Multiple sequence alignment - TraesCS3D01G218900

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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 TraesCS3D01G218900 chr3D 100.000 2911 0 0 1 2911 298058819 298061729 0.000000e+00 5376
1 TraesCS3D01G218900 chr3B 88.354 1391 59 37 2 1303 393228920 393230296 0.000000e+00 1576
2 TraesCS3D01G218900 chr3B 91.250 640 44 8 1316 1951 393230205 393230836 0.000000e+00 861
3 TraesCS3D01G218900 chr3B 90.852 634 32 12 2249 2871 393246399 393247017 0.000000e+00 826
4 TraesCS3D01G218900 chr3B 94.872 78 2 1 2135 2212 130128828 130128753 1.420000e-23 121
5 TraesCS3D01G218900 chr3B 91.011 89 2 5 2135 2222 657345241 657345158 6.590000e-22 115
6 TraesCS3D01G218900 chr3A 93.529 850 47 5 1291 2136 395762197 395763042 0.000000e+00 1258
7 TraesCS3D01G218900 chr3A 97.009 702 18 2 2211 2911 395763111 395763810 0.000000e+00 1177
8 TraesCS3D01G218900 chr3A 89.263 801 43 22 1 788 395760966 395761736 0.000000e+00 963
9 TraesCS3D01G218900 chr3A 90.449 534 44 5 789 1319 395761768 395762297 0.000000e+00 697
10 TraesCS3D01G218900 chr7D 96.000 75 1 1 2135 2209 418729659 418729587 1.420000e-23 121
11 TraesCS3D01G218900 chr7B 96.000 75 1 1 2135 2209 640932075 640932003 1.420000e-23 121
12 TraesCS3D01G218900 chr5B 96.000 75 1 1 2135 2209 655250562 655250634 1.420000e-23 121
13 TraesCS3D01G218900 chr2A 96.000 75 1 1 2135 2209 3779054 3779126 1.420000e-23 121
14 TraesCS3D01G218900 chr2A 94.805 77 2 1 2135 2211 760159161 760159235 5.100000e-23 119
15 TraesCS3D01G218900 chr7A 94.805 77 2 1 2135 2211 618186309 618186383 5.100000e-23 119
16 TraesCS3D01G218900 chr6A 94.667 75 2 1 2135 2209 10113059 10113131 6.590000e-22 115


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 TraesCS3D01G218900 chr3D 298058819 298061729 2910 False 5376.00 5376 100.0000 1 2911 1 chr3D.!!$F1 2910
1 TraesCS3D01G218900 chr3B 393228920 393230836 1916 False 1218.50 1576 89.8020 2 1951 2 chr3B.!!$F2 1949
2 TraesCS3D01G218900 chr3B 393246399 393247017 618 False 826.00 826 90.8520 2249 2871 1 chr3B.!!$F1 622
3 TraesCS3D01G218900 chr3A 395760966 395763810 2844 False 1023.75 1258 92.5625 1 2911 4 chr3A.!!$F1 2910

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
434 444 0.543883 TTGCAGAGACTGGGAGAGCT 60.544 55.0 0.0 0.0 31.21 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2179 2278 0.036294 GAAAAGGAGGACGACCCCTG 60.036 60.0 12.98 0.0 37.09 4.45 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
30 32 5.104941 TCCATGTAGATCAAACCGAATGTCT 60.105 40.000 0.00 0.00 0.00 3.41
61 63 0.885879 TTCTGCTGCATGCCTGAAAG 59.114 50.000 16.68 6.41 42.00 2.62
82 84 2.675348 GGCTGAAGCTATCACTGACAAC 59.325 50.000 1.74 0.00 41.70 3.32
83 85 2.675348 GCTGAAGCTATCACTGACAACC 59.325 50.000 0.00 0.00 38.21 3.77
434 444 0.543883 TTGCAGAGACTGGGAGAGCT 60.544 55.000 0.00 0.00 31.21 4.09
452 462 1.403780 GCTATTCACAGGGAACGTCGT 60.404 52.381 0.00 0.00 38.60 4.34
510 525 1.450312 CCCACTGGATGAGCGGAAC 60.450 63.158 0.00 0.00 0.00 3.62
637 652 2.682856 AGACGTGATGTTTTGCACTGTT 59.317 40.909 0.00 0.00 32.98 3.16
638 653 3.128589 AGACGTGATGTTTTGCACTGTTT 59.871 39.130 0.00 0.00 32.98 2.83
640 655 3.857093 ACGTGATGTTTTGCACTGTTTTC 59.143 39.130 0.00 0.00 32.98 2.29
642 657 5.163703 ACGTGATGTTTTGCACTGTTTTCTA 60.164 36.000 0.00 0.00 32.98 2.10
643 658 5.396362 CGTGATGTTTTGCACTGTTTTCTAG 59.604 40.000 0.00 0.00 32.98 2.43
644 659 6.265577 GTGATGTTTTGCACTGTTTTCTAGT 58.734 36.000 0.00 0.00 32.44 2.57
646 661 6.751425 TGATGTTTTGCACTGTTTTCTAGTTG 59.249 34.615 0.00 0.00 0.00 3.16
647 662 6.260870 TGTTTTGCACTGTTTTCTAGTTGA 57.739 33.333 0.00 0.00 0.00 3.18
648 663 6.090129 TGTTTTGCACTGTTTTCTAGTTGAC 58.910 36.000 0.00 0.00 0.00 3.18
678 700 0.937304 CTGACACGTGTTGGAGTTGG 59.063 55.000 24.26 3.55 0.00 3.77
734 763 3.173151 TCATCTAGAACCTGCTTGTCCA 58.827 45.455 0.00 0.00 0.00 4.02
738 767 1.966451 GAACCTGCTTGTCCACCCG 60.966 63.158 0.00 0.00 0.00 5.28
756 792 1.398390 CCGCTTGTTATCTGGTTCTGC 59.602 52.381 0.00 0.00 0.00 4.26
788 824 0.931702 TGCGTGAACGTAACCAACAG 59.068 50.000 4.59 0.00 42.22 3.16
789 825 1.210870 GCGTGAACGTAACCAACAGA 58.789 50.000 4.59 0.00 42.22 3.41
790 826 1.796459 GCGTGAACGTAACCAACAGAT 59.204 47.619 4.59 0.00 42.22 2.90
791 827 2.222445 GCGTGAACGTAACCAACAGATT 59.778 45.455 4.59 0.00 42.22 2.40
792 828 3.429543 GCGTGAACGTAACCAACAGATTA 59.570 43.478 4.59 0.00 42.22 1.75
793 829 4.664891 GCGTGAACGTAACCAACAGATTAC 60.665 45.833 4.59 0.00 42.22 1.89
843 913 2.413310 ATATGTGGTTCGGTTGGGTC 57.587 50.000 0.00 0.00 0.00 4.46
956 1026 1.702957 ACCAGCAACTAAGGCTTGGTA 59.297 47.619 16.99 0.00 40.23 3.25
1030 1100 3.453717 TGAGATCTGCCTGTTAGCAATCT 59.546 43.478 0.00 9.43 43.52 2.40
1063 1133 0.539051 CCCCTCCGGATGATGATAGC 59.461 60.000 3.57 0.00 0.00 2.97
1065 1135 1.566211 CCTCCGGATGATGATAGCCT 58.434 55.000 3.57 0.00 0.00 4.58
1068 1138 1.002430 TCCGGATGATGATAGCCTTGC 59.998 52.381 0.00 0.00 0.00 4.01
1083 1153 2.360165 GCCTTGCTATCCATGTCTTTGG 59.640 50.000 0.00 0.00 38.18 3.28
1166 1236 3.083997 GACCTGGATCCGCACCCT 61.084 66.667 7.39 0.00 0.00 4.34
1172 1242 3.785859 GATCCGCACCCTCTGCCA 61.786 66.667 0.00 0.00 43.84 4.92
1217 1305 4.462280 CCTTACCCGCCACCGTCC 62.462 72.222 0.00 0.00 0.00 4.79
1226 1314 4.135153 CCACCGTCCGAGCCAGAG 62.135 72.222 0.00 0.00 0.00 3.35
1227 1315 4.803426 CACCGTCCGAGCCAGAGC 62.803 72.222 0.00 0.00 40.32 4.09
1230 1318 4.803426 CGTCCGAGCCAGAGCCAC 62.803 72.222 0.00 0.00 41.25 5.01
1231 1319 4.803426 GTCCGAGCCAGAGCCACG 62.803 72.222 0.00 0.00 41.25 4.94
1238 1326 4.463879 CCAGAGCCACGGCCAGAG 62.464 72.222 2.24 0.00 43.17 3.35
1249 1337 3.458653 GCCAGAGCCAAAGCCAAA 58.541 55.556 0.00 0.00 41.25 3.28
1250 1338 1.291272 GCCAGAGCCAAAGCCAAAG 59.709 57.895 0.00 0.00 41.25 2.77
1251 1339 1.291272 CCAGAGCCAAAGCCAAAGC 59.709 57.895 0.00 0.00 41.25 3.51
1252 1340 1.291272 CAGAGCCAAAGCCAAAGCC 59.709 57.895 0.00 0.00 41.25 4.35
1253 1341 1.154688 AGAGCCAAAGCCAAAGCCT 59.845 52.632 0.00 0.00 41.25 4.58
1254 1342 0.897401 AGAGCCAAAGCCAAAGCCTC 60.897 55.000 0.00 0.00 41.25 4.70
1255 1343 1.152483 AGCCAAAGCCAAAGCCTCA 60.152 52.632 0.00 0.00 41.25 3.86
1256 1344 1.183676 AGCCAAAGCCAAAGCCTCAG 61.184 55.000 0.00 0.00 41.25 3.35
1257 1345 1.291272 CCAAAGCCAAAGCCTCAGC 59.709 57.895 0.00 0.00 41.25 4.26
1258 1346 1.291272 CAAAGCCAAAGCCTCAGCC 59.709 57.895 0.00 0.00 41.25 4.85
1259 1347 1.154688 AAAGCCAAAGCCTCAGCCT 59.845 52.632 0.00 0.00 41.25 4.58
1260 1348 1.183676 AAAGCCAAAGCCTCAGCCTG 61.184 55.000 0.00 0.00 41.25 4.85
1261 1349 2.034687 GCCAAAGCCTCAGCCTGA 59.965 61.111 0.00 0.00 41.25 3.86
1262 1350 2.045131 GCCAAAGCCTCAGCCTGAG 61.045 63.158 14.99 14.99 43.91 3.35
1263 1351 2.045131 CCAAAGCCTCAGCCTGAGC 61.045 63.158 16.49 11.53 42.98 4.26
1264 1352 2.045131 CAAAGCCTCAGCCTGAGCC 61.045 63.158 16.49 5.24 42.98 4.70
1265 1353 2.229928 AAAGCCTCAGCCTGAGCCT 61.230 57.895 16.49 7.92 42.98 4.58
1266 1354 2.481307 AAAGCCTCAGCCTGAGCCTG 62.481 60.000 16.49 4.20 42.98 4.85
1267 1355 3.397439 GCCTCAGCCTGAGCCTGA 61.397 66.667 16.49 0.00 42.98 3.86
1268 1356 2.901813 CCTCAGCCTGAGCCTGAG 59.098 66.667 16.49 13.12 42.98 3.35
1269 1357 2.187424 CTCAGCCTGAGCCTGAGC 59.813 66.667 9.13 0.00 37.72 4.26
1270 1358 3.388703 CTCAGCCTGAGCCTGAGCC 62.389 68.421 9.13 0.00 37.72 4.70
1271 1359 3.714001 CAGCCTGAGCCTGAGCCA 61.714 66.667 0.00 0.00 41.25 4.75
1272 1360 3.715097 AGCCTGAGCCTGAGCCAC 61.715 66.667 0.00 0.00 41.25 5.01
1280 1368 4.020617 CCTGAGCCACAGCCGGAA 62.021 66.667 5.05 0.00 44.52 4.30
1316 1404 2.643232 GCCAGAGCCAAAGCCCAAG 61.643 63.158 0.00 0.00 41.25 3.61
1319 1407 2.283460 GAGCCAAAGCCCAAGCCT 60.283 61.111 0.00 0.00 41.25 4.58
1320 1408 2.283460 AGCCAAAGCCCAAGCCTC 60.283 61.111 0.00 0.00 41.25 4.70
1325 1413 2.849962 AAAGCCCAAGCCTCAGCCT 61.850 57.895 0.00 0.00 41.25 4.58
1331 1419 2.610233 AAGCCTCAGCCTGAGCCT 60.610 61.111 16.49 7.92 42.98 4.58
1332 1420 2.969162 AAGCCTCAGCCTGAGCCTG 61.969 63.158 16.49 4.20 42.98 4.85
1333 1421 3.397439 GCCTCAGCCTGAGCCTGA 61.397 66.667 16.49 0.00 42.98 3.86
1334 1422 2.901813 CCTCAGCCTGAGCCTGAG 59.098 66.667 16.49 13.12 42.98 3.35
1335 1423 2.187424 CTCAGCCTGAGCCTGAGC 59.813 66.667 9.13 0.00 37.72 4.26
1336 1424 3.388703 CTCAGCCTGAGCCTGAGCC 62.389 68.421 9.13 0.00 37.72 4.70
1337 1425 3.714001 CAGCCTGAGCCTGAGCCA 61.714 66.667 0.00 0.00 41.25 4.75
1338 1426 3.715097 AGCCTGAGCCTGAGCCAC 61.715 66.667 0.00 0.00 41.25 5.01
1339 1427 4.025858 GCCTGAGCCTGAGCCACA 62.026 66.667 0.00 0.00 41.25 4.17
1340 1428 2.268280 CCTGAGCCTGAGCCACAG 59.732 66.667 2.06 2.06 45.36 3.66
1341 1429 2.436292 CTGAGCCTGAGCCACAGC 60.436 66.667 3.37 0.52 44.52 4.40
1342 1430 3.972971 CTGAGCCTGAGCCACAGCC 62.973 68.421 3.37 0.00 44.52 4.85
1346 1434 4.020617 CCTGAGCCACAGCCGGAA 62.021 66.667 5.05 0.00 44.52 4.30
1347 1435 2.743928 CTGAGCCACAGCCGGAAC 60.744 66.667 5.05 0.00 41.25 3.62
1348 1436 4.329545 TGAGCCACAGCCGGAACC 62.330 66.667 5.05 0.00 41.25 3.62
1349 1437 4.329545 GAGCCACAGCCGGAACCA 62.330 66.667 5.05 0.00 41.25 3.67
1350 1438 4.335647 AGCCACAGCCGGAACCAG 62.336 66.667 5.05 0.00 41.25 4.00
1351 1439 4.329545 GCCACAGCCGGAACCAGA 62.330 66.667 5.05 0.00 0.00 3.86
1352 1440 2.046892 CCACAGCCGGAACCAGAG 60.047 66.667 5.05 0.00 0.00 3.35
1353 1441 2.743928 CACAGCCGGAACCAGAGC 60.744 66.667 5.05 0.00 0.00 4.09
1354 1442 4.021925 ACAGCCGGAACCAGAGCC 62.022 66.667 5.05 0.00 0.00 4.70
1361 1449 2.125350 GAACCAGAGCCTGAGCCG 60.125 66.667 4.00 0.00 41.25 5.52
1612 1706 0.889186 AGCATGTTCAACCCGTCCAC 60.889 55.000 0.00 0.00 0.00 4.02
1637 1731 2.636412 CCGGAAGCTCTGTCGTGGA 61.636 63.158 0.00 0.00 0.00 4.02
1647 1741 2.959030 CTCTGTCGTGGAATATCCTCCA 59.041 50.000 0.00 0.00 43.45 3.86
1707 1802 6.936900 ACTGACATTGCTCATATAATGTACCC 59.063 38.462 0.00 0.00 44.88 3.69
1712 1807 7.998383 ACATTGCTCATATAATGTACCCAGAAA 59.002 33.333 0.00 0.00 43.54 2.52
1752 1847 3.896888 TGAACCTGATCAGCAACCAATTT 59.103 39.130 17.76 0.00 0.00 1.82
1754 1849 3.233507 ACCTGATCAGCAACCAATTTGT 58.766 40.909 17.76 2.75 37.54 2.83
1787 1882 0.100682 TTCCGCTGACGATGCTACTC 59.899 55.000 0.00 0.00 43.93 2.59
1793 1888 2.803451 CTGACGATGCTACTCCTGTTC 58.197 52.381 0.00 0.00 0.00 3.18
1794 1889 2.164422 CTGACGATGCTACTCCTGTTCA 59.836 50.000 0.00 0.00 0.00 3.18
1795 1890 2.760650 TGACGATGCTACTCCTGTTCAT 59.239 45.455 0.00 0.00 0.00 2.57
1799 1894 5.003804 ACGATGCTACTCCTGTTCATTTTT 58.996 37.500 0.00 0.00 0.00 1.94
1843 1939 6.357240 GTGTAACTCTGAAAGAAAAATGCGAC 59.643 38.462 0.00 0.00 46.34 5.19
1883 1979 2.399356 TTCGTGCGTGTGGTGCAAA 61.399 52.632 0.00 0.00 45.23 3.68
1942 2038 2.047151 CTCCGTCTCTCTCAGCGAGC 62.047 65.000 0.00 0.00 39.70 5.03
2056 2152 5.013568 ACGATTATGTCACCGGATAACAA 57.986 39.130 9.46 0.00 0.00 2.83
2066 2165 2.353579 ACCGGATAACAATTACTTGCGC 59.646 45.455 9.46 0.00 35.69 6.09
2083 2182 1.470098 GCGCTGTCAGGTCATCAAAAT 59.530 47.619 0.00 0.00 0.00 1.82
2106 2205 1.013596 CACGGAACAAACTGCACTGA 58.986 50.000 0.00 0.00 0.00 3.41
2120 2219 2.902486 TGCACTGATCAGGAAGAGTTCT 59.098 45.455 26.08 0.00 0.00 3.01
2136 2235 9.310449 GGAAGAGTTCTCAGGTATACCAATATA 57.690 37.037 23.87 3.50 38.89 0.86
2161 2260 3.829886 ATAAAATGGCCGTATGCATCG 57.170 42.857 0.19 7.03 43.89 3.84
2162 2261 1.388547 AAAATGGCCGTATGCATCGT 58.611 45.000 0.19 0.00 43.89 3.73
2164 2263 0.884704 AATGGCCGTATGCATCGTCC 60.885 55.000 0.19 7.07 43.89 4.79
2165 2264 2.038814 ATGGCCGTATGCATCGTCCA 62.039 55.000 18.67 18.67 43.89 4.02
2166 2265 1.956170 GGCCGTATGCATCGTCCAG 60.956 63.158 0.19 0.00 43.89 3.86
2167 2266 1.067416 GCCGTATGCATCGTCCAGA 59.933 57.895 0.19 0.00 40.77 3.86
2168 2267 0.319900 GCCGTATGCATCGTCCAGAT 60.320 55.000 0.19 0.00 41.01 2.90
2178 2277 1.227205 CGTCCAGATGCAGAGAGGC 60.227 63.158 0.00 0.00 0.00 4.70
2179 2278 1.145819 GTCCAGATGCAGAGAGGCC 59.854 63.158 0.00 0.00 0.00 5.19
2180 2279 1.306397 TCCAGATGCAGAGAGGCCA 60.306 57.895 5.01 0.00 0.00 5.36
2181 2280 1.146485 CCAGATGCAGAGAGGCCAG 59.854 63.158 5.01 0.00 0.00 4.85
2182 2281 1.146485 CAGATGCAGAGAGGCCAGG 59.854 63.158 5.01 0.00 0.00 4.45
2183 2282 2.071262 AGATGCAGAGAGGCCAGGG 61.071 63.158 5.01 0.00 0.00 4.45
2184 2283 3.095163 ATGCAGAGAGGCCAGGGG 61.095 66.667 5.01 0.00 0.00 4.79
2185 2284 3.958629 ATGCAGAGAGGCCAGGGGT 62.959 63.158 5.01 0.00 0.00 4.95
2186 2285 3.791586 GCAGAGAGGCCAGGGGTC 61.792 72.222 5.01 0.00 0.00 4.46
2187 2286 3.465403 CAGAGAGGCCAGGGGTCG 61.465 72.222 5.01 0.00 29.39 4.79
2188 2287 3.999285 AGAGAGGCCAGGGGTCGT 61.999 66.667 5.01 0.00 29.39 4.34
2189 2288 3.462678 GAGAGGCCAGGGGTCGTC 61.463 72.222 5.01 0.00 29.39 4.20
2195 2294 2.284699 CCAGGGGTCGTCCTCCTT 60.285 66.667 6.10 0.00 33.94 3.36
2196 2295 1.918800 CCAGGGGTCGTCCTCCTTT 60.919 63.158 6.10 0.00 33.94 3.11
2197 2296 1.489560 CCAGGGGTCGTCCTCCTTTT 61.490 60.000 6.10 0.00 33.94 2.27
2198 2297 0.036294 CAGGGGTCGTCCTCCTTTTC 60.036 60.000 6.10 0.00 33.94 2.29
2199 2298 0.178900 AGGGGTCGTCCTCCTTTTCT 60.179 55.000 0.00 0.00 33.94 2.52
2201 2300 1.904537 GGGGTCGTCCTCCTTTTCTAA 59.095 52.381 0.00 0.00 35.33 2.10
2202 2301 2.303890 GGGGTCGTCCTCCTTTTCTAAA 59.696 50.000 0.00 0.00 35.33 1.85
2203 2302 3.244665 GGGGTCGTCCTCCTTTTCTAAAA 60.245 47.826 0.00 0.00 35.33 1.52
2204 2303 4.392047 GGGTCGTCCTCCTTTTCTAAAAA 58.608 43.478 0.00 0.00 0.00 1.94
2349 2448 2.270257 GCAGGCACACAAGGCATCA 61.270 57.895 0.00 0.00 36.37 3.07
2372 2471 1.660355 CCGACCGATCATCCGACAT 59.340 57.895 0.00 0.00 0.00 3.06
2373 2472 0.664466 CCGACCGATCATCCGACATG 60.664 60.000 0.00 0.00 0.00 3.21
2641 2745 5.009110 CAGACTCGATCCTGCAATTAGTAGA 59.991 44.000 1.94 0.00 30.56 2.59
2683 2787 6.925718 CAGAGAGTATCCGATGCAAAATTAGA 59.074 38.462 0.00 0.00 33.66 2.10
2778 2882 5.906073 ACAAGTTCAAGTTTCATTTGGGAG 58.094 37.500 0.00 0.00 0.00 4.30
2781 2885 5.208121 AGTTCAAGTTTCATTTGGGAGGAA 58.792 37.500 0.00 0.00 0.00 3.36
2782 2886 5.660864 AGTTCAAGTTTCATTTGGGAGGAAA 59.339 36.000 0.00 0.00 0.00 3.13
2783 2887 5.789643 TCAAGTTTCATTTGGGAGGAAAG 57.210 39.130 0.00 0.00 31.75 2.62
2784 2888 5.454062 TCAAGTTTCATTTGGGAGGAAAGA 58.546 37.500 0.00 0.00 31.75 2.52
2869 2977 4.806892 TGGGCACAGATTTATGGAATCAT 58.193 39.130 0.00 0.00 45.42 2.45
2870 2978 5.210430 TGGGCACAGATTTATGGAATCATT 58.790 37.500 0.00 0.00 45.42 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 32 1.949525 GCAGCAGAACCAGTTTCTCAA 59.050 47.619 0.00 0.00 43.23 3.02
61 63 2.675348 GTTGTCAGTGATAGCTTCAGCC 59.325 50.000 0.00 0.00 43.38 4.85
62 64 2.675348 GGTTGTCAGTGATAGCTTCAGC 59.325 50.000 0.00 0.00 42.49 4.26
63 65 3.265791 GGGTTGTCAGTGATAGCTTCAG 58.734 50.000 0.00 0.00 34.17 3.02
64 66 2.027192 GGGGTTGTCAGTGATAGCTTCA 60.027 50.000 0.00 0.00 0.00 3.02
65 67 2.633488 GGGGTTGTCAGTGATAGCTTC 58.367 52.381 0.00 0.00 0.00 3.86
66 68 1.282157 GGGGGTTGTCAGTGATAGCTT 59.718 52.381 0.00 0.00 0.00 3.74
67 69 0.912486 GGGGGTTGTCAGTGATAGCT 59.088 55.000 0.00 0.00 0.00 3.32
68 70 3.478540 GGGGGTTGTCAGTGATAGC 57.521 57.895 0.00 0.00 0.00 2.97
89 91 0.250467 GCTCCTGCACCAAGTCAAGA 60.250 55.000 0.00 0.00 39.41 3.02
434 444 1.670674 GCACGACGTTCCCTGTGAATA 60.671 52.381 0.00 0.00 34.90 1.75
510 525 9.804758 AACTAGAAATATCTACCGTCTTCTTTG 57.195 33.333 0.00 0.00 37.10 2.77
659 681 0.937304 CCAACTCCAACACGTGTCAG 59.063 55.000 23.61 19.35 0.00 3.51
734 763 1.628846 AGAACCAGATAACAAGCGGGT 59.371 47.619 0.00 0.00 0.00 5.28
738 767 2.436417 TGGCAGAACCAGATAACAAGC 58.564 47.619 0.00 0.00 46.36 4.01
756 792 1.063006 CACGCATCATTCGGCTTGG 59.937 57.895 0.00 0.00 0.00 3.61
812 882 5.163561 CCGAACCACATATTAGTGCCATTTT 60.164 40.000 0.00 0.00 38.18 1.82
843 913 2.746362 CTCTGTTTCTGCAAAGCTAGGG 59.254 50.000 0.00 0.00 0.00 3.53
956 1026 7.624549 ACATCGCCTTATATATGAACTGGATT 58.375 34.615 0.00 0.00 0.00 3.01
1030 1100 0.895100 GAGGGGCAGCATTTGTGTCA 60.895 55.000 0.00 0.00 0.00 3.58
1063 1133 3.624777 ACCAAAGACATGGATAGCAAGG 58.375 45.455 0.00 0.00 43.54 3.61
1065 1135 4.406456 ACAACCAAAGACATGGATAGCAA 58.594 39.130 0.00 0.00 43.54 3.91
1068 1138 5.241506 ACACAACAACCAAAGACATGGATAG 59.758 40.000 0.00 0.00 43.54 2.08
1083 1153 1.039856 ATTGCAGGGGACACAACAAC 58.960 50.000 0.00 0.00 32.44 3.32
1199 1269 4.462280 GACGGTGGCGGGTAAGGG 62.462 72.222 0.00 0.00 0.00 3.95
1221 1309 4.463879 CTCTGGCCGTGGCTCTGG 62.464 72.222 11.25 0.00 41.60 3.86
1232 1320 1.291272 CTTTGGCTTTGGCTCTGGC 59.709 57.895 0.00 0.00 38.73 4.85
1233 1321 1.291272 GCTTTGGCTTTGGCTCTGG 59.709 57.895 0.00 0.00 38.73 3.86
1234 1322 1.183676 AGGCTTTGGCTTTGGCTCTG 61.184 55.000 0.00 0.00 33.67 3.35
1235 1323 0.897401 GAGGCTTTGGCTTTGGCTCT 60.897 55.000 15.85 3.26 45.85 4.09
1236 1324 1.588597 GAGGCTTTGGCTTTGGCTC 59.411 57.895 10.53 10.53 43.97 4.70
1237 1325 1.152483 TGAGGCTTTGGCTTTGGCT 60.152 52.632 0.00 0.00 38.98 4.75
1238 1326 1.291272 CTGAGGCTTTGGCTTTGGC 59.709 57.895 0.00 0.00 38.98 4.52
1239 1327 1.291272 GCTGAGGCTTTGGCTTTGG 59.709 57.895 0.00 0.00 38.98 3.28
1240 1328 1.183676 AGGCTGAGGCTTTGGCTTTG 61.184 55.000 1.28 0.00 38.98 2.77
1241 1329 1.154688 AGGCTGAGGCTTTGGCTTT 59.845 52.632 1.28 0.00 38.98 3.51
1242 1330 1.605738 CAGGCTGAGGCTTTGGCTT 60.606 57.895 9.42 0.96 38.98 4.35
1243 1331 2.035312 CAGGCTGAGGCTTTGGCT 59.965 61.111 9.42 10.14 42.48 4.75
1244 1332 2.034687 TCAGGCTGAGGCTTTGGC 59.965 61.111 14.43 6.21 35.88 4.52
1245 1333 2.045131 GCTCAGGCTGAGGCTTTGG 61.045 63.158 37.73 18.02 44.43 3.28
1246 1334 3.588336 GCTCAGGCTGAGGCTTTG 58.412 61.111 37.73 18.69 44.43 2.77
1255 1343 3.715097 GTGGCTCAGGCTCAGGCT 61.715 66.667 14.06 0.00 39.66 4.58
1256 1344 3.972971 CTGTGGCTCAGGCTCAGGC 62.973 68.421 19.93 4.61 40.23 4.85
1257 1345 2.268280 CTGTGGCTCAGGCTCAGG 59.732 66.667 19.93 4.32 40.23 3.86
1258 1346 2.436292 GCTGTGGCTCAGGCTCAG 60.436 66.667 22.59 22.59 43.78 3.35
1263 1351 4.020617 TTCCGGCTGTGGCTCAGG 62.021 66.667 17.40 3.09 43.78 3.86
1264 1352 2.743928 GTTCCGGCTGTGGCTCAG 60.744 66.667 12.07 12.07 46.12 3.35
1265 1353 4.329545 GGTTCCGGCTGTGGCTCA 62.330 66.667 0.00 0.00 38.73 4.26
1266 1354 4.329545 TGGTTCCGGCTGTGGCTC 62.330 66.667 0.00 0.00 38.73 4.70
1267 1355 4.335647 CTGGTTCCGGCTGTGGCT 62.336 66.667 0.00 0.00 38.73 4.75
1268 1356 4.329545 TCTGGTTCCGGCTGTGGC 62.330 66.667 0.00 0.00 37.82 5.01
1269 1357 2.046892 CTCTGGTTCCGGCTGTGG 60.047 66.667 0.00 0.00 0.00 4.17
1270 1358 2.743928 GCTCTGGTTCCGGCTGTG 60.744 66.667 0.00 0.00 0.00 3.66
1271 1359 4.021925 GGCTCTGGTTCCGGCTGT 62.022 66.667 0.00 0.00 0.00 4.40
1272 1360 3.965539 CTGGCTCTGGTTCCGGCTG 62.966 68.421 0.00 0.00 0.00 4.85
1280 1368 3.699894 CGTGGCTCTGGCTCTGGT 61.700 66.667 0.00 0.00 38.73 4.00
1331 1419 4.329545 GGTTCCGGCTGTGGCTCA 62.330 66.667 0.00 0.00 38.73 4.26
1332 1420 4.329545 TGGTTCCGGCTGTGGCTC 62.330 66.667 0.00 0.00 38.73 4.70
1333 1421 4.335647 CTGGTTCCGGCTGTGGCT 62.336 66.667 0.00 0.00 38.73 4.75
1334 1422 4.329545 TCTGGTTCCGGCTGTGGC 62.330 66.667 0.00 0.00 37.82 5.01
1335 1423 2.046892 CTCTGGTTCCGGCTGTGG 60.047 66.667 0.00 0.00 0.00 4.17
1336 1424 2.743928 GCTCTGGTTCCGGCTGTG 60.744 66.667 0.00 0.00 0.00 3.66
1337 1425 4.021925 GGCTCTGGTTCCGGCTGT 62.022 66.667 0.00 0.00 0.00 4.40
1338 1426 3.710722 AGGCTCTGGTTCCGGCTG 61.711 66.667 0.00 0.00 31.88 4.85
1339 1427 3.710722 CAGGCTCTGGTTCCGGCT 61.711 66.667 0.00 0.00 0.00 5.52
1340 1428 3.672295 CTCAGGCTCTGGTTCCGGC 62.672 68.421 0.00 0.00 31.51 6.13
1341 1429 2.581354 CTCAGGCTCTGGTTCCGG 59.419 66.667 0.00 0.00 31.51 5.14
1342 1430 2.125350 GCTCAGGCTCTGGTTCCG 60.125 66.667 2.86 0.00 35.22 4.30
1343 1431 2.270527 GGCTCAGGCTCTGGTTCC 59.729 66.667 0.00 0.00 38.73 3.62
1344 1432 2.125350 CGGCTCAGGCTCTGGTTC 60.125 66.667 0.00 0.00 38.73 3.62
1345 1433 3.710722 CCGGCTCAGGCTCTGGTT 61.711 66.667 0.00 0.00 38.73 3.67
1346 1434 4.704103 TCCGGCTCAGGCTCTGGT 62.704 66.667 0.00 0.00 38.73 4.00
1347 1435 3.847602 CTCCGGCTCAGGCTCTGG 61.848 72.222 0.00 0.00 38.73 3.86
1348 1436 4.527583 GCTCCGGCTCAGGCTCTG 62.528 72.222 0.00 0.00 38.73 3.35
1353 1441 3.847602 CTCAGGCTCCGGCTCAGG 61.848 72.222 0.00 0.00 35.88 3.86
1354 1442 4.527583 GCTCAGGCTCCGGCTCAG 62.528 72.222 0.00 0.00 35.88 3.35
1386 1474 3.640407 TGGCTTCGGCTCTGGCTT 61.640 61.111 0.00 0.00 41.44 4.35
1391 1479 3.630013 TGCTGTGGCTTCGGCTCT 61.630 61.111 13.21 0.00 40.06 4.09
1637 1731 4.366267 AGGCGAGGAATATGGAGGATATT 58.634 43.478 0.00 0.00 39.56 1.28
1647 1741 2.096248 GATCGAGGAGGCGAGGAATAT 58.904 52.381 0.00 0.00 44.26 1.28
1650 1744 2.187493 CGATCGAGGAGGCGAGGAA 61.187 63.158 10.26 0.00 44.26 3.36
1652 1746 2.902846 ACGATCGAGGAGGCGAGG 60.903 66.667 24.34 0.00 44.26 4.63
1686 1780 7.078249 TCTGGGTACATTATATGAGCAATGT 57.922 36.000 6.77 6.77 45.07 2.71
1707 1802 5.100751 GTCTGTGGACTGAATGTTTTCTG 57.899 43.478 0.00 0.00 39.24 3.02
1752 1847 4.273235 CAGCGGAATGAAGCATTACATACA 59.727 41.667 3.54 0.00 34.57 2.29
1754 1849 4.511454 GTCAGCGGAATGAAGCATTACATA 59.489 41.667 3.54 0.00 34.57 2.29
1799 1894 5.885449 ACACATTTGAAATGAAGGGGAAA 57.115 34.783 23.37 0.00 0.00 3.13
1843 1939 7.220683 ACGAACAAATTCAAAGTTCAACATCAG 59.779 33.333 0.00 0.00 41.17 2.90
1942 2038 0.248498 CTGCATGCCATTCTCTTGCG 60.248 55.000 16.68 0.00 37.40 4.85
2031 2127 7.451501 TGTTATCCGGTGACATAATCGTATA 57.548 36.000 0.00 0.00 0.00 1.47
2056 2152 1.001974 TGACCTGACAGCGCAAGTAAT 59.998 47.619 11.47 0.00 41.68 1.89
2066 2165 2.730090 GCGCATTTTGATGACCTGACAG 60.730 50.000 0.30 0.00 0.00 3.51
2083 2182 2.712539 CAGTTTGTTCCGTGCGCA 59.287 55.556 5.66 5.66 0.00 6.09
2106 2205 5.836358 GGTATACCTGAGAACTCTTCCTGAT 59.164 44.000 15.09 0.00 0.00 2.90
2136 2235 6.806249 CGATGCATACGGCCATTTTATTAATT 59.194 34.615 2.24 0.00 43.89 1.40
2139 2238 4.757657 ACGATGCATACGGCCATTTTATTA 59.242 37.500 18.34 0.00 43.89 0.98
2140 2239 3.568007 ACGATGCATACGGCCATTTTATT 59.432 39.130 18.34 0.00 43.89 1.40
2141 2240 3.146066 ACGATGCATACGGCCATTTTAT 58.854 40.909 18.34 0.00 43.89 1.40
2142 2241 2.546368 GACGATGCATACGGCCATTTTA 59.454 45.455 18.34 0.00 43.89 1.52
2143 2242 1.333619 GACGATGCATACGGCCATTTT 59.666 47.619 18.34 1.14 43.89 1.82
2144 2243 0.944386 GACGATGCATACGGCCATTT 59.056 50.000 18.34 0.00 43.89 2.32
2145 2244 2.616969 GACGATGCATACGGCCATT 58.383 52.632 18.34 0.00 43.89 3.16
2149 2248 0.319900 ATCTGGACGATGCATACGGC 60.320 55.000 18.34 16.22 45.13 5.68
2158 2257 1.039068 CCTCTCTGCATCTGGACGAT 58.961 55.000 0.00 0.00 0.00 3.73
2161 2260 1.145819 GGCCTCTCTGCATCTGGAC 59.854 63.158 0.00 0.00 0.00 4.02
2162 2261 1.306397 TGGCCTCTCTGCATCTGGA 60.306 57.895 3.32 0.00 0.00 3.86
2164 2263 1.146485 CCTGGCCTCTCTGCATCTG 59.854 63.158 3.32 0.00 0.00 2.90
2165 2264 2.071262 CCCTGGCCTCTCTGCATCT 61.071 63.158 3.32 0.00 0.00 2.90
2166 2265 2.509916 CCCTGGCCTCTCTGCATC 59.490 66.667 3.32 0.00 0.00 3.91
2167 2266 3.095163 CCCCTGGCCTCTCTGCAT 61.095 66.667 3.32 0.00 0.00 3.96
2168 2267 4.664267 ACCCCTGGCCTCTCTGCA 62.664 66.667 3.32 0.00 0.00 4.41
2169 2268 3.791586 GACCCCTGGCCTCTCTGC 61.792 72.222 3.32 0.00 0.00 4.26
2170 2269 3.465403 CGACCCCTGGCCTCTCTG 61.465 72.222 3.32 0.00 0.00 3.35
2172 2271 3.462678 GACGACCCCTGGCCTCTC 61.463 72.222 3.32 0.00 0.00 3.20
2178 2277 1.489560 AAAAGGAGGACGACCCCTGG 61.490 60.000 12.98 0.00 37.09 4.45
2179 2278 0.036294 GAAAAGGAGGACGACCCCTG 60.036 60.000 12.98 0.00 37.09 4.45
2180 2279 0.178900 AGAAAAGGAGGACGACCCCT 60.179 55.000 0.00 4.23 38.08 4.79
2181 2280 1.565067 TAGAAAAGGAGGACGACCCC 58.435 55.000 0.00 1.75 36.73 4.95
2182 2281 3.690475 TTTAGAAAAGGAGGACGACCC 57.310 47.619 0.00 0.00 36.73 4.46
2204 2303 8.511321 TCTTGATACAATACTTGTGCGATTTTT 58.489 29.630 2.85 0.00 45.03 1.94
2205 2304 8.039603 TCTTGATACAATACTTGTGCGATTTT 57.960 30.769 2.85 0.00 45.03 1.82
2206 2305 7.609760 TCTTGATACAATACTTGTGCGATTT 57.390 32.000 2.85 0.00 45.03 2.17
2207 2306 6.238211 GCTCTTGATACAATACTTGTGCGATT 60.238 38.462 2.85 0.00 45.03 3.34
2208 2307 5.235186 GCTCTTGATACAATACTTGTGCGAT 59.765 40.000 2.85 0.00 45.03 4.58
2209 2308 4.566759 GCTCTTGATACAATACTTGTGCGA 59.433 41.667 2.85 0.00 45.03 5.10
2349 2448 1.244697 CGGATGATCGGTCGGGATCT 61.245 60.000 11.45 1.09 42.63 2.75
2372 2471 3.417224 CGACCTCGACGACGTCCA 61.417 66.667 21.63 8.86 43.02 4.02
2373 2472 3.114616 TCGACCTCGACGACGTCC 61.115 66.667 21.63 6.76 44.22 4.79
2641 2745 1.141657 TCTGCAGCCTCTGTTCTGTTT 59.858 47.619 9.47 0.00 33.43 2.83
2683 2787 9.601217 GTACAGGTTGAAATGATAGTAGAACAT 57.399 33.333 0.00 0.00 0.00 2.71
2700 2804 1.163420 TGCCGCAACTGTACAGGTTG 61.163 55.000 26.12 24.22 44.60 3.77
2778 2882 5.221126 GGGCAGACATGTCATATTTCTTTCC 60.221 44.000 27.02 7.97 30.39 3.13
2781 2885 4.858850 TGGGCAGACATGTCATATTTCTT 58.141 39.130 27.02 1.19 30.39 2.52
2782 2886 4.508551 TGGGCAGACATGTCATATTTCT 57.491 40.909 27.02 1.97 30.39 2.52
2783 2887 5.581126 TTTGGGCAGACATGTCATATTTC 57.419 39.130 27.02 11.71 30.39 2.17
2784 2888 5.682990 GCATTTGGGCAGACATGTCATATTT 60.683 40.000 27.02 3.53 30.39 1.40
2879 2987 5.773575 TGTCTAATGATTCCATAGCTCGTC 58.226 41.667 0.00 0.00 31.59 4.20
2882 2990 5.994054 TGCTTGTCTAATGATTCCATAGCTC 59.006 40.000 0.00 0.00 31.52 4.09


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

AutoCloner maintained by Alex Coulton.