Multiple sequence alignment - TraesCS4A01G026000

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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 TraesCS4A01G026000 chr4A 100.000 2606 0 0 1 2606 17886880 17889485 0.000000e+00 4813.0
1 TraesCS4A01G026000 chr4A 95.265 718 6 15 1 692 118951959 118951244 0.000000e+00 1112.0
2 TraesCS4A01G026000 chr4A 100.000 30 0 0 700 729 78253483 78253454 3.620000e-04 56.5
3 TraesCS4A01G026000 chr5A 94.069 1703 49 14 909 2606 4080666 4082321 0.000000e+00 2538.0
4 TraesCS4A01G026000 chr5A 86.469 303 18 4 797 1080 4710247 4709949 7.000000e-81 311.0
5 TraesCS4A01G026000 chr6B 99.213 508 3 1 1 507 232746748 232746241 0.000000e+00 915.0
6 TraesCS4A01G026000 chr6B 96.842 190 5 1 503 691 232746213 232746024 1.510000e-82 316.0
7 TraesCS4A01G026000 chr3A 99.214 509 1 3 1 507 704648140 704648647 0.000000e+00 915.0
8 TraesCS4A01G026000 chr3A 83.576 481 74 5 1136 1614 449656805 449656328 1.840000e-121 446.0
9 TraesCS4A01G026000 chr3A 97.396 192 4 1 503 693 704648675 704648866 2.500000e-85 326.0
10 TraesCS4A01G026000 chr3A 96.842 190 5 1 503 691 459079619 459079430 1.510000e-82 316.0
11 TraesCS4A01G026000 chr2A 99.211 507 2 2 1 505 48841572 48842078 0.000000e+00 913.0
12 TraesCS4A01G026000 chr2A 99.016 508 3 2 1 507 398876015 398876521 0.000000e+00 909.0
13 TraesCS4A01G026000 chr2A 87.908 612 70 2 995 1604 764913449 764914058 0.000000e+00 717.0
14 TraesCS4A01G026000 chr2A 97.238 181 5 0 503 683 48842108 48842288 9.060000e-80 307.0
15 TraesCS4A01G026000 chr2A 100.000 30 0 0 700 729 92977045 92977074 3.620000e-04 56.5
16 TraesCS4A01G026000 chr2A 100.000 30 0 0 700 729 719361229 719361258 3.620000e-04 56.5
17 TraesCS4A01G026000 chr1A 99.018 509 3 2 1 507 353632815 353633323 0.000000e+00 911.0
18 TraesCS4A01G026000 chr1A 97.849 186 4 0 503 688 109417175 109416990 3.240000e-84 322.0
19 TraesCS4A01G026000 chr1A 97.849 186 4 0 503 688 353633351 353633536 3.240000e-84 322.0
20 TraesCS4A01G026000 chr7B 99.016 508 3 2 1 507 78118828 78119334 0.000000e+00 909.0
21 TraesCS4A01G026000 chr7B 98.242 512 4 3 1 507 741262570 741263081 0.000000e+00 891.0
22 TraesCS4A01G026000 chr7B 88.817 617 69 0 988 1604 372008137 372008753 0.000000e+00 758.0
23 TraesCS4A01G026000 chr7B 98.925 186 2 0 503 688 741263109 741263294 1.490000e-87 333.0
24 TraesCS4A01G026000 chr7B 100.000 30 0 0 700 729 380855523 380855552 3.620000e-04 56.5
25 TraesCS4A01G026000 chr7B 100.000 30 0 0 700 729 481113084 481113055 3.620000e-04 56.5
26 TraesCS4A01G026000 chr7A 98.625 509 4 3 1 507 615547425 615546918 0.000000e+00 898.0
27 TraesCS4A01G026000 chr7A 88.746 622 69 1 984 1604 424534678 424535299 0.000000e+00 760.0
28 TraesCS4A01G026000 chr7A 98.913 184 2 0 505 688 615546888 615546705 1.930000e-86 329.0
29 TraesCS4A01G026000 chr7D 89.661 619 59 3 988 1604 376941113 376941728 0.000000e+00 784.0
30 TraesCS4A01G026000 chr2B 87.520 617 77 0 988 1604 798294659 798295275 0.000000e+00 713.0
31 TraesCS4A01G026000 chr2B 87.833 600 69 2 1007 1604 798702764 798702167 0.000000e+00 701.0
32 TraesCS4A01G026000 chr2B 100.000 30 0 0 700 729 138119715 138119686 3.620000e-04 56.5
33 TraesCS4A01G026000 chr2B 100.000 30 0 0 700 729 304258651 304258680 3.620000e-04 56.5
34 TraesCS4A01G026000 chr5B 92.421 409 19 6 864 1261 6869260 6869667 8.090000e-160 573.0
35 TraesCS4A01G026000 chr3D 81.037 617 98 10 1001 1614 332327014 332326414 8.440000e-130 473.0
36 TraesCS4A01G026000 chr3B 85.149 101 12 3 590 688 188866145 188866046 1.650000e-17 100.0
37 TraesCS4A01G026000 chr1B 100.000 30 0 0 700 729 634683869 634683898 3.620000e-04 56.5


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 TraesCS4A01G026000 chr4A 17886880 17889485 2605 False 4813.0 4813 100.0000 1 2606 1 chr4A.!!$F1 2605
1 TraesCS4A01G026000 chr4A 118951244 118951959 715 True 1112.0 1112 95.2650 1 692 1 chr4A.!!$R2 691
2 TraesCS4A01G026000 chr5A 4080666 4082321 1655 False 2538.0 2538 94.0690 909 2606 1 chr5A.!!$F1 1697
3 TraesCS4A01G026000 chr6B 232746024 232746748 724 True 615.5 915 98.0275 1 691 2 chr6B.!!$R1 690
4 TraesCS4A01G026000 chr3A 704648140 704648866 726 False 620.5 915 98.3050 1 693 2 chr3A.!!$F1 692
5 TraesCS4A01G026000 chr2A 398876015 398876521 506 False 909.0 909 99.0160 1 507 1 chr2A.!!$F2 506
6 TraesCS4A01G026000 chr2A 764913449 764914058 609 False 717.0 717 87.9080 995 1604 1 chr2A.!!$F4 609
7 TraesCS4A01G026000 chr2A 48841572 48842288 716 False 610.0 913 98.2245 1 683 2 chr2A.!!$F5 682
8 TraesCS4A01G026000 chr1A 353632815 353633536 721 False 616.5 911 98.4335 1 688 2 chr1A.!!$F1 687
9 TraesCS4A01G026000 chr7B 78118828 78119334 506 False 909.0 909 99.0160 1 507 1 chr7B.!!$F1 506
10 TraesCS4A01G026000 chr7B 372008137 372008753 616 False 758.0 758 88.8170 988 1604 1 chr7B.!!$F2 616
11 TraesCS4A01G026000 chr7B 741262570 741263294 724 False 612.0 891 98.5835 1 688 2 chr7B.!!$F4 687
12 TraesCS4A01G026000 chr7A 424534678 424535299 621 False 760.0 760 88.7460 984 1604 1 chr7A.!!$F1 620
13 TraesCS4A01G026000 chr7A 615546705 615547425 720 True 613.5 898 98.7690 1 688 2 chr7A.!!$R1 687
14 TraesCS4A01G026000 chr7D 376941113 376941728 615 False 784.0 784 89.6610 988 1604 1 chr7D.!!$F1 616
15 TraesCS4A01G026000 chr2B 798294659 798295275 616 False 713.0 713 87.5200 988 1604 1 chr2B.!!$F2 616
16 TraesCS4A01G026000 chr2B 798702167 798702764 597 True 701.0 701 87.8330 1007 1604 1 chr2B.!!$R2 597
17 TraesCS4A01G026000 chr3D 332326414 332327014 600 True 473.0 473 81.0370 1001 1614 1 chr3D.!!$R1 613

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
743 784 0.035458 AAAGACTTGGTCTCCGGCTG 59.965 55.0 0.0 0.0 42.59 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2128 2174 0.106708 TCGGGATCCTTACATGCAGC 59.893 55.0 12.58 0.0 0.0 5.25 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
557 598 5.935206 TCGCACCTCTATAAAACAATGAACA 59.065 36.000 0.00 0.00 0.00 3.18
735 776 8.850007 AAAGAGGTAAAGATAAAGACTTGGTC 57.150 34.615 0.00 0.00 0.00 4.02
736 777 7.800300 AGAGGTAAAGATAAAGACTTGGTCT 57.200 36.000 0.00 0.00 45.64 3.85
737 778 7.842982 AGAGGTAAAGATAAAGACTTGGTCTC 58.157 38.462 0.49 0.00 42.59 3.36
738 779 6.948589 AGGTAAAGATAAAGACTTGGTCTCC 58.051 40.000 0.49 2.33 42.59 3.71
739 780 5.811100 GGTAAAGATAAAGACTTGGTCTCCG 59.189 44.000 0.49 0.00 42.59 4.63
740 781 4.473477 AAGATAAAGACTTGGTCTCCGG 57.527 45.455 0.00 0.00 42.59 5.14
741 782 2.168728 AGATAAAGACTTGGTCTCCGGC 59.831 50.000 0.00 0.00 42.59 6.13
742 783 1.640917 TAAAGACTTGGTCTCCGGCT 58.359 50.000 0.00 0.00 42.59 5.52
743 784 0.035458 AAAGACTTGGTCTCCGGCTG 59.965 55.000 0.00 0.00 42.59 4.85
744 785 1.831652 AAGACTTGGTCTCCGGCTGG 61.832 60.000 4.71 4.71 42.59 4.85
745 786 3.316573 GACTTGGTCTCCGGCTGGG 62.317 68.421 12.87 2.35 35.24 4.45
746 787 3.003173 CTTGGTCTCCGGCTGGGA 61.003 66.667 12.87 5.09 44.68 4.37
747 788 2.528127 TTGGTCTCCGGCTGGGAA 60.528 61.111 12.87 0.00 46.61 3.97
748 789 2.124507 CTTGGTCTCCGGCTGGGAAA 62.125 60.000 12.87 0.00 46.61 3.13
749 790 2.046217 GGTCTCCGGCTGGGAAAC 60.046 66.667 12.87 7.52 46.61 2.78
750 791 2.593956 GGTCTCCGGCTGGGAAACT 61.594 63.158 12.87 0.00 46.61 2.66
751 792 1.079057 GTCTCCGGCTGGGAAACTC 60.079 63.158 12.87 0.00 46.61 3.01
752 793 2.125512 CTCCGGCTGGGAAACTCG 60.126 66.667 12.87 0.00 46.61 4.18
753 794 2.920912 TCCGGCTGGGAAACTCGT 60.921 61.111 12.87 0.00 43.62 4.18
754 795 2.434359 CCGGCTGGGAAACTCGTC 60.434 66.667 2.57 0.00 38.47 4.20
755 796 2.434359 CGGCTGGGAAACTCGTCC 60.434 66.667 0.00 0.00 36.90 4.79
762 803 3.347411 GGAAACTCGTCCCATCTCG 57.653 57.895 0.00 0.00 0.00 4.04
763 804 0.815734 GGAAACTCGTCCCATCTCGA 59.184 55.000 0.00 0.00 34.88 4.04
764 805 1.203994 GGAAACTCGTCCCATCTCGAA 59.796 52.381 0.00 0.00 35.69 3.71
765 806 2.159085 GGAAACTCGTCCCATCTCGAAT 60.159 50.000 0.00 0.00 35.69 3.34
766 807 2.873133 AACTCGTCCCATCTCGAATC 57.127 50.000 0.00 0.00 35.69 2.52
767 808 0.663688 ACTCGTCCCATCTCGAATCG 59.336 55.000 0.00 0.00 35.69 3.34
768 809 0.945099 CTCGTCCCATCTCGAATCGA 59.055 55.000 4.91 4.91 35.69 3.59
769 810 1.537638 CTCGTCCCATCTCGAATCGAT 59.462 52.381 5.59 0.00 34.61 3.59
770 811 1.535896 TCGTCCCATCTCGAATCGATC 59.464 52.381 5.59 0.00 34.61 3.69
771 812 1.401670 CGTCCCATCTCGAATCGATCC 60.402 57.143 5.59 0.00 34.61 3.36
772 813 0.881796 TCCCATCTCGAATCGATCCG 59.118 55.000 5.59 0.00 34.61 4.18
773 814 0.598562 CCCATCTCGAATCGATCCGT 59.401 55.000 5.59 0.00 34.61 4.69
774 815 1.000163 CCCATCTCGAATCGATCCGTT 60.000 52.381 5.59 0.00 34.61 4.44
775 816 2.545952 CCCATCTCGAATCGATCCGTTT 60.546 50.000 5.59 0.00 34.61 3.60
776 817 2.472861 CCATCTCGAATCGATCCGTTTG 59.527 50.000 5.59 0.59 34.61 2.93
777 818 1.556564 TCTCGAATCGATCCGTTTGC 58.443 50.000 5.59 0.00 34.61 3.68
778 819 1.134367 TCTCGAATCGATCCGTTTGCT 59.866 47.619 5.59 0.00 34.61 3.91
779 820 1.927174 CTCGAATCGATCCGTTTGCTT 59.073 47.619 5.59 0.00 34.61 3.91
780 821 2.343101 TCGAATCGATCCGTTTGCTTT 58.657 42.857 3.35 0.00 0.00 3.51
781 822 2.739913 TCGAATCGATCCGTTTGCTTTT 59.260 40.909 3.35 0.00 0.00 2.27
782 823 3.187637 TCGAATCGATCCGTTTGCTTTTT 59.812 39.130 3.35 0.00 0.00 1.94
829 870 6.847421 ACGGAGTAGTTTCCAATAGTTAGT 57.153 37.500 0.00 0.00 41.94 2.24
830 871 7.237209 ACGGAGTAGTTTCCAATAGTTAGTT 57.763 36.000 0.00 0.00 41.94 2.24
831 872 7.674120 ACGGAGTAGTTTCCAATAGTTAGTTT 58.326 34.615 0.00 0.00 41.94 2.66
832 873 7.816513 ACGGAGTAGTTTCCAATAGTTAGTTTC 59.183 37.037 0.00 0.00 41.94 2.78
833 874 7.816031 CGGAGTAGTTTCCAATAGTTAGTTTCA 59.184 37.037 0.00 0.00 37.05 2.69
834 875 9.152595 GGAGTAGTTTCCAATAGTTAGTTTCAG 57.847 37.037 0.00 0.00 37.20 3.02
835 876 9.152595 GAGTAGTTTCCAATAGTTAGTTTCAGG 57.847 37.037 0.00 0.00 0.00 3.86
836 877 8.101419 AGTAGTTTCCAATAGTTAGTTTCAGGG 58.899 37.037 0.00 0.00 0.00 4.45
837 878 6.246163 AGTTTCCAATAGTTAGTTTCAGGGG 58.754 40.000 0.00 0.00 0.00 4.79
838 879 5.853572 TTCCAATAGTTAGTTTCAGGGGT 57.146 39.130 0.00 0.00 0.00 4.95
839 880 5.853572 TCCAATAGTTAGTTTCAGGGGTT 57.146 39.130 0.00 0.00 0.00 4.11
840 881 5.566469 TCCAATAGTTAGTTTCAGGGGTTG 58.434 41.667 0.00 0.00 0.00 3.77
841 882 5.073965 TCCAATAGTTAGTTTCAGGGGTTGT 59.926 40.000 0.00 0.00 0.00 3.32
842 883 5.773176 CCAATAGTTAGTTTCAGGGGTTGTT 59.227 40.000 0.00 0.00 0.00 2.83
843 884 6.266786 CCAATAGTTAGTTTCAGGGGTTGTTT 59.733 38.462 0.00 0.00 0.00 2.83
844 885 6.894339 ATAGTTAGTTTCAGGGGTTGTTTG 57.106 37.500 0.00 0.00 0.00 2.93
845 886 4.862371 AGTTAGTTTCAGGGGTTGTTTGA 58.138 39.130 0.00 0.00 0.00 2.69
846 887 4.887655 AGTTAGTTTCAGGGGTTGTTTGAG 59.112 41.667 0.00 0.00 0.00 3.02
847 888 3.662759 AGTTTCAGGGGTTGTTTGAGA 57.337 42.857 0.00 0.00 0.00 3.27
848 889 3.976015 AGTTTCAGGGGTTGTTTGAGAA 58.024 40.909 0.00 0.00 0.00 2.87
849 890 4.546674 AGTTTCAGGGGTTGTTTGAGAAT 58.453 39.130 0.00 0.00 0.00 2.40
850 891 4.962362 AGTTTCAGGGGTTGTTTGAGAATT 59.038 37.500 0.00 0.00 0.00 2.17
851 892 4.935352 TTCAGGGGTTGTTTGAGAATTG 57.065 40.909 0.00 0.00 0.00 2.32
852 893 4.177537 TCAGGGGTTGTTTGAGAATTGA 57.822 40.909 0.00 0.00 0.00 2.57
853 894 4.144297 TCAGGGGTTGTTTGAGAATTGAG 58.856 43.478 0.00 0.00 0.00 3.02
854 895 4.141274 TCAGGGGTTGTTTGAGAATTGAGA 60.141 41.667 0.00 0.00 0.00 3.27
855 896 4.022849 CAGGGGTTGTTTGAGAATTGAGAC 60.023 45.833 0.00 0.00 0.00 3.36
856 897 3.058224 GGGGTTGTTTGAGAATTGAGACG 60.058 47.826 0.00 0.00 0.00 4.18
857 898 3.564225 GGGTTGTTTGAGAATTGAGACGT 59.436 43.478 0.00 0.00 0.00 4.34
858 899 4.319549 GGGTTGTTTGAGAATTGAGACGTC 60.320 45.833 7.70 7.70 0.00 4.34
859 900 4.511826 GGTTGTTTGAGAATTGAGACGTCT 59.488 41.667 20.18 20.18 0.00 4.18
860 901 5.333416 GGTTGTTTGAGAATTGAGACGTCTC 60.333 44.000 33.76 33.76 43.15 3.36
861 902 4.307432 TGTTTGAGAATTGAGACGTCTCC 58.693 43.478 36.01 23.27 42.20 3.71
862 903 2.921634 TGAGAATTGAGACGTCTCCG 57.078 50.000 36.01 0.00 42.20 4.63
863 904 1.472878 TGAGAATTGAGACGTCTCCGG 59.527 52.381 36.01 0.00 42.20 5.14
864 905 0.173708 AGAATTGAGACGTCTCCGGC 59.826 55.000 36.01 23.94 44.68 6.13
871 912 2.480100 GACGTCTCCGGCTACTTCT 58.520 57.895 8.70 0.00 39.71 2.85
872 913 0.377905 GACGTCTCCGGCTACTTCTC 59.622 60.000 8.70 0.00 39.71 2.87
873 914 1.031029 ACGTCTCCGGCTACTTCTCC 61.031 60.000 0.00 0.00 38.78 3.71
874 915 0.748729 CGTCTCCGGCTACTTCTCCT 60.749 60.000 0.00 0.00 0.00 3.69
875 916 0.741915 GTCTCCGGCTACTTCTCCTG 59.258 60.000 0.00 0.00 0.00 3.86
876 917 0.331954 TCTCCGGCTACTTCTCCTGT 59.668 55.000 0.00 0.00 0.00 4.00
877 918 0.741915 CTCCGGCTACTTCTCCTGTC 59.258 60.000 0.00 0.00 0.00 3.51
878 919 0.683504 TCCGGCTACTTCTCCTGTCC 60.684 60.000 0.00 0.00 0.00 4.02
879 920 1.677637 CCGGCTACTTCTCCTGTCCC 61.678 65.000 0.00 0.00 0.00 4.46
880 921 1.817209 GGCTACTTCTCCTGTCCCG 59.183 63.158 0.00 0.00 0.00 5.14
881 922 1.142097 GCTACTTCTCCTGTCCCGC 59.858 63.158 0.00 0.00 0.00 6.13
882 923 1.605058 GCTACTTCTCCTGTCCCGCA 61.605 60.000 0.00 0.00 0.00 5.69
883 924 0.895530 CTACTTCTCCTGTCCCGCAA 59.104 55.000 0.00 0.00 0.00 4.85
884 925 0.606604 TACTTCTCCTGTCCCGCAAC 59.393 55.000 0.00 0.00 0.00 4.17
885 926 1.371183 CTTCTCCTGTCCCGCAACA 59.629 57.895 0.00 0.00 0.00 3.33
886 927 0.250295 CTTCTCCTGTCCCGCAACAA 60.250 55.000 0.00 0.00 0.00 2.83
887 928 0.400213 TTCTCCTGTCCCGCAACAAT 59.600 50.000 0.00 0.00 0.00 2.71
888 929 1.271856 TCTCCTGTCCCGCAACAATA 58.728 50.000 0.00 0.00 0.00 1.90
889 930 1.626321 TCTCCTGTCCCGCAACAATAA 59.374 47.619 0.00 0.00 0.00 1.40
890 931 2.238646 TCTCCTGTCCCGCAACAATAAT 59.761 45.455 0.00 0.00 0.00 1.28
891 932 3.016736 CTCCTGTCCCGCAACAATAATT 58.983 45.455 0.00 0.00 0.00 1.40
892 933 2.752354 TCCTGTCCCGCAACAATAATTG 59.248 45.455 0.00 0.00 0.00 2.32
900 941 2.314323 CAACAATAATTGCCCTGCCC 57.686 50.000 0.00 0.00 0.00 5.36
901 942 1.134431 CAACAATAATTGCCCTGCCCC 60.134 52.381 0.00 0.00 0.00 5.80
902 943 0.339510 ACAATAATTGCCCTGCCCCT 59.660 50.000 0.00 0.00 0.00 4.79
903 944 1.043022 CAATAATTGCCCTGCCCCTC 58.957 55.000 0.00 0.00 0.00 4.30
904 945 0.468029 AATAATTGCCCTGCCCCTCG 60.468 55.000 0.00 0.00 0.00 4.63
905 946 2.983725 ATAATTGCCCTGCCCCTCGC 62.984 60.000 0.00 0.00 38.31 5.03
937 978 3.656045 CGCCGTTCGCTGGGTTTT 61.656 61.111 0.00 0.00 34.21 2.43
944 985 1.512156 TTCGCTGGGTTTTCGCCTTC 61.512 55.000 0.00 0.00 0.00 3.46
945 986 2.561373 GCTGGGTTTTCGCCTTCG 59.439 61.111 0.00 0.00 0.00 3.79
957 1003 3.694535 TCGCCTTCGTTAGATCTCTTC 57.305 47.619 0.00 0.00 36.96 2.87
963 1009 3.784701 TCGTTAGATCTCTTCCTGTGC 57.215 47.619 0.00 0.00 0.00 4.57
990 1036 0.525668 CTACCTAGCTGCCGTGAACG 60.526 60.000 0.00 0.00 39.44 3.95
1050 1096 2.543687 ACTTCGAGGGCGACGTCATG 62.544 60.000 17.16 0.67 44.36 3.07
1356 1402 2.029073 CTCAGCAACGACCACGGT 59.971 61.111 0.00 0.00 44.46 4.83
1616 1662 1.857217 CGACTACTGAGATGCATGCAC 59.143 52.381 25.37 16.77 0.00 4.57
1656 1702 2.540515 CTGTCCTGCAATACCTACGTG 58.459 52.381 0.00 0.00 0.00 4.49
1657 1703 1.897133 TGTCCTGCAATACCTACGTGT 59.103 47.619 0.00 0.00 0.00 4.49
1658 1704 3.090790 TGTCCTGCAATACCTACGTGTA 58.909 45.455 0.00 0.00 0.00 2.90
1659 1705 3.119388 TGTCCTGCAATACCTACGTGTAC 60.119 47.826 0.00 0.00 0.00 2.90
1660 1706 3.129988 GTCCTGCAATACCTACGTGTACT 59.870 47.826 0.00 0.00 0.00 2.73
1661 1707 4.336433 GTCCTGCAATACCTACGTGTACTA 59.664 45.833 0.00 0.00 0.00 1.82
1662 1708 4.577693 TCCTGCAATACCTACGTGTACTAG 59.422 45.833 0.00 0.00 0.00 2.57
1663 1709 4.288531 CTGCAATACCTACGTGTACTAGC 58.711 47.826 0.00 0.00 0.00 3.42
1664 1710 3.949754 TGCAATACCTACGTGTACTAGCT 59.050 43.478 0.00 0.00 0.00 3.32
1665 1711 4.036027 TGCAATACCTACGTGTACTAGCTC 59.964 45.833 0.00 0.00 0.00 4.09
1666 1712 4.275443 GCAATACCTACGTGTACTAGCTCT 59.725 45.833 0.00 0.00 0.00 4.09
1667 1713 5.221009 GCAATACCTACGTGTACTAGCTCTT 60.221 44.000 0.00 0.00 0.00 2.85
1668 1714 6.017605 GCAATACCTACGTGTACTAGCTCTTA 60.018 42.308 0.00 0.00 0.00 2.10
1669 1715 7.467811 GCAATACCTACGTGTACTAGCTCTTAA 60.468 40.741 0.00 0.00 0.00 1.85
1670 1716 7.727331 ATACCTACGTGTACTAGCTCTTAAG 57.273 40.000 0.00 0.00 0.00 1.85
1671 1717 5.495640 ACCTACGTGTACTAGCTCTTAAGT 58.504 41.667 0.00 0.00 0.00 2.24
1672 1718 6.644347 ACCTACGTGTACTAGCTCTTAAGTA 58.356 40.000 0.00 0.00 0.00 2.24
1673 1719 6.536941 ACCTACGTGTACTAGCTCTTAAGTAC 59.463 42.308 14.91 14.91 45.40 2.73
1674 1720 6.760770 CCTACGTGTACTAGCTCTTAAGTACT 59.239 42.308 20.06 7.63 45.41 2.73
1675 1721 7.923344 CCTACGTGTACTAGCTCTTAAGTACTA 59.077 40.741 20.06 8.21 45.41 1.82
1676 1722 7.769272 ACGTGTACTAGCTCTTAAGTACTAG 57.231 40.000 20.06 22.22 45.41 2.57
1677 1723 7.327214 ACGTGTACTAGCTCTTAAGTACTAGT 58.673 38.462 27.57 27.57 45.41 2.57
1733 1779 5.906073 TCGATCTGTAATGAAGAATCAGCA 58.094 37.500 0.00 0.00 39.39 4.41
1760 1806 3.676291 TGGTGATGATGAGTTGTCGAA 57.324 42.857 0.00 0.00 0.00 3.71
1802 1848 2.514824 GCCATGGCGACTCCCTTC 60.515 66.667 23.48 0.00 0.00 3.46
1809 1855 1.038130 GGCGACTCCCTTCTGCTAGA 61.038 60.000 0.00 0.00 0.00 2.43
1905 1951 4.034510 GCAATTCTTCGGTCCTCAACTATG 59.965 45.833 0.00 0.00 0.00 2.23
1920 1966 7.286546 TCCTCAACTATGATCTCTTTCTCGATT 59.713 37.037 0.00 0.00 34.37 3.34
2139 2185 1.059369 GTCGTGCGCTGCATGTAAG 59.941 57.895 9.73 0.00 44.84 2.34
2146 2192 1.224069 CGCTGCATGTAAGGATCCCG 61.224 60.000 8.55 0.00 0.00 5.14
2151 2197 2.172505 TGCATGTAAGGATCCCGATGTT 59.827 45.455 8.55 0.00 0.00 2.71
2164 2210 2.612212 CCCGATGTTTATGCACCTGTAC 59.388 50.000 0.00 0.00 0.00 2.90
2165 2211 3.531538 CCGATGTTTATGCACCTGTACT 58.468 45.455 0.00 0.00 0.00 2.73
2166 2212 3.309682 CCGATGTTTATGCACCTGTACTG 59.690 47.826 0.00 0.00 0.00 2.74
2167 2213 3.932710 CGATGTTTATGCACCTGTACTGT 59.067 43.478 0.00 0.00 0.00 3.55
2168 2214 5.106442 CGATGTTTATGCACCTGTACTGTA 58.894 41.667 0.00 0.00 0.00 2.74
2169 2215 5.579119 CGATGTTTATGCACCTGTACTGTAA 59.421 40.000 0.00 0.00 0.00 2.41
2170 2216 6.455113 CGATGTTTATGCACCTGTACTGTAAC 60.455 42.308 0.00 0.00 0.00 2.50
2171 2217 4.998672 TGTTTATGCACCTGTACTGTAACC 59.001 41.667 0.00 0.00 0.00 2.85
2172 2218 4.893829 TTATGCACCTGTACTGTAACCA 57.106 40.909 0.00 0.00 0.00 3.67
2173 2219 2.831685 TGCACCTGTACTGTAACCAG 57.168 50.000 0.00 0.00 44.68 4.00
2199 2245 4.454678 TGGCAATACACAGGAGATTCATC 58.545 43.478 0.00 0.00 0.00 2.92
2253 2299 2.482333 CCTCTACCTCTCCCACGCG 61.482 68.421 3.53 3.53 0.00 6.01
2254 2300 2.439701 TCTACCTCTCCCACGCGG 60.440 66.667 12.47 0.00 0.00 6.46
2274 2320 2.952245 GGCTGATGGCGATCATGC 59.048 61.111 12.12 15.87 42.94 4.06
2331 2377 0.806102 CCTATTGACGTGTGCCCTCG 60.806 60.000 0.00 0.00 0.00 4.63
2355 2401 0.099082 CTGGCTACGGACGAGAACTC 59.901 60.000 0.00 0.00 0.00 3.01
2379 2425 1.977544 CCGTCGGTCTCCCTCTTGT 60.978 63.158 2.08 0.00 0.00 3.16
2380 2426 1.533469 CCGTCGGTCTCCCTCTTGTT 61.533 60.000 2.08 0.00 0.00 2.83
2383 2429 1.619332 GTCGGTCTCCCTCTTGTTTCT 59.381 52.381 0.00 0.00 0.00 2.52
2402 2448 1.073199 CTCCCACCCAACCTGTGTC 59.927 63.158 0.00 0.00 31.71 3.67
2403 2449 2.281484 CCCACCCAACCTGTGTCG 60.281 66.667 0.00 0.00 31.71 4.35
2404 2450 2.978010 CCACCCAACCTGTGTCGC 60.978 66.667 0.00 0.00 31.71 5.19
2405 2451 2.978010 CACCCAACCTGTGTCGCC 60.978 66.667 0.00 0.00 0.00 5.54
2406 2452 4.619227 ACCCAACCTGTGTCGCCG 62.619 66.667 0.00 0.00 0.00 6.46
2409 2455 4.988598 CAACCTGTGTCGCCGGCT 62.989 66.667 26.68 0.00 0.00 5.52
2490 2536 2.416107 CTTCAAGCTGGCCCTGGACA 62.416 60.000 0.00 0.00 0.00 4.02
2555 2601 0.037882 CGTGCTATGATGCGGAGGAT 60.038 55.000 0.00 0.00 45.36 3.24
2573 2619 3.691342 CACGTCCGGGAAGCCTCA 61.691 66.667 10.02 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
557 598 1.227853 GACCAAATATCGCCGCCCT 60.228 57.895 0.00 0.00 0.00 5.19
709 750 9.939802 GACCAAGTCTTTATCTTTACCTCTTTA 57.060 33.333 0.00 0.00 0.00 1.85
710 751 8.661345 AGACCAAGTCTTTATCTTTACCTCTTT 58.339 33.333 0.00 0.00 40.28 2.52
711 752 8.208575 AGACCAAGTCTTTATCTTTACCTCTT 57.791 34.615 0.00 0.00 40.28 2.85
712 753 7.093245 GGAGACCAAGTCTTTATCTTTACCTCT 60.093 40.741 0.00 0.00 43.53 3.69
713 754 7.042950 GGAGACCAAGTCTTTATCTTTACCTC 58.957 42.308 0.00 0.00 43.53 3.85
714 755 6.351117 CGGAGACCAAGTCTTTATCTTTACCT 60.351 42.308 0.00 0.00 43.53 3.08
715 756 5.811100 CGGAGACCAAGTCTTTATCTTTACC 59.189 44.000 0.00 0.00 43.53 2.85
716 757 5.811100 CCGGAGACCAAGTCTTTATCTTTAC 59.189 44.000 0.00 0.00 43.53 2.01
717 758 5.626116 GCCGGAGACCAAGTCTTTATCTTTA 60.626 44.000 5.05 0.00 43.53 1.85
718 759 4.833390 CCGGAGACCAAGTCTTTATCTTT 58.167 43.478 0.00 0.00 43.53 2.52
719 760 3.369576 GCCGGAGACCAAGTCTTTATCTT 60.370 47.826 5.05 0.00 43.53 2.40
720 761 2.168728 GCCGGAGACCAAGTCTTTATCT 59.831 50.000 5.05 0.00 43.53 1.98
721 762 2.168728 AGCCGGAGACCAAGTCTTTATC 59.831 50.000 5.05 0.00 43.53 1.75
722 763 2.093447 CAGCCGGAGACCAAGTCTTTAT 60.093 50.000 5.05 0.00 43.53 1.40
723 764 1.275291 CAGCCGGAGACCAAGTCTTTA 59.725 52.381 5.05 0.00 43.53 1.85
724 765 0.035458 CAGCCGGAGACCAAGTCTTT 59.965 55.000 5.05 0.00 43.53 2.52
725 766 1.674057 CAGCCGGAGACCAAGTCTT 59.326 57.895 5.05 0.00 43.53 3.01
726 767 2.286523 CCAGCCGGAGACCAAGTCT 61.287 63.158 5.05 0.00 46.42 3.24
727 768 2.266055 CCAGCCGGAGACCAAGTC 59.734 66.667 5.05 0.00 0.00 3.01
728 769 3.322466 CCCAGCCGGAGACCAAGT 61.322 66.667 5.05 0.00 0.00 3.16
729 770 2.124507 TTTCCCAGCCGGAGACCAAG 62.125 60.000 5.05 0.00 43.39 3.61
730 771 2.150719 TTTCCCAGCCGGAGACCAA 61.151 57.895 5.05 0.00 43.39 3.67
731 772 2.528127 TTTCCCAGCCGGAGACCA 60.528 61.111 5.05 0.00 43.39 4.02
732 773 2.046217 GTTTCCCAGCCGGAGACC 60.046 66.667 5.05 0.00 43.39 3.85
733 774 1.079057 GAGTTTCCCAGCCGGAGAC 60.079 63.158 5.05 3.52 44.53 3.36
734 775 2.646175 CGAGTTTCCCAGCCGGAGA 61.646 63.158 5.05 0.00 43.39 3.71
735 776 2.125512 CGAGTTTCCCAGCCGGAG 60.126 66.667 5.05 0.00 43.39 4.63
736 777 2.920912 ACGAGTTTCCCAGCCGGA 60.921 61.111 5.05 0.00 39.68 5.14
737 778 2.434359 GACGAGTTTCCCAGCCGG 60.434 66.667 0.00 0.00 0.00 6.13
738 779 2.434359 GGACGAGTTTCCCAGCCG 60.434 66.667 0.00 0.00 0.00 5.52
744 785 0.815734 TCGAGATGGGACGAGTTTCC 59.184 55.000 0.00 0.00 34.49 3.13
745 786 2.649331 TTCGAGATGGGACGAGTTTC 57.351 50.000 0.00 0.00 39.59 2.78
746 787 2.479730 CGATTCGAGATGGGACGAGTTT 60.480 50.000 0.00 0.00 39.59 2.66
747 788 1.065701 CGATTCGAGATGGGACGAGTT 59.934 52.381 0.00 0.00 39.59 3.01
748 789 0.663688 CGATTCGAGATGGGACGAGT 59.336 55.000 0.00 0.00 39.59 4.18
749 790 0.945099 TCGATTCGAGATGGGACGAG 59.055 55.000 4.29 0.00 39.59 4.18
750 791 1.535896 GATCGATTCGAGATGGGACGA 59.464 52.381 14.81 0.00 39.91 4.20
751 792 1.401670 GGATCGATTCGAGATGGGACG 60.402 57.143 14.81 0.00 39.91 4.79
752 793 1.401670 CGGATCGATTCGAGATGGGAC 60.402 57.143 21.78 0.00 39.91 4.46
753 794 0.881796 CGGATCGATTCGAGATGGGA 59.118 55.000 21.78 0.00 39.91 4.37
754 795 0.598562 ACGGATCGATTCGAGATGGG 59.401 55.000 31.98 1.85 39.91 4.00
755 796 2.423926 AACGGATCGATTCGAGATGG 57.576 50.000 31.98 2.63 39.91 3.51
756 797 2.097202 GCAAACGGATCGATTCGAGATG 60.097 50.000 31.98 24.27 39.91 2.90
757 798 2.128035 GCAAACGGATCGATTCGAGAT 58.872 47.619 31.98 14.62 39.91 2.75
758 799 1.134367 AGCAAACGGATCGATTCGAGA 59.866 47.619 31.98 0.00 39.91 4.04
759 800 1.560923 AGCAAACGGATCGATTCGAG 58.439 50.000 31.98 20.38 39.91 4.04
760 801 2.004583 AAGCAAACGGATCGATTCGA 57.995 45.000 31.98 11.73 41.13 3.71
761 802 2.806288 AAAGCAAACGGATCGATTCG 57.194 45.000 24.35 24.35 0.00 3.34
793 834 8.733458 GGAAACTACTCCGTATTTGGTATTTTT 58.267 33.333 0.00 0.00 0.00 1.94
794 835 7.884354 TGGAAACTACTCCGTATTTGGTATTTT 59.116 33.333 0.00 0.00 38.44 1.82
795 836 7.396418 TGGAAACTACTCCGTATTTGGTATTT 58.604 34.615 0.00 0.00 38.44 1.40
796 837 6.949715 TGGAAACTACTCCGTATTTGGTATT 58.050 36.000 0.00 0.00 38.44 1.89
797 838 6.549433 TGGAAACTACTCCGTATTTGGTAT 57.451 37.500 0.00 0.00 38.44 2.73
798 839 5.999205 TGGAAACTACTCCGTATTTGGTA 57.001 39.130 0.00 0.00 38.44 3.25
799 840 4.895668 TGGAAACTACTCCGTATTTGGT 57.104 40.909 0.00 0.00 38.44 3.67
800 841 7.046033 ACTATTGGAAACTACTCCGTATTTGG 58.954 38.462 0.00 0.00 38.44 3.28
801 842 8.488651 AACTATTGGAAACTACTCCGTATTTG 57.511 34.615 0.00 0.00 38.44 2.32
802 843 9.813446 CTAACTATTGGAAACTACTCCGTATTT 57.187 33.333 0.00 0.00 38.44 1.40
803 844 8.975295 ACTAACTATTGGAAACTACTCCGTATT 58.025 33.333 0.00 0.00 38.44 1.89
804 845 8.530804 ACTAACTATTGGAAACTACTCCGTAT 57.469 34.615 0.00 0.00 38.44 3.06
805 846 7.944729 ACTAACTATTGGAAACTACTCCGTA 57.055 36.000 0.00 0.00 38.44 4.02
806 847 6.847421 ACTAACTATTGGAAACTACTCCGT 57.153 37.500 0.00 0.00 38.44 4.69
807 848 7.816031 TGAAACTAACTATTGGAAACTACTCCG 59.184 37.037 0.00 0.00 38.44 4.63
808 849 9.152595 CTGAAACTAACTATTGGAAACTACTCC 57.847 37.037 0.00 0.00 35.88 3.85
809 850 9.152595 CCTGAAACTAACTATTGGAAACTACTC 57.847 37.037 0.00 0.00 0.00 2.59
810 851 8.101419 CCCTGAAACTAACTATTGGAAACTACT 58.899 37.037 0.00 0.00 0.00 2.57
811 852 7.336176 CCCCTGAAACTAACTATTGGAAACTAC 59.664 40.741 0.00 0.00 0.00 2.73
812 853 7.017850 ACCCCTGAAACTAACTATTGGAAACTA 59.982 37.037 0.00 0.00 0.00 2.24
813 854 6.183361 ACCCCTGAAACTAACTATTGGAAACT 60.183 38.462 0.00 0.00 0.00 2.66
814 855 6.008331 ACCCCTGAAACTAACTATTGGAAAC 58.992 40.000 0.00 0.00 0.00 2.78
815 856 6.208840 ACCCCTGAAACTAACTATTGGAAA 57.791 37.500 0.00 0.00 0.00 3.13
816 857 5.853572 ACCCCTGAAACTAACTATTGGAA 57.146 39.130 0.00 0.00 0.00 3.53
817 858 5.073965 ACAACCCCTGAAACTAACTATTGGA 59.926 40.000 0.00 0.00 0.00 3.53
818 859 5.321927 ACAACCCCTGAAACTAACTATTGG 58.678 41.667 0.00 0.00 0.00 3.16
819 860 6.894339 AACAACCCCTGAAACTAACTATTG 57.106 37.500 0.00 0.00 0.00 1.90
820 861 7.064229 TCAAACAACCCCTGAAACTAACTATT 58.936 34.615 0.00 0.00 0.00 1.73
821 862 6.607019 TCAAACAACCCCTGAAACTAACTAT 58.393 36.000 0.00 0.00 0.00 2.12
822 863 6.003859 TCAAACAACCCCTGAAACTAACTA 57.996 37.500 0.00 0.00 0.00 2.24
823 864 4.862371 TCAAACAACCCCTGAAACTAACT 58.138 39.130 0.00 0.00 0.00 2.24
824 865 4.885325 TCTCAAACAACCCCTGAAACTAAC 59.115 41.667 0.00 0.00 0.00 2.34
825 866 5.118729 TCTCAAACAACCCCTGAAACTAA 57.881 39.130 0.00 0.00 0.00 2.24
826 867 4.781775 TCTCAAACAACCCCTGAAACTA 57.218 40.909 0.00 0.00 0.00 2.24
827 868 3.662759 TCTCAAACAACCCCTGAAACT 57.337 42.857 0.00 0.00 0.00 2.66
828 869 4.937201 ATTCTCAAACAACCCCTGAAAC 57.063 40.909 0.00 0.00 0.00 2.78
829 870 4.959210 TCAATTCTCAAACAACCCCTGAAA 59.041 37.500 0.00 0.00 0.00 2.69
830 871 4.541705 TCAATTCTCAAACAACCCCTGAA 58.458 39.130 0.00 0.00 0.00 3.02
831 872 4.141274 TCTCAATTCTCAAACAACCCCTGA 60.141 41.667 0.00 0.00 0.00 3.86
832 873 4.022849 GTCTCAATTCTCAAACAACCCCTG 60.023 45.833 0.00 0.00 0.00 4.45
833 874 4.145052 GTCTCAATTCTCAAACAACCCCT 58.855 43.478 0.00 0.00 0.00 4.79
834 875 3.058224 CGTCTCAATTCTCAAACAACCCC 60.058 47.826 0.00 0.00 0.00 4.95
835 876 3.564225 ACGTCTCAATTCTCAAACAACCC 59.436 43.478 0.00 0.00 0.00 4.11
836 877 4.511826 AGACGTCTCAATTCTCAAACAACC 59.488 41.667 13.58 0.00 0.00 3.77
837 878 5.333416 GGAGACGTCTCAATTCTCAAACAAC 60.333 44.000 38.52 17.71 44.60 3.32
838 879 4.750098 GGAGACGTCTCAATTCTCAAACAA 59.250 41.667 38.52 0.00 44.60 2.83
839 880 4.307432 GGAGACGTCTCAATTCTCAAACA 58.693 43.478 38.52 0.00 44.60 2.83
840 881 4.912528 GGAGACGTCTCAATTCTCAAAC 57.087 45.455 38.52 18.74 44.60 2.93
856 897 0.741915 CAGGAGAAGTAGCCGGAGAC 59.258 60.000 5.05 0.69 0.00 3.36
857 898 0.331954 ACAGGAGAAGTAGCCGGAGA 59.668 55.000 5.05 0.00 0.00 3.71
858 899 0.741915 GACAGGAGAAGTAGCCGGAG 59.258 60.000 5.05 0.00 0.00 4.63
859 900 0.683504 GGACAGGAGAAGTAGCCGGA 60.684 60.000 5.05 0.00 0.00 5.14
860 901 1.677637 GGGACAGGAGAAGTAGCCGG 61.678 65.000 0.00 0.00 0.00 6.13
861 902 1.817209 GGGACAGGAGAAGTAGCCG 59.183 63.158 0.00 0.00 0.00 5.52
862 903 1.817209 CGGGACAGGAGAAGTAGCC 59.183 63.158 0.00 0.00 0.00 3.93
863 904 1.142097 GCGGGACAGGAGAAGTAGC 59.858 63.158 0.00 0.00 0.00 3.58
864 905 0.895530 TTGCGGGACAGGAGAAGTAG 59.104 55.000 0.00 0.00 0.00 2.57
865 906 0.606604 GTTGCGGGACAGGAGAAGTA 59.393 55.000 0.00 0.00 0.00 2.24
866 907 1.371558 GTTGCGGGACAGGAGAAGT 59.628 57.895 0.00 0.00 0.00 3.01
867 908 0.250295 TTGTTGCGGGACAGGAGAAG 60.250 55.000 0.00 0.00 0.00 2.85
868 909 0.400213 ATTGTTGCGGGACAGGAGAA 59.600 50.000 0.00 0.00 0.00 2.87
869 910 1.271856 TATTGTTGCGGGACAGGAGA 58.728 50.000 0.00 0.00 0.00 3.71
870 911 2.107950 TTATTGTTGCGGGACAGGAG 57.892 50.000 0.00 0.00 0.00 3.69
871 912 2.752354 CAATTATTGTTGCGGGACAGGA 59.248 45.455 0.00 0.00 0.00 3.86
872 913 2.735126 GCAATTATTGTTGCGGGACAGG 60.735 50.000 6.81 0.00 44.20 4.00
873 914 2.529151 GCAATTATTGTTGCGGGACAG 58.471 47.619 6.81 0.00 44.20 3.51
874 915 2.645730 GCAATTATTGTTGCGGGACA 57.354 45.000 6.81 0.00 44.20 4.02
881 922 1.134431 GGGGCAGGGCAATTATTGTTG 60.134 52.381 6.81 4.72 0.00 3.33
882 923 1.203237 GGGGCAGGGCAATTATTGTT 58.797 50.000 6.81 0.00 0.00 2.83
883 924 0.339510 AGGGGCAGGGCAATTATTGT 59.660 50.000 6.81 0.00 0.00 2.71
884 925 1.043022 GAGGGGCAGGGCAATTATTG 58.957 55.000 0.00 0.00 0.00 1.90
885 926 0.468029 CGAGGGGCAGGGCAATTATT 60.468 55.000 0.00 0.00 0.00 1.40
886 927 1.151450 CGAGGGGCAGGGCAATTAT 59.849 57.895 0.00 0.00 0.00 1.28
887 928 2.595095 CGAGGGGCAGGGCAATTA 59.405 61.111 0.00 0.00 0.00 1.40
898 939 4.821589 GAGAAGCGTGGCGAGGGG 62.822 72.222 0.00 0.00 0.00 4.79
925 966 1.512156 GAAGGCGAAAACCCAGCGAA 61.512 55.000 0.00 0.00 0.00 4.70
937 978 2.358267 GGAAGAGATCTAACGAAGGCGA 59.642 50.000 0.00 0.00 41.64 5.54
944 985 2.159366 ACGCACAGGAAGAGATCTAACG 60.159 50.000 0.00 0.00 0.00 3.18
945 986 3.512033 ACGCACAGGAAGAGATCTAAC 57.488 47.619 0.00 0.00 0.00 2.34
957 1003 0.884704 AGGTAGCACAAACGCACAGG 60.885 55.000 0.00 0.00 0.00 4.00
990 1036 1.810853 GGTGGCCATTGCGATTTGC 60.811 57.895 9.72 0.00 46.70 3.68
1050 1096 1.375523 GGACGTGATGGTGGTGGTC 60.376 63.158 0.00 0.00 0.00 4.02
1356 1402 3.998672 GTGTTGGCGACCCCGAGA 61.999 66.667 1.61 0.00 38.22 4.04
1402 1448 3.479203 CCACGGCCTGCCCATCTA 61.479 66.667 0.00 0.00 0.00 1.98
1616 1662 2.582498 GAAGACGGCCGTGGATCG 60.582 66.667 39.65 4.80 39.52 3.69
1656 1702 6.257630 ACGCACTAGTACTTAAGAGCTAGTAC 59.742 42.308 26.84 23.17 44.44 2.73
1657 1703 6.344500 ACGCACTAGTACTTAAGAGCTAGTA 58.656 40.000 26.84 11.84 41.26 1.82
1658 1704 5.184711 ACGCACTAGTACTTAAGAGCTAGT 58.815 41.667 24.30 24.30 43.19 2.57
1659 1705 5.738118 ACGCACTAGTACTTAAGAGCTAG 57.262 43.478 23.45 23.45 37.52 3.42
1660 1706 6.320171 CAAACGCACTAGTACTTAAGAGCTA 58.680 40.000 10.09 9.56 0.00 3.32
1661 1707 5.162075 CAAACGCACTAGTACTTAAGAGCT 58.838 41.667 10.09 8.91 0.00 4.09
1662 1708 4.326548 CCAAACGCACTAGTACTTAAGAGC 59.673 45.833 10.09 2.68 0.00 4.09
1663 1709 5.706916 TCCAAACGCACTAGTACTTAAGAG 58.293 41.667 10.09 0.00 0.00 2.85
1664 1710 5.710513 TCCAAACGCACTAGTACTTAAGA 57.289 39.130 10.09 0.00 0.00 2.10
1665 1711 6.672357 GCAATCCAAACGCACTAGTACTTAAG 60.672 42.308 0.00 0.00 0.00 1.85
1666 1712 5.121142 GCAATCCAAACGCACTAGTACTTAA 59.879 40.000 0.00 0.00 0.00 1.85
1667 1713 4.628333 GCAATCCAAACGCACTAGTACTTA 59.372 41.667 0.00 0.00 0.00 2.24
1668 1714 3.435671 GCAATCCAAACGCACTAGTACTT 59.564 43.478 0.00 0.00 0.00 2.24
1669 1715 3.000727 GCAATCCAAACGCACTAGTACT 58.999 45.455 0.00 0.00 0.00 2.73
1670 1716 3.000727 AGCAATCCAAACGCACTAGTAC 58.999 45.455 0.00 0.00 0.00 2.73
1671 1717 3.328382 AGCAATCCAAACGCACTAGTA 57.672 42.857 0.00 0.00 0.00 1.82
1672 1718 2.185004 AGCAATCCAAACGCACTAGT 57.815 45.000 0.00 0.00 0.00 2.57
1673 1719 4.678509 TTAAGCAATCCAAACGCACTAG 57.321 40.909 0.00 0.00 0.00 2.57
1674 1720 5.637006 AATTAAGCAATCCAAACGCACTA 57.363 34.783 0.00 0.00 0.00 2.74
1675 1721 4.519540 AATTAAGCAATCCAAACGCACT 57.480 36.364 0.00 0.00 0.00 4.40
1676 1722 6.885735 AATAATTAAGCAATCCAAACGCAC 57.114 33.333 0.00 0.00 0.00 5.34
1677 1723 7.067615 TCCTAATAATTAAGCAATCCAAACGCA 59.932 33.333 0.00 0.00 0.00 5.24
1733 1779 5.319453 ACAACTCATCATCACCAATGTCTT 58.681 37.500 0.00 0.00 36.68 3.01
1760 1806 8.951243 GCCATCAACTCTTTATAAGAAAAGTCT 58.049 33.333 0.00 0.00 37.65 3.24
1771 1817 2.961062 GCCATGGCCATCAACTCTTTAT 59.039 45.455 27.24 0.00 34.56 1.40
1785 1831 2.514824 GAAGGGAGTCGCCATGGC 60.515 66.667 27.67 27.67 38.95 4.40
1802 1848 9.817809 TTTGTATCCAAAGTTACTATCTAGCAG 57.182 33.333 0.00 0.00 35.67 4.24
1809 1855 9.174166 GTGGACATTTGTATCCAAAGTTACTAT 57.826 33.333 0.00 0.00 46.53 2.12
1839 1885 3.496884 GTCGAGTCATGGCAAAGTTAACA 59.503 43.478 8.61 0.00 0.00 2.41
1905 1951 8.750298 TGGGGTAATATAATCGAGAAAGAGATC 58.250 37.037 0.00 0.00 0.00 2.75
1920 1966 3.898741 TGCACGAGTGATGGGGTAATATA 59.101 43.478 7.50 0.00 0.00 0.86
1927 1973 0.523072 CTTTTGCACGAGTGATGGGG 59.477 55.000 7.50 0.00 0.00 4.96
2099 2145 2.167398 GAGTGGTGGCGCTGGACTAA 62.167 60.000 7.64 0.00 0.00 2.24
2128 2174 0.106708 TCGGGATCCTTACATGCAGC 59.893 55.000 12.58 0.00 0.00 5.25
2139 2185 1.880027 GGTGCATAAACATCGGGATCC 59.120 52.381 1.92 1.92 0.00 3.36
2146 2192 6.183360 GGTTACAGTACAGGTGCATAAACATC 60.183 42.308 0.00 0.00 0.00 3.06
2151 2197 4.827692 CTGGTTACAGTACAGGTGCATAA 58.172 43.478 0.00 0.00 39.92 1.90
2165 2211 5.561679 TGTGTATTGCCATAACTGGTTACA 58.438 37.500 0.00 0.00 45.10 2.41
2166 2212 5.065988 CCTGTGTATTGCCATAACTGGTTAC 59.934 44.000 0.00 0.00 45.10 2.50
2167 2213 5.045505 TCCTGTGTATTGCCATAACTGGTTA 60.046 40.000 11.69 0.00 45.10 2.85
2168 2214 4.016444 CCTGTGTATTGCCATAACTGGTT 58.984 43.478 0.00 0.00 45.10 3.67
2169 2215 3.265737 TCCTGTGTATTGCCATAACTGGT 59.734 43.478 11.69 0.00 45.10 4.00
2170 2216 3.879295 CTCCTGTGTATTGCCATAACTGG 59.121 47.826 8.40 8.40 46.17 4.00
2171 2217 4.769688 TCTCCTGTGTATTGCCATAACTG 58.230 43.478 0.00 0.00 0.00 3.16
2172 2218 5.636903 ATCTCCTGTGTATTGCCATAACT 57.363 39.130 0.00 0.00 0.00 2.24
2173 2219 5.822519 TGAATCTCCTGTGTATTGCCATAAC 59.177 40.000 0.00 0.00 0.00 1.89
2174 2220 6.000246 TGAATCTCCTGTGTATTGCCATAA 58.000 37.500 0.00 0.00 0.00 1.90
2189 2235 7.415653 GGTTACCAAACTGAATGATGAATCTCC 60.416 40.741 0.00 0.00 35.81 3.71
2199 2245 3.820467 TGCTCTGGTTACCAAACTGAATG 59.180 43.478 5.31 0.00 35.81 2.67
2253 2299 2.663188 GATCGCCATCAGCCGTCC 60.663 66.667 0.00 0.00 38.78 4.79
2254 2300 1.301244 ATGATCGCCATCAGCCGTC 60.301 57.895 0.00 0.00 42.53 4.79
2290 2336 2.584418 CCTGCAGTGAGATCCGCG 60.584 66.667 13.81 0.00 0.00 6.46
2331 2377 2.202623 CGTCCGTAGCCAGAGCAC 60.203 66.667 0.00 0.00 43.56 4.40
2379 2425 0.771127 CAGGTTGGGTGGGAGAGAAA 59.229 55.000 0.00 0.00 0.00 2.52
2380 2426 0.401395 ACAGGTTGGGTGGGAGAGAA 60.401 55.000 0.00 0.00 0.00 2.87
2383 2429 1.385347 ACACAGGTTGGGTGGGAGA 60.385 57.895 0.00 0.00 40.54 3.71
2490 2536 1.654220 AGCGCGTGAATTTTGTGCT 59.346 47.368 8.43 7.50 44.03 4.40
2555 2601 3.379445 GAGGCTTCCCGGACGTGA 61.379 66.667 0.73 0.00 35.76 4.35
2573 2619 2.463589 TTTTGGACATCCGGCGAGCT 62.464 55.000 9.30 0.00 39.43 4.09


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

AutoCloner maintained by Alex Coulton.