Multiple sequence alignment - TraesCS3D01G418300

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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 TraesCS3D01G418300 chr3D 100.000 2685 0 0 1 2685 531051594 531048910 0.000000e+00 4959
1 TraesCS3D01G418300 chr3B 86.694 2202 130 71 256 2399 701413428 701411332 0.000000e+00 2292
2 TraesCS3D01G418300 chr3B 92.157 306 17 3 1 299 701413753 701413448 2.470000e-115 425
3 TraesCS3D01G418300 chr3B 83.117 308 28 12 2398 2685 701411250 701410947 2.650000e-65 259
4 TraesCS3D01G418300 chr3A 89.303 1907 81 43 805 2652 664690661 664688819 0.000000e+00 2278
5 TraesCS3D01G418300 chr3A 87.737 685 47 14 1 665 664691602 664690935 0.000000e+00 765
6 TraesCS3D01G418300 chr6A 83.102 361 33 13 2264 2603 588758916 588759269 1.210000e-78 303
7 TraesCS3D01G418300 chr6A 82.825 361 36 15 2264 2603 32422528 32422173 1.560000e-77 300
8 TraesCS3D01G418300 chr6A 82.825 361 36 15 2264 2603 32530143 32529788 1.560000e-77 300
9 TraesCS3D01G418300 chr6A 82.825 361 36 15 2264 2603 32556328 32555973 1.560000e-77 300
10 TraesCS3D01G418300 chr2B 90.323 124 12 0 2529 2652 132707037 132707160 2.140000e-36 163


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 TraesCS3D01G418300 chr3D 531048910 531051594 2684 True 4959.0 4959 100.000000 1 2685 1 chr3D.!!$R1 2684
1 TraesCS3D01G418300 chr3B 701410947 701413753 2806 True 992.0 2292 87.322667 1 2685 3 chr3B.!!$R1 2684
2 TraesCS3D01G418300 chr3A 664688819 664691602 2783 True 1521.5 2278 88.520000 1 2652 2 chr3A.!!$R1 2651

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
666 762 0.178955 CATGGGCATAGGCATGGGAA 60.179 55.0 0.15 0.0 43.71 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1756 2034 0.111639 GGCAACCCCAGAAGTAACCA 59.888 55.0 0.0 0.0 0.0 3.67 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
31 32 3.637273 GACCACAGGGCGAAGGGT 61.637 66.667 0.00 0.00 37.90 4.34
32 33 2.203877 ACCACAGGGCGAAGGGTA 60.204 61.111 0.00 0.00 37.90 3.69
41 43 1.320507 GGCGAAGGGTAGAGAGGTAG 58.679 60.000 0.00 0.00 0.00 3.18
67 74 2.258286 GCAAAACTTGGCGCCGAT 59.742 55.556 23.90 6.50 0.00 4.18
102 109 1.596220 CGCCATCATGATCTTGTTGCG 60.596 52.381 4.86 18.99 0.00 4.85
326 399 2.344025 GTAACAGTGTGGAATCGTCCC 58.656 52.381 0.00 0.00 44.23 4.46
353 426 0.962855 GGGCACTTCCTCTCAAAGCC 60.963 60.000 0.00 0.00 39.86 4.35
373 446 2.851824 CCGCCGCACAAATTTTATTCTC 59.148 45.455 0.00 0.00 0.00 2.87
403 479 7.357429 TGACACTTGTGATGATGATCTAGAT 57.643 36.000 4.47 4.47 0.00 1.98
418 497 7.390013 TGATCTAGATAGTACAGTACCACCT 57.610 40.000 4.89 4.66 0.00 4.00
421 500 9.962809 GATCTAGATAGTACAGTACCACCTAAT 57.037 37.037 4.89 3.83 0.00 1.73
422 501 9.962809 ATCTAGATAGTACAGTACCACCTAATC 57.037 37.037 2.53 2.37 0.00 1.75
439 518 6.963805 CACCTAATCGAAGAAGCTTGATTTTC 59.036 38.462 2.10 1.69 43.58 2.29
453 532 5.860716 GCTTGATTTTCAATTCCTGACTGAC 59.139 40.000 0.00 0.00 35.59 3.51
463 542 1.595993 CCTGACTGACGATCCGGTGT 61.596 60.000 0.00 0.00 0.00 4.16
469 548 2.360852 ACGATCCGGTGTCCGTCT 60.361 61.111 0.00 0.00 46.80 4.18
470 549 2.320339 GACGATCCGGTGTCCGTCTC 62.320 65.000 22.76 7.88 46.80 3.36
510 589 4.637483 ACAACAGTGTCAATTTGTCCTG 57.363 40.909 0.00 4.24 29.49 3.86
512 591 1.956477 ACAGTGTCAATTTGTCCTGGC 59.044 47.619 13.30 0.00 0.00 4.85
524 607 0.957888 GTCCTGGCCTCTTGCAAGAC 60.958 60.000 25.16 16.01 44.57 3.01
599 686 4.838152 CGCCATCCCAGTGACCCG 62.838 72.222 0.00 0.00 0.00 5.28
627 714 1.537638 CGTCCACATCGAGATCCTAGG 59.462 57.143 0.82 0.82 0.00 3.02
629 716 1.133482 TCCACATCGAGATCCTAGGCA 60.133 52.381 2.96 0.00 0.00 4.75
630 717 1.688735 CCACATCGAGATCCTAGGCAA 59.311 52.381 2.96 0.00 0.00 4.52
637 733 2.352617 CGAGATCCTAGGCAAGATCAGC 60.353 54.545 2.96 0.00 41.16 4.26
650 746 4.917998 GCAAGATCAGCAGCAATTATCATG 59.082 41.667 5.41 0.00 0.00 3.07
656 752 3.508402 CAGCAGCAATTATCATGGGCATA 59.492 43.478 0.00 0.00 0.00 3.14
662 758 4.679639 GCAATTATCATGGGCATAGGCATG 60.680 45.833 0.15 0.00 43.71 4.06
665 761 1.067173 TCATGGGCATAGGCATGGGA 61.067 55.000 0.15 0.00 43.71 4.37
666 762 0.178955 CATGGGCATAGGCATGGGAA 60.179 55.000 0.15 0.00 43.71 3.97
682 778 1.202475 GGGAAGGAAGATCTCGAGTGC 60.202 57.143 13.13 5.76 0.00 4.40
683 779 1.535015 GGAAGGAAGATCTCGAGTGCG 60.535 57.143 13.13 0.00 39.35 5.34
684 780 0.179124 AAGGAAGATCTCGAGTGCGC 60.179 55.000 13.13 0.00 37.46 6.09
685 781 1.941734 GGAAGATCTCGAGTGCGCG 60.942 63.158 13.13 0.00 37.46 6.86
686 782 1.941734 GAAGATCTCGAGTGCGCGG 60.942 63.158 13.13 0.00 37.46 6.46
708 804 1.019278 ATGAACGCGCCAAAGTCGAT 61.019 50.000 5.73 0.00 0.00 3.59
711 807 3.864686 CGCGCCAAAGTCGATGGG 61.865 66.667 0.00 0.00 38.44 4.00
773 1022 6.509656 CGTATTATTTACTGCCACTCCTGTA 58.490 40.000 0.00 0.00 0.00 2.74
775 1024 7.328737 CGTATTATTTACTGCCACTCCTGTATC 59.671 40.741 0.00 0.00 0.00 2.24
777 1026 2.848678 TACTGCCACTCCTGTATCCT 57.151 50.000 0.00 0.00 0.00 3.24
778 1027 1.198713 ACTGCCACTCCTGTATCCTG 58.801 55.000 0.00 0.00 0.00 3.86
779 1028 0.467384 CTGCCACTCCTGTATCCTGG 59.533 60.000 0.00 0.00 0.00 4.45
780 1029 0.252696 TGCCACTCCTGTATCCTGGT 60.253 55.000 0.00 0.00 0.00 4.00
781 1030 0.912486 GCCACTCCTGTATCCTGGTT 59.088 55.000 0.00 0.00 0.00 3.67
782 1031 1.282157 GCCACTCCTGTATCCTGGTTT 59.718 52.381 0.00 0.00 0.00 3.27
783 1032 2.681097 GCCACTCCTGTATCCTGGTTTC 60.681 54.545 0.00 0.00 0.00 2.78
784 1033 2.840651 CCACTCCTGTATCCTGGTTTCT 59.159 50.000 0.00 0.00 0.00 2.52
785 1034 4.030913 CCACTCCTGTATCCTGGTTTCTA 58.969 47.826 0.00 0.00 0.00 2.10
789 1038 6.551601 CACTCCTGTATCCTGGTTTCTATACT 59.448 42.308 0.00 0.00 0.00 2.12
799 1048 3.382546 TGGTTTCTATACTAGCGTCCACC 59.617 47.826 0.00 0.00 0.00 4.61
983 1237 1.003696 GAAAAGGACCTCACTCCCCAG 59.996 57.143 0.00 0.00 0.00 4.45
1089 1343 1.449956 GCTGCTCTTCCTCCTGCTG 60.450 63.158 0.00 0.00 0.00 4.41
1090 1344 1.449956 CTGCTCTTCCTCCTGCTGC 60.450 63.158 0.00 0.00 0.00 5.25
1091 1345 1.901654 CTGCTCTTCCTCCTGCTGCT 61.902 60.000 0.00 0.00 0.00 4.24
1132 1386 0.736325 CCACTCTTCACCGGTAAGCG 60.736 60.000 6.87 9.31 0.00 4.68
1133 1387 1.080025 ACTCTTCACCGGTAAGCGC 60.080 57.895 6.87 0.00 0.00 5.92
1134 1388 1.810030 CTCTTCACCGGTAAGCGCC 60.810 63.158 6.87 0.00 0.00 6.53
1135 1389 2.227089 CTCTTCACCGGTAAGCGCCT 62.227 60.000 6.87 0.00 0.00 5.52
1136 1390 0.966875 TCTTCACCGGTAAGCGCCTA 60.967 55.000 6.87 0.00 0.00 3.93
1137 1391 0.804933 CTTCACCGGTAAGCGCCTAC 60.805 60.000 6.87 7.67 0.00 3.18
1138 1392 1.534336 TTCACCGGTAAGCGCCTACA 61.534 55.000 17.49 0.00 0.00 2.74
1139 1393 1.808390 CACCGGTAAGCGCCTACAC 60.808 63.158 17.49 6.55 0.00 2.90
1140 1394 2.202837 CCGGTAAGCGCCTACACC 60.203 66.667 17.49 12.02 0.00 4.16
1141 1395 2.718073 CCGGTAAGCGCCTACACCT 61.718 63.158 17.49 0.00 0.00 4.00
1143 1397 1.143401 GGTAAGCGCCTACACCTCC 59.857 63.158 17.49 0.00 0.00 4.30
1144 1398 1.328430 GGTAAGCGCCTACACCTCCT 61.328 60.000 17.49 0.00 0.00 3.69
1145 1399 0.179108 GTAAGCGCCTACACCTCCTG 60.179 60.000 11.29 0.00 0.00 3.86
1148 1402 2.893398 CGCCTACACCTCCTGTCC 59.107 66.667 0.00 0.00 33.91 4.02
1149 1403 1.682684 CGCCTACACCTCCTGTCCT 60.683 63.158 0.00 0.00 33.91 3.85
1150 1404 1.901085 GCCTACACCTCCTGTCCTG 59.099 63.158 0.00 0.00 33.91 3.86
1151 1405 1.901085 CCTACACCTCCTGTCCTGC 59.099 63.158 0.00 0.00 33.91 4.85
1152 1406 0.616111 CCTACACCTCCTGTCCTGCT 60.616 60.000 0.00 0.00 33.91 4.24
1153 1407 1.270907 CTACACCTCCTGTCCTGCTT 58.729 55.000 0.00 0.00 33.91 3.91
1154 1408 0.976641 TACACCTCCTGTCCTGCTTG 59.023 55.000 0.00 0.00 33.91 4.01
1155 1409 1.673665 CACCTCCTGTCCTGCTTGC 60.674 63.158 0.00 0.00 0.00 4.01
1156 1410 2.435586 CCTCCTGTCCTGCTTGCG 60.436 66.667 0.00 0.00 0.00 4.85
1194 1448 0.901580 CTTGGCCCTGACATTGCCTT 60.902 55.000 14.45 0.00 45.56 4.35
1204 1458 0.964358 ACATTGCCTTGCCTGCTCTC 60.964 55.000 0.00 0.00 0.00 3.20
1205 1459 1.748122 ATTGCCTTGCCTGCTCTCG 60.748 57.895 0.00 0.00 0.00 4.04
1443 1703 3.585428 AACATCCCCAACCGCCCA 61.585 61.111 0.00 0.00 0.00 5.36
1473 1733 2.203788 TCCTTCACGCCCAGGTCT 60.204 61.111 0.00 0.00 0.00 3.85
1519 1779 2.107903 GCTCTGCTTCTGCTCTGCC 61.108 63.158 0.00 0.00 40.48 4.85
1531 1791 2.757508 TCTGCCCTGCTCTCGAGG 60.758 66.667 13.56 4.50 0.00 4.63
1576 1846 7.287235 AGGGCGATAGTAAGTATTTTAGAGTGT 59.713 37.037 0.00 0.00 39.35 3.55
1577 1847 7.381678 GGGCGATAGTAAGTATTTTAGAGTGTG 59.618 40.741 0.00 0.00 39.35 3.82
1579 1849 7.381678 GCGATAGTAAGTATTTTAGAGTGTGGG 59.618 40.741 0.00 0.00 39.35 4.61
1580 1850 8.411683 CGATAGTAAGTATTTTAGAGTGTGGGT 58.588 37.037 0.00 0.00 0.00 4.51
1584 1859 2.899303 ATTTTAGAGTGTGGGTGGGG 57.101 50.000 0.00 0.00 0.00 4.96
1708 1984 1.938585 TGGTGTAGCTGCTACCTCTT 58.061 50.000 30.80 0.00 36.24 2.85
1731 2007 4.955450 TGATGGATGGAATTGGTTGGTTAG 59.045 41.667 0.00 0.00 0.00 2.34
1732 2008 3.096092 TGGATGGAATTGGTTGGTTAGC 58.904 45.455 0.00 0.00 0.00 3.09
1743 2021 2.956333 GGTTGGTTAGCAAAAGAGTGGT 59.044 45.455 0.00 0.00 0.00 4.16
1755 2033 5.523369 CAAAAGAGTGGTTGATTTGGAGAC 58.477 41.667 0.00 0.00 0.00 3.36
1756 2034 4.713792 AAGAGTGGTTGATTTGGAGACT 57.286 40.909 0.00 0.00 0.00 3.24
1757 2035 4.013267 AGAGTGGTTGATTTGGAGACTG 57.987 45.455 0.00 0.00 0.00 3.51
1758 2036 3.077359 GAGTGGTTGATTTGGAGACTGG 58.923 50.000 0.00 0.00 0.00 4.00
1759 2037 2.443255 AGTGGTTGATTTGGAGACTGGT 59.557 45.455 0.00 0.00 0.00 4.00
1760 2038 3.117512 AGTGGTTGATTTGGAGACTGGTT 60.118 43.478 0.00 0.00 0.00 3.67
1761 2039 4.104102 AGTGGTTGATTTGGAGACTGGTTA 59.896 41.667 0.00 0.00 0.00 2.85
1762 2040 4.215613 GTGGTTGATTTGGAGACTGGTTAC 59.784 45.833 0.00 0.00 0.00 2.50
1763 2041 4.104102 TGGTTGATTTGGAGACTGGTTACT 59.896 41.667 0.00 0.00 0.00 2.24
1764 2042 5.070685 GGTTGATTTGGAGACTGGTTACTT 58.929 41.667 0.00 0.00 0.00 2.24
1765 2043 5.181433 GGTTGATTTGGAGACTGGTTACTTC 59.819 44.000 0.00 0.00 0.00 3.01
1766 2044 5.825593 TGATTTGGAGACTGGTTACTTCT 57.174 39.130 0.00 0.00 0.00 2.85
1767 2045 5.551233 TGATTTGGAGACTGGTTACTTCTG 58.449 41.667 0.00 0.00 0.00 3.02
1768 2046 4.351874 TTTGGAGACTGGTTACTTCTGG 57.648 45.455 0.00 0.00 0.00 3.86
1769 2047 2.257207 TGGAGACTGGTTACTTCTGGG 58.743 52.381 0.00 0.00 0.00 4.45
1770 2048 1.555533 GGAGACTGGTTACTTCTGGGG 59.444 57.143 0.00 0.00 0.00 4.96
1771 2049 2.258109 GAGACTGGTTACTTCTGGGGT 58.742 52.381 0.00 0.00 0.00 4.95
1772 2050 2.638363 GAGACTGGTTACTTCTGGGGTT 59.362 50.000 0.00 0.00 0.00 4.11
1773 2051 2.372172 AGACTGGTTACTTCTGGGGTTG 59.628 50.000 0.00 0.00 0.00 3.77
1774 2052 1.202891 ACTGGTTACTTCTGGGGTTGC 60.203 52.381 0.00 0.00 0.00 4.17
1775 2053 0.111639 TGGTTACTTCTGGGGTTGCC 59.888 55.000 0.00 0.00 0.00 4.52
1776 2054 0.404426 GGTTACTTCTGGGGTTGCCT 59.596 55.000 0.00 0.00 0.00 4.75
1777 2055 1.203013 GGTTACTTCTGGGGTTGCCTT 60.203 52.381 0.00 0.00 0.00 4.35
1778 2056 1.886542 GTTACTTCTGGGGTTGCCTTG 59.113 52.381 0.00 0.00 0.00 3.61
1779 2057 1.145571 TACTTCTGGGGTTGCCTTGT 58.854 50.000 0.00 0.00 0.00 3.16
1780 2058 0.468029 ACTTCTGGGGTTGCCTTGTG 60.468 55.000 0.00 0.00 0.00 3.33
1781 2059 1.152567 TTCTGGGGTTGCCTTGTGG 60.153 57.895 0.00 0.00 0.00 4.17
1861 2139 8.638629 AGATAGATTAGTTAATAGTGCGGAGT 57.361 34.615 0.00 0.00 0.00 3.85
1878 2156 3.995048 CGGAGTTTCAGTACCTTTCCTTC 59.005 47.826 0.00 0.00 0.00 3.46
1891 2170 3.561725 CCTTTCCTTCGAATGCTGGTATC 59.438 47.826 0.00 0.00 0.00 2.24
1892 2171 4.446371 CTTTCCTTCGAATGCTGGTATCT 58.554 43.478 0.00 0.00 0.00 1.98
1893 2172 5.453339 CCTTTCCTTCGAATGCTGGTATCTA 60.453 44.000 0.00 0.00 0.00 1.98
1894 2173 5.808366 TTCCTTCGAATGCTGGTATCTAT 57.192 39.130 0.00 0.00 0.00 1.98
1895 2174 5.808366 TCCTTCGAATGCTGGTATCTATT 57.192 39.130 0.00 0.00 0.00 1.73
1914 2193 6.190587 TCTATTCTCTTGTGTCTCCATCTCA 58.809 40.000 0.00 0.00 0.00 3.27
1980 2268 3.614616 GGCTGTGTTCTTCATAGTCGAAG 59.385 47.826 0.00 0.00 43.17 3.79
2002 2290 4.482386 GCATTTATACATGCCTGCAGATG 58.518 43.478 17.39 14.50 43.38 2.90
2012 2300 6.509656 ACATGCCTGCAGATGTTATTATTTG 58.490 36.000 17.39 0.00 0.00 2.32
2013 2301 6.097270 ACATGCCTGCAGATGTTATTATTTGT 59.903 34.615 17.39 0.07 0.00 2.83
2014 2302 6.528537 TGCCTGCAGATGTTATTATTTGTT 57.471 33.333 17.39 0.00 0.00 2.83
2015 2303 7.637631 TGCCTGCAGATGTTATTATTTGTTA 57.362 32.000 17.39 0.00 0.00 2.41
2016 2304 7.706159 TGCCTGCAGATGTTATTATTTGTTAG 58.294 34.615 17.39 0.00 0.00 2.34
2017 2305 7.339212 TGCCTGCAGATGTTATTATTTGTTAGT 59.661 33.333 17.39 0.00 0.00 2.24
2018 2306 7.645340 GCCTGCAGATGTTATTATTTGTTAGTG 59.355 37.037 17.39 0.00 0.00 2.74
2020 2308 9.494479 CTGCAGATGTTATTATTTGTTAGTGTG 57.506 33.333 8.42 0.00 0.00 3.82
2021 2309 7.967854 TGCAGATGTTATTATTTGTTAGTGTGC 59.032 33.333 0.00 0.00 0.00 4.57
2022 2310 7.164171 GCAGATGTTATTATTTGTTAGTGTGCG 59.836 37.037 0.00 0.00 0.00 5.34
2023 2311 8.175069 CAGATGTTATTATTTGTTAGTGTGCGT 58.825 33.333 0.00 0.00 0.00 5.24
2170 2460 7.022979 GCCTTGATTTATTTTGTGGCAATTTC 58.977 34.615 0.00 0.00 38.99 2.17
2172 2462 8.016801 CCTTGATTTATTTTGTGGCAATTTCAC 58.983 33.333 0.00 2.61 35.82 3.18
2216 2517 8.740906 TGTTCTTTTGGTAGTTTAACACATTGA 58.259 29.630 0.00 0.00 0.00 2.57
2229 2530 3.412386 ACACATTGACTGCTCCTTTACC 58.588 45.455 0.00 0.00 0.00 2.85
2329 2631 3.634568 TGCAGTGGTTTTAATGGAACG 57.365 42.857 0.00 0.00 0.00 3.95
2349 2658 6.431198 AACGTGAAGTTTTCATTACACTGT 57.569 33.333 0.00 0.00 40.88 3.55
2353 2662 8.452534 ACGTGAAGTTTTCATTACACTGTTTTA 58.547 29.630 0.00 0.00 42.47 1.52
2389 2703 9.453572 ACATTCATTCTACTACACACAATTCAT 57.546 29.630 0.00 0.00 0.00 2.57
2502 2910 7.159437 TGAACAAATTAAAAGACAATGCACG 57.841 32.000 0.00 0.00 0.00 5.34
2552 2967 6.509039 ACTTGTTTCTAAGTTAACGAAGCACG 60.509 38.462 9.59 10.25 41.75 5.34
2573 2988 6.129194 GCACGTTCTGTTGTTTAATCCAAATC 60.129 38.462 0.00 0.00 0.00 2.17
2590 3005 7.033530 TCCAAATCGTGTTATCAAAAGTTGT 57.966 32.000 0.00 0.00 0.00 3.32
2644 3059 1.597742 AAGACATTCAGCTGCGTTGT 58.402 45.000 9.47 12.05 0.00 3.32
2647 3062 1.264020 GACATTCAGCTGCGTTGTGAA 59.736 47.619 17.18 4.79 34.79 3.18
2652 3067 0.164647 CAGCTGCGTTGTGAAGCTAC 59.835 55.000 0.00 0.00 45.33 3.58
2653 3068 0.034059 AGCTGCGTTGTGAAGCTACT 59.966 50.000 0.00 0.00 45.26 2.57
2654 3069 0.440371 GCTGCGTTGTGAAGCTACTC 59.560 55.000 0.00 0.00 34.05 2.59
2655 3070 1.071605 CTGCGTTGTGAAGCTACTCC 58.928 55.000 0.00 0.00 0.00 3.85
2656 3071 0.679505 TGCGTTGTGAAGCTACTCCT 59.320 50.000 0.00 0.00 0.00 3.69
2657 3072 1.890489 TGCGTTGTGAAGCTACTCCTA 59.110 47.619 0.00 0.00 0.00 2.94
2658 3073 2.297880 TGCGTTGTGAAGCTACTCCTAA 59.702 45.455 0.00 0.00 0.00 2.69
2659 3074 2.924290 GCGTTGTGAAGCTACTCCTAAG 59.076 50.000 0.00 0.00 0.00 2.18
2660 3075 3.512680 CGTTGTGAAGCTACTCCTAAGG 58.487 50.000 0.00 0.00 0.00 2.69
2661 3076 3.263261 GTTGTGAAGCTACTCCTAAGGC 58.737 50.000 0.00 0.00 0.00 4.35
2662 3077 2.536066 TGTGAAGCTACTCCTAAGGCA 58.464 47.619 0.00 0.00 0.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 4.251103 TGCACCTCATTCTACCTCTCTA 57.749 45.455 0.00 0.00 0.00 2.43
32 33 3.107402 TGCACCTCATTCTACCTCTCT 57.893 47.619 0.00 0.00 0.00 3.10
41 43 2.407090 GCCAAGTTTTGCACCTCATTC 58.593 47.619 0.00 0.00 0.00 2.67
64 71 0.247655 CGATGCCACAACCGAAATCG 60.248 55.000 0.00 0.00 39.44 3.34
67 74 2.950673 GCGATGCCACAACCGAAA 59.049 55.556 0.00 0.00 0.00 3.46
102 109 3.490933 GGTTGCCTCACAAAACTTTCTCC 60.491 47.826 0.00 0.00 40.82 3.71
162 170 2.703416 GGCGCCTTATCATCATCATCA 58.297 47.619 22.15 0.00 0.00 3.07
326 399 1.561542 AGAGGAAGTGCCCTATGGTTG 59.438 52.381 0.00 0.00 36.49 3.77
353 426 2.851824 GGAGAATAAAATTTGTGCGGCG 59.148 45.455 0.51 0.51 0.00 6.46
373 446 4.999311 TCATCATCACAAGTGTCAAGAAGG 59.001 41.667 0.00 0.00 0.00 3.46
403 479 6.653020 TCTTCGATTAGGTGGTACTGTACTA 58.347 40.000 16.79 8.88 0.00 1.82
418 497 9.559958 GAATTGAAAATCAAGCTTCTTCGATTA 57.440 29.630 15.80 3.00 40.05 1.75
421 500 6.207417 AGGAATTGAAAATCAAGCTTCTTCGA 59.793 34.615 0.00 0.00 40.05 3.71
422 501 6.307318 CAGGAATTGAAAATCAAGCTTCTTCG 59.693 38.462 0.00 0.00 40.05 3.79
439 518 2.196749 CGGATCGTCAGTCAGGAATTG 58.803 52.381 0.00 0.00 0.00 2.32
463 542 2.435586 GACGGACGGAGAGACGGA 60.436 66.667 0.00 0.00 38.39 4.69
469 548 0.251297 TAAACCTGGACGGACGGAGA 60.251 55.000 0.00 0.00 36.31 3.71
470 549 0.604578 TTAAACCTGGACGGACGGAG 59.395 55.000 0.00 0.00 36.31 4.63
510 589 1.377856 GGAGGTCTTGCAAGAGGCC 60.378 63.158 29.13 25.41 43.89 5.19
512 591 0.035630 CAGGGAGGTCTTGCAAGAGG 60.036 60.000 29.13 3.31 35.32 3.69
545 628 4.595116 GGCAGATGATGATTCTGTTTTCG 58.405 43.478 2.97 0.00 42.12 3.46
599 686 1.517257 CGATGTGGACGAGGCTGAC 60.517 63.158 0.00 0.00 0.00 3.51
627 714 4.563337 TGATAATTGCTGCTGATCTTGC 57.437 40.909 0.00 0.00 0.00 4.01
629 716 4.523173 CCCATGATAATTGCTGCTGATCTT 59.477 41.667 0.00 0.00 0.00 2.40
630 717 4.079970 CCCATGATAATTGCTGCTGATCT 58.920 43.478 0.00 0.00 0.00 2.75
637 733 3.119245 GCCTATGCCCATGATAATTGCTG 60.119 47.826 0.00 0.00 0.00 4.41
650 746 1.228675 CCTTCCCATGCCTATGCCC 60.229 63.158 0.00 0.00 36.33 5.36
656 752 1.773653 GAGATCTTCCTTCCCATGCCT 59.226 52.381 0.00 0.00 0.00 4.75
662 758 1.202475 GCACTCGAGATCTTCCTTCCC 60.202 57.143 21.68 0.00 0.00 3.97
665 761 0.179124 GCGCACTCGAGATCTTCCTT 60.179 55.000 21.68 0.00 38.10 3.36
666 762 1.435515 GCGCACTCGAGATCTTCCT 59.564 57.895 21.68 0.00 38.10 3.36
684 780 2.304516 CTTTGGCGCGTTCATACCCG 62.305 60.000 8.43 0.00 0.00 5.28
685 781 1.303091 ACTTTGGCGCGTTCATACCC 61.303 55.000 8.43 0.00 0.00 3.69
686 782 0.096454 GACTTTGGCGCGTTCATACC 59.904 55.000 8.43 0.00 0.00 2.73
711 807 4.829518 GTTGAAATCGCGCGCCCC 62.830 66.667 27.95 14.30 0.00 5.80
719 815 2.478746 CGGCCCGTGTTGAAATCG 59.521 61.111 0.00 0.00 0.00 3.34
773 1022 4.523558 GGACGCTAGTATAGAAACCAGGAT 59.476 45.833 0.00 0.00 42.77 3.24
775 1024 3.635373 TGGACGCTAGTATAGAAACCAGG 59.365 47.826 0.00 0.00 42.77 4.45
777 1026 3.382546 GGTGGACGCTAGTATAGAAACCA 59.617 47.826 0.00 0.00 42.77 3.67
778 1027 3.243670 GGGTGGACGCTAGTATAGAAACC 60.244 52.174 0.00 0.00 42.77 3.27
779 1028 3.549625 CGGGTGGACGCTAGTATAGAAAC 60.550 52.174 0.00 0.00 42.77 2.78
780 1029 2.620115 CGGGTGGACGCTAGTATAGAAA 59.380 50.000 0.00 0.00 42.77 2.52
781 1030 2.224606 CGGGTGGACGCTAGTATAGAA 58.775 52.381 0.00 0.00 42.77 2.10
782 1031 1.544093 CCGGGTGGACGCTAGTATAGA 60.544 57.143 0.00 0.00 38.19 1.98
783 1032 0.879765 CCGGGTGGACGCTAGTATAG 59.120 60.000 0.00 0.00 38.77 1.31
784 1033 0.183492 ACCGGGTGGACGCTAGTATA 59.817 55.000 6.32 0.00 39.21 1.47
785 1034 1.076485 ACCGGGTGGACGCTAGTAT 60.076 57.895 6.32 0.00 39.21 2.12
1132 1386 1.901085 CAGGACAGGAGGTGTAGGC 59.099 63.158 0.00 0.00 40.56 3.93
1133 1387 0.616111 AGCAGGACAGGAGGTGTAGG 60.616 60.000 0.00 0.00 40.56 3.18
1134 1388 1.066573 CAAGCAGGACAGGAGGTGTAG 60.067 57.143 0.00 0.00 40.56 2.74
1135 1389 0.976641 CAAGCAGGACAGGAGGTGTA 59.023 55.000 0.00 0.00 40.56 2.90
1136 1390 1.757306 CAAGCAGGACAGGAGGTGT 59.243 57.895 0.00 0.00 44.49 4.16
1137 1391 1.673665 GCAAGCAGGACAGGAGGTG 60.674 63.158 0.00 0.00 0.00 4.00
1138 1392 2.753029 GCAAGCAGGACAGGAGGT 59.247 61.111 0.00 0.00 0.00 3.85
1139 1393 2.435586 CGCAAGCAGGACAGGAGG 60.436 66.667 0.00 0.00 0.00 4.30
1151 1405 4.496927 GGAATTGGGCGGCGCAAG 62.497 66.667 34.36 3.20 39.50 4.01
1416 1676 3.088532 GTTGGGGATGTTGCAGTTGATA 58.911 45.455 0.00 0.00 0.00 2.15
1443 1703 2.739932 CGTGAAGGAGCAGAATCCGAAT 60.740 50.000 0.00 0.00 44.65 3.34
1473 1733 2.031012 CAGTGGAGGCAGTCGCAA 59.969 61.111 0.00 0.00 41.24 4.85
1519 1779 1.039785 TCATCACCCTCGAGAGCAGG 61.040 60.000 15.71 9.08 0.00 4.85
1531 1791 1.747355 CTCAACATTGCCCTCATCACC 59.253 52.381 0.00 0.00 0.00 4.02
1534 1794 1.396653 CCCTCAACATTGCCCTCATC 58.603 55.000 0.00 0.00 0.00 2.92
1576 1846 0.863956 ATGTCCTTTTTCCCCACCCA 59.136 50.000 0.00 0.00 0.00 4.51
1577 1847 1.203125 TCATGTCCTTTTTCCCCACCC 60.203 52.381 0.00 0.00 0.00 4.61
1579 1849 2.558359 CTGTCATGTCCTTTTTCCCCAC 59.442 50.000 0.00 0.00 0.00 4.61
1580 1850 2.875296 CTGTCATGTCCTTTTTCCCCA 58.125 47.619 0.00 0.00 0.00 4.96
1708 1984 3.471430 ACCAACCAATTCCATCCATCA 57.529 42.857 0.00 0.00 0.00 3.07
1731 2007 4.037923 TCTCCAAATCAACCACTCTTTTGC 59.962 41.667 0.00 0.00 0.00 3.68
1732 2008 5.300286 AGTCTCCAAATCAACCACTCTTTTG 59.700 40.000 0.00 0.00 0.00 2.44
1743 2021 5.997746 CAGAAGTAACCAGTCTCCAAATCAA 59.002 40.000 0.00 0.00 0.00 2.57
1755 2033 1.534729 GCAACCCCAGAAGTAACCAG 58.465 55.000 0.00 0.00 0.00 4.00
1756 2034 0.111639 GGCAACCCCAGAAGTAACCA 59.888 55.000 0.00 0.00 0.00 3.67
1757 2035 0.404426 AGGCAACCCCAGAAGTAACC 59.596 55.000 0.00 0.00 35.39 2.85
1758 2036 1.886542 CAAGGCAACCCCAGAAGTAAC 59.113 52.381 0.00 0.00 35.39 2.50
1759 2037 1.497286 ACAAGGCAACCCCAGAAGTAA 59.503 47.619 0.00 0.00 35.39 2.24
1760 2038 1.145571 ACAAGGCAACCCCAGAAGTA 58.854 50.000 0.00 0.00 35.39 2.24
1761 2039 0.468029 CACAAGGCAACCCCAGAAGT 60.468 55.000 0.00 0.00 35.39 3.01
1762 2040 1.181098 CCACAAGGCAACCCCAGAAG 61.181 60.000 0.00 0.00 35.39 2.85
1763 2041 1.152567 CCACAAGGCAACCCCAGAA 60.153 57.895 0.00 0.00 35.39 3.02
1764 2042 2.520458 CCACAAGGCAACCCCAGA 59.480 61.111 0.00 0.00 35.39 3.86
1774 2052 0.963962 AACAGAGCAATGCCACAAGG 59.036 50.000 0.00 0.00 38.23 3.61
1775 2053 2.608752 GGAAACAGAGCAATGCCACAAG 60.609 50.000 0.00 0.00 0.00 3.16
1776 2054 1.340889 GGAAACAGAGCAATGCCACAA 59.659 47.619 0.00 0.00 0.00 3.33
1777 2055 0.961019 GGAAACAGAGCAATGCCACA 59.039 50.000 0.00 0.00 0.00 4.17
1778 2056 1.200948 GAGGAAACAGAGCAATGCCAC 59.799 52.381 0.00 0.00 0.00 5.01
1779 2057 1.074405 AGAGGAAACAGAGCAATGCCA 59.926 47.619 0.00 0.00 0.00 4.92
1780 2058 1.742268 GAGAGGAAACAGAGCAATGCC 59.258 52.381 0.00 0.00 0.00 4.40
1781 2059 2.430465 TGAGAGGAAACAGAGCAATGC 58.570 47.619 0.00 0.00 0.00 3.56
1861 2139 4.454504 GCATTCGAAGGAAAGGTACTGAAA 59.545 41.667 15.01 0.00 40.86 2.69
1878 2156 6.145209 CACAAGAGAATAGATACCAGCATTCG 59.855 42.308 0.00 0.00 33.57 3.34
1947 2226 5.827797 TGAAGAACACAGCCTTCTAAATGTT 59.172 36.000 0.00 0.00 39.47 2.71
2002 2290 8.414173 CAACAACGCACACTAACAAATAATAAC 58.586 33.333 0.00 0.00 0.00 1.89
2012 2300 2.817538 ACACAACAACGCACACTAAC 57.182 45.000 0.00 0.00 0.00 2.34
2013 2301 2.159503 CCAACACAACAACGCACACTAA 60.160 45.455 0.00 0.00 0.00 2.24
2014 2302 1.398739 CCAACACAACAACGCACACTA 59.601 47.619 0.00 0.00 0.00 2.74
2015 2303 0.170116 CCAACACAACAACGCACACT 59.830 50.000 0.00 0.00 0.00 3.55
2016 2304 0.169230 TCCAACACAACAACGCACAC 59.831 50.000 0.00 0.00 0.00 3.82
2017 2305 1.064803 GATCCAACACAACAACGCACA 59.935 47.619 0.00 0.00 0.00 4.57
2018 2306 1.753956 GATCCAACACAACAACGCAC 58.246 50.000 0.00 0.00 0.00 5.34
2020 2308 0.584396 TCGATCCAACACAACAACGC 59.416 50.000 0.00 0.00 0.00 4.84
2021 2309 2.159707 GGATCGATCCAACACAACAACG 60.160 50.000 34.65 0.00 46.38 4.10
2022 2310 3.471495 GGATCGATCCAACACAACAAC 57.529 47.619 34.65 6.83 46.38 3.32
2050 2340 3.904339 AGAAGGTGCTAAAGAGGAGTTGA 59.096 43.478 0.00 0.00 0.00 3.18
2177 2467 5.823045 ACCAAAAGAACAGGTCAACTTCTAG 59.177 40.000 0.00 0.00 0.00 2.43
2194 2484 7.167468 GCAGTCAATGTGTTAAACTACCAAAAG 59.833 37.037 0.00 0.00 0.00 2.27
2216 2517 3.595190 AAAGGTTGGTAAAGGAGCAGT 57.405 42.857 0.00 0.00 36.76 4.40
2229 2530 4.459337 CCAACTAGGCTTCCTTAAAGGTTG 59.541 45.833 0.00 0.00 36.53 3.77
2305 2606 2.298729 TCCATTAAAACCACTGCAAGCC 59.701 45.455 0.00 0.00 37.60 4.35
2315 2617 6.752815 TGAAAACTTCACGTTCCATTAAAACC 59.247 34.615 0.00 0.00 33.90 3.27
2358 2672 8.083462 TGTGTGTAGTAGAATGAATGTTTGAC 57.917 34.615 0.00 0.00 0.00 3.18
2552 2967 6.915843 ACACGATTTGGATTAAACAACAGAAC 59.084 34.615 0.00 0.00 0.00 3.01
2573 2988 4.843147 TCTGCACAACTTTTGATAACACG 58.157 39.130 0.00 0.00 0.00 4.49
2590 3005 3.797451 TCAAAAGCAACACATTCTGCA 57.203 38.095 0.00 0.00 41.17 4.41
2644 3059 4.202419 TGTTTTGCCTTAGGAGTAGCTTCA 60.202 41.667 0.69 0.00 0.00 3.02
2647 3062 3.328050 AGTGTTTTGCCTTAGGAGTAGCT 59.672 43.478 0.69 0.00 0.00 3.32
2652 3067 8.506168 TCATATAAAGTGTTTTGCCTTAGGAG 57.494 34.615 0.69 0.00 0.00 3.69
2653 3068 8.902806 CATCATATAAAGTGTTTTGCCTTAGGA 58.097 33.333 0.69 0.00 0.00 2.94
2654 3069 8.686334 ACATCATATAAAGTGTTTTGCCTTAGG 58.314 33.333 0.00 0.00 0.00 2.69
2657 3072 9.855021 GTAACATCATATAAAGTGTTTTGCCTT 57.145 29.630 5.63 0.00 36.34 4.35
2658 3073 9.243105 AGTAACATCATATAAAGTGTTTTGCCT 57.757 29.630 5.63 0.00 36.34 4.75


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

AutoCloner maintained by Alex Coulton.