Multiple sequence alignment - TraesCS3A01G130400

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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 TraesCS3A01G130400 chr3A 100.000 3060 0 0 1 3060 107415364 107418423 0.000000e+00 5651.0
1 TraesCS3A01G130400 chr3A 92.727 55 1 2 1816 1870 63476203 63476152 3.270000e-10 76.8
2 TraesCS3A01G130400 chr3A 94.737 38 2 0 2810 2847 691088418 691088455 3.290000e-05 60.2
3 TraesCS3A01G130400 chr3B 91.842 1140 45 19 825 1942 140984370 140985483 0.000000e+00 1546.0
4 TraesCS3A01G130400 chr3B 99.388 654 4 0 1 654 764096425 764097078 0.000000e+00 1186.0
5 TraesCS3A01G130400 chr3B 99.233 652 5 0 1 652 771346193 771345542 0.000000e+00 1177.0
6 TraesCS3A01G130400 chr3B 88.087 277 28 2 2032 2303 140985604 140985880 1.060000e-84 324.0
7 TraesCS3A01G130400 chr3B 87.273 55 3 4 666 719 595269972 595269921 3.290000e-05 60.2
8 TraesCS3A01G130400 chr2B 99.540 652 3 0 1 652 501738336 501738987 0.000000e+00 1188.0
9 TraesCS3A01G130400 chr7A 99.387 652 4 0 1 652 570180773 570181424 0.000000e+00 1182.0
10 TraesCS3A01G130400 chr7A 93.023 43 3 0 669 711 477121279 477121321 2.550000e-06 63.9
11 TraesCS3A01G130400 chr3D 93.218 811 44 8 868 1674 91366896 91367699 0.000000e+00 1182.0
12 TraesCS3A01G130400 chr3D 86.582 790 45 23 2021 2769 91369307 91370076 0.000000e+00 815.0
13 TraesCS3A01G130400 chr3D 89.911 337 16 5 1673 2008 91368915 91369234 4.720000e-113 418.0
14 TraesCS3A01G130400 chr3D 95.312 128 5 1 2930 3057 91371567 91371693 5.170000e-48 202.0
15 TraesCS3A01G130400 chr3D 89.091 55 3 2 1816 1870 50400333 50400282 7.080000e-07 65.8
16 TraesCS3A01G130400 chr2A 99.387 652 4 0 1 652 43151458 43152109 0.000000e+00 1182.0
17 TraesCS3A01G130400 chr4A 99.234 653 5 0 1 653 677985967 677986619 0.000000e+00 1179.0
18 TraesCS3A01G130400 chr4B 99.233 652 5 0 1 652 17247630 17248281 0.000000e+00 1177.0
19 TraesCS3A01G130400 chr4B 99.080 652 6 0 1 652 6669151 6668500 0.000000e+00 1171.0
20 TraesCS3A01G130400 chr1A 99.081 653 5 1 1 653 545865414 545866065 0.000000e+00 1171.0
21 TraesCS3A01G130400 chr1A 94.872 39 2 0 669 707 1310257 1310295 9.160000e-06 62.1
22 TraesCS3A01G130400 chr4D 87.387 111 11 3 1075 1183 10743983 10744092 1.150000e-24 124.0
23 TraesCS3A01G130400 chr4D 100.000 35 0 0 673 707 8670251 8670217 7.080000e-07 65.8
24 TraesCS3A01G130400 chr6A 78.037 214 32 11 1078 1282 3856000 3855793 1.490000e-23 121.0
25 TraesCS3A01G130400 chr6B 78.836 189 27 10 1080 1257 8997122 8997308 6.930000e-22 115.0
26 TraesCS3A01G130400 chr6B 91.489 47 2 2 662 707 84933539 84933584 2.550000e-06 63.9
27 TraesCS3A01G130400 chr1B 87.879 66 6 1 666 731 144121737 144121674 3.270000e-10 76.8
28 TraesCS3A01G130400 chr5B 97.368 38 1 0 670 707 600518726 600518763 7.080000e-07 65.8
29 TraesCS3A01G130400 chr6D 95.000 40 2 0 668 707 455101317 455101278 2.550000e-06 63.9
30 TraesCS3A01G130400 chr1D 93.023 43 3 0 668 710 71022219 71022177 2.550000e-06 63.9


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 TraesCS3A01G130400 chr3A 107415364 107418423 3059 False 5651.00 5651 100.00000 1 3060 1 chr3A.!!$F1 3059
1 TraesCS3A01G130400 chr3B 764096425 764097078 653 False 1186.00 1186 99.38800 1 654 1 chr3B.!!$F1 653
2 TraesCS3A01G130400 chr3B 771345542 771346193 651 True 1177.00 1177 99.23300 1 652 1 chr3B.!!$R2 651
3 TraesCS3A01G130400 chr3B 140984370 140985880 1510 False 935.00 1546 89.96450 825 2303 2 chr3B.!!$F2 1478
4 TraesCS3A01G130400 chr2B 501738336 501738987 651 False 1188.00 1188 99.54000 1 652 1 chr2B.!!$F1 651
5 TraesCS3A01G130400 chr7A 570180773 570181424 651 False 1182.00 1182 99.38700 1 652 1 chr7A.!!$F2 651
6 TraesCS3A01G130400 chr3D 91366896 91371693 4797 False 654.25 1182 91.25575 868 3057 4 chr3D.!!$F1 2189
7 TraesCS3A01G130400 chr2A 43151458 43152109 651 False 1182.00 1182 99.38700 1 652 1 chr2A.!!$F1 651
8 TraesCS3A01G130400 chr4A 677985967 677986619 652 False 1179.00 1179 99.23400 1 653 1 chr4A.!!$F1 652
9 TraesCS3A01G130400 chr4B 17247630 17248281 651 False 1177.00 1177 99.23300 1 652 1 chr4B.!!$F1 651
10 TraesCS3A01G130400 chr4B 6668500 6669151 651 True 1171.00 1171 99.08000 1 652 1 chr4B.!!$R1 651
11 TraesCS3A01G130400 chr1A 545865414 545866065 651 False 1171.00 1171 99.08100 1 653 1 chr1A.!!$F2 652

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
844 845 1.123928 GTGAACCGGGGAGATGATCT 58.876 55.0 6.32 0.0 0.0 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2456 3866 0.178938 TTTCTGCCCTTTGCCATCCA 60.179 50.0 0.0 0.0 40.16 3.41 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
657 658 7.778470 ACAACTCTATATTCTAACAAGCAGC 57.222 36.000 0.00 0.00 0.00 5.25
658 659 7.331026 ACAACTCTATATTCTAACAAGCAGCA 58.669 34.615 0.00 0.00 0.00 4.41
659 660 7.278868 ACAACTCTATATTCTAACAAGCAGCAC 59.721 37.037 0.00 0.00 0.00 4.40
660 661 6.878317 ACTCTATATTCTAACAAGCAGCACA 58.122 36.000 0.00 0.00 0.00 4.57
661 662 7.504403 ACTCTATATTCTAACAAGCAGCACAT 58.496 34.615 0.00 0.00 0.00 3.21
662 663 7.989741 ACTCTATATTCTAACAAGCAGCACATT 59.010 33.333 0.00 0.00 0.00 2.71
663 664 8.146479 TCTATATTCTAACAAGCAGCACATTG 57.854 34.615 0.00 0.00 0.00 2.82
664 665 6.764308 ATATTCTAACAAGCAGCACATTGT 57.236 33.333 0.00 0.00 41.28 2.71
665 666 7.864108 ATATTCTAACAAGCAGCACATTGTA 57.136 32.000 0.00 0.00 38.66 2.41
666 667 5.611796 TTCTAACAAGCAGCACATTGTAG 57.388 39.130 0.00 0.00 38.66 2.74
667 668 4.641396 TCTAACAAGCAGCACATTGTAGT 58.359 39.130 0.00 0.00 38.66 2.73
668 669 5.789521 TCTAACAAGCAGCACATTGTAGTA 58.210 37.500 0.00 0.00 38.66 1.82
669 670 6.406370 TCTAACAAGCAGCACATTGTAGTAT 58.594 36.000 0.00 0.00 38.66 2.12
670 671 7.552459 TCTAACAAGCAGCACATTGTAGTATA 58.448 34.615 0.00 0.00 38.66 1.47
671 672 6.668541 AACAAGCAGCACATTGTAGTATAG 57.331 37.500 0.00 0.00 38.66 1.31
672 673 5.734720 ACAAGCAGCACATTGTAGTATAGT 58.265 37.500 0.00 0.00 37.85 2.12
673 674 6.873997 ACAAGCAGCACATTGTAGTATAGTA 58.126 36.000 0.00 0.00 37.85 1.82
674 675 6.757010 ACAAGCAGCACATTGTAGTATAGTAC 59.243 38.462 10.34 10.34 37.85 2.73
675 676 6.716934 AGCAGCACATTGTAGTATAGTACT 57.283 37.500 16.79 0.00 42.68 2.73
676 677 7.113658 AGCAGCACATTGTAGTATAGTACTT 57.886 36.000 16.79 4.20 40.14 2.24
677 678 7.203910 AGCAGCACATTGTAGTATAGTACTTC 58.796 38.462 16.79 0.00 40.14 3.01
678 679 6.421202 GCAGCACATTGTAGTATAGTACTTCC 59.579 42.308 16.79 0.00 40.14 3.46
679 680 7.684670 GCAGCACATTGTAGTATAGTACTTCCT 60.685 40.741 16.79 0.00 40.14 3.36
680 681 7.863375 CAGCACATTGTAGTATAGTACTTCCTC 59.137 40.741 16.79 4.57 40.14 3.71
681 682 7.014422 AGCACATTGTAGTATAGTACTTCCTCC 59.986 40.741 16.79 4.37 40.14 4.30
682 683 7.361127 CACATTGTAGTATAGTACTTCCTCCG 58.639 42.308 16.79 3.84 40.14 4.63
683 684 7.013083 CACATTGTAGTATAGTACTTCCTCCGT 59.987 40.741 16.79 4.33 40.14 4.69
684 685 7.228308 ACATTGTAGTATAGTACTTCCTCCGTC 59.772 40.741 16.79 0.00 40.14 4.79
685 686 5.615289 TGTAGTATAGTACTTCCTCCGTCC 58.385 45.833 16.79 0.00 40.14 4.79
686 687 4.097551 AGTATAGTACTTCCTCCGTCCC 57.902 50.000 0.00 0.00 34.86 4.46
687 688 3.461085 AGTATAGTACTTCCTCCGTCCCA 59.539 47.826 0.00 0.00 34.86 4.37
688 689 3.614568 ATAGTACTTCCTCCGTCCCAT 57.385 47.619 0.00 0.00 0.00 4.00
689 690 4.736611 ATAGTACTTCCTCCGTCCCATA 57.263 45.455 0.00 0.00 0.00 2.74
690 691 3.393426 AGTACTTCCTCCGTCCCATAA 57.607 47.619 0.00 0.00 0.00 1.90
691 692 3.924922 AGTACTTCCTCCGTCCCATAAT 58.075 45.455 0.00 0.00 0.00 1.28
692 693 5.070823 AGTACTTCCTCCGTCCCATAATA 57.929 43.478 0.00 0.00 0.00 0.98
693 694 5.652324 AGTACTTCCTCCGTCCCATAATAT 58.348 41.667 0.00 0.00 0.00 1.28
694 695 6.797707 AGTACTTCCTCCGTCCCATAATATA 58.202 40.000 0.00 0.00 0.00 0.86
695 696 7.243824 AGTACTTCCTCCGTCCCATAATATAA 58.756 38.462 0.00 0.00 0.00 0.98
696 697 7.731688 AGTACTTCCTCCGTCCCATAATATAAA 59.268 37.037 0.00 0.00 0.00 1.40
697 698 7.383156 ACTTCCTCCGTCCCATAATATAAAA 57.617 36.000 0.00 0.00 0.00 1.52
698 699 7.450903 ACTTCCTCCGTCCCATAATATAAAAG 58.549 38.462 0.00 0.00 0.00 2.27
699 700 5.801380 TCCTCCGTCCCATAATATAAAAGC 58.199 41.667 0.00 0.00 0.00 3.51
700 701 5.308497 TCCTCCGTCCCATAATATAAAAGCA 59.692 40.000 0.00 0.00 0.00 3.91
701 702 6.012858 TCCTCCGTCCCATAATATAAAAGCAT 60.013 38.462 0.00 0.00 0.00 3.79
702 703 6.659242 CCTCCGTCCCATAATATAAAAGCATT 59.341 38.462 0.00 0.00 0.00 3.56
703 704 7.176690 CCTCCGTCCCATAATATAAAAGCATTT 59.823 37.037 0.00 0.00 42.41 2.32
721 722 7.294017 AGCATTTTTGTCATATTATGGGAGG 57.706 36.000 3.89 0.00 0.00 4.30
722 723 6.268387 AGCATTTTTGTCATATTATGGGAGGG 59.732 38.462 3.89 0.00 0.00 4.30
723 724 6.267471 GCATTTTTGTCATATTATGGGAGGGA 59.733 38.462 3.89 0.00 0.00 4.20
724 725 7.524367 GCATTTTTGTCATATTATGGGAGGGAG 60.524 40.741 3.89 0.00 0.00 4.30
725 726 6.840090 TTTTGTCATATTATGGGAGGGAGA 57.160 37.500 3.89 0.00 0.00 3.71
726 727 6.439636 TTTGTCATATTATGGGAGGGAGAG 57.560 41.667 3.89 0.00 0.00 3.20
727 728 5.354184 TGTCATATTATGGGAGGGAGAGA 57.646 43.478 3.89 0.00 0.00 3.10
728 729 5.336945 TGTCATATTATGGGAGGGAGAGAG 58.663 45.833 3.89 0.00 0.00 3.20
729 730 5.162826 TGTCATATTATGGGAGGGAGAGAGT 60.163 44.000 3.89 0.00 0.00 3.24
730 731 6.046762 TGTCATATTATGGGAGGGAGAGAGTA 59.953 42.308 3.89 0.00 0.00 2.59
731 732 7.129425 GTCATATTATGGGAGGGAGAGAGTAT 58.871 42.308 3.89 0.00 0.00 2.12
732 733 8.282982 GTCATATTATGGGAGGGAGAGAGTATA 58.717 40.741 3.89 0.00 0.00 1.47
733 734 9.030611 TCATATTATGGGAGGGAGAGAGTATAT 57.969 37.037 3.89 0.00 0.00 0.86
734 735 9.087871 CATATTATGGGAGGGAGAGAGTATATG 57.912 40.741 0.00 0.00 0.00 1.78
735 736 3.176924 TGGGAGGGAGAGAGTATATGC 57.823 52.381 0.00 0.00 0.00 3.14
736 737 2.724672 TGGGAGGGAGAGAGTATATGCT 59.275 50.000 0.00 0.00 0.00 3.79
737 738 3.923425 TGGGAGGGAGAGAGTATATGCTA 59.077 47.826 0.00 0.00 0.00 3.49
738 739 4.017958 TGGGAGGGAGAGAGTATATGCTAG 60.018 50.000 0.00 0.00 0.00 3.42
739 740 3.951680 GGAGGGAGAGAGTATATGCTAGC 59.048 52.174 8.10 8.10 0.00 3.42
740 741 4.568804 GGAGGGAGAGAGTATATGCTAGCA 60.569 50.000 21.85 21.85 0.00 3.49
741 742 4.599041 AGGGAGAGAGTATATGCTAGCAG 58.401 47.826 23.89 0.00 0.00 4.24
742 743 4.044065 AGGGAGAGAGTATATGCTAGCAGT 59.956 45.833 23.89 16.20 0.00 4.40
743 744 5.251932 AGGGAGAGAGTATATGCTAGCAGTA 59.748 44.000 23.89 15.17 0.00 2.74
744 745 5.355910 GGGAGAGAGTATATGCTAGCAGTAC 59.644 48.000 23.89 24.42 0.00 2.73
745 746 6.177610 GGAGAGAGTATATGCTAGCAGTACT 58.822 44.000 30.55 30.55 35.47 2.73
746 747 7.332557 GGAGAGAGTATATGCTAGCAGTACTA 58.667 42.308 30.33 18.04 34.03 1.82
747 748 7.825270 GGAGAGAGTATATGCTAGCAGTACTAA 59.175 40.741 30.33 12.87 34.03 2.24
748 749 9.391006 GAGAGAGTATATGCTAGCAGTACTAAT 57.609 37.037 30.33 24.68 34.03 1.73
749 750 9.747898 AGAGAGTATATGCTAGCAGTACTAATT 57.252 33.333 30.33 22.72 34.03 1.40
754 755 9.915629 GTATATGCTAGCAGTACTAATTTCTGT 57.084 33.333 23.89 3.20 0.00 3.41
757 758 8.879342 ATGCTAGCAGTACTAATTTCTGTTAG 57.121 34.615 23.89 9.66 42.02 2.34
760 761 8.346476 CTAGCAGTACTAATTTCTGTTAGCAG 57.654 38.462 0.00 0.00 43.87 4.24
761 762 6.702329 AGCAGTACTAATTTCTGTTAGCAGT 58.298 36.000 6.47 0.00 43.05 4.40
762 763 7.837863 AGCAGTACTAATTTCTGTTAGCAGTA 58.162 34.615 6.47 0.00 43.05 2.74
763 764 8.311836 AGCAGTACTAATTTCTGTTAGCAGTAA 58.688 33.333 6.47 3.79 43.05 2.24
764 765 8.596380 GCAGTACTAATTTCTGTTAGCAGTAAG 58.404 37.037 6.47 1.72 43.05 2.34
765 766 9.856488 CAGTACTAATTTCTGTTAGCAGTAAGA 57.144 33.333 6.47 0.00 43.05 2.10
768 769 8.635877 ACTAATTTCTGTTAGCAGTAAGATCG 57.364 34.615 6.47 0.00 43.05 3.69
769 770 8.467598 ACTAATTTCTGTTAGCAGTAAGATCGA 58.532 33.333 6.47 0.00 43.05 3.59
770 771 7.763172 AATTTCTGTTAGCAGTAAGATCGAG 57.237 36.000 6.47 0.00 43.05 4.04
771 772 4.294416 TCTGTTAGCAGTAAGATCGAGC 57.706 45.455 6.47 0.00 43.05 5.03
772 773 3.948473 TCTGTTAGCAGTAAGATCGAGCT 59.052 43.478 0.00 0.00 43.05 4.09
773 774 4.033990 TGTTAGCAGTAAGATCGAGCTG 57.966 45.455 2.80 1.74 36.80 4.24
774 775 3.444034 TGTTAGCAGTAAGATCGAGCTGT 59.556 43.478 2.80 0.00 36.80 4.40
775 776 2.861462 AGCAGTAAGATCGAGCTGTC 57.139 50.000 2.80 0.02 33.67 3.51
776 777 2.095461 AGCAGTAAGATCGAGCTGTCA 58.905 47.619 2.80 0.00 33.67 3.58
777 778 2.098934 AGCAGTAAGATCGAGCTGTCAG 59.901 50.000 2.80 0.00 33.67 3.51
778 779 2.098280 GCAGTAAGATCGAGCTGTCAGA 59.902 50.000 2.80 0.00 0.00 3.27
779 780 3.243367 GCAGTAAGATCGAGCTGTCAGAT 60.243 47.826 2.80 0.00 0.00 2.90
780 781 4.736168 GCAGTAAGATCGAGCTGTCAGATT 60.736 45.833 2.80 0.00 0.00 2.40
781 782 5.506483 GCAGTAAGATCGAGCTGTCAGATTA 60.506 44.000 2.80 0.00 0.00 1.75
782 783 6.142139 CAGTAAGATCGAGCTGTCAGATTAG 58.858 44.000 2.80 0.00 0.00 1.73
783 784 4.582701 AAGATCGAGCTGTCAGATTAGG 57.417 45.455 2.80 0.00 0.00 2.69
784 785 2.890311 AGATCGAGCTGTCAGATTAGGG 59.110 50.000 0.39 0.00 0.00 3.53
785 786 2.437085 TCGAGCTGTCAGATTAGGGA 57.563 50.000 3.32 0.00 0.00 4.20
786 787 2.302260 TCGAGCTGTCAGATTAGGGAG 58.698 52.381 3.32 0.00 0.00 4.30
787 788 2.092375 TCGAGCTGTCAGATTAGGGAGA 60.092 50.000 3.32 0.00 0.00 3.71
788 789 2.034053 CGAGCTGTCAGATTAGGGAGAC 59.966 54.545 3.32 0.00 0.00 3.36
789 790 3.295973 GAGCTGTCAGATTAGGGAGACT 58.704 50.000 3.32 0.00 32.41 3.24
790 791 3.295973 AGCTGTCAGATTAGGGAGACTC 58.704 50.000 3.32 0.00 32.41 3.36
791 792 3.027412 GCTGTCAGATTAGGGAGACTCA 58.973 50.000 3.32 0.00 32.41 3.41
792 793 3.640967 GCTGTCAGATTAGGGAGACTCAT 59.359 47.826 3.32 0.00 32.41 2.90
793 794 4.261994 GCTGTCAGATTAGGGAGACTCATC 60.262 50.000 3.32 0.00 31.31 2.92
794 795 3.885901 TGTCAGATTAGGGAGACTCATCG 59.114 47.826 4.53 0.00 35.44 3.84
795 796 3.886505 GTCAGATTAGGGAGACTCATCGT 59.113 47.826 4.53 0.00 35.44 3.73
796 797 4.339814 GTCAGATTAGGGAGACTCATCGTT 59.660 45.833 4.53 0.00 35.44 3.85
797 798 4.339530 TCAGATTAGGGAGACTCATCGTTG 59.660 45.833 4.53 0.00 35.44 4.10
798 799 4.339530 CAGATTAGGGAGACTCATCGTTGA 59.660 45.833 4.53 0.00 35.44 3.18
799 800 4.339814 AGATTAGGGAGACTCATCGTTGAC 59.660 45.833 4.53 0.00 35.44 3.18
800 801 2.223803 AGGGAGACTCATCGTTGACT 57.776 50.000 4.53 0.00 0.00 3.41
801 802 3.367646 AGGGAGACTCATCGTTGACTA 57.632 47.619 4.53 0.00 0.00 2.59
802 803 3.698289 AGGGAGACTCATCGTTGACTAA 58.302 45.455 4.53 0.00 0.00 2.24
803 804 4.282496 AGGGAGACTCATCGTTGACTAAT 58.718 43.478 4.53 0.00 0.00 1.73
804 805 4.098654 AGGGAGACTCATCGTTGACTAATG 59.901 45.833 4.53 0.00 0.00 1.90
805 806 4.363999 GGAGACTCATCGTTGACTAATGG 58.636 47.826 4.53 0.00 0.00 3.16
806 807 4.098044 GGAGACTCATCGTTGACTAATGGA 59.902 45.833 4.53 0.00 0.00 3.41
807 808 5.394224 GGAGACTCATCGTTGACTAATGGAA 60.394 44.000 4.53 0.00 0.00 3.53
808 809 5.411781 AGACTCATCGTTGACTAATGGAAC 58.588 41.667 0.00 0.00 0.00 3.62
833 834 3.058450 TGTATTGTTGTACGTGAACCGG 58.942 45.455 0.00 0.00 42.24 5.28
844 845 1.123928 GTGAACCGGGGAGATGATCT 58.876 55.000 6.32 0.00 0.00 2.75
861 862 5.036117 TGATCTAGGTTTGACTAATGGCC 57.964 43.478 0.00 0.00 0.00 5.36
863 864 5.903010 TGATCTAGGTTTGACTAATGGCCTA 59.097 40.000 3.32 0.00 0.00 3.93
864 865 5.871396 TCTAGGTTTGACTAATGGCCTAG 57.129 43.478 3.32 0.00 44.03 3.02
865 866 5.525484 TCTAGGTTTGACTAATGGCCTAGA 58.475 41.667 3.32 12.48 46.98 2.43
897 898 1.802337 CGATAGAATCCCGGCCGTCA 61.802 60.000 26.12 10.46 39.76 4.35
928 930 4.032900 AGTTGCACATTTACTAATCTCGCG 59.967 41.667 0.00 0.00 0.00 5.87
929 931 2.284150 TGCACATTTACTAATCTCGCGC 59.716 45.455 0.00 0.00 0.00 6.86
937 939 1.202313 ACTAATCTCGCGCTTCACTCC 60.202 52.381 5.56 0.00 0.00 3.85
959 962 3.414700 CTCAGTTCACCGCCACGC 61.415 66.667 0.00 0.00 0.00 5.34
976 979 1.674611 CGCTGCACACGTGTAGTAGC 61.675 60.000 31.18 31.18 43.78 3.58
1055 1058 2.264480 CTCCACGCCGACAATGGA 59.736 61.111 0.00 0.00 40.27 3.41
1098 1101 1.372997 GAAGCTCTTCGTGGACGCA 60.373 57.895 0.00 0.00 39.60 5.24
1380 1383 2.184579 GAGCTCTACACGTGCCCC 59.815 66.667 17.22 0.00 32.66 5.80
1413 1416 3.889134 CTGCTTGGAGTGCGCCAGA 62.889 63.158 4.18 0.00 39.52 3.86
1424 1427 3.411351 CGCCAGAAACGTGACGGG 61.411 66.667 10.66 0.79 0.00 5.28
1514 1517 1.753078 CCAGGTCCTCATCGACGGA 60.753 63.158 0.00 0.00 33.30 4.69
1515 1518 1.109920 CCAGGTCCTCATCGACGGAT 61.110 60.000 3.58 0.00 33.30 4.18
1715 2938 0.609406 GGGTTCAAGGAGGTGGCTTC 60.609 60.000 0.00 0.00 0.00 3.86
1729 2952 4.286032 AGGTGGCTTCATTACTACTGTTCA 59.714 41.667 0.00 0.00 0.00 3.18
1882 3125 1.401409 CGTTTTCCGAGTAGCCGTACA 60.401 52.381 0.00 0.00 39.56 2.90
1900 3143 3.744719 CGACCTCGGCTCGTTCCA 61.745 66.667 0.00 0.00 35.37 3.53
1948 3264 3.562973 CCTGCATTACAAGGTATCAGCAG 59.437 47.826 0.00 0.00 45.62 4.24
1956 3272 0.763652 AGGTATCAGCAGCTGGATGG 59.236 55.000 22.62 0.00 32.50 3.51
1961 3277 1.222661 CAGCAGCTGGATGGCAGTA 59.777 57.895 17.12 0.00 34.17 2.74
1972 3288 5.380043 CTGGATGGCAGTAAAATCCACTAT 58.620 41.667 1.18 0.00 43.85 2.12
1973 3289 6.508030 TGGATGGCAGTAAAATCCACTATA 57.492 37.500 1.18 0.00 43.85 1.31
1989 3306 8.666129 ATCCACTATATAGCTAGCTAAAACCA 57.334 34.615 27.47 6.83 31.73 3.67
1992 3309 8.368668 CCACTATATAGCTAGCTAAAACCAAGT 58.631 37.037 27.47 19.63 31.73 3.16
2010 3327 5.232463 CCAAGTTTGGTTTGATTCTGATGG 58.768 41.667 2.66 0.00 43.43 3.51
2013 3330 5.139727 AGTTTGGTTTGATTCTGATGGTCA 58.860 37.500 0.00 0.00 0.00 4.02
2014 3331 5.776716 AGTTTGGTTTGATTCTGATGGTCAT 59.223 36.000 0.00 0.00 0.00 3.06
2018 3335 6.425735 TGGTTTGATTCTGATGGTCATATGT 58.574 36.000 1.90 0.00 0.00 2.29
2019 3336 7.572814 TGGTTTGATTCTGATGGTCATATGTA 58.427 34.615 1.90 0.00 0.00 2.29
2029 3406 6.910191 TGATGGTCATATGTATTGGGTTCTT 58.090 36.000 1.90 0.00 0.00 2.52
2030 3407 6.998074 TGATGGTCATATGTATTGGGTTCTTC 59.002 38.462 1.90 0.00 0.00 2.87
2050 3427 7.490657 TCTTCCAGGTTTTAATAGCAGTAGA 57.509 36.000 0.00 0.00 0.00 2.59
2054 3436 6.598064 TCCAGGTTTTAATAGCAGTAGAAAGC 59.402 38.462 0.00 0.00 0.00 3.51
2128 3510 5.511373 CCAGAATCTACTCCAACACTGACAA 60.511 44.000 0.00 0.00 0.00 3.18
2141 3523 5.250235 ACACTGACAATACACTATCGGAG 57.750 43.478 0.00 0.00 0.00 4.63
2145 3527 5.500645 TGACAATACACTATCGGAGTCAG 57.499 43.478 0.00 0.00 35.64 3.51
2151 3533 6.961360 ATACACTATCGGAGTCAGATTCAA 57.039 37.500 11.15 0.00 35.64 2.69
2217 3599 2.334023 AGAGGAACACAAGGAGAAGCT 58.666 47.619 0.00 0.00 0.00 3.74
2219 3601 1.771255 AGGAACACAAGGAGAAGCTGT 59.229 47.619 0.00 0.00 0.00 4.40
2255 3637 3.126831 GCGTCATGAAACCTAGGAGATG 58.873 50.000 17.98 11.17 0.00 2.90
2271 3653 7.279758 CCTAGGAGATGTTCAGAAATGAACTTC 59.720 40.741 20.66 20.66 45.98 3.01
2370 3780 1.338105 TGAGCCTATGAGTGTGTGTGC 60.338 52.381 0.00 0.00 0.00 4.57
2382 3792 1.669437 TGTGTGCGTGTGTGTGTGT 60.669 52.632 0.00 0.00 0.00 3.72
2388 3798 1.418342 GCGTGTGTGTGTGTCGTTCT 61.418 55.000 0.00 0.00 0.00 3.01
2391 3801 0.108377 TGTGTGTGTGTCGTTCTGCT 60.108 50.000 0.00 0.00 0.00 4.24
2416 3826 7.047891 TGTAACTTGTTTCTGAATCTGTGTCT 58.952 34.615 0.00 0.00 0.00 3.41
2431 3841 1.373497 GTCTGGCGTGTGGACTGAG 60.373 63.158 0.00 0.00 31.48 3.35
2447 3857 5.465390 TGGACTGAGTTGTCGATTTAACTTG 59.535 40.000 12.08 10.83 37.27 3.16
2469 3879 1.895238 CAAGCTGGATGGCAAAGGG 59.105 57.895 0.00 0.00 34.17 3.95
2645 4066 2.125552 CACGGCGAATCTGGCTGA 60.126 61.111 16.62 0.00 40.04 4.26
2646 4067 2.169789 CACGGCGAATCTGGCTGAG 61.170 63.158 16.62 0.00 40.04 3.35
2647 4068 3.267860 CGGCGAATCTGGCTGAGC 61.268 66.667 0.00 0.00 39.13 4.26
2648 4069 2.188994 GGCGAATCTGGCTGAGCT 59.811 61.111 3.72 0.00 0.00 4.09
2649 4070 2.178890 GGCGAATCTGGCTGAGCTG 61.179 63.158 3.72 0.00 0.00 4.24
2650 4071 2.821688 GCGAATCTGGCTGAGCTGC 61.822 63.158 3.72 0.00 0.00 5.25
2651 4072 2.523507 CGAATCTGGCTGAGCTGCG 61.524 63.158 3.72 0.00 0.00 5.18
2652 4073 1.153489 GAATCTGGCTGAGCTGCGA 60.153 57.895 3.72 0.00 0.00 5.10
2706 4127 1.134175 CCTGCTCGTCTTCTTCTCTCC 59.866 57.143 0.00 0.00 0.00 3.71
2715 4136 3.757493 GTCTTCTTCTCTCCGTAGAACCA 59.243 47.826 0.00 0.00 32.18 3.67
2773 4194 1.093159 CAACAATGCAGCTCTCTCCC 58.907 55.000 0.00 0.00 0.00 4.30
2777 4230 2.037901 CAATGCAGCTCTCTCCCTAGA 58.962 52.381 0.00 0.00 0.00 2.43
2790 4243 6.160576 CTCTCCCTAGAGTAGTACGTACTT 57.839 45.833 31.58 16.31 42.48 2.24
2798 4251 3.935828 GAGTAGTACGTACTTCCTCCGTT 59.064 47.826 31.58 10.91 42.48 4.44
2799 4252 3.935828 AGTAGTACGTACTTCCTCCGTTC 59.064 47.826 31.58 11.75 39.06 3.95
2800 4253 2.087646 AGTACGTACTTCCTCCGTTCC 58.912 52.381 22.45 0.00 36.12 3.62
2801 4254 1.812571 GTACGTACTTCCTCCGTTCCA 59.187 52.381 18.47 0.00 36.12 3.53
2807 4260 4.328169 CGTACTTCCTCCGTTCCAAAATAC 59.672 45.833 0.00 0.00 0.00 1.89
2808 4261 3.332034 ACTTCCTCCGTTCCAAAATACG 58.668 45.455 0.00 0.00 37.50 3.06
2809 4262 3.244318 ACTTCCTCCGTTCCAAAATACGT 60.244 43.478 0.00 0.00 36.09 3.57
2810 4263 4.021192 ACTTCCTCCGTTCCAAAATACGTA 60.021 41.667 0.00 0.00 36.09 3.57
2811 4264 3.848726 TCCTCCGTTCCAAAATACGTAC 58.151 45.455 0.00 0.00 36.09 3.67
2812 4265 3.257873 TCCTCCGTTCCAAAATACGTACA 59.742 43.478 0.00 0.00 36.09 2.90
2813 4266 3.995705 CCTCCGTTCCAAAATACGTACAA 59.004 43.478 0.00 0.00 36.09 2.41
2814 4267 4.451774 CCTCCGTTCCAAAATACGTACAAA 59.548 41.667 0.00 0.00 36.09 2.83
2815 4268 5.341407 TCCGTTCCAAAATACGTACAAAC 57.659 39.130 0.00 0.00 36.09 2.93
2817 4270 5.177327 TCCGTTCCAAAATACGTACAAACTC 59.823 40.000 0.00 0.00 36.09 3.01
2818 4271 5.068256 CGTTCCAAAATACGTACAAACTCG 58.932 41.667 0.00 0.00 33.33 4.18
2819 4272 5.107913 CGTTCCAAAATACGTACAAACTCGA 60.108 40.000 0.00 0.00 33.33 4.04
2820 4273 6.294363 GTTCCAAAATACGTACAAACTCGAG 58.706 40.000 11.84 11.84 0.00 4.04
2821 4274 5.531634 TCCAAAATACGTACAAACTCGAGT 58.468 37.500 13.58 13.58 0.00 4.18
2822 4275 5.630680 TCCAAAATACGTACAAACTCGAGTC 59.369 40.000 20.33 4.72 0.00 3.36
2823 4276 5.403166 CCAAAATACGTACAAACTCGAGTCA 59.597 40.000 20.33 1.60 0.00 3.41
2824 4277 6.286941 CAAAATACGTACAAACTCGAGTCAC 58.713 40.000 20.33 13.10 0.00 3.67
2828 4281 5.368256 ACGTACAAACTCGAGTCACTTAT 57.632 39.130 20.33 1.04 0.00 1.73
2830 4283 6.211515 ACGTACAAACTCGAGTCACTTATTT 58.788 36.000 20.33 4.41 0.00 1.40
2831 4284 6.698766 ACGTACAAACTCGAGTCACTTATTTT 59.301 34.615 20.33 3.59 0.00 1.82
2832 4285 7.001922 CGTACAAACTCGAGTCACTTATTTTG 58.998 38.462 20.33 18.12 0.00 2.44
2833 4286 6.300354 ACAAACTCGAGTCACTTATTTTGG 57.700 37.500 20.33 0.00 0.00 3.28
2834 4287 6.053005 ACAAACTCGAGTCACTTATTTTGGA 58.947 36.000 20.33 0.00 0.00 3.53
2835 4288 6.540914 ACAAACTCGAGTCACTTATTTTGGAA 59.459 34.615 20.33 0.00 0.00 3.53
2836 4289 6.541111 AACTCGAGTCACTTATTTTGGAAC 57.459 37.500 20.33 0.00 0.00 3.62
2837 4290 4.684703 ACTCGAGTCACTTATTTTGGAACG 59.315 41.667 13.58 0.00 0.00 3.95
2838 4291 3.991773 TCGAGTCACTTATTTTGGAACGG 59.008 43.478 0.00 0.00 0.00 4.44
2839 4292 3.124636 CGAGTCACTTATTTTGGAACGGG 59.875 47.826 0.00 0.00 0.00 5.28
2840 4293 3.418047 AGTCACTTATTTTGGAACGGGG 58.582 45.455 0.00 0.00 0.00 5.73
2841 4294 2.490509 GTCACTTATTTTGGAACGGGGG 59.509 50.000 0.00 0.00 0.00 5.40
2842 4295 2.375845 TCACTTATTTTGGAACGGGGGA 59.624 45.455 0.00 0.00 0.00 4.81
2849 4321 1.138568 TTGGAACGGGGGAAGTACAA 58.861 50.000 0.00 0.00 0.00 2.41
2854 4326 3.431346 GGAACGGGGGAAGTACAAGATAC 60.431 52.174 0.00 0.00 0.00 2.24
2883 4355 5.066593 CCCTTTGCTCTAGTGACTTCTTTT 58.933 41.667 0.00 0.00 0.00 2.27
2987 5737 7.281100 GGCAAAGTTCATATAGCAGTTCTACTT 59.719 37.037 0.00 0.00 0.00 2.24
2989 5739 8.535592 CAAAGTTCATATAGCAGTTCTACTTCG 58.464 37.037 0.00 0.00 0.00 3.79
3017 5767 2.229792 ACAATCGTTTCATGTGGCTGT 58.770 42.857 0.00 0.00 0.00 4.40
3034 5784 2.767505 CTGTAGTGGTCGAGCCTTTTT 58.232 47.619 12.85 0.00 38.35 1.94
3048 5798 4.968259 AGCCTTTTTGGGATTTTAACCAC 58.032 39.130 0.00 0.00 36.27 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
331 332 6.836242 GAGGTAATTTCATCCTCTGGAAGAT 58.164 40.000 0.00 0.00 45.62 2.40
418 419 4.008074 AGAAACCACACATCATCGTCTT 57.992 40.909 0.00 0.00 0.00 3.01
654 655 7.717568 AGGAAGTACTATACTACAATGTGCTG 58.282 38.462 0.00 0.00 38.26 4.41
655 656 7.014422 GGAGGAAGTACTATACTACAATGTGCT 59.986 40.741 0.00 0.00 38.26 4.40
656 657 7.146648 GGAGGAAGTACTATACTACAATGTGC 58.853 42.308 0.00 0.00 38.26 4.57
657 658 7.013083 ACGGAGGAAGTACTATACTACAATGTG 59.987 40.741 0.00 0.00 38.26 3.21
658 659 7.059156 ACGGAGGAAGTACTATACTACAATGT 58.941 38.462 0.00 0.00 38.26 2.71
659 660 7.308469 GGACGGAGGAAGTACTATACTACAATG 60.308 44.444 0.00 0.00 38.26 2.82
660 661 6.714356 GGACGGAGGAAGTACTATACTACAAT 59.286 42.308 0.00 0.00 38.26 2.71
661 662 6.058183 GGACGGAGGAAGTACTATACTACAA 58.942 44.000 0.00 0.00 38.26 2.41
662 663 5.455326 GGGACGGAGGAAGTACTATACTACA 60.455 48.000 0.00 0.00 38.26 2.74
663 664 5.000591 GGGACGGAGGAAGTACTATACTAC 58.999 50.000 0.00 0.00 38.26 2.73
664 665 4.660303 TGGGACGGAGGAAGTACTATACTA 59.340 45.833 0.00 0.00 38.26 1.82
665 666 3.461085 TGGGACGGAGGAAGTACTATACT 59.539 47.826 0.00 0.00 41.73 2.12
666 667 3.825328 TGGGACGGAGGAAGTACTATAC 58.175 50.000 0.00 0.00 0.00 1.47
667 668 4.736611 ATGGGACGGAGGAAGTACTATA 57.263 45.455 0.00 0.00 0.00 1.31
668 669 3.614568 ATGGGACGGAGGAAGTACTAT 57.385 47.619 0.00 0.00 0.00 2.12
669 670 4.524802 TTATGGGACGGAGGAAGTACTA 57.475 45.455 0.00 0.00 0.00 1.82
670 671 3.393426 TTATGGGACGGAGGAAGTACT 57.607 47.619 0.00 0.00 0.00 2.73
671 672 5.997384 ATATTATGGGACGGAGGAAGTAC 57.003 43.478 0.00 0.00 0.00 2.73
672 673 8.495160 TTTTATATTATGGGACGGAGGAAGTA 57.505 34.615 0.00 0.00 0.00 2.24
673 674 7.383156 TTTTATATTATGGGACGGAGGAAGT 57.617 36.000 0.00 0.00 0.00 3.01
674 675 6.371825 GCTTTTATATTATGGGACGGAGGAAG 59.628 42.308 0.00 0.00 0.00 3.46
675 676 6.183361 TGCTTTTATATTATGGGACGGAGGAA 60.183 38.462 0.00 0.00 0.00 3.36
676 677 5.308497 TGCTTTTATATTATGGGACGGAGGA 59.692 40.000 0.00 0.00 0.00 3.71
677 678 5.556915 TGCTTTTATATTATGGGACGGAGG 58.443 41.667 0.00 0.00 0.00 4.30
678 679 7.687941 AATGCTTTTATATTATGGGACGGAG 57.312 36.000 0.00 0.00 0.00 4.63
679 680 8.472007 AAAATGCTTTTATATTATGGGACGGA 57.528 30.769 0.00 0.00 0.00 4.69
680 681 8.977505 CAAAAATGCTTTTATATTATGGGACGG 58.022 33.333 0.00 0.00 32.85 4.79
681 682 9.528018 ACAAAAATGCTTTTATATTATGGGACG 57.472 29.630 0.00 0.00 32.85 4.79
694 695 9.603921 CTCCCATAATATGACAAAAATGCTTTT 57.396 29.630 1.10 0.00 35.02 2.27
695 696 8.206189 CCTCCCATAATATGACAAAAATGCTTT 58.794 33.333 1.10 0.00 0.00 3.51
696 697 7.202029 CCCTCCCATAATATGACAAAAATGCTT 60.202 37.037 1.10 0.00 0.00 3.91
697 698 6.268387 CCCTCCCATAATATGACAAAAATGCT 59.732 38.462 1.10 0.00 0.00 3.79
698 699 6.267471 TCCCTCCCATAATATGACAAAAATGC 59.733 38.462 1.10 0.00 0.00 3.56
699 700 7.725397 TCTCCCTCCCATAATATGACAAAAATG 59.275 37.037 1.10 0.00 0.00 2.32
700 701 7.825709 TCTCCCTCCCATAATATGACAAAAAT 58.174 34.615 1.10 0.00 0.00 1.82
701 702 7.128728 TCTCTCCCTCCCATAATATGACAAAAA 59.871 37.037 1.10 0.00 0.00 1.94
702 703 6.619437 TCTCTCCCTCCCATAATATGACAAAA 59.381 38.462 1.10 0.00 0.00 2.44
703 704 6.150332 TCTCTCCCTCCCATAATATGACAAA 58.850 40.000 1.10 0.00 0.00 2.83
704 705 5.726560 TCTCTCCCTCCCATAATATGACAA 58.273 41.667 1.10 0.00 0.00 3.18
705 706 5.162826 ACTCTCTCCCTCCCATAATATGACA 60.163 44.000 1.10 0.00 0.00 3.58
706 707 5.337788 ACTCTCTCCCTCCCATAATATGAC 58.662 45.833 1.10 0.00 0.00 3.06
707 708 5.623551 ACTCTCTCCCTCCCATAATATGA 57.376 43.478 1.10 0.00 0.00 2.15
708 709 9.087871 CATATACTCTCTCCCTCCCATAATATG 57.912 40.741 0.00 0.00 0.00 1.78
709 710 7.732593 GCATATACTCTCTCCCTCCCATAATAT 59.267 40.741 0.00 0.00 0.00 1.28
710 711 7.069986 GCATATACTCTCTCCCTCCCATAATA 58.930 42.308 0.00 0.00 0.00 0.98
711 712 5.902431 GCATATACTCTCTCCCTCCCATAAT 59.098 44.000 0.00 0.00 0.00 1.28
712 713 5.016782 AGCATATACTCTCTCCCTCCCATAA 59.983 44.000 0.00 0.00 0.00 1.90
713 714 4.546195 AGCATATACTCTCTCCCTCCCATA 59.454 45.833 0.00 0.00 0.00 2.74
714 715 3.339436 AGCATATACTCTCTCCCTCCCAT 59.661 47.826 0.00 0.00 0.00 4.00
715 716 2.724672 AGCATATACTCTCTCCCTCCCA 59.275 50.000 0.00 0.00 0.00 4.37
716 717 3.466395 AGCATATACTCTCTCCCTCCC 57.534 52.381 0.00 0.00 0.00 4.30
717 718 3.951680 GCTAGCATATACTCTCTCCCTCC 59.048 52.174 10.63 0.00 0.00 4.30
718 719 4.594970 TGCTAGCATATACTCTCTCCCTC 58.405 47.826 14.93 0.00 0.00 4.30
719 720 4.044065 ACTGCTAGCATATACTCTCTCCCT 59.956 45.833 19.72 0.00 0.00 4.20
720 721 4.340617 ACTGCTAGCATATACTCTCTCCC 58.659 47.826 19.72 0.00 0.00 4.30
721 722 6.177610 AGTACTGCTAGCATATACTCTCTCC 58.822 44.000 25.46 8.43 0.00 3.71
722 723 8.780846 TTAGTACTGCTAGCATATACTCTCTC 57.219 38.462 30.63 11.98 33.04 3.20
723 724 9.747898 AATTAGTACTGCTAGCATATACTCTCT 57.252 33.333 30.63 19.66 33.04 3.10
728 729 9.915629 ACAGAAATTAGTACTGCTAGCATATAC 57.084 33.333 19.72 21.68 35.38 1.47
731 732 9.967346 CTAACAGAAATTAGTACTGCTAGCATA 57.033 33.333 19.72 10.08 35.38 3.14
732 733 7.439655 GCTAACAGAAATTAGTACTGCTAGCAT 59.560 37.037 19.72 11.11 46.43 3.79
733 734 6.757010 GCTAACAGAAATTAGTACTGCTAGCA 59.243 38.462 18.22 18.22 46.43 3.49
734 735 6.757010 TGCTAACAGAAATTAGTACTGCTAGC 59.243 38.462 8.10 8.10 46.89 3.42
752 753 3.444034 ACAGCTCGATCTTACTGCTAACA 59.556 43.478 5.85 0.00 33.35 2.41
753 754 4.035278 ACAGCTCGATCTTACTGCTAAC 57.965 45.455 5.85 0.00 33.35 2.34
754 755 3.694566 TGACAGCTCGATCTTACTGCTAA 59.305 43.478 5.85 0.00 33.35 3.09
755 756 3.279434 TGACAGCTCGATCTTACTGCTA 58.721 45.455 5.85 0.00 33.35 3.49
756 757 2.095461 TGACAGCTCGATCTTACTGCT 58.905 47.619 5.85 0.00 33.35 4.24
757 758 2.098280 TCTGACAGCTCGATCTTACTGC 59.902 50.000 0.00 0.00 33.35 4.40
758 759 4.566545 ATCTGACAGCTCGATCTTACTG 57.433 45.455 0.00 4.69 36.22 2.74
759 760 5.240623 CCTAATCTGACAGCTCGATCTTACT 59.759 44.000 0.00 0.00 0.00 2.24
760 761 5.457140 CCTAATCTGACAGCTCGATCTTAC 58.543 45.833 0.00 0.00 0.00 2.34
761 762 4.520874 CCCTAATCTGACAGCTCGATCTTA 59.479 45.833 0.00 0.00 0.00 2.10
762 763 3.320541 CCCTAATCTGACAGCTCGATCTT 59.679 47.826 0.00 0.00 0.00 2.40
763 764 2.890311 CCCTAATCTGACAGCTCGATCT 59.110 50.000 0.00 0.00 0.00 2.75
764 765 2.887783 TCCCTAATCTGACAGCTCGATC 59.112 50.000 0.00 0.00 0.00 3.69
765 766 2.890311 CTCCCTAATCTGACAGCTCGAT 59.110 50.000 0.00 0.00 0.00 3.59
766 767 2.092375 TCTCCCTAATCTGACAGCTCGA 60.092 50.000 0.00 0.00 0.00 4.04
767 768 2.034053 GTCTCCCTAATCTGACAGCTCG 59.966 54.545 0.00 0.00 0.00 5.03
768 769 3.295973 AGTCTCCCTAATCTGACAGCTC 58.704 50.000 0.00 0.00 32.41 4.09
769 770 3.295973 GAGTCTCCCTAATCTGACAGCT 58.704 50.000 0.00 0.00 32.41 4.24
770 771 3.027412 TGAGTCTCCCTAATCTGACAGC 58.973 50.000 0.00 0.00 32.41 4.40
771 772 4.023279 CGATGAGTCTCCCTAATCTGACAG 60.023 50.000 0.00 0.00 29.59 3.51
772 773 3.885901 CGATGAGTCTCCCTAATCTGACA 59.114 47.826 0.00 0.00 29.59 3.58
773 774 3.886505 ACGATGAGTCTCCCTAATCTGAC 59.113 47.826 0.00 0.00 29.59 3.51
774 775 4.171878 ACGATGAGTCTCCCTAATCTGA 57.828 45.455 0.00 0.00 29.59 3.27
775 776 4.339530 TCAACGATGAGTCTCCCTAATCTG 59.660 45.833 0.00 0.00 29.59 2.90
776 777 4.339814 GTCAACGATGAGTCTCCCTAATCT 59.660 45.833 0.00 0.00 35.88 2.40
777 778 4.339814 AGTCAACGATGAGTCTCCCTAATC 59.660 45.833 0.00 0.00 33.92 1.75
778 779 4.282496 AGTCAACGATGAGTCTCCCTAAT 58.718 43.478 0.00 0.00 33.92 1.73
779 780 3.698289 AGTCAACGATGAGTCTCCCTAA 58.302 45.455 0.00 0.00 33.92 2.69
780 781 3.367646 AGTCAACGATGAGTCTCCCTA 57.632 47.619 0.00 0.00 33.92 3.53
781 782 2.223803 AGTCAACGATGAGTCTCCCT 57.776 50.000 0.00 0.00 33.92 4.20
782 783 4.363999 CATTAGTCAACGATGAGTCTCCC 58.636 47.826 6.26 0.00 39.87 4.30
783 784 4.098044 TCCATTAGTCAACGATGAGTCTCC 59.902 45.833 6.26 0.00 39.87 3.71
784 785 5.250235 TCCATTAGTCAACGATGAGTCTC 57.750 43.478 6.26 0.00 39.87 3.36
785 786 5.047306 TGTTCCATTAGTCAACGATGAGTCT 60.047 40.000 6.26 0.00 39.87 3.24
786 787 5.062308 GTGTTCCATTAGTCAACGATGAGTC 59.938 44.000 6.26 0.00 39.87 3.36
787 788 4.929808 GTGTTCCATTAGTCAACGATGAGT 59.070 41.667 8.19 8.19 42.01 3.41
788 789 5.171476 AGTGTTCCATTAGTCAACGATGAG 58.829 41.667 0.00 0.00 35.88 2.90
789 790 5.147330 AGTGTTCCATTAGTCAACGATGA 57.853 39.130 0.00 0.00 0.00 2.92
790 791 5.179368 ACAAGTGTTCCATTAGTCAACGATG 59.821 40.000 0.00 0.00 0.00 3.84
791 792 5.305585 ACAAGTGTTCCATTAGTCAACGAT 58.694 37.500 0.00 0.00 0.00 3.73
792 793 4.699637 ACAAGTGTTCCATTAGTCAACGA 58.300 39.130 0.00 0.00 0.00 3.85
793 794 6.721571 ATACAAGTGTTCCATTAGTCAACG 57.278 37.500 0.00 0.00 0.00 4.10
794 795 7.871853 ACAATACAAGTGTTCCATTAGTCAAC 58.128 34.615 0.00 0.00 0.00 3.18
795 796 8.349245 CAACAATACAAGTGTTCCATTAGTCAA 58.651 33.333 0.00 0.00 37.09 3.18
796 797 7.500892 ACAACAATACAAGTGTTCCATTAGTCA 59.499 33.333 0.00 0.00 37.09 3.41
797 798 7.871853 ACAACAATACAAGTGTTCCATTAGTC 58.128 34.615 0.00 0.00 37.09 2.59
798 799 7.817418 ACAACAATACAAGTGTTCCATTAGT 57.183 32.000 0.00 0.00 37.09 2.24
799 800 7.955324 CGTACAACAATACAAGTGTTCCATTAG 59.045 37.037 0.00 0.00 37.09 1.73
800 801 7.441760 ACGTACAACAATACAAGTGTTCCATTA 59.558 33.333 0.00 0.00 37.09 1.90
801 802 6.261381 ACGTACAACAATACAAGTGTTCCATT 59.739 34.615 0.00 0.00 37.09 3.16
802 803 5.761234 ACGTACAACAATACAAGTGTTCCAT 59.239 36.000 0.00 0.00 37.09 3.41
803 804 5.006844 CACGTACAACAATACAAGTGTTCCA 59.993 40.000 0.00 0.00 37.09 3.53
804 805 5.234757 TCACGTACAACAATACAAGTGTTCC 59.765 40.000 0.00 0.00 37.09 3.62
805 806 6.276611 TCACGTACAACAATACAAGTGTTC 57.723 37.500 0.00 0.00 37.09 3.18
806 807 6.457257 GGTTCACGTACAACAATACAAGTGTT 60.457 38.462 10.75 0.00 39.79 3.32
807 808 5.006941 GGTTCACGTACAACAATACAAGTGT 59.993 40.000 10.75 0.00 0.00 3.55
808 809 5.437263 GGTTCACGTACAACAATACAAGTG 58.563 41.667 10.75 0.00 0.00 3.16
809 810 4.209703 CGGTTCACGTACAACAATACAAGT 59.790 41.667 10.75 0.00 37.93 3.16
810 811 4.376615 CCGGTTCACGTACAACAATACAAG 60.377 45.833 10.75 0.00 42.24 3.16
811 812 3.493877 CCGGTTCACGTACAACAATACAA 59.506 43.478 10.75 0.00 42.24 2.41
812 813 3.058450 CCGGTTCACGTACAACAATACA 58.942 45.455 10.75 0.00 42.24 2.29
813 814 2.412770 CCCGGTTCACGTACAACAATAC 59.587 50.000 0.00 0.00 42.24 1.89
814 815 2.612471 CCCCGGTTCACGTACAACAATA 60.612 50.000 0.00 0.00 42.24 1.90
815 816 1.515081 CCCGGTTCACGTACAACAAT 58.485 50.000 0.00 0.00 42.24 2.71
816 817 0.532417 CCCCGGTTCACGTACAACAA 60.532 55.000 0.00 0.00 42.24 2.83
817 818 1.069427 CCCCGGTTCACGTACAACA 59.931 57.895 0.00 0.00 42.24 3.33
818 819 0.668401 CTCCCCGGTTCACGTACAAC 60.668 60.000 0.00 0.00 42.24 3.32
819 820 0.827089 TCTCCCCGGTTCACGTACAA 60.827 55.000 0.00 0.00 42.24 2.41
820 821 0.612732 ATCTCCCCGGTTCACGTACA 60.613 55.000 0.00 0.00 42.24 2.90
821 822 0.179119 CATCTCCCCGGTTCACGTAC 60.179 60.000 0.00 0.00 42.24 3.67
822 823 0.323633 TCATCTCCCCGGTTCACGTA 60.324 55.000 0.00 0.00 42.24 3.57
823 824 0.976073 ATCATCTCCCCGGTTCACGT 60.976 55.000 0.00 0.00 42.24 4.49
833 834 6.732896 TTAGTCAAACCTAGATCATCTCCC 57.267 41.667 0.00 0.00 0.00 4.30
844 845 4.098960 CGTCTAGGCCATTAGTCAAACCTA 59.901 45.833 5.01 0.00 0.00 3.08
928 930 0.980423 ACTGAGAAGGGGAGTGAAGC 59.020 55.000 0.00 0.00 0.00 3.86
929 931 2.634940 TGAACTGAGAAGGGGAGTGAAG 59.365 50.000 0.00 0.00 0.00 3.02
937 939 1.376037 GGCGGTGAACTGAGAAGGG 60.376 63.158 0.00 0.00 0.00 3.95
959 962 2.786854 CTAGCTACTACACGTGTGCAG 58.213 52.381 30.83 22.55 0.00 4.41
1047 1050 1.509923 GCCTGCTGCTTCCATTGTC 59.490 57.895 0.00 0.00 36.87 3.18
1380 1383 0.747255 AGCAGTAGATACCGGCACTG 59.253 55.000 0.00 8.82 41.06 3.66
1413 1416 2.049433 CTCTCGCCCGTCACGTTT 60.049 61.111 0.00 0.00 0.00 3.60
1514 1517 2.436646 CCGTCTCGCCTTTGCCAT 60.437 61.111 0.00 0.00 0.00 4.40
1515 1518 4.697756 CCCGTCTCGCCTTTGCCA 62.698 66.667 0.00 0.00 0.00 4.92
1566 1572 1.426621 GATGTACCTCGTCGCGTCA 59.573 57.895 5.77 0.00 0.00 4.35
1568 1574 2.402388 CGATGTACCTCGTCGCGT 59.598 61.111 11.85 0.00 46.19 6.01
1715 2938 7.974675 ACGGAATGAATTGAACAGTAGTAATG 58.025 34.615 0.00 0.00 0.00 1.90
1729 2952 7.614494 AGATGAAAATGGAAACGGAATGAATT 58.386 30.769 0.00 0.00 0.00 2.17
1948 3264 2.099756 GTGGATTTTACTGCCATCCAGC 59.900 50.000 0.19 0.00 45.80 4.85
1956 3272 8.254508 AGCTAGCTATATAGTGGATTTTACTGC 58.745 37.037 17.69 4.06 0.00 4.40
1972 3288 7.859325 CCAAACTTGGTTTTAGCTAGCTATA 57.141 36.000 24.69 17.40 43.43 1.31
1973 3289 6.759497 CCAAACTTGGTTTTAGCTAGCTAT 57.241 37.500 24.69 4.85 43.43 2.97
1989 3306 5.598005 TGACCATCAGAATCAAACCAAACTT 59.402 36.000 0.00 0.00 0.00 2.66
1992 3309 7.396907 ACATATGACCATCAGAATCAAACCAAA 59.603 33.333 10.38 0.00 0.00 3.28
2001 3318 7.095183 ACCCAATACATATGACCATCAGAAT 57.905 36.000 10.38 0.00 0.00 2.40
2008 3325 5.192722 TGGAAGAACCCAATACATATGACCA 59.807 40.000 10.38 0.00 38.00 4.02
2009 3326 5.690865 TGGAAGAACCCAATACATATGACC 58.309 41.667 10.38 0.00 38.00 4.02
2010 3327 5.765182 CCTGGAAGAACCCAATACATATGAC 59.235 44.000 10.38 0.00 35.47 3.06
2013 3330 5.994416 ACCTGGAAGAACCCAATACATAT 57.006 39.130 0.00 0.00 35.47 1.78
2014 3331 5.789574 AACCTGGAAGAACCCAATACATA 57.210 39.130 0.00 0.00 35.47 2.29
2018 3335 7.340999 GCTATTAAAACCTGGAAGAACCCAATA 59.659 37.037 0.00 0.00 35.47 1.90
2019 3336 6.154534 GCTATTAAAACCTGGAAGAACCCAAT 59.845 38.462 0.00 0.00 35.47 3.16
2029 3406 6.598064 GCTTTCTACTGCTATTAAAACCTGGA 59.402 38.462 0.00 0.00 0.00 3.86
2030 3407 6.599638 AGCTTTCTACTGCTATTAAAACCTGG 59.400 38.462 0.00 0.00 37.81 4.45
2050 3427 4.815533 TGCAAGATGTCTCTAGAGCTTT 57.184 40.909 15.35 1.44 0.00 3.51
2078 3460 7.097834 AGGCTCATTTAAGTACTGAACTGTAC 58.902 38.462 9.52 11.98 42.09 2.90
2080 3462 6.115448 AGGCTCATTTAAGTACTGAACTGT 57.885 37.500 9.52 0.00 38.88 3.55
2128 3510 6.961360 TTGAATCTGACTCCGATAGTGTAT 57.039 37.500 0.00 0.00 39.07 2.29
2151 3533 8.715088 GCTGCATAAAGAACAAGAATTTGAATT 58.285 29.630 0.00 0.00 37.73 2.17
2195 3577 3.904339 AGCTTCTCCTTGTGTTCCTCTTA 59.096 43.478 0.00 0.00 0.00 2.10
2196 3578 2.708325 AGCTTCTCCTTGTGTTCCTCTT 59.292 45.455 0.00 0.00 0.00 2.85
2204 3586 1.155042 GCTGACAGCTTCTCCTTGTG 58.845 55.000 20.41 0.00 38.45 3.33
2217 3599 4.383861 CTGCCCGCTCTGCTGACA 62.384 66.667 0.00 0.00 0.00 3.58
2271 3653 3.951775 ACTCTTGGCTGTTACAGAGAG 57.048 47.619 20.81 20.81 37.30 3.20
2322 3704 1.659098 CCTATGGTTTCGCTTGACGTC 59.341 52.381 9.11 9.11 44.19 4.34
2357 3739 0.461870 ACACACGCACACACACTCAT 60.462 50.000 0.00 0.00 0.00 2.90
2360 3770 1.375396 ACACACACGCACACACACT 60.375 52.632 0.00 0.00 0.00 3.55
2370 3780 0.297525 CAGAACGACACACACACACG 59.702 55.000 0.00 0.00 0.00 4.49
2382 3792 4.270084 CAGAAACAAGTTACAGCAGAACGA 59.730 41.667 0.00 0.00 31.85 3.85
2388 3798 5.822519 ACAGATTCAGAAACAAGTTACAGCA 59.177 36.000 0.00 0.00 0.00 4.41
2391 3801 7.011389 CAGACACAGATTCAGAAACAAGTTACA 59.989 37.037 0.00 0.00 0.00 2.41
2416 3826 1.227527 CAACTCAGTCCACACGCCA 60.228 57.895 0.00 0.00 0.00 5.69
2431 3841 3.884169 TGCAGCAAGTTAAATCGACAAC 58.116 40.909 0.00 0.00 0.00 3.32
2447 3857 2.162338 TTTGCCATCCAGCTTGCAGC 62.162 55.000 0.47 0.47 42.84 5.25
2456 3866 0.178938 TTTCTGCCCTTTGCCATCCA 60.179 50.000 0.00 0.00 40.16 3.41
2469 3879 8.299570 TCAGTTTCTTTCTATTTCCATTTCTGC 58.700 33.333 0.00 0.00 0.00 4.26
2476 3886 7.470009 GCCAAGTTCAGTTTCTTTCTATTTCCA 60.470 37.037 0.00 0.00 0.00 3.53
2477 3887 6.863645 GCCAAGTTCAGTTTCTTTCTATTTCC 59.136 38.462 0.00 0.00 0.00 3.13
2545 3955 4.253257 GACGCGAGCGAGGGGTAG 62.253 72.222 24.72 0.00 42.83 3.18
2595 4009 3.531538 ACCAGTTGTAATGCCTGATACG 58.468 45.455 0.00 0.00 0.00 3.06
2647 4068 4.731612 ACCTGCTCGCAGTCGCAG 62.732 66.667 16.82 4.39 46.43 5.18
2648 4069 4.299547 AACCTGCTCGCAGTCGCA 62.300 61.111 16.82 0.00 42.15 5.10
2649 4070 3.782244 CAACCTGCTCGCAGTCGC 61.782 66.667 16.82 0.00 42.15 5.19
2650 4071 3.114616 CCAACCTGCTCGCAGTCG 61.115 66.667 16.82 5.98 42.15 4.18
2651 4072 1.739562 CTCCAACCTGCTCGCAGTC 60.740 63.158 16.82 0.00 42.15 3.51
2652 4073 2.345244 CTCCAACCTGCTCGCAGT 59.655 61.111 16.82 3.60 42.15 4.40
2706 4127 2.813908 GGCGGCTGTGGTTCTACG 60.814 66.667 0.00 0.00 0.00 3.51
2715 4136 2.348104 TGATCGTACTGGCGGCTGT 61.348 57.895 24.13 24.13 0.00 4.40
2769 4190 5.070313 AGGAAGTACGTACTACTCTAGGGAG 59.930 48.000 27.59 0.00 39.39 4.30
2770 4191 4.965532 AGGAAGTACGTACTACTCTAGGGA 59.034 45.833 27.59 0.00 34.26 4.20
2771 4192 5.289083 AGGAAGTACGTACTACTCTAGGG 57.711 47.826 27.59 0.00 34.26 3.53
2772 4193 5.296748 GGAGGAAGTACGTACTACTCTAGG 58.703 50.000 34.82 0.00 38.96 3.02
2773 4194 4.981674 CGGAGGAAGTACGTACTACTCTAG 59.018 50.000 34.82 28.99 38.96 2.43
2777 4230 3.618690 ACGGAGGAAGTACGTACTACT 57.381 47.619 27.59 25.84 39.30 2.57
2778 4231 3.064134 GGAACGGAGGAAGTACGTACTAC 59.936 52.174 27.59 22.03 40.31 2.73
2790 4243 3.257873 TGTACGTATTTTGGAACGGAGGA 59.742 43.478 0.00 0.00 43.25 3.71
2798 4251 5.531634 ACTCGAGTTTGTACGTATTTTGGA 58.468 37.500 13.58 0.00 0.00 3.53
2799 4252 5.403166 TGACTCGAGTTTGTACGTATTTTGG 59.597 40.000 21.08 0.00 0.00 3.28
2800 4253 6.143438 AGTGACTCGAGTTTGTACGTATTTTG 59.857 38.462 21.08 0.00 0.00 2.44
2801 4254 6.211515 AGTGACTCGAGTTTGTACGTATTTT 58.788 36.000 21.08 0.00 0.00 1.82
2807 4260 6.686130 AAATAAGTGACTCGAGTTTGTACG 57.314 37.500 21.08 0.00 0.00 3.67
2808 4261 7.170320 TCCAAAATAAGTGACTCGAGTTTGTAC 59.830 37.037 21.08 15.71 0.00 2.90
2809 4262 7.211573 TCCAAAATAAGTGACTCGAGTTTGTA 58.788 34.615 21.08 10.21 0.00 2.41
2810 4263 6.053005 TCCAAAATAAGTGACTCGAGTTTGT 58.947 36.000 21.08 5.70 0.00 2.83
2811 4264 6.539649 TCCAAAATAAGTGACTCGAGTTTG 57.460 37.500 21.08 16.23 0.00 2.93
2812 4265 6.292703 CGTTCCAAAATAAGTGACTCGAGTTT 60.293 38.462 21.08 12.75 0.00 2.66
2813 4266 5.176958 CGTTCCAAAATAAGTGACTCGAGTT 59.823 40.000 21.08 6.08 0.00 3.01
2814 4267 4.684703 CGTTCCAAAATAAGTGACTCGAGT 59.315 41.667 20.18 20.18 0.00 4.18
2815 4268 4.091509 CCGTTCCAAAATAAGTGACTCGAG 59.908 45.833 11.84 11.84 0.00 4.04
2817 4270 3.124636 CCCGTTCCAAAATAAGTGACTCG 59.875 47.826 0.00 0.00 0.00 4.18
2818 4271 3.439129 CCCCGTTCCAAAATAAGTGACTC 59.561 47.826 0.00 0.00 0.00 3.36
2819 4272 3.418047 CCCCGTTCCAAAATAAGTGACT 58.582 45.455 0.00 0.00 0.00 3.41
2820 4273 2.490509 CCCCCGTTCCAAAATAAGTGAC 59.509 50.000 0.00 0.00 0.00 3.67
2821 4274 2.375845 TCCCCCGTTCCAAAATAAGTGA 59.624 45.455 0.00 0.00 0.00 3.41
2822 4275 2.797786 TCCCCCGTTCCAAAATAAGTG 58.202 47.619 0.00 0.00 0.00 3.16
2823 4276 3.181426 ACTTCCCCCGTTCCAAAATAAGT 60.181 43.478 0.00 0.00 0.00 2.24
2824 4277 3.427573 ACTTCCCCCGTTCCAAAATAAG 58.572 45.455 0.00 0.00 0.00 1.73
2828 4281 1.493871 TGTACTTCCCCCGTTCCAAAA 59.506 47.619 0.00 0.00 0.00 2.44
2830 4283 1.072648 CTTGTACTTCCCCCGTTCCAA 59.927 52.381 0.00 0.00 0.00 3.53
2831 4284 0.688487 CTTGTACTTCCCCCGTTCCA 59.312 55.000 0.00 0.00 0.00 3.53
2832 4285 0.978907 TCTTGTACTTCCCCCGTTCC 59.021 55.000 0.00 0.00 0.00 3.62
2833 4286 3.450096 AGTATCTTGTACTTCCCCCGTTC 59.550 47.826 0.00 0.00 0.00 3.95
2834 4287 3.197116 CAGTATCTTGTACTTCCCCCGTT 59.803 47.826 0.00 0.00 0.00 4.44
2835 4288 2.764572 CAGTATCTTGTACTTCCCCCGT 59.235 50.000 0.00 0.00 0.00 5.28
2836 4289 3.028850 TCAGTATCTTGTACTTCCCCCG 58.971 50.000 0.00 0.00 0.00 5.73
2837 4290 4.683671 GCTTCAGTATCTTGTACTTCCCCC 60.684 50.000 0.00 0.00 0.00 5.40
2838 4291 4.443621 GCTTCAGTATCTTGTACTTCCCC 58.556 47.826 0.00 0.00 0.00 4.81
2839 4292 4.443621 GGCTTCAGTATCTTGTACTTCCC 58.556 47.826 0.00 0.00 0.00 3.97
2840 4293 4.162509 AGGGCTTCAGTATCTTGTACTTCC 59.837 45.833 0.00 0.00 0.00 3.46
2841 4294 5.346181 AGGGCTTCAGTATCTTGTACTTC 57.654 43.478 0.00 0.00 0.00 3.01
2842 4295 5.763876 AAGGGCTTCAGTATCTTGTACTT 57.236 39.130 0.00 0.00 0.00 2.24
2908 4380 9.554395 TTTGATAATGAACACTTTCAGTCTACA 57.446 29.630 0.00 0.00 45.07 2.74
2911 4383 9.956720 CTTTTTGATAATGAACACTTTCAGTCT 57.043 29.630 0.00 0.00 45.07 3.24
2920 4392 7.387397 TGGGCATTTCTTTTTGATAATGAACAC 59.613 33.333 0.00 0.00 31.25 3.32
2928 4400 9.199645 TCTAATCATGGGCATTTCTTTTTGATA 57.800 29.630 0.00 0.00 0.00 2.15
2929 4401 8.081517 TCTAATCATGGGCATTTCTTTTTGAT 57.918 30.769 0.00 0.00 0.00 2.57
2930 4402 7.479352 TCTAATCATGGGCATTTCTTTTTGA 57.521 32.000 0.00 0.00 0.00 2.69
2931 4403 7.982919 TCATCTAATCATGGGCATTTCTTTTTG 59.017 33.333 0.00 0.00 0.00 2.44
2932 4404 8.081517 TCATCTAATCATGGGCATTTCTTTTT 57.918 30.769 0.00 0.00 0.00 1.94
2987 5737 2.029739 TGAAACGATTGTAGTCCTGCGA 60.030 45.455 0.00 0.00 0.00 5.10
2989 5739 3.684788 ACATGAAACGATTGTAGTCCTGC 59.315 43.478 0.00 0.00 0.00 4.85
3017 5767 1.271163 CCCAAAAAGGCTCGACCACTA 60.271 52.381 6.78 0.00 43.14 2.74


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

AutoCloner maintained by Alex Coulton.