTGTCAAGCTCG 60.243 43.478 0.00 0.00 39.91 5.03
2036 10235 4.305989 TGGTCACAAAATTGTCAAGCTC 57.694 40.909 0.00 0.00 39.91 4.09
2037 10236 4.942761 ATGGTCACAAAATTGTCAAGCT 57.057 36.364 0.00 0.00 39.91 3.74
2038 10237 6.624423 AGATATGGTCACAAAATTGTCAAGC 58.376 36.000 0.00 0.00 39.91 4.01
2039 10238 7.756722 GGAAGATATGGTCACAAAATTGTCAAG 59.243 37.037 0.00 0.00 39.91 3.02
2040 10239 7.232330 TGGAAGATATGGTCACAAAATTGTCAA 59.768 33.333 0.00 0.00 39.91 3.18
2041 10240 6.718912 TGGAAGATATGGTCACAAAATTGTCA 59.281 34.615 0.00 0.00 39.91 3.58
2042 10241 7.156876 TGGAAGATATGGTCACAAAATTGTC 57.843 36.000 0.00 0.00 39.91 3.18
2043 10242 7.722949 ATGGAAGATATGGTCACAAAATTGT 57.277 32.000 0.00 0.00 43.36 2.71
2044 10243 7.493320 CCAATGGAAGATATGGTCACAAAATTG 59.507 37.037 0.00 0.00 0.00 2.32
2045 10244 7.180766 ACCAATGGAAGATATGGTCACAAAATT 59.819 33.333 6.16 0.00 42.36 1.82
2046 10245 6.669154 ACCAATGGAAGATATGGTCACAAAAT 59.331 34.615 6.16 0.00 42.36 1.82
2047 10246 6.015918 ACCAATGGAAGATATGGTCACAAAA 58.984 36.000 6.16 0.00 42.36 2.44
2048 10247 5.579047 ACCAATGGAAGATATGGTCACAAA 58.421 37.500 6.16 0.00 42.36 2.83
2049 10248 5.191727 ACCAATGGAAGATATGGTCACAA 57.808 39.130 6.16 0.00 42.36 3.33
2050 10249 4.860802 ACCAATGGAAGATATGGTCACA 57.139 40.909 6.16 0.00 42.36 3.58
2051 10250 6.260936 CAGTAACCAATGGAAGATATGGTCAC 59.739 42.308 6.16 0.00 45.15 3.67
2052 10251 6.157820 TCAGTAACCAATGGAAGATATGGTCA 59.842 38.462 6.16 0.00 45.15 4.02
2055 10254 6.830912 TCTCAGTAACCAATGGAAGATATGG 58.169 40.000 6.16 0.00 38.91 2.74
2076 10275 7.539366 GTGTGACTTATCAGACTGTACTTTCTC 59.461 40.741 1.59 0.00 44.00 2.87
2077 10276 7.014326 TGTGTGACTTATCAGACTGTACTTTCT 59.986 37.037 1.59 0.00 46.76 2.52
2165 10364 1.431036 GGAGTCGTAGCCGTGGTAC 59.569 63.158 3.94 3.94 33.76 3.34
2172 10371 3.258372 TGATTGATATGGGAGTCGTAGCC 59.742 47.826 0.00 0.00 0.00 3.93
2200 10399 8.097662 TGGTGTTGGTTTTCATTTTAAGTCTTT 58.902 29.630 0.00 0.00 0.00 2.52
2263 10462 3.499737 GAATCACGTGCCAGCCGG 61.500 66.667 11.67 0.00 0.00 6.13
2287 10486 5.013079 ACTTTTAGATCACTGGTGGATGTGA 59.987 40.000 0.00 0.00 45.56 3.58


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

AutoCloner maintained by Alex Coulton.