Multiple sequence alignment - TraesCS5B01G225200

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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 TraesCS5B01G225200 chr5B 100.000 6308 0 0 1 6308 400665717 400672024 0.000000e+00 11649.0
1 TraesCS5B01G225200 chr5A 94.402 4502 167 35 1 4453 442352416 442356881 0.000000e+00 6839.0
2 TraesCS5B01G225200 chr5A 95.680 926 32 6 4877 5800 442357644 442358563 0.000000e+00 1482.0
3 TraesCS5B01G225200 chr5A 90.514 506 35 4 5801 6298 442358987 442359487 0.000000e+00 656.0
4 TraesCS5B01G225200 chr5A 91.398 372 20 2 4455 4820 442357282 442357647 3.400000e-137 499.0
5 TraesCS5B01G225200 chr5A 87.826 115 11 2 6168 6282 442377598 442377709 1.430000e-26 132.0
6 TraesCS5B01G225200 chr5D 94.093 3877 112 39 890 4740 341193868 341197653 0.000000e+00 5782.0
7 TraesCS5B01G225200 chr5D 93.602 1438 57 9 4877 6298 341197908 341199326 0.000000e+00 2113.0
8 TraesCS5B01G225200 chr5D 94.139 563 27 3 1 562 341192735 341193292 0.000000e+00 852.0
9 TraesCS5B01G225200 chr5D 87.283 692 69 13 2078 2763 553326797 553327475 0.000000e+00 773.0
10 TraesCS5B01G225200 chr7A 79.801 302 55 3 2425 2726 52969730 52969435 1.380000e-51 215.0
11 TraesCS5B01G225200 chr7D 85.465 172 23 2 5139 5309 49883914 49883744 1.810000e-40 178.0
12 TraesCS5B01G225200 chr3D 100.000 28 0 0 4858 4885 328393086 328393113 1.100000e-02 52.8
13 TraesCS5B01G225200 chr3B 88.636 44 3 2 4858 4899 802995997 802995954 1.100000e-02 52.8


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 TraesCS5B01G225200 chr5B 400665717 400672024 6307 False 11649.000000 11649 100.000000 1 6308 1 chr5B.!!$F1 6307
1 TraesCS5B01G225200 chr5A 442352416 442359487 7071 False 2369.000000 6839 92.998500 1 6298 4 chr5A.!!$F2 6297
2 TraesCS5B01G225200 chr5D 341192735 341199326 6591 False 2915.666667 5782 93.944667 1 6298 3 chr5D.!!$F2 6297
3 TraesCS5B01G225200 chr5D 553326797 553327475 678 False 773.000000 773 87.283000 2078 2763 1 chr5D.!!$F1 685

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
481 487 0.108472 GTTAGGTGAGGTGGTACCGC 60.108 60.000 17.55 17.55 44.90 5.68 F
1167 1496 0.179009 TGCATGCCAGAGCTATTCCC 60.179 55.000 16.68 0.00 40.80 3.97 F
1704 2058 0.528017 TGTGCCGACTTTGTGCAAAA 59.472 45.000 0.00 0.00 36.65 2.44 F
3499 3874 0.454196 GGTTGACGTTGCTGGTGTTT 59.546 50.000 0.00 0.00 0.00 2.83 F
4996 5966 1.073125 CCAACATATATGGTCCGGGCA 59.927 52.381 16.96 0.00 33.08 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1420 1753 2.586079 GAAGCATCGCTAGCGCCA 60.586 61.111 31.82 16.86 38.25 5.69 R
2780 3148 2.163818 TCTTCTGGCCTACAAACACG 57.836 50.000 3.32 0.00 0.00 4.49 R
3639 4014 3.497332 AGAAGCATGCATGGCTATGAAT 58.503 40.909 27.34 5.87 41.66 2.57 R
5204 6174 1.187087 GACTTCTGTGATCGGGAGGT 58.813 55.000 0.00 0.00 30.00 3.85 R
6140 7541 0.410270 ACTTCTTCGACCCCTCTCCT 59.590 55.000 0.00 0.00 0.00 3.69 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
40 45 4.320456 AGGCACCAGAGCACACCG 62.320 66.667 0.00 0.00 35.83 4.94
70 75 4.003788 CCGTCTCAACCCGTGGCT 62.004 66.667 0.00 0.00 0.00 4.75
256 261 1.173913 GCCCGGCTAGAAATGTTTGT 58.826 50.000 0.71 0.00 0.00 2.83
297 302 0.900182 GGAAGGGAGCTTGGGGTTTG 60.900 60.000 0.00 0.00 0.00 2.93
334 340 1.947456 GTTTGGCCATCCGGAATCTAC 59.053 52.381 9.01 0.00 34.14 2.59
363 369 3.250280 TGATTCGTATCTCGCTGTCTACC 59.750 47.826 3.59 0.00 39.67 3.18
373 379 0.458716 GCTGTCTACCCTGCGAGTTC 60.459 60.000 0.00 0.00 0.00 3.01
397 403 3.869272 CGGAATGCACGCAGAGCC 61.869 66.667 0.00 0.00 45.43 4.70
410 416 1.604185 GCAGAGCCGGTGTGATATCTC 60.604 57.143 1.90 0.63 0.00 2.75
416 422 2.031870 CCGGTGTGATATCTCAGGACA 58.968 52.381 7.71 0.00 30.18 4.02
465 471 5.504994 GCGTTCTGAACTTTTGATGGTGTTA 60.505 40.000 17.60 0.00 0.00 2.41
466 472 6.136071 CGTTCTGAACTTTTGATGGTGTTAG 58.864 40.000 17.60 0.00 0.00 2.34
467 473 6.438763 GTTCTGAACTTTTGATGGTGTTAGG 58.561 40.000 13.13 0.00 0.00 2.69
468 474 5.690865 TCTGAACTTTTGATGGTGTTAGGT 58.309 37.500 0.00 0.00 0.00 3.08
469 475 5.530915 TCTGAACTTTTGATGGTGTTAGGTG 59.469 40.000 0.00 0.00 0.00 4.00
470 476 5.441500 TGAACTTTTGATGGTGTTAGGTGA 58.558 37.500 0.00 0.00 0.00 4.02
481 487 0.108472 GTTAGGTGAGGTGGTACCGC 60.108 60.000 17.55 17.55 44.90 5.68
542 548 1.957186 GTCGGCAAAGGCACGTGTA 60.957 57.895 18.38 0.00 43.71 2.90
568 574 3.474600 TGGTTGGAATTTTGCATGTTGG 58.525 40.909 0.00 0.00 0.00 3.77
581 587 2.033550 GCATGTTGGTGTCCGTGTAAAA 59.966 45.455 0.00 0.00 0.00 1.52
582 588 3.489398 GCATGTTGGTGTCCGTGTAAAAA 60.489 43.478 0.00 0.00 0.00 1.94
591 597 6.421202 TGGTGTCCGTGTAAAAATTAATTTGC 59.579 34.615 14.04 8.40 0.00 3.68
595 601 8.350722 TGTCCGTGTAAAAATTAATTTGCTGTA 58.649 29.630 14.04 2.77 0.00 2.74
598 604 7.274686 CCGTGTAAAAATTAATTTGCTGTAGGG 59.725 37.037 14.04 10.56 0.00 3.53
609 615 1.343985 TGCTGTAGGGAGGGCATCTTA 60.344 52.381 0.00 0.00 0.00 2.10
640 647 1.584380 CTTCTTGCTGCTGCCTGGTC 61.584 60.000 13.47 0.00 38.71 4.02
656 663 1.249407 GGTCCGGTTTTAATGTGCCA 58.751 50.000 0.00 0.00 0.00 4.92
668 675 2.589798 ATGTGCCATGCTTGTATTGC 57.410 45.000 0.00 0.00 0.00 3.56
690 704 6.015282 TGCTGGAGTAGATGATCATGAGTAT 58.985 40.000 14.30 0.00 0.00 2.12
725 739 7.275888 TGCTCTTGTCTTATGATGTGTTTTT 57.724 32.000 0.00 0.00 0.00 1.94
922 1251 5.069119 CAGGCTGTTTTTACCTCTCCTTTTT 59.931 40.000 6.28 0.00 0.00 1.94
1092 1421 0.257039 ATCCAACCAGGGATCAGTGC 59.743 55.000 0.00 0.00 44.40 4.40
1147 1476 1.174783 CAGAAAAGGCTCTGCTGCAT 58.825 50.000 1.31 0.00 36.67 3.96
1167 1496 0.179009 TGCATGCCAGAGCTATTCCC 60.179 55.000 16.68 0.00 40.80 3.97
1263 1592 6.683974 AGTTTGCCACATATTACAGATGTC 57.316 37.500 0.00 0.00 35.31 3.06
1296 1625 2.884639 GCCAAGGCTCACTACTTTTTCA 59.115 45.455 3.29 0.00 38.26 2.69
1413 1746 8.774586 ACAAAGAACATATGTTACTGACAGAAC 58.225 33.333 20.83 9.72 42.62 3.01
1419 1752 1.616865 TGTTACTGACAGAACTCCCCG 59.383 52.381 10.08 0.00 33.40 5.73
1420 1753 1.617357 GTTACTGACAGAACTCCCCGT 59.383 52.381 10.08 0.00 0.00 5.28
1696 2050 1.981256 AGGTTGAATGTGCCGACTTT 58.019 45.000 0.00 0.00 0.00 2.66
1704 2058 0.528017 TGTGCCGACTTTGTGCAAAA 59.472 45.000 0.00 0.00 36.65 2.44
1705 2059 1.199624 GTGCCGACTTTGTGCAAAAG 58.800 50.000 15.42 15.42 36.65 2.27
1706 2060 0.814457 TGCCGACTTTGTGCAAAAGT 59.186 45.000 19.96 19.96 42.62 2.66
1707 2061 1.199624 GCCGACTTTGTGCAAAAGTG 58.800 50.000 22.97 16.75 40.27 3.16
1737 2094 6.959639 ATTTCTTCTCTTTGTAAACTGCCA 57.040 33.333 0.00 0.00 0.00 4.92
1844 2202 5.069501 TCGACTAAAGAAGCCTTACCTTC 57.930 43.478 0.00 0.00 41.15 3.46
1924 2282 3.244044 CCTCTAATACTTCTGCTGGAGCC 60.244 52.174 0.00 0.00 41.18 4.70
1976 2334 3.262420 GAACATTGGTACGCTCTGATGT 58.738 45.455 0.00 0.00 0.00 3.06
2001 2359 4.695217 TGGTTTGTCTTTTCTGTGACAC 57.305 40.909 0.00 0.00 42.06 3.67
2017 2375 4.445052 TGTGACACACGTTACCTTTTATCG 59.555 41.667 3.56 0.00 37.14 2.92
2058 2416 8.816640 AAATGTTAGCTTATGTGAGTTTTTGG 57.183 30.769 0.00 0.00 0.00 3.28
2059 2417 7.759489 ATGTTAGCTTATGTGAGTTTTTGGA 57.241 32.000 0.00 0.00 0.00 3.53
2060 2418 7.759489 TGTTAGCTTATGTGAGTTTTTGGAT 57.241 32.000 0.00 0.00 0.00 3.41
2061 2419 8.177119 TGTTAGCTTATGTGAGTTTTTGGATT 57.823 30.769 0.00 0.00 0.00 3.01
2062 2420 8.637986 TGTTAGCTTATGTGAGTTTTTGGATTT 58.362 29.630 0.00 0.00 0.00 2.17
2063 2421 8.915654 GTTAGCTTATGTGAGTTTTTGGATTTG 58.084 33.333 0.00 0.00 0.00 2.32
2064 2422 7.054491 AGCTTATGTGAGTTTTTGGATTTGT 57.946 32.000 0.00 0.00 0.00 2.83
2082 2444 7.095144 TGGATTTGTCATTTGATTGTTGAATGC 60.095 33.333 0.00 0.00 32.28 3.56
2083 2445 7.095144 GGATTTGTCATTTGATTGTTGAATGCA 60.095 33.333 0.00 0.00 32.28 3.96
2337 2704 7.759489 ACATGCCTGAAGTTTAAATAAGTGA 57.241 32.000 0.00 0.00 0.00 3.41
2536 2903 0.767375 ATGCCGGTAAGGATGCATCT 59.233 50.000 25.28 10.06 40.21 2.90
2570 2938 7.255590 CCTGATGTTGTAAGGAAGTTGATGTTT 60.256 37.037 0.00 0.00 32.43 2.83
2620 2988 1.871080 ACCTTCAGCTTTCACGTGAG 58.129 50.000 19.11 9.44 0.00 3.51
2977 3345 7.631717 AAGGAGCATTTAGTTCTATTTCCAC 57.368 36.000 0.00 0.00 0.00 4.02
3160 3531 2.428491 CCCAAAGTACACCAATACGCA 58.572 47.619 0.00 0.00 0.00 5.24
3203 3574 9.640963 ACTTTTCATAGAAGTACATGTACTGTC 57.359 33.333 33.49 28.50 44.96 3.51
3434 3809 3.119137 AGACTTTTGGTTTTGACACAGCC 60.119 43.478 0.00 0.00 0.00 4.85
3499 3874 0.454196 GGTTGACGTTGCTGGTGTTT 59.546 50.000 0.00 0.00 0.00 2.83
3521 3896 8.962679 TGTTTGTGTTCTTTTACTATGGAAACT 58.037 29.630 0.00 0.00 0.00 2.66
3639 4014 4.591321 ATTAATGGGAAGAAGCACTGGA 57.409 40.909 0.00 0.00 0.00 3.86
3745 4120 6.475504 TGATGGAGCTTCAAATCTGTCTTTA 58.524 36.000 0.00 0.00 0.00 1.85
3764 4139 8.757789 TGTCTTTACTTCACATTTACTAACACG 58.242 33.333 0.00 0.00 0.00 4.49
3821 4196 2.566833 TGGAGAACATGGTGTCTTGG 57.433 50.000 7.95 0.00 0.00 3.61
4052 4427 7.702348 GGAAATGTGATACTTAGTGATTTTGGC 59.298 37.037 0.00 0.00 0.00 4.52
4095 4470 3.866883 ATGCTCGTTTTAAACCCCATG 57.133 42.857 1.97 0.00 0.00 3.66
4152 4527 8.812513 TGATGATAGGTGTTTGAAATCATCTT 57.187 30.769 18.96 0.00 46.78 2.40
4193 4568 5.552178 CTGAAGCCAGTTCCTACTTTACTT 58.448 41.667 0.00 0.00 35.70 2.24
4337 4713 8.658499 GGTTGTCACCAGTTTTATATAGTAGG 57.342 38.462 0.00 0.00 43.61 3.18
4402 4789 5.643777 CCGATTCACAATCTACTGGAAAGTT 59.356 40.000 0.00 0.00 35.73 2.66
4404 4791 6.402550 CGATTCACAATCTACTGGAAAGTTGG 60.403 42.308 0.00 0.00 35.73 3.77
4406 4793 5.935945 TCACAATCTACTGGAAAGTTGGAA 58.064 37.500 0.00 0.00 0.00 3.53
4453 4840 5.796424 ATTGTGTTTTGCTGGAAAGAGAT 57.204 34.783 0.00 0.00 0.00 2.75
4538 5324 1.270550 CTGGCACAAATGGAACTGGTC 59.729 52.381 0.00 0.00 38.70 4.02
4541 5327 2.299867 GGCACAAATGGAACTGGTCAAT 59.700 45.455 0.00 0.00 0.00 2.57
4652 5444 6.070481 TGCCAGTGTATAACTTATGAACCTCA 60.070 38.462 0.00 0.00 36.83 3.86
4669 5461 6.040278 TGAACCTCATTTTCTGTACATGCAAA 59.960 34.615 0.00 0.00 0.00 3.68
4708 5500 7.819521 ATTTCATGATAGGAGACCATATCCA 57.180 36.000 0.00 0.00 39.47 3.41
4709 5501 7.819521 TTTCATGATAGGAGACCATATCCAT 57.180 36.000 0.00 0.00 39.47 3.41
4710 5502 8.915813 TTTCATGATAGGAGACCATATCCATA 57.084 34.615 0.00 0.00 39.47 2.74
4711 5503 9.511404 TTTCATGATAGGAGACCATATCCATAT 57.489 33.333 0.00 0.00 39.47 1.78
4795 5765 7.223193 TGTTATAACATTTGTATTCCTCCGTCG 59.777 37.037 14.35 0.00 33.17 5.12
4820 5790 9.445786 CGTTTTGATATTTTGTCAAGTTGTACT 57.554 29.630 2.11 0.00 36.96 2.73
4825 5795 9.431887 TGATATTTTGTCAAGTTGTACTACTCC 57.568 33.333 10.44 3.22 0.00 3.85
4826 5796 8.788325 ATATTTTGTCAAGTTGTACTACTCCC 57.212 34.615 10.44 2.90 0.00 4.30
4827 5797 5.881923 TTTGTCAAGTTGTACTACTCCCT 57.118 39.130 10.44 0.00 0.00 4.20
4828 5798 5.464030 TTGTCAAGTTGTACTACTCCCTC 57.536 43.478 10.44 3.46 0.00 4.30
4829 5799 3.830755 TGTCAAGTTGTACTACTCCCTCC 59.169 47.826 10.44 0.00 0.00 4.30
4830 5800 3.830755 GTCAAGTTGTACTACTCCCTCCA 59.169 47.826 10.44 0.00 0.00 3.86
4831 5801 4.466726 GTCAAGTTGTACTACTCCCTCCAT 59.533 45.833 10.44 0.00 0.00 3.41
4832 5802 5.655532 GTCAAGTTGTACTACTCCCTCCATA 59.344 44.000 10.44 0.00 0.00 2.74
4833 5803 6.154021 GTCAAGTTGTACTACTCCCTCCATAA 59.846 42.308 10.44 0.00 0.00 1.90
4834 5804 6.727231 TCAAGTTGTACTACTCCCTCCATAAA 59.273 38.462 10.44 0.00 0.00 1.40
4835 5805 7.236019 TCAAGTTGTACTACTCCCTCCATAAAA 59.764 37.037 10.44 0.00 0.00 1.52
4836 5806 7.563724 AGTTGTACTACTCCCTCCATAAAAA 57.436 36.000 3.98 0.00 0.00 1.94
4866 5836 7.923414 AAGAGCGTTTAGACCATATTTCTTT 57.077 32.000 0.00 0.00 0.00 2.52
4868 5838 8.421673 AGAGCGTTTAGACCATATTTCTTTAC 57.578 34.615 0.00 0.00 0.00 2.01
4869 5839 7.222224 AGAGCGTTTAGACCATATTTCTTTACG 59.778 37.037 0.00 0.00 34.44 3.18
4870 5840 6.257193 AGCGTTTAGACCATATTTCTTTACGG 59.743 38.462 13.74 0.00 33.11 4.02
4871 5841 6.256321 GCGTTTAGACCATATTTCTTTACGGA 59.744 38.462 13.74 0.00 33.11 4.69
4872 5842 7.516312 GCGTTTAGACCATATTTCTTTACGGAG 60.516 40.741 13.74 0.00 33.11 4.63
4873 5843 7.042925 CGTTTAGACCATATTTCTTTACGGAGG 60.043 40.741 0.00 0.00 30.86 4.30
4874 5844 5.291905 AGACCATATTTCTTTACGGAGGG 57.708 43.478 0.00 0.00 0.00 4.30
4875 5845 4.966805 AGACCATATTTCTTTACGGAGGGA 59.033 41.667 0.00 0.00 0.00 4.20
4876 5846 5.070580 AGACCATATTTCTTTACGGAGGGAG 59.929 44.000 0.00 0.00 0.00 4.30
4877 5847 4.720273 ACCATATTTCTTTACGGAGGGAGT 59.280 41.667 0.00 0.00 0.00 3.85
4878 5848 5.901276 ACCATATTTCTTTACGGAGGGAGTA 59.099 40.000 0.00 0.00 0.00 2.59
4879 5849 6.183360 ACCATATTTCTTTACGGAGGGAGTAC 60.183 42.308 0.00 0.00 0.00 2.73
4892 5862 5.358090 GGAGGGAGTACATAGCAACTAAAC 58.642 45.833 0.00 0.00 0.00 2.01
4912 5882 8.397906 ACTAAACGATTTGATGTCATTGGTATG 58.602 33.333 0.00 0.00 0.00 2.39
4996 5966 1.073125 CCAACATATATGGTCCGGGCA 59.927 52.381 16.96 0.00 33.08 5.36
5041 6011 1.102809 TCTTGTGCACTGTGCTTGGG 61.103 55.000 30.43 18.53 45.31 4.12
5122 6092 7.774625 TCCATCATATCTAGTTTGCATTTGACA 59.225 33.333 0.00 0.00 0.00 3.58
5204 6174 5.657826 ATTTGCAACACACATTATGCCTA 57.342 34.783 0.00 0.00 38.00 3.93
5506 6478 1.198637 GTCCATGAACAACAGAGCTGC 59.801 52.381 0.00 0.00 0.00 5.25
5644 6616 3.710326 TCCACGACCGATTTCTATGAG 57.290 47.619 0.00 0.00 0.00 2.90
5650 6622 5.520288 CACGACCGATTTCTATGAGTGATTT 59.480 40.000 0.00 0.00 0.00 2.17
5711 6683 8.315391 TGTTCTTTAATTCACTGATGACTCTG 57.685 34.615 0.00 0.00 33.38 3.35
5740 6712 0.958822 ACCATGAACAAAAGCGGGAC 59.041 50.000 0.00 0.00 0.00 4.46
5758 6730 2.281762 GGACGACGATGTATTCAAGTGC 59.718 50.000 0.00 0.00 0.00 4.40
5768 6740 7.979537 ACGATGTATTCAAGTGCAAGTATCTAA 59.020 33.333 0.00 0.00 0.00 2.10
5781 6753 7.698130 GTGCAAGTATCTAATCAATCGCTTTTT 59.302 33.333 0.00 0.00 0.00 1.94
5893 7291 0.321671 GTAGCTGCAACAGACTGGGA 59.678 55.000 7.51 0.00 32.44 4.37
5936 7334 4.501571 CGGATACAACCATTACAGGGAGAG 60.502 50.000 0.00 0.00 0.00 3.20
5963 7361 5.983720 ACTCGATAGGATGGTAAACATTTCG 59.016 40.000 0.00 0.00 40.72 3.46
5972 7370 3.319405 TGGTAAACATTTCGGCACACAAT 59.681 39.130 0.00 0.00 0.00 2.71
5984 7382 4.637977 TCGGCACACAATATAAGCAAATCA 59.362 37.500 0.00 0.00 0.00 2.57
5987 7385 6.332630 GGCACACAATATAAGCAAATCAAGT 58.667 36.000 0.00 0.00 0.00 3.16
6078 7479 3.131933 CAGACCAGTCTTTGATCGGAGAT 59.868 47.826 0.00 0.00 38.80 2.75
6096 7497 5.685075 CGGAGATTGGCAAACTCTAATACCT 60.685 44.000 29.02 0.00 0.00 3.08
6098 7499 7.280356 GGAGATTGGCAAACTCTAATACCTAA 58.720 38.462 29.02 0.00 0.00 2.69
6245 7651 5.487433 GAATTTGGTTGGGGATTTCGATTT 58.513 37.500 0.00 0.00 0.00 2.17
6246 7652 6.613153 AATTTGGTTGGGGATTTCGATTTA 57.387 33.333 0.00 0.00 0.00 1.40
6247 7653 5.652994 TTTGGTTGGGGATTTCGATTTAG 57.347 39.130 0.00 0.00 0.00 1.85
6282 7688 0.034477 CGGAACTAGGGTTTGGCCAT 60.034 55.000 6.09 0.00 39.65 4.40
6286 7692 0.912487 ACTAGGGTTTGGCCATCCGA 60.912 55.000 6.09 4.55 39.65 4.55
6302 7708 3.723348 GAAACACGGCGGCCTGTC 61.723 66.667 18.34 0.00 0.00 3.51
6303 7709 4.555709 AAACACGGCGGCCTGTCA 62.556 61.111 18.34 0.00 0.00 3.58
6304 7710 4.555709 AACACGGCGGCCTGTCAA 62.556 61.111 18.34 0.00 0.00 3.18
6307 7713 4.329545 ACGGCGGCCTGTCAACAT 62.330 61.111 18.34 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
238 243 2.420022 CTCACAAACATTTCTAGCCGGG 59.580 50.000 2.18 0.00 0.00 5.73
256 261 2.637872 CCTTCAAACTCTGGTACCCTCA 59.362 50.000 10.07 0.00 0.00 3.86
297 302 0.898326 AACCAACCGGCCTTCCAATC 60.898 55.000 0.00 0.00 34.57 2.67
334 340 2.408704 GCGAGATACGAATCAAATCGGG 59.591 50.000 1.59 0.00 46.82 5.14
343 349 2.553172 GGGTAGACAGCGAGATACGAAT 59.447 50.000 0.00 0.00 45.77 3.34
397 403 2.690497 ACTGTCCTGAGATATCACACCG 59.310 50.000 5.32 0.00 0.00 4.94
410 416 0.311165 ACGAACGAGACACTGTCCTG 59.689 55.000 5.51 1.48 32.18 3.86
416 422 2.190981 GAACAACACGAACGAGACACT 58.809 47.619 0.14 0.00 0.00 3.55
465 471 2.203728 TGCGGTACCACCTCACCT 60.204 61.111 13.54 0.00 35.66 4.00
466 472 1.823169 TTCTGCGGTACCACCTCACC 61.823 60.000 13.54 0.00 35.66 4.02
467 473 0.249398 ATTCTGCGGTACCACCTCAC 59.751 55.000 13.54 0.00 35.66 3.51
468 474 0.535335 GATTCTGCGGTACCACCTCA 59.465 55.000 13.54 2.98 35.66 3.86
469 475 0.824759 AGATTCTGCGGTACCACCTC 59.175 55.000 13.54 0.00 35.66 3.85
470 476 0.537188 CAGATTCTGCGGTACCACCT 59.463 55.000 13.54 0.00 35.66 4.00
481 487 5.518128 CGAAGGTACATTGAGTCAGATTCTG 59.482 44.000 7.38 7.38 0.00 3.02
542 548 6.112927 ACATGCAAAATTCCAACCAACTAT 57.887 33.333 0.00 0.00 0.00 2.12
568 574 7.168469 ACAGCAAATTAATTTTTACACGGACAC 59.832 33.333 10.77 0.00 0.00 3.67
581 587 3.960755 GCCCTCCCTACAGCAAATTAATT 59.039 43.478 0.00 0.00 0.00 1.40
582 588 3.052944 TGCCCTCCCTACAGCAAATTAAT 60.053 43.478 0.00 0.00 30.97 1.40
591 597 3.309296 TCTTAAGATGCCCTCCCTACAG 58.691 50.000 0.00 0.00 0.00 2.74
595 601 3.126453 ACATTCTTAAGATGCCCTCCCT 58.874 45.455 5.89 0.00 0.00 4.20
598 604 6.122964 AGGTAAACATTCTTAAGATGCCCTC 58.877 40.000 5.89 0.00 0.00 4.30
656 663 4.760530 TCTACTCCAGCAATACAAGCAT 57.239 40.909 0.00 0.00 0.00 3.79
668 675 8.806429 AGTATACTCATGATCATCTACTCCAG 57.194 38.462 4.86 0.00 0.00 3.86
690 704 5.386958 AAGACAAGAGCATTCGTGTAGTA 57.613 39.130 0.00 0.00 44.40 1.82
730 744 5.097742 TCACAGAGACTGAACCAGAAAAA 57.902 39.130 5.76 0.00 35.18 1.94
846 860 5.348164 ACGGTTCCAAAGAAAAACAATCAG 58.652 37.500 0.00 0.00 32.58 2.90
860 874 3.256383 TCGAAATACTGAGACGGTTCCAA 59.744 43.478 0.00 0.00 0.00 3.53
922 1251 4.042809 TCATCCCTCCTCAAGCAAAAGTAA 59.957 41.667 0.00 0.00 0.00 2.24
923 1252 3.587061 TCATCCCTCCTCAAGCAAAAGTA 59.413 43.478 0.00 0.00 0.00 2.24
1062 1391 2.440599 GTTGGATGCCCCCACAGT 59.559 61.111 0.00 0.00 35.62 3.55
1092 1421 7.390440 TCATTTAAGTGAGTGAAACCATACTGG 59.610 37.037 0.00 0.00 45.02 4.00
1147 1476 1.683943 GGAATAGCTCTGGCATGCAA 58.316 50.000 21.36 7.49 41.70 4.08
1167 1496 3.532542 GAAATCCAGGTCTAAGTTCCCG 58.467 50.000 0.00 0.00 0.00 5.14
1263 1592 4.012374 TGAGCCTTGGCTCTAAATCAAAG 58.988 43.478 33.12 0.00 37.68 2.77
1290 1619 6.871492 GGAACCTGTTTTTCTTCAGTGAAAAA 59.129 34.615 7.06 10.02 46.87 1.94
1296 1625 4.645136 GGAAGGAACCTGTTTTTCTTCAGT 59.355 41.667 16.15 0.00 0.00 3.41
1419 1752 2.875786 GAAGCATCGCTAGCGCCAC 61.876 63.158 31.82 21.37 38.25 5.01
1420 1753 2.586079 GAAGCATCGCTAGCGCCA 60.586 61.111 31.82 16.86 38.25 5.69
1572 1926 3.791320 AGTTTCCCTGAGGTACATCTCA 58.209 45.455 9.22 5.44 41.03 3.27
1704 2058 7.573968 ACAAAGAGAAGAAATAGTTTGCACT 57.426 32.000 0.00 0.00 36.99 4.40
1705 2059 9.730420 TTTACAAAGAGAAGAAATAGTTTGCAC 57.270 29.630 0.00 0.00 0.00 4.57
1706 2060 9.730420 GTTTACAAAGAGAAGAAATAGTTTGCA 57.270 29.630 0.00 0.00 0.00 4.08
1707 2061 9.952188 AGTTTACAAAGAGAAGAAATAGTTTGC 57.048 29.630 0.00 0.00 0.00 3.68
1709 2063 9.952188 GCAGTTTACAAAGAGAAGAAATAGTTT 57.048 29.630 0.00 0.00 0.00 2.66
1710 2064 8.568794 GGCAGTTTACAAAGAGAAGAAATAGTT 58.431 33.333 0.00 0.00 0.00 2.24
1711 2065 7.719633 TGGCAGTTTACAAAGAGAAGAAATAGT 59.280 33.333 0.00 0.00 0.00 2.12
1712 2066 8.099364 TGGCAGTTTACAAAGAGAAGAAATAG 57.901 34.615 0.00 0.00 0.00 1.73
1713 2067 8.458573 TTGGCAGTTTACAAAGAGAAGAAATA 57.541 30.769 0.00 0.00 0.00 1.40
1714 2068 6.959639 TGGCAGTTTACAAAGAGAAGAAAT 57.040 33.333 0.00 0.00 0.00 2.17
1715 2069 6.767524 TTGGCAGTTTACAAAGAGAAGAAA 57.232 33.333 0.00 0.00 0.00 2.52
1811 2169 6.854892 GGCTTCTTTAGTCGAAGGTTTAAAAC 59.145 38.462 0.00 0.00 38.59 2.43
1816 2174 4.353383 AGGCTTCTTTAGTCGAAGGTTT 57.647 40.909 0.00 0.00 38.59 3.27
1924 2282 2.941064 ACAATCAGGATCAATGCACTCG 59.059 45.455 0.00 0.00 0.00 4.18
1976 2334 5.941058 TGTCACAGAAAAGACAAACCAACTA 59.059 36.000 0.00 0.00 41.42 2.24
2058 2416 7.798801 TGCATTCAACAATCAAATGACAAATC 58.201 30.769 0.00 0.00 33.22 2.17
2059 2417 7.731882 TGCATTCAACAATCAAATGACAAAT 57.268 28.000 0.00 0.00 33.22 2.32
2060 2418 7.731882 ATGCATTCAACAATCAAATGACAAA 57.268 28.000 0.00 0.00 33.22 2.83
2061 2419 7.441458 TGAATGCATTCAACAATCAAATGACAA 59.559 29.630 34.23 9.47 43.26 3.18
2062 2420 6.929606 TGAATGCATTCAACAATCAAATGACA 59.070 30.769 34.23 10.42 43.26 3.58
2063 2421 7.354025 TGAATGCATTCAACAATCAAATGAC 57.646 32.000 34.23 7.99 43.26 3.06
2082 2444 9.539139 GAATCACGAGAATATAGCAATTGAATG 57.461 33.333 10.34 0.00 0.00 2.67
2083 2445 9.499479 AGAATCACGAGAATATAGCAATTGAAT 57.501 29.630 10.34 4.30 0.00 2.57
2172 2536 3.581770 AGTATATTTCCTTACGAGGCCCC 59.418 47.826 0.00 0.00 43.21 5.80
2277 2641 7.492344 GCCAATTTTGAACGATATTGAAAGGAT 59.508 33.333 0.00 0.00 31.29 3.24
2510 2877 3.489229 GCATCCTTACCGGCATTTCTTTC 60.489 47.826 0.00 0.00 0.00 2.62
2536 2903 3.270027 CTTACAACATCAGGCGAATGGA 58.730 45.455 7.01 0.00 0.00 3.41
2570 2938 7.068839 ACCAAAATGTAATTCCACGGCATAATA 59.931 33.333 0.00 0.00 33.67 0.98
2620 2988 4.142381 GCAAGATTTATGTTCTCCACCACC 60.142 45.833 0.00 0.00 0.00 4.61
2780 3148 2.163818 TCTTCTGGCCTACAAACACG 57.836 50.000 3.32 0.00 0.00 4.49
2912 3280 8.720562 CAAAAGTACATCAATGACAGTATGACA 58.279 33.333 0.00 0.00 46.13 3.58
2913 3281 8.177663 CCAAAAGTACATCAATGACAGTATGAC 58.822 37.037 0.00 0.00 39.69 3.06
2914 3282 8.100164 TCCAAAAGTACATCAATGACAGTATGA 58.900 33.333 0.00 0.00 39.69 2.15
2915 3283 8.177663 GTCCAAAAGTACATCAATGACAGTATG 58.822 37.037 0.00 0.00 46.00 2.39
2916 3284 7.882791 TGTCCAAAAGTACATCAATGACAGTAT 59.117 33.333 0.00 0.00 0.00 2.12
2917 3285 7.220740 TGTCCAAAAGTACATCAATGACAGTA 58.779 34.615 0.00 0.00 0.00 2.74
2918 3286 6.061441 TGTCCAAAAGTACATCAATGACAGT 58.939 36.000 0.00 0.00 0.00 3.55
2919 3287 6.558771 TGTCCAAAAGTACATCAATGACAG 57.441 37.500 0.00 0.00 0.00 3.51
2977 3345 6.415280 GTCAGATTACTGTGCTATACTTGACG 59.585 42.308 0.00 0.00 43.81 4.35
3521 3896 9.184523 CCATATACCAAATTCACTCCACTTAAA 57.815 33.333 0.00 0.00 0.00 1.52
3639 4014 3.497332 AGAAGCATGCATGGCTATGAAT 58.503 40.909 27.34 5.87 41.66 2.57
3745 4120 4.384846 CGCTCGTGTTAGTAAATGTGAAGT 59.615 41.667 0.00 0.00 0.00 3.01
3821 4196 3.691118 TCCAGTAAATGCTCAAGATGTGC 59.309 43.478 0.00 0.00 37.38 4.57
4052 4427 1.066908 ACCTTTTGTTGCATGTGGACG 59.933 47.619 0.00 0.00 0.00 4.79
4122 4497 9.904198 TGATTTCAAACACCTATCATCATCTAA 57.096 29.630 0.00 0.00 0.00 2.10
4152 4527 5.509163 GCTTCAGTAGAGTTGACTGGTTACA 60.509 44.000 3.15 0.00 43.76 2.41
4230 4606 3.677156 AGGCCCTTGATTTTCTAGCAT 57.323 42.857 0.00 0.00 0.00 3.79
4295 4671 6.474427 GTGACAACCAGCATAAATCATTCATG 59.526 38.462 0.00 0.00 0.00 3.07
4331 4707 3.276857 CACTTCTGTACGAGCCCTACTA 58.723 50.000 0.00 0.00 0.00 1.82
4332 4708 2.093106 CACTTCTGTACGAGCCCTACT 58.907 52.381 0.00 0.00 0.00 2.57
4333 4709 1.817447 ACACTTCTGTACGAGCCCTAC 59.183 52.381 0.00 0.00 0.00 3.18
4334 4710 2.211250 ACACTTCTGTACGAGCCCTA 57.789 50.000 0.00 0.00 0.00 3.53
4335 4711 2.093106 CTACACTTCTGTACGAGCCCT 58.907 52.381 0.00 0.00 0.00 5.19
4337 4713 3.572604 AACTACACTTCTGTACGAGCC 57.427 47.619 0.00 0.00 0.00 4.70
4380 4767 6.655003 TCCAACTTTCCAGTAGATTGTGAATC 59.345 38.462 0.00 0.00 33.00 2.52
4736 5528 7.825270 ACATGTCAATACGGGAACAGTATTTAA 59.175 33.333 0.00 0.00 41.31 1.52
4778 5748 4.998672 TCAAAACGACGGAGGAATACAAAT 59.001 37.500 0.00 0.00 0.00 2.32
4781 5751 3.663995 TCAAAACGACGGAGGAATACA 57.336 42.857 0.00 0.00 0.00 2.29
4840 5810 9.614792 AAAGAAATATGGTCTAAACGCTCTTAT 57.385 29.630 0.00 0.00 0.00 1.73
4842 5812 7.923414 AAAGAAATATGGTCTAAACGCTCTT 57.077 32.000 0.00 0.00 0.00 2.85
4843 5813 7.222224 CGTAAAGAAATATGGTCTAAACGCTCT 59.778 37.037 9.13 0.00 31.11 4.09
4844 5814 7.335491 CGTAAAGAAATATGGTCTAAACGCTC 58.665 38.462 9.13 0.00 31.11 5.03
4845 5815 6.257193 CCGTAAAGAAATATGGTCTAAACGCT 59.743 38.462 13.18 0.00 34.50 5.07
4846 5816 6.256321 TCCGTAAAGAAATATGGTCTAAACGC 59.744 38.462 13.18 0.00 34.50 4.84
4847 5817 7.042925 CCTCCGTAAAGAAATATGGTCTAAACG 60.043 40.741 12.36 12.36 35.10 3.60
4848 5818 7.226128 CCCTCCGTAAAGAAATATGGTCTAAAC 59.774 40.741 0.00 0.00 34.21 2.01
4849 5819 7.126115 TCCCTCCGTAAAGAAATATGGTCTAAA 59.874 37.037 0.00 0.00 34.21 1.85
4850 5820 6.612456 TCCCTCCGTAAAGAAATATGGTCTAA 59.388 38.462 0.00 0.00 34.21 2.10
4851 5821 6.138263 TCCCTCCGTAAAGAAATATGGTCTA 58.862 40.000 0.00 0.00 34.21 2.59
4852 5822 4.966805 TCCCTCCGTAAAGAAATATGGTCT 59.033 41.667 0.00 0.00 34.21 3.85
4853 5823 5.163332 ACTCCCTCCGTAAAGAAATATGGTC 60.163 44.000 0.00 0.00 34.21 4.02
4854 5824 4.720273 ACTCCCTCCGTAAAGAAATATGGT 59.280 41.667 0.00 0.00 34.21 3.55
4855 5825 5.291905 ACTCCCTCCGTAAAGAAATATGG 57.708 43.478 0.00 0.00 33.90 2.74
4856 5826 6.812998 TGTACTCCCTCCGTAAAGAAATATG 58.187 40.000 0.00 0.00 0.00 1.78
4857 5827 7.613551 ATGTACTCCCTCCGTAAAGAAATAT 57.386 36.000 0.00 0.00 0.00 1.28
4858 5828 7.255730 GCTATGTACTCCCTCCGTAAAGAAATA 60.256 40.741 0.00 0.00 0.00 1.40
4859 5829 5.952347 ATGTACTCCCTCCGTAAAGAAAT 57.048 39.130 0.00 0.00 0.00 2.17
4860 5830 5.163478 GCTATGTACTCCCTCCGTAAAGAAA 60.163 44.000 0.00 0.00 0.00 2.52
4861 5831 4.340381 GCTATGTACTCCCTCCGTAAAGAA 59.660 45.833 0.00 0.00 0.00 2.52
4862 5832 3.887716 GCTATGTACTCCCTCCGTAAAGA 59.112 47.826 0.00 0.00 0.00 2.52
4863 5833 3.635373 TGCTATGTACTCCCTCCGTAAAG 59.365 47.826 0.00 0.00 0.00 1.85
4864 5834 3.634504 TGCTATGTACTCCCTCCGTAAA 58.365 45.455 0.00 0.00 0.00 2.01
4865 5835 3.301794 TGCTATGTACTCCCTCCGTAA 57.698 47.619 0.00 0.00 0.00 3.18
4866 5836 2.954318 GTTGCTATGTACTCCCTCCGTA 59.046 50.000 0.00 0.00 0.00 4.02
4867 5837 1.755380 GTTGCTATGTACTCCCTCCGT 59.245 52.381 0.00 0.00 0.00 4.69
4868 5838 2.032620 AGTTGCTATGTACTCCCTCCG 58.967 52.381 0.00 0.00 0.00 4.63
4869 5839 5.358090 GTTTAGTTGCTATGTACTCCCTCC 58.642 45.833 0.00 0.00 0.00 4.30
4870 5840 5.041940 CGTTTAGTTGCTATGTACTCCCTC 58.958 45.833 0.00 0.00 0.00 4.30
4871 5841 4.708421 TCGTTTAGTTGCTATGTACTCCCT 59.292 41.667 0.00 0.00 0.00 4.20
4872 5842 5.002464 TCGTTTAGTTGCTATGTACTCCC 57.998 43.478 0.00 0.00 0.00 4.30
4873 5843 7.277098 TCAAATCGTTTAGTTGCTATGTACTCC 59.723 37.037 0.00 0.00 33.18 3.85
4874 5844 8.181487 TCAAATCGTTTAGTTGCTATGTACTC 57.819 34.615 0.00 0.00 33.18 2.59
4875 5845 8.604035 CATCAAATCGTTTAGTTGCTATGTACT 58.396 33.333 0.00 0.00 33.18 2.73
4876 5846 8.388103 ACATCAAATCGTTTAGTTGCTATGTAC 58.612 33.333 0.00 0.00 32.23 2.90
4877 5847 8.487313 ACATCAAATCGTTTAGTTGCTATGTA 57.513 30.769 0.00 0.00 32.23 2.29
4878 5848 7.119116 TGACATCAAATCGTTTAGTTGCTATGT 59.881 33.333 0.00 0.00 34.93 2.29
4879 5849 7.463544 TGACATCAAATCGTTTAGTTGCTATG 58.536 34.615 0.00 0.00 33.18 2.23
4912 5882 3.703001 TGTTTCTTGATCTGGGGAGTC 57.297 47.619 0.00 0.00 0.00 3.36
5041 6011 5.576774 GGGACATAAACTTACAGCATTTTGC 59.423 40.000 0.00 0.00 45.46 3.68
5122 6092 7.794683 TCCATGGACCTAGAGGAGTTAATATTT 59.205 37.037 11.44 0.00 38.94 1.40
5157 6127 2.359850 GTGATGCCGCTGAACCCA 60.360 61.111 0.00 0.00 0.00 4.51
5204 6174 1.187087 GACTTCTGTGATCGGGAGGT 58.813 55.000 0.00 0.00 30.00 3.85
5448 6420 2.552315 TGAAACAAGCCGATTGAGTTCC 59.448 45.455 2.79 0.00 41.83 3.62
5506 6478 1.002468 CGGGACAACTTGAGCTTTGTG 60.002 52.381 6.24 0.00 36.06 3.33
5597 6569 1.290203 AGGCATTTCGCTACACATCG 58.710 50.000 0.00 0.00 41.91 3.84
5644 6616 7.462109 TTCAGCACAACATAAAACAAATCAC 57.538 32.000 0.00 0.00 0.00 3.06
5650 6622 4.916983 AGCTTCAGCACAACATAAAACA 57.083 36.364 0.75 0.00 45.16 2.83
5658 6630 3.971032 AGTGTTTAGCTTCAGCACAAC 57.029 42.857 12.97 4.13 45.16 3.32
5711 6683 5.499139 TTTTGTTCATGGTGTGACTTCTC 57.501 39.130 0.00 0.00 36.32 2.87
5740 6712 3.367932 ACTTGCACTTGAATACATCGTCG 59.632 43.478 0.00 0.00 0.00 5.12
5786 6758 0.467804 GCAGGGCCCTTTTGTTTCAA 59.532 50.000 26.10 0.00 0.00 2.69
5803 6781 4.770010 CCTTGACTTAATAAAGTTGGGGCA 59.230 41.667 0.00 0.00 46.09 5.36
5866 7261 2.878406 TCTGTTGCAGCTACTTTTGGTC 59.122 45.455 8.50 0.00 0.00 4.02
5893 7291 5.623169 TCCGTGGGTTAACTTTGATAAACT 58.377 37.500 5.42 0.00 0.00 2.66
5936 7334 3.181469 TGTTTACCATCCTATCGAGTGCC 60.181 47.826 0.00 0.00 0.00 5.01
5963 7361 6.332630 ACTTGATTTGCTTATATTGTGTGCC 58.667 36.000 0.00 0.00 0.00 5.01
5972 7370 9.120538 GTAATTGGGAGACTTGATTTGCTTATA 57.879 33.333 0.00 0.00 0.00 0.98
5984 7382 7.040548 GCGTACTAGATAGTAATTGGGAGACTT 60.041 40.741 0.00 0.00 40.20 3.01
5987 7385 5.709164 GGCGTACTAGATAGTAATTGGGAGA 59.291 44.000 0.00 0.00 40.20 3.71
6043 7444 8.836413 CAAAGACTGGTCTGTTCTTATTTTGTA 58.164 33.333 3.88 0.00 40.36 2.41
6078 7479 5.811190 TGCTTAGGTATTAGAGTTTGCCAA 58.189 37.500 0.00 0.00 0.00 4.52
6096 7497 6.501781 GGTAGTATCGCTAAACTCTTGCTTA 58.498 40.000 0.00 0.00 0.00 3.09
6098 7499 4.497674 CGGTAGTATCGCTAAACTCTTGCT 60.498 45.833 0.00 0.00 0.00 3.91
6139 7540 0.820871 CTTCTTCGACCCCTCTCCTG 59.179 60.000 0.00 0.00 0.00 3.86
6140 7541 0.410270 ACTTCTTCGACCCCTCTCCT 59.590 55.000 0.00 0.00 0.00 3.69
6286 7692 4.555709 TGACAGGCCGCCGTGTTT 62.556 61.111 13.59 0.00 39.93 2.83


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

AutoCloner maintained by Alex Coulton.