Multiple sequence alignment - TraesCS6A01G034800

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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 TraesCS6A01G034800 chr6A 100.000 2885 0 0 1 2885 16682324 16685208 0.000000e+00 5328
1 TraesCS6A01G034800 chr6A 92.188 448 31 3 886 1330 16658875 16658429 5.250000e-177 630
2 TraesCS6A01G034800 chr6A 86.948 521 49 15 812 1326 16594039 16593532 4.170000e-158 568
3 TraesCS6A01G034800 chr6A 85.353 553 60 17 1328 1866 16658496 16657951 1.170000e-153 553
4 TraesCS6A01G034800 chr6A 84.457 534 58 20 814 1330 16802290 16801765 1.190000e-138 503
5 TraesCS6A01G034800 chr6D 92.273 1566 81 14 1325 2873 16503099 16504641 0.000000e+00 2185
6 TraesCS6A01G034800 chr6D 90.909 1342 84 17 7 1330 16501847 16503168 0.000000e+00 1768
7 TraesCS6A01G034800 chr6D 85.475 537 54 15 796 1326 16510493 16511011 3.270000e-149 538
8 TraesCS6A01G034800 chr6D 86.546 498 53 13 1358 1848 16389870 16389380 1.180000e-148 536
9 TraesCS6A01G034800 chr6D 87.810 443 41 7 891 1325 16307425 16306988 9.220000e-140 507
10 TraesCS6A01G034800 chr6D 87.239 431 27 19 886 1295 29089507 29089930 1.570000e-127 466
11 TraesCS6A01G034800 chr6B 91.745 424 25 8 1360 1775 59233020 59233441 5.360000e-162 580
12 TraesCS6A01G034800 chr6B 93.923 362 20 2 1328 1689 28980036 28979677 1.950000e-151 545
13 TraesCS6A01G034800 chr6B 92.857 378 22 4 1360 1733 59295166 59295542 7.030000e-151 544
14 TraesCS6A01G034800 chr6B 92.593 378 23 4 1360 1733 28714278 28714654 3.270000e-149 538
15 TraesCS6A01G034800 chr6B 94.286 350 19 1 1328 1677 29060406 29060058 4.230000e-148 534
16 TraesCS6A01G034800 chr6B 88.993 427 43 2 891 1317 28256807 28256385 2.550000e-145 525
17 TraesCS6A01G034800 chr6B 87.257 463 42 15 886 1338 28925849 28926304 1.980000e-141 512
18 TraesCS6A01G034800 chr6B 84.942 518 63 12 1328 1837 28926230 28926740 7.130000e-141 510
19 TraesCS6A01G034800 chr6B 84.884 516 56 14 814 1326 29068641 29068145 4.290000e-138 501


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 TraesCS6A01G034800 chr6A 16682324 16685208 2884 False 5328.0 5328 100.0000 1 2885 1 chr6A.!!$F1 2884
1 TraesCS6A01G034800 chr6A 16657951 16658875 924 True 591.5 630 88.7705 886 1866 2 chr6A.!!$R3 980
2 TraesCS6A01G034800 chr6A 16593532 16594039 507 True 568.0 568 86.9480 812 1326 1 chr6A.!!$R1 514
3 TraesCS6A01G034800 chr6A 16801765 16802290 525 True 503.0 503 84.4570 814 1330 1 chr6A.!!$R2 516
4 TraesCS6A01G034800 chr6D 16501847 16504641 2794 False 1976.5 2185 91.5910 7 2873 2 chr6D.!!$F3 2866
5 TraesCS6A01G034800 chr6D 16510493 16511011 518 False 538.0 538 85.4750 796 1326 1 chr6D.!!$F1 530
6 TraesCS6A01G034800 chr6B 28925849 28926740 891 False 511.0 512 86.0995 886 1837 2 chr6B.!!$F4 951

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
396 404 0.031857 CACGCACCCAAGCAAATCAA 59.968 50.0 0.0 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2125 2165 0.031994 GCATGGCTTTTGTGGTTCGT 59.968 50.0 0.0 0.0 0.0 3.85 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
35 36 1.369091 GCTCGGGTGTGGCAATGTAG 61.369 60.000 0.00 0.00 0.00 2.74
69 70 5.581126 TGTCAAAGGATAATGCACAATCC 57.419 39.130 17.69 17.69 41.77 3.01
70 71 5.015515 TGTCAAAGGATAATGCACAATCCA 58.984 37.500 24.16 7.18 43.55 3.41
105 106 4.448732 TCTCACAAAGTCACATGAATCACG 59.551 41.667 0.00 0.00 0.00 4.35
112 113 3.798878 AGTCACATGAATCACGCTAATCG 59.201 43.478 0.00 0.00 45.38 3.34
155 163 9.915629 AGTAACATTAAACACAAAGTTCAACAA 57.084 25.926 0.00 0.00 40.26 2.83
176 184 9.373750 CAACAAATAATAGTAACATCTCATGCG 57.626 33.333 0.00 0.00 0.00 4.73
177 185 7.576236 ACAAATAATAGTAACATCTCATGCGC 58.424 34.615 0.00 0.00 0.00 6.09
178 186 7.442364 ACAAATAATAGTAACATCTCATGCGCT 59.558 33.333 9.73 0.00 0.00 5.92
218 226 6.234177 AGACAAAGGACCAGAGTAATGAAAG 58.766 40.000 0.00 0.00 0.00 2.62
224 232 4.081087 GGACCAGAGTAATGAAAGTAGGCA 60.081 45.833 0.00 0.00 0.00 4.75
263 271 7.394016 TGAACAGACTAATGAAAATAGGCTCA 58.606 34.615 0.00 0.00 36.59 4.26
320 328 7.697710 CACAAATGTGTCATATACATGTTCACC 59.302 37.037 2.30 0.00 41.10 4.02
393 401 0.749649 TTTCACGCACCCAAGCAAAT 59.250 45.000 0.00 0.00 0.00 2.32
394 402 0.313672 TTCACGCACCCAAGCAAATC 59.686 50.000 0.00 0.00 0.00 2.17
396 404 0.031857 CACGCACCCAAGCAAATCAA 59.968 50.000 0.00 0.00 0.00 2.57
402 410 3.493176 GCACCCAAGCAAATCAACTTCTT 60.493 43.478 0.00 0.00 0.00 2.52
473 483 1.269174 CGACATTGACAATGGCCACAA 59.731 47.619 27.46 8.55 44.30 3.33
476 486 3.666274 ACATTGACAATGGCCACAATTG 58.334 40.909 27.46 12.39 43.21 2.32
605 616 9.167311 ACATTTTAGTCTATGGAGTGATGAAAC 57.833 33.333 11.18 0.00 0.00 2.78
664 675 3.949754 CACACATGATGAATGGGCTTACT 59.050 43.478 0.00 0.00 44.25 2.24
697 711 9.593134 AAAATGTGATTAGCTACAACAACAAAA 57.407 25.926 0.00 0.00 0.00 2.44
698 712 9.762933 AAATGTGATTAGCTACAACAACAAAAT 57.237 25.926 0.00 0.00 0.00 1.82
728 742 9.001049 GTTATACATATAAGCAGATTCGTCTCG 57.999 37.037 0.00 0.00 0.00 4.04
764 778 3.244875 TGGCTGCAAGATAAGAGTGGAAA 60.245 43.478 0.50 0.00 34.07 3.13
809 823 8.137437 ACAAAGACAATCATCAAGTGGTAAAAG 58.863 33.333 0.00 0.00 0.00 2.27
846 860 1.416401 GATTGGCCGATTAGACCCTCA 59.584 52.381 7.01 0.00 0.00 3.86
874 889 1.026718 GTGCCCCCAAACTGATCTCG 61.027 60.000 0.00 0.00 0.00 4.04
1268 1291 1.878522 GCCGAGGTACGCACAGATG 60.879 63.158 0.00 0.00 41.07 2.90
1269 1292 1.511305 CCGAGGTACGCACAGATGT 59.489 57.895 0.00 0.00 41.07 3.06
1270 1293 0.525668 CCGAGGTACGCACAGATGTC 60.526 60.000 0.00 0.00 41.07 3.06
1271 1294 0.525668 CGAGGTACGCACAGATGTCC 60.526 60.000 0.00 0.00 34.51 4.02
1272 1295 0.818296 GAGGTACGCACAGATGTCCT 59.182 55.000 0.00 0.00 0.00 3.85
1273 1296 0.818296 AGGTACGCACAGATGTCCTC 59.182 55.000 0.00 0.00 0.00 3.71
1274 1297 0.179108 GGTACGCACAGATGTCCTCC 60.179 60.000 0.00 0.00 0.00 4.30
1275 1298 0.179108 GTACGCACAGATGTCCTCCC 60.179 60.000 0.00 0.00 0.00 4.30
1276 1299 0.324368 TACGCACAGATGTCCTCCCT 60.324 55.000 0.00 0.00 0.00 4.20
1277 1300 1.142748 CGCACAGATGTCCTCCCTC 59.857 63.158 0.00 0.00 0.00 4.30
1278 1301 1.524482 GCACAGATGTCCTCCCTCC 59.476 63.158 0.00 0.00 0.00 4.30
1279 1302 0.980231 GCACAGATGTCCTCCCTCCT 60.980 60.000 0.00 0.00 0.00 3.69
1280 1303 1.118838 CACAGATGTCCTCCCTCCTC 58.881 60.000 0.00 0.00 0.00 3.71
1281 1304 0.396417 ACAGATGTCCTCCCTCCTCG 60.396 60.000 0.00 0.00 0.00 4.63
1282 1305 0.106469 CAGATGTCCTCCCTCCTCGA 60.106 60.000 0.00 0.00 0.00 4.04
1283 1306 0.184933 AGATGTCCTCCCTCCTCGAG 59.815 60.000 5.13 5.13 0.00 4.04
1291 1314 4.026300 CCTCCTCGAGGCTGTTCT 57.974 61.111 27.39 0.00 43.29 3.01
1292 1315 1.515020 CCTCCTCGAGGCTGTTCTG 59.485 63.158 27.39 9.58 43.29 3.02
1293 1316 1.153667 CTCCTCGAGGCTGTTCTGC 60.154 63.158 27.39 0.00 34.44 4.26
1294 1317 1.603236 CTCCTCGAGGCTGTTCTGCT 61.603 60.000 27.39 0.00 34.44 4.24
1295 1318 1.153667 CCTCGAGGCTGTTCTGCTC 60.154 63.158 20.67 0.00 0.00 4.26
1296 1319 1.603236 CCTCGAGGCTGTTCTGCTCT 61.603 60.000 20.67 0.00 0.00 4.09
1297 1320 0.458197 CTCGAGGCTGTTCTGCTCTG 60.458 60.000 3.91 0.00 0.00 3.35
1298 1321 1.181741 TCGAGGCTGTTCTGCTCTGT 61.182 55.000 0.00 0.00 0.00 3.41
1299 1322 0.320247 CGAGGCTGTTCTGCTCTGTT 60.320 55.000 0.00 0.00 0.00 3.16
1300 1323 1.437625 GAGGCTGTTCTGCTCTGTTC 58.562 55.000 0.00 0.00 0.00 3.18
1301 1324 1.001860 GAGGCTGTTCTGCTCTGTTCT 59.998 52.381 0.00 0.00 0.00 3.01
1302 1325 1.419387 AGGCTGTTCTGCTCTGTTCTT 59.581 47.619 0.00 0.00 0.00 2.52
1303 1326 1.534595 GGCTGTTCTGCTCTGTTCTTG 59.465 52.381 2.15 0.00 0.00 3.02
1304 1327 1.069364 GCTGTTCTGCTCTGTTCTTGC 60.069 52.381 0.00 0.00 0.00 4.01
1305 1328 2.216046 CTGTTCTGCTCTGTTCTTGCA 58.784 47.619 0.00 0.00 35.30 4.08
1306 1329 1.942657 TGTTCTGCTCTGTTCTTGCAC 59.057 47.619 0.00 0.00 32.91 4.57
1307 1330 2.216898 GTTCTGCTCTGTTCTTGCACT 58.783 47.619 0.00 0.00 32.91 4.40
1308 1331 1.875009 TCTGCTCTGTTCTTGCACTG 58.125 50.000 0.00 0.00 32.91 3.66
1309 1332 1.139654 TCTGCTCTGTTCTTGCACTGT 59.860 47.619 0.00 0.00 32.91 3.55
1310 1333 1.945394 CTGCTCTGTTCTTGCACTGTT 59.055 47.619 0.00 0.00 32.91 3.16
1311 1334 1.942657 TGCTCTGTTCTTGCACTGTTC 59.057 47.619 0.00 0.00 0.00 3.18
1312 1335 1.070309 GCTCTGTTCTTGCACTGTTCG 60.070 52.381 0.00 0.00 0.00 3.95
1313 1336 2.473816 CTCTGTTCTTGCACTGTTCGA 58.526 47.619 0.00 0.00 0.00 3.71
1314 1337 2.201732 TCTGTTCTTGCACTGTTCGAC 58.798 47.619 0.00 0.00 0.00 4.20
1315 1338 0.927537 TGTTCTTGCACTGTTCGACG 59.072 50.000 0.00 0.00 0.00 5.12
1316 1339 0.232303 GTTCTTGCACTGTTCGACGG 59.768 55.000 0.00 0.00 0.00 4.79
1317 1340 0.103390 TTCTTGCACTGTTCGACGGA 59.897 50.000 0.00 0.00 0.00 4.69
1318 1341 0.317160 TCTTGCACTGTTCGACGGAT 59.683 50.000 0.00 0.00 0.00 4.18
1319 1342 0.439985 CTTGCACTGTTCGACGGATG 59.560 55.000 0.00 0.00 0.00 3.51
1320 1343 0.032815 TTGCACTGTTCGACGGATGA 59.967 50.000 0.00 0.00 0.00 2.92
1321 1344 0.666274 TGCACTGTTCGACGGATGAC 60.666 55.000 0.00 0.00 0.00 3.06
1322 1345 0.388649 GCACTGTTCGACGGATGACT 60.389 55.000 0.00 0.00 0.00 3.41
1323 1346 1.340658 CACTGTTCGACGGATGACTG 58.659 55.000 0.00 0.00 0.00 3.51
1324 1347 1.068541 CACTGTTCGACGGATGACTGA 60.069 52.381 0.00 0.00 0.00 3.41
1325 1348 1.068472 ACTGTTCGACGGATGACTGAC 60.068 52.381 0.00 0.00 0.00 3.51
1326 1349 0.109919 TGTTCGACGGATGACTGACG 60.110 55.000 0.00 0.00 40.60 4.35
1327 1350 0.797249 GTTCGACGGATGACTGACGG 60.797 60.000 0.00 0.00 39.94 4.79
1328 1351 0.956902 TTCGACGGATGACTGACGGA 60.957 55.000 0.00 0.00 39.94 4.69
1329 1352 0.746923 TCGACGGATGACTGACGGAT 60.747 55.000 0.00 0.00 39.94 4.18
1350 1373 1.198094 TTTCCTGTCCCCGAGCATCA 61.198 55.000 0.00 0.00 33.17 3.07
1382 1410 2.861935 GTTCTTCTTGTGTTCGACGGAA 59.138 45.455 0.00 0.00 0.00 4.30
1387 1415 3.264104 TCTTGTGTTCGACGGAAAACTT 58.736 40.909 0.00 0.00 40.44 2.66
1423 1456 1.836802 GAATCTCAGGTCCTGGAGCTT 59.163 52.381 24.99 11.08 38.40 3.74
1519 1552 4.774503 GAGCTCGGCAGGCTGCTT 62.775 66.667 35.73 17.92 44.28 3.91
1566 1599 2.009774 CGTCATCCCCAACATCAACTC 58.990 52.381 0.00 0.00 0.00 3.01
1577 1610 1.376424 ATCAACTCCCGTGCTGCTG 60.376 57.895 0.00 0.00 0.00 4.41
1635 1668 0.321996 GTCGCCCAAGAAGAAGACCT 59.678 55.000 0.00 0.00 0.00 3.85
1785 1825 1.410517 CTGCCCTTAGATTCGCTGAGA 59.589 52.381 0.00 0.00 32.19 3.27
1793 1833 1.065854 AGATTCGCTGAGAAAGGGTGG 60.066 52.381 0.00 0.00 42.91 4.61
1798 1838 1.678728 CGCTGAGAAAGGGTGGCATTA 60.679 52.381 0.00 0.00 34.19 1.90
1870 1910 8.260818 TCTTAATTCTCTTGTTCTATCTGTGGG 58.739 37.037 0.00 0.00 0.00 4.61
1873 1913 4.416516 TCTCTTGTTCTATCTGTGGGTGA 58.583 43.478 0.00 0.00 0.00 4.02
1882 1922 5.684704 TCTATCTGTGGGTGAAATTGATCC 58.315 41.667 0.00 0.00 0.00 3.36
1893 1933 6.381133 GGGTGAAATTGATCCTGTTAATCCTT 59.619 38.462 0.00 0.00 0.00 3.36
1897 1937 7.178983 TGAAATTGATCCTGTTAATCCTTGCTT 59.821 33.333 0.00 0.00 0.00 3.91
1901 1941 3.955471 TCCTGTTAATCCTTGCTTCCTG 58.045 45.455 0.00 0.00 0.00 3.86
1911 1951 2.622942 CCTTGCTTCCTGTGCTGTTTTA 59.377 45.455 0.00 0.00 0.00 1.52
1912 1952 3.256631 CCTTGCTTCCTGTGCTGTTTTAT 59.743 43.478 0.00 0.00 0.00 1.40
1913 1953 4.479619 CTTGCTTCCTGTGCTGTTTTATC 58.520 43.478 0.00 0.00 0.00 1.75
1914 1954 2.819608 TGCTTCCTGTGCTGTTTTATCC 59.180 45.455 0.00 0.00 0.00 2.59
1915 1955 3.084786 GCTTCCTGTGCTGTTTTATCCT 58.915 45.455 0.00 0.00 0.00 3.24
1916 1956 4.261801 GCTTCCTGTGCTGTTTTATCCTA 58.738 43.478 0.00 0.00 0.00 2.94
1921 1961 5.720041 TCCTGTGCTGTTTTATCCTAGTACT 59.280 40.000 0.00 0.00 0.00 2.73
1950 1990 7.715265 TCTCACTTATATCGGCTGAAAAATC 57.285 36.000 0.00 0.00 0.00 2.17
1960 2000 2.840038 GGCTGAAAAATCCCCCAATTCT 59.160 45.455 0.00 0.00 0.00 2.40
1970 2010 2.097825 CCCCCAATTCTTTGCTCTCTG 58.902 52.381 0.00 0.00 0.00 3.35
1979 2019 7.147949 CCAATTCTTTGCTCTCTGAATTATGGT 60.148 37.037 0.00 0.00 37.12 3.55
1988 2028 6.688637 TCTCTGAATTATGGTGCTCAATTG 57.311 37.500 0.00 0.00 0.00 2.32
2049 2089 8.228464 CACAATCATATTACTATTGAGCTGCAG 58.772 37.037 10.11 10.11 35.18 4.41
2052 2092 7.530426 TCATATTACTATTGAGCTGCAGAGA 57.470 36.000 20.43 0.00 0.00 3.10
2093 2133 1.530293 CAGCTTTCTGTCAGTCAGCAC 59.470 52.381 20.95 2.03 43.32 4.40
2156 2196 0.333993 AGCCATGCCAAGACATTCCT 59.666 50.000 0.00 0.00 0.00 3.36
2169 2209 5.551760 AGACATTCCTGCAGTTAATTTCG 57.448 39.130 13.81 3.61 0.00 3.46
2170 2210 4.096732 ACATTCCTGCAGTTAATTTCGC 57.903 40.909 13.81 0.00 0.00 4.70
2186 2226 1.573108 TCGCCTTGATCTTTCCCTCT 58.427 50.000 0.00 0.00 0.00 3.69
2219 2259 8.099364 AGTTCTTTACATGTTGTATTCACAGG 57.901 34.615 2.30 0.00 35.67 4.00
2264 2304 3.108357 GAGCCGGCCGTATGCAAAC 62.108 63.158 26.15 11.87 43.89 2.93
2284 2324 1.699634 CTGAAGTTTGGGGAGTCAGGA 59.300 52.381 0.00 0.00 33.57 3.86
2285 2325 1.420138 TGAAGTTTGGGGAGTCAGGAC 59.580 52.381 0.00 0.00 0.00 3.85
2286 2326 1.700186 GAAGTTTGGGGAGTCAGGACT 59.300 52.381 0.70 0.70 45.84 3.85
2371 2411 9.833917 AGGTACTAATTTAGATTGACCTAAAGC 57.166 33.333 10.39 0.00 38.29 3.51
2388 2428 5.922544 CCTAAAGCAGAAACAAACATTGAGG 59.077 40.000 0.00 0.00 0.00 3.86
2455 2495 5.473162 TGATGTTTCACTTCGTTCCATCAAT 59.527 36.000 0.00 0.00 35.56 2.57
2554 2595 8.807667 ACTTTGAATTGAACACATTGATTCTC 57.192 30.769 0.00 0.00 0.00 2.87
2564 2620 4.271049 ACACATTGATTCTCCGCTAAATCG 59.729 41.667 0.00 0.00 35.16 3.34
2592 2648 3.233507 ACCAAAACTAGTACCGAGTCCA 58.766 45.455 0.00 0.00 0.00 4.02
2593 2649 3.836562 ACCAAAACTAGTACCGAGTCCAT 59.163 43.478 0.00 0.00 0.00 3.41
2619 2675 6.426646 AAGGTCTTGTGCTAAGGATATAGG 57.573 41.667 2.24 0.00 0.00 2.57
2658 2714 5.645624 TCTTGTTTTTCATGCTGTTTTCGA 58.354 33.333 0.00 0.00 0.00 3.71
2661 2717 3.641437 TTTTCATGCTGTTTTCGAGGG 57.359 42.857 0.00 0.00 0.00 4.30
2669 2725 6.260050 TCATGCTGTTTTCGAGGGTTTATATC 59.740 38.462 0.00 0.00 0.00 1.63
2721 2777 8.825745 TGTTACATTTTTCTTTTGCTGAATTCC 58.174 29.630 2.27 0.00 0.00 3.01
2722 2778 8.825745 GTTACATTTTTCTTTTGCTGAATTCCA 58.174 29.630 2.27 0.00 0.00 3.53
2723 2779 9.558396 TTACATTTTTCTTTTGCTGAATTCCAT 57.442 25.926 2.27 0.00 0.00 3.41
2774 2830 9.454859 CCTCTGTTGTCTCTATTTATTTTTCCT 57.545 33.333 0.00 0.00 0.00 3.36
2792 2848 9.899226 ATTTTTCCTATTCGTCTTCTTTCAAAG 57.101 29.630 0.00 0.00 0.00 2.77
2793 2849 8.446599 TTTTCCTATTCGTCTTCTTTCAAAGT 57.553 30.769 0.00 0.00 0.00 2.66
2797 2853 8.557029 TCCTATTCGTCTTCTTTCAAAGTTTTC 58.443 33.333 0.00 0.00 0.00 2.29
2825 2881 7.529880 TTTTACTTTTTCGTCGACTTTCTCT 57.470 32.000 14.70 0.00 0.00 3.10
2847 2904 9.284594 TCTCTTATTTGTTTTTGTTTTGTCTCG 57.715 29.630 0.00 0.00 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.388308 CCGAGCTCCTAAGACATCATTG 58.612 50.000 8.47 0.00 0.00 2.82
1 2 2.366916 CCCGAGCTCCTAAGACATCATT 59.633 50.000 8.47 0.00 0.00 2.57
2 3 1.967066 CCCGAGCTCCTAAGACATCAT 59.033 52.381 8.47 0.00 0.00 2.45
3 4 1.342076 ACCCGAGCTCCTAAGACATCA 60.342 52.381 8.47 0.00 0.00 3.07
4 5 1.067821 CACCCGAGCTCCTAAGACATC 59.932 57.143 8.47 0.00 0.00 3.06
5 6 1.115467 CACCCGAGCTCCTAAGACAT 58.885 55.000 8.47 0.00 0.00 3.06
35 36 2.026262 TCCTTTGACATAGTCCCCAAGC 60.026 50.000 0.00 0.00 0.00 4.01
69 70 6.016860 TGACTTTGTGAGATGAAAATGGAGTG 60.017 38.462 0.00 0.00 0.00 3.51
70 71 6.016777 GTGACTTTGTGAGATGAAAATGGAGT 60.017 38.462 0.00 0.00 0.00 3.85
155 163 6.931281 ACAGCGCATGAGATGTTACTATTATT 59.069 34.615 14.86 0.00 37.48 1.40
169 177 2.284263 TCACTCTTACAGCGCATGAG 57.716 50.000 11.47 11.51 0.00 2.90
193 201 5.825593 TCATTACTCTGGTCCTTTGTCTT 57.174 39.130 0.00 0.00 0.00 3.01
201 209 4.081087 TGCCTACTTTCATTACTCTGGTCC 60.081 45.833 0.00 0.00 0.00 4.46
203 211 5.499004 TTGCCTACTTTCATTACTCTGGT 57.501 39.130 0.00 0.00 0.00 4.00
256 264 8.330247 TGTTAACCCTTGTTATTAATGAGCCTA 58.670 33.333 2.48 0.00 36.84 3.93
257 265 7.179269 TGTTAACCCTTGTTATTAATGAGCCT 58.821 34.615 2.48 0.00 36.84 4.58
300 308 5.427378 CTGGGTGAACATGTATATGACACA 58.573 41.667 23.01 12.57 42.17 3.72
320 328 7.542130 GTCAATGGTATGTTTAAAAAGAGCTGG 59.458 37.037 4.03 0.00 0.00 4.85
360 368 8.151596 TGGGTGCGTGAAATGTTTCTATATATA 58.848 33.333 6.99 0.00 38.02 0.86
361 369 6.995686 TGGGTGCGTGAAATGTTTCTATATAT 59.004 34.615 6.99 0.00 38.02 0.86
362 370 6.350103 TGGGTGCGTGAAATGTTTCTATATA 58.650 36.000 6.99 0.00 38.02 0.86
363 371 5.189928 TGGGTGCGTGAAATGTTTCTATAT 58.810 37.500 6.99 0.00 38.02 0.86
364 372 4.580868 TGGGTGCGTGAAATGTTTCTATA 58.419 39.130 6.99 0.00 38.02 1.31
393 401 8.492673 AATCATGCGAGTAATAAAGAAGTTGA 57.507 30.769 0.00 0.00 0.00 3.18
394 402 8.390354 TGAATCATGCGAGTAATAAAGAAGTTG 58.610 33.333 0.00 0.00 0.00 3.16
396 404 8.554528 CATGAATCATGCGAGTAATAAAGAAGT 58.445 33.333 10.55 0.00 35.02 3.01
402 410 8.382030 ACAATCATGAATCATGCGAGTAATAA 57.618 30.769 17.81 0.00 41.18 1.40
449 457 1.745087 GGCCATTGTCAATGTCGTCAT 59.255 47.619 21.32 0.00 37.18 3.06
450 458 1.164411 GGCCATTGTCAATGTCGTCA 58.836 50.000 21.32 0.00 37.18 4.35
473 483 9.951866 AAAATAAGGATGGGTAAGGATAACAAT 57.048 29.630 0.00 0.00 0.00 2.71
512 523 4.160814 TGGAAGGTATATGCGTTGTACAGT 59.839 41.667 3.37 0.00 0.00 3.55
574 585 9.739276 ATCACTCCATAGACTAAAATGTTCAAA 57.261 29.630 0.00 0.00 0.00 2.69
605 616 3.417069 TCGGGTATTGGCCATATTCAG 57.583 47.619 6.09 0.00 0.00 3.02
728 742 3.401182 TGCAGCCAATTGATTTTTCACC 58.599 40.909 7.12 0.00 0.00 4.02
809 823 3.631227 CCAATCAGAGAGCAGGGATTTTC 59.369 47.826 0.00 0.00 0.00 2.29
884 899 2.671070 CCGTTGGATCTGCAGGGT 59.329 61.111 15.13 2.64 0.00 4.34
956 972 2.438795 TGGGCGCGGGTTTTATCC 60.439 61.111 8.83 0.00 0.00 2.59
1275 1298 1.153667 GCAGAACAGCCTCGAGGAG 60.154 63.158 35.69 26.48 37.39 3.69
1276 1299 1.599606 GAGCAGAACAGCCTCGAGGA 61.600 60.000 35.69 0.00 37.39 3.71
1277 1300 1.153667 GAGCAGAACAGCCTCGAGG 60.154 63.158 27.83 27.83 38.53 4.63
1278 1301 0.458197 CAGAGCAGAACAGCCTCGAG 60.458 60.000 5.13 5.13 34.23 4.04
1279 1302 1.181741 ACAGAGCAGAACAGCCTCGA 61.182 55.000 0.00 0.00 34.23 4.04
1280 1303 0.320247 AACAGAGCAGAACAGCCTCG 60.320 55.000 0.00 0.00 34.23 4.63
1281 1304 1.001860 AGAACAGAGCAGAACAGCCTC 59.998 52.381 0.00 0.00 34.23 4.70
1282 1305 1.055040 AGAACAGAGCAGAACAGCCT 58.945 50.000 0.00 0.00 34.23 4.58
1283 1306 1.534595 CAAGAACAGAGCAGAACAGCC 59.465 52.381 0.00 0.00 34.23 4.85
1284 1307 1.069364 GCAAGAACAGAGCAGAACAGC 60.069 52.381 0.00 0.00 0.00 4.40
1285 1308 2.032204 GTGCAAGAACAGAGCAGAACAG 60.032 50.000 0.00 0.00 39.21 3.16
1286 1309 1.942657 GTGCAAGAACAGAGCAGAACA 59.057 47.619 0.00 0.00 39.21 3.18
1287 1310 2.032204 CAGTGCAAGAACAGAGCAGAAC 60.032 50.000 0.00 0.00 39.21 3.01
1288 1311 2.216046 CAGTGCAAGAACAGAGCAGAA 58.784 47.619 0.00 0.00 39.21 3.02
1289 1312 1.139654 ACAGTGCAAGAACAGAGCAGA 59.860 47.619 0.00 0.00 39.21 4.26
1290 1313 1.590932 ACAGTGCAAGAACAGAGCAG 58.409 50.000 0.00 0.00 39.21 4.24
1291 1314 1.942657 GAACAGTGCAAGAACAGAGCA 59.057 47.619 0.00 0.00 35.63 4.26
1292 1315 1.070309 CGAACAGTGCAAGAACAGAGC 60.070 52.381 0.00 0.00 0.00 4.09
1293 1316 2.219674 GTCGAACAGTGCAAGAACAGAG 59.780 50.000 0.00 0.00 0.00 3.35
1294 1317 2.201732 GTCGAACAGTGCAAGAACAGA 58.798 47.619 0.00 0.00 0.00 3.41
1295 1318 1.071239 CGTCGAACAGTGCAAGAACAG 60.071 52.381 0.00 0.00 0.00 3.16
1296 1319 0.927537 CGTCGAACAGTGCAAGAACA 59.072 50.000 0.00 0.00 0.00 3.18
1297 1320 0.232303 CCGTCGAACAGTGCAAGAAC 59.768 55.000 0.00 0.00 0.00 3.01
1298 1321 0.103390 TCCGTCGAACAGTGCAAGAA 59.897 50.000 0.00 0.00 0.00 2.52
1299 1322 0.317160 ATCCGTCGAACAGTGCAAGA 59.683 50.000 0.00 0.00 0.00 3.02
1300 1323 0.439985 CATCCGTCGAACAGTGCAAG 59.560 55.000 0.00 0.00 0.00 4.01
1301 1324 0.032815 TCATCCGTCGAACAGTGCAA 59.967 50.000 0.00 0.00 0.00 4.08
1302 1325 0.666274 GTCATCCGTCGAACAGTGCA 60.666 55.000 0.00 0.00 0.00 4.57
1303 1326 0.388649 AGTCATCCGTCGAACAGTGC 60.389 55.000 0.00 0.00 0.00 4.40
1304 1327 1.068541 TCAGTCATCCGTCGAACAGTG 60.069 52.381 0.00 0.00 0.00 3.66
1305 1328 1.068472 GTCAGTCATCCGTCGAACAGT 60.068 52.381 0.00 0.00 0.00 3.55
1306 1329 1.618861 GTCAGTCATCCGTCGAACAG 58.381 55.000 0.00 0.00 0.00 3.16
1307 1330 0.109919 CGTCAGTCATCCGTCGAACA 60.110 55.000 0.00 0.00 0.00 3.18
1308 1331 0.797249 CCGTCAGTCATCCGTCGAAC 60.797 60.000 0.00 0.00 0.00 3.95
1309 1332 0.956902 TCCGTCAGTCATCCGTCGAA 60.957 55.000 0.00 0.00 0.00 3.71
1310 1333 0.746923 ATCCGTCAGTCATCCGTCGA 60.747 55.000 0.00 0.00 0.00 4.20
1311 1334 0.317103 GATCCGTCAGTCATCCGTCG 60.317 60.000 0.00 0.00 0.00 5.12
1312 1335 1.025812 AGATCCGTCAGTCATCCGTC 58.974 55.000 0.00 0.00 0.00 4.79
1313 1336 1.475403 AAGATCCGTCAGTCATCCGT 58.525 50.000 0.00 0.00 0.00 4.69
1314 1337 2.464865 GAAAGATCCGTCAGTCATCCG 58.535 52.381 0.00 0.00 0.00 4.18
1315 1338 2.827652 GGAAAGATCCGTCAGTCATCC 58.172 52.381 0.00 0.00 35.59 3.51
1326 1349 0.466124 CTCGGGGACAGGAAAGATCC 59.534 60.000 0.00 0.00 46.98 3.36
1327 1350 0.179070 GCTCGGGGACAGGAAAGATC 60.179 60.000 0.00 0.00 0.00 2.75
1328 1351 0.909610 TGCTCGGGGACAGGAAAGAT 60.910 55.000 0.00 0.00 0.00 2.40
1329 1352 0.909610 ATGCTCGGGGACAGGAAAGA 60.910 55.000 0.00 0.00 0.00 2.52
1350 1373 4.125703 CACAAGAAGAACAGAGCAGAACT 58.874 43.478 0.00 0.00 0.00 3.01
1387 1415 7.444183 ACCTGAGATTCAAAAACGAAATCTGTA 59.556 33.333 1.82 0.00 0.00 2.74
1549 1582 1.767759 GGGAGTTGATGTTGGGGATG 58.232 55.000 0.00 0.00 0.00 3.51
1635 1668 0.699577 TTCTTGGGGGACTTGGTGGA 60.700 55.000 0.00 0.00 0.00 4.02
1785 1825 3.091545 CACAGACATAATGCCACCCTTT 58.908 45.455 0.00 0.00 0.00 3.11
1793 1833 6.763135 TCCTACAGAAATCACAGACATAATGC 59.237 38.462 0.00 0.00 0.00 3.56
1798 1838 6.118170 CCATTCCTACAGAAATCACAGACAT 58.882 40.000 0.00 0.00 38.21 3.06
1865 1905 3.524095 ACAGGATCAATTTCACCCACA 57.476 42.857 0.00 0.00 0.00 4.17
1870 1910 6.753744 GCAAGGATTAACAGGATCAATTTCAC 59.246 38.462 0.00 0.00 0.00 3.18
1873 1913 7.364144 GGAAGCAAGGATTAACAGGATCAATTT 60.364 37.037 0.00 0.00 0.00 1.82
1882 1922 3.119708 GCACAGGAAGCAAGGATTAACAG 60.120 47.826 0.00 0.00 0.00 3.16
1893 1933 2.819608 GGATAAAACAGCACAGGAAGCA 59.180 45.455 0.00 0.00 0.00 3.91
1897 1937 5.720041 AGTACTAGGATAAAACAGCACAGGA 59.280 40.000 0.00 0.00 0.00 3.86
1916 1956 9.080097 AGCCGATATAAGTGAGAATTTAGTACT 57.920 33.333 0.00 0.00 0.00 2.73
1921 1961 9.607988 TTTTCAGCCGATATAAGTGAGAATTTA 57.392 29.630 0.00 0.00 0.00 1.40
1934 1974 2.176798 TGGGGGATTTTTCAGCCGATAT 59.823 45.455 0.00 0.00 0.00 1.63
1939 1979 2.840038 AGAATTGGGGGATTTTTCAGCC 59.160 45.455 0.00 0.00 0.00 4.85
1940 1980 4.558226 AAGAATTGGGGGATTTTTCAGC 57.442 40.909 0.00 0.00 0.00 4.26
1950 1990 2.097825 CAGAGAGCAAAGAATTGGGGG 58.902 52.381 0.00 0.00 37.02 5.40
1960 2000 4.592942 AGCACCATAATTCAGAGAGCAAA 58.407 39.130 0.00 0.00 0.00 3.68
1970 2010 5.638657 TGTTTGCAATTGAGCACCATAATTC 59.361 36.000 10.34 0.00 45.61 2.17
1979 2019 4.052608 CAATCAGTGTTTGCAATTGAGCA 58.947 39.130 10.34 0.00 43.99 4.26
1988 2028 8.863049 CATAAGGAATTTACAATCAGTGTTTGC 58.137 33.333 12.82 0.00 41.98 3.68
2021 2061 8.562892 GCAGCTCAATAGTAATATGATTGTGTT 58.437 33.333 0.00 0.00 33.27 3.32
2060 2100 1.329906 GAAAGCTGATCATGAGGTGCG 59.670 52.381 0.09 0.00 0.00 5.34
2067 2107 4.251268 TGACTGACAGAAAGCTGATCATG 58.749 43.478 10.08 0.00 45.17 3.07
2093 2133 3.616956 TGAGCAAGTCTAAGATGGTGG 57.383 47.619 0.00 0.00 0.00 4.61
2125 2165 0.031994 GCATGGCTTTTGTGGTTCGT 59.968 50.000 0.00 0.00 0.00 3.85
2156 2196 4.009675 AGATCAAGGCGAAATTAACTGCA 58.990 39.130 0.00 0.00 0.00 4.41
2169 2209 2.797177 ACAGAGGGAAAGATCAAGGC 57.203 50.000 0.00 0.00 0.00 4.35
2170 2210 5.046304 TCAACTACAGAGGGAAAGATCAAGG 60.046 44.000 0.00 0.00 0.00 3.61
2186 2226 9.772973 ATACAACATGTAAAGAACTCAACTACA 57.227 29.630 0.00 0.00 36.31 2.74
2219 2259 2.799978 CAACCGGAAGAATTTGTTTGGC 59.200 45.455 9.46 0.00 0.00 4.52
2264 2304 1.699634 TCCTGACTCCCCAAACTTCAG 59.300 52.381 0.00 0.00 34.63 3.02
2284 2324 5.061179 GTGGTTTGTTACATACACCTGAGT 58.939 41.667 8.09 0.00 36.21 3.41
2285 2325 5.060506 TGTGGTTTGTTACATACACCTGAG 58.939 41.667 8.09 0.00 36.21 3.35
2286 2326 5.037383 TGTGGTTTGTTACATACACCTGA 57.963 39.130 8.09 0.00 36.21 3.86
2287 2327 5.759506 TTGTGGTTTGTTACATACACCTG 57.240 39.130 8.09 0.00 36.21 4.00
2288 2328 5.068067 GGTTTGTGGTTTGTTACATACACCT 59.932 40.000 8.09 0.00 36.21 4.00
2289 2329 5.163540 TGGTTTGTGGTTTGTTACATACACC 60.164 40.000 8.09 6.81 36.21 4.16
2290 2330 5.892568 TGGTTTGTGGTTTGTTACATACAC 58.107 37.500 8.09 7.69 36.21 2.90
2295 2335 5.923733 AATCTGGTTTGTGGTTTGTTACA 57.076 34.783 0.00 0.00 0.00 2.41
2371 2411 9.918630 ATCTTAATTCCTCAATGTTTGTTTCTG 57.081 29.630 0.00 0.00 0.00 3.02
2431 2471 4.384940 TGATGGAACGAAGTGAAACATCA 58.615 39.130 0.00 0.00 45.00 3.07
2533 2574 5.619757 GCGGAGAATCAATGTGTTCAATTCA 60.620 40.000 0.00 0.00 36.25 2.57
2547 2588 2.866156 CAAGCGATTTAGCGGAGAATCA 59.134 45.455 0.00 0.00 43.00 2.57
2554 2595 0.523335 GGTTGCAAGCGATTTAGCGG 60.523 55.000 13.62 0.00 43.00 5.52
2564 2620 3.608474 CGGTACTAGTTTTGGTTGCAAGC 60.608 47.826 21.51 21.51 0.00 4.01
2592 2648 2.912956 TCCTTAGCACAAGACCTTCCAT 59.087 45.455 0.00 0.00 0.00 3.41
2593 2649 2.334977 TCCTTAGCACAAGACCTTCCA 58.665 47.619 0.00 0.00 0.00 3.53
2619 2675 4.531659 ACAAGAGAAGCGTACACAAAAC 57.468 40.909 0.00 0.00 0.00 2.43
2774 2830 7.501225 AGGGAAAACTTTGAAAGAAGACGAATA 59.499 33.333 12.53 0.00 0.00 1.75
2778 2834 5.500645 AGGGAAAACTTTGAAAGAAGACG 57.499 39.130 12.53 0.00 0.00 4.18
2779 2835 8.547967 AAAAAGGGAAAACTTTGAAAGAAGAC 57.452 30.769 12.53 0.83 40.36 3.01
2780 2836 9.647797 GTAAAAAGGGAAAACTTTGAAAGAAGA 57.352 29.630 12.53 0.00 40.36 2.87
2781 2837 9.653287 AGTAAAAAGGGAAAACTTTGAAAGAAG 57.347 29.630 12.53 0.00 40.36 2.85
2788 2844 8.714179 ACGAAAAAGTAAAAAGGGAAAACTTTG 58.286 29.630 0.00 0.00 40.36 2.77
2791 2847 6.748658 CGACGAAAAAGTAAAAAGGGAAAACT 59.251 34.615 0.00 0.00 0.00 2.66
2792 2848 6.746822 TCGACGAAAAAGTAAAAAGGGAAAAC 59.253 34.615 0.00 0.00 0.00 2.43
2793 2849 6.746822 GTCGACGAAAAAGTAAAAAGGGAAAA 59.253 34.615 0.00 0.00 0.00 2.29
2797 2853 5.413969 AGTCGACGAAAAAGTAAAAAGGG 57.586 39.130 10.46 0.00 0.00 3.95
2825 2881 8.934507 ATCCGAGACAAAACAAAAACAAATAA 57.065 26.923 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.