Multiple sequence alignment - TraesCS3D01G481800

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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 TraesCS3D01G481800 chr3D 100.000 4523 0 0 1 4523 579585289 579589811 0.000000e+00 8353.0
1 TraesCS3D01G481800 chr3D 89.773 1721 158 13 1819 3528 579422239 579420526 0.000000e+00 2187.0
2 TraesCS3D01G481800 chr3D 91.301 1391 119 2 1 1390 579423880 579422491 0.000000e+00 1897.0
3 TraesCS3D01G481800 chr3D 91.860 1339 105 4 1 1336 579396190 579394853 0.000000e+00 1866.0
4 TraesCS3D01G481800 chr3D 93.602 844 49 4 2792 3631 579383798 579382956 0.000000e+00 1254.0
5 TraesCS3D01G481800 chr3D 89.501 981 82 9 1819 2796 579394576 579393614 0.000000e+00 1221.0
6 TraesCS3D01G481800 chr3D 92.179 179 14 0 3351 3529 579367490 579367312 2.090000e-63 254.0
7 TraesCS3D01G481800 chr3D 82.418 273 24 14 1571 1822 422528787 422529056 2.740000e-52 217.0
8 TraesCS3D01G481800 chr3D 77.746 355 50 19 3566 3895 579367315 579366965 1.660000e-44 191.0
9 TraesCS3D01G481800 chr3D 80.451 266 28 12 1578 1822 590409732 590409470 1.000000e-41 182.0
10 TraesCS3D01G481800 chr3D 80.597 134 10 5 1410 1543 579422389 579422272 6.230000e-14 89.8
11 TraesCS3D01G481800 chr3D 79.104 134 11 6 1410 1543 579394725 579394609 4.850000e-10 76.8
12 TraesCS3D01G481800 chr3A 91.717 3344 182 41 1230 4523 714644930 714648228 0.000000e+00 4553.0
13 TraesCS3D01G481800 chr3A 89.623 2467 186 39 1819 4266 714590052 714587637 0.000000e+00 3073.0
14 TraesCS3D01G481800 chr3A 91.977 1396 107 5 1 1391 714591687 714590292 0.000000e+00 1953.0
15 TraesCS3D01G481800 chr3A 94.231 1248 69 1 1 1248 714643670 714644914 0.000000e+00 1903.0
16 TraesCS3D01G481800 chr3A 90.290 587 56 1 796 1381 714627775 714628361 0.000000e+00 767.0
17 TraesCS3D01G481800 chr3A 87.370 673 75 6 2904 3572 714602902 714602236 0.000000e+00 763.0
18 TraesCS3D01G481800 chr3A 82.642 265 24 13 1571 1815 566874641 566874379 9.850000e-52 215.0
19 TraesCS3D01G481800 chr3B 92.434 1771 103 13 1819 3569 773900182 773901941 0.000000e+00 2499.0
20 TraesCS3D01G481800 chr3B 88.933 1771 173 10 1819 3572 773759468 773757704 0.000000e+00 2163.0
21 TraesCS3D01G481800 chr3B 94.543 1246 68 0 1 1246 773898610 773899855 0.000000e+00 1925.0
22 TraesCS3D01G481800 chr3B 89.337 1388 130 5 4 1390 773761090 773759720 0.000000e+00 1727.0
23 TraesCS3D01G481800 chr3B 91.831 661 45 6 2873 3527 773743745 773743088 0.000000e+00 913.0
24 TraesCS3D01G481800 chr3B 87.150 428 18 8 3600 4025 773901939 773902331 6.900000e-123 451.0
25 TraesCS3D01G481800 chr3B 93.561 264 14 1 4059 4319 773902323 773902586 1.530000e-104 390.0
26 TraesCS3D01G481800 chr3B 81.741 471 67 14 3569 4022 773743086 773742618 4.270000e-100 375.0
27 TraesCS3D01G481800 chr3B 95.395 152 7 0 1239 1390 773899882 773900033 4.520000e-60 243.0
28 TraesCS3D01G481800 chr3B 91.579 95 8 0 3566 3660 773730251 773730157 1.020000e-26 132.0
29 TraesCS3D01G481800 chr3B 87.778 90 11 0 3566 3655 773734517 773734428 6.190000e-19 106.0
30 TraesCS3D01G481800 chr3B 100.000 32 0 0 3983 4014 773751913 773751882 4.890000e-05 60.2
31 TraesCS3D01G481800 chr3B 100.000 31 0 0 1410 1440 773900068 773900098 1.760000e-04 58.4
32 TraesCS3D01G481800 chr4A 83.969 262 23 12 1581 1825 47750939 47751198 2.720000e-57 233.0
33 TraesCS3D01G481800 chr4A 80.769 260 31 6 1581 1822 605143245 605142987 7.730000e-43 185.0
34 TraesCS3D01G481800 chr2B 83.846 260 21 10 1581 1822 225571375 225571631 1.270000e-55 228.0
35 TraesCS3D01G481800 chr2B 79.087 263 31 15 1581 1822 620624231 620623972 4.680000e-35 159.0
36 TraesCS3D01G481800 chr2B 90.526 95 9 0 1581 1675 106941230 106941324 4.750000e-25 126.0
37 TraesCS3D01G481800 chr4D 82.772 267 22 12 1581 1825 416060963 416060699 2.740000e-52 217.0
38 TraesCS3D01G481800 chr5B 82.397 267 19 10 1581 1822 316713424 316713161 1.650000e-49 207.0
39 TraesCS3D01G481800 chr7A 80.443 271 31 10 1573 1822 163129200 163128931 2.150000e-43 187.0
40 TraesCS3D01G481800 chr1B 80.392 255 43 7 1573 1822 685647054 685646802 2.150000e-43 187.0
41 TraesCS3D01G481800 chrUn 80.545 257 31 6 1581 1819 451281487 451281232 3.590000e-41 180.0
42 TraesCS3D01G481800 chr2A 86.755 151 18 2 1672 1822 726429816 726429964 2.800000e-37 167.0
43 TraesCS3D01G481800 chr4B 85.897 156 17 5 1672 1825 512757927 512757775 1.300000e-35 161.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G481800 chr3D 579585289 579589811 4522 False 8353.000000 8353 100.000000 1 4523 1 chr3D.!!$F2 4522
1 TraesCS3D01G481800 chr3D 579420526 579423880 3354 True 1391.266667 2187 87.223667 1 3528 3 chr3D.!!$R5 3527
2 TraesCS3D01G481800 chr3D 579382956 579383798 842 True 1254.000000 1254 93.602000 2792 3631 1 chr3D.!!$R1 839
3 TraesCS3D01G481800 chr3D 579393614 579396190 2576 True 1054.600000 1866 86.821667 1 2796 3 chr3D.!!$R4 2795
4 TraesCS3D01G481800 chr3D 579366965 579367490 525 True 222.500000 254 84.962500 3351 3895 2 chr3D.!!$R3 544
5 TraesCS3D01G481800 chr3A 714643670 714648228 4558 False 3228.000000 4553 92.974000 1 4523 2 chr3A.!!$F2 4522
6 TraesCS3D01G481800 chr3A 714587637 714591687 4050 True 2513.000000 3073 90.800000 1 4266 2 chr3A.!!$R3 4265
7 TraesCS3D01G481800 chr3A 714627775 714628361 586 False 767.000000 767 90.290000 796 1381 1 chr3A.!!$F1 585
8 TraesCS3D01G481800 chr3A 714602236 714602902 666 True 763.000000 763 87.370000 2904 3572 1 chr3A.!!$R2 668
9 TraesCS3D01G481800 chr3B 773757704 773761090 3386 True 1945.000000 2163 89.135000 4 3572 2 chr3B.!!$R5 3568
10 TraesCS3D01G481800 chr3B 773898610 773902586 3976 False 927.733333 2499 93.847167 1 4319 6 chr3B.!!$F1 4318
11 TraesCS3D01G481800 chr3B 773742618 773743745 1127 True 644.000000 913 86.786000 2873 4022 2 chr3B.!!$R4 1149

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
534 535 0.987294 ATGACCTTGACACTCCCCTG 59.013 55.0 0.0 0.0 0.00 4.45 F
1881 2196 0.768622 TCAGGGAAAGGGCGAAAGAA 59.231 50.0 0.0 0.0 0.00 2.52 F
2427 2747 0.683504 GGCTCGGTAGAGGTTCTGGA 60.684 60.0 0.0 0.0 44.51 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2205 2524 0.109723 AGCCGCCTTGTCCTAACAAA 59.890 50.0 0.00 0.00 44.53 2.83 R
3160 3501 2.728690 TTGCAGACATTGGCAATGAC 57.271 45.0 38.83 32.99 44.41 3.06 R
4052 4513 0.036105 ACAACATGCTCCGCAGATCA 60.036 50.0 0.00 0.00 43.65 2.92 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
127 128 5.221702 ACCCCCTCAAATTCAACTGAAAATG 60.222 40.000 0.00 0.00 37.61 2.32
361 362 8.267620 TGGAAATCTTGTAGTCCTATCATCAT 57.732 34.615 0.00 0.00 0.00 2.45
367 368 7.455891 TCTTGTAGTCCTATCATCATACGGTA 58.544 38.462 0.00 0.00 0.00 4.02
413 414 1.594293 CAAGCGACACCGTCCTTGT 60.594 57.895 13.02 0.00 36.76 3.16
534 535 0.987294 ATGACCTTGACACTCCCCTG 59.013 55.000 0.00 0.00 0.00 4.45
846 850 1.559219 TGTGGTGCATATGGCTACTGT 59.441 47.619 4.56 0.00 45.15 3.55
865 869 3.715628 GTGACAACACAGAGGCAATTT 57.284 42.857 0.00 0.00 45.32 1.82
992 996 3.054361 GGAGAGGCCAATTTCTTGACCTA 60.054 47.826 5.01 0.00 44.40 3.08
1027 1031 2.755650 CTCCAGACAAGTTTGTACGCT 58.244 47.619 0.00 0.00 42.43 5.07
1147 1151 1.181098 GGATGCAACAAGGTGCCTGT 61.181 55.000 7.74 0.00 44.26 4.00
1161 1165 2.602676 CCTGTTGTGGACCGGGGAT 61.603 63.158 6.32 0.00 0.00 3.85
1212 1216 2.868583 CGGCAATGAGAACCTGTATCTG 59.131 50.000 0.00 0.00 0.00 2.90
1235 1273 3.610911 GGCTTGCTACCTTGTCAAGTAT 58.389 45.455 11.61 2.23 39.36 2.12
1336 1376 4.552166 TGACAACTTGCTGCTTTAACTC 57.448 40.909 0.00 0.00 0.00 3.01
1350 1390 7.164335 GCTGCTTTAACTCGCTAATAAATTGTC 59.836 37.037 0.00 0.00 0.00 3.18
1391 1460 1.207593 CCACTACACGCAGCAAAGC 59.792 57.895 0.00 0.00 0.00 3.51
1392 1461 1.506309 CCACTACACGCAGCAAAGCA 61.506 55.000 0.00 0.00 0.00 3.91
1394 1463 1.021202 ACTACACGCAGCAAAGCAAA 58.979 45.000 0.00 0.00 0.00 3.68
1395 1464 1.403679 ACTACACGCAGCAAAGCAAAA 59.596 42.857 0.00 0.00 0.00 2.44
1396 1465 2.034558 ACTACACGCAGCAAAGCAAAAT 59.965 40.909 0.00 0.00 0.00 1.82
1397 1466 1.490621 ACACGCAGCAAAGCAAAATC 58.509 45.000 0.00 0.00 0.00 2.17
1399 1468 1.190763 CACGCAGCAAAGCAAAATCAC 59.809 47.619 0.00 0.00 0.00 3.06
1400 1469 1.067516 ACGCAGCAAAGCAAAATCACT 59.932 42.857 0.00 0.00 0.00 3.41
1401 1470 2.293122 ACGCAGCAAAGCAAAATCACTA 59.707 40.909 0.00 0.00 0.00 2.74
1403 1472 3.610114 CGCAGCAAAGCAAAATCACTACT 60.610 43.478 0.00 0.00 0.00 2.57
1405 1474 4.149396 GCAGCAAAGCAAAATCACTACTTG 59.851 41.667 0.00 0.00 0.00 3.16
1406 1475 4.149396 CAGCAAAGCAAAATCACTACTTGC 59.851 41.667 0.00 0.00 44.61 4.01
1407 1476 3.429881 GCAAAGCAAAATCACTACTTGCC 59.570 43.478 2.58 0.00 45.23 4.52
1408 1477 4.619973 CAAAGCAAAATCACTACTTGCCA 58.380 39.130 2.58 0.00 45.23 4.92
1479 1751 2.666272 TGCCAAAATGGTGGTACAGA 57.334 45.000 0.00 0.00 41.80 3.41
1480 1752 2.235016 TGCCAAAATGGTGGTACAGAC 58.765 47.619 0.00 0.00 41.80 3.51
1482 1754 2.625790 GCCAAAATGGTGGTACAGACAA 59.374 45.455 0.00 0.00 41.80 3.18
1483 1755 3.552068 GCCAAAATGGTGGTACAGACAAC 60.552 47.826 0.00 0.00 41.80 3.32
1484 1756 3.634448 CCAAAATGGTGGTACAGACAACA 59.366 43.478 0.00 0.00 41.80 3.33
1485 1757 4.499019 CCAAAATGGTGGTACAGACAACAC 60.499 45.833 0.00 0.00 41.80 3.32
1486 1758 3.857157 AATGGTGGTACAGACAACACT 57.143 42.857 0.00 0.00 41.80 3.55
1487 1759 2.613026 TGGTGGTACAGACAACACTG 57.387 50.000 0.00 0.00 41.80 3.66
1514 1786 1.530013 GCATTGAGCCCAAGTGCACT 61.530 55.000 15.25 15.25 37.08 4.40
1555 1853 9.983804 GATGCAATTAACTAAACTGTAGGTTAC 57.016 33.333 0.00 0.00 37.12 2.50
1556 1854 9.734984 ATGCAATTAACTAAACTGTAGGTTACT 57.265 29.630 0.00 0.00 37.12 2.24
1557 1855 9.211485 TGCAATTAACTAAACTGTAGGTTACTC 57.789 33.333 0.00 0.00 37.12 2.59
1558 1856 8.378421 GCAATTAACTAAACTGTAGGTTACTCG 58.622 37.037 0.00 0.00 37.12 4.18
1559 1857 9.415544 CAATTAACTAAACTGTAGGTTACTCGT 57.584 33.333 0.00 0.00 37.12 4.18
1560 1858 8.976986 ATTAACTAAACTGTAGGTTACTCGTG 57.023 34.615 0.00 0.00 37.12 4.35
1561 1859 6.639632 AACTAAACTGTAGGTTACTCGTGA 57.360 37.500 0.00 0.00 37.12 4.35
1562 1860 6.830873 ACTAAACTGTAGGTTACTCGTGAT 57.169 37.500 0.00 0.00 37.12 3.06
1563 1861 7.928307 ACTAAACTGTAGGTTACTCGTGATA 57.072 36.000 0.00 0.00 37.12 2.15
1564 1862 7.983307 ACTAAACTGTAGGTTACTCGTGATAG 58.017 38.462 0.00 0.00 37.12 2.08
1565 1863 6.830873 AAACTGTAGGTTACTCGTGATAGT 57.169 37.500 0.00 0.00 37.12 2.12
1566 1864 6.434018 AACTGTAGGTTACTCGTGATAGTC 57.566 41.667 0.00 0.00 36.23 2.59
1567 1865 5.494724 ACTGTAGGTTACTCGTGATAGTCA 58.505 41.667 0.00 0.00 0.00 3.41
1568 1866 5.585445 ACTGTAGGTTACTCGTGATAGTCAG 59.415 44.000 0.00 0.00 0.00 3.51
1569 1867 5.737860 TGTAGGTTACTCGTGATAGTCAGA 58.262 41.667 0.00 0.00 0.00 3.27
1570 1868 5.583854 TGTAGGTTACTCGTGATAGTCAGAC 59.416 44.000 0.00 0.00 0.00 3.51
1571 1869 4.586884 AGGTTACTCGTGATAGTCAGACA 58.413 43.478 2.66 0.00 0.00 3.41
1572 1870 5.008331 AGGTTACTCGTGATAGTCAGACAA 58.992 41.667 2.66 0.00 0.00 3.18
1573 1871 5.475909 AGGTTACTCGTGATAGTCAGACAAA 59.524 40.000 2.66 0.00 0.00 2.83
1574 1872 6.015688 AGGTTACTCGTGATAGTCAGACAAAA 60.016 38.462 2.66 0.00 0.00 2.44
1575 1873 6.643770 GGTTACTCGTGATAGTCAGACAAAAA 59.356 38.462 2.66 0.00 0.00 1.94
1576 1874 7.148787 GGTTACTCGTGATAGTCAGACAAAAAG 60.149 40.741 2.66 0.00 0.00 2.27
1577 1875 5.844004 ACTCGTGATAGTCAGACAAAAAGT 58.156 37.500 2.66 0.00 0.00 2.66
1578 1876 6.978338 ACTCGTGATAGTCAGACAAAAAGTA 58.022 36.000 2.66 0.00 0.00 2.24
1579 1877 6.862090 ACTCGTGATAGTCAGACAAAAAGTAC 59.138 38.462 2.66 0.00 0.00 2.73
1589 1887 6.015265 GTCAGACAAAAAGTACTACTCCCTCT 60.015 42.308 0.00 0.00 0.00 3.69
1594 1892 5.741962 AAAAGTACTACTCCCTCTGTTCC 57.258 43.478 0.00 0.00 0.00 3.62
1639 1937 3.779759 TCCAAAAGTCAAACATGTGCAC 58.220 40.909 10.75 10.75 0.00 4.57
1650 1948 1.474478 ACATGTGCACGTTTGACCAAA 59.526 42.857 9.37 0.00 0.00 3.28
1782 2096 6.826893 AACATACACAAATTTGACTTGCAC 57.173 33.333 24.64 0.00 0.00 4.57
1783 2097 5.900425 ACATACACAAATTTGACTTGCACA 58.100 33.333 24.64 2.88 0.00 4.57
1794 2108 6.984740 TTTGACTTGCACAAAAATCGATAC 57.015 33.333 0.00 0.00 34.89 2.24
1881 2196 0.768622 TCAGGGAAAGGGCGAAAGAA 59.231 50.000 0.00 0.00 0.00 2.52
1888 2203 1.156736 AAGGGCGAAAGAACATCGTG 58.843 50.000 0.00 0.00 42.15 4.35
1892 2207 2.540101 GGGCGAAAGAACATCGTGATAG 59.460 50.000 0.00 0.00 42.15 2.08
1942 2257 3.871006 TGTTGCTGATACTTCTATTGGCG 59.129 43.478 0.00 0.00 0.00 5.69
1986 2301 9.981114 CAAGTTTAAAGGTAGTCCATTGATTTT 57.019 29.630 0.00 0.00 35.89 1.82
2046 2365 8.178313 GCCTTTCTAAGACAACAAAGATGATAC 58.822 37.037 0.00 0.00 0.00 2.24
2127 2446 2.481276 CGCATTAGTGATGGACTCGGAA 60.481 50.000 0.00 0.00 35.96 4.30
2193 2512 3.111098 GCTGCAACAAACAACTTCTCTG 58.889 45.455 0.00 0.00 0.00 3.35
2203 2522 6.601613 ACAAACAACTTCTCTGTGTCCAATTA 59.398 34.615 0.00 0.00 0.00 1.40
2204 2523 7.122055 ACAAACAACTTCTCTGTGTCCAATTAA 59.878 33.333 0.00 0.00 0.00 1.40
2205 2524 7.823745 AACAACTTCTCTGTGTCCAATTAAT 57.176 32.000 0.00 0.00 0.00 1.40
2206 2525 7.823745 ACAACTTCTCTGTGTCCAATTAATT 57.176 32.000 0.00 0.00 0.00 1.40
2215 2534 8.106247 TCTGTGTCCAATTAATTTGTTAGGAC 57.894 34.615 20.18 20.18 43.24 3.85
2288 2607 6.318648 TGTCCCTAATTGCACTGAAATATGAC 59.681 38.462 0.00 0.00 0.00 3.06
2314 2634 4.751767 TTGTCCCTTTTTGCTGTGATTT 57.248 36.364 0.00 0.00 0.00 2.17
2315 2635 4.057406 TGTCCCTTTTTGCTGTGATTTG 57.943 40.909 0.00 0.00 0.00 2.32
2413 2733 3.251004 AGAAGTTGCTGTTAAAAGGCTCG 59.749 43.478 0.00 0.00 0.00 5.03
2427 2747 0.683504 GGCTCGGTAGAGGTTCTGGA 60.684 60.000 0.00 0.00 44.51 3.86
2433 2753 1.273098 GGTAGAGGTTCTGGACAGGGA 60.273 57.143 0.00 0.00 0.00 4.20
2702 3034 1.811965 TCATTGGCCAACACGATTCAG 59.188 47.619 23.27 2.54 0.00 3.02
2744 3077 3.013921 GAGGGCTACTCTATCTCCATCG 58.986 54.545 2.33 0.00 43.14 3.84
2908 3247 8.340618 AGTTGTCGGAACATAGTAAGTACTAA 57.659 34.615 0.00 0.00 41.64 2.24
3039 3380 2.568623 TGGAAGGCCTCTTTTCTGTC 57.431 50.000 5.23 0.00 32.52 3.51
3066 3407 3.555168 CCGATGTCTATAGCTTTGGGGTC 60.555 52.174 0.00 0.00 0.00 4.46
3193 3537 1.879380 TCTGCAATTCCTTTGACCACG 59.121 47.619 0.00 0.00 37.53 4.94
3198 3542 1.892209 ATTCCTTTGACCACGTGACC 58.108 50.000 19.30 8.69 0.00 4.02
3572 3932 2.222027 CACTGTTTCCTGTTCTCCCAC 58.778 52.381 0.00 0.00 0.00 4.61
3948 4367 1.009829 CTGAACGATTGGCTACTGGC 58.990 55.000 0.00 0.00 40.90 4.85
4025 4486 7.722363 TCCTTTATTCATGTTAGTCGAGCATA 58.278 34.615 0.00 0.00 0.00 3.14
4026 4487 8.367911 TCCTTTATTCATGTTAGTCGAGCATAT 58.632 33.333 0.00 0.00 0.00 1.78
4052 4513 1.592669 GCGGCTCATGCTATCACGT 60.593 57.895 0.00 0.00 39.59 4.49
4226 4690 0.681733 ACACGCACTGGAGTCTTCAT 59.318 50.000 0.00 0.00 0.00 2.57
4285 4750 2.291856 CCTCTGGGGTTCCACTCTC 58.708 63.158 0.00 0.00 38.32 3.20
4292 4757 1.700186 GGGGTTCCACTCTCTGAAGTT 59.300 52.381 0.00 0.00 0.00 2.66
4322 4787 7.067494 AGCATACCAATTTGTGATTCCTTCTAC 59.933 37.037 0.00 0.00 0.00 2.59
4332 4797 5.997746 TGTGATTCCTTCTACAAAAGAGTGG 59.002 40.000 0.00 0.00 35.05 4.00
4338 4803 2.266279 TCTACAAAAGAGTGGGAGGGG 58.734 52.381 0.00 0.00 0.00 4.79
4339 4804 1.282157 CTACAAAAGAGTGGGAGGGGG 59.718 57.143 0.00 0.00 0.00 5.40
4421 4888 7.996385 CCACTTCTAAGGGGTATTGTATTTTG 58.004 38.462 2.62 0.00 44.84 2.44
4422 4889 7.832187 CCACTTCTAAGGGGTATTGTATTTTGA 59.168 37.037 2.62 0.00 44.84 2.69
4423 4890 9.408648 CACTTCTAAGGGGTATTGTATTTTGAT 57.591 33.333 0.00 0.00 0.00 2.57
4424 4891 9.628500 ACTTCTAAGGGGTATTGTATTTTGATC 57.372 33.333 0.00 0.00 0.00 2.92
4451 4918 0.110486 ATGGTCCAACGCCTTTGACT 59.890 50.000 0.00 0.00 37.39 3.41
4453 4920 1.515521 GGTCCAACGCCTTTGACTGG 61.516 60.000 0.92 0.00 37.39 4.00
4457 4924 1.597027 AACGCCTTTGACTGGACGG 60.597 57.895 0.00 0.00 0.00 4.79
4467 4934 1.067846 TGACTGGACGGAATCTTGACG 60.068 52.381 0.00 0.00 0.00 4.35
4482 4949 1.218316 GACGGAAGGGCATTCGAGT 59.782 57.895 10.52 10.52 38.95 4.18
4511 4978 6.954232 TCGGGAGTAAATCTAAGGACAAAAT 58.046 36.000 0.00 0.00 0.00 1.82
4519 4986 7.765695 AAATCTAAGGACAAAATTGAGCAGA 57.234 32.000 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
163 164 3.231736 AACCCAGACGACGGTGCT 61.232 61.111 0.00 0.00 30.96 4.40
189 190 2.562738 AGCATCGGTGATCGGATTATCA 59.437 45.455 0.00 0.00 39.77 2.15
237 238 3.477530 GGACAACACAAGGCTAGAGTTT 58.522 45.455 0.00 0.00 0.00 2.66
534 535 1.363744 CATTCCAGACGAAGGACTGC 58.636 55.000 0.00 0.00 34.05 4.40
846 850 2.622942 GGAAATTGCCTCTGTGTTGTCA 59.377 45.455 0.00 0.00 0.00 3.58
977 981 2.424956 GCTGGCTAGGTCAAGAAATTGG 59.575 50.000 0.00 0.00 0.00 3.16
1008 1012 2.869801 CAAGCGTACAAACTTGTCTGGA 59.130 45.455 10.59 0.00 42.35 3.86
1027 1031 5.769662 AGTCATCATAGCTTTTGTTCCACAA 59.230 36.000 0.00 0.00 36.11 3.33
1147 1151 0.620410 ATCAGATCCCCGGTCCACAA 60.620 55.000 0.00 0.00 0.00 3.33
1161 1165 3.054875 CACCCTTCTCCACATCAATCAGA 60.055 47.826 0.00 0.00 0.00 3.27
1212 1216 1.234615 TTGACAAGGTAGCAAGCCGC 61.235 55.000 0.00 0.00 42.91 6.53
1235 1273 5.869579 ACAAGAGCAATAGAAAGAGGAACA 58.130 37.500 0.00 0.00 0.00 3.18
1336 1376 5.868257 TCAGCAACTGACAATTTATTAGCG 58.132 37.500 0.00 0.00 35.39 4.26
1350 1390 1.002033 GAGCCAAAGTGTCAGCAACTG 60.002 52.381 0.00 0.00 0.00 3.16
1391 1460 3.928375 GGCAATGGCAAGTAGTGATTTTG 59.072 43.478 0.58 0.00 43.71 2.44
1392 1461 3.577848 TGGCAATGGCAAGTAGTGATTTT 59.422 39.130 7.14 0.00 43.71 1.82
1394 1463 2.806434 TGGCAATGGCAAGTAGTGATT 58.194 42.857 7.14 0.00 43.71 2.57
1395 1464 2.512692 TGGCAATGGCAAGTAGTGAT 57.487 45.000 7.14 0.00 43.71 3.06
1396 1465 2.512692 ATGGCAATGGCAAGTAGTGA 57.487 45.000 14.81 0.00 42.43 3.41
1397 1466 3.255725 CAAATGGCAATGGCAAGTAGTG 58.744 45.455 14.81 4.05 42.43 2.74
1399 1468 2.273557 GCAAATGGCAATGGCAAGTAG 58.726 47.619 14.81 5.61 42.43 2.57
1400 1469 2.383368 GCAAATGGCAATGGCAAGTA 57.617 45.000 14.81 0.00 42.43 2.24
1401 1470 3.236604 GCAAATGGCAATGGCAAGT 57.763 47.368 14.81 1.64 42.43 3.16
1457 1729 1.274728 TGTACCACCATTTTGGCATGC 59.725 47.619 9.90 9.90 42.67 4.06
1458 1730 2.824936 TCTGTACCACCATTTTGGCATG 59.175 45.455 0.00 0.00 42.67 4.06
1479 1751 5.463061 GCTCAATGCATTTTAACAGTGTTGT 59.537 36.000 18.90 0.00 42.31 3.32
1480 1752 5.107375 GGCTCAATGCATTTTAACAGTGTTG 60.107 40.000 18.90 3.04 45.15 3.33
1482 1754 4.559153 GGCTCAATGCATTTTAACAGTGT 58.441 39.130 9.83 0.00 45.15 3.55
1483 1755 3.928375 GGGCTCAATGCATTTTAACAGTG 59.072 43.478 9.83 0.00 45.15 3.66
1484 1756 3.577848 TGGGCTCAATGCATTTTAACAGT 59.422 39.130 9.83 0.00 45.15 3.55
1485 1757 4.191033 TGGGCTCAATGCATTTTAACAG 57.809 40.909 9.83 2.27 45.15 3.16
1486 1758 4.040217 ACTTGGGCTCAATGCATTTTAACA 59.960 37.500 9.83 2.94 45.15 2.41
1487 1759 4.389687 CACTTGGGCTCAATGCATTTTAAC 59.610 41.667 9.83 0.78 45.15 2.01
1488 1760 4.567971 CACTTGGGCTCAATGCATTTTAA 58.432 39.130 9.83 0.00 45.15 1.52
1489 1761 3.617045 GCACTTGGGCTCAATGCATTTTA 60.617 43.478 21.45 0.00 45.15 1.52
1490 1762 2.872842 GCACTTGGGCTCAATGCATTTT 60.873 45.455 21.45 0.00 45.15 1.82
1491 1763 1.338389 GCACTTGGGCTCAATGCATTT 60.338 47.619 21.45 0.00 45.15 2.32
1492 1764 0.248289 GCACTTGGGCTCAATGCATT 59.752 50.000 21.45 5.99 45.15 3.56
1493 1765 0.901114 TGCACTTGGGCTCAATGCAT 60.901 50.000 23.77 0.00 41.18 3.96
1494 1766 1.531128 TGCACTTGGGCTCAATGCA 60.531 52.632 23.77 23.77 43.70 3.96
1495 1767 1.080298 GTGCACTTGGGCTCAATGC 60.080 57.895 20.28 20.28 41.94 3.56
1496 1768 0.963962 AAGTGCACTTGGGCTCAATG 59.036 50.000 30.66 1.73 34.38 2.82
1497 1769 1.202976 AGAAGTGCACTTGGGCTCAAT 60.203 47.619 35.67 9.42 36.11 2.57
1498 1770 0.183492 AGAAGTGCACTTGGGCTCAA 59.817 50.000 35.67 0.00 36.11 3.02
1514 1786 9.638239 GTTAATTGCATCAGGAATGTTTTAGAA 57.362 29.630 0.00 0.00 35.82 2.10
1555 1853 7.085116 AGTACTTTTTGTCTGACTATCACGAG 58.915 38.462 9.51 1.41 0.00 4.18
1556 1854 6.978338 AGTACTTTTTGTCTGACTATCACGA 58.022 36.000 9.51 0.00 0.00 4.35
1557 1855 8.021973 AGTAGTACTTTTTGTCTGACTATCACG 58.978 37.037 9.51 0.00 0.00 4.35
1558 1856 9.344309 GAGTAGTACTTTTTGTCTGACTATCAC 57.656 37.037 9.51 0.00 0.00 3.06
1559 1857 8.521176 GGAGTAGTACTTTTTGTCTGACTATCA 58.479 37.037 9.51 0.00 0.00 2.15
1560 1858 7.975058 GGGAGTAGTACTTTTTGTCTGACTATC 59.025 40.741 9.51 0.00 0.00 2.08
1561 1859 7.674772 AGGGAGTAGTACTTTTTGTCTGACTAT 59.325 37.037 9.51 0.00 0.00 2.12
1562 1860 7.008941 AGGGAGTAGTACTTTTTGTCTGACTA 58.991 38.462 9.51 0.00 0.00 2.59
1563 1861 5.839606 AGGGAGTAGTACTTTTTGTCTGACT 59.160 40.000 9.51 0.00 0.00 3.41
1564 1862 6.015265 AGAGGGAGTAGTACTTTTTGTCTGAC 60.015 42.308 0.00 0.00 0.00 3.51
1565 1863 6.015350 CAGAGGGAGTAGTACTTTTTGTCTGA 60.015 42.308 16.47 0.00 0.00 3.27
1566 1864 6.159988 CAGAGGGAGTAGTACTTTTTGTCTG 58.840 44.000 0.00 8.90 0.00 3.51
1567 1865 5.839606 ACAGAGGGAGTAGTACTTTTTGTCT 59.160 40.000 0.00 0.75 0.00 3.41
1568 1866 6.099159 ACAGAGGGAGTAGTACTTTTTGTC 57.901 41.667 0.00 0.00 0.00 3.18
1569 1867 6.464039 GGAACAGAGGGAGTAGTACTTTTTGT 60.464 42.308 0.00 3.09 0.00 2.83
1570 1868 5.932883 GGAACAGAGGGAGTAGTACTTTTTG 59.067 44.000 0.00 2.52 0.00 2.44
1571 1869 5.605488 TGGAACAGAGGGAGTAGTACTTTTT 59.395 40.000 0.00 0.00 0.00 1.94
1572 1870 5.152934 TGGAACAGAGGGAGTAGTACTTTT 58.847 41.667 0.00 0.00 0.00 2.27
1573 1871 4.748701 TGGAACAGAGGGAGTAGTACTTT 58.251 43.478 0.00 0.00 0.00 2.66
1574 1872 4.399483 TGGAACAGAGGGAGTAGTACTT 57.601 45.455 0.00 0.00 0.00 2.24
1575 1873 4.399483 TTGGAACAGAGGGAGTAGTACT 57.601 45.455 1.37 1.37 42.39 2.73
1576 1874 5.479124 TTTTGGAACAGAGGGAGTAGTAC 57.521 43.478 0.00 0.00 42.39 2.73
1577 1875 7.989947 ATATTTTGGAACAGAGGGAGTAGTA 57.010 36.000 0.00 0.00 42.39 1.82
1578 1876 6.893020 ATATTTTGGAACAGAGGGAGTAGT 57.107 37.500 0.00 0.00 42.39 2.73
1579 1877 7.934120 CCTTATATTTTGGAACAGAGGGAGTAG 59.066 40.741 0.00 0.00 42.39 2.57
1619 1917 2.535166 CGTGCACATGTTTGACTTTTGG 59.465 45.455 18.64 0.00 0.00 3.28
1620 1918 3.178267 ACGTGCACATGTTTGACTTTTG 58.822 40.909 18.64 0.00 0.00 2.44
1622 1920 3.502191 AACGTGCACATGTTTGACTTT 57.498 38.095 18.64 0.00 37.24 2.66
1767 2081 6.703857 TCGATTTTTGTGCAAGTCAAATTTG 58.296 32.000 12.15 12.15 35.25 2.32
1768 2082 6.900568 TCGATTTTTGTGCAAGTCAAATTT 57.099 29.167 2.22 0.00 35.25 1.82
1769 2083 7.651304 TGTATCGATTTTTGTGCAAGTCAAATT 59.349 29.630 1.71 0.00 35.25 1.82
1770 2084 7.114811 GTGTATCGATTTTTGTGCAAGTCAAAT 59.885 33.333 1.71 0.00 35.25 2.32
1794 2108 5.302059 TCTCTCCGTTCCAGAATATAAGGTG 59.698 44.000 0.00 0.00 0.00 4.00
1807 2121 6.628185 TGTAAATCTTTACTCTCTCCGTTCC 58.372 40.000 12.61 0.00 42.61 3.62
1881 2196 6.040504 TGCTGGTATAACTTCTATCACGATGT 59.959 38.462 0.00 0.00 0.00 3.06
1888 2203 8.286097 GCTGAAATTGCTGGTATAACTTCTATC 58.714 37.037 0.00 0.00 0.00 2.08
1892 2207 6.194796 TGCTGAAATTGCTGGTATAACTTC 57.805 37.500 0.00 0.00 0.00 3.01
1942 2257 1.533625 TGCAGAACCATACAAGGCAC 58.466 50.000 0.00 0.00 0.00 5.01
1998 2315 4.022416 GCCACAATATGTGTCTTCCAAACA 60.022 41.667 9.42 0.00 46.45 2.83
2026 2343 9.868277 AGAGAAGTATCATCTTTGTTGTCTTAG 57.132 33.333 0.00 0.00 0.00 2.18
2046 2365 5.702670 TCTTGTCATGTTTGCCTAAGAGAAG 59.297 40.000 0.00 0.00 0.00 2.85
2127 2446 6.983906 AAATGGAAGTTCATGAGTTTCCTT 57.016 33.333 27.16 21.95 39.80 3.36
2160 2479 0.663153 GTTGCAGCGACTGTTTCCTT 59.337 50.000 5.41 0.00 33.43 3.36
2167 2486 1.191096 GTTGTTTGTTGCAGCGACTG 58.809 50.000 14.20 2.92 34.12 3.51
2193 2512 7.812669 CCTTGTCCTAACAAATTAATTGGACAC 59.187 37.037 25.61 9.97 44.53 3.67
2203 2522 1.544246 GCCGCCTTGTCCTAACAAATT 59.456 47.619 0.00 0.00 44.53 1.82
2204 2523 1.173913 GCCGCCTTGTCCTAACAAAT 58.826 50.000 0.00 0.00 44.53 2.32
2205 2524 0.109723 AGCCGCCTTGTCCTAACAAA 59.890 50.000 0.00 0.00 44.53 2.83
2206 2525 0.109723 AAGCCGCCTTGTCCTAACAA 59.890 50.000 0.00 0.00 43.06 2.83
2215 2534 0.958822 ACTTTACCAAAGCCGCCTTG 59.041 50.000 0.00 0.00 42.27 3.61
2288 2607 4.874966 TCACAGCAAAAAGGGACAAAATTG 59.125 37.500 0.00 0.00 0.00 2.32
2314 2634 9.309516 GATACGAAATAGTATGGTTCAGTTTCA 57.690 33.333 0.00 0.00 37.43 2.69
2315 2635 8.762426 GGATACGAAATAGTATGGTTCAGTTTC 58.238 37.037 0.00 0.00 37.43 2.78
2335 2655 6.018994 CCAACGAGGAGAAAATTAAGGATACG 60.019 42.308 0.00 0.00 41.08 3.06
2413 2733 1.196012 CCCTGTCCAGAACCTCTACC 58.804 60.000 0.00 0.00 0.00 3.18
2427 2747 4.362677 TCCTAAACTCTATTGCTCCCTGT 58.637 43.478 0.00 0.00 0.00 4.00
2433 2753 8.763601 ACTACTTCATTCCTAAACTCTATTGCT 58.236 33.333 0.00 0.00 0.00 3.91
2621 2946 6.545666 ACGGATTATGATTTAAGATGTGGCAA 59.454 34.615 0.00 0.00 0.00 4.52
2653 2985 4.341806 TGGCTTCTTTTCAGAATCTGCAAA 59.658 37.500 5.18 6.64 38.42 3.68
2702 3034 7.387643 CCCTCTAGCCACTCCTTTTATTATAC 58.612 42.308 0.00 0.00 0.00 1.47
2744 3077 6.286758 TGAATTATCATCAGCCTTGAGTCTC 58.713 40.000 0.00 0.00 36.61 3.36
2754 3087 7.563020 TCAGATCCCTATGAATTATCATCAGC 58.437 38.462 0.00 0.00 42.75 4.26
2942 3281 6.125327 TGTGCATTTCGAGTTGAGTTTAAA 57.875 33.333 0.00 0.00 0.00 1.52
3039 3380 4.747108 CCAAAGCTATAGACATCGGACTTG 59.253 45.833 3.21 0.00 0.00 3.16
3066 3407 4.023707 CCACTTACAGTTTCCAAGAGCAAG 60.024 45.833 0.00 0.00 0.00 4.01
3090 3431 5.455056 TCTCGGTTGAGCTAATCCTTATC 57.545 43.478 0.00 0.00 42.26 1.75
3091 3432 5.128827 TGTTCTCGGTTGAGCTAATCCTTAT 59.871 40.000 0.00 0.00 42.26 1.73
3160 3501 2.728690 TTGCAGACATTGGCAATGAC 57.271 45.000 38.83 32.99 44.41 3.06
3572 3932 3.000078 GCAAAATCATCTCAATGCAAGCG 60.000 43.478 0.00 0.00 34.10 4.68
4025 4486 1.352352 AGCATGAGCCGCCCTATTAAT 59.648 47.619 0.00 0.00 43.56 1.40
4026 4487 0.764890 AGCATGAGCCGCCCTATTAA 59.235 50.000 0.00 0.00 43.56 1.40
4052 4513 0.036105 ACAACATGCTCCGCAGATCA 60.036 50.000 0.00 0.00 43.65 2.92
4251 4716 3.324846 CCAGAGGTATTAGTAGCATGCCA 59.675 47.826 15.66 0.00 0.00 4.92
4338 4803 9.964303 AAAAATGAAAGAAATAAACAAATGCCC 57.036 25.926 0.00 0.00 0.00 5.36
4367 4832 1.891933 TATGCCCCTTCCACATGAGA 58.108 50.000 0.00 0.00 0.00 3.27
4368 4833 2.301346 GTTATGCCCCTTCCACATGAG 58.699 52.381 0.00 0.00 0.00 2.90
4369 4834 1.064017 GGTTATGCCCCTTCCACATGA 60.064 52.381 0.00 0.00 0.00 3.07
4414 4881 8.062065 TGGACCATTACTTTGGATCAAAATAC 57.938 34.615 0.00 0.00 39.25 1.89
4416 4883 7.386059 GTTGGACCATTACTTTGGATCAAAAT 58.614 34.615 0.00 0.00 39.25 1.82
4417 4884 6.515862 CGTTGGACCATTACTTTGGATCAAAA 60.516 38.462 0.00 0.00 39.25 2.44
4419 4886 4.457603 CGTTGGACCATTACTTTGGATCAA 59.542 41.667 0.00 0.00 39.25 2.57
4420 4887 4.006989 CGTTGGACCATTACTTTGGATCA 58.993 43.478 0.00 0.00 39.25 2.92
4421 4888 3.181500 GCGTTGGACCATTACTTTGGATC 60.181 47.826 0.00 0.00 39.25 3.36
4422 4889 2.752903 GCGTTGGACCATTACTTTGGAT 59.247 45.455 0.00 0.00 39.25 3.41
4423 4890 2.156098 GCGTTGGACCATTACTTTGGA 58.844 47.619 0.00 0.00 39.25 3.53
4424 4891 1.201414 GGCGTTGGACCATTACTTTGG 59.799 52.381 0.00 0.00 42.82 3.28
4451 4918 0.970640 TTCCGTCAAGATTCCGTCCA 59.029 50.000 0.00 0.00 0.00 4.02
4453 4920 1.641577 CCTTCCGTCAAGATTCCGTC 58.358 55.000 0.00 0.00 33.29 4.79
4457 4924 2.044123 ATGCCCTTCCGTCAAGATTC 57.956 50.000 0.00 0.00 33.29 2.52
4467 4934 1.209747 AGGTTACTCGAATGCCCTTCC 59.790 52.381 0.00 0.00 0.00 3.46
4482 4949 5.595952 GTCCTTAGATTTACTCCCGAGGTTA 59.404 44.000 0.00 0.00 0.00 2.85
4489 4956 8.575649 TCAATTTTGTCCTTAGATTTACTCCC 57.424 34.615 0.00 0.00 0.00 4.30
4494 4961 8.730680 GTCTGCTCAATTTTGTCCTTAGATTTA 58.269 33.333 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.