Multiple sequence alignment - TraesCS5D01G222400

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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 TraesCS5D01G222400 chr5D 100.000 2357 0 0 1 2357 330074418 330072062 0.000000e+00 4353
1 TraesCS5D01G222400 chr5B 87.500 1520 85 45 621 2102 383031674 383030222 0.000000e+00 1657
2 TraesCS5D01G222400 chr5B 89.450 436 25 11 13 439 383032213 383031790 4.460000e-147 531
3 TraesCS5D01G222400 chr5A 88.673 874 38 17 621 1458 426746847 426747695 0.000000e+00 1009
4 TraesCS5D01G222400 chr5A 90.435 345 21 8 1769 2112 426747886 426748219 5.980000e-121 444
5 TraesCS5D01G222400 chr5A 90.435 230 14 4 1516 1744 426747668 426747890 1.770000e-76 296
6 TraesCS5D01G222400 chr5A 83.972 287 23 10 159 439 426746466 426746735 1.080000e-63 254
7 TraesCS5D01G222400 chr5A 86.061 165 4 5 13 158 426746234 426746398 2.420000e-35 159
8 TraesCS5D01G222400 chr5A 77.551 245 32 16 2135 2357 426748303 426748546 2.460000e-25 126


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 TraesCS5D01G222400 chr5D 330072062 330074418 2356 True 4353.000000 4353 100.000000 1 2357 1 chr5D.!!$R1 2356
1 TraesCS5D01G222400 chr5B 383030222 383032213 1991 True 1094.000000 1657 88.475000 13 2102 2 chr5B.!!$R1 2089
2 TraesCS5D01G222400 chr5A 426746234 426748546 2312 False 381.333333 1009 86.187833 13 2357 6 chr5A.!!$F1 2344

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
93 94 0.384309 GCTGTTTTTATAGGGCGGGC 59.616 55.0 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1498 1645 0.036858 TGTGCTGCGTACATGGCTTA 60.037 50.0 0.0 0.0 0.0 3.09 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
91 92 2.614057 CTCTGCTGTTTTTATAGGGCGG 59.386 50.000 0.00 0.00 0.00 6.13
93 94 0.384309 GCTGTTTTTATAGGGCGGGC 59.616 55.000 0.00 0.00 0.00 6.13
163 254 6.952743 GCAGCTGGATGCATGTAATATATAC 58.047 40.000 17.12 0.00 45.77 1.47
169 260 6.705825 TGGATGCATGTAATATATACGATGGC 59.294 38.462 2.46 0.00 0.00 4.40
216 312 5.238583 TCTTCTAGGCTAGCTTGTTTGAAC 58.761 41.667 16.85 0.00 0.00 3.18
281 380 3.065510 CGCAGAGTGAGCTAAGCTAGTTA 59.934 47.826 0.00 0.00 39.88 2.24
282 381 4.438880 CGCAGAGTGAGCTAAGCTAGTTAA 60.439 45.833 0.00 0.00 39.88 2.01
283 382 5.596845 GCAGAGTGAGCTAAGCTAGTTAAT 58.403 41.667 0.00 0.00 39.88 1.40
284 383 6.045955 GCAGAGTGAGCTAAGCTAGTTAATT 58.954 40.000 0.00 0.00 39.88 1.40
318 417 2.425143 TCCATCATGACTTTGAGGGC 57.575 50.000 0.00 0.00 45.09 5.19
364 463 2.897350 GCGCCCATACTGGAGTGC 60.897 66.667 0.00 0.15 40.96 4.40
377 476 1.063792 TGGAGTGCCCGGTACTACATA 60.064 52.381 16.19 0.00 34.33 2.29
426 528 3.677156 AGGATTGCTGCCCTCTTTATT 57.323 42.857 0.00 0.00 0.00 1.40
431 533 6.944862 AGGATTGCTGCCCTCTTTATTATAAG 59.055 38.462 0.00 0.00 0.00 1.73
434 536 8.946797 ATTGCTGCCCTCTTTATTATAAGAAT 57.053 30.769 0.00 0.00 33.96 2.40
480 582 4.278669 TGCAAAGGTATTCCGTTTTAGCAA 59.721 37.500 0.00 0.00 39.05 3.91
482 584 5.867174 GCAAAGGTATTCCGTTTTAGCAAAT 59.133 36.000 0.00 0.00 39.05 2.32
483 585 6.367695 GCAAAGGTATTCCGTTTTAGCAAATT 59.632 34.615 0.00 0.00 39.05 1.82
485 587 6.584185 AGGTATTCCGTTTTAGCAAATTGT 57.416 33.333 0.00 0.00 39.05 2.71
486 588 6.386654 AGGTATTCCGTTTTAGCAAATTGTG 58.613 36.000 0.00 0.00 39.05 3.33
487 589 7.064029 AGGTATTCCGTTTTAGCAAATTGTGC 61.064 38.462 0.00 0.00 45.83 4.57
571 673 5.551233 ACAGTGCACAGCTCTTAAGAATTA 58.449 37.500 21.04 0.00 29.56 1.40
576 678 6.149474 GTGCACAGCTCTTAAGAATTAAAGGA 59.851 38.462 13.17 0.00 40.54 3.36
577 679 6.714810 TGCACAGCTCTTAAGAATTAAAGGAA 59.285 34.615 6.63 0.00 40.54 3.36
579 681 7.699812 GCACAGCTCTTAAGAATTAAAGGAATG 59.300 37.037 6.63 0.00 40.54 2.67
605 710 5.669798 AATATAGGTTGGCCCTTGAAGAT 57.330 39.130 0.00 0.00 42.73 2.40
610 715 2.899900 GGTTGGCCCTTGAAGATCTTTT 59.100 45.455 9.87 0.00 0.00 2.27
641 746 5.696724 TCGATGAAGAACTTTCTTTGAGGAC 59.303 40.000 5.71 0.00 46.84 3.85
654 759 5.505780 TCTTTGAGGACCTGAAAACTTTCA 58.494 37.500 7.57 4.87 44.31 2.69
662 767 3.065371 ACCTGAAAACTTTCAAGACGCTG 59.935 43.478 7.60 0.00 45.61 5.18
691 796 3.574614 CCAAATAAAGCCTGTTGGTTCG 58.425 45.455 0.00 0.00 36.55 3.95
692 797 2.986479 CAAATAAAGCCTGTTGGTTCGC 59.014 45.455 0.00 0.00 32.32 4.70
718 823 1.534717 GGCCTGGCCCAATATGCAT 60.535 57.895 27.77 3.79 44.06 3.96
730 835 5.292589 GCCCAATATGCATTTCTGAAAGTTG 59.707 40.000 3.54 4.39 33.76 3.16
735 840 4.305989 TGCATTTCTGAAAGTTGGTGAC 57.694 40.909 8.95 0.23 33.76 3.67
736 841 3.068024 TGCATTTCTGAAAGTTGGTGACC 59.932 43.478 8.95 0.00 33.76 4.02
759 864 1.557099 TCCGTGTAGTCTGGAGCATT 58.443 50.000 0.00 0.00 0.00 3.56
920 1048 3.071459 GACAACCGCACATCGCTCG 62.071 63.158 0.00 0.00 39.08 5.03
924 1052 4.498520 CCGCACATCGCTCGACCT 62.499 66.667 0.00 0.00 39.08 3.85
927 1055 0.595053 CGCACATCGCTCGACCTTAT 60.595 55.000 0.00 0.00 39.08 1.73
939 1067 3.659786 TCGACCTTATAATTCATGGCCG 58.340 45.455 0.00 0.00 0.00 6.13
996 1135 5.006746 CGCAAGAATTCCAAGTACAGTATCC 59.993 44.000 0.65 0.00 43.02 2.59
1021 1160 3.501911 CCCGGCCATTCCCTCCAT 61.502 66.667 2.24 0.00 0.00 3.41
1362 1506 4.662468 ACGATCGTACTACTAGTCTCCA 57.338 45.455 21.32 0.00 0.00 3.86
1391 1536 2.729882 CCGAAGTTGACGAAACGAGATT 59.270 45.455 0.00 0.00 44.04 2.40
1397 1542 7.529519 CGAAGTTGACGAAACGAGATTTTATTT 59.470 33.333 0.00 0.00 44.04 1.40
1405 1550 9.685005 ACGAAACGAGATTTTATTTTAAGATCG 57.315 29.630 0.00 0.00 0.00 3.69
1434 1581 2.973694 AAATCGGCTACGTGGTACAT 57.026 45.000 0.00 0.00 44.52 2.29
1445 1592 4.859304 ACGTGGTACATAGTTCAGTTCA 57.141 40.909 0.00 0.00 44.52 3.18
1452 1599 6.722590 TGGTACATAGTTCAGTTCAGTTCCTA 59.277 38.462 0.00 0.00 0.00 2.94
1456 1603 8.974060 ACATAGTTCAGTTCAGTTCCTAAAAA 57.026 30.769 0.00 0.00 0.00 1.94
1483 1630 8.726988 ACGGGTTAATAATATGATCAAATTCGG 58.273 33.333 0.00 0.00 0.00 4.30
1484 1631 7.696453 CGGGTTAATAATATGATCAAATTCGGC 59.304 37.037 0.00 0.00 0.00 5.54
1485 1632 7.696453 GGGTTAATAATATGATCAAATTCGGCG 59.304 37.037 0.00 0.00 0.00 6.46
1486 1633 7.218204 GGTTAATAATATGATCAAATTCGGCGC 59.782 37.037 0.00 0.00 0.00 6.53
1487 1634 5.878332 ATAATATGATCAAATTCGGCGCA 57.122 34.783 10.83 0.00 0.00 6.09
1488 1635 3.542712 ATATGATCAAATTCGGCGCAC 57.457 42.857 10.83 0.00 0.00 5.34
1489 1636 1.093972 ATGATCAAATTCGGCGCACA 58.906 45.000 10.83 0.00 0.00 4.57
1490 1637 1.093972 TGATCAAATTCGGCGCACAT 58.906 45.000 10.83 0.00 0.00 3.21
1491 1638 1.202166 TGATCAAATTCGGCGCACATG 60.202 47.619 10.83 0.00 0.00 3.21
1492 1639 0.810648 ATCAAATTCGGCGCACATGT 59.189 45.000 10.83 0.00 0.00 3.21
1493 1640 0.595588 TCAAATTCGGCGCACATGTT 59.404 45.000 10.83 0.00 0.00 2.71
1494 1641 1.000827 TCAAATTCGGCGCACATGTTT 60.001 42.857 10.83 0.09 0.00 2.83
1495 1642 2.226674 TCAAATTCGGCGCACATGTTTA 59.773 40.909 10.83 0.00 0.00 2.01
1496 1643 3.119673 TCAAATTCGGCGCACATGTTTAT 60.120 39.130 10.83 0.00 0.00 1.40
1497 1644 2.755836 ATTCGGCGCACATGTTTATC 57.244 45.000 10.83 0.00 0.00 1.75
1498 1645 1.732941 TTCGGCGCACATGTTTATCT 58.267 45.000 10.83 0.00 0.00 1.98
1499 1646 2.588027 TCGGCGCACATGTTTATCTA 57.412 45.000 10.83 0.00 0.00 1.98
1500 1647 2.894902 TCGGCGCACATGTTTATCTAA 58.105 42.857 10.83 0.00 0.00 2.10
1501 1648 2.863740 TCGGCGCACATGTTTATCTAAG 59.136 45.455 10.83 0.00 0.00 2.18
1502 1649 2.599848 CGGCGCACATGTTTATCTAAGC 60.600 50.000 10.83 0.00 0.00 3.09
1503 1650 2.287009 GGCGCACATGTTTATCTAAGCC 60.287 50.000 10.83 0.00 0.00 4.35
1504 1651 2.354510 GCGCACATGTTTATCTAAGCCA 59.645 45.455 0.30 0.00 0.00 4.75
1505 1652 3.003689 GCGCACATGTTTATCTAAGCCAT 59.996 43.478 0.30 0.00 0.00 4.40
1506 1653 4.530388 CGCACATGTTTATCTAAGCCATG 58.470 43.478 0.00 0.00 0.00 3.66
1507 1654 4.035558 CGCACATGTTTATCTAAGCCATGT 59.964 41.667 0.00 0.00 32.80 3.21
1508 1655 5.236263 CGCACATGTTTATCTAAGCCATGTA 59.764 40.000 0.00 0.00 31.60 2.29
1509 1656 6.430451 GCACATGTTTATCTAAGCCATGTAC 58.570 40.000 0.00 7.54 31.60 2.90
1510 1657 6.649436 CACATGTTTATCTAAGCCATGTACG 58.351 40.000 0.00 0.00 31.60 3.67
1511 1658 5.236478 ACATGTTTATCTAAGCCATGTACGC 59.764 40.000 12.12 0.00 31.12 4.42
1512 1659 4.760878 TGTTTATCTAAGCCATGTACGCA 58.239 39.130 0.00 0.00 0.00 5.24
1513 1660 4.808895 TGTTTATCTAAGCCATGTACGCAG 59.191 41.667 0.00 0.00 0.00 5.18
1565 1712 8.706492 AAAATTCAATCGGAGTACGTATGTAA 57.294 30.769 0.00 0.00 44.69 2.41
1566 1713 8.882415 AAATTCAATCGGAGTACGTATGTAAT 57.118 30.769 0.00 0.00 44.69 1.89
1567 1714 9.970395 AAATTCAATCGGAGTACGTATGTAATA 57.030 29.630 0.00 0.00 44.69 0.98
1569 1716 9.622004 ATTCAATCGGAGTACGTATGTAATAAG 57.378 33.333 0.00 0.00 44.69 1.73
1574 1726 8.087982 TCGGAGTACGTATGTAATAAGTAAGG 57.912 38.462 0.00 0.00 43.51 2.69
1631 1783 1.738099 GTCGCTGACTCACCGCAAT 60.738 57.895 2.10 0.00 0.00 3.56
1733 1886 1.197721 GGCAAAGACACATCCACTTCG 59.802 52.381 0.00 0.00 0.00 3.79
1817 1970 4.708601 CGTAGTTTCCATCGACAAAAAGG 58.291 43.478 0.00 0.00 0.00 3.11
1818 1971 4.449743 CGTAGTTTCCATCGACAAAAAGGA 59.550 41.667 0.00 0.00 0.00 3.36
1819 1972 5.049954 CGTAGTTTCCATCGACAAAAAGGAA 60.050 40.000 0.00 0.00 36.63 3.36
1820 1973 5.845391 AGTTTCCATCGACAAAAAGGAAA 57.155 34.783 0.00 0.00 43.80 3.13
1821 1974 5.831997 AGTTTCCATCGACAAAAAGGAAAG 58.168 37.500 5.27 0.00 45.83 2.62
1822 1975 4.846779 TTCCATCGACAAAAAGGAAAGG 57.153 40.909 0.00 0.00 35.57 3.11
1823 1976 4.093472 TCCATCGACAAAAAGGAAAGGA 57.907 40.909 0.00 0.00 0.00 3.36
1828 1981 6.460953 CCATCGACAAAAAGGAAAGGAAAAGA 60.461 38.462 0.00 0.00 0.00 2.52
1830 1983 6.560711 TCGACAAAAAGGAAAGGAAAAGAAG 58.439 36.000 0.00 0.00 0.00 2.85
1836 1989 9.091784 CAAAAAGGAAAGGAAAAGAAGAAGAAG 57.908 33.333 0.00 0.00 0.00 2.85
1838 1991 8.595362 AAAGGAAAGGAAAAGAAGAAGAAGAA 57.405 30.769 0.00 0.00 0.00 2.52
1852 2011 3.836365 AGAAGAAATCCTAGCTGAGGC 57.164 47.619 0.00 0.00 46.25 4.70
1868 2027 4.754114 GCTGAGGCTGAAGGTGAAATATAG 59.246 45.833 0.00 0.00 35.22 1.31
1871 2030 5.163301 TGAGGCTGAAGGTGAAATATAGGAC 60.163 44.000 0.00 0.00 0.00 3.85
1872 2031 4.971924 AGGCTGAAGGTGAAATATAGGACT 59.028 41.667 0.00 0.00 0.00 3.85
1873 2032 6.143915 AGGCTGAAGGTGAAATATAGGACTA 58.856 40.000 0.00 0.00 0.00 2.59
1874 2033 6.789959 AGGCTGAAGGTGAAATATAGGACTAT 59.210 38.462 0.00 0.00 0.00 2.12
1875 2034 7.956315 AGGCTGAAGGTGAAATATAGGACTATA 59.044 37.037 1.83 1.83 33.09 1.31
1876 2035 8.254508 GGCTGAAGGTGAAATATAGGACTATAG 58.745 40.741 0.00 0.00 32.18 1.31
1878 2037 9.535170 CTGAAGGTGAAATATAGGACTATAGGA 57.465 37.037 4.43 0.00 32.18 2.94
1879 2038 9.892444 TGAAGGTGAAATATAGGACTATAGGAA 57.108 33.333 4.43 0.00 32.18 3.36
1918 2077 4.495422 AGTTACTGCTATGAAACTGACCG 58.505 43.478 0.00 0.00 31.20 4.79
1947 2106 9.757227 GGATAATGGATCGAGGAATATAAAGAG 57.243 37.037 0.00 0.00 35.12 2.85
1954 2113 4.283722 TCGAGGAATATAAAGAGAAGGGGC 59.716 45.833 0.00 0.00 0.00 5.80
2022 2181 7.148474 CGAATTCAGTATTTCTCTTTTCCCGAA 60.148 37.037 6.22 0.00 0.00 4.30
2088 2248 3.187700 ACGCGATTGATGTTACTTCCTC 58.812 45.455 15.93 0.00 0.00 3.71
2119 2329 0.035739 GTGGTAACTCAGCGGGGAAA 59.964 55.000 0.00 0.00 37.61 3.13
2131 2341 0.179081 CGGGGAAAATCGAGTCTCCC 60.179 60.000 16.06 16.06 45.99 4.30
2142 2363 3.977312 TCGAGTCTCCCCTTAGATTCAA 58.023 45.455 0.00 0.00 33.16 2.69
2149 2370 7.366226 AGTCTCCCCTTAGATTCAAAGATCTA 58.634 38.462 0.00 0.00 37.54 1.98
2158 2379 6.516739 AGATTCAAAGATCTACTCGTGACA 57.483 37.500 0.00 0.00 34.68 3.58
2173 2394 7.352719 ACTCGTGACAGTCTATTTTTCAATC 57.647 36.000 1.31 0.00 0.00 2.67
2174 2395 7.155328 ACTCGTGACAGTCTATTTTTCAATCT 58.845 34.615 1.31 0.00 0.00 2.40
2176 2397 8.378172 TCGTGACAGTCTATTTTTCAATCTTT 57.622 30.769 1.31 0.00 0.00 2.52
2178 2399 9.107367 CGTGACAGTCTATTTTTCAATCTTTTC 57.893 33.333 1.31 0.00 0.00 2.29
2179 2400 9.399403 GTGACAGTCTATTTTTCAATCTTTTCC 57.601 33.333 1.31 0.00 0.00 3.13
2180 2401 9.354673 TGACAGTCTATTTTTCAATCTTTTCCT 57.645 29.630 1.31 0.00 0.00 3.36
2199 2432 4.344978 TCCTCTCTCTTTTCTGATTCCGA 58.655 43.478 0.00 0.00 0.00 4.55
2201 2434 4.159506 CCTCTCTCTTTTCTGATTCCGACT 59.840 45.833 0.00 0.00 0.00 4.18
2207 2440 3.319137 TTTCTGATTCCGACTGTGGAG 57.681 47.619 0.00 0.00 39.72 3.86
2210 2443 2.690497 TCTGATTCCGACTGTGGAGATC 59.310 50.000 0.00 0.00 39.72 2.75
2214 2447 3.526931 TTCCGACTGTGGAGATCAATC 57.473 47.619 0.00 0.00 39.72 2.67
2215 2448 1.405463 TCCGACTGTGGAGATCAATCG 59.595 52.381 0.00 0.00 33.05 3.34
2216 2449 1.405463 CCGACTGTGGAGATCAATCGA 59.595 52.381 0.00 0.00 32.51 3.59
2240 2473 2.125832 TAAAACGCTCGGCTCCGG 60.126 61.111 8.59 0.00 40.25 5.14
2250 2483 3.062466 GGCTCCGGTTTGCCCTTC 61.062 66.667 19.83 1.37 43.11 3.46
2255 2488 0.538746 TCCGGTTTGCCCTTCCTTTC 60.539 55.000 0.00 0.00 0.00 2.62
2258 2491 0.679505 GGTTTGCCCTTCCTTTCCAC 59.320 55.000 0.00 0.00 0.00 4.02
2263 2496 1.272092 TGCCCTTCCTTTCCACTCATG 60.272 52.381 0.00 0.00 0.00 3.07
2264 2497 1.272147 GCCCTTCCTTTCCACTCATGT 60.272 52.381 0.00 0.00 0.00 3.21
2265 2498 2.716217 CCCTTCCTTTCCACTCATGTC 58.284 52.381 0.00 0.00 0.00 3.06
2266 2499 2.307098 CCCTTCCTTTCCACTCATGTCT 59.693 50.000 0.00 0.00 0.00 3.41
2267 2500 3.519510 CCCTTCCTTTCCACTCATGTCTA 59.480 47.826 0.00 0.00 0.00 2.59
2268 2501 4.508662 CCTTCCTTTCCACTCATGTCTAC 58.491 47.826 0.00 0.00 0.00 2.59
2269 2502 4.223923 CCTTCCTTTCCACTCATGTCTACT 59.776 45.833 0.00 0.00 0.00 2.57
2270 2503 5.407407 TTCCTTTCCACTCATGTCTACTC 57.593 43.478 0.00 0.00 0.00 2.59
2271 2504 4.678256 TCCTTTCCACTCATGTCTACTCT 58.322 43.478 0.00 0.00 0.00 3.24
2272 2505 5.827756 TCCTTTCCACTCATGTCTACTCTA 58.172 41.667 0.00 0.00 0.00 2.43
2284 2517 2.695666 GTCTACTCTAGGCCATGAGCAA 59.304 50.000 20.50 11.03 46.50 3.91
2286 2519 3.969976 TCTACTCTAGGCCATGAGCAATT 59.030 43.478 20.50 7.67 46.50 2.32
2287 2520 2.928334 ACTCTAGGCCATGAGCAATTG 58.072 47.619 20.50 0.00 46.50 2.32
2288 2521 2.507058 ACTCTAGGCCATGAGCAATTGA 59.493 45.455 20.50 0.00 46.50 2.57
2289 2522 3.139850 CTCTAGGCCATGAGCAATTGAG 58.860 50.000 10.34 1.78 46.50 3.02
2290 2523 1.607628 CTAGGCCATGAGCAATTGAGC 59.392 52.381 10.34 0.00 46.50 4.26
2293 2526 1.138266 GGCCATGAGCAATTGAGCATT 59.862 47.619 10.34 0.00 46.50 3.56
2294 2527 2.419574 GGCCATGAGCAATTGAGCATTT 60.420 45.455 10.34 0.00 46.50 2.32
2332 2584 6.480320 TCCATTACCAAAACATTTTCAAACGG 59.520 34.615 0.00 0.00 0.00 4.44
2333 2585 6.480320 CCATTACCAAAACATTTTCAAACGGA 59.520 34.615 0.00 0.00 0.00 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.064060 GCTAAACGCAGCGATCCATTT 59.936 47.619 24.65 13.54 38.92 2.32
1 2 0.657840 GCTAAACGCAGCGATCCATT 59.342 50.000 24.65 10.37 38.92 3.16
2 3 2.311294 GCTAAACGCAGCGATCCAT 58.689 52.632 24.65 4.83 38.92 3.41
3 4 3.794270 GCTAAACGCAGCGATCCA 58.206 55.556 24.65 0.00 38.92 3.41
163 254 2.420022 CAGACTAACCAAAAGGCCATCG 59.580 50.000 5.01 0.00 0.00 3.84
169 260 4.828829 ACGATACCAGACTAACCAAAAGG 58.171 43.478 0.00 0.00 0.00 3.11
239 338 1.630148 CGTCGGTGATCTGTTTCCTC 58.370 55.000 0.00 0.00 0.00 3.71
242 341 1.702299 CGCGTCGGTGATCTGTTTC 59.298 57.895 0.00 0.00 0.00 2.78
281 380 1.824852 GGAATTGGAAGCACCCGAATT 59.175 47.619 0.00 0.00 38.00 2.17
282 381 1.272425 TGGAATTGGAAGCACCCGAAT 60.272 47.619 0.00 0.00 38.00 3.34
283 382 0.111446 TGGAATTGGAAGCACCCGAA 59.889 50.000 0.00 0.00 38.00 4.30
284 383 0.331278 ATGGAATTGGAAGCACCCGA 59.669 50.000 0.00 0.00 38.00 5.14
318 417 2.643551 ACTGGAGGCAACATTATTCCG 58.356 47.619 0.00 0.00 41.41 4.30
364 463 2.866460 GCTGTGCATATGTAGTACCGGG 60.866 54.545 6.32 0.00 0.00 5.73
393 495 4.406943 CAGCAATCCTTTAAGAACTTCGC 58.593 43.478 0.00 0.00 0.00 4.70
537 639 4.157656 AGCTGTGCACTGTTCTAACAAAAA 59.842 37.500 22.70 0.00 38.66 1.94
538 640 3.694072 AGCTGTGCACTGTTCTAACAAAA 59.306 39.130 22.70 0.00 38.66 2.44
539 641 3.278574 AGCTGTGCACTGTTCTAACAAA 58.721 40.909 22.70 0.00 38.66 2.83
540 642 2.872245 GAGCTGTGCACTGTTCTAACAA 59.128 45.455 26.06 0.20 38.66 2.83
541 643 2.103094 AGAGCTGTGCACTGTTCTAACA 59.897 45.455 31.78 4.66 34.63 2.41
542 644 2.760374 AGAGCTGTGCACTGTTCTAAC 58.240 47.619 31.78 13.27 34.63 2.34
543 645 3.475566 AAGAGCTGTGCACTGTTCTAA 57.524 42.857 32.52 7.02 35.14 2.10
544 646 4.280929 TCTTAAGAGCTGTGCACTGTTCTA 59.719 41.667 32.52 21.63 35.14 2.10
545 647 3.070159 TCTTAAGAGCTGTGCACTGTTCT 59.930 43.478 28.97 28.97 37.07 3.01
546 648 3.393800 TCTTAAGAGCTGTGCACTGTTC 58.606 45.455 26.04 26.04 28.62 3.18
547 649 3.475566 TCTTAAGAGCTGTGCACTGTT 57.524 42.857 22.70 18.11 28.62 3.16
548 650 3.475566 TTCTTAAGAGCTGTGCACTGT 57.524 42.857 22.70 11.17 28.62 3.55
549 651 6.486253 TTAATTCTTAAGAGCTGTGCACTG 57.514 37.500 19.41 18.94 28.62 3.66
550 652 6.150140 CCTTTAATTCTTAAGAGCTGTGCACT 59.850 38.462 19.41 0.00 0.00 4.40
551 653 6.149474 TCCTTTAATTCTTAAGAGCTGTGCAC 59.851 38.462 10.75 10.75 0.00 4.57
552 654 6.237901 TCCTTTAATTCTTAAGAGCTGTGCA 58.762 36.000 5.12 0.00 0.00 4.57
553 655 6.743575 TCCTTTAATTCTTAAGAGCTGTGC 57.256 37.500 5.12 0.00 0.00 4.57
554 656 8.950210 TCATTCCTTTAATTCTTAAGAGCTGTG 58.050 33.333 5.12 0.00 0.00 3.66
571 673 7.454694 GGGCCAACCTATATTAATCATTCCTTT 59.545 37.037 4.39 0.00 35.85 3.11
614 719 8.094548 TCCTCAAAGAAAGTTCTTCATCGATTA 58.905 33.333 6.76 0.00 46.22 1.75
616 721 6.370166 GTCCTCAAAGAAAGTTCTTCATCGAT 59.630 38.462 6.76 0.00 46.22 3.59
617 722 5.696724 GTCCTCAAAGAAAGTTCTTCATCGA 59.303 40.000 6.76 0.00 46.22 3.59
618 723 5.106908 GGTCCTCAAAGAAAGTTCTTCATCG 60.107 44.000 6.76 0.00 46.22 3.84
619 724 6.000840 AGGTCCTCAAAGAAAGTTCTTCATC 58.999 40.000 6.76 0.00 46.22 2.92
620 725 5.767168 CAGGTCCTCAAAGAAAGTTCTTCAT 59.233 40.000 6.76 0.00 46.22 2.57
627 732 5.510430 AGTTTTCAGGTCCTCAAAGAAAGT 58.490 37.500 0.00 0.00 30.83 2.66
628 733 6.456795 AAGTTTTCAGGTCCTCAAAGAAAG 57.543 37.500 0.00 0.00 30.83 2.62
630 735 5.949354 TGAAAGTTTTCAGGTCCTCAAAGAA 59.051 36.000 3.28 0.00 41.88 2.52
631 736 5.505780 TGAAAGTTTTCAGGTCCTCAAAGA 58.494 37.500 3.28 0.00 41.88 2.52
632 737 5.835113 TGAAAGTTTTCAGGTCCTCAAAG 57.165 39.130 3.28 0.00 41.88 2.77
633 738 5.949354 TCTTGAAAGTTTTCAGGTCCTCAAA 59.051 36.000 14.01 0.00 46.68 2.69
641 746 3.312421 TCAGCGTCTTGAAAGTTTTCAGG 59.688 43.478 9.65 9.65 46.68 3.86
654 759 4.699522 GGGCCGGTTCAGCGTCTT 62.700 66.667 1.90 0.00 0.00 3.01
662 767 0.174845 GGCTTTATTTGGGCCGGTTC 59.825 55.000 1.90 0.00 36.37 3.62
691 796 3.847621 GGCCAGGCCTAATGAAGC 58.152 61.111 24.99 1.34 46.69 3.86
718 823 3.374042 TGGGTCACCAACTTTCAGAAA 57.626 42.857 0.00 0.00 45.87 2.52
730 835 0.611714 ACTACACGGAATGGGTCACC 59.388 55.000 0.00 0.00 37.24 4.02
735 840 1.137086 CTCCAGACTACACGGAATGGG 59.863 57.143 0.00 0.00 0.00 4.00
736 841 1.471676 GCTCCAGACTACACGGAATGG 60.472 57.143 0.00 0.00 0.00 3.16
759 864 0.037590 CCCACACGGATTTTCTCCCA 59.962 55.000 0.00 0.00 41.49 4.37
920 1048 3.751518 ACCGGCCATGAATTATAAGGTC 58.248 45.455 0.00 0.00 0.00 3.85
924 1052 5.630121 AGAATGACCGGCCATGAATTATAA 58.370 37.500 3.17 0.00 0.00 0.98
927 1055 3.576078 AGAATGACCGGCCATGAATTA 57.424 42.857 3.17 0.00 0.00 1.40
939 1067 4.096833 TGATGTGCTGCAAATAGAATGACC 59.903 41.667 5.05 0.00 0.00 4.02
980 1115 6.121776 ACATGTTGGATACTGTACTTGGAA 57.878 37.500 0.00 0.00 37.61 3.53
981 1116 5.338056 GGACATGTTGGATACTGTACTTGGA 60.338 44.000 0.00 0.00 37.61 3.53
982 1117 4.876107 GGACATGTTGGATACTGTACTTGG 59.124 45.833 0.00 0.00 37.61 3.61
983 1118 4.876107 GGGACATGTTGGATACTGTACTTG 59.124 45.833 0.00 0.00 37.61 3.16
986 1121 3.454375 CGGGACATGTTGGATACTGTAC 58.546 50.000 0.00 0.00 37.61 2.90
988 1123 1.209504 CCGGGACATGTTGGATACTGT 59.790 52.381 0.00 0.00 37.61 3.55
996 1135 1.666209 GGAATGGCCGGGACATGTTG 61.666 60.000 17.98 0.00 28.30 3.33
1021 1160 1.052124 AGGACCAGTGGGACGAACAA 61.052 55.000 15.21 0.00 38.05 2.83
1344 1483 5.743117 ACAACTGGAGACTAGTAGTACGAT 58.257 41.667 1.88 0.00 0.00 3.73
1362 1506 3.441496 TCGTCAACTTCGGTTACAACT 57.559 42.857 0.00 0.00 36.26 3.16
1397 1542 7.494625 AGCCGATTTTATTTCAGACGATCTTAA 59.505 33.333 0.00 0.00 0.00 1.85
1405 1550 5.490213 CACGTAGCCGATTTTATTTCAGAC 58.510 41.667 0.00 0.00 37.88 3.51
1458 1605 7.696453 GCCGAATTTGATCATATTATTAACCCG 59.304 37.037 10.85 8.52 0.00 5.28
1459 1606 7.696453 CGCCGAATTTGATCATATTATTAACCC 59.304 37.037 10.85 0.00 0.00 4.11
1473 1620 0.810648 ACATGTGCGCCGAATTTGAT 59.189 45.000 4.18 0.00 0.00 2.57
1477 1624 2.682856 AGATAAACATGTGCGCCGAATT 59.317 40.909 4.18 0.00 0.00 2.17
1479 1626 1.732941 AGATAAACATGTGCGCCGAA 58.267 45.000 4.18 0.00 0.00 4.30
1481 1628 2.599848 GCTTAGATAAACATGTGCGCCG 60.600 50.000 4.18 0.00 0.00 6.46
1482 1629 2.287009 GGCTTAGATAAACATGTGCGCC 60.287 50.000 4.18 0.00 0.00 6.53
1483 1630 2.354510 TGGCTTAGATAAACATGTGCGC 59.645 45.455 0.00 0.00 0.00 6.09
1484 1631 4.530388 CATGGCTTAGATAAACATGTGCG 58.470 43.478 0.00 0.00 35.44 5.34
1488 1635 5.236263 TGCGTACATGGCTTAGATAAACATG 59.764 40.000 0.00 12.06 43.29 3.21
1489 1636 5.364778 TGCGTACATGGCTTAGATAAACAT 58.635 37.500 0.00 0.00 0.00 2.71
1490 1637 4.760878 TGCGTACATGGCTTAGATAAACA 58.239 39.130 0.00 0.00 0.00 2.83
1491 1638 4.318831 GCTGCGTACATGGCTTAGATAAAC 60.319 45.833 0.00 0.00 0.00 2.01
1492 1639 3.807622 GCTGCGTACATGGCTTAGATAAA 59.192 43.478 0.00 0.00 0.00 1.40
1493 1640 3.181470 TGCTGCGTACATGGCTTAGATAA 60.181 43.478 0.00 0.00 0.00 1.75
1494 1641 2.364002 TGCTGCGTACATGGCTTAGATA 59.636 45.455 0.00 0.00 0.00 1.98
1495 1642 1.138859 TGCTGCGTACATGGCTTAGAT 59.861 47.619 0.00 0.00 0.00 1.98
1496 1643 0.534873 TGCTGCGTACATGGCTTAGA 59.465 50.000 0.00 0.00 0.00 2.10
1497 1644 0.652592 GTGCTGCGTACATGGCTTAG 59.347 55.000 0.00 0.00 0.00 2.18
1498 1645 0.036858 TGTGCTGCGTACATGGCTTA 60.037 50.000 0.00 0.00 0.00 3.09
1499 1646 0.888736 TTGTGCTGCGTACATGGCTT 60.889 50.000 0.00 0.00 0.00 4.35
1500 1647 0.888736 TTTGTGCTGCGTACATGGCT 60.889 50.000 0.00 0.00 0.00 4.75
1501 1648 0.454957 CTTTGTGCTGCGTACATGGC 60.455 55.000 0.00 0.00 0.00 4.40
1502 1649 0.874390 ACTTTGTGCTGCGTACATGG 59.126 50.000 0.00 0.00 0.00 3.66
1503 1650 2.032117 TGAACTTTGTGCTGCGTACATG 60.032 45.455 0.00 0.00 0.00 3.21
1504 1651 2.217750 TGAACTTTGTGCTGCGTACAT 58.782 42.857 0.00 0.00 0.00 2.29
1505 1652 1.657822 TGAACTTTGTGCTGCGTACA 58.342 45.000 0.00 0.00 0.00 2.90
1506 1653 2.748461 TTGAACTTTGTGCTGCGTAC 57.252 45.000 0.00 0.00 0.00 3.67
1507 1654 3.313803 TGAATTGAACTTTGTGCTGCGTA 59.686 39.130 0.00 0.00 0.00 4.42
1508 1655 2.098934 TGAATTGAACTTTGTGCTGCGT 59.901 40.909 0.00 0.00 0.00 5.24
1509 1656 2.722629 CTGAATTGAACTTTGTGCTGCG 59.277 45.455 0.00 0.00 0.00 5.18
1510 1657 3.709987 ACTGAATTGAACTTTGTGCTGC 58.290 40.909 0.00 0.00 0.00 5.25
1511 1658 4.741676 GGAACTGAATTGAACTTTGTGCTG 59.258 41.667 0.00 0.00 0.00 4.41
1512 1659 4.646492 AGGAACTGAATTGAACTTTGTGCT 59.354 37.500 0.00 0.00 37.18 4.40
1513 1660 4.936891 AGGAACTGAATTGAACTTTGTGC 58.063 39.130 0.00 0.00 37.18 4.57
1543 1690 9.622004 CTTATTACATACGTACTCCGATTGAAT 57.378 33.333 0.00 0.00 40.70 2.57
1567 1714 9.694137 GAGATGTCTATTTTATACGCCTTACTT 57.306 33.333 0.00 0.00 0.00 2.24
1569 1716 8.305317 AGGAGATGTCTATTTTATACGCCTTAC 58.695 37.037 0.00 0.00 0.00 2.34
1574 1726 6.688578 TGGAGGAGATGTCTATTTTATACGC 58.311 40.000 0.00 0.00 0.00 4.42
1626 1778 2.919229 ACGTAGGAAAAGTACGATTGCG 59.081 45.455 9.47 0.00 44.90 4.85
1631 1783 6.144402 GTCATTTTCACGTAGGAAAAGTACGA 59.856 38.462 16.07 9.19 46.45 3.43
1733 1886 1.139058 ACATTAGACAGTGGCCGATCC 59.861 52.381 0.00 0.00 0.00 3.36
1817 1970 8.855110 AGGATTTCTTCTTCTTCTTTTCCTTTC 58.145 33.333 0.00 0.00 0.00 2.62
1818 1971 8.774546 AGGATTTCTTCTTCTTCTTTTCCTTT 57.225 30.769 0.00 0.00 0.00 3.11
1819 1972 9.513906 CTAGGATTTCTTCTTCTTCTTTTCCTT 57.486 33.333 0.00 0.00 32.42 3.36
1820 1973 7.609918 GCTAGGATTTCTTCTTCTTCTTTTCCT 59.390 37.037 0.00 0.00 34.43 3.36
1821 1974 7.609918 AGCTAGGATTTCTTCTTCTTCTTTTCC 59.390 37.037 0.00 0.00 0.00 3.13
1822 1975 8.450180 CAGCTAGGATTTCTTCTTCTTCTTTTC 58.550 37.037 0.00 0.00 0.00 2.29
1823 1976 8.160106 TCAGCTAGGATTTCTTCTTCTTCTTTT 58.840 33.333 0.00 0.00 0.00 2.27
1852 2011 9.535170 TCCTATAGTCCTATATTTCACCTTCAG 57.465 37.037 0.00 0.00 0.00 3.02
1918 2077 4.559862 ATTCCTCGATCCATTATCCACC 57.440 45.455 0.00 0.00 0.00 4.61
1947 2106 1.671328 GATACTGCTTTTCGCCCCTTC 59.329 52.381 0.00 0.00 38.05 3.46
2088 2248 1.072331 AGTTACCACTTGCTCCACTGG 59.928 52.381 0.00 0.00 0.00 4.00
2119 2329 4.547671 TGAATCTAAGGGGAGACTCGATT 58.452 43.478 0.00 0.00 34.16 3.34
2131 2341 7.646130 GTCACGAGTAGATCTTTGAATCTAAGG 59.354 40.741 0.00 0.00 39.37 2.69
2142 2363 7.633193 AAATAGACTGTCACGAGTAGATCTT 57.367 36.000 10.88 0.00 0.00 2.40
2149 2370 7.155328 AGATTGAAAAATAGACTGTCACGAGT 58.845 34.615 10.88 0.00 0.00 4.18
2173 2394 6.091986 CGGAATCAGAAAAGAGAGAGGAAAAG 59.908 42.308 0.00 0.00 0.00 2.27
2174 2395 5.934625 CGGAATCAGAAAAGAGAGAGGAAAA 59.065 40.000 0.00 0.00 0.00 2.29
2176 2397 4.772624 TCGGAATCAGAAAAGAGAGAGGAA 59.227 41.667 0.00 0.00 0.00 3.36
2178 2399 4.159506 AGTCGGAATCAGAAAAGAGAGAGG 59.840 45.833 0.00 0.00 0.00 3.69
2179 2400 5.101628 CAGTCGGAATCAGAAAAGAGAGAG 58.898 45.833 0.00 0.00 0.00 3.20
2180 2401 4.524714 ACAGTCGGAATCAGAAAAGAGAGA 59.475 41.667 0.00 0.00 0.00 3.10
2210 2443 5.126423 CGAGCGTTTTAGATTGATCGATTG 58.874 41.667 0.00 0.00 0.00 2.67
2214 2447 2.347661 GCCGAGCGTTTTAGATTGATCG 60.348 50.000 0.00 0.00 0.00 3.69
2215 2448 2.866762 AGCCGAGCGTTTTAGATTGATC 59.133 45.455 0.00 0.00 0.00 2.92
2216 2449 2.866762 GAGCCGAGCGTTTTAGATTGAT 59.133 45.455 0.00 0.00 0.00 2.57
2219 2452 1.653151 GGAGCCGAGCGTTTTAGATT 58.347 50.000 0.00 0.00 0.00 2.40
2240 2473 1.613925 GAGTGGAAAGGAAGGGCAAAC 59.386 52.381 0.00 0.00 0.00 2.93
2250 2483 5.068460 CCTAGAGTAGACATGAGTGGAAAGG 59.932 48.000 0.00 0.00 0.00 3.11
2255 2488 2.625790 GGCCTAGAGTAGACATGAGTGG 59.374 54.545 0.00 0.00 0.00 4.00
2258 2491 4.148079 TCATGGCCTAGAGTAGACATGAG 58.852 47.826 10.26 0.00 41.05 2.90
2263 2496 2.311463 TGCTCATGGCCTAGAGTAGAC 58.689 52.381 21.06 9.15 40.92 2.59
2264 2497 2.755952 TGCTCATGGCCTAGAGTAGA 57.244 50.000 21.06 7.71 40.92 2.59
2265 2498 4.063689 CAATTGCTCATGGCCTAGAGTAG 58.936 47.826 21.06 6.65 40.92 2.57
2266 2499 3.711190 TCAATTGCTCATGGCCTAGAGTA 59.289 43.478 21.06 16.21 40.92 2.59
2267 2500 2.507058 TCAATTGCTCATGGCCTAGAGT 59.493 45.455 21.06 4.44 40.92 3.24
2268 2501 3.139850 CTCAATTGCTCATGGCCTAGAG 58.860 50.000 17.48 17.48 40.92 2.43
2269 2502 2.747467 GCTCAATTGCTCATGGCCTAGA 60.747 50.000 3.32 0.08 40.92 2.43
2270 2503 1.607628 GCTCAATTGCTCATGGCCTAG 59.392 52.381 3.32 0.00 40.92 3.02
2271 2504 1.064537 TGCTCAATTGCTCATGGCCTA 60.065 47.619 3.32 0.00 40.92 3.93
2272 2505 0.323999 TGCTCAATTGCTCATGGCCT 60.324 50.000 3.32 0.00 40.92 5.19
2284 2517 5.552870 ACCTACTCCGATAAATGCTCAAT 57.447 39.130 0.00 0.00 0.00 2.57
2286 2519 4.202223 GGAACCTACTCCGATAAATGCTCA 60.202 45.833 0.00 0.00 0.00 4.26
2287 2520 4.202223 TGGAACCTACTCCGATAAATGCTC 60.202 45.833 0.00 0.00 38.44 4.26
2288 2521 3.709653 TGGAACCTACTCCGATAAATGCT 59.290 43.478 0.00 0.00 38.44 3.79
2289 2522 4.067972 TGGAACCTACTCCGATAAATGC 57.932 45.455 0.00 0.00 38.44 3.56
2290 2523 6.649557 GGTAATGGAACCTACTCCGATAAATG 59.350 42.308 0.00 0.00 38.44 2.32
2293 2526 5.210430 TGGTAATGGAACCTACTCCGATAA 58.790 41.667 0.00 0.00 40.44 1.75
2294 2527 4.806892 TGGTAATGGAACCTACTCCGATA 58.193 43.478 0.00 0.00 40.44 2.92


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

AutoCloner maintained by Alex Coulton.