Multiple sequence alignment - TraesCS3B01G376200

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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 TraesCS3B01G376200 chr3B 100.000 5357 0 0 1 5357 592534828 592529472 0.000000e+00 9893
1 TraesCS3B01G376200 chr3D 93.045 4946 200 75 472 5357 450296280 450291419 0.000000e+00 7095
2 TraesCS3B01G376200 chr3D 89.381 452 17 9 1 451 450296766 450296345 1.700000e-149 540
3 TraesCS3B01G376200 chr3A 92.153 2536 109 45 2876 5357 593702928 593700429 0.000000e+00 3498
4 TraesCS3B01G376200 chr3A 96.805 1659 48 4 1098 2755 593704727 593703073 0.000000e+00 2765
5 TraesCS3B01G376200 chr3A 89.498 438 21 11 653 1079 593705451 593705028 1.020000e-146 531
6 TraesCS3B01G376200 chr3A 87.800 459 22 21 4 455 593706127 593705696 1.720000e-139 507
7 TraesCS3B01G376200 chr3A 86.555 119 14 2 450 566 593705661 593705543 4.350000e-26 130
8 TraesCS3B01G376200 chr3A 91.011 89 5 2 2749 2834 593703007 593702919 3.390000e-22 117


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 TraesCS3B01G376200 chr3B 592529472 592534828 5356 True 9893.0 9893 100.000 1 5357 1 chr3B.!!$R1 5356
1 TraesCS3B01G376200 chr3D 450291419 450296766 5347 True 3817.5 7095 91.213 1 5357 2 chr3D.!!$R1 5356
2 TraesCS3B01G376200 chr3A 593700429 593706127 5698 True 1258.0 3498 90.637 4 5357 6 chr3A.!!$R1 5353

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
395 403 0.322277 TCTTCCGTCTCGCTACAGGT 60.322 55.000 0.00 0.0 0.00 4.00 F
511 568 1.021968 AATTCCGGCGTTATCAAGGC 58.978 50.000 6.01 0.0 41.32 4.35 F
1575 1967 1.050988 ATGGTATCTGGTCGCTGCCT 61.051 55.000 0.00 0.0 0.00 4.75 F
2683 3077 1.073603 TGTGCATGTGTGGGAATCTGA 59.926 47.619 0.00 0.0 0.00 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2220 2612 1.005630 GTCGAGCACTTCCAGCAGT 60.006 57.895 0.00 0.0 0.00 4.40 R
2469 2861 2.062971 AGGCATGCAGGGAAATACAG 57.937 50.000 21.36 0.0 0.00 2.74 R
2940 3409 0.037232 GAAGACTGGTCAGGTTCCCG 60.037 60.000 3.51 0.0 0.00 5.14 R
4532 5002 0.248565 AGAATCGCAGAGAAGCAGCA 59.751 50.000 0.00 0.0 43.63 4.41 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
19 20 0.815095 CAAGGCGGGTAAATTCCACC 59.185 55.000 1.34 1.34 35.15 4.61
60 61 1.889105 CACTTGCACTGCTCACCGT 60.889 57.895 1.98 0.00 0.00 4.83
61 62 1.153168 ACTTGCACTGCTCACCGTT 60.153 52.632 1.98 0.00 0.00 4.44
395 403 0.322277 TCTTCCGTCTCGCTACAGGT 60.322 55.000 0.00 0.00 0.00 4.00
399 407 2.161855 TCCGTCTCGCTACAGGTAAAA 58.838 47.619 0.00 0.00 0.00 1.52
400 408 2.557924 TCCGTCTCGCTACAGGTAAAAA 59.442 45.455 0.00 0.00 0.00 1.94
401 409 3.194116 TCCGTCTCGCTACAGGTAAAAAT 59.806 43.478 0.00 0.00 0.00 1.82
402 410 3.306166 CCGTCTCGCTACAGGTAAAAATG 59.694 47.826 0.00 0.00 0.00 2.32
403 411 3.924686 CGTCTCGCTACAGGTAAAAATGT 59.075 43.478 0.00 0.00 0.00 2.71
404 412 5.097529 CGTCTCGCTACAGGTAAAAATGTA 58.902 41.667 0.00 0.00 0.00 2.29
408 416 7.756722 GTCTCGCTACAGGTAAAAATGTAGTAA 59.243 37.037 12.47 2.80 46.89 2.24
427 437 9.967451 TGTAGTAATCCATTCAAACCAAAGATA 57.033 29.630 0.00 0.00 0.00 1.98
464 513 5.804979 GGAAATGTTATTGTGAAATCGGGTG 59.195 40.000 0.00 0.00 0.00 4.61
476 525 6.098552 TGTGAAATCGGGTGATAATAGTGGTA 59.901 38.462 0.00 0.00 33.40 3.25
511 568 1.021968 AATTCCGGCGTTATCAAGGC 58.978 50.000 6.01 0.00 41.32 4.35
518 575 1.400494 GGCGTTATCAAGGCGTGAATT 59.600 47.619 7.31 0.00 42.87 2.17
562 619 2.689983 GTGGCAATCAATCCGGAAGATT 59.310 45.455 22.76 22.76 46.54 2.40
574 631 5.429681 TCCGGAAGATTGGATTTCTACAA 57.570 39.130 0.00 0.00 0.00 2.41
588 645 9.098355 TGGATTTCTACAAGACGATTTTATCTG 57.902 33.333 0.00 0.00 0.00 2.90
589 646 8.064814 GGATTTCTACAAGACGATTTTATCTGC 58.935 37.037 0.00 0.00 0.00 4.26
590 647 8.723942 ATTTCTACAAGACGATTTTATCTGCT 57.276 30.769 0.00 0.00 0.00 4.24
591 648 7.525688 TTCTACAAGACGATTTTATCTGCTG 57.474 36.000 0.00 0.00 0.00 4.41
592 649 6.631016 TCTACAAGACGATTTTATCTGCTGT 58.369 36.000 0.00 0.00 0.00 4.40
593 650 5.536554 ACAAGACGATTTTATCTGCTGTG 57.463 39.130 0.00 0.00 0.00 3.66
594 651 4.997395 ACAAGACGATTTTATCTGCTGTGT 59.003 37.500 0.00 0.00 0.00 3.72
595 652 6.163476 ACAAGACGATTTTATCTGCTGTGTA 58.837 36.000 0.00 0.00 0.00 2.90
596 653 6.311445 ACAAGACGATTTTATCTGCTGTGTAG 59.689 38.462 0.00 0.00 0.00 2.74
597 654 5.967088 AGACGATTTTATCTGCTGTGTAGT 58.033 37.500 0.00 0.00 0.00 2.73
598 655 5.807520 AGACGATTTTATCTGCTGTGTAGTG 59.192 40.000 0.00 0.00 0.00 2.74
599 656 5.479306 ACGATTTTATCTGCTGTGTAGTGT 58.521 37.500 0.00 0.00 0.00 3.55
600 657 5.932303 ACGATTTTATCTGCTGTGTAGTGTT 59.068 36.000 0.00 0.00 0.00 3.32
601 658 7.094631 ACGATTTTATCTGCTGTGTAGTGTTA 58.905 34.615 0.00 0.00 0.00 2.41
602 659 7.063074 ACGATTTTATCTGCTGTGTAGTGTTAC 59.937 37.037 0.00 0.00 0.00 2.50
603 660 7.062956 CGATTTTATCTGCTGTGTAGTGTTACA 59.937 37.037 0.00 0.00 37.45 2.41
604 661 8.792830 ATTTTATCTGCTGTGTAGTGTTACAT 57.207 30.769 0.00 0.00 41.56 2.29
605 662 7.827819 TTTATCTGCTGTGTAGTGTTACATC 57.172 36.000 0.00 0.00 41.56 3.06
606 663 4.864704 TCTGCTGTGTAGTGTTACATCA 57.135 40.909 0.00 0.00 41.56 3.07
607 664 4.809673 TCTGCTGTGTAGTGTTACATCAG 58.190 43.478 0.00 0.00 41.56 2.90
608 665 3.925379 TGCTGTGTAGTGTTACATCAGG 58.075 45.455 13.73 0.00 41.56 3.86
817 912 3.124297 GCTAGCTCATTAATAGCGCAAGG 59.876 47.826 11.47 0.00 44.87 3.61
871 967 4.021925 GTTCACAGCCTCCCCGCT 62.022 66.667 0.00 0.00 40.65 5.52
1557 1949 3.626924 GCTGGCCCGATACCCGAT 61.627 66.667 0.00 0.00 41.76 4.18
1575 1967 1.050988 ATGGTATCTGGTCGCTGCCT 61.051 55.000 0.00 0.00 0.00 4.75
1629 2021 2.203182 TCGGGGAGTGTTCCTGGT 59.797 61.111 0.00 0.00 43.49 4.00
1767 2159 1.079405 CTTCTTCACCGGCGGCTTA 60.079 57.895 28.71 8.86 0.00 3.09
1866 2258 1.749033 GATCGGGGAGATGTGGTCC 59.251 63.158 0.00 0.00 40.26 4.46
1942 2334 3.034721 TCGCGAAATGTAAGAACCTGT 57.965 42.857 6.20 0.00 0.00 4.00
2229 2621 2.268920 GGGATGCGACTGCTGGAA 59.731 61.111 0.00 0.00 43.34 3.53
2241 2633 2.089349 GCTGGAAGTGCTCGACGTC 61.089 63.158 5.18 5.18 35.30 4.34
2283 2675 2.351276 GTGCCACCGGAGATTGGT 59.649 61.111 9.46 0.00 41.47 3.67
2325 2717 1.849039 CTGAGGATGGGGGACAATTCT 59.151 52.381 0.00 0.00 0.00 2.40
2424 2816 1.950216 TGCCGCACTAAATTTGACACA 59.050 42.857 0.00 0.00 0.00 3.72
2469 2861 9.052759 TGAAGTTGACTAGGTCTATTTGTTTTC 57.947 33.333 0.00 0.00 33.15 2.29
2683 3077 1.073603 TGTGCATGTGTGGGAATCTGA 59.926 47.619 0.00 0.00 0.00 3.27
2740 3134 6.729690 ATAGAAAGTCTAGCAAGCTGATCT 57.270 37.500 4.53 3.83 31.67 2.75
2741 3135 4.757594 AGAAAGTCTAGCAAGCTGATCTG 58.242 43.478 4.53 0.00 0.00 2.90
2801 3270 4.134563 TGAGTACTCAAAAAGTGAAGCCC 58.865 43.478 23.24 0.00 39.11 5.19
2815 3284 3.267860 GCCCGCAGATCGAGCAAG 61.268 66.667 2.38 0.00 41.84 4.01
2845 3314 8.854614 AACTCAGTTATACTCTGCTTGATTTT 57.145 30.769 0.00 0.00 33.48 1.82
2851 3320 8.940952 AGTTATACTCTGCTTGATTTTCTGAAC 58.059 33.333 0.00 0.00 0.00 3.18
2852 3321 8.721478 GTTATACTCTGCTTGATTTTCTGAACA 58.279 33.333 0.00 0.00 0.00 3.18
2858 3327 6.942005 TCTGCTTGATTTTCTGAACATTAGGA 59.058 34.615 0.00 0.00 0.00 2.94
2940 3409 0.744771 GACCGATTCCAAGCACCCTC 60.745 60.000 0.00 0.00 0.00 4.30
3174 3643 4.639906 TGCGGTGCTGTCATGCCA 62.640 61.111 0.00 0.00 0.00 4.92
3234 3703 2.727123 TGTCACAATCCACACCAAGT 57.273 45.000 0.00 0.00 0.00 3.16
3345 3814 4.692625 GTGATCACTGTAACTGTGCTCAAT 59.307 41.667 18.83 0.00 39.04 2.57
3489 3958 0.394192 CAGAGTTCAGCACTGGTGGA 59.606 55.000 8.35 0.00 35.01 4.02
3702 4171 3.646162 TGAGAGGCTTTTACTGGACTTCA 59.354 43.478 0.00 0.00 0.00 3.02
3771 4240 1.002868 GCACCTCCATGAGTGCACT 60.003 57.895 21.88 21.88 37.00 4.40
3774 4243 0.612229 ACCTCCATGAGTGCACTGAG 59.388 55.000 27.27 22.70 0.00 3.35
3930 4399 1.144057 CAGGGTCGGTGACTATGGC 59.856 63.158 0.00 0.00 32.47 4.40
3952 4421 1.264749 TGCAAGCCTACTCCCGATGT 61.265 55.000 0.00 0.00 0.00 3.06
3954 4423 1.138266 GCAAGCCTACTCCCGATGTTA 59.862 52.381 0.00 0.00 0.00 2.41
3996 4465 1.649321 AGATCCAGAGTGCACTTGGA 58.351 50.000 33.47 33.47 0.00 3.53
3999 4468 3.972638 AGATCCAGAGTGCACTTGGATAT 59.027 43.478 36.74 33.94 39.26 1.63
4080 4549 2.203480 GGGGTGCTTGCACTGGAA 60.203 61.111 22.55 0.00 0.00 3.53
4257 4726 2.594303 CTGGGCCTCGTTTGCACA 60.594 61.111 4.53 0.00 40.50 4.57
4311 4780 4.441634 GGCGAGGTGTTGAGTATACTTGAT 60.442 45.833 6.88 0.00 0.00 2.57
4323 4792 3.550437 ATACTTGATGTGGTGAGGAGC 57.450 47.619 0.00 0.00 0.00 4.70
4326 4795 0.842030 TTGATGTGGTGAGGAGCCCT 60.842 55.000 0.00 0.00 36.03 5.19
4353 4822 1.580658 AGTCCAGGGGATGAGATGGTA 59.419 52.381 0.00 0.00 32.73 3.25
4355 4824 3.406152 AGTCCAGGGGATGAGATGGTATA 59.594 47.826 0.00 0.00 32.73 1.47
4358 4827 3.054802 CCAGGGGATGAGATGGTATAAGC 60.055 52.174 0.00 0.00 0.00 3.09
4359 4828 3.584406 CAGGGGATGAGATGGTATAAGCA 59.416 47.826 0.00 0.00 0.00 3.91
4360 4829 4.042062 CAGGGGATGAGATGGTATAAGCAA 59.958 45.833 0.00 0.00 0.00 3.91
4361 4830 4.288105 AGGGGATGAGATGGTATAAGCAAG 59.712 45.833 0.00 0.00 0.00 4.01
4362 4831 4.566488 GGGGATGAGATGGTATAAGCAAGG 60.566 50.000 0.00 0.00 0.00 3.61
4363 4832 4.042187 GGGATGAGATGGTATAAGCAAGGT 59.958 45.833 0.00 0.00 0.00 3.50
4364 4833 5.241662 GGATGAGATGGTATAAGCAAGGTC 58.758 45.833 0.00 0.00 0.00 3.85
4365 4834 5.012561 GGATGAGATGGTATAAGCAAGGTCT 59.987 44.000 0.00 0.00 0.00 3.85
4366 4835 5.537300 TGAGATGGTATAAGCAAGGTCTC 57.463 43.478 0.00 0.00 32.73 3.36
4367 4836 5.211973 TGAGATGGTATAAGCAAGGTCTCT 58.788 41.667 8.71 0.00 33.08 3.10
4371 4840 6.825721 AGATGGTATAAGCAAGGTCTCTTTTG 59.174 38.462 0.00 0.00 0.00 2.44
4372 4841 6.121776 TGGTATAAGCAAGGTCTCTTTTGA 57.878 37.500 0.00 0.00 0.00 2.69
4377 4846 5.506686 AAGCAAGGTCTCTTTTGAAACTC 57.493 39.130 0.00 0.00 0.00 3.01
4383 4852 5.995446 AGGTCTCTTTTGAAACTCTGTTCT 58.005 37.500 0.00 0.00 0.00 3.01
4385 4854 5.586643 GGTCTCTTTTGAAACTCTGTTCTGT 59.413 40.000 0.00 0.00 0.00 3.41
4390 4859 4.944962 TTGAAACTCTGTTCTGTGTGTG 57.055 40.909 0.00 0.00 0.00 3.82
4406 4875 2.039084 TGTGTGCCTGGGTTTTTGTTTT 59.961 40.909 0.00 0.00 0.00 2.43
4447 4916 3.490851 CCGGTTGGGAAGAAGGGA 58.509 61.111 0.00 0.00 38.47 4.20
4450 4919 1.198759 CGGTTGGGAAGAAGGGAGGA 61.199 60.000 0.00 0.00 0.00 3.71
4454 4923 0.475632 TGGGAAGAAGGGAGGAAGCA 60.476 55.000 0.00 0.00 0.00 3.91
4456 4925 1.075536 GGGAAGAAGGGAGGAAGCAAA 59.924 52.381 0.00 0.00 0.00 3.68
4508 4978 6.319141 AGCTTGTAGTTTGGTTCTGAAATC 57.681 37.500 0.00 0.00 0.00 2.17
4529 4999 4.740822 GGGGGTTGGCGATGCTGT 62.741 66.667 0.00 0.00 0.00 4.40
4532 5002 1.665442 GGGTTGGCGATGCTGTTTT 59.335 52.632 0.00 0.00 0.00 2.43
4533 5003 0.667184 GGGTTGGCGATGCTGTTTTG 60.667 55.000 0.00 0.00 0.00 2.44
4534 5004 1.284297 GGTTGGCGATGCTGTTTTGC 61.284 55.000 0.00 0.00 0.00 3.68
4546 5016 0.308684 TGTTTTGCTGCTTCTCTGCG 59.691 50.000 0.00 0.00 41.87 5.18
4582 5053 4.640771 TCCTTGGATGAAACTGTAGCTT 57.359 40.909 0.00 0.00 0.00 3.74
4594 5065 2.257894 CTGTAGCTTTCTCTGCTCGTG 58.742 52.381 0.00 0.00 41.46 4.35
4599 5070 0.671781 CTTTCTCTGCTCGTGTGGGG 60.672 60.000 0.00 0.00 0.00 4.96
4600 5071 1.407656 TTTCTCTGCTCGTGTGGGGT 61.408 55.000 0.00 0.00 0.00 4.95
4601 5072 0.541063 TTCTCTGCTCGTGTGGGGTA 60.541 55.000 0.00 0.00 0.00 3.69
4603 5074 0.537188 CTCTGCTCGTGTGGGGTATT 59.463 55.000 0.00 0.00 0.00 1.89
4604 5075 0.249120 TCTGCTCGTGTGGGGTATTG 59.751 55.000 0.00 0.00 0.00 1.90
4606 5077 2.112815 GCTCGTGTGGGGTATTGCC 61.113 63.158 0.00 0.00 0.00 4.52
4607 5078 1.813753 CTCGTGTGGGGTATTGCCG 60.814 63.158 0.00 0.00 38.44 5.69
4613 5084 2.280186 GGGGTATTGCCGCGAGAG 60.280 66.667 8.23 0.00 40.49 3.20
4615 5086 2.499685 GGTATTGCCGCGAGAGGT 59.500 61.111 8.23 0.00 0.00 3.85
4616 5087 1.153429 GGTATTGCCGCGAGAGGTT 60.153 57.895 8.23 0.00 0.00 3.50
4701 5177 8.791675 TGTGCTGATAAATGTGACTTTGATTTA 58.208 29.630 0.00 0.00 0.00 1.40
4702 5178 9.065871 GTGCTGATAAATGTGACTTTGATTTAC 57.934 33.333 0.00 0.00 0.00 2.01
4703 5179 8.791675 TGCTGATAAATGTGACTTTGATTTACA 58.208 29.630 0.00 0.00 0.00 2.41
4704 5180 9.793252 GCTGATAAATGTGACTTTGATTTACAT 57.207 29.630 0.00 0.00 33.73 2.29
4776 5256 2.229675 TTACTCATCTGATGCTGCCG 57.770 50.000 12.78 1.89 0.00 5.69
4791 5272 0.250684 TGCCGATCTTTTCACTGCCA 60.251 50.000 0.00 0.00 0.00 4.92
4807 5307 3.838317 ACTGCCACCTATTCACTAACAGA 59.162 43.478 0.00 0.00 0.00 3.41
4818 5318 9.612620 CCTATTCACTAACAGAAAAATGTTCAC 57.387 33.333 0.00 0.00 42.33 3.18
4850 5350 7.687941 ACTGTTTCGATTCCATTACTGATTT 57.312 32.000 0.00 0.00 0.00 2.17
4854 5354 8.183536 TGTTTCGATTCCATTACTGATTTCATG 58.816 33.333 0.00 0.00 0.00 3.07
4857 5357 6.483307 TCGATTCCATTACTGATTTCATGACC 59.517 38.462 0.00 0.00 0.00 4.02
4866 5366 5.043903 ACTGATTTCATGACCGTAATCTCG 58.956 41.667 15.47 10.57 0.00 4.04
4873 5373 5.222631 TCATGACCGTAATCTCGATGATTG 58.777 41.667 15.84 6.28 44.40 2.67
4890 5390 0.620556 TTGCCCTTCTGATCCAGTCC 59.379 55.000 0.00 0.00 32.61 3.85
4898 5404 4.324099 CCTTCTGATCCAGTCCATCAAAGT 60.324 45.833 0.00 0.00 32.61 2.66
4902 5408 4.074259 TGATCCAGTCCATCAAAGTTGTG 58.926 43.478 0.00 0.00 0.00 3.33
4905 5411 3.631686 TCCAGTCCATCAAAGTTGTGTTG 59.368 43.478 0.00 0.00 0.00 3.33
4907 5413 2.362077 AGTCCATCAAAGTTGTGTTGCC 59.638 45.455 0.00 0.00 0.00 4.52
4909 5415 2.361757 TCCATCAAAGTTGTGTTGCCAG 59.638 45.455 0.00 0.00 0.00 4.85
4961 5467 1.911702 AACGCTAGGCCTTTCTCCCC 61.912 60.000 12.58 0.00 0.00 4.81
4965 5471 1.382695 TAGGCCTTTCTCCCCTCCG 60.383 63.158 12.58 0.00 0.00 4.63
4967 5473 3.009714 GCCTTTCTCCCCTCCGGT 61.010 66.667 0.00 0.00 0.00 5.28
4968 5474 2.603652 GCCTTTCTCCCCTCCGGTT 61.604 63.158 0.00 0.00 0.00 4.44
4969 5475 2.075837 CCTTTCTCCCCTCCGGTTT 58.924 57.895 0.00 0.00 0.00 3.27
4975 5481 2.361230 CCCCTCCGGTTTGAAGGC 60.361 66.667 0.00 0.00 0.00 4.35
4976 5482 2.434331 CCCTCCGGTTTGAAGGCA 59.566 61.111 0.00 0.00 0.00 4.75
5011 5517 0.477204 ATCCATGGATCACAGCCTGG 59.523 55.000 22.15 0.00 0.00 4.45
5012 5518 0.915872 TCCATGGATCACAGCCTGGT 60.916 55.000 11.44 0.00 0.00 4.00
5013 5519 0.750546 CCATGGATCACAGCCTGGTG 60.751 60.000 5.56 0.00 40.16 4.17
5014 5520 0.750546 CATGGATCACAGCCTGGTGG 60.751 60.000 0.00 0.00 39.27 4.61
5015 5521 1.210204 ATGGATCACAGCCTGGTGGT 61.210 55.000 0.00 0.00 39.27 4.16
5017 5523 1.377725 GATCACAGCCTGGTGGTGG 60.378 63.158 16.26 2.96 46.86 4.61
5110 5616 4.248842 CGCCAGTCACCACCACCA 62.249 66.667 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.967779 ACCTTCAAATTTTCGGTGGGG 59.032 47.619 2.83 0.00 0.00 4.96
20 21 3.389221 CAACCTTCAAATTTTCGGTGGG 58.611 45.455 4.15 0.00 0.00 4.61
399 407 9.308000 TCTTTGGTTTGAATGGATTACTACATT 57.692 29.630 0.00 0.00 39.81 2.71
400 408 8.877864 TCTTTGGTTTGAATGGATTACTACAT 57.122 30.769 0.00 0.00 0.00 2.29
401 409 8.877864 ATCTTTGGTTTGAATGGATTACTACA 57.122 30.769 0.00 0.00 0.00 2.74
464 513 5.035443 GCCATCGTCGATACCACTATTATC 58.965 45.833 7.56 0.00 0.00 1.75
511 568 7.377397 TGGAAATTTAAGACGTTTCAATTCACG 59.623 33.333 0.00 0.83 42.29 4.35
518 575 5.470777 ACCGATGGAAATTTAAGACGTTTCA 59.529 36.000 0.00 0.00 34.40 2.69
562 619 9.098355 CAGATAAAATCGTCTTGTAGAAATCCA 57.902 33.333 0.00 0.00 0.00 3.41
568 625 6.531594 CACAGCAGATAAAATCGTCTTGTAGA 59.468 38.462 0.00 0.00 0.00 2.59
574 631 5.807520 CACTACACAGCAGATAAAATCGTCT 59.192 40.000 0.00 0.00 0.00 4.18
588 645 3.262420 CCCTGATGTAACACTACACAGC 58.738 50.000 0.00 0.00 40.84 4.40
589 646 3.260884 ACCCCTGATGTAACACTACACAG 59.739 47.826 0.00 0.00 40.84 3.66
590 647 3.007506 CACCCCTGATGTAACACTACACA 59.992 47.826 0.00 0.00 40.84 3.72
591 648 3.596214 CACCCCTGATGTAACACTACAC 58.404 50.000 0.00 0.00 40.84 2.90
592 649 2.569853 CCACCCCTGATGTAACACTACA 59.430 50.000 0.00 0.00 42.22 2.74
593 650 2.835764 TCCACCCCTGATGTAACACTAC 59.164 50.000 0.00 0.00 0.00 2.73
594 651 3.193395 TCCACCCCTGATGTAACACTA 57.807 47.619 0.00 0.00 0.00 2.74
595 652 2.038863 TCCACCCCTGATGTAACACT 57.961 50.000 0.00 0.00 0.00 3.55
596 653 3.366052 AATCCACCCCTGATGTAACAC 57.634 47.619 0.00 0.00 0.00 3.32
597 654 4.396357 AAAATCCACCCCTGATGTAACA 57.604 40.909 0.00 0.00 0.00 2.41
724 817 3.611766 TCCGATTTGTTTCTCCTCCTC 57.388 47.619 0.00 0.00 0.00 3.71
725 818 4.367039 TTTCCGATTTGTTTCTCCTCCT 57.633 40.909 0.00 0.00 0.00 3.69
726 819 4.519350 ACTTTTCCGATTTGTTTCTCCTCC 59.481 41.667 0.00 0.00 0.00 4.30
727 820 5.690997 ACTTTTCCGATTTGTTTCTCCTC 57.309 39.130 0.00 0.00 0.00 3.71
1145 1537 4.112341 CGTCGTCCTCGGTCCACC 62.112 72.222 0.00 0.00 37.69 4.61
1557 1949 1.264749 AAGGCAGCGACCAGATACCA 61.265 55.000 0.69 0.00 0.00 3.25
1575 1967 2.035155 TCCAGAGACCGGAGCGAA 59.965 61.111 9.46 0.00 0.00 4.70
1866 2258 3.710722 AGGTCAAGCCGCTCCAGG 61.711 66.667 0.00 0.00 43.70 4.45
1942 2334 2.903357 GCTGAGATCGGCCTCCAA 59.097 61.111 0.00 0.00 42.27 3.53
2218 2610 2.091112 CGAGCACTTCCAGCAGTCG 61.091 63.158 0.00 0.00 0.00 4.18
2220 2612 1.005630 GTCGAGCACTTCCAGCAGT 60.006 57.895 0.00 0.00 0.00 4.40
2406 2798 5.218885 TGAATTGTGTCAAATTTAGTGCGG 58.781 37.500 0.00 0.00 29.89 5.69
2412 2804 8.980610 CAAGCAATCTGAATTGTGTCAAATTTA 58.019 29.630 0.00 0.00 43.54 1.40
2424 2816 7.516198 ACTTCACTAACAAGCAATCTGAATT 57.484 32.000 0.00 0.00 0.00 2.17
2469 2861 2.062971 AGGCATGCAGGGAAATACAG 57.937 50.000 21.36 0.00 0.00 2.74
2550 2942 9.551734 GTTTAGGACTCCTAACAGAAAACTAAA 57.448 33.333 16.05 0.00 44.64 1.85
2683 3077 3.321497 TGCAAAGTTTGAAACAAACGCT 58.679 36.364 19.82 9.35 35.42 5.07
2724 3118 3.130164 TCTGTCAGATCAGCTTGCTAGAC 59.870 47.826 0.00 0.00 35.63 2.59
2793 3262 1.880340 CTCGATCTGCGGGCTTCAC 60.880 63.158 0.00 0.00 41.33 3.18
2801 3270 4.045104 AGTTTATACTTGCTCGATCTGCG 58.955 43.478 0.00 0.00 42.69 5.18
2834 3303 7.094463 ACTCCTAATGTTCAGAAAATCAAGCAG 60.094 37.037 0.00 0.00 0.00 4.24
2835 3304 6.716628 ACTCCTAATGTTCAGAAAATCAAGCA 59.283 34.615 0.00 0.00 0.00 3.91
2836 3305 7.094634 TGACTCCTAATGTTCAGAAAATCAAGC 60.095 37.037 0.00 0.00 0.00 4.01
2837 3306 8.327941 TGACTCCTAATGTTCAGAAAATCAAG 57.672 34.615 0.00 0.00 0.00 3.02
2838 3307 8.868522 ATGACTCCTAATGTTCAGAAAATCAA 57.131 30.769 0.00 0.00 0.00 2.57
2879 3348 1.927487 ATCCCTGCATTCACAAGCAA 58.073 45.000 0.00 0.00 40.73 3.91
2940 3409 0.037232 GAAGACTGGTCAGGTTCCCG 60.037 60.000 3.51 0.00 0.00 5.14
2949 3418 1.070758 TCAACAGCCTGAAGACTGGTC 59.929 52.381 0.00 0.00 38.25 4.02
3174 3643 2.433436 GGGTTGAGTACAATCGGCTTT 58.567 47.619 0.00 0.00 37.94 3.51
3234 3703 1.002134 GTGCTTGCTGCTAGGGGAA 60.002 57.895 12.76 0.00 43.37 3.97
3345 3814 4.994201 GCTGCACGGACACGACGA 62.994 66.667 0.00 0.00 44.60 4.20
3771 4240 2.634940 CCAGGAAAGAGTGTTCTCCTCA 59.365 50.000 2.18 0.00 41.26 3.86
3774 4243 3.604582 CATCCAGGAAAGAGTGTTCTCC 58.395 50.000 0.00 0.00 41.26 3.71
3855 4324 4.174009 ACTTGAGATTGTAATGGACGACG 58.826 43.478 0.00 0.00 0.00 5.12
3930 4399 1.450312 CGGGAGTAGGCTTGCAAGG 60.450 63.158 27.10 9.80 0.00 3.61
3942 4411 2.501492 CCGGTCTAACATCGGGAGT 58.499 57.895 0.00 0.00 40.07 3.85
3952 4421 1.136305 GCTCAGCACATACCGGTCTAA 59.864 52.381 12.40 0.00 0.00 2.10
3954 4423 1.257750 TGCTCAGCACATACCGGTCT 61.258 55.000 12.40 0.00 31.71 3.85
3996 4465 2.009774 GCGAATTCTGGCGCCATATAT 58.990 47.619 32.87 20.07 46.93 0.86
3999 4468 3.731136 GCGAATTCTGGCGCCATA 58.269 55.556 32.87 21.93 46.93 2.74
4080 4549 1.604378 CCTCCTGCCCGTCAAGATT 59.396 57.895 0.00 0.00 0.00 2.40
4257 4726 4.063967 TTCGACGGCACCTGCGAT 62.064 61.111 0.00 0.00 43.26 4.58
4323 4792 1.992277 CCCTGGACTGTCCTGAGGG 60.992 68.421 28.37 28.37 41.73 4.30
4326 4795 0.618680 CATCCCCTGGACTGTCCTGA 60.619 60.000 28.83 18.92 37.65 3.86
4353 4822 7.001073 AGAGTTTCAAAAGAGACCTTGCTTAT 58.999 34.615 0.00 0.00 31.91 1.73
4355 4824 5.067023 CAGAGTTTCAAAAGAGACCTTGCTT 59.933 40.000 0.00 0.00 31.91 3.91
4358 4827 6.317391 AGAACAGAGTTTCAAAAGAGACCTTG 59.683 38.462 0.00 0.00 31.91 3.61
4359 4828 6.317391 CAGAACAGAGTTTCAAAAGAGACCTT 59.683 38.462 0.00 0.00 0.00 3.50
4360 4829 5.819901 CAGAACAGAGTTTCAAAAGAGACCT 59.180 40.000 0.00 0.00 0.00 3.85
4361 4830 5.586643 ACAGAACAGAGTTTCAAAAGAGACC 59.413 40.000 0.00 0.00 0.00 3.85
4362 4831 6.092807 ACACAGAACAGAGTTTCAAAAGAGAC 59.907 38.462 0.00 0.00 0.00 3.36
4363 4832 6.092670 CACACAGAACAGAGTTTCAAAAGAGA 59.907 38.462 0.00 0.00 0.00 3.10
4364 4833 6.128172 ACACACAGAACAGAGTTTCAAAAGAG 60.128 38.462 0.00 0.00 0.00 2.85
4365 4834 5.705441 ACACACAGAACAGAGTTTCAAAAGA 59.295 36.000 0.00 0.00 0.00 2.52
4366 4835 5.796935 CACACACAGAACAGAGTTTCAAAAG 59.203 40.000 0.00 0.00 0.00 2.27
4367 4836 5.698832 CACACACAGAACAGAGTTTCAAAA 58.301 37.500 0.00 0.00 0.00 2.44
4371 4840 2.032178 GGCACACACAGAACAGAGTTTC 59.968 50.000 0.00 0.00 0.00 2.78
4372 4841 2.017049 GGCACACACAGAACAGAGTTT 58.983 47.619 0.00 0.00 0.00 2.66
4377 4846 1.168407 CCCAGGCACACACAGAACAG 61.168 60.000 0.00 0.00 0.00 3.16
4383 4852 0.534412 CAAAAACCCAGGCACACACA 59.466 50.000 0.00 0.00 0.00 3.72
4385 4854 1.270907 AACAAAAACCCAGGCACACA 58.729 45.000 0.00 0.00 0.00 3.72
4390 4859 5.018539 AGTAGAAAAACAAAAACCCAGGC 57.981 39.130 0.00 0.00 0.00 4.85
4406 4875 7.470563 CGGGCATCATATATGCATCTAGTAGAA 60.471 40.741 0.19 0.00 46.21 2.10
4447 4916 2.787994 CATCACCACTCTTTGCTTCCT 58.212 47.619 0.00 0.00 0.00 3.36
4450 4919 1.985473 TGCATCACCACTCTTTGCTT 58.015 45.000 0.00 0.00 34.47 3.91
4454 4923 2.559668 CCACAATGCATCACCACTCTTT 59.440 45.455 0.00 0.00 0.00 2.52
4456 4925 1.352017 TCCACAATGCATCACCACTCT 59.648 47.619 0.00 0.00 0.00 3.24
4481 4951 5.676552 TCAGAACCAAACTACAAGCTACAA 58.323 37.500 0.00 0.00 0.00 2.41
4487 4957 8.507249 CCTAAGATTTCAGAACCAAACTACAAG 58.493 37.037 0.00 0.00 0.00 3.16
4508 4978 1.823899 GCATCGCCAACCCCCTAAG 60.824 63.158 0.00 0.00 0.00 2.18
4529 4999 1.527034 ATCGCAGAGAAGCAGCAAAA 58.473 45.000 0.00 0.00 43.63 2.44
4532 5002 0.248565 AGAATCGCAGAGAAGCAGCA 59.751 50.000 0.00 0.00 43.63 4.41
4533 5003 1.367659 AAGAATCGCAGAGAAGCAGC 58.632 50.000 0.00 0.00 43.63 5.25
4534 5004 2.095532 CCAAAGAATCGCAGAGAAGCAG 59.904 50.000 0.00 0.00 43.63 4.24
4546 5016 5.982890 TCCAAGGAATGAACCAAAGAATC 57.017 39.130 0.00 0.00 0.00 2.52
4582 5053 0.541063 TACCCCACACGAGCAGAGAA 60.541 55.000 0.00 0.00 0.00 2.87
4594 5065 2.895372 CTCGCGGCAATACCCCAC 60.895 66.667 6.13 0.00 33.26 4.61
4599 5070 0.739813 ACAACCTCTCGCGGCAATAC 60.740 55.000 6.13 0.00 0.00 1.89
4600 5071 0.739462 CACAACCTCTCGCGGCAATA 60.739 55.000 6.13 0.00 0.00 1.90
4601 5072 2.034879 CACAACCTCTCGCGGCAAT 61.035 57.895 6.13 0.00 0.00 3.56
4603 5074 4.680237 CCACAACCTCTCGCGGCA 62.680 66.667 6.13 0.00 0.00 5.69
4612 5083 3.628646 GAGATGCCGGCCACAACCT 62.629 63.158 26.77 11.42 0.00 3.50
4613 5084 3.134127 GAGATGCCGGCCACAACC 61.134 66.667 26.77 6.34 0.00 3.77
4615 5086 4.776322 CCGAGATGCCGGCCACAA 62.776 66.667 26.77 4.98 43.25 3.33
4701 5177 9.363763 CAGAAGATGTTCGAGCAATATATATGT 57.636 33.333 5.91 0.00 37.79 2.29
4702 5178 8.326713 GCAGAAGATGTTCGAGCAATATATATG 58.673 37.037 5.91 1.46 38.04 1.78
4703 5179 8.256605 AGCAGAAGATGTTCGAGCAATATATAT 58.743 33.333 19.70 0.00 39.59 0.86
4704 5180 7.606349 AGCAGAAGATGTTCGAGCAATATATA 58.394 34.615 19.70 0.00 39.59 0.86
4717 5194 4.581824 ACACATTGTGAAGCAGAAGATGTT 59.418 37.500 23.12 0.00 36.96 2.71
4762 5242 1.880271 AAGATCGGCAGCATCAGATG 58.120 50.000 5.98 5.98 0.00 2.90
4763 5243 2.634815 AAAGATCGGCAGCATCAGAT 57.365 45.000 0.00 0.00 0.00 2.90
4776 5256 4.943705 TGAATAGGTGGCAGTGAAAAGATC 59.056 41.667 0.00 0.00 0.00 2.75
4791 5272 9.349713 TGAACATTTTTCTGTTAGTGAATAGGT 57.650 29.630 0.00 0.00 39.40 3.08
4807 5307 4.104776 CAGTCGTTGCTGTGAACATTTTT 58.895 39.130 0.00 0.00 0.00 1.94
4832 5332 6.483307 GGTCATGAAATCAGTAATGGAATCGA 59.517 38.462 0.00 0.00 0.00 3.59
4833 5333 6.564686 CGGTCATGAAATCAGTAATGGAATCG 60.565 42.308 0.00 0.00 0.00 3.34
4834 5334 6.260936 ACGGTCATGAAATCAGTAATGGAATC 59.739 38.462 0.00 0.00 0.00 2.52
4835 5335 6.122277 ACGGTCATGAAATCAGTAATGGAAT 58.878 36.000 0.00 0.00 0.00 3.01
4836 5336 5.496556 ACGGTCATGAAATCAGTAATGGAA 58.503 37.500 0.00 0.00 0.00 3.53
4837 5337 5.097742 ACGGTCATGAAATCAGTAATGGA 57.902 39.130 0.00 0.00 0.00 3.41
4838 5338 6.918892 TTACGGTCATGAAATCAGTAATGG 57.081 37.500 0.00 0.00 0.00 3.16
4839 5339 8.370493 AGATTACGGTCATGAAATCAGTAATG 57.630 34.615 18.39 0.00 34.64 1.90
4840 5340 7.382488 CGAGATTACGGTCATGAAATCAGTAAT 59.618 37.037 16.44 15.88 36.42 1.89
4841 5341 6.695713 CGAGATTACGGTCATGAAATCAGTAA 59.304 38.462 16.44 12.75 32.04 2.24
4842 5342 6.038936 TCGAGATTACGGTCATGAAATCAGTA 59.961 38.462 16.44 5.87 32.04 2.74
4843 5343 5.043903 CGAGATTACGGTCATGAAATCAGT 58.956 41.667 16.44 6.70 32.04 3.41
4850 5350 5.222631 CAATCATCGAGATTACGGTCATGA 58.777 41.667 8.98 0.00 45.06 3.07
4854 5354 2.731976 GGCAATCATCGAGATTACGGTC 59.268 50.000 8.98 0.00 45.06 4.79
4857 5357 3.032017 AGGGCAATCATCGAGATTACG 57.968 47.619 8.98 0.00 45.06 3.18
4866 5366 3.147629 CTGGATCAGAAGGGCAATCATC 58.852 50.000 0.00 0.00 32.44 2.92
4873 5373 0.842635 ATGGACTGGATCAGAAGGGC 59.157 55.000 1.59 0.00 35.18 5.19
4890 5390 2.129607 GCTGGCAACACAACTTTGATG 58.870 47.619 0.00 0.00 46.17 3.07
4898 5404 1.685517 TGCAAATAGCTGGCAACACAA 59.314 42.857 0.00 0.00 44.67 3.33
4902 5408 3.040409 GCTGCAAATAGCTGGCAAC 57.960 52.632 0.00 0.00 45.94 4.17
4909 5415 0.179163 GGTCAACGGCTGCAAATAGC 60.179 55.000 0.50 0.00 45.96 2.97
4940 5446 0.249398 GGAGAAAGGCCTAGCGTTCA 59.751 55.000 5.16 0.00 35.55 3.18
4945 5451 1.701031 GGAGGGGAGAAAGGCCTAGC 61.701 65.000 5.16 0.00 0.00 3.42
4961 5467 1.291877 CGAGTGCCTTCAAACCGGAG 61.292 60.000 9.46 0.00 0.00 4.63
4965 5471 0.310854 CCAACGAGTGCCTTCAAACC 59.689 55.000 0.00 0.00 0.00 3.27
4967 5473 1.593196 CTCCAACGAGTGCCTTCAAA 58.407 50.000 0.00 0.00 0.00 2.69
4968 5474 0.884704 GCTCCAACGAGTGCCTTCAA 60.885 55.000 0.00 0.00 38.49 2.69
4969 5475 1.301716 GCTCCAACGAGTGCCTTCA 60.302 57.895 0.00 0.00 38.49 3.02
4975 5481 1.363744 GATCCTTGCTCCAACGAGTG 58.636 55.000 0.00 0.00 38.49 3.51
4976 5482 0.250513 GGATCCTTGCTCCAACGAGT 59.749 55.000 3.84 0.00 38.49 4.18
5110 5616 2.173569 CCCCCTCGATTCAATTCCTCTT 59.826 50.000 0.00 0.00 0.00 2.85
5189 5706 2.181021 GTGAATGCTGCCTGCTGC 59.819 61.111 13.30 13.30 43.37 5.25
5320 5849 3.121778 GCAAAACAGCATCATTTTCGACC 59.878 43.478 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.