Multiple sequence alignment - TraesCS6B01G316500

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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 TraesCS6B01G316500 chr6B 100.000 2315 0 0 1 2315 564308497 564310811 0.000000e+00 4276.0
1 TraesCS6B01G316500 chr3B 95.394 1346 60 1 1 1344 571018235 571019580 0.000000e+00 2141.0
2 TraesCS6B01G316500 chr3B 91.450 1345 112 3 1 1344 808035094 808036436 0.000000e+00 1844.0
3 TraesCS6B01G316500 chr7B 95.167 1345 65 0 1 1345 722949211 722947867 0.000000e+00 2124.0
4 TraesCS6B01G316500 chr1B 95.026 1347 67 0 1 1347 41706535 41705189 0.000000e+00 2117.0
5 TraesCS6B01G316500 chr1B 94.056 1346 77 3 1 1344 31660985 31662329 0.000000e+00 2039.0
6 TraesCS6B01G316500 chr7A 94.577 1346 73 0 1 1346 29988489 29987144 0.000000e+00 2082.0
7 TraesCS6B01G316500 chr7D 88.410 1346 146 10 1 1342 139749775 139748436 0.000000e+00 1613.0
8 TraesCS6B01G316500 chr4D 88.336 1346 148 9 1 1342 482768186 482769526 0.000000e+00 1607.0
9 TraesCS6B01G316500 chr4D 89.583 48 3 1 1350 1397 95820983 95821028 2.480000e-05 60.2
10 TraesCS6B01G316500 chrUn 85.757 1348 182 8 1 1344 298402286 298403627 0.000000e+00 1417.0
11 TraesCS6B01G316500 chr6A 88.447 805 50 18 1397 2197 519234899 519235664 0.000000e+00 931.0
12 TraesCS6B01G316500 chr6D 95.852 458 8 3 1859 2315 377846157 377846604 0.000000e+00 730.0
13 TraesCS6B01G316500 chr6D 87.395 357 37 6 1397 1752 377839979 377840328 9.960000e-109 403.0
14 TraesCS6B01G316500 chr6D 88.889 90 7 2 1780 1867 377840326 377840414 8.750000e-20 108.0
15 TraesCS6B01G316500 chr3D 100.000 31 0 0 1368 1398 27246132 27246162 8.930000e-05 58.4


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 TraesCS6B01G316500 chr6B 564308497 564310811 2314 False 4276 4276 100.000 1 2315 1 chr6B.!!$F1 2314
1 TraesCS6B01G316500 chr3B 571018235 571019580 1345 False 2141 2141 95.394 1 1344 1 chr3B.!!$F1 1343
2 TraesCS6B01G316500 chr3B 808035094 808036436 1342 False 1844 1844 91.450 1 1344 1 chr3B.!!$F2 1343
3 TraesCS6B01G316500 chr7B 722947867 722949211 1344 True 2124 2124 95.167 1 1345 1 chr7B.!!$R1 1344
4 TraesCS6B01G316500 chr1B 41705189 41706535 1346 True 2117 2117 95.026 1 1347 1 chr1B.!!$R1 1346
5 TraesCS6B01G316500 chr1B 31660985 31662329 1344 False 2039 2039 94.056 1 1344 1 chr1B.!!$F1 1343
6 TraesCS6B01G316500 chr7A 29987144 29988489 1345 True 2082 2082 94.577 1 1346 1 chr7A.!!$R1 1345
7 TraesCS6B01G316500 chr7D 139748436 139749775 1339 True 1613 1613 88.410 1 1342 1 chr7D.!!$R1 1341
8 TraesCS6B01G316500 chr4D 482768186 482769526 1340 False 1607 1607 88.336 1 1342 1 chr4D.!!$F2 1341
9 TraesCS6B01G316500 chrUn 298402286 298403627 1341 False 1417 1417 85.757 1 1344 1 chrUn.!!$F1 1343
10 TraesCS6B01G316500 chr6A 519234899 519235664 765 False 931 931 88.447 1397 2197 1 chr6A.!!$F1 800

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
477 481 1.745115 TGCCCTAGTTGCATGCGAC 60.745 57.895 27.71 27.71 32.85 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2203 2210 0.031994 CAGGGGCTTGGTTTGTTTCG 59.968 55.0 0.0 0.0 0.0 3.46 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
61 62 6.426633 TCTCAATCGTGTTTCTGCATTTCTAA 59.573 34.615 0.00 0.00 0.00 2.10
180 184 4.208047 CGATCTGATTTCATCTCGTGGTTC 59.792 45.833 0.00 0.00 0.00 3.62
182 186 3.260632 TCTGATTTCATCTCGTGGTTCCA 59.739 43.478 0.00 0.00 0.00 3.53
400 404 3.650139 CAGAAGTGTAAGGTGCTACGTT 58.350 45.455 0.00 0.00 0.00 3.99
412 416 4.038402 AGGTGCTACGTTATATACCCACAC 59.962 45.833 0.00 0.00 0.00 3.82
413 417 4.038402 GGTGCTACGTTATATACCCACACT 59.962 45.833 0.00 0.00 0.00 3.55
477 481 1.745115 TGCCCTAGTTGCATGCGAC 60.745 57.895 27.71 27.71 32.85 5.19
537 541 2.273912 ACTCCCACCGGACGAGTTC 61.274 63.158 9.46 0.00 33.01 3.01
573 577 4.507335 GGAAGGGAATGGCTTATGCATCTA 60.507 45.833 0.19 0.00 41.91 1.98
574 578 4.729552 AGGGAATGGCTTATGCATCTAA 57.270 40.909 0.19 0.00 41.91 2.10
687 691 3.286751 GCGCCTGTTTCAGCCACA 61.287 61.111 0.00 0.00 0.00 4.17
714 718 6.012858 TGGAGTTCCTGGACAGTTATTACAAT 60.013 38.462 0.00 0.00 36.82 2.71
720 724 8.877864 TCCTGGACAGTTATTACAATTCAATT 57.122 30.769 0.00 0.00 0.00 2.32
740 744 2.256117 AAGCTTGCTGGTCGTTACTT 57.744 45.000 0.00 0.00 0.00 2.24
943 948 4.851843 TCAAGGACAGATCATCTTTGCAT 58.148 39.130 13.76 0.00 34.18 3.96
1144 1149 6.546428 TGGTTCTAGAGATTAAGGAGTTGG 57.454 41.667 0.00 0.00 0.00 3.77
1158 1163 4.695606 AGGAGTTGGTGAGTAATAGGGAA 58.304 43.478 0.00 0.00 0.00 3.97
1264 1269 2.746277 GGTTGCGCTCGGTTCCAT 60.746 61.111 9.73 0.00 0.00 3.41
1386 1391 3.274196 CGTTACAACGCACATGCTC 57.726 52.632 1.04 0.00 46.06 4.26
1387 1392 0.790207 CGTTACAACGCACATGCTCT 59.210 50.000 1.04 0.00 46.06 4.09
1388 1393 1.194547 CGTTACAACGCACATGCTCTT 59.805 47.619 1.04 0.00 46.06 2.85
1389 1394 2.349438 CGTTACAACGCACATGCTCTTT 60.349 45.455 1.04 0.00 46.06 2.52
1390 1395 3.628017 GTTACAACGCACATGCTCTTTT 58.372 40.909 1.82 0.00 39.32 2.27
1391 1396 2.124011 ACAACGCACATGCTCTTTTG 57.876 45.000 1.82 3.17 39.32 2.44
1392 1397 0.780002 CAACGCACATGCTCTTTTGC 59.220 50.000 1.82 0.00 39.32 3.68
1393 1398 0.670162 AACGCACATGCTCTTTTGCT 59.330 45.000 1.82 0.00 39.32 3.91
1394 1399 1.522668 ACGCACATGCTCTTTTGCTA 58.477 45.000 1.82 0.00 39.32 3.49
1395 1400 1.466167 ACGCACATGCTCTTTTGCTAG 59.534 47.619 1.82 0.00 39.32 3.42
1451 1456 6.711194 ACTAGTAAAGCAGGGAGAAGAAAAAC 59.289 38.462 0.00 0.00 0.00 2.43
1466 1471 7.652727 AGAAGAAAAACAAAGGTAGATGAAGC 58.347 34.615 0.00 0.00 0.00 3.86
1469 1474 4.773323 AAACAAAGGTAGATGAAGCTGC 57.227 40.909 0.00 0.00 0.00 5.25
1471 1476 4.026356 ACAAAGGTAGATGAAGCTGCTT 57.974 40.909 15.92 15.92 0.00 3.91
1472 1477 4.401925 ACAAAGGTAGATGAAGCTGCTTT 58.598 39.130 17.10 0.58 0.00 3.51
1476 1481 5.683876 AGGTAGATGAAGCTGCTTTAGAA 57.316 39.130 17.10 3.58 0.00 2.10
1482 1487 7.282332 AGATGAAGCTGCTTTAGAAACTTTT 57.718 32.000 17.10 0.00 0.00 2.27
1484 1489 5.043248 TGAAGCTGCTTTAGAAACTTTTGC 58.957 37.500 17.10 0.00 0.00 3.68
1504 1509 2.224314 GCAGAAACCAACACTAGCAGAC 59.776 50.000 0.00 0.00 0.00 3.51
1531 1536 2.017049 CCCTGAAGATTTTAGCCACCG 58.983 52.381 0.00 0.00 0.00 4.94
1588 1593 4.260784 GGGCGATAAACTTCACTTGCTATG 60.261 45.833 0.00 0.00 0.00 2.23
1611 1616 2.096218 GCTCAACAGTCTTAAACCAGCG 60.096 50.000 0.00 0.00 0.00 5.18
1629 1634 1.730446 GCGTCAGCAGCCTTTGATTTC 60.730 52.381 0.00 0.00 44.35 2.17
1637 1642 3.007290 GCAGCCTTTGATTTCCTCCTTTT 59.993 43.478 0.00 0.00 0.00 2.27
1687 1692 8.470002 AGAAATCCAATAGGCAATCAGTTTAAC 58.530 33.333 0.00 0.00 33.74 2.01
1688 1693 6.715347 ATCCAATAGGCAATCAGTTTAACC 57.285 37.500 0.00 0.00 33.74 2.85
1689 1694 5.575157 TCCAATAGGCAATCAGTTTAACCA 58.425 37.500 0.00 0.00 33.74 3.67
1690 1695 6.013379 TCCAATAGGCAATCAGTTTAACCAA 58.987 36.000 0.00 0.00 33.74 3.67
1691 1696 6.495181 TCCAATAGGCAATCAGTTTAACCAAA 59.505 34.615 0.00 0.00 33.74 3.28
1692 1697 6.813152 CCAATAGGCAATCAGTTTAACCAAAG 59.187 38.462 0.00 0.00 0.00 2.77
1693 1698 7.378181 CAATAGGCAATCAGTTTAACCAAAGT 58.622 34.615 0.00 0.00 0.00 2.66
1694 1699 5.200368 AGGCAATCAGTTTAACCAAAGTG 57.800 39.130 0.00 0.00 43.61 3.16
1711 1716 8.599624 ACCAAAGTGAAAGGATCATTCATAAT 57.400 30.769 14.09 4.19 40.97 1.28
1735 1740 8.976986 ATTTTTCTCTCAAAAATCCGATGAAG 57.023 30.769 0.20 0.00 35.59 3.02
1736 1741 7.744087 TTTTCTCTCAAAAATCCGATGAAGA 57.256 32.000 0.00 0.00 0.00 2.87
1737 1742 7.744087 TTTCTCTCAAAAATCCGATGAAGAA 57.256 32.000 0.00 0.00 0.00 2.52
1748 1753 7.928307 AATCCGATGAAGAATTTTCTCTCAA 57.072 32.000 0.00 0.00 36.28 3.02
1770 1775 9.415544 CTCAAAAATCCAATAAAACTTCTCTGG 57.584 33.333 0.00 0.00 0.00 3.86
1771 1776 9.142014 TCAAAAATCCAATAAAACTTCTCTGGA 57.858 29.630 0.00 0.00 37.37 3.86
1772 1777 9.762933 CAAAAATCCAATAAAACTTCTCTGGAA 57.237 29.630 0.00 0.00 36.59 3.53
1778 1783 8.296713 TCCAATAAAACTTCTCTGGAAAAATCG 58.703 33.333 0.00 0.00 30.12 3.34
1786 1791 7.588512 ACTTCTCTGGAAAAATCGAAAATCAG 58.411 34.615 0.00 0.00 0.00 2.90
1812 1817 0.306533 TCGTTTCGTTGGAAGCTTGC 59.693 50.000 11.58 11.58 32.80 4.01
1814 1819 1.758783 GTTTCGTTGGAAGCTTGCAG 58.241 50.000 20.42 10.59 32.80 4.41
1815 1820 1.065551 GTTTCGTTGGAAGCTTGCAGT 59.934 47.619 20.42 0.00 32.80 4.40
1816 1821 2.248280 TTCGTTGGAAGCTTGCAGTA 57.752 45.000 20.42 4.39 0.00 2.74
1822 1827 2.683968 TGGAAGCTTGCAGTAAGTACG 58.316 47.619 17.55 0.00 38.70 3.67
2036 2042 4.137872 GCGGCCCTGCGTACAGTA 62.138 66.667 0.00 0.00 42.81 2.74
2060 2066 2.257541 GACAGGGAGGGAGGGGATGA 62.258 65.000 0.00 0.00 0.00 2.92
2106 2112 0.179034 GCTGGTGCATAGGGAAGGAG 60.179 60.000 0.00 0.00 39.41 3.69
2107 2113 0.179034 CTGGTGCATAGGGAAGGAGC 60.179 60.000 0.00 0.00 0.00 4.70
2109 2115 0.179034 GGTGCATAGGGAAGGAGCTG 60.179 60.000 0.00 0.00 0.00 4.24
2112 2118 1.704007 GCATAGGGAAGGAGCTGGCT 61.704 60.000 0.00 0.00 0.00 4.75
2137 2143 0.242286 GCGAGAGAGCTCACAGAACA 59.758 55.000 17.77 0.00 41.36 3.18
2144 2150 2.970974 GCTCACAGAACAAGGCGGC 61.971 63.158 0.00 0.00 0.00 6.53
2201 2208 2.853542 TGCACTGGAGCAGGGGAA 60.854 61.111 0.00 0.00 40.11 3.97
2202 2209 2.436109 GCACTGGAGCAGGGGAAA 59.564 61.111 0.00 0.00 35.08 3.13
2203 2210 1.973812 GCACTGGAGCAGGGGAAAC 60.974 63.158 0.00 0.00 35.08 2.78
2204 2211 1.672356 CACTGGAGCAGGGGAAACG 60.672 63.158 0.00 0.00 35.51 3.60
2205 2212 1.841556 ACTGGAGCAGGGGAAACGA 60.842 57.895 0.00 0.00 35.51 3.85
2206 2213 1.374947 CTGGAGCAGGGGAAACGAA 59.625 57.895 0.00 0.00 0.00 3.85
2207 2214 0.250727 CTGGAGCAGGGGAAACGAAA 60.251 55.000 0.00 0.00 0.00 3.46
2208 2215 0.536460 TGGAGCAGGGGAAACGAAAC 60.536 55.000 0.00 0.00 0.00 2.78
2209 2216 0.536460 GGAGCAGGGGAAACGAAACA 60.536 55.000 0.00 0.00 0.00 2.83
2210 2217 1.314730 GAGCAGGGGAAACGAAACAA 58.685 50.000 0.00 0.00 0.00 2.83
2211 2218 1.679153 GAGCAGGGGAAACGAAACAAA 59.321 47.619 0.00 0.00 0.00 2.83
2212 2219 1.407618 AGCAGGGGAAACGAAACAAAC 59.592 47.619 0.00 0.00 0.00 2.93
2213 2220 1.537348 GCAGGGGAAACGAAACAAACC 60.537 52.381 0.00 0.00 0.00 3.27
2214 2221 1.751924 CAGGGGAAACGAAACAAACCA 59.248 47.619 0.00 0.00 0.00 3.67
2215 2222 2.166664 CAGGGGAAACGAAACAAACCAA 59.833 45.455 0.00 0.00 0.00 3.67
2216 2223 2.429250 AGGGGAAACGAAACAAACCAAG 59.571 45.455 0.00 0.00 0.00 3.61
2217 2224 2.198406 GGGAAACGAAACAAACCAAGC 58.802 47.619 0.00 0.00 0.00 4.01
2218 2225 2.198406 GGAAACGAAACAAACCAAGCC 58.802 47.619 0.00 0.00 0.00 4.35
2219 2226 2.198406 GAAACGAAACAAACCAAGCCC 58.802 47.619 0.00 0.00 0.00 5.19
2220 2227 0.462375 AACGAAACAAACCAAGCCCC 59.538 50.000 0.00 0.00 0.00 5.80
2221 2228 0.396556 ACGAAACAAACCAAGCCCCT 60.397 50.000 0.00 0.00 0.00 4.79
2222 2229 0.031994 CGAAACAAACCAAGCCCCTG 59.968 55.000 0.00 0.00 0.00 4.45
2223 2230 0.249868 GAAACAAACCAAGCCCCTGC 60.250 55.000 0.00 0.00 37.95 4.85
2224 2231 1.695114 AAACAAACCAAGCCCCTGCC 61.695 55.000 0.00 0.00 38.69 4.85
2225 2232 3.313524 CAAACCAAGCCCCTGCCC 61.314 66.667 0.00 0.00 38.69 5.36
2226 2233 3.521452 AAACCAAGCCCCTGCCCT 61.521 61.111 0.00 0.00 38.69 5.19
2227 2234 3.529835 AAACCAAGCCCCTGCCCTC 62.530 63.158 0.00 0.00 38.69 4.30
2230 2237 3.399181 CAAGCCCCTGCCCTCGTA 61.399 66.667 0.00 0.00 38.69 3.43
2231 2238 3.400054 AAGCCCCTGCCCTCGTAC 61.400 66.667 0.00 0.00 38.69 3.67
2232 2239 4.715130 AGCCCCTGCCCTCGTACA 62.715 66.667 0.00 0.00 38.69 2.90
2233 2240 4.162690 GCCCCTGCCCTCGTACAG 62.163 72.222 0.00 0.00 0.00 2.74
2234 2241 2.363795 CCCCTGCCCTCGTACAGA 60.364 66.667 0.00 0.00 35.90 3.41
2235 2242 2.427245 CCCCTGCCCTCGTACAGAG 61.427 68.421 7.49 7.49 46.44 3.35
2236 2243 1.682684 CCCTGCCCTCGTACAGAGT 60.683 63.158 11.85 0.00 45.44 3.24
2237 2244 0.395311 CCCTGCCCTCGTACAGAGTA 60.395 60.000 11.85 0.00 45.44 2.59
2238 2245 0.739561 CCTGCCCTCGTACAGAGTAC 59.260 60.000 11.85 0.00 45.44 2.73
2239 2246 1.682394 CCTGCCCTCGTACAGAGTACT 60.682 57.143 0.00 0.00 45.44 2.73
2240 2247 1.402259 CTGCCCTCGTACAGAGTACTG 59.598 57.143 0.00 0.00 45.44 2.74
2241 2248 1.003928 TGCCCTCGTACAGAGTACTGA 59.996 52.381 0.00 4.41 46.03 3.41
2242 2249 2.299521 GCCCTCGTACAGAGTACTGAT 58.700 52.381 0.00 0.00 46.03 2.90
2243 2250 3.118149 TGCCCTCGTACAGAGTACTGATA 60.118 47.826 0.00 0.00 46.03 2.15
2244 2251 3.250521 GCCCTCGTACAGAGTACTGATAC 59.749 52.174 0.00 0.00 46.03 2.24
2245 2252 3.493877 CCCTCGTACAGAGTACTGATACG 59.506 52.174 17.82 17.82 46.03 3.06
2246 2253 4.118410 CCTCGTACAGAGTACTGATACGT 58.882 47.826 20.84 0.00 46.03 3.57
2247 2254 4.025896 CCTCGTACAGAGTACTGATACGTG 60.026 50.000 20.84 18.95 46.03 4.49
2248 2255 3.308053 TCGTACAGAGTACTGATACGTGC 59.692 47.826 20.84 7.15 46.03 5.34
2249 2256 3.063045 CGTACAGAGTACTGATACGTGCA 59.937 47.826 16.51 0.00 46.03 4.57
2250 2257 3.766676 ACAGAGTACTGATACGTGCAG 57.233 47.619 15.91 15.91 46.03 4.41
2251 2258 2.159366 ACAGAGTACTGATACGTGCAGC 60.159 50.000 17.02 5.36 46.03 5.25
2252 2259 3.101980 CAGAGTACTGATACGTGCAGCG 61.102 54.545 17.02 7.07 46.03 5.18
2253 2260 0.100682 AGTACTGATACGTGCAGCGG 59.899 55.000 17.02 0.84 46.52 5.52
2254 2261 1.226859 TACTGATACGTGCAGCGGC 60.227 57.895 17.02 0.31 46.52 6.53
2255 2262 2.930012 TACTGATACGTGCAGCGGCG 62.930 60.000 17.02 0.51 46.52 6.46
2256 2263 4.123009 TGATACGTGCAGCGGCGA 62.123 61.111 12.98 0.00 46.52 5.54
2257 2264 3.617538 GATACGTGCAGCGGCGAC 61.618 66.667 12.98 1.23 46.52 5.19
2258 2265 4.429212 ATACGTGCAGCGGCGACA 62.429 61.111 12.98 1.48 46.52 4.35
2267 2274 4.735132 GCGGCGACACCAGCACTA 62.735 66.667 12.98 0.00 39.03 2.74
2268 2275 2.507102 CGGCGACACCAGCACTAG 60.507 66.667 0.00 0.00 39.03 2.57
2269 2276 2.815647 GGCGACACCAGCACTAGC 60.816 66.667 0.00 0.00 38.86 3.42
2286 2293 2.411701 CGCCAGCGAGAACCGATA 59.588 61.111 6.06 0.00 42.83 2.92
2287 2294 1.007271 CGCCAGCGAGAACCGATAT 60.007 57.895 6.06 0.00 42.83 1.63
2288 2295 1.278172 CGCCAGCGAGAACCGATATG 61.278 60.000 6.06 0.00 42.83 1.78
2289 2296 0.249489 GCCAGCGAGAACCGATATGT 60.249 55.000 0.00 0.00 41.76 2.29
2290 2297 1.806623 GCCAGCGAGAACCGATATGTT 60.807 52.381 0.00 0.00 41.76 2.71
2291 2298 2.545113 GCCAGCGAGAACCGATATGTTA 60.545 50.000 0.00 0.00 41.76 2.41
2292 2299 3.713288 CCAGCGAGAACCGATATGTTAA 58.287 45.455 0.00 0.00 41.76 2.01
2293 2300 3.489785 CCAGCGAGAACCGATATGTTAAC 59.510 47.826 0.00 0.00 41.76 2.01
2294 2301 3.489785 CAGCGAGAACCGATATGTTAACC 59.510 47.826 2.48 0.00 41.76 2.85
2295 2302 2.798847 GCGAGAACCGATATGTTAACCC 59.201 50.000 2.48 0.00 41.76 4.11
2296 2303 3.047796 CGAGAACCGATATGTTAACCCG 58.952 50.000 2.48 1.87 41.76 5.28
2297 2304 3.387397 GAGAACCGATATGTTAACCCGG 58.613 50.000 18.10 18.10 45.09 5.73
2300 2307 1.873698 CCGATATGTTAACCCGGTGG 58.126 55.000 0.00 0.00 35.83 4.61
2301 2308 1.413445 CCGATATGTTAACCCGGTGGA 59.587 52.381 0.00 0.00 35.83 4.02
2302 2309 2.158928 CCGATATGTTAACCCGGTGGAA 60.159 50.000 0.00 0.00 35.83 3.53
2303 2310 2.867975 CGATATGTTAACCCGGTGGAAC 59.132 50.000 0.00 8.18 34.81 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
180 184 1.884235 AAACGCCACTCTTCTCTTGG 58.116 50.000 0.00 0.00 0.00 3.61
182 186 3.394719 GAGAAAACGCCACTCTTCTCTT 58.605 45.455 3.92 0.00 40.33 2.85
400 404 7.609146 CCGACAAGTAGATAGTGTGGGTATATA 59.391 40.741 0.00 0.00 36.65 0.86
412 416 4.519350 TCCACATAGCCGACAAGTAGATAG 59.481 45.833 0.00 0.00 0.00 2.08
413 417 4.277672 GTCCACATAGCCGACAAGTAGATA 59.722 45.833 0.00 0.00 0.00 1.98
537 541 1.209504 TCCCTTCCGTTATCAAGCAGG 59.790 52.381 0.00 0.00 0.00 4.85
573 577 8.443160 CGTACATCATTTGAAACTCTACACATT 58.557 33.333 0.00 0.00 0.00 2.71
574 578 7.064609 CCGTACATCATTTGAAACTCTACACAT 59.935 37.037 0.00 0.00 0.00 3.21
687 691 1.807814 AACTGTCCAGGAACTCCACT 58.192 50.000 0.00 0.00 34.60 4.00
714 718 3.146066 ACGACCAGCAAGCTTAATTGAA 58.854 40.909 0.00 0.00 31.55 2.69
720 724 3.396260 AAGTAACGACCAGCAAGCTTA 57.604 42.857 0.00 0.00 0.00 3.09
740 744 5.477607 TCCTTTTAGAATCTCGTCCACAA 57.522 39.130 0.00 0.00 0.00 3.33
809 814 1.617357 CCGGCCAAGGTAGAGGTATAC 59.383 57.143 2.24 0.00 0.00 1.47
1144 1149 7.711339 CAGAGGTACAAATTCCCTATTACTCAC 59.289 40.741 0.00 0.00 0.00 3.51
1158 1163 7.272037 ACGACAAATTTTCAGAGGTACAAAT 57.728 32.000 0.00 0.00 0.00 2.32
1264 1269 4.016444 GGCCACAAATCCTCAATACAAGA 58.984 43.478 0.00 0.00 0.00 3.02
1377 1382 3.565905 AACTAGCAAAAGAGCATGTGC 57.434 42.857 0.00 0.00 42.49 4.57
1378 1383 5.611796 TGTAACTAGCAAAAGAGCATGTG 57.388 39.130 0.00 0.00 36.85 3.21
1379 1384 5.939883 TGATGTAACTAGCAAAAGAGCATGT 59.060 36.000 0.00 0.00 36.85 3.21
1380 1385 6.426980 TGATGTAACTAGCAAAAGAGCATG 57.573 37.500 0.00 0.00 36.85 4.06
1381 1386 7.452880 TTTGATGTAACTAGCAAAAGAGCAT 57.547 32.000 0.00 0.00 36.85 3.79
1382 1387 6.875948 TTTGATGTAACTAGCAAAAGAGCA 57.124 33.333 0.00 0.00 36.85 4.26
1383 1388 9.443283 CATATTTGATGTAACTAGCAAAAGAGC 57.557 33.333 0.00 0.00 34.38 4.09
1438 1443 6.715264 TCATCTACCTTTGTTTTTCTTCTCCC 59.285 38.462 0.00 0.00 0.00 4.30
1451 1456 5.877012 TCTAAAGCAGCTTCATCTACCTTTG 59.123 40.000 8.48 0.00 0.00 2.77
1466 1471 6.019559 GGTTTCTGCAAAAGTTTCTAAAGCAG 60.020 38.462 15.13 15.13 46.76 4.24
1469 1474 7.330700 TGTTGGTTTCTGCAAAAGTTTCTAAAG 59.669 33.333 0.00 0.00 0.00 1.85
1471 1476 6.588373 GTGTTGGTTTCTGCAAAAGTTTCTAA 59.412 34.615 0.00 0.00 0.00 2.10
1472 1477 6.071616 AGTGTTGGTTTCTGCAAAAGTTTCTA 60.072 34.615 0.00 0.00 0.00 2.10
1476 1481 4.535526 AGTGTTGGTTTCTGCAAAAGTT 57.464 36.364 0.00 0.00 0.00 2.66
1482 1487 2.158827 TCTGCTAGTGTTGGTTTCTGCA 60.159 45.455 0.00 0.00 0.00 4.41
1484 1489 2.808543 GGTCTGCTAGTGTTGGTTTCTG 59.191 50.000 0.00 0.00 0.00 3.02
1504 1509 1.826385 AAAATCTTCAGGGCTGACGG 58.174 50.000 0.00 0.00 39.66 4.79
1531 1536 2.247267 CACGACGTTTTGCGGACC 59.753 61.111 0.00 0.00 46.52 4.46
1562 1567 3.119495 GCAAGTGAAGTTTATCGCCCATT 60.119 43.478 0.00 0.00 0.00 3.16
1588 1593 2.814336 CTGGTTTAAGACTGTTGAGCCC 59.186 50.000 0.00 0.00 0.00 5.19
1611 1616 2.163211 GAGGAAATCAAAGGCTGCTGAC 59.837 50.000 0.00 0.00 0.00 3.51
1647 1652 7.968014 ATTGGATTTCTAGCTGATCCTTTTT 57.032 32.000 16.29 2.69 40.01 1.94
1648 1653 7.723172 CCTATTGGATTTCTAGCTGATCCTTTT 59.277 37.037 16.29 7.80 40.01 2.27
1649 1654 7.230027 CCTATTGGATTTCTAGCTGATCCTTT 58.770 38.462 16.29 9.43 40.01 3.11
1650 1655 6.746614 GCCTATTGGATTTCTAGCTGATCCTT 60.747 42.308 16.29 9.66 40.01 3.36
1651 1656 5.280419 GCCTATTGGATTTCTAGCTGATCCT 60.280 44.000 16.29 5.23 40.01 3.24
1652 1657 4.940654 GCCTATTGGATTTCTAGCTGATCC 59.059 45.833 0.00 4.93 39.81 3.36
1655 1660 5.372343 TTGCCTATTGGATTTCTAGCTGA 57.628 39.130 0.00 0.00 34.57 4.26
1666 1671 5.575157 TGGTTAAACTGATTGCCTATTGGA 58.425 37.500 0.00 0.00 34.57 3.53
1687 1692 9.880157 AAATTATGAATGATCCTTTCACTTTGG 57.120 29.630 9.61 0.00 37.11 3.28
1711 1716 8.165239 TCTTCATCGGATTTTTGAGAGAAAAA 57.835 30.769 0.00 0.00 32.75 1.94
1729 1734 9.918630 TGGATTTTTGAGAGAAAATTCTTCATC 57.081 29.630 0.00 0.00 38.85 2.92
1762 1767 7.810658 TCTGATTTTCGATTTTTCCAGAGAAG 58.189 34.615 0.00 0.00 32.35 2.85
1769 1774 7.322222 CGAGCATATCTGATTTTCGATTTTTCC 59.678 37.037 0.00 0.00 0.00 3.13
1770 1775 7.852945 ACGAGCATATCTGATTTTCGATTTTTC 59.147 33.333 14.92 0.00 0.00 2.29
1771 1776 7.697691 ACGAGCATATCTGATTTTCGATTTTT 58.302 30.769 14.92 0.00 0.00 1.94
1772 1777 7.251704 ACGAGCATATCTGATTTTCGATTTT 57.748 32.000 14.92 0.00 0.00 1.82
1773 1778 6.851222 ACGAGCATATCTGATTTTCGATTT 57.149 33.333 14.92 0.00 0.00 2.17
1774 1779 6.851222 AACGAGCATATCTGATTTTCGATT 57.149 33.333 14.92 7.00 0.00 3.34
1775 1780 6.346120 CGAAACGAGCATATCTGATTTTCGAT 60.346 38.462 18.84 7.22 44.14 3.59
1776 1781 5.051708 CGAAACGAGCATATCTGATTTTCGA 60.052 40.000 18.84 0.00 44.14 3.71
1777 1782 5.126423 CGAAACGAGCATATCTGATTTTCG 58.874 41.667 13.39 13.39 38.43 3.46
1778 1783 6.037423 ACGAAACGAGCATATCTGATTTTC 57.963 37.500 0.00 0.00 0.00 2.29
1783 1788 3.119280 TCCAACGAAACGAGCATATCTGA 60.119 43.478 0.00 0.00 0.00 3.27
1786 1791 3.544244 GCTTCCAACGAAACGAGCATATC 60.544 47.826 0.00 0.00 0.00 1.63
1812 1817 3.128242 CAGTGGTACCCTCGTACTTACTG 59.872 52.174 10.07 9.03 44.38 2.74
1814 1819 2.159324 GCAGTGGTACCCTCGTACTTAC 60.159 54.545 10.07 0.00 43.78 2.34
1815 1820 2.094675 GCAGTGGTACCCTCGTACTTA 58.905 52.381 10.07 0.00 43.78 2.24
1816 1821 0.893447 GCAGTGGTACCCTCGTACTT 59.107 55.000 10.07 0.00 43.78 2.24
1822 1827 0.905337 ACTCCAGCAGTGGTACCCTC 60.905 60.000 10.07 2.55 45.28 4.30
1830 1835 1.251527 ACCCGTCTACTCCAGCAGTG 61.252 60.000 0.00 0.00 36.43 3.66
1991 1996 5.406780 AGCTCACGTCTCAGTTTATTTTCTG 59.593 40.000 0.00 0.00 0.00 3.02
1992 1997 5.542779 AGCTCACGTCTCAGTTTATTTTCT 58.457 37.500 0.00 0.00 0.00 2.52
1993 1998 5.405571 TGAGCTCACGTCTCAGTTTATTTTC 59.594 40.000 13.74 0.00 35.81 2.29
1995 2000 4.686554 GTGAGCTCACGTCTCAGTTTATTT 59.313 41.667 29.84 0.00 40.82 1.40
1998 2003 3.284323 GTGAGCTCACGTCTCAGTTTA 57.716 47.619 29.84 0.00 40.82 2.01
2036 2042 2.641746 CCTCCCTCCCTGTCCCTCT 61.642 68.421 0.00 0.00 0.00 3.69
2060 2066 0.684479 TAGCCTCGCTGACCAGTGAT 60.684 55.000 12.94 2.73 45.68 3.06
2112 2118 1.077429 TGAGCTCTCTCGCTGGCTA 60.077 57.895 16.19 0.00 42.26 3.93
2119 2125 2.594321 CTTGTTCTGTGAGCTCTCTCG 58.406 52.381 16.19 7.24 42.26 4.04
2192 2199 1.407618 GTTTGTTTCGTTTCCCCTGCT 59.592 47.619 0.00 0.00 0.00 4.24
2197 2204 2.198406 GCTTGGTTTGTTTCGTTTCCC 58.802 47.619 0.00 0.00 0.00 3.97
2198 2205 2.198406 GGCTTGGTTTGTTTCGTTTCC 58.802 47.619 0.00 0.00 0.00 3.13
2199 2206 2.198406 GGGCTTGGTTTGTTTCGTTTC 58.802 47.619 0.00 0.00 0.00 2.78
2200 2207 1.134640 GGGGCTTGGTTTGTTTCGTTT 60.135 47.619 0.00 0.00 0.00 3.60
2201 2208 0.462375 GGGGCTTGGTTTGTTTCGTT 59.538 50.000 0.00 0.00 0.00 3.85
2202 2209 0.396556 AGGGGCTTGGTTTGTTTCGT 60.397 50.000 0.00 0.00 0.00 3.85
2203 2210 0.031994 CAGGGGCTTGGTTTGTTTCG 59.968 55.000 0.00 0.00 0.00 3.46
2204 2211 0.249868 GCAGGGGCTTGGTTTGTTTC 60.250 55.000 0.00 0.00 36.96 2.78
2205 2212 1.695114 GGCAGGGGCTTGGTTTGTTT 61.695 55.000 0.00 0.00 40.87 2.83
2206 2213 2.140138 GGCAGGGGCTTGGTTTGTT 61.140 57.895 0.00 0.00 40.87 2.83
2207 2214 2.524148 GGCAGGGGCTTGGTTTGT 60.524 61.111 0.00 0.00 40.87 2.83
2208 2215 3.313524 GGGCAGGGGCTTGGTTTG 61.314 66.667 0.00 0.00 40.87 2.93
2209 2216 3.521452 AGGGCAGGGGCTTGGTTT 61.521 61.111 0.00 0.00 40.87 3.27
2210 2217 3.984732 GAGGGCAGGGGCTTGGTT 61.985 66.667 0.00 0.00 40.87 3.67
2213 2220 3.399181 TACGAGGGCAGGGGCTTG 61.399 66.667 0.00 0.00 40.87 4.01
2214 2221 3.400054 GTACGAGGGCAGGGGCTT 61.400 66.667 0.00 0.00 40.87 4.35
2215 2222 4.715130 TGTACGAGGGCAGGGGCT 62.715 66.667 0.00 0.00 40.87 5.19
2216 2223 4.162690 CTGTACGAGGGCAGGGGC 62.163 72.222 0.00 0.00 40.13 5.80
2217 2224 2.363795 TCTGTACGAGGGCAGGGG 60.364 66.667 0.00 0.00 33.81 4.79
2218 2225 0.395311 TACTCTGTACGAGGGCAGGG 60.395 60.000 15.76 0.00 44.33 4.45
2219 2226 0.739561 GTACTCTGTACGAGGGCAGG 59.260 60.000 15.76 0.00 44.33 4.85
2220 2227 1.402259 CAGTACTCTGTACGAGGGCAG 59.598 57.143 15.76 0.00 44.33 4.85
2221 2228 1.003928 TCAGTACTCTGTACGAGGGCA 59.996 52.381 15.76 2.47 44.33 5.36
2222 2229 1.747709 TCAGTACTCTGTACGAGGGC 58.252 55.000 15.76 9.62 44.33 5.19
2223 2230 3.493877 CGTATCAGTACTCTGTACGAGGG 59.506 52.174 19.02 5.46 44.30 4.30
2224 2231 4.025896 CACGTATCAGTACTCTGTACGAGG 60.026 50.000 25.68 17.51 44.30 4.63
2225 2232 4.550447 GCACGTATCAGTACTCTGTACGAG 60.550 50.000 25.68 21.19 44.30 4.18
2226 2233 3.308053 GCACGTATCAGTACTCTGTACGA 59.692 47.826 25.68 8.89 44.30 3.43
2227 2234 3.063045 TGCACGTATCAGTACTCTGTACG 59.937 47.826 20.81 20.81 45.39 3.67
2228 2235 4.589252 CTGCACGTATCAGTACTCTGTAC 58.411 47.826 8.39 0.05 41.91 2.90
2229 2236 3.064958 GCTGCACGTATCAGTACTCTGTA 59.935 47.826 15.57 0.00 41.91 2.74
2230 2237 2.159366 GCTGCACGTATCAGTACTCTGT 60.159 50.000 15.57 0.00 41.91 3.41
2231 2238 2.455032 GCTGCACGTATCAGTACTCTG 58.545 52.381 15.57 0.00 42.54 3.35
2232 2239 1.064208 CGCTGCACGTATCAGTACTCT 59.936 52.381 15.57 0.00 36.87 3.24
2233 2240 1.467875 CGCTGCACGTATCAGTACTC 58.532 55.000 15.57 2.13 36.87 2.59
2234 2241 0.100682 CCGCTGCACGTATCAGTACT 59.899 55.000 15.57 0.00 41.42 2.73
2235 2242 1.480219 GCCGCTGCACGTATCAGTAC 61.480 60.000 15.57 0.00 41.42 2.73
2236 2243 1.226859 GCCGCTGCACGTATCAGTA 60.227 57.895 15.57 0.00 41.42 2.74
2237 2244 2.509336 GCCGCTGCACGTATCAGT 60.509 61.111 15.57 0.00 41.42 3.41
2238 2245 3.620428 CGCCGCTGCACGTATCAG 61.620 66.667 11.40 11.40 41.42 2.90
2239 2246 4.123009 TCGCCGCTGCACGTATCA 62.123 61.111 11.15 0.00 41.42 2.15
2240 2247 3.617538 GTCGCCGCTGCACGTATC 61.618 66.667 11.15 1.91 41.42 2.24
2241 2248 4.429212 TGTCGCCGCTGCACGTAT 62.429 61.111 11.15 0.00 41.42 3.06
2250 2257 4.735132 TAGTGCTGGTGTCGCCGC 62.735 66.667 10.96 10.96 41.21 6.53
2251 2258 2.507102 CTAGTGCTGGTGTCGCCG 60.507 66.667 0.00 0.00 41.21 6.46
2252 2259 2.815647 GCTAGTGCTGGTGTCGCC 60.816 66.667 0.00 0.00 36.03 5.54
2253 2260 3.181967 CGCTAGTGCTGGTGTCGC 61.182 66.667 0.00 0.00 36.97 5.19
2254 2261 3.181967 GCGCTAGTGCTGGTGTCG 61.182 66.667 20.99 0.00 36.97 4.35
2255 2262 2.815647 GGCGCTAGTGCTGGTGTC 60.816 66.667 26.36 6.23 36.97 3.67
2256 2263 3.596066 CTGGCGCTAGTGCTGGTGT 62.596 63.158 26.36 0.00 36.97 4.16
2257 2264 2.816958 CTGGCGCTAGTGCTGGTG 60.817 66.667 26.36 11.16 36.97 4.17
2258 2265 4.767255 GCTGGCGCTAGTGCTGGT 62.767 66.667 26.36 0.00 36.97 4.00
2260 2267 4.801624 TCGCTGGCGCTAGTGCTG 62.802 66.667 27.33 19.64 39.59 4.41
2261 2268 4.504916 CTCGCTGGCGCTAGTGCT 62.505 66.667 27.33 0.00 39.59 4.40
2262 2269 3.989698 TTCTCGCTGGCGCTAGTGC 62.990 63.158 27.33 20.17 39.59 4.40
2263 2270 2.161486 GTTCTCGCTGGCGCTAGTG 61.161 63.158 26.40 26.40 39.59 2.74
2264 2271 2.182030 GTTCTCGCTGGCGCTAGT 59.818 61.111 22.50 0.00 39.59 2.57
2265 2272 2.583593 GGTTCTCGCTGGCGCTAG 60.584 66.667 17.52 17.52 39.59 3.42
2266 2273 4.492160 CGGTTCTCGCTGGCGCTA 62.492 66.667 7.64 0.00 39.59 4.26
2268 2275 3.768185 TATCGGTTCTCGCTGGCGC 62.768 63.158 10.28 0.00 39.59 6.53
2269 2276 1.007271 ATATCGGTTCTCGCTGGCG 60.007 57.895 8.80 8.80 39.05 5.69
2270 2277 0.249489 ACATATCGGTTCTCGCTGGC 60.249 55.000 0.00 0.00 39.05 4.85
2271 2278 2.225068 AACATATCGGTTCTCGCTGG 57.775 50.000 0.00 0.00 39.05 4.85
2272 2279 3.489785 GGTTAACATATCGGTTCTCGCTG 59.510 47.826 8.10 0.00 39.05 5.18
2273 2280 3.492137 GGGTTAACATATCGGTTCTCGCT 60.492 47.826 8.10 0.00 39.05 4.93
2274 2281 2.798847 GGGTTAACATATCGGTTCTCGC 59.201 50.000 8.10 0.00 39.05 5.03
2275 2282 3.047796 CGGGTTAACATATCGGTTCTCG 58.952 50.000 8.10 0.00 40.90 4.04
2276 2283 3.387397 CCGGGTTAACATATCGGTTCTC 58.613 50.000 8.10 0.00 36.38 2.87
2277 2284 3.464111 CCGGGTTAACATATCGGTTCT 57.536 47.619 8.10 0.00 36.38 3.01
2281 2288 1.413445 TCCACCGGGTTAACATATCGG 59.587 52.381 19.83 19.83 45.42 4.18
2282 2289 2.867975 GTTCCACCGGGTTAACATATCG 59.132 50.000 6.32 5.56 34.93 2.92
2283 2290 3.118149 AGGTTCCACCGGGTTAACATATC 60.118 47.826 18.81 6.37 44.90 1.63
2284 2291 2.848071 AGGTTCCACCGGGTTAACATAT 59.152 45.455 18.81 6.34 44.90 1.78
2285 2292 2.027007 CAGGTTCCACCGGGTTAACATA 60.027 50.000 18.81 0.00 44.90 2.29
2286 2293 1.069775 AGGTTCCACCGGGTTAACAT 58.930 50.000 18.81 12.11 44.90 2.71
2287 2294 0.108963 CAGGTTCCACCGGGTTAACA 59.891 55.000 18.81 0.00 44.90 2.41
2288 2295 1.239296 GCAGGTTCCACCGGGTTAAC 61.239 60.000 6.32 11.89 44.90 2.01
2289 2296 1.073548 GCAGGTTCCACCGGGTTAA 59.926 57.895 6.32 0.00 44.90 2.01
2290 2297 2.751688 GCAGGTTCCACCGGGTTA 59.248 61.111 6.32 0.00 44.90 2.85
2291 2298 4.636435 CGCAGGTTCCACCGGGTT 62.636 66.667 6.32 0.00 44.90 4.11


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

AutoCloner maintained by Alex Coulton.