Multiple sequence alignment - TraesCS7A01G243500

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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 TraesCS7A01G243500 chr7A 100.000 2339 0 0 1 2339 219377056 219379394 0.000000e+00 4320.0
1 TraesCS7A01G243500 chr2D 88.986 1371 139 9 1 1362 622369651 622368284 0.000000e+00 1685.0
2 TraesCS7A01G243500 chr2D 81.790 324 55 4 1410 1733 348074775 348075094 3.830000e-68 268.0
3 TraesCS7A01G243500 chr2D 94.545 55 1 1 1925 1979 348075294 348075346 1.490000e-12 84.2
4 TraesCS7A01G243500 chr4D 88.222 1367 154 7 1 1361 349920260 349921625 0.000000e+00 1626.0
5 TraesCS7A01G243500 chr4D 87.282 1376 160 12 1 1364 28465767 28464395 0.000000e+00 1557.0
6 TraesCS7A01G243500 chr5B 87.819 1371 155 9 1 1361 521394987 521396355 0.000000e+00 1596.0
7 TraesCS7A01G243500 chr1A 87.473 1381 157 10 1 1369 260841558 260842934 0.000000e+00 1578.0
8 TraesCS7A01G243500 chr1A 77.907 516 75 28 1406 1919 330752142 330752620 3.800000e-73 285.0
9 TraesCS7A01G243500 chr6D 87.518 1370 160 8 1 1361 132391900 132393267 0.000000e+00 1572.0
10 TraesCS7A01G243500 chr6D 87.381 1371 159 10 1 1361 60313482 60314848 0.000000e+00 1561.0
11 TraesCS7A01G243500 chr1D 87.464 1372 158 11 1 1361 360147464 360146096 0.000000e+00 1568.0
12 TraesCS7A01G243500 chr5A 87.372 1370 162 7 1 1361 343044036 343042669 0.000000e+00 1561.0
13 TraesCS7A01G243500 chr2B 79.127 527 82 21 1414 1928 516101371 516100861 2.880000e-89 339.0
14 TraesCS7A01G243500 chr2B 81.598 413 30 21 1941 2338 516100806 516100425 1.360000e-77 300.0
15 TraesCS7A01G243500 chr2B 80.760 421 39 15 1931 2338 592573419 592573028 8.180000e-75 291.0
16 TraesCS7A01G243500 chr5D 81.455 426 32 20 1927 2338 240171402 240171010 2.920000e-79 305.0
17 TraesCS7A01G243500 chr5D 80.328 427 45 14 1925 2338 51195893 51196293 1.060000e-73 287.0
18 TraesCS7A01G243500 chr5D 80.140 428 48 15 1925 2338 51156397 51156801 3.800000e-73 285.0
19 TraesCS7A01G243500 chr5D 77.203 522 81 28 1397 1916 51195354 51195839 1.070000e-68 270.0
20 TraesCS7A01G243500 chr5D 79.446 433 48 15 1925 2338 51176895 51177305 3.830000e-68 268.0
21 TraesCS7A01G243500 chr5D 83.951 243 23 8 1926 2155 339303332 339303571 3.910000e-53 219.0
22 TraesCS7A01G243500 chr4A 78.168 513 74 24 1406 1916 527574905 527575381 2.270000e-75 292.0
23 TraesCS7A01G243500 chr3B 80.769 416 40 20 1935 2338 52855712 52856099 2.940000e-74 289.0
24 TraesCS7A01G243500 chr3D 77.451 510 78 25 1405 1911 75765615 75766090 1.070000e-68 270.0
25 TraesCS7A01G243500 chr3D 83.750 160 25 1 1404 1562 448617271 448617112 1.450000e-32 150.0
26 TraesCS7A01G243500 chr3D 93.878 49 1 1 1931 1979 75766147 75766193 3.220000e-09 73.1
27 TraesCS7A01G243500 chr6B 80.000 410 41 18 1941 2338 578018012 578017632 4.960000e-67 265.0
28 TraesCS7A01G243500 chr3A 76.998 513 80 20 1402 1911 323387291 323386814 2.310000e-65 259.0
29 TraesCS7A01G243500 chr3A 84.766 256 16 13 1927 2168 486210531 486210777 3.890000e-58 235.0
30 TraesCS7A01G243500 chr3A 85.714 133 14 4 1791 1919 744851028 744850897 4.050000e-28 135.0
31 TraesCS7A01G243500 chr3A 87.368 95 12 0 2244 2338 486210784 486210878 2.460000e-20 110.0
32 TraesCS7A01G243500 chr4B 81.250 272 32 10 1927 2184 369779358 369779624 3.940000e-48 202.0
33 TraesCS7A01G243500 chr2A 82.843 204 32 3 1413 1615 622473712 622473511 1.850000e-41 180.0


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 TraesCS7A01G243500 chr7A 219377056 219379394 2338 False 4320.0 4320 100.0000 1 2339 1 chr7A.!!$F1 2338
1 TraesCS7A01G243500 chr2D 622368284 622369651 1367 True 1685.0 1685 88.9860 1 1362 1 chr2D.!!$R1 1361
2 TraesCS7A01G243500 chr4D 349920260 349921625 1365 False 1626.0 1626 88.2220 1 1361 1 chr4D.!!$F1 1360
3 TraesCS7A01G243500 chr4D 28464395 28465767 1372 True 1557.0 1557 87.2820 1 1364 1 chr4D.!!$R1 1363
4 TraesCS7A01G243500 chr5B 521394987 521396355 1368 False 1596.0 1596 87.8190 1 1361 1 chr5B.!!$F1 1360
5 TraesCS7A01G243500 chr1A 260841558 260842934 1376 False 1578.0 1578 87.4730 1 1369 1 chr1A.!!$F1 1368
6 TraesCS7A01G243500 chr6D 132391900 132393267 1367 False 1572.0 1572 87.5180 1 1361 1 chr6D.!!$F2 1360
7 TraesCS7A01G243500 chr6D 60313482 60314848 1366 False 1561.0 1561 87.3810 1 1361 1 chr6D.!!$F1 1360
8 TraesCS7A01G243500 chr1D 360146096 360147464 1368 True 1568.0 1568 87.4640 1 1361 1 chr1D.!!$R1 1360
9 TraesCS7A01G243500 chr5A 343042669 343044036 1367 True 1561.0 1561 87.3720 1 1361 1 chr5A.!!$R1 1360
10 TraesCS7A01G243500 chr2B 516100425 516101371 946 True 319.5 339 80.3625 1414 2338 2 chr2B.!!$R2 924
11 TraesCS7A01G243500 chr5D 51195354 51196293 939 False 278.5 287 78.7655 1397 2338 2 chr5D.!!$F4 941

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
931 947 0.179081 GGGTACGATGGGAGCAGTTC 60.179 60.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2163 2270 0.105862 CCCAAGGATGATGCACCCAT 60.106 55.0 3.34 3.34 0.0 4.0 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 21 1.002624 GCGAGTGGGGAATGGACAA 60.003 57.895 0.00 0.00 0.00 3.18
34 35 7.828717 GGGGAATGGACAAAACATCAATATTTT 59.171 33.333 0.00 0.00 0.00 1.82
110 117 4.159693 GGGGGACAATTATCAAAAGTGGTC 59.840 45.833 0.00 0.00 0.00 4.02
111 118 4.770010 GGGGACAATTATCAAAAGTGGTCA 59.230 41.667 0.00 0.00 0.00 4.02
128 135 0.321564 TCAACCTGATTGACCCTGCG 60.322 55.000 0.00 0.00 42.62 5.18
136 143 1.940613 GATTGACCCTGCGTCCAATAC 59.059 52.381 0.00 0.00 41.18 1.89
194 201 3.425359 CCATTGACGCACAACAGATTCTC 60.425 47.826 0.00 0.00 41.52 2.87
225 232 3.314913 ACTTTCGCAACATGACATGACAA 59.685 39.130 22.19 4.22 0.00 3.18
247 254 8.310122 ACAAATTTCATTGCCTGGAGTTATAT 57.690 30.769 0.00 0.00 33.52 0.86
251 258 7.572523 TTTCATTGCCTGGAGTTATATGAAG 57.427 36.000 0.00 0.00 33.59 3.02
271 278 6.774673 TGAAGAATGGTATGTTCTTGGTACA 58.225 36.000 5.91 0.00 43.80 2.90
309 316 4.975147 TGGAGTGGAATTATCAGTATGGGT 59.025 41.667 0.00 0.00 36.16 4.51
401 410 4.871933 ATCTTGTCCGGCAAAAGAAAAT 57.128 36.364 14.64 0.24 36.53 1.82
442 451 1.066929 CATGTCACACTCCCATGTCGA 60.067 52.381 0.00 0.00 33.06 4.20
483 492 2.094675 CATGAAGGTCTCGCCCATTTT 58.905 47.619 0.00 0.00 38.26 1.82
492 501 2.307686 TCTCGCCCATTTTCCCTACTTT 59.692 45.455 0.00 0.00 0.00 2.66
526 535 6.887376 TTAGAAGATACGAAACACATGCTC 57.113 37.500 0.00 0.00 0.00 4.26
602 611 9.905713 AGATTATTGATAAAGCTTGTGAGGTTA 57.094 29.630 0.00 0.00 42.47 2.85
615 624 3.244078 TGTGAGGTTAATCGTGCTGAAGT 60.244 43.478 0.00 0.00 0.00 3.01
699 708 9.347934 CCAAGATGTACGAGAAATAATAGCTAG 57.652 37.037 0.00 0.00 0.00 3.42
736 745 4.519540 ATGGTGGGAAAGACGAAAATTG 57.480 40.909 0.00 0.00 0.00 2.32
737 746 2.035321 TGGTGGGAAAGACGAAAATTGC 59.965 45.455 0.00 0.00 0.00 3.56
763 772 5.105997 GCACAAGGAATTAACTCAGAATGCT 60.106 40.000 0.00 0.00 34.76 3.79
775 784 7.838079 AACTCAGAATGCTACTCAGATATCT 57.162 36.000 0.00 0.00 34.76 1.98
827 836 7.177216 ACTTTGTAAATGCATCATCTCCAAAGA 59.823 33.333 24.86 4.67 36.34 2.52
853 869 5.236334 TCCATGAAAGGGGGTGGTATTATA 58.764 41.667 0.00 0.00 39.14 0.98
861 877 4.930764 AGGGGGTGGTATTATACTCCTAGA 59.069 45.833 2.21 0.00 37.60 2.43
886 902 7.607250 AGGTTTTGTGAAACTTAATGTTGACA 58.393 30.769 2.51 0.00 43.68 3.58
924 940 0.616395 TGCTGAAGGGTACGATGGGA 60.616 55.000 0.00 0.00 0.00 4.37
931 947 0.179081 GGGTACGATGGGAGCAGTTC 60.179 60.000 0.00 0.00 0.00 3.01
1034 1050 5.595952 CCTTAGCTCTCAAATTTGGCCTAAT 59.404 40.000 17.90 6.60 0.00 1.73
1077 1093 4.982295 TGTAATCGCCTAATCATCAACTCG 59.018 41.667 0.00 0.00 0.00 4.18
1084 1100 5.062683 CGCCTAATCATCAACTCGGATAATG 59.937 44.000 0.00 0.00 0.00 1.90
1104 1120 2.237143 TGTGGAGGTGATTGAGACCATC 59.763 50.000 0.00 0.00 35.76 3.51
1179 1195 5.726980 ACCACTATGCATGTGATTTTGTT 57.273 34.783 22.76 0.00 37.60 2.83
1182 1198 8.518430 ACCACTATGCATGTGATTTTGTTATA 57.482 30.769 22.76 0.00 37.60 0.98
1279 1299 4.561530 CGACTTCAGATTGGTTTGAGGAGA 60.562 45.833 0.00 0.00 0.00 3.71
1381 1401 8.894768 AAAAAGGTGGATATCTATTTCTCTCG 57.105 34.615 2.05 0.00 0.00 4.04
1382 1402 7.841282 AAAGGTGGATATCTATTTCTCTCGA 57.159 36.000 2.05 0.00 0.00 4.04
1383 1403 7.841282 AAGGTGGATATCTATTTCTCTCGAA 57.159 36.000 2.05 0.00 0.00 3.71
1384 1404 7.841282 AGGTGGATATCTATTTCTCTCGAAA 57.159 36.000 2.05 0.00 42.83 3.46
1385 1405 7.891561 AGGTGGATATCTATTTCTCTCGAAAG 58.108 38.462 2.05 0.00 42.01 2.62
1386 1406 7.726291 AGGTGGATATCTATTTCTCTCGAAAGA 59.274 37.037 2.05 0.00 42.01 2.52
1387 1407 7.810759 GGTGGATATCTATTTCTCTCGAAAGAC 59.189 40.741 2.05 0.00 42.01 3.01
1388 1408 7.810759 GTGGATATCTATTTCTCTCGAAAGACC 59.189 40.741 2.05 0.00 42.01 3.85
1389 1409 7.505923 TGGATATCTATTTCTCTCGAAAGACCA 59.494 37.037 2.05 0.00 42.01 4.02
1390 1410 8.527810 GGATATCTATTTCTCTCGAAAGACCAT 58.472 37.037 2.05 0.00 42.01 3.55
1393 1413 7.883391 TCTATTTCTCTCGAAAGACCATACT 57.117 36.000 0.00 0.00 42.01 2.12
1394 1414 7.708051 TCTATTTCTCTCGAAAGACCATACTG 58.292 38.462 0.00 0.00 42.01 2.74
1395 1415 3.784701 TCTCTCGAAAGACCATACTGC 57.215 47.619 0.00 0.00 35.39 4.40
1398 1418 2.832129 TCTCGAAAGACCATACTGCCTT 59.168 45.455 0.00 0.00 35.39 4.35
1402 1422 4.020928 TCGAAAGACCATACTGCCTTTGTA 60.021 41.667 0.00 0.00 33.31 2.41
1406 1426 3.583086 AGACCATACTGCCTTTGTACACT 59.417 43.478 0.00 0.00 0.00 3.55
1408 1428 4.725490 ACCATACTGCCTTTGTACACTTT 58.275 39.130 0.00 0.00 0.00 2.66
1411 1431 3.290948 ACTGCCTTTGTACACTTTGGA 57.709 42.857 0.00 0.00 0.00 3.53
1423 1443 2.559231 ACACTTTGGACGTGTTTGGTTT 59.441 40.909 0.00 0.00 42.56 3.27
1436 1456 0.541764 TTGGTTTCCTGGGTGCATCC 60.542 55.000 9.82 9.82 0.00 3.51
1483 1503 3.971702 GGGCTGGCCTGGTTGAGT 61.972 66.667 13.80 0.00 36.10 3.41
1495 1515 4.053295 CCTGGTTGAGTTGATGCAAAAAG 58.947 43.478 0.00 0.00 0.00 2.27
1496 1516 4.441913 CCTGGTTGAGTTGATGCAAAAAGT 60.442 41.667 0.00 0.00 0.00 2.66
1503 1523 6.728200 TGAGTTGATGCAAAAAGTAGTTGAG 58.272 36.000 0.00 0.00 0.00 3.02
1508 1528 7.977789 TGATGCAAAAAGTAGTTGAGATGTA 57.022 32.000 0.00 0.00 0.00 2.29
1534 1554 2.777114 TGGTGTACTGCATGATATGGGT 59.223 45.455 0.00 0.00 0.00 4.51
1539 1559 2.130193 ACTGCATGATATGGGTCAGGT 58.870 47.619 0.00 0.00 32.79 4.00
1541 1561 3.053395 ACTGCATGATATGGGTCAGGTTT 60.053 43.478 0.00 0.00 32.79 3.27
1563 1583 7.755373 GGTTTAGCTCAGATTTTGTTTGGTATC 59.245 37.037 0.00 0.00 0.00 2.24
1592 1612 4.467438 TCTGAGGTTGTATGAGAGATGCAA 59.533 41.667 0.00 0.00 0.00 4.08
1602 1622 8.822652 TGTATGAGAGATGCAACATACAATAG 57.177 34.615 20.45 0.00 46.19 1.73
1606 1626 7.729116 TGAGAGATGCAACATACAATAGATGA 58.271 34.615 0.00 0.00 0.00 2.92
1615 1635 7.975616 GCAACATACAATAGATGATGTTTGGTT 59.024 33.333 0.00 0.00 37.52 3.67
1618 1638 8.840321 ACATACAATAGATGATGTTTGGTTAGC 58.160 33.333 0.00 0.00 34.22 3.09
1630 1650 4.155826 TGTTTGGTTAGCTGTATGATGTGC 59.844 41.667 0.00 0.00 0.00 4.57
1636 1656 5.973565 GGTTAGCTGTATGATGTGCAATTTC 59.026 40.000 0.00 0.00 0.00 2.17
1640 1660 4.796830 GCTGTATGATGTGCAATTTCACTG 59.203 41.667 9.63 0.00 37.81 3.66
1645 1693 5.313520 TGATGTGCAATTTCACTGTATGG 57.686 39.130 9.63 0.00 37.81 2.74
1651 1699 4.039004 TGCAATTTCACTGTATGGTGCTTT 59.961 37.500 0.00 0.00 37.16 3.51
1652 1700 4.386652 GCAATTTCACTGTATGGTGCTTTG 59.613 41.667 0.00 0.00 37.16 2.77
1654 1702 6.676950 CAATTTCACTGTATGGTGCTTTGTA 58.323 36.000 0.00 0.00 37.16 2.41
1655 1703 5.682943 TTTCACTGTATGGTGCTTTGTAC 57.317 39.130 0.00 0.00 37.16 2.90
1656 1704 4.344359 TCACTGTATGGTGCTTTGTACA 57.656 40.909 0.00 0.00 37.16 2.90
1657 1705 4.905429 TCACTGTATGGTGCTTTGTACAT 58.095 39.130 0.00 0.00 37.16 2.29
1658 1706 6.043854 TCACTGTATGGTGCTTTGTACATA 57.956 37.500 0.00 0.00 37.16 2.29
1659 1707 5.872617 TCACTGTATGGTGCTTTGTACATAC 59.127 40.000 0.00 0.00 43.55 2.39
1662 1710 6.676237 TGTATGGTGCTTTGTACATACATG 57.324 37.500 11.11 0.00 46.16 3.21
1663 1711 6.176896 TGTATGGTGCTTTGTACATACATGT 58.823 36.000 2.69 2.69 46.16 3.21
1664 1712 7.331791 TGTATGGTGCTTTGTACATACATGTA 58.668 34.615 8.27 8.27 46.16 2.29
1668 1716 8.116651 TGGTGCTTTGTACATACATGTAAAAT 57.883 30.769 10.14 1.00 44.11 1.82
1669 1717 8.240682 TGGTGCTTTGTACATACATGTAAAATC 58.759 33.333 10.14 2.21 44.11 2.17
1671 1719 9.277565 GTGCTTTGTACATACATGTAAAATCAG 57.722 33.333 10.14 3.67 44.11 2.90
1692 1740 7.724305 TCAGTTACAAAATAGTTCTGGTGAC 57.276 36.000 0.00 0.00 0.00 3.67
1698 1746 5.477984 ACAAAATAGTTCTGGTGACATGCAT 59.522 36.000 0.00 0.00 41.51 3.96
1701 1749 3.430042 AGTTCTGGTGACATGCATTCT 57.570 42.857 0.00 0.00 41.51 2.40
1703 1751 4.910195 AGTTCTGGTGACATGCATTCTAA 58.090 39.130 0.00 0.00 41.51 2.10
1704 1752 4.697352 AGTTCTGGTGACATGCATTCTAAC 59.303 41.667 0.00 0.00 41.51 2.34
1705 1753 4.558226 TCTGGTGACATGCATTCTAACT 57.442 40.909 0.00 0.00 41.51 2.24
1712 1760 6.763135 GGTGACATGCATTCTAACTCAGATAA 59.237 38.462 0.00 0.00 31.77 1.75
1718 1766 8.886719 CATGCATTCTAACTCAGATAACTTTGA 58.113 33.333 0.00 0.00 31.77 2.69
1765 1813 9.617523 AAAGTGATCTCATGTTTCCAAATTTTT 57.382 25.926 0.00 0.00 0.00 1.94
1805 1853 6.524358 CATGTATGCAAAATGGCAGAGATGC 61.524 44.000 6.92 9.53 45.48 3.91
1808 1856 2.094390 TGCAAAATGGCAGAGATGCTTC 60.094 45.455 15.25 0.00 39.25 3.86
1843 1891 4.190772 CAAAATTTCAGCAACACCTTGGT 58.809 39.130 0.00 0.00 38.70 3.67
1885 1934 7.251704 AGCAGTTTATATGACACATAAGCAC 57.748 36.000 3.58 0.00 0.00 4.40
1919 2013 8.292444 ACATAATAGCTAAAGAAATGCACCAA 57.708 30.769 0.00 0.00 0.00 3.67
1923 2017 5.064441 AGCTAAAGAAATGCACCAACATC 57.936 39.130 0.00 0.00 0.00 3.06
1929 2023 4.147321 AGAAATGCACCAACATCAGAGTT 58.853 39.130 0.00 0.00 0.00 3.01
1933 2027 1.195448 GCACCAACATCAGAGTTCACG 59.805 52.381 0.00 0.00 0.00 4.35
1938 2032 5.867174 CACCAACATCAGAGTTCACGTATTA 59.133 40.000 0.00 0.00 0.00 0.98
1939 2033 6.035005 CACCAACATCAGAGTTCACGTATTAG 59.965 42.308 0.00 0.00 0.00 1.73
1978 2072 6.213397 TCCATATGGTCCATATTACAGTCCAG 59.787 42.308 20.05 7.22 35.18 3.86
1981 2075 8.762645 CATATGGTCCATATTACAGTCCAGTAT 58.237 37.037 20.05 0.00 35.18 2.12
1985 2079 8.177456 TGGTCCATATTACAGTCCAGTATATCT 58.823 37.037 0.00 0.00 0.00 1.98
2143 2250 8.188373 CAACTTGGATAGGTGAATTGGCACAA 62.188 42.308 0.00 0.00 44.60 3.33
2163 2270 0.478072 ATTTGCTCACACTCCACCCA 59.522 50.000 0.00 0.00 0.00 4.51
2177 2284 4.186136 CCCATGGGTGCATCATCC 57.814 61.111 23.93 0.00 34.72 3.51
2178 2285 1.540166 CCCATGGGTGCATCATCCT 59.460 57.895 23.93 0.00 35.30 3.24
2182 2289 0.105862 ATGGGTGCATCATCCTTGGG 60.106 55.000 0.00 0.00 35.30 4.12
2183 2290 2.129785 GGGTGCATCATCCTTGGGC 61.130 63.158 0.00 0.00 30.73 5.36
2184 2291 2.484062 GGTGCATCATCCTTGGGCG 61.484 63.158 0.00 0.00 0.00 6.13
2185 2292 2.829914 TGCATCATCCTTGGGCGC 60.830 61.111 0.00 0.00 0.00 6.53
2186 2293 2.517875 GCATCATCCTTGGGCGCT 60.518 61.111 7.64 0.00 0.00 5.92
2187 2294 2.123428 GCATCATCCTTGGGCGCTT 61.123 57.895 7.64 0.00 0.00 4.68
2188 2295 2.028130 CATCATCCTTGGGCGCTTC 58.972 57.895 7.64 0.02 0.00 3.86
2189 2296 0.749091 CATCATCCTTGGGCGCTTCA 60.749 55.000 7.64 3.23 0.00 3.02
2190 2297 0.184451 ATCATCCTTGGGCGCTTCAT 59.816 50.000 7.64 0.00 0.00 2.57
2191 2298 0.464373 TCATCCTTGGGCGCTTCATC 60.464 55.000 7.64 0.00 0.00 2.92
2194 2301 1.454479 CCTTGGGCGCTTCATCCAT 60.454 57.895 7.64 0.00 0.00 3.41
2199 2306 3.957535 GCGCTTCATCCATGGGCG 61.958 66.667 23.01 23.01 45.38 6.13
2231 2338 1.687612 CACTCCATCCTTGGGCACT 59.312 57.895 0.00 0.00 43.81 4.40
2232 2339 0.393537 CACTCCATCCTTGGGCACTC 60.394 60.000 0.00 0.00 43.81 3.51
2233 2340 1.225704 CTCCATCCTTGGGCACTCC 59.774 63.158 0.00 0.00 43.81 3.85
2234 2341 1.541118 TCCATCCTTGGGCACTCCA 60.541 57.895 0.00 0.00 43.81 3.86
2235 2342 0.920763 TCCATCCTTGGGCACTCCAT 60.921 55.000 0.00 0.00 46.52 3.41
2236 2343 0.466922 CCATCCTTGGGCACTCCATC 60.467 60.000 0.00 0.00 46.52 3.51
2237 2344 0.549950 CATCCTTGGGCACTCCATCT 59.450 55.000 0.00 0.00 46.52 2.90
2238 2345 1.064166 CATCCTTGGGCACTCCATCTT 60.064 52.381 0.00 0.00 46.52 2.40
2239 2346 1.075601 TCCTTGGGCACTCCATCTTT 58.924 50.000 0.00 0.00 46.52 2.52
2257 2364 1.379916 TGGGCACTCCACCATTGAG 59.620 57.895 0.00 0.00 41.46 3.02
2287 2394 1.052617 TGGTGAATGACCCAACGAGA 58.947 50.000 0.00 0.00 45.45 4.04
2291 2398 1.079127 AATGACCCAACGAGAGCGG 60.079 57.895 0.00 0.00 43.17 5.52
2293 2400 4.373116 GACCCAACGAGAGCGGCA 62.373 66.667 1.45 0.00 43.17 5.69
2320 2427 3.056891 TGTGACATCTGCACGAATGAGTA 60.057 43.478 6.09 0.00 39.07 2.59
2338 2445 0.042731 TAGCTCCTAGCCCTGTTGGT 59.957 55.000 0.00 0.00 43.77 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 7.049754 GGCATCTTCCCAAAATATTGATGTTT 58.950 34.615 9.92 0.00 38.94 2.83
34 35 1.355718 GGGATCCAGGCATCTTCCCA 61.356 60.000 15.23 0.00 44.58 4.37
110 117 0.606401 ACGCAGGGTCAATCAGGTTG 60.606 55.000 0.00 0.00 39.25 3.77
111 118 0.321653 GACGCAGGGTCAATCAGGTT 60.322 55.000 12.66 0.00 45.36 3.50
136 143 5.365025 TGTCTAATCAGATCCTCTTCCCAAG 59.635 44.000 0.00 0.00 32.09 3.61
143 150 8.420222 CACATAGTTTGTCTAATCAGATCCTCT 58.580 37.037 0.00 0.00 36.00 3.69
194 201 1.879380 TGTTGCGAAAGTGGGATTGAG 59.121 47.619 0.00 0.00 0.00 3.02
225 232 8.537728 TTCATATAACTCCAGGCAATGAAATT 57.462 30.769 0.00 0.00 36.63 1.82
247 254 6.774673 TGTACCAAGAACATACCATTCTTCA 58.225 36.000 0.00 0.00 43.06 3.02
251 258 7.679638 GCAGATTGTACCAAGAACATACCATTC 60.680 40.741 0.00 0.00 0.00 2.67
348 355 7.619698 CCATATCTGACACCATATAGGGTTAGA 59.380 40.741 6.28 11.21 43.89 2.10
417 426 3.673902 CATGGGAGTGTGACATGTAACA 58.326 45.455 12.32 12.32 37.72 2.41
426 435 0.888619 GACTCGACATGGGAGTGTGA 59.111 55.000 21.83 0.00 44.41 3.58
442 451 4.878439 TGTGTTTATTAGCGAGTGTGACT 58.122 39.130 0.00 0.00 0.00 3.41
492 501 5.752650 TCGTATCTTCTAAACCCTGAGAGA 58.247 41.667 0.00 0.00 0.00 3.10
526 535 4.416505 CTTTGCTTTACTGCAGAGGAAG 57.583 45.455 23.35 19.78 44.27 3.46
602 611 1.538047 ATTGCCACTTCAGCACGATT 58.462 45.000 0.00 0.00 40.69 3.34
615 624 5.665812 AGTAGAAGGTATTCCAGTATTGCCA 59.334 40.000 0.00 0.00 35.94 4.92
677 686 9.894783 TGAACTAGCTATTATTTCTCGTACATC 57.105 33.333 0.00 0.00 0.00 3.06
699 708 3.553096 CCACCATAGATACCGAGCTGAAC 60.553 52.174 0.00 0.00 0.00 3.18
707 716 3.552273 CGTCTTTCCCACCATAGATACCG 60.552 52.174 0.00 0.00 0.00 4.02
736 745 3.753272 TCTGAGTTAATTCCTTGTGCAGC 59.247 43.478 0.00 0.00 0.00 5.25
737 746 5.947228 TTCTGAGTTAATTCCTTGTGCAG 57.053 39.130 0.00 0.00 0.00 4.41
775 784 2.551270 GTGAGGGCTATGATCCCCATA 58.449 52.381 7.44 0.00 45.03 2.74
827 836 1.509548 CCACCCCCTTTCATGGAGGT 61.510 60.000 13.00 0.00 33.80 3.85
853 869 5.632034 AGTTTCACAAAACCTCTAGGAGT 57.368 39.130 2.23 0.00 44.87 3.85
861 877 7.544217 GTGTCAACATTAAGTTTCACAAAACCT 59.456 33.333 0.00 0.00 44.87 3.50
886 902 4.398358 CAGCATGTCATGATCAAAAGAGGT 59.602 41.667 17.24 0.00 0.00 3.85
924 940 1.610363 TGTCGTCTCTCAGAACTGCT 58.390 50.000 0.00 0.00 0.00 4.24
931 947 2.820787 ACCTACCTTTGTCGTCTCTCAG 59.179 50.000 0.00 0.00 0.00 3.35
1034 1050 1.680651 CCCGCCCTTTGTGCCAATA 60.681 57.895 0.00 0.00 0.00 1.90
1041 1057 0.323087 GATTACACCCCGCCCTTTGT 60.323 55.000 0.00 0.00 0.00 2.83
1077 1093 5.059833 GTCTCAATCACCTCCACATTATCC 58.940 45.833 0.00 0.00 0.00 2.59
1084 1100 2.420687 GGATGGTCTCAATCACCTCCAC 60.421 54.545 0.00 0.00 34.12 4.02
1104 1120 1.141881 CGATTGTCCTCCGTCCTGG 59.858 63.158 0.00 0.00 40.09 4.45
1131 1147 0.179156 CATCGAAAATTGCTGCCGCT 60.179 50.000 0.70 0.00 36.97 5.52
1211 1231 6.595716 AGCGAGTTCATGAGCTACTTTATTTT 59.404 34.615 12.49 0.00 38.29 1.82
1374 1394 3.119101 GGCAGTATGGTCTTTCGAGAGAA 60.119 47.826 7.31 0.00 43.01 2.87
1375 1395 2.427453 GGCAGTATGGTCTTTCGAGAGA 59.573 50.000 0.68 0.68 35.86 3.10
1376 1396 2.428890 AGGCAGTATGGTCTTTCGAGAG 59.571 50.000 0.00 0.00 35.86 3.20
1377 1397 2.457598 AGGCAGTATGGTCTTTCGAGA 58.542 47.619 0.00 0.00 35.86 4.04
1378 1398 2.969628 AGGCAGTATGGTCTTTCGAG 57.030 50.000 0.00 0.00 35.86 4.04
1379 1399 3.244422 ACAAAGGCAGTATGGTCTTTCGA 60.244 43.478 0.00 0.00 40.52 3.71
1380 1400 3.074412 ACAAAGGCAGTATGGTCTTTCG 58.926 45.455 0.00 0.00 40.52 3.46
1381 1401 5.001232 TGTACAAAGGCAGTATGGTCTTTC 58.999 41.667 0.00 0.00 40.52 2.62
1382 1402 4.760204 GTGTACAAAGGCAGTATGGTCTTT 59.240 41.667 0.00 0.00 43.08 2.52
1383 1403 4.041691 AGTGTACAAAGGCAGTATGGTCTT 59.958 41.667 0.00 0.00 35.86 3.01
1384 1404 3.583086 AGTGTACAAAGGCAGTATGGTCT 59.417 43.478 0.00 0.00 35.86 3.85
1385 1405 3.939066 AGTGTACAAAGGCAGTATGGTC 58.061 45.455 0.00 0.00 35.86 4.02
1386 1406 4.367039 AAGTGTACAAAGGCAGTATGGT 57.633 40.909 0.00 0.00 35.86 3.55
1387 1407 4.082787 CCAAAGTGTACAAAGGCAGTATGG 60.083 45.833 0.00 0.00 35.86 2.74
1388 1408 4.759693 TCCAAAGTGTACAAAGGCAGTATG 59.240 41.667 0.00 0.00 40.87 2.39
1389 1409 4.760204 GTCCAAAGTGTACAAAGGCAGTAT 59.240 41.667 0.00 0.00 0.00 2.12
1390 1410 4.131596 GTCCAAAGTGTACAAAGGCAGTA 58.868 43.478 0.00 0.00 0.00 2.74
1391 1411 2.949644 GTCCAAAGTGTACAAAGGCAGT 59.050 45.455 0.00 0.00 0.00 4.40
1392 1412 2.032030 CGTCCAAAGTGTACAAAGGCAG 60.032 50.000 0.00 0.00 0.00 4.85
1393 1413 1.944024 CGTCCAAAGTGTACAAAGGCA 59.056 47.619 0.00 0.00 0.00 4.75
1394 1414 1.944709 ACGTCCAAAGTGTACAAAGGC 59.055 47.619 0.00 0.00 0.00 4.35
1395 1415 3.602390 CACGTCCAAAGTGTACAAAGG 57.398 47.619 0.00 0.00 35.08 3.11
1406 1426 2.164624 CAGGAAACCAAACACGTCCAAA 59.835 45.455 0.00 0.00 0.00 3.28
1408 1428 1.384525 CAGGAAACCAAACACGTCCA 58.615 50.000 0.00 0.00 0.00 4.02
1411 1431 0.033894 ACCCAGGAAACCAAACACGT 60.034 50.000 0.00 0.00 0.00 4.49
1452 1472 3.066814 GCCCCAGCCAAGCTCAAG 61.067 66.667 0.00 0.00 36.40 3.02
1453 1473 3.583380 AGCCCCAGCCAAGCTCAA 61.583 61.111 0.00 0.00 41.25 3.02
1454 1474 4.355720 CAGCCCCAGCCAAGCTCA 62.356 66.667 0.00 0.00 41.25 4.26
1483 1503 7.275888 ACATCTCAACTACTTTTTGCATCAA 57.724 32.000 0.00 0.00 0.00 2.57
1495 1515 7.817962 AGTACACCAAACATACATCTCAACTAC 59.182 37.037 0.00 0.00 0.00 2.73
1496 1516 7.817478 CAGTACACCAAACATACATCTCAACTA 59.183 37.037 0.00 0.00 0.00 2.24
1503 1523 5.353956 TCATGCAGTACACCAAACATACATC 59.646 40.000 0.00 0.00 0.00 3.06
1508 1528 5.300034 CCATATCATGCAGTACACCAAACAT 59.700 40.000 0.00 0.00 0.00 2.71
1534 1554 6.239008 CCAAACAAAATCTGAGCTAAACCTGA 60.239 38.462 0.00 0.00 0.00 3.86
1539 1559 8.635765 AGATACCAAACAAAATCTGAGCTAAA 57.364 30.769 0.00 0.00 0.00 1.85
1541 1561 7.362056 GCAAGATACCAAACAAAATCTGAGCTA 60.362 37.037 0.00 0.00 32.19 3.32
1563 1583 4.763073 TCTCATACAACCTCAGATGCAAG 58.237 43.478 0.00 0.00 0.00 4.01
1592 1612 8.840321 GCTAACCAAACATCATCTATTGTATGT 58.160 33.333 0.00 0.00 34.11 2.29
1600 1620 7.791029 TCATACAGCTAACCAAACATCATCTA 58.209 34.615 0.00 0.00 0.00 1.98
1602 1622 6.925610 TCATACAGCTAACCAAACATCATC 57.074 37.500 0.00 0.00 0.00 2.92
1606 1626 5.163622 GCACATCATACAGCTAACCAAACAT 60.164 40.000 0.00 0.00 0.00 2.71
1615 1635 5.882000 AGTGAAATTGCACATCATACAGCTA 59.118 36.000 18.97 0.00 41.19 3.32
1616 1636 4.703575 AGTGAAATTGCACATCATACAGCT 59.296 37.500 18.97 0.00 41.19 4.24
1618 1638 5.946298 ACAGTGAAATTGCACATCATACAG 58.054 37.500 18.97 1.03 41.19 2.74
1630 1650 5.531634 ACAAAGCACCATACAGTGAAATTG 58.468 37.500 0.00 0.52 40.34 2.32
1636 1656 5.641636 TGTATGTACAAAGCACCATACAGTG 59.358 40.000 0.00 0.00 42.66 3.66
1640 1660 6.677781 ACATGTATGTACAAAGCACCATAC 57.322 37.500 0.00 0.00 39.68 2.39
1645 1693 9.277565 CTGATTTTACATGTATGTACAAAGCAC 57.722 33.333 6.36 0.00 42.48 4.40
1664 1712 9.965824 CACCAGAACTATTTTGTAACTGATTTT 57.034 29.630 0.00 0.00 31.35 1.82
1668 1716 7.276658 TGTCACCAGAACTATTTTGTAACTGA 58.723 34.615 0.00 0.00 31.35 3.41
1669 1717 7.490962 TGTCACCAGAACTATTTTGTAACTG 57.509 36.000 0.00 0.00 0.00 3.16
1671 1719 6.801862 GCATGTCACCAGAACTATTTTGTAAC 59.198 38.462 0.00 0.00 0.00 2.50
1675 1723 5.375417 TGCATGTCACCAGAACTATTTTG 57.625 39.130 0.00 0.00 0.00 2.44
1678 1726 5.503927 AGAATGCATGTCACCAGAACTATT 58.496 37.500 0.00 0.00 0.00 1.73
1682 1730 4.697352 AGTTAGAATGCATGTCACCAGAAC 59.303 41.667 0.00 0.00 0.00 3.01
1685 1733 4.256110 TGAGTTAGAATGCATGTCACCAG 58.744 43.478 0.00 0.00 0.00 4.00
1687 1735 4.507710 TCTGAGTTAGAATGCATGTCACC 58.492 43.478 0.00 0.00 30.84 4.02
1692 1740 8.886719 TCAAAGTTATCTGAGTTAGAATGCATG 58.113 33.333 0.00 0.00 39.30 4.06
1741 1789 8.206189 ACAAAAATTTGGAAACATGAGATCACT 58.794 29.630 10.38 0.00 42.34 3.41
1742 1790 8.369218 ACAAAAATTTGGAAACATGAGATCAC 57.631 30.769 10.38 0.00 42.34 3.06
1745 1793 8.961294 TTGACAAAAATTTGGAAACATGAGAT 57.039 26.923 10.38 0.00 42.34 2.75
1776 1824 5.593502 TCTGCCATTTTGCATACATGTGATA 59.406 36.000 9.11 0.00 41.16 2.15
1786 1834 2.596904 GCATCTCTGCCATTTTGCAT 57.403 45.000 0.00 0.00 42.88 3.96
1873 1922 6.978343 TGTACCATAAAGTGCTTATGTGTC 57.022 37.500 4.15 0.00 43.76 3.67
1893 1942 8.972458 TGGTGCATTTCTTTAGCTATTATGTA 57.028 30.769 0.00 0.00 0.00 2.29
1897 1946 7.695480 TGTTGGTGCATTTCTTTAGCTATTA 57.305 32.000 0.00 0.00 0.00 0.98
1919 2013 8.678593 TCTATCTAATACGTGAACTCTGATGT 57.321 34.615 0.00 0.00 0.00 3.06
1923 2017 6.017026 TGGCTCTATCTAATACGTGAACTCTG 60.017 42.308 0.00 0.00 0.00 3.35
1929 2023 6.459670 TTTGTGGCTCTATCTAATACGTGA 57.540 37.500 0.00 0.00 0.00 4.35
1938 2032 5.311649 ACCATATGGATTTGTGGCTCTATCT 59.688 40.000 28.77 0.00 38.94 1.98
1939 2033 5.564550 ACCATATGGATTTGTGGCTCTATC 58.435 41.667 28.77 0.00 38.94 2.08
2028 2123 7.987458 ACATGGACCTTATGTTATGTTCTGTAG 59.013 37.037 0.00 0.00 35.32 2.74
2120 2227 3.245229 TGTGCCAATTCACCTATCCAAGT 60.245 43.478 0.00 0.00 36.17 3.16
2126 2233 4.937015 GCAAATTTGTGCCAATTCACCTAT 59.063 37.500 19.03 0.00 38.66 2.57
2137 2244 2.397549 GAGTGTGAGCAAATTTGTGCC 58.602 47.619 19.03 9.28 46.14 5.01
2143 2250 1.133513 TGGGTGGAGTGTGAGCAAATT 60.134 47.619 0.00 0.00 0.00 1.82
2163 2270 0.105862 CCCAAGGATGATGCACCCAT 60.106 55.000 3.34 3.34 0.00 4.00
2168 2275 2.829914 GCGCCCAAGGATGATGCA 60.830 61.111 0.00 0.00 0.00 3.96
2171 2278 0.184451 ATGAAGCGCCCAAGGATGAT 59.816 50.000 2.29 0.00 0.00 2.45
2177 2284 1.731433 CCATGGATGAAGCGCCCAAG 61.731 60.000 5.56 0.06 33.15 3.61
2178 2285 1.753848 CCATGGATGAAGCGCCCAA 60.754 57.895 5.56 0.00 33.15 4.12
2182 2289 3.957535 CGCCCATGGATGAAGCGC 61.958 66.667 15.22 0.00 41.09 5.92
2183 2290 3.957535 GCGCCCATGGATGAAGCG 61.958 66.667 23.01 23.01 46.16 4.68
2184 2291 2.517875 AGCGCCCATGGATGAAGC 60.518 61.111 15.22 10.79 0.00 3.86
2185 2292 1.895707 GGAGCGCCCATGGATGAAG 60.896 63.158 15.22 0.00 34.14 3.02
2186 2293 2.192979 GGAGCGCCCATGGATGAA 59.807 61.111 15.22 0.00 34.14 2.57
2187 2294 3.089217 TGGAGCGCCCATGGATGA 61.089 61.111 15.22 0.00 40.82 2.92
2239 2346 1.379916 CTCAATGGTGGAGTGCCCA 59.620 57.895 0.00 0.00 44.25 5.36
2252 2359 1.004044 CACCACCTCTCCAAGCTCAAT 59.996 52.381 0.00 0.00 0.00 2.57
2257 2364 1.003580 TCATTCACCACCTCTCCAAGC 59.996 52.381 0.00 0.00 0.00 4.01
2287 2394 3.557903 ATGTCACAGGCTTGCCGCT 62.558 57.895 5.95 0.00 39.13 5.52
2291 2398 1.239296 TGCAGATGTCACAGGCTTGC 61.239 55.000 0.00 0.00 0.00 4.01
2293 2400 0.952497 CGTGCAGATGTCACAGGCTT 60.952 55.000 0.00 0.00 34.27 4.35
2296 2403 1.395954 CATTCGTGCAGATGTCACAGG 59.604 52.381 0.00 0.00 34.27 4.00
2299 2406 2.341257 ACTCATTCGTGCAGATGTCAC 58.659 47.619 0.00 0.00 0.00 3.67
2320 2427 1.229658 ACCAACAGGGCTAGGAGCT 60.230 57.895 0.00 0.00 41.99 4.09


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

AutoCloner maintained by Alex Coulton.