Multiple sequence alignment - TraesCS2B01G527100

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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 TraesCS2B01G527100 chr2B 100.000 2606 0 0 1 2606 721714686 721717291 0.000000e+00 4813.0
1 TraesCS2B01G527100 chr2B 100.000 94 0 0 1 94 685272701 685272608 9.590000e-40 174.0
2 TraesCS2B01G527100 chr2B 95.455 44 0 2 2121 2164 721716726 721716767 4.650000e-08 69.4
3 TraesCS2B01G527100 chr2B 95.455 44 0 2 2041 2082 721716806 721716849 4.650000e-08 69.4
4 TraesCS2B01G527100 chr2D 90.643 2052 87 43 98 2098 594448867 594450864 0.000000e+00 2628.0
5 TraesCS2B01G527100 chr2D 91.232 422 13 7 2198 2606 594450860 594451270 1.050000e-153 553.0
6 TraesCS2B01G527100 chr2D 97.917 96 2 0 1 96 645613145 645613050 1.600000e-37 167.0
7 TraesCS2B01G527100 chr2A 90.873 1501 67 29 626 2104 728941091 728942543 0.000000e+00 1949.0
8 TraesCS2B01G527100 chr2A 93.034 445 20 2 2162 2606 728942561 728942994 7.860000e-180 640.0
9 TraesCS2B01G527100 chr2A 84.000 550 29 30 121 633 728930120 728930647 8.440000e-130 473.0
10 TraesCS2B01G527100 chr4B 98.947 95 1 0 1 95 99436949 99437043 1.240000e-38 171.0
11 TraesCS2B01G527100 chr7B 98.936 94 1 0 1 94 140609498 140609405 4.460000e-38 169.0
12 TraesCS2B01G527100 chr7B 98.936 94 1 0 1 94 320319938 320320031 4.460000e-38 169.0
13 TraesCS2B01G527100 chr5B 98.936 94 1 0 1 94 53449614 53449707 4.460000e-38 169.0
14 TraesCS2B01G527100 chr3B 97.917 96 2 0 1 96 797131884 797131789 1.600000e-37 167.0
15 TraesCS2B01G527100 chr3A 96.970 99 3 0 1 99 726020392 726020294 1.600000e-37 167.0
16 TraesCS2B01G527100 chr1B 97.895 95 2 0 1 95 567855478 567855572 5.770000e-37 165.0


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 TraesCS2B01G527100 chr2B 721714686 721717291 2605 False 1650.6 4813 96.9700 1 2606 3 chr2B.!!$F1 2605
1 TraesCS2B01G527100 chr2D 594448867 594451270 2403 False 1590.5 2628 90.9375 98 2606 2 chr2D.!!$F1 2508
2 TraesCS2B01G527100 chr2A 728941091 728942994 1903 False 1294.5 1949 91.9535 626 2606 2 chr2A.!!$F2 1980
3 TraesCS2B01G527100 chr2A 728930120 728930647 527 False 473.0 473 84.0000 121 633 1 chr2A.!!$F1 512

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
90 91 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.0 13.64 4.95 46.06 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1669 1743 1.270094 TGGTACGTGCAGGAAGAAGTG 60.27 52.381 14.38 0.0 0.0 3.16 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
45 46 9.117183 TCTAGAACTAAAATACGTCTAGATGCA 57.883 33.333 12.04 0.00 32.48 3.96
46 47 9.900710 CTAGAACTAAAATACGTCTAGATGCAT 57.099 33.333 12.04 0.00 0.00 3.96
47 48 8.804688 AGAACTAAAATACGTCTAGATGCATC 57.195 34.615 19.37 19.37 0.00 3.91
48 49 7.868415 AGAACTAAAATACGTCTAGATGCATCC 59.132 37.037 23.06 6.84 0.00 3.51
49 50 6.456501 ACTAAAATACGTCTAGATGCATCCC 58.543 40.000 23.06 7.99 0.00 3.85
50 51 3.963428 AATACGTCTAGATGCATCCCC 57.037 47.619 23.06 7.64 0.00 4.81
51 52 2.677542 TACGTCTAGATGCATCCCCT 57.322 50.000 23.06 7.62 0.00 4.79
52 53 1.794714 ACGTCTAGATGCATCCCCTT 58.205 50.000 23.06 7.24 0.00 3.95
53 54 2.119495 ACGTCTAGATGCATCCCCTTT 58.881 47.619 23.06 6.85 0.00 3.11
54 55 2.505819 ACGTCTAGATGCATCCCCTTTT 59.494 45.455 23.06 6.10 0.00 2.27
55 56 3.709653 ACGTCTAGATGCATCCCCTTTTA 59.290 43.478 23.06 6.97 0.00 1.52
56 57 4.348168 ACGTCTAGATGCATCCCCTTTTAT 59.652 41.667 23.06 4.58 0.00 1.40
57 58 5.163195 ACGTCTAGATGCATCCCCTTTTATT 60.163 40.000 23.06 3.84 0.00 1.40
58 59 5.409826 CGTCTAGATGCATCCCCTTTTATTC 59.590 44.000 23.06 0.00 0.00 1.75
59 60 6.299141 GTCTAGATGCATCCCCTTTTATTCA 58.701 40.000 23.06 0.00 0.00 2.57
60 61 6.944862 GTCTAGATGCATCCCCTTTTATTCAT 59.055 38.462 23.06 2.35 0.00 2.57
61 62 7.449704 GTCTAGATGCATCCCCTTTTATTCATT 59.550 37.037 23.06 1.91 0.00 2.57
62 63 8.006564 TCTAGATGCATCCCCTTTTATTCATTT 58.993 33.333 23.06 1.25 0.00 2.32
63 64 7.441903 AGATGCATCCCCTTTTATTCATTTT 57.558 32.000 23.06 0.00 0.00 1.82
64 65 7.277396 AGATGCATCCCCTTTTATTCATTTTG 58.723 34.615 23.06 0.00 0.00 2.44
65 66 6.617782 TGCATCCCCTTTTATTCATTTTGA 57.382 33.333 0.00 0.00 0.00 2.69
66 67 7.197901 TGCATCCCCTTTTATTCATTTTGAT 57.802 32.000 0.00 0.00 0.00 2.57
67 68 7.049133 TGCATCCCCTTTTATTCATTTTGATG 58.951 34.615 0.00 0.00 0.00 3.07
68 69 7.092979 TGCATCCCCTTTTATTCATTTTGATGA 60.093 33.333 0.00 0.00 0.00 2.92
69 70 7.225341 GCATCCCCTTTTATTCATTTTGATGAC 59.775 37.037 0.00 0.00 0.00 3.06
70 71 7.789202 TCCCCTTTTATTCATTTTGATGACA 57.211 32.000 0.00 0.00 0.00 3.58
71 72 8.200024 TCCCCTTTTATTCATTTTGATGACAA 57.800 30.769 0.00 0.00 0.00 3.18
72 73 8.313292 TCCCCTTTTATTCATTTTGATGACAAG 58.687 33.333 0.00 0.00 37.32 3.16
73 74 8.096414 CCCCTTTTATTCATTTTGATGACAAGT 58.904 33.333 0.00 0.00 37.32 3.16
80 81 8.915871 ATTCATTTTGATGACAAGTATTTCCG 57.084 30.769 0.00 0.00 37.32 4.30
81 82 6.851609 TCATTTTGATGACAAGTATTTCCGG 58.148 36.000 0.00 0.00 37.32 5.14
82 83 6.657117 TCATTTTGATGACAAGTATTTCCGGA 59.343 34.615 0.00 0.00 37.32 5.14
83 84 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
84 85 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
85 86 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
86 87 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
87 88 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
88 89 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
89 90 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
90 91 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
91 92 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
92 93 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
93 94 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
94 95 0.967380 TTTCCGGACGGAGGGAGTAC 60.967 60.000 13.64 0.00 46.06 2.73
95 96 2.832201 CCGGACGGAGGGAGTACC 60.832 72.222 4.40 0.00 37.50 3.34
96 97 2.044650 CGGACGGAGGGAGTACCA 60.045 66.667 0.00 0.00 43.89 3.25
104 105 0.754587 GAGGGAGTACCACCTACGGG 60.755 65.000 5.97 0.00 43.89 5.28
106 107 0.615827 GGGAGTACCACCTACGGGTT 60.616 60.000 6.65 0.00 44.73 4.11
116 117 1.133730 ACCTACGGGTTTTTGGCAAGA 60.134 47.619 0.00 0.00 44.73 3.02
117 118 1.268625 CCTACGGGTTTTTGGCAAGAC 59.731 52.381 0.00 3.67 0.00 3.01
172 174 0.613777 ACCTTGGTCCCTCGTTGATC 59.386 55.000 0.00 0.00 0.00 2.92
241 247 1.451028 GGCCTGGCTAGTTGCTCTG 60.451 63.158 19.68 0.00 42.39 3.35
246 252 0.107508 TGGCTAGTTGCTCTGGATGC 60.108 55.000 0.00 0.00 42.39 3.91
247 253 0.107508 GGCTAGTTGCTCTGGATGCA 60.108 55.000 0.00 0.00 42.39 3.96
248 254 1.476471 GGCTAGTTGCTCTGGATGCAT 60.476 52.381 0.00 0.00 40.34 3.96
249 255 1.602851 GCTAGTTGCTCTGGATGCATG 59.397 52.381 2.46 0.00 40.34 4.06
290 296 0.912486 GTTACCTGCCCATCCAGAGT 59.088 55.000 0.00 0.00 34.77 3.24
297 303 1.360551 CCCATCCAGAGTAGACGCG 59.639 63.158 3.53 3.53 0.00 6.01
301 307 2.324332 ATCCAGAGTAGACGCGTGCG 62.324 60.000 20.70 13.39 46.03 5.34
467 481 1.483827 TCACTGGCTCTTCCTAGCATG 59.516 52.381 0.00 0.00 44.64 4.06
469 483 0.179702 CTGGCTCTTCCTAGCATGCA 59.820 55.000 21.98 5.01 44.64 3.96
470 484 0.841961 TGGCTCTTCCTAGCATGCAT 59.158 50.000 21.98 7.68 44.64 3.96
472 486 1.878734 GGCTCTTCCTAGCATGCATTC 59.121 52.381 21.98 0.00 44.64 2.67
473 487 1.878734 GCTCTTCCTAGCATGCATTCC 59.121 52.381 21.98 0.00 42.30 3.01
474 488 2.502295 CTCTTCCTAGCATGCATTCCC 58.498 52.381 21.98 0.00 0.00 3.97
475 489 2.106166 CTCTTCCTAGCATGCATTCCCT 59.894 50.000 21.98 0.00 0.00 4.20
486 500 1.204146 GCATTCCCTCCCTGTGACTA 58.796 55.000 0.00 0.00 0.00 2.59
530 548 2.005971 GGTAACCACCACACTCGATC 57.994 55.000 0.00 0.00 45.04 3.69
547 565 0.627451 ATCACATCACATGCACCCCT 59.373 50.000 0.00 0.00 0.00 4.79
551 569 0.253894 CATCACATGCACCCCTCTCA 59.746 55.000 0.00 0.00 0.00 3.27
600 652 5.590259 AGAAATGTACATACACTCATTGGCC 59.410 40.000 9.21 0.00 39.30 5.36
721 773 0.311790 ATCACAACAGCACAAAGGCG 59.688 50.000 0.00 0.00 39.27 5.52
802 856 3.076785 TCCTCACCTTCTTCTTCCTCTCT 59.923 47.826 0.00 0.00 0.00 3.10
803 857 3.447229 CCTCACCTTCTTCTTCCTCTCTC 59.553 52.174 0.00 0.00 0.00 3.20
819 873 0.326618 TCTCTCTCCCCCACCCAATC 60.327 60.000 0.00 0.00 0.00 2.67
820 874 0.327000 CTCTCTCCCCCACCCAATCT 60.327 60.000 0.00 0.00 0.00 2.40
821 875 0.326618 TCTCTCCCCCACCCAATCTC 60.327 60.000 0.00 0.00 0.00 2.75
836 890 2.591193 ATCTCCTCCTCCCCCACGAC 62.591 65.000 0.00 0.00 0.00 4.34
901 955 2.736826 CCTCCCGCCTTTCCTCTCC 61.737 68.421 0.00 0.00 0.00 3.71
905 967 1.990060 CCGCCTTTCCTCTCCCTCA 60.990 63.158 0.00 0.00 0.00 3.86
908 970 1.207791 GCCTTTCCTCTCCCTCATCA 58.792 55.000 0.00 0.00 0.00 3.07
932 994 0.478507 CTCCTCCTCCTCCTCCTCTC 59.521 65.000 0.00 0.00 0.00 3.20
933 995 0.047176 TCCTCCTCCTCCTCCTCTCT 59.953 60.000 0.00 0.00 0.00 3.10
935 997 1.290732 CCTCCTCCTCCTCCTCTCTTT 59.709 57.143 0.00 0.00 0.00 2.52
936 998 2.666317 CTCCTCCTCCTCCTCTCTTTC 58.334 57.143 0.00 0.00 0.00 2.62
937 999 2.244769 CTCCTCCTCCTCCTCTCTTTCT 59.755 54.545 0.00 0.00 0.00 2.52
938 1000 2.243736 TCCTCCTCCTCCTCTCTTTCTC 59.756 54.545 0.00 0.00 0.00 2.87
939 1001 2.244769 CCTCCTCCTCCTCTCTTTCTCT 59.755 54.545 0.00 0.00 0.00 3.10
940 1002 3.555966 CTCCTCCTCCTCTCTTTCTCTC 58.444 54.545 0.00 0.00 0.00 3.20
941 1003 3.197983 TCCTCCTCCTCTCTTTCTCTCT 58.802 50.000 0.00 0.00 0.00 3.10
942 1004 3.053693 TCCTCCTCCTCTCTTTCTCTCTG 60.054 52.174 0.00 0.00 0.00 3.35
943 1005 2.689983 CTCCTCCTCTCTTTCTCTCTGC 59.310 54.545 0.00 0.00 0.00 4.26
944 1006 1.405105 CCTCCTCTCTTTCTCTCTGCG 59.595 57.143 0.00 0.00 0.00 5.18
945 1007 2.364632 CTCCTCTCTTTCTCTCTGCGA 58.635 52.381 0.00 0.00 0.00 5.10
971 1033 1.139058 GTGTGGTGAGTTGAGGTGAGT 59.861 52.381 0.00 0.00 0.00 3.41
979 1041 3.259374 TGAGTTGAGGTGAGTTGAGGATC 59.741 47.826 0.00 0.00 0.00 3.36
991 1053 0.252057 TGAGGATCTTGGGTGGACGA 60.252 55.000 0.00 0.00 34.92 4.20
1048 1110 0.316841 AAACCCTAACCGCGTCGTTA 59.683 50.000 4.92 6.57 0.00 3.18
1054 1116 1.865788 TAACCGCGTCGTTACCAGCT 61.866 55.000 4.92 0.00 0.00 4.24
1059 1124 1.146358 GCGTCGTTACCAGCTCATCC 61.146 60.000 0.00 0.00 0.00 3.51
1062 1127 1.141881 CGTTACCAGCTCATCCGCT 59.858 57.895 0.00 0.00 41.90 5.52
1203 1268 2.832498 GCCTACTCCTCCATGGCC 59.168 66.667 6.96 0.00 37.81 5.36
1511 1579 2.728817 CGCCGGGATGGAGTACTC 59.271 66.667 14.87 14.87 42.00 2.59
1607 1675 2.579860 ACCTCTTCTCCTGCCAATGATT 59.420 45.455 0.00 0.00 0.00 2.57
1618 1686 1.605710 GCCAATGATTCATCCAGTCCG 59.394 52.381 0.00 0.00 0.00 4.79
1619 1687 2.923121 CCAATGATTCATCCAGTCCGT 58.077 47.619 0.00 0.00 0.00 4.69
1620 1688 2.874701 CCAATGATTCATCCAGTCCGTC 59.125 50.000 0.00 0.00 0.00 4.79
1669 1743 8.786955 CGGTCGATCGAGTAATTCTAAATTATC 58.213 37.037 20.09 0.00 0.00 1.75
1804 1882 0.786581 ATCGATCGCGCATGATCAAC 59.213 50.000 20.54 0.00 44.02 3.18
1818 1896 6.471146 GCATGATCAACATAGAGGATTACCT 58.529 40.000 0.00 0.00 42.64 3.08
1877 1956 6.951971 AGGAAGATTGGTGGAGTATATATGC 58.048 40.000 0.00 0.00 0.00 3.14
1891 1970 0.106868 ATATGCTGAGCTGCTGGCAA 60.107 50.000 23.80 15.97 44.79 4.52
2030 2111 7.631822 AGATAATCGATCGATATGGAGTTACG 58.368 38.462 29.57 0.00 39.80 3.18
2045 2130 7.806409 TGGAGTTACGTATATACTAGTGCAA 57.194 36.000 5.39 0.00 0.00 4.08
2063 2148 6.220201 AGTGCAATGTTGTTGGGTTAATTAC 58.780 36.000 0.00 0.00 0.00 1.89
2064 2149 6.041523 AGTGCAATGTTGTTGGGTTAATTACT 59.958 34.615 0.00 0.00 0.00 2.24
2065 2150 6.704050 GTGCAATGTTGTTGGGTTAATTACTT 59.296 34.615 0.00 0.00 0.00 2.24
2066 2151 6.926272 TGCAATGTTGTTGGGTTAATTACTTC 59.074 34.615 0.00 0.00 0.00 3.01
2121 2206 9.715119 TGAACTACATATATATGCTAGATGGGT 57.285 33.333 24.17 10.00 37.19 4.51
2122 2207 9.973450 GAACTACATATATATGCTAGATGGGTG 57.027 37.037 24.17 5.26 37.19 4.61
2123 2208 7.957002 ACTACATATATATGCTAGATGGGTGC 58.043 38.462 24.17 0.00 37.19 5.01
2124 2209 7.786943 ACTACATATATATGCTAGATGGGTGCT 59.213 37.037 24.17 8.24 37.19 4.40
2125 2210 9.301897 CTACATATATATGCTAGATGGGTGCTA 57.698 37.037 20.46 2.61 37.19 3.49
2126 2211 8.733092 ACATATATATGCTAGATGGGTGCTAT 57.267 34.615 20.46 0.00 37.19 2.97
2127 2212 9.828691 ACATATATATGCTAGATGGGTGCTATA 57.171 33.333 20.46 0.00 37.19 1.31
2130 2215 8.733092 ATATATGCTAGATGGGTGCTATATGT 57.267 34.615 0.00 0.00 0.00 2.29
2131 2216 5.768980 ATGCTAGATGGGTGCTATATGTT 57.231 39.130 0.00 0.00 0.00 2.71
2132 2217 4.898320 TGCTAGATGGGTGCTATATGTTG 58.102 43.478 0.00 0.00 0.00 3.33
2133 2218 4.347876 TGCTAGATGGGTGCTATATGTTGT 59.652 41.667 0.00 0.00 0.00 3.32
2134 2219 5.163205 TGCTAGATGGGTGCTATATGTTGTT 60.163 40.000 0.00 0.00 0.00 2.83
2135 2220 5.180117 GCTAGATGGGTGCTATATGTTGTTG 59.820 44.000 0.00 0.00 0.00 3.33
2136 2221 4.464008 AGATGGGTGCTATATGTTGTTGG 58.536 43.478 0.00 0.00 0.00 3.77
2137 2222 3.011566 TGGGTGCTATATGTTGTTGGG 57.988 47.619 0.00 0.00 0.00 4.12
2138 2223 2.310349 TGGGTGCTATATGTTGTTGGGT 59.690 45.455 0.00 0.00 0.00 4.51
2139 2224 3.245443 TGGGTGCTATATGTTGTTGGGTT 60.245 43.478 0.00 0.00 0.00 4.11
2140 2225 4.018324 TGGGTGCTATATGTTGTTGGGTTA 60.018 41.667 0.00 0.00 0.00 2.85
2141 2226 4.951094 GGGTGCTATATGTTGTTGGGTTAA 59.049 41.667 0.00 0.00 0.00 2.01
2142 2227 5.596772 GGGTGCTATATGTTGTTGGGTTAAT 59.403 40.000 0.00 0.00 0.00 1.40
2143 2228 6.097696 GGGTGCTATATGTTGTTGGGTTAATT 59.902 38.462 0.00 0.00 0.00 1.40
2144 2229 7.285858 GGGTGCTATATGTTGTTGGGTTAATTA 59.714 37.037 0.00 0.00 0.00 1.40
2145 2230 8.132995 GGTGCTATATGTTGTTGGGTTAATTAC 58.867 37.037 0.00 0.00 0.00 1.89
2146 2231 8.899771 GTGCTATATGTTGTTGGGTTAATTACT 58.100 33.333 0.00 0.00 0.00 2.24
2147 2232 9.469097 TGCTATATGTTGTTGGGTTAATTACTT 57.531 29.630 0.00 0.00 0.00 2.24
2148 2233 9.946165 GCTATATGTTGTTGGGTTAATTACTTC 57.054 33.333 0.00 0.00 0.00 3.01
2153 2238 8.239038 TGTTGTTGGGTTAATTACTTCATTGA 57.761 30.769 0.00 0.00 0.00 2.57
2154 2239 8.865090 TGTTGTTGGGTTAATTACTTCATTGAT 58.135 29.630 0.00 0.00 0.00 2.57
2155 2240 9.353999 GTTGTTGGGTTAATTACTTCATTGATC 57.646 33.333 0.00 0.00 0.00 2.92
2156 2241 8.877864 TGTTGGGTTAATTACTTCATTGATCT 57.122 30.769 0.00 0.00 0.00 2.75
2157 2242 9.967451 TGTTGGGTTAATTACTTCATTGATCTA 57.033 29.630 0.00 0.00 0.00 1.98
2159 2244 8.657074 TGGGTTAATTACTTCATTGATCTACG 57.343 34.615 0.00 0.00 0.00 3.51
2160 2245 7.225931 TGGGTTAATTACTTCATTGATCTACGC 59.774 37.037 0.00 0.00 0.00 4.42
2185 2270 3.395607 ACCATGTCATGTGGGTGCTATAT 59.604 43.478 11.84 0.00 41.14 0.86
2225 2310 7.895962 AGATGTGTAGGTTATGAGGCATATCTA 59.104 37.037 0.00 0.00 34.61 1.98
2238 2323 6.665680 TGAGGCATATCTATACTCTTCCCTTC 59.334 42.308 0.00 0.00 0.00 3.46
2368 2453 4.725790 AAGCATAGCAATGTTTCCTTCC 57.274 40.909 0.00 0.00 31.60 3.46
2369 2454 3.700538 AGCATAGCAATGTTTCCTTCCA 58.299 40.909 0.00 0.00 35.38 3.53
2370 2455 4.284178 AGCATAGCAATGTTTCCTTCCAT 58.716 39.130 0.00 0.00 35.38 3.41
2371 2456 4.098960 AGCATAGCAATGTTTCCTTCCATG 59.901 41.667 0.00 0.00 35.38 3.66
2454 2547 8.072321 TGATTGCTCTAGAATCAAAGAGTAGT 57.928 34.615 12.27 6.51 41.13 2.73
2455 2548 8.535335 TGATTGCTCTAGAATCAAAGAGTAGTT 58.465 33.333 12.27 2.87 41.13 2.24
2456 2549 8.940768 ATTGCTCTAGAATCAAAGAGTAGTTC 57.059 34.615 12.27 0.00 41.13 3.01
2457 2550 6.868622 TGCTCTAGAATCAAAGAGTAGTTCC 58.131 40.000 12.27 0.00 41.13 3.62
2458 2551 6.127310 TGCTCTAGAATCAAAGAGTAGTTCCC 60.127 42.308 12.27 0.00 41.13 3.97
2459 2552 6.097696 GCTCTAGAATCAAAGAGTAGTTCCCT 59.902 42.308 12.27 0.00 41.13 4.20
2460 2553 7.648039 TCTAGAATCAAAGAGTAGTTCCCTC 57.352 40.000 0.00 0.00 0.00 4.30
2567 2665 2.840511 TGAGGGGTGGTTATGCTTAGA 58.159 47.619 0.00 0.00 0.00 2.10
2589 2687 9.575868 TTAGATTGTTTGGTGGAGTGTTTATTA 57.424 29.630 0.00 0.00 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 9.117183 TGCATCTAGACGTATTTTAGTTCTAGA 57.883 33.333 8.64 8.64 38.94 2.43
20 21 9.900710 ATGCATCTAGACGTATTTTAGTTCTAG 57.099 33.333 0.00 0.00 0.00 2.43
21 22 9.894783 GATGCATCTAGACGTATTTTAGTTCTA 57.105 33.333 19.70 0.00 0.00 2.10
22 23 7.868415 GGATGCATCTAGACGTATTTTAGTTCT 59.132 37.037 25.28 0.00 0.00 3.01
23 24 7.116519 GGGATGCATCTAGACGTATTTTAGTTC 59.883 40.741 25.28 2.81 0.00 3.01
24 25 6.929606 GGGATGCATCTAGACGTATTTTAGTT 59.070 38.462 25.28 0.00 0.00 2.24
25 26 6.456501 GGGATGCATCTAGACGTATTTTAGT 58.543 40.000 25.28 0.00 0.00 2.24
26 27 5.869888 GGGGATGCATCTAGACGTATTTTAG 59.130 44.000 25.28 0.00 0.00 1.85
27 28 5.542635 AGGGGATGCATCTAGACGTATTTTA 59.457 40.000 25.28 0.00 0.00 1.52
28 29 4.348168 AGGGGATGCATCTAGACGTATTTT 59.652 41.667 25.28 0.00 0.00 1.82
29 30 3.904339 AGGGGATGCATCTAGACGTATTT 59.096 43.478 25.28 0.00 0.00 1.40
30 31 3.511477 AGGGGATGCATCTAGACGTATT 58.489 45.455 25.28 0.13 0.00 1.89
31 32 3.176924 AGGGGATGCATCTAGACGTAT 57.823 47.619 25.28 0.00 0.00 3.06
32 33 2.677542 AGGGGATGCATCTAGACGTA 57.322 50.000 25.28 0.00 0.00 3.57
33 34 1.794714 AAGGGGATGCATCTAGACGT 58.205 50.000 25.28 12.28 0.00 4.34
34 35 2.918712 AAAGGGGATGCATCTAGACG 57.081 50.000 25.28 0.00 0.00 4.18
35 36 6.299141 TGAATAAAAGGGGATGCATCTAGAC 58.701 40.000 25.28 13.29 0.00 2.59
36 37 6.514012 TGAATAAAAGGGGATGCATCTAGA 57.486 37.500 25.28 0.00 0.00 2.43
37 38 7.771927 AATGAATAAAAGGGGATGCATCTAG 57.228 36.000 25.28 0.00 0.00 2.43
38 39 8.423349 CAAAATGAATAAAAGGGGATGCATCTA 58.577 33.333 25.28 9.84 0.00 1.98
39 40 7.126115 TCAAAATGAATAAAAGGGGATGCATCT 59.874 33.333 25.28 7.83 0.00 2.90
40 41 7.274447 TCAAAATGAATAAAAGGGGATGCATC 58.726 34.615 18.81 18.81 0.00 3.91
41 42 7.197901 TCAAAATGAATAAAAGGGGATGCAT 57.802 32.000 0.00 0.00 0.00 3.96
42 43 6.617782 TCAAAATGAATAAAAGGGGATGCA 57.382 33.333 0.00 0.00 0.00 3.96
43 44 7.225341 GTCATCAAAATGAATAAAAGGGGATGC 59.775 37.037 0.00 0.00 43.42 3.91
44 45 8.259411 TGTCATCAAAATGAATAAAAGGGGATG 58.741 33.333 0.00 0.00 43.42 3.51
45 46 8.378115 TGTCATCAAAATGAATAAAAGGGGAT 57.622 30.769 0.00 0.00 43.42 3.85
46 47 7.789202 TGTCATCAAAATGAATAAAAGGGGA 57.211 32.000 0.00 0.00 43.42 4.81
47 48 8.096414 ACTTGTCATCAAAATGAATAAAAGGGG 58.904 33.333 0.00 0.00 43.42 4.79
55 56 7.975616 CCGGAAATACTTGTCATCAAAATGAAT 59.024 33.333 0.00 0.00 43.42 2.57
56 57 7.175816 TCCGGAAATACTTGTCATCAAAATGAA 59.824 33.333 0.00 0.00 43.42 2.57
57 58 6.657117 TCCGGAAATACTTGTCATCAAAATGA 59.343 34.615 0.00 0.00 39.63 2.57
58 59 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
59 60 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
60 61 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
61 62 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
62 63 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
63 64 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
64 65 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
65 66 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
66 67 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
67 68 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
68 69 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
69 70 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
70 71 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
71 72 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
72 73 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
73 74 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
74 75 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
75 76 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
76 77 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
77 78 2.273449 GTACTCCCTCCGTCCGGA 59.727 66.667 0.00 0.00 42.90 5.14
78 79 2.832201 GGTACTCCCTCCGTCCGG 60.832 72.222 0.00 0.00 0.00 5.14
79 80 2.044650 TGGTACTCCCTCCGTCCG 60.045 66.667 0.00 0.00 0.00 4.79
80 81 2.056815 GGTGGTACTCCCTCCGTCC 61.057 68.421 0.00 0.00 37.14 4.79
81 82 3.613527 GGTGGTACTCCCTCCGTC 58.386 66.667 0.00 0.00 37.14 4.79
84 85 2.804549 CGTAGGTGGTACTCCCTCC 58.195 63.158 7.08 0.00 44.18 4.30
172 174 0.463295 ATGAACCTCCGCTGATGCAG 60.463 55.000 0.00 0.00 39.64 4.41
182 184 1.742268 GCAAGCAAGAGATGAACCTCC 59.258 52.381 0.00 0.00 33.76 4.30
290 296 0.041224 GATCATCTCGCACGCGTCTA 60.041 55.000 9.86 0.00 40.74 2.59
301 307 2.551887 TGTGAGCTAGCTCGATCATCTC 59.448 50.000 33.55 18.16 45.48 2.75
311 321 0.879400 GATGCGCATGTGAGCTAGCT 60.879 55.000 30.76 19.45 41.53 3.32
312 322 1.568514 GATGCGCATGTGAGCTAGC 59.431 57.895 30.76 6.62 41.53 3.42
313 323 1.554891 CGGATGCGCATGTGAGCTAG 61.555 60.000 30.76 7.55 41.53 3.42
314 324 1.592400 CGGATGCGCATGTGAGCTA 60.592 57.895 30.76 0.00 41.53 3.32
432 442 3.244044 GCCAGTGAACAACTCTCTCTTCT 60.244 47.826 0.00 0.00 36.83 2.85
433 443 3.063485 GCCAGTGAACAACTCTCTCTTC 58.937 50.000 0.00 0.00 36.83 2.87
434 444 2.703007 AGCCAGTGAACAACTCTCTCTT 59.297 45.455 0.00 0.00 36.83 2.85
435 445 2.298729 GAGCCAGTGAACAACTCTCTCT 59.701 50.000 0.00 0.00 36.83 3.10
467 481 1.134371 GTAGTCACAGGGAGGGAATGC 60.134 57.143 0.00 0.00 0.00 3.56
469 483 2.950990 AGTAGTCACAGGGAGGGAAT 57.049 50.000 0.00 0.00 0.00 3.01
470 484 2.623502 GCTAGTAGTCACAGGGAGGGAA 60.624 54.545 0.00 0.00 0.00 3.97
472 486 1.063567 AGCTAGTAGTCACAGGGAGGG 60.064 57.143 0.00 0.00 0.00 4.30
473 487 2.445682 AGCTAGTAGTCACAGGGAGG 57.554 55.000 0.00 0.00 0.00 4.30
474 488 7.584122 TTAATTAGCTAGTAGTCACAGGGAG 57.416 40.000 0.00 0.00 0.00 4.30
475 489 8.005388 AGATTAATTAGCTAGTAGTCACAGGGA 58.995 37.037 0.00 0.00 0.00 4.20
529 547 0.035152 GAGGGGTGCATGTGATGTGA 60.035 55.000 0.00 0.00 0.00 3.58
530 548 0.034767 AGAGGGGTGCATGTGATGTG 60.035 55.000 0.00 0.00 0.00 3.21
587 639 1.004277 GGGACAAGGCCAATGAGTGTA 59.996 52.381 14.81 0.00 0.00 2.90
600 652 1.949525 CAGTTGACAACCAGGGACAAG 59.050 52.381 14.72 0.00 0.00 3.16
802 856 0.326618 GAGATTGGGTGGGGGAGAGA 60.327 60.000 0.00 0.00 0.00 3.10
803 857 1.348775 GGAGATTGGGTGGGGGAGAG 61.349 65.000 0.00 0.00 0.00 3.20
819 873 2.760385 GTCGTGGGGGAGGAGGAG 60.760 72.222 0.00 0.00 0.00 3.69
820 874 4.393778 GGTCGTGGGGGAGGAGGA 62.394 72.222 0.00 0.00 0.00 3.71
836 890 2.493273 TTAAAAGGCAGGAGGGGCGG 62.493 60.000 0.00 0.00 38.57 6.13
901 955 0.264359 AGGAGGAGAGGGTGATGAGG 59.736 60.000 0.00 0.00 0.00 3.86
905 967 0.560688 GAGGAGGAGGAGAGGGTGAT 59.439 60.000 0.00 0.00 0.00 3.06
908 970 1.230819 AGGAGGAGGAGGAGAGGGT 60.231 63.158 0.00 0.00 0.00 4.34
939 1001 4.056125 CCACACCTCGCTCGCAGA 62.056 66.667 0.00 0.00 0.00 4.26
940 1002 4.363990 ACCACACCTCGCTCGCAG 62.364 66.667 0.00 0.00 0.00 5.18
941 1003 4.662961 CACCACACCTCGCTCGCA 62.663 66.667 0.00 0.00 0.00 5.10
942 1004 4.357947 TCACCACACCTCGCTCGC 62.358 66.667 0.00 0.00 0.00 5.03
943 1005 2.126307 CTCACCACACCTCGCTCG 60.126 66.667 0.00 0.00 0.00 5.03
944 1006 0.946221 CAACTCACCACACCTCGCTC 60.946 60.000 0.00 0.00 0.00 5.03
945 1007 1.069765 CAACTCACCACACCTCGCT 59.930 57.895 0.00 0.00 0.00 4.93
971 1033 0.613260 CGTCCACCCAAGATCCTCAA 59.387 55.000 0.00 0.00 0.00 3.02
979 1041 3.530910 AACGGCTCGTCCACCCAAG 62.531 63.158 0.69 0.00 39.99 3.61
1185 1250 2.423446 GCCATGGAGGAGTAGGCG 59.577 66.667 18.40 0.00 41.22 5.52
1607 1675 2.387757 TGATGATGACGGACTGGATGA 58.612 47.619 0.00 0.00 0.00 2.92
1618 1686 4.944317 AGGATGCATGATGATGATGATGAC 59.056 41.667 2.46 0.00 0.00 3.06
1619 1687 5.179452 AGGATGCATGATGATGATGATGA 57.821 39.130 2.46 0.00 0.00 2.92
1620 1688 4.336713 GGAGGATGCATGATGATGATGATG 59.663 45.833 2.46 0.00 0.00 3.07
1669 1743 1.270094 TGGTACGTGCAGGAAGAAGTG 60.270 52.381 14.38 0.00 0.00 3.16
1804 1882 1.338200 GCCGGCAGGTAATCCTCTATG 60.338 57.143 24.80 0.00 43.07 2.23
1818 1896 3.916438 TAACTCTCCCCTGCCGGCA 62.916 63.158 30.59 30.59 0.00 5.69
1877 1956 2.033757 ACCTTGCCAGCAGCTCAG 59.966 61.111 0.00 0.00 44.23 3.35
1891 1970 9.892130 CTTTTCTCACCTACTAATAATTCACCT 57.108 33.333 0.00 0.00 0.00 4.00
2030 2111 7.497909 ACCCAACAACATTGCACTAGTATATAC 59.502 37.037 4.60 4.60 0.00 1.47
2045 2130 8.865090 TCAATGAAGTAATTAACCCAACAACAT 58.135 29.630 0.00 0.00 0.00 2.71
2063 2148 9.964253 GAACATATTATGCGTAGATCAATGAAG 57.036 33.333 3.52 0.00 0.00 3.02
2064 2149 9.710900 AGAACATATTATGCGTAGATCAATGAA 57.289 29.630 3.52 0.00 0.00 2.57
2065 2150 9.710900 AAGAACATATTATGCGTAGATCAATGA 57.289 29.630 3.52 0.00 0.00 2.57
2066 2151 9.750882 CAAGAACATATTATGCGTAGATCAATG 57.249 33.333 3.52 0.00 0.00 2.82
2104 2189 9.828691 ACATATAGCACCCATCTAGCATATATA 57.171 33.333 0.00 0.00 0.00 0.86
2106 2191 8.424133 CAACATATAGCACCCATCTAGCATATA 58.576 37.037 0.00 0.00 0.00 0.86
2108 2193 6.213397 ACAACATATAGCACCCATCTAGCATA 59.787 38.462 0.00 0.00 0.00 3.14
2111 2196 4.899502 ACAACATATAGCACCCATCTAGC 58.100 43.478 0.00 0.00 0.00 3.42
2112 2197 5.702670 CCAACAACATATAGCACCCATCTAG 59.297 44.000 0.00 0.00 0.00 2.43
2113 2198 5.456042 CCCAACAACATATAGCACCCATCTA 60.456 44.000 0.00 0.00 0.00 1.98
2114 2199 4.464008 CCAACAACATATAGCACCCATCT 58.536 43.478 0.00 0.00 0.00 2.90
2118 2203 3.012934 ACCCAACAACATATAGCACCC 57.987 47.619 0.00 0.00 0.00 4.61
2119 2204 6.709018 ATTAACCCAACAACATATAGCACC 57.291 37.500 0.00 0.00 0.00 5.01
2121 2206 9.469097 AAGTAATTAACCCAACAACATATAGCA 57.531 29.630 0.00 0.00 0.00 3.49
2122 2207 9.946165 GAAGTAATTAACCCAACAACATATAGC 57.054 33.333 0.00 0.00 0.00 2.97
2127 2212 8.865090 TCAATGAAGTAATTAACCCAACAACAT 58.135 29.630 0.00 0.00 0.00 2.71
2128 2213 8.239038 TCAATGAAGTAATTAACCCAACAACA 57.761 30.769 0.00 0.00 0.00 3.33
2129 2214 9.353999 GATCAATGAAGTAATTAACCCAACAAC 57.646 33.333 0.00 0.00 0.00 3.32
2130 2215 9.308000 AGATCAATGAAGTAATTAACCCAACAA 57.692 29.630 0.00 0.00 0.00 2.83
2131 2216 8.877864 AGATCAATGAAGTAATTAACCCAACA 57.122 30.769 0.00 0.00 0.00 3.33
2133 2218 9.104965 CGTAGATCAATGAAGTAATTAACCCAA 57.895 33.333 0.00 0.00 0.00 4.12
2134 2219 7.225931 GCGTAGATCAATGAAGTAATTAACCCA 59.774 37.037 0.00 0.00 0.00 4.51
2135 2220 7.225931 TGCGTAGATCAATGAAGTAATTAACCC 59.774 37.037 0.00 0.00 0.00 4.11
2136 2221 8.138365 TGCGTAGATCAATGAAGTAATTAACC 57.862 34.615 0.00 0.00 0.00 2.85
2139 2224 9.419297 GGTATGCGTAGATCAATGAAGTAATTA 57.581 33.333 0.00 0.00 0.00 1.40
2140 2225 7.931407 TGGTATGCGTAGATCAATGAAGTAATT 59.069 33.333 0.00 0.00 0.00 1.40
2141 2226 7.441836 TGGTATGCGTAGATCAATGAAGTAAT 58.558 34.615 0.00 0.00 0.00 1.89
2142 2227 6.811954 TGGTATGCGTAGATCAATGAAGTAA 58.188 36.000 0.00 0.00 0.00 2.24
2143 2228 6.399639 TGGTATGCGTAGATCAATGAAGTA 57.600 37.500 0.00 0.00 0.00 2.24
2144 2229 5.276461 TGGTATGCGTAGATCAATGAAGT 57.724 39.130 0.00 0.00 0.00 3.01
2145 2230 5.698089 ACATGGTATGCGTAGATCAATGAAG 59.302 40.000 0.00 0.00 0.00 3.02
2146 2231 5.610398 ACATGGTATGCGTAGATCAATGAA 58.390 37.500 0.00 0.00 0.00 2.57
2147 2232 5.213891 ACATGGTATGCGTAGATCAATGA 57.786 39.130 0.00 0.00 0.00 2.57
2148 2233 4.990426 TGACATGGTATGCGTAGATCAATG 59.010 41.667 0.00 0.00 0.00 2.82
2149 2234 5.213891 TGACATGGTATGCGTAGATCAAT 57.786 39.130 0.00 0.00 0.00 2.57
2150 2235 4.664150 TGACATGGTATGCGTAGATCAA 57.336 40.909 0.00 0.00 0.00 2.57
2151 2236 4.039124 ACATGACATGGTATGCGTAGATCA 59.961 41.667 19.39 0.00 33.60 2.92
2152 2237 4.386954 CACATGACATGGTATGCGTAGATC 59.613 45.833 19.39 0.00 33.60 2.75
2153 2238 4.309933 CACATGACATGGTATGCGTAGAT 58.690 43.478 19.39 0.00 33.60 1.98
2154 2239 3.492482 CCACATGACATGGTATGCGTAGA 60.492 47.826 19.39 0.00 32.08 2.59
2155 2240 2.802247 CCACATGACATGGTATGCGTAG 59.198 50.000 19.39 0.00 32.08 3.51
2156 2241 2.484594 CCCACATGACATGGTATGCGTA 60.485 50.000 19.39 0.00 35.23 4.42
2157 2242 1.667236 CCACATGACATGGTATGCGT 58.333 50.000 19.39 0.00 32.08 5.24
2158 2243 0.946528 CCCACATGACATGGTATGCG 59.053 55.000 19.39 0.00 35.23 4.73
2159 2244 1.677576 CACCCACATGACATGGTATGC 59.322 52.381 19.39 0.00 35.23 3.14
2160 2245 1.677576 GCACCCACATGACATGGTATG 59.322 52.381 19.39 12.23 35.23 2.39
2185 2270 8.941995 ACCTACACATCTATAGCTTCAAGATA 57.058 34.615 0.00 0.00 0.00 1.98
2225 2310 4.961585 AGGTAACAGGAAGGGAAGAGTAT 58.038 43.478 0.00 0.00 41.41 2.12
2238 2323 5.866207 ACCTACAAGAGAAAAGGTAACAGG 58.134 41.667 0.00 0.00 40.57 4.00
2344 2429 4.361451 AGGAAACATTGCTATGCTTTCG 57.639 40.909 19.12 0.00 35.25 3.46
2454 2547 0.329261 CATGTGCAGGGAAGAGGGAA 59.671 55.000 0.00 0.00 0.00 3.97
2455 2548 1.993653 CATGTGCAGGGAAGAGGGA 59.006 57.895 0.00 0.00 0.00 4.20
2456 2549 1.751927 GCATGTGCAGGGAAGAGGG 60.752 63.158 0.00 0.00 41.59 4.30
2457 2550 3.915575 GCATGTGCAGGGAAGAGG 58.084 61.111 0.00 0.00 41.59 3.69
2567 2665 7.453126 TGGATAATAAACACTCCACCAAACAAT 59.547 33.333 0.00 0.00 32.92 2.71


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

AutoCloner maintained by Alex Coulton.