Multiple sequence alignment - TraesCS1D01G373800

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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 TraesCS1D01G373800 chr1D 100.000 2866 0 0 1 2866 451523538 451526403 0.000000e+00 5293.0
1 TraesCS1D01G373800 chr1D 96.149 727 24 4 1 726 451504807 451505530 0.000000e+00 1184.0
2 TraesCS1D01G373800 chr1D 92.393 723 53 2 1 721 343859861 343860583 0.000000e+00 1029.0
3 TraesCS1D01G373800 chr1D 92.138 636 19 18 1095 1712 451625161 451625783 0.000000e+00 869.0
4 TraesCS1D01G373800 chr1D 86.410 780 65 20 947 1710 464802684 464801930 0.000000e+00 815.0
5 TraesCS1D01G373800 chr1D 79.104 134 24 4 2373 2505 451293944 451294074 3.930000e-14 89.8
6 TraesCS1D01G373800 chr1A 93.563 1072 49 12 792 1855 546212104 546213163 0.000000e+00 1580.0
7 TraesCS1D01G373800 chr1A 89.460 759 58 18 947 1690 557099805 557099054 0.000000e+00 939.0
8 TraesCS1D01G373800 chr1A 93.701 127 8 0 2740 2866 546213277 546213403 1.050000e-44 191.0
9 TraesCS1D01G373800 chr1B 90.476 1113 65 13 726 1821 620551308 620552396 0.000000e+00 1430.0
10 TraesCS1D01G373800 chr1B 92.062 1033 46 15 790 1790 620130150 620129122 0.000000e+00 1421.0
11 TraesCS1D01G373800 chr1B 93.750 880 26 7 1095 1960 620900100 620900964 0.000000e+00 1293.0
12 TraesCS1D01G373800 chr1B 91.398 837 45 16 1095 1919 621059335 621060156 0.000000e+00 1122.0
13 TraesCS1D01G373800 chr1B 88.590 929 54 9 1961 2866 620901002 620901901 0.000000e+00 1081.0
14 TraesCS1D01G373800 chr1B 88.372 774 56 22 947 1710 641523761 641523012 0.000000e+00 900.0
15 TraesCS1D01G373800 chr1B 91.837 637 17 22 1095 1712 620786143 620786763 0.000000e+00 856.0
16 TraesCS1D01G373800 chr1B 88.706 425 30 6 1961 2370 621060225 621060646 1.190000e-138 503.0
17 TraesCS1D01G373800 chr1B 87.948 307 18 10 2486 2786 620552823 620553116 7.600000e-91 344.0
18 TraesCS1D01G373800 chr1B 81.928 249 14 11 2649 2866 620787497 620787745 6.310000e-42 182.0
19 TraesCS1D01G373800 chr1B 95.312 64 3 0 726 789 620130324 620130261 5.050000e-18 102.0
20 TraesCS1D01G373800 chr1B 78.723 141 27 3 2373 2513 620495438 620495301 1.090000e-14 91.6
21 TraesCS1D01G373800 chr2D 93.004 729 47 4 1 726 421230547 421229820 0.000000e+00 1061.0
22 TraesCS1D01G373800 chr2D 92.181 729 53 4 1 726 421217654 421216927 0.000000e+00 1027.0
23 TraesCS1D01G373800 chr4D 92.857 728 49 3 1 726 42501443 42500717 0.000000e+00 1053.0
24 TraesCS1D01G373800 chr4D 88.889 54 6 0 1603 1656 40206381 40206434 1.840000e-07 67.6
25 TraesCS1D01G373800 chr5D 92.582 728 50 4 1 726 520610994 520611719 0.000000e+00 1042.0
26 TraesCS1D01G373800 chr5D 92.033 728 55 3 1 726 252556942 252557668 0.000000e+00 1020.0
27 TraesCS1D01G373800 chr3D 92.170 728 54 3 1 726 434973112 434972386 0.000000e+00 1026.0
28 TraesCS1D01G373800 chrUn 92.022 727 55 3 1 726 111920889 111920165 0.000000e+00 1018.0
29 TraesCS1D01G373800 chrUn 88.432 778 67 17 947 1710 74602022 74602790 0.000000e+00 917.0
30 TraesCS1D01G373800 chrUn 92.958 71 5 0 816 886 74601964 74602034 1.400000e-18 104.0
31 TraesCS1D01G373800 chr6D 91.098 674 39 13 947 1605 431856231 431856898 0.000000e+00 893.0
32 TraesCS1D01G373800 chr6B 88.015 776 62 21 947 1710 651990697 651991453 0.000000e+00 889.0
33 TraesCS1D01G373800 chr3A 82.377 732 63 36 867 1570 66253834 66254527 6.890000e-161 577.0
34 TraesCS1D01G373800 chr5B 79.461 482 66 17 1485 1941 503732420 503731947 7.710000e-81 311.0


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 TraesCS1D01G373800 chr1D 451523538 451526403 2865 False 5293.0 5293 100.0000 1 2866 1 chr1D.!!$F4 2865
1 TraesCS1D01G373800 chr1D 451504807 451505530 723 False 1184.0 1184 96.1490 1 726 1 chr1D.!!$F3 725
2 TraesCS1D01G373800 chr1D 343859861 343860583 722 False 1029.0 1029 92.3930 1 721 1 chr1D.!!$F1 720
3 TraesCS1D01G373800 chr1D 451625161 451625783 622 False 869.0 869 92.1380 1095 1712 1 chr1D.!!$F5 617
4 TraesCS1D01G373800 chr1D 464801930 464802684 754 True 815.0 815 86.4100 947 1710 1 chr1D.!!$R1 763
5 TraesCS1D01G373800 chr1A 557099054 557099805 751 True 939.0 939 89.4600 947 1690 1 chr1A.!!$R1 743
6 TraesCS1D01G373800 chr1A 546212104 546213403 1299 False 885.5 1580 93.6320 792 2866 2 chr1A.!!$F1 2074
7 TraesCS1D01G373800 chr1B 620900100 620901901 1801 False 1187.0 1293 91.1700 1095 2866 2 chr1B.!!$F3 1771
8 TraesCS1D01G373800 chr1B 641523012 641523761 749 True 900.0 900 88.3720 947 1710 1 chr1B.!!$R2 763
9 TraesCS1D01G373800 chr1B 620551308 620553116 1808 False 887.0 1430 89.2120 726 2786 2 chr1B.!!$F1 2060
10 TraesCS1D01G373800 chr1B 621059335 621060646 1311 False 812.5 1122 90.0520 1095 2370 2 chr1B.!!$F4 1275
11 TraesCS1D01G373800 chr1B 620129122 620130324 1202 True 761.5 1421 93.6870 726 1790 2 chr1B.!!$R3 1064
12 TraesCS1D01G373800 chr1B 620786143 620787745 1602 False 519.0 856 86.8825 1095 2866 2 chr1B.!!$F2 1771
13 TraesCS1D01G373800 chr2D 421229820 421230547 727 True 1061.0 1061 93.0040 1 726 1 chr2D.!!$R2 725
14 TraesCS1D01G373800 chr2D 421216927 421217654 727 True 1027.0 1027 92.1810 1 726 1 chr2D.!!$R1 725
15 TraesCS1D01G373800 chr4D 42500717 42501443 726 True 1053.0 1053 92.8570 1 726 1 chr4D.!!$R1 725
16 TraesCS1D01G373800 chr5D 520610994 520611719 725 False 1042.0 1042 92.5820 1 726 1 chr5D.!!$F2 725
17 TraesCS1D01G373800 chr5D 252556942 252557668 726 False 1020.0 1020 92.0330 1 726 1 chr5D.!!$F1 725
18 TraesCS1D01G373800 chr3D 434972386 434973112 726 True 1026.0 1026 92.1700 1 726 1 chr3D.!!$R1 725
19 TraesCS1D01G373800 chrUn 111920165 111920889 724 True 1018.0 1018 92.0220 1 726 1 chrUn.!!$R1 725
20 TraesCS1D01G373800 chrUn 74601964 74602790 826 False 510.5 917 90.6950 816 1710 2 chrUn.!!$F1 894
21 TraesCS1D01G373800 chr6D 431856231 431856898 667 False 893.0 893 91.0980 947 1605 1 chr6D.!!$F1 658
22 TraesCS1D01G373800 chr6B 651990697 651991453 756 False 889.0 889 88.0150 947 1710 1 chr6B.!!$F1 763
23 TraesCS1D01G373800 chr3A 66253834 66254527 693 False 577.0 577 82.3770 867 1570 1 chr3A.!!$F1 703

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
616 618 0.031917 TCCTACACCCGGCCAGATTA 60.032 55.0 2.24 0.0 0.0 1.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2177 2745 1.140312 AGGTTTCTTCAGTGGGCAGA 58.86 50.0 0.0 0.0 0.0 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
24 25 2.284331 TCCTAGCAGTCGGCCCAA 60.284 61.111 0.00 0.00 46.50 4.12
101 103 0.784495 TAGCCCATCTCCCCGTATCT 59.216 55.000 0.00 0.00 0.00 1.98
440 442 1.973281 CCCTGACCAAGCATGCGTT 60.973 57.895 13.01 4.25 0.00 4.84
579 581 4.821589 GGAGAAGCCGGCGACCAG 62.822 72.222 23.20 0.00 0.00 4.00
580 582 3.760035 GAGAAGCCGGCGACCAGA 61.760 66.667 23.20 0.00 0.00 3.86
581 583 3.708220 GAGAAGCCGGCGACCAGAG 62.708 68.421 23.20 0.00 0.00 3.35
582 584 3.760035 GAAGCCGGCGACCAGAGA 61.760 66.667 23.20 0.00 0.00 3.10
583 585 3.708220 GAAGCCGGCGACCAGAGAG 62.708 68.421 23.20 0.00 0.00 3.20
584 586 4.742649 AGCCGGCGACCAGAGAGA 62.743 66.667 23.20 0.00 0.00 3.10
585 587 4.500116 GCCGGCGACCAGAGAGAC 62.500 72.222 12.58 0.00 0.00 3.36
586 588 2.752238 CCGGCGACCAGAGAGACT 60.752 66.667 9.30 0.00 0.00 3.24
587 589 2.487428 CGGCGACCAGAGAGACTG 59.513 66.667 0.00 0.00 45.36 3.51
600 602 4.098847 GACTGACAGTCGGGTCCT 57.901 61.111 19.41 0.00 35.28 3.85
601 603 3.261250 GACTGACAGTCGGGTCCTA 57.739 57.895 19.41 0.00 35.28 2.94
602 604 0.810016 GACTGACAGTCGGGTCCTAC 59.190 60.000 19.41 0.00 35.28 3.18
603 605 0.111832 ACTGACAGTCGGGTCCTACA 59.888 55.000 14.20 0.00 36.97 2.74
604 606 0.526662 CTGACAGTCGGGTCCTACAC 59.473 60.000 0.74 0.00 36.97 2.90
605 607 0.896940 TGACAGTCGGGTCCTACACC 60.897 60.000 0.00 0.00 45.97 4.16
612 614 3.782443 GGTCCTACACCCGGCCAG 61.782 72.222 2.24 0.00 39.69 4.85
613 615 2.682494 GTCCTACACCCGGCCAGA 60.682 66.667 2.24 0.00 0.00 3.86
614 616 2.064581 GTCCTACACCCGGCCAGAT 61.065 63.158 2.24 0.00 0.00 2.90
615 617 1.306654 TCCTACACCCGGCCAGATT 60.307 57.895 2.24 0.00 0.00 2.40
616 618 0.031917 TCCTACACCCGGCCAGATTA 60.032 55.000 2.24 0.00 0.00 1.75
617 619 0.106149 CCTACACCCGGCCAGATTAC 59.894 60.000 2.24 0.00 0.00 1.89
618 620 0.106149 CTACACCCGGCCAGATTACC 59.894 60.000 2.24 0.00 0.00 2.85
619 621 0.618107 TACACCCGGCCAGATTACCA 60.618 55.000 2.24 0.00 0.00 3.25
620 622 1.279025 ACACCCGGCCAGATTACCAT 61.279 55.000 2.24 0.00 0.00 3.55
621 623 0.106719 CACCCGGCCAGATTACCATT 60.107 55.000 2.24 0.00 0.00 3.16
622 624 0.106719 ACCCGGCCAGATTACCATTG 60.107 55.000 2.24 0.00 0.00 2.82
623 625 0.106719 CCCGGCCAGATTACCATTGT 60.107 55.000 2.24 0.00 0.00 2.71
624 626 1.142060 CCCGGCCAGATTACCATTGTA 59.858 52.381 2.24 0.00 0.00 2.41
625 627 2.218603 CCGGCCAGATTACCATTGTAC 58.781 52.381 2.24 0.00 0.00 2.90
626 628 2.218603 CGGCCAGATTACCATTGTACC 58.781 52.381 2.24 0.00 0.00 3.34
627 629 2.583143 GGCCAGATTACCATTGTACCC 58.417 52.381 0.00 0.00 0.00 3.69
628 630 2.583143 GCCAGATTACCATTGTACCCC 58.417 52.381 0.00 0.00 0.00 4.95
629 631 2.174854 GCCAGATTACCATTGTACCCCT 59.825 50.000 0.00 0.00 0.00 4.79
630 632 3.820557 CCAGATTACCATTGTACCCCTG 58.179 50.000 0.00 0.00 0.00 4.45
631 633 3.435026 CCAGATTACCATTGTACCCCTGG 60.435 52.174 0.00 0.00 34.51 4.45
632 634 2.783510 AGATTACCATTGTACCCCTGGG 59.216 50.000 5.50 5.50 42.03 4.45
652 654 2.848694 GGGGGTAGGCCTATATAAACCC 59.151 54.545 25.63 25.63 44.86 4.11
654 656 2.848694 GGGTAGGCCTATATAAACCCCC 59.151 54.545 23.88 18.69 40.62 5.40
655 657 3.534192 GGTAGGCCTATATAAACCCCCA 58.466 50.000 17.38 0.00 0.00 4.96
656 658 3.522343 GGTAGGCCTATATAAACCCCCAG 59.478 52.174 17.38 0.00 0.00 4.45
657 659 2.644151 AGGCCTATATAAACCCCCAGG 58.356 52.381 1.29 0.00 40.04 4.45
658 660 2.185931 AGGCCTATATAAACCCCCAGGA 59.814 50.000 1.29 0.00 36.73 3.86
659 661 2.307980 GGCCTATATAAACCCCCAGGAC 59.692 54.545 0.00 0.00 36.73 3.85
660 662 2.983898 GCCTATATAAACCCCCAGGACA 59.016 50.000 0.00 0.00 36.73 4.02
661 663 3.244805 GCCTATATAAACCCCCAGGACAC 60.245 52.174 0.00 0.00 36.73 3.67
662 664 3.329814 CCTATATAAACCCCCAGGACACC 59.670 52.174 0.00 0.00 36.73 4.16
663 665 1.598869 TATAAACCCCCAGGACACCC 58.401 55.000 0.00 0.00 36.73 4.61
664 666 0.478789 ATAAACCCCCAGGACACCCA 60.479 55.000 0.00 0.00 36.73 4.51
665 667 0.478789 TAAACCCCCAGGACACCCAT 60.479 55.000 0.00 0.00 36.73 4.00
666 668 2.092904 AAACCCCCAGGACACCCATG 62.093 60.000 0.00 0.00 36.73 3.66
667 669 4.447342 CCCCCAGGACACCCATGC 62.447 72.222 0.00 0.00 33.47 4.06
668 670 3.660571 CCCCAGGACACCCATGCA 61.661 66.667 0.00 0.00 33.88 3.96
669 671 2.440147 CCCAGGACACCCATGCAA 59.560 61.111 0.00 0.00 33.88 4.08
670 672 1.228831 CCCAGGACACCCATGCAAA 60.229 57.895 0.00 0.00 33.88 3.68
671 673 1.252904 CCCAGGACACCCATGCAAAG 61.253 60.000 0.00 0.00 33.88 2.77
672 674 1.252904 CCAGGACACCCATGCAAAGG 61.253 60.000 3.89 3.89 33.88 3.11
678 680 4.537260 CCCATGCAAAGGGTTCCA 57.463 55.556 17.30 0.00 41.61 3.53
679 681 2.757313 CCCATGCAAAGGGTTCCAA 58.243 52.632 17.30 0.00 41.61 3.53
680 682 0.321346 CCCATGCAAAGGGTTCCAAC 59.679 55.000 17.30 0.00 41.61 3.77
695 697 6.738832 GGTTCCAACCTGTTAGAATTAGAC 57.261 41.667 0.83 0.00 45.75 2.59
696 698 6.473758 GGTTCCAACCTGTTAGAATTAGACT 58.526 40.000 0.83 0.00 45.75 3.24
697 699 6.594547 GGTTCCAACCTGTTAGAATTAGACTC 59.405 42.308 0.83 0.00 45.75 3.36
698 700 6.928348 TCCAACCTGTTAGAATTAGACTCA 57.072 37.500 0.00 0.00 0.00 3.41
699 701 6.698380 TCCAACCTGTTAGAATTAGACTCAC 58.302 40.000 0.00 0.00 0.00 3.51
700 702 6.269077 TCCAACCTGTTAGAATTAGACTCACA 59.731 38.462 0.00 0.00 0.00 3.58
701 703 6.369065 CCAACCTGTTAGAATTAGACTCACAC 59.631 42.308 0.00 0.00 0.00 3.82
702 704 6.038997 ACCTGTTAGAATTAGACTCACACC 57.961 41.667 0.00 0.00 0.00 4.16
703 705 5.780793 ACCTGTTAGAATTAGACTCACACCT 59.219 40.000 0.00 0.00 0.00 4.00
704 706 6.952358 ACCTGTTAGAATTAGACTCACACCTA 59.048 38.462 0.00 0.00 0.00 3.08
705 707 7.122948 ACCTGTTAGAATTAGACTCACACCTAG 59.877 40.741 0.00 0.00 0.00 3.02
706 708 7.406031 TGTTAGAATTAGACTCACACCTAGG 57.594 40.000 7.41 7.41 0.00 3.02
707 709 6.380274 TGTTAGAATTAGACTCACACCTAGGG 59.620 42.308 14.81 4.64 0.00 3.53
708 710 4.290942 AGAATTAGACTCACACCTAGGGG 58.709 47.826 10.33 10.33 38.88 4.79
709 711 2.544844 TTAGACTCACACCTAGGGGG 57.455 55.000 17.43 8.65 41.89 5.40
710 712 1.690010 TAGACTCACACCTAGGGGGA 58.310 55.000 17.43 8.98 38.76 4.81
711 713 0.336737 AGACTCACACCTAGGGGGAG 59.663 60.000 21.53 21.53 38.76 4.30
712 714 0.335361 GACTCACACCTAGGGGGAGA 59.665 60.000 27.03 18.63 38.76 3.71
713 715 0.790993 ACTCACACCTAGGGGGAGAA 59.209 55.000 27.03 6.62 38.76 2.87
714 716 1.273324 ACTCACACCTAGGGGGAGAAG 60.273 57.143 27.03 16.17 38.76 2.85
715 717 1.007238 CTCACACCTAGGGGGAGAAGA 59.993 57.143 17.43 4.20 38.76 2.87
716 718 1.007238 TCACACCTAGGGGGAGAAGAG 59.993 57.143 17.43 0.00 38.76 2.85
717 719 1.007238 CACACCTAGGGGGAGAAGAGA 59.993 57.143 17.43 0.00 38.76 3.10
718 720 1.289530 ACACCTAGGGGGAGAAGAGAG 59.710 57.143 17.43 0.00 38.76 3.20
719 721 0.263468 ACCTAGGGGGAGAAGAGAGC 59.737 60.000 14.81 0.00 38.76 4.09
720 722 0.263172 CCTAGGGGGAGAAGAGAGCA 59.737 60.000 0.00 0.00 37.23 4.26
721 723 1.343478 CCTAGGGGGAGAAGAGAGCAA 60.343 57.143 0.00 0.00 37.23 3.91
722 724 2.472029 CTAGGGGGAGAAGAGAGCAAA 58.528 52.381 0.00 0.00 0.00 3.68
723 725 1.284313 AGGGGGAGAAGAGAGCAAAG 58.716 55.000 0.00 0.00 0.00 2.77
724 726 0.393673 GGGGGAGAAGAGAGCAAAGC 60.394 60.000 0.00 0.00 0.00 3.51
758 760 1.889170 CTGCTGGCCTACGATCTGATA 59.111 52.381 3.32 0.00 0.00 2.15
794 906 0.176680 CACTGGCAGCTACTGTAGGG 59.823 60.000 15.89 0.00 33.43 3.53
801 913 0.983378 AGCTACTGTAGGGCCCAAGG 60.983 60.000 27.56 13.46 0.00 3.61
1054 1191 0.846427 TCTGCAATTCCCCACCTCCT 60.846 55.000 0.00 0.00 0.00 3.69
1056 1193 1.139498 TGCAATTCCCCACCTCCTCA 61.139 55.000 0.00 0.00 0.00 3.86
1057 1194 0.681243 GCAATTCCCCACCTCCTCAC 60.681 60.000 0.00 0.00 0.00 3.51
1058 1195 0.995024 CAATTCCCCACCTCCTCACT 59.005 55.000 0.00 0.00 0.00 3.41
1573 1801 2.378886 TCACCTCCTCCTAGACAGTTGA 59.621 50.000 0.00 0.00 0.00 3.18
1806 2205 3.251571 GTCGCCTTGTTGGTAGTAAGAG 58.748 50.000 0.00 0.00 38.35 2.85
1840 2248 4.202040 TGGTGCAAACAGTGATTCAGAAAG 60.202 41.667 0.00 0.00 0.00 2.62
1935 2352 5.946298 TCATTTCTTAGCAATGCAAGTCAG 58.054 37.500 8.35 0.00 32.49 3.51
2134 2702 4.152402 CCGTCCATTTCTTGTACTGAACAG 59.848 45.833 0.00 0.00 39.87 3.16
2177 2745 5.009610 TGCTTCTTTGTTTTATTTCCTCGCT 59.990 36.000 0.00 0.00 0.00 4.93
2302 2884 0.392336 TGTTCTGCATTGCCAAACCC 59.608 50.000 16.17 0.00 0.00 4.11
2384 2974 1.523258 GCAGCTGCGTGATGGAGAT 60.523 57.895 25.23 0.00 38.54 2.75
2395 2986 1.065199 TGATGGAGATGGTGTGAAGGC 60.065 52.381 0.00 0.00 0.00 4.35
2414 3005 2.594303 CAGCGGTGGTTTCTGCCA 60.594 61.111 6.74 0.00 40.22 4.92
2418 3009 4.043200 GGTGGTTTCTGCCAGCGC 62.043 66.667 0.00 0.00 45.40 5.92
2498 3089 2.819595 CATCCACCAAGCCGTCCG 60.820 66.667 0.00 0.00 0.00 4.79
2536 3127 8.893727 GGATGTAAAACAGAGCATACAAGTAAT 58.106 33.333 0.00 0.00 32.53 1.89
2543 3134 7.133891 ACAGAGCATACAAGTAATTGTGTTC 57.866 36.000 18.30 9.94 36.44 3.18
2559 3150 2.607635 GTGTTCGCTTCAGTGTCAAGAA 59.392 45.455 0.00 0.00 0.00 2.52
2624 3215 5.212194 TGAATTGCTTTAGAACGCAGAAAC 58.788 37.500 0.00 0.00 37.46 2.78
2787 3412 6.476243 TTAAGAAGTCCAAATACAAGCGAC 57.524 37.500 0.00 0.00 0.00 5.19
2822 3447 0.469917 AACTGGACAGACAGGGTGTG 59.530 55.000 6.29 0.00 42.75 3.82
2843 3468 5.487488 TGTGGTAGGGAGAATCATGTAAACT 59.513 40.000 0.00 0.00 36.25 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 93 2.116772 CGGCCCTAGATACGGGGA 59.883 66.667 0.00 0.00 45.18 4.81
440 442 7.951591 TGATTACTGTAGCTGTGATGCTAATA 58.048 34.615 0.00 0.00 45.64 0.98
562 564 4.821589 CTGGTCGCCGGCTTCTCC 62.822 72.222 26.68 20.02 0.00 3.71
563 565 3.708220 CTCTGGTCGCCGGCTTCTC 62.708 68.421 26.68 11.74 0.00 2.87
564 566 3.764466 CTCTGGTCGCCGGCTTCT 61.764 66.667 26.68 0.00 0.00 2.85
565 567 3.708220 CTCTCTGGTCGCCGGCTTC 62.708 68.421 26.68 16.73 0.00 3.86
566 568 3.764466 CTCTCTGGTCGCCGGCTT 61.764 66.667 26.68 0.00 0.00 4.35
567 569 4.742649 TCTCTCTGGTCGCCGGCT 62.743 66.667 26.68 0.00 0.00 5.52
568 570 4.500116 GTCTCTCTGGTCGCCGGC 62.500 72.222 19.07 19.07 0.00 6.13
569 571 2.752238 AGTCTCTCTGGTCGCCGG 60.752 66.667 0.00 0.00 0.00 6.13
570 572 2.041115 TCAGTCTCTCTGGTCGCCG 61.041 63.158 0.00 0.00 43.76 6.46
571 573 1.244697 TGTCAGTCTCTCTGGTCGCC 61.245 60.000 0.00 0.00 43.76 5.54
572 574 0.170116 CTGTCAGTCTCTCTGGTCGC 59.830 60.000 0.00 0.00 43.76 5.19
573 575 1.466950 GACTGTCAGTCTCTCTGGTCG 59.533 57.143 23.25 0.00 41.88 4.79
574 576 1.466950 CGACTGTCAGTCTCTCTGGTC 59.533 57.143 26.46 2.70 42.92 4.02
575 577 1.529226 CGACTGTCAGTCTCTCTGGT 58.471 55.000 26.46 0.00 42.92 4.00
576 578 0.808125 CCGACTGTCAGTCTCTCTGG 59.192 60.000 26.46 17.49 42.92 3.86
577 579 0.808125 CCCGACTGTCAGTCTCTCTG 59.192 60.000 26.46 13.09 42.92 3.35
578 580 0.402504 ACCCGACTGTCAGTCTCTCT 59.597 55.000 26.46 7.31 42.92 3.10
579 581 0.806241 GACCCGACTGTCAGTCTCTC 59.194 60.000 26.46 15.50 42.92 3.20
580 582 0.609681 GGACCCGACTGTCAGTCTCT 60.610 60.000 26.46 11.45 42.92 3.10
581 583 0.609681 AGGACCCGACTGTCAGTCTC 60.610 60.000 26.46 18.34 42.92 3.36
582 584 0.697079 TAGGACCCGACTGTCAGTCT 59.303 55.000 26.46 11.54 42.92 3.24
583 585 0.810016 GTAGGACCCGACTGTCAGTC 59.190 60.000 21.13 21.13 41.71 3.51
584 586 0.111832 TGTAGGACCCGACTGTCAGT 59.888 55.000 4.81 4.81 36.97 3.41
585 587 0.526662 GTGTAGGACCCGACTGTCAG 59.473 60.000 8.73 0.00 36.97 3.51
586 588 0.896940 GGTGTAGGACCCGACTGTCA 60.897 60.000 8.73 0.00 39.10 3.58
587 589 1.888736 GGTGTAGGACCCGACTGTC 59.111 63.158 0.00 0.00 39.10 3.51
588 590 4.108673 GGTGTAGGACCCGACTGT 57.891 61.111 1.24 0.00 39.10 3.55
595 597 3.782443 CTGGCCGGGTGTAGGACC 61.782 72.222 2.57 0.00 45.28 4.46
596 598 1.623542 AATCTGGCCGGGTGTAGGAC 61.624 60.000 12.87 0.00 37.28 3.85
597 599 0.031917 TAATCTGGCCGGGTGTAGGA 60.032 55.000 12.87 0.00 0.00 2.94
598 600 0.106149 GTAATCTGGCCGGGTGTAGG 59.894 60.000 12.87 0.00 0.00 3.18
599 601 0.106149 GGTAATCTGGCCGGGTGTAG 59.894 60.000 12.87 0.00 0.00 2.74
600 602 0.618107 TGGTAATCTGGCCGGGTGTA 60.618 55.000 12.87 0.00 0.00 2.90
601 603 1.279025 ATGGTAATCTGGCCGGGTGT 61.279 55.000 12.87 0.00 0.00 4.16
602 604 0.106719 AATGGTAATCTGGCCGGGTG 60.107 55.000 12.87 0.00 0.00 4.61
603 605 0.106719 CAATGGTAATCTGGCCGGGT 60.107 55.000 12.87 0.00 0.00 5.28
604 606 0.106719 ACAATGGTAATCTGGCCGGG 60.107 55.000 12.87 0.00 0.00 5.73
605 607 2.218603 GTACAATGGTAATCTGGCCGG 58.781 52.381 4.71 4.71 0.00 6.13
606 608 2.218603 GGTACAATGGTAATCTGGCCG 58.781 52.381 0.00 0.00 0.00 6.13
607 609 2.583143 GGGTACAATGGTAATCTGGCC 58.417 52.381 0.00 0.00 0.00 5.36
608 610 2.174854 AGGGGTACAATGGTAATCTGGC 59.825 50.000 0.00 0.00 0.00 4.85
609 611 3.435026 CCAGGGGTACAATGGTAATCTGG 60.435 52.174 9.20 9.20 37.11 3.86
610 612 3.435026 CCCAGGGGTACAATGGTAATCTG 60.435 52.174 0.00 0.00 31.85 2.90
611 613 2.783510 CCCAGGGGTACAATGGTAATCT 59.216 50.000 0.00 0.00 31.85 2.40
612 614 2.158519 CCCCAGGGGTACAATGGTAATC 60.159 54.545 18.09 0.00 38.25 1.75
613 615 1.856920 CCCCAGGGGTACAATGGTAAT 59.143 52.381 18.09 0.00 38.25 1.89
614 616 1.300927 CCCCAGGGGTACAATGGTAA 58.699 55.000 18.09 0.00 38.25 2.85
615 617 3.030635 CCCCAGGGGTACAATGGTA 57.969 57.895 18.09 0.00 38.25 3.25
616 618 3.850061 CCCCAGGGGTACAATGGT 58.150 61.111 18.09 0.00 38.25 3.55
631 633 2.848694 GGGTTTATATAGGCCTACCCCC 59.151 54.545 23.88 17.51 39.42 5.40
633 635 2.848694 GGGGGTTTATATAGGCCTACCC 59.151 54.545 25.63 25.63 43.59 3.69
634 636 3.522343 CTGGGGGTTTATATAGGCCTACC 59.478 52.174 16.61 13.48 0.00 3.18
635 637 3.522343 CCTGGGGGTTTATATAGGCCTAC 59.478 52.174 16.61 3.08 0.00 3.18
636 638 3.410337 TCCTGGGGGTTTATATAGGCCTA 59.590 47.826 16.60 16.60 0.00 3.93
637 639 2.185931 TCCTGGGGGTTTATATAGGCCT 59.814 50.000 11.78 11.78 0.00 5.19
638 640 2.307980 GTCCTGGGGGTTTATATAGGCC 59.692 54.545 0.00 0.00 0.00 5.19
639 641 2.983898 TGTCCTGGGGGTTTATATAGGC 59.016 50.000 0.00 0.00 0.00 3.93
640 642 3.329814 GGTGTCCTGGGGGTTTATATAGG 59.670 52.174 0.00 0.00 0.00 2.57
641 643 3.329814 GGGTGTCCTGGGGGTTTATATAG 59.670 52.174 0.00 0.00 0.00 1.31
642 644 3.312231 TGGGTGTCCTGGGGGTTTATATA 60.312 47.826 0.00 0.00 0.00 0.86
643 645 2.141067 GGGTGTCCTGGGGGTTTATAT 58.859 52.381 0.00 0.00 0.00 0.86
644 646 1.203583 TGGGTGTCCTGGGGGTTTATA 60.204 52.381 0.00 0.00 0.00 0.98
645 647 0.478789 TGGGTGTCCTGGGGGTTTAT 60.479 55.000 0.00 0.00 0.00 1.40
646 648 0.478789 ATGGGTGTCCTGGGGGTTTA 60.479 55.000 0.00 0.00 0.00 2.01
647 649 1.782608 ATGGGTGTCCTGGGGGTTT 60.783 57.895 0.00 0.00 0.00 3.27
648 650 2.121042 ATGGGTGTCCTGGGGGTT 60.121 61.111 0.00 0.00 0.00 4.11
649 651 2.941025 CATGGGTGTCCTGGGGGT 60.941 66.667 0.00 0.00 0.00 4.95
650 652 4.447342 GCATGGGTGTCCTGGGGG 62.447 72.222 0.00 0.00 0.00 5.40
651 653 2.728460 TTTGCATGGGTGTCCTGGGG 62.728 60.000 0.00 0.00 0.00 4.96
652 654 1.228831 TTTGCATGGGTGTCCTGGG 60.229 57.895 0.00 0.00 0.00 4.45
653 655 1.252904 CCTTTGCATGGGTGTCCTGG 61.253 60.000 0.00 0.00 0.00 4.45
654 656 1.252904 CCCTTTGCATGGGTGTCCTG 61.253 60.000 15.09 0.00 39.82 3.86
655 657 1.077265 CCCTTTGCATGGGTGTCCT 59.923 57.895 15.09 0.00 39.82 3.85
656 658 3.698765 CCCTTTGCATGGGTGTCC 58.301 61.111 15.09 0.00 39.82 4.02
662 664 0.321346 GGTTGGAACCCTTTGCATGG 59.679 55.000 0.00 0.00 43.43 3.66
663 665 3.912899 GGTTGGAACCCTTTGCATG 57.087 52.632 0.00 0.00 43.43 4.06
673 675 7.117956 GTGAGTCTAATTCTAACAGGTTGGAAC 59.882 40.741 12.26 2.04 41.64 3.62
674 676 7.159372 GTGAGTCTAATTCTAACAGGTTGGAA 58.841 38.462 12.38 12.38 42.71 3.53
675 677 6.269077 TGTGAGTCTAATTCTAACAGGTTGGA 59.731 38.462 0.00 0.00 0.00 3.53
676 678 6.369065 GTGTGAGTCTAATTCTAACAGGTTGG 59.631 42.308 0.00 0.00 28.17 3.77
677 679 6.369065 GGTGTGAGTCTAATTCTAACAGGTTG 59.631 42.308 0.00 0.00 28.17 3.77
678 680 6.270231 AGGTGTGAGTCTAATTCTAACAGGTT 59.730 38.462 0.00 0.00 28.17 3.50
679 681 5.780793 AGGTGTGAGTCTAATTCTAACAGGT 59.219 40.000 0.00 0.00 28.17 4.00
680 682 6.287589 AGGTGTGAGTCTAATTCTAACAGG 57.712 41.667 0.00 0.00 28.17 4.00
681 683 7.416890 CCCTAGGTGTGAGTCTAATTCTAACAG 60.417 44.444 8.29 0.00 28.17 3.16
682 684 6.380274 CCCTAGGTGTGAGTCTAATTCTAACA 59.620 42.308 8.29 0.00 0.00 2.41
683 685 6.183360 CCCCTAGGTGTGAGTCTAATTCTAAC 60.183 46.154 8.29 0.00 0.00 2.34
684 686 5.897824 CCCCTAGGTGTGAGTCTAATTCTAA 59.102 44.000 8.29 0.00 0.00 2.10
685 687 5.455872 CCCCTAGGTGTGAGTCTAATTCTA 58.544 45.833 8.29 0.00 0.00 2.10
686 688 4.290942 CCCCTAGGTGTGAGTCTAATTCT 58.709 47.826 8.29 0.00 0.00 2.40
687 689 3.388350 CCCCCTAGGTGTGAGTCTAATTC 59.612 52.174 8.29 0.00 0.00 2.17
688 690 3.013648 TCCCCCTAGGTGTGAGTCTAATT 59.986 47.826 8.29 0.00 36.75 1.40
689 691 2.590611 TCCCCCTAGGTGTGAGTCTAAT 59.409 50.000 8.29 0.00 36.75 1.73
690 692 2.005350 TCCCCCTAGGTGTGAGTCTAA 58.995 52.381 8.29 0.00 36.75 2.10
691 693 1.569548 CTCCCCCTAGGTGTGAGTCTA 59.430 57.143 8.29 0.00 36.75 2.59
692 694 0.336737 CTCCCCCTAGGTGTGAGTCT 59.663 60.000 8.29 0.00 36.75 3.24
693 695 0.335361 TCTCCCCCTAGGTGTGAGTC 59.665 60.000 8.29 0.00 36.75 3.36
694 696 0.790993 TTCTCCCCCTAGGTGTGAGT 59.209 55.000 8.29 0.00 36.75 3.41
695 697 1.007238 TCTTCTCCCCCTAGGTGTGAG 59.993 57.143 8.29 10.21 36.75 3.51
696 698 1.007238 CTCTTCTCCCCCTAGGTGTGA 59.993 57.143 8.29 2.24 36.75 3.58
697 699 1.007238 TCTCTTCTCCCCCTAGGTGTG 59.993 57.143 8.29 0.00 36.75 3.82
698 700 1.289530 CTCTCTTCTCCCCCTAGGTGT 59.710 57.143 8.29 0.00 36.75 4.16
699 701 2.032151 GCTCTCTTCTCCCCCTAGGTG 61.032 61.905 8.29 0.00 36.75 4.00
700 702 0.263468 GCTCTCTTCTCCCCCTAGGT 59.737 60.000 8.29 0.00 36.75 3.08
701 703 0.263172 TGCTCTCTTCTCCCCCTAGG 59.737 60.000 0.06 0.06 0.00 3.02
702 704 2.166907 TTGCTCTCTTCTCCCCCTAG 57.833 55.000 0.00 0.00 0.00 3.02
703 705 2.472029 CTTTGCTCTCTTCTCCCCCTA 58.528 52.381 0.00 0.00 0.00 3.53
704 706 1.284313 CTTTGCTCTCTTCTCCCCCT 58.716 55.000 0.00 0.00 0.00 4.79
705 707 0.393673 GCTTTGCTCTCTTCTCCCCC 60.394 60.000 0.00 0.00 0.00 5.40
706 708 0.393673 GGCTTTGCTCTCTTCTCCCC 60.394 60.000 0.00 0.00 0.00 4.81
707 709 0.326264 TGGCTTTGCTCTCTTCTCCC 59.674 55.000 0.00 0.00 0.00 4.30
708 710 2.083002 CTTGGCTTTGCTCTCTTCTCC 58.917 52.381 0.00 0.00 0.00 3.71
709 711 1.468127 GCTTGGCTTTGCTCTCTTCTC 59.532 52.381 0.00 0.00 0.00 2.87
710 712 1.202855 TGCTTGGCTTTGCTCTCTTCT 60.203 47.619 0.00 0.00 0.00 2.85
711 713 1.068679 GTGCTTGGCTTTGCTCTCTTC 60.069 52.381 0.00 0.00 0.00 2.87
712 714 0.957362 GTGCTTGGCTTTGCTCTCTT 59.043 50.000 0.00 0.00 0.00 2.85
713 715 0.179009 TGTGCTTGGCTTTGCTCTCT 60.179 50.000 0.00 0.00 0.00 3.10
714 716 0.039708 GTGTGCTTGGCTTTGCTCTC 60.040 55.000 0.00 0.00 0.00 3.20
715 717 0.752743 TGTGTGCTTGGCTTTGCTCT 60.753 50.000 0.00 0.00 0.00 4.09
716 718 0.316204 ATGTGTGCTTGGCTTTGCTC 59.684 50.000 0.00 0.00 0.00 4.26
717 719 0.032952 CATGTGTGCTTGGCTTTGCT 59.967 50.000 0.00 0.00 0.00 3.91
718 720 0.947180 CCATGTGTGCTTGGCTTTGC 60.947 55.000 0.00 0.00 33.91 3.68
719 721 3.204505 CCATGTGTGCTTGGCTTTG 57.795 52.632 0.00 0.00 33.91 2.77
724 726 2.260434 GCAGCCATGTGTGCTTGG 59.740 61.111 8.85 0.00 41.38 3.61
758 760 4.697352 GCCAGTGATACAAACTTGATCACT 59.303 41.667 20.19 20.19 45.66 3.41
794 906 2.203209 CGGATACTGCCCTTGGGC 60.203 66.667 22.91 22.91 0.00 5.36
801 913 2.029623 TGTAGTTCTCCGGATACTGCC 58.970 52.381 22.89 15.70 0.00 4.85
808 920 2.764572 GGGAATTCTGTAGTTCTCCGGA 59.235 50.000 2.93 2.93 0.00 5.14
842 954 3.309296 TGGTGGGCAACTGGAAATTTTA 58.691 40.909 0.00 0.00 0.00 1.52
1054 1191 1.388531 GAGGGAGAGGTGGGAGTGA 59.611 63.158 0.00 0.00 0.00 3.41
1056 1193 1.079438 GTGAGGGAGAGGTGGGAGT 59.921 63.158 0.00 0.00 0.00 3.85
1057 1194 0.686112 GAGTGAGGGAGAGGTGGGAG 60.686 65.000 0.00 0.00 0.00 4.30
1058 1195 1.388531 GAGTGAGGGAGAGGTGGGA 59.611 63.158 0.00 0.00 0.00 4.37
1573 1801 1.208052 AGCCAACTACATCTGTCGCAT 59.792 47.619 0.00 0.00 0.00 4.73
1744 2143 3.434299 CCCATGAAATTCAGCAAAAGCAC 59.566 43.478 1.10 0.00 0.00 4.40
1745 2144 3.324268 TCCCATGAAATTCAGCAAAAGCA 59.676 39.130 1.10 0.00 0.00 3.91
1746 2145 3.929094 TCCCATGAAATTCAGCAAAAGC 58.071 40.909 1.10 0.00 0.00 3.51
1806 2205 2.223782 TGTTTGCACCACAGAATTCAGC 60.224 45.455 8.44 2.58 0.00 4.26
1840 2248 4.510711 CACCAATACAGAGATGCATCACTC 59.489 45.833 27.81 17.38 0.00 3.51
1935 2352 1.177401 GAACCAGGGATCTGCAAACC 58.823 55.000 0.00 0.00 39.61 3.27
2103 2671 3.069443 ACAAGAAATGGACGGCAATTTGT 59.931 39.130 8.79 0.42 0.00 2.83
2177 2745 1.140312 AGGTTTCTTCAGTGGGCAGA 58.860 50.000 0.00 0.00 0.00 4.26
2210 2780 2.789917 GCTTCAGCTCCATGTGCG 59.210 61.111 0.00 0.00 38.21 5.34
2240 2822 2.225491 GACGCTGCTATTTCAACCACAA 59.775 45.455 0.00 0.00 0.00 3.33
2302 2884 5.212194 CAAGATTAACAAAACAGACGGGTG 58.788 41.667 0.00 0.00 0.00 4.61
2342 2924 6.457934 GCACATGTATTGGACTCTGAAGATTG 60.458 42.308 0.00 0.00 0.00 2.67
2351 2933 2.353889 CAGCTGCACATGTATTGGACTC 59.646 50.000 0.00 0.00 0.00 3.36
2395 2986 4.389576 GCAGAAACCACCGCTGCG 62.390 66.667 16.34 16.34 44.52 5.18
2498 3089 2.721425 TTACATCCATCGGTTTCCCC 57.279 50.000 0.00 0.00 0.00 4.81
2536 3127 2.017138 TGACACTGAAGCGAACACAA 57.983 45.000 0.00 0.00 0.00 3.33
2559 3150 6.010219 ACCAAATTAATGCTTCCTAGTGTGT 58.990 36.000 0.00 0.00 0.00 3.72
2570 3161 6.704310 AGCAAAAGATGACCAAATTAATGCT 58.296 32.000 0.00 0.00 34.68 3.79
2624 3215 3.947910 AATTGGCAAAGGTGATGTCTG 57.052 42.857 3.01 0.00 0.00 3.51
2787 3412 2.943690 CCAGTTCCTTCATCTGCATCAG 59.056 50.000 0.00 0.00 0.00 2.90
2822 3447 6.522946 GGTAGTTTACATGATTCTCCCTACC 58.477 44.000 0.00 5.90 36.29 3.18
2843 3468 0.530744 GTGATGTCTGCCACTCGGTA 59.469 55.000 0.00 0.00 33.28 4.02


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

AutoCloner maintained by Alex Coulton.