Multiple sequence alignment - TraesCS5B01G511600

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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 TraesCS5B01G511600 chr5B 100.000 6827 0 0 1 6827 676932407 676925581 0.000000e+00 12608.0
1 TraesCS5B01G511600 chr5B 96.970 99 2 1 4218 4316 678507379 678507282 1.520000e-36 165.0
2 TraesCS5B01G511600 chr5B 96.907 97 3 0 4212 4308 676928097 676928193 5.480000e-36 163.0
3 TraesCS5B01G511600 chr4A 96.743 4268 85 29 1 4221 634836131 634840391 0.000000e+00 7062.0
4 TraesCS5B01G511600 chr4A 92.802 2584 95 30 4303 6827 634840389 634842940 0.000000e+00 3657.0
5 TraesCS5B01G511600 chr4A 97.959 98 2 0 4219 4316 697942077 697941980 3.270000e-38 171.0
6 TraesCS5B01G511600 chr4A 97.938 97 2 0 4362 4458 58113534 58113438 1.180000e-37 169.0
7 TraesCS5B01G511600 chr4A 97.938 97 2 0 4362 4458 115567140 115567236 1.180000e-37 169.0
8 TraesCS5B01G511600 chr4A 90.678 118 8 2 4362 4479 39876333 39876447 3.300000e-33 154.0
9 TraesCS5B01G511600 chr4A 88.710 62 2 1 3590 3646 634839817 634839878 3.420000e-08 71.3
10 TraesCS5B01G511600 chr5D 97.276 3267 72 7 1 3251 536421127 536417862 0.000000e+00 5524.0
11 TraesCS5B01G511600 chr5D 92.861 1723 72 20 4472 6155 536416628 536414918 0.000000e+00 2453.0
12 TraesCS5B01G511600 chr5D 95.503 845 26 8 3382 4221 536417523 536416686 0.000000e+00 1339.0
13 TraesCS5B01G511600 chr5D 87.004 454 30 11 6191 6631 536414912 536414475 1.030000e-132 484.0
14 TraesCS5B01G511600 chr5D 94.366 142 5 1 3245 3383 536417824 536417683 1.490000e-51 215.0
15 TraesCS5B01G511600 chr7B 97.959 98 2 0 4211 4308 432933332 432933235 3.270000e-38 171.0
16 TraesCS5B01G511600 chr7B 93.636 110 4 3 4197 4304 110241860 110241968 1.970000e-35 161.0
17 TraesCS5B01G511600 chr7B 91.453 117 6 4 4197 4310 48864089 48864204 2.550000e-34 158.0
18 TraesCS5B01G511600 chr7D 97.938 97 2 0 4362 4458 397569629 397569533 1.180000e-37 169.0
19 TraesCS5B01G511600 chr4B 97.938 97 2 0 4362 4458 494225877 494225781 1.180000e-37 169.0
20 TraesCS5B01G511600 chr4B 96.117 103 2 2 4214 4314 250706482 250706584 4.240000e-37 167.0
21 TraesCS5B01G511600 chr3D 97.938 97 2 0 4362 4458 260983796 260983892 1.180000e-37 169.0
22 TraesCS5B01G511600 chr3D 97.938 97 2 0 4362 4458 313292465 313292369 1.180000e-37 169.0
23 TraesCS5B01G511600 chr3D 97.059 34 1 0 757 790 346090884 346090917 2.660000e-04 58.4
24 TraesCS5B01G511600 chr1D 97.938 97 2 0 4362 4458 105351573 105351669 1.180000e-37 169.0
25 TraesCS5B01G511600 chr6B 90.000 120 8 4 4194 4312 676296643 676296527 1.190000e-32 152.0
26 TraesCS5B01G511600 chr6B 88.983 118 13 0 516 633 86095925 86095808 5.520000e-31 147.0
27 TraesCS5B01G511600 chr3B 90.435 115 11 0 4194 4308 204288924 204289038 1.190000e-32 152.0
28 TraesCS5B01G511600 chr3B 97.297 37 1 0 749 785 641665998 641665962 5.720000e-06 63.9
29 TraesCS5B01G511600 chr7A 85.897 78 11 0 6637 6714 74415898 74415821 4.390000e-12 84.2
30 TraesCS5B01G511600 chr7A 88.889 63 7 0 6653 6715 251743273 251743335 2.040000e-10 78.7
31 TraesCS5B01G511600 chr5A 97.436 39 1 0 747 785 290394474 290394512 4.420000e-07 67.6
32 TraesCS5B01G511600 chr2B 95.000 40 2 0 746 785 116390684 116390723 5.720000e-06 63.9
33 TraesCS5B01G511600 chr2B 94.444 36 1 1 751 786 706722765 706722731 3.000000e-03 54.7
34 TraesCS5B01G511600 chr6A 80.000 85 12 4 701 783 486352133 486352214 2.660000e-04 58.4
35 TraesCS5B01G511600 chr3A 94.595 37 2 0 692 728 621664434 621664470 2.660000e-04 58.4


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 TraesCS5B01G511600 chr5B 676925581 676932407 6826 True 12608.000000 12608 100.000000 1 6827 1 chr5B.!!$R1 6826
1 TraesCS5B01G511600 chr4A 634836131 634842940 6809 False 3596.766667 7062 92.751667 1 6827 3 chr4A.!!$F3 6826
2 TraesCS5B01G511600 chr5D 536414475 536421127 6652 True 2003.000000 5524 93.402000 1 6631 5 chr5D.!!$R1 6630

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
657 680 0.178992 CTGGACTTGCACTTGGGGAA 60.179 55.0 0.0 0.0 0.00 3.97 F
1014 1055 0.173255 AAATCATGGCGCGAAAAGGG 59.827 50.0 12.1 0.0 0.00 3.95 F
1548 1589 0.804544 CAGCTTTCATGGCAATGGCG 60.805 55.0 0.0 0.0 42.47 5.69 F
2722 2768 0.679640 TCGGCATTTGGATTTCGCCT 60.680 50.0 0.0 0.0 40.72 5.52 F
4111 4372 0.314935 CTTGCAACTGCCATCGGTTT 59.685 50.0 0.0 0.0 39.67 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1548 1589 0.455815 CATAGGCACGCCCTTTTTCC 59.544 55.0 3.95 0.00 43.06 3.13 R
2705 2751 0.532115 ACAGGCGAAATCCAAATGCC 59.468 50.0 0.00 0.00 46.07 4.40 R
2791 2837 2.611292 GGCACTCATACAGCTGACATTC 59.389 50.0 23.35 1.27 0.00 2.67 R
4286 4548 0.033796 TGTACTCCCTCCGTTCCGAT 60.034 55.0 0.00 0.00 0.00 4.18 R
5894 6221 0.179045 CCAGTCTTTAGCATCCGGGG 60.179 60.0 0.00 0.00 0.00 5.73 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
323 345 9.944663 TGTTGTTATGTTTAGAGATGTTGTTTC 57.055 29.630 0.00 0.00 0.00 2.78
330 352 8.050778 TGTTTAGAGATGTTGTTTCTGTTGTT 57.949 30.769 0.00 0.00 0.00 2.83
331 353 9.168451 TGTTTAGAGATGTTGTTTCTGTTGTTA 57.832 29.630 0.00 0.00 0.00 2.41
332 354 9.651718 GTTTAGAGATGTTGTTTCTGTTGTTAG 57.348 33.333 0.00 0.00 0.00 2.34
333 355 8.958119 TTAGAGATGTTGTTTCTGTTGTTAGT 57.042 30.769 0.00 0.00 0.00 2.24
378 401 3.084039 CCTAGTGAGCTTGCCAATTTCA 58.916 45.455 0.00 0.00 0.00 2.69
410 433 1.531602 GCTGTTTGGTTCCTGCCCT 60.532 57.895 0.00 0.00 0.00 5.19
648 671 1.902508 CCCTAAGAGTCTGGACTTGCA 59.097 52.381 4.67 0.00 42.66 4.08
657 680 0.178992 CTGGACTTGCACTTGGGGAA 60.179 55.000 0.00 0.00 0.00 3.97
669 692 1.542915 CTTGGGGAAAGTGATGTGCTG 59.457 52.381 0.00 0.00 0.00 4.41
672 695 1.815003 GGGGAAAGTGATGTGCTGAAG 59.185 52.381 0.00 0.00 0.00 3.02
690 721 3.054139 TGAAGCTCTATGACATTGGCCTT 60.054 43.478 3.32 0.00 0.00 4.35
694 725 2.617308 CTCTATGACATTGGCCTTGCAG 59.383 50.000 3.32 0.00 0.00 4.41
723 755 5.394333 GCTACTCCCTCCGATCCATATTAAC 60.394 48.000 0.00 0.00 0.00 2.01
728 760 4.322801 CCCTCCGATCCATATTAACTGTCC 60.323 50.000 0.00 0.00 0.00 4.02
731 763 4.527038 TCCGATCCATATTAACTGTCCCTC 59.473 45.833 0.00 0.00 0.00 4.30
733 765 5.230942 CGATCCATATTAACTGTCCCTCAC 58.769 45.833 0.00 0.00 0.00 3.51
748 780 5.063880 GTCCCTCACAATATGGTTCCATAC 58.936 45.833 12.94 0.00 32.57 2.39
772 804 8.099364 ACTAATTCAGCGACAATTAATATGGG 57.901 34.615 0.00 0.00 0.00 4.00
985 1026 3.262420 CCTAAACTGAGAATCCACCACG 58.738 50.000 0.00 0.00 0.00 4.94
1014 1055 0.173255 AAATCATGGCGCGAAAAGGG 59.827 50.000 12.10 0.00 0.00 3.95
1015 1056 1.666209 AATCATGGCGCGAAAAGGGG 61.666 55.000 12.10 0.00 0.00 4.79
1389 1430 8.074370 GGTAAAAACTCATCAGTAGAACAAACC 58.926 37.037 0.00 0.00 30.14 3.27
1548 1589 0.804544 CAGCTTTCATGGCAATGGCG 60.805 55.000 0.00 0.00 42.47 5.69
1825 1866 8.406297 TCTTTTTCTTCTTTTCTAGTTGCCTTC 58.594 33.333 0.00 0.00 0.00 3.46
1911 1952 0.978907 TCCTCTCATGAGTGCAAGCA 59.021 50.000 21.92 0.19 38.61 3.91
1987 2031 2.362736 TCTGCAGTTGATGATGCCTTC 58.637 47.619 14.67 0.00 41.85 3.46
2456 2502 9.525409 CTGAATTTGTCTTTCTTTTCAACTGAT 57.475 29.630 0.00 0.00 0.00 2.90
2705 2751 1.139989 ATTGCGCCGATCACTATTCG 58.860 50.000 4.18 0.00 36.38 3.34
2722 2768 0.679640 TCGGCATTTGGATTTCGCCT 60.680 50.000 0.00 0.00 40.72 5.52
2791 2837 8.742554 AAAAAGGTGATGCTAAAGATAAAACG 57.257 30.769 0.00 0.00 0.00 3.60
3367 3462 3.648339 TTTTGAAGTGCATGAGAAGGC 57.352 42.857 0.00 0.00 0.00 4.35
3666 3924 2.237143 CCTAGTGGAAGTTGATCTGGCA 59.763 50.000 0.00 0.00 34.57 4.92
3691 3950 7.645058 AGGAATTGGTATGGATTTTACTGTG 57.355 36.000 0.00 0.00 0.00 3.66
4111 4372 0.314935 CTTGCAACTGCCATCGGTTT 59.685 50.000 0.00 0.00 39.67 3.27
4196 4458 6.931281 TGGTCTGAGATAAAAACAGAAGACAG 59.069 38.462 0.00 0.00 41.31 3.51
4228 4490 5.168647 AGATGTAGTATCTACTCCCTCCG 57.831 47.826 8.13 0.00 37.73 4.63
4229 4491 4.598373 AGATGTAGTATCTACTCCCTCCGT 59.402 45.833 8.13 0.00 37.73 4.69
4230 4492 4.785346 TGTAGTATCTACTCCCTCCGTT 57.215 45.455 8.13 0.00 37.73 4.44
4231 4493 4.712476 TGTAGTATCTACTCCCTCCGTTC 58.288 47.826 8.13 0.00 37.73 3.95
4232 4494 3.226682 AGTATCTACTCCCTCCGTTCC 57.773 52.381 0.00 0.00 0.00 3.62
4233 4495 1.878734 GTATCTACTCCCTCCGTTCCG 59.121 57.143 0.00 0.00 0.00 4.30
4234 4496 0.549950 ATCTACTCCCTCCGTTCCGA 59.450 55.000 0.00 0.00 0.00 4.55
4235 4497 0.549950 TCTACTCCCTCCGTTCCGAT 59.450 55.000 0.00 0.00 0.00 4.18
4236 4498 1.064166 TCTACTCCCTCCGTTCCGATT 60.064 52.381 0.00 0.00 0.00 3.34
4237 4499 1.755380 CTACTCCCTCCGTTCCGATTT 59.245 52.381 0.00 0.00 0.00 2.17
4238 4500 1.856629 ACTCCCTCCGTTCCGATTTA 58.143 50.000 0.00 0.00 0.00 1.40
4239 4501 1.479730 ACTCCCTCCGTTCCGATTTAC 59.520 52.381 0.00 0.00 0.00 2.01
4240 4502 1.755380 CTCCCTCCGTTCCGATTTACT 59.245 52.381 0.00 0.00 0.00 2.24
4241 4503 1.753073 TCCCTCCGTTCCGATTTACTC 59.247 52.381 0.00 0.00 0.00 2.59
4243 4505 1.133790 CCTCCGTTCCGATTTACTCGT 59.866 52.381 0.00 0.00 46.18 4.18
4244 4506 2.448219 CTCCGTTCCGATTTACTCGTC 58.552 52.381 0.00 0.00 46.18 4.20
4245 4507 1.186030 CCGTTCCGATTTACTCGTCG 58.814 55.000 0.00 0.00 46.18 5.12
4246 4508 1.466360 CCGTTCCGATTTACTCGTCGT 60.466 52.381 0.00 0.00 46.18 4.34
4247 4509 1.576246 CGTTCCGATTTACTCGTCGTG 59.424 52.381 0.00 0.00 46.18 4.35
4248 4510 1.916000 GTTCCGATTTACTCGTCGTGG 59.084 52.381 0.00 0.00 46.18 4.94
4249 4511 1.167851 TCCGATTTACTCGTCGTGGT 58.832 50.000 0.00 0.00 46.18 4.16
4250 4512 1.541147 TCCGATTTACTCGTCGTGGTT 59.459 47.619 0.00 0.00 46.18 3.67
4251 4513 2.030007 TCCGATTTACTCGTCGTGGTTT 60.030 45.455 0.00 0.00 46.18 3.27
4252 4514 2.733026 CCGATTTACTCGTCGTGGTTTT 59.267 45.455 0.00 0.00 46.18 2.43
4253 4515 3.919804 CCGATTTACTCGTCGTGGTTTTA 59.080 43.478 0.00 0.00 46.18 1.52
4254 4516 4.030977 CCGATTTACTCGTCGTGGTTTTAG 59.969 45.833 0.00 0.00 46.18 1.85
4255 4517 4.618489 CGATTTACTCGTCGTGGTTTTAGT 59.382 41.667 0.00 0.00 42.56 2.24
4256 4518 5.117592 CGATTTACTCGTCGTGGTTTTAGTT 59.882 40.000 0.00 0.00 42.56 2.24
4257 4519 5.888412 TTTACTCGTCGTGGTTTTAGTTC 57.112 39.130 0.00 0.00 0.00 3.01
4258 4520 3.441496 ACTCGTCGTGGTTTTAGTTCA 57.559 42.857 0.00 0.00 0.00 3.18
4259 4521 3.784338 ACTCGTCGTGGTTTTAGTTCAA 58.216 40.909 0.00 0.00 0.00 2.69
4260 4522 4.183101 ACTCGTCGTGGTTTTAGTTCAAA 58.817 39.130 0.00 0.00 0.00 2.69
4261 4523 4.812626 ACTCGTCGTGGTTTTAGTTCAAAT 59.187 37.500 0.00 0.00 0.00 2.32
4262 4524 5.295045 ACTCGTCGTGGTTTTAGTTCAAATT 59.705 36.000 0.00 0.00 0.00 1.82
4263 4525 6.121613 TCGTCGTGGTTTTAGTTCAAATTT 57.878 33.333 0.00 0.00 0.00 1.82
4264 4526 5.966503 TCGTCGTGGTTTTAGTTCAAATTTG 59.033 36.000 12.15 12.15 0.00 2.32
4265 4527 5.966503 CGTCGTGGTTTTAGTTCAAATTTGA 59.033 36.000 16.91 16.91 34.92 2.69
4266 4528 6.469595 CGTCGTGGTTTTAGTTCAAATTTGAA 59.530 34.615 26.01 26.01 44.31 2.69
4279 4541 7.743520 TTCAAATTTGAACTAAAACCACGAC 57.256 32.000 26.01 0.00 41.88 4.34
4280 4542 5.966503 TCAAATTTGAACTAAAACCACGACG 59.033 36.000 18.45 0.00 33.55 5.12
4281 4543 5.738118 AATTTGAACTAAAACCACGACGA 57.262 34.783 0.00 0.00 0.00 4.20
4282 4544 4.782252 TTTGAACTAAAACCACGACGAG 57.218 40.909 0.00 0.00 0.00 4.18
4283 4545 3.441496 TGAACTAAAACCACGACGAGT 57.559 42.857 0.00 0.00 0.00 4.18
4284 4546 4.566545 TGAACTAAAACCACGACGAGTA 57.433 40.909 0.00 0.00 0.00 2.59
4285 4547 4.930963 TGAACTAAAACCACGACGAGTAA 58.069 39.130 0.00 0.00 0.00 2.24
4286 4548 5.347342 TGAACTAAAACCACGACGAGTAAA 58.653 37.500 0.00 0.00 0.00 2.01
4287 4549 5.984926 TGAACTAAAACCACGACGAGTAAAT 59.015 36.000 0.00 0.00 0.00 1.40
4288 4550 6.144402 TGAACTAAAACCACGACGAGTAAATC 59.856 38.462 0.00 0.00 0.00 2.17
4376 4638 7.882791 TCTTTAGAAAGTATCAATGTGCCAGAA 59.117 33.333 2.10 0.00 37.31 3.02
4458 4720 5.416083 GGACTAAAGGCTTTGTTGTTGTTT 58.584 37.500 22.32 0.00 0.00 2.83
4459 4721 6.406065 GGGACTAAAGGCTTTGTTGTTGTTTA 60.406 38.462 22.32 0.00 0.00 2.01
4460 4722 6.695713 GGACTAAAGGCTTTGTTGTTGTTTAG 59.304 38.462 22.32 9.75 33.93 1.85
4461 4723 7.399245 ACTAAAGGCTTTGTTGTTGTTTAGA 57.601 32.000 22.32 0.00 32.68 2.10
4462 4724 7.832769 ACTAAAGGCTTTGTTGTTGTTTAGAA 58.167 30.769 22.32 0.00 32.68 2.10
4463 4725 8.308207 ACTAAAGGCTTTGTTGTTGTTTAGAAA 58.692 29.630 22.32 0.00 32.68 2.52
4466 4728 7.399245 AGGCTTTGTTGTTGTTTAGAAAGTA 57.601 32.000 0.00 0.00 0.00 2.24
4467 4729 7.255569 AGGCTTTGTTGTTGTTTAGAAAGTAC 58.744 34.615 0.00 0.00 0.00 2.73
4469 4731 7.431376 GGCTTTGTTGTTGTTTAGAAAGTACTC 59.569 37.037 0.00 0.00 0.00 2.59
4470 4732 7.431376 GCTTTGTTGTTGTTTAGAAAGTACTCC 59.569 37.037 0.00 0.00 0.00 3.85
4739 5006 3.054878 GGTTGCTTTTGATTCTGTGCTG 58.945 45.455 0.00 0.00 0.00 4.41
5190 5466 5.964958 TCTGTTTGAATCACTGAAATCCC 57.035 39.130 0.00 0.00 0.00 3.85
5288 5566 6.183360 CCACTGTTAGTTTGAAGTTTAGCCAA 60.183 38.462 0.00 0.00 0.00 4.52
5312 5592 1.833630 CTCTGGGCATTGTCTCCAGTA 59.166 52.381 16.56 7.88 45.97 2.74
5325 5605 7.450124 TTGTCTCCAGTACTCAGTTTACTAG 57.550 40.000 0.00 0.00 0.00 2.57
5328 5608 8.327271 TGTCTCCAGTACTCAGTTTACTAGTAT 58.673 37.037 2.79 0.00 0.00 2.12
5329 5609 9.176460 GTCTCCAGTACTCAGTTTACTAGTATT 57.824 37.037 2.79 0.00 0.00 1.89
5553 5864 2.047274 AGATGCCCACCGAACACG 60.047 61.111 0.00 0.00 0.00 4.49
5616 5927 0.960861 GTAGTGGCAAAGGGAGCACC 60.961 60.000 0.00 0.00 40.67 5.01
5859 6179 7.120138 TGGTCTGGGAAAAGATAAATAAACGAC 59.880 37.037 0.00 0.00 0.00 4.34
5863 6183 9.908152 CTGGGAAAAGATAAATAAACGACTTTT 57.092 29.630 0.00 0.00 39.26 2.27
5864 6184 9.685828 TGGGAAAAGATAAATAAACGACTTTTG 57.314 29.630 0.00 0.00 37.57 2.44
5865 6185 9.902196 GGGAAAAGATAAATAAACGACTTTTGA 57.098 29.630 0.00 0.00 37.57 2.69
5894 6221 2.030274 ACAAATGGCCAACTTAGTTCGC 60.030 45.455 10.96 6.16 0.00 4.70
5918 6246 1.336125 GGATGCTAAAGACTGGCATGC 59.664 52.381 9.90 9.90 45.14 4.06
5920 6248 1.456296 TGCTAAAGACTGGCATGCTG 58.544 50.000 18.92 13.27 0.00 4.41
5940 6268 1.153823 GCGTACGCTGAGACACCAT 60.154 57.895 31.95 0.00 38.26 3.55
5941 6269 1.140407 GCGTACGCTGAGACACCATC 61.140 60.000 31.95 0.00 38.26 3.51
6006 6334 5.468746 AGAATCGAAATTCAGACGGAAAACA 59.531 36.000 1.86 0.00 43.21 2.83
6061 6389 7.094549 TGGATGTATTGTTACTTGCCTTACAAC 60.095 37.037 0.00 0.00 33.77 3.32
6087 6415 5.018149 GGCCCAAAAATGTTACCCTAAGTA 58.982 41.667 0.00 0.00 0.00 2.24
6136 6464 5.480205 GAAACTTGTCTATTCTTCTCGGGT 58.520 41.667 0.00 0.00 0.00 5.28
6137 6465 4.722361 ACTTGTCTATTCTTCTCGGGTC 57.278 45.455 0.00 0.00 0.00 4.46
6138 6466 4.087182 ACTTGTCTATTCTTCTCGGGTCA 58.913 43.478 0.00 0.00 0.00 4.02
6146 6474 1.140052 TCTTCTCGGGTCAAACTTGCA 59.860 47.619 0.00 0.00 0.00 4.08
6147 6475 2.154462 CTTCTCGGGTCAAACTTGCAT 58.846 47.619 0.00 0.00 0.00 3.96
6148 6476 2.270352 TCTCGGGTCAAACTTGCATT 57.730 45.000 0.00 0.00 0.00 3.56
6149 6477 2.582052 TCTCGGGTCAAACTTGCATTT 58.418 42.857 0.00 0.00 0.00 2.32
6150 6478 3.745799 TCTCGGGTCAAACTTGCATTTA 58.254 40.909 0.00 0.00 0.00 1.40
6151 6479 4.331968 TCTCGGGTCAAACTTGCATTTAT 58.668 39.130 0.00 0.00 0.00 1.40
6152 6480 4.764823 TCTCGGGTCAAACTTGCATTTATT 59.235 37.500 0.00 0.00 0.00 1.40
6153 6481 5.242838 TCTCGGGTCAAACTTGCATTTATTT 59.757 36.000 0.00 0.00 0.00 1.40
6154 6482 5.848406 TCGGGTCAAACTTGCATTTATTTT 58.152 33.333 0.00 0.00 0.00 1.82
6158 6486 9.360093 CGGGTCAAACTTGCATTTATTTTATTA 57.640 29.630 0.00 0.00 0.00 0.98
6219 6547 7.864379 AGAAATGTTTATCTTGACTTTGCTGTG 59.136 33.333 0.00 0.00 0.00 3.66
6234 6562 1.808945 GCTGTGGTTCTCATGGTCTTG 59.191 52.381 0.00 0.00 0.00 3.02
6246 6585 6.166279 TCTCATGGTCTTGAACACTTGATAC 58.834 40.000 0.00 0.00 0.00 2.24
6292 6631 2.412847 GCTGAATTGTCCAGTTGTACGC 60.413 50.000 0.00 0.00 34.29 4.42
6298 6637 1.301401 TCCAGTTGTACGCAGCCAC 60.301 57.895 0.00 0.00 0.00 5.01
6331 6670 2.897326 ACCATTAAGCTCCCAACCAAAC 59.103 45.455 0.00 0.00 0.00 2.93
6425 6764 3.808116 CAGTGACATGTCTCTGCTTTG 57.192 47.619 33.13 18.07 42.05 2.77
6426 6765 3.136763 CAGTGACATGTCTCTGCTTTGT 58.863 45.455 33.13 10.42 42.05 2.83
6427 6766 3.059120 CAGTGACATGTCTCTGCTTTGTG 60.059 47.826 33.13 16.92 42.05 3.33
6428 6767 1.875514 TGACATGTCTCTGCTTTGTGC 59.124 47.619 25.55 0.00 43.25 4.57
6429 6768 2.149578 GACATGTCTCTGCTTTGTGCT 58.850 47.619 18.83 0.00 43.37 4.40
6430 6769 2.551459 GACATGTCTCTGCTTTGTGCTT 59.449 45.455 18.83 0.00 43.37 3.91
6511 6850 4.523943 TGGTGAGCTTTAGCATCATGTTTT 59.476 37.500 4.33 0.00 45.16 2.43
6588 6928 3.433615 GCCTCACTAGCTTTGTGTACAAG 59.566 47.826 15.88 0.00 37.15 3.16
6606 6946 7.697291 GTGTACAAGCACAGAGATTAGTACTAC 59.303 40.741 0.91 0.00 39.07 2.73
6641 6981 5.778750 TGTAGCCCTTTATATGGACTACTCC 59.221 44.000 14.91 0.00 34.82 3.85
6648 6988 6.782988 CCTTTATATGGACTACTCCCTCTGAA 59.217 42.308 0.00 0.00 35.34 3.02
6662 7002 4.410228 TCCCTCTGAACCCAAATAGATGAG 59.590 45.833 0.00 0.00 0.00 2.90
6672 7012 9.274206 GAACCCAAATAGATGAGGTATAAACTC 57.726 37.037 0.00 0.00 35.55 3.01
6675 7015 8.432805 CCCAAATAGATGAGGTATAAACTCAGT 58.567 37.037 12.35 6.57 46.98 3.41
6684 7024 8.331730 TGAGGTATAAACTCAGTTAAAAAGGC 57.668 34.615 0.00 0.00 39.87 4.35
6690 7030 5.535753 AACTCAGTTAAAAAGGCAATGCT 57.464 34.783 4.82 0.00 0.00 3.79
6709 7049 7.569957 GCAATGCTTTCTAAGTTTGACCAAATG 60.570 37.037 0.00 0.00 32.36 2.32
6725 7065 4.099573 ACCAAATGTATACTCCCTCTGTCG 59.900 45.833 4.17 0.00 0.00 4.35
6747 7087 4.099573 CGGTCTGTCCCACAATATAAGACT 59.900 45.833 0.00 0.00 34.41 3.24
6773 7113 3.009723 TGCAAGCTAGCCATAACTTGAC 58.990 45.455 12.13 5.54 37.30 3.18
6777 7117 5.634896 CAAGCTAGCCATAACTTGACAAAG 58.365 41.667 12.13 0.00 37.30 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 0.853530 AAGCAAGGAACCCTCACCTT 59.146 50.000 0.00 0.00 45.87 3.50
323 345 9.150348 ACAAAATTCCTCAAAAACTAACAACAG 57.850 29.630 0.00 0.00 0.00 3.16
330 352 6.227298 TGGCACAAAATTCCTCAAAAACTA 57.773 33.333 0.00 0.00 31.92 2.24
331 353 5.096443 TGGCACAAAATTCCTCAAAAACT 57.904 34.783 0.00 0.00 31.92 2.66
378 401 4.149598 CCAAACAGCCCCTTAACTAACTT 58.850 43.478 0.00 0.00 0.00 2.66
476 499 2.781158 AAAGCGCTGGCAAAACGGT 61.781 52.632 12.58 3.49 43.41 4.83
657 680 2.855209 AGAGCTTCAGCACATCACTT 57.145 45.000 0.75 0.00 45.16 3.16
669 692 3.205784 AGGCCAATGTCATAGAGCTTC 57.794 47.619 5.01 0.00 0.00 3.86
672 695 1.336125 GCAAGGCCAATGTCATAGAGC 59.664 52.381 5.01 0.00 0.00 4.09
690 721 1.831736 GGAGGGAGTAGCTAAACTGCA 59.168 52.381 9.96 0.00 39.40 4.41
694 725 2.296752 GGATCGGAGGGAGTAGCTAAAC 59.703 54.545 0.00 0.00 0.00 2.01
723 755 3.054434 TGGAACCATATTGTGAGGGACAG 60.054 47.826 0.00 0.00 35.44 3.51
728 760 8.924511 AATTAGTATGGAACCATATTGTGAGG 57.075 34.615 15.28 0.00 40.49 3.86
731 763 8.292448 GCTGAATTAGTATGGAACCATATTGTG 58.708 37.037 15.28 4.92 40.49 3.33
733 765 7.387673 TCGCTGAATTAGTATGGAACCATATTG 59.612 37.037 15.28 2.07 40.49 1.90
748 780 8.099364 ACCCATATTAATTGTCGCTGAATTAG 57.901 34.615 0.00 0.00 29.28 1.73
772 804 2.168728 AGATTTTGCTACTCCCTCCGAC 59.831 50.000 0.00 0.00 0.00 4.79
941 982 1.900245 TGCATCACAGCAGTTCACAT 58.100 45.000 0.00 0.00 40.11 3.21
985 1026 2.476854 GCGCCATGATTTCACTCAAGAC 60.477 50.000 0.00 0.00 0.00 3.01
1014 1055 2.551032 CGGACCACTTTTACTTTGACCC 59.449 50.000 0.00 0.00 0.00 4.46
1015 1056 3.469739 TCGGACCACTTTTACTTTGACC 58.530 45.455 0.00 0.00 0.00 4.02
1389 1430 3.731867 GCTCTGTCAAAATACGCAATGGG 60.732 47.826 0.00 0.00 0.00 4.00
1548 1589 0.455815 CATAGGCACGCCCTTTTTCC 59.544 55.000 3.95 0.00 43.06 3.13
1825 1866 7.370383 AGCACAGTAAACATTAAATTGTCAGG 58.630 34.615 0.00 0.00 0.00 3.86
1987 2031 6.205658 GCAAGAGAGCATAATAAACCCTTAGG 59.794 42.308 0.00 0.00 40.04 2.69
2705 2751 0.532115 ACAGGCGAAATCCAAATGCC 59.468 50.000 0.00 0.00 46.07 4.40
2791 2837 2.611292 GGCACTCATACAGCTGACATTC 59.389 50.000 23.35 1.27 0.00 2.67
3666 3924 7.363793 GCACAGTAAAATCCATACCAATTCCTT 60.364 37.037 0.00 0.00 0.00 3.36
3691 3950 8.958043 CAAGAACATTGAACTTAACTAAACTGC 58.042 33.333 0.00 0.00 0.00 4.40
3766 4026 8.907222 AATGCTTTTCCAAACATTAAATCAGT 57.093 26.923 0.00 0.00 31.20 3.41
4111 4372 8.792633 CATTTCCCAAACACTAGTCTCATAAAA 58.207 33.333 0.00 0.00 0.00 1.52
4233 4495 6.144402 TGAACTAAAACCACGACGAGTAAATC 59.856 38.462 0.00 0.00 0.00 2.17
4234 4496 5.984926 TGAACTAAAACCACGACGAGTAAAT 59.015 36.000 0.00 0.00 0.00 1.40
4235 4497 5.347342 TGAACTAAAACCACGACGAGTAAA 58.653 37.500 0.00 0.00 0.00 2.01
4236 4498 4.930963 TGAACTAAAACCACGACGAGTAA 58.069 39.130 0.00 0.00 0.00 2.24
4237 4499 4.566545 TGAACTAAAACCACGACGAGTA 57.433 40.909 0.00 0.00 0.00 2.59
4238 4500 3.441496 TGAACTAAAACCACGACGAGT 57.559 42.857 0.00 0.00 0.00 4.18
4239 4501 4.782252 TTTGAACTAAAACCACGACGAG 57.218 40.909 0.00 0.00 0.00 4.18
4240 4502 5.738118 AATTTGAACTAAAACCACGACGA 57.262 34.783 0.00 0.00 0.00 4.20
4241 4503 5.966503 TCAAATTTGAACTAAAACCACGACG 59.033 36.000 18.45 0.00 33.55 5.12
4242 4504 7.743520 TTCAAATTTGAACTAAAACCACGAC 57.256 32.000 26.01 0.00 41.88 4.34
4255 4517 6.469595 CGTCGTGGTTTTAGTTCAAATTTGAA 59.530 34.615 26.01 26.01 44.31 2.69
4256 4518 5.966503 CGTCGTGGTTTTAGTTCAAATTTGA 59.033 36.000 16.91 16.91 34.92 2.69
4257 4519 5.966503 TCGTCGTGGTTTTAGTTCAAATTTG 59.033 36.000 12.15 12.15 0.00 2.32
4258 4520 6.121613 TCGTCGTGGTTTTAGTTCAAATTT 57.878 33.333 0.00 0.00 0.00 1.82
4259 4521 5.295045 ACTCGTCGTGGTTTTAGTTCAAATT 59.705 36.000 0.00 0.00 0.00 1.82
4260 4522 4.812626 ACTCGTCGTGGTTTTAGTTCAAAT 59.187 37.500 0.00 0.00 0.00 2.32
4261 4523 4.183101 ACTCGTCGTGGTTTTAGTTCAAA 58.817 39.130 0.00 0.00 0.00 2.69
4262 4524 3.784338 ACTCGTCGTGGTTTTAGTTCAA 58.216 40.909 0.00 0.00 0.00 2.69
4263 4525 3.441496 ACTCGTCGTGGTTTTAGTTCA 57.559 42.857 0.00 0.00 0.00 3.18
4264 4526 5.888412 TTTACTCGTCGTGGTTTTAGTTC 57.112 39.130 0.00 0.00 0.00 3.01
4265 4527 5.117592 CGATTTACTCGTCGTGGTTTTAGTT 59.882 40.000 0.00 0.00 42.56 2.24
4266 4528 4.618489 CGATTTACTCGTCGTGGTTTTAGT 59.382 41.667 0.00 0.00 42.56 2.24
4267 4529 4.030977 CCGATTTACTCGTCGTGGTTTTAG 59.969 45.833 0.00 0.00 46.18 1.85
4268 4530 3.919804 CCGATTTACTCGTCGTGGTTTTA 59.080 43.478 0.00 0.00 46.18 1.52
4269 4531 2.733026 CCGATTTACTCGTCGTGGTTTT 59.267 45.455 0.00 0.00 46.18 2.43
4270 4532 2.030007 TCCGATTTACTCGTCGTGGTTT 60.030 45.455 0.00 0.00 46.18 3.27
4271 4533 1.541147 TCCGATTTACTCGTCGTGGTT 59.459 47.619 0.00 0.00 46.18 3.67
4272 4534 1.167851 TCCGATTTACTCGTCGTGGT 58.832 50.000 0.00 0.00 46.18 4.16
4273 4535 1.916000 GTTCCGATTTACTCGTCGTGG 59.084 52.381 0.00 0.00 46.18 4.94
4274 4536 1.576246 CGTTCCGATTTACTCGTCGTG 59.424 52.381 0.00 0.00 46.18 4.35
4275 4537 1.466360 CCGTTCCGATTTACTCGTCGT 60.466 52.381 0.00 0.00 46.18 4.34
4276 4538 1.186030 CCGTTCCGATTTACTCGTCG 58.814 55.000 0.00 0.00 46.18 5.12
4277 4539 2.448219 CTCCGTTCCGATTTACTCGTC 58.552 52.381 0.00 0.00 46.18 4.20
4278 4540 1.133790 CCTCCGTTCCGATTTACTCGT 59.866 52.381 0.00 0.00 46.18 4.18
4280 4542 1.753073 TCCCTCCGTTCCGATTTACTC 59.247 52.381 0.00 0.00 0.00 2.59
4281 4543 1.755380 CTCCCTCCGTTCCGATTTACT 59.245 52.381 0.00 0.00 0.00 2.24
4282 4544 1.479730 ACTCCCTCCGTTCCGATTTAC 59.520 52.381 0.00 0.00 0.00 2.01
4283 4545 1.856629 ACTCCCTCCGTTCCGATTTA 58.143 50.000 0.00 0.00 0.00 1.40
4284 4546 1.479730 GTACTCCCTCCGTTCCGATTT 59.520 52.381 0.00 0.00 0.00 2.17
4285 4547 1.109609 GTACTCCCTCCGTTCCGATT 58.890 55.000 0.00 0.00 0.00 3.34
4286 4548 0.033796 TGTACTCCCTCCGTTCCGAT 60.034 55.000 0.00 0.00 0.00 4.18
4287 4549 0.033796 ATGTACTCCCTCCGTTCCGA 60.034 55.000 0.00 0.00 0.00 4.55
4288 4550 1.683943 TATGTACTCCCTCCGTTCCG 58.316 55.000 0.00 0.00 0.00 4.30
4289 4551 5.796424 TTAATATGTACTCCCTCCGTTCC 57.204 43.478 0.00 0.00 0.00 3.62
4290 4552 7.889469 TGTATTAATATGTACTCCCTCCGTTC 58.111 38.462 0.00 0.00 0.00 3.95
4291 4553 7.525029 GCTGTATTAATATGTACTCCCTCCGTT 60.525 40.741 0.00 0.00 0.00 4.44
4292 4554 6.071503 GCTGTATTAATATGTACTCCCTCCGT 60.072 42.308 0.00 0.00 0.00 4.69
4293 4555 6.153000 AGCTGTATTAATATGTACTCCCTCCG 59.847 42.308 0.00 0.00 0.00 4.63
4294 4556 7.483580 AGCTGTATTAATATGTACTCCCTCC 57.516 40.000 0.00 0.00 0.00 4.30
4295 4557 8.585881 TGAAGCTGTATTAATATGTACTCCCTC 58.414 37.037 0.00 0.00 0.00 4.30
4296 4558 8.492415 TGAAGCTGTATTAATATGTACTCCCT 57.508 34.615 0.00 0.00 0.00 4.20
4356 4618 4.458989 TGGTTCTGGCACATTGATACTTTC 59.541 41.667 0.00 0.00 38.20 2.62
4389 4651 2.540101 GTGAAACCCATAAGATCTCGCG 59.460 50.000 0.00 0.00 0.00 5.87
4466 4728 8.410673 ATGAGTAGTCATATTTGATACGGAGT 57.589 34.615 11.48 0.00 41.96 3.85
4467 4729 8.735315 AGATGAGTAGTCATATTTGATACGGAG 58.265 37.037 13.11 0.00 43.92 4.63
4469 4731 8.515414 TCAGATGAGTAGTCATATTTGATACGG 58.485 37.037 13.11 0.13 43.92 4.02
5288 5566 2.309755 TGGAGACAATGCCCAGAGATTT 59.690 45.455 0.00 0.00 37.44 2.17
5354 5634 8.693542 TTTAGTACGTTTACTGCTTTCCTATC 57.306 34.615 0.00 0.00 39.06 2.08
5514 5825 5.060427 TCATTCCCTGGAGAAGAAAACAA 57.940 39.130 0.00 0.00 0.00 2.83
5553 5864 2.281484 TGGAAGGTCGGCTTGTGC 60.281 61.111 0.00 0.00 38.76 4.57
5616 5927 4.052518 CCACCCCTTGGCCCTGAG 62.053 72.222 0.00 0.00 39.07 3.35
5836 6156 8.857694 AAGTCGTTTATTTATCTTTTCCCAGA 57.142 30.769 0.00 0.00 0.00 3.86
5838 6158 9.685828 CAAAAGTCGTTTATTTATCTTTTCCCA 57.314 29.630 0.00 0.00 34.39 4.37
5859 6179 5.163513 GGCCATTTGTGATACACTCAAAAG 58.836 41.667 0.00 0.00 42.47 2.27
5863 6183 3.431673 TGGCCATTTGTGATACACTCA 57.568 42.857 0.00 0.00 35.11 3.41
5864 6184 3.758554 AGTTGGCCATTTGTGATACACTC 59.241 43.478 6.09 0.00 35.11 3.51
5865 6185 3.766545 AGTTGGCCATTTGTGATACACT 58.233 40.909 6.09 0.00 35.11 3.55
5866 6186 4.519540 AAGTTGGCCATTTGTGATACAC 57.480 40.909 6.09 0.00 34.56 2.90
5867 6187 5.321102 ACTAAGTTGGCCATTTGTGATACA 58.679 37.500 6.09 0.00 0.00 2.29
5868 6188 5.897377 ACTAAGTTGGCCATTTGTGATAC 57.103 39.130 6.09 0.00 0.00 2.24
5869 6189 5.123186 CGAACTAAGTTGGCCATTTGTGATA 59.877 40.000 6.09 0.00 0.00 2.15
5870 6190 4.082787 CGAACTAAGTTGGCCATTTGTGAT 60.083 41.667 6.09 0.00 0.00 3.06
5871 6191 3.252215 CGAACTAAGTTGGCCATTTGTGA 59.748 43.478 6.09 0.00 0.00 3.58
5894 6221 0.179045 CCAGTCTTTAGCATCCGGGG 60.179 60.000 0.00 0.00 0.00 5.73
5940 6268 0.392060 TCGAGTCGGGATGTTCGAGA 60.392 55.000 13.54 0.00 37.18 4.04
5941 6269 0.248134 GTCGAGTCGGGATGTTCGAG 60.248 60.000 13.54 0.00 42.03 4.04
6000 6328 6.968904 CCATACACATACATGCTCTTGTTTTC 59.031 38.462 0.00 0.00 0.00 2.29
6006 6334 4.155063 TGCCATACACATACATGCTCTT 57.845 40.909 0.00 0.00 0.00 2.85
6061 6389 1.203758 GGGTAACATTTTTGGGCCTCG 59.796 52.381 4.53 0.00 39.74 4.63
6154 6482 9.953565 AGTACTACCACTTCAGCAAAATTAATA 57.046 29.630 0.00 0.00 0.00 0.98
6158 6486 5.473504 CCAGTACTACCACTTCAGCAAAATT 59.526 40.000 0.00 0.00 0.00 1.82
6169 6497 4.838986 ACTGTTCATTCCAGTACTACCACT 59.161 41.667 0.00 0.00 41.24 4.00
6172 6500 6.770746 TCTACTGTTCATTCCAGTACTACC 57.229 41.667 0.00 0.00 42.83 3.18
6173 6501 9.088512 CATTTCTACTGTTCATTCCAGTACTAC 57.911 37.037 0.00 0.00 42.83 2.73
6174 6502 8.812972 ACATTTCTACTGTTCATTCCAGTACTA 58.187 33.333 0.00 0.00 42.83 1.82
6194 6522 7.115378 CCACAGCAAAGTCAAGATAAACATTTC 59.885 37.037 0.00 0.00 0.00 2.17
6219 6547 3.744660 AGTGTTCAAGACCATGAGAACC 58.255 45.455 0.00 0.00 39.57 3.62
6277 6616 0.882927 GGCTGCGTACAACTGGACAA 60.883 55.000 0.00 0.00 0.00 3.18
6292 6631 0.320771 GTACTGGTGAGTGGTGGCTG 60.321 60.000 0.00 0.00 33.21 4.85
6298 6637 3.055094 AGCTTAATGGTACTGGTGAGTGG 60.055 47.826 0.00 0.00 33.21 4.00
6424 6763 3.670359 GCTTAATCATCACGCAAAGCACA 60.670 43.478 0.00 0.00 39.24 4.57
6425 6764 2.848302 GCTTAATCATCACGCAAAGCAC 59.152 45.455 0.00 0.00 39.24 4.40
6426 6765 2.749076 AGCTTAATCATCACGCAAAGCA 59.251 40.909 7.52 0.00 41.31 3.91
6427 6766 3.357897 GAGCTTAATCATCACGCAAAGC 58.642 45.455 0.00 0.00 39.62 3.51
6428 6767 3.306973 TCGAGCTTAATCATCACGCAAAG 59.693 43.478 0.00 0.00 0.00 2.77
6429 6768 3.258228 TCGAGCTTAATCATCACGCAAA 58.742 40.909 0.00 0.00 0.00 3.68
6430 6769 2.887337 TCGAGCTTAATCATCACGCAA 58.113 42.857 0.00 0.00 0.00 4.85
6511 6850 9.490379 GAAAAGGTGACTGAGATTTCTAACTTA 57.510 33.333 0.00 0.00 42.68 2.24
6544 6883 2.648059 GGACCCAGACTGATTGGATTG 58.352 52.381 3.32 0.00 37.96 2.67
6559 6898 3.851128 GCTAGTGAGGCGGGACCC 61.851 72.222 0.00 0.00 40.58 4.46
6588 6928 8.703604 TTGATTTGTAGTACTAATCTCTGTGC 57.296 34.615 26.81 9.65 39.77 4.57
6641 6981 4.164988 ACCTCATCTATTTGGGTTCAGAGG 59.835 45.833 0.00 0.00 44.28 3.69
6648 6988 8.331931 TGAGTTTATACCTCATCTATTTGGGT 57.668 34.615 0.00 0.00 34.12 4.51
6662 7002 9.353999 CATTGCCTTTTTAACTGAGTTTATACC 57.646 33.333 1.97 0.00 0.00 2.73
6672 7012 7.653311 ACTTAGAAAGCATTGCCTTTTTAACTG 59.347 33.333 4.70 4.23 35.31 3.16
6673 7013 7.726216 ACTTAGAAAGCATTGCCTTTTTAACT 58.274 30.769 4.70 2.46 35.31 2.24
6675 7015 8.825745 CAAACTTAGAAAGCATTGCCTTTTTAA 58.174 29.630 4.70 9.68 35.31 1.52
6678 7018 6.479990 GTCAAACTTAGAAAGCATTGCCTTTT 59.520 34.615 4.70 0.00 35.31 2.27
6684 7024 7.439056 ACATTTGGTCAAACTTAGAAAGCATTG 59.561 33.333 0.00 0.00 32.51 2.82
6709 7049 2.879646 CAGACCGACAGAGGGAGTATAC 59.120 54.545 0.00 0.00 35.02 1.47
6715 7055 1.304217 GGACAGACCGACAGAGGGA 60.304 63.158 0.00 0.00 35.02 4.20
6725 7065 5.104900 ACAGTCTTATATTGTGGGACAGACC 60.105 44.000 0.00 0.00 41.80 3.85
6747 7087 3.826157 AGTTATGGCTAGCTTGCAAAACA 59.174 39.130 21.53 10.51 34.04 2.83


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

AutoCloner maintained by Alex Coulton.