Multiple sequence alignment - TraesCS6A01G112500

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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 TraesCS6A01G112500 chr6A 100.000 5078 0 0 1 5078 81852385 81847308 0.000000e+00 9378.0
1 TraesCS6A01G112500 chr6A 97.619 546 13 0 1 546 64566991 64566446 0.000000e+00 937.0
2 TraesCS6A01G112500 chr6D 92.642 4050 167 35 606 4589 65908669 65912653 0.000000e+00 5707.0
3 TraesCS6A01G112500 chr6D 95.806 453 11 4 4591 5035 65912782 65913234 0.000000e+00 725.0
4 TraesCS6A01G112500 chr6D 82.667 75 12 1 3214 3287 194175718 194175792 1.180000e-06 65.8
5 TraesCS6A01G112500 chr6B 91.500 2894 140 35 582 3428 141016788 141019622 0.000000e+00 3884.0
6 TraesCS6A01G112500 chr6B 93.260 1647 45 12 3421 5035 141020408 141022020 0.000000e+00 2366.0
7 TraesCS6A01G112500 chr6B 97.628 548 13 0 1 548 557937992 557938539 0.000000e+00 941.0
8 TraesCS6A01G112500 chr6B 84.507 71 8 3 3219 3287 387077735 387077804 3.280000e-07 67.6
9 TraesCS6A01G112500 chr3B 90.390 1051 46 10 917 1954 784741203 784742211 0.000000e+00 1330.0
10 TraesCS6A01G112500 chr3B 93.451 794 32 4 917 1696 784731434 784732221 0.000000e+00 1160.0
11 TraesCS6A01G112500 chr3B 95.082 549 23 3 1 545 59468508 59469056 0.000000e+00 861.0
12 TraesCS6A01G112500 chr3B 93.385 257 8 6 1698 1954 784732195 784732442 6.210000e-99 372.0
13 TraesCS6A01G112500 chr3B 83.810 105 15 2 3234 3336 63412981 63412877 1.160000e-16 99.0
14 TraesCS6A01G112500 chr4A 97.985 546 11 0 1 546 36020705 36020160 0.000000e+00 948.0
15 TraesCS6A01G112500 chr2B 97.441 547 11 1 1 547 392862987 392862444 0.000000e+00 929.0
16 TraesCS6A01G112500 chr5A 97.253 546 15 0 1 546 438852666 438852121 0.000000e+00 926.0
17 TraesCS6A01G112500 chr7B 96.886 546 17 0 1 546 742588237 742588782 0.000000e+00 915.0
18 TraesCS6A01G112500 chr1D 94.536 549 26 2 1 545 48875630 48875082 0.000000e+00 845.0
19 TraesCS6A01G112500 chr7D 93.606 563 27 5 1 557 611342239 611341680 0.000000e+00 832.0
20 TraesCS6A01G112500 chr3A 95.612 433 17 2 2018 2450 735590756 735591186 0.000000e+00 693.0


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 TraesCS6A01G112500 chr6A 81847308 81852385 5077 True 9378 9378 100.000 1 5078 1 chr6A.!!$R2 5077
1 TraesCS6A01G112500 chr6A 64566446 64566991 545 True 937 937 97.619 1 546 1 chr6A.!!$R1 545
2 TraesCS6A01G112500 chr6D 65908669 65913234 4565 False 3216 5707 94.224 606 5035 2 chr6D.!!$F2 4429
3 TraesCS6A01G112500 chr6B 141016788 141022020 5232 False 3125 3884 92.380 582 5035 2 chr6B.!!$F3 4453
4 TraesCS6A01G112500 chr6B 557937992 557938539 547 False 941 941 97.628 1 548 1 chr6B.!!$F2 547
5 TraesCS6A01G112500 chr3B 784741203 784742211 1008 False 1330 1330 90.390 917 1954 1 chr3B.!!$F2 1037
6 TraesCS6A01G112500 chr3B 59468508 59469056 548 False 861 861 95.082 1 545 1 chr3B.!!$F1 544
7 TraesCS6A01G112500 chr3B 784731434 784732442 1008 False 766 1160 93.418 917 1954 2 chr3B.!!$F3 1037
8 TraesCS6A01G112500 chr4A 36020160 36020705 545 True 948 948 97.985 1 546 1 chr4A.!!$R1 545
9 TraesCS6A01G112500 chr2B 392862444 392862987 543 True 929 929 97.441 1 547 1 chr2B.!!$R1 546
10 TraesCS6A01G112500 chr5A 438852121 438852666 545 True 926 926 97.253 1 546 1 chr5A.!!$R1 545
11 TraesCS6A01G112500 chr7B 742588237 742588782 545 False 915 915 96.886 1 546 1 chr7B.!!$F1 545
12 TraesCS6A01G112500 chr1D 48875082 48875630 548 True 845 845 94.536 1 545 1 chr1D.!!$R1 544
13 TraesCS6A01G112500 chr7D 611341680 611342239 559 True 832 832 93.606 1 557 1 chr7D.!!$R1 556

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
558 565 1.000717 ACGCTCCCAACAAAATTTCGG 60.001 47.619 0.00 0.00 0.00 4.30 F
1804 1859 0.874390 TTGCACTTCAGTTCATCGCC 59.126 50.000 0.00 0.00 0.00 5.54 F
1954 2009 1.302366 TGGCATGCTTAATCTCTGCG 58.698 50.000 18.92 0.00 33.69 5.18 F
3044 3123 0.111253 AAAGTCCTCCAAGGCCTGTG 59.889 55.000 5.69 7.02 34.61 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2537 2611 1.064240 ACAGATGAGATGGCATGGCAA 60.064 47.619 27.04 10.17 0.00 4.52 R
2951 3029 0.658536 GAACAGAAGCACGCAACTGC 60.659 55.000 12.86 0.00 37.44 4.40 R
3472 4345 0.751643 GCAACAGGGCCCGAATGTAT 60.752 55.000 18.44 3.97 0.00 2.29 R
5043 6074 0.512952 CACGCAGACAGTAAGGCAAC 59.487 55.000 0.00 0.00 0.00 4.17 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
45 46 5.981174 TGTGCAGAGATCATATTCAACTCA 58.019 37.500 0.00 0.00 0.00 3.41
53 54 9.842775 AGAGATCATATTCAACTCAATTTGCTA 57.157 29.630 0.00 0.00 0.00 3.49
243 244 4.285260 AGCTTTTCTGGCCAATTTCTTCAT 59.715 37.500 7.01 0.00 0.00 2.57
355 356 2.584391 GGAGGAAGTGTGGGCGAGT 61.584 63.158 0.00 0.00 0.00 4.18
367 368 2.742372 GCGAGTTGTGCGTGGGAT 60.742 61.111 0.00 0.00 0.00 3.85
414 421 1.566231 AGCGATGGGGGAGATTTTCTT 59.434 47.619 0.00 0.00 0.00 2.52
548 555 1.218316 CCCACTAGACGCTCCCAAC 59.782 63.158 0.00 0.00 0.00 3.77
549 556 1.541310 CCCACTAGACGCTCCCAACA 61.541 60.000 0.00 0.00 0.00 3.33
551 558 1.270625 CCACTAGACGCTCCCAACAAA 60.271 52.381 0.00 0.00 0.00 2.83
552 559 2.489971 CACTAGACGCTCCCAACAAAA 58.510 47.619 0.00 0.00 0.00 2.44
553 560 3.074412 CACTAGACGCTCCCAACAAAAT 58.926 45.455 0.00 0.00 0.00 1.82
554 561 3.502211 CACTAGACGCTCCCAACAAAATT 59.498 43.478 0.00 0.00 0.00 1.82
555 562 4.023193 CACTAGACGCTCCCAACAAAATTT 60.023 41.667 0.00 0.00 0.00 1.82
556 563 3.643159 AGACGCTCCCAACAAAATTTC 57.357 42.857 0.00 0.00 0.00 2.17
557 564 2.031157 AGACGCTCCCAACAAAATTTCG 60.031 45.455 0.00 0.00 0.00 3.46
558 565 1.000717 ACGCTCCCAACAAAATTTCGG 60.001 47.619 0.00 0.00 0.00 4.30
559 566 1.000717 CGCTCCCAACAAAATTTCGGT 60.001 47.619 0.00 0.00 0.00 4.69
560 567 2.403259 GCTCCCAACAAAATTTCGGTG 58.597 47.619 0.00 0.00 0.00 4.94
561 568 2.223947 GCTCCCAACAAAATTTCGGTGT 60.224 45.455 0.00 0.00 0.00 4.16
562 569 3.380142 CTCCCAACAAAATTTCGGTGTG 58.620 45.455 0.00 0.00 0.00 3.82
563 570 3.024547 TCCCAACAAAATTTCGGTGTGA 58.975 40.909 0.00 0.00 0.00 3.58
564 571 3.447586 TCCCAACAAAATTTCGGTGTGAA 59.552 39.130 0.00 0.00 33.85 3.18
577 584 7.737972 TTTCGGTGTGAAATCAAATAGAGAA 57.262 32.000 0.00 0.00 41.59 2.87
578 585 7.737972 TTCGGTGTGAAATCAAATAGAGAAA 57.262 32.000 0.00 0.00 32.37 2.52
579 586 7.129109 TCGGTGTGAAATCAAATAGAGAAAC 57.871 36.000 0.00 0.00 0.00 2.78
580 587 6.708502 TCGGTGTGAAATCAAATAGAGAAACA 59.291 34.615 0.00 0.00 0.00 2.83
654 661 3.303135 AGCGAACGAGAGCCCACA 61.303 61.111 0.00 0.00 0.00 4.17
655 662 2.811317 GCGAACGAGAGCCCACAG 60.811 66.667 0.00 0.00 0.00 3.66
656 663 2.811317 CGAACGAGAGCCCACAGC 60.811 66.667 0.00 0.00 44.25 4.40
690 697 1.153107 CAGCCAATCGAGGATGCCA 60.153 57.895 0.00 0.00 38.36 4.92
715 722 1.065401 CACCTGCAAGCGACAGAAAAA 59.935 47.619 5.39 0.00 37.32 1.94
720 727 2.421775 TGCAAGCGACAGAAAAAGACAA 59.578 40.909 0.00 0.00 0.00 3.18
756 763 1.122019 AGAACGTCCTCCACCAAGCT 61.122 55.000 0.00 0.00 0.00 3.74
768 775 2.027625 CCAAGCTCGAACCGACCAC 61.028 63.158 0.00 0.00 0.00 4.16
769 776 1.300620 CAAGCTCGAACCGACCACA 60.301 57.895 0.00 0.00 0.00 4.17
770 777 1.006102 AAGCTCGAACCGACCACAG 60.006 57.895 0.00 0.00 0.00 3.66
771 778 3.112709 GCTCGAACCGACCACAGC 61.113 66.667 0.00 0.00 0.00 4.40
772 779 2.432628 CTCGAACCGACCACAGCC 60.433 66.667 0.00 0.00 0.00 4.85
935 949 4.733725 TCCTAGCGGCCAGGGGTT 62.734 66.667 14.54 0.00 33.66 4.11
946 960 1.604378 CAGGGGTTGATTCGAGCCT 59.396 57.895 19.21 5.46 35.84 4.58
1017 1031 3.520691 AGGATGATGATGGGGTTCATG 57.479 47.619 0.00 0.00 36.48 3.07
1018 1032 3.058341 AGGATGATGATGGGGTTCATGA 58.942 45.455 0.00 0.00 36.48 3.07
1019 1033 3.661161 AGGATGATGATGGGGTTCATGAT 59.339 43.478 0.00 0.00 36.48 2.45
1370 1412 0.923358 AGGTGGTGGTTTGGTCTTCA 59.077 50.000 0.00 0.00 0.00 3.02
1418 1472 7.259161 CCTGTAGACTTAGTTTTAGCTAGTGG 58.741 42.308 0.00 0.00 0.00 4.00
1699 1754 4.159693 CCAGGTAGTGTCATGCTACTGTAA 59.840 45.833 10.74 0.00 38.92 2.41
1700 1755 5.337250 CCAGGTAGTGTCATGCTACTGTAAA 60.337 44.000 10.74 0.00 38.92 2.01
1701 1756 5.577164 CAGGTAGTGTCATGCTACTGTAAAC 59.423 44.000 10.74 2.91 38.92 2.01
1702 1757 4.868734 GGTAGTGTCATGCTACTGTAAACC 59.131 45.833 10.74 7.26 38.92 3.27
1703 1758 4.891992 AGTGTCATGCTACTGTAAACCT 57.108 40.909 1.51 0.00 0.00 3.50
1704 1759 4.822026 AGTGTCATGCTACTGTAAACCTC 58.178 43.478 1.51 0.00 0.00 3.85
1705 1760 3.933332 GTGTCATGCTACTGTAAACCTCC 59.067 47.826 0.00 0.00 0.00 4.30
1706 1761 3.580895 TGTCATGCTACTGTAAACCTCCA 59.419 43.478 0.00 0.00 0.00 3.86
1707 1762 4.184629 GTCATGCTACTGTAAACCTCCAG 58.815 47.826 0.00 0.00 34.82 3.86
1708 1763 3.197766 TCATGCTACTGTAAACCTCCAGG 59.802 47.826 0.00 0.00 42.17 4.45
1719 1774 3.768633 CCTCCAGGTAGTGTCATGC 57.231 57.895 0.00 0.00 0.00 4.06
1720 1775 1.198713 CCTCCAGGTAGTGTCATGCT 58.801 55.000 0.00 0.00 0.00 3.79
1721 1776 2.388735 CCTCCAGGTAGTGTCATGCTA 58.611 52.381 0.00 0.00 0.00 3.49
1722 1777 2.101582 CCTCCAGGTAGTGTCATGCTAC 59.898 54.545 1.52 1.52 38.38 3.58
1723 1778 3.027412 CTCCAGGTAGTGTCATGCTACT 58.973 50.000 8.35 7.62 38.92 2.57
1804 1859 0.874390 TTGCACTTCAGTTCATCGCC 59.126 50.000 0.00 0.00 0.00 5.54
1819 1874 5.339008 TCATCGCCACACTTACTATCTTT 57.661 39.130 0.00 0.00 0.00 2.52
1820 1875 5.348986 TCATCGCCACACTTACTATCTTTC 58.651 41.667 0.00 0.00 0.00 2.62
1821 1876 5.127194 TCATCGCCACACTTACTATCTTTCT 59.873 40.000 0.00 0.00 0.00 2.52
1822 1877 6.320418 TCATCGCCACACTTACTATCTTTCTA 59.680 38.462 0.00 0.00 0.00 2.10
1847 1902 6.068670 TCTATGCTAGTATGCCTACTGTCAA 58.931 40.000 11.50 0.00 38.65 3.18
1874 1929 1.417890 GGGCTGTGTCAGTGGCTATAT 59.582 52.381 0.00 0.00 33.43 0.86
1885 1940 7.657761 GTGTCAGTGGCTATATATAAAGCAGTT 59.342 37.037 9.23 0.00 40.61 3.16
1886 1941 7.872993 TGTCAGTGGCTATATATAAAGCAGTTC 59.127 37.037 9.23 0.00 40.61 3.01
1887 1942 7.332182 GTCAGTGGCTATATATAAAGCAGTTCC 59.668 40.741 9.23 0.00 40.61 3.62
1888 1943 7.016170 TCAGTGGCTATATATAAAGCAGTTCCA 59.984 37.037 9.23 0.00 40.61 3.53
1946 2001 2.169330 TGCAGTCAATGGCATGCTTAA 58.831 42.857 18.92 4.07 39.42 1.85
1954 2009 1.302366 TGGCATGCTTAATCTCTGCG 58.698 50.000 18.92 0.00 33.69 5.18
1962 2017 3.124560 GCTTAATCTCTGCGGTACCTTC 58.875 50.000 10.90 2.05 0.00 3.46
1977 2032 5.575995 CGGTACCTTCTCTTTACTGCTTTAC 59.424 44.000 10.90 0.00 0.00 2.01
2051 2109 8.712285 AACATCATCTTTTATGGCTCAAAATG 57.288 30.769 0.00 0.00 0.00 2.32
2065 2123 5.393461 GGCTCAAAATGTTTCACTGGGATAG 60.393 44.000 0.00 0.00 0.00 2.08
2174 2232 4.486125 TGGTATGAGCTTCAGCATTGTA 57.514 40.909 0.75 0.00 45.16 2.41
2257 2323 6.373216 TGACCAGTATTAATGGCAAGTTACAC 59.627 38.462 10.01 0.00 41.87 2.90
2299 2373 3.968649 TGCATTTTTCAGTGCTTCTGTC 58.031 40.909 8.75 0.00 43.97 3.51
2322 2396 7.877612 TGTCTAAATGAGCATTCTTTCACTACA 59.122 33.333 0.00 0.00 0.00 2.74
2325 2399 3.942829 TGAGCATTCTTTCACTACAGGG 58.057 45.455 0.00 0.00 0.00 4.45
2368 2442 9.846248 AGTATTTTATTCAGACATTTCTTGCAC 57.154 29.630 0.00 0.00 0.00 4.57
2371 2445 4.778534 ATTCAGACATTTCTTGCACCTG 57.221 40.909 0.00 0.00 0.00 4.00
2481 2555 6.412214 CATCCCATATCAACATCAGATGCTA 58.588 40.000 10.59 0.00 0.00 3.49
2495 2569 4.588106 TCAGATGCTAGGAGAGGAAATCAG 59.412 45.833 0.00 0.00 0.00 2.90
2537 2611 7.456725 CCCATTGTGGAAGATATGATAGAAGT 58.543 38.462 0.00 0.00 40.96 3.01
2572 2646 2.491675 TCTGTCTAGCGAGGACAAGA 57.508 50.000 9.80 7.42 42.15 3.02
2802 2879 6.716284 TCTGGGTCAAATGTCATGTATAACA 58.284 36.000 0.00 0.00 0.00 2.41
2837 2914 4.565022 TCAACATTCTGTAAGCATGACGA 58.435 39.130 0.00 0.00 40.15 4.20
2838 2915 4.627035 TCAACATTCTGTAAGCATGACGAG 59.373 41.667 0.00 0.00 40.15 4.18
2855 2932 1.654105 CGAGAGTGTTACATTCACGCC 59.346 52.381 13.35 0.00 40.28 5.68
2917 2995 8.624367 TTAGATAGAAATCGGAGAGGTAGAAG 57.376 38.462 0.00 0.00 43.63 2.85
2951 3029 1.833630 TGAGGCATGTAGAAGGTGAGG 59.166 52.381 0.00 0.00 0.00 3.86
2977 3055 1.487482 CGTGCTTCTGTTCTGTTCGA 58.513 50.000 0.00 0.00 0.00 3.71
3044 3123 0.111253 AAAGTCCTCCAAGGCCTGTG 59.889 55.000 5.69 7.02 34.61 3.66
3155 3234 2.846193 TGCACAGAACTGTAAAGGTCC 58.154 47.619 7.15 0.00 42.83 4.46
3169 3248 4.882842 AAAGGTCCAAGTGTTTTGTTGT 57.117 36.364 0.00 0.00 0.00 3.32
3310 3389 2.355363 CGAACGCCAGTGGTCGAA 60.355 61.111 25.89 0.00 33.72 3.71
3428 3507 3.499338 TGCATTGCCTATTATTGGGAGG 58.501 45.455 6.12 0.00 0.00 4.30
3447 4320 2.824341 AGGTAAGACGACGGTCAATTCT 59.176 45.455 9.10 3.72 45.92 2.40
3472 4345 5.518848 AGAAAACACATTCTGCATGTTGA 57.481 34.783 3.51 0.00 44.40 3.18
3630 4521 7.317390 TCCTTTAGTTTTTGTTTGGTCTGTTC 58.683 34.615 0.00 0.00 0.00 3.18
3749 4640 6.699575 ATAACCCCATCATTTTCTTTCTCG 57.300 37.500 0.00 0.00 0.00 4.04
3841 4732 1.547901 GCTTGGCCTTAGTTCCTTGGT 60.548 52.381 3.32 0.00 0.00 3.67
4027 4918 2.674033 GGCACCAGCACTGCATGA 60.674 61.111 3.30 0.00 44.61 3.07
4032 4923 2.693762 CCAGCACTGCATGAACCCG 61.694 63.158 3.30 0.00 0.00 5.28
4094 4985 2.932614 GGTGACAAATCTGGAGATGTCG 59.067 50.000 11.28 0.00 32.98 4.35
4095 4986 2.932614 GTGACAAATCTGGAGATGTCGG 59.067 50.000 11.28 0.00 32.98 4.79
4226 5117 5.130311 TGTGCATAATAGTCCCTCTTTAGCA 59.870 40.000 0.00 0.00 0.00 3.49
4231 5122 8.097662 GCATAATAGTCCCTCTTTAGCATAGTT 58.902 37.037 0.00 0.00 0.00 2.24
4394 5285 4.807834 TGGTATTGTTGTTGCAACATGTTG 59.192 37.500 31.48 30.20 43.14 3.33
4518 5411 2.519013 GACAATGAAGGGGCTCAACTT 58.481 47.619 0.00 0.00 0.00 2.66
4536 5429 5.185249 TCAACTTGTATGTACTCCCTCTGTC 59.815 44.000 0.00 0.00 0.00 3.51
4589 5609 8.753175 CGTCTTATACTGTTTATTTACAGAGGC 58.247 37.037 10.46 0.00 46.72 4.70
4670 5690 1.078709 AATTGACGTCCGCTGACATG 58.921 50.000 14.12 0.00 41.85 3.21
4786 5816 2.159382 CCTGGAATTGCAACTTACGGT 58.841 47.619 0.00 0.00 0.00 4.83
4896 5926 4.104102 TCACCCTACATCAGAGGTTTTGTT 59.896 41.667 0.00 0.00 31.52 2.83
4923 5953 5.998981 CCACAGTTAAAACATGTAGGGTGTA 59.001 40.000 0.00 0.00 0.00 2.90
4972 6003 5.280368 CCTTGCATATGTATCTCATCTGGGT 60.280 44.000 4.29 0.00 37.91 4.51
5005 6036 5.504665 CGGATGTAGGCTGAAAATCATGTTC 60.505 44.000 0.00 0.00 0.00 3.18
5035 6066 1.604604 TTGGTTGCCTTACTGTCTGC 58.395 50.000 0.00 0.00 0.00 4.26
5036 6067 0.602638 TGGTTGCCTTACTGTCTGCG 60.603 55.000 0.00 0.00 0.00 5.18
5037 6068 0.602905 GGTTGCCTTACTGTCTGCGT 60.603 55.000 0.00 0.00 0.00 5.24
5038 6069 0.512952 GTTGCCTTACTGTCTGCGTG 59.487 55.000 0.00 0.00 0.00 5.34
5039 6070 0.105964 TTGCCTTACTGTCTGCGTGT 59.894 50.000 0.00 0.00 0.00 4.49
5040 6071 0.105964 TGCCTTACTGTCTGCGTGTT 59.894 50.000 0.00 0.00 0.00 3.32
5041 6072 1.226746 GCCTTACTGTCTGCGTGTTT 58.773 50.000 0.00 0.00 0.00 2.83
5042 6073 1.069906 GCCTTACTGTCTGCGTGTTTG 60.070 52.381 0.00 0.00 0.00 2.93
5043 6074 1.531149 CCTTACTGTCTGCGTGTTTGG 59.469 52.381 0.00 0.00 0.00 3.28
5044 6075 2.210116 CTTACTGTCTGCGTGTTTGGT 58.790 47.619 0.00 0.00 0.00 3.67
5045 6076 2.319136 TACTGTCTGCGTGTTTGGTT 57.681 45.000 0.00 0.00 0.00 3.67
5046 6077 0.732571 ACTGTCTGCGTGTTTGGTTG 59.267 50.000 0.00 0.00 0.00 3.77
5047 6078 0.592247 CTGTCTGCGTGTTTGGTTGC 60.592 55.000 0.00 0.00 0.00 4.17
5048 6079 1.299089 GTCTGCGTGTTTGGTTGCC 60.299 57.895 0.00 0.00 0.00 4.52
5049 6080 1.453015 TCTGCGTGTTTGGTTGCCT 60.453 52.632 0.00 0.00 0.00 4.75
5050 6081 1.034838 TCTGCGTGTTTGGTTGCCTT 61.035 50.000 0.00 0.00 0.00 4.35
5051 6082 0.665835 CTGCGTGTTTGGTTGCCTTA 59.334 50.000 0.00 0.00 0.00 2.69
5052 6083 0.382515 TGCGTGTTTGGTTGCCTTAC 59.617 50.000 0.00 0.00 0.00 2.34
5053 6084 0.666374 GCGTGTTTGGTTGCCTTACT 59.334 50.000 0.00 0.00 0.00 2.24
5054 6085 1.599419 GCGTGTTTGGTTGCCTTACTG 60.599 52.381 0.00 0.00 0.00 2.74
5055 6086 1.673920 CGTGTTTGGTTGCCTTACTGT 59.326 47.619 0.00 0.00 0.00 3.55
5056 6087 2.286772 CGTGTTTGGTTGCCTTACTGTC 60.287 50.000 0.00 0.00 0.00 3.51
5057 6088 2.949644 GTGTTTGGTTGCCTTACTGTCT 59.050 45.455 0.00 0.00 0.00 3.41
5058 6089 2.948979 TGTTTGGTTGCCTTACTGTCTG 59.051 45.455 0.00 0.00 0.00 3.51
5059 6090 1.604604 TTGGTTGCCTTACTGTCTGC 58.395 50.000 0.00 0.00 0.00 4.26
5060 6091 0.602638 TGGTTGCCTTACTGTCTGCG 60.603 55.000 0.00 0.00 0.00 5.18
5061 6092 0.602905 GGTTGCCTTACTGTCTGCGT 60.603 55.000 0.00 0.00 0.00 5.24
5062 6093 0.512952 GTTGCCTTACTGTCTGCGTG 59.487 55.000 0.00 0.00 0.00 5.34
5063 6094 0.105964 TTGCCTTACTGTCTGCGTGT 59.894 50.000 0.00 0.00 0.00 4.49
5064 6095 0.105964 TGCCTTACTGTCTGCGTGTT 59.894 50.000 0.00 0.00 0.00 3.32
5065 6096 1.226746 GCCTTACTGTCTGCGTGTTT 58.773 50.000 0.00 0.00 0.00 2.83
5066 6097 1.069906 GCCTTACTGTCTGCGTGTTTG 60.070 52.381 0.00 0.00 0.00 2.93
5067 6098 1.531149 CCTTACTGTCTGCGTGTTTGG 59.469 52.381 0.00 0.00 0.00 3.28
5068 6099 2.210116 CTTACTGTCTGCGTGTTTGGT 58.790 47.619 0.00 0.00 0.00 3.67
5069 6100 2.319136 TACTGTCTGCGTGTTTGGTT 57.681 45.000 0.00 0.00 0.00 3.67
5070 6101 0.732571 ACTGTCTGCGTGTTTGGTTG 59.267 50.000 0.00 0.00 0.00 3.77
5071 6102 0.592247 CTGTCTGCGTGTTTGGTTGC 60.592 55.000 0.00 0.00 0.00 4.17
5072 6103 1.299089 GTCTGCGTGTTTGGTTGCC 60.299 57.895 0.00 0.00 0.00 4.52
5073 6104 1.453015 TCTGCGTGTTTGGTTGCCT 60.453 52.632 0.00 0.00 0.00 4.75
5074 6105 1.299316 CTGCGTGTTTGGTTGCCTG 60.299 57.895 0.00 0.00 0.00 4.85
5075 6106 2.003658 CTGCGTGTTTGGTTGCCTGT 62.004 55.000 0.00 0.00 0.00 4.00
5076 6107 1.140804 GCGTGTTTGGTTGCCTGTT 59.859 52.632 0.00 0.00 0.00 3.16
5077 6108 0.869880 GCGTGTTTGGTTGCCTGTTC 60.870 55.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 7.309438 GGAAGAAGGAACATGAAGTAGCAAATT 60.309 37.037 0.00 0.00 0.00 1.82
53 54 5.310409 TGAAGGAAGAAGGAACATGAAGT 57.690 39.130 0.00 0.00 0.00 3.01
243 244 2.715046 CCATGGCAGAGCAAAACTAGA 58.285 47.619 0.00 0.00 0.00 2.43
355 356 3.353029 CACGCATCCCACGCACAA 61.353 61.111 0.00 0.00 0.00 3.33
367 368 0.107410 GATAACCACATCCCCACGCA 60.107 55.000 0.00 0.00 0.00 5.24
414 421 2.494530 GCCCACGCTCCCAACAAAA 61.495 57.895 0.00 0.00 0.00 2.44
455 462 2.167037 CCCCCTTGGTCCCAGGAAA 61.167 63.158 10.73 0.00 0.00 3.13
554 561 7.227711 TGTTTCTCTATTTGATTTCACACCGAA 59.772 33.333 0.00 0.00 0.00 4.30
555 562 6.708502 TGTTTCTCTATTTGATTTCACACCGA 59.291 34.615 0.00 0.00 0.00 4.69
556 563 6.898041 TGTTTCTCTATTTGATTTCACACCG 58.102 36.000 0.00 0.00 0.00 4.94
557 564 9.528018 TTTTGTTTCTCTATTTGATTTCACACC 57.472 29.630 0.00 0.00 0.00 4.16
571 578 9.857957 AACACCGTTTTAAATTTTGTTTCTCTA 57.142 25.926 0.00 0.00 0.00 2.43
572 579 8.766000 AACACCGTTTTAAATTTTGTTTCTCT 57.234 26.923 0.00 0.00 0.00 3.10
600 607 7.035612 ACAAAAAGCACGAGAAAATTCTTCTT 58.964 30.769 0.00 0.00 37.73 2.52
601 608 6.564328 ACAAAAAGCACGAGAAAATTCTTCT 58.436 32.000 0.00 3.49 37.73 2.85
602 609 6.344234 CGACAAAAAGCACGAGAAAATTCTTC 60.344 38.462 0.00 0.00 37.73 2.87
604 611 4.970003 CGACAAAAAGCACGAGAAAATTCT 59.030 37.500 0.00 0.00 41.00 2.40
715 722 0.033894 AAAACGTGGTGGGGTTGTCT 60.034 50.000 0.00 0.00 0.00 3.41
720 727 1.152839 CTGGAAAACGTGGTGGGGT 60.153 57.895 0.00 0.00 0.00 4.95
756 763 3.998672 GGGCTGTGGTCGGTTCGA 61.999 66.667 0.00 0.00 0.00 3.71
921 935 2.265467 GAATCAACCCCTGGCCGCTA 62.265 60.000 0.00 0.00 0.00 4.26
935 949 4.161295 CGGGGCAGGCTCGAATCA 62.161 66.667 11.71 0.00 0.00 2.57
1017 1031 0.472044 GCTCCTTCCTCTTCCCCATC 59.528 60.000 0.00 0.00 0.00 3.51
1018 1032 0.045469 AGCTCCTTCCTCTTCCCCAT 59.955 55.000 0.00 0.00 0.00 4.00
1019 1033 0.911525 CAGCTCCTTCCTCTTCCCCA 60.912 60.000 0.00 0.00 0.00 4.96
1190 1217 0.179145 ATCGACTGGAAGCGTAACCG 60.179 55.000 0.00 0.00 37.60 4.44
1202 1229 0.671472 TGCACCAGAAGCATCGACTG 60.671 55.000 0.00 0.00 37.02 3.51
1274 1302 1.142870 AGCAGCTACTTCAACCAACCA 59.857 47.619 0.00 0.00 0.00 3.67
1299 1327 0.168788 CAAACCTAGCATGCACACGG 59.831 55.000 21.98 15.74 0.00 4.94
1418 1472 7.118390 GGTATCCATCTAGCAATACACATGAAC 59.882 40.741 0.00 0.00 0.00 3.18
1640 1695 3.059352 ACAAACCAGCTCATCCACTAC 57.941 47.619 0.00 0.00 0.00 2.73
1701 1756 1.198713 AGCATGACACTACCTGGAGG 58.801 55.000 0.00 0.00 42.17 4.30
1702 1757 3.027412 AGTAGCATGACACTACCTGGAG 58.973 50.000 0.00 0.00 40.77 3.86
1703 1758 2.760650 CAGTAGCATGACACTACCTGGA 59.239 50.000 0.00 0.00 40.77 3.86
1704 1759 2.497675 ACAGTAGCATGACACTACCTGG 59.502 50.000 0.00 0.00 40.77 4.45
1705 1760 3.876274 ACAGTAGCATGACACTACCTG 57.124 47.619 0.00 2.63 40.77 4.00
1706 1761 6.546428 AAATACAGTAGCATGACACTACCT 57.454 37.500 0.00 0.00 40.77 3.08
1707 1762 7.762615 TGTAAAATACAGTAGCATGACACTACC 59.237 37.037 0.00 0.00 40.77 3.18
1708 1763 8.592998 GTGTAAAATACAGTAGCATGACACTAC 58.407 37.037 0.00 0.00 39.77 2.73
1709 1764 8.308207 TGTGTAAAATACAGTAGCATGACACTA 58.692 33.333 0.00 0.00 39.77 2.74
1710 1765 7.158697 TGTGTAAAATACAGTAGCATGACACT 58.841 34.615 0.00 0.00 39.77 3.55
1711 1766 7.359262 TGTGTAAAATACAGTAGCATGACAC 57.641 36.000 0.00 0.00 39.77 3.67
1712 1767 7.971183 TTGTGTAAAATACAGTAGCATGACA 57.029 32.000 0.00 0.00 39.77 3.58
1721 1776 8.915036 TGGGTTTGTAATTGTGTAAAATACAGT 58.085 29.630 0.00 0.00 39.77 3.55
1722 1777 9.405587 CTGGGTTTGTAATTGTGTAAAATACAG 57.594 33.333 0.00 0.00 39.77 2.74
1723 1778 9.132923 TCTGGGTTTGTAATTGTGTAAAATACA 57.867 29.630 0.00 0.00 36.08 2.29
1770 1825 6.480763 TGAAGTGCAATCCAGGTAATCTAAA 58.519 36.000 0.00 0.00 0.00 1.85
1819 1874 7.634718 ACAGTAGGCATACTAGCATAGATAGA 58.365 38.462 11.26 0.00 42.77 1.98
1820 1875 7.554476 TGACAGTAGGCATACTAGCATAGATAG 59.446 40.741 11.26 0.00 42.77 2.08
1821 1876 7.402862 TGACAGTAGGCATACTAGCATAGATA 58.597 38.462 11.26 0.00 42.77 1.98
1822 1877 6.249192 TGACAGTAGGCATACTAGCATAGAT 58.751 40.000 11.26 0.00 42.77 1.98
1874 1929 4.790937 TGCATGGATGGAACTGCTTTATA 58.209 39.130 0.00 0.00 35.66 0.98
1885 1940 2.458620 TCAAGCAAATGCATGGATGGA 58.541 42.857 10.34 0.00 45.16 3.41
1886 1941 2.971660 TCAAGCAAATGCATGGATGG 57.028 45.000 10.34 0.00 45.16 3.51
1887 1942 3.049912 CGATCAAGCAAATGCATGGATG 58.950 45.455 10.34 1.12 45.16 3.51
1888 1943 2.953648 TCGATCAAGCAAATGCATGGAT 59.046 40.909 10.34 8.13 45.16 3.41
1946 2001 2.445682 AGAGAAGGTACCGCAGAGAT 57.554 50.000 6.18 0.00 0.00 2.75
1954 2009 6.461640 TGTAAAGCAGTAAAGAGAAGGTACC 58.538 40.000 2.73 2.73 0.00 3.34
1998 2053 5.163364 TGCAAAAGTATCTTGAAAGGGCAAA 60.163 36.000 0.00 0.00 0.00 3.68
2048 2106 4.574674 TGAGCTATCCCAGTGAAACATT 57.425 40.909 0.00 0.00 41.43 2.71
2051 2109 4.943705 TCAAATGAGCTATCCCAGTGAAAC 59.056 41.667 0.00 0.00 0.00 2.78
2065 2123 8.733458 TCCATAACTGCATATAATCAAATGAGC 58.267 33.333 0.00 0.00 0.00 4.26
2142 2200 3.110705 AGCTCATACCAACAGAGGACAT 58.889 45.455 0.00 0.00 0.00 3.06
2213 2271 5.538053 TGGTCATTAAACTGAATGCAAGGAA 59.462 36.000 0.00 0.00 36.85 3.36
2299 2373 7.201679 CCCTGTAGTGAAAGAATGCTCATTTAG 60.202 40.741 0.00 0.00 0.00 1.85
2322 2396 2.584835 TGCAGCAACAGATAAACCCT 57.415 45.000 0.00 0.00 0.00 4.34
2325 2399 7.873739 AAAATACTTGCAGCAACAGATAAAC 57.126 32.000 2.83 0.00 0.00 2.01
2481 2555 1.558756 CCACTGCTGATTTCCTCTCCT 59.441 52.381 0.00 0.00 0.00 3.69
2495 2569 1.508088 GGCATGTTAGCACCACTGC 59.492 57.895 0.00 0.00 44.63 4.40
2504 2578 3.355378 TCTTCCACAATGGGCATGTTAG 58.645 45.455 0.00 0.00 38.32 2.34
2537 2611 1.064240 ACAGATGAGATGGCATGGCAA 60.064 47.619 27.04 10.17 0.00 4.52
2744 2819 2.146342 GCACAATGTGAGTACTGCAGT 58.854 47.619 25.12 25.12 35.23 4.40
2778 2853 6.716284 TGTTATACATGACATTTGACCCAGA 58.284 36.000 0.00 0.00 0.00 3.86
2837 2914 3.402628 AAGGCGTGAATGTAACACTCT 57.597 42.857 0.00 0.00 36.29 3.24
2838 2915 5.796350 ATTAAGGCGTGAATGTAACACTC 57.204 39.130 0.00 0.00 36.29 3.51
2903 2980 3.244805 TGTCTGTTCTTCTACCTCTCCGA 60.245 47.826 0.00 0.00 0.00 4.55
2917 2995 1.070758 TGCCTCACCTCTTGTCTGTTC 59.929 52.381 0.00 0.00 0.00 3.18
2951 3029 0.658536 GAACAGAAGCACGCAACTGC 60.659 55.000 12.86 0.00 37.44 4.40
2977 3055 3.889859 ATCAGAGAGAGCCAGAGAGAT 57.110 47.619 0.00 0.00 0.00 2.75
3107 3186 4.899502 GCATATAGCACCACTGGAAGTAT 58.100 43.478 0.71 0.00 45.93 2.12
3108 3187 4.336889 GCATATAGCACCACTGGAAGTA 57.663 45.455 0.71 0.00 45.93 2.24
3131 3210 5.228945 ACCTTTACAGTTCTGTGCATACT 57.771 39.130 14.69 0.00 0.00 2.12
3169 3248 3.324556 TCATATGCACTAGCTACATGGCA 59.675 43.478 0.00 6.09 42.74 4.92
3211 3290 3.501385 CCTCCCCCTTTAACCATGTTTCA 60.501 47.826 0.00 0.00 0.00 2.69
3212 3291 3.096852 CCTCCCCCTTTAACCATGTTTC 58.903 50.000 0.00 0.00 0.00 2.78
3297 3376 2.022129 GTGAGTTCGACCACTGGCG 61.022 63.158 0.00 0.20 0.00 5.69
3412 3491 4.039973 CGTCTTACCTCCCAATAATAGGCA 59.960 45.833 0.00 0.00 33.42 4.75
3428 3507 6.088824 TCTTTAGAATTGACCGTCGTCTTAC 58.911 40.000 4.95 0.00 39.94 2.34
3472 4345 0.751643 GCAACAGGGCCCGAATGTAT 60.752 55.000 18.44 3.97 0.00 2.29
3508 4381 9.704098 GAATACTAAGAAAAGAAAAGCCGTATG 57.296 33.333 0.00 0.00 0.00 2.39
3512 4385 7.148623 ACGAGAATACTAAGAAAAGAAAAGCCG 60.149 37.037 0.00 0.00 0.00 5.52
3604 4495 7.234661 ACAGACCAAACAAAAACTAAAGGAA 57.765 32.000 0.00 0.00 0.00 3.36
3630 4521 6.294473 ACCCAATCATGCTCAAAGTATAGAG 58.706 40.000 0.00 0.00 35.01 2.43
3749 4640 6.169094 TGATTGAAAGGTTGATCTGAGAGAC 58.831 40.000 0.00 0.00 0.00 3.36
4032 4923 4.133796 GGGTTTGGCAGCGATGGC 62.134 66.667 21.51 21.51 40.37 4.40
4044 4935 4.250305 ACTGGCGCTGACGGGTTT 62.250 61.111 7.64 0.00 40.57 3.27
4094 4985 4.815108 CCTGCGGTTAAGGGGGCC 62.815 72.222 0.00 0.00 0.00 5.80
4095 4986 2.200923 TAACCTGCGGTTAAGGGGGC 62.201 60.000 14.96 0.00 44.94 5.80
4214 5105 6.139671 AGATCAGAACTATGCTAAAGAGGGA 58.860 40.000 0.00 0.00 0.00 4.20
4509 5402 3.197983 AGGGAGTACATACAAGTTGAGCC 59.802 47.826 10.54 0.00 0.00 4.70
4518 5411 7.727578 TTTATTGACAGAGGGAGTACATACA 57.272 36.000 0.00 0.00 0.00 2.29
4536 5429 9.844790 TTTTAGATCACTGTCTTGCATTTATTG 57.155 29.630 0.00 0.00 0.00 1.90
4589 5609 5.050644 TGCAAGCTTGATGAAATGTACTG 57.949 39.130 30.39 0.00 0.00 2.74
4786 5816 2.754552 GTGCAATCATGTTCCCTGCTTA 59.245 45.455 0.00 0.00 34.10 3.09
4896 5926 5.067273 CCCTACATGTTTTAACTGTGGTCA 58.933 41.667 2.30 0.00 0.00 4.02
4923 5953 4.202050 GGGAAACGATGCAAGCTATCAAAT 60.202 41.667 0.00 0.00 0.00 2.32
4972 6003 2.021068 GCCTACATCCGCTCAGCTGA 62.021 60.000 17.19 17.19 0.00 4.26
5005 6036 1.826720 AGGCAACCAAACCATATGCAG 59.173 47.619 0.00 0.00 38.73 4.41
5035 6066 1.673920 ACAGTAAGGCAACCAAACACG 59.326 47.619 0.00 0.00 37.17 4.49
5036 6067 2.949644 AGACAGTAAGGCAACCAAACAC 59.050 45.455 0.00 0.00 37.17 3.32
5037 6068 2.948979 CAGACAGTAAGGCAACCAAACA 59.051 45.455 0.00 0.00 37.17 2.83
5038 6069 2.287608 GCAGACAGTAAGGCAACCAAAC 60.288 50.000 0.00 0.00 37.17 2.93
5039 6070 1.953686 GCAGACAGTAAGGCAACCAAA 59.046 47.619 0.00 0.00 37.17 3.28
5040 6071 1.604604 GCAGACAGTAAGGCAACCAA 58.395 50.000 0.00 0.00 37.17 3.67
5041 6072 0.602638 CGCAGACAGTAAGGCAACCA 60.603 55.000 0.00 0.00 37.17 3.67
5042 6073 0.602905 ACGCAGACAGTAAGGCAACC 60.603 55.000 0.00 0.00 37.17 3.77
5043 6074 0.512952 CACGCAGACAGTAAGGCAAC 59.487 55.000 0.00 0.00 0.00 4.17
5044 6075 0.105964 ACACGCAGACAGTAAGGCAA 59.894 50.000 0.00 0.00 0.00 4.52
5045 6076 0.105964 AACACGCAGACAGTAAGGCA 59.894 50.000 0.00 0.00 0.00 4.75
5046 6077 1.069906 CAAACACGCAGACAGTAAGGC 60.070 52.381 0.00 0.00 0.00 4.35
5047 6078 1.531149 CCAAACACGCAGACAGTAAGG 59.469 52.381 0.00 0.00 0.00 2.69
5048 6079 2.210116 ACCAAACACGCAGACAGTAAG 58.790 47.619 0.00 0.00 0.00 2.34
5049 6080 2.319136 ACCAAACACGCAGACAGTAA 57.681 45.000 0.00 0.00 0.00 2.24
5050 6081 1.937223 CAACCAAACACGCAGACAGTA 59.063 47.619 0.00 0.00 0.00 2.74
5051 6082 0.732571 CAACCAAACACGCAGACAGT 59.267 50.000 0.00 0.00 0.00 3.55
5052 6083 0.592247 GCAACCAAACACGCAGACAG 60.592 55.000 0.00 0.00 0.00 3.51
5053 6084 1.431440 GCAACCAAACACGCAGACA 59.569 52.632 0.00 0.00 0.00 3.41
5054 6085 1.299089 GGCAACCAAACACGCAGAC 60.299 57.895 0.00 0.00 0.00 3.51
5055 6086 1.453015 AGGCAACCAAACACGCAGA 60.453 52.632 0.00 0.00 37.17 4.26
5056 6087 1.299316 CAGGCAACCAAACACGCAG 60.299 57.895 0.00 0.00 37.17 5.18
5057 6088 1.599606 AACAGGCAACCAAACACGCA 61.600 50.000 0.00 0.00 37.17 5.24
5058 6089 0.869880 GAACAGGCAACCAAACACGC 60.870 55.000 0.00 0.00 37.17 5.34
5059 6090 3.250220 GAACAGGCAACCAAACACG 57.750 52.632 0.00 0.00 37.17 4.49


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

AutoCloner maintained by Alex Coulton.