Multiple sequence alignment - TraesCS7B01G241700

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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 TraesCS7B01G241700 chr7B 100.000 2213 0 0 1 2213 449554270 449552058 0.000000e+00 4087.0
1 TraesCS7B01G241700 chr7B 83.721 129 21 0 62 190 355873067 355872939 2.980000e-24 122.0
2 TraesCS7B01G241700 chr7B 80.000 155 26 5 101 252 165581315 165581467 2.320000e-20 110.0
3 TraesCS7B01G241700 chr7D 95.377 1341 46 8 1 1337 433012790 433014118 0.000000e+00 2119.0
4 TraesCS7B01G241700 chr7D 87.719 228 10 8 1360 1571 433014109 433014334 1.310000e-62 250.0
5 TraesCS7B01G241700 chr7D 80.612 196 17 3 61 255 312466907 312467082 4.960000e-27 132.0
6 TraesCS7B01G241700 chr7D 97.826 46 1 0 1570 1615 433014671 433014716 1.820000e-11 80.5
7 TraesCS7B01G241700 chr7A 84.328 670 60 22 890 1518 499572462 499571797 4.040000e-172 614.0
8 TraesCS7B01G241700 chr7A 94.859 389 17 2 890 1276 483962135 483962522 2.430000e-169 604.0
9 TraesCS7B01G241700 chr7A 82.343 606 65 21 1609 2210 483963310 483963877 2.550000e-134 488.0
10 TraesCS7B01G241700 chr7A 79.621 633 61 41 252 860 483961548 483962136 2.060000e-105 392.0
11 TraesCS7B01G241700 chr7A 79.055 635 56 32 252 860 499573044 499572461 4.490000e-97 364.0
12 TraesCS7B01G241700 chr7A 84.977 213 26 5 1000 1212 692313216 692313010 6.190000e-51 211.0
13 TraesCS7B01G241700 chr7A 85.156 128 19 0 63 190 396986693 396986566 4.960000e-27 132.0
14 TraesCS7B01G241700 chr7A 89.247 93 10 0 61 153 381245702 381245610 1.390000e-22 117.0
15 TraesCS7B01G241700 chr7A 96.364 55 2 0 1283 1337 483962553 483962607 8.410000e-15 91.6
16 TraesCS7B01G241700 chr7A 84.884 86 11 2 1 84 499573094 499573009 3.920000e-13 86.1
17 TraesCS7B01G241700 chr7A 91.379 58 5 0 1 58 483961498 483961555 1.820000e-11 80.5
18 TraesCS7B01G241700 chr1A 85.915 213 30 0 1000 1212 6765453 6765241 6.150000e-56 228.0
19 TraesCS7B01G241700 chr1B 81.818 242 37 5 975 1209 639448317 639448558 1.730000e-46 196.0
20 TraesCS7B01G241700 chr2A 85.052 194 13 6 62 255 155591083 155590906 1.350000e-42 183.0
21 TraesCS7B01G241700 chr2A 89.623 106 9 2 159 262 511475230 511475125 1.380000e-27 134.0
22 TraesCS7B01G241700 chr2A 93.976 83 5 0 173 255 727187095 727187177 2.310000e-25 126.0
23 TraesCS7B01G241700 chr2D 81.910 199 15 3 57 255 342099810 342099633 4.920000e-32 148.0
24 TraesCS7B01G241700 chr3A 81.218 197 14 7 61 255 275277335 275277510 1.070000e-28 137.0
25 TraesCS7B01G241700 chr5D 80.928 194 15 9 62 254 13715040 13715212 1.380000e-27 134.0
26 TraesCS7B01G241700 chr6B 80.729 192 17 7 65 255 555341823 555341995 4.960000e-27 132.0


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 TraesCS7B01G241700 chr7B 449552058 449554270 2212 True 4087.00 4087 100.000000 1 2213 1 chr7B.!!$R2 2212
1 TraesCS7B01G241700 chr7D 433012790 433014716 1926 False 816.50 2119 93.640667 1 1615 3 chr7D.!!$F2 1614
2 TraesCS7B01G241700 chr7A 499571797 499573094 1297 True 354.70 614 82.755667 1 1518 3 chr7A.!!$R4 1517
3 TraesCS7B01G241700 chr7A 483961498 483963877 2379 False 331.22 604 88.913200 1 2210 5 chr7A.!!$F1 2209

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
220 221 0.032416 TCCCTACTCAGCACCCTACC 60.032 60.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1780 2381 0.168788 CGTCGTCCTACGCCACTTAA 59.831 55.0 0.0 0.0 42.21 1.85 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
78 79 2.783284 CGTGCATTGTTCCAAATATCGC 59.217 45.455 0.00 0.00 0.00 4.58
115 116 6.565234 CATCTCGGTCAGTTAATCACTACTT 58.435 40.000 0.00 0.00 32.76 2.24
119 120 4.625742 CGGTCAGTTAATCACTACTTGGTG 59.374 45.833 0.00 0.00 38.44 4.17
150 151 8.204836 ACCGAGTAGCTGATTAACTGATTTATT 58.795 33.333 0.00 0.00 0.00 1.40
154 155 9.686683 AGTAGCTGATTAACTGATTTATTGGTT 57.313 29.630 0.00 0.00 0.00 3.67
184 185 7.272037 ACTAATTTATTGGCCGATTAACTGG 57.728 36.000 11.78 2.69 0.00 4.00
217 218 2.868964 TTATCCCTACTCAGCACCCT 57.131 50.000 0.00 0.00 0.00 4.34
220 221 0.032416 TCCCTACTCAGCACCCTACC 60.032 60.000 0.00 0.00 0.00 3.18
227 228 1.046472 TCAGCACCCTACCGGTATGG 61.046 60.000 28.54 28.54 46.14 2.74
314 315 9.983804 GGTCTATATAGGTTTTCTTTTTCAACG 57.016 33.333 9.89 0.00 0.00 4.10
348 367 5.880887 TCTATCTCTGTATGTAGCGTATGGG 59.119 44.000 0.00 0.00 0.00 4.00
394 413 0.792640 CTCGAGTGCTGCATTTCGTT 59.207 50.000 26.95 4.94 34.83 3.85
466 485 7.699566 TGGAAACGGCATGTTCTTATTTATAC 58.300 34.615 0.00 0.00 40.84 1.47
467 486 7.554835 TGGAAACGGCATGTTCTTATTTATACT 59.445 33.333 0.00 0.00 40.84 2.12
468 487 8.068380 GGAAACGGCATGTTCTTATTTATACTC 58.932 37.037 0.00 0.00 40.84 2.59
485 507 1.006043 ACTCCCCTCTCGACTCATTGA 59.994 52.381 0.00 0.00 0.00 2.57
571 601 1.136828 TGTGAGGTAGGTGGCTGTTT 58.863 50.000 0.00 0.00 0.00 2.83
718 753 3.585748 TCTTTCGAGAAAACAGCAACG 57.414 42.857 0.00 0.00 0.00 4.10
719 754 2.036933 CTTTCGAGAAAACAGCAACGC 58.963 47.619 0.00 0.00 0.00 4.84
723 758 1.732259 CGAGAAAACAGCAACGCCTAT 59.268 47.619 0.00 0.00 0.00 2.57
770 809 6.774354 AACATTTTAGTTGCTGCAGAATTG 57.226 33.333 20.43 10.43 0.00 2.32
815 855 2.203549 GAGGGGAGCCAGGTTGAAGG 62.204 65.000 0.00 0.00 0.00 3.46
878 919 0.179034 CTAACTGCCTCCTGATGCCC 60.179 60.000 0.00 0.00 0.00 5.36
879 920 0.913934 TAACTGCCTCCTGATGCCCA 60.914 55.000 0.00 0.00 0.00 5.36
880 921 1.792757 AACTGCCTCCTGATGCCCAA 61.793 55.000 0.00 0.00 0.00 4.12
891 932 1.311859 GATGCCCAATGCGAGATTCA 58.688 50.000 0.00 0.00 45.60 2.57
897 938 2.096496 CCCAATGCGAGATTCACACTTC 59.904 50.000 0.00 0.00 0.00 3.01
1170 1213 1.374252 GAAGAAGAAGGACGCCGCA 60.374 57.895 0.00 0.00 0.00 5.69
1280 1323 8.319143 TCTAAACTAGTTACCTCACAATTTGC 57.681 34.615 8.92 0.00 0.00 3.68
1325 1392 5.075493 AGATAGAGCTTTTTATGGCATGGG 58.925 41.667 10.98 0.00 0.00 4.00
1326 1393 3.105959 AGAGCTTTTTATGGCATGGGT 57.894 42.857 10.98 0.74 0.00 4.51
1327 1394 2.762327 AGAGCTTTTTATGGCATGGGTG 59.238 45.455 10.98 0.00 0.00 4.61
1328 1395 2.760092 GAGCTTTTTATGGCATGGGTGA 59.240 45.455 10.98 0.00 0.00 4.02
1329 1396 3.172339 AGCTTTTTATGGCATGGGTGAA 58.828 40.909 10.98 0.00 0.00 3.18
1330 1397 3.196254 AGCTTTTTATGGCATGGGTGAAG 59.804 43.478 10.98 8.13 0.00 3.02
1331 1398 3.055891 GCTTTTTATGGCATGGGTGAAGT 60.056 43.478 10.98 0.00 0.00 3.01
1332 1399 4.747810 CTTTTTATGGCATGGGTGAAGTC 58.252 43.478 10.98 0.00 0.00 3.01
1333 1400 2.435372 TTATGGCATGGGTGAAGTCC 57.565 50.000 10.98 0.00 0.00 3.85
1334 1401 1.294041 TATGGCATGGGTGAAGTCCA 58.706 50.000 10.98 0.00 38.82 4.02
1335 1402 0.033796 ATGGCATGGGTGAAGTCCAG 60.034 55.000 0.00 0.00 37.75 3.86
1336 1403 1.133181 TGGCATGGGTGAAGTCCAGA 61.133 55.000 0.00 0.00 37.75 3.86
1337 1404 0.257039 GGCATGGGTGAAGTCCAGAT 59.743 55.000 0.00 0.00 37.75 2.90
1338 1405 1.341383 GGCATGGGTGAAGTCCAGATT 60.341 52.381 0.00 0.00 37.75 2.40
1339 1406 2.450476 GCATGGGTGAAGTCCAGATTT 58.550 47.619 0.00 0.00 37.75 2.17
1340 1407 2.827921 GCATGGGTGAAGTCCAGATTTT 59.172 45.455 0.00 0.00 37.75 1.82
1341 1408 3.259123 GCATGGGTGAAGTCCAGATTTTT 59.741 43.478 0.00 0.00 37.75 1.94
1416 1543 0.885879 TGGCCGCGGATATACTACTG 59.114 55.000 33.48 0.00 0.00 2.74
1449 1576 2.937469 TTTGGAGGCACATTATTGCG 57.063 45.000 0.00 0.00 44.00 4.85
1459 1586 3.316283 CACATTATTGCGGTTTGTTGCT 58.684 40.909 0.00 0.00 0.00 3.91
1460 1587 4.480541 CACATTATTGCGGTTTGTTGCTA 58.519 39.130 0.00 0.00 0.00 3.49
1520 1651 1.290134 GACCCCCTGATCAACCTTCT 58.710 55.000 0.00 0.00 0.00 2.85
1525 1688 4.017126 CCCCCTGATCAACCTTCTTAAAC 58.983 47.826 0.00 0.00 0.00 2.01
1530 1693 6.294176 CCCTGATCAACCTTCTTAAACTGTTG 60.294 42.308 0.00 0.00 38.07 3.33
1537 1700 4.137543 CCTTCTTAAACTGTTGCACCTCT 58.862 43.478 0.00 0.00 0.00 3.69
1620 2221 1.066143 ACAAATGTAGGCTCCCACTCG 60.066 52.381 0.00 0.00 0.00 4.18
1623 2224 0.106167 ATGTAGGCTCCCACTCGCTA 60.106 55.000 0.00 0.00 0.00 4.26
1625 2226 1.144298 TGTAGGCTCCCACTCGCTATA 59.856 52.381 0.00 0.00 0.00 1.31
1630 2231 3.090037 GGCTCCCACTCGCTATATCTTA 58.910 50.000 0.00 0.00 0.00 2.10
1638 2239 8.500238 TCCCACTCGCTATATCTTATAGGATTA 58.500 37.037 2.29 0.00 0.00 1.75
1657 2258 6.014840 AGGATTACAGACGAGAAAAGGTGTTA 60.015 38.462 0.00 0.00 0.00 2.41
1658 2259 6.647895 GGATTACAGACGAGAAAAGGTGTTAA 59.352 38.462 0.00 0.00 0.00 2.01
1659 2260 7.172019 GGATTACAGACGAGAAAAGGTGTTAAA 59.828 37.037 0.00 0.00 0.00 1.52
1660 2261 7.846644 TTACAGACGAGAAAAGGTGTTAAAA 57.153 32.000 0.00 0.00 0.00 1.52
1661 2262 6.115450 ACAGACGAGAAAAGGTGTTAAAAC 57.885 37.500 0.00 0.00 0.00 2.43
1662 2263 5.644636 ACAGACGAGAAAAGGTGTTAAAACA 59.355 36.000 0.00 0.00 36.38 2.83
1663 2264 6.183360 ACAGACGAGAAAAGGTGTTAAAACAG 60.183 38.462 0.00 0.00 40.05 3.16
1664 2265 6.036735 CAGACGAGAAAAGGTGTTAAAACAGA 59.963 38.462 0.00 0.00 40.05 3.41
1665 2266 6.596497 AGACGAGAAAAGGTGTTAAAACAGAA 59.404 34.615 0.00 0.00 40.05 3.02
1674 2275 9.984190 AAAGGTGTTAAAACAGAAAGTAAACAA 57.016 25.926 0.00 0.00 40.05 2.83
1696 2297 0.373716 GAAGAACGTGCTATTGCCGG 59.626 55.000 0.00 0.00 37.25 6.13
1708 2309 4.887071 TGCTATTGCCGGAATTCAAATAGT 59.113 37.500 5.05 0.00 38.71 2.12
1710 2311 5.008613 GCTATTGCCGGAATTCAAATAGTGA 59.991 40.000 5.05 0.00 0.00 3.41
1712 2313 2.675844 TGCCGGAATTCAAATAGTGACG 59.324 45.455 5.05 0.00 35.39 4.35
1717 2318 1.014352 ATTCAAATAGTGACGCGCCC 58.986 50.000 5.73 0.00 35.39 6.13
1732 2333 4.828296 CCCATGCACAGGAGCCCC 62.828 72.222 8.56 0.00 0.00 5.80
1752 2353 3.136077 CCCTGGATCAGAGATCAACATGT 59.864 47.826 9.02 0.00 32.44 3.21
1755 2356 2.877168 GGATCAGAGATCAACATGTGCC 59.123 50.000 0.00 0.00 0.00 5.01
1757 2358 1.276138 TCAGAGATCAACATGTGCCGT 59.724 47.619 0.00 0.00 0.00 5.68
1761 2362 1.155889 GATCAACATGTGCCGTGACA 58.844 50.000 0.00 0.00 0.00 3.58
1771 2372 2.105128 CCGTGACATCTCCCGAGC 59.895 66.667 0.00 0.00 0.00 5.03
1772 2373 2.278206 CGTGACATCTCCCGAGCG 60.278 66.667 0.00 0.00 0.00 5.03
1780 2381 4.421479 CTCCCGAGCGCGAAGTGT 62.421 66.667 12.10 0.00 41.96 3.55
1789 2390 1.129809 CGCGAAGTGTTAAGTGGCG 59.870 57.895 0.00 0.00 36.05 5.69
1790 2391 1.554042 CGCGAAGTGTTAAGTGGCGT 61.554 55.000 0.00 0.00 37.61 5.68
1795 2396 2.738013 AGTGTTAAGTGGCGTAGGAC 57.262 50.000 0.00 0.00 0.00 3.85
1807 2408 0.448990 CGTAGGACGACGTTGGATCA 59.551 55.000 7.90 0.00 46.05 2.92
1808 2409 1.065102 CGTAGGACGACGTTGGATCAT 59.935 52.381 7.90 0.00 46.05 2.45
1821 2422 1.401905 TGGATCATAGATCGGCGATCG 59.598 52.381 35.80 25.14 43.17 3.69
1825 2426 2.052690 ATAGATCGGCGATCGGGGG 61.053 63.158 35.80 0.00 43.17 5.40
1826 2427 2.494777 ATAGATCGGCGATCGGGGGA 62.495 60.000 35.80 23.02 43.17 4.81
1838 2441 1.185618 TCGGGGGACACACTGAGAAG 61.186 60.000 0.00 0.00 0.00 2.85
1842 2445 1.002544 GGGGACACACTGAGAAGGAAG 59.997 57.143 0.00 0.00 0.00 3.46
1847 2450 5.172205 GGACACACTGAGAAGGAAGATAAC 58.828 45.833 0.00 0.00 0.00 1.89
1848 2451 5.046950 GGACACACTGAGAAGGAAGATAACT 60.047 44.000 0.00 0.00 0.00 2.24
1849 2452 5.788450 ACACACTGAGAAGGAAGATAACTG 58.212 41.667 0.00 0.00 0.00 3.16
1850 2453 5.540337 ACACACTGAGAAGGAAGATAACTGA 59.460 40.000 0.00 0.00 0.00 3.41
1851 2454 6.042093 ACACACTGAGAAGGAAGATAACTGAA 59.958 38.462 0.00 0.00 0.00 3.02
1852 2455 6.589523 CACACTGAGAAGGAAGATAACTGAAG 59.410 42.308 0.00 0.00 0.00 3.02
1853 2456 6.495181 ACACTGAGAAGGAAGATAACTGAAGA 59.505 38.462 0.00 0.00 0.00 2.87
1854 2457 7.180051 ACACTGAGAAGGAAGATAACTGAAGAT 59.820 37.037 0.00 0.00 0.00 2.40
1855 2458 7.492020 CACTGAGAAGGAAGATAACTGAAGATG 59.508 40.741 0.00 0.00 0.00 2.90
1856 2459 6.344500 TGAGAAGGAAGATAACTGAAGATGC 58.656 40.000 0.00 0.00 0.00 3.91
1857 2460 6.155910 TGAGAAGGAAGATAACTGAAGATGCT 59.844 38.462 0.00 0.00 0.00 3.79
1858 2461 7.343057 TGAGAAGGAAGATAACTGAAGATGCTA 59.657 37.037 0.00 0.00 0.00 3.49
1859 2462 7.496747 AGAAGGAAGATAACTGAAGATGCTAC 58.503 38.462 0.00 0.00 0.00 3.58
1860 2463 6.798427 AGGAAGATAACTGAAGATGCTACA 57.202 37.500 0.00 0.00 0.00 2.74
1861 2464 6.578023 AGGAAGATAACTGAAGATGCTACAC 58.422 40.000 0.00 0.00 0.00 2.90
1862 2465 6.382570 AGGAAGATAACTGAAGATGCTACACT 59.617 38.462 0.00 0.00 0.00 3.55
1867 2470 5.931441 AACTGAAGATGCTACACTTTGAC 57.069 39.130 0.00 0.00 0.00 3.18
1872 2475 6.573434 TGAAGATGCTACACTTTGACGATAT 58.427 36.000 0.00 0.00 0.00 1.63
1874 2477 6.834959 AGATGCTACACTTTGACGATATTG 57.165 37.500 0.00 0.00 0.00 1.90
1892 2495 8.965819 ACGATATTGAGACATATATTCAGAGCT 58.034 33.333 0.00 0.00 0.00 4.09
1893 2496 9.235537 CGATATTGAGACATATATTCAGAGCTG 57.764 37.037 0.00 0.00 0.00 4.24
1894 2497 9.531942 GATATTGAGACATATATTCAGAGCTGG 57.468 37.037 0.00 0.00 0.00 4.85
1896 2499 6.737720 TGAGACATATATTCAGAGCTGGTT 57.262 37.500 0.00 0.00 0.00 3.67
1898 2501 6.107901 AGACATATATTCAGAGCTGGTTCC 57.892 41.667 0.00 0.00 0.00 3.62
1899 2502 5.843421 AGACATATATTCAGAGCTGGTTCCT 59.157 40.000 0.00 0.00 0.00 3.36
1900 2503 5.862845 ACATATATTCAGAGCTGGTTCCTG 58.137 41.667 0.00 0.00 0.00 3.86
1901 2504 5.604231 ACATATATTCAGAGCTGGTTCCTGA 59.396 40.000 0.00 0.00 35.38 3.86
1902 2505 2.777832 ATTCAGAGCTGGTTCCTGAC 57.222 50.000 0.00 0.00 36.75 3.51
1903 2506 1.423584 TTCAGAGCTGGTTCCTGACA 58.576 50.000 0.00 0.00 36.75 3.58
1905 2508 1.980765 TCAGAGCTGGTTCCTGACAAT 59.019 47.619 0.00 0.00 32.57 2.71
1906 2509 2.082231 CAGAGCTGGTTCCTGACAATG 58.918 52.381 0.00 0.00 0.00 2.82
1907 2510 0.807496 GAGCTGGTTCCTGACAATGC 59.193 55.000 0.00 0.00 0.00 3.56
1909 2512 1.598701 GCTGGTTCCTGACAATGCCC 61.599 60.000 0.00 0.00 0.00 5.36
1910 2513 0.967380 CTGGTTCCTGACAATGCCCC 60.967 60.000 0.00 0.00 0.00 5.80
1911 2514 1.682344 GGTTCCTGACAATGCCCCC 60.682 63.158 0.00 0.00 0.00 5.40
1928 2531 0.182299 CCCCCTCCTTGAGATTCAGC 59.818 60.000 0.00 0.00 0.00 4.26
1929 2532 1.211456 CCCCTCCTTGAGATTCAGCT 58.789 55.000 0.00 0.00 0.00 4.24
1930 2533 1.140652 CCCCTCCTTGAGATTCAGCTC 59.859 57.143 0.00 0.00 35.46 4.09
1931 2534 1.202510 CCCTCCTTGAGATTCAGCTCG 60.203 57.143 0.00 0.00 37.73 5.03
1932 2535 1.569708 CTCCTTGAGATTCAGCTCGC 58.430 55.000 0.00 0.00 37.73 5.03
1933 2536 1.136695 CTCCTTGAGATTCAGCTCGCT 59.863 52.381 0.00 0.00 37.73 4.93
1968 2571 6.641161 AAGCCTGGGAAAATTTTATGGATT 57.359 33.333 2.75 6.11 0.00 3.01
1994 2597 0.460987 GAGTCCTCCAATGTCGCCTG 60.461 60.000 0.00 0.00 0.00 4.85
2021 2624 3.703052 GGAGGCATGTTCTTCCATTTGAT 59.297 43.478 0.00 0.00 0.00 2.57
2032 2635 5.879763 TCTTCCATTTGATCTTCCACTGAA 58.120 37.500 0.00 0.00 0.00 3.02
2033 2636 6.487828 TCTTCCATTTGATCTTCCACTGAAT 58.512 36.000 0.00 0.00 0.00 2.57
2034 2637 6.376299 TCTTCCATTTGATCTTCCACTGAATG 59.624 38.462 0.00 0.00 0.00 2.67
2065 2668 3.467803 GATACTGATGTTACCCTGCACC 58.532 50.000 0.00 0.00 0.00 5.01
2081 2684 1.679032 GCACCCGAGGAATAAGCTTGT 60.679 52.381 9.86 0.00 0.00 3.16
2086 2689 2.678336 CCGAGGAATAAGCTTGTGTTCC 59.322 50.000 22.51 22.51 40.28 3.62
2097 2700 5.948992 AGCTTGTGTTCCAGTAATTCTTC 57.051 39.130 0.00 0.00 0.00 2.87
2099 2702 4.378459 GCTTGTGTTCCAGTAATTCTTCCG 60.378 45.833 0.00 0.00 0.00 4.30
2100 2703 4.610605 TGTGTTCCAGTAATTCTTCCGA 57.389 40.909 0.00 0.00 0.00 4.55
2104 2708 3.777465 TCCAGTAATTCTTCCGACTCG 57.223 47.619 0.00 0.00 0.00 4.18
2132 2736 7.567250 TGAGGATTGTACCATCAGGATTAAGTA 59.433 37.037 9.01 0.00 38.69 2.24
2133 2737 7.967908 AGGATTGTACCATCAGGATTAAGTAG 58.032 38.462 9.01 0.00 38.69 2.57
2134 2738 7.569111 AGGATTGTACCATCAGGATTAAGTAGT 59.431 37.037 9.01 0.00 38.69 2.73
2135 2739 7.657761 GGATTGTACCATCAGGATTAAGTAGTG 59.342 40.741 9.01 0.00 38.69 2.74
2137 2741 5.365605 TGTACCATCAGGATTAAGTAGTGGG 59.634 44.000 0.00 0.00 38.69 4.61
2138 2742 4.371681 ACCATCAGGATTAAGTAGTGGGT 58.628 43.478 0.00 0.00 38.69 4.51
2139 2743 4.164221 ACCATCAGGATTAAGTAGTGGGTG 59.836 45.833 0.00 0.00 38.69 4.61
2140 2744 4.444876 CCATCAGGATTAAGTAGTGGGTGG 60.445 50.000 0.00 0.00 36.89 4.61
2141 2745 3.798515 TCAGGATTAAGTAGTGGGTGGT 58.201 45.455 0.00 0.00 0.00 4.16
2210 2815 4.724074 CATGGAATGTATGGTGCAGTTT 57.276 40.909 0.00 0.00 40.20 2.66
2211 2816 4.426416 CATGGAATGTATGGTGCAGTTTG 58.574 43.478 0.00 0.00 40.20 2.93
2212 2817 2.824936 TGGAATGTATGGTGCAGTTTGG 59.175 45.455 0.00 0.00 0.00 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 79 1.502231 CGAGATGCCGATTAACTGGG 58.498 55.000 0.00 0.00 0.00 4.45
119 120 4.013702 TCAGCTACTCGGTGACCC 57.986 61.111 0.00 0.00 44.63 4.46
127 128 9.331282 ACCAATAAATCAGTTAATCAGCTACTC 57.669 33.333 0.00 0.00 0.00 2.59
150 151 6.039941 CGGCCAATAAATTAGTTATCCAACCA 59.960 38.462 2.24 0.00 35.05 3.67
154 155 9.575868 TTAATCGGCCAATAAATTAGTTATCCA 57.424 29.630 2.24 0.00 30.74 3.41
163 164 5.654650 TGTCCAGTTAATCGGCCAATAAATT 59.345 36.000 2.24 0.00 0.00 1.82
184 185 6.465084 AGTAGGGATAAATAGGCGAATTGTC 58.535 40.000 0.00 0.00 0.00 3.18
227 228 6.567050 TGTTCAGGATATCGTTAACTGGTAC 58.433 40.000 18.34 11.55 0.00 3.34
237 238 3.558931 TGCCAATGTTCAGGATATCGT 57.441 42.857 0.00 0.00 0.00 3.73
314 315 6.976088 ACATACAGAGATAGAGCACATGTAC 58.024 40.000 0.00 0.00 0.00 2.90
348 367 8.084684 ACCTCAGCTTAATTTCTTCATGTTTTC 58.915 33.333 0.00 0.00 0.00 2.29
394 413 8.314751 TGAGATTTGTTGGGTGAACTTTTTAAA 58.685 29.630 0.00 0.00 35.37 1.52
442 461 7.927048 AGTATAAATAAGAACATGCCGTTTCC 58.073 34.615 0.00 0.00 38.19 3.13
448 467 6.543735 AGGGGAGTATAAATAAGAACATGCC 58.456 40.000 0.00 0.00 0.00 4.40
466 485 1.769026 TCAATGAGTCGAGAGGGGAG 58.231 55.000 0.00 0.00 0.00 4.30
467 486 2.231716 TTCAATGAGTCGAGAGGGGA 57.768 50.000 0.00 0.00 0.00 4.81
468 487 2.224161 GGATTCAATGAGTCGAGAGGGG 60.224 54.545 0.00 0.00 0.00 4.79
565 595 6.292389 AGCACAATATCGAATCTAAACAGC 57.708 37.500 0.00 0.00 0.00 4.40
571 601 8.414003 ACTCTAACAAGCACAATATCGAATCTA 58.586 33.333 0.00 0.00 0.00 1.98
770 809 4.611366 GCTGTTACACAATTTAACACTCGC 59.389 41.667 0.00 0.00 35.07 5.03
791 831 2.188215 AACCTGGCTCCCCTCTAGCT 62.188 60.000 0.00 0.00 39.97 3.32
815 855 2.884827 GCACATGGCTTCAATTTCCTC 58.115 47.619 0.00 0.00 40.25 3.71
878 919 4.627035 TGTAGAAGTGTGAATCTCGCATTG 59.373 41.667 0.00 0.00 39.28 2.82
879 920 4.820897 TGTAGAAGTGTGAATCTCGCATT 58.179 39.130 0.00 0.00 39.28 3.56
880 921 4.456280 TGTAGAAGTGTGAATCTCGCAT 57.544 40.909 0.00 0.00 39.28 4.73
891 932 4.286297 TGCAAAGGCTATGTAGAAGTGT 57.714 40.909 0.00 0.00 41.91 3.55
897 938 7.760794 TCAATTCAAAATGCAAAGGCTATGTAG 59.239 33.333 0.00 0.00 41.91 2.74
1241 1284 2.496470 AGTTTAGAAGCTCGGTACAGGG 59.504 50.000 0.00 0.00 0.00 4.45
1344 1411 5.104277 TCTGGACTTCACTTACCCTCAAAAA 60.104 40.000 0.00 0.00 0.00 1.94
1345 1412 4.410883 TCTGGACTTCACTTACCCTCAAAA 59.589 41.667 0.00 0.00 0.00 2.44
1346 1413 3.971305 TCTGGACTTCACTTACCCTCAAA 59.029 43.478 0.00 0.00 0.00 2.69
1347 1414 3.583228 TCTGGACTTCACTTACCCTCAA 58.417 45.455 0.00 0.00 0.00 3.02
1348 1415 3.254093 TCTGGACTTCACTTACCCTCA 57.746 47.619 0.00 0.00 0.00 3.86
1349 1416 4.828072 ATTCTGGACTTCACTTACCCTC 57.172 45.455 0.00 0.00 0.00 4.30
1350 1417 5.785940 ACTAATTCTGGACTTCACTTACCCT 59.214 40.000 0.00 0.00 0.00 4.34
1351 1418 6.051179 ACTAATTCTGGACTTCACTTACCC 57.949 41.667 0.00 0.00 0.00 3.69
1352 1419 9.099454 CATTACTAATTCTGGACTTCACTTACC 57.901 37.037 0.00 0.00 0.00 2.85
1353 1420 8.604890 GCATTACTAATTCTGGACTTCACTTAC 58.395 37.037 0.00 0.00 0.00 2.34
1354 1421 8.540388 AGCATTACTAATTCTGGACTTCACTTA 58.460 33.333 0.00 0.00 0.00 2.24
1355 1422 7.398024 AGCATTACTAATTCTGGACTTCACTT 58.602 34.615 0.00 0.00 0.00 3.16
1356 1423 6.951971 AGCATTACTAATTCTGGACTTCACT 58.048 36.000 0.00 0.00 0.00 3.41
1416 1543 3.129462 GCCTCCAAAAATTCTACTCCAGC 59.871 47.826 0.00 0.00 0.00 4.85
1520 1651 6.544197 TGTTTCATAGAGGTGCAACAGTTTAA 59.456 34.615 3.64 0.00 39.98 1.52
1525 1688 5.437289 TTTGTTTCATAGAGGTGCAACAG 57.563 39.130 3.64 0.00 36.77 3.16
1530 1693 4.006319 AGAGCTTTGTTTCATAGAGGTGC 58.994 43.478 0.00 0.00 0.00 5.01
1537 1700 5.183713 CCATGTTGGAGAGCTTTGTTTCATA 59.816 40.000 0.00 0.00 40.96 2.15
1630 2231 6.154706 ACACCTTTTCTCGTCTGTAATCCTAT 59.845 38.462 0.00 0.00 0.00 2.57
1638 2239 5.644636 TGTTTTAACACCTTTTCTCGTCTGT 59.355 36.000 0.00 0.00 33.17 3.41
1643 2244 7.248437 ACTTTCTGTTTTAACACCTTTTCTCG 58.752 34.615 0.00 0.00 34.70 4.04
1658 2259 9.931210 CGTTCTTCTATTGTTTACTTTCTGTTT 57.069 29.630 0.00 0.00 0.00 2.83
1659 2260 9.106070 ACGTTCTTCTATTGTTTACTTTCTGTT 57.894 29.630 0.00 0.00 0.00 3.16
1660 2261 8.548721 CACGTTCTTCTATTGTTTACTTTCTGT 58.451 33.333 0.00 0.00 0.00 3.41
1661 2262 7.530861 GCACGTTCTTCTATTGTTTACTTTCTG 59.469 37.037 0.00 0.00 0.00 3.02
1662 2263 7.441458 AGCACGTTCTTCTATTGTTTACTTTCT 59.559 33.333 0.00 0.00 0.00 2.52
1663 2264 7.573627 AGCACGTTCTTCTATTGTTTACTTTC 58.426 34.615 0.00 0.00 0.00 2.62
1664 2265 7.492352 AGCACGTTCTTCTATTGTTTACTTT 57.508 32.000 0.00 0.00 0.00 2.66
1665 2266 8.773404 ATAGCACGTTCTTCTATTGTTTACTT 57.227 30.769 0.00 0.00 0.00 2.24
1674 2275 3.123804 CGGCAATAGCACGTTCTTCTAT 58.876 45.455 0.00 0.00 44.61 1.98
1693 2294 2.285602 CGCGTCACTATTTGAATTCCGG 60.286 50.000 2.27 0.00 35.39 5.14
1696 2297 2.538939 GGGCGCGTCACTATTTGAATTC 60.539 50.000 14.93 0.00 35.39 2.17
1732 2333 3.560481 GCACATGTTGATCTCTGATCCAG 59.440 47.826 0.00 0.00 0.00 3.86
1739 2340 1.276138 TCACGGCACATGTTGATCTCT 59.724 47.619 0.00 0.00 0.00 3.10
1757 2358 4.193334 CGCGCTCGGGAGATGTCA 62.193 66.667 5.56 0.00 38.80 3.58
1761 2362 3.141488 ACTTCGCGCTCGGGAGAT 61.141 61.111 5.56 0.00 38.30 2.75
1771 2372 1.129809 CGCCACTTAACACTTCGCG 59.870 57.895 0.00 0.00 0.00 5.87
1772 2373 1.389106 CTACGCCACTTAACACTTCGC 59.611 52.381 0.00 0.00 0.00 4.70
1780 2381 0.168788 CGTCGTCCTACGCCACTTAA 59.831 55.000 0.00 0.00 42.21 1.85
1789 2390 2.865343 ATGATCCAACGTCGTCCTAC 57.135 50.000 0.00 0.00 0.00 3.18
1790 2391 3.812262 TCTATGATCCAACGTCGTCCTA 58.188 45.455 0.00 0.00 0.00 2.94
1795 2396 2.585845 CCGATCTATGATCCAACGTCG 58.414 52.381 0.00 0.00 0.00 5.12
1807 2408 2.052690 CCCCCGATCGCCGATCTAT 61.053 63.158 23.28 0.00 41.76 1.98
1808 2409 2.675423 CCCCCGATCGCCGATCTA 60.675 66.667 23.28 0.00 41.76 1.98
1821 2422 0.836400 TCCTTCTCAGTGTGTCCCCC 60.836 60.000 0.00 0.00 0.00 5.40
1825 2426 5.866633 CAGTTATCTTCCTTCTCAGTGTGTC 59.133 44.000 0.00 0.00 0.00 3.67
1826 2427 5.540337 TCAGTTATCTTCCTTCTCAGTGTGT 59.460 40.000 0.00 0.00 0.00 3.72
1838 2441 6.578023 AGTGTAGCATCTTCAGTTATCTTCC 58.422 40.000 0.00 0.00 0.00 3.46
1842 2445 7.463383 CGTCAAAGTGTAGCATCTTCAGTTATC 60.463 40.741 0.00 0.00 0.00 1.75
1847 2450 4.237724 TCGTCAAAGTGTAGCATCTTCAG 58.762 43.478 0.00 0.00 0.00 3.02
1848 2451 4.251543 TCGTCAAAGTGTAGCATCTTCA 57.748 40.909 0.00 0.00 0.00 3.02
1849 2452 7.222805 TCAATATCGTCAAAGTGTAGCATCTTC 59.777 37.037 0.00 0.00 0.00 2.87
1850 2453 7.041721 TCAATATCGTCAAAGTGTAGCATCTT 58.958 34.615 0.00 0.00 0.00 2.40
1851 2454 6.573434 TCAATATCGTCAAAGTGTAGCATCT 58.427 36.000 0.00 0.00 0.00 2.90
1852 2455 6.697455 TCTCAATATCGTCAAAGTGTAGCATC 59.303 38.462 0.00 0.00 0.00 3.91
1853 2456 6.477033 GTCTCAATATCGTCAAAGTGTAGCAT 59.523 38.462 0.00 0.00 0.00 3.79
1854 2457 5.805486 GTCTCAATATCGTCAAAGTGTAGCA 59.195 40.000 0.00 0.00 0.00 3.49
1855 2458 5.805486 TGTCTCAATATCGTCAAAGTGTAGC 59.195 40.000 0.00 0.00 0.00 3.58
1856 2459 7.993821 ATGTCTCAATATCGTCAAAGTGTAG 57.006 36.000 0.00 0.00 0.00 2.74
1867 2470 9.235537 CAGCTCTGAATATATGTCTCAATATCG 57.764 37.037 0.00 0.00 0.00 2.92
1872 2475 6.737720 ACCAGCTCTGAATATATGTCTCAA 57.262 37.500 0.00 0.00 0.00 3.02
1874 2477 6.014669 AGGAACCAGCTCTGAATATATGTCTC 60.015 42.308 0.00 0.00 0.00 3.36
1888 2491 0.807496 GCATTGTCAGGAACCAGCTC 59.193 55.000 0.00 0.00 0.00 4.09
1890 2493 1.598701 GGGCATTGTCAGGAACCAGC 61.599 60.000 0.00 0.00 0.00 4.85
1892 2495 1.076549 GGGGCATTGTCAGGAACCA 59.923 57.895 0.00 0.00 0.00 3.67
1893 2496 1.682344 GGGGGCATTGTCAGGAACC 60.682 63.158 0.00 0.00 0.00 3.62
1894 2497 4.018409 GGGGGCATTGTCAGGAAC 57.982 61.111 0.00 0.00 0.00 3.62
1909 2512 0.182299 GCTGAATCTCAAGGAGGGGG 59.818 60.000 0.00 0.00 0.00 5.40
1910 2513 1.140652 GAGCTGAATCTCAAGGAGGGG 59.859 57.143 0.00 0.00 33.41 4.79
1911 2514 1.202510 CGAGCTGAATCTCAAGGAGGG 60.203 57.143 0.00 0.00 33.41 4.30
1914 2517 1.135915 GAGCGAGCTGAATCTCAAGGA 59.864 52.381 0.84 0.00 33.41 3.36
1915 2518 1.136695 AGAGCGAGCTGAATCTCAAGG 59.863 52.381 0.84 0.00 33.41 3.61
1916 2519 2.159268 TGAGAGCGAGCTGAATCTCAAG 60.159 50.000 15.47 0.00 43.81 3.02
1918 2521 1.467920 TGAGAGCGAGCTGAATCTCA 58.532 50.000 14.34 14.34 44.38 3.27
1919 2522 2.462889 CTTGAGAGCGAGCTGAATCTC 58.537 52.381 0.84 10.38 38.91 2.75
1921 2524 0.929615 GCTTGAGAGCGAGCTGAATC 59.070 55.000 0.84 0.00 46.18 2.52
1922 2525 3.062585 GCTTGAGAGCGAGCTGAAT 57.937 52.632 0.84 0.00 46.18 2.57
1923 2526 4.586618 GCTTGAGAGCGAGCTGAA 57.413 55.556 0.84 0.00 46.18 3.02
1932 2535 4.009015 GGCTTTGGGGCTTGAGAG 57.991 61.111 0.00 0.00 37.53 3.20
1962 2565 1.694696 GAGGACTCCGCCTTAATCCAT 59.305 52.381 0.00 0.00 38.73 3.41
1984 2587 3.376935 CTCCGGAGCAGGCGACATT 62.377 63.158 20.67 0.00 0.00 2.71
1994 2597 1.078143 AAGAACATGCCTCCGGAGC 60.078 57.895 26.87 20.75 0.00 4.70
2021 2624 4.566278 CCCAGTCATTCATTCAGTGGAAGA 60.566 45.833 0.00 0.00 36.25 2.87
2032 2635 5.901413 ACATCAGTATCCCAGTCATTCAT 57.099 39.130 0.00 0.00 0.00 2.57
2033 2636 5.698741 AACATCAGTATCCCAGTCATTCA 57.301 39.130 0.00 0.00 0.00 2.57
2034 2637 5.992217 GGTAACATCAGTATCCCAGTCATTC 59.008 44.000 0.00 0.00 0.00 2.67
2065 2668 2.678336 GGAACACAAGCTTATTCCTCGG 59.322 50.000 21.08 2.65 38.08 4.63
2081 2684 4.617530 CGAGTCGGAAGAATTACTGGAACA 60.618 45.833 4.10 0.00 45.01 3.18
2086 2689 4.921547 TCATCGAGTCGGAAGAATTACTG 58.078 43.478 13.54 0.00 45.01 2.74
2097 2700 2.287668 GGTACAATCCTCATCGAGTCGG 60.288 54.545 13.54 0.00 0.00 4.79
2132 2736 1.754745 CTACAGCACACCACCCACT 59.245 57.895 0.00 0.00 0.00 4.00
2133 2737 1.302511 CCTACAGCACACCACCCAC 60.303 63.158 0.00 0.00 0.00 4.61
2134 2738 2.525124 CCCTACAGCACACCACCCA 61.525 63.158 0.00 0.00 0.00 4.51
2135 2739 1.562672 ATCCCTACAGCACACCACCC 61.563 60.000 0.00 0.00 0.00 4.61
2137 2741 0.392998 CCATCCCTACAGCACACCAC 60.393 60.000 0.00 0.00 0.00 4.16
2138 2742 1.990424 CCATCCCTACAGCACACCA 59.010 57.895 0.00 0.00 0.00 4.17
2139 2743 1.452108 GCCATCCCTACAGCACACC 60.452 63.158 0.00 0.00 0.00 4.16
2140 2744 1.452108 GGCCATCCCTACAGCACAC 60.452 63.158 0.00 0.00 0.00 3.82
2141 2745 1.207488 AAGGCCATCCCTACAGCACA 61.207 55.000 5.01 0.00 45.62 4.57
2172 2776 4.230455 TCCATGTTCCCAATTGAAAAGGT 58.770 39.130 7.12 0.00 0.00 3.50


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

AutoCloner maintained by Alex Coulton.