Multiple sequence alignment - TraesCS3B01G366700

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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 TraesCS3B01G366700 chr3B 100.000 2874 0 0 1 2874 578981988 578979115 0.000000e+00 5308
1 TraesCS3B01G366700 chr3D 90.233 2795 165 42 118 2869 441577518 441580247 0.000000e+00 3550
2 TraesCS3B01G366700 chr3A 87.490 2566 172 59 79 2575 582351023 582353508 0.000000e+00 2822
3 TraesCS3B01G366700 chr3A 92.459 305 17 5 2570 2874 582353609 582353907 5.690000e-117 431


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 TraesCS3B01G366700 chr3B 578979115 578981988 2873 True 5308.0 5308 100.0000 1 2874 1 chr3B.!!$R1 2873
1 TraesCS3B01G366700 chr3D 441577518 441580247 2729 False 3550.0 3550 90.2330 118 2869 1 chr3D.!!$F1 2751
2 TraesCS3B01G366700 chr3A 582351023 582353907 2884 False 1626.5 2822 89.9745 79 2874 2 chr3A.!!$F1 2795

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
387 388 0.034186 TTCGCCTCGTTACCCTCCTA 60.034 55.0 0.0 0.0 0.0 2.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1946 2042 0.248289 GTTGGCTCCATTGCAATGCT 59.752 50.0 30.15 0.0 35.08 3.79 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
17 18 2.338620 TTGGTGAGTCTCGTGGCG 59.661 61.111 0.00 0.00 0.00 5.69
18 19 3.220999 TTGGTGAGTCTCGTGGCGG 62.221 63.158 0.00 0.00 0.00 6.13
19 20 3.681835 GGTGAGTCTCGTGGCGGT 61.682 66.667 0.00 0.00 0.00 5.68
20 21 2.430921 GTGAGTCTCGTGGCGGTG 60.431 66.667 0.00 0.00 0.00 4.94
21 22 3.680786 TGAGTCTCGTGGCGGTGG 61.681 66.667 0.00 0.00 0.00 4.61
22 23 3.681835 GAGTCTCGTGGCGGTGGT 61.682 66.667 0.00 0.00 0.00 4.16
23 24 3.916392 GAGTCTCGTGGCGGTGGTG 62.916 68.421 0.00 0.00 0.00 4.17
29 30 4.887190 GTGGCGGTGGTGGTGGTT 62.887 66.667 0.00 0.00 0.00 3.67
30 31 4.885270 TGGCGGTGGTGGTGGTTG 62.885 66.667 0.00 0.00 0.00 3.77
42 43 4.966787 TGGTTGCGCCCCTTGGTC 62.967 66.667 4.18 0.00 36.04 4.02
48 49 4.619227 CGCCCCTTGGTCGTGTGT 62.619 66.667 0.00 0.00 0.00 3.72
49 50 2.978010 GCCCCTTGGTCGTGTGTG 60.978 66.667 0.00 0.00 0.00 3.82
50 51 2.508928 CCCCTTGGTCGTGTGTGT 59.491 61.111 0.00 0.00 0.00 3.72
51 52 1.891919 CCCCTTGGTCGTGTGTGTG 60.892 63.158 0.00 0.00 0.00 3.82
52 53 1.153249 CCCTTGGTCGTGTGTGTGT 60.153 57.895 0.00 0.00 0.00 3.72
53 54 1.436195 CCCTTGGTCGTGTGTGTGTG 61.436 60.000 0.00 0.00 0.00 3.82
54 55 0.742990 CCTTGGTCGTGTGTGTGTGT 60.743 55.000 0.00 0.00 0.00 3.72
55 56 1.471851 CCTTGGTCGTGTGTGTGTGTA 60.472 52.381 0.00 0.00 0.00 2.90
56 57 2.479837 CTTGGTCGTGTGTGTGTGTAT 58.520 47.619 0.00 0.00 0.00 2.29
57 58 1.859383 TGGTCGTGTGTGTGTGTATG 58.141 50.000 0.00 0.00 0.00 2.39
58 59 1.144969 GGTCGTGTGTGTGTGTATGG 58.855 55.000 0.00 0.00 0.00 2.74
59 60 1.144969 GTCGTGTGTGTGTGTATGGG 58.855 55.000 0.00 0.00 0.00 4.00
60 61 0.034198 TCGTGTGTGTGTGTATGGGG 59.966 55.000 0.00 0.00 0.00 4.96
61 62 0.953471 CGTGTGTGTGTGTATGGGGG 60.953 60.000 0.00 0.00 0.00 5.40
62 63 0.109723 GTGTGTGTGTGTATGGGGGT 59.890 55.000 0.00 0.00 0.00 4.95
63 64 0.109532 TGTGTGTGTGTATGGGGGTG 59.890 55.000 0.00 0.00 0.00 4.61
64 65 0.608035 GTGTGTGTGTATGGGGGTGG 60.608 60.000 0.00 0.00 0.00 4.61
65 66 1.001393 GTGTGTGTATGGGGGTGGG 60.001 63.158 0.00 0.00 0.00 4.61
66 67 2.235028 TGTGTGTATGGGGGTGGGG 61.235 63.158 0.00 0.00 0.00 4.96
67 68 2.211575 TGTGTATGGGGGTGGGGT 59.788 61.111 0.00 0.00 0.00 4.95
68 69 2.235028 TGTGTATGGGGGTGGGGTG 61.235 63.158 0.00 0.00 0.00 4.61
69 70 1.926489 GTGTATGGGGGTGGGGTGA 60.926 63.158 0.00 0.00 0.00 4.02
70 71 1.618143 TGTATGGGGGTGGGGTGAG 60.618 63.158 0.00 0.00 0.00 3.51
71 72 2.043772 TATGGGGGTGGGGTGAGG 59.956 66.667 0.00 0.00 0.00 3.86
72 73 3.668859 TATGGGGGTGGGGTGAGGG 62.669 68.421 0.00 0.00 0.00 4.30
77 78 2.204029 GGTGGGGTGAGGGGTGTA 60.204 66.667 0.00 0.00 0.00 2.90
89 90 1.705997 GGGGTGTAGCTATGGGTGGG 61.706 65.000 0.00 0.00 0.00 4.61
92 93 0.463833 GTGTAGCTATGGGTGGGCAC 60.464 60.000 0.00 0.00 0.00 5.01
97 98 3.334891 TATGGGTGGGCACGGCTT 61.335 61.111 0.00 0.00 0.00 4.35
106 107 1.578206 GGGCACGGCTTGTTCTCTTC 61.578 60.000 0.00 0.00 0.00 2.87
109 110 1.593196 CACGGCTTGTTCTCTTCCAA 58.407 50.000 0.00 0.00 0.00 3.53
114 115 1.160137 CTTGTTCTCTTCCAAGGGCG 58.840 55.000 0.00 0.00 35.51 6.13
123 124 1.202099 TTCCAAGGGCGGTGGTATCA 61.202 55.000 5.13 0.00 37.43 2.15
151 152 1.139498 TGGATTTGGAGGCCTGGACA 61.139 55.000 12.00 3.00 0.00 4.02
166 167 1.550130 GGACATCGGTGGGTCTTCCA 61.550 60.000 0.00 0.00 44.79 3.53
221 222 2.203422 CACTGGCGGGTTCCCAAA 60.203 61.111 8.70 0.00 30.66 3.28
242 243 1.865725 CGAAAACTCCGCGATTTGTC 58.134 50.000 8.23 0.71 0.00 3.18
243 244 1.193650 CGAAAACTCCGCGATTTGTCA 59.806 47.619 8.23 0.00 0.00 3.58
251 252 0.930310 CGCGATTTGTCATCGATGGT 59.070 50.000 24.61 6.71 43.59 3.55
259 260 0.530650 GTCATCGATGGTGGCGACAT 60.531 55.000 24.61 0.00 46.14 3.06
265 266 2.906182 GATGGTGGCGACATCTGCGA 62.906 60.000 1.65 0.00 43.86 5.10
309 310 1.851267 GTTGTGGTTCCCCTTCCCT 59.149 57.895 0.00 0.00 0.00 4.20
312 313 0.996762 TGTGGTTCCCCTTCCCTTGT 60.997 55.000 0.00 0.00 0.00 3.16
320 321 0.322008 CCCTTCCCTTGTCAGTGCTC 60.322 60.000 0.00 0.00 0.00 4.26
321 322 0.322008 CCTTCCCTTGTCAGTGCTCC 60.322 60.000 0.00 0.00 0.00 4.70
385 386 1.141234 CTTCGCCTCGTTACCCTCC 59.859 63.158 0.00 0.00 0.00 4.30
387 388 0.034186 TTCGCCTCGTTACCCTCCTA 60.034 55.000 0.00 0.00 0.00 2.94
430 438 0.451383 TGCTTATTGTCATGGCGTGC 59.549 50.000 0.65 0.00 0.00 5.34
443 451 4.717629 CGTGCCGTCGCCTTCTGA 62.718 66.667 0.00 0.00 0.00 3.27
447 455 2.995872 GCCGTCGCCTTCTGACTCT 61.996 63.158 0.00 0.00 34.17 3.24
449 457 1.581954 CGTCGCCTTCTGACTCTGT 59.418 57.895 0.00 0.00 34.17 3.41
452 460 0.811915 TCGCCTTCTGACTCTGTAGC 59.188 55.000 0.00 0.00 0.00 3.58
467 475 3.369643 TAGCGCTCATGCTCGGCAA 62.370 57.895 16.34 0.00 45.87 4.52
495 503 6.153756 AGTCGTGTTGTTTTTAGTGCTTTTT 58.846 32.000 0.00 0.00 0.00 1.94
556 564 6.642733 TCTCTTTGATCTAATTTGAGGGGT 57.357 37.500 0.00 0.00 0.00 4.95
579 589 2.906389 GGGGAGCCTTTTCCATTCTTTT 59.094 45.455 0.00 0.00 39.09 2.27
590 600 5.447624 TTCCATTCTTTTTCGAAGGTTCC 57.552 39.130 0.00 0.00 0.00 3.62
601 611 4.437772 TCGAAGGTTCCGTTTTTGTTTT 57.562 36.364 0.00 0.00 0.00 2.43
603 613 4.858140 TCGAAGGTTCCGTTTTTGTTTTTC 59.142 37.500 0.00 0.00 0.00 2.29
604 614 4.031991 CGAAGGTTCCGTTTTTGTTTTTCC 59.968 41.667 0.00 0.00 0.00 3.13
606 616 5.918426 AGGTTCCGTTTTTGTTTTTCCTA 57.082 34.783 0.00 0.00 0.00 2.94
607 617 5.898174 AGGTTCCGTTTTTGTTTTTCCTAG 58.102 37.500 0.00 0.00 0.00 3.02
609 619 5.394443 GGTTCCGTTTTTGTTTTTCCTAGGT 60.394 40.000 9.08 0.00 0.00 3.08
611 621 6.375945 TCCGTTTTTGTTTTTCCTAGGTAC 57.624 37.500 9.08 4.11 0.00 3.34
632 663 3.375922 ACAGGTACAACCAAACAAACTCG 59.624 43.478 0.00 0.00 41.95 4.18
761 820 4.815308 TCAAAAACATTAGGAAACGACCGA 59.185 37.500 0.00 0.00 34.73 4.69
771 830 2.039062 AAACGACCGAAACGTGTGGC 62.039 55.000 0.00 0.00 43.16 5.01
851 910 4.265056 GGCCAACCCCACGTCTGT 62.265 66.667 0.00 0.00 0.00 3.41
860 919 0.590732 CCCACGTCTGTATACGCGTC 60.591 60.000 18.63 1.04 46.71 5.19
861 920 0.376152 CCACGTCTGTATACGCGTCT 59.624 55.000 18.63 9.26 46.71 4.18
883 943 1.658095 GCGTTAGCTTTGCTCTCTCTG 59.342 52.381 0.00 0.00 40.44 3.35
891 951 3.808618 GCTTTGCTCTCTCTGGAAGGAAA 60.809 47.826 0.00 0.00 0.00 3.13
949 1009 1.214589 GCTAAGTCCAACCGAGCGA 59.785 57.895 0.00 0.00 0.00 4.93
952 1012 2.537792 TAAGTCCAACCGAGCGAGCG 62.538 60.000 0.00 0.00 0.00 5.03
1168 1241 4.733725 TCCCCAACCCTAGCGGCT 62.734 66.667 7.98 7.98 33.26 5.52
1616 1698 0.035820 GGTGGTGCTGGAACGGAATA 60.036 55.000 0.00 0.00 36.31 1.75
1630 1712 2.198406 CGGAATATTTCGTTGCGAGGA 58.802 47.619 8.05 0.00 41.99 3.71
1631 1713 2.800544 CGGAATATTTCGTTGCGAGGAT 59.199 45.455 8.05 0.00 41.99 3.24
1632 1714 3.247648 CGGAATATTTCGTTGCGAGGATT 59.752 43.478 8.05 0.00 41.99 3.01
1633 1715 4.260620 CGGAATATTTCGTTGCGAGGATTT 60.261 41.667 8.05 0.00 41.99 2.17
1634 1716 4.970003 GGAATATTTCGTTGCGAGGATTTG 59.030 41.667 0.00 0.00 37.14 2.32
1635 1717 2.919666 ATTTCGTTGCGAGGATTTGG 57.080 45.000 0.00 0.00 37.14 3.28
1636 1718 1.600023 TTTCGTTGCGAGGATTTGGT 58.400 45.000 0.00 0.00 37.14 3.67
1637 1719 1.153353 TTCGTTGCGAGGATTTGGTC 58.847 50.000 0.00 0.00 37.14 4.02
1758 1853 5.277828 GGTTGAGATCGTGTAAAACAGCTTT 60.278 40.000 0.00 0.00 0.00 3.51
1775 1870 6.508777 ACAGCTTTGTAAATTTCGGCTAAAA 58.491 32.000 0.00 0.00 0.00 1.52
1814 1909 7.377766 TCTGGTTGTGCTTGTCTATAAATTC 57.622 36.000 0.00 0.00 0.00 2.17
1882 1978 3.953712 TGAGCTTTATGGTCGACAGAA 57.046 42.857 18.91 4.89 45.46 3.02
1884 1980 2.605366 GAGCTTTATGGTCGACAGAAGC 59.395 50.000 24.45 24.45 45.31 3.86
1903 1999 0.530870 CGCTAGCTTCCTAAGGCACC 60.531 60.000 13.93 0.00 0.00 5.01
1907 2003 1.362224 AGCTTCCTAAGGCACCTGAA 58.638 50.000 0.00 0.00 0.00 3.02
1915 2011 0.609131 AAGGCACCTGAACGAATGGG 60.609 55.000 0.00 0.00 0.00 4.00
1917 2013 0.608035 GGCACCTGAACGAATGGGAA 60.608 55.000 0.00 0.00 0.00 3.97
1919 2015 1.133025 GCACCTGAACGAATGGGAATG 59.867 52.381 0.00 0.00 0.00 2.67
1920 2016 2.710377 CACCTGAACGAATGGGAATGA 58.290 47.619 0.00 0.00 0.00 2.57
1921 2017 2.420022 CACCTGAACGAATGGGAATGAC 59.580 50.000 0.00 0.00 0.00 3.06
1922 2018 2.039746 ACCTGAACGAATGGGAATGACA 59.960 45.455 0.00 0.00 0.00 3.58
1923 2019 3.282021 CCTGAACGAATGGGAATGACAT 58.718 45.455 0.00 0.00 0.00 3.06
1924 2020 3.696051 CCTGAACGAATGGGAATGACATT 59.304 43.478 0.00 0.00 40.98 2.71
1925 2021 4.158394 CCTGAACGAATGGGAATGACATTT 59.842 41.667 1.39 0.00 38.57 2.32
1926 2022 5.309323 TGAACGAATGGGAATGACATTTC 57.691 39.130 1.39 0.00 38.57 2.17
1927 2023 4.764308 TGAACGAATGGGAATGACATTTCA 59.236 37.500 8.73 7.95 38.57 2.69
1928 2024 4.970662 ACGAATGGGAATGACATTTCAG 57.029 40.909 8.73 0.43 38.57 3.02
1929 2025 4.335416 ACGAATGGGAATGACATTTCAGT 58.665 39.130 8.73 6.90 38.57 3.41
1930 2026 4.156556 ACGAATGGGAATGACATTTCAGTG 59.843 41.667 8.73 4.95 38.57 3.66
1931 2027 4.395854 CGAATGGGAATGACATTTCAGTGA 59.604 41.667 8.73 0.00 38.57 3.41
1932 2028 5.106197 CGAATGGGAATGACATTTCAGTGAA 60.106 40.000 8.73 0.08 38.57 3.18
1933 2029 6.570186 CGAATGGGAATGACATTTCAGTGAAA 60.570 38.462 20.14 20.14 38.57 2.69
1934 2030 6.862469 ATGGGAATGACATTTCAGTGAAAT 57.138 33.333 22.70 22.70 42.14 2.17
1935 2031 6.669125 TGGGAATGACATTTCAGTGAAATT 57.331 33.333 25.20 17.24 39.82 1.82
1936 2032 7.773489 TGGGAATGACATTTCAGTGAAATTA 57.227 32.000 25.20 16.01 39.82 1.40
1937 2033 7.601856 TGGGAATGACATTTCAGTGAAATTAC 58.398 34.615 25.20 20.83 39.82 1.89
1938 2034 7.451255 TGGGAATGACATTTCAGTGAAATTACT 59.549 33.333 25.20 12.68 39.82 2.24
1939 2035 8.306761 GGGAATGACATTTCAGTGAAATTACTT 58.693 33.333 25.20 16.57 39.82 2.24
1940 2036 9.346725 GGAATGACATTTCAGTGAAATTACTTC 57.653 33.333 25.20 21.76 39.82 3.01
1941 2037 9.346725 GAATGACATTTCAGTGAAATTACTTCC 57.653 33.333 25.20 11.92 39.82 3.46
1942 2038 6.898041 TGACATTTCAGTGAAATTACTTCCG 58.102 36.000 25.20 15.69 39.82 4.30
1943 2039 6.485313 TGACATTTCAGTGAAATTACTTCCGT 59.515 34.615 25.20 18.33 39.82 4.69
1944 2040 6.899114 ACATTTCAGTGAAATTACTTCCGTC 58.101 36.000 25.20 0.00 39.82 4.79
1945 2041 6.710744 ACATTTCAGTGAAATTACTTCCGTCT 59.289 34.615 25.20 1.64 39.82 4.18
1946 2042 7.876068 ACATTTCAGTGAAATTACTTCCGTCTA 59.124 33.333 25.20 0.00 39.82 2.59
1947 2043 7.884816 TTTCAGTGAAATTACTTCCGTCTAG 57.115 36.000 14.35 0.00 32.53 2.43
1948 2044 5.408356 TCAGTGAAATTACTTCCGTCTAGC 58.592 41.667 0.00 0.00 32.53 3.42
1949 2045 5.047590 TCAGTGAAATTACTTCCGTCTAGCA 60.048 40.000 0.00 0.00 32.53 3.49
1950 2046 5.812642 CAGTGAAATTACTTCCGTCTAGCAT 59.187 40.000 0.00 0.00 32.53 3.79
2038 2161 2.957402 AACTTGAGCATGGACCTGAA 57.043 45.000 0.00 0.00 0.00 3.02
2039 2162 2.191128 ACTTGAGCATGGACCTGAAC 57.809 50.000 0.00 0.00 0.00 3.18
2040 2163 1.421268 ACTTGAGCATGGACCTGAACA 59.579 47.619 0.00 0.00 0.00 3.18
2042 2165 0.320683 TGAGCATGGACCTGAACACG 60.321 55.000 0.00 0.00 0.00 4.49
2044 2167 0.108585 AGCATGGACCTGAACACGTT 59.891 50.000 0.00 0.00 0.00 3.99
2045 2168 0.517316 GCATGGACCTGAACACGTTC 59.483 55.000 2.89 2.89 39.91 3.95
2046 2169 1.877637 CATGGACCTGAACACGTTCA 58.122 50.000 11.85 11.85 46.27 3.18
2047 2170 1.531149 CATGGACCTGAACACGTTCAC 59.469 52.381 8.51 0.56 43.90 3.18
2048 2171 0.528901 TGGACCTGAACACGTTCACG 60.529 55.000 8.51 7.76 43.90 4.35
2049 2172 1.563173 GACCTGAACACGTTCACGC 59.437 57.895 8.51 0.00 43.90 5.34
2050 2173 1.149361 GACCTGAACACGTTCACGCA 61.149 55.000 8.51 0.00 43.90 5.24
2051 2174 0.531974 ACCTGAACACGTTCACGCAT 60.532 50.000 8.51 0.00 43.90 4.73
2052 2175 1.269883 ACCTGAACACGTTCACGCATA 60.270 47.619 8.51 0.00 43.90 3.14
2105 2228 6.252967 TGTTCATGTAGCCATAAGTTGTTG 57.747 37.500 0.00 0.00 0.00 3.33
2106 2229 5.767665 TGTTCATGTAGCCATAAGTTGTTGT 59.232 36.000 0.00 0.00 0.00 3.32
2107 2230 6.264292 TGTTCATGTAGCCATAAGTTGTTGTT 59.736 34.615 0.00 0.00 0.00 2.83
2108 2231 6.252967 TCATGTAGCCATAAGTTGTTGTTG 57.747 37.500 0.00 0.00 0.00 3.33
2109 2232 5.767665 TCATGTAGCCATAAGTTGTTGTTGT 59.232 36.000 0.00 0.00 0.00 3.32
2124 2247 5.635866 TGTTGTTGTTGTCAGTAACATGTG 58.364 37.500 0.00 0.00 40.00 3.21
2159 2292 7.553760 TCTCTGATCTATAATAGCAGCTCTCAG 59.446 40.741 0.00 0.55 0.00 3.35
2219 2352 5.697178 GTGAGGAGGAGTAAAACAGAGAAAC 59.303 44.000 0.00 0.00 0.00 2.78
2289 2423 3.582647 TGCATCCTAGAGGTGTTCTTCAA 59.417 43.478 0.00 0.00 37.36 2.69
2290 2424 4.041567 TGCATCCTAGAGGTGTTCTTCAAA 59.958 41.667 0.00 0.00 37.36 2.69
2291 2425 5.003804 GCATCCTAGAGGTGTTCTTCAAAA 58.996 41.667 0.00 0.00 37.36 2.44
2309 2443 3.951563 AAAGCTGGTATGCTGGGATTA 57.048 42.857 0.00 0.00 43.24 1.75
2312 2446 2.027745 AGCTGGTATGCTGGGATTATCG 60.028 50.000 0.00 0.00 42.33 2.92
2316 2450 3.074412 GGTATGCTGGGATTATCGTTGG 58.926 50.000 0.00 0.00 0.00 3.77
2344 2478 1.956477 GTTGATGCTTCTGGTGGTGTT 59.044 47.619 0.88 0.00 0.00 3.32
2434 2568 0.732880 ATCGAACCTCTTGTGTCGCG 60.733 55.000 0.00 0.00 0.00 5.87
2558 2695 8.972127 TCATACTTATAAAAGTCAGAGCAGTCT 58.028 33.333 0.00 0.00 42.42 3.24
2617 2857 5.393461 GCAAAGAGCAAACATAGCATACCTT 60.393 40.000 0.00 0.00 44.79 3.50
2642 2882 7.547697 TTAGTGTGCCACCTATATTATGCTA 57.452 36.000 0.00 0.00 34.49 3.49
2647 2887 8.258007 GTGTGCCACCTATATTATGCTAAGATA 58.742 37.037 0.00 0.00 0.00 1.98
2691 2931 6.483640 GCTTTCACCCAGAGTATATGTTTAGG 59.516 42.308 0.00 0.00 0.00 2.69
2738 2978 8.243426 CCTTATGCAGCTTTAAATTAACAGACA 58.757 33.333 0.00 0.00 0.00 3.41
2754 2994 3.817084 ACAGACATGTGTTGACATTGGAG 59.183 43.478 1.15 0.00 41.12 3.86
2763 3003 3.066621 TGTTGACATTGGAGTTGCTGTTC 59.933 43.478 0.00 0.00 0.00 3.18
2870 3111 5.765182 ACATTGTGTCCCAACTTCTAGAAAG 59.235 40.000 6.63 3.77 35.44 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.338620 CGCCACGAGACTCACCAA 59.661 61.111 2.82 0.00 0.00 3.67
1 2 3.680786 CCGCCACGAGACTCACCA 61.681 66.667 2.82 0.00 0.00 4.17
2 3 3.681835 ACCGCCACGAGACTCACC 61.682 66.667 2.82 0.00 0.00 4.02
3 4 2.430921 CACCGCCACGAGACTCAC 60.431 66.667 2.82 0.00 0.00 3.51
4 5 3.680786 CCACCGCCACGAGACTCA 61.681 66.667 2.82 0.00 0.00 3.41
5 6 3.681835 ACCACCGCCACGAGACTC 61.682 66.667 0.00 0.00 0.00 3.36
6 7 3.991051 CACCACCGCCACGAGACT 61.991 66.667 0.00 0.00 0.00 3.24
12 13 4.887190 AACCACCACCACCGCCAC 62.887 66.667 0.00 0.00 0.00 5.01
13 14 4.885270 CAACCACCACCACCGCCA 62.885 66.667 0.00 0.00 0.00 5.69
25 26 4.966787 GACCAAGGGGCGCAACCA 62.967 66.667 20.55 0.00 42.05 3.67
32 33 2.978010 CACACACGACCAAGGGGC 60.978 66.667 0.00 0.00 37.90 5.80
33 34 1.891919 CACACACACGACCAAGGGG 60.892 63.158 0.00 0.00 41.29 4.79
34 35 1.153249 ACACACACACGACCAAGGG 60.153 57.895 0.00 0.00 0.00 3.95
35 36 0.742990 ACACACACACACGACCAAGG 60.743 55.000 0.00 0.00 0.00 3.61
36 37 1.929230 TACACACACACACGACCAAG 58.071 50.000 0.00 0.00 0.00 3.61
37 38 2.205911 CATACACACACACACGACCAA 58.794 47.619 0.00 0.00 0.00 3.67
38 39 1.539280 CCATACACACACACACGACCA 60.539 52.381 0.00 0.00 0.00 4.02
39 40 1.144969 CCATACACACACACACGACC 58.855 55.000 0.00 0.00 0.00 4.79
40 41 1.144969 CCCATACACACACACACGAC 58.855 55.000 0.00 0.00 0.00 4.34
41 42 0.034198 CCCCATACACACACACACGA 59.966 55.000 0.00 0.00 0.00 4.35
42 43 0.953471 CCCCCATACACACACACACG 60.953 60.000 0.00 0.00 0.00 4.49
43 44 0.109723 ACCCCCATACACACACACAC 59.890 55.000 0.00 0.00 0.00 3.82
44 45 0.109532 CACCCCCATACACACACACA 59.890 55.000 0.00 0.00 0.00 3.72
45 46 0.608035 CCACCCCCATACACACACAC 60.608 60.000 0.00 0.00 0.00 3.82
46 47 1.764422 CCACCCCCATACACACACA 59.236 57.895 0.00 0.00 0.00 3.72
47 48 1.001393 CCCACCCCCATACACACAC 60.001 63.158 0.00 0.00 0.00 3.82
48 49 2.235028 CCCCACCCCCATACACACA 61.235 63.158 0.00 0.00 0.00 3.72
49 50 2.235761 ACCCCACCCCCATACACAC 61.236 63.158 0.00 0.00 0.00 3.82
50 51 2.211575 ACCCCACCCCCATACACA 59.788 61.111 0.00 0.00 0.00 3.72
51 52 1.921869 CTCACCCCACCCCCATACAC 61.922 65.000 0.00 0.00 0.00 2.90
52 53 1.618143 CTCACCCCACCCCCATACA 60.618 63.158 0.00 0.00 0.00 2.29
53 54 2.383601 CCTCACCCCACCCCCATAC 61.384 68.421 0.00 0.00 0.00 2.39
54 55 2.043772 CCTCACCCCACCCCCATA 59.956 66.667 0.00 0.00 0.00 2.74
59 60 3.876255 TACACCCCTCACCCCACCC 62.876 68.421 0.00 0.00 0.00 4.61
60 61 2.204029 TACACCCCTCACCCCACC 60.204 66.667 0.00 0.00 0.00 4.61
61 62 2.967946 GCTACACCCCTCACCCCAC 61.968 68.421 0.00 0.00 0.00 4.61
62 63 1.817572 TAGCTACACCCCTCACCCCA 61.818 60.000 0.00 0.00 0.00 4.96
63 64 0.400093 ATAGCTACACCCCTCACCCC 60.400 60.000 0.00 0.00 0.00 4.95
64 65 0.759346 CATAGCTACACCCCTCACCC 59.241 60.000 0.00 0.00 0.00 4.61
65 66 0.759346 CCATAGCTACACCCCTCACC 59.241 60.000 0.00 0.00 0.00 4.02
66 67 0.759346 CCCATAGCTACACCCCTCAC 59.241 60.000 0.00 0.00 0.00 3.51
67 68 0.341961 ACCCATAGCTACACCCCTCA 59.658 55.000 0.00 0.00 0.00 3.86
68 69 0.759346 CACCCATAGCTACACCCCTC 59.241 60.000 0.00 0.00 0.00 4.30
69 70 0.694444 CCACCCATAGCTACACCCCT 60.694 60.000 0.00 0.00 0.00 4.79
70 71 1.705997 CCCACCCATAGCTACACCCC 61.706 65.000 0.00 0.00 0.00 4.95
71 72 1.837090 CCCACCCATAGCTACACCC 59.163 63.158 0.00 0.00 0.00 4.61
72 73 1.148498 GCCCACCCATAGCTACACC 59.852 63.158 0.00 0.00 0.00 4.16
73 74 0.463833 GTGCCCACCCATAGCTACAC 60.464 60.000 0.00 0.00 0.00 2.90
74 75 1.912220 GTGCCCACCCATAGCTACA 59.088 57.895 0.00 0.00 0.00 2.74
75 76 1.227556 CGTGCCCACCCATAGCTAC 60.228 63.158 0.00 0.00 0.00 3.58
76 77 2.439960 CCGTGCCCACCCATAGCTA 61.440 63.158 0.00 0.00 0.00 3.32
77 78 3.797353 CCGTGCCCACCCATAGCT 61.797 66.667 0.00 0.00 0.00 3.32
89 90 0.884704 TGGAAGAGAACAAGCCGTGC 60.885 55.000 0.00 0.00 0.00 5.34
92 93 1.160137 CCTTGGAAGAGAACAAGCCG 58.840 55.000 0.00 0.00 42.01 5.52
97 98 1.374947 CCGCCCTTGGAAGAGAACA 59.625 57.895 0.00 0.00 0.00 3.18
106 107 1.451387 GTGATACCACCGCCCTTGG 60.451 63.158 0.00 0.00 40.32 3.61
109 110 1.120530 CTAAGTGATACCACCGCCCT 58.879 55.000 0.00 0.00 44.22 5.19
114 115 5.552870 ATCCACATCTAAGTGATACCACC 57.447 43.478 0.00 0.00 44.22 4.61
123 124 3.372025 GGCCTCCAAATCCACATCTAAGT 60.372 47.826 0.00 0.00 0.00 2.24
166 167 1.687612 CACTGAGCCCACCCTTGAT 59.312 57.895 0.00 0.00 0.00 2.57
242 243 0.249615 AGATGTCGCCACCATCGATG 60.250 55.000 18.76 18.76 42.78 3.84
243 244 0.249615 CAGATGTCGCCACCATCGAT 60.250 55.000 0.00 0.00 42.78 3.59
251 252 2.125952 CACTCGCAGATGTCGCCA 60.126 61.111 0.00 0.00 33.89 5.69
265 266 4.434520 GCCTTTAAGAGAATAGCGACACT 58.565 43.478 0.00 0.00 0.00 3.55
276 277 2.400399 CACAACGACGCCTTTAAGAGA 58.600 47.619 0.00 0.00 0.00 3.10
282 283 1.441732 GGAACCACAACGACGCCTTT 61.442 55.000 0.00 0.00 0.00 3.11
309 310 1.112916 TCACCTCGGAGCACTGACAA 61.113 55.000 0.00 0.00 0.00 3.18
312 313 0.033504 GTTTCACCTCGGAGCACTGA 59.966 55.000 0.00 0.00 0.00 3.41
320 321 0.676782 GGACATGGGTTTCACCTCGG 60.677 60.000 0.00 0.00 38.64 4.63
321 322 1.019278 CGGACATGGGTTTCACCTCG 61.019 60.000 0.00 0.00 38.64 4.63
385 386 2.076622 CTCCACGACGATGCCCCTAG 62.077 65.000 0.00 0.00 0.00 3.02
387 388 3.461773 CTCCACGACGATGCCCCT 61.462 66.667 0.00 0.00 0.00 4.79
394 396 4.988716 ACCTGGGCTCCACGACGA 62.989 66.667 0.00 0.00 0.00 4.20
406 408 1.406539 GCCATGACAATAAGCACCTGG 59.593 52.381 0.00 0.00 0.00 4.45
430 438 1.153939 CAGAGTCAGAAGGCGACGG 60.154 63.158 0.00 0.00 38.46 4.79
436 444 0.814457 AGCGCTACAGAGTCAGAAGG 59.186 55.000 8.99 0.00 0.00 3.46
443 451 4.823276 GCATGAGCGCTACAGAGT 57.177 55.556 11.50 0.00 0.00 3.24
545 553 2.096168 CTCCCCCACCCCTCAAATT 58.904 57.895 0.00 0.00 0.00 1.82
546 554 2.626467 GCTCCCCCACCCCTCAAAT 61.626 63.158 0.00 0.00 0.00 2.32
551 559 4.635963 AAAGGCTCCCCCACCCCT 62.636 66.667 0.00 0.00 35.39 4.79
552 560 3.600981 AAAAGGCTCCCCCACCCC 61.601 66.667 0.00 0.00 35.39 4.95
556 564 0.041090 GAATGGAAAAGGCTCCCCCA 59.959 55.000 4.53 4.53 34.22 4.96
579 589 4.437772 AAACAAAAACGGAACCTTCGAA 57.562 36.364 0.00 0.00 0.00 3.71
590 600 6.183360 ACCTGTACCTAGGAAAAACAAAAACG 60.183 38.462 17.98 2.40 40.42 3.60
601 611 4.130719 TGGTTGTACCTGTACCTAGGAA 57.869 45.455 17.98 0.00 40.42 3.36
603 613 4.040706 TGTTTGGTTGTACCTGTACCTAGG 59.959 45.833 7.41 7.41 43.71 3.02
604 614 5.217978 TGTTTGGTTGTACCTGTACCTAG 57.782 43.478 5.07 0.00 39.58 3.02
606 616 4.506937 TTGTTTGGTTGTACCTGTACCT 57.493 40.909 5.07 0.00 39.58 3.08
607 617 4.641541 AGTTTGTTTGGTTGTACCTGTACC 59.358 41.667 5.07 0.00 39.58 3.34
609 619 4.571580 CGAGTTTGTTTGGTTGTACCTGTA 59.428 41.667 0.00 0.00 39.58 2.74
611 621 3.242936 CCGAGTTTGTTTGGTTGTACCTG 60.243 47.826 0.00 0.00 39.58 4.00
632 663 3.663025 AGCACAACATTAAATTGCACCC 58.337 40.909 0.00 0.00 35.57 4.61
761 820 4.142902 CGAGAATAGAATTGCCACACGTTT 60.143 41.667 0.00 0.00 0.00 3.60
771 830 3.448686 ACTGCGTCCGAGAATAGAATTG 58.551 45.455 0.00 0.00 0.00 2.32
797 856 0.111253 CCCTGCCTTGTCTTGTTCCT 59.889 55.000 0.00 0.00 0.00 3.36
860 919 0.642800 GAGAGCAAAGCTAACGCGAG 59.357 55.000 15.93 0.36 39.88 5.03
861 920 0.243907 AGAGAGCAAAGCTAACGCGA 59.756 50.000 15.93 0.00 39.88 5.87
867 926 2.499289 CCTTCCAGAGAGAGCAAAGCTA 59.501 50.000 0.00 0.00 39.88 3.32
868 927 1.278699 CCTTCCAGAGAGAGCAAAGCT 59.721 52.381 0.00 0.00 43.88 3.74
883 943 7.952671 ACTACCTTTTCAATTTCTTTCCTTCC 58.047 34.615 0.00 0.00 0.00 3.46
891 951 4.394729 TGGCGACTACCTTTTCAATTTCT 58.605 39.130 0.00 0.00 0.00 2.52
921 981 2.182030 GACTTAGCTGGCTCGCGT 59.818 61.111 5.77 0.00 34.40 6.01
955 1015 4.994756 GGGTGGGTGGGTGCCTTG 62.995 72.222 0.00 0.00 0.00 3.61
1148 1221 1.993391 CCGCTAGGGTTGGGGAGAA 60.993 63.158 6.02 0.00 39.53 2.87
1616 1698 2.159382 ACCAAATCCTCGCAACGAAAT 58.841 42.857 0.00 0.00 34.74 2.17
1630 1712 1.710244 TGTGACATCCCTGGACCAAAT 59.290 47.619 0.00 0.00 0.00 2.32
1631 1713 1.144691 TGTGACATCCCTGGACCAAA 58.855 50.000 0.00 0.00 0.00 3.28
1632 1714 0.400213 GTGTGACATCCCTGGACCAA 59.600 55.000 0.00 0.00 0.00 3.67
1633 1715 0.766288 TGTGTGACATCCCTGGACCA 60.766 55.000 0.00 0.00 0.00 4.02
1634 1716 0.400213 TTGTGTGACATCCCTGGACC 59.600 55.000 0.00 0.00 0.00 4.46
1635 1717 2.496899 ATTGTGTGACATCCCTGGAC 57.503 50.000 0.00 0.00 0.00 4.02
1636 1718 2.644299 AGAATTGTGTGACATCCCTGGA 59.356 45.455 0.00 0.00 0.00 3.86
1637 1719 3.077484 AGAATTGTGTGACATCCCTGG 57.923 47.619 0.00 0.00 0.00 4.45
1638 1720 4.520111 TGAAAGAATTGTGTGACATCCCTG 59.480 41.667 0.00 0.00 0.00 4.45
1639 1721 4.728772 TGAAAGAATTGTGTGACATCCCT 58.271 39.130 0.00 0.00 0.00 4.20
1640 1722 5.649782 ATGAAAGAATTGTGTGACATCCC 57.350 39.130 0.00 0.00 0.00 3.85
1641 1723 7.615582 TCTATGAAAGAATTGTGTGACATCC 57.384 36.000 0.00 0.00 0.00 3.51
1642 1724 8.886719 TCATCTATGAAAGAATTGTGTGACATC 58.113 33.333 0.00 0.00 37.89 3.06
1758 1853 8.064814 GCAAAATGTTTTTAGCCGAAATTTACA 58.935 29.630 0.00 0.00 0.00 2.41
1775 1870 4.099881 ACAACCAGATCACTGCAAAATGTT 59.900 37.500 0.00 0.00 42.25 2.71
1814 1909 6.698766 GCAGAATAATAAAACCATGAAGCTGG 59.301 38.462 0.00 0.00 42.35 4.85
1884 1980 0.530870 GGTGCCTTAGGAAGCTAGCG 60.531 60.000 9.55 0.00 0.00 4.26
1903 1999 4.970662 AATGTCATTCCCATTCGTTCAG 57.029 40.909 0.00 0.00 0.00 3.02
1907 2003 4.156556 CACTGAAATGTCATTCCCATTCGT 59.843 41.667 0.00 0.00 31.49 3.85
1915 2011 9.346725 GGAAGTAATTTCACTGAAATGTCATTC 57.653 33.333 16.18 15.76 40.77 2.67
1917 2013 7.174946 ACGGAAGTAATTTCACTGAAATGTCAT 59.825 33.333 16.18 5.05 46.88 3.06
1919 2015 6.899114 ACGGAAGTAATTTCACTGAAATGTC 58.101 36.000 16.18 12.27 46.88 3.06
1920 2016 6.877611 ACGGAAGTAATTTCACTGAAATGT 57.122 33.333 16.18 9.87 46.88 2.71
1932 2028 9.279108 CCATTGCAATGCTAGACGGAAGTAATT 62.279 40.741 30.15 0.00 38.79 1.40
1933 2029 7.897298 CCATTGCAATGCTAGACGGAAGTAAT 61.897 42.308 30.15 0.00 38.79 1.89
1934 2030 6.653228 CCATTGCAATGCTAGACGGAAGTAA 61.653 44.000 30.15 0.00 38.79 2.24
1935 2031 5.215809 CCATTGCAATGCTAGACGGAAGTA 61.216 45.833 30.15 0.00 38.79 2.24
1936 2032 4.485016 CCATTGCAATGCTAGACGGAAGT 61.485 47.826 30.15 0.00 40.46 3.01
1937 2033 2.032550 CCATTGCAATGCTAGACGGAAG 59.967 50.000 30.15 11.45 35.08 3.46
1938 2034 2.016318 CCATTGCAATGCTAGACGGAA 58.984 47.619 30.15 0.00 35.08 4.30
1939 2035 1.209261 TCCATTGCAATGCTAGACGGA 59.791 47.619 30.15 18.84 35.08 4.69
1940 2036 1.600957 CTCCATTGCAATGCTAGACGG 59.399 52.381 30.15 16.94 35.08 4.79
1941 2037 1.003116 GCTCCATTGCAATGCTAGACG 60.003 52.381 30.15 17.20 35.08 4.18
1942 2038 1.336125 GGCTCCATTGCAATGCTAGAC 59.664 52.381 30.15 25.95 35.08 2.59
1943 2039 1.064537 TGGCTCCATTGCAATGCTAGA 60.065 47.619 30.15 21.29 35.08 2.43
1944 2040 1.395635 TGGCTCCATTGCAATGCTAG 58.604 50.000 30.15 27.04 35.08 3.42
1945 2041 1.477700 GTTGGCTCCATTGCAATGCTA 59.522 47.619 30.15 19.86 35.08 3.49
1946 2042 0.248289 GTTGGCTCCATTGCAATGCT 59.752 50.000 30.15 0.00 35.08 3.79
1947 2043 0.248289 AGTTGGCTCCATTGCAATGC 59.752 50.000 30.15 20.39 35.08 3.56
1948 2044 2.028839 TCAAGTTGGCTCCATTGCAATG 60.029 45.455 28.91 28.91 36.17 2.82
1949 2045 2.028748 GTCAAGTTGGCTCCATTGCAAT 60.029 45.455 5.99 5.99 34.04 3.56
1950 2046 1.340889 GTCAAGTTGGCTCCATTGCAA 59.659 47.619 0.00 0.00 34.04 4.08
1990 2112 6.746364 GCTGCTCTTCTATTTTGAGTTTCATG 59.254 38.462 0.00 0.00 0.00 3.07
1997 2119 8.885494 AGTTATAGCTGCTCTTCTATTTTGAG 57.115 34.615 4.91 0.00 0.00 3.02
1999 2121 9.102757 TCAAGTTATAGCTGCTCTTCTATTTTG 57.897 33.333 4.91 2.91 0.00 2.44
2038 2161 4.185394 TCCATTATTATGCGTGAACGTGT 58.815 39.130 4.59 0.00 42.22 4.49
2039 2162 4.787381 TCCATTATTATGCGTGAACGTG 57.213 40.909 4.59 0.00 42.22 4.49
2040 2163 4.814234 ACATCCATTATTATGCGTGAACGT 59.186 37.500 4.59 0.00 42.22 3.99
2042 2165 8.503196 TGATTACATCCATTATTATGCGTGAAC 58.497 33.333 0.00 0.00 0.00 3.18
2044 2167 8.093927 TCTGATTACATCCATTATTATGCGTGA 58.906 33.333 0.00 0.00 0.00 4.35
2045 2168 8.255394 TCTGATTACATCCATTATTATGCGTG 57.745 34.615 0.00 0.00 0.00 5.34
2046 2169 7.550551 CCTCTGATTACATCCATTATTATGCGT 59.449 37.037 0.00 0.00 0.00 5.24
2047 2170 7.550551 ACCTCTGATTACATCCATTATTATGCG 59.449 37.037 0.00 0.00 0.00 4.73
2048 2171 8.798859 ACCTCTGATTACATCCATTATTATGC 57.201 34.615 0.00 0.00 0.00 3.14
2051 2174 9.559732 CACAACCTCTGATTACATCCATTATTA 57.440 33.333 0.00 0.00 0.00 0.98
2052 2175 8.274322 TCACAACCTCTGATTACATCCATTATT 58.726 33.333 0.00 0.00 0.00 1.40
2159 2292 5.417580 TCAAGTACATAAAATGGGAAGGCAC 59.582 40.000 0.00 0.00 33.60 5.01
2219 2352 4.335315 AGTTCATGTATGCAAATACCCACG 59.665 41.667 0.00 0.00 0.00 4.94
2257 2390 3.387374 CCTCTAGGATGCACTGACATTCT 59.613 47.826 0.00 0.00 39.33 2.40
2289 2423 2.834638 AATCCCAGCATACCAGCTTT 57.165 45.000 0.00 0.00 43.70 3.51
2290 2424 3.557898 CGATAATCCCAGCATACCAGCTT 60.558 47.826 0.00 0.00 43.70 3.74
2309 2443 2.665649 TCAACGTATGAGCCAACGAT 57.334 45.000 1.45 0.00 41.55 3.73
2312 2446 2.009774 AGCATCAACGTATGAGCCAAC 58.990 47.619 2.44 0.00 42.53 3.77
2316 2450 2.286294 CCAGAAGCATCAACGTATGAGC 59.714 50.000 2.44 7.82 42.53 4.26
2344 2478 0.521291 GCTATTTGCTGCACCGTTCA 59.479 50.000 0.00 0.00 38.95 3.18
2364 2498 3.054875 AGCTGTCCTTCATAATGTGCAGA 60.055 43.478 0.00 0.00 0.00 4.26
2371 2505 4.346418 CAGGAGGTAGCTGTCCTTCATAAT 59.654 45.833 16.91 0.00 41.57 1.28
2434 2568 6.702282 GGAATAGTGCTCACCAGACTAAATAC 59.298 42.308 0.00 0.00 0.00 1.89
2585 2722 8.469200 TGCTATGTTTGCTCTTTGCTATATTTT 58.531 29.630 0.00 0.00 43.37 1.82
2589 2829 7.173218 GGTATGCTATGTTTGCTCTTTGCTATA 59.827 37.037 0.00 0.00 43.37 1.31
2642 2882 9.614792 AGCAAGAACCGAAATATAAACTATCTT 57.385 29.630 0.00 0.00 0.00 2.40
2647 2887 8.021396 GTGAAAGCAAGAACCGAAATATAAACT 58.979 33.333 0.00 0.00 0.00 2.66
2738 2978 3.005050 CAGCAACTCCAATGTCAACACAT 59.995 43.478 0.00 0.00 45.89 3.21
2754 2994 9.124807 GGTAAAATTTATGTAGTGAACAGCAAC 57.875 33.333 0.00 0.00 42.70 4.17
2763 3003 8.739972 AGCCTTTCAGGTAAAATTTATGTAGTG 58.260 33.333 0.00 0.00 37.80 2.74


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

AutoCloner maintained by Alex Coulton.