Multiple sequence alignment - TraesCS4B01G388300

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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 TraesCS4B01G388300 chr4B 100.000 2805 0 0 1 2805 665558825 665561629 0.000000e+00 5180.0
1 TraesCS4B01G388300 chr4B 92.602 1987 72 24 707 2685 625975959 625977878 0.000000e+00 2785.0
2 TraesCS4B01G388300 chr4B 92.085 1415 93 10 707 2110 665876324 665874918 0.000000e+00 1975.0
3 TraesCS4B01G388300 chr4B 94.111 866 43 5 1888 2749 666581159 666580298 0.000000e+00 1310.0
4 TraesCS4B01G388300 chr4B 86.494 1044 128 5 707 1744 666582194 666581158 0.000000e+00 1134.0
5 TraesCS4B01G388300 chr4B 97.391 575 15 0 1 575 625975393 625975967 0.000000e+00 979.0
6 TraesCS4B01G388300 chr4B 91.958 572 46 0 4 575 665876887 665876316 0.000000e+00 802.0
7 TraesCS4B01G388300 chr4B 78.186 463 53 23 2289 2720 625873268 625873713 4.640000e-63 252.0
8 TraesCS4B01G388300 chr5A 92.155 1415 92 10 707 2110 705843309 705841903 0.000000e+00 1980.0
9 TraesCS4B01G388300 chr5A 92.917 960 59 5 1476 2428 705565215 705566172 0.000000e+00 1387.0
10 TraesCS4B01G388300 chr5A 92.133 572 45 0 4 575 705843872 705843301 0.000000e+00 808.0
11 TraesCS4B01G388300 chr5A 86.415 530 63 7 50 575 706083483 706084007 3.130000e-159 571.0
12 TraesCS4B01G388300 chr5A 90.099 101 8 2 611 711 676909671 676909769 2.270000e-26 130.0
13 TraesCS4B01G388300 chrUn 92.440 1164 78 6 707 1861 108322490 108323652 0.000000e+00 1653.0
14 TraesCS4B01G388300 chrUn 93.333 570 38 0 6 575 108321929 108322498 0.000000e+00 843.0
15 TraesCS4B01G388300 chrUn 86.553 528 66 5 50 575 134253516 134252992 6.740000e-161 577.0
16 TraesCS4B01G388300 chrUn 86.553 528 66 5 50 575 134268314 134268838 6.740000e-161 577.0
17 TraesCS4B01G388300 chrUn 94.512 164 9 0 1947 2110 108323667 108323830 1.290000e-63 254.0
18 TraesCS4B01G388300 chrUn 92.857 98 7 0 2331 2428 108429066 108428969 2.910000e-30 143.0
19 TraesCS4B01G388300 chrUn 90.741 54 3 2 2685 2738 371225357 371225408 1.390000e-08 71.3
20 TraesCS4B01G388300 chr6B 84.665 1089 151 7 708 1788 88218617 88217537 0.000000e+00 1072.0
21 TraesCS4B01G388300 chr6B 87.875 866 105 0 712 1577 643264834 643265699 0.000000e+00 1018.0
22 TraesCS4B01G388300 chr6B 86.822 516 62 6 50 562 88219135 88218623 3.130000e-159 571.0
23 TraesCS4B01G388300 chr6B 97.761 134 2 1 575 707 63664808 63664941 2.170000e-56 230.0
24 TraesCS4B01G388300 chr6B 94.737 133 7 0 574 706 2310169 2310037 1.020000e-49 207.0
25 TraesCS4B01G388300 chr6B 93.443 122 8 0 576 697 177568398 177568519 6.170000e-42 182.0
26 TraesCS4B01G388300 chr6A 88.209 882 104 0 707 1588 572137684 572138565 0.000000e+00 1053.0
27 TraesCS4B01G388300 chr6A 84.520 562 80 5 6 563 572137122 572137680 1.470000e-152 549.0
28 TraesCS4B01G388300 chr6D 87.755 882 108 0 707 1588 427484329 427485210 0.000000e+00 1031.0
29 TraesCS4B01G388300 chr4A 99.242 132 1 0 574 705 199942227 199942096 3.610000e-59 239.0
30 TraesCS4B01G388300 chr5B 98.485 132 2 0 575 706 440262457 440262588 1.680000e-57 233.0
31 TraesCS4B01G388300 chr5B 96.117 103 4 0 576 678 613278237 613278339 4.810000e-38 169.0
32 TraesCS4B01G388300 chr5B 84.559 136 15 4 574 706 372024135 372024003 2.270000e-26 130.0
33 TraesCS4B01G388300 chr5B 81.022 137 22 2 1811 1947 705329026 705328894 3.820000e-19 106.0
34 TraesCS4B01G388300 chr1A 97.761 134 3 0 576 709 530170450 530170317 6.040000e-57 231.0
35 TraesCS4B01G388300 chr1A 74.825 143 34 2 1836 1977 368375947 368375806 2.330000e-06 63.9
36 TraesCS4B01G388300 chr7A 98.450 129 2 0 575 703 575223143 575223015 7.820000e-56 228.0
37 TraesCS4B01G388300 chr7B 96.800 125 4 0 578 702 10922583 10922459 2.830000e-50 209.0
38 TraesCS4B01G388300 chr5D 78.039 255 34 10 1791 2043 557510753 557510987 1.050000e-29 141.0
39 TraesCS4B01G388300 chr1D 84.127 63 10 0 1836 1898 295278583 295278521 8.390000e-06 62.1
40 TraesCS4B01G388300 chr1B 84.127 63 10 0 1836 1898 396601535 396601473 8.390000e-06 62.1


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 TraesCS4B01G388300 chr4B 665558825 665561629 2804 False 5180.000000 5180 100.000000 1 2805 1 chr4B.!!$F2 2804
1 TraesCS4B01G388300 chr4B 625975393 625977878 2485 False 1882.000000 2785 94.996500 1 2685 2 chr4B.!!$F3 2684
2 TraesCS4B01G388300 chr4B 665874918 665876887 1969 True 1388.500000 1975 92.021500 4 2110 2 chr4B.!!$R1 2106
3 TraesCS4B01G388300 chr4B 666580298 666582194 1896 True 1222.000000 1310 90.302500 707 2749 2 chr4B.!!$R2 2042
4 TraesCS4B01G388300 chr5A 705841903 705843872 1969 True 1394.000000 1980 92.144000 4 2110 2 chr5A.!!$R1 2106
5 TraesCS4B01G388300 chr5A 705565215 705566172 957 False 1387.000000 1387 92.917000 1476 2428 1 chr5A.!!$F2 952
6 TraesCS4B01G388300 chr5A 706083483 706084007 524 False 571.000000 571 86.415000 50 575 1 chr5A.!!$F3 525
7 TraesCS4B01G388300 chrUn 108321929 108323830 1901 False 916.666667 1653 93.428333 6 2110 3 chrUn.!!$F3 2104
8 TraesCS4B01G388300 chrUn 134252992 134253516 524 True 577.000000 577 86.553000 50 575 1 chrUn.!!$R2 525
9 TraesCS4B01G388300 chrUn 134268314 134268838 524 False 577.000000 577 86.553000 50 575 1 chrUn.!!$F1 525
10 TraesCS4B01G388300 chr6B 643264834 643265699 865 False 1018.000000 1018 87.875000 712 1577 1 chr6B.!!$F3 865
11 TraesCS4B01G388300 chr6B 88217537 88219135 1598 True 821.500000 1072 85.743500 50 1788 2 chr6B.!!$R2 1738
12 TraesCS4B01G388300 chr6A 572137122 572138565 1443 False 801.000000 1053 86.364500 6 1588 2 chr6A.!!$F1 1582
13 TraesCS4B01G388300 chr6D 427484329 427485210 881 False 1031.000000 1031 87.755000 707 1588 1 chr6D.!!$F1 881

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
649 655 0.036022 TGAATGCCACGTGTCATCCA 59.964 50.0 13.12 2.86 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1990 2008 1.195115 CTTCCTCCAGGGATTCGACA 58.805 55.0 0.0 0.0 44.66 4.35 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
104 109 3.813443 AGGTGTGGATGTTGATATCTGC 58.187 45.455 3.98 0.00 0.00 4.26
175 180 7.329471 TCATTCTAGAAACTTGTCTGACAATCG 59.671 37.037 22.28 14.55 37.48 3.34
565 571 6.912051 GTGAATGGGCAAAAATTTCAAGAAAC 59.088 34.615 0.00 0.00 32.51 2.78
566 572 6.039159 TGAATGGGCAAAAATTTCAAGAAACC 59.961 34.615 0.00 0.00 32.51 3.27
567 573 5.109500 TGGGCAAAAATTTCAAGAAACCT 57.891 34.783 0.00 0.00 32.51 3.50
568 574 4.880696 TGGGCAAAAATTTCAAGAAACCTG 59.119 37.500 0.00 0.00 32.51 4.00
569 575 4.881273 GGGCAAAAATTTCAAGAAACCTGT 59.119 37.500 0.00 0.00 32.51 4.00
570 576 5.356751 GGGCAAAAATTTCAAGAAACCTGTT 59.643 36.000 0.00 0.00 32.51 3.16
571 577 6.127758 GGGCAAAAATTTCAAGAAACCTGTTT 60.128 34.615 0.00 0.00 32.51 2.83
572 578 6.746822 GGCAAAAATTTCAAGAAACCTGTTTG 59.253 34.615 0.00 3.12 32.51 2.93
573 579 7.361628 GGCAAAAATTTCAAGAAACCTGTTTGA 60.362 33.333 12.58 0.00 32.51 2.69
574 580 7.481483 GCAAAAATTTCAAGAAACCTGTTTGAC 59.519 33.333 12.58 4.56 32.51 3.18
575 581 6.885735 AAATTTCAAGAAACCTGTTTGACG 57.114 33.333 0.00 0.00 32.51 4.35
576 582 4.364415 TTTCAAGAAACCTGTTTGACGG 57.636 40.909 0.00 0.00 31.11 4.79
577 583 3.269538 TCAAGAAACCTGTTTGACGGA 57.730 42.857 0.00 0.00 32.11 4.69
578 584 3.611970 TCAAGAAACCTGTTTGACGGAA 58.388 40.909 0.00 0.00 32.11 4.30
579 585 4.011023 TCAAGAAACCTGTTTGACGGAAA 58.989 39.130 0.00 0.00 32.11 3.13
580 586 4.459685 TCAAGAAACCTGTTTGACGGAAAA 59.540 37.500 0.00 0.00 32.11 2.29
581 587 5.047943 TCAAGAAACCTGTTTGACGGAAAAA 60.048 36.000 0.00 0.00 32.11 1.94
614 620 6.678568 AGACCAGGTCTCATATAAATCAGG 57.321 41.667 17.31 0.00 38.71 3.86
615 621 6.146760 AGACCAGGTCTCATATAAATCAGGT 58.853 40.000 17.31 0.00 38.71 4.00
616 622 6.042552 AGACCAGGTCTCATATAAATCAGGTG 59.957 42.308 17.31 0.00 38.71 4.00
617 623 5.905331 ACCAGGTCTCATATAAATCAGGTGA 59.095 40.000 0.00 0.00 0.00 4.02
618 624 6.042552 ACCAGGTCTCATATAAATCAGGTGAG 59.957 42.308 0.00 0.00 38.07 3.51
619 625 6.268617 CCAGGTCTCATATAAATCAGGTGAGA 59.731 42.308 0.00 0.00 41.99 3.27
622 628 6.672266 TCTCATATAAATCAGGTGAGACCC 57.328 41.667 0.00 0.00 40.06 4.46
623 629 5.243954 TCTCATATAAATCAGGTGAGACCCG 59.756 44.000 0.00 0.00 40.06 5.28
624 630 2.622064 ATAAATCAGGTGAGACCCGC 57.378 50.000 0.00 0.00 39.75 6.13
625 631 0.539986 TAAATCAGGTGAGACCCGCC 59.460 55.000 0.00 0.00 45.81 6.13
626 632 2.198304 AAATCAGGTGAGACCCGCCC 62.198 60.000 0.00 0.00 46.65 6.13
627 633 3.625632 ATCAGGTGAGACCCGCCCT 62.626 63.158 0.00 0.00 46.65 5.19
628 634 4.087892 CAGGTGAGACCCGCCCTG 62.088 72.222 0.00 0.00 46.65 4.45
629 635 4.316823 AGGTGAGACCCGCCCTGA 62.317 66.667 0.00 0.00 46.65 3.86
630 636 3.083997 GGTGAGACCCGCCCTGAT 61.084 66.667 0.00 0.00 39.55 2.90
631 637 2.187946 GTGAGACCCGCCCTGATG 59.812 66.667 0.00 0.00 0.00 3.07
632 638 2.038813 TGAGACCCGCCCTGATGA 59.961 61.111 0.00 0.00 0.00 2.92
633 639 1.612146 TGAGACCCGCCCTGATGAA 60.612 57.895 0.00 0.00 0.00 2.57
634 640 0.982852 TGAGACCCGCCCTGATGAAT 60.983 55.000 0.00 0.00 0.00 2.57
635 641 0.533755 GAGACCCGCCCTGATGAATG 60.534 60.000 0.00 0.00 0.00 2.67
636 642 2.124151 ACCCGCCCTGATGAATGC 60.124 61.111 0.00 0.00 0.00 3.56
637 643 2.908940 CCCGCCCTGATGAATGCC 60.909 66.667 0.00 0.00 0.00 4.40
638 644 2.124193 CCGCCCTGATGAATGCCA 60.124 61.111 0.00 0.00 0.00 4.92
639 645 2.484062 CCGCCCTGATGAATGCCAC 61.484 63.158 0.00 0.00 0.00 5.01
640 646 2.827051 CGCCCTGATGAATGCCACG 61.827 63.158 0.00 0.00 0.00 4.94
641 647 1.750399 GCCCTGATGAATGCCACGT 60.750 57.895 0.00 0.00 0.00 4.49
642 648 1.996786 GCCCTGATGAATGCCACGTG 61.997 60.000 9.08 9.08 0.00 4.49
643 649 0.677731 CCCTGATGAATGCCACGTGT 60.678 55.000 15.65 0.00 0.00 4.49
644 650 0.729116 CCTGATGAATGCCACGTGTC 59.271 55.000 15.65 0.98 0.00 3.67
645 651 1.441738 CTGATGAATGCCACGTGTCA 58.558 50.000 15.65 8.63 0.00 3.58
646 652 2.011947 CTGATGAATGCCACGTGTCAT 58.988 47.619 16.60 16.60 33.45 3.06
647 653 2.009051 TGATGAATGCCACGTGTCATC 58.991 47.619 27.38 27.38 44.33 2.92
648 654 1.331756 GATGAATGCCACGTGTCATCC 59.668 52.381 25.32 11.52 40.23 3.51
649 655 0.036022 TGAATGCCACGTGTCATCCA 59.964 50.000 13.12 2.86 0.00 3.41
650 656 1.339920 TGAATGCCACGTGTCATCCAT 60.340 47.619 13.12 0.00 0.00 3.41
651 657 1.331756 GAATGCCACGTGTCATCCATC 59.668 52.381 13.12 3.25 0.00 3.51
652 658 0.252761 ATGCCACGTGTCATCCATCA 59.747 50.000 15.65 0.00 0.00 3.07
653 659 0.391528 TGCCACGTGTCATCCATCAG 60.392 55.000 15.65 0.00 0.00 2.90
654 660 0.108186 GCCACGTGTCATCCATCAGA 60.108 55.000 15.65 0.00 0.00 3.27
655 661 1.675714 GCCACGTGTCATCCATCAGAA 60.676 52.381 15.65 0.00 0.00 3.02
656 662 2.910199 CCACGTGTCATCCATCAGAAT 58.090 47.619 15.65 0.00 0.00 2.40
657 663 2.610833 CCACGTGTCATCCATCAGAATG 59.389 50.000 15.65 0.00 37.54 2.67
661 667 3.209410 GTGTCATCCATCAGAATGGGTC 58.791 50.000 4.68 0.00 43.29 4.46
662 668 3.117745 TGTCATCCATCAGAATGGGTCT 58.882 45.455 4.68 0.00 43.29 3.85
663 669 3.135348 TGTCATCCATCAGAATGGGTCTC 59.865 47.826 4.68 0.00 43.29 3.36
664 670 3.135348 GTCATCCATCAGAATGGGTCTCA 59.865 47.826 4.68 0.00 43.29 3.27
665 671 3.135348 TCATCCATCAGAATGGGTCTCAC 59.865 47.826 4.68 0.00 43.29 3.51
666 672 2.441001 ATCCATCAGAATGGGTCTCACC 59.559 50.000 4.68 0.00 43.29 4.02
667 673 3.893100 ATCCATCAGAATGGGTCTCACCT 60.893 47.826 4.68 0.00 43.29 4.00
668 674 2.915349 CATCAGAATGGGTCTCACCTG 58.085 52.381 0.00 0.00 38.64 4.00
669 675 0.615331 TCAGAATGGGTCTCACCTGC 59.385 55.000 0.22 0.00 38.64 4.85
670 676 0.617413 CAGAATGGGTCTCACCTGCT 59.383 55.000 0.00 0.00 38.64 4.24
671 677 1.833630 CAGAATGGGTCTCACCTGCTA 59.166 52.381 0.00 0.00 38.64 3.49
672 678 2.237143 CAGAATGGGTCTCACCTGCTAA 59.763 50.000 0.00 0.00 38.64 3.09
673 679 3.118112 CAGAATGGGTCTCACCTGCTAAT 60.118 47.826 0.00 0.00 38.64 1.73
674 680 3.135530 AGAATGGGTCTCACCTGCTAATC 59.864 47.826 0.00 0.00 38.64 1.75
675 681 1.204146 TGGGTCTCACCTGCTAATCC 58.796 55.000 0.00 0.00 38.64 3.01
676 682 0.105039 GGGTCTCACCTGCTAATCCG 59.895 60.000 0.00 0.00 38.64 4.18
677 683 0.824759 GGTCTCACCTGCTAATCCGT 59.175 55.000 0.00 0.00 34.73 4.69
678 684 1.471676 GGTCTCACCTGCTAATCCGTG 60.472 57.143 0.00 0.00 34.73 4.94
679 685 1.476891 GTCTCACCTGCTAATCCGTGA 59.523 52.381 0.00 0.00 34.26 4.35
680 686 2.215907 CTCACCTGCTAATCCGTGAG 57.784 55.000 2.01 2.01 44.38 3.51
681 687 1.847328 TCACCTGCTAATCCGTGAGA 58.153 50.000 0.00 0.00 31.80 3.27
682 688 1.476891 TCACCTGCTAATCCGTGAGAC 59.523 52.381 0.00 0.00 31.80 3.36
683 689 0.824759 ACCTGCTAATCCGTGAGACC 59.175 55.000 0.00 0.00 0.00 3.85
684 690 1.115467 CCTGCTAATCCGTGAGACCT 58.885 55.000 0.00 0.00 0.00 3.85
685 691 1.202463 CCTGCTAATCCGTGAGACCTG 60.202 57.143 0.00 0.00 0.00 4.00
686 692 0.824109 TGCTAATCCGTGAGACCTGG 59.176 55.000 0.00 0.00 0.00 4.45
687 693 0.824759 GCTAATCCGTGAGACCTGGT 59.175 55.000 0.00 0.00 0.00 4.00
688 694 1.202428 GCTAATCCGTGAGACCTGGTC 60.202 57.143 19.20 19.20 0.00 4.02
689 695 2.379972 CTAATCCGTGAGACCTGGTCT 58.620 52.381 28.70 28.70 46.42 3.85
773 779 1.969862 CTGCAAGGAAAAGGGGCTG 59.030 57.895 0.00 0.00 0.00 4.85
783 789 1.187567 AAAGGGGCTGCATCCACAAC 61.188 55.000 12.22 0.00 29.87 3.32
817 823 2.183679 ACAGATCGCCTCTTCTTCCTT 58.816 47.619 0.00 0.00 29.16 3.36
864 870 4.626287 GCATTCCCTCATTACCAGAAGTGA 60.626 45.833 0.00 0.00 0.00 3.41
984 990 2.094066 CAATCCGCCGCCAAAAAGC 61.094 57.895 0.00 0.00 0.00 3.51
1180 1186 4.324267 AGTTGATACAGTTGCTTACCACC 58.676 43.478 0.00 0.00 0.00 4.61
1369 1375 4.320456 CCCAGACAGGCACGCTGT 62.320 66.667 0.00 0.00 37.81 4.40
1381 1387 2.346803 GCACGCTGTTTGAGATTCCTA 58.653 47.619 0.00 0.00 0.00 2.94
1648 1657 8.621532 TTAATGCTTATATTTAGGAGCTGTGG 57.378 34.615 0.00 0.00 36.16 4.17
1677 1686 7.384439 TCTGTGTTTAAACATTGAGTTGACA 57.616 32.000 23.11 12.12 41.19 3.58
1685 1694 4.371624 ACATTGAGTTGACATGGAGGAA 57.628 40.909 0.00 0.00 0.00 3.36
1901 1919 4.541973 AATGATCTTGAAAAGGTTGGGC 57.458 40.909 0.00 0.00 46.24 5.36
1911 1929 4.712337 TGAAAAGGTTGGGCTTGTTTCTTA 59.288 37.500 0.00 0.00 0.00 2.10
2039 2058 8.267894 AGTAATTTACTTATGCCATCTGTGAGT 58.732 33.333 3.16 0.00 34.86 3.41
2059 2088 8.836413 TGTGAGTTTCTTTAGTTTCTTACCATG 58.164 33.333 0.00 0.00 0.00 3.66
2060 2089 8.837389 GTGAGTTTCTTTAGTTTCTTACCATGT 58.163 33.333 0.00 0.00 0.00 3.21
2066 2095 9.457436 TTCTTTAGTTTCTTACCATGTATTCCC 57.543 33.333 0.00 0.00 0.00 3.97
2067 2096 8.607713 TCTTTAGTTTCTTACCATGTATTCCCA 58.392 33.333 0.00 0.00 0.00 4.37
2068 2097 9.408648 CTTTAGTTTCTTACCATGTATTCCCAT 57.591 33.333 0.00 0.00 0.00 4.00
2137 2166 3.278574 TGGTAACATCCTGCTAACATGC 58.721 45.455 0.00 0.00 46.17 4.06
2194 2224 4.509600 GGAAGTTGCTCGAGGAGATAATTG 59.490 45.833 15.58 0.00 0.00 2.32
2276 2306 5.129320 TGTCACTGGATAGTATGATTGCACT 59.871 40.000 0.00 0.00 34.74 4.40
2358 2388 7.397221 TCATTGACTGTTCCTGTATCAGAAAT 58.603 34.615 0.00 0.00 32.44 2.17
2359 2389 7.335171 TCATTGACTGTTCCTGTATCAGAAATG 59.665 37.037 0.00 0.00 37.67 2.32
2409 2439 7.792383 CACTTCTGTGAGAAATTTATGCTTG 57.208 36.000 0.00 0.00 46.55 4.01
2487 2517 4.825422 ACATATATGCCACATCTCCTTCG 58.175 43.478 12.79 0.00 0.00 3.79
2521 2551 5.730550 AGAAAATACAAGAGCACACGGATA 58.269 37.500 0.00 0.00 0.00 2.59
2555 2585 1.658673 GAACCGTCACTCCGTCAGT 59.341 57.895 0.00 0.00 34.67 3.41
2614 2644 8.792633 TCTTTCAGGTGAATATTTGTTAAGTGG 58.207 33.333 0.00 0.00 33.54 4.00
2674 2704 6.825213 ACTGCATCTTTTACTGATCATTGCTA 59.175 34.615 0.00 0.00 0.00 3.49
2716 2746 7.064134 GTCTGACGTGAAACATATGGTCATTTA 59.936 37.037 7.80 0.00 35.74 1.40
2734 2764 9.722056 GGTCATTTAAGTAATAGCAACATTGAG 57.278 33.333 0.00 0.00 0.00 3.02
2749 2779 8.462016 AGCAACATTGAGGTAAATTACTTGATC 58.538 33.333 2.96 0.00 0.00 2.92
2753 2783 9.685276 ACATTGAGGTAAATTACTTGATCATCA 57.315 29.630 0.00 0.00 0.00 3.07
2779 2809 9.998106 ATAGTTTGATACACTAGAACTTGTTGT 57.002 29.630 0.00 0.00 33.13 3.32
2780 2810 8.142994 AGTTTGATACACTAGAACTTGTTGTG 57.857 34.615 0.00 0.00 35.09 3.33
2781 2811 7.226720 AGTTTGATACACTAGAACTTGTTGTGG 59.773 37.037 0.00 1.22 33.44 4.17
2782 2812 6.169557 TGATACACTAGAACTTGTTGTGGT 57.830 37.500 0.00 1.75 33.44 4.16
2783 2813 6.588204 TGATACACTAGAACTTGTTGTGGTT 58.412 36.000 0.00 0.00 33.44 3.67
2784 2814 7.728148 TGATACACTAGAACTTGTTGTGGTTA 58.272 34.615 0.00 0.00 33.44 2.85
2785 2815 7.654520 TGATACACTAGAACTTGTTGTGGTTAC 59.345 37.037 0.00 0.00 33.44 2.50
2786 2816 5.985911 ACACTAGAACTTGTTGTGGTTACT 58.014 37.500 0.00 0.00 33.44 2.24
2787 2817 6.412214 ACACTAGAACTTGTTGTGGTTACTT 58.588 36.000 0.00 0.00 33.44 2.24
2788 2818 6.882678 ACACTAGAACTTGTTGTGGTTACTTT 59.117 34.615 0.00 0.00 33.44 2.66
2789 2819 8.042515 ACACTAGAACTTGTTGTGGTTACTTTA 58.957 33.333 0.00 0.00 33.44 1.85
2790 2820 9.052759 CACTAGAACTTGTTGTGGTTACTTTAT 57.947 33.333 0.00 0.00 0.00 1.40
2791 2821 9.623000 ACTAGAACTTGTTGTGGTTACTTTATT 57.377 29.630 0.00 0.00 0.00 1.40
2792 2822 9.878599 CTAGAACTTGTTGTGGTTACTTTATTG 57.121 33.333 0.00 0.00 0.00 1.90
2793 2823 7.712797 AGAACTTGTTGTGGTTACTTTATTGG 58.287 34.615 0.00 0.00 0.00 3.16
2794 2824 6.399639 ACTTGTTGTGGTTACTTTATTGGG 57.600 37.500 0.00 0.00 0.00 4.12
2795 2825 5.303333 ACTTGTTGTGGTTACTTTATTGGGG 59.697 40.000 0.00 0.00 0.00 4.96
2796 2826 4.805744 TGTTGTGGTTACTTTATTGGGGT 58.194 39.130 0.00 0.00 0.00 4.95
2797 2827 5.209659 TGTTGTGGTTACTTTATTGGGGTT 58.790 37.500 0.00 0.00 0.00 4.11
2798 2828 5.302313 TGTTGTGGTTACTTTATTGGGGTTC 59.698 40.000 0.00 0.00 0.00 3.62
2799 2829 5.327737 TGTGGTTACTTTATTGGGGTTCT 57.672 39.130 0.00 0.00 0.00 3.01
2800 2830 5.074115 TGTGGTTACTTTATTGGGGTTCTG 58.926 41.667 0.00 0.00 0.00 3.02
2801 2831 5.163077 TGTGGTTACTTTATTGGGGTTCTGA 60.163 40.000 0.00 0.00 0.00 3.27
2802 2832 5.771165 GTGGTTACTTTATTGGGGTTCTGAA 59.229 40.000 0.00 0.00 0.00 3.02
2803 2833 6.265876 GTGGTTACTTTATTGGGGTTCTGAAA 59.734 38.462 0.00 0.00 0.00 2.69
2804 2834 6.839657 TGGTTACTTTATTGGGGTTCTGAAAA 59.160 34.615 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 6.038492 CCATCAAGGCAACAATTTCAAAAAGT 59.962 34.615 0.00 0.00 41.41 2.66
71 74 4.163078 ACATCCACACCTAGGAGAATTCAG 59.837 45.833 17.98 1.37 38.83 3.02
104 109 7.015226 TGCTCCAATTGAATCAACTAATACG 57.985 36.000 7.12 0.00 0.00 3.06
175 180 1.067354 ACGTCAAACCACGAGATACCC 60.067 52.381 0.00 0.00 42.69 3.69
591 597 6.042552 CACCTGATTTATATGAGACCTGGTCT 59.957 42.308 28.70 28.70 46.42 3.85
592 598 6.042093 TCACCTGATTTATATGAGACCTGGTC 59.958 42.308 19.20 19.20 0.00 4.02
593 599 5.905331 TCACCTGATTTATATGAGACCTGGT 59.095 40.000 0.00 0.00 0.00 4.00
594 600 6.268617 TCTCACCTGATTTATATGAGACCTGG 59.731 42.308 0.00 0.00 40.59 4.45
595 601 7.295322 TCTCACCTGATTTATATGAGACCTG 57.705 40.000 0.00 0.00 40.59 4.00
599 605 6.672266 GGGTCTCACCTGATTTATATGAGA 57.328 41.667 0.00 0.00 42.63 3.27
612 618 3.625632 ATCAGGGCGGGTCTCACCT 62.626 63.158 0.00 0.00 38.64 4.00
613 619 3.083997 ATCAGGGCGGGTCTCACC 61.084 66.667 0.00 0.00 37.60 4.02
614 620 1.899437 TTCATCAGGGCGGGTCTCAC 61.899 60.000 0.00 0.00 0.00 3.51
615 621 0.982852 ATTCATCAGGGCGGGTCTCA 60.983 55.000 0.00 0.00 0.00 3.27
616 622 0.533755 CATTCATCAGGGCGGGTCTC 60.534 60.000 0.00 0.00 0.00 3.36
617 623 1.528824 CATTCATCAGGGCGGGTCT 59.471 57.895 0.00 0.00 0.00 3.85
618 624 2.189499 GCATTCATCAGGGCGGGTC 61.189 63.158 0.00 0.00 0.00 4.46
619 625 2.124151 GCATTCATCAGGGCGGGT 60.124 61.111 0.00 0.00 0.00 5.28
620 626 2.908940 GGCATTCATCAGGGCGGG 60.909 66.667 0.00 0.00 0.00 6.13
621 627 2.124193 TGGCATTCATCAGGGCGG 60.124 61.111 0.00 0.00 0.00 6.13
622 628 2.827051 CGTGGCATTCATCAGGGCG 61.827 63.158 0.00 0.00 0.00 6.13
623 629 1.750399 ACGTGGCATTCATCAGGGC 60.750 57.895 0.00 0.00 0.00 5.19
624 630 0.677731 ACACGTGGCATTCATCAGGG 60.678 55.000 21.57 0.00 0.00 4.45
625 631 0.729116 GACACGTGGCATTCATCAGG 59.271 55.000 18.77 0.00 0.00 3.86
626 632 1.441738 TGACACGTGGCATTCATCAG 58.558 50.000 23.03 0.00 0.00 2.90
627 633 2.009051 GATGACACGTGGCATTCATCA 58.991 47.619 36.07 20.33 45.42 3.07
628 634 1.331756 GGATGACACGTGGCATTCATC 59.668 52.381 36.07 30.49 45.42 2.92
629 635 1.339920 TGGATGACACGTGGCATTCAT 60.340 47.619 36.64 26.22 43.95 2.57
630 636 0.036022 TGGATGACACGTGGCATTCA 59.964 50.000 36.64 36.64 46.54 2.57
631 637 1.331756 GATGGATGACACGTGGCATTC 59.668 52.381 36.07 34.16 45.42 2.67
632 638 1.339920 TGATGGATGACACGTGGCATT 60.340 47.619 36.07 22.11 45.42 3.56
634 640 0.391528 CTGATGGATGACACGTGGCA 60.392 55.000 29.28 29.28 37.54 4.92
635 641 0.108186 TCTGATGGATGACACGTGGC 60.108 55.000 21.57 19.24 0.00 5.01
636 642 2.385013 TTCTGATGGATGACACGTGG 57.615 50.000 21.57 1.66 0.00 4.94
637 643 3.938778 CATTCTGATGGATGACACGTG 57.061 47.619 15.48 15.48 0.00 4.49
648 654 2.915349 CAGGTGAGACCCATTCTGATG 58.085 52.381 0.00 0.00 39.75 3.07
649 655 1.211457 GCAGGTGAGACCCATTCTGAT 59.789 52.381 0.00 0.00 39.75 2.90
650 656 0.615331 GCAGGTGAGACCCATTCTGA 59.385 55.000 0.00 0.00 39.75 3.27
651 657 0.617413 AGCAGGTGAGACCCATTCTG 59.383 55.000 0.00 0.00 39.75 3.02
652 658 2.254152 TAGCAGGTGAGACCCATTCT 57.746 50.000 0.00 0.00 39.75 2.40
653 659 3.471680 GATTAGCAGGTGAGACCCATTC 58.528 50.000 0.00 0.00 39.75 2.67
654 660 2.173569 GGATTAGCAGGTGAGACCCATT 59.826 50.000 0.00 0.00 39.75 3.16
655 661 1.771255 GGATTAGCAGGTGAGACCCAT 59.229 52.381 0.00 0.00 39.75 4.00
656 662 1.204146 GGATTAGCAGGTGAGACCCA 58.796 55.000 0.00 0.00 39.75 4.51
657 663 0.105039 CGGATTAGCAGGTGAGACCC 59.895 60.000 0.00 0.00 39.75 4.46
658 664 0.824759 ACGGATTAGCAGGTGAGACC 59.175 55.000 0.00 0.00 38.99 3.85
659 665 1.476891 TCACGGATTAGCAGGTGAGAC 59.523 52.381 0.00 0.00 34.71 3.36
660 666 1.847328 TCACGGATTAGCAGGTGAGA 58.153 50.000 0.00 0.00 34.71 3.27
662 668 1.476891 GTCTCACGGATTAGCAGGTGA 59.523 52.381 0.00 0.00 37.77 4.02
663 669 1.471676 GGTCTCACGGATTAGCAGGTG 60.472 57.143 0.00 0.00 0.00 4.00
664 670 0.824759 GGTCTCACGGATTAGCAGGT 59.175 55.000 0.00 0.00 0.00 4.00
665 671 1.115467 AGGTCTCACGGATTAGCAGG 58.885 55.000 0.00 0.00 0.00 4.85
666 672 1.202463 CCAGGTCTCACGGATTAGCAG 60.202 57.143 0.00 0.00 0.00 4.24
667 673 0.824109 CCAGGTCTCACGGATTAGCA 59.176 55.000 0.00 0.00 0.00 3.49
668 674 0.824759 ACCAGGTCTCACGGATTAGC 59.175 55.000 0.00 0.00 0.00 3.09
669 675 2.379972 AGACCAGGTCTCACGGATTAG 58.620 52.381 17.31 0.00 38.71 1.73
670 676 2.526888 AGACCAGGTCTCACGGATTA 57.473 50.000 17.31 0.00 38.71 1.75
671 677 3.383162 AGACCAGGTCTCACGGATT 57.617 52.632 17.31 0.00 38.71 3.01
699 705 4.442753 GGCTGAATGTCAAACAGGGAAAAA 60.443 41.667 10.28 0.00 33.00 1.94
700 706 3.069443 GGCTGAATGTCAAACAGGGAAAA 59.931 43.478 10.28 0.00 33.00 2.29
701 707 2.627699 GGCTGAATGTCAAACAGGGAAA 59.372 45.455 10.28 0.00 33.00 3.13
702 708 2.238521 GGCTGAATGTCAAACAGGGAA 58.761 47.619 10.28 0.00 33.00 3.97
703 709 1.144708 TGGCTGAATGTCAAACAGGGA 59.855 47.619 10.28 0.00 33.00 4.20
704 710 1.542915 CTGGCTGAATGTCAAACAGGG 59.457 52.381 10.28 0.00 30.92 4.45
705 711 2.486982 CTCTGGCTGAATGTCAAACAGG 59.513 50.000 10.28 0.00 33.58 4.00
773 779 2.070783 CAATTGGCAAGTTGTGGATGC 58.929 47.619 5.96 0.00 39.33 3.91
783 789 3.730061 GCGATCTGTTCTCAATTGGCAAG 60.730 47.826 5.96 0.00 0.00 4.01
817 823 2.836981 CAAATATGGTCTTTGGGGGCAA 59.163 45.455 0.00 0.00 31.43 4.52
856 862 1.681166 CCAGGAAGGCCATCACTTCTG 60.681 57.143 10.67 7.57 42.96 3.02
864 870 2.971598 CGTGTCCCAGGAAGGCCAT 61.972 63.158 5.01 0.00 36.29 4.40
984 990 3.061295 CGTCCATGACATCTTTCTGAACG 59.939 47.826 0.00 0.00 32.09 3.95
1180 1186 3.117171 GCGCCTCAGCACTGACAG 61.117 66.667 0.00 0.00 39.83 3.51
1369 1375 9.388506 GAGAGATTTCACATTAGGAATCTCAAA 57.611 33.333 20.97 0.00 34.71 2.69
1642 1651 5.154222 GTTTAAACACAGATAAGCCACAGC 58.846 41.667 13.51 0.00 40.32 4.40
1648 1657 8.905702 CAACTCAATGTTTAAACACAGATAAGC 58.094 33.333 22.78 0.00 42.51 3.09
1677 1686 7.950124 TCTTTCTCCAAAATAAACTTCCTCCAT 59.050 33.333 0.00 0.00 0.00 3.41
1784 1802 5.478407 GCACTAGCAAACAATAAATTGGGT 58.522 37.500 7.56 0.00 40.37 4.51
1911 1929 7.151976 GCCAACCAAAATATACAGACAAAGTT 58.848 34.615 0.00 0.00 0.00 2.66
1990 2008 1.195115 CTTCCTCCAGGGATTCGACA 58.805 55.000 0.00 0.00 44.66 4.35
2152 2182 3.050089 TCCCCTGTTTCAGAACCTTACA 58.950 45.455 0.00 0.00 34.80 2.41
2487 2517 6.675728 GCTCTTGTATTTTCTCCAAATCGGAC 60.676 42.308 0.00 0.00 39.64 4.79
2506 2536 3.238108 ACTTCTATCCGTGTGCTCTTG 57.762 47.619 0.00 0.00 0.00 3.02
2507 2537 4.219944 TGTTACTTCTATCCGTGTGCTCTT 59.780 41.667 0.00 0.00 0.00 2.85
2521 2551 5.421056 TGACGGTTCCAGATATGTTACTTCT 59.579 40.000 0.00 0.00 0.00 2.85
2555 2585 5.279006 CGGTTATATTCTGCTCTGGCTAAGA 60.279 44.000 0.00 0.00 39.59 2.10
2674 2704 7.769507 TCACGTCAGACAAGATAAGTACTAGAT 59.230 37.037 0.00 0.00 0.00 1.98
2680 2710 6.741109 TGTTTCACGTCAGACAAGATAAGTA 58.259 36.000 0.41 0.00 0.00 2.24
2681 2711 5.597806 TGTTTCACGTCAGACAAGATAAGT 58.402 37.500 0.41 0.00 0.00 2.24
2682 2712 6.712241 ATGTTTCACGTCAGACAAGATAAG 57.288 37.500 0.41 0.00 0.00 1.73
2683 2713 7.277760 CCATATGTTTCACGTCAGACAAGATAA 59.722 37.037 1.24 0.00 0.00 1.75
2753 2783 9.998106 ACAACAAGTTCTAGTGTATCAAACTAT 57.002 29.630 0.00 0.00 30.37 2.12
2754 2784 9.256477 CACAACAAGTTCTAGTGTATCAAACTA 57.744 33.333 0.00 0.00 30.37 2.24
2755 2785 7.226720 CCACAACAAGTTCTAGTGTATCAAACT 59.773 37.037 0.00 0.00 0.00 2.66
2756 2786 7.012044 ACCACAACAAGTTCTAGTGTATCAAAC 59.988 37.037 0.00 0.00 0.00 2.93
2757 2787 7.051623 ACCACAACAAGTTCTAGTGTATCAAA 58.948 34.615 0.00 0.00 0.00 2.69
2758 2788 6.588204 ACCACAACAAGTTCTAGTGTATCAA 58.412 36.000 0.00 0.00 0.00 2.57
2759 2789 6.169557 ACCACAACAAGTTCTAGTGTATCA 57.830 37.500 0.00 0.00 0.00 2.15
2760 2790 7.871463 AGTAACCACAACAAGTTCTAGTGTATC 59.129 37.037 0.00 0.00 0.00 2.24
2761 2791 7.732996 AGTAACCACAACAAGTTCTAGTGTAT 58.267 34.615 0.00 0.00 0.00 2.29
2762 2792 7.116075 AGTAACCACAACAAGTTCTAGTGTA 57.884 36.000 0.00 0.00 0.00 2.90
2763 2793 5.985911 AGTAACCACAACAAGTTCTAGTGT 58.014 37.500 0.00 0.00 0.00 3.55
2764 2794 6.920569 AAGTAACCACAACAAGTTCTAGTG 57.079 37.500 0.00 0.00 0.00 2.74
2765 2795 9.623000 AATAAAGTAACCACAACAAGTTCTAGT 57.377 29.630 0.00 0.00 0.00 2.57
2766 2796 9.878599 CAATAAAGTAACCACAACAAGTTCTAG 57.121 33.333 0.00 0.00 0.00 2.43
2767 2797 8.842280 CCAATAAAGTAACCACAACAAGTTCTA 58.158 33.333 0.00 0.00 0.00 2.10
2768 2798 7.201875 CCCAATAAAGTAACCACAACAAGTTCT 60.202 37.037 0.00 0.00 0.00 3.01
2769 2799 6.921307 CCCAATAAAGTAACCACAACAAGTTC 59.079 38.462 0.00 0.00 0.00 3.01
2770 2800 6.183360 CCCCAATAAAGTAACCACAACAAGTT 60.183 38.462 0.00 0.00 0.00 2.66
2771 2801 5.303333 CCCCAATAAAGTAACCACAACAAGT 59.697 40.000 0.00 0.00 0.00 3.16
2772 2802 5.303333 ACCCCAATAAAGTAACCACAACAAG 59.697 40.000 0.00 0.00 0.00 3.16
2773 2803 5.209659 ACCCCAATAAAGTAACCACAACAA 58.790 37.500 0.00 0.00 0.00 2.83
2774 2804 4.805744 ACCCCAATAAAGTAACCACAACA 58.194 39.130 0.00 0.00 0.00 3.33
2775 2805 5.537295 AGAACCCCAATAAAGTAACCACAAC 59.463 40.000 0.00 0.00 0.00 3.32
2776 2806 5.536916 CAGAACCCCAATAAAGTAACCACAA 59.463 40.000 0.00 0.00 0.00 3.33
2777 2807 5.074115 CAGAACCCCAATAAAGTAACCACA 58.926 41.667 0.00 0.00 0.00 4.17
2778 2808 5.318630 TCAGAACCCCAATAAAGTAACCAC 58.681 41.667 0.00 0.00 0.00 4.16
2779 2809 5.586155 TCAGAACCCCAATAAAGTAACCA 57.414 39.130 0.00 0.00 0.00 3.67
2780 2810 6.904463 TTTCAGAACCCCAATAAAGTAACC 57.096 37.500 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.