Multiple sequence alignment - TraesCS7A01G049700

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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 TraesCS7A01G049700 chr7A 100.000 2426 0 0 1 2426 23114222 23116647 0.000000e+00 4481.0
1 TraesCS7A01G049700 chr7A 95.214 585 27 1 1841 2424 280088648 280088064 0.000000e+00 924.0
2 TraesCS7A01G049700 chr7A 85.962 577 49 16 260 824 41256908 41256352 2.690000e-164 588.0
3 TraesCS7A01G049700 chr7A 84.153 183 14 2 1084 1253 65476517 65476697 1.930000e-36 163.0
4 TraesCS7A01G049700 chr7A 95.238 42 2 0 188 229 23148802 23148843 1.560000e-07 67.6
5 TraesCS7A01G049700 chr6A 97.089 1477 39 1 260 1736 378261872 378260400 0.000000e+00 2486.0
6 TraesCS7A01G049700 chr6A 98.997 698 6 1 1729 2426 378260354 378259658 0.000000e+00 1249.0
7 TraesCS7A01G049700 chr6A 95.214 585 27 1 1841 2424 596718706 596719290 0.000000e+00 924.0
8 TraesCS7A01G049700 chr6A 90.343 321 27 4 260 579 108087797 108087480 3.730000e-113 418.0
9 TraesCS7A01G049700 chr6A 89.535 86 8 1 1185 1269 596718096 596718181 9.170000e-20 108.0
10 TraesCS7A01G049700 chr2B 92.012 651 42 7 1780 2424 747759619 747760265 0.000000e+00 905.0
11 TraesCS7A01G049700 chr1D 94.188 585 30 2 1841 2424 292572631 292572050 0.000000e+00 889.0
12 TraesCS7A01G049700 chr7D 95.298 553 25 1 1841 2392 45850567 45850015 0.000000e+00 876.0
13 TraesCS7A01G049700 chr2A 94.991 559 25 3 1870 2426 192216651 192217208 0.000000e+00 874.0
14 TraesCS7A01G049700 chr2A 86.014 572 58 15 260 824 720444597 720444041 5.780000e-166 593.0
15 TraesCS7A01G049700 chr6B 92.881 590 35 6 1841 2426 658977748 658977162 0.000000e+00 850.0
16 TraesCS7A01G049700 chr6B 87.918 389 46 1 1261 1648 474200485 474200873 7.910000e-125 457.0
17 TraesCS7A01G049700 chr6B 87.661 389 47 1 1261 1648 474197207 474197595 3.680000e-123 451.0
18 TraesCS7A01G049700 chr6B 87.766 188 19 3 640 824 678290029 678289843 1.460000e-52 217.0
19 TraesCS7A01G049700 chr4B 87.883 685 69 12 1750 2426 365826255 365826933 0.000000e+00 793.0
20 TraesCS7A01G049700 chr1B 86.268 568 55 11 260 824 554137996 554138543 1.610000e-166 595.0
21 TraesCS7A01G049700 chr7B 85.814 571 57 11 258 824 7260509 7261059 3.480000e-163 584.0
22 TraesCS7A01G049700 chr3A 85.639 571 62 12 260 824 611173348 611173904 1.250000e-162 582.0
23 TraesCS7A01G049700 chr3A 91.562 320 26 1 248 566 742905558 742905877 7.960000e-120 440.0
24 TraesCS7A01G049700 chr5A 86.531 490 53 11 1259 1736 328014907 328014419 5.940000e-146 527.0
25 TraesCS7A01G049700 chr3D 86.157 484 54 10 1259 1736 56605819 56606295 5.980000e-141 510.0
26 TraesCS7A01G049700 chr3D 87.368 285 24 9 1463 1736 416395679 416395962 1.400000e-82 316.0
27 TraesCS7A01G049700 chr3B 90.343 321 26 4 260 579 71305660 71305344 1.340000e-112 416.0
28 TraesCS7A01G049700 chr3B 97.872 47 1 0 778 824 770063202 770063248 5.560000e-12 82.4
29 TraesCS7A01G049700 chr5B 90.909 308 27 1 260 566 113545200 113545507 1.740000e-111 412.0
30 TraesCS7A01G049700 chr5B 90.031 321 28 4 260 579 308575671 308575354 1.740000e-111 412.0
31 TraesCS7A01G049700 chr2D 84.595 370 32 13 460 824 634785980 634786329 6.420000e-91 344.0
32 TraesCS7A01G049700 chr1A 85.246 183 12 3 1084 1253 118288719 118288539 8.920000e-40 174.0


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 TraesCS7A01G049700 chr7A 23114222 23116647 2425 False 4481.0 4481 100.0000 1 2426 1 chr7A.!!$F1 2425
1 TraesCS7A01G049700 chr7A 280088064 280088648 584 True 924.0 924 95.2140 1841 2424 1 chr7A.!!$R2 583
2 TraesCS7A01G049700 chr7A 41256352 41256908 556 True 588.0 588 85.9620 260 824 1 chr7A.!!$R1 564
3 TraesCS7A01G049700 chr6A 378259658 378261872 2214 True 1867.5 2486 98.0430 260 2426 2 chr6A.!!$R2 2166
4 TraesCS7A01G049700 chr6A 596718096 596719290 1194 False 516.0 924 92.3745 1185 2424 2 chr6A.!!$F1 1239
5 TraesCS7A01G049700 chr2B 747759619 747760265 646 False 905.0 905 92.0120 1780 2424 1 chr2B.!!$F1 644
6 TraesCS7A01G049700 chr1D 292572050 292572631 581 True 889.0 889 94.1880 1841 2424 1 chr1D.!!$R1 583
7 TraesCS7A01G049700 chr7D 45850015 45850567 552 True 876.0 876 95.2980 1841 2392 1 chr7D.!!$R1 551
8 TraesCS7A01G049700 chr2A 192216651 192217208 557 False 874.0 874 94.9910 1870 2426 1 chr2A.!!$F1 556
9 TraesCS7A01G049700 chr2A 720444041 720444597 556 True 593.0 593 86.0140 260 824 1 chr2A.!!$R1 564
10 TraesCS7A01G049700 chr6B 658977162 658977748 586 True 850.0 850 92.8810 1841 2426 1 chr6B.!!$R1 585
11 TraesCS7A01G049700 chr6B 474197207 474200873 3666 False 454.0 457 87.7895 1261 1648 2 chr6B.!!$F1 387
12 TraesCS7A01G049700 chr4B 365826255 365826933 678 False 793.0 793 87.8830 1750 2426 1 chr4B.!!$F1 676
13 TraesCS7A01G049700 chr1B 554137996 554138543 547 False 595.0 595 86.2680 260 824 1 chr1B.!!$F1 564
14 TraesCS7A01G049700 chr7B 7260509 7261059 550 False 584.0 584 85.8140 258 824 1 chr7B.!!$F1 566
15 TraesCS7A01G049700 chr3A 611173348 611173904 556 False 582.0 582 85.6390 260 824 1 chr3A.!!$F1 564

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
181 182 0.034896 CCAGCCGGACTTGTGTAGTT 59.965 55.0 5.05 0.0 37.17 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1685 1928 2.777832 ACCTGAAGACATGAGGCTTC 57.222 50.0 15.71 15.71 40.62 3.86 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
27 28 9.834628 TTGATAGCTTTGTTAATTTAAAGTCGG 57.165 29.630 0.00 0.00 36.52 4.79
28 29 9.005777 TGATAGCTTTGTTAATTTAAAGTCGGT 57.994 29.630 0.00 0.00 36.52 4.69
29 30 9.486857 GATAGCTTTGTTAATTTAAAGTCGGTC 57.513 33.333 0.00 0.00 36.52 4.79
30 31 7.506328 AGCTTTGTTAATTTAAAGTCGGTCT 57.494 32.000 0.00 0.00 36.52 3.85
31 32 7.582352 AGCTTTGTTAATTTAAAGTCGGTCTC 58.418 34.615 0.00 0.00 36.52 3.36
32 33 7.444487 AGCTTTGTTAATTTAAAGTCGGTCTCT 59.556 33.333 0.00 0.00 36.52 3.10
33 34 8.074370 GCTTTGTTAATTTAAAGTCGGTCTCTT 58.926 33.333 0.00 0.00 36.52 2.85
34 35 9.595357 CTTTGTTAATTTAAAGTCGGTCTCTTC 57.405 33.333 0.00 0.00 0.00 2.87
35 36 7.342318 TGTTAATTTAAAGTCGGTCTCTTCG 57.658 36.000 0.00 0.00 0.00 3.79
36 37 4.923264 AATTTAAAGTCGGTCTCTTCGC 57.077 40.909 0.00 0.00 0.00 4.70
37 38 3.655276 TTTAAAGTCGGTCTCTTCGCT 57.345 42.857 0.00 0.00 0.00 4.93
38 39 4.771590 TTTAAAGTCGGTCTCTTCGCTA 57.228 40.909 0.00 0.00 0.00 4.26
39 40 2.923605 AAAGTCGGTCTCTTCGCTAG 57.076 50.000 0.00 0.00 0.00 3.42
40 41 0.452585 AAGTCGGTCTCTTCGCTAGC 59.547 55.000 4.06 4.06 0.00 3.42
41 42 1.064458 GTCGGTCTCTTCGCTAGCC 59.936 63.158 9.66 0.00 0.00 3.93
42 43 1.077644 TCGGTCTCTTCGCTAGCCT 60.078 57.895 9.66 0.00 0.00 4.58
43 44 0.680280 TCGGTCTCTTCGCTAGCCTT 60.680 55.000 9.66 0.00 0.00 4.35
44 45 0.248702 CGGTCTCTTCGCTAGCCTTC 60.249 60.000 9.66 0.00 0.00 3.46
45 46 0.103390 GGTCTCTTCGCTAGCCTTCC 59.897 60.000 9.66 0.00 0.00 3.46
46 47 1.107945 GTCTCTTCGCTAGCCTTCCT 58.892 55.000 9.66 0.00 0.00 3.36
47 48 1.478916 GTCTCTTCGCTAGCCTTCCTT 59.521 52.381 9.66 0.00 0.00 3.36
48 49 1.751924 TCTCTTCGCTAGCCTTCCTTC 59.248 52.381 9.66 0.00 0.00 3.46
49 50 1.754226 CTCTTCGCTAGCCTTCCTTCT 59.246 52.381 9.66 0.00 0.00 2.85
50 51 2.952978 CTCTTCGCTAGCCTTCCTTCTA 59.047 50.000 9.66 0.00 0.00 2.10
51 52 3.362706 TCTTCGCTAGCCTTCCTTCTAA 58.637 45.455 9.66 0.00 0.00 2.10
52 53 3.767673 TCTTCGCTAGCCTTCCTTCTAAA 59.232 43.478 9.66 0.00 0.00 1.85
53 54 4.222145 TCTTCGCTAGCCTTCCTTCTAAAA 59.778 41.667 9.66 0.00 0.00 1.52
54 55 4.546829 TCGCTAGCCTTCCTTCTAAAAA 57.453 40.909 9.66 0.00 0.00 1.94
71 72 2.856091 AAAAAGAAGACGACGCGATG 57.144 45.000 15.93 7.01 0.00 3.84
72 73 0.438830 AAAAGAAGACGACGCGATGC 59.561 50.000 15.93 0.00 0.00 3.91
73 74 0.666274 AAAGAAGACGACGCGATGCA 60.666 50.000 15.93 0.00 0.00 3.96
74 75 1.344942 AAGAAGACGACGCGATGCAC 61.345 55.000 15.93 2.62 0.00 4.57
75 76 3.114483 GAAGACGACGCGATGCACG 62.114 63.158 15.93 12.58 45.66 5.34
80 81 4.134187 GACGCGATGCACGGTGTG 62.134 66.667 15.93 0.00 42.83 3.82
84 85 3.490759 CGATGCACGGTGTGGCTC 61.491 66.667 10.24 1.34 38.46 4.70
85 86 3.490759 GATGCACGGTGTGGCTCG 61.491 66.667 10.24 0.00 33.64 5.03
86 87 4.314440 ATGCACGGTGTGGCTCGT 62.314 61.111 10.24 0.00 40.49 4.18
90 91 2.029073 ACGGTGTGGCTCGTGAAG 59.971 61.111 0.00 0.00 38.25 3.02
91 92 2.738521 CGGTGTGGCTCGTGAAGG 60.739 66.667 0.00 0.00 0.00 3.46
92 93 2.426023 GGTGTGGCTCGTGAAGGT 59.574 61.111 0.00 0.00 0.00 3.50
93 94 1.961277 GGTGTGGCTCGTGAAGGTG 60.961 63.158 0.00 0.00 0.00 4.00
94 95 1.961277 GTGTGGCTCGTGAAGGTGG 60.961 63.158 0.00 0.00 0.00 4.61
95 96 2.426023 GTGGCTCGTGAAGGTGGT 59.574 61.111 0.00 0.00 0.00 4.16
96 97 1.668151 GTGGCTCGTGAAGGTGGTC 60.668 63.158 0.00 0.00 0.00 4.02
97 98 1.837051 TGGCTCGTGAAGGTGGTCT 60.837 57.895 0.00 0.00 0.00 3.85
98 99 1.374758 GGCTCGTGAAGGTGGTCTG 60.375 63.158 0.00 0.00 0.00 3.51
99 100 1.374758 GCTCGTGAAGGTGGTCTGG 60.375 63.158 0.00 0.00 0.00 3.86
100 101 1.374758 CTCGTGAAGGTGGTCTGGC 60.375 63.158 0.00 0.00 0.00 4.85
101 102 2.358737 CGTGAAGGTGGTCTGGCC 60.359 66.667 0.00 0.00 37.90 5.36
102 103 2.836154 GTGAAGGTGGTCTGGCCA 59.164 61.111 4.71 4.71 46.95 5.36
111 112 4.052518 GTCTGGCCAGGGGTGCAT 62.053 66.667 32.23 0.00 0.00 3.96
112 113 4.051167 TCTGGCCAGGGGTGCATG 62.051 66.667 32.23 4.54 0.00 4.06
115 116 4.702274 GGCCAGGGGTGCATGGTT 62.702 66.667 0.00 0.00 38.91 3.67
116 117 3.070576 GCCAGGGGTGCATGGTTC 61.071 66.667 5.97 0.00 38.91 3.62
117 118 2.751436 CCAGGGGTGCATGGTTCG 60.751 66.667 0.00 0.00 0.00 3.95
118 119 2.751436 CAGGGGTGCATGGTTCGG 60.751 66.667 0.00 0.00 0.00 4.30
119 120 4.047125 AGGGGTGCATGGTTCGGG 62.047 66.667 0.00 0.00 0.00 5.14
120 121 4.041762 GGGGTGCATGGTTCGGGA 62.042 66.667 0.00 0.00 0.00 5.14
121 122 2.034999 GGGTGCATGGTTCGGGAA 59.965 61.111 0.00 0.00 0.00 3.97
122 123 2.046285 GGGTGCATGGTTCGGGAAG 61.046 63.158 0.00 0.00 0.00 3.46
123 124 1.303317 GGTGCATGGTTCGGGAAGT 60.303 57.895 0.00 0.00 0.00 3.01
124 125 0.893727 GGTGCATGGTTCGGGAAGTT 60.894 55.000 0.00 0.00 0.00 2.66
125 126 0.240945 GTGCATGGTTCGGGAAGTTG 59.759 55.000 0.00 0.00 0.00 3.16
126 127 1.212751 GCATGGTTCGGGAAGTTGC 59.787 57.895 0.00 0.00 0.00 4.17
127 128 1.523154 GCATGGTTCGGGAAGTTGCA 61.523 55.000 0.00 0.00 0.00 4.08
128 129 0.958091 CATGGTTCGGGAAGTTGCAA 59.042 50.000 0.00 0.00 0.00 4.08
129 130 1.339610 CATGGTTCGGGAAGTTGCAAA 59.660 47.619 0.00 0.00 0.00 3.68
130 131 1.698506 TGGTTCGGGAAGTTGCAAAT 58.301 45.000 0.00 0.00 0.00 2.32
131 132 1.339610 TGGTTCGGGAAGTTGCAAATG 59.660 47.619 0.00 0.00 0.00 2.32
132 133 1.336795 GGTTCGGGAAGTTGCAAATGG 60.337 52.381 0.00 0.00 0.00 3.16
133 134 1.339929 GTTCGGGAAGTTGCAAATGGT 59.660 47.619 0.00 0.00 0.00 3.55
134 135 0.958091 TCGGGAAGTTGCAAATGGTG 59.042 50.000 0.00 0.00 0.00 4.17
175 176 4.681978 GACGCCAGCCGGACTTGT 62.682 66.667 5.05 0.00 42.52 3.16
176 177 4.988598 ACGCCAGCCGGACTTGTG 62.989 66.667 5.05 7.31 42.52 3.33
177 178 4.988598 CGCCAGCCGGACTTGTGT 62.989 66.667 5.05 0.00 0.00 3.72
178 179 2.345991 GCCAGCCGGACTTGTGTA 59.654 61.111 5.05 0.00 0.00 2.90
179 180 1.741770 GCCAGCCGGACTTGTGTAG 60.742 63.158 5.05 0.00 0.00 2.74
180 181 1.671742 CCAGCCGGACTTGTGTAGT 59.328 57.895 5.05 0.00 40.71 2.73
181 182 0.034896 CCAGCCGGACTTGTGTAGTT 59.965 55.000 5.05 0.00 37.17 2.24
182 183 1.148310 CAGCCGGACTTGTGTAGTTG 58.852 55.000 5.05 0.00 37.17 3.16
183 184 0.756903 AGCCGGACTTGTGTAGTTGT 59.243 50.000 5.05 0.00 37.17 3.32
184 185 0.865769 GCCGGACTTGTGTAGTTGTG 59.134 55.000 5.05 0.00 37.17 3.33
185 186 1.508632 CCGGACTTGTGTAGTTGTGG 58.491 55.000 0.00 0.00 37.17 4.17
186 187 1.069513 CCGGACTTGTGTAGTTGTGGA 59.930 52.381 0.00 0.00 37.17 4.02
187 188 2.404215 CGGACTTGTGTAGTTGTGGAG 58.596 52.381 0.00 0.00 37.17 3.86
188 189 2.223971 CGGACTTGTGTAGTTGTGGAGT 60.224 50.000 0.00 0.00 37.17 3.85
189 190 3.005050 CGGACTTGTGTAGTTGTGGAGTA 59.995 47.826 0.00 0.00 37.17 2.59
190 191 4.304939 GGACTTGTGTAGTTGTGGAGTAC 58.695 47.826 0.00 0.00 37.17 2.73
191 192 4.202182 GGACTTGTGTAGTTGTGGAGTACA 60.202 45.833 0.00 0.00 40.91 2.90
200 201 2.342279 TGGAGTACACACTGCCGC 59.658 61.111 0.00 0.00 42.16 6.53
201 202 2.809601 GGAGTACACACTGCCGCG 60.810 66.667 0.00 0.00 37.16 6.46
202 203 3.479269 GAGTACACACTGCCGCGC 61.479 66.667 0.00 0.00 34.21 6.86
219 220 4.785453 CCCCTCGCAGGCTTGACC 62.785 72.222 0.00 0.00 32.73 4.02
220 221 4.785453 CCCTCGCAGGCTTGACCC 62.785 72.222 0.00 0.00 40.58 4.46
221 222 4.020617 CCTCGCAGGCTTGACCCA 62.021 66.667 0.00 0.00 40.58 4.51
222 223 2.743928 CTCGCAGGCTTGACCCAC 60.744 66.667 0.00 0.00 40.58 4.61
223 224 3.535629 CTCGCAGGCTTGACCCACA 62.536 63.158 0.00 0.00 40.58 4.17
224 225 3.052082 CGCAGGCTTGACCCACAG 61.052 66.667 0.00 0.00 40.58 3.66
225 226 3.368571 GCAGGCTTGACCCACAGC 61.369 66.667 0.00 0.00 40.58 4.40
226 227 2.113774 CAGGCTTGACCCACAGCA 59.886 61.111 0.00 0.00 40.58 4.41
227 228 1.529010 CAGGCTTGACCCACAGCAA 60.529 57.895 0.00 0.00 40.58 3.91
228 229 0.896940 CAGGCTTGACCCACAGCAAT 60.897 55.000 0.00 0.00 40.58 3.56
229 230 0.896940 AGGCTTGACCCACAGCAATG 60.897 55.000 0.00 0.00 40.58 2.82
230 231 1.588082 GCTTGACCCACAGCAATGG 59.412 57.895 0.00 0.00 39.71 3.16
231 232 0.895100 GCTTGACCCACAGCAATGGA 60.895 55.000 7.80 0.00 43.02 3.41
232 233 1.171308 CTTGACCCACAGCAATGGAG 58.829 55.000 7.80 1.38 43.02 3.86
233 234 0.895100 TTGACCCACAGCAATGGAGC 60.895 55.000 7.80 0.61 43.02 4.70
234 235 2.036256 ACCCACAGCAATGGAGCC 59.964 61.111 7.80 0.00 43.02 4.70
235 236 3.136123 CCCACAGCAATGGAGCCG 61.136 66.667 7.80 0.00 43.02 5.52
236 237 3.818787 CCACAGCAATGGAGCCGC 61.819 66.667 0.00 0.00 43.02 6.53
237 238 3.818787 CACAGCAATGGAGCCGCC 61.819 66.667 0.00 0.00 34.23 6.13
247 248 2.032680 TGGAGCCGCCATTAGTTTAC 57.967 50.000 0.00 0.00 43.33 2.01
248 249 1.306148 GGAGCCGCCATTAGTTTACC 58.694 55.000 0.00 0.00 36.34 2.85
249 250 1.134189 GGAGCCGCCATTAGTTTACCT 60.134 52.381 0.00 0.00 36.34 3.08
250 251 2.640184 GAGCCGCCATTAGTTTACCTT 58.360 47.619 0.00 0.00 0.00 3.50
251 252 3.014623 GAGCCGCCATTAGTTTACCTTT 58.985 45.455 0.00 0.00 0.00 3.11
252 253 2.752903 AGCCGCCATTAGTTTACCTTTG 59.247 45.455 0.00 0.00 0.00 2.77
253 254 2.159296 GCCGCCATTAGTTTACCTTTGG 60.159 50.000 0.00 0.00 0.00 3.28
254 255 2.425668 CCGCCATTAGTTTACCTTTGGG 59.574 50.000 0.00 0.00 38.88 4.12
256 257 3.119637 CGCCATTAGTTTACCTTTGGGTG 60.120 47.826 0.00 0.00 46.75 4.61
333 334 7.759489 TTGTTAGATATGTTGCTTGGTTCTT 57.241 32.000 0.00 0.00 0.00 2.52
336 337 9.290988 TGTTAGATATGTTGCTTGGTTCTTAAA 57.709 29.630 0.00 0.00 0.00 1.52
427 428 1.376683 GACCGCCAAGCACCATGTA 60.377 57.895 0.00 0.00 0.00 2.29
441 442 3.383505 CACCATGTATACTTCCGTCTGGA 59.616 47.826 4.17 0.00 44.61 3.86
443 444 4.039245 ACCATGTATACTTCCGTCTGGATG 59.961 45.833 4.17 0.00 45.91 3.51
458 459 5.506708 GTCTGGATGTAAATACCCCACTTT 58.493 41.667 0.00 0.00 0.00 2.66
462 463 8.340757 TCTGGATGTAAATACCCCACTTTTATT 58.659 33.333 0.00 0.00 0.00 1.40
642 644 0.859232 CACCGTCCTTGACAAGAACG 59.141 55.000 18.87 18.87 32.09 3.95
676 694 1.927174 CGATCTTCAACATCGACCACC 59.073 52.381 0.00 0.00 44.95 4.61
1094 1114 3.636231 CCCCACACCGGCTCAAGA 61.636 66.667 0.00 0.00 0.00 3.02
1183 1203 0.179161 ATCAAGGAAGCGACGAGACG 60.179 55.000 0.00 0.00 0.00 4.18
1701 1944 3.264947 CATTCGAAGCCTCATGTCTTCA 58.735 45.455 18.04 6.71 38.80 3.02
2341 5208 4.505191 CCTCTGAAGCATTTGTTGTTGTTG 59.495 41.667 0.00 0.00 0.00 3.33
2395 5262 4.112634 GTTCTTGCACACTCGCTATATGA 58.887 43.478 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.834628 CCGACTTTAAATTAACAAAGCTATCAA 57.165 29.630 0.00 0.00 35.58 2.57
2 3 9.005777 ACCGACTTTAAATTAACAAAGCTATCA 57.994 29.630 0.00 0.00 35.58 2.15
3 4 9.486857 GACCGACTTTAAATTAACAAAGCTATC 57.513 33.333 0.00 0.00 35.58 2.08
4 5 9.227777 AGACCGACTTTAAATTAACAAAGCTAT 57.772 29.630 0.00 0.00 35.58 2.97
5 6 8.611654 AGACCGACTTTAAATTAACAAAGCTA 57.388 30.769 0.00 0.00 35.58 3.32
6 7 7.444487 AGAGACCGACTTTAAATTAACAAAGCT 59.556 33.333 6.90 0.00 35.58 3.74
7 8 7.582352 AGAGACCGACTTTAAATTAACAAAGC 58.418 34.615 6.90 0.00 35.58 3.51
8 9 9.595357 GAAGAGACCGACTTTAAATTAACAAAG 57.405 33.333 0.00 5.86 37.69 2.77
9 10 8.277713 CGAAGAGACCGACTTTAAATTAACAAA 58.722 33.333 0.00 0.00 0.00 2.83
10 11 7.569957 GCGAAGAGACCGACTTTAAATTAACAA 60.570 37.037 0.00 0.00 0.00 2.83
11 12 6.128742 GCGAAGAGACCGACTTTAAATTAACA 60.129 38.462 0.00 0.00 0.00 2.41
12 13 6.090493 AGCGAAGAGACCGACTTTAAATTAAC 59.910 38.462 0.00 0.00 0.00 2.01
13 14 6.161381 AGCGAAGAGACCGACTTTAAATTAA 58.839 36.000 0.00 0.00 0.00 1.40
14 15 5.717119 AGCGAAGAGACCGACTTTAAATTA 58.283 37.500 0.00 0.00 0.00 1.40
15 16 4.566987 AGCGAAGAGACCGACTTTAAATT 58.433 39.130 0.00 0.00 0.00 1.82
16 17 4.189639 AGCGAAGAGACCGACTTTAAAT 57.810 40.909 0.00 0.00 0.00 1.40
17 18 3.655276 AGCGAAGAGACCGACTTTAAA 57.345 42.857 0.00 0.00 0.00 1.52
18 19 3.427233 GCTAGCGAAGAGACCGACTTTAA 60.427 47.826 0.00 0.00 0.00 1.52
19 20 2.097142 GCTAGCGAAGAGACCGACTTTA 59.903 50.000 0.00 0.00 0.00 1.85
20 21 1.135344 GCTAGCGAAGAGACCGACTTT 60.135 52.381 0.00 0.00 0.00 2.66
21 22 0.452585 GCTAGCGAAGAGACCGACTT 59.547 55.000 0.00 0.00 0.00 3.01
22 23 1.378124 GGCTAGCGAAGAGACCGACT 61.378 60.000 9.00 0.00 0.00 4.18
23 24 1.064458 GGCTAGCGAAGAGACCGAC 59.936 63.158 9.00 0.00 0.00 4.79
24 25 0.680280 AAGGCTAGCGAAGAGACCGA 60.680 55.000 9.00 0.00 0.00 4.69
25 26 0.248702 GAAGGCTAGCGAAGAGACCG 60.249 60.000 9.00 0.00 0.00 4.79
26 27 0.103390 GGAAGGCTAGCGAAGAGACC 59.897 60.000 9.00 1.62 0.00 3.85
27 28 1.107945 AGGAAGGCTAGCGAAGAGAC 58.892 55.000 9.00 0.00 0.00 3.36
28 29 1.751924 GAAGGAAGGCTAGCGAAGAGA 59.248 52.381 9.00 0.00 0.00 3.10
29 30 1.754226 AGAAGGAAGGCTAGCGAAGAG 59.246 52.381 9.00 0.00 0.00 2.85
30 31 1.853963 AGAAGGAAGGCTAGCGAAGA 58.146 50.000 9.00 0.00 0.00 2.87
31 32 3.802948 TTAGAAGGAAGGCTAGCGAAG 57.197 47.619 9.00 0.00 0.00 3.79
32 33 4.546829 TTTTAGAAGGAAGGCTAGCGAA 57.453 40.909 9.00 0.00 0.00 4.70
33 34 4.546829 TTTTTAGAAGGAAGGCTAGCGA 57.453 40.909 9.00 0.00 0.00 4.93
52 53 1.136336 GCATCGCGTCGTCTTCTTTTT 60.136 47.619 5.77 0.00 0.00 1.94
53 54 0.438830 GCATCGCGTCGTCTTCTTTT 59.561 50.000 5.77 0.00 0.00 2.27
54 55 0.666274 TGCATCGCGTCGTCTTCTTT 60.666 50.000 5.77 0.00 0.00 2.52
55 56 1.080772 TGCATCGCGTCGTCTTCTT 60.081 52.632 5.77 0.00 0.00 2.52
56 57 1.801913 GTGCATCGCGTCGTCTTCT 60.802 57.895 5.77 0.00 0.00 2.85
57 58 2.689766 GTGCATCGCGTCGTCTTC 59.310 61.111 5.77 0.00 0.00 2.87
58 59 3.172575 CGTGCATCGCGTCGTCTT 61.173 61.111 5.77 0.00 32.40 3.01
63 64 4.134187 CACACCGTGCATCGCGTC 62.134 66.667 5.77 0.00 38.35 5.19
67 68 3.490759 GAGCCACACCGTGCATCG 61.491 66.667 0.00 0.00 39.52 3.84
68 69 3.490759 CGAGCCACACCGTGCATC 61.491 66.667 0.00 0.00 31.34 3.91
69 70 4.314440 ACGAGCCACACCGTGCAT 62.314 61.111 0.00 0.00 37.64 3.96
73 74 2.029073 CTTCACGAGCCACACCGT 59.971 61.111 0.00 0.00 39.88 4.83
74 75 2.738521 CCTTCACGAGCCACACCG 60.739 66.667 0.00 0.00 0.00 4.94
75 76 1.961277 CACCTTCACGAGCCACACC 60.961 63.158 0.00 0.00 0.00 4.16
76 77 1.961277 CCACCTTCACGAGCCACAC 60.961 63.158 0.00 0.00 0.00 3.82
77 78 2.377628 GACCACCTTCACGAGCCACA 62.378 60.000 0.00 0.00 0.00 4.17
78 79 1.668151 GACCACCTTCACGAGCCAC 60.668 63.158 0.00 0.00 0.00 5.01
79 80 1.837051 AGACCACCTTCACGAGCCA 60.837 57.895 0.00 0.00 0.00 4.75
80 81 1.374758 CAGACCACCTTCACGAGCC 60.375 63.158 0.00 0.00 0.00 4.70
81 82 1.374758 CCAGACCACCTTCACGAGC 60.375 63.158 0.00 0.00 0.00 5.03
82 83 1.374758 GCCAGACCACCTTCACGAG 60.375 63.158 0.00 0.00 0.00 4.18
83 84 2.741092 GCCAGACCACCTTCACGA 59.259 61.111 0.00 0.00 0.00 4.35
84 85 2.358737 GGCCAGACCACCTTCACG 60.359 66.667 0.00 0.00 38.86 4.35
85 86 1.302832 CTGGCCAGACCACCTTCAC 60.303 63.158 29.88 0.00 46.36 3.18
86 87 2.528818 CCTGGCCAGACCACCTTCA 61.529 63.158 34.91 0.00 46.36 3.02
87 88 2.352805 CCTGGCCAGACCACCTTC 59.647 66.667 34.91 0.00 46.36 3.46
88 89 3.260100 CCCTGGCCAGACCACCTT 61.260 66.667 34.91 0.00 46.36 3.50
91 92 4.351054 CACCCCTGGCCAGACCAC 62.351 72.222 34.91 0.00 46.36 4.16
94 95 4.052518 ATGCACCCCTGGCCAGAC 62.053 66.667 34.91 17.11 0.00 3.51
95 96 4.051167 CATGCACCCCTGGCCAGA 62.051 66.667 34.91 13.64 0.00 3.86
98 99 4.702274 AACCATGCACCCCTGGCC 62.702 66.667 3.91 0.00 35.88 5.36
99 100 3.070576 GAACCATGCACCCCTGGC 61.071 66.667 3.91 0.00 35.88 4.85
100 101 2.751436 CGAACCATGCACCCCTGG 60.751 66.667 2.41 2.41 38.55 4.45
101 102 2.751436 CCGAACCATGCACCCCTG 60.751 66.667 0.00 0.00 0.00 4.45
102 103 4.047125 CCCGAACCATGCACCCCT 62.047 66.667 0.00 0.00 0.00 4.79
103 104 3.577334 TTCCCGAACCATGCACCCC 62.577 63.158 0.00 0.00 0.00 4.95
104 105 2.034999 TTCCCGAACCATGCACCC 59.965 61.111 0.00 0.00 0.00 4.61
105 106 0.893727 AACTTCCCGAACCATGCACC 60.894 55.000 0.00 0.00 0.00 5.01
106 107 0.240945 CAACTTCCCGAACCATGCAC 59.759 55.000 0.00 0.00 0.00 4.57
107 108 1.523154 GCAACTTCCCGAACCATGCA 61.523 55.000 0.00 0.00 32.80 3.96
108 109 1.212751 GCAACTTCCCGAACCATGC 59.787 57.895 0.00 0.00 0.00 4.06
109 110 0.958091 TTGCAACTTCCCGAACCATG 59.042 50.000 0.00 0.00 0.00 3.66
110 111 1.698506 TTTGCAACTTCCCGAACCAT 58.301 45.000 0.00 0.00 0.00 3.55
111 112 1.339610 CATTTGCAACTTCCCGAACCA 59.660 47.619 0.00 0.00 0.00 3.67
112 113 1.336795 CCATTTGCAACTTCCCGAACC 60.337 52.381 0.00 0.00 0.00 3.62
113 114 1.339929 ACCATTTGCAACTTCCCGAAC 59.660 47.619 0.00 0.00 0.00 3.95
114 115 1.339610 CACCATTTGCAACTTCCCGAA 59.660 47.619 0.00 0.00 0.00 4.30
115 116 0.958091 CACCATTTGCAACTTCCCGA 59.042 50.000 0.00 0.00 0.00 5.14
116 117 3.495124 CACCATTTGCAACTTCCCG 57.505 52.632 0.00 0.00 0.00 5.14
158 159 4.681978 ACAAGTCCGGCTGGCGTC 62.682 66.667 22.22 14.27 34.14 5.19
159 160 4.988598 CACAAGTCCGGCTGGCGT 62.989 66.667 22.22 0.65 34.14 5.68
160 161 3.583276 TACACAAGTCCGGCTGGCG 62.583 63.158 17.39 17.39 34.14 5.69
161 162 1.741770 CTACACAAGTCCGGCTGGC 60.742 63.158 6.73 1.77 34.14 4.85
162 163 0.034896 AACTACACAAGTCCGGCTGG 59.965 55.000 4.71 4.71 37.50 4.85
163 164 1.148310 CAACTACACAAGTCCGGCTG 58.852 55.000 0.00 0.00 37.50 4.85
164 165 0.756903 ACAACTACACAAGTCCGGCT 59.243 50.000 0.00 0.00 37.50 5.52
165 166 0.865769 CACAACTACACAAGTCCGGC 59.134 55.000 0.00 0.00 37.50 6.13
166 167 1.069513 TCCACAACTACACAAGTCCGG 59.930 52.381 0.00 0.00 37.50 5.14
167 168 2.223971 ACTCCACAACTACACAAGTCCG 60.224 50.000 0.00 0.00 37.50 4.79
168 169 3.470645 ACTCCACAACTACACAAGTCC 57.529 47.619 0.00 0.00 37.50 3.85
169 170 4.743644 GTGTACTCCACAACTACACAAGTC 59.256 45.833 0.00 0.00 43.92 3.01
170 171 4.690122 GTGTACTCCACAACTACACAAGT 58.310 43.478 0.00 0.00 43.92 3.16
182 183 2.027625 GCGGCAGTGTGTACTCCAC 61.028 63.158 7.83 7.83 44.78 4.02
183 184 2.342279 GCGGCAGTGTGTACTCCA 59.658 61.111 0.00 0.00 34.07 3.86
184 185 2.809601 CGCGGCAGTGTGTACTCC 60.810 66.667 0.00 0.00 34.07 3.85
185 186 3.479269 GCGCGGCAGTGTGTACTC 61.479 66.667 8.83 0.00 34.07 2.59
202 203 4.785453 GGTCAAGCCTGCGAGGGG 62.785 72.222 4.65 0.00 35.37 4.79
203 204 4.785453 GGGTCAAGCCTGCGAGGG 62.785 72.222 4.65 0.00 35.37 4.30
204 205 4.020617 TGGGTCAAGCCTGCGAGG 62.021 66.667 0.00 0.00 38.80 4.63
205 206 2.743928 GTGGGTCAAGCCTGCGAG 60.744 66.667 0.00 0.00 37.43 5.03
206 207 3.535629 CTGTGGGTCAAGCCTGCGA 62.536 63.158 0.00 0.00 37.43 5.10
207 208 3.052082 CTGTGGGTCAAGCCTGCG 61.052 66.667 0.00 0.00 37.43 5.18
208 209 3.368571 GCTGTGGGTCAAGCCTGC 61.369 66.667 0.00 0.00 37.43 4.85
209 210 0.896940 ATTGCTGTGGGTCAAGCCTG 60.897 55.000 0.00 0.00 37.43 4.85
210 211 0.896940 CATTGCTGTGGGTCAAGCCT 60.897 55.000 0.00 0.00 37.43 4.58
211 212 1.588082 CATTGCTGTGGGTCAAGCC 59.412 57.895 0.00 0.00 0.00 4.35
212 213 0.895100 TCCATTGCTGTGGGTCAAGC 60.895 55.000 7.89 0.00 39.80 4.01
213 214 1.171308 CTCCATTGCTGTGGGTCAAG 58.829 55.000 7.89 0.00 39.80 3.02
214 215 0.895100 GCTCCATTGCTGTGGGTCAA 60.895 55.000 7.89 0.00 39.80 3.18
215 216 1.303561 GCTCCATTGCTGTGGGTCA 60.304 57.895 7.89 0.00 39.80 4.02
216 217 2.048603 GGCTCCATTGCTGTGGGTC 61.049 63.158 7.89 1.49 39.80 4.46
217 218 2.036256 GGCTCCATTGCTGTGGGT 59.964 61.111 7.89 0.00 39.80 4.51
218 219 3.136123 CGGCTCCATTGCTGTGGG 61.136 66.667 7.89 1.50 39.80 4.61
219 220 3.818787 GCGGCTCCATTGCTGTGG 61.819 66.667 0.00 1.95 41.12 4.17
220 221 3.818787 GGCGGCTCCATTGCTGTG 61.819 66.667 0.00 0.00 41.12 3.66
221 222 4.349503 TGGCGGCTCCATTGCTGT 62.350 61.111 11.43 0.00 40.72 4.40
229 230 1.134189 AGGTAAACTAATGGCGGCTCC 60.134 52.381 11.43 0.00 0.00 4.70
230 231 2.327200 AGGTAAACTAATGGCGGCTC 57.673 50.000 11.43 0.00 0.00 4.70
231 232 2.752903 CAAAGGTAAACTAATGGCGGCT 59.247 45.455 11.43 0.00 0.00 5.52
232 233 2.159296 CCAAAGGTAAACTAATGGCGGC 60.159 50.000 0.00 0.00 31.82 6.53
233 234 2.425668 CCCAAAGGTAAACTAATGGCGG 59.574 50.000 0.00 0.00 35.83 6.13
234 235 3.775661 CCCAAAGGTAAACTAATGGCG 57.224 47.619 0.00 0.00 35.83 5.69
333 334 4.521256 GCCAAGGAAGTACATGGTTGTTTA 59.479 41.667 0.00 0.00 37.28 2.01
336 337 2.108250 AGCCAAGGAAGTACATGGTTGT 59.892 45.455 0.00 0.00 39.98 3.32
364 365 9.905713 TTGAGAGCCAAGAAATTACATAGTTAT 57.094 29.630 0.00 0.00 0.00 1.89
395 396 3.741249 TGGCGGTCAAGTAAACACATAA 58.259 40.909 0.00 0.00 0.00 1.90
642 644 2.203070 ATCGCCGGAGTTGCATCC 60.203 61.111 5.05 0.00 35.88 3.51
676 694 0.784178 CGATGTCAGTGTTGTGTCCG 59.216 55.000 0.00 0.00 0.00 4.79
923 943 6.274001 ACTCAATCGATAGTATTTGTTGCG 57.726 37.500 0.00 0.00 37.40 4.85
1111 1131 4.803426 CCGCTCCAGTCTCCACGC 62.803 72.222 0.00 0.00 0.00 5.34
1573 1615 7.395206 GGGTAACAAATTTAGAAGGAGCCTAAA 59.605 37.037 0.00 0.00 38.18 1.85
1685 1928 2.777832 ACCTGAAGACATGAGGCTTC 57.222 50.000 15.71 15.71 40.62 3.86
1701 1944 9.453572 CATATGGATGCAGTTTATGTAATACCT 57.546 33.333 0.00 0.00 0.00 3.08
2395 5262 7.497579 TGATATTAGCACACAATACCATTTCGT 59.502 33.333 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.