Multiple sequence alignment - TraesCS6B01G027200

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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 TraesCS6B01G027200 chr6B 100.000 2396 0 0 1 2396 16246175 16248570 0.000000e+00 4425
1 TraesCS6B01G027200 chr6B 85.207 676 97 3 719 1392 16241320 16241994 0.000000e+00 691
2 TraesCS6B01G027200 chr6B 100.000 121 0 0 2621 2741 16248795 16248915 9.880000e-55 224
3 TraesCS6B01G027200 chr6A 91.333 1673 117 15 719 2386 8754620 8752971 0.000000e+00 2261
4 TraesCS6B01G027200 chr6A 86.640 1003 133 1 719 1721 8868632 8867631 0.000000e+00 1109
5 TraesCS6B01G027200 chr6A 86.341 1003 136 1 719 1721 8792303 8791302 0.000000e+00 1092
6 TraesCS6B01G027200 chr6A 89.916 119 12 0 2621 2739 8752940 8752822 1.310000e-33 154
7 TraesCS6B01G027200 chr6D 89.069 1665 155 17 727 2386 8316195 8314553 0.000000e+00 2041
8 TraesCS6B01G027200 chr6D 86.915 1047 132 5 719 1762 8348501 8347457 0.000000e+00 1170
9 TraesCS6B01G027200 chr6D 84.369 1094 156 12 719 1805 8386161 8385076 0.000000e+00 1059
10 TraesCS6B01G027200 chr1B 97.143 735 7 2 1 722 619101957 619102690 0.000000e+00 1229
11 TraesCS6B01G027200 chr4D 84.111 1007 143 6 724 1716 477912367 477913370 0.000000e+00 957
12 TraesCS6B01G027200 chr4B 83.877 1011 144 12 724 1719 604139733 604140739 0.000000e+00 946
13 TraesCS6B01G027200 chr4B 80.916 786 78 37 1 727 567440029 567439257 3.080000e-154 555
14 TraesCS6B01G027200 chr7B 89.392 707 19 9 1 678 741862155 741861476 0.000000e+00 839
15 TraesCS6B01G027200 chr5A 84.453 804 117 6 919 1720 680709640 680710437 0.000000e+00 785
16 TraesCS6B01G027200 chr4A 83.146 623 92 5 719 1329 684610666 684611287 8.570000e-155 556
17 TraesCS6B01G027200 chr1D 77.582 794 100 47 1 722 413945954 413946741 2.540000e-110 409
18 TraesCS6B01G027200 chr2B 80.000 505 58 28 92 565 726556747 726556255 1.570000e-87 333


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 TraesCS6B01G027200 chr6B 16246175 16248915 2740 False 2324.5 4425 100.0000 1 2741 2 chr6B.!!$F2 2740
1 TraesCS6B01G027200 chr6B 16241320 16241994 674 False 691.0 691 85.2070 719 1392 1 chr6B.!!$F1 673
2 TraesCS6B01G027200 chr6A 8752822 8754620 1798 True 1207.5 2261 90.6245 719 2739 2 chr6A.!!$R3 2020
3 TraesCS6B01G027200 chr6A 8867631 8868632 1001 True 1109.0 1109 86.6400 719 1721 1 chr6A.!!$R2 1002
4 TraesCS6B01G027200 chr6A 8791302 8792303 1001 True 1092.0 1092 86.3410 719 1721 1 chr6A.!!$R1 1002
5 TraesCS6B01G027200 chr6D 8314553 8316195 1642 True 2041.0 2041 89.0690 727 2386 1 chr6D.!!$R1 1659
6 TraesCS6B01G027200 chr6D 8347457 8348501 1044 True 1170.0 1170 86.9150 719 1762 1 chr6D.!!$R2 1043
7 TraesCS6B01G027200 chr6D 8385076 8386161 1085 True 1059.0 1059 84.3690 719 1805 1 chr6D.!!$R3 1086
8 TraesCS6B01G027200 chr1B 619101957 619102690 733 False 1229.0 1229 97.1430 1 722 1 chr1B.!!$F1 721
9 TraesCS6B01G027200 chr4D 477912367 477913370 1003 False 957.0 957 84.1110 724 1716 1 chr4D.!!$F1 992
10 TraesCS6B01G027200 chr4B 604139733 604140739 1006 False 946.0 946 83.8770 724 1719 1 chr4B.!!$F1 995
11 TraesCS6B01G027200 chr4B 567439257 567440029 772 True 555.0 555 80.9160 1 727 1 chr4B.!!$R1 726
12 TraesCS6B01G027200 chr7B 741861476 741862155 679 True 839.0 839 89.3920 1 678 1 chr7B.!!$R1 677
13 TraesCS6B01G027200 chr5A 680709640 680710437 797 False 785.0 785 84.4530 919 1720 1 chr5A.!!$F1 801
14 TraesCS6B01G027200 chr4A 684610666 684611287 621 False 556.0 556 83.1460 719 1329 1 chr4A.!!$F1 610
15 TraesCS6B01G027200 chr1D 413945954 413946741 787 False 409.0 409 77.5820 1 722 1 chr1D.!!$F1 721

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
642 710 0.036388 TTTTCGCACTAGCCCAGAGG 60.036 55.0 0.0 0.0 37.52 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1974 2087 0.184211 AAGTAACAAAGTGGGCGGGT 59.816 50.0 0.0 0.0 0.0 5.28 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
329 340 1.237533 TGTGTACTGGTTCGCGTCTA 58.762 50.000 5.77 0.00 0.00 2.59
548 616 2.906354 AGGAAGGAATCGATTTCACCG 58.094 47.619 18.62 0.00 35.94 4.94
549 617 2.500098 AGGAAGGAATCGATTTCACCGA 59.500 45.455 18.62 0.00 40.53 4.69
550 618 3.055385 AGGAAGGAATCGATTTCACCGAA 60.055 43.478 18.62 0.00 39.62 4.30
551 619 3.687698 GGAAGGAATCGATTTCACCGAAA 59.312 43.478 18.62 0.00 39.62 3.46
552 620 4.436986 GGAAGGAATCGATTTCACCGAAAC 60.437 45.833 18.62 6.82 39.62 2.78
553 621 3.670625 AGGAATCGATTTCACCGAAACA 58.329 40.909 18.62 0.00 39.62 2.83
554 622 4.069304 AGGAATCGATTTCACCGAAACAA 58.931 39.130 18.62 0.00 39.62 2.83
555 623 4.517453 AGGAATCGATTTCACCGAAACAAA 59.483 37.500 18.62 0.00 39.62 2.83
556 624 5.009210 AGGAATCGATTTCACCGAAACAAAA 59.991 36.000 18.62 0.00 39.62 2.44
557 625 5.342259 GGAATCGATTTCACCGAAACAAAAG 59.658 40.000 12.81 0.00 39.62 2.27
558 626 4.217754 TCGATTTCACCGAAACAAAAGG 57.782 40.909 0.00 0.00 34.23 3.11
559 627 3.878103 TCGATTTCACCGAAACAAAAGGA 59.122 39.130 0.00 0.00 34.23 3.36
560 628 4.335874 TCGATTTCACCGAAACAAAAGGAA 59.664 37.500 0.00 0.00 34.23 3.36
561 629 5.009210 TCGATTTCACCGAAACAAAAGGAAT 59.991 36.000 0.00 0.00 34.23 3.01
562 630 6.205076 TCGATTTCACCGAAACAAAAGGAATA 59.795 34.615 0.00 0.00 34.23 1.75
563 631 6.523201 CGATTTCACCGAAACAAAAGGAATAG 59.477 38.462 0.00 0.00 34.23 1.73
564 632 6.945938 TTTCACCGAAACAAAAGGAATAGA 57.054 33.333 0.00 0.00 0.00 1.98
565 633 6.554334 TTCACCGAAACAAAAGGAATAGAG 57.446 37.500 0.00 0.00 0.00 2.43
566 634 5.617252 TCACCGAAACAAAAGGAATAGAGT 58.383 37.500 0.00 0.00 0.00 3.24
567 635 5.699458 TCACCGAAACAAAAGGAATAGAGTC 59.301 40.000 0.00 0.00 0.00 3.36
568 636 5.701290 CACCGAAACAAAAGGAATAGAGTCT 59.299 40.000 0.00 0.00 0.00 3.24
569 637 5.701290 ACCGAAACAAAAGGAATAGAGTCTG 59.299 40.000 1.86 0.00 0.00 3.51
570 638 5.390991 CCGAAACAAAAGGAATAGAGTCTGC 60.391 44.000 1.86 0.00 0.00 4.26
571 639 5.390991 CGAAACAAAAGGAATAGAGTCTGCC 60.391 44.000 1.86 1.61 0.00 4.85
572 640 3.600388 ACAAAAGGAATAGAGTCTGCCG 58.400 45.455 1.86 0.00 0.00 5.69
573 641 2.939103 CAAAAGGAATAGAGTCTGCCGG 59.061 50.000 1.86 0.00 0.00 6.13
574 642 0.466124 AAGGAATAGAGTCTGCCGGC 59.534 55.000 22.73 22.73 0.00 6.13
575 643 1.300233 GGAATAGAGTCTGCCGGCG 60.300 63.158 23.90 16.91 0.00 6.46
576 644 1.437986 GAATAGAGTCTGCCGGCGT 59.562 57.895 23.90 5.96 0.00 5.68
577 645 0.595310 GAATAGAGTCTGCCGGCGTC 60.595 60.000 23.90 15.51 0.00 5.19
578 646 2.017559 AATAGAGTCTGCCGGCGTCC 62.018 60.000 23.90 11.64 0.00 4.79
579 647 3.931190 TAGAGTCTGCCGGCGTCCA 62.931 63.158 23.90 2.23 0.00 4.02
592 660 4.643387 GTCCACGCCTGGTTGCCT 62.643 66.667 1.44 0.00 38.90 4.75
593 661 3.884774 TCCACGCCTGGTTGCCTT 61.885 61.111 1.44 0.00 38.90 4.35
594 662 2.912025 CCACGCCTGGTTGCCTTT 60.912 61.111 0.00 0.00 32.03 3.11
595 663 2.644992 CACGCCTGGTTGCCTTTC 59.355 61.111 0.00 0.00 0.00 2.62
596 664 1.898574 CACGCCTGGTTGCCTTTCT 60.899 57.895 0.00 0.00 0.00 2.52
597 665 0.605319 CACGCCTGGTTGCCTTTCTA 60.605 55.000 0.00 0.00 0.00 2.10
598 666 0.321653 ACGCCTGGTTGCCTTTCTAG 60.322 55.000 0.00 0.00 0.00 2.43
599 667 1.648467 CGCCTGGTTGCCTTTCTAGC 61.648 60.000 0.00 0.00 0.00 3.42
600 668 1.315981 GCCTGGTTGCCTTTCTAGCC 61.316 60.000 0.00 0.00 0.00 3.93
601 669 0.038166 CCTGGTTGCCTTTCTAGCCA 59.962 55.000 0.00 0.00 0.00 4.75
602 670 1.168714 CTGGTTGCCTTTCTAGCCAC 58.831 55.000 0.00 0.00 0.00 5.01
603 671 0.605319 TGGTTGCCTTTCTAGCCACG 60.605 55.000 0.00 0.00 0.00 4.94
604 672 1.305930 GGTTGCCTTTCTAGCCACGG 61.306 60.000 0.00 0.00 0.00 4.94
605 673 1.674322 TTGCCTTTCTAGCCACGGC 60.674 57.895 0.00 0.00 41.06 5.68
606 674 2.824489 GCCTTTCTAGCCACGGCC 60.824 66.667 3.95 0.00 43.17 6.13
607 675 2.124695 CCTTTCTAGCCACGGCCC 60.125 66.667 3.95 0.00 43.17 5.80
608 676 2.668632 CTTTCTAGCCACGGCCCA 59.331 61.111 3.95 0.00 43.17 5.36
609 677 1.745489 CTTTCTAGCCACGGCCCAC 60.745 63.158 3.95 0.00 43.17 4.61
620 688 3.563512 GGCCCACGACCCATAGAT 58.436 61.111 0.00 0.00 0.00 1.98
621 689 1.837090 GGCCCACGACCCATAGATT 59.163 57.895 0.00 0.00 0.00 2.40
622 690 0.182775 GGCCCACGACCCATAGATTT 59.817 55.000 0.00 0.00 0.00 2.17
623 691 1.409661 GGCCCACGACCCATAGATTTT 60.410 52.381 0.00 0.00 0.00 1.82
624 692 2.375146 GCCCACGACCCATAGATTTTT 58.625 47.619 0.00 0.00 0.00 1.94
641 709 1.808411 TTTTTCGCACTAGCCCAGAG 58.192 50.000 0.00 0.00 37.52 3.35
642 710 0.036388 TTTTCGCACTAGCCCAGAGG 60.036 55.000 0.00 0.00 37.52 3.69
653 721 1.604378 CCCAGAGGCCTTGTACTGG 59.396 63.158 25.01 25.01 46.37 4.00
656 724 1.561643 CAGAGGCCTTGTACTGGAGA 58.438 55.000 6.77 0.00 0.00 3.71
657 725 1.480137 CAGAGGCCTTGTACTGGAGAG 59.520 57.143 6.77 0.00 0.00 3.20
658 726 0.827368 GAGGCCTTGTACTGGAGAGG 59.173 60.000 6.77 3.38 0.00 3.69
659 727 0.618968 AGGCCTTGTACTGGAGAGGG 60.619 60.000 0.00 0.00 0.00 4.30
660 728 1.627297 GGCCTTGTACTGGAGAGGGG 61.627 65.000 0.00 0.00 0.00 4.79
661 729 1.908483 CCTTGTACTGGAGAGGGGC 59.092 63.158 0.00 0.00 0.00 5.80
662 730 1.627297 CCTTGTACTGGAGAGGGGCC 61.627 65.000 0.00 0.00 0.00 5.80
663 731 1.615424 TTGTACTGGAGAGGGGCCC 60.615 63.158 17.12 17.12 0.00 5.80
664 732 2.768769 GTACTGGAGAGGGGCCCC 60.769 72.222 35.90 35.90 0.00 5.80
673 741 3.906980 AGGGGCCCCTCGATTATG 58.093 61.111 39.79 0.00 44.43 1.90
674 742 1.847968 AGGGGCCCCTCGATTATGG 60.848 63.158 39.79 0.00 44.43 2.74
675 743 2.757077 GGGCCCCTCGATTATGGG 59.243 66.667 12.23 0.36 42.98 4.00
679 747 2.757077 CCCTCGATTATGGGGGCC 59.243 66.667 0.00 0.00 39.76 5.80
680 748 2.757077 CCTCGATTATGGGGGCCC 59.243 66.667 15.76 15.76 0.00 5.80
681 749 2.347490 CTCGATTATGGGGGCCCG 59.653 66.667 17.79 2.66 39.42 6.13
682 750 3.246112 TCGATTATGGGGGCCCGG 61.246 66.667 17.79 0.00 39.42 5.73
683 751 4.344865 CGATTATGGGGGCCCGGG 62.345 72.222 19.09 19.09 39.42 5.73
684 752 3.979497 GATTATGGGGGCCCGGGG 61.979 72.222 25.28 9.31 39.42 5.73
685 753 4.875301 ATTATGGGGGCCCGGGGT 62.875 66.667 25.28 4.08 39.42 4.95
912 981 0.108329 CCCGACCTTCATACGCAGTT 60.108 55.000 0.00 0.00 37.78 3.16
1190 1295 1.666700 TGTGTACGTGAACTTTGGCAC 59.333 47.619 0.00 0.00 0.00 5.01
1209 1314 3.364549 CACCACCACCATAATGACCAAT 58.635 45.455 0.00 0.00 0.00 3.16
1278 1383 0.558220 TCCTCTGGATCATCCGTCCT 59.442 55.000 0.00 0.00 40.17 3.85
1298 1403 2.303549 GACCTCATCAGGGGCGACAG 62.304 65.000 0.00 0.00 45.53 3.51
1354 1460 1.021390 CGAGTGTGGTCTCATTGCCC 61.021 60.000 0.00 0.00 34.46 5.36
1356 1462 1.074775 GTGTGGTCTCATTGCCCCA 59.925 57.895 0.00 0.00 0.00 4.96
1365 1471 4.008669 ATTGCCCCATGGTGCCCA 62.009 61.111 17.16 3.58 38.19 5.36
1525 1631 1.259142 CCAATGCACTGAATGGGGCA 61.259 55.000 0.00 0.00 41.00 5.36
1544 1650 2.291365 CATTGGCATGGAGATCGACAA 58.709 47.619 0.00 0.00 0.00 3.18
1726 1833 1.289530 AGGTGCTAGCTCCTACTCCTT 59.710 52.381 31.92 10.65 38.06 3.36
1730 1837 1.781786 CTAGCTCCTACTCCTTGCCA 58.218 55.000 0.00 0.00 0.00 4.92
1743 1850 0.798776 CTTGCCACTCTGCGTAAAGG 59.201 55.000 0.00 0.00 0.00 3.11
1750 1857 4.260784 GCCACTCTGCGTAAAGGAATAATG 60.261 45.833 0.00 0.00 0.00 1.90
1766 1877 4.796110 ATAATGGTGTACCTGCTCCAAT 57.204 40.909 2.32 0.00 35.91 3.16
1769 1880 1.271325 TGGTGTACCTGCTCCAATGTG 60.271 52.381 2.32 0.00 36.82 3.21
1771 1882 2.504367 GTGTACCTGCTCCAATGTGTT 58.496 47.619 0.00 0.00 0.00 3.32
1772 1883 2.484264 GTGTACCTGCTCCAATGTGTTC 59.516 50.000 0.00 0.00 0.00 3.18
1792 1904 5.220381 GTTCTTTTCTCAATCCCGGTTTTC 58.780 41.667 0.00 0.00 0.00 2.29
1793 1905 4.465886 TCTTTTCTCAATCCCGGTTTTCA 58.534 39.130 0.00 0.00 0.00 2.69
1831 1944 1.615384 CCTTCTTTTGGAGGAGGCAGG 60.615 57.143 0.00 0.00 44.34 4.85
1837 1950 0.987294 TTGGAGGAGGCAGGAAGAAG 59.013 55.000 0.00 0.00 0.00 2.85
1845 1958 1.073284 AGGCAGGAAGAAGCGGTTTTA 59.927 47.619 0.00 0.00 0.00 1.52
1862 1975 7.384387 AGCGGTTTTAAGAATATCTCGGTAATC 59.616 37.037 0.00 0.00 0.00 1.75
1863 1976 7.384387 GCGGTTTTAAGAATATCTCGGTAATCT 59.616 37.037 0.00 0.00 0.00 2.40
1864 1977 9.257651 CGGTTTTAAGAATATCTCGGTAATCTT 57.742 33.333 0.00 0.00 30.92 2.40
1888 2001 6.399639 AGTAATTACCGCCCAATAAAATGG 57.600 37.500 12.05 0.00 40.35 3.16
1897 2010 7.342581 ACCGCCCAATAAAATGGAATAAATTT 58.657 30.769 0.00 0.00 43.54 1.82
1937 2050 7.678947 TGGTGCCAAAAATAAATGTAATTGG 57.321 32.000 0.00 0.00 36.10 3.16
1943 2056 8.970859 CCAAAAATAAATGTAATTGGCCCATA 57.029 30.769 0.00 0.00 36.10 2.74
1950 2063 5.612725 ATGTAATTGGCCCATAGTTTTGG 57.387 39.130 0.00 0.00 36.46 3.28
1951 2064 4.678256 TGTAATTGGCCCATAGTTTTGGA 58.322 39.130 0.00 0.00 39.25 3.53
1969 2082 8.218488 AGTTTTGGAATTAGTAGTTCTTGTCCT 58.782 33.333 5.50 0.00 0.00 3.85
1974 2087 6.295688 GGAATTAGTAGTTCTTGTCCTGGTGA 60.296 42.308 5.50 0.00 0.00 4.02
1986 2099 3.491598 CTGGTGACCCGCCCACTTT 62.492 63.158 0.00 0.00 35.05 2.66
2003 2116 4.401202 CCACTTTGTTACTTCCCACAAGTT 59.599 41.667 0.00 0.00 34.43 2.66
2004 2117 5.339990 CACTTTGTTACTTCCCACAAGTTG 58.660 41.667 0.00 0.00 34.43 3.16
2014 2129 4.028993 TCCCACAAGTTGATTCTAACCC 57.971 45.455 10.54 0.00 0.00 4.11
2037 2152 0.686224 ACCGGGTGTATGGACGAAAA 59.314 50.000 6.32 0.00 0.00 2.29
2038 2153 1.279846 ACCGGGTGTATGGACGAAAAT 59.720 47.619 6.32 0.00 0.00 1.82
2040 2155 1.668751 CGGGTGTATGGACGAAAATGG 59.331 52.381 0.00 0.00 0.00 3.16
2042 2157 1.404035 GGTGTATGGACGAAAATGGCC 59.596 52.381 0.00 0.00 0.00 5.36
2043 2158 2.088423 GTGTATGGACGAAAATGGCCA 58.912 47.619 8.56 8.56 34.45 5.36
2044 2159 2.088423 TGTATGGACGAAAATGGCCAC 58.912 47.619 8.16 0.00 32.42 5.01
2045 2160 2.290641 TGTATGGACGAAAATGGCCACT 60.291 45.455 8.16 0.00 32.42 4.00
2052 2167 0.808755 GAAAATGGCCACTACCACCG 59.191 55.000 8.16 0.00 44.17 4.94
2093 2208 2.850321 CAACGATTGCATACACACACC 58.150 47.619 0.00 0.00 0.00 4.16
2094 2209 2.472695 ACGATTGCATACACACACCT 57.527 45.000 0.00 0.00 0.00 4.00
2095 2210 2.778299 ACGATTGCATACACACACCTT 58.222 42.857 0.00 0.00 0.00 3.50
2100 2215 6.596106 ACGATTGCATACACACACCTTATTTA 59.404 34.615 0.00 0.00 0.00 1.40
2163 2279 5.221481 TGTTGGACGGTAACAGTAATTCTCA 60.221 40.000 0.00 0.00 33.43 3.27
2172 2288 7.120726 CGGTAACAGTAATTCTCAAAAGGGAAT 59.879 37.037 0.00 0.00 34.14 3.01
2181 2297 2.733026 CTCAAAAGGGAATGCAAAAGCG 59.267 45.455 0.00 0.00 0.00 4.68
2209 2325 4.687483 ACCAGACAGTTTTCGTAAATACCG 59.313 41.667 0.00 0.00 0.00 4.02
2211 2327 5.164022 CCAGACAGTTTTCGTAAATACCGAC 60.164 44.000 0.00 0.00 33.41 4.79
2246 2363 4.077300 TGGACATGCTCCATGAGATAAC 57.923 45.455 11.78 0.00 44.99 1.89
2266 2389 7.569111 AGATAACTTATAAGGAGGACACACCAT 59.431 37.037 16.73 0.00 42.04 3.55
2283 2406 5.545658 CACCATCGTGTTTTTAGCTACAT 57.454 39.130 0.00 0.00 35.10 2.29
2307 2430 2.114616 GGAGAGATGTGTGAGTGGGAT 58.885 52.381 0.00 0.00 0.00 3.85
2309 2432 3.706594 GGAGAGATGTGTGAGTGGGATTA 59.293 47.826 0.00 0.00 0.00 1.75
2310 2433 4.162320 GGAGAGATGTGTGAGTGGGATTAA 59.838 45.833 0.00 0.00 0.00 1.40
2327 2450 5.754778 GGATTAATTATCCCGGTTTCAACG 58.245 41.667 0.00 0.00 46.20 4.10
2342 2465 4.974368 TTCAACGAGGTGTCAATGTTTT 57.026 36.364 0.00 0.00 0.00 2.43
2343 2466 4.545823 TCAACGAGGTGTCAATGTTTTC 57.454 40.909 0.00 0.00 0.00 2.29
2359 2482 3.128589 TGTTTTCGCTTAGCAATCCCATC 59.871 43.478 4.70 0.00 0.00 3.51
2386 2509 3.024784 CGTGTGCATATGCCGCAT 58.975 55.556 24.54 11.38 42.32 4.73
2387 2510 1.082561 CGTGTGCATATGCCGCATC 60.083 57.895 24.54 15.12 42.32 3.91
2388 2511 1.774046 CGTGTGCATATGCCGCATCA 61.774 55.000 24.54 12.56 42.32 3.07
2389 2512 0.381445 GTGTGCATATGCCGCATCAA 59.619 50.000 24.54 1.08 42.32 2.57
2390 2513 1.101331 TGTGCATATGCCGCATCAAA 58.899 45.000 24.54 0.28 42.32 2.69
2392 2515 2.883386 TGTGCATATGCCGCATCAAATA 59.117 40.909 24.54 0.00 42.32 1.40
2650 2773 9.512588 GGATATCATGACCTTTTGTAATGAGAT 57.487 33.333 4.83 0.53 46.04 2.75
2658 2781 4.858692 CCTTTTGTAATGAGATGCGTTTGG 59.141 41.667 0.00 0.00 0.00 3.28
2659 2782 3.485947 TTGTAATGAGATGCGTTTGGC 57.514 42.857 0.00 0.00 43.96 4.52
2669 2792 1.591327 GCGTTTGGCCTGTGTTTGG 60.591 57.895 3.32 0.00 34.80 3.28
2672 2795 1.801025 CGTTTGGCCTGTGTTTGGAAC 60.801 52.381 3.32 0.00 0.00 3.62
2678 2801 1.877443 GCCTGTGTTTGGAACGTGTAT 59.123 47.619 0.00 0.00 0.00 2.29
2680 2803 3.124636 GCCTGTGTTTGGAACGTGTATAG 59.875 47.826 0.00 0.00 0.00 1.31
2702 2825 4.699257 AGGACTTGCTCAACATCTGATTTC 59.301 41.667 0.00 0.00 32.14 2.17
2703 2826 4.142513 GGACTTGCTCAACATCTGATTTCC 60.143 45.833 0.00 0.00 32.14 3.13
2715 2838 5.301805 ACATCTGATTTCCGTTTGAAAGGTT 59.698 36.000 0.00 0.00 45.74 3.50
2716 2839 5.845391 TCTGATTTCCGTTTGAAAGGTTT 57.155 34.783 0.00 0.00 45.74 3.27
2727 2850 5.230182 GTTTGAAAGGTTTATGCAAGAGGG 58.770 41.667 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
329 340 3.271729 TGCTTCGTCGAACTCTAGATCT 58.728 45.455 2.90 0.00 0.00 2.75
548 616 5.390991 CGGCAGACTCTATTCCTTTTGTTTC 60.391 44.000 0.00 0.00 0.00 2.78
549 617 4.455877 CGGCAGACTCTATTCCTTTTGTTT 59.544 41.667 0.00 0.00 0.00 2.83
550 618 4.003648 CGGCAGACTCTATTCCTTTTGTT 58.996 43.478 0.00 0.00 0.00 2.83
551 619 3.600388 CGGCAGACTCTATTCCTTTTGT 58.400 45.455 0.00 0.00 0.00 2.83
552 620 2.939103 CCGGCAGACTCTATTCCTTTTG 59.061 50.000 0.00 0.00 0.00 2.44
553 621 2.681097 GCCGGCAGACTCTATTCCTTTT 60.681 50.000 24.80 0.00 0.00 2.27
554 622 1.134371 GCCGGCAGACTCTATTCCTTT 60.134 52.381 24.80 0.00 0.00 3.11
555 623 0.466124 GCCGGCAGACTCTATTCCTT 59.534 55.000 24.80 0.00 0.00 3.36
556 624 1.739338 CGCCGGCAGACTCTATTCCT 61.739 60.000 28.98 0.00 0.00 3.36
557 625 1.300233 CGCCGGCAGACTCTATTCC 60.300 63.158 28.98 0.00 0.00 3.01
558 626 0.595310 GACGCCGGCAGACTCTATTC 60.595 60.000 28.98 7.10 0.00 1.75
559 627 1.437986 GACGCCGGCAGACTCTATT 59.562 57.895 28.98 1.00 0.00 1.73
560 628 2.491022 GGACGCCGGCAGACTCTAT 61.491 63.158 28.98 1.76 0.00 1.98
561 629 3.138798 GGACGCCGGCAGACTCTA 61.139 66.667 28.98 0.00 0.00 2.43
581 649 2.184323 GCTAGAAAGGCAACCAGGC 58.816 57.895 0.00 0.00 44.61 4.85
590 658 2.124695 GGGCCGTGGCTAGAAAGG 60.125 66.667 11.25 0.00 41.60 3.11
591 659 1.745489 GTGGGCCGTGGCTAGAAAG 60.745 63.158 11.25 0.00 41.60 2.62
592 660 2.349755 GTGGGCCGTGGCTAGAAA 59.650 61.111 11.25 0.00 41.60 2.52
593 661 4.077184 CGTGGGCCGTGGCTAGAA 62.077 66.667 11.25 0.00 41.60 2.10
595 663 4.814294 GTCGTGGGCCGTGGCTAG 62.814 72.222 11.25 0.37 41.60 3.42
600 668 3.733344 CTATGGGTCGTGGGCCGTG 62.733 68.421 0.00 0.00 37.94 4.94
601 669 3.467226 CTATGGGTCGTGGGCCGT 61.467 66.667 0.00 0.00 37.94 5.68
602 670 2.040009 AATCTATGGGTCGTGGGCCG 62.040 60.000 0.00 0.00 38.13 6.13
603 671 0.182775 AAATCTATGGGTCGTGGGCC 59.817 55.000 0.00 0.00 0.00 5.80
604 672 2.052782 AAAATCTATGGGTCGTGGGC 57.947 50.000 0.00 0.00 0.00 5.36
622 690 1.610624 CCTCTGGGCTAGTGCGAAAAA 60.611 52.381 0.00 0.00 40.82 1.94
623 691 0.036388 CCTCTGGGCTAGTGCGAAAA 60.036 55.000 0.00 0.00 40.82 2.29
624 692 1.596934 CCTCTGGGCTAGTGCGAAA 59.403 57.895 0.00 0.00 40.82 3.46
625 693 3.298958 CCTCTGGGCTAGTGCGAA 58.701 61.111 0.00 0.00 40.82 4.70
635 703 0.909610 TCCAGTACAAGGCCTCTGGG 60.910 60.000 29.00 15.98 45.07 4.45
636 704 0.539051 CTCCAGTACAAGGCCTCTGG 59.461 60.000 25.70 25.70 46.00 3.86
637 705 1.480137 CTCTCCAGTACAAGGCCTCTG 59.520 57.143 5.23 9.22 0.00 3.35
638 706 1.621072 CCTCTCCAGTACAAGGCCTCT 60.621 57.143 5.23 0.00 0.00 3.69
639 707 0.827368 CCTCTCCAGTACAAGGCCTC 59.173 60.000 5.23 0.00 0.00 4.70
640 708 0.618968 CCCTCTCCAGTACAAGGCCT 60.619 60.000 0.00 0.00 0.00 5.19
641 709 1.627297 CCCCTCTCCAGTACAAGGCC 61.627 65.000 0.00 0.00 0.00 5.19
642 710 1.908483 CCCCTCTCCAGTACAAGGC 59.092 63.158 0.00 0.00 0.00 4.35
643 711 1.627297 GGCCCCTCTCCAGTACAAGG 61.627 65.000 0.00 0.00 0.00 3.61
644 712 1.627297 GGGCCCCTCTCCAGTACAAG 61.627 65.000 12.23 0.00 0.00 3.16
645 713 1.615424 GGGCCCCTCTCCAGTACAA 60.615 63.158 12.23 0.00 0.00 2.41
646 714 2.040606 GGGCCCCTCTCCAGTACA 59.959 66.667 12.23 0.00 0.00 2.90
647 715 2.768769 GGGGCCCCTCTCCAGTAC 60.769 72.222 35.49 1.84 0.00 2.73
648 716 2.958739 AGGGGCCCCTCTCCAGTA 60.959 66.667 39.79 0.00 44.43 2.74
657 725 2.757077 CCATAATCGAGGGGCCCC 59.243 66.667 35.90 35.90 0.00 5.80
658 726 2.757077 CCCATAATCGAGGGGCCC 59.243 66.667 17.12 17.12 43.81 5.80
662 730 2.757077 GGCCCCCATAATCGAGGG 59.243 66.667 0.36 0.36 45.04 4.30
663 731 2.757077 GGGCCCCCATAATCGAGG 59.243 66.667 12.23 0.00 35.81 4.63
664 732 2.347490 CGGGCCCCCATAATCGAG 59.653 66.667 18.66 0.00 35.37 4.04
665 733 3.246112 CCGGGCCCCCATAATCGA 61.246 66.667 18.66 0.00 35.37 3.59
666 734 4.344865 CCCGGGCCCCCATAATCG 62.345 72.222 18.66 0.62 35.37 3.34
667 735 3.979497 CCCCGGGCCCCCATAATC 61.979 72.222 17.73 0.00 35.37 1.75
668 736 4.875301 ACCCCGGGCCCCCATAAT 62.875 66.667 17.73 0.00 35.37 1.28
715 783 3.958860 ACAGCTGGACACAGGCCC 61.959 66.667 19.93 0.00 45.04 5.80
716 784 2.670934 CACAGCTGGACACAGGCC 60.671 66.667 19.93 0.00 45.04 5.19
717 785 2.670934 CCACAGCTGGACACAGGC 60.671 66.667 19.93 0.00 45.04 4.85
721 789 2.203337 TTGCCCACAGCTGGACAC 60.203 61.111 19.93 5.38 44.23 3.67
872 941 3.263425 GGAAGTCCCTGAACCTCATGTTA 59.737 47.826 0.00 0.00 37.29 2.41
912 981 2.436646 GTAGTCGTCCGGGGTCGA 60.437 66.667 0.00 7.44 39.00 4.20
1190 1295 3.630168 TCATTGGTCATTATGGTGGTGG 58.370 45.455 0.00 0.00 0.00 4.61
1209 1314 0.528017 CGAACTCTACCAGCTGCTCA 59.472 55.000 8.66 0.00 0.00 4.26
1243 1348 1.888512 GAGGAAATGCTTGCCACTCAA 59.111 47.619 0.00 0.00 0.00 3.02
1278 1383 2.038813 TCGCCCCTGATGAGGTCA 59.961 61.111 0.00 0.00 37.73 4.02
1322 1428 3.608662 ACTCGGCGGTTTCGACCA 61.609 61.111 7.21 0.00 42.49 4.02
1365 1471 4.568152 GTGATTTAACACCTGCTGTTGT 57.432 40.909 0.35 0.00 43.38 3.32
1380 1486 2.035626 CCCACTGCCGGGTGATTT 59.964 61.111 11.95 0.00 41.83 2.17
1414 1520 1.891919 GTGTTGAGTTCCAGCCGCA 60.892 57.895 0.00 0.00 0.00 5.69
1525 1631 2.292267 GTTGTCGATCTCCATGCCAAT 58.708 47.619 0.00 0.00 0.00 3.16
1544 1650 3.240203 CGTCACGCCGAACATTGT 58.760 55.556 0.00 0.00 0.00 2.71
1726 1833 0.394938 TTCCTTTACGCAGAGTGGCA 59.605 50.000 0.00 0.00 0.00 4.92
1730 1837 4.876107 CACCATTATTCCTTTACGCAGAGT 59.124 41.667 0.00 0.00 0.00 3.24
1743 1850 4.150897 TGGAGCAGGTACACCATTATTC 57.849 45.455 0.38 0.00 38.89 1.75
1750 1857 1.271379 ACACATTGGAGCAGGTACACC 60.271 52.381 0.00 0.00 0.00 4.16
1766 1877 3.146066 CCGGGATTGAGAAAAGAACACA 58.854 45.455 0.00 0.00 0.00 3.72
1769 1880 4.848562 AAACCGGGATTGAGAAAAGAAC 57.151 40.909 6.32 0.00 0.00 3.01
1771 1882 4.465886 TGAAAACCGGGATTGAGAAAAGA 58.534 39.130 6.32 0.00 0.00 2.52
1772 1883 4.518970 TCTGAAAACCGGGATTGAGAAAAG 59.481 41.667 6.32 0.00 0.00 2.27
1792 1904 0.464554 GGATTTTCCGGCCTCCTCTG 60.465 60.000 0.00 0.00 0.00 3.35
1793 1905 1.636769 GGGATTTTCCGGCCTCCTCT 61.637 60.000 0.00 0.00 37.43 3.69
1828 1941 5.629079 ATTCTTAAAACCGCTTCTTCCTG 57.371 39.130 0.00 0.00 0.00 3.86
1829 1942 7.339482 AGATATTCTTAAAACCGCTTCTTCCT 58.661 34.615 0.00 0.00 0.00 3.36
1831 1944 7.338462 CGAGATATTCTTAAAACCGCTTCTTC 58.662 38.462 0.00 0.00 0.00 2.87
1837 1950 6.833342 TTACCGAGATATTCTTAAAACCGC 57.167 37.500 0.00 0.00 0.00 5.68
1862 1975 8.079809 CCATTTTATTGGGCGGTAATTACTAAG 58.920 37.037 15.05 8.36 32.80 2.18
1863 1976 7.778853 TCCATTTTATTGGGCGGTAATTACTAA 59.221 33.333 15.05 1.98 37.37 2.24
1864 1977 7.288560 TCCATTTTATTGGGCGGTAATTACTA 58.711 34.615 15.05 0.00 37.37 1.82
1865 1978 6.130569 TCCATTTTATTGGGCGGTAATTACT 58.869 36.000 15.05 0.00 37.37 2.24
1866 1979 6.394025 TCCATTTTATTGGGCGGTAATTAC 57.606 37.500 7.09 7.09 37.37 1.89
1867 1980 7.604657 ATTCCATTTTATTGGGCGGTAATTA 57.395 32.000 0.00 0.00 37.37 1.40
1868 1981 5.941555 TTCCATTTTATTGGGCGGTAATT 57.058 34.783 0.00 0.00 37.37 1.40
1869 1982 7.604657 TTATTCCATTTTATTGGGCGGTAAT 57.395 32.000 0.00 0.00 37.37 1.89
1870 1983 7.419711 TTTATTCCATTTTATTGGGCGGTAA 57.580 32.000 0.00 0.00 37.37 2.85
1897 2010 4.195416 GGCACCAAGGTTTTTGAATTCAA 58.805 39.130 16.91 16.91 0.00 2.69
1904 2017 4.979943 ATTTTTGGCACCAAGGTTTTTG 57.020 36.364 1.79 0.00 37.24 2.44
1911 2024 8.235905 CCAATTACATTTATTTTTGGCACCAAG 58.764 33.333 1.79 0.00 37.24 3.61
1937 2050 7.556635 AGAACTACTAATTCCAAAACTATGGGC 59.443 37.037 0.00 0.00 41.05 5.36
1943 2056 8.218488 AGGACAAGAACTACTAATTCCAAAACT 58.782 33.333 0.00 0.00 0.00 2.66
1950 2063 6.590677 GTCACCAGGACAAGAACTACTAATTC 59.409 42.308 0.00 0.00 46.19 2.17
1951 2064 6.465084 GTCACCAGGACAAGAACTACTAATT 58.535 40.000 0.00 0.00 46.19 1.40
1969 2082 3.494254 AAAGTGGGCGGGTCACCA 61.494 61.111 0.00 0.00 35.87 4.17
1974 2087 0.184211 AAGTAACAAAGTGGGCGGGT 59.816 50.000 0.00 0.00 0.00 5.28
1986 2099 5.690865 AGAATCAACTTGTGGGAAGTAACA 58.309 37.500 0.00 0.00 0.00 2.41
2014 2129 1.438814 GTCCATACACCCGGTACCG 59.561 63.158 27.68 27.68 34.07 4.02
2026 2141 2.799126 AGTGGCCATTTTCGTCCATA 57.201 45.000 9.72 0.00 0.00 2.74
2037 2152 4.467084 CGCGGTGGTAGTGGCCAT 62.467 66.667 9.72 0.00 41.08 4.40
2042 2157 3.118454 CTTGGCGCGGTGGTAGTG 61.118 66.667 8.83 0.00 0.00 2.74
2043 2158 4.388499 CCTTGGCGCGGTGGTAGT 62.388 66.667 8.83 0.00 0.00 2.73
2052 2167 3.741476 CTTCACAGGCCTTGGCGC 61.741 66.667 0.00 0.00 0.00 6.53
2091 2206 8.548877 TGAGCTCTGAATAGGTTTAAATAAGGT 58.451 33.333 16.19 0.00 0.00 3.50
2092 2207 8.964476 TGAGCTCTGAATAGGTTTAAATAAGG 57.036 34.615 16.19 0.00 0.00 2.69
2100 2215 7.765695 TTTGATTTGAGCTCTGAATAGGTTT 57.234 32.000 16.19 0.00 0.00 3.27
2140 2256 5.232463 TGAGAATTACTGTTACCGTCCAAC 58.768 41.667 0.00 0.00 0.00 3.77
2181 2297 2.294979 ACGAAAACTGTCTGGTTTCCC 58.705 47.619 12.96 0.00 46.64 3.97
2191 2307 3.674753 CGGTCGGTATTTACGAAAACTGT 59.325 43.478 0.00 0.00 42.55 3.55
2246 2363 4.099573 ACGATGGTGTGTCCTCCTTATAAG 59.900 45.833 5.43 5.43 37.07 1.73
2266 2389 4.020928 TCCCTGATGTAGCTAAAAACACGA 60.021 41.667 0.00 0.00 0.00 4.35
2283 2406 2.174360 CACTCACACATCTCTCCCTGA 58.826 52.381 0.00 0.00 0.00 3.86
2307 2430 4.877251 CCTCGTTGAAACCGGGATAATTAA 59.123 41.667 6.32 0.00 0.00 1.40
2309 2432 3.275999 CCTCGTTGAAACCGGGATAATT 58.724 45.455 6.32 0.00 0.00 1.40
2310 2433 2.237893 ACCTCGTTGAAACCGGGATAAT 59.762 45.455 6.32 0.00 0.00 1.28
2327 2450 3.626028 AAGCGAAAACATTGACACCTC 57.374 42.857 0.00 0.00 0.00 3.85
2342 2465 2.092968 ACAAGATGGGATTGCTAAGCGA 60.093 45.455 0.00 0.00 0.00 4.93
2343 2466 2.292267 ACAAGATGGGATTGCTAAGCG 58.708 47.619 0.00 0.00 0.00 4.68
2359 2482 1.240641 TATGCACACGCCCCAACAAG 61.241 55.000 0.00 0.00 37.32 3.16
2650 2773 1.140589 CAAACACAGGCCAAACGCA 59.859 52.632 5.01 0.00 40.31 5.24
2658 2781 1.301423 TACACGTTCCAAACACAGGC 58.699 50.000 0.00 0.00 0.00 4.85
2659 2782 3.682858 CCTATACACGTTCCAAACACAGG 59.317 47.826 0.00 0.00 0.00 4.00
2669 2792 4.106029 TGAGCAAGTCCTATACACGTTC 57.894 45.455 0.00 0.00 0.00 3.95
2672 2795 3.845178 TGTTGAGCAAGTCCTATACACG 58.155 45.455 0.00 0.00 0.00 4.49
2678 2801 5.426689 AATCAGATGTTGAGCAAGTCCTA 57.573 39.130 0.00 0.00 39.68 2.94
2680 2803 4.142513 GGAAATCAGATGTTGAGCAAGTCC 60.143 45.833 0.00 0.00 39.68 3.85
2702 2825 4.865776 TCTTGCATAAACCTTTCAAACGG 58.134 39.130 0.00 0.00 0.00 4.44
2703 2826 4.917415 CCTCTTGCATAAACCTTTCAAACG 59.083 41.667 0.00 0.00 0.00 3.60


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

AutoCloner maintained by Alex Coulton.