Multiple sequence alignment - TraesCS3A01G243800

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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 TraesCS3A01G243800 chr3A 100.000 3866 0 0 1 3866 457079493 457083358 0 7140
1 TraesCS3A01G243800 chr3B 94.698 2999 93 24 883 3866 446176979 446174032 0 4597
2 TraesCS3A01G243800 chr3D 95.603 2365 74 13 746 3101 346648341 346645998 0 3764
3 TraesCS3A01G243800 chr3D 94.737 741 22 4 3126 3866 346645650 346644927 0 1136
4 TraesCS3A01G243800 chr2D 90.995 633 48 4 2 627 572445701 572446331 0 845
5 TraesCS3A01G243800 chr2D 90.909 627 55 2 2 627 355809417 355810042 0 841
6 TraesCS3A01G243800 chr2D 90.895 626 55 1 2 627 572449992 572450615 0 839
7 TraesCS3A01G243800 chr2D 90.735 626 57 1 2 627 357342475 357343099 0 833
8 TraesCS3A01G243800 chr1D 91.054 626 53 3 2 627 206139127 206139749 0 843
9 TraesCS3A01G243800 chr1D 90.379 634 50 6 1 627 220852896 220852267 0 822
10 TraesCS3A01G243800 chr6D 90.735 626 55 1 2 627 211651157 211650535 0 832
11 TraesCS3A01G243800 chr6A 90.590 627 57 2 2 627 166340465 166339840 0 830
12 TraesCS3A01G243800 chr4D 90.521 633 52 3 1 627 126307766 126308396 0 830


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 TraesCS3A01G243800 chr3A 457079493 457083358 3865 False 7140 7140 100.000 1 3866 1 chr3A.!!$F1 3865
1 TraesCS3A01G243800 chr3B 446174032 446176979 2947 True 4597 4597 94.698 883 3866 1 chr3B.!!$R1 2983
2 TraesCS3A01G243800 chr3D 346644927 346648341 3414 True 2450 3764 95.170 746 3866 2 chr3D.!!$R1 3120
3 TraesCS3A01G243800 chr2D 572445701 572450615 4914 False 842 845 90.945 2 627 2 chr2D.!!$F3 625
4 TraesCS3A01G243800 chr2D 355809417 355810042 625 False 841 841 90.909 2 627 1 chr2D.!!$F1 625
5 TraesCS3A01G243800 chr2D 357342475 357343099 624 False 833 833 90.735 2 627 1 chr2D.!!$F2 625
6 TraesCS3A01G243800 chr1D 206139127 206139749 622 False 843 843 91.054 2 627 1 chr1D.!!$F1 625
7 TraesCS3A01G243800 chr1D 220852267 220852896 629 True 822 822 90.379 1 627 1 chr1D.!!$R1 626
8 TraesCS3A01G243800 chr6D 211650535 211651157 622 True 832 832 90.735 2 627 1 chr6D.!!$R1 625
9 TraesCS3A01G243800 chr6A 166339840 166340465 625 True 830 830 90.590 2 627 1 chr6A.!!$R1 625
10 TraesCS3A01G243800 chr4D 126307766 126308396 630 False 830 830 90.521 1 627 1 chr4D.!!$F1 626

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
718 5014 0.034059 CAACGGGCTGTCAGAGTCTT 59.966 55.0 3.32 0.0 0.0 3.01 F
2268 6577 0.842030 ATGAAGGTGTCTGGGGAGCA 60.842 55.0 0.00 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2577 6886 0.538516 TTGCGGTGTACCCTTGCAAT 60.539 50.0 0.00 0.0 40.31 3.56 R
3182 7817 1.291877 CTCGTGGCACCACAGCTTAC 61.292 60.0 19.38 0.0 46.47 2.34 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
163 165 0.898326 TTGACCGCTACCTCTCAGCA 60.898 55.000 0.00 0.00 39.04 4.41
275 277 0.104304 AGACTTCAACAACGGCGTCT 59.896 50.000 15.17 0.00 0.00 4.18
531 4827 6.919721 ACGTTTTAGTTAGAACACCCGTATA 58.080 36.000 0.00 0.00 0.00 1.47
548 4844 4.758165 CCGTATACAAACCAACAACTTCCT 59.242 41.667 3.32 0.00 0.00 3.36
551 4847 6.017770 CGTATACAAACCAACAACTTCCTCAA 60.018 38.462 3.32 0.00 0.00 3.02
579 4875 1.896220 AGAAAAATGTGCCGAGCAGA 58.104 45.000 0.00 0.00 40.08 4.26
636 4932 8.432805 AGATAGAACACCCATATACTTTGAAGG 58.567 37.037 0.00 0.00 0.00 3.46
637 4933 6.388619 AGAACACCCATATACTTTGAAGGT 57.611 37.500 0.00 0.00 0.00 3.50
638 4934 6.790319 AGAACACCCATATACTTTGAAGGTT 58.210 36.000 0.00 0.00 0.00 3.50
639 4935 6.659242 AGAACACCCATATACTTTGAAGGTTG 59.341 38.462 0.00 0.00 0.00 3.77
640 4936 6.134535 ACACCCATATACTTTGAAGGTTGA 57.865 37.500 0.00 0.00 0.00 3.18
641 4937 5.944007 ACACCCATATACTTTGAAGGTTGAC 59.056 40.000 0.00 0.00 0.00 3.18
642 4938 5.064707 CACCCATATACTTTGAAGGTTGACG 59.935 44.000 0.00 0.00 0.00 4.35
643 4939 5.183228 CCCATATACTTTGAAGGTTGACGT 58.817 41.667 0.00 0.00 0.00 4.34
644 4940 6.070653 ACCCATATACTTTGAAGGTTGACGTA 60.071 38.462 0.00 0.00 0.00 3.57
645 4941 6.990349 CCCATATACTTTGAAGGTTGACGTAT 59.010 38.462 0.00 0.00 0.00 3.06
646 4942 7.170998 CCCATATACTTTGAAGGTTGACGTATC 59.829 40.741 0.00 0.00 0.00 2.24
647 4943 7.709182 CCATATACTTTGAAGGTTGACGTATCA 59.291 37.037 0.00 0.00 0.00 2.15
648 4944 8.755941 CATATACTTTGAAGGTTGACGTATCAG 58.244 37.037 0.00 0.00 35.83 2.90
649 4945 4.315803 ACTTTGAAGGTTGACGTATCAGG 58.684 43.478 0.00 0.00 35.83 3.86
650 4946 4.039973 ACTTTGAAGGTTGACGTATCAGGA 59.960 41.667 0.00 0.00 35.83 3.86
651 4947 4.819105 TTGAAGGTTGACGTATCAGGAT 57.181 40.909 0.00 0.00 35.83 3.24
652 4948 4.386867 TGAAGGTTGACGTATCAGGATC 57.613 45.455 0.00 0.00 35.83 3.36
653 4949 3.767131 TGAAGGTTGACGTATCAGGATCA 59.233 43.478 0.00 0.00 35.83 2.92
654 4950 4.405680 TGAAGGTTGACGTATCAGGATCAT 59.594 41.667 0.00 0.00 35.83 2.45
655 4951 5.596772 TGAAGGTTGACGTATCAGGATCATA 59.403 40.000 0.00 0.00 35.83 2.15
656 4952 6.097696 TGAAGGTTGACGTATCAGGATCATAA 59.902 38.462 0.00 0.00 35.83 1.90
657 4953 6.479972 AGGTTGACGTATCAGGATCATAAA 57.520 37.500 0.00 0.00 35.83 1.40
658 4954 7.067496 AGGTTGACGTATCAGGATCATAAAT 57.933 36.000 0.00 0.00 35.83 1.40
659 4955 8.190326 AGGTTGACGTATCAGGATCATAAATA 57.810 34.615 0.00 0.00 35.83 1.40
660 4956 8.307483 AGGTTGACGTATCAGGATCATAAATAG 58.693 37.037 0.00 0.00 35.83 1.73
661 4957 8.304596 GGTTGACGTATCAGGATCATAAATAGA 58.695 37.037 0.00 0.00 35.83 1.98
662 4958 9.692749 GTTGACGTATCAGGATCATAAATAGAA 57.307 33.333 0.00 0.00 35.83 2.10
663 4959 9.914131 TTGACGTATCAGGATCATAAATAGAAG 57.086 33.333 0.00 0.00 35.83 2.85
664 4960 9.297037 TGACGTATCAGGATCATAAATAGAAGA 57.703 33.333 0.00 0.00 0.00 2.87
681 4977 9.965902 AAATAGAAGAAATCAAGAAAGGCTAGA 57.034 29.630 0.00 0.00 0.00 2.43
682 4978 9.612066 AATAGAAGAAATCAAGAAAGGCTAGAG 57.388 33.333 0.00 0.00 0.00 2.43
683 4979 7.014988 AGAAGAAATCAAGAAAGGCTAGAGT 57.985 36.000 0.00 0.00 0.00 3.24
684 4980 7.457561 AGAAGAAATCAAGAAAGGCTAGAGTT 58.542 34.615 0.00 0.00 0.00 3.01
685 4981 7.941790 AGAAGAAATCAAGAAAGGCTAGAGTTT 59.058 33.333 0.00 0.00 0.00 2.66
686 4982 7.680442 AGAAATCAAGAAAGGCTAGAGTTTC 57.320 36.000 8.50 8.50 33.59 2.78
687 4983 6.370166 AGAAATCAAGAAAGGCTAGAGTTTCG 59.630 38.462 0.00 0.00 37.67 3.46
688 4984 4.602340 TCAAGAAAGGCTAGAGTTTCGT 57.398 40.909 0.00 0.00 37.67 3.85
689 4985 4.957296 TCAAGAAAGGCTAGAGTTTCGTT 58.043 39.130 0.00 0.00 37.67 3.85
690 4986 6.092955 TCAAGAAAGGCTAGAGTTTCGTTA 57.907 37.500 0.00 0.00 37.67 3.18
691 4987 5.924825 TCAAGAAAGGCTAGAGTTTCGTTAC 59.075 40.000 0.00 0.00 37.67 2.50
692 4988 5.464030 AGAAAGGCTAGAGTTTCGTTACA 57.536 39.130 0.00 0.00 37.67 2.41
693 4989 5.850614 AGAAAGGCTAGAGTTTCGTTACAA 58.149 37.500 0.00 0.00 37.67 2.41
694 4990 6.465084 AGAAAGGCTAGAGTTTCGTTACAAT 58.535 36.000 0.00 0.00 37.67 2.71
695 4991 7.609056 AGAAAGGCTAGAGTTTCGTTACAATA 58.391 34.615 0.00 0.00 37.67 1.90
696 4992 8.258708 AGAAAGGCTAGAGTTTCGTTACAATAT 58.741 33.333 0.00 0.00 37.67 1.28
697 4993 8.421673 AAAGGCTAGAGTTTCGTTACAATATC 57.578 34.615 0.00 0.00 0.00 1.63
698 4994 7.349412 AGGCTAGAGTTTCGTTACAATATCT 57.651 36.000 0.00 0.00 0.00 1.98
699 4995 7.427214 AGGCTAGAGTTTCGTTACAATATCTC 58.573 38.462 0.00 0.00 0.00 2.75
700 4996 7.068348 AGGCTAGAGTTTCGTTACAATATCTCA 59.932 37.037 0.00 0.00 0.00 3.27
701 4997 7.705325 GGCTAGAGTTTCGTTACAATATCTCAA 59.295 37.037 0.00 0.00 0.00 3.02
702 4998 8.533153 GCTAGAGTTTCGTTACAATATCTCAAC 58.467 37.037 0.00 0.00 0.00 3.18
703 4999 7.507672 AGAGTTTCGTTACAATATCTCAACG 57.492 36.000 8.55 8.55 43.76 4.10
704 5000 6.530534 AGAGTTTCGTTACAATATCTCAACGG 59.469 38.462 12.77 0.42 42.90 4.44
705 5001 5.579511 AGTTTCGTTACAATATCTCAACGGG 59.420 40.000 12.77 0.00 42.90 5.28
706 5002 3.450578 TCGTTACAATATCTCAACGGGC 58.549 45.455 12.77 0.00 42.90 6.13
707 5003 3.131577 TCGTTACAATATCTCAACGGGCT 59.868 43.478 12.77 0.00 42.90 5.19
708 5004 3.245284 CGTTACAATATCTCAACGGGCTG 59.755 47.826 0.00 0.00 39.92 4.85
709 5005 4.189231 GTTACAATATCTCAACGGGCTGT 58.811 43.478 0.00 0.00 0.00 4.40
710 5006 2.906354 ACAATATCTCAACGGGCTGTC 58.094 47.619 0.00 0.00 0.00 3.51
711 5007 2.236146 ACAATATCTCAACGGGCTGTCA 59.764 45.455 0.00 0.00 0.00 3.58
712 5008 2.868583 CAATATCTCAACGGGCTGTCAG 59.131 50.000 0.00 0.00 0.00 3.51
713 5009 1.847328 TATCTCAACGGGCTGTCAGA 58.153 50.000 3.32 4.92 0.00 3.27
714 5010 0.534412 ATCTCAACGGGCTGTCAGAG 59.466 55.000 17.97 17.97 35.23 3.35
715 5011 0.827925 TCTCAACGGGCTGTCAGAGT 60.828 55.000 21.25 0.00 35.37 3.24
716 5012 0.389166 CTCAACGGGCTGTCAGAGTC 60.389 60.000 16.53 0.00 31.51 3.36
717 5013 0.827925 TCAACGGGCTGTCAGAGTCT 60.828 55.000 3.32 0.00 0.00 3.24
718 5014 0.034059 CAACGGGCTGTCAGAGTCTT 59.966 55.000 3.32 0.00 0.00 3.01
719 5015 1.272490 CAACGGGCTGTCAGAGTCTTA 59.728 52.381 3.32 0.00 0.00 2.10
720 5016 1.178276 ACGGGCTGTCAGAGTCTTAG 58.822 55.000 3.32 0.00 0.00 2.18
721 5017 1.271982 ACGGGCTGTCAGAGTCTTAGA 60.272 52.381 3.32 0.00 0.00 2.10
722 5018 2.028130 CGGGCTGTCAGAGTCTTAGAT 58.972 52.381 3.32 0.00 0.00 1.98
723 5019 2.034053 CGGGCTGTCAGAGTCTTAGATC 59.966 54.545 3.32 0.00 0.00 2.75
724 5020 2.364002 GGGCTGTCAGAGTCTTAGATCC 59.636 54.545 3.32 0.00 0.00 3.36
725 5021 3.027412 GGCTGTCAGAGTCTTAGATCCA 58.973 50.000 3.32 0.00 0.00 3.41
726 5022 3.181480 GGCTGTCAGAGTCTTAGATCCAC 60.181 52.174 3.32 0.00 0.00 4.02
727 5023 3.181480 GCTGTCAGAGTCTTAGATCCACC 60.181 52.174 3.32 0.00 0.00 4.61
728 5024 4.277476 CTGTCAGAGTCTTAGATCCACCT 58.723 47.826 0.00 0.00 0.00 4.00
729 5025 5.441500 CTGTCAGAGTCTTAGATCCACCTA 58.558 45.833 0.00 0.00 0.00 3.08
730 5026 6.019656 TGTCAGAGTCTTAGATCCACCTAT 57.980 41.667 0.00 0.00 0.00 2.57
731 5027 6.065374 TGTCAGAGTCTTAGATCCACCTATC 58.935 44.000 0.00 0.00 0.00 2.08
732 5028 6.126332 TGTCAGAGTCTTAGATCCACCTATCT 60.126 42.308 0.00 0.00 39.54 1.98
733 5029 7.072581 TGTCAGAGTCTTAGATCCACCTATCTA 59.927 40.741 0.00 0.00 37.41 1.98
734 5030 8.107095 GTCAGAGTCTTAGATCCACCTATCTAT 58.893 40.741 0.00 0.00 38.08 1.98
735 5031 8.325787 TCAGAGTCTTAGATCCACCTATCTATC 58.674 40.741 0.00 0.00 38.08 2.08
736 5032 8.106462 CAGAGTCTTAGATCCACCTATCTATCA 58.894 40.741 0.00 0.00 38.08 2.15
737 5033 8.107095 AGAGTCTTAGATCCACCTATCTATCAC 58.893 40.741 0.00 0.00 38.08 3.06
738 5034 7.760607 AGTCTTAGATCCACCTATCTATCACA 58.239 38.462 0.00 0.00 38.08 3.58
739 5035 8.397957 AGTCTTAGATCCACCTATCTATCACAT 58.602 37.037 0.00 0.00 38.08 3.21
740 5036 8.465999 GTCTTAGATCCACCTATCTATCACATG 58.534 40.741 0.00 0.00 38.08 3.21
741 5037 5.674052 AGATCCACCTATCTATCACATGC 57.326 43.478 0.00 0.00 34.40 4.06
742 5038 3.942130 TCCACCTATCTATCACATGCG 57.058 47.619 0.00 0.00 0.00 4.73
743 5039 2.562738 TCCACCTATCTATCACATGCGG 59.437 50.000 0.00 0.00 0.00 5.69
744 5040 2.562738 CCACCTATCTATCACATGCGGA 59.437 50.000 0.00 0.00 0.00 5.54
825 5121 3.467803 GTCTGCTAGACTTGGTTTGTGT 58.532 45.455 0.00 0.00 41.88 3.72
826 5122 3.495001 GTCTGCTAGACTTGGTTTGTGTC 59.505 47.826 0.00 0.00 41.88 3.67
829 5125 2.808543 GCTAGACTTGGTTTGTGTCAGG 59.191 50.000 0.00 0.00 33.56 3.86
840 5136 2.839486 TGTGTCAGGAAGATCACCAC 57.161 50.000 10.74 3.14 31.47 4.16
847 5143 3.381590 TCAGGAAGATCACCACATAGTCG 59.618 47.826 10.74 0.00 0.00 4.18
943 5252 6.376864 TGAAATATGAACGAACCCATGACAAT 59.623 34.615 0.00 0.00 0.00 2.71
944 5253 5.756195 ATATGAACGAACCCATGACAATG 57.244 39.130 0.00 0.00 0.00 2.82
988 5297 1.325640 CGCTCCATGTCTGAAATCACG 59.674 52.381 0.00 0.00 0.00 4.35
1494 5803 2.410638 TATCCATGTACGCGGCGGTC 62.411 60.000 27.37 18.25 0.00 4.79
1833 6142 1.257750 ACTCCTATGTGTGCAGCCGA 61.258 55.000 0.00 0.00 0.00 5.54
1870 6179 2.337532 CACTGGGCACTGCTTTGC 59.662 61.111 0.00 1.80 42.18 3.68
1931 6240 1.634702 GAGGTGTTCGAGAGCATGAC 58.365 55.000 0.00 0.00 0.00 3.06
1962 6271 2.920384 TACACCTGGACCAGCGCA 60.920 61.111 16.72 0.00 0.00 6.09
2029 6338 1.275010 TGTTCAAGCGTATGGAGAGCA 59.725 47.619 0.00 0.00 0.00 4.26
2144 6453 3.623060 TCGATGAAGGATAAGCACAAAGC 59.377 43.478 0.00 0.00 46.19 3.51
2200 6509 0.981183 TTTGTATGGTCGAGCAGGGT 59.019 50.000 23.06 8.93 0.00 4.34
2268 6577 0.842030 ATGAAGGTGTCTGGGGAGCA 60.842 55.000 0.00 0.00 0.00 4.26
2300 6609 1.144969 TCTCGGATTCACAACAACGC 58.855 50.000 0.00 0.00 0.00 4.84
2590 6899 1.630369 AGCTGAGATTGCAAGGGTACA 59.370 47.619 4.94 0.21 0.00 2.90
2611 6920 3.004315 CACCGCAAACACAAAAGAGGTAT 59.996 43.478 0.00 0.00 0.00 2.73
2613 6922 4.822896 ACCGCAAACACAAAAGAGGTATTA 59.177 37.500 0.00 0.00 0.00 0.98
2715 7024 4.208632 CCAGAAGGCACGGTGATC 57.791 61.111 13.29 6.61 0.00 2.92
2838 7147 2.738314 GTTTCACCATTTCAAGCATGGC 59.262 45.455 0.03 0.00 44.69 4.40
2870 7179 5.590259 CCTGTAGGGATTACTGGTGATTTTG 59.410 44.000 3.02 0.00 43.04 2.44
2873 7182 5.982890 AGGGATTACTGGTGATTTTGTTG 57.017 39.130 0.00 0.00 0.00 3.33
2893 7202 1.671845 GTGTAACTGTTCCCGTGCAAA 59.328 47.619 0.00 0.00 0.00 3.68
3079 7389 3.488090 GCGCGTTCCTACACAGGC 61.488 66.667 8.43 0.00 42.30 4.85
3080 7390 2.048597 CGCGTTCCTACACAGGCA 60.049 61.111 0.00 0.00 42.30 4.75
3081 7391 1.666553 CGCGTTCCTACACAGGCAA 60.667 57.895 0.00 0.00 42.30 4.52
3082 7392 1.225376 CGCGTTCCTACACAGGCAAA 61.225 55.000 0.00 0.00 42.30 3.68
3182 7817 3.408634 TCAAGTAAAGAAGAAAGGGCGG 58.591 45.455 0.00 0.00 0.00 6.13
3243 7879 0.820891 CAATCAGGGGAATCCAGCGG 60.821 60.000 0.09 0.00 38.24 5.52
3331 7967 1.135257 CCAGAGCTTCGTGATCTTCGT 60.135 52.381 9.75 0.00 39.74 3.85
3352 7988 2.422591 GCCAGGCAGCAAAGCAAA 59.577 55.556 6.55 0.00 35.83 3.68
3408 8044 8.630054 TTTTGATAACTGTATTTAGCACTGGT 57.370 30.769 0.00 0.00 27.27 4.00
3409 8045 9.727859 TTTTGATAACTGTATTTAGCACTGGTA 57.272 29.630 0.00 0.00 27.27 3.25
3410 8046 8.942338 TTGATAACTGTATTTAGCACTGGTAG 57.058 34.615 0.00 0.00 27.27 3.18
3411 8047 8.301252 TGATAACTGTATTTAGCACTGGTAGA 57.699 34.615 0.00 0.00 0.00 2.59
3412 8048 8.414003 TGATAACTGTATTTAGCACTGGTAGAG 58.586 37.037 0.00 0.00 0.00 2.43
3431 8071 4.860022 AGAGGAGAGAAGGAGAGAAGAAG 58.140 47.826 0.00 0.00 0.00 2.85
3503 8143 5.825507 ACAAAATCTTCACAGAAACAGAGC 58.174 37.500 0.00 0.00 30.76 4.09
3579 8219 2.109387 ACACTGGCAAACCGCGTA 59.891 55.556 4.92 0.00 43.84 4.42
3708 8348 1.856265 GCAAACTGGAAGGAGTGGCG 61.856 60.000 0.00 0.00 39.30 5.69
3751 8391 7.639113 AGTAACCTGTCAAAAATTGAAGTGA 57.361 32.000 0.00 0.00 42.15 3.41
3768 8408 6.539173 TGAAGTGAGGCTAGGTTAAAATTCA 58.461 36.000 0.00 0.00 0.00 2.57
3770 8410 4.944317 AGTGAGGCTAGGTTAAAATTCAGC 59.056 41.667 0.00 0.00 0.00 4.26
3830 8470 9.619316 CAAATATGAAAATACGAAGTTGGAACA 57.381 29.630 0.00 0.00 37.78 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
145 147 1.304134 TGCTGAGAGGTAGCGGTCA 60.304 57.895 0.00 0.27 44.01 4.02
275 277 1.848932 CTGTCGTTGTCGTCCTCCGA 61.849 60.000 0.00 0.00 45.00 4.55
482 4778 9.269415 GTTTGCGACGAGTGTTTTATATTTAAT 57.731 29.630 0.00 0.00 0.00 1.40
531 4827 4.340617 TCTTGAGGAAGTTGTTGGTTTGT 58.659 39.130 0.00 0.00 0.00 2.83
548 4844 4.810491 GCACATTTTTCTTTGGCTTCTTGA 59.190 37.500 0.00 0.00 0.00 3.02
551 4847 3.732212 GGCACATTTTTCTTTGGCTTCT 58.268 40.909 0.00 0.00 0.00 2.85
560 4856 1.896220 TCTGCTCGGCACATTTTTCT 58.104 45.000 0.00 0.00 33.79 2.52
562 4858 3.665745 AATTCTGCTCGGCACATTTTT 57.334 38.095 0.00 0.00 33.79 1.94
579 4875 2.923605 GCGATCAAGTGCTGCACAAATT 60.924 45.455 31.90 16.59 36.74 1.82
627 4923 4.039973 TCCTGATACGTCAACCTTCAAAGT 59.960 41.667 0.00 0.00 33.05 2.66
628 4924 4.566004 TCCTGATACGTCAACCTTCAAAG 58.434 43.478 0.00 0.00 33.05 2.77
629 4925 4.610605 TCCTGATACGTCAACCTTCAAA 57.389 40.909 0.00 0.00 33.05 2.69
630 4926 4.221924 TGATCCTGATACGTCAACCTTCAA 59.778 41.667 0.00 0.00 33.05 2.69
631 4927 3.767131 TGATCCTGATACGTCAACCTTCA 59.233 43.478 0.00 0.00 33.05 3.02
632 4928 4.386867 TGATCCTGATACGTCAACCTTC 57.613 45.455 0.00 0.00 33.05 3.46
633 4929 6.479972 TTATGATCCTGATACGTCAACCTT 57.520 37.500 0.00 0.00 33.05 3.50
634 4930 6.479972 TTTATGATCCTGATACGTCAACCT 57.520 37.500 0.00 0.00 33.05 3.50
635 4931 8.304596 TCTATTTATGATCCTGATACGTCAACC 58.695 37.037 0.00 0.00 33.05 3.77
636 4932 9.692749 TTCTATTTATGATCCTGATACGTCAAC 57.307 33.333 0.00 0.00 33.05 3.18
637 4933 9.914131 CTTCTATTTATGATCCTGATACGTCAA 57.086 33.333 0.00 0.00 33.05 3.18
638 4934 9.297037 TCTTCTATTTATGATCCTGATACGTCA 57.703 33.333 0.00 0.00 0.00 4.35
655 4951 9.965902 TCTAGCCTTTCTTGATTTCTTCTATTT 57.034 29.630 0.00 0.00 0.00 1.40
656 4952 9.612066 CTCTAGCCTTTCTTGATTTCTTCTATT 57.388 33.333 0.00 0.00 0.00 1.73
657 4953 8.767436 ACTCTAGCCTTTCTTGATTTCTTCTAT 58.233 33.333 0.00 0.00 0.00 1.98
658 4954 8.140112 ACTCTAGCCTTTCTTGATTTCTTCTA 57.860 34.615 0.00 0.00 0.00 2.10
659 4955 7.014988 ACTCTAGCCTTTCTTGATTTCTTCT 57.985 36.000 0.00 0.00 0.00 2.85
660 4956 7.680442 AACTCTAGCCTTTCTTGATTTCTTC 57.320 36.000 0.00 0.00 0.00 2.87
661 4957 7.095017 CGAAACTCTAGCCTTTCTTGATTTCTT 60.095 37.037 9.16 0.00 31.17 2.52
662 4958 6.370166 CGAAACTCTAGCCTTTCTTGATTTCT 59.630 38.462 9.16 0.00 31.17 2.52
663 4959 6.147985 ACGAAACTCTAGCCTTTCTTGATTTC 59.852 38.462 0.00 0.00 0.00 2.17
664 4960 5.998363 ACGAAACTCTAGCCTTTCTTGATTT 59.002 36.000 0.00 0.00 0.00 2.17
665 4961 5.552178 ACGAAACTCTAGCCTTTCTTGATT 58.448 37.500 0.00 0.00 0.00 2.57
666 4962 5.153950 ACGAAACTCTAGCCTTTCTTGAT 57.846 39.130 0.00 0.00 0.00 2.57
667 4963 4.602340 ACGAAACTCTAGCCTTTCTTGA 57.398 40.909 0.00 0.00 0.00 3.02
668 4964 5.694910 TGTAACGAAACTCTAGCCTTTCTTG 59.305 40.000 0.00 0.72 0.00 3.02
669 4965 5.850614 TGTAACGAAACTCTAGCCTTTCTT 58.149 37.500 0.00 6.33 0.00 2.52
670 4966 5.464030 TGTAACGAAACTCTAGCCTTTCT 57.536 39.130 0.00 0.00 0.00 2.52
671 4967 6.723131 ATTGTAACGAAACTCTAGCCTTTC 57.277 37.500 0.00 3.13 0.00 2.62
672 4968 8.258708 AGATATTGTAACGAAACTCTAGCCTTT 58.741 33.333 0.00 0.00 0.00 3.11
673 4969 7.783042 AGATATTGTAACGAAACTCTAGCCTT 58.217 34.615 0.00 0.00 0.00 4.35
674 4970 7.068348 TGAGATATTGTAACGAAACTCTAGCCT 59.932 37.037 0.00 0.00 0.00 4.58
675 4971 7.201145 TGAGATATTGTAACGAAACTCTAGCC 58.799 38.462 0.00 0.00 0.00 3.93
676 4972 8.533153 GTTGAGATATTGTAACGAAACTCTAGC 58.467 37.037 0.00 0.00 0.00 3.42
677 4973 8.734933 CGTTGAGATATTGTAACGAAACTCTAG 58.265 37.037 11.49 0.00 46.18 2.43
678 4974 7.699391 CCGTTGAGATATTGTAACGAAACTCTA 59.301 37.037 16.05 0.00 46.18 2.43
679 4975 6.530534 CCGTTGAGATATTGTAACGAAACTCT 59.469 38.462 16.05 0.00 46.18 3.24
680 4976 6.237755 CCCGTTGAGATATTGTAACGAAACTC 60.238 42.308 16.05 0.00 46.18 3.01
681 4977 5.579511 CCCGTTGAGATATTGTAACGAAACT 59.420 40.000 16.05 0.00 46.18 2.66
682 4978 5.725864 GCCCGTTGAGATATTGTAACGAAAC 60.726 44.000 16.05 0.00 46.18 2.78
683 4979 4.330620 GCCCGTTGAGATATTGTAACGAAA 59.669 41.667 16.05 0.00 46.18 3.46
684 4980 3.866910 GCCCGTTGAGATATTGTAACGAA 59.133 43.478 16.05 0.00 46.18 3.85
685 4981 3.131577 AGCCCGTTGAGATATTGTAACGA 59.868 43.478 16.05 0.00 46.18 3.85
686 4982 3.245284 CAGCCCGTTGAGATATTGTAACG 59.755 47.826 0.00 0.00 43.79 3.18
687 4983 4.189231 ACAGCCCGTTGAGATATTGTAAC 58.811 43.478 0.00 0.00 0.00 2.50
688 4984 4.081365 TGACAGCCCGTTGAGATATTGTAA 60.081 41.667 0.00 0.00 0.00 2.41
689 4985 3.449377 TGACAGCCCGTTGAGATATTGTA 59.551 43.478 0.00 0.00 0.00 2.41
690 4986 2.236146 TGACAGCCCGTTGAGATATTGT 59.764 45.455 0.00 0.00 0.00 2.71
691 4987 2.868583 CTGACAGCCCGTTGAGATATTG 59.131 50.000 0.00 0.00 0.00 1.90
692 4988 2.766263 TCTGACAGCCCGTTGAGATATT 59.234 45.455 0.00 0.00 0.00 1.28
693 4989 2.363680 CTCTGACAGCCCGTTGAGATAT 59.636 50.000 0.00 0.00 33.13 1.63
694 4990 1.751351 CTCTGACAGCCCGTTGAGATA 59.249 52.381 0.00 0.00 33.13 1.98
695 4991 0.534412 CTCTGACAGCCCGTTGAGAT 59.466 55.000 0.00 0.00 33.13 2.75
696 4992 0.827925 ACTCTGACAGCCCGTTGAGA 60.828 55.000 0.00 2.44 34.53 3.27
697 4993 0.389166 GACTCTGACAGCCCGTTGAG 60.389 60.000 0.00 0.00 35.73 3.02
698 4994 0.827925 AGACTCTGACAGCCCGTTGA 60.828 55.000 0.00 0.00 0.00 3.18
699 4995 0.034059 AAGACTCTGACAGCCCGTTG 59.966 55.000 0.00 0.00 0.00 4.10
700 4996 1.546476 CTAAGACTCTGACAGCCCGTT 59.454 52.381 0.00 0.00 0.00 4.44
701 4997 1.178276 CTAAGACTCTGACAGCCCGT 58.822 55.000 0.00 0.00 0.00 5.28
702 4998 1.464734 TCTAAGACTCTGACAGCCCG 58.535 55.000 0.00 0.00 0.00 6.13
703 4999 2.364002 GGATCTAAGACTCTGACAGCCC 59.636 54.545 0.00 0.00 0.00 5.19
704 5000 3.027412 TGGATCTAAGACTCTGACAGCC 58.973 50.000 0.00 0.00 0.00 4.85
705 5001 3.181480 GGTGGATCTAAGACTCTGACAGC 60.181 52.174 0.00 0.00 0.00 4.40
706 5002 4.277476 AGGTGGATCTAAGACTCTGACAG 58.723 47.826 0.00 0.00 0.00 3.51
707 5003 4.323569 AGGTGGATCTAAGACTCTGACA 57.676 45.455 0.00 0.00 0.00 3.58
708 5004 6.303839 AGATAGGTGGATCTAAGACTCTGAC 58.696 44.000 0.00 0.00 34.29 3.51
709 5005 6.523035 AGATAGGTGGATCTAAGACTCTGA 57.477 41.667 0.00 0.00 34.29 3.27
710 5006 8.106462 TGATAGATAGGTGGATCTAAGACTCTG 58.894 40.741 0.00 0.00 40.85 3.35
711 5007 8.107095 GTGATAGATAGGTGGATCTAAGACTCT 58.893 40.741 0.00 0.00 40.85 3.24
712 5008 7.885922 TGTGATAGATAGGTGGATCTAAGACTC 59.114 40.741 0.00 0.00 40.85 3.36
713 5009 7.760607 TGTGATAGATAGGTGGATCTAAGACT 58.239 38.462 0.00 0.00 40.85 3.24
714 5010 8.465999 CATGTGATAGATAGGTGGATCTAAGAC 58.534 40.741 0.00 0.00 40.85 3.01
715 5011 7.123397 GCATGTGATAGATAGGTGGATCTAAGA 59.877 40.741 0.00 0.00 40.85 2.10
716 5012 7.264221 GCATGTGATAGATAGGTGGATCTAAG 58.736 42.308 0.00 0.00 40.85 2.18
717 5013 6.127619 CGCATGTGATAGATAGGTGGATCTAA 60.128 42.308 0.00 0.00 40.85 2.10
718 5014 5.358160 CGCATGTGATAGATAGGTGGATCTA 59.642 44.000 0.00 0.00 41.53 1.98
719 5015 4.159321 CGCATGTGATAGATAGGTGGATCT 59.841 45.833 0.00 0.00 39.54 2.75
720 5016 4.428209 CGCATGTGATAGATAGGTGGATC 58.572 47.826 0.00 0.00 0.00 3.36
721 5017 3.196469 CCGCATGTGATAGATAGGTGGAT 59.804 47.826 8.11 0.00 0.00 3.41
722 5018 2.562738 CCGCATGTGATAGATAGGTGGA 59.437 50.000 8.11 0.00 0.00 4.02
723 5019 2.562738 TCCGCATGTGATAGATAGGTGG 59.437 50.000 8.11 0.00 0.00 4.61
724 5020 3.942130 TCCGCATGTGATAGATAGGTG 57.058 47.619 8.11 0.00 0.00 4.00
725 5021 5.394663 GCTAATCCGCATGTGATAGATAGGT 60.395 44.000 8.11 0.00 0.00 3.08
726 5022 5.046529 GCTAATCCGCATGTGATAGATAGG 58.953 45.833 8.11 0.89 0.00 2.57
727 5023 5.900425 AGCTAATCCGCATGTGATAGATAG 58.100 41.667 8.11 4.47 0.00 2.08
728 5024 5.654209 AGAGCTAATCCGCATGTGATAGATA 59.346 40.000 8.11 0.00 0.00 1.98
729 5025 4.465660 AGAGCTAATCCGCATGTGATAGAT 59.534 41.667 8.11 6.04 0.00 1.98
730 5026 3.829026 AGAGCTAATCCGCATGTGATAGA 59.171 43.478 8.11 0.00 0.00 1.98
731 5027 4.185467 AGAGCTAATCCGCATGTGATAG 57.815 45.455 8.11 8.34 0.00 2.08
732 5028 4.607293 AAGAGCTAATCCGCATGTGATA 57.393 40.909 8.11 0.00 0.00 2.15
733 5029 3.482156 AAGAGCTAATCCGCATGTGAT 57.518 42.857 8.11 0.63 0.00 3.06
734 5030 2.988010 AAGAGCTAATCCGCATGTGA 57.012 45.000 8.11 0.00 0.00 3.58
735 5031 4.142622 TGAAAAAGAGCTAATCCGCATGTG 60.143 41.667 0.00 0.00 0.00 3.21
736 5032 4.009675 TGAAAAAGAGCTAATCCGCATGT 58.990 39.130 0.00 0.00 0.00 3.21
737 5033 4.095483 AGTGAAAAAGAGCTAATCCGCATG 59.905 41.667 0.00 0.00 0.00 4.06
738 5034 4.095483 CAGTGAAAAAGAGCTAATCCGCAT 59.905 41.667 0.00 0.00 0.00 4.73
739 5035 3.436704 CAGTGAAAAAGAGCTAATCCGCA 59.563 43.478 0.00 0.00 0.00 5.69
740 5036 3.684788 TCAGTGAAAAAGAGCTAATCCGC 59.315 43.478 0.00 0.00 0.00 5.54
741 5037 6.428385 AATCAGTGAAAAAGAGCTAATCCG 57.572 37.500 0.00 0.00 0.00 4.18
742 5038 8.499403 ACTAATCAGTGAAAAAGAGCTAATCC 57.501 34.615 0.00 0.00 32.25 3.01
810 5106 4.407621 TCTTCCTGACACAAACCAAGTCTA 59.592 41.667 0.00 0.00 33.56 2.59
811 5107 3.199946 TCTTCCTGACACAAACCAAGTCT 59.800 43.478 0.00 0.00 33.56 3.24
812 5108 3.541632 TCTTCCTGACACAAACCAAGTC 58.458 45.455 0.00 0.00 0.00 3.01
813 5109 3.644966 TCTTCCTGACACAAACCAAGT 57.355 42.857 0.00 0.00 0.00 3.16
814 5110 4.023707 GTGATCTTCCTGACACAAACCAAG 60.024 45.833 0.00 0.00 34.05 3.61
815 5111 3.882888 GTGATCTTCCTGACACAAACCAA 59.117 43.478 0.00 0.00 34.05 3.67
816 5112 3.476552 GTGATCTTCCTGACACAAACCA 58.523 45.455 0.00 0.00 34.05 3.67
817 5113 2.814336 GGTGATCTTCCTGACACAAACC 59.186 50.000 0.00 0.00 35.33 3.27
818 5114 3.251004 GTGGTGATCTTCCTGACACAAAC 59.749 47.826 0.00 0.00 35.33 2.93
819 5115 3.118075 TGTGGTGATCTTCCTGACACAAA 60.118 43.478 0.00 0.00 34.80 2.83
820 5116 2.437651 TGTGGTGATCTTCCTGACACAA 59.562 45.455 0.00 0.00 34.80 3.33
821 5117 2.046292 TGTGGTGATCTTCCTGACACA 58.954 47.619 0.00 0.00 35.29 3.72
822 5118 2.839486 TGTGGTGATCTTCCTGACAC 57.161 50.000 8.50 0.00 0.00 3.67
823 5119 4.096681 ACTATGTGGTGATCTTCCTGACA 58.903 43.478 8.50 6.25 0.00 3.58
824 5120 4.688021 GACTATGTGGTGATCTTCCTGAC 58.312 47.826 8.50 1.75 0.00 3.51
825 5121 3.381590 CGACTATGTGGTGATCTTCCTGA 59.618 47.826 8.50 0.00 0.00 3.86
826 5122 3.131223 ACGACTATGTGGTGATCTTCCTG 59.869 47.826 0.00 0.00 0.00 3.86
829 5125 5.647589 TGTTACGACTATGTGGTGATCTTC 58.352 41.667 0.00 0.00 0.00 2.87
840 5136 9.135843 TGTACTGAAATTTCTGTTACGACTATG 57.864 33.333 28.57 4.47 39.57 2.23
847 5143 6.801862 GGCACATGTACTGAAATTTCTGTTAC 59.198 38.462 28.57 23.06 39.57 2.50
988 5297 1.794222 CCGCCATCTTGTTCGGAAC 59.206 57.895 13.86 13.86 44.23 3.62
1217 5526 3.319198 GGAGGAGGCCGTTGTGGA 61.319 66.667 0.00 0.00 42.00 4.02
1305 5614 2.818432 GAGGAAGGTGAACGAGTAGTGA 59.182 50.000 0.00 0.00 0.00 3.41
1534 5843 4.082523 CACCACGTCCGGGCTCAT 62.083 66.667 3.66 0.00 0.00 2.90
1634 5943 1.918293 TTCCAGGCGACATGGTCCT 60.918 57.895 9.69 0.00 39.01 3.85
1752 6061 2.826337 AGTGAGCACTGACACCAGA 58.174 52.632 1.71 0.00 43.02 3.86
1833 6142 3.325201 GACCGAAACCCGCATCCCT 62.325 63.158 0.00 0.00 36.84 4.20
1845 6154 2.110213 GTGCCCAGTGTGACCGAA 59.890 61.111 0.00 0.00 0.00 4.30
1931 6240 3.262420 CAGGTGTAGATGTTCCTTTCGG 58.738 50.000 0.00 0.00 0.00 4.30
2200 6509 3.639672 ATTGACAGCATCATCCAGACA 57.360 42.857 0.00 0.00 37.11 3.41
2268 6577 1.531423 TCCGAGAAGCGTTGAGTAGT 58.469 50.000 0.00 0.00 38.67 2.73
2300 6609 3.039202 GCGTGTTTGCCCAGATCGG 62.039 63.158 0.00 0.00 0.00 4.18
2577 6886 0.538516 TTGCGGTGTACCCTTGCAAT 60.539 50.000 0.00 0.00 40.31 3.56
2590 6899 1.470051 ACCTCTTTTGTGTTTGCGGT 58.530 45.000 0.00 0.00 0.00 5.68
2715 7024 4.172505 CTCTCAAGTTCTTCACGATCCTG 58.827 47.826 0.00 0.00 0.00 3.86
2838 7147 3.449227 TCCCTACAGGAGCACGCG 61.449 66.667 3.53 3.53 40.93 6.01
2870 7179 1.003223 GCACGGGAACAGTTACACAAC 60.003 52.381 0.00 0.00 34.67 3.32
2873 7182 1.301423 TTGCACGGGAACAGTTACAC 58.699 50.000 0.00 0.00 0.00 2.90
2893 7202 6.151663 TGATTGCGAATGGATCATCAAAAT 57.848 33.333 0.00 0.00 0.00 1.82
3079 7389 2.868899 AGTTCTTCCCAGCCTCTTTTG 58.131 47.619 0.00 0.00 0.00 2.44
3080 7390 3.117512 TGAAGTTCTTCCCAGCCTCTTTT 60.118 43.478 4.17 0.00 0.00 2.27
3081 7391 2.443255 TGAAGTTCTTCCCAGCCTCTTT 59.557 45.455 4.17 0.00 0.00 2.52
3082 7392 2.057922 TGAAGTTCTTCCCAGCCTCTT 58.942 47.619 4.17 0.00 0.00 2.85
3182 7817 1.291877 CTCGTGGCACCACAGCTTAC 61.292 60.000 19.38 0.00 46.47 2.34
3331 7967 2.282674 CTTTGCTGCCTGGCCTGA 60.283 61.111 17.53 0.00 0.00 3.86
3401 8037 1.754226 CCTTCTCTCCTCTACCAGTGC 59.246 57.143 0.00 0.00 0.00 4.40
3402 8038 3.053991 TCTCCTTCTCTCCTCTACCAGTG 60.054 52.174 0.00 0.00 0.00 3.66
3403 8039 3.194620 TCTCCTTCTCTCCTCTACCAGT 58.805 50.000 0.00 0.00 0.00 4.00
3404 8040 3.458118 TCTCTCCTTCTCTCCTCTACCAG 59.542 52.174 0.00 0.00 0.00 4.00
3405 8041 3.465832 TCTCTCCTTCTCTCCTCTACCA 58.534 50.000 0.00 0.00 0.00 3.25
3406 8042 4.165372 TCTTCTCTCCTTCTCTCCTCTACC 59.835 50.000 0.00 0.00 0.00 3.18
3407 8043 5.367945 TCTTCTCTCCTTCTCTCCTCTAC 57.632 47.826 0.00 0.00 0.00 2.59
3408 8044 5.491078 ACTTCTTCTCTCCTTCTCTCCTCTA 59.509 44.000 0.00 0.00 0.00 2.43
3409 8045 4.292306 ACTTCTTCTCTCCTTCTCTCCTCT 59.708 45.833 0.00 0.00 0.00 3.69
3410 8046 4.600062 ACTTCTTCTCTCCTTCTCTCCTC 58.400 47.826 0.00 0.00 0.00 3.71
3411 8047 4.675063 ACTTCTTCTCTCCTTCTCTCCT 57.325 45.455 0.00 0.00 0.00 3.69
3412 8048 7.418337 AATTACTTCTTCTCTCCTTCTCTCC 57.582 40.000 0.00 0.00 0.00 3.71
3503 8143 4.588084 CGAACAAACTGGTGTGCG 57.412 55.556 0.53 0.53 43.80 5.34
3579 8219 9.899661 TTTGACCTTATGTTTAGCATATACACT 57.100 29.630 0.00 0.00 39.56 3.55
3708 8348 4.243007 ACTAATGGCAAGCACACTTTTC 57.757 40.909 0.00 0.00 32.29 2.29
3751 8391 3.054655 TCCGCTGAATTTTAACCTAGCCT 60.055 43.478 0.00 0.00 0.00 4.58
3768 8408 1.947456 GTTTGTCTTGGTTCTTCCGCT 59.053 47.619 0.00 0.00 39.52 5.52
3770 8410 5.744666 TTAAGTTTGTCTTGGTTCTTCCG 57.255 39.130 0.00 0.00 39.52 4.30
3825 8465 4.025015 CATGCTATGCTTCAACTGTTCC 57.975 45.455 0.00 0.00 0.00 3.62


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

AutoCloner maintained by Alex Coulton.