Multiple sequence alignment - TraesCS4A01G093500

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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 TraesCS4A01G093500 chr4A 100.000 5881 0 0 1 5881 100969587 100963707 0.000000e+00 10861.0
1 TraesCS4A01G093500 chr4D 93.781 4711 192 44 1207 5875 364028530 364033181 0.000000e+00 6983.0
2 TraesCS4A01G093500 chr4D 88.486 1103 36 28 93 1162 364027486 364028530 0.000000e+00 1249.0
3 TraesCS4A01G093500 chr4D 94.872 78 4 0 1 78 481055512 481055589 8.000000e-24 122.0
4 TraesCS4A01G093500 chr4B 94.206 4246 172 34 85 4297 449502074 449506278 0.000000e+00 6410.0
5 TraesCS4A01G093500 chr4B 95.874 1115 21 5 4295 5398 449506307 449507407 0.000000e+00 1781.0
6 TraesCS4A01G093500 chr4B 95.335 493 15 2 5394 5881 449509609 449510098 0.000000e+00 776.0
7 TraesCS4A01G093500 chr5D 90.588 85 8 0 1 85 495380113 495380029 4.820000e-21 113.0
8 TraesCS4A01G093500 chr5A 90.000 70 7 0 3 72 616750680 616750749 2.260000e-14 91.6


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 TraesCS4A01G093500 chr4A 100963707 100969587 5880 True 10861 10861 100.000000 1 5881 1 chr4A.!!$R1 5880
1 TraesCS4A01G093500 chr4D 364027486 364033181 5695 False 4116 6983 91.133500 93 5875 2 chr4D.!!$F2 5782
2 TraesCS4A01G093500 chr4B 449502074 449510098 8024 False 2989 6410 95.138333 85 5881 3 chr4B.!!$F1 5796

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
208 213 0.035739 TACCACCAAAGCTCGAACCC 59.964 55.0 0.00 0.0 0.00 4.11 F
1811 1855 0.179121 TAGTGGCGACCATGTTAGCG 60.179 55.0 0.00 0.0 35.28 4.26 F
2233 2284 1.024271 TCGCTTGGCCTATTTGATGC 58.976 50.0 3.32 0.0 0.00 3.91 F
2925 2981 0.039618 TTCCTCCAATGCCCCTGAAC 59.960 55.0 0.00 0.0 0.00 3.18 F
3721 3790 0.106769 TTCTGCAGCCAAGGAACACA 60.107 50.0 9.47 0.0 0.00 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2058 2106 0.247736 ACCTTCATGAGCCGACACTC 59.752 55.0 0.00 0.00 37.19 3.51 R
2634 2689 0.669318 TACGTTTGGCTTCCTCTGCG 60.669 55.0 0.00 0.00 0.00 5.18 R
3995 4064 0.393537 GGTGAGGACCCTGCAGAATG 60.394 60.0 17.39 5.77 36.03 2.67 R
4007 4078 0.770499 TTTCAGGCATGTGGTGAGGA 59.230 50.0 0.00 0.00 0.00 3.71 R
5715 8045 0.110486 TGTTCAACTTCCTCCTGCCC 59.890 55.0 0.00 0.00 0.00 5.36 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
20 21 3.788333 CGCATCTGTGGGAAATTCATT 57.212 42.857 0.00 0.00 40.48 2.57
21 22 3.441163 CGCATCTGTGGGAAATTCATTG 58.559 45.455 0.00 0.00 40.48 2.82
22 23 3.192466 GCATCTGTGGGAAATTCATTGC 58.808 45.455 0.00 0.00 0.00 3.56
23 24 3.368635 GCATCTGTGGGAAATTCATTGCA 60.369 43.478 0.00 0.00 0.00 4.08
24 25 4.823157 CATCTGTGGGAAATTCATTGCAA 58.177 39.130 0.00 0.00 0.00 4.08
25 26 4.524316 TCTGTGGGAAATTCATTGCAAG 57.476 40.909 4.94 0.00 0.00 4.01
26 27 2.997986 CTGTGGGAAATTCATTGCAAGC 59.002 45.455 4.94 0.00 0.00 4.01
27 28 2.367894 TGTGGGAAATTCATTGCAAGCA 59.632 40.909 4.94 0.00 0.00 3.91
28 29 2.738314 GTGGGAAATTCATTGCAAGCAC 59.262 45.455 4.94 0.00 0.00 4.40
29 30 2.633967 TGGGAAATTCATTGCAAGCACT 59.366 40.909 4.94 0.00 0.00 4.40
30 31 3.256558 GGGAAATTCATTGCAAGCACTC 58.743 45.455 4.94 0.00 0.00 3.51
31 32 2.919229 GGAAATTCATTGCAAGCACTCG 59.081 45.455 4.94 0.00 0.00 4.18
32 33 3.568538 GAAATTCATTGCAAGCACTCGT 58.431 40.909 4.94 0.00 0.00 4.18
33 34 2.907910 ATTCATTGCAAGCACTCGTC 57.092 45.000 4.94 0.00 0.00 4.20
34 35 1.592064 TTCATTGCAAGCACTCGTCA 58.408 45.000 4.94 0.00 0.00 4.35
35 36 1.812235 TCATTGCAAGCACTCGTCAT 58.188 45.000 4.94 0.00 0.00 3.06
36 37 1.733912 TCATTGCAAGCACTCGTCATC 59.266 47.619 4.94 0.00 0.00 2.92
37 38 0.723414 ATTGCAAGCACTCGTCATCG 59.277 50.000 4.94 0.00 38.55 3.84
38 39 0.319469 TTGCAAGCACTCGTCATCGA 60.319 50.000 0.00 0.00 44.12 3.59
46 47 2.491621 TCGTCATCGAGCAGCCTG 59.508 61.111 0.00 0.00 41.35 4.85
47 48 3.260483 CGTCATCGAGCAGCCTGC 61.260 66.667 9.13 9.13 45.46 4.85
48 49 2.894387 GTCATCGAGCAGCCTGCC 60.894 66.667 14.25 4.00 46.52 4.85
49 50 4.519437 TCATCGAGCAGCCTGCCG 62.519 66.667 14.25 16.39 46.52 5.69
70 71 4.150994 GGCGAAAACCCACAGACA 57.849 55.556 0.00 0.00 0.00 3.41
71 72 1.652563 GGCGAAAACCCACAGACAC 59.347 57.895 0.00 0.00 0.00 3.67
72 73 1.652563 GCGAAAACCCACAGACACC 59.347 57.895 0.00 0.00 0.00 4.16
73 74 1.098712 GCGAAAACCCACAGACACCA 61.099 55.000 0.00 0.00 0.00 4.17
74 75 1.384525 CGAAAACCCACAGACACCAA 58.615 50.000 0.00 0.00 0.00 3.67
75 76 1.746220 CGAAAACCCACAGACACCAAA 59.254 47.619 0.00 0.00 0.00 3.28
76 77 2.360801 CGAAAACCCACAGACACCAAAT 59.639 45.455 0.00 0.00 0.00 2.32
77 78 3.566322 CGAAAACCCACAGACACCAAATA 59.434 43.478 0.00 0.00 0.00 1.40
78 79 4.217550 CGAAAACCCACAGACACCAAATAT 59.782 41.667 0.00 0.00 0.00 1.28
79 80 5.619086 CGAAAACCCACAGACACCAAATATC 60.619 44.000 0.00 0.00 0.00 1.63
80 81 4.380843 AACCCACAGACACCAAATATCA 57.619 40.909 0.00 0.00 0.00 2.15
81 82 4.380843 ACCCACAGACACCAAATATCAA 57.619 40.909 0.00 0.00 0.00 2.57
82 83 4.934356 ACCCACAGACACCAAATATCAAT 58.066 39.130 0.00 0.00 0.00 2.57
83 84 6.073447 ACCCACAGACACCAAATATCAATA 57.927 37.500 0.00 0.00 0.00 1.90
84 85 6.672593 ACCCACAGACACCAAATATCAATAT 58.327 36.000 0.00 0.00 0.00 1.28
85 86 7.811282 ACCCACAGACACCAAATATCAATATA 58.189 34.615 0.00 0.00 0.00 0.86
86 87 8.448008 ACCCACAGACACCAAATATCAATATAT 58.552 33.333 0.00 0.00 0.00 0.86
87 88 8.733458 CCCACAGACACCAAATATCAATATATG 58.267 37.037 0.00 0.00 0.00 1.78
88 89 9.288576 CCACAGACACCAAATATCAATATATGT 57.711 33.333 0.00 0.00 0.00 2.29
90 91 9.208022 ACAGACACCAAATATCAATATATGTCG 57.792 33.333 0.00 0.00 0.00 4.35
91 92 9.423061 CAGACACCAAATATCAATATATGTCGA 57.577 33.333 0.00 0.00 0.00 4.20
116 117 2.363788 TTAGTGTTACGCTGGCTCTG 57.636 50.000 8.86 0.00 0.00 3.35
183 188 1.762460 CGTGGATGACCCTAGCCCT 60.762 63.158 0.00 0.00 35.38 5.19
204 209 1.295423 GGCTACCACCAAAGCTCGA 59.705 57.895 0.00 0.00 38.80 4.04
205 210 0.321298 GGCTACCACCAAAGCTCGAA 60.321 55.000 0.00 0.00 38.80 3.71
207 212 1.439679 CTACCACCAAAGCTCGAACC 58.560 55.000 0.00 0.00 0.00 3.62
208 213 0.035739 TACCACCAAAGCTCGAACCC 59.964 55.000 0.00 0.00 0.00 4.11
337 347 2.357154 CGGGGGAGAATTCATTCCAAGT 60.357 50.000 14.00 0.00 37.51 3.16
386 396 2.042435 CCGGCTCCTCCTCCTCTT 60.042 66.667 0.00 0.00 0.00 2.85
420 439 3.545426 CGTTTCTCCTCCACGAAAAACAC 60.545 47.826 0.00 0.00 35.93 3.32
597 616 2.109799 CCAGCCATCGCCGAAGAT 59.890 61.111 0.00 0.00 34.57 2.40
660 693 1.035932 TTTACGCGGAGGAGAGGAGG 61.036 60.000 12.47 0.00 0.00 4.30
755 788 4.680237 CTGTCGCGGCCAACTCCA 62.680 66.667 8.89 0.00 0.00 3.86
756 789 4.980805 TGTCGCGGCCAACTCCAC 62.981 66.667 8.89 0.00 0.00 4.02
761 794 4.263572 CGGCCAACTCCACCACCA 62.264 66.667 2.24 0.00 0.00 4.17
762 795 2.597510 GGCCAACTCCACCACCAC 60.598 66.667 0.00 0.00 0.00 4.16
763 796 2.597510 GCCAACTCCACCACCACC 60.598 66.667 0.00 0.00 0.00 4.61
831 867 1.306141 TCCTCCGTCCATTCCAGCT 60.306 57.895 0.00 0.00 0.00 4.24
853 889 2.031120 CTCTTGCTTCTCGATCCTCCT 58.969 52.381 0.00 0.00 0.00 3.69
854 890 2.028130 TCTTGCTTCTCGATCCTCCTC 58.972 52.381 0.00 0.00 0.00 3.71
855 891 1.068434 CTTGCTTCTCGATCCTCCTCC 59.932 57.143 0.00 0.00 0.00 4.30
856 892 0.757188 TGCTTCTCGATCCTCCTCCC 60.757 60.000 0.00 0.00 0.00 4.30
857 893 0.469144 GCTTCTCGATCCTCCTCCCT 60.469 60.000 0.00 0.00 0.00 4.20
858 894 2.032151 GCTTCTCGATCCTCCTCCCTT 61.032 57.143 0.00 0.00 0.00 3.95
1072 1110 0.817013 CTCTCTGCTCCTCTGTGTCC 59.183 60.000 0.00 0.00 0.00 4.02
1087 1125 4.844085 TCTGTGTCCCCTCTTCTATTTTCA 59.156 41.667 0.00 0.00 0.00 2.69
1088 1126 5.046304 TCTGTGTCCCCTCTTCTATTTTCAG 60.046 44.000 0.00 0.00 0.00 3.02
1162 1200 3.692406 ACCAGCCGTCGTTCTCCC 61.692 66.667 0.00 0.00 0.00 4.30
1165 1203 4.070552 AGCCGTCGTTCTCCCTGC 62.071 66.667 0.00 0.00 0.00 4.85
1167 1205 4.452733 CCGTCGTTCTCCCTGCCC 62.453 72.222 0.00 0.00 0.00 5.36
1172 1210 1.376037 CGTTCTCCCTGCCCTTGTC 60.376 63.158 0.00 0.00 0.00 3.18
1198 1236 5.010314 TGTCTCGCTAGAGGTTAACTTTTGA 59.990 40.000 5.42 0.00 44.47 2.69
1203 1241 5.122396 CGCTAGAGGTTAACTTTTGATTGCT 59.878 40.000 5.42 0.00 0.00 3.91
1205 1243 6.149474 GCTAGAGGTTAACTTTTGATTGCTGA 59.851 38.462 5.42 0.00 0.00 4.26
1214 1252 5.693814 ACTTTTGATTGCTGACTTTCGATC 58.306 37.500 0.00 0.00 0.00 3.69
1260 1298 6.809196 ACTTTTAGATTAGAGAACGCAGAGTG 59.191 38.462 0.00 0.00 0.00 3.51
1477 1515 5.337578 AACCACTTTGTTTATGCACTTGT 57.662 34.783 0.00 0.00 0.00 3.16
1504 1542 8.659527 TGTATTTTGAGGCTGATATCCATTAGA 58.340 33.333 0.00 0.00 0.00 2.10
1516 1554 1.407618 TCCATTAGACCGGTCACATCG 59.592 52.381 35.00 18.74 0.00 3.84
1532 1570 4.312231 CGTGTGCAGTGCAACCCG 62.312 66.667 21.67 17.66 41.47 5.28
1581 1619 6.867816 TGTTGCAATCAATCAATGTAGGAAAC 59.132 34.615 0.59 0.00 34.29 2.78
1610 1648 9.515020 TTTCAATCAACATTTTCTAACAGTCAC 57.485 29.630 0.00 0.00 0.00 3.67
1682 1720 3.736094 TCCAGGATAAAGTGAGGTCCAT 58.264 45.455 0.00 0.00 33.12 3.41
1687 1725 4.540099 AGGATAAAGTGAGGTCCATCCAAA 59.460 41.667 5.25 0.00 39.02 3.28
1746 1790 1.525077 TTGGTGACTGAACCGGTGC 60.525 57.895 8.52 6.80 43.73 5.01
1754 1798 1.272769 ACTGAACCGGTGCTAGAACTC 59.727 52.381 15.35 2.57 0.00 3.01
1795 1839 3.340727 GTGATTAGCACGGCGTAGT 57.659 52.632 14.22 5.22 37.83 2.73
1811 1855 0.179121 TAGTGGCGACCATGTTAGCG 60.179 55.000 0.00 0.00 35.28 4.26
1878 1922 4.012374 CCTGTTCAATGCAGGTATTCTGT 58.988 43.478 3.37 0.00 46.22 3.41
1891 1935 5.923114 CAGGTATTCTGTATTCGTCATCTGG 59.077 44.000 0.00 0.00 38.64 3.86
1898 1942 3.689161 TGTATTCGTCATCTGGCCTTTTG 59.311 43.478 3.32 0.00 0.00 2.44
1903 1949 2.613691 GTCATCTGGCCTTTTGCAATG 58.386 47.619 3.32 0.00 43.89 2.82
1906 1952 4.098349 GTCATCTGGCCTTTTGCAATGATA 59.902 41.667 3.32 0.00 43.89 2.15
1911 1957 3.773667 TGGCCTTTTGCAATGATATTCCA 59.226 39.130 3.32 0.00 43.89 3.53
1919 1965 9.321562 CTTTTGCAATGATATTCCAATTAAGCT 57.678 29.630 0.00 0.00 0.00 3.74
1923 1969 7.288389 TGCAATGATATTCCAATTAAGCTCCTT 59.712 33.333 0.00 0.00 0.00 3.36
2006 2054 1.268539 GGTGCCGAACAAGAACAGTTG 60.269 52.381 0.00 0.00 0.00 3.16
2041 2089 8.093927 TGTACATCACATAGTGACTGAAATTCA 58.906 33.333 1.43 0.00 45.65 2.57
2079 2129 1.079503 GTGTCGGCTCATGAAGGTTC 58.920 55.000 0.00 0.00 0.00 3.62
2109 2159 6.000219 TGCTCATGAAAGTTCTAAAGCTTCT 59.000 36.000 0.00 0.00 0.00 2.85
2110 2160 6.072838 TGCTCATGAAAGTTCTAAAGCTTCTG 60.073 38.462 0.00 0.00 0.00 3.02
2111 2161 6.072783 GCTCATGAAAGTTCTAAAGCTTCTGT 60.073 38.462 0.00 0.00 0.00 3.41
2112 2162 7.194607 TCATGAAAGTTCTAAAGCTTCTGTG 57.805 36.000 0.00 0.00 0.00 3.66
2120 2170 4.973168 TCTAAAGCTTCTGTGTGACCATT 58.027 39.130 0.00 0.00 0.00 3.16
2233 2284 1.024271 TCGCTTGGCCTATTTGATGC 58.976 50.000 3.32 0.00 0.00 3.91
2235 2286 1.268896 CGCTTGGCCTATTTGATGCTG 60.269 52.381 3.32 0.00 0.00 4.41
2243 2294 3.621268 GCCTATTTGATGCTGACGTAACA 59.379 43.478 0.00 0.00 0.00 2.41
2445 2496 5.067805 AGTCCGCCATTTTTCTTTCATATCC 59.932 40.000 0.00 0.00 0.00 2.59
2493 2544 4.806964 GCATTCAATTCACCCCCACATTTT 60.807 41.667 0.00 0.00 0.00 1.82
2511 2565 7.144661 CACATTTTTAGCACTTCATGTTACCA 58.855 34.615 0.00 0.00 0.00 3.25
2522 2576 7.089538 CACTTCATGTTACCATATTTTGTGCA 58.910 34.615 0.00 0.00 0.00 4.57
2634 2689 2.479389 CCGTCAGATTGCACTCTCTCTC 60.479 54.545 3.15 0.00 0.00 3.20
2653 2708 0.669318 CGCAGAGGAAGCCAAACGTA 60.669 55.000 0.00 0.00 0.00 3.57
2720 2776 6.801862 CCTTTCTGGTTAAAAATCTGTTAGCG 59.198 38.462 0.00 0.00 0.00 4.26
2788 2844 2.159170 GGGAGAGAACGATGAAGACCTG 60.159 54.545 0.00 0.00 0.00 4.00
2925 2981 0.039618 TTCCTCCAATGCCCCTGAAC 59.960 55.000 0.00 0.00 0.00 3.18
3061 3117 0.179059 TCCGTTGCTCTTCTTGCACA 60.179 50.000 0.00 0.00 40.40 4.57
3220 3281 9.856162 AAAATAGAAAGTAACTGTCACCCTTTA 57.144 29.630 0.00 0.00 0.00 1.85
3565 3634 5.104569 ACAAATTTTCCCTTCTGCTTTTCCA 60.105 36.000 0.00 0.00 0.00 3.53
3634 3703 1.337110 GCAAAACATCCGCAGCGTTC 61.337 55.000 15.05 0.00 0.00 3.95
3636 3705 0.881118 AAAACATCCGCAGCGTTCAT 59.119 45.000 15.05 0.00 0.00 2.57
3638 3707 2.023741 CATCCGCAGCGTTCATGC 59.976 61.111 15.05 0.00 40.35 4.06
3721 3790 0.106769 TTCTGCAGCCAAGGAACACA 60.107 50.000 9.47 0.00 0.00 3.72
3724 3793 1.136695 CTGCAGCCAAGGAACACAAAA 59.863 47.619 0.00 0.00 0.00 2.44
3913 3982 1.470098 CTCAACGAAGCAATGGAAGGG 59.530 52.381 0.00 0.00 0.00 3.95
3943 4012 7.497579 TGCAAAGTGAGTTCTTATGTTCAGTTA 59.502 33.333 0.00 0.00 33.37 2.24
3961 4030 5.471797 TCAGTTAATTGGTCGAAGCAAATCA 59.528 36.000 0.00 0.00 39.20 2.57
3962 4031 6.016693 TCAGTTAATTGGTCGAAGCAAATCAA 60.017 34.615 0.00 0.00 39.20 2.57
3963 4032 6.640499 CAGTTAATTGGTCGAAGCAAATCAAA 59.360 34.615 0.00 0.00 39.20 2.69
3974 4043 5.225949 CGAAGCAAATCAAAGCGTAATCTTC 59.774 40.000 0.00 0.00 35.48 2.87
3975 4044 5.627499 AGCAAATCAAAGCGTAATCTTCA 57.373 34.783 0.00 0.00 35.48 3.02
3986 4055 9.128107 CAAAGCGTAATCTTCACAAATGTTAAT 57.872 29.630 0.00 0.00 0.00 1.40
3996 4065 9.452287 TCTTCACAAATGTTAATGATCATCTCA 57.548 29.630 9.06 8.99 38.53 3.27
4007 4078 2.775960 TGATCATCTCATTCTGCAGGGT 59.224 45.455 15.13 0.00 0.00 4.34
4049 4120 1.112113 GAGGCCTATGTCTGTCGGAA 58.888 55.000 4.42 0.00 0.00 4.30
4105 4176 3.445096 CAGCCTAAATTGACTTTCAGGGG 59.555 47.826 0.00 0.00 0.00 4.79
4140 4212 6.317391 CCAGTAGATGATTCTTTTTGACCCTC 59.683 42.308 0.00 0.00 33.17 4.30
4231 4303 1.785041 GCCACAAAAGCTGACTCGCA 61.785 55.000 0.00 0.00 0.00 5.10
4310 4413 4.582869 TCACTGAGATCAGAACCAAATGG 58.417 43.478 16.52 0.00 46.59 3.16
4655 4761 0.600255 ACGCTCAACCTTCAACCTCG 60.600 55.000 0.00 0.00 0.00 4.63
4682 4788 1.095600 CATCCTCGTCGTCTTCCTCA 58.904 55.000 0.00 0.00 0.00 3.86
4938 5044 6.707599 CAGAGATCATGTGCACATACATAG 57.292 41.667 30.92 18.53 39.17 2.23
5069 5175 6.000219 CAGGATGGAAGGTGTAATAAGATGG 59.000 44.000 0.00 0.00 0.00 3.51
5166 5274 9.278978 TGTAAAGTCAAGTTGTCTATTATTGCA 57.721 29.630 2.98 1.93 0.00 4.08
5348 5464 7.954666 ATTTAGCCAGTTCTTAATTTAGCCA 57.045 32.000 0.00 0.00 0.00 4.75
5349 5465 7.391148 TTTAGCCAGTTCTTAATTTAGCCAG 57.609 36.000 0.00 0.00 0.00 4.85
5350 5466 4.923415 AGCCAGTTCTTAATTTAGCCAGT 58.077 39.130 0.00 0.00 0.00 4.00
5351 5467 5.325239 AGCCAGTTCTTAATTTAGCCAGTT 58.675 37.500 0.00 0.00 0.00 3.16
5352 5468 5.416013 AGCCAGTTCTTAATTTAGCCAGTTC 59.584 40.000 0.00 0.00 0.00 3.01
5353 5469 5.416013 GCCAGTTCTTAATTTAGCCAGTTCT 59.584 40.000 0.00 0.00 0.00 3.01
5465 7790 0.249489 AGTTGACGTCTGCTGTGGAC 60.249 55.000 17.92 3.02 0.00 4.02
5643 7968 7.846644 AAGAAACAAAAATGCAGTCAATCAA 57.153 28.000 0.00 0.00 0.00 2.57
5715 8045 0.104120 TAATCACCATGCGAGGACGG 59.896 55.000 0.69 0.00 40.15 4.79
5746 8076 6.273071 AGGAAGTTGAACACTTTTACAATGC 58.727 36.000 0.00 0.00 46.53 3.56
5753 8083 2.552315 ACACTTTTACAATGCCAGACCG 59.448 45.455 0.00 0.00 0.00 4.79
5842 8172 9.303116 AGTTTATCACTAGAGGATCGATACATT 57.697 33.333 10.99 0.00 42.67 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.441163 CAATGAATTTCCCACAGATGCG 58.559 45.455 0.00 0.00 0.00 4.73
1 2 3.192466 GCAATGAATTTCCCACAGATGC 58.808 45.455 0.00 0.00 0.00 3.91
2 3 4.459390 TGCAATGAATTTCCCACAGATG 57.541 40.909 0.00 0.00 0.00 2.90
3 4 4.622220 GCTTGCAATGAATTTCCCACAGAT 60.622 41.667 0.00 0.00 0.00 2.90
6 7 2.367894 TGCTTGCAATGAATTTCCCACA 59.632 40.909 0.00 0.00 0.00 4.17
7 8 2.738314 GTGCTTGCAATGAATTTCCCAC 59.262 45.455 0.00 0.00 0.00 4.61
9 10 3.256558 GAGTGCTTGCAATGAATTTCCC 58.743 45.455 0.00 0.00 0.00 3.97
10 11 2.919229 CGAGTGCTTGCAATGAATTTCC 59.081 45.455 0.00 0.00 0.00 3.13
11 12 3.568538 ACGAGTGCTTGCAATGAATTTC 58.431 40.909 0.00 0.00 0.00 2.17
12 13 3.004629 TGACGAGTGCTTGCAATGAATTT 59.995 39.130 0.00 0.00 0.00 1.82
13 14 2.553602 TGACGAGTGCTTGCAATGAATT 59.446 40.909 0.00 0.00 0.00 2.17
14 15 2.153645 TGACGAGTGCTTGCAATGAAT 58.846 42.857 0.00 0.00 0.00 2.57
15 16 1.592064 TGACGAGTGCTTGCAATGAA 58.408 45.000 0.00 0.00 0.00 2.57
16 17 1.733912 GATGACGAGTGCTTGCAATGA 59.266 47.619 0.00 0.00 0.00 2.57
17 18 1.528400 CGATGACGAGTGCTTGCAATG 60.528 52.381 0.00 0.00 42.66 2.82
18 19 0.723414 CGATGACGAGTGCTTGCAAT 59.277 50.000 0.00 0.00 42.66 3.56
19 20 0.319469 TCGATGACGAGTGCTTGCAA 60.319 50.000 0.00 0.00 43.81 4.08
20 21 1.288752 TCGATGACGAGTGCTTGCA 59.711 52.632 0.00 0.00 43.81 4.08
21 22 4.169102 TCGATGACGAGTGCTTGC 57.831 55.556 0.00 0.00 43.81 4.01
29 30 2.491621 CAGGCTGCTCGATGACGA 59.508 61.111 0.00 0.00 46.56 4.20
30 31 3.260483 GCAGGCTGCTCGATGACG 61.260 66.667 31.37 0.00 40.96 4.35
31 32 2.894387 GGCAGGCTGCTCGATGAC 60.894 66.667 35.73 16.00 44.28 3.06
32 33 4.519437 CGGCAGGCTGCTCGATGA 62.519 66.667 35.73 0.00 44.28 2.92
53 54 1.652563 GTGTCTGTGGGTTTTCGCC 59.347 57.895 0.00 0.00 0.00 5.54
54 55 1.098712 TGGTGTCTGTGGGTTTTCGC 61.099 55.000 0.00 0.00 0.00 4.70
55 56 1.384525 TTGGTGTCTGTGGGTTTTCG 58.615 50.000 0.00 0.00 0.00 3.46
56 57 5.242838 TGATATTTGGTGTCTGTGGGTTTTC 59.757 40.000 0.00 0.00 0.00 2.29
57 58 5.144100 TGATATTTGGTGTCTGTGGGTTTT 58.856 37.500 0.00 0.00 0.00 2.43
58 59 4.735369 TGATATTTGGTGTCTGTGGGTTT 58.265 39.130 0.00 0.00 0.00 3.27
59 60 4.380843 TGATATTTGGTGTCTGTGGGTT 57.619 40.909 0.00 0.00 0.00 4.11
60 61 4.380843 TTGATATTTGGTGTCTGTGGGT 57.619 40.909 0.00 0.00 0.00 4.51
61 62 8.733458 CATATATTGATATTTGGTGTCTGTGGG 58.267 37.037 0.00 0.00 0.00 4.61
62 63 9.288576 ACATATATTGATATTTGGTGTCTGTGG 57.711 33.333 6.45 0.00 0.00 4.17
64 65 9.208022 CGACATATATTGATATTTGGTGTCTGT 57.792 33.333 0.00 0.00 0.00 3.41
65 66 9.423061 TCGACATATATTGATATTTGGTGTCTG 57.577 33.333 0.00 0.00 0.00 3.51
68 69 9.725019 ACATCGACATATATTGATATTTGGTGT 57.275 29.630 0.00 0.00 0.00 4.16
82 83 9.333497 GCGTAACACTAATAACATCGACATATA 57.667 33.333 0.00 0.00 0.00 0.86
83 84 8.080417 AGCGTAACACTAATAACATCGACATAT 58.920 33.333 0.00 0.00 0.00 1.78
84 85 7.377662 CAGCGTAACACTAATAACATCGACATA 59.622 37.037 0.00 0.00 0.00 2.29
85 86 6.198403 CAGCGTAACACTAATAACATCGACAT 59.802 38.462 0.00 0.00 0.00 3.06
86 87 5.513849 CAGCGTAACACTAATAACATCGACA 59.486 40.000 0.00 0.00 0.00 4.35
87 88 5.051907 CCAGCGTAACACTAATAACATCGAC 60.052 44.000 0.00 0.00 0.00 4.20
88 89 5.038683 CCAGCGTAACACTAATAACATCGA 58.961 41.667 0.00 0.00 0.00 3.59
89 90 4.317839 GCCAGCGTAACACTAATAACATCG 60.318 45.833 0.00 0.00 0.00 3.84
90 91 4.809426 AGCCAGCGTAACACTAATAACATC 59.191 41.667 0.00 0.00 0.00 3.06
91 92 4.766375 AGCCAGCGTAACACTAATAACAT 58.234 39.130 0.00 0.00 0.00 2.71
97 98 1.616865 ACAGAGCCAGCGTAACACTAA 59.383 47.619 0.00 0.00 0.00 2.24
116 117 6.417635 CACCATTGATCACACAGTTAAACAAC 59.582 38.462 0.00 0.00 0.00 3.32
420 439 5.502220 CGTTGGCTTTTCCATTTCTTTGTTG 60.502 40.000 0.00 0.00 46.04 3.33
582 601 2.550830 AATTATCTTCGGCGATGGCT 57.449 45.000 20.67 12.03 39.81 4.75
583 602 2.095718 GGAAATTATCTTCGGCGATGGC 60.096 50.000 20.67 0.00 38.90 4.40
584 603 3.403038 AGGAAATTATCTTCGGCGATGG 58.597 45.455 20.67 12.57 0.00 3.51
590 609 5.050295 GTCGGCTTTAGGAAATTATCTTCGG 60.050 44.000 0.00 0.00 0.00 4.30
597 616 2.282407 GCCGTCGGCTTTAGGAAATTA 58.718 47.619 28.98 0.00 46.69 1.40
755 788 1.133809 AGCTATGTGGTGGTGGTGGT 61.134 55.000 0.00 0.00 0.00 4.16
756 789 0.038166 AAGCTATGTGGTGGTGGTGG 59.962 55.000 0.00 0.00 0.00 4.61
757 790 1.909700 AAAGCTATGTGGTGGTGGTG 58.090 50.000 0.00 0.00 0.00 4.17
758 791 4.018415 AGAATAAAGCTATGTGGTGGTGGT 60.018 41.667 0.00 0.00 0.00 4.16
759 792 4.526970 AGAATAAAGCTATGTGGTGGTGG 58.473 43.478 0.00 0.00 0.00 4.61
760 793 4.576463 GGAGAATAAAGCTATGTGGTGGTG 59.424 45.833 0.00 0.00 0.00 4.17
761 794 4.227300 TGGAGAATAAAGCTATGTGGTGGT 59.773 41.667 0.00 0.00 0.00 4.16
762 795 4.780815 TGGAGAATAAAGCTATGTGGTGG 58.219 43.478 0.00 0.00 0.00 4.61
763 796 6.115446 TCTTGGAGAATAAAGCTATGTGGTG 58.885 40.000 0.00 0.00 0.00 4.17
831 867 2.028130 GAGGATCGAGAAGCAAGAGGA 58.972 52.381 0.00 0.00 0.00 3.71
853 889 2.614013 GGGAGCAGGGGAAAGGGA 60.614 66.667 0.00 0.00 0.00 4.20
854 890 3.744155 GGGGAGCAGGGGAAAGGG 61.744 72.222 0.00 0.00 0.00 3.95
855 891 4.115199 CGGGGAGCAGGGGAAAGG 62.115 72.222 0.00 0.00 0.00 3.11
961 997 1.804151 CGTTCCAACCCGGCATATATG 59.196 52.381 8.45 8.45 33.14 1.78
1072 1110 7.985752 ACGGTAATTACTGAAAATAGAAGAGGG 59.014 37.037 27.43 0.00 36.44 4.30
1162 1200 1.294659 GCGAGACAAGACAAGGGCAG 61.295 60.000 0.00 0.00 0.00 4.85
1165 1203 1.819288 TCTAGCGAGACAAGACAAGGG 59.181 52.381 0.00 0.00 0.00 3.95
1167 1205 2.490115 ACCTCTAGCGAGACAAGACAAG 59.510 50.000 0.00 0.00 39.74 3.16
1172 1210 4.705337 AGTTAACCTCTAGCGAGACAAG 57.295 45.455 0.88 0.00 39.74 3.16
1198 1236 3.686726 GGTTCAGATCGAAAGTCAGCAAT 59.313 43.478 0.00 0.00 34.69 3.56
1203 1241 2.609491 CCACGGTTCAGATCGAAAGTCA 60.609 50.000 0.00 0.00 34.69 3.41
1205 1243 1.337823 CCCACGGTTCAGATCGAAAGT 60.338 52.381 0.00 3.79 34.69 2.66
1260 1298 1.369625 AAATGGATCGCCGACAGTTC 58.630 50.000 0.00 0.00 36.79 3.01
1460 1498 9.635632 CAAAATACAACAAGTGCATAAACAAAG 57.364 29.630 0.00 0.00 0.00 2.77
1477 1515 9.288576 CTAATGGATATCAGCCTCAAAATACAA 57.711 33.333 4.83 0.00 0.00 2.41
1516 1554 3.209097 ACGGGTTGCACTGCACAC 61.209 61.111 2.26 5.60 38.71 3.82
1581 1619 8.143835 ACTGTTAGAAAATGTTGATTGAAAGGG 58.856 33.333 0.00 0.00 0.00 3.95
1610 1648 3.434641 CCCTCTTGTGAATATAGCATGCG 59.565 47.826 13.01 0.00 0.00 4.73
1662 1700 3.181450 GGATGGACCTCACTTTATCCTGG 60.181 52.174 0.00 0.00 33.12 4.45
1672 1710 4.636206 GTCACTATTTTGGATGGACCTCAC 59.364 45.833 0.00 0.00 39.86 3.51
1682 1720 5.305585 GTCAGGTTCAGTCACTATTTTGGA 58.694 41.667 0.00 0.00 0.00 3.53
1687 1725 3.261897 CAGGGTCAGGTTCAGTCACTATT 59.738 47.826 0.00 0.00 0.00 1.73
1729 1773 1.116536 TAGCACCGGTTCAGTCACCA 61.117 55.000 2.97 0.00 36.49 4.17
1762 1806 9.077674 CGTGCTAATCACAGTTATATATCTTCC 57.922 37.037 0.00 0.00 45.92 3.46
1795 1839 1.447140 GTCGCTAACATGGTCGCCA 60.447 57.895 1.07 1.01 38.19 5.69
1800 1844 0.676782 GCTTGGGTCGCTAACATGGT 60.677 55.000 0.00 0.00 0.00 3.55
1811 1855 1.273327 CCACAGGAAATTGCTTGGGTC 59.727 52.381 0.00 0.00 0.00 4.46
1876 1920 3.627395 AAAGGCCAGATGACGAATACA 57.373 42.857 5.01 0.00 0.00 2.29
1878 1922 2.682856 GCAAAAGGCCAGATGACGAATA 59.317 45.455 5.01 0.00 36.11 1.75
1891 1935 6.930667 AATTGGAATATCATTGCAAAAGGC 57.069 33.333 1.71 0.00 45.13 4.35
1898 1942 7.224522 AGGAGCTTAATTGGAATATCATTGC 57.775 36.000 0.00 0.00 0.00 3.56
1947 1993 9.598517 TCAAATCAAATCTTAACTGCAGTTTTT 57.401 25.926 35.20 25.22 39.31 1.94
1948 1994 9.252962 CTCAAATCAAATCTTAACTGCAGTTTT 57.747 29.630 35.20 21.15 39.31 2.43
1950 1996 7.864379 CACTCAAATCAAATCTTAACTGCAGTT 59.136 33.333 32.97 32.97 41.73 3.16
1951 1997 7.365741 CACTCAAATCAAATCTTAACTGCAGT 58.634 34.615 15.25 15.25 0.00 4.40
1952 1998 6.805271 CCACTCAAATCAAATCTTAACTGCAG 59.195 38.462 13.48 13.48 0.00 4.41
1953 1999 6.489700 TCCACTCAAATCAAATCTTAACTGCA 59.510 34.615 0.00 0.00 0.00 4.41
1955 2001 9.918630 AAATCCACTCAAATCAAATCTTAACTG 57.081 29.630 0.00 0.00 0.00 3.16
1957 2003 9.358872 GGAAATCCACTCAAATCAAATCTTAAC 57.641 33.333 0.00 0.00 35.64 2.01
1958 2004 9.087871 TGGAAATCCACTCAAATCAAATCTTAA 57.912 29.630 0.00 0.00 42.01 1.85
1959 2005 8.648698 TGGAAATCCACTCAAATCAAATCTTA 57.351 30.769 0.00 0.00 42.01 2.10
1960 2006 7.543359 TGGAAATCCACTCAAATCAAATCTT 57.457 32.000 0.00 0.00 42.01 2.40
2006 2054 5.974158 CACTATGTGATGTACAGACTACAGC 59.026 44.000 0.33 0.00 43.80 4.40
2041 2089 7.813148 GCCGACACTCACAGTTATATGTATATT 59.187 37.037 0.00 0.00 0.00 1.28
2058 2106 0.247736 ACCTTCATGAGCCGACACTC 59.752 55.000 0.00 0.00 37.19 3.51
2079 2129 3.336468 AGAACTTTCATGAGCAGCTCTG 58.664 45.455 23.15 17.39 0.00 3.35
2120 2170 3.054728 TCAGGTGAAAGTTTGGAGTGACA 60.055 43.478 0.00 0.00 0.00 3.58
2233 2284 1.530720 TGTGCAGCAATGTTACGTCAG 59.469 47.619 0.00 0.00 0.00 3.51
2235 2286 1.262950 TGTGTGCAGCAATGTTACGTC 59.737 47.619 0.00 0.00 0.00 4.34
2243 2294 3.216800 TCTTCTTTCTGTGTGCAGCAAT 58.783 40.909 0.00 0.00 42.29 3.56
2445 2496 4.994907 TCATGCAATGGAATTTCAGGAG 57.005 40.909 0.00 0.00 46.73 3.69
2511 2565 8.706492 ATTTGTTCGATGATTGCACAAAATAT 57.294 26.923 13.21 0.00 39.94 1.28
2522 2576 5.824904 AAGCAGCTATTTGTTCGATGATT 57.175 34.783 0.00 0.00 0.00 2.57
2634 2689 0.669318 TACGTTTGGCTTCCTCTGCG 60.669 55.000 0.00 0.00 0.00 5.18
2720 2776 3.575965 ATTCAACCGAAATCAAGCACC 57.424 42.857 0.00 0.00 34.01 5.01
2788 2844 2.681064 TCCTGCATTGCCTTGGCC 60.681 61.111 9.35 0.00 0.00 5.36
2797 2853 2.936919 TGTTCAGACTGTCCTGCATT 57.063 45.000 3.76 0.00 34.28 3.56
2925 2981 3.839293 AGCTTCTTTACACACTAGCTCG 58.161 45.455 0.00 0.00 34.04 5.03
3061 3117 2.125961 GGTCTCGCGGATAGGGTGT 61.126 63.158 6.13 0.00 0.00 4.16
3167 3225 9.706691 CTAAGACACCTGAATACAGTTTAAAGA 57.293 33.333 0.00 0.00 42.05 2.52
3206 3267 5.445964 ACACAAAGATAAAGGGTGACAGTT 58.554 37.500 0.00 0.00 33.82 3.16
3209 3270 5.300792 GGAAACACAAAGATAAAGGGTGACA 59.699 40.000 0.00 0.00 33.82 3.58
3220 3281 3.636764 GGTGAACTGGGAAACACAAAGAT 59.363 43.478 0.00 0.00 35.33 2.40
3421 3490 4.351938 CCCGTCCTGTTCGTCGCA 62.352 66.667 0.00 0.00 0.00 5.10
3424 3493 2.027625 CAAGCCCGTCCTGTTCGTC 61.028 63.158 0.00 0.00 0.00 4.20
3565 3634 7.265673 CAAGCATTCATCTCCTGAAAATTGAT 58.734 34.615 0.00 0.00 46.62 2.57
3617 3686 0.881118 ATGAACGCTGCGGATGTTTT 59.119 45.000 26.95 10.09 0.00 2.43
3721 3790 4.307432 CGTCTCCCAGCGACATATATTTT 58.693 43.478 0.00 0.00 0.00 1.82
3724 3793 1.819288 CCGTCTCCCAGCGACATATAT 59.181 52.381 0.00 0.00 0.00 0.86
3892 3961 1.135575 CCTTCCATTGCTTCGTTGAGC 60.136 52.381 2.11 2.11 43.00 4.26
3901 3970 1.000396 GCACTCCCCTTCCATTGCT 60.000 57.895 0.00 0.00 0.00 3.91
3913 3982 4.757149 ACATAAGAACTCACTTTGCACTCC 59.243 41.667 0.00 0.00 0.00 3.85
3943 4012 3.989817 GCTTTGATTTGCTTCGACCAATT 59.010 39.130 0.00 0.00 0.00 2.32
3946 4015 1.069296 CGCTTTGATTTGCTTCGACCA 60.069 47.619 0.00 0.00 0.00 4.02
3961 4030 9.128107 CATTAACATTTGTGAAGATTACGCTTT 57.872 29.630 0.00 0.00 0.00 3.51
3962 4031 8.511321 TCATTAACATTTGTGAAGATTACGCTT 58.489 29.630 0.00 0.00 0.00 4.68
3963 4032 8.039603 TCATTAACATTTGTGAAGATTACGCT 57.960 30.769 0.00 0.00 0.00 5.07
3986 4055 2.775960 ACCCTGCAGAATGAGATGATCA 59.224 45.455 17.39 0.00 43.70 2.92
3995 4064 0.393537 GGTGAGGACCCTGCAGAATG 60.394 60.000 17.39 5.77 36.03 2.67
3996 4065 0.842030 TGGTGAGGACCCTGCAGAAT 60.842 55.000 17.39 1.52 42.34 2.40
4007 4078 0.770499 TTTCAGGCATGTGGTGAGGA 59.230 50.000 0.00 0.00 0.00 3.71
4037 4108 1.550327 TCTGCTCTTCCGACAGACAT 58.450 50.000 0.00 0.00 35.58 3.06
4140 4212 2.359107 TGAGAAGCCAAGCCGCAG 60.359 61.111 0.00 0.00 0.00 5.18
4231 4303 6.545908 CAAGAATTGCAGTGACCTCACATCT 61.546 44.000 8.14 0.00 44.02 2.90
4374 4477 2.025887 AGCCAGTTAGTAGCCTGCAATT 60.026 45.455 0.00 0.00 0.00 2.32
4509 4612 6.636850 GGTGCCATTAATCGAACAATCATAAC 59.363 38.462 0.00 0.00 0.00 1.89
4655 4761 2.033550 AGACGACGAGGATGAAGCATAC 59.966 50.000 0.00 0.00 0.00 2.39
4682 4788 3.903714 TCTTGGATGATGGTGGTCGATAT 59.096 43.478 0.00 0.00 0.00 1.63
4887 4993 4.080582 TCTCCGATATGGACATGGTGTTTT 60.081 41.667 0.00 0.00 43.74 2.43
4938 5044 3.827008 TCTGTAGCACATTCATCTCCC 57.173 47.619 0.00 0.00 0.00 4.30
5069 5175 8.836413 TGCTAGTTACATTGGTATTTCTTATGC 58.164 33.333 0.00 0.00 0.00 3.14
5166 5274 2.305635 TGATCGGTGCCCATGCTTATAT 59.694 45.455 0.00 0.00 38.71 0.86
5167 5275 1.696884 TGATCGGTGCCCATGCTTATA 59.303 47.619 0.00 0.00 38.71 0.98
5341 5457 5.130350 ACTTGCACTTAAGAACTGGCTAAA 58.870 37.500 10.09 0.00 0.00 1.85
5342 5458 4.714632 ACTTGCACTTAAGAACTGGCTAA 58.285 39.130 10.09 2.41 0.00 3.09
5343 5459 4.202315 TGACTTGCACTTAAGAACTGGCTA 60.202 41.667 10.09 1.47 0.00 3.93
5344 5460 3.142174 GACTTGCACTTAAGAACTGGCT 58.858 45.455 10.09 0.00 0.00 4.75
5345 5461 2.878406 TGACTTGCACTTAAGAACTGGC 59.122 45.455 10.09 5.33 0.00 4.85
5346 5462 4.380531 TCTGACTTGCACTTAAGAACTGG 58.619 43.478 10.09 0.00 0.00 4.00
5347 5463 5.991328 TTCTGACTTGCACTTAAGAACTG 57.009 39.130 10.09 0.00 0.00 3.16
5348 5464 6.016777 CCATTTCTGACTTGCACTTAAGAACT 60.017 38.462 10.09 0.00 0.00 3.01
5349 5465 6.017109 TCCATTTCTGACTTGCACTTAAGAAC 60.017 38.462 10.09 0.86 0.00 3.01
5350 5466 6.061441 TCCATTTCTGACTTGCACTTAAGAA 58.939 36.000 10.09 0.00 0.00 2.52
5351 5467 5.620206 TCCATTTCTGACTTGCACTTAAGA 58.380 37.500 10.09 0.00 0.00 2.10
5352 5468 5.947228 TCCATTTCTGACTTGCACTTAAG 57.053 39.130 0.00 0.00 0.00 1.85
5353 5469 5.009610 GGTTCCATTTCTGACTTGCACTTAA 59.990 40.000 0.00 0.00 0.00 1.85
5465 7790 1.369625 GTATGGACCGCAAGAACTGG 58.630 55.000 0.00 0.00 43.02 4.00
5551 7876 5.593909 ACAACTCATGGTGAAGACAAAATGA 59.406 36.000 0.00 0.00 32.74 2.57
5715 8045 0.110486 TGTTCAACTTCCTCCTGCCC 59.890 55.000 0.00 0.00 0.00 5.36
5746 8076 4.188462 TGTTGCAATATTACTCGGTCTGG 58.812 43.478 0.59 0.00 0.00 3.86
5753 8083 6.838198 TGTACCGATGTTGCAATATTACTC 57.162 37.500 10.25 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.