Multiple sequence alignment - TraesCS3B01G280600

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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 TraesCS3B01G280600 chr3B 100.000 5354 0 0 1 5354 450855788 450850435 0.000000e+00 9888.0
1 TraesCS3B01G280600 chr3B 98.039 51 1 0 5302 5352 745460102 745460052 7.390000e-14 89.8
2 TraesCS3B01G280600 chr3A 94.016 4746 160 51 588 5272 470105292 470100610 0.000000e+00 7077.0
3 TraesCS3B01G280600 chr3D 97.270 3223 59 15 781 3988 352153677 352150469 0.000000e+00 5437.0
4 TraesCS3B01G280600 chr3D 88.064 1307 91 27 3995 5272 352150394 352149124 0.000000e+00 1489.0
5 TraesCS3B01G280600 chr3D 92.091 569 38 6 1 566 539552174 539552738 0.000000e+00 795.0
6 TraesCS3B01G280600 chr3D 92.091 569 32 8 1 566 84506798 84507356 0.000000e+00 789.0
7 TraesCS3B01G280600 chr3D 95.918 245 7 3 585 828 352154287 352154045 1.400000e-105 394.0
8 TraesCS3B01G280600 chr3D 96.517 201 5 1 813 1013 352154033 352153835 1.110000e-86 331.0
9 TraesCS3B01G280600 chr3D 93.846 65 3 1 3908 3972 352150448 352150385 4.410000e-16 97.1
10 TraesCS3B01G280600 chr3D 100.000 28 0 0 3368 3395 352150470 352150443 1.000000e-02 52.8
11 TraesCS3B01G280600 chr1B 92.281 570 40 4 1 566 391420589 391420020 0.000000e+00 806.0
12 TraesCS3B01G280600 chrUn 92.267 569 37 6 1 566 36297942 36298506 0.000000e+00 800.0
13 TraesCS3B01G280600 chr6B 92.254 568 38 6 1 563 640128940 640129506 0.000000e+00 800.0
14 TraesCS3B01G280600 chr6B 98.039 51 1 0 5304 5354 622622759 622622809 7.390000e-14 89.8
15 TraesCS3B01G280600 chr6B 97.917 48 1 0 5302 5349 697953870 697953917 3.440000e-12 84.2
16 TraesCS3B01G280600 chr6D 91.916 569 35 8 1 566 357779694 357779134 0.000000e+00 785.0
17 TraesCS3B01G280600 chr5D 91.916 569 34 4 1 566 7054931 7054372 0.000000e+00 785.0
18 TraesCS3B01G280600 chr5D 96.226 53 2 0 5302 5354 341080827 341080879 2.660000e-13 87.9
19 TraesCS3B01G280600 chr4B 91.564 569 44 4 1 566 595287239 595287806 0.000000e+00 782.0
20 TraesCS3B01G280600 chr4B 98.039 51 1 0 5302 5352 573076857 573076907 7.390000e-14 89.8
21 TraesCS3B01G280600 chr2B 91.844 564 38 7 1 560 111464260 111464819 0.000000e+00 780.0
22 TraesCS3B01G280600 chr5A 100.000 53 0 0 5302 5354 569997506 569997558 1.230000e-16 99.0
23 TraesCS3B01G280600 chr7D 98.113 53 1 0 5302 5354 414312869 414312817 5.710000e-15 93.5
24 TraesCS3B01G280600 chr2D 98.113 53 1 0 5302 5354 186827354 186827302 5.710000e-15 93.5
25 TraesCS3B01G280600 chr2D 96.226 53 2 0 5302 5354 15493362 15493310 2.660000e-13 87.9
26 TraesCS3B01G280600 chr1A 88.462 52 4 2 4922 4972 402931576 402931626 1.610000e-05 62.1


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 TraesCS3B01G280600 chr3B 450850435 450855788 5353 True 9888.00 9888 100.000000 1 5354 1 chr3B.!!$R1 5353
1 TraesCS3B01G280600 chr3A 470100610 470105292 4682 True 7077.00 7077 94.016000 588 5272 1 chr3A.!!$R1 4684
2 TraesCS3B01G280600 chr3D 352149124 352154287 5163 True 1300.15 5437 95.269167 585 5272 6 chr3D.!!$R1 4687
3 TraesCS3B01G280600 chr3D 539552174 539552738 564 False 795.00 795 92.091000 1 566 1 chr3D.!!$F2 565
4 TraesCS3B01G280600 chr3D 84506798 84507356 558 False 789.00 789 92.091000 1 566 1 chr3D.!!$F1 565
5 TraesCS3B01G280600 chr1B 391420020 391420589 569 True 806.00 806 92.281000 1 566 1 chr1B.!!$R1 565
6 TraesCS3B01G280600 chrUn 36297942 36298506 564 False 800.00 800 92.267000 1 566 1 chrUn.!!$F1 565
7 TraesCS3B01G280600 chr6B 640128940 640129506 566 False 800.00 800 92.254000 1 563 1 chr6B.!!$F2 562
8 TraesCS3B01G280600 chr6D 357779134 357779694 560 True 785.00 785 91.916000 1 566 1 chr6D.!!$R1 565
9 TraesCS3B01G280600 chr5D 7054372 7054931 559 True 785.00 785 91.916000 1 566 1 chr5D.!!$R1 565
10 TraesCS3B01G280600 chr4B 595287239 595287806 567 False 782.00 782 91.564000 1 566 1 chr4B.!!$F2 565
11 TraesCS3B01G280600 chr2B 111464260 111464819 559 False 780.00 780 91.844000 1 560 1 chr2B.!!$F1 559

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
579 592 0.032813 AGGGTCATGGATTTGGCCTG 60.033 55.0 3.32 0.0 41.32 4.85 F
580 593 0.033208 GGGTCATGGATTTGGCCTGA 60.033 55.0 3.32 0.0 41.32 3.86 F
1329 1758 0.112412 AACGCCCAACCTCCTGATTT 59.888 50.0 0.00 0.0 0.00 2.17 F
2841 3274 0.032912 TCACCGGGAGTAGCATGGTA 60.033 55.0 6.32 0.0 0.00 3.25 F
3534 3996 1.022451 TTCCGTGCCGAGGTAAATGC 61.022 55.0 0.00 0.0 0.00 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1844 2276 2.093500 ACATCTCATAGCCGCAGTTTGA 60.093 45.455 0.00 0.0 0.00 2.69 R
2072 2504 4.468510 ACCGAGTGAATAAACCATACCAGA 59.531 41.667 0.00 0.0 0.00 3.86 R
3289 3751 1.756375 GCTGTGCGAGCTGAATACCG 61.756 60.000 0.00 0.0 45.21 4.02 R
4273 4809 0.244994 GCTGGAGCTTCGAGTTCAGA 59.755 55.000 4.42 0.0 38.21 3.27 R
5291 5873 0.250684 TGGCTCAATGAAGACGCCAA 60.251 50.000 10.92 0.0 46.76 4.52 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
314 324 1.768684 GAAGAGTGGAGTGGGGTGCA 61.769 60.000 0.00 0.00 0.00 4.57
454 465 3.284449 GGCGCAAACTTGGGTCGT 61.284 61.111 10.83 0.00 42.44 4.34
472 484 1.003112 TGGATGGGTCGAAAACGGG 60.003 57.895 0.00 0.00 0.00 5.28
566 579 1.760875 GCCGGACAGGATAGGGTCA 60.761 63.158 5.05 0.00 45.00 4.02
567 580 1.122019 GCCGGACAGGATAGGGTCAT 61.122 60.000 5.05 0.00 45.00 3.06
568 581 0.681733 CCGGACAGGATAGGGTCATG 59.318 60.000 0.00 0.00 45.00 3.07
569 582 0.681733 CGGACAGGATAGGGTCATGG 59.318 60.000 0.00 0.00 42.75 3.66
570 583 1.757764 CGGACAGGATAGGGTCATGGA 60.758 57.143 0.00 0.00 42.75 3.41
571 584 2.625639 GGACAGGATAGGGTCATGGAT 58.374 52.381 0.00 0.00 42.75 3.41
572 585 2.982488 GGACAGGATAGGGTCATGGATT 59.018 50.000 0.00 0.00 42.75 3.01
573 586 3.395941 GGACAGGATAGGGTCATGGATTT 59.604 47.826 0.00 0.00 42.75 2.17
574 587 4.392940 GACAGGATAGGGTCATGGATTTG 58.607 47.826 0.00 0.00 42.75 2.32
575 588 3.139025 ACAGGATAGGGTCATGGATTTGG 59.861 47.826 0.00 0.00 42.75 3.28
576 589 2.108952 AGGATAGGGTCATGGATTTGGC 59.891 50.000 0.00 0.00 0.00 4.52
577 590 2.519013 GATAGGGTCATGGATTTGGCC 58.481 52.381 0.00 0.00 40.82 5.36
578 591 1.607225 TAGGGTCATGGATTTGGCCT 58.393 50.000 3.32 0.00 41.32 5.19
579 592 0.032813 AGGGTCATGGATTTGGCCTG 60.033 55.000 3.32 0.00 41.32 4.85
580 593 0.033208 GGGTCATGGATTTGGCCTGA 60.033 55.000 3.32 0.00 41.32 3.86
581 594 1.106285 GGTCATGGATTTGGCCTGAC 58.894 55.000 3.32 7.44 38.40 3.51
582 595 1.616725 GGTCATGGATTTGGCCTGACA 60.617 52.381 17.75 5.26 38.40 3.58
583 596 1.474077 GTCATGGATTTGGCCTGACAC 59.526 52.381 12.74 0.00 36.72 3.67
593 606 0.822121 GGCCTGACACGAGGGTTTTT 60.822 55.000 0.00 0.00 33.17 1.94
698 712 2.024655 AGATCGTGGAGTAGGTAACCCA 60.025 50.000 0.00 0.00 37.17 4.51
710 724 5.845065 AGTAGGTAACCCAAGAAAAGAGACT 59.155 40.000 0.00 0.00 37.17 3.24
715 729 4.092116 ACCCAAGAAAAGAGACTGAAGG 57.908 45.455 0.00 0.00 0.00 3.46
742 756 6.525628 TGAGATTAACTAACGAACGATGACAC 59.474 38.462 0.14 0.00 0.00 3.67
938 1367 1.283321 ACATTTGCCTCTTCCTCCCTC 59.717 52.381 0.00 0.00 0.00 4.30
967 1396 2.018086 CCCCTCCCCCTCTCTCTCT 61.018 68.421 0.00 0.00 0.00 3.10
968 1397 1.541672 CCCTCCCCCTCTCTCTCTC 59.458 68.421 0.00 0.00 0.00 3.20
1329 1758 0.112412 AACGCCCAACCTCCTGATTT 59.888 50.000 0.00 0.00 0.00 2.17
1362 1791 8.233190 ACATTTTTCTCTTGAGATTCATCGTTC 58.767 33.333 0.82 0.00 0.00 3.95
1674 2106 2.694109 GACTCTTAATGTAGGGACGCCT 59.306 50.000 0.00 0.00 0.00 5.52
1844 2276 4.968719 TGATCAGTGGTATCAATACTGGGT 59.031 41.667 0.00 0.00 41.54 4.51
1977 2409 2.046120 GCTGCTGCAAGAGAGGCT 60.046 61.111 11.11 0.00 39.41 4.58
2072 2504 9.784531 CTGTGTCCCAAATCTACTATATCATTT 57.215 33.333 0.00 0.00 0.00 2.32
2096 2528 5.657745 TCTGGTATGGTTTATTCACTCGGTA 59.342 40.000 0.00 0.00 0.00 4.02
2442 2874 3.119173 GCTATTGCTATTGTTTGTGGCCA 60.119 43.478 0.00 0.00 36.03 5.36
2446 2878 2.961741 TGCTATTGTTTGTGGCCAAGAA 59.038 40.909 7.24 1.60 0.00 2.52
2525 2957 8.262933 ACCAATTACGTTTATTAGAGGCTAGTT 58.737 33.333 0.00 0.00 0.00 2.24
2588 3021 7.441836 AGAATGTATGTTGTCAGTGAACTACA 58.558 34.615 0.00 3.63 38.81 2.74
2637 3070 2.105006 GTGATGCACACCTCACTGAT 57.895 50.000 10.29 0.00 43.05 2.90
2841 3274 0.032912 TCACCGGGAGTAGCATGGTA 60.033 55.000 6.32 0.00 0.00 3.25
3105 3547 5.695816 GCAAAAATCTTCAGCACATTGGTAA 59.304 36.000 0.00 0.00 0.00 2.85
3164 3626 3.309296 TCTCTCTCTCTCTCTCTCTCCC 58.691 54.545 0.00 0.00 0.00 4.30
3289 3751 1.324740 TGGGCATGCATCAAAGCCTC 61.325 55.000 21.36 13.73 46.23 4.70
3534 3996 1.022451 TTCCGTGCCGAGGTAAATGC 61.022 55.000 0.00 0.00 0.00 3.56
3679 4141 9.650714 TGTAAATAGCCTAAGGTGATTCTAGTA 57.349 33.333 0.00 0.00 0.00 1.82
3910 4376 8.981659 CAAATGAACCTAAGGAATAAGGGAAAT 58.018 33.333 0.00 0.00 37.18 2.17
3970 4436 7.899973 AGAATACCTTTGAATCAAGCATGTTT 58.100 30.769 0.00 0.00 0.00 2.83
3990 4456 7.513190 TGTTTGTAAGCACATTTAAACACAC 57.487 32.000 0.00 0.00 34.52 3.82
4005 4539 2.368439 ACACACTCAAAGCTTTCTGCA 58.632 42.857 9.23 0.00 45.94 4.41
4030 4564 5.772393 TCCTTTTCTTACCTGGCTTCATA 57.228 39.130 0.00 0.00 0.00 2.15
4114 4650 4.021192 GCCTTGGAAAATGGATTTGTGAGA 60.021 41.667 0.00 0.00 0.00 3.27
4148 4684 4.892345 TCTCTCTCTCTCTCTCTCTCTCTG 59.108 50.000 0.00 0.00 0.00 3.35
4149 4685 4.614475 TCTCTCTCTCTCTCTCTCTCTGT 58.386 47.826 0.00 0.00 0.00 3.41
4196 4732 1.468520 GTGTGTGTGTGCTGTGTTCTT 59.531 47.619 0.00 0.00 0.00 2.52
4273 4809 4.002506 TGCACGGCCATGTCGAGT 62.003 61.111 2.24 0.00 33.65 4.18
4504 5040 1.034356 TTGTTGGTCTTCTCCGACGA 58.966 50.000 0.00 0.00 42.98 4.20
4594 5130 1.676529 GGCGACTGCATCTACTAGACA 59.323 52.381 0.00 0.00 45.35 3.41
4646 5182 2.100749 GTGGTTTGTTCCAGAAAGGTGG 59.899 50.000 0.00 0.00 38.23 4.61
4715 5252 6.183360 TGGACCATGTCGTACGAAAATATTTG 60.183 38.462 21.39 9.25 32.65 2.32
4720 5257 5.236282 TGTCGTACGAAAATATTTGGACCA 58.764 37.500 21.39 5.90 30.84 4.02
4773 5325 1.102154 TTTGTTGGTGTGAGCAGTGG 58.898 50.000 0.00 0.00 0.00 4.00
4819 5373 3.835395 AGAGTTCTTCGGGTCATTCTCTT 59.165 43.478 0.00 0.00 0.00 2.85
4832 5386 5.932303 GGTCATTCTCTTGTGCTAGTGTTAA 59.068 40.000 0.00 0.00 0.00 2.01
4843 5397 3.263170 TGCTAGTGTTAAGGCATCTCCAA 59.737 43.478 0.00 0.00 37.29 3.53
4844 5398 3.873952 GCTAGTGTTAAGGCATCTCCAAG 59.126 47.826 0.00 0.00 37.29 3.61
4853 5407 1.450312 CATCTCCAAGGTGGACGCC 60.450 63.158 0.00 0.00 42.67 5.68
4876 5430 2.355115 GGACGCCCCCAAATGTCT 59.645 61.111 0.00 0.00 0.00 3.41
4879 5433 1.586154 GACGCCCCCAAATGTCTGTG 61.586 60.000 0.00 0.00 0.00 3.66
4893 5447 2.084546 GTCTGTGGACATGTTAAGGCC 58.915 52.381 0.00 0.00 41.75 5.19
4895 5449 1.812571 CTGTGGACATGTTAAGGCCAC 59.187 52.381 21.15 21.15 46.97 5.01
4900 5454 0.331616 ACATGTTAAGGCCACCCCTC 59.668 55.000 5.01 0.00 45.62 4.30
4901 5455 0.331278 CATGTTAAGGCCACCCCTCA 59.669 55.000 5.01 0.00 45.62 3.86
4902 5456 1.080638 ATGTTAAGGCCACCCCTCAA 58.919 50.000 5.01 0.00 45.62 3.02
4903 5457 0.854218 TGTTAAGGCCACCCCTCAAA 59.146 50.000 5.01 0.00 45.62 2.69
4904 5458 1.431243 TGTTAAGGCCACCCCTCAAAT 59.569 47.619 5.01 0.00 45.62 2.32
4905 5459 2.158234 TGTTAAGGCCACCCCTCAAATT 60.158 45.455 5.01 0.00 45.62 1.82
4906 5460 2.903784 GTTAAGGCCACCCCTCAAATTT 59.096 45.455 5.01 0.00 45.62 1.82
4907 5461 2.116869 AAGGCCACCCCTCAAATTTT 57.883 45.000 5.01 0.00 45.62 1.82
4908 5462 2.116869 AGGCCACCCCTCAAATTTTT 57.883 45.000 5.01 0.00 41.21 1.94
4909 5463 1.977854 AGGCCACCCCTCAAATTTTTC 59.022 47.619 5.01 0.00 41.21 2.29
4910 5464 1.003118 GGCCACCCCTCAAATTTTTCC 59.997 52.381 0.00 0.00 0.00 3.13
4911 5465 1.977854 GCCACCCCTCAAATTTTTCCT 59.022 47.619 0.00 0.00 0.00 3.36
5080 5648 5.952526 ACTTAATTAAACCAACCTGGACG 57.047 39.130 0.00 0.00 40.96 4.79
5083 5651 0.885596 TTAAACCAACCTGGACGCCG 60.886 55.000 0.00 0.00 40.96 6.46
5128 5709 0.820074 ACTCATCTAGGAGGGACGCG 60.820 60.000 3.53 3.53 39.27 6.01
5196 5778 3.717294 ATCGGGGCGGCTTCTTGT 61.717 61.111 9.56 0.00 0.00 3.16
5197 5779 3.682292 ATCGGGGCGGCTTCTTGTC 62.682 63.158 9.56 0.00 0.00 3.18
5198 5780 4.394712 CGGGGCGGCTTCTTGTCT 62.395 66.667 9.56 0.00 0.00 3.41
5199 5781 2.747855 GGGGCGGCTTCTTGTCTG 60.748 66.667 9.56 0.00 0.00 3.51
5200 5782 2.347490 GGGCGGCTTCTTGTCTGA 59.653 61.111 9.56 0.00 0.00 3.27
5201 5783 2.035442 GGGCGGCTTCTTGTCTGAC 61.035 63.158 9.56 0.00 0.00 3.51
5202 5784 2.383527 GGCGGCTTCTTGTCTGACG 61.384 63.158 0.00 0.00 0.00 4.35
5203 5785 1.372997 GCGGCTTCTTGTCTGACGA 60.373 57.895 2.98 0.00 0.00 4.20
5205 5787 0.039074 CGGCTTCTTGTCTGACGACT 60.039 55.000 2.98 0.00 40.86 4.18
5206 5788 1.603172 CGGCTTCTTGTCTGACGACTT 60.603 52.381 2.98 0.00 40.86 3.01
5213 5795 4.373116 TCTGACGACTTGCCGCCC 62.373 66.667 0.00 0.00 0.00 6.13
5283 5865 5.156804 GGCGACCAAGTAAAGTGATAATG 57.843 43.478 0.00 0.00 0.00 1.90
5284 5866 4.634443 GGCGACCAAGTAAAGTGATAATGT 59.366 41.667 0.00 0.00 0.00 2.71
5285 5867 5.813672 GGCGACCAAGTAAAGTGATAATGTA 59.186 40.000 0.00 0.00 0.00 2.29
5286 5868 6.238022 GGCGACCAAGTAAAGTGATAATGTAC 60.238 42.308 0.00 0.00 0.00 2.90
5287 5869 6.238022 GCGACCAAGTAAAGTGATAATGTACC 60.238 42.308 0.00 0.00 0.00 3.34
5288 5870 7.039882 CGACCAAGTAAAGTGATAATGTACCT 58.960 38.462 0.00 0.00 0.00 3.08
5289 5871 7.222224 CGACCAAGTAAAGTGATAATGTACCTC 59.778 40.741 0.00 0.00 0.00 3.85
5290 5872 7.336396 ACCAAGTAAAGTGATAATGTACCTCC 58.664 38.462 0.00 0.00 0.00 4.30
5291 5873 7.182206 ACCAAGTAAAGTGATAATGTACCTCCT 59.818 37.037 0.00 0.00 0.00 3.69
5292 5874 8.047310 CCAAGTAAAGTGATAATGTACCTCCTT 58.953 37.037 0.00 0.00 0.00 3.36
5293 5875 8.883731 CAAGTAAAGTGATAATGTACCTCCTTG 58.116 37.037 0.00 0.00 0.00 3.61
5294 5876 7.565680 AGTAAAGTGATAATGTACCTCCTTGG 58.434 38.462 0.00 0.00 42.93 3.61
5295 5877 4.423625 AGTGATAATGTACCTCCTTGGC 57.576 45.455 0.00 0.00 40.22 4.52
5296 5878 3.131396 GTGATAATGTACCTCCTTGGCG 58.869 50.000 0.00 0.00 40.22 5.69
5297 5879 2.769663 TGATAATGTACCTCCTTGGCGT 59.230 45.455 0.00 0.00 40.22 5.68
5298 5880 2.973694 TAATGTACCTCCTTGGCGTC 57.026 50.000 0.00 0.00 40.22 5.19
5299 5881 1.276622 AATGTACCTCCTTGGCGTCT 58.723 50.000 0.00 0.00 40.22 4.18
5300 5882 1.276622 ATGTACCTCCTTGGCGTCTT 58.723 50.000 0.00 0.00 40.22 3.01
5301 5883 0.606604 TGTACCTCCTTGGCGTCTTC 59.393 55.000 0.00 0.00 40.22 2.87
5302 5884 0.606604 GTACCTCCTTGGCGTCTTCA 59.393 55.000 0.00 0.00 40.22 3.02
5303 5885 1.207329 GTACCTCCTTGGCGTCTTCAT 59.793 52.381 0.00 0.00 40.22 2.57
5304 5886 0.693049 ACCTCCTTGGCGTCTTCATT 59.307 50.000 0.00 0.00 40.22 2.57
5305 5887 1.089920 CCTCCTTGGCGTCTTCATTG 58.910 55.000 0.00 0.00 0.00 2.82
5306 5888 1.339055 CCTCCTTGGCGTCTTCATTGA 60.339 52.381 0.00 0.00 0.00 2.57
5307 5889 2.005451 CTCCTTGGCGTCTTCATTGAG 58.995 52.381 0.00 0.00 0.00 3.02
5308 5890 0.449388 CCTTGGCGTCTTCATTGAGC 59.551 55.000 0.00 0.00 0.00 4.26
5310 5892 4.301505 GGCGTCTTCATTGAGCCA 57.698 55.556 9.20 0.00 46.48 4.75
5311 5893 2.555123 GGCGTCTTCATTGAGCCAA 58.445 52.632 9.20 0.00 46.48 4.52
5312 5894 0.449388 GGCGTCTTCATTGAGCCAAG 59.551 55.000 9.20 0.00 46.48 3.61
5313 5895 1.160137 GCGTCTTCATTGAGCCAAGT 58.840 50.000 0.00 0.00 0.00 3.16
5314 5896 1.135859 GCGTCTTCATTGAGCCAAGTG 60.136 52.381 0.00 0.00 0.00 3.16
5315 5897 2.146342 CGTCTTCATTGAGCCAAGTGT 58.854 47.619 0.00 0.00 0.00 3.55
5316 5898 2.096069 CGTCTTCATTGAGCCAAGTGTG 60.096 50.000 0.00 0.00 0.00 3.82
5325 5907 4.258206 CCAAGTGTGGTTGCACCT 57.742 55.556 6.83 0.00 40.42 4.00
5326 5908 3.412722 CCAAGTGTGGTTGCACCTA 57.587 52.632 6.83 0.00 40.42 3.08
5327 5909 0.951558 CCAAGTGTGGTTGCACCTAC 59.048 55.000 6.83 0.00 40.42 3.18
5328 5910 1.476833 CCAAGTGTGGTTGCACCTACT 60.477 52.381 0.00 5.05 40.42 2.57
5329 5911 1.873591 CAAGTGTGGTTGCACCTACTC 59.126 52.381 0.00 0.00 39.58 2.59
5330 5912 0.396811 AGTGTGGTTGCACCTACTCC 59.603 55.000 0.00 0.00 39.58 3.85
5331 5913 0.107831 GTGTGGTTGCACCTACTCCA 59.892 55.000 0.00 0.00 39.58 3.86
5332 5914 0.840617 TGTGGTTGCACCTACTCCAA 59.159 50.000 0.00 0.00 39.58 3.53
5333 5915 1.213182 TGTGGTTGCACCTACTCCAAA 59.787 47.619 0.00 0.00 39.58 3.28
5334 5916 2.158534 TGTGGTTGCACCTACTCCAAAT 60.159 45.455 0.00 0.00 39.58 2.32
5335 5917 2.890945 GTGGTTGCACCTACTCCAAATT 59.109 45.455 6.83 0.00 39.58 1.82
5336 5918 3.057526 GTGGTTGCACCTACTCCAAATTC 60.058 47.826 6.83 0.00 39.58 2.17
5337 5919 3.153919 GGTTGCACCTACTCCAAATTCA 58.846 45.455 0.00 0.00 34.73 2.57
5338 5920 3.191371 GGTTGCACCTACTCCAAATTCAG 59.809 47.826 0.00 0.00 34.73 3.02
5339 5921 4.072131 GTTGCACCTACTCCAAATTCAGA 58.928 43.478 0.00 0.00 0.00 3.27
5340 5922 4.574674 TGCACCTACTCCAAATTCAGAT 57.425 40.909 0.00 0.00 0.00 2.90
5341 5923 4.264253 TGCACCTACTCCAAATTCAGATG 58.736 43.478 0.00 0.00 0.00 2.90
5342 5924 3.065925 GCACCTACTCCAAATTCAGATGC 59.934 47.826 0.00 0.00 0.00 3.91
5343 5925 4.521146 CACCTACTCCAAATTCAGATGCT 58.479 43.478 0.00 0.00 0.00 3.79
5344 5926 4.574013 CACCTACTCCAAATTCAGATGCTC 59.426 45.833 0.00 0.00 0.00 4.26
5345 5927 4.472833 ACCTACTCCAAATTCAGATGCTCT 59.527 41.667 0.00 0.00 0.00 4.09
5346 5928 5.055812 CCTACTCCAAATTCAGATGCTCTC 58.944 45.833 0.00 0.00 0.00 3.20
5347 5929 4.840716 ACTCCAAATTCAGATGCTCTCT 57.159 40.909 0.00 0.00 33.14 3.10
5348 5930 5.176741 ACTCCAAATTCAGATGCTCTCTT 57.823 39.130 0.00 0.00 29.16 2.85
5349 5931 5.184711 ACTCCAAATTCAGATGCTCTCTTC 58.815 41.667 0.00 0.00 29.16 2.87
5350 5932 4.186926 TCCAAATTCAGATGCTCTCTTCG 58.813 43.478 0.00 0.00 29.16 3.79
5351 5933 3.242673 CCAAATTCAGATGCTCTCTTCGC 60.243 47.826 0.00 0.00 29.16 4.70
5352 5934 1.850377 ATTCAGATGCTCTCTTCGCG 58.150 50.000 0.00 0.00 29.16 5.87
5353 5935 0.811281 TTCAGATGCTCTCTTCGCGA 59.189 50.000 3.71 3.71 29.16 5.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 111 2.217038 TTGGTCTTGAGCTCGCCCT 61.217 57.895 9.64 0.00 0.00 5.19
278 288 0.193574 TTCTCCACTCTTCCCCACCT 59.806 55.000 0.00 0.00 0.00 4.00
279 289 0.615850 CTTCTCCACTCTTCCCCACC 59.384 60.000 0.00 0.00 0.00 4.61
566 579 0.327924 TCGTGTCAGGCCAAATCCAT 59.672 50.000 5.01 0.00 0.00 3.41
567 580 0.321564 CTCGTGTCAGGCCAAATCCA 60.322 55.000 5.01 0.00 0.00 3.41
568 581 1.026718 CCTCGTGTCAGGCCAAATCC 61.027 60.000 5.01 0.00 0.00 3.01
569 582 1.026718 CCCTCGTGTCAGGCCAAATC 61.027 60.000 5.01 0.00 31.23 2.17
570 583 1.002134 CCCTCGTGTCAGGCCAAAT 60.002 57.895 5.01 0.00 31.23 2.32
571 584 1.990160 AACCCTCGTGTCAGGCCAAA 61.990 55.000 5.01 0.00 31.23 3.28
572 585 1.990160 AAACCCTCGTGTCAGGCCAA 61.990 55.000 5.01 0.00 31.23 4.52
573 586 1.990160 AAAACCCTCGTGTCAGGCCA 61.990 55.000 5.01 0.00 31.23 5.36
574 587 0.822121 AAAAACCCTCGTGTCAGGCC 60.822 55.000 0.00 0.00 31.23 5.19
575 588 0.591659 GAAAAACCCTCGTGTCAGGC 59.408 55.000 0.00 0.00 31.23 4.85
576 589 1.961793 TGAAAAACCCTCGTGTCAGG 58.038 50.000 0.00 0.00 0.00 3.86
577 590 4.102649 GTTTTGAAAAACCCTCGTGTCAG 58.897 43.478 7.31 0.00 41.77 3.51
578 591 4.099380 GTTTTGAAAAACCCTCGTGTCA 57.901 40.909 7.31 0.00 41.77 3.58
593 606 5.009210 CCGTTTGATTTGTCCCTAGTTTTGA 59.991 40.000 0.00 0.00 0.00 2.69
698 712 4.656112 TCTCACCCTTCAGTCTCTTTTCTT 59.344 41.667 0.00 0.00 0.00 2.52
710 724 5.988310 TCGTTAGTTAATCTCACCCTTCA 57.012 39.130 0.00 0.00 0.00 3.02
715 729 6.020837 GTCATCGTTCGTTAGTTAATCTCACC 60.021 42.308 0.00 0.00 0.00 4.02
742 756 3.622163 TGTGCCAAAATTGCTTTGTCAAG 59.378 39.130 0.00 0.00 42.57 3.02
967 1396 4.090588 GATGGACGGGCGTTGGGA 62.091 66.667 0.00 0.00 0.00 4.37
968 1397 4.096003 AGATGGACGGGCGTTGGG 62.096 66.667 0.00 0.00 0.00 4.12
1329 1758 8.833231 AATCTCAAGAGAAAAATGTAACGAGA 57.167 30.769 3.59 0.00 41.36 4.04
1377 1807 2.047061 AGGGAGTTACAGCAGTTCACA 58.953 47.619 0.00 0.00 0.00 3.58
1385 1815 4.689612 TGATGGATTAGGGAGTTACAGC 57.310 45.455 0.00 0.00 0.00 4.40
1674 2106 4.776435 TGCCAATGAGATAGAATCCACA 57.224 40.909 0.00 0.00 0.00 4.17
1844 2276 2.093500 ACATCTCATAGCCGCAGTTTGA 60.093 45.455 0.00 0.00 0.00 2.69
1977 2409 4.726035 TGAAGGTACCCCACACATTAAA 57.274 40.909 8.74 0.00 0.00 1.52
2072 2504 4.468510 ACCGAGTGAATAAACCATACCAGA 59.531 41.667 0.00 0.00 0.00 3.86
2096 2528 6.503524 CACCACTTGTTATTAGCTTGTGTTT 58.496 36.000 0.00 0.00 0.00 2.83
2588 3021 5.705441 TCAAATGGCTAGACACTTCGAAAAT 59.295 36.000 0.00 0.00 0.00 1.82
3025 3467 6.983906 AACAGAAGATTCCAAAATGACCTT 57.016 33.333 0.00 0.00 0.00 3.50
3289 3751 1.756375 GCTGTGCGAGCTGAATACCG 61.756 60.000 0.00 0.00 45.21 4.02
3494 3956 7.093992 CGGAAAGATTTCTTCACTACTTCTCT 58.906 38.462 5.37 0.00 37.35 3.10
3534 3996 5.750547 TGCTATACAAGAGCTCTCGAAAATG 59.249 40.000 18.55 12.94 40.76 2.32
3927 4393 8.214364 AGGTATTCTAGATGAATTTTGGAGGAC 58.786 37.037 0.00 0.00 42.28 3.85
3970 4436 6.685527 TGAGTGTGTTTAAATGTGCTTACA 57.314 33.333 0.00 0.00 0.00 2.41
3990 4456 2.818432 AGGATGTGCAGAAAGCTTTGAG 59.182 45.455 18.30 9.72 45.94 3.02
4005 4539 4.202567 TGAAGCCAGGTAAGAAAAGGATGT 60.203 41.667 0.00 0.00 0.00 3.06
4046 4580 1.788258 TCTTTGTGCAGCTTCTCGAG 58.212 50.000 5.93 5.93 0.00 4.04
4114 4650 5.714863 AGAGAGAGAGAGAGAGAGAGAGAT 58.285 45.833 0.00 0.00 0.00 2.75
4148 4684 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
4149 4685 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
4196 4732 1.065709 GGGAAACGATTAGGCACCTGA 60.066 52.381 0.00 0.00 0.00 3.86
4273 4809 0.244994 GCTGGAGCTTCGAGTTCAGA 59.755 55.000 4.42 0.00 38.21 3.27
4318 4854 4.223032 AGCTTCCTTTTCTTCGGATACAGA 59.777 41.667 0.00 0.00 0.00 3.41
4594 5130 1.372501 AGTGGGGAGTGGCAGTATTT 58.627 50.000 0.00 0.00 0.00 1.40
4646 5182 2.747686 ACCCATCCGGTGACACAC 59.252 61.111 8.08 0.00 46.09 3.82
4715 5252 3.119495 GCATTTCAGGTTACATGTGGTCC 60.119 47.826 9.11 8.06 0.00 4.46
4745 5282 4.209080 GCTCACACCAACAAACTAAATTGC 59.791 41.667 0.00 0.00 33.52 3.56
4819 5373 3.369471 GGAGATGCCTTAACACTAGCACA 60.369 47.826 0.00 0.00 38.21 4.57
4832 5386 4.587520 TCCACCTTGGAGATGCCT 57.412 55.556 0.00 0.00 42.67 4.75
4843 5397 1.909781 TCCGTTTAGGCGTCCACCT 60.910 57.895 0.00 0.00 44.31 4.00
4844 5398 1.739196 GTCCGTTTAGGCGTCCACC 60.739 63.158 0.00 0.00 40.77 4.61
4853 5407 0.678684 ATTTGGGGGCGTCCGTTTAG 60.679 55.000 0.00 0.00 36.01 1.85
4876 5430 1.546773 GGTGGCCTTAACATGTCCACA 60.547 52.381 26.23 8.25 46.62 4.17
4879 5433 0.683179 GGGGTGGCCTTAACATGTCC 60.683 60.000 3.32 0.00 0.00 4.02
4884 5438 0.854218 TTTGAGGGGTGGCCTTAACA 59.146 50.000 3.32 0.00 0.00 2.41
4893 5447 6.419484 AAACTAGGAAAAATTTGAGGGGTG 57.581 37.500 0.00 0.00 0.00 4.61
4895 5449 8.425703 TGTTTAAACTAGGAAAAATTTGAGGGG 58.574 33.333 18.72 0.00 0.00 4.79
4907 5461 9.187455 GCGAATTTGAAATGTTTAAACTAGGAA 57.813 29.630 18.72 7.23 0.00 3.36
4908 5462 8.353684 TGCGAATTTGAAATGTTTAAACTAGGA 58.646 29.630 18.72 0.00 0.00 2.94
4909 5463 8.514136 TGCGAATTTGAAATGTTTAAACTAGG 57.486 30.769 18.72 0.00 0.00 3.02
5054 5622 7.707464 CGTCCAGGTTGGTTTAATTAAGTTTTT 59.293 33.333 0.00 0.00 39.03 1.94
5055 5623 7.204604 CGTCCAGGTTGGTTTAATTAAGTTTT 58.795 34.615 0.00 0.00 39.03 2.43
5056 5624 6.736519 GCGTCCAGGTTGGTTTAATTAAGTTT 60.737 38.462 0.00 0.00 39.03 2.66
5057 5625 5.278610 GCGTCCAGGTTGGTTTAATTAAGTT 60.279 40.000 0.00 0.00 39.03 2.66
5111 5688 2.194212 GCGCGTCCCTCCTAGATGA 61.194 63.158 8.43 0.00 0.00 2.92
5151 5732 1.153289 CCACGGAGGATGAGCAAGG 60.153 63.158 0.00 0.00 41.22 3.61
5196 5778 4.373116 GGGCGGCAAGTCGTCAGA 62.373 66.667 12.47 0.00 36.35 3.27
5199 5781 4.699522 AAGGGGCGGCAAGTCGTC 62.700 66.667 12.47 0.00 0.00 4.20
5200 5782 4.699522 GAAGGGGCGGCAAGTCGT 62.700 66.667 12.47 0.00 0.00 4.34
5272 5854 5.193679 GCCAAGGAGGTACATTATCACTTT 58.806 41.667 0.00 0.00 40.61 2.66
5273 5855 4.683400 CGCCAAGGAGGTACATTATCACTT 60.683 45.833 0.00 0.00 40.61 3.16
5274 5856 3.181465 CGCCAAGGAGGTACATTATCACT 60.181 47.826 0.00 0.00 40.61 3.41
5275 5857 3.131396 CGCCAAGGAGGTACATTATCAC 58.869 50.000 0.00 0.00 40.61 3.06
5276 5858 2.769663 ACGCCAAGGAGGTACATTATCA 59.230 45.455 0.00 0.00 40.61 2.15
5277 5859 3.069729 AGACGCCAAGGAGGTACATTATC 59.930 47.826 0.00 0.00 40.61 1.75
5278 5860 3.039011 AGACGCCAAGGAGGTACATTAT 58.961 45.455 0.00 0.00 40.61 1.28
5279 5861 2.463752 AGACGCCAAGGAGGTACATTA 58.536 47.619 0.00 0.00 40.61 1.90
5280 5862 1.276622 AGACGCCAAGGAGGTACATT 58.723 50.000 0.00 0.00 40.61 2.71
5281 5863 1.207329 GAAGACGCCAAGGAGGTACAT 59.793 52.381 0.00 0.00 40.61 2.29
5282 5864 0.606604 GAAGACGCCAAGGAGGTACA 59.393 55.000 0.00 0.00 40.61 2.90
5283 5865 0.606604 TGAAGACGCCAAGGAGGTAC 59.393 55.000 0.00 0.00 40.61 3.34
5284 5866 1.568504 ATGAAGACGCCAAGGAGGTA 58.431 50.000 0.00 0.00 40.61 3.08
5285 5867 0.693049 AATGAAGACGCCAAGGAGGT 59.307 50.000 0.00 0.00 40.61 3.85
5286 5868 1.089920 CAATGAAGACGCCAAGGAGG 58.910 55.000 0.00 0.00 41.84 4.30
5287 5869 2.005451 CTCAATGAAGACGCCAAGGAG 58.995 52.381 0.00 0.00 0.00 3.69
5288 5870 1.945819 GCTCAATGAAGACGCCAAGGA 60.946 52.381 0.00 0.00 0.00 3.36
5289 5871 0.449388 GCTCAATGAAGACGCCAAGG 59.551 55.000 0.00 0.00 0.00 3.61
5290 5872 0.449388 GGCTCAATGAAGACGCCAAG 59.551 55.000 6.39 0.00 40.41 3.61
5291 5873 0.250684 TGGCTCAATGAAGACGCCAA 60.251 50.000 10.92 0.00 46.76 4.52
5292 5874 4.301505 GGCTCAATGAAGACGCCA 57.698 55.556 6.39 0.00 40.41 5.69
5293 5875 0.449388 CTTGGCTCAATGAAGACGCC 59.551 55.000 4.49 4.49 41.06 5.68
5294 5876 1.135859 CACTTGGCTCAATGAAGACGC 60.136 52.381 0.00 0.00 0.00 5.19
5295 5877 2.096069 CACACTTGGCTCAATGAAGACG 60.096 50.000 0.00 0.00 0.00 4.18
5296 5878 2.227388 CCACACTTGGCTCAATGAAGAC 59.773 50.000 0.00 0.00 35.56 3.01
5297 5879 2.507484 CCACACTTGGCTCAATGAAGA 58.493 47.619 0.00 0.00 35.56 2.87
5317 5899 4.072131 TCTGAATTTGGAGTAGGTGCAAC 58.928 43.478 0.00 0.00 35.99 4.17
5318 5900 4.365514 TCTGAATTTGGAGTAGGTGCAA 57.634 40.909 0.00 0.00 34.08 4.08
5319 5901 4.264253 CATCTGAATTTGGAGTAGGTGCA 58.736 43.478 0.00 0.00 0.00 4.57
5320 5902 3.065925 GCATCTGAATTTGGAGTAGGTGC 59.934 47.826 0.00 0.00 38.19 5.01
5321 5903 4.521146 AGCATCTGAATTTGGAGTAGGTG 58.479 43.478 0.00 0.00 0.00 4.00
5322 5904 4.775236 GAGCATCTGAATTTGGAGTAGGT 58.225 43.478 0.00 0.00 0.00 3.08


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

AutoCloner maintained by Alex Coulton.