Multiple sequence alignment - TraesCS5D01G232100

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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 TraesCS5D01G232100 chr5D 100.000 3011 0 0 1 3011 339094036 339091026 0.000000e+00 5561
1 TraesCS5D01G232100 chr5D 78.837 808 126 26 1688 2466 339086504 339085713 1.250000e-138 503
2 TraesCS5D01G232100 chr5D 81.239 549 76 10 1697 2219 339067460 339066913 4.640000e-113 418
3 TraesCS5D01G232100 chr5A 94.848 1805 71 6 954 2738 439855434 439853632 0.000000e+00 2798
4 TraesCS5D01G232100 chr5A 85.185 513 36 12 420 928 439856014 439855538 9.700000e-135 490
5 TraesCS5D01G232100 chr5A 78.533 750 114 25 1753 2466 439825796 439825058 1.650000e-122 449
6 TraesCS5D01G232100 chr5A 82.000 550 70 15 1697 2219 439773389 439772842 9.910000e-120 440
7 TraesCS5D01G232100 chr5A 84.211 190 27 2 147 336 439856243 439856057 6.630000e-42 182
8 TraesCS5D01G232100 chr5B 96.134 1526 46 1 928 2440 398064932 398063407 0.000000e+00 2479
9 TraesCS5D01G232100 chr5B 84.468 940 101 21 1 928 398065880 398064974 0.000000e+00 885
10 TraesCS5D01G232100 chr5B 82.194 556 73 12 1688 2219 398059705 398059152 3.540000e-124 455
11 TraesCS5D01G232100 chr5B 81.701 541 72 10 1697 2211 397966172 397965633 2.770000e-115 425
12 TraesCS5D01G232100 chr5B 93.750 208 12 1 2803 3009 398062657 398062450 8.110000e-81 311
13 TraesCS5D01G232100 chr5B 83.432 169 13 5 2626 2779 398063366 398063198 3.130000e-30 143
14 TraesCS5D01G232100 chr5B 82.639 144 21 4 2326 2466 398058950 398058808 1.130000e-24 124
15 TraesCS5D01G232100 chr2A 94.947 1029 32 5 1832 2841 236918919 236917892 0.000000e+00 1594


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 TraesCS5D01G232100 chr5D 339091026 339094036 3010 True 5561.000000 5561 100.000000 1 3011 1 chr5D.!!$R3 3010
1 TraesCS5D01G232100 chr5D 339085713 339086504 791 True 503.000000 503 78.837000 1688 2466 1 chr5D.!!$R2 778
2 TraesCS5D01G232100 chr5D 339066913 339067460 547 True 418.000000 418 81.239000 1697 2219 1 chr5D.!!$R1 522
3 TraesCS5D01G232100 chr5A 439853632 439856243 2611 True 1156.666667 2798 88.081333 147 2738 3 chr5A.!!$R3 2591
4 TraesCS5D01G232100 chr5A 439825058 439825796 738 True 449.000000 449 78.533000 1753 2466 1 chr5A.!!$R2 713
5 TraesCS5D01G232100 chr5A 439772842 439773389 547 True 440.000000 440 82.000000 1697 2219 1 chr5A.!!$R1 522
6 TraesCS5D01G232100 chr5B 398058808 398065880 7072 True 732.833333 2479 87.102833 1 3009 6 chr5B.!!$R2 3008
7 TraesCS5D01G232100 chr5B 397965633 397966172 539 True 425.000000 425 81.701000 1697 2211 1 chr5B.!!$R1 514
8 TraesCS5D01G232100 chr2A 236917892 236918919 1027 True 1594.000000 1594 94.947000 1832 2841 1 chr2A.!!$R1 1009

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
92 94 0.163788 CGTTGCTTGCTAGTTGACCG 59.836 55.0 0.0 0.0 0.0 4.79 F
1326 1421 0.035056 ACGATGGCAAAGGGAAGGAG 60.035 55.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1686 1784 0.320421 TGCAGTAGAAGTCGTTGGCC 60.320 55.0 0.00 0.00 0.00 5.36 R
2661 7384 0.035881 CTGAGAAACTGGCCAGCTCA 59.964 55.0 33.06 30.54 34.71 4.26 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
50 51 8.361592 ACTGCCGTGTACTTGTATAATATTTC 57.638 34.615 0.00 0.00 0.00 2.17
66 67 6.597832 AATATTTCCCCATTCAAAACGTGA 57.402 33.333 0.00 0.00 0.00 4.35
67 68 4.519540 ATTTCCCCATTCAAAACGTGAG 57.480 40.909 0.00 0.00 37.61 3.51
69 70 2.500229 TCCCCATTCAAAACGTGAGAC 58.500 47.619 0.00 0.00 37.61 3.36
71 72 2.484264 CCCCATTCAAAACGTGAGACTC 59.516 50.000 0.00 0.00 37.61 3.36
92 94 0.163788 CGTTGCTTGCTAGTTGACCG 59.836 55.000 0.00 0.00 0.00 4.79
101 103 2.624364 TGCTAGTTGACCGAGTTGTGTA 59.376 45.455 0.00 0.00 0.00 2.90
111 113 2.357009 CCGAGTTGTGTATAGCGGTAGT 59.643 50.000 0.00 0.00 34.45 2.73
121 123 1.538047 TAGCGGTAGTTTCGTGGTCT 58.462 50.000 0.00 0.00 0.00 3.85
126 128 2.667724 CGGTAGTTTCGTGGTCTGAGAC 60.668 54.545 3.47 3.47 0.00 3.36
145 147 5.470098 TGAGACTCCACAAATGCTTTACTTC 59.530 40.000 0.00 0.00 0.00 3.01
171 173 8.266392 TGATTGTTTTGCTTGTGATTCTTTTT 57.734 26.923 0.00 0.00 0.00 1.94
196 198 1.139095 GGTAACCGGAGAGCGTCTG 59.861 63.158 9.46 0.00 0.00 3.51
212 214 2.035632 GTCTGGTGGGTCCTAGATGAG 58.964 57.143 0.00 0.00 37.07 2.90
216 218 2.023015 TGGTGGGTCCTAGATGAGTGAT 60.023 50.000 0.00 0.00 37.07 3.06
220 222 3.706594 TGGGTCCTAGATGAGTGATCAAC 59.293 47.826 0.00 0.00 32.86 3.18
262 264 1.072331 GAACTCACCACCACCATCACT 59.928 52.381 0.00 0.00 0.00 3.41
279 281 7.007723 ACCATCACTAACCCAAATTTGTAAGA 58.992 34.615 16.73 5.54 0.00 2.10
280 282 7.039993 ACCATCACTAACCCAAATTTGTAAGAC 60.040 37.037 16.73 0.00 0.00 3.01
287 289 9.280174 CTAACCCAAATTTGTAAGACAGTAGAA 57.720 33.333 16.73 0.00 0.00 2.10
305 307 9.431887 ACAGTAGAATTTTATAAACGAAGAGCA 57.568 29.630 0.00 0.00 0.00 4.26
336 338 1.863454 CCTCGATGAAGGAGCGAAATG 59.137 52.381 0.00 0.00 43.11 2.32
350 352 2.548920 GCGAAATGGGGATAGAGTGAGG 60.549 54.545 0.00 0.00 0.00 3.86
358 360 2.501723 GGGATAGAGTGAGGCAGTGAAA 59.498 50.000 0.00 0.00 0.00 2.69
361 363 2.376808 AGAGTGAGGCAGTGAAATCG 57.623 50.000 0.00 0.00 0.00 3.34
362 364 0.723981 GAGTGAGGCAGTGAAATCGC 59.276 55.000 0.00 0.00 0.00 4.58
363 365 0.322975 AGTGAGGCAGTGAAATCGCT 59.677 50.000 0.00 0.00 37.13 4.93
431 438 7.218773 CGCCTTATTCATTGTTTATCAAGTGTG 59.781 37.037 0.00 0.00 39.55 3.82
440 447 5.185454 TGTTTATCAAGTGTGGAGGCATAG 58.815 41.667 0.00 0.00 0.00 2.23
452 459 2.429610 GGAGGCATAGTCAACGTAGGAA 59.570 50.000 0.00 0.00 0.00 3.36
491 500 2.618442 TGTCCGATGATATGCTTGCA 57.382 45.000 0.00 0.00 0.00 4.08
513 522 1.078426 GGTTAGTCTGCATGCCCGT 60.078 57.895 16.68 0.00 0.00 5.28
528 537 2.097791 TGCCCGTTTGTGTTACAAGAAC 59.902 45.455 0.00 0.00 39.53 3.01
573 583 4.379186 CGAGCATATTTGAATGAGGGCATC 60.379 45.833 0.00 0.00 32.35 3.91
574 584 4.737578 AGCATATTTGAATGAGGGCATCT 58.262 39.130 0.00 0.00 32.35 2.90
594 604 6.295292 GCATCTTTTTGGAGTTTGGGTAATCT 60.295 38.462 0.00 0.00 0.00 2.40
605 615 7.027874 AGTTTGGGTAATCTAATCACTTCCA 57.972 36.000 0.00 0.00 0.00 3.53
683 693 6.377146 ACAATACCTAATCAGCAACCGAAAAT 59.623 34.615 0.00 0.00 0.00 1.82
685 695 5.059404 ACCTAATCAGCAACCGAAAATTG 57.941 39.130 0.00 0.00 0.00 2.32
686 696 4.764823 ACCTAATCAGCAACCGAAAATTGA 59.235 37.500 0.00 0.00 0.00 2.57
690 700 4.377839 TCAGCAACCGAAAATTGAAACA 57.622 36.364 0.00 0.00 0.00 2.83
735 745 8.716646 TTGAAATCGAGATGTCAGCTATAAAA 57.283 30.769 6.13 0.00 36.49 1.52
736 746 8.893219 TGAAATCGAGATGTCAGCTATAAAAT 57.107 30.769 1.99 0.00 30.42 1.82
739 749 9.553064 AAATCGAGATGTCAGCTATAAAATCTT 57.447 29.630 0.00 0.00 0.00 2.40
740 750 7.936950 TCGAGATGTCAGCTATAAAATCTTG 57.063 36.000 0.00 0.00 0.00 3.02
741 751 7.492524 TCGAGATGTCAGCTATAAAATCTTGT 58.507 34.615 0.00 0.00 30.69 3.16
742 752 7.436376 TCGAGATGTCAGCTATAAAATCTTGTG 59.564 37.037 0.00 0.79 30.69 3.33
743 753 7.256756 AGATGTCAGCTATAAAATCTTGTGC 57.743 36.000 0.00 0.00 0.00 4.57
744 754 6.825213 AGATGTCAGCTATAAAATCTTGTGCA 59.175 34.615 0.00 0.00 0.00 4.57
745 755 6.816134 TGTCAGCTATAAAATCTTGTGCAA 57.184 33.333 0.00 0.00 0.00 4.08
746 756 7.395190 TGTCAGCTATAAAATCTTGTGCAAT 57.605 32.000 0.00 0.00 0.00 3.56
747 757 7.252708 TGTCAGCTATAAAATCTTGTGCAATG 58.747 34.615 0.00 0.00 0.00 2.82
748 758 7.094248 TGTCAGCTATAAAATCTTGTGCAATGT 60.094 33.333 0.00 0.00 0.00 2.71
811 828 0.463833 GCCCGACCCATGGAGTTTAG 60.464 60.000 15.22 0.00 0.00 1.85
830 847 9.226345 GAGTTTAGTCTTTTGTTGAATGTTCTG 57.774 33.333 0.00 0.00 0.00 3.02
840 857 4.743151 TGTTGAATGTTCTGTCTCACGTAC 59.257 41.667 0.00 0.00 0.00 3.67
841 858 4.848562 TGAATGTTCTGTCTCACGTACT 57.151 40.909 0.00 0.00 0.00 2.73
842 859 4.546570 TGAATGTTCTGTCTCACGTACTG 58.453 43.478 0.00 0.00 0.00 2.74
843 860 4.037565 TGAATGTTCTGTCTCACGTACTGT 59.962 41.667 0.00 0.00 0.00 3.55
844 861 5.239963 TGAATGTTCTGTCTCACGTACTGTA 59.760 40.000 0.00 0.00 0.00 2.74
910 927 9.399797 TGATGATTTGAGTTACTTGATTGCTAT 57.600 29.630 0.00 0.00 0.00 2.97
918 935 5.416952 AGTTACTTGATTGCTATTGCTGCTT 59.583 36.000 0.00 0.00 40.48 3.91
937 1005 4.083855 TGCTTCTCAATCTGCTTAACAACG 60.084 41.667 0.00 0.00 0.00 4.10
956 1051 3.884169 ACGATGTTGGATGTGTTTTTCG 58.116 40.909 0.00 0.00 0.00 3.46
989 1084 5.106555 CCAAGTCACTACGAATCTGCATTTT 60.107 40.000 0.00 0.00 0.00 1.82
1326 1421 0.035056 ACGATGGCAAAGGGAAGGAG 60.035 55.000 0.00 0.00 0.00 3.69
1365 1460 2.437413 GAAGAATTCGGGCAAGGTTCT 58.563 47.619 0.00 0.00 34.17 3.01
1686 1784 0.664166 GTTCCAGCGGCACAACAATG 60.664 55.000 1.45 0.00 0.00 2.82
2490 7213 6.066032 TCATCATGTCAGTACTATCGGGTTA 58.934 40.000 0.00 0.00 0.00 2.85
2531 7254 9.299465 GCTCTACTAGGGTATTACTACTGATTT 57.701 37.037 0.00 0.00 0.00 2.17
2582 7305 8.286097 GCTCTGATGCCATTACTAATTTTAGTC 58.714 37.037 6.26 0.00 42.66 2.59
2589 7312 7.042992 TGCCATTACTAATTTTAGTCGACATCG 60.043 37.037 19.50 0.00 42.66 3.84
2624 7347 9.765795 AACTATATGAGCTCCATTAGTAAACAC 57.234 33.333 12.15 0.00 36.71 3.32
2661 7384 6.126097 TGTTCTGGGGATTATTCCTGATGAAT 60.126 38.462 3.75 0.00 45.64 2.57
2744 7470 0.746063 CAAACACTGTGCATGTGGGT 59.254 50.000 21.31 6.68 39.52 4.51
2747 7473 0.111061 ACACTGTGCATGTGGGTGAT 59.889 50.000 21.31 3.39 39.52 3.06
2797 7523 7.614494 TCTGCTACTTAACTTATTAACCCGTT 58.386 34.615 0.00 0.00 0.00 4.44
2841 7570 5.743026 TTTTGCGAGAACACACTATTTGA 57.257 34.783 0.00 0.00 0.00 2.69
2842 7571 4.725556 TTGCGAGAACACACTATTTGAC 57.274 40.909 0.00 0.00 0.00 3.18
2843 7572 3.990092 TGCGAGAACACACTATTTGACT 58.010 40.909 0.00 0.00 0.00 3.41
2844 7573 5.128992 TGCGAGAACACACTATTTGACTA 57.871 39.130 0.00 0.00 0.00 2.59
2845 7574 5.534407 TGCGAGAACACACTATTTGACTAA 58.466 37.500 0.00 0.00 0.00 2.24
2846 7575 5.633601 TGCGAGAACACACTATTTGACTAAG 59.366 40.000 0.00 0.00 0.00 2.18
2847 7576 5.444745 GCGAGAACACACTATTTGACTAAGC 60.445 44.000 0.00 0.00 0.00 3.09
2848 7577 5.633601 CGAGAACACACTATTTGACTAAGCA 59.366 40.000 0.00 0.00 0.00 3.91
2849 7578 6.400091 CGAGAACACACTATTTGACTAAGCAC 60.400 42.308 0.00 0.00 0.00 4.40
2850 7579 6.525629 AGAACACACTATTTGACTAAGCACT 58.474 36.000 0.00 0.00 0.00 4.40
2851 7580 7.667557 AGAACACACTATTTGACTAAGCACTA 58.332 34.615 0.00 0.00 0.00 2.74
2852 7581 8.314751 AGAACACACTATTTGACTAAGCACTAT 58.685 33.333 0.00 0.00 0.00 2.12
2853 7582 8.848474 AACACACTATTTGACTAAGCACTATT 57.152 30.769 0.00 0.00 0.00 1.73
2854 7583 9.938280 AACACACTATTTGACTAAGCACTATTA 57.062 29.630 0.00 0.00 0.00 0.98
2855 7584 9.938280 ACACACTATTTGACTAAGCACTATTAA 57.062 29.630 0.00 0.00 0.00 1.40
2880 7609 9.492973 AATTTGAATCTTACCATTTTTGTCTGG 57.507 29.630 0.00 0.00 38.55 3.86
2881 7610 6.588719 TGAATCTTACCATTTTTGTCTGGG 57.411 37.500 0.00 0.00 36.82 4.45
2882 7611 6.074648 TGAATCTTACCATTTTTGTCTGGGT 58.925 36.000 0.00 0.00 36.82 4.51
2883 7612 6.208599 TGAATCTTACCATTTTTGTCTGGGTC 59.791 38.462 0.00 0.00 36.82 4.46
2884 7613 5.055265 TCTTACCATTTTTGTCTGGGTCA 57.945 39.130 0.00 0.00 36.82 4.02
2885 7614 4.825085 TCTTACCATTTTTGTCTGGGTCAC 59.175 41.667 0.00 0.00 36.82 3.67
2886 7615 3.025322 ACCATTTTTGTCTGGGTCACA 57.975 42.857 0.00 0.00 36.82 3.58
2887 7616 3.370104 ACCATTTTTGTCTGGGTCACAA 58.630 40.909 0.00 0.00 36.82 3.33
2888 7617 3.772025 ACCATTTTTGTCTGGGTCACAAA 59.228 39.130 0.00 0.00 41.05 2.83
2889 7618 4.408596 ACCATTTTTGTCTGGGTCACAAAT 59.591 37.500 0.00 0.00 42.04 2.32
2890 7619 4.751098 CCATTTTTGTCTGGGTCACAAATG 59.249 41.667 9.24 9.24 42.04 2.32
2891 7620 4.399004 TTTTTGTCTGGGTCACAAATGG 57.601 40.909 0.00 0.00 42.04 3.16
2892 7621 2.746279 TTGTCTGGGTCACAAATGGT 57.254 45.000 0.00 0.00 30.67 3.55
2893 7622 2.746279 TGTCTGGGTCACAAATGGTT 57.254 45.000 0.00 0.00 0.00 3.67
2894 7623 3.866703 TGTCTGGGTCACAAATGGTTA 57.133 42.857 0.00 0.00 0.00 2.85
2895 7624 4.380843 TGTCTGGGTCACAAATGGTTAT 57.619 40.909 0.00 0.00 0.00 1.89
2896 7625 5.506730 TGTCTGGGTCACAAATGGTTATA 57.493 39.130 0.00 0.00 0.00 0.98
2897 7626 5.250200 TGTCTGGGTCACAAATGGTTATAC 58.750 41.667 0.00 0.00 0.00 1.47
2898 7627 5.013704 TGTCTGGGTCACAAATGGTTATACT 59.986 40.000 0.00 0.00 0.00 2.12
2899 7628 6.213802 TGTCTGGGTCACAAATGGTTATACTA 59.786 38.462 0.00 0.00 0.00 1.82
2900 7629 7.092623 TGTCTGGGTCACAAATGGTTATACTAT 60.093 37.037 0.00 0.00 0.00 2.12
2901 7630 7.773690 GTCTGGGTCACAAATGGTTATACTATT 59.226 37.037 0.00 0.00 30.15 1.73
2902 7631 7.773224 TCTGGGTCACAAATGGTTATACTATTG 59.227 37.037 0.00 0.00 29.42 1.90
2903 7632 6.831353 TGGGTCACAAATGGTTATACTATTGG 59.169 38.462 0.00 0.00 29.42 3.16
2904 7633 7.057894 GGGTCACAAATGGTTATACTATTGGA 58.942 38.462 0.00 0.00 29.42 3.53
2905 7634 7.724061 GGGTCACAAATGGTTATACTATTGGAT 59.276 37.037 0.00 0.00 29.42 3.41
2906 7635 8.567948 GGTCACAAATGGTTATACTATTGGATG 58.432 37.037 0.00 0.00 29.42 3.51
2907 7636 9.337396 GTCACAAATGGTTATACTATTGGATGA 57.663 33.333 0.00 0.00 29.42 2.92
2908 7637 9.913310 TCACAAATGGTTATACTATTGGATGAA 57.087 29.630 0.00 0.00 29.42 2.57
2910 7639 8.850156 ACAAATGGTTATACTATTGGATGAAGC 58.150 33.333 0.00 0.00 29.42 3.86
2911 7640 9.071276 CAAATGGTTATACTATTGGATGAAGCT 57.929 33.333 0.00 0.00 29.42 3.74
2912 7641 9.646522 AAATGGTTATACTATTGGATGAAGCTT 57.353 29.630 0.00 0.00 29.42 3.74
2913 7642 9.646522 AATGGTTATACTATTGGATGAAGCTTT 57.353 29.630 0.00 0.00 27.71 3.51
2915 7644 9.555727 TGGTTATACTATTGGATGAAGCTTTAC 57.444 33.333 0.00 0.00 0.00 2.01
2916 7645 9.555727 GGTTATACTATTGGATGAAGCTTTACA 57.444 33.333 0.00 0.00 0.00 2.41
2920 7649 7.944729 ACTATTGGATGAAGCTTTACAATGT 57.055 32.000 15.93 10.36 31.71 2.71
2921 7650 7.765307 ACTATTGGATGAAGCTTTACAATGTG 58.235 34.615 15.93 11.67 31.71 3.21
2922 7651 6.594788 ATTGGATGAAGCTTTACAATGTGT 57.405 33.333 7.65 0.00 0.00 3.72
2923 7652 7.701539 ATTGGATGAAGCTTTACAATGTGTA 57.298 32.000 7.65 0.00 0.00 2.90
2924 7653 7.701539 TTGGATGAAGCTTTACAATGTGTAT 57.298 32.000 0.00 0.00 32.20 2.29
2925 7654 7.701539 TGGATGAAGCTTTACAATGTGTATT 57.298 32.000 0.00 0.00 32.20 1.89
2926 7655 8.800370 TGGATGAAGCTTTACAATGTGTATTA 57.200 30.769 0.00 0.00 32.20 0.98
2927 7656 8.673711 TGGATGAAGCTTTACAATGTGTATTAC 58.326 33.333 0.00 0.00 32.20 1.89
2928 7657 8.673711 GGATGAAGCTTTACAATGTGTATTACA 58.326 33.333 0.00 0.00 44.87 2.41
2942 7671 7.030075 TGTGTATTACATAGCGCTACTAACA 57.970 36.000 21.49 14.75 33.42 2.41
2943 7672 7.482474 TGTGTATTACATAGCGCTACTAACAA 58.518 34.615 21.49 9.98 33.42 2.83
2944 7673 7.433131 TGTGTATTACATAGCGCTACTAACAAC 59.567 37.037 21.49 17.59 33.42 3.32
2945 7674 6.919662 TGTATTACATAGCGCTACTAACAACC 59.080 38.462 21.49 5.39 33.57 3.77
2946 7675 5.587388 TTACATAGCGCTACTAACAACCT 57.413 39.130 21.49 0.00 33.57 3.50
2947 7676 4.467198 ACATAGCGCTACTAACAACCTT 57.533 40.909 21.49 0.00 33.57 3.50
2948 7677 4.181578 ACATAGCGCTACTAACAACCTTG 58.818 43.478 21.49 12.32 33.57 3.61
2949 7678 4.081862 ACATAGCGCTACTAACAACCTTGA 60.082 41.667 21.49 0.00 33.57 3.02
2950 7679 2.960819 AGCGCTACTAACAACCTTGAG 58.039 47.619 8.99 0.00 0.00 3.02
2951 7680 2.299297 AGCGCTACTAACAACCTTGAGT 59.701 45.455 8.99 0.00 0.00 3.41
2952 7681 3.064931 GCGCTACTAACAACCTTGAGTT 58.935 45.455 0.00 0.00 40.16 3.01
2953 7682 4.021719 AGCGCTACTAACAACCTTGAGTTA 60.022 41.667 8.99 0.00 36.18 2.24
2954 7683 4.868734 GCGCTACTAACAACCTTGAGTTAT 59.131 41.667 0.00 0.00 36.18 1.89
2955 7684 5.350640 GCGCTACTAACAACCTTGAGTTATT 59.649 40.000 0.00 0.00 36.18 1.40
2956 7685 6.128363 GCGCTACTAACAACCTTGAGTTATTT 60.128 38.462 0.00 0.00 36.18 1.40
2957 7686 7.453838 CGCTACTAACAACCTTGAGTTATTTC 58.546 38.462 0.00 0.00 36.18 2.17
2958 7687 7.117236 CGCTACTAACAACCTTGAGTTATTTCA 59.883 37.037 0.00 0.00 36.18 2.69
2959 7688 8.228464 GCTACTAACAACCTTGAGTTATTTCAC 58.772 37.037 0.00 0.00 36.18 3.18
2960 7689 9.268268 CTACTAACAACCTTGAGTTATTTCACA 57.732 33.333 0.00 0.00 36.18 3.58
2961 7690 8.691661 ACTAACAACCTTGAGTTATTTCACAT 57.308 30.769 0.00 0.00 36.18 3.21
2962 7691 9.131791 ACTAACAACCTTGAGTTATTTCACATT 57.868 29.630 0.00 0.00 36.18 2.71
3007 7736 8.997301 ATATAAAAGGAGGAGAGAATATGGGT 57.003 34.615 0.00 0.00 0.00 4.51
3008 7737 7.713704 ATAAAAGGAGGAGAGAATATGGGTT 57.286 36.000 0.00 0.00 0.00 4.11
3009 7738 8.814448 ATAAAAGGAGGAGAGAATATGGGTTA 57.186 34.615 0.00 0.00 0.00 2.85
3010 7739 6.502074 AAAGGAGGAGAGAATATGGGTTAC 57.498 41.667 0.00 0.00 0.00 2.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 1.086696 TACACGGCAGTACGTACTCC 58.913 55.000 25.10 24.09 46.75 3.85
50 51 2.484264 GAGTCTCACGTTTTGAATGGGG 59.516 50.000 0.00 0.00 32.21 4.96
69 70 0.179240 CAACTAGCAAGCAACGCGAG 60.179 55.000 15.93 5.94 38.01 5.03
71 72 0.451135 GTCAACTAGCAAGCAACGCG 60.451 55.000 3.53 3.53 0.00 6.01
92 94 4.498323 CGAAACTACCGCTATACACAACTC 59.502 45.833 0.00 0.00 0.00 3.01
101 103 2.097825 AGACCACGAAACTACCGCTAT 58.902 47.619 0.00 0.00 0.00 2.97
111 113 1.340248 GTGGAGTCTCAGACCACGAAA 59.660 52.381 0.00 0.00 43.21 3.46
121 123 4.973168 AGTAAAGCATTTGTGGAGTCTCA 58.027 39.130 1.47 0.00 39.63 3.27
126 128 5.947228 TCAGAAGTAAAGCATTTGTGGAG 57.053 39.130 0.00 0.00 39.63 3.86
134 136 6.752168 AGCAAAACAATCAGAAGTAAAGCAT 58.248 32.000 0.00 0.00 0.00 3.79
145 147 7.473027 AAAGAATCACAAGCAAAACAATCAG 57.527 32.000 0.00 0.00 0.00 2.90
174 176 0.393820 ACGCTCTCCGGTTACCAAAA 59.606 50.000 0.00 0.00 42.52 2.44
175 177 0.037975 GACGCTCTCCGGTTACCAAA 60.038 55.000 0.00 0.00 42.52 3.28
177 179 1.303888 AGACGCTCTCCGGTTACCA 60.304 57.895 0.00 0.00 42.52 3.25
178 180 1.139095 CAGACGCTCTCCGGTTACC 59.861 63.158 0.00 0.00 42.52 2.85
179 181 1.139095 CCAGACGCTCTCCGGTTAC 59.861 63.158 0.00 0.00 42.52 2.50
180 182 1.303888 ACCAGACGCTCTCCGGTTA 60.304 57.895 0.00 0.00 42.52 2.85
186 188 2.574399 GACCCACCAGACGCTCTC 59.426 66.667 0.00 0.00 0.00 3.20
196 198 2.160721 TCACTCATCTAGGACCCACC 57.839 55.000 0.00 0.00 39.35 4.61
212 214 4.818546 CCACTCTATCCCAATGTTGATCAC 59.181 45.833 0.00 0.00 0.00 3.06
216 218 2.509548 CCCCACTCTATCCCAATGTTGA 59.490 50.000 0.00 0.00 0.00 3.18
220 222 0.846015 TGCCCCACTCTATCCCAATG 59.154 55.000 0.00 0.00 0.00 2.82
262 264 9.802039 ATTCTACTGTCTTACAAATTTGGGTTA 57.198 29.630 21.74 3.19 0.00 2.85
279 281 9.431887 TGCTCTTCGTTTATAAAATTCTACTGT 57.568 29.630 0.00 0.00 0.00 3.55
287 289 7.201732 CCACCAGATGCTCTTCGTTTATAAAAT 60.202 37.037 0.00 0.00 0.00 1.82
293 295 2.354704 CCCACCAGATGCTCTTCGTTTA 60.355 50.000 0.00 0.00 0.00 2.01
305 307 0.032117 TCATCGAGGACCCACCAGAT 60.032 55.000 0.00 0.00 42.04 2.90
336 338 0.755686 CACTGCCTCACTCTATCCCC 59.244 60.000 0.00 0.00 0.00 4.81
365 367 4.904590 TTGGGTTGGTGGTGGCGG 62.905 66.667 0.00 0.00 0.00 6.13
366 368 1.753368 AATTTGGGTTGGTGGTGGCG 61.753 55.000 0.00 0.00 0.00 5.69
367 369 0.472044 AAATTTGGGTTGGTGGTGGC 59.528 50.000 0.00 0.00 0.00 5.01
401 408 9.950680 CTTGATAAACAATGAATAAGGCGTATT 57.049 29.630 5.34 5.34 37.88 1.89
405 412 7.218773 CACACTTGATAAACAATGAATAAGGCG 59.781 37.037 0.00 0.00 37.88 5.52
408 415 9.778993 CTCCACACTTGATAAACAATGAATAAG 57.221 33.333 0.00 0.00 37.88 1.73
413 420 4.458989 GCCTCCACACTTGATAAACAATGA 59.541 41.667 0.00 0.00 37.88 2.57
415 422 4.406456 TGCCTCCACACTTGATAAACAAT 58.594 39.130 0.00 0.00 37.88 2.71
431 438 2.029623 TCCTACGTTGACTATGCCTCC 58.970 52.381 0.00 0.00 0.00 4.30
440 447 4.260375 GCACATGATGATTCCTACGTTGAC 60.260 45.833 0.00 0.00 0.00 3.18
452 459 3.512329 ACATTTGGTGTGCACATGATGAT 59.488 39.130 24.69 10.90 40.28 2.45
491 500 0.034089 GGCATGCAGACTAACCCCTT 60.034 55.000 21.36 0.00 0.00 3.95
513 522 8.740906 TGTTAGATTTGGTTCTTGTAACACAAA 58.259 29.630 0.00 0.00 37.69 2.83
528 537 5.294306 TCGCTCTAAGCAATGTTAGATTTGG 59.706 40.000 0.00 0.00 42.58 3.28
573 583 8.802267 TGATTAGATTACCCAAACTCCAAAAAG 58.198 33.333 0.00 0.00 0.00 2.27
574 584 8.581578 GTGATTAGATTACCCAAACTCCAAAAA 58.418 33.333 0.00 0.00 0.00 1.94
605 615 7.606073 GGTTAACCATGCCATGTTTTAGAAAAT 59.394 33.333 20.12 0.00 35.64 1.82
683 693 6.403866 AGTTGAACCATATTGCTGTTTCAA 57.596 33.333 0.00 0.00 0.00 2.69
685 695 7.377766 TCTAGTTGAACCATATTGCTGTTTC 57.622 36.000 0.00 0.00 0.00 2.78
686 696 7.944729 ATCTAGTTGAACCATATTGCTGTTT 57.055 32.000 0.00 0.00 0.00 2.83
723 733 7.253422 ACATTGCACAAGATTTTATAGCTGAC 58.747 34.615 0.00 0.00 0.00 3.51
735 745 7.554118 AGCTTACTACATTACATTGCACAAGAT 59.446 33.333 0.00 0.00 0.00 2.40
736 746 6.878923 AGCTTACTACATTACATTGCACAAGA 59.121 34.615 0.00 0.00 0.00 3.02
739 749 7.447374 AAAGCTTACTACATTACATTGCACA 57.553 32.000 0.00 0.00 0.00 4.57
740 750 8.742554 AAAAAGCTTACTACATTACATTGCAC 57.257 30.769 0.00 0.00 0.00 4.57
794 808 1.831736 AGACTAAACTCCATGGGTCGG 59.168 52.381 13.02 2.73 0.00 4.79
797 811 5.061721 ACAAAAGACTAAACTCCATGGGT 57.938 39.130 13.02 5.94 0.00 4.51
811 828 6.688813 GTGAGACAGAACATTCAACAAAAGAC 59.311 38.462 0.00 0.00 0.00 3.01
830 847 8.851960 TGAATATGAAATACAGTACGTGAGAC 57.148 34.615 0.00 0.00 0.00 3.36
868 885 7.888546 TCAAATCATCAGCCATCTATCATGATT 59.111 33.333 14.65 0.00 40.87 2.57
877 894 5.999044 AGTAACTCAAATCATCAGCCATCT 58.001 37.500 0.00 0.00 0.00 2.90
910 927 2.195741 AGCAGATTGAGAAGCAGCAA 57.804 45.000 0.00 0.00 31.22 3.91
918 935 5.237815 ACATCGTTGTTAAGCAGATTGAGA 58.762 37.500 0.00 0.00 29.55 3.27
937 1005 5.518487 ACAAACGAAAAACACATCCAACATC 59.482 36.000 0.00 0.00 0.00 3.06
956 1051 4.362279 TCGTAGTGACTTGGTGTACAAAC 58.638 43.478 0.00 0.00 38.91 2.93
1071 1166 0.392336 AAACCGCACATGCCATTGTT 59.608 45.000 0.00 0.00 37.91 2.83
1074 1169 1.374505 GCAAACCGCACATGCCATT 60.375 52.632 0.00 0.00 41.79 3.16
1119 1214 4.761739 TCACAATTCTCAGGTTTCCATGAC 59.238 41.667 0.00 0.00 0.00 3.06
1305 1400 0.322456 CCTTCCCTTTGCCATCGTCA 60.322 55.000 0.00 0.00 0.00 4.35
1308 1403 1.379642 GCTCCTTCCCTTTGCCATCG 61.380 60.000 0.00 0.00 0.00 3.84
1365 1460 4.471908 ATCATCGTGCCGCTGCCA 62.472 61.111 0.00 0.00 36.33 4.92
1389 1484 0.379669 CGATCATCAGCCTGCAAACC 59.620 55.000 0.00 0.00 0.00 3.27
1431 1526 3.561310 TGATATGATCGCAGTTTTCAGGC 59.439 43.478 0.00 0.00 0.00 4.85
1686 1784 0.320421 TGCAGTAGAAGTCGTTGGCC 60.320 55.000 0.00 0.00 0.00 5.36
2531 7254 4.745125 GCACGAGCTAATGAATGCTAACTA 59.255 41.667 0.00 0.00 39.91 2.24
2582 7305 0.670546 AGTTGCCACTTCCGATGTCG 60.671 55.000 0.00 0.00 39.44 4.35
2589 7312 4.061596 GAGCTCATATAGTTGCCACTTCC 58.938 47.826 9.40 0.00 34.06 3.46
2661 7384 0.035881 CTGAGAAACTGGCCAGCTCA 59.964 55.000 33.06 30.54 34.71 4.26
2787 7513 7.825761 AGTTAAGTAGCATGTAAACGGGTTAAT 59.174 33.333 0.00 0.00 0.00 1.40
2854 7583 9.492973 CCAGACAAAAATGGTAAGATTCAAATT 57.507 29.630 0.00 0.00 0.00 1.82
2855 7584 8.096414 CCCAGACAAAAATGGTAAGATTCAAAT 58.904 33.333 0.00 0.00 34.58 2.32
2856 7585 7.070571 ACCCAGACAAAAATGGTAAGATTCAAA 59.929 33.333 0.00 0.00 34.58 2.69
2857 7586 6.553100 ACCCAGACAAAAATGGTAAGATTCAA 59.447 34.615 0.00 0.00 34.58 2.69
2858 7587 6.074648 ACCCAGACAAAAATGGTAAGATTCA 58.925 36.000 0.00 0.00 34.58 2.57
2859 7588 6.208599 TGACCCAGACAAAAATGGTAAGATTC 59.791 38.462 0.00 0.00 34.58 2.52
2860 7589 6.015434 GTGACCCAGACAAAAATGGTAAGATT 60.015 38.462 0.00 0.00 34.58 2.40
2861 7590 5.476945 GTGACCCAGACAAAAATGGTAAGAT 59.523 40.000 0.00 0.00 34.58 2.40
2862 7591 4.825085 GTGACCCAGACAAAAATGGTAAGA 59.175 41.667 0.00 0.00 34.58 2.10
2863 7592 4.582656 TGTGACCCAGACAAAAATGGTAAG 59.417 41.667 0.00 0.00 34.58 2.34
2864 7593 4.537751 TGTGACCCAGACAAAAATGGTAA 58.462 39.130 0.00 0.00 34.58 2.85
2865 7594 4.171878 TGTGACCCAGACAAAAATGGTA 57.828 40.909 0.00 0.00 34.58 3.25
2866 7595 3.025322 TGTGACCCAGACAAAAATGGT 57.975 42.857 0.00 0.00 34.58 3.55
2867 7596 4.399004 TTTGTGACCCAGACAAAAATGG 57.601 40.909 0.00 0.00 39.71 3.16
2868 7597 4.751098 CCATTTGTGACCCAGACAAAAATG 59.249 41.667 12.70 12.70 44.32 2.32
2869 7598 4.408596 ACCATTTGTGACCCAGACAAAAAT 59.591 37.500 0.00 0.00 44.32 1.82
2870 7599 3.772025 ACCATTTGTGACCCAGACAAAAA 59.228 39.130 0.00 0.00 44.32 1.94
2871 7600 3.370104 ACCATTTGTGACCCAGACAAAA 58.630 40.909 0.00 0.00 44.32 2.44
2872 7601 3.025322 ACCATTTGTGACCCAGACAAA 57.975 42.857 0.00 0.00 45.01 2.83
2873 7602 2.746279 ACCATTTGTGACCCAGACAA 57.254 45.000 0.00 0.00 0.00 3.18
2874 7603 2.746279 AACCATTTGTGACCCAGACA 57.254 45.000 0.00 0.00 0.00 3.41
2875 7604 5.497474 AGTATAACCATTTGTGACCCAGAC 58.503 41.667 0.00 0.00 0.00 3.51
2876 7605 5.772393 AGTATAACCATTTGTGACCCAGA 57.228 39.130 0.00 0.00 0.00 3.86
2877 7606 7.013274 CCAATAGTATAACCATTTGTGACCCAG 59.987 40.741 0.00 0.00 0.00 4.45
2878 7607 6.831353 CCAATAGTATAACCATTTGTGACCCA 59.169 38.462 0.00 0.00 0.00 4.51
2879 7608 7.057894 TCCAATAGTATAACCATTTGTGACCC 58.942 38.462 0.00 0.00 0.00 4.46
2880 7609 8.567948 CATCCAATAGTATAACCATTTGTGACC 58.432 37.037 0.00 0.00 0.00 4.02
2881 7610 9.337396 TCATCCAATAGTATAACCATTTGTGAC 57.663 33.333 0.00 0.00 0.00 3.67
2882 7611 9.913310 TTCATCCAATAGTATAACCATTTGTGA 57.087 29.630 0.00 0.00 0.00 3.58
2884 7613 8.850156 GCTTCATCCAATAGTATAACCATTTGT 58.150 33.333 0.00 0.00 0.00 2.83
2885 7614 9.071276 AGCTTCATCCAATAGTATAACCATTTG 57.929 33.333 0.00 0.00 0.00 2.32
2886 7615 9.646522 AAGCTTCATCCAATAGTATAACCATTT 57.353 29.630 0.00 0.00 0.00 2.32
2887 7616 9.646522 AAAGCTTCATCCAATAGTATAACCATT 57.353 29.630 0.00 0.00 0.00 3.16
2889 7618 9.555727 GTAAAGCTTCATCCAATAGTATAACCA 57.444 33.333 0.00 0.00 0.00 3.67
2890 7619 9.555727 TGTAAAGCTTCATCCAATAGTATAACC 57.444 33.333 0.00 0.00 0.00 2.85
2894 7623 9.632638 ACATTGTAAAGCTTCATCCAATAGTAT 57.367 29.630 0.00 0.00 0.00 2.12
2895 7624 8.892723 CACATTGTAAAGCTTCATCCAATAGTA 58.107 33.333 0.00 0.00 0.00 1.82
2896 7625 7.394359 ACACATTGTAAAGCTTCATCCAATAGT 59.606 33.333 0.00 5.82 0.00 2.12
2897 7626 7.765307 ACACATTGTAAAGCTTCATCCAATAG 58.235 34.615 0.00 5.28 0.00 1.73
2898 7627 7.701539 ACACATTGTAAAGCTTCATCCAATA 57.298 32.000 0.00 0.00 0.00 1.90
2899 7628 6.594788 ACACATTGTAAAGCTTCATCCAAT 57.405 33.333 0.00 3.39 0.00 3.16
2900 7629 7.701539 ATACACATTGTAAAGCTTCATCCAA 57.298 32.000 0.00 0.93 36.31 3.53
2901 7630 7.701539 AATACACATTGTAAAGCTTCATCCA 57.298 32.000 0.00 0.00 36.31 3.41
2902 7631 8.673711 TGTAATACACATTGTAAAGCTTCATCC 58.326 33.333 0.00 0.00 36.31 3.51
2906 7635 9.651718 GCTATGTAATACACATTGTAAAGCTTC 57.348 33.333 0.00 0.00 46.01 3.86
2907 7636 8.335356 CGCTATGTAATACACATTGTAAAGCTT 58.665 33.333 0.00 0.00 46.01 3.74
2908 7637 7.518370 GCGCTATGTAATACACATTGTAAAGCT 60.518 37.037 0.00 0.00 46.01 3.74
2909 7638 6.573725 GCGCTATGTAATACACATTGTAAAGC 59.426 38.462 0.00 0.00 46.01 3.51
2910 7639 7.851508 AGCGCTATGTAATACACATTGTAAAG 58.148 34.615 8.99 0.00 46.01 1.85
2911 7640 7.780008 AGCGCTATGTAATACACATTGTAAA 57.220 32.000 8.99 0.00 46.01 2.01
2912 7641 8.139350 AGTAGCGCTATGTAATACACATTGTAA 58.861 33.333 21.96 0.00 46.01 2.41
2913 7642 7.654568 AGTAGCGCTATGTAATACACATTGTA 58.345 34.615 21.96 0.00 46.01 2.41
2914 7643 6.513180 AGTAGCGCTATGTAATACACATTGT 58.487 36.000 21.96 0.00 46.01 2.71
2915 7644 8.425491 GTTAGTAGCGCTATGTAATACACATTG 58.575 37.037 21.96 0.00 46.01 2.82
2916 7645 8.139350 TGTTAGTAGCGCTATGTAATACACATT 58.861 33.333 21.96 0.00 46.01 2.71
2918 7647 7.030075 TGTTAGTAGCGCTATGTAATACACA 57.970 36.000 21.96 12.72 42.69 3.72
2919 7648 7.096312 GGTTGTTAGTAGCGCTATGTAATACAC 60.096 40.741 21.96 16.18 0.00 2.90
2920 7649 6.919662 GGTTGTTAGTAGCGCTATGTAATACA 59.080 38.462 21.96 15.19 0.00 2.29
2921 7650 7.144000 AGGTTGTTAGTAGCGCTATGTAATAC 58.856 38.462 21.96 19.16 0.00 1.89
2922 7651 7.281040 AGGTTGTTAGTAGCGCTATGTAATA 57.719 36.000 21.96 15.85 0.00 0.98
2923 7652 6.158023 AGGTTGTTAGTAGCGCTATGTAAT 57.842 37.500 21.96 0.97 0.00 1.89
2924 7653 5.587388 AGGTTGTTAGTAGCGCTATGTAA 57.413 39.130 21.96 17.63 0.00 2.41
2925 7654 5.125900 TCAAGGTTGTTAGTAGCGCTATGTA 59.874 40.000 21.96 12.59 0.00 2.29
2926 7655 4.081862 TCAAGGTTGTTAGTAGCGCTATGT 60.082 41.667 21.96 13.65 0.00 2.29
2927 7656 4.430007 TCAAGGTTGTTAGTAGCGCTATG 58.570 43.478 21.96 10.56 0.00 2.23
2928 7657 4.159879 ACTCAAGGTTGTTAGTAGCGCTAT 59.840 41.667 21.96 12.03 0.00 2.97
2929 7658 3.508793 ACTCAAGGTTGTTAGTAGCGCTA 59.491 43.478 14.45 14.45 0.00 4.26
2930 7659 2.299297 ACTCAAGGTTGTTAGTAGCGCT 59.701 45.455 17.26 17.26 0.00 5.92
2931 7660 2.685100 ACTCAAGGTTGTTAGTAGCGC 58.315 47.619 0.00 0.00 0.00 5.92
2932 7661 6.963049 AATAACTCAAGGTTGTTAGTAGCG 57.037 37.500 0.00 0.00 37.46 4.26
2933 7662 8.228464 GTGAAATAACTCAAGGTTGTTAGTAGC 58.772 37.037 0.00 0.00 38.09 3.58
2934 7663 9.268268 TGTGAAATAACTCAAGGTTGTTAGTAG 57.732 33.333 0.00 0.00 38.09 2.57
2935 7664 9.787435 ATGTGAAATAACTCAAGGTTGTTAGTA 57.213 29.630 0.00 0.00 38.09 1.82
2936 7665 8.691661 ATGTGAAATAACTCAAGGTTGTTAGT 57.308 30.769 0.00 0.00 38.09 2.24
2981 7710 9.411848 ACCCATATTCTCTCCTCCTTTTATATT 57.588 33.333 0.00 0.00 0.00 1.28
2982 7711 8.997301 ACCCATATTCTCTCCTCCTTTTATAT 57.003 34.615 0.00 0.00 0.00 0.86
2983 7712 8.814448 AACCCATATTCTCTCCTCCTTTTATA 57.186 34.615 0.00 0.00 0.00 0.98
2984 7713 7.713704 AACCCATATTCTCTCCTCCTTTTAT 57.286 36.000 0.00 0.00 0.00 1.40
2985 7714 8.030913 GTAACCCATATTCTCTCCTCCTTTTA 57.969 38.462 0.00 0.00 0.00 1.52
2986 7715 6.901300 GTAACCCATATTCTCTCCTCCTTTT 58.099 40.000 0.00 0.00 0.00 2.27
2987 7716 6.502074 GTAACCCATATTCTCTCCTCCTTT 57.498 41.667 0.00 0.00 0.00 3.11


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

AutoCloner maintained by Alex Coulton.