Multiple sequence alignment - TraesCS6B01G065500

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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 TraesCS6B01G065500 chr6B 100.000 5672 0 0 1 5672 43347469 43353140 0.000000e+00 10475.0
1 TraesCS6B01G065500 chr6B 90.875 2674 180 23 613 3276 43498350 43500969 0.000000e+00 3528.0
2 TraesCS6B01G065500 chr6B 88.362 2466 234 25 705 3169 43281514 43283927 0.000000e+00 2915.0
3 TraesCS6B01G065500 chr6B 86.171 2625 305 31 666 3283 44099996 44102569 0.000000e+00 2784.0
4 TraesCS6B01G065500 chr6B 89.537 1424 109 13 3275 4693 43501014 43502402 0.000000e+00 1768.0
5 TraesCS6B01G065500 chr6B 86.451 1454 168 21 3316 4760 43284214 43285647 0.000000e+00 1567.0
6 TraesCS6B01G065500 chr6B 82.576 1320 186 31 3393 4690 44102630 44103927 0.000000e+00 1123.0
7 TraesCS6B01G065500 chr6B 86.842 380 40 3 252 628 43497958 43498330 3.160000e-112 416.0
8 TraesCS6B01G065500 chr6B 77.817 284 41 15 349 618 43281182 43281457 7.610000e-34 156.0
9 TraesCS6B01G065500 chr6B 75.486 257 34 14 4 252 43348012 43348247 1.300000e-16 99.0
10 TraesCS6B01G065500 chr6A 95.908 5645 185 25 1 5625 24852788 24858406 0.000000e+00 9103.0
11 TraesCS6B01G065500 chr6A 90.121 3057 222 39 247 3276 25017216 25020219 0.000000e+00 3899.0
12 TraesCS6B01G065500 chr6A 88.554 2490 228 26 705 3193 24838500 24840933 0.000000e+00 2966.0
13 TraesCS6B01G065500 chr6A 85.267 1724 193 34 3354 5058 24841082 24842763 0.000000e+00 1720.0
14 TraesCS6B01G065500 chr6A 88.395 1439 107 17 3275 4693 25020300 25021698 0.000000e+00 1677.0
15 TraesCS6B01G065500 chr6A 78.505 321 37 18 475 774 24852721 24853030 1.260000e-41 182.0
16 TraesCS6B01G065500 chr6A 74.609 256 37 13 4 252 24853339 24853573 2.820000e-13 87.9
17 TraesCS6B01G065500 chr6A 78.014 141 24 5 112 247 25017621 25017759 1.310000e-11 82.4
18 TraesCS6B01G065500 chr6A 97.297 37 1 0 5497 5533 569998437 569998473 4.740000e-06 63.9
19 TraesCS6B01G065500 chr6A 94.595 37 1 1 5501 5536 12321360 12321324 7.940000e-04 56.5
20 TraesCS6B01G065500 chrUn 96.622 3286 90 8 1 3276 94178598 94181872 0.000000e+00 5433.0
21 TraesCS6B01G065500 chrUn 90.409 3055 219 23 247 3276 94220198 94223203 0.000000e+00 3951.0
22 TraesCS6B01G065500 chrUn 94.924 2246 97 13 3275 5511 94181977 94184214 0.000000e+00 3500.0
23 TraesCS6B01G065500 chrUn 88.773 2494 225 30 705 3193 94047291 94049734 0.000000e+00 3003.0
24 TraesCS6B01G065500 chrUn 86.949 2475 263 31 666 3129 94817855 94820280 0.000000e+00 2726.0
25 TraesCS6B01G065500 chrUn 91.656 755 46 9 3275 4025 94223247 94223988 0.000000e+00 1029.0
26 TraesCS6B01G065500 chrUn 87.821 739 73 10 3354 4082 94049898 94050629 0.000000e+00 850.0
27 TraesCS6B01G065500 chrUn 81.952 953 113 26 4118 5058 94050634 94051539 0.000000e+00 752.0
28 TraesCS6B01G065500 chrUn 86.818 660 64 6 4032 4690 94224155 94224792 0.000000e+00 715.0
29 TraesCS6B01G065500 chrUn 82.301 339 41 13 5086 5422 94051538 94051859 5.600000e-70 276.0
30 TraesCS6B01G065500 chrUn 88.649 185 13 2 5485 5669 94184220 94184396 9.570000e-53 219.0
31 TraesCS6B01G065500 chrUn 89.209 139 11 3 475 610 94178531 94178668 2.720000e-38 171.0
32 TraesCS6B01G065500 chrUn 78.231 294 37 13 349 618 94046940 94047230 4.550000e-36 163.0
33 TraesCS6B01G065500 chrUn 75.097 257 35 14 4 252 94179150 94179385 6.050000e-15 93.5
34 TraesCS6B01G065500 chr1D 90.196 51 4 1 5486 5536 255504286 255504237 1.320000e-06 65.8
35 TraesCS6B01G065500 chr3D 97.143 35 0 1 5500 5533 539118936 539118902 2.210000e-04 58.4
36 TraesCS6B01G065500 chr3D 94.595 37 1 1 5500 5535 369623889 369623853 7.940000e-04 56.5
37 TraesCS6B01G065500 chr4D 94.595 37 1 1 5500 5535 382692509 382692473 7.940000e-04 56.5
38 TraesCS6B01G065500 chr1A 97.059 34 0 1 5500 5532 331548462 331548495 7.940000e-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 TraesCS6B01G065500 chr6B 43347469 43353140 5671 False 10475.000000 10475 100.000000 1 5672 1 chr6B.!!$F1 5671
1 TraesCS6B01G065500 chr6B 44099996 44103927 3931 False 1953.500000 2784 84.373500 666 4690 2 chr6B.!!$F5 4024
2 TraesCS6B01G065500 chr6B 43497958 43502402 4444 False 1904.000000 3528 89.084667 252 4693 3 chr6B.!!$F4 4441
3 TraesCS6B01G065500 chr6B 43281182 43285647 4465 False 1546.000000 2915 84.210000 349 4760 3 chr6B.!!$F3 4411
4 TraesCS6B01G065500 chr6A 24852721 24858406 5685 False 4642.500000 9103 87.206500 1 5625 2 chr6A.!!$F4 5624
5 TraesCS6B01G065500 chr6A 24838500 24842763 4263 False 2343.000000 2966 86.910500 705 5058 2 chr6A.!!$F3 4353
6 TraesCS6B01G065500 chr6A 25017216 25021698 4482 False 1886.133333 3899 85.510000 112 4693 3 chr6A.!!$F5 4581
7 TraesCS6B01G065500 chrUn 94817855 94820280 2425 False 2726.000000 2726 86.949000 666 3129 1 chrUn.!!$F1 2463
8 TraesCS6B01G065500 chrUn 94220198 94224792 4594 False 1898.333333 3951 89.627667 247 4690 3 chrUn.!!$F4 4443
9 TraesCS6B01G065500 chrUn 94178531 94184396 5865 False 1883.300000 5433 88.900200 1 5669 5 chrUn.!!$F3 5668
10 TraesCS6B01G065500 chrUn 94046940 94051859 4919 False 1008.800000 3003 83.815600 349 5422 5 chrUn.!!$F2 5073

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
202 274 0.307760 CAAGTCGCTTTCTTTGCCGT 59.692 50.0 0.00 0.00 0.00 5.68 F
1270 1458 0.398696 TGGCATGGTTCAAGGTACGT 59.601 50.0 0.00 0.00 0.00 3.57 F
1686 1875 0.244721 AAAGCGCTGCAAAATCTCCC 59.755 50.0 12.58 0.00 0.00 4.30 F
2328 2523 0.664761 AAGCATCATCGGAAATGGCG 59.335 50.0 6.05 0.00 0.00 5.69 F
3469 3996 0.111061 TGATTGCCTGCAGGTTCAGT 59.889 50.0 32.81 19.92 37.57 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1638 1827 1.067425 TGCATCATCCAAAGCAGCAAC 60.067 47.619 0.0 0.0 32.48 4.17 R
2311 2506 0.317269 CACGCCATTTCCGATGATGC 60.317 55.000 0.0 0.0 0.00 3.91 R
2982 3179 0.941542 CAACCCTGTAACACACCACG 59.058 55.000 0.0 0.0 0.00 4.94 R
4216 4926 0.251742 TCCCTTGGAAATGCCTGGTG 60.252 55.000 0.0 0.0 37.63 4.17 R
4716 5428 0.820871 TCACACAAAACAGTTGCCCC 59.179 50.000 0.0 0.0 0.00 5.80 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
38 106 2.154462 CTTTCTTGGATGCTTGTCGGT 58.846 47.619 0.00 0.00 0.00 4.69
134 206 7.425606 ACTTTTGTGTTGCTTACTAGAAATGG 58.574 34.615 0.00 0.00 0.00 3.16
138 210 3.756434 TGTTGCTTACTAGAAATGGGTGC 59.244 43.478 0.00 0.00 0.00 5.01
150 222 6.041423 AGAAATGGGTGCATTTCCTTAAAG 57.959 37.500 4.33 0.00 46.94 1.85
177 249 5.749596 TTTGTCAAATCGTCTGTCATTGT 57.250 34.783 0.00 0.00 0.00 2.71
179 251 5.342806 TGTCAAATCGTCTGTCATTGTTC 57.657 39.130 0.00 0.00 0.00 3.18
180 252 5.056480 TGTCAAATCGTCTGTCATTGTTCT 58.944 37.500 0.00 0.00 0.00 3.01
181 253 5.177511 TGTCAAATCGTCTGTCATTGTTCTC 59.822 40.000 0.00 0.00 0.00 2.87
182 254 5.406780 GTCAAATCGTCTGTCATTGTTCTCT 59.593 40.000 0.00 0.00 0.00 3.10
184 256 4.790765 ATCGTCTGTCATTGTTCTCTCA 57.209 40.909 0.00 0.00 0.00 3.27
186 258 4.550422 TCGTCTGTCATTGTTCTCTCAAG 58.450 43.478 0.00 0.00 0.00 3.02
187 259 4.038042 TCGTCTGTCATTGTTCTCTCAAGT 59.962 41.667 0.00 0.00 0.00 3.16
188 260 4.384247 CGTCTGTCATTGTTCTCTCAAGTC 59.616 45.833 0.00 0.00 0.00 3.01
189 261 4.384247 GTCTGTCATTGTTCTCTCAAGTCG 59.616 45.833 0.00 0.00 0.00 4.18
190 262 3.059884 TGTCATTGTTCTCTCAAGTCGC 58.940 45.455 0.00 0.00 0.00 5.19
191 263 3.243873 TGTCATTGTTCTCTCAAGTCGCT 60.244 43.478 0.00 0.00 0.00 4.93
194 266 4.449068 TCATTGTTCTCTCAAGTCGCTTTC 59.551 41.667 0.00 0.00 0.00 2.62
195 267 3.735237 TGTTCTCTCAAGTCGCTTTCT 57.265 42.857 0.00 0.00 0.00 2.52
196 268 4.060038 TGTTCTCTCAAGTCGCTTTCTT 57.940 40.909 0.00 0.00 0.00 2.52
198 270 4.271049 TGTTCTCTCAAGTCGCTTTCTTTG 59.729 41.667 0.00 0.00 0.00 2.77
199 271 2.802816 TCTCTCAAGTCGCTTTCTTTGC 59.197 45.455 0.00 0.00 0.00 3.68
202 274 0.307760 CAAGTCGCTTTCTTTGCCGT 59.692 50.000 0.00 0.00 0.00 5.68
203 275 1.529438 CAAGTCGCTTTCTTTGCCGTA 59.471 47.619 0.00 0.00 0.00 4.02
204 276 2.094762 AGTCGCTTTCTTTGCCGTAT 57.905 45.000 0.00 0.00 0.00 3.06
206 278 2.415512 AGTCGCTTTCTTTGCCGTATTC 59.584 45.455 0.00 0.00 0.00 1.75
207 279 2.158841 GTCGCTTTCTTTGCCGTATTCA 59.841 45.455 0.00 0.00 0.00 2.57
209 281 3.438781 TCGCTTTCTTTGCCGTATTCAAT 59.561 39.130 0.00 0.00 0.00 2.57
210 282 3.786048 CGCTTTCTTTGCCGTATTCAATC 59.214 43.478 0.00 0.00 0.00 2.67
212 284 4.380444 GCTTTCTTTGCCGTATTCAATCCA 60.380 41.667 0.00 0.00 0.00 3.41
213 285 5.679638 GCTTTCTTTGCCGTATTCAATCCAT 60.680 40.000 0.00 0.00 0.00 3.41
239 311 7.585286 TTTTATCACTGCAATTGCTTCATTC 57.415 32.000 29.37 0.99 42.66 2.67
240 312 4.794278 ATCACTGCAATTGCTTCATTCA 57.206 36.364 29.37 8.03 42.66 2.57
241 313 4.587584 TCACTGCAATTGCTTCATTCAA 57.412 36.364 29.37 7.29 42.66 2.69
243 315 5.543714 TCACTGCAATTGCTTCATTCAAAT 58.456 33.333 29.37 0.00 42.66 2.32
245 317 6.073494 TCACTGCAATTGCTTCATTCAAATTG 60.073 34.615 29.37 11.37 42.66 2.32
248 320 6.224584 TGCAATTGCTTCATTCAAATTGAGA 58.775 32.000 29.37 1.54 42.66 3.27
278 351 2.096909 CGTTTACCGTCAGTTGCTGAAG 60.097 50.000 0.00 2.98 42.46 3.02
279 352 1.508632 TTACCGTCAGTTGCTGAAGC 58.491 50.000 0.00 0.00 42.46 3.86
286 359 0.596577 CAGTTGCTGAAGCTGTGCAT 59.403 50.000 8.93 0.00 42.66 3.96
290 363 0.879090 TGCTGAAGCTGTGCATGAAG 59.121 50.000 0.00 0.00 42.66 3.02
308 381 3.505184 CGGACGAAAATGCCGGGG 61.505 66.667 2.18 0.00 41.29 5.73
417 500 4.923281 GCTCTGTTTTGTTTGTCTGTTTGT 59.077 37.500 0.00 0.00 0.00 2.83
696 859 7.387673 TGTGTTTAGTCGAATCATCTGTCATTT 59.612 33.333 0.00 0.00 0.00 2.32
912 1094 5.755375 CCACGATAACATCTGCTCTATGTTT 59.245 40.000 14.22 5.86 43.31 2.83
913 1095 6.258727 CCACGATAACATCTGCTCTATGTTTT 59.741 38.462 14.22 8.74 43.31 2.43
947 1135 6.216868 ACAGGGGGTTTCTAACACATAAGTAT 59.783 38.462 0.00 0.00 36.19 2.12
1085 1273 1.219393 GTTTAGCTGCGAGGCCTCT 59.781 57.895 29.73 13.77 0.00 3.69
1142 1330 2.111043 CACTGGAGGTGTTGCCGT 59.889 61.111 0.00 0.00 43.70 5.68
1162 1350 2.760799 TTGCCATCCATGCAGCCC 60.761 61.111 0.00 0.00 40.35 5.19
1270 1458 0.398696 TGGCATGGTTCAAGGTACGT 59.601 50.000 0.00 0.00 0.00 3.57
1281 1469 7.385267 TGGTTCAAGGTACGTTAGCTTTAATA 58.615 34.615 0.00 0.00 43.37 0.98
1286 1474 6.284891 AGGTACGTTAGCTTTAATACCACA 57.715 37.500 15.38 0.00 35.53 4.17
1307 1495 7.098477 CCACACATTCATTTGGTATTGTTGAT 58.902 34.615 0.00 0.00 0.00 2.57
1342 1531 5.545063 TCTCTTGTGGAGTTGTGACAATA 57.455 39.130 0.00 0.00 42.40 1.90
1347 1536 6.653320 TCTTGTGGAGTTGTGACAATAATACC 59.347 38.462 0.00 2.24 0.00 2.73
1348 1537 4.932799 TGTGGAGTTGTGACAATAATACCG 59.067 41.667 0.00 0.00 0.00 4.02
1601 1790 3.008049 ACAACCACTGGAAGATAGTGACC 59.992 47.826 0.71 0.00 46.52 4.02
1638 1827 3.691049 ATGTTTATGGTCGAAATGGCG 57.309 42.857 0.00 0.00 0.00 5.69
1686 1875 0.244721 AAAGCGCTGCAAAATCTCCC 59.755 50.000 12.58 0.00 0.00 4.30
1748 1937 7.951591 AGCTCATAAATTTGTTGGTTAGTGTT 58.048 30.769 0.00 0.00 0.00 3.32
1890 2079 4.346127 ACTGGCTGTCTGCATATCTTGATA 59.654 41.667 3.96 0.00 45.15 2.15
2311 2506 7.916914 TTCATCCTGCATATGACATCATAAG 57.083 36.000 6.97 3.06 41.60 1.73
2328 2523 0.664761 AAGCATCATCGGAAATGGCG 59.335 50.000 6.05 0.00 0.00 5.69
2525 2720 2.794350 GCAGTTGAAAATTGGTGTTCCG 59.206 45.455 0.00 0.00 33.69 4.30
2982 3179 2.819608 TGCAGCCATTTACTTTGGAGAC 59.180 45.455 0.00 0.00 36.26 3.36
3381 3894 8.463930 TTTTCTGTTTTCACATACTTCTCCAT 57.536 30.769 0.00 0.00 30.39 3.41
3383 3896 9.739276 TTTCTGTTTTCACATACTTCTCCATAT 57.261 29.630 0.00 0.00 30.39 1.78
3384 3897 8.722480 TCTGTTTTCACATACTTCTCCATATG 57.278 34.615 0.00 0.00 35.33 1.78
3469 3996 0.111061 TGATTGCCTGCAGGTTCAGT 59.889 50.000 32.81 19.92 37.57 3.41
3525 4052 9.880157 GTAAACCAACCTTCTCTATTATGTGTA 57.120 33.333 0.00 0.00 0.00 2.90
3651 4194 7.229306 TCCTGATCATATGGCTATTTGTTGTTC 59.771 37.037 2.13 0.00 0.00 3.18
3916 4459 0.608856 ATGGCCATTGTTGACGAGCA 60.609 50.000 14.09 0.00 0.00 4.26
4198 4906 9.651913 ACTTTGTTTCACAAATCAAAATGTAGT 57.348 25.926 2.62 0.00 45.79 2.73
4216 4926 5.001232 TGTAGTGCCTTACAAGTTCATTCC 58.999 41.667 0.00 0.00 30.94 3.01
4540 5250 1.200020 GCAAGGATCCACCAAAGAACG 59.800 52.381 15.82 0.00 42.04 3.95
4631 5341 0.398318 GAGATAGAAAGGCCGGCCAT 59.602 55.000 45.13 34.11 38.92 4.40
4645 5355 1.881925 CGGCCATGGAAGTCAGAAACA 60.882 52.381 18.40 0.00 0.00 2.83
4646 5356 1.541588 GGCCATGGAAGTCAGAAACAC 59.458 52.381 18.40 0.00 0.00 3.32
4706 5417 4.048241 AGCTAGTTCGTGCTTTATCTCC 57.952 45.455 0.00 0.00 35.86 3.71
4710 5422 4.015872 AGTTCGTGCTTTATCTCCCAAA 57.984 40.909 0.00 0.00 0.00 3.28
4836 5548 7.093902 GGGTTCAAATACTTCTTAAAGGAAGGG 60.094 40.741 8.77 0.00 44.82 3.95
5058 5775 3.746949 GACTGATCCTGCCGGCTGG 62.747 68.421 38.86 38.86 38.77 4.85
5061 5778 3.474570 GATCCTGCCGGCTGGAGT 61.475 66.667 44.51 34.88 45.06 3.85
5107 5824 7.078851 CGATGCCTGTAGATTGTAGTACTAAG 58.921 42.308 3.61 0.00 0.00 2.18
5109 5826 5.892119 TGCCTGTAGATTGTAGTACTAAGCT 59.108 40.000 3.61 2.69 0.00 3.74
5150 5867 0.541863 AGTTTAGATGGAGCCACCCG 59.458 55.000 0.00 0.00 38.00 5.28
5168 5885 6.677187 GCCACCCGAAAGATATGTTAGTTTTC 60.677 42.308 0.00 0.00 0.00 2.29
5169 5886 6.598064 CCACCCGAAAGATATGTTAGTTTTCT 59.402 38.462 0.00 0.00 0.00 2.52
5446 6164 0.187117 TTTGGTGGTTCTGGGATGCA 59.813 50.000 0.00 0.00 0.00 3.96
5452 6170 1.144708 TGGTTCTGGGATGCAACTGAA 59.855 47.619 0.00 0.00 0.00 3.02
5469 6187 4.205587 ACTGAATCAGATCAATCCCAAGC 58.794 43.478 18.20 0.00 35.18 4.01
5483 6201 0.970937 CCAAGCTACTCCCTCCGTCA 60.971 60.000 0.00 0.00 0.00 4.35
5488 6206 2.158445 AGCTACTCCCTCCGTCACATAT 60.158 50.000 0.00 0.00 0.00 1.78
5491 6209 4.082679 GCTACTCCCTCCGTCACATATTAG 60.083 50.000 0.00 0.00 0.00 1.73
5493 6211 4.742012 ACTCCCTCCGTCACATATTAGAT 58.258 43.478 0.00 0.00 0.00 1.98
5494 6212 5.888901 ACTCCCTCCGTCACATATTAGATA 58.111 41.667 0.00 0.00 0.00 1.98
5532 6285 0.417841 TGGGAAGGAGGGAGTAGCTT 59.582 55.000 0.00 0.00 0.00 3.74
5533 6286 1.203440 TGGGAAGGAGGGAGTAGCTTT 60.203 52.381 0.00 0.00 0.00 3.51
5538 6291 4.399219 GAAGGAGGGAGTAGCTTTTTGTT 58.601 43.478 0.00 0.00 0.00 2.83
5561 6314 7.773224 TGTTTCTCTCAAATCTTACTGGAACAA 59.227 33.333 0.00 0.00 38.70 2.83
5572 6325 0.532862 CTGGAACAACGAGCCACTGT 60.533 55.000 0.00 0.00 38.70 3.55
5625 6378 3.731652 TGCATCTGTTTTGGTTCTTGG 57.268 42.857 0.00 0.00 0.00 3.61
5626 6379 2.224018 TGCATCTGTTTTGGTTCTTGGC 60.224 45.455 0.00 0.00 0.00 4.52
5627 6380 2.036346 GCATCTGTTTTGGTTCTTGGCT 59.964 45.455 0.00 0.00 0.00 4.75
5628 6381 3.493176 GCATCTGTTTTGGTTCTTGGCTT 60.493 43.478 0.00 0.00 0.00 4.35
5629 6382 4.301628 CATCTGTTTTGGTTCTTGGCTTC 58.698 43.478 0.00 0.00 0.00 3.86
5630 6383 3.631250 TCTGTTTTGGTTCTTGGCTTCT 58.369 40.909 0.00 0.00 0.00 2.85
5631 6384 4.023291 TCTGTTTTGGTTCTTGGCTTCTT 58.977 39.130 0.00 0.00 0.00 2.52
5632 6385 4.114794 CTGTTTTGGTTCTTGGCTTCTTG 58.885 43.478 0.00 0.00 0.00 3.02
5636 6389 0.040067 GGTTCTTGGCTTCTTGCGTG 60.040 55.000 0.00 0.00 44.05 5.34
5643 6396 2.970974 GCTTCTTGCGTGCACCTCC 61.971 63.158 12.15 0.20 0.00 4.30
5669 6422 8.712363 CGAGAAATATACCATACCAATCACAAG 58.288 37.037 0.00 0.00 0.00 3.16
5670 6423 9.561069 GAGAAATATACCATACCAATCACAAGT 57.439 33.333 0.00 0.00 0.00 3.16
5671 6424 9.342308 AGAAATATACCATACCAATCACAAGTG 57.658 33.333 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.506500 AGAAAGTCAAGAAGCAATATGTGG 57.493 37.500 0.00 0.00 0.00 4.17
1 2 6.805271 CCAAGAAAGTCAAGAAGCAATATGTG 59.195 38.462 0.00 0.00 0.00 3.21
2 3 6.716628 TCCAAGAAAGTCAAGAAGCAATATGT 59.283 34.615 0.00 0.00 0.00 2.29
3 4 7.149569 TCCAAGAAAGTCAAGAAGCAATATG 57.850 36.000 0.00 0.00 0.00 1.78
4 5 7.630082 GCATCCAAGAAAGTCAAGAAGCAATAT 60.630 37.037 0.00 0.00 0.00 1.28
5 6 6.349611 GCATCCAAGAAAGTCAAGAAGCAATA 60.350 38.462 0.00 0.00 0.00 1.90
158 230 5.406780 AGAGAACAATGACAGACGATTTGAC 59.593 40.000 0.00 0.00 0.00 3.18
159 231 5.541845 AGAGAACAATGACAGACGATTTGA 58.458 37.500 0.00 0.00 0.00 2.69
160 232 5.406477 TGAGAGAACAATGACAGACGATTTG 59.594 40.000 0.00 0.00 0.00 2.32
161 233 5.541845 TGAGAGAACAATGACAGACGATTT 58.458 37.500 0.00 0.00 0.00 2.17
164 236 4.038042 ACTTGAGAGAACAATGACAGACGA 59.962 41.667 0.00 0.00 0.00 4.20
165 237 4.302455 ACTTGAGAGAACAATGACAGACG 58.698 43.478 0.00 0.00 0.00 4.18
166 238 4.384247 CGACTTGAGAGAACAATGACAGAC 59.616 45.833 0.00 0.00 0.00 3.51
167 239 4.550422 CGACTTGAGAGAACAATGACAGA 58.450 43.478 0.00 0.00 0.00 3.41
168 240 3.122613 GCGACTTGAGAGAACAATGACAG 59.877 47.826 0.00 0.00 0.00 3.51
169 241 3.059884 GCGACTTGAGAGAACAATGACA 58.940 45.455 0.00 0.00 0.00 3.58
170 242 3.321497 AGCGACTTGAGAGAACAATGAC 58.679 45.455 0.00 0.00 0.00 3.06
171 243 3.667497 AGCGACTTGAGAGAACAATGA 57.333 42.857 0.00 0.00 0.00 2.57
172 244 4.450419 AGAAAGCGACTTGAGAGAACAATG 59.550 41.667 0.00 0.00 0.00 2.82
173 245 4.636249 AGAAAGCGACTTGAGAGAACAAT 58.364 39.130 0.00 0.00 0.00 2.71
174 246 4.060038 AGAAAGCGACTTGAGAGAACAA 57.940 40.909 0.00 0.00 0.00 2.83
176 248 4.767075 CAAAGAAAGCGACTTGAGAGAAC 58.233 43.478 0.00 0.00 0.00 3.01
177 249 3.248602 GCAAAGAAAGCGACTTGAGAGAA 59.751 43.478 0.00 0.00 0.00 2.87
179 251 2.096019 GGCAAAGAAAGCGACTTGAGAG 60.096 50.000 0.00 0.00 0.00 3.20
180 252 1.873591 GGCAAAGAAAGCGACTTGAGA 59.126 47.619 0.00 0.00 0.00 3.27
181 253 1.398960 CGGCAAAGAAAGCGACTTGAG 60.399 52.381 0.00 0.00 0.00 3.02
182 254 0.586319 CGGCAAAGAAAGCGACTTGA 59.414 50.000 0.00 0.00 0.00 3.02
184 256 1.873698 TACGGCAAAGAAAGCGACTT 58.126 45.000 0.00 0.00 0.00 3.01
186 258 2.158841 TGAATACGGCAAAGAAAGCGAC 59.841 45.455 0.00 0.00 0.00 5.19
187 259 2.418692 TGAATACGGCAAAGAAAGCGA 58.581 42.857 0.00 0.00 0.00 4.93
188 260 2.892373 TGAATACGGCAAAGAAAGCG 57.108 45.000 0.00 0.00 0.00 4.68
189 261 4.105486 GGATTGAATACGGCAAAGAAAGC 58.895 43.478 0.00 0.00 0.00 3.51
190 262 5.309323 TGGATTGAATACGGCAAAGAAAG 57.691 39.130 0.00 0.00 0.00 2.62
191 263 5.913137 ATGGATTGAATACGGCAAAGAAA 57.087 34.783 0.00 0.00 0.00 2.52
194 266 6.966435 AAAAATGGATTGAATACGGCAAAG 57.034 33.333 0.00 0.00 0.00 2.77
219 291 4.794278 TGAATGAAGCAATTGCAGTGAT 57.206 36.364 30.89 15.57 45.16 3.06
220 292 4.587584 TTGAATGAAGCAATTGCAGTGA 57.412 36.364 30.89 13.94 45.16 3.41
221 293 5.856126 ATTTGAATGAAGCAATTGCAGTG 57.144 34.783 30.89 0.00 45.16 3.66
222 294 5.992829 TCAATTTGAATGAAGCAATTGCAGT 59.007 32.000 30.89 18.85 45.16 4.40
223 295 6.367695 TCTCAATTTGAATGAAGCAATTGCAG 59.632 34.615 30.89 14.51 45.16 4.41
224 296 6.224584 TCTCAATTTGAATGAAGCAATTGCA 58.775 32.000 30.89 12.29 45.16 4.08
225 297 6.715344 TCTCAATTTGAATGAAGCAATTGC 57.285 33.333 23.05 23.05 42.49 3.56
226 298 9.755064 GAAATCTCAATTTGAATGAAGCAATTG 57.245 29.630 0.00 0.00 35.21 2.32
227 299 9.496873 TGAAATCTCAATTTGAATGAAGCAATT 57.503 25.926 0.01 0.00 35.21 2.32
229 301 8.145767 ACTGAAATCTCAATTTGAATGAAGCAA 58.854 29.630 0.01 0.00 35.21 3.91
231 303 7.275123 GGACTGAAATCTCAATTTGAATGAAGC 59.725 37.037 0.01 0.00 35.21 3.86
232 304 7.484007 CGGACTGAAATCTCAATTTGAATGAAG 59.516 37.037 0.01 0.00 35.21 3.02
233 305 7.040478 ACGGACTGAAATCTCAATTTGAATGAA 60.040 33.333 0.01 0.00 35.21 2.57
235 307 6.615088 ACGGACTGAAATCTCAATTTGAATG 58.385 36.000 0.01 0.00 35.21 2.67
236 308 6.824305 ACGGACTGAAATCTCAATTTGAAT 57.176 33.333 0.01 0.00 35.21 2.57
237 309 6.633500 AACGGACTGAAATCTCAATTTGAA 57.367 33.333 0.01 0.00 35.21 2.69
239 311 6.801862 GGTAAACGGACTGAAATCTCAATTTG 59.198 38.462 0.00 0.00 35.21 2.32
240 312 6.348213 CGGTAAACGGACTGAAATCTCAATTT 60.348 38.462 0.00 0.00 37.04 1.82
241 313 5.121768 CGGTAAACGGACTGAAATCTCAATT 59.878 40.000 0.00 0.00 39.42 2.32
243 315 3.991773 CGGTAAACGGACTGAAATCTCAA 59.008 43.478 0.00 0.00 39.42 3.02
278 351 2.482374 GTCCGCTTCATGCACAGC 59.518 61.111 4.58 4.58 43.06 4.40
279 352 1.291184 TTCGTCCGCTTCATGCACAG 61.291 55.000 0.00 0.00 43.06 3.66
286 359 1.873165 GGCATTTTCGTCCGCTTCA 59.127 52.632 0.00 0.00 0.00 3.02
290 363 4.174129 CCCGGCATTTTCGTCCGC 62.174 66.667 0.00 0.00 41.68 5.54
295 368 4.474846 CACGCCCCGGCATTTTCG 62.475 66.667 6.52 0.00 42.06 3.46
308 381 0.724785 GGTAAACAAAGAGCGCACGC 60.725 55.000 11.47 6.99 42.33 5.34
696 859 3.636764 GAGGAAAAGCAACTTGGGAGAAA 59.363 43.478 0.00 0.00 0.00 2.52
947 1135 5.512753 TGCTTGTCTTCATGTTAGCAAAA 57.487 34.783 0.00 0.00 35.86 2.44
1085 1273 8.877864 AAGAATAGACCCAATATTCACAACAA 57.122 30.769 8.06 0.00 40.55 2.83
1142 1330 2.352821 GCTGCATGGATGGCAACCA 61.353 57.895 19.40 19.40 41.39 3.67
1162 1350 6.416631 TGGATCAGAGTTGATATCTTCCAG 57.583 41.667 3.98 0.00 44.01 3.86
1270 1458 9.853555 CAAATGAATGTGTGGTATTAAAGCTAA 57.146 29.630 0.00 0.00 0.00 3.09
1281 1469 6.041409 TCAACAATACCAAATGAATGTGTGGT 59.959 34.615 0.00 0.00 46.12 4.16
1307 1495 7.224297 ACTCCACAAGAGAAGCAAAAACTATA 58.776 34.615 0.00 0.00 46.50 1.31
1342 1531 5.204409 TGATACAAGGAATACGCGGTATT 57.796 39.130 12.47 12.09 40.82 1.89
1347 1536 2.743938 AGCTGATACAAGGAATACGCG 58.256 47.619 3.53 3.53 0.00 6.01
1348 1537 4.786609 GCAAAGCTGATACAAGGAATACGC 60.787 45.833 0.00 0.00 0.00 4.42
1638 1827 1.067425 TGCATCATCCAAAGCAGCAAC 60.067 47.619 0.00 0.00 32.48 4.17
1686 1875 1.686587 GGAAGGAAACCCAACCTTGTG 59.313 52.381 0.00 0.00 45.08 3.33
1748 1937 8.913487 TGATAACACGAGACTCCATATAACTA 57.087 34.615 0.00 0.00 0.00 2.24
2311 2506 0.317269 CACGCCATTTCCGATGATGC 60.317 55.000 0.00 0.00 0.00 3.91
2328 2523 1.496934 CAAAAACCAATGGTCCGCAC 58.503 50.000 4.95 0.00 33.12 5.34
2525 2720 9.788960 ACAAACTCTTTGAAACTAAATCTGTTC 57.211 29.630 1.75 0.00 43.26 3.18
2769 2966 6.152932 AGCATGGTATGATGAAATGGTTTC 57.847 37.500 0.00 0.00 40.08 2.78
2805 3002 1.213296 TTCCTGCAGGATAAGACCCC 58.787 55.000 35.42 0.00 44.98 4.95
2806 3003 3.481453 GAATTCCTGCAGGATAAGACCC 58.519 50.000 35.42 16.21 44.98 4.46
2807 3004 3.134458 CGAATTCCTGCAGGATAAGACC 58.866 50.000 35.42 19.04 44.98 3.85
2808 3005 4.060038 TCGAATTCCTGCAGGATAAGAC 57.940 45.455 35.42 21.80 44.98 3.01
2982 3179 0.941542 CAACCCTGTAACACACCACG 59.058 55.000 0.00 0.00 0.00 4.94
3384 3897 9.450807 GCCATGATAAGAACATTTGTAATACAC 57.549 33.333 0.00 0.00 0.00 2.90
3525 4052 7.457561 ACAAAATGTTACCTATGGCCAAAAAT 58.542 30.769 10.96 0.00 0.00 1.82
3916 4459 4.959839 ACAAAAACAGTTCAACATAGGGGT 59.040 37.500 0.00 0.00 0.00 4.95
4128 4835 3.070018 GCCGCAGATAAGTGCAGATAAT 58.930 45.455 0.00 0.00 44.21 1.28
4133 4840 2.012237 CAGCCGCAGATAAGTGCAG 58.988 57.895 0.00 0.00 44.21 4.41
4198 4906 3.153919 GGTGGAATGAACTTGTAAGGCA 58.846 45.455 0.00 0.00 0.00 4.75
4216 4926 0.251742 TCCCTTGGAAATGCCTGGTG 60.252 55.000 0.00 0.00 37.63 4.17
4540 5250 2.105128 CATGGACCGCCTCTCGTC 59.895 66.667 0.00 0.00 36.19 4.20
4631 5341 1.810031 CGCTGGTGTTTCTGACTTCCA 60.810 52.381 0.00 0.00 34.03 3.53
4645 5355 4.618227 GCTTTCCATTTCAATAACGCTGGT 60.618 41.667 0.00 0.00 0.00 4.00
4646 5356 3.859386 GCTTTCCATTTCAATAACGCTGG 59.141 43.478 0.00 0.00 0.00 4.85
4706 5417 4.362476 GTTGCCCCGCTGCTTTGG 62.362 66.667 0.00 0.00 0.00 3.28
4710 5422 4.586235 AACAGTTGCCCCGCTGCT 62.586 61.111 0.00 0.00 36.26 4.24
4716 5428 0.820871 TCACACAAAACAGTTGCCCC 59.179 50.000 0.00 0.00 0.00 5.80
4917 5630 2.237143 CTCTGAAGTGGCAAGATACCCA 59.763 50.000 0.00 0.00 0.00 4.51
4998 5712 3.577649 AGTGACACAATCCTACTGACG 57.422 47.619 8.59 0.00 0.00 4.35
5046 5763 2.284331 TAACTCCAGCCGGCAGGA 60.284 61.111 35.28 35.28 41.02 3.86
5058 5775 5.118203 GTCACACATCAAACGGTACTAACTC 59.882 44.000 0.00 0.00 0.00 3.01
5061 5778 3.982701 CGTCACACATCAAACGGTACTAA 59.017 43.478 0.00 0.00 0.00 2.24
5107 5824 7.809806 ACTAGTTTATGAACAAGCATCAAAAGC 59.190 33.333 2.93 0.00 38.26 3.51
5174 5891 9.113838 CAGACAAAACAGAGTATATAAGCCAAT 57.886 33.333 0.00 0.00 0.00 3.16
5321 6039 9.449719 TGGCTTTCTTCTTAACTTTCCTAATAG 57.550 33.333 0.00 0.00 0.00 1.73
5400 6118 5.918426 TTTGCATCAATTGGAGCTAATCA 57.082 34.783 19.06 1.76 0.00 2.57
5446 6164 4.643784 GCTTGGGATTGATCTGATTCAGTT 59.356 41.667 13.23 5.27 32.61 3.16
5452 6170 4.041444 GGAGTAGCTTGGGATTGATCTGAT 59.959 45.833 0.00 0.00 0.00 2.90
5469 6187 5.314529 TCTAATATGTGACGGAGGGAGTAG 58.685 45.833 0.00 0.00 0.00 2.57
5518 6271 4.104897 AGAAACAAAAAGCTACTCCCTCCT 59.895 41.667 0.00 0.00 0.00 3.69
5532 6285 8.746052 TCCAGTAAGATTTGAGAGAAACAAAA 57.254 30.769 0.00 0.00 39.95 2.44
5533 6286 8.621286 GTTCCAGTAAGATTTGAGAGAAACAAA 58.379 33.333 0.00 0.00 40.62 2.83
5538 6291 6.423905 CGTTGTTCCAGTAAGATTTGAGAGAA 59.576 38.462 0.00 0.00 0.00 2.87
5561 6314 2.213499 CTTTTGAGAACAGTGGCTCGT 58.787 47.619 9.74 0.00 33.89 4.18
5572 6325 6.219417 TGCAAGAATTTCCACTTTTGAGAA 57.781 33.333 0.00 0.00 0.00 2.87
5625 6378 2.558313 GAGGTGCACGCAAGAAGC 59.442 61.111 11.45 0.00 43.62 3.86
5626 6379 2.671177 CGGAGGTGCACGCAAGAAG 61.671 63.158 11.45 0.00 43.62 2.85
5627 6380 2.664851 CGGAGGTGCACGCAAGAA 60.665 61.111 11.45 0.00 43.62 2.52
5628 6381 3.573772 CTCGGAGGTGCACGCAAGA 62.574 63.158 11.45 7.11 43.62 3.02
5630 6383 2.652382 TTTCTCGGAGGTGCACGCAA 62.652 55.000 11.45 0.00 0.00 4.85
5631 6384 2.449031 ATTTCTCGGAGGTGCACGCA 62.449 55.000 11.45 0.00 0.00 5.24
5632 6385 0.459585 TATTTCTCGGAGGTGCACGC 60.460 55.000 11.45 5.21 0.00 5.34
5636 6389 3.746045 TGGTATATTTCTCGGAGGTGC 57.254 47.619 4.96 0.00 0.00 5.01
5643 6396 8.601845 TTGTGATTGGTATGGTATATTTCTCG 57.398 34.615 0.00 0.00 0.00 4.04


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

AutoCloner maintained by Alex Coulton.