Multiple sequence alignment - TraesCS6D01G397700

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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 TraesCS6D01G397700 chr6D 100.000 2501 0 0 1 2501 469371538 469374038 0.000000e+00 4619.0
1 TraesCS6D01G397700 chr6A 97.349 1358 36 0 91 1448 614504987 614506344 0.000000e+00 2309.0
2 TraesCS6D01G397700 chr6A 91.082 841 24 2 1661 2501 614506464 614507253 0.000000e+00 1090.0
3 TraesCS6D01G397700 chr6A 94.783 115 2 1 1486 1600 614506351 614506461 2.560000e-40 176.0
4 TraesCS6D01G397700 chr6A 100.000 43 0 0 1 43 614504946 614504988 2.060000e-11 80.5
5 TraesCS6D01G397700 chr5B 76.614 1069 206 26 404 1456 684067603 684066563 1.310000e-152 549.0
6 TraesCS6D01G397700 chr5B 74.190 988 199 42 488 1441 685070392 685069427 6.580000e-96 361.0
7 TraesCS6D01G397700 chr5B 73.377 1078 213 52 414 1455 685048992 685047953 1.430000e-87 333.0
8 TraesCS6D01G397700 chr5B 73.434 990 206 37 488 1437 684050675 684049703 4.010000e-83 318.0
9 TraesCS6D01G397700 chr4A 75.794 1070 213 31 404 1456 626976503 626977543 1.340000e-137 499.0
10 TraesCS6D01G397700 chr4A 72.840 1134 231 49 360 1437 626989149 626990261 1.440000e-82 316.0
11 TraesCS6D01G397700 chr5D 75.607 1070 214 30 404 1456 542097558 542096519 1.040000e-133 486.0
12 TraesCS6D01G397700 chr5D 72.009 886 195 33 589 1437 542386157 542385288 1.950000e-51 213.0
13 TraesCS6D01G397700 chr7B 73.309 547 105 28 414 941 87210273 87210797 1.990000e-36 163.0


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 TraesCS6D01G397700 chr6D 469371538 469374038 2500 False 4619.000 4619 100.0000 1 2501 1 chr6D.!!$F1 2500
1 TraesCS6D01G397700 chr6A 614504946 614507253 2307 False 913.875 2309 95.8035 1 2501 4 chr6A.!!$F1 2500
2 TraesCS6D01G397700 chr5B 684066563 684067603 1040 True 549.000 549 76.6140 404 1456 1 chr5B.!!$R2 1052
3 TraesCS6D01G397700 chr5B 685069427 685070392 965 True 361.000 361 74.1900 488 1441 1 chr5B.!!$R4 953
4 TraesCS6D01G397700 chr5B 685047953 685048992 1039 True 333.000 333 73.3770 414 1455 1 chr5B.!!$R3 1041
5 TraesCS6D01G397700 chr5B 684049703 684050675 972 True 318.000 318 73.4340 488 1437 1 chr5B.!!$R1 949
6 TraesCS6D01G397700 chr4A 626976503 626977543 1040 False 499.000 499 75.7940 404 1456 1 chr4A.!!$F1 1052
7 TraesCS6D01G397700 chr4A 626989149 626990261 1112 False 316.000 316 72.8400 360 1437 1 chr4A.!!$F2 1077
8 TraesCS6D01G397700 chr5D 542096519 542097558 1039 True 486.000 486 75.6070 404 1456 1 chr5D.!!$R1 1052
9 TraesCS6D01G397700 chr5D 542385288 542386157 869 True 213.000 213 72.0090 589 1437 1 chr5D.!!$R2 848

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
88 89 0.034863 GGTTTTGGGGCATAGACCGA 60.035 55.0 0.00 0.00 0.0 4.69 F
107 108 0.534412 ACCAGGACAATCTCGAGCAG 59.466 55.0 7.81 2.15 0.0 4.24 F
1456 1509 0.538746 TCTGTATATGAGGCGGCGGA 60.539 55.0 9.78 0.00 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1457 1510 0.322098 TACAACCTTGGTCCGCCATG 60.322 55.0 0.00 0.0 45.56 3.66 R
1458 1511 0.322187 GTACAACCTTGGTCCGCCAT 60.322 55.0 0.00 0.0 45.56 4.40 R
2299 2352 0.765510 GACTATCCGGGGCCTTGATT 59.234 55.0 0.84 0.0 0.00 2.57 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
41 42 3.374745 CAATGGTGTGTGCTGAGAAAAC 58.625 45.455 0.00 0.00 0.00 2.43
42 43 2.121291 TGGTGTGTGCTGAGAAAACA 57.879 45.000 0.00 0.00 0.00 2.83
43 44 2.653726 TGGTGTGTGCTGAGAAAACAT 58.346 42.857 0.00 0.00 0.00 2.71
44 45 3.814625 TGGTGTGTGCTGAGAAAACATA 58.185 40.909 0.00 0.00 0.00 2.29
45 46 3.814842 TGGTGTGTGCTGAGAAAACATAG 59.185 43.478 0.00 0.00 0.00 2.23
46 47 3.815401 GGTGTGTGCTGAGAAAACATAGT 59.185 43.478 0.00 0.00 0.00 2.12
47 48 4.083802 GGTGTGTGCTGAGAAAACATAGTC 60.084 45.833 0.00 0.00 0.00 2.59
48 49 4.752101 GTGTGTGCTGAGAAAACATAGTCT 59.248 41.667 0.00 0.00 0.00 3.24
49 50 4.751600 TGTGTGCTGAGAAAACATAGTCTG 59.248 41.667 0.00 0.00 0.00 3.51
50 51 4.153117 GTGTGCTGAGAAAACATAGTCTGG 59.847 45.833 0.00 0.00 0.00 3.86
51 52 3.126000 GTGCTGAGAAAACATAGTCTGGC 59.874 47.826 0.00 0.00 0.00 4.85
52 53 3.008375 TGCTGAGAAAACATAGTCTGGCT 59.992 43.478 0.00 0.00 0.00 4.75
53 54 4.006319 GCTGAGAAAACATAGTCTGGCTT 58.994 43.478 0.00 0.00 0.00 4.35
54 55 4.457257 GCTGAGAAAACATAGTCTGGCTTT 59.543 41.667 0.00 0.00 0.00 3.51
55 56 5.048434 GCTGAGAAAACATAGTCTGGCTTTT 60.048 40.000 0.00 0.00 0.00 2.27
56 57 6.317789 TGAGAAAACATAGTCTGGCTTTTG 57.682 37.500 0.00 0.00 0.00 2.44
57 58 5.827797 TGAGAAAACATAGTCTGGCTTTTGT 59.172 36.000 0.00 0.00 0.00 2.83
58 59 6.076981 AGAAAACATAGTCTGGCTTTTGTG 57.923 37.500 0.00 0.00 0.00 3.33
59 60 4.853924 AAACATAGTCTGGCTTTTGTGG 57.146 40.909 0.00 0.00 0.00 4.17
60 61 3.788227 ACATAGTCTGGCTTTTGTGGA 57.212 42.857 0.00 0.00 0.00 4.02
61 62 4.307032 ACATAGTCTGGCTTTTGTGGAT 57.693 40.909 0.00 0.00 0.00 3.41
62 63 4.265073 ACATAGTCTGGCTTTTGTGGATC 58.735 43.478 0.00 0.00 0.00 3.36
63 64 2.206576 AGTCTGGCTTTTGTGGATCC 57.793 50.000 4.20 4.20 0.00 3.36
64 65 0.804989 GTCTGGCTTTTGTGGATCCG 59.195 55.000 7.39 0.00 0.00 4.18
65 66 0.960364 TCTGGCTTTTGTGGATCCGC 60.960 55.000 18.84 18.84 0.00 5.54
66 67 1.937546 CTGGCTTTTGTGGATCCGCC 61.938 60.000 22.48 19.32 38.01 6.13
67 68 1.976474 GGCTTTTGTGGATCCGCCA 60.976 57.895 22.48 9.11 46.96 5.69
75 76 2.577490 TGGATCCGCCATGGTTTTG 58.423 52.632 14.67 0.93 43.33 2.44
76 77 0.969917 TGGATCCGCCATGGTTTTGG 60.970 55.000 14.67 10.61 43.33 3.28
77 78 1.675720 GGATCCGCCATGGTTTTGGG 61.676 60.000 14.67 7.53 39.52 4.12
78 79 1.675720 GATCCGCCATGGTTTTGGGG 61.676 60.000 14.67 4.60 46.41 4.96
79 80 4.081185 CCGCCATGGTTTTGGGGC 62.081 66.667 14.67 0.00 45.72 5.80
80 81 3.309506 CGCCATGGTTTTGGGGCA 61.310 61.111 14.67 0.00 46.75 5.36
81 82 2.658064 CGCCATGGTTTTGGGGCAT 61.658 57.895 14.67 0.00 46.75 4.40
82 83 1.326213 CGCCATGGTTTTGGGGCATA 61.326 55.000 14.67 0.00 46.75 3.14
83 84 0.465287 GCCATGGTTTTGGGGCATAG 59.535 55.000 14.67 0.00 45.70 2.23
84 85 1.964344 GCCATGGTTTTGGGGCATAGA 60.964 52.381 14.67 0.00 45.70 1.98
85 86 1.756538 CCATGGTTTTGGGGCATAGAC 59.243 52.381 2.57 0.00 32.80 2.59
86 87 1.756538 CATGGTTTTGGGGCATAGACC 59.243 52.381 0.00 0.00 0.00 3.85
87 88 0.322997 TGGTTTTGGGGCATAGACCG 60.323 55.000 0.00 0.00 0.00 4.79
88 89 0.034863 GGTTTTGGGGCATAGACCGA 60.035 55.000 0.00 0.00 0.00 4.69
89 90 1.092348 GTTTTGGGGCATAGACCGAC 58.908 55.000 0.00 0.00 0.00 4.79
107 108 0.534412 ACCAGGACAATCTCGAGCAG 59.466 55.000 7.81 2.15 0.00 4.24
126 127 1.080093 GCCGTCCTCACGTTCATCA 60.080 57.895 0.00 0.00 45.17 3.07
134 135 2.002586 CTCACGTTCATCACCATGGAC 58.997 52.381 21.47 3.52 35.33 4.02
224 225 2.261671 GCATCCGTGACACCGAGT 59.738 61.111 0.00 0.00 0.00 4.18
239 240 4.075793 AGTAGGCGAGGGAGGGCA 62.076 66.667 0.00 0.00 0.00 5.36
310 311 7.554118 AGAGCTTTTACTGCAAGATTAAGCATA 59.446 33.333 17.16 0.00 42.08 3.14
341 342 9.547753 AGGTATCACATGTAATACAAGATTGAC 57.452 33.333 18.80 3.75 31.33 3.18
452 453 6.381420 TCTTGTGTAAGGAAAAATGGGAAACA 59.619 34.615 0.00 0.00 34.59 2.83
486 488 1.808411 TTCCACCGCTCAATCTTCAC 58.192 50.000 0.00 0.00 0.00 3.18
522 524 5.881777 TGGATCATGTAGACGCTAGTATC 57.118 43.478 0.00 0.00 0.00 2.24
528 530 1.600957 GTAGACGCTAGTATCCGCACA 59.399 52.381 0.00 0.00 0.00 4.57
812 847 7.977853 GCTTATCCAAATCAAACTGAATGATGT 59.022 33.333 0.00 0.00 37.58 3.06
943 981 2.567049 GACGAGTACACGCAGCCT 59.433 61.111 12.79 0.00 36.70 4.58
1140 1193 3.508793 AGCTCATTGCAGCACTTACATTT 59.491 39.130 0.00 0.00 45.94 2.32
1363 1416 1.239296 GCCAGTGCTTGCAGACATGA 61.239 55.000 0.00 0.00 33.53 3.07
1375 1428 2.416747 CAGACATGAGAAGCACGGAAA 58.583 47.619 0.00 0.00 0.00 3.13
1384 1437 6.465439 TGAGAAGCACGGAAAAGATAGATA 57.535 37.500 0.00 0.00 0.00 1.98
1456 1509 0.538746 TCTGTATATGAGGCGGCGGA 60.539 55.000 9.78 0.00 0.00 5.54
1457 1510 0.388649 CTGTATATGAGGCGGCGGAC 60.389 60.000 9.78 0.00 0.00 4.79
1458 1511 1.110518 TGTATATGAGGCGGCGGACA 61.111 55.000 9.78 6.16 0.00 4.02
1459 1512 0.246635 GTATATGAGGCGGCGGACAT 59.753 55.000 9.78 18.60 0.00 3.06
1460 1513 0.246360 TATATGAGGCGGCGGACATG 59.754 55.000 21.65 0.00 0.00 3.21
1461 1514 2.454832 ATATGAGGCGGCGGACATGG 62.455 60.000 21.65 0.00 0.00 3.66
1476 1529 3.564775 TGGCGGACCAAGGTTGTA 58.435 55.556 0.00 0.00 45.37 2.41
1477 1530 1.071814 TGGCGGACCAAGGTTGTAC 59.928 57.895 0.00 0.00 45.37 2.90
1478 1531 1.673337 GGCGGACCAAGGTTGTACC 60.673 63.158 0.00 0.00 35.34 3.34
1493 1546 4.338400 GGTTGTACCTGAAATAGCCATTCC 59.662 45.833 0.00 0.00 34.73 3.01
1600 1653 8.149973 TCTTTAGTGTAATTTTGACAGGTGTC 57.850 34.615 2.99 2.99 44.97 3.67
1601 1654 7.990886 TCTTTAGTGTAATTTTGACAGGTGTCT 59.009 33.333 11.31 0.00 44.99 3.41
1602 1655 7.724305 TTAGTGTAATTTTGACAGGTGTCTC 57.276 36.000 11.31 0.00 44.99 3.36
1603 1656 5.680619 AGTGTAATTTTGACAGGTGTCTCA 58.319 37.500 11.31 0.00 44.99 3.27
1604 1657 6.119536 AGTGTAATTTTGACAGGTGTCTCAA 58.880 36.000 11.31 4.69 44.99 3.02
1605 1658 6.601613 AGTGTAATTTTGACAGGTGTCTCAAA 59.398 34.615 11.31 10.11 44.99 2.69
1606 1659 7.122055 AGTGTAATTTTGACAGGTGTCTCAAAA 59.878 33.333 11.31 10.81 44.99 2.44
1607 1660 7.432252 GTGTAATTTTGACAGGTGTCTCAAAAG 59.568 37.037 11.31 0.00 44.99 2.27
1608 1661 6.773976 AATTTTGACAGGTGTCTCAAAAGA 57.226 33.333 11.31 0.00 44.99 2.52
1609 1662 6.773976 ATTTTGACAGGTGTCTCAAAAGAA 57.226 33.333 11.31 0.00 44.99 2.52
1610 1663 6.773976 TTTTGACAGGTGTCTCAAAAGAAT 57.226 33.333 11.31 0.00 44.99 2.40
1611 1664 7.873719 TTTTGACAGGTGTCTCAAAAGAATA 57.126 32.000 11.31 0.00 44.99 1.75
1612 1665 8.463930 TTTTGACAGGTGTCTCAAAAGAATAT 57.536 30.769 11.31 0.00 44.99 1.28
1613 1666 7.439157 TTGACAGGTGTCTCAAAAGAATATG 57.561 36.000 11.31 0.00 44.99 1.78
1614 1667 5.412594 TGACAGGTGTCTCAAAAGAATATGC 59.587 40.000 11.31 0.00 44.99 3.14
1615 1668 5.316167 ACAGGTGTCTCAAAAGAATATGCA 58.684 37.500 0.00 0.00 31.93 3.96
1616 1669 5.182001 ACAGGTGTCTCAAAAGAATATGCAC 59.818 40.000 0.00 0.00 31.93 4.57
1617 1670 5.413833 CAGGTGTCTCAAAAGAATATGCACT 59.586 40.000 0.00 0.00 31.93 4.40
1618 1671 5.645497 AGGTGTCTCAAAAGAATATGCACTC 59.355 40.000 0.00 0.00 31.93 3.51
1619 1672 5.163713 GGTGTCTCAAAAGAATATGCACTCC 60.164 44.000 0.00 0.00 31.93 3.85
1620 1673 5.645497 GTGTCTCAAAAGAATATGCACTCCT 59.355 40.000 0.00 0.00 31.93 3.69
1621 1674 5.645067 TGTCTCAAAAGAATATGCACTCCTG 59.355 40.000 0.00 0.00 31.93 3.86
1622 1675 4.637534 TCTCAAAAGAATATGCACTCCTGC 59.362 41.667 0.00 0.00 44.52 4.85
1623 1676 7.788585 GTCTCAAAAGAATATGCACTCCTGCA 61.789 42.308 0.00 0.00 44.99 4.41
1624 1677 9.679721 GTCTCAAAAGAATATGCACTCCTGCAC 62.680 44.444 0.00 0.00 44.27 4.57
1633 1686 2.772287 GCACTCCTGCACTTCTTTAGT 58.228 47.619 0.00 0.00 43.62 2.24
1634 1687 3.926616 GCACTCCTGCACTTCTTTAGTA 58.073 45.455 0.00 0.00 43.62 1.82
1635 1688 4.508662 GCACTCCTGCACTTCTTTAGTAT 58.491 43.478 0.00 0.00 43.62 2.12
1636 1689 5.661458 GCACTCCTGCACTTCTTTAGTATA 58.339 41.667 0.00 0.00 43.62 1.47
1637 1690 6.106673 GCACTCCTGCACTTCTTTAGTATAA 58.893 40.000 0.00 0.00 43.62 0.98
1638 1691 6.763610 GCACTCCTGCACTTCTTTAGTATAAT 59.236 38.462 0.00 0.00 43.62 1.28
1639 1692 7.926555 GCACTCCTGCACTTCTTTAGTATAATA 59.073 37.037 0.00 0.00 43.62 0.98
1640 1693 9.817809 CACTCCTGCACTTCTTTAGTATAATAA 57.182 33.333 0.00 0.00 34.56 1.40
1730 1783 9.101655 CGATAGTGCATATTCAAATGGATATGA 57.898 33.333 20.90 7.47 29.43 2.15
1868 1921 2.624846 TTATCCCCTCCCCCAGATTT 57.375 50.000 0.00 0.00 0.00 2.17
1890 1943 7.712264 TTTTACAAATTCTGACATGGCAAAG 57.288 32.000 1.11 0.00 0.00 2.77
1893 1946 4.250464 CAAATTCTGACATGGCAAAGCAT 58.750 39.130 1.11 0.00 0.00 3.79
1894 1947 5.047164 ACAAATTCTGACATGGCAAAGCATA 60.047 36.000 1.11 0.00 0.00 3.14
1895 1948 5.864418 AATTCTGACATGGCAAAGCATAT 57.136 34.783 1.11 0.00 0.00 1.78
1896 1949 5.864418 ATTCTGACATGGCAAAGCATATT 57.136 34.783 1.11 0.00 0.00 1.28
1897 1950 5.664294 TTCTGACATGGCAAAGCATATTT 57.336 34.783 1.11 0.00 0.00 1.40
1898 1951 6.772360 TTCTGACATGGCAAAGCATATTTA 57.228 33.333 1.11 0.00 0.00 1.40
1899 1952 6.135290 TCTGACATGGCAAAGCATATTTAC 57.865 37.500 1.11 0.00 0.00 2.01
1900 1953 5.651576 TCTGACATGGCAAAGCATATTTACA 59.348 36.000 1.11 0.00 0.00 2.41
1901 1954 6.321945 TCTGACATGGCAAAGCATATTTACAT 59.678 34.615 1.11 0.00 0.00 2.29
1902 1955 6.274579 TGACATGGCAAAGCATATTTACATG 58.725 36.000 0.00 0.00 40.04 3.21
1903 1956 6.224665 ACATGGCAAAGCATATTTACATGT 57.775 33.333 2.69 2.69 41.78 3.21
1904 1957 6.642430 ACATGGCAAAGCATATTTACATGTT 58.358 32.000 2.30 0.00 43.41 2.71
1905 1958 7.104939 ACATGGCAAAGCATATTTACATGTTT 58.895 30.769 2.30 0.00 43.41 2.83
1906 1959 7.278424 ACATGGCAAAGCATATTTACATGTTTC 59.722 33.333 2.30 0.00 43.41 2.78
1907 1960 6.695429 TGGCAAAGCATATTTACATGTTTCA 58.305 32.000 2.30 0.00 30.15 2.69
1908 1961 6.589523 TGGCAAAGCATATTTACATGTTTCAC 59.410 34.615 2.30 0.00 30.15 3.18
1909 1962 6.589523 GGCAAAGCATATTTACATGTTTCACA 59.410 34.615 2.30 0.00 30.15 3.58
1910 1963 7.278424 GGCAAAGCATATTTACATGTTTCACAT 59.722 33.333 2.30 0.00 39.91 3.21
1958 2011 7.697352 TCAAATTGCAAAGTCAACATAAGTG 57.303 32.000 1.71 0.00 0.00 3.16
1959 2012 6.200665 TCAAATTGCAAAGTCAACATAAGTGC 59.799 34.615 1.71 0.00 0.00 4.40
1982 2035 6.139672 CAAATCAAATTGCACGGAACTTAC 57.860 37.500 0.00 0.00 0.00 2.34
2043 2096 9.964303 TTTACACGTACTTGATAGTTTACTGAA 57.036 29.630 6.33 0.00 35.78 3.02
2044 2097 9.964303 TTACACGTACTTGATAGTTTACTGAAA 57.036 29.630 6.33 0.00 35.78 2.69
2045 2098 8.516811 ACACGTACTTGATAGTTTACTGAAAG 57.483 34.615 6.33 0.00 36.37 2.62
2046 2099 7.115947 ACACGTACTTGATAGTTTACTGAAAGC 59.884 37.037 6.33 0.00 34.48 3.51
2047 2100 7.328737 CACGTACTTGATAGTTTACTGAAAGCT 59.671 37.037 0.00 0.00 34.48 3.74
2048 2101 8.517878 ACGTACTTGATAGTTTACTGAAAGCTA 58.482 33.333 0.00 0.00 34.48 3.32
2049 2102 9.517609 CGTACTTGATAGTTTACTGAAAGCTAT 57.482 33.333 0.00 0.00 34.48 2.97
2058 2111 7.908453 AGTTTACTGAAAGCTATCTACAAGGT 58.092 34.615 0.00 0.00 37.60 3.50
2059 2112 8.035984 AGTTTACTGAAAGCTATCTACAAGGTC 58.964 37.037 0.00 0.00 37.60 3.85
2060 2113 7.476540 TTACTGAAAGCTATCTACAAGGTCA 57.523 36.000 0.00 0.00 37.60 4.02
2061 2114 6.360370 ACTGAAAGCTATCTACAAGGTCAA 57.640 37.500 0.00 0.00 37.60 3.18
2062 2115 6.769512 ACTGAAAGCTATCTACAAGGTCAAA 58.230 36.000 0.00 0.00 37.60 2.69
2063 2116 7.224297 ACTGAAAGCTATCTACAAGGTCAAAA 58.776 34.615 0.00 0.00 37.60 2.44
2064 2117 7.719633 ACTGAAAGCTATCTACAAGGTCAAAAA 59.280 33.333 0.00 0.00 37.60 1.94
2104 2157 0.111639 TGTTACAGGCCCTTCCAACC 59.888 55.000 0.00 0.00 37.29 3.77
2134 2187 1.269448 GGCATTTTCAAGTTCTCGGCA 59.731 47.619 0.00 0.00 0.00 5.69
2135 2188 2.288152 GGCATTTTCAAGTTCTCGGCAA 60.288 45.455 0.00 0.00 0.00 4.52
2288 2341 3.119101 GGACCTCATAGCTTCTCGACAAA 60.119 47.826 0.00 0.00 0.00 2.83
2424 2477 3.672808 ACTGCATGAAAAGACCTCTCTG 58.327 45.455 0.00 0.00 0.00 3.35
2454 2507 1.404391 CAGCTTGCTAATGGCCAGAAG 59.596 52.381 13.05 12.35 40.92 2.85
2478 2531 3.739300 CCGTGACGACACTTACTCAAATT 59.261 43.478 15.65 0.00 43.99 1.82
2496 2549 4.985044 AATTCAGTTAAACGACGGTCAG 57.015 40.909 9.10 3.87 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 3.629398 GGATCCACAAAAGCCAGACTATG 59.371 47.826 6.95 0.00 0.00 2.23
42 43 3.682718 CGGATCCACAAAAGCCAGACTAT 60.683 47.826 13.41 0.00 0.00 2.12
43 44 2.354704 CGGATCCACAAAAGCCAGACTA 60.355 50.000 13.41 0.00 0.00 2.59
44 45 1.611673 CGGATCCACAAAAGCCAGACT 60.612 52.381 13.41 0.00 0.00 3.24
45 46 0.804989 CGGATCCACAAAAGCCAGAC 59.195 55.000 13.41 0.00 0.00 3.51
46 47 0.960364 GCGGATCCACAAAAGCCAGA 60.960 55.000 13.41 0.00 0.00 3.86
47 48 1.508088 GCGGATCCACAAAAGCCAG 59.492 57.895 13.41 0.00 0.00 4.85
48 49 1.976474 GGCGGATCCACAAAAGCCA 60.976 57.895 18.18 0.00 43.65 4.75
49 50 1.976474 TGGCGGATCCACAAAAGCC 60.976 57.895 16.72 16.72 40.72 4.35
50 51 3.680156 TGGCGGATCCACAAAAGC 58.320 55.556 13.41 5.49 40.72 3.51
58 59 1.675720 CCCAAAACCATGGCGGATCC 61.676 60.000 13.04 0.00 39.26 3.36
59 60 1.675720 CCCCAAAACCATGGCGGATC 61.676 60.000 13.04 0.00 39.26 3.36
60 61 1.685421 CCCCAAAACCATGGCGGAT 60.685 57.895 13.04 0.00 39.26 4.18
61 62 2.283532 CCCCAAAACCATGGCGGA 60.284 61.111 13.04 0.00 39.26 5.54
62 63 4.081185 GCCCCAAAACCATGGCGG 62.081 66.667 13.04 7.41 39.26 6.13
64 65 0.465287 CTATGCCCCAAAACCATGGC 59.535 55.000 13.04 0.00 44.27 4.40
65 66 1.756538 GTCTATGCCCCAAAACCATGG 59.243 52.381 11.19 11.19 40.35 3.66
66 67 1.756538 GGTCTATGCCCCAAAACCATG 59.243 52.381 0.00 0.00 0.00 3.66
67 68 1.684869 CGGTCTATGCCCCAAAACCAT 60.685 52.381 0.00 0.00 0.00 3.55
68 69 0.322997 CGGTCTATGCCCCAAAACCA 60.323 55.000 0.00 0.00 0.00 3.67
69 70 0.034863 TCGGTCTATGCCCCAAAACC 60.035 55.000 0.00 0.00 0.00 3.27
70 71 1.092348 GTCGGTCTATGCCCCAAAAC 58.908 55.000 0.00 0.00 0.00 2.43
71 72 0.034863 GGTCGGTCTATGCCCCAAAA 60.035 55.000 0.00 0.00 0.00 2.44
72 73 1.202099 TGGTCGGTCTATGCCCCAAA 61.202 55.000 0.00 0.00 0.00 3.28
73 74 1.613928 TGGTCGGTCTATGCCCCAA 60.614 57.895 0.00 0.00 0.00 4.12
74 75 2.039787 TGGTCGGTCTATGCCCCA 59.960 61.111 0.00 0.00 0.00 4.96
75 76 2.808206 CCTGGTCGGTCTATGCCCC 61.808 68.421 0.00 0.00 0.00 5.80
76 77 1.760875 TCCTGGTCGGTCTATGCCC 60.761 63.158 0.00 0.00 0.00 5.36
77 78 1.327690 TGTCCTGGTCGGTCTATGCC 61.328 60.000 0.00 0.00 0.00 4.40
78 79 0.535335 TTGTCCTGGTCGGTCTATGC 59.465 55.000 0.00 0.00 0.00 3.14
79 80 2.695666 AGATTGTCCTGGTCGGTCTATG 59.304 50.000 0.00 0.00 0.00 2.23
80 81 2.959707 GAGATTGTCCTGGTCGGTCTAT 59.040 50.000 0.00 0.00 0.00 1.98
81 82 2.376109 GAGATTGTCCTGGTCGGTCTA 58.624 52.381 0.00 0.00 0.00 2.59
82 83 1.187087 GAGATTGTCCTGGTCGGTCT 58.813 55.000 0.00 0.00 0.00 3.85
83 84 0.179134 CGAGATTGTCCTGGTCGGTC 60.179 60.000 0.00 0.00 0.00 4.79
84 85 0.611062 TCGAGATTGTCCTGGTCGGT 60.611 55.000 2.85 0.00 0.00 4.69
85 86 0.101399 CTCGAGATTGTCCTGGTCGG 59.899 60.000 6.58 0.00 0.00 4.79
86 87 0.526524 GCTCGAGATTGTCCTGGTCG 60.527 60.000 18.75 0.00 0.00 4.79
87 88 0.532573 TGCTCGAGATTGTCCTGGTC 59.467 55.000 18.75 0.00 0.00 4.02
88 89 0.534412 CTGCTCGAGATTGTCCTGGT 59.466 55.000 18.75 0.00 0.00 4.00
89 90 0.179089 CCTGCTCGAGATTGTCCTGG 60.179 60.000 18.75 6.80 0.00 4.45
126 127 2.264794 GAGAACGCCGTCCATGGT 59.735 61.111 12.58 0.00 0.00 3.55
134 135 3.883744 AACCTGCAGGAGAACGCCG 62.884 63.158 39.19 9.60 38.94 6.46
135 136 2.032681 AACCTGCAGGAGAACGCC 59.967 61.111 39.19 0.00 38.94 5.68
205 206 3.295304 CTCGGTGTCACGGATGCCA 62.295 63.158 13.06 0.00 0.00 4.92
239 240 0.108138 CCATCTTCTTTCTCGGCGGT 60.108 55.000 7.21 0.00 0.00 5.68
245 246 1.932511 CGCAGAGCCATCTTCTTTCTC 59.067 52.381 0.00 0.00 31.64 2.87
341 342 8.298854 TCCAAACTGATGTTTTGATGAGTTATG 58.701 33.333 0.00 0.00 43.13 1.90
452 453 4.096382 GCGGTGGAATGAACTTGATATTGT 59.904 41.667 0.00 0.00 0.00 2.71
486 488 3.851458 TGATCCATCTCAAGTCCATGG 57.149 47.619 4.97 4.97 38.83 3.66
522 524 3.127376 TGATGTGATCTTCATTTGTGCGG 59.873 43.478 0.00 0.00 0.00 5.69
528 530 7.028926 GAAGATGCTGATGTGATCTTCATTT 57.971 36.000 13.55 0.00 46.10 2.32
812 847 0.107643 TGGCTGTTGGACAACGATCA 59.892 50.000 10.27 5.63 43.94 2.92
943 981 2.198827 AGGTTGATTTCATCACCGCA 57.801 45.000 0.00 0.00 39.39 5.69
1140 1193 4.988716 ACGGTCGTGCCCTCCTGA 62.989 66.667 0.00 0.00 0.00 3.86
1363 1416 5.740513 GCCTATCTATCTTTTCCGTGCTTCT 60.741 44.000 0.00 0.00 0.00 2.85
1375 1428 2.175202 CCGCCTGAGCCTATCTATCTT 58.825 52.381 0.00 0.00 34.57 2.40
1426 1479 5.424895 GCCTCATATACAGATTCTCCCAGAT 59.575 44.000 0.00 0.00 0.00 2.90
1456 1509 1.603455 CAACCTTGGTCCGCCATGT 60.603 57.895 0.00 0.00 45.56 3.21
1457 1510 0.322098 TACAACCTTGGTCCGCCATG 60.322 55.000 0.00 0.00 45.56 3.66
1458 1511 0.322187 GTACAACCTTGGTCCGCCAT 60.322 55.000 0.00 0.00 45.56 4.40
1459 1512 1.071814 GTACAACCTTGGTCCGCCA 59.928 57.895 0.00 0.00 44.38 5.69
1460 1513 1.673337 GGTACAACCTTGGTCCGCC 60.673 63.158 0.00 0.00 34.73 6.13
1461 1514 3.976758 GGTACAACCTTGGTCCGC 58.023 61.111 0.00 0.00 34.73 5.54
1470 1523 4.338400 GGAATGGCTATTTCAGGTACAACC 59.662 45.833 0.00 0.00 38.99 3.77
1471 1524 4.947388 TGGAATGGCTATTTCAGGTACAAC 59.053 41.667 0.00 0.00 28.47 3.32
1472 1525 5.186256 TGGAATGGCTATTTCAGGTACAA 57.814 39.130 0.00 0.00 28.47 2.41
1473 1526 4.853468 TGGAATGGCTATTTCAGGTACA 57.147 40.909 0.00 0.00 28.47 2.90
1474 1527 4.580580 CCTTGGAATGGCTATTTCAGGTAC 59.419 45.833 11.53 0.00 33.41 3.34
1475 1528 4.229582 ACCTTGGAATGGCTATTTCAGGTA 59.770 41.667 17.71 0.06 34.39 3.08
1476 1529 3.011708 ACCTTGGAATGGCTATTTCAGGT 59.988 43.478 15.09 15.09 33.41 4.00
1477 1530 3.382546 CACCTTGGAATGGCTATTTCAGG 59.617 47.826 14.14 14.14 33.41 3.86
1478 1531 4.272489 TCACCTTGGAATGGCTATTTCAG 58.728 43.478 3.77 0.00 33.41 3.02
1479 1532 4.263905 ACTCACCTTGGAATGGCTATTTCA 60.264 41.667 0.00 0.00 33.71 2.69
1480 1533 4.096984 CACTCACCTTGGAATGGCTATTTC 59.903 45.833 0.00 0.00 33.71 2.17
1481 1534 4.019174 CACTCACCTTGGAATGGCTATTT 58.981 43.478 0.00 0.00 33.71 1.40
1482 1535 3.266772 TCACTCACCTTGGAATGGCTATT 59.733 43.478 0.00 0.00 33.71 1.73
1483 1536 2.846206 TCACTCACCTTGGAATGGCTAT 59.154 45.455 0.00 0.00 33.71 2.97
1484 1537 2.265367 TCACTCACCTTGGAATGGCTA 58.735 47.619 0.00 0.00 33.71 3.93
1493 1546 4.129380 TCATGACAAGTTCACTCACCTTG 58.871 43.478 0.00 0.00 41.02 3.61
1582 1635 7.338196 TCTTTTGAGACACCTGTCAAAATTACA 59.662 33.333 8.14 0.00 46.39 2.41
1614 1667 9.817809 TTATTATACTAAAGAAGTGCAGGAGTG 57.182 33.333 0.00 0.00 39.39 3.51
1638 1691 9.418045 GCACTACTTTTGAATATTGCCTTTTTA 57.582 29.630 0.00 0.00 0.00 1.52
1639 1692 7.930865 TGCACTACTTTTGAATATTGCCTTTTT 59.069 29.630 0.00 0.00 0.00 1.94
1640 1693 7.441017 TGCACTACTTTTGAATATTGCCTTTT 58.559 30.769 0.00 0.00 0.00 2.27
1641 1694 6.991938 TGCACTACTTTTGAATATTGCCTTT 58.008 32.000 0.00 0.00 0.00 3.11
1642 1695 6.588719 TGCACTACTTTTGAATATTGCCTT 57.411 33.333 0.00 0.00 0.00 4.35
1643 1696 6.780457 ATGCACTACTTTTGAATATTGCCT 57.220 33.333 0.00 0.00 0.00 4.75
1644 1697 9.185192 GAATATGCACTACTTTTGAATATTGCC 57.815 33.333 0.00 0.00 0.00 4.52
1645 1698 9.734620 TGAATATGCACTACTTTTGAATATTGC 57.265 29.630 0.00 0.00 0.00 3.56
1656 1709 8.186821 GCTCATTCTTTTGAATATGCACTACTT 58.813 33.333 0.00 0.00 46.51 2.24
1657 1710 7.337689 TGCTCATTCTTTTGAATATGCACTACT 59.662 33.333 0.00 0.00 46.51 2.57
1658 1711 7.475015 TGCTCATTCTTTTGAATATGCACTAC 58.525 34.615 0.00 0.00 46.51 2.73
1659 1712 7.628769 TGCTCATTCTTTTGAATATGCACTA 57.371 32.000 0.00 0.00 46.51 2.74
1704 1757 9.101655 TCATATCCATTTGAATATGCACTATCG 57.898 33.333 0.00 0.00 0.00 2.92
1722 1775 9.753674 AATAAGTTCAAAAGGAGTTCATATCCA 57.246 29.630 0.00 0.00 39.47 3.41
1757 1810 8.507249 GCTTAGTGTTTGAGATACTTGTCAAAT 58.493 33.333 2.25 0.00 44.17 2.32
1868 1921 5.221402 TGCTTTGCCATGTCAGAATTTGTAA 60.221 36.000 0.00 0.00 0.00 2.41
1902 1955 4.276926 GGATAGAGGGAATGCATGTGAAAC 59.723 45.833 0.00 0.00 37.35 2.78
1903 1956 4.079844 TGGATAGAGGGAATGCATGTGAAA 60.080 41.667 0.00 0.00 0.00 2.69
1904 1957 3.459227 TGGATAGAGGGAATGCATGTGAA 59.541 43.478 0.00 0.00 0.00 3.18
1905 1958 3.047857 TGGATAGAGGGAATGCATGTGA 58.952 45.455 0.00 0.00 0.00 3.58
1906 1959 3.497103 TGGATAGAGGGAATGCATGTG 57.503 47.619 0.00 0.00 0.00 3.21
1907 1960 3.654321 TGATGGATAGAGGGAATGCATGT 59.346 43.478 0.00 0.00 35.78 3.21
1908 1961 4.262617 CTGATGGATAGAGGGAATGCATG 58.737 47.826 0.00 0.00 35.78 4.06
1909 1962 3.308259 GCTGATGGATAGAGGGAATGCAT 60.308 47.826 0.00 0.00 38.01 3.96
1910 1963 2.039480 GCTGATGGATAGAGGGAATGCA 59.961 50.000 0.00 0.00 0.00 3.96
1911 1964 2.039480 TGCTGATGGATAGAGGGAATGC 59.961 50.000 0.00 0.00 0.00 3.56
1912 1965 4.362470 TTGCTGATGGATAGAGGGAATG 57.638 45.455 0.00 0.00 0.00 2.67
1913 1966 4.600547 TGATTGCTGATGGATAGAGGGAAT 59.399 41.667 0.00 0.00 0.00 3.01
1914 1967 3.975982 TGATTGCTGATGGATAGAGGGAA 59.024 43.478 0.00 0.00 0.00 3.97
1915 1968 3.590714 TGATTGCTGATGGATAGAGGGA 58.409 45.455 0.00 0.00 0.00 4.20
1916 1969 4.362470 TTGATTGCTGATGGATAGAGGG 57.638 45.455 0.00 0.00 0.00 4.30
1917 1970 6.678878 CAATTTGATTGCTGATGGATAGAGG 58.321 40.000 0.00 0.00 32.92 3.69
1959 2012 5.689514 TGTAAGTTCCGTGCAATTTGATTTG 59.310 36.000 0.00 0.00 0.00 2.32
2087 2140 2.047769 TAGGTTGGAAGGGCCTGTAA 57.952 50.000 6.92 0.00 37.63 2.41
2134 2187 5.255687 TGCATTAAGTCATCACACATCCTT 58.744 37.500 0.00 0.00 0.00 3.36
2135 2188 4.847198 TGCATTAAGTCATCACACATCCT 58.153 39.130 0.00 0.00 0.00 3.24
2288 2341 2.831526 GGGCCTTGATTAAACACCATGT 59.168 45.455 0.84 0.00 0.00 3.21
2299 2352 0.765510 GACTATCCGGGGCCTTGATT 59.234 55.000 0.84 0.00 0.00 2.57
2424 2477 2.257676 GCAAGCTGCACCTTGAGC 59.742 61.111 23.05 7.08 43.79 4.26
2478 2531 1.955778 TCCTGACCGTCGTTTAACTGA 59.044 47.619 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.