Multiple sequence alignment - TraesCS4B01G077800

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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 TraesCS4B01G077800 chr4B 100.000 3885 0 0 1 3885 74684169 74680285 0.000000e+00 7175.0
1 TraesCS4B01G077800 chr4D 91.312 3637 153 72 321 3860 50772600 50769030 0.000000e+00 4815.0
2 TraesCS4B01G077800 chr4D 88.806 134 5 4 54 187 50775469 50775346 5.200000e-34 156.0
3 TraesCS4B01G077800 chr4D 100.000 31 0 0 1 31 50775504 50775474 1.510000e-04 58.4
4 TraesCS4B01G077800 chr4A 90.103 3698 187 77 276 3885 546209424 546213030 0.000000e+00 4636.0
5 TraesCS4B01G077800 chr4A 91.275 149 4 6 39 185 546209261 546209402 1.100000e-45 195.0
6 TraesCS4B01G077800 chr4A 91.892 74 4 2 171 243 652852223 652852295 6.870000e-18 102.0
7 TraesCS4B01G077800 chr4A 94.231 52 1 2 3 54 546209196 546209245 1.160000e-10 78.7
8 TraesCS4B01G077800 chr5D 85.135 592 80 4 2263 2850 89381395 89381982 2.000000e-167 599.0
9 TraesCS4B01G077800 chr5D 83.989 356 53 4 1808 2161 89380935 89381288 4.810000e-89 339.0
10 TraesCS4B01G077800 chr5D 77.904 439 72 20 993 1414 89379990 89380420 2.320000e-62 250.0
11 TraesCS4B01G077800 chr5A 84.641 599 84 6 2256 2850 83277858 83278452 1.200000e-164 590.0
12 TraesCS4B01G077800 chr5A 83.146 356 56 4 1808 2161 83277404 83277757 4.840000e-84 322.0
13 TraesCS4B01G077800 chr5A 77.500 440 72 22 993 1414 83276469 83276899 5.020000e-59 239.0
14 TraesCS4B01G077800 chr5B 84.797 592 82 4 2263 2850 94676973 94676386 4.320000e-164 588.0
15 TraesCS4B01G077800 chr5B 82.730 359 58 4 1808 2164 94677444 94677088 2.250000e-82 316.0
16 TraesCS4B01G077800 chr5B 91.667 72 6 0 180 251 706851755 706851826 2.470000e-17 100.0
17 TraesCS4B01G077800 chr2D 81.674 442 77 4 2304 2743 136832834 136833273 7.930000e-97 364.0
18 TraesCS4B01G077800 chr2D 91.139 79 4 3 191 266 562685744 562685666 1.910000e-18 104.0
19 TraesCS4B01G077800 chr2D 78.846 156 20 11 1205 1348 136832035 136832189 4.130000e-15 93.5
20 TraesCS4B01G077800 chr2A 81.336 434 77 4 2307 2738 164704329 164703898 2.220000e-92 350.0
21 TraesCS4B01G077800 chr2A 77.112 367 68 9 1808 2160 164704823 164704459 8.510000e-47 198.0
22 TraesCS4B01G077800 chr2A 81.308 107 18 2 1303 1408 164705024 164704919 6.920000e-13 86.1
23 TraesCS4B01G077800 chr3A 94.521 73 4 0 179 251 227483588 227483660 3.170000e-21 113.0
24 TraesCS4B01G077800 chr1B 90.909 77 6 1 185 261 472926077 472926002 6.870000e-18 102.0
25 TraesCS4B01G077800 chr2B 87.952 83 10 0 184 266 183932335 183932253 8.880000e-17 99.0
26 TraesCS4B01G077800 chr2B 81.308 107 18 2 1303 1408 195529767 195529872 6.920000e-13 86.1
27 TraesCS4B01G077800 chrUn 87.500 88 6 4 166 251 85071736 85071820 3.200000e-16 97.1
28 TraesCS4B01G077800 chr7B 87.805 82 8 2 186 266 409921388 409921308 1.150000e-15 95.3
29 TraesCS4B01G077800 chr6B 85.882 85 12 0 186 270 199745204 199745288 1.490000e-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 TraesCS4B01G077800 chr4B 74680285 74684169 3884 True 7175.000000 7175 100.000000 1 3885 1 chr4B.!!$R1 3884
1 TraesCS4B01G077800 chr4D 50769030 50775504 6474 True 1676.466667 4815 93.372667 1 3860 3 chr4D.!!$R1 3859
2 TraesCS4B01G077800 chr4A 546209196 546213030 3834 False 1636.566667 4636 91.869667 3 3885 3 chr4A.!!$F2 3882
3 TraesCS4B01G077800 chr5D 89379990 89381982 1992 False 396.000000 599 82.342667 993 2850 3 chr5D.!!$F1 1857
4 TraesCS4B01G077800 chr5A 83276469 83278452 1983 False 383.666667 590 81.762333 993 2850 3 chr5A.!!$F1 1857
5 TraesCS4B01G077800 chr5B 94676386 94677444 1058 True 452.000000 588 83.763500 1808 2850 2 chr5B.!!$R1 1042
6 TraesCS4B01G077800 chr2D 136832035 136833273 1238 False 228.750000 364 80.260000 1205 2743 2 chr2D.!!$F1 1538
7 TraesCS4B01G077800 chr2A 164703898 164705024 1126 True 211.366667 350 79.918667 1303 2738 3 chr2A.!!$R1 1435

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
268 300 0.033796 TTCGGATGGAGGGAGTACGT 60.034 55.000 0.00 0.00 0.0 3.57 F
703 3455 0.040646 TTAACTGAGCTCGGGGAGGA 59.959 55.000 26.07 5.02 0.0 3.71 F
1005 3788 0.320683 CACGCTCACTGTCCATGGAA 60.321 55.000 18.20 6.23 0.0 3.53 F
1665 4516 1.446792 CTTCGCCGATGTCTGCTGT 60.447 57.895 0.00 0.00 0.0 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1395 4217 1.332144 AAGCGCTTACGATGGGGGTA 61.332 55.0 23.72 0.0 43.93 3.69 R
2317 5593 1.192146 CCCCGTTCACCTTCCTCTCA 61.192 60.0 0.00 0.0 0.00 3.27 R
2467 5743 1.806461 GCGTCAGGTGTGAGTCCTCA 61.806 60.0 0.00 0.0 37.24 3.86 R
3015 6296 0.963856 TGCCTCATGCTGCTTCCTTG 60.964 55.0 0.00 0.0 42.00 3.61 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
37 38 3.393609 CTCCCACCTAACCTAATAACCCC 59.606 52.174 0.00 0.00 0.00 4.95
39 40 3.528491 CCCACCTAACCTAATAACCCCAA 59.472 47.826 0.00 0.00 0.00 4.12
42 43 3.528905 ACCTAACCTAATAACCCCAACCC 59.471 47.826 0.00 0.00 0.00 4.11
43 44 2.812836 AACCTAATAACCCCAACCCG 57.187 50.000 0.00 0.00 0.00 5.28
44 45 1.969713 ACCTAATAACCCCAACCCGA 58.030 50.000 0.00 0.00 0.00 5.14
45 46 1.841919 ACCTAATAACCCCAACCCGAG 59.158 52.381 0.00 0.00 0.00 4.63
46 47 1.841919 CCTAATAACCCCAACCCGAGT 59.158 52.381 0.00 0.00 0.00 4.18
111 143 1.151668 GACCCTACATCATCATGCGC 58.848 55.000 0.00 0.00 32.57 6.09
132 164 1.541233 GCGATTACCATCCACCCTCAG 60.541 57.143 0.00 0.00 0.00 3.35
133 165 1.541233 CGATTACCATCCACCCTCAGC 60.541 57.143 0.00 0.00 0.00 4.26
134 166 1.490490 GATTACCATCCACCCTCAGCA 59.510 52.381 0.00 0.00 0.00 4.41
135 167 1.595311 TTACCATCCACCCTCAGCAT 58.405 50.000 0.00 0.00 0.00 3.79
136 168 1.131638 TACCATCCACCCTCAGCATC 58.868 55.000 0.00 0.00 0.00 3.91
137 169 0.915872 ACCATCCACCCTCAGCATCA 60.916 55.000 0.00 0.00 0.00 3.07
141 173 0.915872 TCCACCCTCAGCATCACCAT 60.916 55.000 0.00 0.00 0.00 3.55
143 175 0.465097 CACCCTCAGCATCACCATCC 60.465 60.000 0.00 0.00 0.00 3.51
168 200 6.202937 CCAACAACAACAAAAGCGACTAATA 58.797 36.000 0.00 0.00 0.00 0.98
196 228 7.865706 ATCAGCAAAATAATACTTCCTTCGT 57.134 32.000 0.00 0.00 0.00 3.85
198 230 7.103641 TCAGCAAAATAATACTTCCTTCGTCT 58.896 34.615 0.00 0.00 0.00 4.18
199 231 7.064609 TCAGCAAAATAATACTTCCTTCGTCTG 59.935 37.037 0.00 0.00 0.00 3.51
200 232 7.064609 CAGCAAAATAATACTTCCTTCGTCTGA 59.935 37.037 0.00 0.00 0.00 3.27
201 233 7.606456 AGCAAAATAATACTTCCTTCGTCTGAA 59.394 33.333 0.00 0.00 0.00 3.02
202 234 8.234546 GCAAAATAATACTTCCTTCGTCTGAAA 58.765 33.333 0.00 0.00 32.66 2.69
209 241 6.787085 ACTTCCTTCGTCTGAAAATACTTG 57.213 37.500 0.00 0.00 32.66 3.16
210 242 6.289064 ACTTCCTTCGTCTGAAAATACTTGT 58.711 36.000 0.00 0.00 32.66 3.16
211 243 6.424207 ACTTCCTTCGTCTGAAAATACTTGTC 59.576 38.462 0.00 0.00 32.66 3.18
212 244 5.849510 TCCTTCGTCTGAAAATACTTGTCA 58.150 37.500 0.00 0.00 32.66 3.58
213 245 6.464222 TCCTTCGTCTGAAAATACTTGTCAT 58.536 36.000 0.00 0.00 32.66 3.06
214 246 6.590292 TCCTTCGTCTGAAAATACTTGTCATC 59.410 38.462 0.00 0.00 32.66 2.92
215 247 6.368791 CCTTCGTCTGAAAATACTTGTCATCA 59.631 38.462 0.00 0.00 32.66 3.07
216 248 7.095229 CCTTCGTCTGAAAATACTTGTCATCAA 60.095 37.037 0.00 0.00 32.66 2.57
217 249 7.722795 TCGTCTGAAAATACTTGTCATCAAA 57.277 32.000 0.00 0.00 32.87 2.69
218 250 8.148807 TCGTCTGAAAATACTTGTCATCAAAA 57.851 30.769 0.00 0.00 32.87 2.44
219 251 8.783093 TCGTCTGAAAATACTTGTCATCAAAAT 58.217 29.630 0.00 0.00 32.87 1.82
220 252 8.843733 CGTCTGAAAATACTTGTCATCAAAATG 58.156 33.333 0.00 0.00 32.87 2.32
221 253 9.132521 GTCTGAAAATACTTGTCATCAAAATGG 57.867 33.333 0.00 0.00 33.42 3.16
222 254 9.076781 TCTGAAAATACTTGTCATCAAAATGGA 57.923 29.630 0.00 0.00 33.42 3.41
223 255 9.865321 CTGAAAATACTTGTCATCAAAATGGAT 57.135 29.630 0.00 0.00 33.42 3.41
231 263 9.918630 ACTTGTCATCAAAATGGATAAAAGAAG 57.081 29.630 0.00 0.00 33.42 2.85
262 294 8.444010 TCTAAATATATTTTCGGATGGAGGGA 57.556 34.615 15.64 0.00 0.00 4.20
263 295 8.540388 TCTAAATATATTTTCGGATGGAGGGAG 58.460 37.037 15.64 3.30 0.00 4.30
264 296 6.704056 AATATATTTTCGGATGGAGGGAGT 57.296 37.500 0.00 0.00 0.00 3.85
265 297 7.808279 AATATATTTTCGGATGGAGGGAGTA 57.192 36.000 0.00 0.00 0.00 2.59
266 298 3.840124 ATTTTCGGATGGAGGGAGTAC 57.160 47.619 0.00 0.00 0.00 2.73
267 299 1.108776 TTTCGGATGGAGGGAGTACG 58.891 55.000 0.00 0.00 0.00 3.67
268 300 0.033796 TTCGGATGGAGGGAGTACGT 60.034 55.000 0.00 0.00 0.00 3.57
269 301 0.839277 TCGGATGGAGGGAGTACGTA 59.161 55.000 0.00 0.00 0.00 3.57
270 302 1.212688 TCGGATGGAGGGAGTACGTAA 59.787 52.381 0.00 0.00 0.00 3.18
272 304 2.747467 CGGATGGAGGGAGTACGTAAGA 60.747 54.545 0.00 0.00 43.62 2.10
273 305 3.294214 GGATGGAGGGAGTACGTAAGAA 58.706 50.000 0.00 0.00 43.62 2.52
274 306 3.703052 GGATGGAGGGAGTACGTAAGAAA 59.297 47.826 0.00 0.00 43.62 2.52
281 313 4.101430 AGGGAGTACGTAAGAAAAACCACA 59.899 41.667 0.00 0.00 43.62 4.17
284 316 5.525012 GGAGTACGTAAGAAAAACCACAAGT 59.475 40.000 0.00 0.00 43.62 3.16
287 319 8.491331 AGTACGTAAGAAAAACCACAAGTAAA 57.509 30.769 0.00 0.00 43.62 2.01
310 342 2.406024 CGCTTGCTTACGAACGAACTAA 59.594 45.455 0.14 0.00 0.00 2.24
317 349 4.143452 GCTTACGAACGAACTAAACACTCC 60.143 45.833 0.14 0.00 0.00 3.85
349 3070 4.502016 CATCTCCCAAGATACGATGGATG 58.498 47.826 0.00 0.00 40.38 3.51
350 3071 3.576861 TCTCCCAAGATACGATGGATGT 58.423 45.455 0.00 0.00 39.12 3.06
379 3101 1.003233 GTTTCTCCAGGAAGCGGCT 60.003 57.895 0.00 0.00 35.16 5.52
450 3172 2.368548 ACATTGCACGGCATAGATAGGA 59.631 45.455 0.00 0.00 38.76 2.94
451 3173 3.008375 ACATTGCACGGCATAGATAGGAT 59.992 43.478 0.00 0.00 38.76 3.24
452 3174 4.222810 ACATTGCACGGCATAGATAGGATA 59.777 41.667 0.00 0.00 38.76 2.59
454 3176 2.166459 TGCACGGCATAGATAGGATAGC 59.834 50.000 0.00 0.00 31.71 2.97
455 3177 2.166459 GCACGGCATAGATAGGATAGCA 59.834 50.000 0.00 0.00 0.00 3.49
456 3178 3.181471 GCACGGCATAGATAGGATAGCAT 60.181 47.826 0.00 0.00 0.00 3.79
457 3179 4.038042 GCACGGCATAGATAGGATAGCATA 59.962 45.833 0.00 0.00 0.00 3.14
458 3180 5.767269 CACGGCATAGATAGGATAGCATAG 58.233 45.833 0.00 0.00 0.00 2.23
459 3181 4.830046 ACGGCATAGATAGGATAGCATAGG 59.170 45.833 0.00 0.00 0.00 2.57
460 3182 4.830046 CGGCATAGATAGGATAGCATAGGT 59.170 45.833 0.00 0.00 0.00 3.08
461 3183 6.004574 CGGCATAGATAGGATAGCATAGGTA 58.995 44.000 0.00 0.00 0.00 3.08
476 3198 0.107654 AGGTAAGATGCCTCCAACGC 60.108 55.000 0.00 0.00 0.00 4.84
501 3233 2.807045 GCTGTGGCTCACGAGTCG 60.807 66.667 11.85 11.85 37.14 4.18
502 3234 2.807045 CTGTGGCTCACGAGTCGC 60.807 66.667 13.59 5.27 43.36 5.19
503 3235 4.700365 TGTGGCTCACGAGTCGCG 62.700 66.667 13.59 2.58 45.81 5.87
554 3287 2.637025 GCAAGCGTCCAAAGCGAA 59.363 55.556 0.00 0.00 40.04 4.70
555 3288 1.441016 GCAAGCGTCCAAAGCGAAG 60.441 57.895 0.00 0.00 40.04 3.79
569 3321 1.497722 CGAAGCAAAGAGGCGAACC 59.502 57.895 0.00 0.00 39.27 3.62
570 3322 1.227999 CGAAGCAAAGAGGCGAACCA 61.228 55.000 0.00 0.00 39.06 3.67
574 3326 1.782028 GCAAAGAGGCGAACCACGTT 61.782 55.000 0.00 0.00 44.60 3.99
576 3328 1.782028 AAAGAGGCGAACCACGTTGC 61.782 55.000 0.00 0.00 44.60 4.17
594 3346 3.141488 CCGTCCCTCGCTACAGCT 61.141 66.667 0.00 0.00 39.32 4.24
601 3353 0.387202 CCTCGCTACAGCTATGCAGT 59.613 55.000 0.00 0.00 39.32 4.40
653 3405 1.810441 CGGAAGAGAGCAGCAGCAG 60.810 63.158 3.17 0.00 45.49 4.24
669 3421 2.219674 CAGCAGACGAACAGAAAGTCAC 59.780 50.000 0.00 0.00 37.36 3.67
698 3450 1.084370 CCGCTTTAACTGAGCTCGGG 61.084 60.000 26.07 15.30 37.99 5.14
700 3452 0.249398 GCTTTAACTGAGCTCGGGGA 59.751 55.000 26.07 10.84 37.18 4.81
702 3454 0.902531 TTTAACTGAGCTCGGGGAGG 59.097 55.000 26.07 6.33 0.00 4.30
703 3455 0.040646 TTAACTGAGCTCGGGGAGGA 59.959 55.000 26.07 5.02 0.00 3.71
767 3534 4.695231 CGTCCGGTCGTCACGCTT 62.695 66.667 13.16 0.00 0.00 4.68
768 3535 3.103911 GTCCGGTCGTCACGCTTG 61.104 66.667 0.00 0.00 0.00 4.01
770 3537 3.403057 CCGGTCGTCACGCTTGTG 61.403 66.667 0.00 0.00 45.26 3.33
778 3545 4.893241 CACGCTTGTGAACCGAAC 57.107 55.556 0.00 0.00 46.91 3.95
779 3546 1.278637 CACGCTTGTGAACCGAACC 59.721 57.895 0.00 0.00 46.91 3.62
869 3643 2.042831 AGTCCAGCTTGCATTCCGC 61.043 57.895 0.00 0.00 42.89 5.54
933 3708 2.217847 CACACCTCCGTATAAATTCGCG 59.782 50.000 0.00 0.00 0.00 5.87
941 3716 2.346924 CGTATAAATTCGCGAACCACCG 60.347 50.000 26.00 16.94 0.00 4.94
1005 3788 0.320683 CACGCTCACTGTCCATGGAA 60.321 55.000 18.20 6.23 0.00 3.53
1395 4217 1.475751 CCGCACCTCAGCATTAAGGAT 60.476 52.381 0.00 0.00 36.46 3.24
1436 4267 4.349365 TCCTCTTCTTCTCCTTCTTCCTC 58.651 47.826 0.00 0.00 0.00 3.71
1437 4268 4.093011 CCTCTTCTTCTCCTTCTTCCTCA 58.907 47.826 0.00 0.00 0.00 3.86
1529 4379 2.416547 ACGAAATGCTCCAGTCAAATCG 59.583 45.455 0.00 0.00 34.20 3.34
1601 4451 6.808212 GTCCTGCATACTGTAAAAACGTAGTA 59.192 38.462 0.00 0.00 45.00 1.82
1602 4452 7.008992 GTCCTGCATACTGTAAAAACGTAGTAG 59.991 40.741 0.00 0.00 45.00 2.57
1603 4453 6.810182 CCTGCATACTGTAAAAACGTAGTAGT 59.190 38.462 0.00 0.00 45.00 2.73
1653 4504 6.685527 AAAATTCTCCTTATCTTCTTCGCC 57.314 37.500 0.00 0.00 0.00 5.54
1665 4516 1.446792 CTTCGCCGATGTCTGCTGT 60.447 57.895 0.00 0.00 0.00 4.40
2034 5283 3.427573 TCCTGAGAAGTGGTACATCGAA 58.572 45.455 0.00 0.00 44.52 3.71
2239 5493 4.761739 TGGAATCTTGGCACTTTTACTCAG 59.238 41.667 0.00 0.00 0.00 3.35
2246 5500 6.321181 TCTTGGCACTTTTACTCAGATGTTTT 59.679 34.615 0.00 0.00 0.00 2.43
2467 5743 0.609131 CCGGCCTTCTTGTCCACATT 60.609 55.000 0.00 0.00 0.00 2.71
2874 6150 0.396060 GAGCTAGCATGGAGGGGAAG 59.604 60.000 18.83 0.00 0.00 3.46
2881 6157 1.143813 CATGGAGGGGAAGCCATACT 58.856 55.000 0.00 0.00 42.81 2.12
2886 6162 2.175715 GGAGGGGAAGCCATACTTGAAT 59.824 50.000 0.00 0.00 39.29 2.57
2928 6204 4.795278 GCCATTGATACTTGCTTCTTTTCG 59.205 41.667 0.00 0.00 0.00 3.46
3012 6289 6.378280 GGAAATTCCAAATGACCTCTGTGTAT 59.622 38.462 7.23 0.00 36.28 2.29
3015 6296 5.023533 TCCAAATGACCTCTGTGTATAGC 57.976 43.478 0.00 0.00 0.00 2.97
3152 6433 3.047877 GACTTGGTGCGTTCCCCG 61.048 66.667 0.00 0.00 40.40 5.73
3194 6480 3.582120 CGTGGTGGCGCTGTTTGT 61.582 61.111 7.64 0.00 0.00 2.83
3232 6518 5.179452 ACTAATTGGTCAGTGGCATTACT 57.821 39.130 0.00 0.00 0.00 2.24
3269 6581 1.134946 GTTTGCTGTGCTTGGTGAAGT 59.865 47.619 0.00 0.00 0.00 3.01
3275 6587 3.214328 CTGTGCTTGGTGAAGTTAACCT 58.786 45.455 10.93 0.00 38.60 3.50
3287 6599 6.049790 GTGAAGTTAACCTTGTCAGAGAAGT 58.950 40.000 6.57 0.00 32.03 3.01
3298 6610 5.201713 TGTCAGAGAAGTGTAACCTCTTG 57.798 43.478 0.00 0.00 37.86 3.02
3319 6631 1.547372 TGAACGGCTGTTAGTACCTCC 59.453 52.381 11.80 0.00 38.78 4.30
3427 6744 6.045955 GCTTTGTTTGTTTCCTTGTAATCCA 58.954 36.000 0.00 0.00 0.00 3.41
3527 6849 5.529581 TTTTTCCTTGGAGATGTTGAACC 57.470 39.130 0.00 0.00 0.00 3.62
3530 6852 0.443869 CTTGGAGATGTTGAACCGCG 59.556 55.000 0.00 0.00 0.00 6.46
3535 6857 1.154225 GATGTTGAACCGCGGCAAG 60.154 57.895 28.58 0.59 0.00 4.01
3536 6858 3.267597 ATGTTGAACCGCGGCAAGC 62.268 57.895 28.58 13.69 43.95 4.01
3590 6912 1.994916 CATTTTACTTTGGCCTGCCG 58.005 50.000 3.32 0.00 39.42 5.69
3615 6937 3.452627 GTGTTGGAGGGAGTAGTGATGAT 59.547 47.826 0.00 0.00 0.00 2.45
3621 6943 5.163269 TGGAGGGAGTAGTGATGATTTCATG 60.163 44.000 0.00 0.00 36.54 3.07
3755 7078 0.108424 CTGTACTCCTGAGCAGCACC 60.108 60.000 0.00 0.00 0.00 5.01
3762 7085 1.217511 CTGAGCAGCACCGATGAGT 59.782 57.895 0.00 0.00 0.00 3.41
3793 7117 4.684242 GCCTTTATTTTTCTTTCGGTGTGG 59.316 41.667 0.00 0.00 0.00 4.17
3795 7119 5.689961 CCTTTATTTTTCTTTCGGTGTGGTG 59.310 40.000 0.00 0.00 0.00 4.17
3796 7120 6.452494 TTTATTTTTCTTTCGGTGTGGTGA 57.548 33.333 0.00 0.00 0.00 4.02
3798 7122 4.364415 TTTTTCTTTCGGTGTGGTGAAG 57.636 40.909 0.00 0.00 0.00 3.02
3799 7123 2.992124 TTCTTTCGGTGTGGTGAAGA 57.008 45.000 0.00 0.00 0.00 2.87
3801 7125 1.760613 TCTTTCGGTGTGGTGAAGACT 59.239 47.619 0.00 0.00 0.00 3.24
3802 7126 1.867233 CTTTCGGTGTGGTGAAGACTG 59.133 52.381 0.00 0.00 0.00 3.51
3803 7127 1.116308 TTCGGTGTGGTGAAGACTGA 58.884 50.000 0.00 0.00 35.71 3.41
3804 7128 1.338107 TCGGTGTGGTGAAGACTGAT 58.662 50.000 0.00 0.00 32.67 2.90
3810 7146 0.615331 TGGTGAAGACTGATGAGGCC 59.385 55.000 0.00 0.00 0.00 5.19
3821 7157 3.797331 TGAGGCCTCACTCACTGG 58.203 61.111 32.00 0.00 42.26 4.00
3822 7158 2.267324 GAGGCCTCACTCACTGGC 59.733 66.667 28.43 0.00 45.42 4.85
3825 7161 2.673523 GCCTCACTCACTGGCCAT 59.326 61.111 5.51 0.00 40.71 4.40
3826 7162 1.748122 GCCTCACTCACTGGCCATG 60.748 63.158 5.51 7.41 40.71 3.66
3827 7163 1.077930 CCTCACTCACTGGCCATGG 60.078 63.158 5.51 7.63 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 5.669477 ACTCTACTACTACTACTCGGGTTG 58.331 45.833 0.00 0.00 0.00 3.77
39 40 6.369629 TCTACTCTACTACTACTACTCGGGT 58.630 44.000 0.00 0.00 0.00 5.28
42 43 8.109705 TGGATCTACTCTACTACTACTACTCG 57.890 42.308 0.00 0.00 0.00 4.18
43 44 9.918630 CTTGGATCTACTCTACTACTACTACTC 57.081 40.741 0.00 0.00 0.00 2.59
44 45 9.659135 TCTTGGATCTACTCTACTACTACTACT 57.341 37.037 0.00 0.00 0.00 2.57
111 143 0.600255 GAGGGTGGATGGTAATCGCG 60.600 60.000 0.00 0.00 33.18 5.87
132 164 0.532115 GTTGTTGGGGATGGTGATGC 59.468 55.000 0.00 0.00 0.00 3.91
133 165 1.921982 TGTTGTTGGGGATGGTGATG 58.078 50.000 0.00 0.00 0.00 3.07
134 166 2.247358 GTTGTTGTTGGGGATGGTGAT 58.753 47.619 0.00 0.00 0.00 3.06
135 167 1.063642 TGTTGTTGTTGGGGATGGTGA 60.064 47.619 0.00 0.00 0.00 4.02
136 168 1.407936 TGTTGTTGTTGGGGATGGTG 58.592 50.000 0.00 0.00 0.00 4.17
137 169 2.166907 TTGTTGTTGTTGGGGATGGT 57.833 45.000 0.00 0.00 0.00 3.55
141 173 1.134965 CGCTTTTGTTGTTGTTGGGGA 60.135 47.619 0.00 0.00 0.00 4.81
143 175 1.923864 GTCGCTTTTGTTGTTGTTGGG 59.076 47.619 0.00 0.00 0.00 4.12
173 205 7.064609 CAGACGAAGGAAGTATTATTTTGCTGA 59.935 37.037 0.00 0.00 0.00 4.26
185 217 7.439381 ACAAGTATTTTCAGACGAAGGAAGTA 58.561 34.615 0.00 0.00 31.28 2.24
187 219 6.423905 TGACAAGTATTTTCAGACGAAGGAAG 59.576 38.462 0.00 0.00 31.28 3.46
188 220 6.285224 TGACAAGTATTTTCAGACGAAGGAA 58.715 36.000 0.00 0.00 31.28 3.36
189 221 5.849510 TGACAAGTATTTTCAGACGAAGGA 58.150 37.500 0.00 0.00 31.28 3.36
190 222 6.368791 TGATGACAAGTATTTTCAGACGAAGG 59.631 38.462 0.00 0.00 31.28 3.46
191 223 7.351414 TGATGACAAGTATTTTCAGACGAAG 57.649 36.000 0.00 0.00 31.28 3.79
192 224 7.722795 TTGATGACAAGTATTTTCAGACGAA 57.277 32.000 0.00 0.00 0.00 3.85
193 225 7.722795 TTTGATGACAAGTATTTTCAGACGA 57.277 32.000 0.00 0.00 37.32 4.20
194 226 8.843733 CATTTTGATGACAAGTATTTTCAGACG 58.156 33.333 0.00 0.00 37.32 4.18
195 227 9.132521 CCATTTTGATGACAAGTATTTTCAGAC 57.867 33.333 0.00 0.00 37.32 3.51
196 228 9.076781 TCCATTTTGATGACAAGTATTTTCAGA 57.923 29.630 0.00 0.00 37.32 3.27
205 237 9.918630 CTTCTTTTATCCATTTTGATGACAAGT 57.081 29.630 0.00 0.00 37.32 3.16
236 268 9.057911 TCCCTCCATCCGAAAATATATTTAGAT 57.942 33.333 11.07 10.65 0.00 1.98
237 269 8.444010 TCCCTCCATCCGAAAATATATTTAGA 57.556 34.615 11.07 9.00 0.00 2.10
238 270 8.322091 ACTCCCTCCATCCGAAAATATATTTAG 58.678 37.037 11.07 8.48 0.00 1.85
239 271 8.214721 ACTCCCTCCATCCGAAAATATATTTA 57.785 34.615 11.07 0.00 0.00 1.40
252 284 2.941480 TCTTACGTACTCCCTCCATCC 58.059 52.381 0.00 0.00 0.00 3.51
254 286 5.485620 GTTTTTCTTACGTACTCCCTCCAT 58.514 41.667 0.00 0.00 0.00 3.41
256 288 4.248859 GGTTTTTCTTACGTACTCCCTCC 58.751 47.826 0.00 0.00 0.00 4.30
257 289 4.687948 GTGGTTTTTCTTACGTACTCCCTC 59.312 45.833 0.00 0.00 0.00 4.30
258 290 4.101430 TGTGGTTTTTCTTACGTACTCCCT 59.899 41.667 0.00 0.00 0.00 4.20
259 291 4.379652 TGTGGTTTTTCTTACGTACTCCC 58.620 43.478 0.00 0.00 0.00 4.30
260 292 5.525012 ACTTGTGGTTTTTCTTACGTACTCC 59.475 40.000 0.00 0.00 0.00 3.85
261 293 6.594284 ACTTGTGGTTTTTCTTACGTACTC 57.406 37.500 0.00 0.00 0.00 2.59
262 294 8.491331 TTTACTTGTGGTTTTTCTTACGTACT 57.509 30.769 0.00 0.00 0.00 2.73
263 295 9.373750 GATTTACTTGTGGTTTTTCTTACGTAC 57.626 33.333 0.00 0.00 0.00 3.67
264 296 8.274939 CGATTTACTTGTGGTTTTTCTTACGTA 58.725 33.333 0.00 0.00 0.00 3.57
265 297 7.127686 CGATTTACTTGTGGTTTTTCTTACGT 58.872 34.615 0.00 0.00 0.00 3.57
266 298 6.085849 GCGATTTACTTGTGGTTTTTCTTACG 59.914 38.462 0.00 0.00 0.00 3.18
267 299 7.136772 AGCGATTTACTTGTGGTTTTTCTTAC 58.863 34.615 0.00 0.00 0.00 2.34
268 300 7.266922 AGCGATTTACTTGTGGTTTTTCTTA 57.733 32.000 0.00 0.00 0.00 2.10
269 301 6.144078 AGCGATTTACTTGTGGTTTTTCTT 57.856 33.333 0.00 0.00 0.00 2.52
270 302 5.767816 AGCGATTTACTTGTGGTTTTTCT 57.232 34.783 0.00 0.00 0.00 2.52
271 303 5.332280 GCAAGCGATTTACTTGTGGTTTTTC 60.332 40.000 5.50 0.00 45.09 2.29
272 304 4.506288 GCAAGCGATTTACTTGTGGTTTTT 59.494 37.500 5.50 0.00 45.09 1.94
273 305 4.048504 GCAAGCGATTTACTTGTGGTTTT 58.951 39.130 5.50 0.00 45.09 2.43
274 306 3.317993 AGCAAGCGATTTACTTGTGGTTT 59.682 39.130 5.50 0.00 45.09 3.27
281 313 4.433805 CGTTCGTAAGCAAGCGATTTACTT 60.434 41.667 4.13 4.13 36.97 2.24
284 316 3.244156 TCGTTCGTAAGCAAGCGATTTA 58.756 40.909 0.00 0.00 36.97 1.40
287 319 1.389106 GTTCGTTCGTAAGCAAGCGAT 59.611 47.619 0.00 0.00 36.97 4.58
317 349 0.685131 TTGGGAGATGCCAATGCCTG 60.685 55.000 1.14 0.00 38.95 4.85
341 3062 1.009078 ATGCACGAACACATCCATCG 58.991 50.000 0.00 0.00 42.05 3.84
349 3070 1.601903 TGGAGAAACATGCACGAACAC 59.398 47.619 0.00 0.00 0.00 3.32
350 3071 1.872952 CTGGAGAAACATGCACGAACA 59.127 47.619 0.00 0.00 0.00 3.18
454 3176 3.393800 CGTTGGAGGCATCTTACCTATG 58.606 50.000 0.00 0.00 37.77 2.23
455 3177 2.224305 GCGTTGGAGGCATCTTACCTAT 60.224 50.000 0.00 0.00 37.77 2.57
456 3178 1.138266 GCGTTGGAGGCATCTTACCTA 59.862 52.381 0.00 0.00 37.77 3.08
457 3179 0.107654 GCGTTGGAGGCATCTTACCT 60.108 55.000 0.00 0.00 41.41 3.08
458 3180 1.095807 GGCGTTGGAGGCATCTTACC 61.096 60.000 0.00 0.00 36.61 2.85
459 3181 1.095807 GGGCGTTGGAGGCATCTTAC 61.096 60.000 0.00 0.00 38.57 2.34
460 3182 1.223487 GGGCGTTGGAGGCATCTTA 59.777 57.895 0.00 0.00 38.57 2.10
461 3183 2.044946 GGGCGTTGGAGGCATCTT 60.045 61.111 0.00 0.00 38.57 2.40
503 3235 2.509561 GTTTCGGAGGAGCTCGCC 60.510 66.667 7.83 10.80 0.00 5.54
504 3236 1.807573 CAGTTTCGGAGGAGCTCGC 60.808 63.158 7.83 1.84 0.00 5.03
505 3237 0.243907 TTCAGTTTCGGAGGAGCTCG 59.756 55.000 7.83 0.00 0.00 5.03
506 3238 2.070028 GTTTCAGTTTCGGAGGAGCTC 58.930 52.381 4.71 4.71 0.00 4.09
507 3239 1.694696 AGTTTCAGTTTCGGAGGAGCT 59.305 47.619 0.00 0.00 0.00 4.09
508 3240 1.801178 CAGTTTCAGTTTCGGAGGAGC 59.199 52.381 0.00 0.00 0.00 4.70
554 3287 1.961277 CGTGGTTCGCCTCTTTGCT 60.961 57.895 0.00 0.00 38.36 3.91
555 3288 1.782028 AACGTGGTTCGCCTCTTTGC 61.782 55.000 0.00 0.00 44.19 3.68
559 3292 2.665185 GCAACGTGGTTCGCCTCT 60.665 61.111 0.00 0.00 44.19 3.69
576 3328 4.208686 GCTGTAGCGAGGGACGGG 62.209 72.222 0.00 0.00 42.83 5.28
588 3340 1.136305 GTCCGGAACTGCATAGCTGTA 59.864 52.381 5.23 0.00 39.66 2.74
594 3346 4.021559 TCCGTCCGGAACTGCATA 57.978 55.556 5.23 0.00 42.05 3.14
638 3390 1.079956 CGTCTGCTGCTGCTCTCTT 60.080 57.895 17.00 0.00 40.48 2.85
646 3398 1.202580 ACTTTCTGTTCGTCTGCTGCT 60.203 47.619 0.00 0.00 0.00 4.24
653 3405 4.328983 TCAGTTTGTGACTTTCTGTTCGTC 59.671 41.667 0.00 0.00 36.10 4.20
669 3421 1.263217 AGTTAAAGCGGCGTCAGTTTG 59.737 47.619 9.37 0.00 0.00 2.93
698 3450 4.459089 GACGCTGGGTGCTCCTCC 62.459 72.222 0.70 0.00 40.11 4.30
702 3454 2.512515 GATGGACGCTGGGTGCTC 60.513 66.667 16.61 8.51 37.93 4.26
703 3455 4.101448 GGATGGACGCTGGGTGCT 62.101 66.667 16.61 3.41 37.93 4.40
708 3475 4.530857 GGGACGGATGGACGCTGG 62.531 72.222 0.00 0.00 37.37 4.85
742 3509 4.918129 CGACCGGACGGGCATACG 62.918 72.222 18.76 9.28 45.70 3.06
743 3510 3.763127 GACGACCGGACGGGCATAC 62.763 68.421 28.68 9.95 45.70 2.39
766 3533 2.968156 CGGCGGTTCGGTTCACAA 60.968 61.111 0.00 0.00 0.00 3.33
767 3534 4.973055 CCGGCGGTTCGGTTCACA 62.973 66.667 19.97 0.00 44.60 3.58
843 3617 1.374758 CAAGCTGGACTGGACCGAC 60.375 63.158 0.00 0.00 0.00 4.79
844 3618 3.059982 CAAGCTGGACTGGACCGA 58.940 61.111 0.00 0.00 0.00 4.69
850 3624 1.798735 CGGAATGCAAGCTGGACTG 59.201 57.895 0.00 0.00 0.00 3.51
851 3625 2.042831 GCGGAATGCAAGCTGGACT 61.043 57.895 0.00 0.00 45.45 3.85
933 3708 2.713154 GTGTGTGTGCGGTGGTTC 59.287 61.111 0.00 0.00 0.00 3.62
941 3716 4.927782 TGCCGAGGGTGTGTGTGC 62.928 66.667 0.00 0.00 0.00 4.57
943 3718 4.626081 GCTGCCGAGGGTGTGTGT 62.626 66.667 0.00 0.00 0.00 3.72
1005 3788 1.003233 GAAGAAGCCCTGCGTCCTT 60.003 57.895 0.00 0.00 37.75 3.36
1105 3888 4.070552 GGAGAACCGGAGCGCAGT 62.071 66.667 9.46 0.00 0.00 4.40
1395 4217 1.332144 AAGCGCTTACGATGGGGGTA 61.332 55.000 23.72 0.00 43.93 3.69
1436 4267 1.968017 ACCAAGACAGCGGCATGTG 60.968 57.895 1.45 0.00 32.25 3.21
1437 4268 1.968017 CACCAAGACAGCGGCATGT 60.968 57.895 1.45 3.63 35.68 3.21
1529 4379 3.812053 ACAGACACAGACATTTGAGAAGC 59.188 43.478 0.00 0.00 0.00 3.86
1601 4451 6.536582 CAGCACTGTAAGCATGAGTAAATACT 59.463 38.462 0.00 0.00 37.60 2.12
1602 4452 6.313905 ACAGCACTGTAAGCATGAGTAAATAC 59.686 38.462 0.35 0.00 42.90 1.89
1603 4453 6.406370 ACAGCACTGTAAGCATGAGTAAATA 58.594 36.000 0.35 0.00 42.90 1.40
1634 4484 3.021695 TCGGCGAAGAAGATAAGGAGAA 58.978 45.455 7.35 0.00 0.00 2.87
1653 4504 4.389992 AGACAACAAATACAGCAGACATCG 59.610 41.667 0.00 0.00 0.00 3.84
1665 4516 4.503910 ACAGCATCGCTAGACAACAAATA 58.496 39.130 0.00 0.00 36.40 1.40
2034 5283 3.314331 CTCCCACCGACAGCCAGT 61.314 66.667 0.00 0.00 0.00 4.00
2239 5493 7.182761 CCTACAAAGACATCGATCAAAACATC 58.817 38.462 0.00 0.00 0.00 3.06
2246 5500 2.766263 AGCCCTACAAAGACATCGATCA 59.234 45.455 0.00 0.00 0.00 2.92
2317 5593 1.192146 CCCCGTTCACCTTCCTCTCA 61.192 60.000 0.00 0.00 0.00 3.27
2467 5743 1.806461 GCGTCAGGTGTGAGTCCTCA 61.806 60.000 0.00 0.00 37.24 3.86
2874 6150 6.000891 TCAATTGCGATATTCAAGTATGGC 57.999 37.500 0.00 0.00 36.63 4.40
2881 6157 6.476380 GCCTGAAAATCAATTGCGATATTCAA 59.524 34.615 0.00 0.00 0.00 2.69
2886 6162 3.698539 TGGCCTGAAAATCAATTGCGATA 59.301 39.130 3.32 0.00 0.00 2.92
2928 6204 4.151335 CACTACTCATCAGTCAGTTGCAAC 59.849 45.833 22.17 22.17 33.62 4.17
3012 6289 1.407851 CCTCATGCTGCTTCCTTGCTA 60.408 52.381 0.00 0.00 0.00 3.49
3015 6296 0.963856 TGCCTCATGCTGCTTCCTTG 60.964 55.000 0.00 0.00 42.00 3.61
3152 6433 3.075148 GCCTTTCTCAGGTAGTTGGAAC 58.925 50.000 0.00 0.00 46.07 3.62
3194 6480 7.186268 ACCAATTAGTATTTGCTAAAGGGGAA 58.814 34.615 11.85 0.00 35.92 3.97
3232 6518 1.999648 AACTGAGCAGCCAATTGGAA 58.000 45.000 29.02 4.63 37.39 3.53
3269 6581 6.099269 AGGTTACACTTCTCTGACAAGGTTAA 59.901 38.462 0.00 0.00 0.00 2.01
3275 6587 5.128827 ACAAGAGGTTACACTTCTCTGACAA 59.871 40.000 0.00 0.00 33.05 3.18
3287 6599 1.414919 AGCCGTTCACAAGAGGTTACA 59.585 47.619 0.00 0.00 0.00 2.41
3298 6610 2.603953 GAGGTACTAACAGCCGTTCAC 58.396 52.381 0.00 0.00 41.55 3.18
3319 6631 8.297426 GGAAGAACTATTTTGGAAAACCTACTG 58.703 37.037 0.00 0.00 0.00 2.74
3330 6642 5.355350 AGATGCGAAGGAAGAACTATTTTGG 59.645 40.000 0.00 0.00 0.00 3.28
3332 6644 6.173339 TGAGATGCGAAGGAAGAACTATTTT 58.827 36.000 0.00 0.00 0.00 1.82
3333 6645 5.734720 TGAGATGCGAAGGAAGAACTATTT 58.265 37.500 0.00 0.00 0.00 1.40
3334 6646 5.344743 TGAGATGCGAAGGAAGAACTATT 57.655 39.130 0.00 0.00 0.00 1.73
3427 6744 8.682936 AGACACTTCACTCATTAGATGTTTTT 57.317 30.769 0.00 0.00 0.00 1.94
3530 6852 4.487412 GATGCCACGCTGCTTGCC 62.487 66.667 0.00 0.00 38.78 4.52
3590 6912 1.002087 CACTACTCCCTCCAACACACC 59.998 57.143 0.00 0.00 0.00 4.16
3654 6976 1.863155 GCCAGGGGTGGAATGGAAGA 61.863 60.000 0.00 0.00 36.09 2.87
3755 7078 3.904136 AAAGGCTCACAAAACTCATCG 57.096 42.857 0.00 0.00 0.00 3.84
3762 7085 7.223777 CCGAAAGAAAAATAAAGGCTCACAAAA 59.776 33.333 0.00 0.00 0.00 2.44
3793 7117 1.552337 TGAGGCCTCATCAGTCTTCAC 59.448 52.381 32.00 1.30 34.14 3.18
3795 7119 1.830477 AGTGAGGCCTCATCAGTCTTC 59.170 52.381 37.07 21.50 42.18 2.87
3796 7120 1.830477 GAGTGAGGCCTCATCAGTCTT 59.170 52.381 37.07 16.79 41.78 3.01
3798 7122 1.134848 GTGAGTGAGGCCTCATCAGTC 60.135 57.143 37.07 27.84 43.03 3.51
3799 7123 0.901124 GTGAGTGAGGCCTCATCAGT 59.099 55.000 37.07 22.01 43.03 3.41
3801 7125 0.900421 CAGTGAGTGAGGCCTCATCA 59.100 55.000 37.07 32.19 43.03 3.07
3802 7126 0.177604 CCAGTGAGTGAGGCCTCATC 59.822 60.000 37.07 30.34 43.03 2.92
3803 7127 1.908340 GCCAGTGAGTGAGGCCTCAT 61.908 60.000 37.07 25.02 43.03 2.90
3804 7128 2.587247 GCCAGTGAGTGAGGCCTCA 61.587 63.158 32.00 32.00 42.58 3.86
3810 7146 0.675837 CACCATGGCCAGTGAGTGAG 60.676 60.000 18.04 5.04 36.01 3.51
3826 7162 2.991540 GGGAAAGGTGGCAGCACC 60.992 66.667 20.04 17.33 45.31 5.01
3827 7163 1.531602 AAGGGAAAGGTGGCAGCAC 60.532 57.895 20.04 9.47 0.00 4.40
3859 7195 4.024048 ACAACAAGAAAGGAGTGCAATACG 60.024 41.667 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.