Multiple sequence alignment - TraesCS5D01G424500

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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 TraesCS5D01G424500 chr5D 100.000 5384 0 0 1 5384 483710915 483716298 0.000000e+00 9943
1 TraesCS5D01G424500 chr5B 94.888 3697 144 19 276 3951 594916216 594919888 0.000000e+00 5738
2 TraesCS5D01G424500 chr5B 91.440 1285 54 20 3980 5247 594919887 594921132 0.000000e+00 1712
3 TraesCS5D01G424500 chr5B 88.809 277 26 3 2 274 594915902 594916177 8.640000e-88 335
4 TraesCS5D01G424500 chr5B 97.222 72 2 0 5290 5361 594921131 594921202 7.320000e-24 122
5 TraesCS5D01G424500 chr5A 94.613 3694 142 33 276 3945 605226724 605230384 0.000000e+00 5666
6 TraesCS5D01G424500 chr5A 93.717 764 36 7 4033 4788 605230385 605231144 0.000000e+00 1134
7 TraesCS5D01G424500 chr5A 90.295 577 44 5 4787 5360 605231303 605231870 0.000000e+00 745
8 TraesCS5D01G424500 chr5A 95.238 273 12 1 2 274 605226414 605226685 1.070000e-116 431


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 TraesCS5D01G424500 chr5D 483710915 483716298 5383 False 9943.00 9943 100.00000 1 5384 1 chr5D.!!$F1 5383
1 TraesCS5D01G424500 chr5B 594915902 594921202 5300 False 1976.75 5738 93.08975 2 5361 4 chr5B.!!$F1 5359
2 TraesCS5D01G424500 chr5A 605226414 605231870 5456 False 1994.00 5666 93.46575 2 5360 4 chr5A.!!$F1 5358

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
426 477 0.108804 TCGAAAGGCGTTGCTCTAGG 60.109 55.0 0.00 0.0 41.80 3.02 F
427 478 0.108804 CGAAAGGCGTTGCTCTAGGA 60.109 55.0 0.00 0.0 34.64 2.94 F
1257 1328 0.384309 TCATCGGCATGTACGTCCTC 59.616 55.0 10.83 0.0 0.00 3.71 F
1926 1997 0.107643 TGTTTGACCTGATGCCACGA 59.892 50.0 0.00 0.0 0.00 4.35 F
3423 3494 1.042229 TTGCAGCAGACAAAAGCCAT 58.958 45.0 0.00 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1236 1307 0.597637 GGACGTACATGCCGATGAGG 60.598 60.000 11.82 0.00 44.97 3.86 R
1777 1848 1.071385 CAACCCAGAGAGCAAGTCAGT 59.929 52.381 0.00 0.00 0.00 3.41 R
2286 2357 1.317613 ACATTTTCACTGCCGCTTCA 58.682 45.000 0.00 0.00 0.00 3.02 R
3670 3741 4.253685 CAATACAGTGGTACCTTGTCCAG 58.746 47.826 21.04 11.31 34.16 3.86 R
5274 5562 0.042731 CCCAGGGGTCCTCTGTTCTA 59.957 60.000 17.89 0.00 0.00 2.10 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 3.815401 TCTGCTTGGACTTGCTTAACTTC 59.185 43.478 0.00 0.00 0.00 3.01
75 76 2.960129 GGAATAGCCACGACGCCG 60.960 66.667 0.00 0.00 42.50 6.46
169 170 6.616947 TGAGAAACGAACTCACATTTTGTTT 58.383 32.000 0.00 0.99 41.35 2.83
194 199 3.361644 GCGATAAATACATGCCAATTGCG 59.638 43.478 0.00 0.00 45.60 4.85
200 205 1.246649 ACATGCCAATTGCGTCTCAA 58.753 45.000 0.00 0.00 45.60 3.02
201 206 1.612950 ACATGCCAATTGCGTCTCAAA 59.387 42.857 0.00 0.00 45.60 2.69
204 209 2.945278 TGCCAATTGCGTCTCAAAATC 58.055 42.857 0.00 0.00 45.60 2.17
209 214 4.934144 GCGTCTCAAAATCGCGAG 57.066 55.556 16.66 0.00 40.51 5.03
234 239 5.716228 ACATAGAAACCATTCCATGAAGCAA 59.284 36.000 0.00 0.00 36.98 3.91
277 282 3.731136 GCAGTGAGCGTGAACCAA 58.269 55.556 0.00 0.00 0.00 3.67
278 283 1.571460 GCAGTGAGCGTGAACCAAG 59.429 57.895 0.00 0.00 0.00 3.61
279 284 1.160329 GCAGTGAGCGTGAACCAAGT 61.160 55.000 0.00 0.00 0.00 3.16
280 285 1.299541 CAGTGAGCGTGAACCAAGTT 58.700 50.000 0.00 0.00 0.00 2.66
311 354 9.921637 GATATTAACCATTTCAACCTTTTGACA 57.078 29.630 0.00 0.00 41.64 3.58
312 355 9.927668 ATATTAACCATTTCAACCTTTTGACAG 57.072 29.630 0.00 0.00 41.64 3.51
313 356 5.675684 AACCATTTCAACCTTTTGACAGT 57.324 34.783 0.00 0.00 41.64 3.55
315 358 6.976934 ACCATTTCAACCTTTTGACAGTAT 57.023 33.333 0.00 0.00 41.64 2.12
318 361 6.863126 CCATTTCAACCTTTTGACAGTATCAC 59.137 38.462 0.00 0.00 41.64 3.06
343 386 0.238289 AGCGGCAAAACATCGAACAG 59.762 50.000 1.45 0.00 0.00 3.16
377 428 2.949909 ATTGCCCCTACACGCACGA 61.950 57.895 0.00 0.00 33.97 4.35
385 436 1.854743 CCTACACGCACGATTCATCTG 59.145 52.381 0.00 0.00 0.00 2.90
388 439 0.723414 CACGCACGATTCATCTGCTT 59.277 50.000 0.00 0.00 32.51 3.91
392 443 2.031314 CGCACGATTCATCTGCTTGAAT 59.969 45.455 9.03 9.03 46.39 2.57
393 444 3.360533 GCACGATTCATCTGCTTGAATG 58.639 45.455 12.70 8.85 44.35 2.67
404 455 1.242076 GCTTGAATGACCAGTGCACT 58.758 50.000 15.25 15.25 0.00 4.40
408 459 4.437930 GCTTGAATGACCAGTGCACTAATC 60.438 45.833 21.20 19.46 0.00 1.75
412 463 3.394674 TGACCAGTGCACTAATCGAAA 57.605 42.857 21.20 1.66 0.00 3.46
414 465 2.673368 GACCAGTGCACTAATCGAAAGG 59.327 50.000 21.20 16.14 0.00 3.11
415 466 1.398390 CCAGTGCACTAATCGAAAGGC 59.602 52.381 21.20 0.00 0.00 4.35
416 467 1.061131 CAGTGCACTAATCGAAAGGCG 59.939 52.381 21.20 0.00 42.69 5.52
417 468 1.076332 GTGCACTAATCGAAAGGCGT 58.924 50.000 10.32 0.00 41.80 5.68
418 469 1.463444 GTGCACTAATCGAAAGGCGTT 59.537 47.619 10.32 0.00 41.80 4.84
419 470 1.463056 TGCACTAATCGAAAGGCGTTG 59.537 47.619 0.00 0.00 41.80 4.10
420 471 1.790481 GCACTAATCGAAAGGCGTTGC 60.790 52.381 0.00 0.00 41.80 4.17
421 472 1.732259 CACTAATCGAAAGGCGTTGCT 59.268 47.619 0.00 0.00 41.80 3.91
422 473 2.000447 ACTAATCGAAAGGCGTTGCTC 59.000 47.619 0.00 0.00 41.80 4.26
423 474 2.271800 CTAATCGAAAGGCGTTGCTCT 58.728 47.619 0.00 0.00 41.80 4.09
424 475 2.380084 AATCGAAAGGCGTTGCTCTA 57.620 45.000 0.00 0.00 41.80 2.43
425 476 1.927895 ATCGAAAGGCGTTGCTCTAG 58.072 50.000 0.00 0.00 41.80 2.43
426 477 0.108804 TCGAAAGGCGTTGCTCTAGG 60.109 55.000 0.00 0.00 41.80 3.02
427 478 0.108804 CGAAAGGCGTTGCTCTAGGA 60.109 55.000 0.00 0.00 34.64 2.94
428 479 1.646189 GAAAGGCGTTGCTCTAGGAG 58.354 55.000 0.00 0.00 0.00 3.69
463 514 2.548295 CCGGCTACCTCGAGCTCTC 61.548 68.421 12.85 0.00 42.43 3.20
481 532 2.356069 TCTCGACGAGATGACATCCTTG 59.644 50.000 23.27 4.90 33.35 3.61
513 564 6.146021 ACAGGAGCATTTTTAATTTTCAAGCG 59.854 34.615 0.00 0.00 0.00 4.68
525 576 3.423154 CAAGCGGCGGGTTCTGTC 61.423 66.667 9.78 0.00 0.00 3.51
536 587 2.079925 GGGTTCTGTCTGTGCTCAATC 58.920 52.381 0.00 0.00 0.00 2.67
884 947 2.760385 AGGCACGAGGGACTAGCC 60.760 66.667 0.00 0.00 46.82 3.93
903 966 3.502979 AGCCCGAGATAGAACGATAGAAC 59.497 47.826 0.00 0.00 41.38 3.01
936 999 2.049063 AGCGCCACGTGAGAGTTC 60.049 61.111 19.30 0.00 0.00 3.01
946 1009 4.556233 CACGTGAGAGTTCAAGTCCATAA 58.444 43.478 10.90 0.00 42.88 1.90
1257 1328 0.384309 TCATCGGCATGTACGTCCTC 59.616 55.000 10.83 0.00 0.00 3.71
1791 1862 1.173043 CGGAGACTGACTTGCTCTCT 58.827 55.000 0.00 0.00 32.50 3.10
1828 1899 1.819632 CTGGCGGTGAAGTATGGGC 60.820 63.158 0.00 0.00 0.00 5.36
1926 1997 0.107643 TGTTTGACCTGATGCCACGA 59.892 50.000 0.00 0.00 0.00 4.35
1992 2063 3.554692 GGGCTTGTCGACGATGCG 61.555 66.667 11.62 0.00 0.00 4.73
2073 2144 3.142174 GAGCTTGTTACCAGCTTTGACT 58.858 45.455 12.23 0.00 39.21 3.41
2286 2357 6.365520 GGGTTATGTTCTTAATGGGATGAGT 58.634 40.000 0.00 0.00 0.00 3.41
2310 2381 1.599419 GCGGCAGTGAAAATGTTTCGT 60.599 47.619 0.00 0.00 32.28 3.85
2487 2558 6.691754 TTAATGGACATGTATGCGAAATGT 57.308 33.333 0.00 0.00 37.24 2.71
2643 2714 3.618690 ATGGAAGGAGTGAAGTACAGC 57.381 47.619 0.00 0.00 0.00 4.40
2652 2723 4.310769 GAGTGAAGTACAGCAATGTGACT 58.689 43.478 0.00 0.00 0.00 3.41
2874 2945 8.972127 TCATGGAATAGTATAATCTCTGCCTAC 58.028 37.037 0.00 0.00 0.00 3.18
3312 3383 2.267961 GGACGGTGGGATGGTGTC 59.732 66.667 0.00 0.00 0.00 3.67
3423 3494 1.042229 TTGCAGCAGACAAAAGCCAT 58.958 45.000 0.00 0.00 0.00 4.40
3617 3688 2.086610 ACCCTTGTTCAACCATTGCT 57.913 45.000 0.00 0.00 0.00 3.91
3632 3703 7.491048 TCAACCATTGCTTTTCTTTGTTCTTAC 59.509 33.333 0.00 0.00 0.00 2.34
3709 3780 2.353357 TTGCTGATCCATCCATGTCC 57.647 50.000 0.00 0.00 0.00 4.02
3747 3819 7.785028 ACACAGGAATCAGGATCAGTTATACTA 59.215 37.037 0.00 0.00 0.00 1.82
3771 3843 6.925610 TCATTGCTAATGAGGTGATAACAC 57.074 37.500 7.27 0.00 42.69 3.32
3884 3964 5.104610 ACCCAAATGCATGCCATTGTATTAA 60.105 36.000 23.14 1.36 43.22 1.40
3885 3965 5.821470 CCCAAATGCATGCCATTGTATTAAA 59.179 36.000 23.14 0.89 43.22 1.52
3886 3966 6.487331 CCCAAATGCATGCCATTGTATTAAAT 59.513 34.615 23.14 3.05 43.22 1.40
3887 3967 7.013464 CCCAAATGCATGCCATTGTATTAAATT 59.987 33.333 23.14 8.25 43.22 1.82
3888 3968 9.053840 CCAAATGCATGCCATTGTATTAAATTA 57.946 29.630 23.14 0.00 43.22 1.40
3957 4037 2.099141 CAGTTAGCCTACTGCAAGCA 57.901 50.000 3.19 0.00 44.83 3.91
3962 4042 4.308526 CCTACTGCAAGCAGGGTG 57.691 61.111 24.29 13.71 44.19 4.61
3963 4043 2.042831 CCTACTGCAAGCAGGGTGC 61.043 63.158 24.29 0.00 44.19 5.01
3972 4052 2.045926 GCAGGGTGCTGGTGTAGG 60.046 66.667 0.00 0.00 40.96 3.18
3973 4053 2.671070 CAGGGTGCTGGTGTAGGG 59.329 66.667 0.00 0.00 0.00 3.53
3974 4054 3.330720 AGGGTGCTGGTGTAGGGC 61.331 66.667 0.00 0.00 0.00 5.19
3975 4055 4.426313 GGGTGCTGGTGTAGGGCC 62.426 72.222 0.00 0.00 0.00 5.80
3976 4056 4.778143 GGTGCTGGTGTAGGGCCG 62.778 72.222 0.00 0.00 0.00 6.13
3977 4057 4.016706 GTGCTGGTGTAGGGCCGT 62.017 66.667 2.24 2.24 0.00 5.68
3978 4058 3.246112 TGCTGGTGTAGGGCCGTT 61.246 61.111 1.81 0.00 0.00 4.44
4013 4093 7.378966 TGTATATAATGCCTCTCTGTTACTGC 58.621 38.462 0.00 0.00 0.00 4.40
4097 4177 3.679025 TGCTTGCTTGTTTTGTTCTGTTG 59.321 39.130 0.00 0.00 0.00 3.33
4259 4343 8.972662 TTATCCCAGTGGAATCTGATATTCTA 57.027 34.615 11.95 0.00 45.98 2.10
4265 4349 8.597167 CCAGTGGAATCTGATATTCTAATGGTA 58.403 37.037 17.27 0.00 44.30 3.25
4579 4665 5.759763 ACTTTTCCACAGAAATTCAAATGGC 59.240 36.000 0.00 0.00 41.55 4.40
4580 4666 3.959535 TCCACAGAAATTCAAATGGCC 57.040 42.857 0.00 0.00 0.00 5.36
4581 4667 3.237746 TCCACAGAAATTCAAATGGCCA 58.762 40.909 8.56 8.56 0.00 5.36
4582 4668 3.839490 TCCACAGAAATTCAAATGGCCAT 59.161 39.130 14.09 14.09 0.00 4.40
4583 4669 3.936453 CCACAGAAATTCAAATGGCCATG 59.064 43.478 21.63 9.94 0.00 3.66
4584 4670 3.936453 CACAGAAATTCAAATGGCCATGG 59.064 43.478 21.63 15.23 0.00 3.66
4585 4671 3.839490 ACAGAAATTCAAATGGCCATGGA 59.161 39.130 21.63 17.49 0.00 3.41
4586 4672 4.286549 ACAGAAATTCAAATGGCCATGGAA 59.713 37.500 26.44 26.44 0.00 3.53
4587 4673 5.045432 ACAGAAATTCAAATGGCCATGGAAT 60.045 36.000 27.87 27.87 31.25 3.01
4588 4674 5.295787 CAGAAATTCAAATGGCCATGGAATG 59.704 40.000 31.29 22.23 46.21 2.67
4589 4675 4.847990 AATTCAAATGGCCATGGAATGT 57.152 36.364 31.29 22.52 44.81 2.71
4590 4676 5.954153 AATTCAAATGGCCATGGAATGTA 57.046 34.783 31.29 18.69 44.81 2.29
4591 4677 6.503560 AATTCAAATGGCCATGGAATGTAT 57.496 33.333 31.29 20.39 44.81 2.29
4592 4678 5.534207 TTCAAATGGCCATGGAATGTATC 57.466 39.130 21.63 0.00 44.81 2.24
4593 4679 4.806892 TCAAATGGCCATGGAATGTATCT 58.193 39.130 21.63 0.00 44.81 1.98
4594 4680 5.210430 TCAAATGGCCATGGAATGTATCTT 58.790 37.500 21.63 2.13 44.81 2.40
4595 4681 5.069383 TCAAATGGCCATGGAATGTATCTTG 59.931 40.000 21.63 15.40 44.81 3.02
4596 4682 3.668141 TGGCCATGGAATGTATCTTGT 57.332 42.857 18.40 0.00 44.81 3.16
4597 4683 3.554934 TGGCCATGGAATGTATCTTGTC 58.445 45.455 18.40 0.00 44.81 3.18
4598 4684 2.887152 GGCCATGGAATGTATCTTGTCC 59.113 50.000 18.40 0.00 44.81 4.02
4599 4685 3.554934 GCCATGGAATGTATCTTGTCCA 58.445 45.455 18.40 0.00 44.81 4.02
4601 4687 4.217118 GCCATGGAATGTATCTTGTCCATC 59.783 45.833 18.40 0.00 45.75 3.51
4602 4688 5.628130 CCATGGAATGTATCTTGTCCATCT 58.372 41.667 5.56 0.00 45.75 2.90
4603 4689 6.066690 CCATGGAATGTATCTTGTCCATCTT 58.933 40.000 5.56 0.00 45.75 2.40
4604 4690 6.016527 CCATGGAATGTATCTTGTCCATCTTG 60.017 42.308 5.56 0.00 45.75 3.02
4605 4691 5.439721 TGGAATGTATCTTGTCCATCTTGG 58.560 41.667 0.00 0.00 35.22 3.61
4700 4814 5.769662 TCAATGCTGACAGTTTATTCCTTGT 59.230 36.000 3.99 0.00 0.00 3.16
4770 4884 8.956426 TGAACCTGGACAACATTATTCTATTTC 58.044 33.333 0.00 0.00 0.00 2.17
4774 4888 7.067372 CCTGGACAACATTATTCTATTTCTGCA 59.933 37.037 0.00 0.00 0.00 4.41
4797 5071 7.775093 TGCACCATAATGTTCTAGAAGCTATTT 59.225 33.333 5.12 0.00 0.00 1.40
5033 5321 1.331214 ACAGGCCTGTCAAAACCATG 58.669 50.000 33.20 5.54 40.24 3.66
5042 5330 2.032799 TGTCAAAACCATGAGAACACGC 59.967 45.455 0.00 0.00 0.00 5.34
5112 5400 2.095461 TGCAGCACAACAAGGTTAACA 58.905 42.857 8.10 0.00 0.00 2.41
5190 5478 7.767659 GGTAATTTTATCGTTTCTCCCTACTGT 59.232 37.037 0.00 0.00 0.00 3.55
5218 5506 7.329499 TGTGTACACCTTACAAACAAGTCTTA 58.671 34.615 22.91 0.00 0.00 2.10
5245 5533 6.788243 TCATTGAATTGATCGCCATATATGC 58.212 36.000 7.24 2.52 0.00 3.14
5246 5534 6.600427 TCATTGAATTGATCGCCATATATGCT 59.400 34.615 7.24 0.00 0.00 3.79
5247 5535 6.822667 TTGAATTGATCGCCATATATGCTT 57.177 33.333 7.24 0.00 0.00 3.91
5248 5536 6.185852 TGAATTGATCGCCATATATGCTTG 57.814 37.500 7.24 0.00 0.00 4.01
5249 5537 5.939296 TGAATTGATCGCCATATATGCTTGA 59.061 36.000 7.24 4.93 0.00 3.02
5250 5538 6.430616 TGAATTGATCGCCATATATGCTTGAA 59.569 34.615 7.24 0.00 0.00 2.69
5251 5539 7.121611 TGAATTGATCGCCATATATGCTTGAAT 59.878 33.333 7.24 0.00 0.00 2.57
5252 5540 6.822667 TTGATCGCCATATATGCTTGAATT 57.177 33.333 7.24 0.00 0.00 2.17
5253 5541 6.426980 TGATCGCCATATATGCTTGAATTC 57.573 37.500 7.24 0.00 0.00 2.17
5254 5542 5.939296 TGATCGCCATATATGCTTGAATTCA 59.061 36.000 3.38 3.38 0.00 2.57
5255 5543 6.600427 TGATCGCCATATATGCTTGAATTCAT 59.400 34.615 9.40 0.00 0.00 2.57
5256 5544 6.185852 TCGCCATATATGCTTGAATTCATG 57.814 37.500 9.40 12.82 0.00 3.07
5257 5545 5.706833 TCGCCATATATGCTTGAATTCATGT 59.293 36.000 19.25 6.48 0.00 3.21
5258 5546 6.025896 CGCCATATATGCTTGAATTCATGTC 58.974 40.000 19.25 13.24 0.00 3.06
5259 5547 6.348704 CGCCATATATGCTTGAATTCATGTCA 60.349 38.462 19.25 17.18 0.00 3.58
5260 5548 6.805271 GCCATATATGCTTGAATTCATGTCAC 59.195 38.462 19.25 6.79 0.00 3.67
5261 5549 7.522562 GCCATATATGCTTGAATTCATGTCACA 60.523 37.037 19.25 11.28 0.00 3.58
5262 5550 8.021396 CCATATATGCTTGAATTCATGTCACAG 58.979 37.037 19.25 9.95 0.00 3.66
5263 5551 4.713824 ATGCTTGAATTCATGTCACAGG 57.286 40.909 19.25 0.00 0.00 4.00
5264 5552 2.821378 TGCTTGAATTCATGTCACAGGG 59.179 45.455 19.25 1.25 0.00 4.45
5265 5553 2.416431 GCTTGAATTCATGTCACAGGGC 60.416 50.000 19.25 6.29 0.00 5.19
5266 5554 2.885135 TGAATTCATGTCACAGGGCT 57.115 45.000 3.38 0.00 0.00 5.19
5267 5555 3.159213 TGAATTCATGTCACAGGGCTT 57.841 42.857 3.38 0.00 0.00 4.35
5268 5556 3.499338 TGAATTCATGTCACAGGGCTTT 58.501 40.909 3.38 0.00 0.00 3.51
5269 5557 3.256383 TGAATTCATGTCACAGGGCTTTG 59.744 43.478 3.38 0.00 0.00 2.77
5270 5558 1.619654 TTCATGTCACAGGGCTTTGG 58.380 50.000 0.00 0.00 0.00 3.28
5271 5559 0.770499 TCATGTCACAGGGCTTTGGA 59.230 50.000 0.00 0.00 0.00 3.53
5272 5560 1.355381 TCATGTCACAGGGCTTTGGAT 59.645 47.619 0.00 0.00 0.00 3.41
5273 5561 1.747355 CATGTCACAGGGCTTTGGATC 59.253 52.381 0.00 0.00 0.00 3.36
5274 5562 1.067295 TGTCACAGGGCTTTGGATCT 58.933 50.000 0.00 0.00 0.00 2.75
5275 5563 2.265367 TGTCACAGGGCTTTGGATCTA 58.735 47.619 0.00 0.00 0.00 1.98
5276 5564 2.237143 TGTCACAGGGCTTTGGATCTAG 59.763 50.000 0.00 0.00 0.00 2.43
5277 5565 2.501723 GTCACAGGGCTTTGGATCTAGA 59.498 50.000 0.00 0.00 0.00 2.43
5278 5566 3.055094 GTCACAGGGCTTTGGATCTAGAA 60.055 47.826 0.00 0.00 0.00 2.10
5279 5567 3.055094 TCACAGGGCTTTGGATCTAGAAC 60.055 47.826 0.00 0.00 0.00 3.01
5280 5568 2.912956 ACAGGGCTTTGGATCTAGAACA 59.087 45.455 0.00 0.00 0.00 3.18
5281 5569 3.054802 ACAGGGCTTTGGATCTAGAACAG 60.055 47.826 0.00 0.00 0.00 3.16
5282 5570 3.198635 CAGGGCTTTGGATCTAGAACAGA 59.801 47.826 0.00 0.00 37.79 3.41
5283 5571 3.454082 AGGGCTTTGGATCTAGAACAGAG 59.546 47.826 11.67 11.67 36.48 3.35
5284 5572 3.432890 GGGCTTTGGATCTAGAACAGAGG 60.433 52.174 15.56 6.49 36.48 3.69
5285 5573 3.452627 GGCTTTGGATCTAGAACAGAGGA 59.547 47.826 15.56 0.00 36.48 3.71
5286 5574 4.438148 GCTTTGGATCTAGAACAGAGGAC 58.562 47.826 15.56 2.39 36.48 3.85
5287 5575 4.682050 GCTTTGGATCTAGAACAGAGGACC 60.682 50.000 15.56 0.00 36.48 4.46
5288 5576 3.033659 TGGATCTAGAACAGAGGACCC 57.966 52.381 0.00 0.00 36.48 4.46
5340 5672 8.352201 CAATAGGTCTGTTCAAATCTTGACAAA 58.648 33.333 0.00 0.00 39.87 2.83
5374 5706 7.757941 TGTTTCATGACTATGGAAATTCACA 57.242 32.000 0.00 0.00 33.63 3.58
5375 5707 8.352137 TGTTTCATGACTATGGAAATTCACAT 57.648 30.769 0.00 0.00 33.63 3.21
5376 5708 8.805175 TGTTTCATGACTATGGAAATTCACATT 58.195 29.630 0.00 0.00 33.63 2.71
5377 5709 9.643693 GTTTCATGACTATGGAAATTCACATTT 57.356 29.630 0.00 0.00 33.63 2.32
5378 5710 9.642327 TTTCATGACTATGGAAATTCACATTTG 57.358 29.630 0.00 0.00 34.97 2.32
5379 5711 7.259882 TCATGACTATGGAAATTCACATTTGC 58.740 34.615 0.00 0.00 40.31 3.68
5380 5712 6.839124 TGACTATGGAAATTCACATTTGCT 57.161 33.333 0.00 0.00 40.49 3.91
5381 5713 6.855836 TGACTATGGAAATTCACATTTGCTC 58.144 36.000 0.00 0.00 40.49 4.26
5382 5714 6.660521 TGACTATGGAAATTCACATTTGCTCT 59.339 34.615 0.00 0.00 40.49 4.09
5383 5715 7.177216 TGACTATGGAAATTCACATTTGCTCTT 59.823 33.333 0.00 0.00 40.49 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.052229 AAGCAGACGGTCCCGACG 62.052 66.667 13.54 4.45 42.83 5.12
33 34 3.175240 CGCTTGGACGTGCTCTCG 61.175 66.667 8.99 4.88 0.00 4.04
75 76 1.689273 TGCACCATAAACCCAAACACC 59.311 47.619 0.00 0.00 0.00 4.16
169 170 5.233902 GCAATTGGCATGTATTTATCGCAAA 59.766 36.000 7.72 0.00 43.97 3.68
200 205 3.857052 TGGTTTCTATGTCTCGCGATTT 58.143 40.909 10.36 0.00 0.00 2.17
201 206 3.520290 TGGTTTCTATGTCTCGCGATT 57.480 42.857 10.36 0.00 0.00 3.34
204 209 2.540101 GGAATGGTTTCTATGTCTCGCG 59.460 50.000 0.00 0.00 32.16 5.87
209 214 5.357878 TGCTTCATGGAATGGTTTCTATGTC 59.642 40.000 10.55 4.48 45.83 3.06
285 328 9.921637 TGTCAAAAGGTTGAAATGGTTAATATC 57.078 29.630 0.00 0.00 45.29 1.63
307 350 2.688446 CCGCTTAGAGGTGATACTGTCA 59.312 50.000 0.00 0.00 0.00 3.58
311 354 1.776662 TGCCGCTTAGAGGTGATACT 58.223 50.000 3.59 0.00 0.00 2.12
312 355 2.596904 TTGCCGCTTAGAGGTGATAC 57.403 50.000 3.59 0.00 0.00 2.24
313 356 3.267483 GTTTTGCCGCTTAGAGGTGATA 58.733 45.455 3.59 0.00 0.00 2.15
315 358 1.202710 TGTTTTGCCGCTTAGAGGTGA 60.203 47.619 3.59 0.00 0.00 4.02
318 361 1.062587 CGATGTTTTGCCGCTTAGAGG 59.937 52.381 0.00 0.00 0.00 3.69
343 386 2.733026 GGCAATGTCACTGCATTTGAAC 59.267 45.455 8.74 0.00 41.78 3.18
385 436 1.242076 AGTGCACTGGTCATTCAAGC 58.758 50.000 20.97 0.00 0.00 4.01
388 439 3.056179 TCGATTAGTGCACTGGTCATTCA 60.056 43.478 29.57 3.27 0.00 2.57
392 443 3.325870 CTTTCGATTAGTGCACTGGTCA 58.674 45.455 29.57 6.24 0.00 4.02
393 444 2.673368 CCTTTCGATTAGTGCACTGGTC 59.327 50.000 29.57 22.92 0.00 4.02
404 455 2.380084 AGAGCAACGCCTTTCGATTA 57.620 45.000 0.00 0.00 41.67 1.75
408 459 0.108804 TCCTAGAGCAACGCCTTTCG 60.109 55.000 0.00 0.00 45.38 3.46
420 471 3.740321 GCAATGAATTCTCGCTCCTAGAG 59.260 47.826 7.05 0.00 37.09 2.43
421 472 3.493350 GGCAATGAATTCTCGCTCCTAGA 60.493 47.826 7.05 0.00 0.00 2.43
422 473 2.805099 GGCAATGAATTCTCGCTCCTAG 59.195 50.000 7.05 0.00 0.00 3.02
423 474 2.485479 GGGCAATGAATTCTCGCTCCTA 60.485 50.000 7.05 0.00 0.00 2.94
424 475 1.673168 GGCAATGAATTCTCGCTCCT 58.327 50.000 7.05 0.00 0.00 3.69
425 476 0.665298 GGGCAATGAATTCTCGCTCC 59.335 55.000 7.05 6.56 0.00 4.70
426 477 0.665298 GGGGCAATGAATTCTCGCTC 59.335 55.000 7.05 6.35 0.00 5.03
427 478 0.753111 GGGGGCAATGAATTCTCGCT 60.753 55.000 7.05 0.00 0.00 4.93
428 479 1.735973 GGGGGCAATGAATTCTCGC 59.264 57.895 7.05 6.41 0.00 5.03
429 480 1.447317 CCGGGGGCAATGAATTCTCG 61.447 60.000 7.05 0.00 0.00 4.04
430 481 2.419057 CCGGGGGCAATGAATTCTC 58.581 57.895 7.05 0.00 0.00 2.87
431 482 4.684623 CCGGGGGCAATGAATTCT 57.315 55.556 7.05 0.00 0.00 2.40
463 514 2.568696 ACAAGGATGTCATCTCGTCG 57.431 50.000 12.54 0.00 33.41 5.12
481 532 1.523758 AAAATGCTCCTGTCCGTGAC 58.476 50.000 0.00 0.00 0.00 3.67
513 564 3.050275 GCACAGACAGAACCCGCC 61.050 66.667 0.00 0.00 0.00 6.13
525 576 1.800805 AAGTCACCGATTGAGCACAG 58.199 50.000 0.00 0.00 33.71 3.66
536 587 1.136085 CAACGCCATTGTAAGTCACCG 60.136 52.381 0.00 0.00 33.20 4.94
884 947 4.986875 TCGTTCTATCGTTCTATCTCGG 57.013 45.455 0.00 0.00 0.00 4.63
903 966 2.528743 GCTCACGTGCCATCCATCG 61.529 63.158 11.67 0.00 0.00 3.84
923 986 1.068588 TGGACTTGAACTCTCACGTGG 59.931 52.381 17.00 6.71 34.39 4.94
936 999 5.634859 GGCAGAAAATTGTGTTATGGACTTG 59.365 40.000 0.00 0.00 0.00 3.16
946 1009 3.243401 GGAAACGAGGCAGAAAATTGTGT 60.243 43.478 0.00 0.00 0.00 3.72
1236 1307 0.597637 GGACGTACATGCCGATGAGG 60.598 60.000 11.82 0.00 44.97 3.86
1777 1848 1.071385 CAACCCAGAGAGCAAGTCAGT 59.929 52.381 0.00 0.00 0.00 3.41
1791 1862 2.203337 GTGTGGAGCTGCAACCCA 60.203 61.111 10.44 0.24 0.00 4.51
1828 1899 2.840066 CGGCGACCTCTGGCTCTAG 61.840 68.421 0.00 0.00 0.00 2.43
1926 1997 3.671716 GTTCCAGGTTACCAAATCGTCT 58.328 45.455 3.51 0.00 0.00 4.18
1992 2063 4.023792 TGCATGTCACAGAACAATCTCAAC 60.024 41.667 0.00 0.00 32.03 3.18
2286 2357 1.317613 ACATTTTCACTGCCGCTTCA 58.682 45.000 0.00 0.00 0.00 3.02
2310 2381 1.440618 TGCCCACTTCCAAGAGGTAA 58.559 50.000 2.58 0.00 35.31 2.85
2487 2558 2.897350 TGGCTAAGGTCAAGTCTACCA 58.103 47.619 0.00 0.00 39.64 3.25
2643 2714 9.814899 GATAGGATGGAAGATATAGTCACATTG 57.185 37.037 0.00 0.00 0.00 2.82
2652 2723 7.634429 GCACATGCTGATAGGATGGAAGATATA 60.634 40.741 13.61 0.00 46.66 0.86
3312 3383 8.737175 TCCTTCATCAATCTTCTCATTTTTGAG 58.263 33.333 0.00 0.00 37.28 3.02
3423 3494 8.311395 ACATGTAAATATCTTCAGAGTCAGGA 57.689 34.615 0.00 0.00 0.00 3.86
3617 3688 6.661805 ACAGAAGGTGGTAAGAACAAAGAAAA 59.338 34.615 0.00 0.00 0.00 2.29
3632 3703 8.786826 TGTATCATTTTAGTTACAGAAGGTGG 57.213 34.615 0.00 0.00 0.00 4.61
3670 3741 4.253685 CAATACAGTGGTACCTTGTCCAG 58.746 47.826 21.04 11.31 34.16 3.86
3709 3780 4.999311 TGATTCCTGTGTCTCATGAAGTTG 59.001 41.667 0.00 0.00 35.02 3.16
3747 3819 7.056006 TGTGTTATCACCTCATTAGCAATGAT 58.944 34.615 10.62 0.00 42.79 2.45
3838 3917 5.505654 GGTGCATGTTCGAGAAGAAGAAAAA 60.506 40.000 0.00 0.00 39.95 1.94
3884 3964 9.205719 GTTCTTAGTTCTTCGACTCCTTTAATT 57.794 33.333 0.00 0.00 0.00 1.40
3885 3965 7.818446 GGTTCTTAGTTCTTCGACTCCTTTAAT 59.182 37.037 0.00 0.00 0.00 1.40
3886 3966 7.150640 GGTTCTTAGTTCTTCGACTCCTTTAA 58.849 38.462 0.00 0.00 0.00 1.52
3887 3967 6.266103 TGGTTCTTAGTTCTTCGACTCCTTTA 59.734 38.462 0.00 0.00 0.00 1.85
3888 3968 5.070047 TGGTTCTTAGTTCTTCGACTCCTTT 59.930 40.000 0.00 0.00 0.00 3.11
3889 3969 4.587684 TGGTTCTTAGTTCTTCGACTCCTT 59.412 41.667 0.00 0.00 0.00 3.36
3955 4035 2.045926 CCTACACCAGCACCCTGC 60.046 66.667 0.00 0.00 45.46 4.85
3956 4036 2.671070 CCCTACACCAGCACCCTG 59.329 66.667 0.00 0.00 38.85 4.45
3957 4037 3.330720 GCCCTACACCAGCACCCT 61.331 66.667 0.00 0.00 0.00 4.34
3958 4038 4.426313 GGCCCTACACCAGCACCC 62.426 72.222 0.00 0.00 0.00 4.61
3959 4039 4.778143 CGGCCCTACACCAGCACC 62.778 72.222 0.00 0.00 0.00 5.01
3960 4040 3.546714 AACGGCCCTACACCAGCAC 62.547 63.158 0.00 0.00 0.00 4.40
3961 4041 3.246112 AACGGCCCTACACCAGCA 61.246 61.111 0.00 0.00 0.00 4.41
3962 4042 2.436115 GAACGGCCCTACACCAGC 60.436 66.667 0.00 0.00 0.00 4.85
3963 4043 0.673644 CAAGAACGGCCCTACACCAG 60.674 60.000 0.00 0.00 0.00 4.00
3964 4044 1.373435 CAAGAACGGCCCTACACCA 59.627 57.895 0.00 0.00 0.00 4.17
3965 4045 0.609662 TACAAGAACGGCCCTACACC 59.390 55.000 0.00 0.00 0.00 4.16
3966 4046 2.685850 ATACAAGAACGGCCCTACAC 57.314 50.000 0.00 0.00 0.00 2.90
3967 4047 4.162698 ACATTATACAAGAACGGCCCTACA 59.837 41.667 0.00 0.00 0.00 2.74
3968 4048 4.700700 ACATTATACAAGAACGGCCCTAC 58.299 43.478 0.00 0.00 0.00 3.18
3969 4049 6.675413 ATACATTATACAAGAACGGCCCTA 57.325 37.500 0.00 0.00 0.00 3.53
3970 4050 3.926058 ACATTATACAAGAACGGCCCT 57.074 42.857 0.00 0.00 0.00 5.19
3971 4051 9.609346 ATTATATACATTATACAAGAACGGCCC 57.391 33.333 0.00 0.00 0.00 5.80
3973 4053 9.916397 GCATTATATACATTATACAAGAACGGC 57.084 33.333 0.00 0.00 0.00 5.68
4013 4093 1.051812 ATCCCTTGCCAGGAGATACG 58.948 55.000 5.14 0.00 44.19 3.06
4063 4143 5.261209 ACAAGCAAGCAAATCACTAAACA 57.739 34.783 0.00 0.00 0.00 2.83
4097 4177 2.632377 TGCCTTCTACAGCAACATAGC 58.368 47.619 0.00 0.00 35.69 2.97
4532 4618 8.418597 AGTACAGTGTTAGGAATTAGAACTCA 57.581 34.615 0.00 0.00 0.00 3.41
4579 4665 5.628130 AGATGGACAAGATACATTCCATGG 58.372 41.667 4.97 4.97 46.75 3.66
4580 4666 6.016527 CCAAGATGGACAAGATACATTCCATG 60.017 42.308 6.70 0.00 46.75 3.66
4582 4668 5.439721 CCAAGATGGACAAGATACATTCCA 58.560 41.667 0.00 0.00 40.96 3.53
4583 4669 4.276926 GCCAAGATGGACAAGATACATTCC 59.723 45.833 0.00 0.00 40.96 3.01
4584 4670 5.429957 GCCAAGATGGACAAGATACATTC 57.570 43.478 0.00 0.00 40.96 2.67
4596 4682 2.158623 GGTGATACATGGCCAAGATGGA 60.159 50.000 16.33 2.98 40.96 3.41
4597 4683 2.158564 AGGTGATACATGGCCAAGATGG 60.159 50.000 16.33 2.51 41.55 3.51
4598 4684 2.882761 CAGGTGATACATGGCCAAGATG 59.117 50.000 16.33 9.36 0.00 2.90
4599 4685 2.511218 ACAGGTGATACATGGCCAAGAT 59.489 45.455 16.33 6.00 33.62 2.40
4600 4686 1.915489 ACAGGTGATACATGGCCAAGA 59.085 47.619 16.33 0.22 33.62 3.02
4601 4687 2.425143 ACAGGTGATACATGGCCAAG 57.575 50.000 10.96 8.43 33.62 3.61
4602 4688 2.573915 TGTACAGGTGATACATGGCCAA 59.426 45.455 10.96 0.00 33.62 4.52
4603 4689 2.192263 TGTACAGGTGATACATGGCCA 58.808 47.619 8.56 8.56 33.62 5.36
4604 4690 3.492102 ATGTACAGGTGATACATGGCC 57.508 47.619 0.33 0.00 40.85 5.36
4605 4691 4.569943 CCTATGTACAGGTGATACATGGC 58.430 47.826 0.33 0.00 42.06 4.40
4700 4814 4.336889 AGCTTGCAGAACTTACACAGTA 57.663 40.909 0.00 0.00 32.94 2.74
4770 4884 5.121811 AGCTTCTAGAACATTATGGTGCAG 58.878 41.667 0.00 0.00 0.00 4.41
4774 4888 9.113838 CACAAATAGCTTCTAGAACATTATGGT 57.886 33.333 0.00 0.00 0.00 3.55
4797 5071 7.762159 GGACAAAACTTTCCAAGAAATTACACA 59.238 33.333 0.00 0.00 0.00 3.72
4926 5204 6.240894 TCAGAACCAACAGAATTAGATGCTT 58.759 36.000 0.00 0.00 0.00 3.91
4928 5206 5.645497 ACTCAGAACCAACAGAATTAGATGC 59.355 40.000 0.00 0.00 0.00 3.91
4929 5207 7.524912 CAACTCAGAACCAACAGAATTAGATG 58.475 38.462 0.00 0.00 0.00 2.90
5024 5305 1.262950 TCGCGTGTTCTCATGGTTTTG 59.737 47.619 5.77 0.00 0.00 2.44
5033 5321 2.058798 TGTTGAATCTCGCGTGTTCTC 58.941 47.619 5.77 3.16 0.00 2.87
5042 5330 4.786507 TGCTGTGAAAATGTTGAATCTCG 58.213 39.130 0.00 0.00 0.00 4.04
5112 5400 2.229792 ACAGGTCACGCACATTTCATT 58.770 42.857 0.00 0.00 0.00 2.57
5190 5478 7.988599 AGACTTGTTTGTAAGGTGTACACATAA 59.011 33.333 26.51 9.16 31.94 1.90
5245 5533 3.087031 AGCCCTGTGACATGAATTCAAG 58.913 45.455 13.09 10.92 0.00 3.02
5246 5534 3.159213 AGCCCTGTGACATGAATTCAA 57.841 42.857 13.09 0.00 0.00 2.69
5247 5535 2.885135 AGCCCTGTGACATGAATTCA 57.115 45.000 11.26 11.26 0.00 2.57
5248 5536 3.367703 CCAAAGCCCTGTGACATGAATTC 60.368 47.826 0.00 0.00 0.00 2.17
5249 5537 2.564062 CCAAAGCCCTGTGACATGAATT 59.436 45.455 0.00 0.00 0.00 2.17
5250 5538 2.173519 CCAAAGCCCTGTGACATGAAT 58.826 47.619 0.00 0.00 0.00 2.57
5251 5539 1.144708 TCCAAAGCCCTGTGACATGAA 59.855 47.619 0.00 0.00 0.00 2.57
5252 5540 0.770499 TCCAAAGCCCTGTGACATGA 59.230 50.000 0.00 0.00 0.00 3.07
5253 5541 1.747355 GATCCAAAGCCCTGTGACATG 59.253 52.381 0.00 0.00 0.00 3.21
5254 5542 1.637553 AGATCCAAAGCCCTGTGACAT 59.362 47.619 0.00 0.00 0.00 3.06
5255 5543 1.067295 AGATCCAAAGCCCTGTGACA 58.933 50.000 0.00 0.00 0.00 3.58
5256 5544 2.501723 TCTAGATCCAAAGCCCTGTGAC 59.498 50.000 0.00 0.00 0.00 3.67
5257 5545 2.832838 TCTAGATCCAAAGCCCTGTGA 58.167 47.619 0.00 0.00 0.00 3.58
5258 5546 3.274288 GTTCTAGATCCAAAGCCCTGTG 58.726 50.000 0.00 0.00 0.00 3.66
5259 5547 2.912956 TGTTCTAGATCCAAAGCCCTGT 59.087 45.455 0.00 0.00 0.00 4.00
5260 5548 3.198635 TCTGTTCTAGATCCAAAGCCCTG 59.801 47.826 0.00 0.00 0.00 4.45
5261 5549 3.454082 CTCTGTTCTAGATCCAAAGCCCT 59.546 47.826 0.00 0.00 34.21 5.19
5262 5550 3.432890 CCTCTGTTCTAGATCCAAAGCCC 60.433 52.174 0.00 0.00 34.21 5.19
5263 5551 3.452627 TCCTCTGTTCTAGATCCAAAGCC 59.547 47.826 0.00 0.00 34.21 4.35
5264 5552 4.438148 GTCCTCTGTTCTAGATCCAAAGC 58.562 47.826 0.00 0.00 34.21 3.51
5265 5553 4.141824 GGGTCCTCTGTTCTAGATCCAAAG 60.142 50.000 0.00 0.00 34.21 2.77
5266 5554 3.775316 GGGTCCTCTGTTCTAGATCCAAA 59.225 47.826 0.00 0.00 34.21 3.28
5267 5555 3.375699 GGGTCCTCTGTTCTAGATCCAA 58.624 50.000 0.00 0.00 34.21 3.53
5268 5556 2.359355 GGGGTCCTCTGTTCTAGATCCA 60.359 54.545 0.00 0.00 34.21 3.41
5269 5557 2.090999 AGGGGTCCTCTGTTCTAGATCC 60.091 54.545 0.00 0.00 34.21 3.36
5270 5558 2.962421 CAGGGGTCCTCTGTTCTAGATC 59.038 54.545 11.02 0.00 34.21 2.75
5271 5559 2.359781 CCAGGGGTCCTCTGTTCTAGAT 60.360 54.545 17.89 0.00 34.21 1.98
5272 5560 1.007238 CCAGGGGTCCTCTGTTCTAGA 59.993 57.143 17.89 0.00 0.00 2.43
5273 5561 1.490574 CCAGGGGTCCTCTGTTCTAG 58.509 60.000 17.89 0.00 0.00 2.43
5274 5562 0.042731 CCCAGGGGTCCTCTGTTCTA 59.957 60.000 17.89 0.00 0.00 2.10
5275 5563 1.229658 CCCAGGGGTCCTCTGTTCT 60.230 63.158 17.89 0.00 0.00 3.01
5276 5564 3.404773 CCCAGGGGTCCTCTGTTC 58.595 66.667 17.89 0.00 0.00 3.18
5286 5574 2.316586 AAGCCATACCACCCAGGGG 61.317 63.158 11.37 6.87 43.89 4.79
5287 5575 1.076777 CAAGCCATACCACCCAGGG 60.077 63.158 2.85 2.85 43.89 4.45
5288 5576 1.076777 CCAAGCCATACCACCCAGG 60.077 63.158 0.00 0.00 45.67 4.45


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

AutoCloner maintained by Alex Coulton.