Multiple sequence alignment - TraesCS5D01G138200

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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 TraesCS5D01G138200 chr5D 100.000 3897 0 0 1 3897 220185684 220189580 0.000000e+00 7197.0
1 TraesCS5D01G138200 chr5D 95.370 216 10 0 226 441 220185705 220185920 1.040000e-90 344.0
2 TraesCS5D01G138200 chr5D 95.370 216 10 0 22 237 220185909 220186124 1.040000e-90 344.0
3 TraesCS5D01G138200 chr5D 85.294 170 23 2 1 169 559390808 559390976 1.440000e-39 174.0
4 TraesCS5D01G138200 chr5B 97.441 2696 49 8 647 3330 243127729 243130416 0.000000e+00 4578.0
5 TraesCS5D01G138200 chr5B 96.629 534 18 0 3330 3863 243130474 243131007 0.000000e+00 887.0
6 TraesCS5D01G138200 chr5B 86.173 405 35 13 236 633 243127354 243127744 6.020000e-113 418.0
7 TraesCS5D01G138200 chr5B 86.722 241 27 4 1 237 243127323 243127562 2.990000e-66 263.0
8 TraesCS5D01G138200 chr5B 82.759 174 22 7 1 169 268136861 268137031 8.720000e-32 148.0
9 TraesCS5D01G138200 chr5B 97.059 34 1 0 3860 3893 243131686 243131719 1.510000e-04 58.4
10 TraesCS5D01G138200 chr5A 96.705 2701 67 12 646 3330 294240919 294243613 0.000000e+00 4475.0
11 TraesCS5D01G138200 chr5A 97.378 534 14 0 3330 3863 294243671 294244204 0.000000e+00 909.0
12 TraesCS5D01G138200 chr5A 87.616 323 33 5 235 553 294225759 294226078 6.150000e-98 368.0
13 TraesCS5D01G138200 chr5A 87.429 175 16 5 1 170 672754118 672753945 3.070000e-46 196.0
14 TraesCS5D01G138200 chr5A 87.857 140 13 3 239 374 672754084 672753945 1.120000e-35 161.0
15 TraesCS5D01G138200 chr5A 91.667 84 6 1 550 633 294240852 294240934 8.850000e-22 115.0
16 TraesCS5D01G138200 chr1D 85.465 172 16 4 1 170 427224834 427224998 1.860000e-38 171.0
17 TraesCS5D01G138200 chr1D 86.957 138 9 4 239 374 427224868 427224998 3.140000e-31 147.0
18 TraesCS5D01G138200 chr1D 91.011 89 4 1 3056 3144 141310836 141310752 2.460000e-22 117.0
19 TraesCS5D01G138200 chr2A 88.194 144 13 3 235 374 764766462 764766605 6.700000e-38 169.0
20 TraesCS5D01G138200 chr3A 82.581 155 16 3 1 155 448322809 448322952 4.090000e-25 126.0
21 TraesCS5D01G138200 chr6B 92.135 89 3 1 3056 3144 613189163 613189079 5.290000e-24 122.0
22 TraesCS5D01G138200 chrUn 92.771 83 2 1 3056 3138 391007177 391007255 2.460000e-22 117.0
23 TraesCS5D01G138200 chr6D 91.011 89 4 1 3056 3144 425588058 425587974 2.460000e-22 117.0
24 TraesCS5D01G138200 chr4D 92.771 83 2 1 3056 3138 123302190 123302268 2.460000e-22 117.0
25 TraesCS5D01G138200 chr4D 92.771 83 2 1 3056 3138 123718807 123718885 2.460000e-22 117.0
26 TraesCS5D01G138200 chr4D 92.771 83 2 1 3056 3138 241164992 241165070 2.460000e-22 117.0
27 TraesCS5D01G138200 chr3D 96.970 33 1 0 235 267 26279615 26279647 5.440000e-04 56.5


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 TraesCS5D01G138200 chr5D 220185684 220189580 3896 False 2628.333333 7197 96.913333 1 3897 3 chr5D.!!$F2 3896
1 TraesCS5D01G138200 chr5B 243127323 243131719 4396 False 1240.880000 4578 92.804800 1 3893 5 chr5B.!!$F2 3892
2 TraesCS5D01G138200 chr5A 294240852 294244204 3352 False 1833.000000 4475 95.250000 550 3863 3 chr5A.!!$F2 3313

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
45 46 0.109412 GATTCTCGTTCGTGTCCGGT 60.109 55.000 0.00 0.0 33.95 5.28 F
52 53 0.242825 GTTCGTGTCCGGTGAGATCA 59.757 55.000 0.00 0.0 33.95 2.92 F
62 63 0.452184 GGTGAGATCAAGAGCGTCGA 59.548 55.000 0.00 0.0 0.00 4.20 F
755 764 0.895559 ACTGCAGCCCTAAACCAAGC 60.896 55.000 15.27 0.0 0.00 4.01 F
826 835 1.070786 GCTGTCCCGAAGTGTTCCA 59.929 57.895 0.00 0.0 0.00 3.53 F
1092 1101 1.409802 CCTGGTAGCGAAGGTAGGAGA 60.410 57.143 0.00 0.0 42.96 3.71 F
1366 1375 2.289072 TGTGAGAGGTGCAGAAGTAAGC 60.289 50.000 0.00 0.0 0.00 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1366 1375 1.815003 GCAGGTCAAAGGTGGAATCAG 59.185 52.381 0.00 0.00 0.00 2.90 R
1973 1985 6.019881 AGCTATTGAAACGTGCAAAAAGAAAC 60.020 34.615 15.35 4.61 0.00 2.78 R
2041 2053 6.808212 AGAATTGTCAATCGGCAATAAAACAG 59.192 34.615 0.00 0.00 34.61 3.16 R
2515 2540 4.608514 TGGGAACTGGCAGGGGGA 62.609 66.667 20.34 0.00 0.00 4.81 R
2603 2631 6.724263 TCACACGGCAATATGAATGAATTAC 58.276 36.000 0.00 0.00 0.00 1.89 R
2830 2858 1.919918 CGTTGTGCATTGGTTGTGTT 58.080 45.000 0.00 0.00 0.00 3.32 R
3221 3250 0.179234 TCCAACTGCTGTGAAACCGA 59.821 50.000 0.00 0.00 34.36 4.69 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
33 34 2.215907 AGCTGGATCGTTGATTCTCG 57.784 50.000 0.00 0.00 0.00 4.04
37 38 2.526077 TGGATCGTTGATTCTCGTTCG 58.474 47.619 0.00 0.00 0.00 3.95
38 39 2.094906 TGGATCGTTGATTCTCGTTCGT 60.095 45.455 0.00 0.00 0.00 3.85
39 40 2.279136 GGATCGTTGATTCTCGTTCGTG 59.721 50.000 0.00 0.00 0.00 4.35
40 41 2.410785 TCGTTGATTCTCGTTCGTGT 57.589 45.000 0.00 0.00 0.00 4.49
41 42 2.313234 TCGTTGATTCTCGTTCGTGTC 58.687 47.619 0.00 0.00 0.00 3.67
42 43 1.385743 CGTTGATTCTCGTTCGTGTCC 59.614 52.381 0.00 0.00 0.00 4.02
43 44 1.385743 GTTGATTCTCGTTCGTGTCCG 59.614 52.381 0.00 0.00 0.00 4.79
44 45 0.109458 TGATTCTCGTTCGTGTCCGG 60.109 55.000 0.00 0.00 33.95 5.14
45 46 0.109412 GATTCTCGTTCGTGTCCGGT 60.109 55.000 0.00 0.00 33.95 5.28
46 47 0.388134 ATTCTCGTTCGTGTCCGGTG 60.388 55.000 0.00 0.00 33.95 4.94
47 48 1.446516 TTCTCGTTCGTGTCCGGTGA 61.447 55.000 0.00 0.00 33.95 4.02
48 49 1.442184 CTCGTTCGTGTCCGGTGAG 60.442 63.158 0.00 0.00 33.95 3.51
49 50 1.848932 CTCGTTCGTGTCCGGTGAGA 61.849 60.000 0.00 0.00 32.49 3.27
50 51 1.211969 CGTTCGTGTCCGGTGAGAT 59.788 57.895 0.00 0.00 33.95 2.75
51 52 0.797249 CGTTCGTGTCCGGTGAGATC 60.797 60.000 0.00 0.00 33.95 2.75
52 53 0.242825 GTTCGTGTCCGGTGAGATCA 59.757 55.000 0.00 0.00 33.95 2.92
53 54 0.963225 TTCGTGTCCGGTGAGATCAA 59.037 50.000 0.00 0.00 33.95 2.57
54 55 0.526211 TCGTGTCCGGTGAGATCAAG 59.474 55.000 0.00 0.00 33.95 3.02
55 56 0.526211 CGTGTCCGGTGAGATCAAGA 59.474 55.000 0.00 0.00 0.00 3.02
56 57 1.468224 CGTGTCCGGTGAGATCAAGAG 60.468 57.143 0.00 0.00 0.00 2.85
57 58 0.532573 TGTCCGGTGAGATCAAGAGC 59.467 55.000 0.00 0.00 0.00 4.09
58 59 0.526524 GTCCGGTGAGATCAAGAGCG 60.527 60.000 0.00 0.00 0.00 5.03
59 60 0.965866 TCCGGTGAGATCAAGAGCGT 60.966 55.000 0.00 0.00 0.00 5.07
60 61 0.526524 CCGGTGAGATCAAGAGCGTC 60.527 60.000 0.00 0.00 0.00 5.19
61 62 0.863538 CGGTGAGATCAAGAGCGTCG 60.864 60.000 0.00 0.00 0.00 5.12
62 63 0.452184 GGTGAGATCAAGAGCGTCGA 59.548 55.000 0.00 0.00 0.00 4.20
63 64 1.135373 GGTGAGATCAAGAGCGTCGAA 60.135 52.381 0.00 0.00 0.00 3.71
64 65 1.914700 GTGAGATCAAGAGCGTCGAAC 59.085 52.381 0.00 0.00 0.00 3.95
65 66 1.539827 TGAGATCAAGAGCGTCGAACA 59.460 47.619 0.00 0.00 0.00 3.18
66 67 2.030274 TGAGATCAAGAGCGTCGAACAA 60.030 45.455 0.00 0.00 0.00 2.83
67 68 2.987149 GAGATCAAGAGCGTCGAACAAA 59.013 45.455 0.00 0.00 0.00 2.83
68 69 2.989840 AGATCAAGAGCGTCGAACAAAG 59.010 45.455 0.00 0.00 0.00 2.77
69 70 2.218953 TCAAGAGCGTCGAACAAAGT 57.781 45.000 0.00 0.00 0.00 2.66
70 71 2.546778 TCAAGAGCGTCGAACAAAGTT 58.453 42.857 0.00 0.00 0.00 2.66
71 72 2.933906 TCAAGAGCGTCGAACAAAGTTT 59.066 40.909 0.00 0.00 0.00 2.66
72 73 3.372822 TCAAGAGCGTCGAACAAAGTTTT 59.627 39.130 0.00 0.00 0.00 2.43
73 74 4.095610 CAAGAGCGTCGAACAAAGTTTTT 58.904 39.130 0.00 0.00 0.00 1.94
116 117 2.542766 CGAAAAGCACCGCACATAAT 57.457 45.000 0.00 0.00 0.00 1.28
117 118 3.666883 CGAAAAGCACCGCACATAATA 57.333 42.857 0.00 0.00 0.00 0.98
118 119 4.209452 CGAAAAGCACCGCACATAATAT 57.791 40.909 0.00 0.00 0.00 1.28
119 120 5.337219 CGAAAAGCACCGCACATAATATA 57.663 39.130 0.00 0.00 0.00 0.86
120 121 5.927030 CGAAAAGCACCGCACATAATATAT 58.073 37.500 0.00 0.00 0.00 0.86
121 122 5.790003 CGAAAAGCACCGCACATAATATATG 59.210 40.000 0.00 0.00 0.00 1.78
122 123 6.565811 CGAAAAGCACCGCACATAATATATGT 60.566 38.462 0.00 0.00 0.00 2.29
123 124 5.862924 AAGCACCGCACATAATATATGTC 57.137 39.130 0.15 0.00 0.00 3.06
124 125 4.253685 AGCACCGCACATAATATATGTCC 58.746 43.478 0.15 0.00 0.00 4.02
125 126 3.062099 GCACCGCACATAATATATGTCCG 59.938 47.826 6.81 6.81 33.37 4.79
126 127 4.242475 CACCGCACATAATATATGTCCGT 58.758 43.478 11.55 2.02 31.81 4.69
127 128 4.091365 CACCGCACATAATATATGTCCGTG 59.909 45.833 11.55 8.85 31.81 4.94
128 129 4.242475 CCGCACATAATATATGTCCGTGT 58.758 43.478 11.55 0.00 31.81 4.49
129 130 4.688879 CCGCACATAATATATGTCCGTGTT 59.311 41.667 11.55 0.00 31.81 3.32
130 131 5.865013 CCGCACATAATATATGTCCGTGTTA 59.135 40.000 11.55 0.00 31.81 2.41
131 132 6.533723 CCGCACATAATATATGTCCGTGTTAT 59.466 38.462 11.55 0.00 31.81 1.89
132 133 7.703197 CCGCACATAATATATGTCCGTGTTATA 59.297 37.037 11.55 0.00 31.81 0.98
133 134 9.078753 CGCACATAATATATGTCCGTGTTATAA 57.921 33.333 5.83 0.00 29.40 0.98
145 146 8.780846 TGTCCGTGTTATAATGTAAATTGAGT 57.219 30.769 0.00 0.00 0.00 3.41
146 147 9.872721 TGTCCGTGTTATAATGTAAATTGAGTA 57.127 29.630 0.00 0.00 0.00 2.59
157 158 8.964420 AATGTAAATTGAGTAATTTGTGTCGG 57.036 30.769 7.94 0.00 44.12 4.79
158 159 7.499321 TGTAAATTGAGTAATTTGTGTCGGT 57.501 32.000 7.94 0.00 44.12 4.69
159 160 8.604640 TGTAAATTGAGTAATTTGTGTCGGTA 57.395 30.769 7.94 0.00 44.12 4.02
160 161 8.714179 TGTAAATTGAGTAATTTGTGTCGGTAG 58.286 33.333 7.94 0.00 44.12 3.18
161 162 7.972832 AAATTGAGTAATTTGTGTCGGTAGA 57.027 32.000 0.00 0.00 43.10 2.59
162 163 7.360575 AATTGAGTAATTTGTGTCGGTAGAC 57.639 36.000 0.00 0.00 39.29 2.59
163 164 4.813027 TGAGTAATTTGTGTCGGTAGACC 58.187 43.478 0.00 0.00 46.51 3.85
164 165 4.281435 TGAGTAATTTGTGTCGGTAGACCA 59.719 41.667 0.00 0.00 46.51 4.02
165 166 5.046878 TGAGTAATTTGTGTCGGTAGACCAT 60.047 40.000 0.00 0.00 46.51 3.55
166 167 5.175859 AGTAATTTGTGTCGGTAGACCATG 58.824 41.667 0.00 0.00 46.51 3.66
167 168 3.973206 ATTTGTGTCGGTAGACCATGA 57.027 42.857 0.00 0.00 46.51 3.07
168 169 3.755112 TTTGTGTCGGTAGACCATGAA 57.245 42.857 0.00 0.00 46.51 2.57
169 170 3.755112 TTGTGTCGGTAGACCATGAAA 57.245 42.857 0.00 0.00 46.51 2.69
170 171 3.755112 TGTGTCGGTAGACCATGAAAA 57.245 42.857 0.00 0.00 46.51 2.29
171 172 4.074627 TGTGTCGGTAGACCATGAAAAA 57.925 40.909 0.00 0.00 46.51 1.94
172 173 4.647611 TGTGTCGGTAGACCATGAAAAAT 58.352 39.130 0.00 0.00 46.51 1.82
173 174 5.067273 TGTGTCGGTAGACCATGAAAAATT 58.933 37.500 0.00 0.00 46.51 1.82
174 175 6.231951 TGTGTCGGTAGACCATGAAAAATTA 58.768 36.000 0.00 0.00 46.51 1.40
175 176 6.882140 TGTGTCGGTAGACCATGAAAAATTAT 59.118 34.615 0.00 0.00 46.51 1.28
176 177 7.392113 TGTGTCGGTAGACCATGAAAAATTATT 59.608 33.333 0.00 0.00 46.51 1.40
177 178 7.908601 GTGTCGGTAGACCATGAAAAATTATTC 59.091 37.037 0.00 0.00 46.51 1.75
178 179 7.608376 TGTCGGTAGACCATGAAAAATTATTCA 59.392 33.333 0.00 0.00 46.51 2.57
179 180 8.122952 GTCGGTAGACCATGAAAAATTATTCAG 58.877 37.037 0.00 0.00 40.60 3.02
180 181 7.282224 TCGGTAGACCATGAAAAATTATTCAGG 59.718 37.037 0.00 0.00 42.21 3.86
181 182 7.067008 CGGTAGACCATGAAAAATTATTCAGGT 59.933 37.037 0.00 9.41 42.21 4.00
182 183 8.749354 GGTAGACCATGAAAAATTATTCAGGTT 58.251 33.333 0.00 0.00 42.21 3.50
214 215 9.920133 AAAAGCAAAACAATGTTTTTAATTGGT 57.080 22.222 20.12 12.71 40.46 3.67
215 216 9.566530 AAAGCAAAACAATGTTTTTAATTGGTC 57.433 25.926 20.12 6.17 38.98 4.02
216 217 8.504812 AGCAAAACAATGTTTTTAATTGGTCT 57.495 26.923 20.12 7.94 38.98 3.85
217 218 9.606631 AGCAAAACAATGTTTTTAATTGGTCTA 57.393 25.926 20.12 0.00 38.98 2.59
218 219 9.862585 GCAAAACAATGTTTTTAATTGGTCTAG 57.137 29.630 20.12 6.99 38.98 2.43
247 248 1.484227 TTGTTGCTCGTTCGTGTCCG 61.484 55.000 0.00 0.00 0.00 4.79
307 308 9.667107 TGATCCGGCTAATATAATAAGGAAAAG 57.333 33.333 0.00 0.00 0.00 2.27
324 325 6.003950 AGGAAAAGCACCGCACATAATATAT 58.996 36.000 0.00 0.00 0.00 0.86
326 327 6.293955 GGAAAAGCACCGCACATAATATATGT 60.294 38.462 0.00 0.00 0.00 2.29
327 328 5.862924 AAGCACCGCACATAATATATGTC 57.137 39.130 0.15 0.00 0.00 3.06
328 329 4.253685 AGCACCGCACATAATATATGTCC 58.746 43.478 0.15 0.00 0.00 4.02
361 362 8.964420 AATGTAAATTGAGTAATTTGTGTCGG 57.036 30.769 7.94 0.00 44.12 4.79
371 373 3.973206 ATTTGTGTCGGTAGACCATGA 57.027 42.857 0.00 0.00 46.51 3.07
376 378 4.647611 TGTGTCGGTAGACCATGAAAAAT 58.352 39.130 0.00 0.00 46.51 1.82
463 467 6.555315 TCTCACTTGAGAGCAAAAAGAAAAC 58.445 36.000 4.76 0.00 45.48 2.43
465 469 6.866480 TCACTTGAGAGCAAAAAGAAAACAT 58.134 32.000 0.00 0.00 32.73 2.71
466 470 7.322664 TCACTTGAGAGCAAAAAGAAAACATT 58.677 30.769 0.00 0.00 32.73 2.71
467 471 7.818930 TCACTTGAGAGCAAAAAGAAAACATTT 59.181 29.630 0.00 0.00 32.73 2.32
470 474 9.481800 CTTGAGAGCAAAAAGAAAACATTTTTC 57.518 29.630 3.62 3.62 37.67 2.29
471 475 8.545229 TGAGAGCAAAAAGAAAACATTTTTCA 57.455 26.923 12.63 0.00 37.67 2.69
477 483 9.351570 GCAAAAAGAAAACATTTTTCATTTGGA 57.648 25.926 24.91 0.00 37.67 3.53
542 548 7.305993 GCTGTGAACAAAGAAATTTAAACTCGG 60.306 37.037 0.00 0.00 0.00 4.63
545 551 7.698970 GTGAACAAAGAAATTTAAACTCGGACA 59.301 33.333 0.00 0.00 0.00 4.02
546 552 8.410141 TGAACAAAGAAATTTAAACTCGGACAT 58.590 29.630 0.00 0.00 0.00 3.06
547 553 9.244799 GAACAAAGAAATTTAAACTCGGACATT 57.755 29.630 0.00 0.00 0.00 2.71
633 642 2.957474 ACCAACCACTGTAAATTGCCT 58.043 42.857 0.00 0.00 0.00 4.75
635 644 3.709141 ACCAACCACTGTAAATTGCCTTT 59.291 39.130 0.00 0.00 0.00 3.11
636 645 4.163268 ACCAACCACTGTAAATTGCCTTTT 59.837 37.500 0.00 0.00 0.00 2.27
637 646 5.122519 CCAACCACTGTAAATTGCCTTTTT 58.877 37.500 0.00 0.00 0.00 1.94
656 665 4.966965 TTTTTGAGCGAACCACTGTAAA 57.033 36.364 0.00 0.00 0.00 2.01
657 666 5.508200 TTTTTGAGCGAACCACTGTAAAT 57.492 34.783 0.00 0.00 0.00 1.40
658 667 6.621316 TTTTTGAGCGAACCACTGTAAATA 57.379 33.333 0.00 0.00 0.00 1.40
659 668 6.811253 TTTTGAGCGAACCACTGTAAATAT 57.189 33.333 0.00 0.00 0.00 1.28
660 669 5.794687 TTGAGCGAACCACTGTAAATATG 57.205 39.130 0.00 0.00 0.00 1.78
661 670 3.621268 TGAGCGAACCACTGTAAATATGC 59.379 43.478 0.00 0.00 0.00 3.14
662 671 2.943033 AGCGAACCACTGTAAATATGCC 59.057 45.455 0.00 0.00 0.00 4.40
663 672 2.032924 GCGAACCACTGTAAATATGCCC 59.967 50.000 0.00 0.00 0.00 5.36
664 673 3.541632 CGAACCACTGTAAATATGCCCT 58.458 45.455 0.00 0.00 0.00 5.19
715 724 1.071605 GGCCGCTGATATCAATCGAC 58.928 55.000 21.61 13.81 34.60 4.20
755 764 0.895559 ACTGCAGCCCTAAACCAAGC 60.896 55.000 15.27 0.00 0.00 4.01
759 768 1.327303 CAGCCCTAAACCAAGCACAA 58.673 50.000 0.00 0.00 0.00 3.33
826 835 1.070786 GCTGTCCCGAAGTGTTCCA 59.929 57.895 0.00 0.00 0.00 3.53
1092 1101 1.409802 CCTGGTAGCGAAGGTAGGAGA 60.410 57.143 0.00 0.00 42.96 3.71
1366 1375 2.289072 TGTGAGAGGTGCAGAAGTAAGC 60.289 50.000 0.00 0.00 0.00 3.09
1509 1518 3.328931 AGACTTGAGGAGGCAAAGATTGA 59.671 43.478 0.00 0.00 35.01 2.57
1831 1840 5.635280 CGCACATCCATTCGATAAAGTAGAT 59.365 40.000 0.00 0.00 0.00 1.98
1973 1985 2.828877 TGTTTGTCAGTAGTTCACCCG 58.171 47.619 0.00 0.00 0.00 5.28
2515 2540 3.586174 CCTATGGATCCTGTGGATGATGT 59.414 47.826 14.23 0.00 43.27 3.06
2603 2631 4.259970 GCTGTATGTGTTATCTTGTCTGCG 60.260 45.833 0.00 0.00 0.00 5.18
2830 2858 2.093075 CGTAGTCTACTCTGAGGTCCCA 60.093 54.545 9.85 0.00 0.00 4.37
2862 2890 1.453015 ACAACGCAAGCACCTCCAA 60.453 52.632 0.00 0.00 45.62 3.53
2902 2930 3.526019 ACCAGAGTAGCCTCTAAGACTCT 59.474 47.826 0.00 0.00 46.52 3.24
3038 3067 7.554959 AGTAATTCCAGAACTCTAGAAACCA 57.445 36.000 0.00 0.00 28.17 3.67
3138 3167 7.093992 CCTTAGTTGTCTGCTATAAGATAGCC 58.906 42.308 14.32 2.18 39.69 3.93
3140 3169 5.848406 AGTTGTCTGCTATAAGATAGCCAC 58.152 41.667 14.32 11.52 39.69 5.01
3158 3187 3.307339 GCCACTTGGAGTCAGATTTCTCT 60.307 47.826 0.00 0.00 37.39 3.10
3175 3204 5.730296 TTCTCTTCCTGGTAGAAAGAGTG 57.270 43.478 17.52 2.03 0.00 3.51
3392 3479 3.075641 GTGAGGGAGACGGGGGTC 61.076 72.222 0.00 0.00 0.00 4.46
3410 3497 2.287915 GGTCATAGGCTGTGTAATTGCG 59.712 50.000 11.19 0.00 0.00 4.85
3427 3514 2.029623 TGCGTTGGGATCTACTAGTCC 58.970 52.381 0.00 0.00 0.00 3.85
3492 3579 1.320344 CCCTAGCGGTGCAGACTGTA 61.320 60.000 3.99 0.00 0.00 2.74
3648 3735 2.386249 TGCGCCGACAAACAAAAATAC 58.614 42.857 4.18 0.00 0.00 1.89
3779 3866 2.142292 AACAGCGCTCCCCATTTCCT 62.142 55.000 7.13 0.00 0.00 3.36
3863 4632 7.588497 AGCACATAGTTCATACATAGTCTGA 57.412 36.000 0.00 0.00 0.00 3.27
3893 4662 5.799213 CATAGGGAAGTTCATCATACTCCC 58.201 45.833 5.01 0.00 35.21 4.30
3894 4663 4.014273 AGGGAAGTTCATCATACTCCCT 57.986 45.455 5.01 1.47 37.93 4.20
3895 4664 3.970640 AGGGAAGTTCATCATACTCCCTC 59.029 47.826 5.01 0.00 38.13 4.30
3896 4665 3.071747 GGGAAGTTCATCATACTCCCTCC 59.928 52.174 5.01 0.00 33.66 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 1.385743 CGGACACGAACGAGAATCAAC 59.614 52.381 0.14 0.00 44.60 3.18
28 29 1.008194 CACCGGACACGAACGAGAA 60.008 57.895 9.46 0.00 44.60 2.87
30 31 1.442184 CTCACCGGACACGAACGAG 60.442 63.158 9.46 0.00 44.60 4.18
33 34 0.242825 TGATCTCACCGGACACGAAC 59.757 55.000 9.46 0.00 44.60 3.95
37 38 1.737363 GCTCTTGATCTCACCGGACAC 60.737 57.143 9.46 0.00 0.00 3.67
38 39 0.532573 GCTCTTGATCTCACCGGACA 59.467 55.000 9.46 0.00 0.00 4.02
39 40 0.526524 CGCTCTTGATCTCACCGGAC 60.527 60.000 9.46 0.00 0.00 4.79
40 41 0.965866 ACGCTCTTGATCTCACCGGA 60.966 55.000 9.46 0.00 0.00 5.14
41 42 0.526524 GACGCTCTTGATCTCACCGG 60.527 60.000 0.00 0.00 0.00 5.28
42 43 0.863538 CGACGCTCTTGATCTCACCG 60.864 60.000 0.00 0.00 0.00 4.94
43 44 0.452184 TCGACGCTCTTGATCTCACC 59.548 55.000 0.00 0.00 0.00 4.02
44 45 1.914700 GTTCGACGCTCTTGATCTCAC 59.085 52.381 0.00 0.00 0.00 3.51
45 46 1.539827 TGTTCGACGCTCTTGATCTCA 59.460 47.619 0.00 0.00 0.00 3.27
46 47 2.264109 TGTTCGACGCTCTTGATCTC 57.736 50.000 0.00 0.00 0.00 2.75
47 48 2.724977 TTGTTCGACGCTCTTGATCT 57.275 45.000 0.00 0.00 0.00 2.75
48 49 2.731976 ACTTTGTTCGACGCTCTTGATC 59.268 45.455 0.00 0.00 0.00 2.92
49 50 2.755650 ACTTTGTTCGACGCTCTTGAT 58.244 42.857 0.00 0.00 0.00 2.57
50 51 2.218953 ACTTTGTTCGACGCTCTTGA 57.781 45.000 0.00 0.00 0.00 3.02
51 52 3.319238 AAACTTTGTTCGACGCTCTTG 57.681 42.857 0.00 0.00 0.00 3.02
52 53 4.351131 AAAAACTTTGTTCGACGCTCTT 57.649 36.364 0.00 0.00 0.00 2.85
72 73 9.256477 CGCTATTATATTAGCCGGATCATAAAA 57.744 33.333 5.05 0.00 41.27 1.52
73 74 8.635328 TCGCTATTATATTAGCCGGATCATAAA 58.365 33.333 5.05 0.00 41.27 1.40
74 75 8.173542 TCGCTATTATATTAGCCGGATCATAA 57.826 34.615 5.05 4.63 41.27 1.90
75 76 7.754851 TCGCTATTATATTAGCCGGATCATA 57.245 36.000 5.05 0.00 41.27 2.15
76 77 6.650427 TCGCTATTATATTAGCCGGATCAT 57.350 37.500 5.05 0.00 41.27 2.45
77 78 6.459670 TTCGCTATTATATTAGCCGGATCA 57.540 37.500 5.05 0.00 41.27 2.92
78 79 7.516943 GCTTTTCGCTATTATATTAGCCGGATC 60.517 40.741 5.05 0.00 41.27 3.36
79 80 6.258068 GCTTTTCGCTATTATATTAGCCGGAT 59.742 38.462 5.05 0.00 41.27 4.18
80 81 5.579511 GCTTTTCGCTATTATATTAGCCGGA 59.420 40.000 5.05 9.43 41.27 5.14
81 82 5.350365 TGCTTTTCGCTATTATATTAGCCGG 59.650 40.000 17.03 0.00 41.27 6.13
82 83 6.241385 GTGCTTTTCGCTATTATATTAGCCG 58.759 40.000 17.03 13.17 41.27 5.52
83 84 6.543736 GGTGCTTTTCGCTATTATATTAGCC 58.456 40.000 17.03 6.33 41.27 3.93
84 85 6.241385 CGGTGCTTTTCGCTATTATATTAGC 58.759 40.000 14.13 14.13 40.98 3.09
97 98 2.542766 ATTATGTGCGGTGCTTTTCG 57.457 45.000 0.00 0.00 0.00 3.46
98 99 6.668323 ACATATATTATGTGCGGTGCTTTTC 58.332 36.000 0.00 0.00 0.00 2.29
99 100 6.293955 GGACATATATTATGTGCGGTGCTTTT 60.294 38.462 4.95 0.00 31.12 2.27
100 101 5.181245 GGACATATATTATGTGCGGTGCTTT 59.819 40.000 4.95 0.00 31.12 3.51
101 102 4.695455 GGACATATATTATGTGCGGTGCTT 59.305 41.667 4.95 0.00 31.12 3.91
102 103 4.253685 GGACATATATTATGTGCGGTGCT 58.746 43.478 4.95 0.00 31.12 4.40
103 104 4.600012 GGACATATATTATGTGCGGTGC 57.400 45.455 4.95 0.00 31.12 5.01
119 120 9.391006 ACTCAATTTACATTATAACACGGACAT 57.609 29.630 0.00 0.00 0.00 3.06
120 121 8.780846 ACTCAATTTACATTATAACACGGACA 57.219 30.769 0.00 0.00 0.00 4.02
132 133 8.573035 ACCGACACAAATTACTCAATTTACATT 58.427 29.630 0.00 0.00 41.41 2.71
133 134 8.106247 ACCGACACAAATTACTCAATTTACAT 57.894 30.769 0.00 0.00 41.41 2.29
134 135 7.499321 ACCGACACAAATTACTCAATTTACA 57.501 32.000 0.00 0.00 41.41 2.41
135 136 8.928733 TCTACCGACACAAATTACTCAATTTAC 58.071 33.333 0.00 0.00 41.41 2.01
136 137 8.928733 GTCTACCGACACAAATTACTCAATTTA 58.071 33.333 0.00 0.00 39.59 1.40
137 138 7.094933 GGTCTACCGACACAAATTACTCAATTT 60.095 37.037 0.00 0.00 41.69 1.82
138 139 6.370718 GGTCTACCGACACAAATTACTCAATT 59.629 38.462 0.00 0.00 42.05 2.32
139 140 5.873164 GGTCTACCGACACAAATTACTCAAT 59.127 40.000 0.00 0.00 42.05 2.57
140 141 5.221481 TGGTCTACCGACACAAATTACTCAA 60.221 40.000 0.00 0.00 42.05 3.02
141 142 4.281435 TGGTCTACCGACACAAATTACTCA 59.719 41.667 0.00 0.00 42.05 3.41
142 143 4.813027 TGGTCTACCGACACAAATTACTC 58.187 43.478 0.00 0.00 42.05 2.59
143 144 4.877378 TGGTCTACCGACACAAATTACT 57.123 40.909 0.00 0.00 42.05 2.24
144 145 5.172934 TCATGGTCTACCGACACAAATTAC 58.827 41.667 0.00 0.00 42.05 1.89
145 146 5.408880 TCATGGTCTACCGACACAAATTA 57.591 39.130 0.00 0.00 42.05 1.40
146 147 4.280436 TCATGGTCTACCGACACAAATT 57.720 40.909 0.00 0.00 42.05 1.82
147 148 3.973206 TCATGGTCTACCGACACAAAT 57.027 42.857 0.00 0.00 42.05 2.32
148 149 3.755112 TTCATGGTCTACCGACACAAA 57.245 42.857 0.00 0.00 42.05 2.83
149 150 3.755112 TTTCATGGTCTACCGACACAA 57.245 42.857 0.00 0.00 42.05 3.33
150 151 3.755112 TTTTCATGGTCTACCGACACA 57.245 42.857 0.00 0.00 42.05 3.72
151 152 5.622770 AATTTTTCATGGTCTACCGACAC 57.377 39.130 0.00 0.00 42.05 3.67
152 153 7.608376 TGAATAATTTTTCATGGTCTACCGACA 59.392 33.333 7.18 0.00 35.00 4.35
153 154 7.981142 TGAATAATTTTTCATGGTCTACCGAC 58.019 34.615 7.18 0.00 32.89 4.79
154 155 7.282224 CCTGAATAATTTTTCATGGTCTACCGA 59.718 37.037 11.11 0.00 35.20 4.69
155 156 7.067008 ACCTGAATAATTTTTCATGGTCTACCG 59.933 37.037 18.16 5.14 34.70 4.02
156 157 8.293699 ACCTGAATAATTTTTCATGGTCTACC 57.706 34.615 18.16 0.00 34.70 3.18
188 189 9.920133 ACCAATTAAAAACATTGTTTTGCTTTT 57.080 22.222 24.13 13.00 32.95 2.27
189 190 9.566530 GACCAATTAAAAACATTGTTTTGCTTT 57.433 25.926 24.13 15.67 32.95 3.51
190 191 8.955388 AGACCAATTAAAAACATTGTTTTGCTT 58.045 25.926 24.13 15.82 32.95 3.91
191 192 8.504812 AGACCAATTAAAAACATTGTTTTGCT 57.495 26.923 24.13 14.22 32.95 3.91
192 193 9.862585 CTAGACCAATTAAAAACATTGTTTTGC 57.137 29.630 24.13 9.73 32.95 3.68
221 222 3.849145 CACGAACGAGCAACAAAGAAAAA 59.151 39.130 0.14 0.00 0.00 1.94
222 223 3.120130 ACACGAACGAGCAACAAAGAAAA 60.120 39.130 0.14 0.00 0.00 2.29
223 224 2.417239 ACACGAACGAGCAACAAAGAAA 59.583 40.909 0.14 0.00 0.00 2.52
224 225 2.004017 ACACGAACGAGCAACAAAGAA 58.996 42.857 0.14 0.00 0.00 2.52
225 226 1.591158 GACACGAACGAGCAACAAAGA 59.409 47.619 0.14 0.00 0.00 2.52
226 227 1.332904 GGACACGAACGAGCAACAAAG 60.333 52.381 0.14 0.00 0.00 2.77
227 228 0.653636 GGACACGAACGAGCAACAAA 59.346 50.000 0.14 0.00 0.00 2.83
228 229 1.484227 CGGACACGAACGAGCAACAA 61.484 55.000 0.14 0.00 44.60 2.83
229 230 1.947146 CGGACACGAACGAGCAACA 60.947 57.895 0.14 0.00 44.60 3.33
230 231 2.654912 CCGGACACGAACGAGCAAC 61.655 63.158 0.00 0.00 44.60 4.17
231 232 2.355363 CCGGACACGAACGAGCAA 60.355 61.111 0.00 0.00 44.60 3.91
232 233 3.598715 ACCGGACACGAACGAGCA 61.599 61.111 9.46 0.00 44.60 4.26
233 234 3.103911 CACCGGACACGAACGAGC 61.104 66.667 9.46 0.00 44.60 5.03
234 235 1.442184 CTCACCGGACACGAACGAG 60.442 63.158 9.46 0.00 44.60 4.18
235 236 1.239296 ATCTCACCGGACACGAACGA 61.239 55.000 9.46 0.00 44.60 3.85
236 237 0.797249 GATCTCACCGGACACGAACG 60.797 60.000 9.46 0.00 44.60 3.95
237 238 0.242825 TGATCTCACCGGACACGAAC 59.757 55.000 9.46 0.00 44.60 3.95
238 239 0.963225 TTGATCTCACCGGACACGAA 59.037 50.000 9.46 0.00 44.60 3.85
239 240 0.526211 CTTGATCTCACCGGACACGA 59.474 55.000 9.46 0.00 44.60 4.35
240 241 0.526211 TCTTGATCTCACCGGACACG 59.474 55.000 9.46 0.00 40.55 4.49
241 242 1.737363 GCTCTTGATCTCACCGGACAC 60.737 57.143 9.46 0.00 0.00 3.67
247 248 2.370281 TCAACGCTCTTGATCTCACC 57.630 50.000 0.00 0.00 0.00 4.02
282 283 8.613482 GCTTTTCCTTATTATATTAGCCGGATC 58.387 37.037 5.05 0.00 0.00 3.36
285 286 7.361799 GGTGCTTTTCCTTATTATATTAGCCGG 60.362 40.741 0.00 0.00 0.00 6.13
300 301 1.904287 TTATGTGCGGTGCTTTTCCT 58.096 45.000 0.00 0.00 0.00 3.36
302 303 6.668323 ACATATATTATGTGCGGTGCTTTTC 58.332 36.000 0.00 0.00 0.00 2.29
307 308 4.600012 GGACATATATTATGTGCGGTGC 57.400 45.455 4.95 0.00 31.12 5.01
324 325 8.780846 ACTCAATTTACATTATAACACGGACA 57.219 30.769 0.00 0.00 0.00 4.02
360 361 8.293699 ACCTGAATAATTTTTCATGGTCTACC 57.706 34.615 18.16 0.00 34.70 3.18
426 428 5.647658 TCTCAAGTGAGAGCAACAAAGAAAA 59.352 36.000 6.92 0.00 45.48 2.29
446 450 8.545229 TGAAAAATGTTTTCTTTTTGCTCTCA 57.455 26.923 13.09 0.00 36.28 3.27
500 506 5.119931 TCACAGCTTCGCAAAATATTTGT 57.880 34.783 0.39 0.00 0.00 2.83
507 513 2.929531 TTGTTCACAGCTTCGCAAAA 57.070 40.000 0.00 0.00 0.00 2.44
508 514 2.421775 TCTTTGTTCACAGCTTCGCAAA 59.578 40.909 0.00 0.00 0.00 3.68
517 523 7.913297 TCCGAGTTTAAATTTCTTTGTTCACAG 59.087 33.333 0.00 0.00 0.00 3.66
559 565 6.321181 GGTAAGATAGTGATCCATGGCAAAAA 59.679 38.462 6.96 0.00 31.81 1.94
593 602 9.010029 GGTTGGTAAGATAGTGATTTTTCTCAA 57.990 33.333 0.00 0.00 0.00 3.02
594 603 8.160765 TGGTTGGTAAGATAGTGATTTTTCTCA 58.839 33.333 0.00 0.00 0.00 3.27
595 604 8.451748 GTGGTTGGTAAGATAGTGATTTTTCTC 58.548 37.037 0.00 0.00 0.00 2.87
635 644 4.966965 TTTACAGTGGTTCGCTCAAAAA 57.033 36.364 0.00 0.00 0.00 1.94
636 645 6.607689 CATATTTACAGTGGTTCGCTCAAAA 58.392 36.000 0.00 0.00 0.00 2.44
637 646 5.391523 GCATATTTACAGTGGTTCGCTCAAA 60.392 40.000 0.00 0.00 0.00 2.69
638 647 4.094294 GCATATTTACAGTGGTTCGCTCAA 59.906 41.667 0.00 0.00 0.00 3.02
639 648 3.621268 GCATATTTACAGTGGTTCGCTCA 59.379 43.478 0.00 0.00 0.00 4.26
640 649 3.002348 GGCATATTTACAGTGGTTCGCTC 59.998 47.826 0.00 0.00 0.00 5.03
641 650 2.943033 GGCATATTTACAGTGGTTCGCT 59.057 45.455 0.00 0.00 0.00 4.93
642 651 2.032924 GGGCATATTTACAGTGGTTCGC 59.967 50.000 0.00 0.00 0.00 4.70
643 652 3.312421 CAGGGCATATTTACAGTGGTTCG 59.688 47.826 0.00 0.00 0.00 3.95
644 653 4.096382 CACAGGGCATATTTACAGTGGTTC 59.904 45.833 0.00 0.00 0.00 3.62
645 654 4.016444 CACAGGGCATATTTACAGTGGTT 58.984 43.478 0.00 0.00 0.00 3.67
646 655 3.620488 CACAGGGCATATTTACAGTGGT 58.380 45.455 0.00 0.00 0.00 4.16
647 656 2.358898 GCACAGGGCATATTTACAGTGG 59.641 50.000 0.00 0.00 43.97 4.00
648 657 3.698029 GCACAGGGCATATTTACAGTG 57.302 47.619 0.00 0.00 43.97 3.66
660 669 2.359230 GACCAGAGTGCACAGGGC 60.359 66.667 21.04 16.16 45.13 5.19
661 670 2.047844 CGACCAGAGTGCACAGGG 60.048 66.667 21.04 18.60 0.00 4.45
662 671 1.892819 ATCCGACCAGAGTGCACAGG 61.893 60.000 21.04 19.27 0.00 4.00
663 672 0.459237 GATCCGACCAGAGTGCACAG 60.459 60.000 21.04 8.31 0.00 3.66
664 673 1.591703 GATCCGACCAGAGTGCACA 59.408 57.895 21.04 0.00 0.00 4.57
715 724 2.519302 GCCGTTGGATCCCATGGG 60.519 66.667 26.30 26.30 32.26 4.00
755 764 1.588674 TGGGTTCTGTTAGCGTTGTG 58.411 50.000 0.00 0.00 0.00 3.33
759 768 1.226030 GCGTTGGGTTCTGTTAGCGT 61.226 55.000 0.00 0.00 0.00 5.07
763 772 1.001633 GAGAGGCGTTGGGTTCTGTTA 59.998 52.381 0.00 0.00 0.00 2.41
1366 1375 1.815003 GCAGGTCAAAGGTGGAATCAG 59.185 52.381 0.00 0.00 0.00 2.90
1509 1518 7.125356 TGCAGCATCTATAGGATATGACTTCAT 59.875 37.037 0.00 0.00 40.22 2.57
1831 1840 6.990349 GTGTTACCTTCATAGCCTGCTTAATA 59.010 38.462 0.00 0.00 0.00 0.98
1973 1985 6.019881 AGCTATTGAAACGTGCAAAAAGAAAC 60.020 34.615 15.35 4.61 0.00 2.78
2041 2053 6.808212 AGAATTGTCAATCGGCAATAAAACAG 59.192 34.615 0.00 0.00 34.61 3.16
2515 2540 4.608514 TGGGAACTGGCAGGGGGA 62.609 66.667 20.34 0.00 0.00 4.81
2603 2631 6.724263 TCACACGGCAATATGAATGAATTAC 58.276 36.000 0.00 0.00 0.00 1.89
2830 2858 1.919918 CGTTGTGCATTGGTTGTGTT 58.080 45.000 0.00 0.00 0.00 3.32
2862 2890 1.995066 TGATCAGATGGCCGGGTGT 60.995 57.895 2.18 0.00 0.00 4.16
2902 2930 7.109232 GCTGTAGCAATCACATTTGGTGCTA 62.109 44.000 11.73 11.73 43.31 3.49
3138 3167 4.934602 GGAAGAGAAATCTGACTCCAAGTG 59.065 45.833 0.00 0.00 34.13 3.16
3140 3169 5.177326 CAGGAAGAGAAATCTGACTCCAAG 58.823 45.833 0.00 0.00 34.13 3.61
3158 3187 5.551233 CATTGTCACTCTTTCTACCAGGAA 58.449 41.667 0.00 0.00 0.00 3.36
3217 3246 0.532862 ACTGCTGTGAAACCGACTGG 60.533 55.000 0.00 0.00 42.84 4.00
3221 3250 0.179234 TCCAACTGCTGTGAAACCGA 59.821 50.000 0.00 0.00 34.36 4.69
3392 3479 3.487376 CCAACGCAATTACACAGCCTATG 60.487 47.826 0.00 0.00 0.00 2.23
3410 3497 2.966516 CCCTGGACTAGTAGATCCCAAC 59.033 54.545 3.59 0.00 33.69 3.77
3427 3514 6.257630 CCTAAAACAACAAACAATGAACCCTG 59.742 38.462 0.00 0.00 0.00 4.45
3560 3647 5.636121 ACGAAATTAGATGCGTGTTTGAGTA 59.364 36.000 0.00 0.00 35.44 2.59
3562 3649 4.783036 CACGAAATTAGATGCGTGTTTGAG 59.217 41.667 0.00 0.00 46.28 3.02
3581 3668 7.434307 TGTTTTCTTTAACACAAAACAACACGA 59.566 29.630 12.75 0.00 43.58 4.35
3779 3866 6.477253 TGCTTGTGTATGTATTTGAGGGTTA 58.523 36.000 0.00 0.00 0.00 2.85
3863 4632 6.753913 TGATGAACTTCCCTATGCTATCTT 57.246 37.500 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.