Multiple sequence alignment - TraesCS6B01G296700

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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 TraesCS6B01G296700 chr6B 100.000 5092 0 0 1 5092 532337556 532342647 0.000000e+00 9404.0
1 TraesCS6B01G296700 chr6B 97.297 37 1 0 939 975 532338461 532338497 4.260000e-06 63.9
2 TraesCS6B01G296700 chr6B 97.297 37 1 0 906 942 532338494 532338530 4.260000e-06 63.9
3 TraesCS6B01G296700 chr6D 95.850 4289 141 23 573 4843 347687968 347683699 0.000000e+00 6900.0
4 TraesCS6B01G296700 chr6D 91.331 496 13 7 1 492 347688438 347687969 0.000000e+00 651.0
5 TraesCS6B01G296700 chr6D 95.312 128 6 0 4842 4969 347683737 347683610 2.400000e-48 204.0
6 TraesCS6B01G296700 chr6A 95.275 3894 114 24 906 4765 495685750 495689607 0.000000e+00 6107.0
7 TraesCS6B01G296700 chr6A 97.239 978 18 5 1 975 495684815 495685786 0.000000e+00 1648.0
8 TraesCS6B01G296700 chr6A 97.368 38 0 1 939 975 495685716 495685753 4.260000e-06 63.9


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 TraesCS6B01G296700 chr6B 532337556 532342647 5091 False 9404.0 9404 100.000000 1 5092 1 chr6B.!!$F1 5091
1 TraesCS6B01G296700 chr6D 347683610 347688438 4828 True 2585.0 6900 94.164333 1 4969 3 chr6D.!!$R1 4968
2 TraesCS6B01G296700 chr6A 495684815 495689607 4792 False 2606.3 6107 96.627333 1 4765 3 chr6A.!!$F1 4764

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
427 434 0.103755 TCAGCGCATCATCTCCAGAC 59.896 55.000 11.47 0.0 0.00 3.51 F
1364 1411 0.452184 AGCCAGTCATGTACTCGTCG 59.548 55.000 0.00 0.0 35.76 5.12 F
2048 2097 0.234884 GTGTCAACACGCTGGTTAGC 59.765 55.000 0.00 0.0 46.62 3.09 F
3268 3320 3.326006 TGTCTTTGCTCTGGAGACTGATT 59.674 43.478 1.35 0.0 40.28 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1753 1802 1.047034 ATACAGGGCACGGGGTAGAC 61.047 60.000 0.00 0.0 0.00 2.59 R
3305 3357 1.675714 CGGACAGCAGCTGGAACATAA 60.676 52.381 26.38 0.0 38.20 1.90 R
3792 3844 1.815003 CAGACCACAAGCTTTGGGATC 59.185 52.381 23.11 15.8 38.59 3.36 R
5018 5096 0.035439 AAACCGTGTGCTCCATAGGG 60.035 55.000 0.00 0.0 36.75 3.53 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 41 1.069973 TGTCATCGAGCGCAAAAAGTG 60.070 47.619 11.47 0.22 0.00 3.16
109 114 0.534412 CCAGCAGTGATCTTCGGAGT 59.466 55.000 0.00 0.00 0.00 3.85
376 381 6.808704 CCTTTCTTTTGTTCTATTGGCTAAGC 59.191 38.462 0.00 0.00 0.00 3.09
395 402 7.168804 GGCTAAGCTTTTATCATCTCATTTTGC 59.831 37.037 3.20 0.00 0.00 3.68
427 434 0.103755 TCAGCGCATCATCTCCAGAC 59.896 55.000 11.47 0.00 0.00 3.51
550 557 5.633830 ACTGTTCTTTCCTGCATGTATTG 57.366 39.130 0.00 0.00 0.00 1.90
562 569 4.891260 TGCATGTATTGGCATGTGAAAAA 58.109 34.783 7.71 0.00 45.75 1.94
745 752 7.699878 TGCTATATTCTGGGACTCTACTATGA 58.300 38.462 0.00 0.00 0.00 2.15
761 768 5.121380 ACTATGATTGCTGTGGGATCTTT 57.879 39.130 0.00 0.00 0.00 2.52
791 798 2.624838 ACCAAATCCAAGACAGCACAAG 59.375 45.455 0.00 0.00 0.00 3.16
979 1020 5.476945 TCCCAAAGGAAAAAGCTTCTATCAC 59.523 40.000 0.00 0.00 40.08 3.06
998 1039 2.722116 CACGCAACAAAATTACCGGAAC 59.278 45.455 9.46 0.00 0.00 3.62
1023 1064 7.951245 ACAATGGATAGGTAACCCTTTTTGTAA 59.049 33.333 0.00 0.00 42.66 2.41
1095 1137 5.125417 TGCATTTTTCTTAGAGCGCCTTATT 59.875 36.000 2.29 0.00 0.00 1.40
1100 1142 6.569179 TTTCTTAGAGCGCCTTATTTTTGT 57.431 33.333 2.29 0.00 0.00 2.83
1214 1260 7.440198 TCCTATGATCACTCTTGCTATCTTTG 58.560 38.462 0.00 0.00 0.00 2.77
1364 1411 0.452184 AGCCAGTCATGTACTCGTCG 59.548 55.000 0.00 0.00 35.76 5.12
1382 1431 2.793790 GTCGCTGATGTTCTCTAGCATG 59.206 50.000 0.00 0.00 35.98 4.06
1391 1440 6.531594 TGATGTTCTCTAGCATGTTACTTTCG 59.468 38.462 0.00 0.00 0.00 3.46
1543 1592 7.298122 AGCACGTGATTGATAACAAAGTTTAG 58.702 34.615 22.23 0.00 39.54 1.85
1564 1613 5.234466 AGAACTACCCCATATCATGCTTC 57.766 43.478 0.00 0.00 0.00 3.86
1605 1654 6.258230 TGTTTCATTTAGGAGTGCAATCTG 57.742 37.500 14.60 4.04 0.00 2.90
1753 1802 6.040616 ACCAGGTAGGATTTCTTATGTACTCG 59.959 42.308 0.00 0.00 41.22 4.18
1762 1811 3.470709 TCTTATGTACTCGTCTACCCCG 58.529 50.000 0.00 0.00 0.00 5.73
1780 1829 2.943033 CCCGTGCCCTGTATTTTTCTAG 59.057 50.000 0.00 0.00 0.00 2.43
1793 1842 9.807649 CTGTATTTTTCTAGCAGCCAAATTAAT 57.192 29.630 0.00 0.00 0.00 1.40
1815 1864 7.907214 AATTGGAAGTCTGACATTAGTGTAC 57.093 36.000 10.88 0.00 39.09 2.90
2048 2097 0.234884 GTGTCAACACGCTGGTTAGC 59.765 55.000 0.00 0.00 46.62 3.09
2120 2169 4.653341 TCTTGAACCCCATGTGTTTCAATT 59.347 37.500 1.64 0.00 0.00 2.32
2585 2634 6.038356 CAGGTCAATATTCATGTTTCCTTGC 58.962 40.000 0.00 0.00 0.00 4.01
2639 2688 5.939883 TCAGCAATTCTTGTGTAAGCAGTAT 59.060 36.000 0.00 0.00 33.82 2.12
3097 3149 6.627087 TCTTTTGTCCTAGATGACATTCCT 57.373 37.500 3.09 0.00 44.27 3.36
3268 3320 3.326006 TGTCTTTGCTCTGGAGACTGATT 59.674 43.478 1.35 0.00 40.28 2.57
3278 3330 5.065914 TCTGGAGACTGATTGGTTTTCTTG 58.934 41.667 0.00 0.00 32.87 3.02
3305 3357 7.867921 TGTTATCCAACCATTAGGATTGTACT 58.132 34.615 0.00 0.00 41.80 2.73
3420 3472 4.320714 CGTTCCTAAAGCCCTTGTTTTACC 60.321 45.833 0.00 0.00 0.00 2.85
3449 3501 3.636764 GGTCCATTTGTTTCAGTTGGAGT 59.363 43.478 0.00 0.00 37.16 3.85
3738 3790 6.264067 ACCAAACAAACTACTAGTCGAGTACT 59.736 38.462 0.00 0.00 39.81 2.73
3783 3835 8.462016 CAAGTTTCCTATATAAAGCTGCTTTGT 58.538 33.333 31.86 28.00 35.21 2.83
3785 3837 7.829211 AGTTTCCTATATAAAGCTGCTTTGTGA 59.171 33.333 31.86 18.24 35.21 3.58
3792 3844 6.695292 ATAAAGCTGCTTTGTGAAATTTCG 57.305 33.333 31.86 0.06 35.21 3.46
3928 3980 2.150397 ACGGTTCAGAAGGTTTCGAG 57.850 50.000 0.00 0.00 34.02 4.04
4136 4191 2.108514 GCTGCAGCGAGGCATGTAA 61.109 57.895 25.23 0.00 43.97 2.41
4159 4214 4.072839 GCTACAGAGCTAAAACCAGGTTT 58.927 43.478 12.23 12.23 45.98 3.27
4183 4238 2.653766 GCGCCAACCGTGTGTTTG 60.654 61.111 0.00 0.00 39.71 2.93
4370 4425 3.132111 GTGGTCTTGGTTTGGTTTGTGAT 59.868 43.478 0.00 0.00 0.00 3.06
4377 4432 6.605594 TCTTGGTTTGGTTTGTGATCTAGTTT 59.394 34.615 0.00 0.00 0.00 2.66
4477 4533 0.591170 TTTGGCTTCGCTTGTACAGC 59.409 50.000 0.00 1.42 46.31 4.40
4536 4592 8.286191 TGCCTGGTCAAATTTTAAATTTGTTT 57.714 26.923 30.15 5.79 39.36 2.83
4549 4605 8.844441 TTTAAATTTGTTTGGTAGTCTGTTCG 57.156 30.769 0.00 0.00 0.00 3.95
4557 4613 7.632721 TGTTTGGTAGTCTGTTCGTATTTTTC 58.367 34.615 0.00 0.00 0.00 2.29
4563 4619 4.271533 AGTCTGTTCGTATTTTTCGTTGCA 59.728 37.500 0.00 0.00 0.00 4.08
4566 4622 3.064958 TGTTCGTATTTTTCGTTGCACCA 59.935 39.130 0.00 0.00 0.00 4.17
4573 4629 3.510388 TTTTCGTTGCACCATGACAAA 57.490 38.095 0.00 0.00 0.00 2.83
4580 4641 1.894466 TGCACCATGACAAATCCCTTG 59.106 47.619 0.00 0.00 41.19 3.61
4598 4659 6.532826 TCCCTTGCATTTTCAAAGCTTTTAT 58.467 32.000 9.53 0.00 0.00 1.40
4609 4670 6.959639 TCAAAGCTTTTATGGTCTCTTTGT 57.040 33.333 9.53 0.00 40.45 2.83
4612 4673 7.706179 TCAAAGCTTTTATGGTCTCTTTGTTTG 59.294 33.333 9.53 0.00 40.45 2.93
4613 4674 6.715347 AGCTTTTATGGTCTCTTTGTTTGT 57.285 33.333 0.00 0.00 0.00 2.83
4614 4675 7.112452 AGCTTTTATGGTCTCTTTGTTTGTT 57.888 32.000 0.00 0.00 0.00 2.83
4615 4676 7.555965 AGCTTTTATGGTCTCTTTGTTTGTTT 58.444 30.769 0.00 0.00 0.00 2.83
4670 4743 3.401182 TGCCTGAAAATTGAAATGGTGC 58.599 40.909 0.00 0.00 0.00 5.01
4718 4794 2.309136 AAAGGATTGGGGTTCCACTG 57.691 50.000 0.00 0.00 43.94 3.66
4739 4817 6.864685 CACTGTCAAATGATAATTGTGCAAGT 59.135 34.615 0.00 0.00 0.00 3.16
4741 4819 6.389091 TGTCAAATGATAATTGTGCAAGTCC 58.611 36.000 0.00 0.00 0.00 3.85
4769 4847 1.678970 GCACCCCTCATTCACACCC 60.679 63.158 0.00 0.00 0.00 4.61
4778 4856 0.253044 CATTCACACCCCGTCCTCAT 59.747 55.000 0.00 0.00 0.00 2.90
4779 4857 0.253044 ATTCACACCCCGTCCTCATG 59.747 55.000 0.00 0.00 0.00 3.07
4789 4867 2.417243 CCCGTCCTCATGGAAAAATTGC 60.417 50.000 0.00 0.00 45.18 3.56
4796 4874 3.401182 TCATGGAAAAATTGCAAGGTGC 58.599 40.909 4.94 0.00 45.29 5.01
4805 4883 4.643795 GCAAGGTGCATGAGGCTA 57.356 55.556 0.00 0.00 44.26 3.93
4806 4884 2.872408 GCAAGGTGCATGAGGCTAA 58.128 52.632 0.00 0.00 44.26 3.09
4807 4885 0.737219 GCAAGGTGCATGAGGCTAAG 59.263 55.000 0.00 0.00 44.26 2.18
4808 4886 1.679944 GCAAGGTGCATGAGGCTAAGA 60.680 52.381 0.00 0.00 44.26 2.10
4809 4887 2.715046 CAAGGTGCATGAGGCTAAGAA 58.285 47.619 0.00 0.00 45.15 2.52
4810 4888 3.084039 CAAGGTGCATGAGGCTAAGAAA 58.916 45.455 0.00 0.00 45.15 2.52
4811 4889 3.439857 AGGTGCATGAGGCTAAGAAAA 57.560 42.857 0.00 0.00 45.15 2.29
4812 4890 3.766545 AGGTGCATGAGGCTAAGAAAAA 58.233 40.909 0.00 0.00 45.15 1.94
4813 4891 4.347607 AGGTGCATGAGGCTAAGAAAAAT 58.652 39.130 0.00 0.00 45.15 1.82
4814 4892 4.159135 AGGTGCATGAGGCTAAGAAAAATG 59.841 41.667 0.00 0.00 45.15 2.32
4815 4893 3.861689 GTGCATGAGGCTAAGAAAAATGC 59.138 43.478 0.00 0.00 45.15 3.56
4816 4894 3.765511 TGCATGAGGCTAAGAAAAATGCT 59.234 39.130 0.00 0.00 45.15 3.79
4817 4895 4.221262 TGCATGAGGCTAAGAAAAATGCTT 59.779 37.500 0.00 0.00 45.15 3.91
4818 4896 4.565564 GCATGAGGCTAAGAAAAATGCTTG 59.434 41.667 0.00 0.00 40.25 4.01
4819 4897 4.789012 TGAGGCTAAGAAAAATGCTTGG 57.211 40.909 0.00 0.00 0.00 3.61
4820 4898 4.406456 TGAGGCTAAGAAAAATGCTTGGA 58.594 39.130 0.00 0.00 0.00 3.53
4821 4899 5.018809 TGAGGCTAAGAAAAATGCTTGGAT 58.981 37.500 0.00 0.00 0.00 3.41
4822 4900 5.126061 TGAGGCTAAGAAAAATGCTTGGATC 59.874 40.000 0.00 0.00 0.00 3.36
4823 4901 5.267587 AGGCTAAGAAAAATGCTTGGATCT 58.732 37.500 0.00 0.00 0.00 2.75
4824 4902 6.426587 AGGCTAAGAAAAATGCTTGGATCTA 58.573 36.000 0.00 0.00 0.00 1.98
4825 4903 7.065504 AGGCTAAGAAAAATGCTTGGATCTAT 58.934 34.615 0.00 0.00 0.00 1.98
4826 4904 8.220559 AGGCTAAGAAAAATGCTTGGATCTATA 58.779 33.333 0.00 0.00 0.00 1.31
4827 4905 8.850156 GGCTAAGAAAAATGCTTGGATCTATAA 58.150 33.333 0.00 0.00 0.00 0.98
4836 4914 9.683069 AAATGCTTGGATCTATAAAATTAAGCG 57.317 29.630 0.00 0.00 41.43 4.68
4837 4915 6.668323 TGCTTGGATCTATAAAATTAAGCGC 58.332 36.000 0.00 0.00 41.43 5.92
4838 4916 6.486657 TGCTTGGATCTATAAAATTAAGCGCT 59.513 34.615 2.64 2.64 41.43 5.92
4839 4917 7.018235 GCTTGGATCTATAAAATTAAGCGCTC 58.982 38.462 12.06 0.00 31.40 5.03
4840 4918 7.435068 TTGGATCTATAAAATTAAGCGCTCC 57.565 36.000 12.06 2.50 0.00 4.70
4880 4958 9.881773 TGGATCTATAAAATTAAGCTTTCCCAT 57.118 29.630 3.20 0.00 0.00 4.00
4898 4976 2.158505 CCATGATTTCTCCTGGGCTCAT 60.159 50.000 0.00 0.00 34.49 2.90
4907 4985 0.319728 CCTGGGCTCATATCGGTGAG 59.680 60.000 0.00 8.43 46.59 3.51
4943 5021 2.977914 CTCACCGAGGATGACATTGTT 58.022 47.619 0.00 0.00 0.00 2.83
4966 5044 8.525316 TGTTTGAAAGCATACAAATGATGATCT 58.475 29.630 0.00 0.00 38.09 2.75
4972 5050 9.793252 AAAGCATACAAATGATGATCTTTACAC 57.207 29.630 0.00 0.00 34.84 2.90
4973 5051 8.510243 AGCATACAAATGATGATCTTTACACA 57.490 30.769 0.00 0.00 34.84 3.72
4974 5052 8.618677 AGCATACAAATGATGATCTTTACACAG 58.381 33.333 0.00 0.00 34.84 3.66
4975 5053 7.377928 GCATACAAATGATGATCTTTACACAGC 59.622 37.037 0.00 0.00 34.84 4.40
4976 5054 5.872635 ACAAATGATGATCTTTACACAGCG 58.127 37.500 0.00 0.00 0.00 5.18
4977 5055 5.643348 ACAAATGATGATCTTTACACAGCGA 59.357 36.000 0.00 0.00 0.00 4.93
4978 5056 5.725110 AATGATGATCTTTACACAGCGAC 57.275 39.130 0.00 0.00 0.00 5.19
4979 5057 4.456280 TGATGATCTTTACACAGCGACT 57.544 40.909 0.00 0.00 0.00 4.18
4980 5058 4.176271 TGATGATCTTTACACAGCGACTG 58.824 43.478 5.47 5.47 37.52 3.51
4981 5059 2.337583 TGATCTTTACACAGCGACTGC 58.662 47.619 6.74 0.00 43.24 4.40
4992 5070 3.296516 GCGACTGCTGCACATAAAC 57.703 52.632 0.00 0.00 38.39 2.01
4993 5071 0.179189 GCGACTGCTGCACATAAACC 60.179 55.000 0.00 0.00 38.39 3.27
4994 5072 0.095245 CGACTGCTGCACATAAACCG 59.905 55.000 0.00 0.00 0.00 4.44
4995 5073 0.179189 GACTGCTGCACATAAACCGC 60.179 55.000 0.00 0.00 0.00 5.68
4996 5074 0.888736 ACTGCTGCACATAAACCGCA 60.889 50.000 0.00 0.00 0.00 5.69
4997 5075 0.240678 CTGCTGCACATAAACCGCAA 59.759 50.000 0.00 0.00 34.75 4.85
4998 5076 0.887247 TGCTGCACATAAACCGCAAT 59.113 45.000 0.00 0.00 34.75 3.56
4999 5077 1.271934 TGCTGCACATAAACCGCAATT 59.728 42.857 0.00 0.00 34.75 2.32
5000 5078 1.919918 GCTGCACATAAACCGCAATTC 59.080 47.619 0.00 0.00 34.75 2.17
5001 5079 2.415893 GCTGCACATAAACCGCAATTCT 60.416 45.455 0.00 0.00 34.75 2.40
5002 5080 3.429085 CTGCACATAAACCGCAATTCTC 58.571 45.455 0.00 0.00 34.75 2.87
5003 5081 2.159585 TGCACATAAACCGCAATTCTCG 60.160 45.455 0.00 0.00 31.46 4.04
5010 5088 3.146783 CCGCAATTCTCGGTAACCA 57.853 52.632 7.35 0.00 41.85 3.67
5011 5089 1.663695 CCGCAATTCTCGGTAACCAT 58.336 50.000 7.35 0.00 41.85 3.55
5012 5090 1.597663 CCGCAATTCTCGGTAACCATC 59.402 52.381 7.35 0.00 41.85 3.51
5013 5091 2.550978 CGCAATTCTCGGTAACCATCT 58.449 47.619 0.00 0.00 0.00 2.90
5014 5092 2.936498 CGCAATTCTCGGTAACCATCTT 59.064 45.455 0.00 0.00 0.00 2.40
5015 5093 4.116961 CGCAATTCTCGGTAACCATCTTA 58.883 43.478 0.00 0.00 0.00 2.10
5016 5094 4.750098 CGCAATTCTCGGTAACCATCTTAT 59.250 41.667 0.00 0.00 0.00 1.73
5017 5095 5.107453 CGCAATTCTCGGTAACCATCTTATC 60.107 44.000 0.00 0.00 0.00 1.75
5018 5096 5.179555 GCAATTCTCGGTAACCATCTTATCC 59.820 44.000 0.00 0.00 0.00 2.59
5019 5097 4.950205 TTCTCGGTAACCATCTTATCCC 57.050 45.455 0.00 0.00 0.00 3.85
5020 5098 3.236896 TCTCGGTAACCATCTTATCCCC 58.763 50.000 0.00 0.00 0.00 4.81
5021 5099 3.116862 TCTCGGTAACCATCTTATCCCCT 60.117 47.826 0.00 0.00 0.00 4.79
5022 5100 4.106825 TCTCGGTAACCATCTTATCCCCTA 59.893 45.833 0.00 0.00 0.00 3.53
5023 5101 5.019657 TCGGTAACCATCTTATCCCCTAT 57.980 43.478 0.00 0.00 0.00 2.57
5024 5102 4.775780 TCGGTAACCATCTTATCCCCTATG 59.224 45.833 0.00 0.00 0.00 2.23
5025 5103 4.081087 CGGTAACCATCTTATCCCCTATGG 60.081 50.000 0.00 0.00 43.73 2.74
5033 5111 3.628989 TCCCCTATGGAGCACACG 58.371 61.111 0.00 0.00 38.61 4.49
5034 5112 2.063979 TCCCCTATGGAGCACACGG 61.064 63.158 0.00 0.00 38.61 4.94
5035 5113 2.367202 CCCCTATGGAGCACACGGT 61.367 63.158 0.00 0.00 35.39 4.83
5036 5114 1.602237 CCCTATGGAGCACACGGTT 59.398 57.895 0.00 0.00 0.00 4.44
5037 5115 0.035439 CCCTATGGAGCACACGGTTT 60.035 55.000 0.00 0.00 0.00 3.27
5038 5116 1.086696 CCTATGGAGCACACGGTTTG 58.913 55.000 0.00 0.00 0.00 2.93
5039 5117 1.338674 CCTATGGAGCACACGGTTTGA 60.339 52.381 0.00 0.00 0.00 2.69
5040 5118 2.422597 CTATGGAGCACACGGTTTGAA 58.577 47.619 0.00 0.00 0.00 2.69
5041 5119 1.686355 ATGGAGCACACGGTTTGAAA 58.314 45.000 0.00 0.00 0.00 2.69
5042 5120 1.021202 TGGAGCACACGGTTTGAAAG 58.979 50.000 0.00 0.00 0.00 2.62
5043 5121 0.317854 GGAGCACACGGTTTGAAAGC 60.318 55.000 0.00 0.00 0.00 3.51
5044 5122 0.663153 GAGCACACGGTTTGAAAGCT 59.337 50.000 5.53 0.00 35.23 3.74
5045 5123 1.065551 GAGCACACGGTTTGAAAGCTT 59.934 47.619 5.53 0.00 33.59 3.74
5046 5124 1.199624 GCACACGGTTTGAAAGCTTG 58.800 50.000 11.32 11.32 34.71 4.01
5047 5125 1.838913 CACACGGTTTGAAAGCTTGG 58.161 50.000 16.16 3.87 33.07 3.61
5048 5126 0.744281 ACACGGTTTGAAAGCTTGGG 59.256 50.000 16.16 1.26 33.07 4.12
5049 5127 0.597377 CACGGTTTGAAAGCTTGGGC 60.597 55.000 0.00 0.00 39.06 5.36
5050 5128 1.006220 CGGTTTGAAAGCTTGGGCC 60.006 57.895 0.00 0.00 39.73 5.80
5051 5129 1.371183 GGTTTGAAAGCTTGGGCCC 59.629 57.895 17.59 17.59 39.73 5.80
5052 5130 1.371183 GTTTGAAAGCTTGGGCCCC 59.629 57.895 22.27 3.22 39.73 5.80
5053 5131 1.121407 GTTTGAAAGCTTGGGCCCCT 61.121 55.000 22.27 6.20 39.73 4.79
5054 5132 0.831711 TTTGAAAGCTTGGGCCCCTC 60.832 55.000 22.27 8.26 39.73 4.30
5055 5133 2.363018 GAAAGCTTGGGCCCCTCC 60.363 66.667 22.27 6.97 39.73 4.30
5065 5143 3.090532 GCCCCTCCCAAGGTCGAT 61.091 66.667 0.00 0.00 41.59 3.59
5066 5144 2.680370 GCCCCTCCCAAGGTCGATT 61.680 63.158 0.00 0.00 41.59 3.34
5067 5145 1.999346 CCCCTCCCAAGGTCGATTT 59.001 57.895 0.00 0.00 41.59 2.17
5068 5146 0.331616 CCCCTCCCAAGGTCGATTTT 59.668 55.000 0.00 0.00 41.59 1.82
5069 5147 1.272480 CCCCTCCCAAGGTCGATTTTT 60.272 52.381 0.00 0.00 41.59 1.94
5091 5169 8.624367 TTTTTGTGTGGCTAGCTATTAAGTAA 57.376 30.769 15.72 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 7.946655 TCAGAATGATGTGGTCGATTATAAC 57.053 36.000 0.00 0.00 42.56 1.89
104 109 6.851330 GTCTTTGATGAACACTTTAAACTCCG 59.149 38.462 0.00 0.00 0.00 4.63
109 114 7.286546 TCCCATGTCTTTGATGAACACTTTAAA 59.713 33.333 0.00 0.00 0.00 1.52
257 262 2.029020 TGCTGTCGTTGAGCATAGAACT 60.029 45.455 0.00 0.00 41.56 3.01
395 402 6.716898 TGATGCGCTGATAAATAGAGAATG 57.283 37.500 9.73 0.00 0.00 2.67
550 557 5.988561 TGGTTGATTTAGTTTTTCACATGCC 59.011 36.000 0.00 0.00 0.00 4.40
562 569 9.739276 TGTTTCAAGAGATATGGTTGATTTAGT 57.261 29.630 0.00 0.00 30.50 2.24
745 752 3.087031 CTCACAAAGATCCCACAGCAAT 58.913 45.455 0.00 0.00 0.00 3.56
979 1020 3.001395 TGTTCCGGTAATTTTGTTGCG 57.999 42.857 0.00 0.00 0.00 4.85
1028 1070 7.180229 TCAATACAACTGTTATCCAGAGGAGAA 59.820 37.037 0.00 0.00 44.49 2.87
1065 1107 4.558496 CGCTCTAAGAAAAATGCAAACCCA 60.558 41.667 0.00 0.00 0.00 4.51
1100 1142 9.231297 CCAACTTCCTTAATCAACTTGAATCTA 57.769 33.333 0.00 0.00 0.00 1.98
1214 1260 3.988379 TCATTGTTTCACAGTTCAGGC 57.012 42.857 0.00 0.00 0.00 4.85
1364 1411 5.355596 AGTAACATGCTAGAGAACATCAGC 58.644 41.667 0.00 0.00 34.54 4.26
1407 1456 5.219633 GCCGCAAAGACTTCAATAAAGAAA 58.780 37.500 0.00 0.00 38.44 2.52
1543 1592 4.999950 CAGAAGCATGATATGGGGTAGTTC 59.000 45.833 0.00 0.00 0.00 3.01
1564 1613 8.991243 ATGAAACAATGGACAATATTCAACAG 57.009 30.769 0.00 0.00 0.00 3.16
1605 1654 7.152645 TGACTCTGTCTTTCATAAGTTGGTAC 58.847 38.462 0.00 0.00 33.15 3.34
1753 1802 1.047034 ATACAGGGCACGGGGTAGAC 61.047 60.000 0.00 0.00 0.00 2.59
1762 1811 3.181496 GCTGCTAGAAAAATACAGGGCAC 60.181 47.826 0.00 0.00 0.00 5.01
1793 1842 6.041637 ACAGTACACTAATGTCAGACTTCCAA 59.958 38.462 1.31 0.00 40.48 3.53
1815 1864 5.248870 AGGCTTTAACAAACAACTCACAG 57.751 39.130 0.00 0.00 0.00 3.66
1858 1907 4.761227 TGCATCAGTTGATCTGCAAAACTA 59.239 37.500 7.69 0.00 43.32 2.24
1860 1909 3.904571 TGCATCAGTTGATCTGCAAAAC 58.095 40.909 7.69 0.00 43.32 2.43
1953 2002 4.034975 GCTAGCTTTAGGACATCTTTGCTG 59.965 45.833 7.70 0.00 0.00 4.41
1992 2041 4.142513 GGTGGTGCAGATGAAATTTCTCTC 60.143 45.833 18.64 14.46 0.00 3.20
2120 2169 1.822990 CAGGTGCTCGGTACCTAAGAA 59.177 52.381 10.90 0.00 46.43 2.52
2585 2634 9.099454 GGAGAATCACAACAAAAGTACTATAGG 57.901 37.037 4.43 0.00 36.25 2.57
2971 3023 3.275143 TGCATATACAAAGAACCACCCG 58.725 45.455 0.00 0.00 0.00 5.28
3097 3149 8.531146 GGAAAATTAGGAAATCCAATGAGTTCA 58.469 33.333 1.67 0.00 45.12 3.18
3305 3357 1.675714 CGGACAGCAGCTGGAACATAA 60.676 52.381 26.38 0.00 38.20 1.90
3420 3472 5.786311 ACTGAAACAAATGGACCAATCATG 58.214 37.500 0.00 0.00 0.00 3.07
3449 3501 5.551233 CAATGTGTCCTGAAACTCCTCTTA 58.449 41.667 0.00 0.00 0.00 2.10
3783 3835 4.280677 ACAAGCTTTGGGATCGAAATTTCA 59.719 37.500 17.99 5.97 34.12 2.69
3785 3837 4.559153 CACAAGCTTTGGGATCGAAATTT 58.441 39.130 0.00 0.00 35.62 1.82
3792 3844 1.815003 CAGACCACAAGCTTTGGGATC 59.185 52.381 23.11 15.80 38.59 3.36
3928 3980 2.742053 TGAGCAAGCTTTTCGGTGATAC 59.258 45.455 0.00 0.00 0.00 2.24
4136 4191 6.262024 CAAACCTGGTTTTAGCTCTGTAGCT 61.262 44.000 21.73 5.11 46.46 3.32
4183 4238 1.598701 GCAAGGACCATGAACAGGCC 61.599 60.000 0.00 0.00 0.00 5.19
4370 4425 7.167635 GCGATATGAACGATTGAGAAAACTAGA 59.832 37.037 0.00 0.00 0.00 2.43
4377 4432 4.740205 GTCTGCGATATGAACGATTGAGAA 59.260 41.667 0.00 0.00 0.00 2.87
4477 4533 5.560148 ACGTGCTCTATTAAATTTCGCAAG 58.440 37.500 0.00 0.00 0.00 4.01
4484 4540 9.257651 GGATACACTAACGTGCTCTATTAAATT 57.742 33.333 0.00 0.00 45.10 1.82
4536 4592 5.531634 ACGAAAAATACGAACAGACTACCA 58.468 37.500 0.00 0.00 34.70 3.25
4544 4600 3.064958 TGGTGCAACGAAAAATACGAACA 59.935 39.130 0.00 0.00 38.12 3.18
4545 4601 3.619729 TGGTGCAACGAAAAATACGAAC 58.380 40.909 0.00 0.00 38.12 3.95
4549 4605 4.541779 TGTCATGGTGCAACGAAAAATAC 58.458 39.130 0.00 0.00 38.12 1.89
4557 4613 1.402720 GGGATTTGTCATGGTGCAACG 60.403 52.381 0.00 0.00 38.12 4.10
4563 4619 2.307496 TGCAAGGGATTTGTCATGGT 57.693 45.000 0.00 0.00 39.08 3.55
4566 4622 5.486735 TGAAAATGCAAGGGATTTGTCAT 57.513 34.783 0.00 0.00 39.08 3.06
4580 4641 6.870439 AGAGACCATAAAAGCTTTGAAAATGC 59.130 34.615 13.54 0.49 46.27 3.56
4670 4743 7.189512 GGATCGAATGGACTAAAAATTGACTG 58.810 38.462 0.00 0.00 0.00 3.51
4706 4782 1.496857 TCATTTGACAGTGGAACCCCA 59.503 47.619 0.00 0.00 40.95 4.96
4718 4794 6.389091 TGGACTTGCACAATTATCATTTGAC 58.611 36.000 0.00 0.00 0.00 3.18
4739 4817 1.494721 GAGGGGTGCAATATCCTTGGA 59.505 52.381 0.00 0.00 0.00 3.53
4741 4819 2.734755 TGAGGGGTGCAATATCCTTG 57.265 50.000 0.00 0.00 0.00 3.61
4769 4847 2.230992 TGCAATTTTTCCATGAGGACGG 59.769 45.455 0.00 0.00 45.73 4.79
4789 4867 2.408271 TCTTAGCCTCATGCACCTTG 57.592 50.000 0.00 0.00 44.83 3.61
4796 4874 5.105635 TCCAAGCATTTTTCTTAGCCTCATG 60.106 40.000 0.00 0.00 0.00 3.07
4810 4888 9.683069 CGCTTAATTTTATAGATCCAAGCATTT 57.317 29.630 0.00 0.00 37.57 2.32
4811 4889 7.809806 GCGCTTAATTTTATAGATCCAAGCATT 59.190 33.333 0.00 0.00 37.57 3.56
4812 4890 7.175641 AGCGCTTAATTTTATAGATCCAAGCAT 59.824 33.333 2.64 0.00 37.57 3.79
4813 4891 6.486657 AGCGCTTAATTTTATAGATCCAAGCA 59.513 34.615 2.64 0.00 37.57 3.91
4814 4892 6.903419 AGCGCTTAATTTTATAGATCCAAGC 58.097 36.000 2.64 0.00 35.08 4.01
4815 4893 7.361286 GGGAGCGCTTAATTTTATAGATCCAAG 60.361 40.741 13.26 0.00 0.00 3.61
4816 4894 6.430000 GGGAGCGCTTAATTTTATAGATCCAA 59.570 38.462 13.26 0.00 0.00 3.53
4817 4895 5.938125 GGGAGCGCTTAATTTTATAGATCCA 59.062 40.000 13.26 0.00 0.00 3.41
4818 4896 5.938125 TGGGAGCGCTTAATTTTATAGATCC 59.062 40.000 13.26 2.15 0.00 3.36
4819 4897 7.361286 CCTTGGGAGCGCTTAATTTTATAGATC 60.361 40.741 13.26 0.00 0.00 2.75
4820 4898 6.431234 CCTTGGGAGCGCTTAATTTTATAGAT 59.569 38.462 13.26 0.00 0.00 1.98
4821 4899 5.763204 CCTTGGGAGCGCTTAATTTTATAGA 59.237 40.000 13.26 0.00 0.00 1.98
4822 4900 5.763204 TCCTTGGGAGCGCTTAATTTTATAG 59.237 40.000 13.26 0.00 0.00 1.31
4823 4901 5.686753 TCCTTGGGAGCGCTTAATTTTATA 58.313 37.500 13.26 0.00 0.00 0.98
4824 4902 4.532834 TCCTTGGGAGCGCTTAATTTTAT 58.467 39.130 13.26 0.00 0.00 1.40
4825 4903 3.958018 TCCTTGGGAGCGCTTAATTTTA 58.042 40.909 13.26 0.00 0.00 1.52
4826 4904 2.802719 TCCTTGGGAGCGCTTAATTTT 58.197 42.857 13.26 0.00 0.00 1.82
4827 4905 2.507407 TCCTTGGGAGCGCTTAATTT 57.493 45.000 13.26 0.00 0.00 1.82
4828 4906 2.507407 TTCCTTGGGAGCGCTTAATT 57.493 45.000 13.26 0.00 31.21 1.40
4829 4907 2.507407 TTTCCTTGGGAGCGCTTAAT 57.493 45.000 13.26 0.00 31.21 1.40
4830 4908 2.279935 TTTTCCTTGGGAGCGCTTAA 57.720 45.000 13.26 6.96 31.21 1.85
4831 4909 2.091541 CATTTTCCTTGGGAGCGCTTA 58.908 47.619 13.26 0.00 31.21 3.09
4832 4910 0.890683 CATTTTCCTTGGGAGCGCTT 59.109 50.000 13.26 0.00 31.21 4.68
4833 4911 1.598701 GCATTTTCCTTGGGAGCGCT 61.599 55.000 11.27 11.27 31.21 5.92
4834 4912 1.153765 GCATTTTCCTTGGGAGCGC 60.154 57.895 0.00 0.00 31.21 5.92
4835 4913 0.890683 AAGCATTTTCCTTGGGAGCG 59.109 50.000 0.00 0.00 31.21 5.03
4836 4914 2.375173 CAAGCATTTTCCTTGGGAGC 57.625 50.000 0.00 0.00 36.82 4.70
4880 4958 3.007290 CGATATGAGCCCAGGAGAAATCA 59.993 47.826 0.00 0.00 0.00 2.57
4898 4976 2.165167 AGGTCAACGAACTCACCGATA 58.835 47.619 0.00 0.00 33.78 2.92
4907 4985 1.865340 GTGAGGTCAAGGTCAACGAAC 59.135 52.381 0.00 0.00 0.00 3.95
4974 5052 0.179189 GGTTTATGTGCAGCAGTCGC 60.179 55.000 0.00 0.00 38.99 5.19
4975 5053 0.095245 CGGTTTATGTGCAGCAGTCG 59.905 55.000 0.00 0.00 0.00 4.18
4976 5054 0.179189 GCGGTTTATGTGCAGCAGTC 60.179 55.000 0.00 0.00 0.00 3.51
4977 5055 0.888736 TGCGGTTTATGTGCAGCAGT 60.889 50.000 0.00 0.00 34.03 4.40
4978 5056 0.240678 TTGCGGTTTATGTGCAGCAG 59.759 50.000 0.00 0.00 40.15 4.24
4979 5057 0.887247 ATTGCGGTTTATGTGCAGCA 59.113 45.000 0.00 0.00 40.15 4.41
4980 5058 1.919918 GAATTGCGGTTTATGTGCAGC 59.080 47.619 0.00 0.00 40.15 5.25
4981 5059 3.429085 GAGAATTGCGGTTTATGTGCAG 58.571 45.455 0.00 0.00 40.15 4.41
4982 5060 2.159585 CGAGAATTGCGGTTTATGTGCA 60.160 45.455 0.00 0.00 36.72 4.57
4983 5061 2.440501 CGAGAATTGCGGTTTATGTGC 58.559 47.619 0.00 0.00 0.00 4.57
4984 5062 3.051606 CCGAGAATTGCGGTTTATGTG 57.948 47.619 7.92 0.00 43.66 3.21
4993 5071 2.550978 AGATGGTTACCGAGAATTGCG 58.449 47.619 0.00 0.00 0.00 4.85
4994 5072 5.179555 GGATAAGATGGTTACCGAGAATTGC 59.820 44.000 0.00 0.00 0.00 3.56
4995 5073 5.701290 GGGATAAGATGGTTACCGAGAATTG 59.299 44.000 0.00 0.00 0.00 2.32
4996 5074 5.221864 GGGGATAAGATGGTTACCGAGAATT 60.222 44.000 0.00 0.00 0.00 2.17
4997 5075 4.286291 GGGGATAAGATGGTTACCGAGAAT 59.714 45.833 0.00 0.00 0.00 2.40
4998 5076 3.644738 GGGGATAAGATGGTTACCGAGAA 59.355 47.826 0.00 0.00 0.00 2.87
4999 5077 3.116862 AGGGGATAAGATGGTTACCGAGA 60.117 47.826 0.00 0.00 0.00 4.04
5000 5078 3.240302 AGGGGATAAGATGGTTACCGAG 58.760 50.000 0.00 0.00 0.00 4.63
5001 5079 3.339713 AGGGGATAAGATGGTTACCGA 57.660 47.619 0.00 0.00 0.00 4.69
5002 5080 4.081087 CCATAGGGGATAAGATGGTTACCG 60.081 50.000 0.00 0.00 40.01 4.02
5003 5081 5.098663 TCCATAGGGGATAAGATGGTTACC 58.901 45.833 0.00 0.00 42.15 2.85
5016 5094 2.063979 CCGTGTGCTCCATAGGGGA 61.064 63.158 0.00 0.00 45.89 4.81
5017 5095 1.910580 AACCGTGTGCTCCATAGGGG 61.911 60.000 0.00 0.00 35.39 4.79
5018 5096 0.035439 AAACCGTGTGCTCCATAGGG 60.035 55.000 0.00 0.00 36.75 3.53
5019 5097 1.086696 CAAACCGTGTGCTCCATAGG 58.913 55.000 0.00 0.00 0.00 2.57
5020 5098 2.093306 TCAAACCGTGTGCTCCATAG 57.907 50.000 0.00 0.00 0.00 2.23
5021 5099 2.552599 TTCAAACCGTGTGCTCCATA 57.447 45.000 0.00 0.00 0.00 2.74
5022 5100 1.608590 CTTTCAAACCGTGTGCTCCAT 59.391 47.619 0.00 0.00 0.00 3.41
5023 5101 1.021202 CTTTCAAACCGTGTGCTCCA 58.979 50.000 0.00 0.00 0.00 3.86
5024 5102 0.317854 GCTTTCAAACCGTGTGCTCC 60.318 55.000 0.00 0.00 0.00 4.70
5025 5103 0.663153 AGCTTTCAAACCGTGTGCTC 59.337 50.000 0.00 0.00 0.00 4.26
5026 5104 1.102978 AAGCTTTCAAACCGTGTGCT 58.897 45.000 0.00 0.00 33.34 4.40
5027 5105 1.199624 CAAGCTTTCAAACCGTGTGC 58.800 50.000 0.00 0.00 0.00 4.57
5028 5106 1.535860 CCCAAGCTTTCAAACCGTGTG 60.536 52.381 0.00 0.00 0.00 3.82
5029 5107 0.744281 CCCAAGCTTTCAAACCGTGT 59.256 50.000 0.00 0.00 0.00 4.49
5030 5108 0.597377 GCCCAAGCTTTCAAACCGTG 60.597 55.000 0.00 0.00 35.50 4.94
5031 5109 1.739667 GCCCAAGCTTTCAAACCGT 59.260 52.632 0.00 0.00 35.50 4.83
5032 5110 1.006220 GGCCCAAGCTTTCAAACCG 60.006 57.895 0.00 0.00 39.73 4.44
5033 5111 1.371183 GGGCCCAAGCTTTCAAACC 59.629 57.895 19.95 0.00 39.73 3.27
5034 5112 1.121407 AGGGGCCCAAGCTTTCAAAC 61.121 55.000 27.72 0.20 39.73 2.93
5035 5113 0.831711 GAGGGGCCCAAGCTTTCAAA 60.832 55.000 27.72 0.00 39.73 2.69
5036 5114 1.228862 GAGGGGCCCAAGCTTTCAA 60.229 57.895 27.72 0.00 39.73 2.69
5037 5115 2.440599 GAGGGGCCCAAGCTTTCA 59.559 61.111 27.72 0.00 39.73 2.69
5038 5116 2.363018 GGAGGGGCCCAAGCTTTC 60.363 66.667 27.72 12.37 39.73 2.62
5066 5144 8.624367 TTACTTAATAGCTAGCCACACAAAAA 57.376 30.769 12.13 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.