Multiple sequence alignment - TraesCS4A01G151300

Loading Multiple Alignment...

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 TraesCS4A01G151300 chr4A 100.000 5119 0 0 1 5119 302722135 302717017 0.000000e+00 9454.0
1 TraesCS4A01G151300 chr4B 94.390 4207 130 39 885 5036 305478066 305482221 0.000000e+00 6364.0
2 TraesCS4A01G151300 chr4B 89.949 587 50 9 1 584 97877770 97877190 0.000000e+00 749.0
3 TraesCS4A01G151300 chr4B 89.267 587 56 7 3 585 97789189 97788606 0.000000e+00 728.0
4 TraesCS4A01G151300 chr4B 100.000 56 0 0 5035 5090 305484817 305484872 2.520000e-18 104.0
5 TraesCS4A01G151300 chr4B 88.571 70 4 3 2167 2234 661199895 661199828 1.180000e-11 82.4
6 TraesCS4A01G151300 chr4D 96.694 2359 48 8 885 3238 202762731 202760398 0.000000e+00 3897.0
7 TraesCS4A01G151300 chr4D 93.392 1029 34 13 3285 4296 202759835 202758824 0.000000e+00 1493.0
8 TraesCS4A01G151300 chr3D 88.534 689 68 10 1 685 379088179 379088860 0.000000e+00 824.0
9 TraesCS4A01G151300 chr3D 89.241 632 59 8 20 647 183589366 183588740 0.000000e+00 782.0
10 TraesCS4A01G151300 chr3D 87.671 73 8 1 2159 2231 474998264 474998193 3.280000e-12 84.2
11 TraesCS4A01G151300 chr5B 89.433 653 54 15 1 647 421455876 421455233 0.000000e+00 809.0
12 TraesCS4A01G151300 chr5B 85.106 705 76 14 1 684 373034875 373035571 0.000000e+00 693.0
13 TraesCS4A01G151300 chr5B 83.262 705 90 20 1 684 411376120 411375423 1.570000e-174 623.0
14 TraesCS4A01G151300 chr7D 88.262 673 46 17 26 684 533429326 533429979 0.000000e+00 774.0
15 TraesCS4A01G151300 chr5A 88.308 650 66 9 1 646 461720577 461719934 0.000000e+00 771.0
16 TraesCS4A01G151300 chr2D 87.037 702 65 17 1 684 89219689 89220382 0.000000e+00 769.0
17 TraesCS4A01G151300 chr2D 86.067 689 71 13 12 684 104872916 104872237 0.000000e+00 717.0
18 TraesCS4A01G151300 chr2D 89.552 67 5 2 2165 2231 495046926 495046990 3.280000e-12 84.2
19 TraesCS4A01G151300 chr7B 86.409 699 74 13 1 684 727667590 727666898 0.000000e+00 745.0
20 TraesCS4A01G151300 chr7B 85.164 701 72 17 1 684 562052432 562053117 0.000000e+00 689.0
21 TraesCS4A01G151300 chr7B 84.113 705 79 21 1 684 138133466 138134158 0.000000e+00 651.0
22 TraesCS4A01G151300 chr6B 84.211 703 78 22 1 684 9796109 9796797 0.000000e+00 652.0
23 TraesCS4A01G151300 chr6B 82.692 104 12 4 2164 2267 49622818 49622721 2.540000e-13 87.9
24 TraesCS4A01G151300 chr6B 89.855 69 6 1 2163 2231 49622748 49622815 2.540000e-13 87.9
25 TraesCS4A01G151300 chr6B 89.552 67 7 0 2165 2231 195461859 195461925 9.130000e-13 86.1
26 TraesCS4A01G151300 chr6B 85.714 77 10 1 2164 2240 49827765 49827690 4.250000e-11 80.5
27 TraesCS4A01G151300 chr2A 87.143 70 7 1 2165 2232 18609651 18609720 1.530000e-10 78.7
28 TraesCS4A01G151300 chr2B 100.000 41 0 0 644 684 537872152 537872192 5.500000e-10 76.8


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 TraesCS4A01G151300 chr4A 302717017 302722135 5118 True 9454 9454 100.000 1 5119 1 chr4A.!!$R1 5118
1 TraesCS4A01G151300 chr4B 305478066 305484872 6806 False 3234 6364 97.195 885 5090 2 chr4B.!!$F1 4205
2 TraesCS4A01G151300 chr4B 97877190 97877770 580 True 749 749 89.949 1 584 1 chr4B.!!$R2 583
3 TraesCS4A01G151300 chr4B 97788606 97789189 583 True 728 728 89.267 3 585 1 chr4B.!!$R1 582
4 TraesCS4A01G151300 chr4D 202758824 202762731 3907 True 2695 3897 95.043 885 4296 2 chr4D.!!$R1 3411
5 TraesCS4A01G151300 chr3D 379088179 379088860 681 False 824 824 88.534 1 685 1 chr3D.!!$F1 684
6 TraesCS4A01G151300 chr3D 183588740 183589366 626 True 782 782 89.241 20 647 1 chr3D.!!$R1 627
7 TraesCS4A01G151300 chr5B 421455233 421455876 643 True 809 809 89.433 1 647 1 chr5B.!!$R2 646
8 TraesCS4A01G151300 chr5B 373034875 373035571 696 False 693 693 85.106 1 684 1 chr5B.!!$F1 683
9 TraesCS4A01G151300 chr5B 411375423 411376120 697 True 623 623 83.262 1 684 1 chr5B.!!$R1 683
10 TraesCS4A01G151300 chr7D 533429326 533429979 653 False 774 774 88.262 26 684 1 chr7D.!!$F1 658
11 TraesCS4A01G151300 chr5A 461719934 461720577 643 True 771 771 88.308 1 646 1 chr5A.!!$R1 645
12 TraesCS4A01G151300 chr2D 89219689 89220382 693 False 769 769 87.037 1 684 1 chr2D.!!$F1 683
13 TraesCS4A01G151300 chr2D 104872237 104872916 679 True 717 717 86.067 12 684 1 chr2D.!!$R1 672
14 TraesCS4A01G151300 chr7B 727666898 727667590 692 True 745 745 86.409 1 684 1 chr7B.!!$R1 683
15 TraesCS4A01G151300 chr7B 562052432 562053117 685 False 689 689 85.164 1 684 1 chr7B.!!$F2 683
16 TraesCS4A01G151300 chr7B 138133466 138134158 692 False 651 651 84.113 1 684 1 chr7B.!!$F1 683
17 TraesCS4A01G151300 chr6B 9796109 9796797 688 False 652 652 84.211 1 684 1 chr6B.!!$F1 683

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
848 896 0.108804 TGCGTCCCTTAGCTTCGAAG 60.109 55.0 21.02 21.02 0.0 3.79 F
2183 2233 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.0 0.00 0.00 0.0 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2754 2805 2.228822 GTGGAATGTTGCGAACTTCCAT 59.771 45.455 17.36 0.0 43.66 3.41 R
4154 4734 0.107508 AGACGATGGCAAGGATGTGG 60.108 55.000 0.00 0.0 0.00 4.17 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
64 69 4.735338 GCTCCTCTTTTTGAAAAGTGTTCG 59.265 41.667 14.03 5.67 44.37 3.95
158 165 9.696917 ACAAAATGTTCATACTTTTTCAGGATC 57.303 29.630 0.00 0.00 38.70 3.36
161 168 7.636150 ATGTTCATACTTTTTCAGGATCTGG 57.364 36.000 0.00 0.00 31.51 3.86
187 194 8.915654 GTCACAAATTCAAAATATGTTCCTGTC 58.084 33.333 0.00 0.00 0.00 3.51
311 323 9.829507 TTTCAATATTTGTCCACAACTTCAAAT 57.170 25.926 0.00 0.00 41.36 2.32
550 580 6.071503 GGTTACTTACCTTGCTCTAGAAGTGA 60.072 42.308 0.00 0.00 44.10 3.41
559 589 2.417933 GCTCTAGAAGTGAACGGTCGTA 59.582 50.000 0.00 0.00 0.00 3.43
614 649 0.440758 TCATTTTTACACCGCTCGCG 59.559 50.000 0.00 0.00 39.44 5.87
695 743 3.001514 TGCTCCTGCAGGAATCCC 58.998 61.111 34.30 22.21 45.31 3.85
696 744 1.617536 TGCTCCTGCAGGAATCCCT 60.618 57.895 34.30 0.00 45.31 4.20
697 745 1.148048 GCTCCTGCAGGAATCCCTC 59.852 63.158 34.30 15.89 44.91 4.30
698 746 1.630126 GCTCCTGCAGGAATCCCTCA 61.630 60.000 34.30 11.53 44.91 3.86
699 747 0.914644 CTCCTGCAGGAATCCCTCAA 59.085 55.000 34.30 10.77 44.91 3.02
700 748 1.283029 CTCCTGCAGGAATCCCTCAAA 59.717 52.381 34.30 10.01 44.91 2.69
701 749 1.710244 TCCTGCAGGAATCCCTCAAAA 59.290 47.619 33.41 5.54 42.02 2.44
702 750 2.109834 TCCTGCAGGAATCCCTCAAAAA 59.890 45.455 33.41 5.30 42.02 1.94
725 773 3.712287 TGCTCCTGCAGGAATCGA 58.288 55.556 34.30 16.43 45.31 3.59
726 774 1.219124 TGCTCCTGCAGGAATCGAC 59.781 57.895 34.30 21.08 45.31 4.20
727 775 1.522580 GCTCCTGCAGGAATCGACC 60.523 63.158 34.30 15.33 44.91 4.79
728 776 1.144936 CTCCTGCAGGAATCGACCC 59.855 63.158 34.30 0.00 44.91 4.46
729 777 2.202932 CCTGCAGGAATCGACCCG 60.203 66.667 29.88 0.00 37.39 5.28
730 778 2.892425 CTGCAGGAATCGACCCGC 60.892 66.667 5.57 12.25 0.00 6.13
731 779 4.467084 TGCAGGAATCGACCCGCC 62.467 66.667 14.75 4.14 0.00 6.13
732 780 4.162690 GCAGGAATCGACCCGCCT 62.163 66.667 0.00 0.00 0.00 5.52
733 781 2.107141 CAGGAATCGACCCGCCTC 59.893 66.667 0.00 0.00 0.00 4.70
734 782 2.363795 AGGAATCGACCCGCCTCA 60.364 61.111 0.00 0.00 0.00 3.86
735 783 1.987855 AGGAATCGACCCGCCTCAA 60.988 57.895 0.00 0.00 0.00 3.02
736 784 1.146263 GGAATCGACCCGCCTCAAT 59.854 57.895 0.00 0.00 0.00 2.57
737 785 1.160329 GGAATCGACCCGCCTCAATG 61.160 60.000 0.00 0.00 0.00 2.82
738 786 1.776034 GAATCGACCCGCCTCAATGC 61.776 60.000 0.00 0.00 0.00 3.56
739 787 2.535485 AATCGACCCGCCTCAATGCA 62.535 55.000 0.00 0.00 0.00 3.96
740 788 2.535485 ATCGACCCGCCTCAATGCAA 62.535 55.000 0.00 0.00 0.00 4.08
741 789 2.331893 CGACCCGCCTCAATGCAAA 61.332 57.895 0.00 0.00 0.00 3.68
742 790 1.861542 CGACCCGCCTCAATGCAAAA 61.862 55.000 0.00 0.00 0.00 2.44
743 791 0.532115 GACCCGCCTCAATGCAAAAT 59.468 50.000 0.00 0.00 0.00 1.82
744 792 1.748493 GACCCGCCTCAATGCAAAATA 59.252 47.619 0.00 0.00 0.00 1.40
745 793 2.362077 GACCCGCCTCAATGCAAAATAT 59.638 45.455 0.00 0.00 0.00 1.28
746 794 2.101249 ACCCGCCTCAATGCAAAATATG 59.899 45.455 0.00 0.00 0.00 1.78
747 795 2.546373 CCCGCCTCAATGCAAAATATGG 60.546 50.000 0.00 0.00 0.00 2.74
748 796 2.101249 CCGCCTCAATGCAAAATATGGT 59.899 45.455 0.00 0.00 0.00 3.55
749 797 3.430651 CCGCCTCAATGCAAAATATGGTT 60.431 43.478 0.00 0.00 0.00 3.67
750 798 4.183101 CGCCTCAATGCAAAATATGGTTT 58.817 39.130 0.00 0.00 0.00 3.27
751 799 5.347342 CGCCTCAATGCAAAATATGGTTTA 58.653 37.500 0.00 0.00 0.00 2.01
752 800 5.809562 CGCCTCAATGCAAAATATGGTTTAA 59.190 36.000 0.00 0.00 0.00 1.52
753 801 6.312426 CGCCTCAATGCAAAATATGGTTTAAA 59.688 34.615 0.00 0.00 0.00 1.52
754 802 7.011295 CGCCTCAATGCAAAATATGGTTTAAAT 59.989 33.333 0.00 0.00 0.00 1.40
755 803 8.676401 GCCTCAATGCAAAATATGGTTTAAATT 58.324 29.630 0.00 0.00 0.00 1.82
779 827 8.654230 TTTGAATCGAAAATGAATCAAAACCA 57.346 26.923 4.90 0.00 42.02 3.67
780 828 8.654230 TTGAATCGAAAATGAATCAAAACCAA 57.346 26.923 0.00 0.00 35.44 3.67
781 829 8.654230 TGAATCGAAAATGAATCAAAACCAAA 57.346 26.923 0.00 0.00 0.00 3.28
782 830 9.102757 TGAATCGAAAATGAATCAAAACCAAAA 57.897 25.926 0.00 0.00 0.00 2.44
783 831 9.584839 GAATCGAAAATGAATCAAAACCAAAAG 57.415 29.630 0.00 0.00 0.00 2.27
784 832 8.885494 ATCGAAAATGAATCAAAACCAAAAGA 57.115 26.923 0.00 0.00 0.00 2.52
785 833 8.709386 TCGAAAATGAATCAAAACCAAAAGAA 57.291 26.923 0.00 0.00 0.00 2.52
786 834 9.155975 TCGAAAATGAATCAAAACCAAAAGAAA 57.844 25.926 0.00 0.00 0.00 2.52
787 835 9.766277 CGAAAATGAATCAAAACCAAAAGAAAA 57.234 25.926 0.00 0.00 0.00 2.29
812 860 7.890879 AAAAACATTTATTTGTTTGCTTCGC 57.109 28.000 3.57 0.00 46.33 4.70
813 861 4.884257 ACATTTATTTGTTTGCTTCGCG 57.116 36.364 0.00 0.00 0.00 5.87
814 862 4.295051 ACATTTATTTGTTTGCTTCGCGT 58.705 34.783 5.77 0.00 0.00 6.01
815 863 4.148000 ACATTTATTTGTTTGCTTCGCGTG 59.852 37.500 5.77 1.17 0.00 5.34
816 864 3.341857 TTATTTGTTTGCTTCGCGTGT 57.658 38.095 5.77 0.00 0.00 4.49
817 865 2.202295 ATTTGTTTGCTTCGCGTGTT 57.798 40.000 5.77 0.00 0.00 3.32
818 866 1.263776 TTTGTTTGCTTCGCGTGTTG 58.736 45.000 5.77 0.00 0.00 3.33
819 867 0.524392 TTGTTTGCTTCGCGTGTTGG 60.524 50.000 5.77 0.00 0.00 3.77
820 868 1.353804 GTTTGCTTCGCGTGTTGGA 59.646 52.632 5.77 0.00 0.00 3.53
821 869 0.928451 GTTTGCTTCGCGTGTTGGAC 60.928 55.000 5.77 0.00 0.00 4.02
822 870 2.054140 TTTGCTTCGCGTGTTGGACC 62.054 55.000 5.77 0.00 0.00 4.46
823 871 4.072088 GCTTCGCGTGTTGGACCG 62.072 66.667 5.77 0.00 0.00 4.79
824 872 2.660552 CTTCGCGTGTTGGACCGT 60.661 61.111 5.77 0.00 0.00 4.83
825 873 2.938823 CTTCGCGTGTTGGACCGTG 61.939 63.158 5.77 0.00 36.00 4.94
826 874 3.719883 TTCGCGTGTTGGACCGTGT 62.720 57.895 5.77 0.00 36.10 4.49
827 875 3.266376 CGCGTGTTGGACCGTGTT 61.266 61.111 0.00 0.00 0.00 3.32
828 876 2.815298 CGCGTGTTGGACCGTGTTT 61.815 57.895 0.00 0.00 0.00 2.83
829 877 1.430228 GCGTGTTGGACCGTGTTTT 59.570 52.632 0.00 0.00 0.00 2.43
830 878 0.863957 GCGTGTTGGACCGTGTTTTG 60.864 55.000 0.00 0.00 0.00 2.44
831 879 0.863957 CGTGTTGGACCGTGTTTTGC 60.864 55.000 0.00 0.00 0.00 3.68
832 880 0.863957 GTGTTGGACCGTGTTTTGCG 60.864 55.000 0.00 0.00 0.00 4.85
833 881 1.306642 TGTTGGACCGTGTTTTGCGT 61.307 50.000 0.00 0.00 0.00 5.24
834 882 0.590481 GTTGGACCGTGTTTTGCGTC 60.590 55.000 0.00 0.00 0.00 5.19
835 883 1.716826 TTGGACCGTGTTTTGCGTCC 61.717 55.000 0.00 0.00 33.46 4.79
836 884 2.635338 GACCGTGTTTTGCGTCCC 59.365 61.111 0.00 0.00 0.00 4.46
837 885 1.890510 GACCGTGTTTTGCGTCCCT 60.891 57.895 0.00 0.00 0.00 4.20
838 886 1.441732 GACCGTGTTTTGCGTCCCTT 61.442 55.000 0.00 0.00 0.00 3.95
839 887 0.179051 ACCGTGTTTTGCGTCCCTTA 60.179 50.000 0.00 0.00 0.00 2.69
840 888 0.515564 CCGTGTTTTGCGTCCCTTAG 59.484 55.000 0.00 0.00 0.00 2.18
841 889 0.110373 CGTGTTTTGCGTCCCTTAGC 60.110 55.000 0.00 0.00 0.00 3.09
842 890 1.235724 GTGTTTTGCGTCCCTTAGCT 58.764 50.000 0.00 0.00 0.00 3.32
843 891 1.607148 GTGTTTTGCGTCCCTTAGCTT 59.393 47.619 0.00 0.00 0.00 3.74
844 892 1.877443 TGTTTTGCGTCCCTTAGCTTC 59.123 47.619 0.00 0.00 0.00 3.86
845 893 1.136057 GTTTTGCGTCCCTTAGCTTCG 60.136 52.381 0.00 0.00 0.00 3.79
846 894 0.319083 TTTGCGTCCCTTAGCTTCGA 59.681 50.000 0.00 0.00 0.00 3.71
847 895 0.319083 TTGCGTCCCTTAGCTTCGAA 59.681 50.000 0.00 0.00 0.00 3.71
848 896 0.108804 TGCGTCCCTTAGCTTCGAAG 60.109 55.000 21.02 21.02 0.00 3.79
849 897 0.172803 GCGTCCCTTAGCTTCGAAGA 59.827 55.000 28.95 5.85 0.00 2.87
850 898 1.403780 GCGTCCCTTAGCTTCGAAGAA 60.404 52.381 28.95 13.68 45.90 2.52
851 899 2.531206 CGTCCCTTAGCTTCGAAGAAG 58.469 52.381 28.95 21.54 45.90 2.85
852 900 2.735762 CGTCCCTTAGCTTCGAAGAAGG 60.736 54.545 27.28 27.28 45.90 3.46
855 903 2.894902 CCTTAGCTTCGAAGAAGGGAC 58.105 52.381 28.95 9.62 45.90 4.46
856 904 2.531206 CTTAGCTTCGAAGAAGGGACG 58.469 52.381 28.95 5.69 45.90 4.79
857 905 0.172803 TAGCTTCGAAGAAGGGACGC 59.827 55.000 28.95 11.38 45.90 5.19
858 906 2.445438 GCTTCGAAGAAGGGACGCG 61.445 63.158 28.95 3.53 45.90 6.01
859 907 1.805945 CTTCGAAGAAGGGACGCGG 60.806 63.158 20.74 0.00 45.90 6.46
860 908 3.927163 TTCGAAGAAGGGACGCGGC 62.927 63.158 12.47 7.53 45.90 6.53
874 922 3.411351 CGGCCGAACCACGACTTG 61.411 66.667 24.07 0.00 45.77 3.16
947 995 2.291282 TGTTGTGGTTGTGGAGGACTTT 60.291 45.455 0.00 0.00 0.00 2.66
1263 1311 2.102553 GCGTCGAGCTAGTGGTCC 59.897 66.667 0.00 0.00 44.04 4.46
1368 1416 2.525629 TCCTCGACAAGGCCACCA 60.526 61.111 5.01 0.00 45.78 4.17
1373 1421 2.113986 GACAAGGCCACCAGCACT 59.886 61.111 5.01 0.00 46.50 4.40
1376 1424 1.970114 CAAGGCCACCAGCACTCTG 60.970 63.158 5.01 0.00 46.50 3.35
1411 1459 0.610232 GCCTCCAACAAGGTGAGCAT 60.610 55.000 0.00 0.00 38.79 3.79
1437 1485 1.444212 CCGATGGCGCCAAAGTTTG 60.444 57.895 36.33 20.57 35.83 2.93
1440 1488 1.418373 GATGGCGCCAAAGTTTGTTC 58.582 50.000 36.33 20.18 0.00 3.18
1776 1825 0.323178 ATCTGAACTGCTGCAAGGGG 60.323 55.000 3.02 0.00 0.00 4.79
2010 2060 6.935167 TGTAGCAGATACTGAATTGAACAGA 58.065 36.000 0.00 0.00 38.55 3.41
2104 2154 7.445402 ACTGTCTTTGCTGTTGACTATATTTGT 59.555 33.333 0.00 0.00 0.00 2.83
2107 2157 9.463443 GTCTTTGCTGTTGACTATATTTGTTTT 57.537 29.630 0.00 0.00 0.00 2.43
2160 2210 3.058224 AGCCTGAGCGTTGAATTTTGTAC 60.058 43.478 0.00 0.00 46.67 2.90
2176 2226 4.972875 ACGGTAGTACTCCCTCCG 57.027 61.111 19.65 19.65 45.53 4.63
2177 2227 4.972875 CGGTAGTACTCCCTCCGT 57.027 61.111 0.00 0.00 36.99 4.69
2178 2228 2.700329 CGGTAGTACTCCCTCCGTC 58.300 63.158 0.00 0.00 36.99 4.79
2179 2229 0.817229 CGGTAGTACTCCCTCCGTCC 60.817 65.000 0.00 0.00 36.99 4.79
2180 2230 0.467106 GGTAGTACTCCCTCCGTCCC 60.467 65.000 0.00 0.00 0.00 4.46
2181 2231 0.257039 GTAGTACTCCCTCCGTCCCA 59.743 60.000 0.00 0.00 0.00 4.37
2182 2232 1.002069 TAGTACTCCCTCCGTCCCAA 58.998 55.000 0.00 0.00 0.00 4.12
2183 2233 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
2184 2234 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
2185 2235 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
2186 2236 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
2187 2237 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
2188 2238 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
2470 2521 5.294306 CACAGACTTGTTACATGTGTGAACT 59.706 40.000 26.63 9.07 36.68 3.01
2522 2573 5.895534 AGCCATTTTCATGATGTTACAGGAT 59.104 36.000 0.00 0.00 30.94 3.24
2619 2670 5.612725 AACATGGTTTGGTTCAGTTGAAT 57.387 34.783 0.00 0.00 36.33 2.57
2858 2909 3.926058 AATATACGGCCACACCTTCTT 57.074 42.857 2.24 0.00 35.61 2.52
2939 2990 5.344933 TGTCTCGAATCGTGTGAATAAGTTG 59.655 40.000 1.52 0.00 0.00 3.16
2945 2996 3.734463 TCGTGTGAATAAGTTGCAGGAA 58.266 40.909 0.00 0.00 0.00 3.36
2995 3046 2.093783 GTCTTTTCGTGTTATCTGGCGG 59.906 50.000 0.00 0.00 0.00 6.13
3086 3137 7.281999 GCTTTATTCTAGACTTGAGCAGGATTT 59.718 37.037 10.75 0.00 0.00 2.17
3183 3237 3.932710 CGTAGGCAGTTTATGTGTGATGT 59.067 43.478 0.00 0.00 0.00 3.06
3205 3259 3.153919 GGGGCACACATTCTTTCTGTTA 58.846 45.455 0.00 0.00 0.00 2.41
3266 3655 6.036953 TGCTACTTTTCCATGTTTTTGCTTTG 59.963 34.615 0.00 0.00 0.00 2.77
3347 3917 4.398988 TGTCTGCCCAATATTGTGCTAAAG 59.601 41.667 21.17 12.03 32.56 1.85
3383 3953 8.814038 AAGAGTTGCTTCACTTATTATTCCAT 57.186 30.769 0.00 0.00 28.17 3.41
3409 3979 9.979578 TGTGATGTAAAATCATTAGCTTTTGTT 57.020 25.926 0.00 0.00 0.00 2.83
3477 4047 5.080337 TCCTATATCACACATCTCCTGTCC 58.920 45.833 0.00 0.00 35.29 4.02
3637 4207 2.362397 ACAGAGAAACACGAGCTTCTGA 59.638 45.455 13.34 0.00 30.63 3.27
3790 4360 4.142271 TGTCAACAGGTGCTTTTAAACCAG 60.142 41.667 0.00 0.00 39.05 4.00
3801 4371 7.492994 GGTGCTTTTAAACCAGTTTTTATGACA 59.507 33.333 0.37 0.00 36.41 3.58
3865 4435 1.404035 GGCGGCGAAAATAACCATCTT 59.596 47.619 12.98 0.00 0.00 2.40
3868 4438 3.311596 GCGGCGAAAATAACCATCTTAGT 59.688 43.478 12.98 0.00 0.00 2.24
4007 4582 9.698309 TTGTTCTGTTTTTGTTTTCTATTGTCA 57.302 25.926 0.00 0.00 0.00 3.58
4064 4641 8.094548 ACTGATATATAATTTGCTTGCTACCGA 58.905 33.333 0.00 0.00 0.00 4.69
4127 4707 5.050634 TCGTGAGTTGAGTCGTAATTTTTGG 60.051 40.000 0.00 0.00 0.00 3.28
4128 4708 5.277154 CGTGAGTTGAGTCGTAATTTTTGGT 60.277 40.000 0.00 0.00 0.00 3.67
4130 4710 6.413818 GTGAGTTGAGTCGTAATTTTTGGTTG 59.586 38.462 0.00 0.00 0.00 3.77
4134 4714 8.626526 AGTTGAGTCGTAATTTTTGGTTGTATT 58.373 29.630 0.00 0.00 0.00 1.89
4152 4732 8.797438 GGTTGTATTTTTCTTCTGGAAAGAGAT 58.203 33.333 0.00 0.00 43.68 2.75
4153 4733 9.617975 GTTGTATTTTTCTTCTGGAAAGAGATG 57.382 33.333 0.00 0.00 43.68 2.90
4154 4734 7.820648 TGTATTTTTCTTCTGGAAAGAGATGC 58.179 34.615 0.00 0.00 43.68 3.91
4155 4735 5.712152 TTTTTCTTCTGGAAAGAGATGCC 57.288 39.130 0.00 0.00 43.68 4.40
4156 4736 4.371624 TTTCTTCTGGAAAGAGATGCCA 57.628 40.909 0.00 0.00 38.81 4.92
4157 4737 3.340814 TCTTCTGGAAAGAGATGCCAC 57.659 47.619 0.00 0.00 0.00 5.01
4158 4738 2.639347 TCTTCTGGAAAGAGATGCCACA 59.361 45.455 0.00 0.00 0.00 4.17
4159 4739 3.265221 TCTTCTGGAAAGAGATGCCACAT 59.735 43.478 0.00 0.00 0.00 3.21
4160 4740 3.272574 TCTGGAAAGAGATGCCACATC 57.727 47.619 0.00 0.00 0.00 3.06
4161 4741 2.092753 TCTGGAAAGAGATGCCACATCC 60.093 50.000 4.00 0.00 0.00 3.51
4162 4742 1.918262 TGGAAAGAGATGCCACATCCT 59.082 47.619 4.00 0.00 0.00 3.24
4193 4773 1.376086 CTGTGATGGTCACCTGCCA 59.624 57.895 7.55 0.00 46.40 4.92
4194 4774 0.957395 CTGTGATGGTCACCTGCCAC 60.957 60.000 7.55 1.02 46.40 5.01
4261 4845 0.394565 GTGAGCTGGTTCTGTGGACT 59.605 55.000 0.00 0.00 0.00 3.85
4292 4876 1.497991 TGTAAGCGTGTGTTCTCTGC 58.502 50.000 0.00 0.00 0.00 4.26
4304 4888 2.158900 TGTTCTCTGCCCTGCTATAAGC 60.159 50.000 0.00 0.00 42.82 3.09
4352 4936 6.653320 AGCACGTAAAAGGTGAATTCTGAATA 59.347 34.615 7.05 0.00 36.17 1.75
4353 4937 7.336931 AGCACGTAAAAGGTGAATTCTGAATAT 59.663 33.333 7.05 0.00 36.17 1.28
4363 4947 7.233348 AGGTGAATTCTGAATATCTCTCTCTCC 59.767 40.741 7.05 6.23 0.00 3.71
4365 4949 6.496565 TGAATTCTGAATATCTCTCTCTCCCC 59.503 42.308 7.05 0.00 0.00 4.81
4366 4950 5.409590 TTCTGAATATCTCTCTCTCCCCA 57.590 43.478 0.00 0.00 0.00 4.96
4368 4952 4.418526 TCTGAATATCTCTCTCTCCCCACT 59.581 45.833 0.00 0.00 0.00 4.00
4395 4996 1.262950 TGAAGTGGAAAACGACGCATG 59.737 47.619 0.00 0.00 0.00 4.06
4410 5011 0.039798 GCATGCAACACTGGTGTGAG 60.040 55.000 14.21 4.93 46.55 3.51
4418 5019 2.670934 CTGGTGTGAGGGCTGTGC 60.671 66.667 0.00 0.00 0.00 4.57
4465 5066 3.056250 CCTATATGAGCAAGGCGATGAGT 60.056 47.826 0.00 0.00 0.00 3.41
4489 5090 5.127682 TGTCATGAACTGCAAGCTCTCTATA 59.872 40.000 0.00 0.00 37.60 1.31
4492 5093 7.328249 GTCATGAACTGCAAGCTCTCTATATAC 59.672 40.741 0.00 0.00 37.60 1.47
4493 5094 6.715347 TGAACTGCAAGCTCTCTATATACA 57.285 37.500 0.00 0.00 37.60 2.29
4494 5095 6.743110 TGAACTGCAAGCTCTCTATATACAG 58.257 40.000 0.00 0.00 37.60 2.74
4504 5105 8.404107 AGCTCTCTATATACAGAAAGGAGTTC 57.596 38.462 0.00 0.00 36.38 3.01
4508 5109 9.083422 TCTCTATATACAGAAAGGAGTTCATGG 57.917 37.037 0.00 0.00 38.86 3.66
4511 5112 3.228188 ACAGAAAGGAGTTCATGGCAA 57.772 42.857 0.00 0.00 38.86 4.52
4580 5181 5.446473 GCTTTCACTATTTGGACTGATCACG 60.446 44.000 0.00 0.00 0.00 4.35
4584 5185 4.564372 CACTATTTGGACTGATCACGAGTG 59.436 45.833 0.00 0.00 0.00 3.51
4608 5209 1.935199 GCTCTCTTTCTGATCAGCAGC 59.065 52.381 18.36 12.82 44.52 5.25
4616 5217 0.671472 CTGATCAGCAGCCGACAACA 60.671 55.000 10.38 0.00 37.90 3.33
4630 5231 1.190763 GACAACAAATTTGCAGCGCAG 59.809 47.619 18.12 1.31 40.61 5.18
4633 5234 0.953727 ACAAATTTGCAGCGCAGAGA 59.046 45.000 18.12 0.00 40.61 3.10
4634 5235 1.337703 ACAAATTTGCAGCGCAGAGAA 59.662 42.857 18.12 0.00 40.61 2.87
4635 5236 1.717645 CAAATTTGCAGCGCAGAGAAC 59.282 47.619 11.47 0.00 40.61 3.01
4636 5237 0.953727 AATTTGCAGCGCAGAGAACA 59.046 45.000 11.47 0.00 40.61 3.18
4637 5238 0.239347 ATTTGCAGCGCAGAGAACAC 59.761 50.000 11.47 0.00 40.61 3.32
4638 5239 1.094650 TTTGCAGCGCAGAGAACACA 61.095 50.000 11.47 0.00 40.61 3.72
4639 5240 1.094650 TTGCAGCGCAGAGAACACAA 61.095 50.000 11.47 0.00 40.61 3.33
4640 5241 1.082496 GCAGCGCAGAGAACACAAC 60.082 57.895 11.47 0.00 0.00 3.32
4652 5263 5.621228 CAGAGAACACAACGCTTACAATTTC 59.379 40.000 0.00 0.00 0.00 2.17
4754 5365 2.165167 CAGGCCATGTCTGTTTGTCAT 58.835 47.619 5.01 0.00 29.72 3.06
4841 5452 4.205065 TCAACAATTGGCCATTCATTCC 57.795 40.909 6.09 0.00 0.00 3.01
4842 5453 3.055240 TCAACAATTGGCCATTCATTCCC 60.055 43.478 6.09 0.00 0.00 3.97
4843 5454 2.836667 ACAATTGGCCATTCATTCCCT 58.163 42.857 6.09 0.00 0.00 4.20
4844 5455 3.183801 ACAATTGGCCATTCATTCCCTT 58.816 40.909 6.09 0.00 0.00 3.95
4845 5456 3.054948 ACAATTGGCCATTCATTCCCTTG 60.055 43.478 6.09 0.00 0.00 3.61
4846 5457 2.619697 TTGGCCATTCATTCCCTTGA 57.380 45.000 6.09 0.00 0.00 3.02
4847 5458 1.851304 TGGCCATTCATTCCCTTGAC 58.149 50.000 0.00 0.00 0.00 3.18
4848 5459 1.076841 TGGCCATTCATTCCCTTGACA 59.923 47.619 0.00 0.00 0.00 3.58
4849 5460 1.753073 GGCCATTCATTCCCTTGACAG 59.247 52.381 0.00 0.00 0.00 3.51
4850 5461 2.621407 GGCCATTCATTCCCTTGACAGA 60.621 50.000 0.00 0.00 0.00 3.41
4851 5462 2.686915 GCCATTCATTCCCTTGACAGAG 59.313 50.000 0.00 0.00 0.00 3.35
4852 5463 3.285484 CCATTCATTCCCTTGACAGAGG 58.715 50.000 0.00 0.00 36.52 3.69
4871 5482 4.010349 GAGGGTTACTCTTTGGAACATGG 58.990 47.826 0.00 0.00 43.14 3.66
4872 5483 3.655777 AGGGTTACTCTTTGGAACATGGA 59.344 43.478 0.00 0.00 39.30 3.41
4935 5546 6.705863 TTGGCTTTGCAAACCAAATTAATT 57.294 29.167 28.58 0.00 42.22 1.40
4949 5560 0.388391 TTAATTGCTGCCTTGCACGC 60.388 50.000 0.00 0.00 43.20 5.34
4950 5561 1.522302 TAATTGCTGCCTTGCACGCA 61.522 50.000 7.40 7.40 43.20 5.24
4951 5562 2.162338 AATTGCTGCCTTGCACGCAT 62.162 50.000 8.04 0.00 43.20 4.73
4952 5563 2.162338 ATTGCTGCCTTGCACGCATT 62.162 50.000 8.04 7.58 43.20 3.56
4954 5565 2.986306 GCTGCCTTGCACGCATTCT 61.986 57.895 8.04 0.00 35.25 2.40
4955 5566 1.154093 CTGCCTTGCACGCATTCTG 60.154 57.895 8.04 0.00 35.25 3.02
4956 5567 2.180017 GCCTTGCACGCATTCTGG 59.820 61.111 0.00 0.00 0.00 3.86
4958 5569 1.865788 GCCTTGCACGCATTCTGGAA 61.866 55.000 0.00 0.00 0.00 3.53
4976 5601 4.030913 TGGAATCACTCCTACTTACCAGG 58.969 47.826 0.00 0.00 45.64 4.45
4991 5616 1.215423 ACCAGGGAGCAAAGAAGTTGT 59.785 47.619 0.00 0.00 39.63 3.32
4996 5621 4.691216 CAGGGAGCAAAGAAGTTGTACTAC 59.309 45.833 0.00 0.00 39.63 2.73
5002 5627 4.385825 CAAAGAAGTTGTACTACTGGCCA 58.614 43.478 10.78 4.71 32.08 5.36
5016 5641 1.200760 TGGCCAGGCTTGAAGCTAGA 61.201 55.000 17.59 0.00 41.99 2.43
5018 5643 1.417890 GGCCAGGCTTGAAGCTAGATA 59.582 52.381 17.59 0.00 41.99 1.98
5090 8311 4.652822 ACCAATCTGAAACCAGTTAGTCC 58.347 43.478 0.00 0.00 33.49 3.85
5091 8312 4.104102 ACCAATCTGAAACCAGTTAGTCCA 59.896 41.667 0.00 0.00 33.49 4.02
5092 8313 5.222130 ACCAATCTGAAACCAGTTAGTCCAT 60.222 40.000 0.00 0.00 33.49 3.41
5093 8314 5.711976 CCAATCTGAAACCAGTTAGTCCATT 59.288 40.000 0.00 0.00 33.49 3.16
5094 8315 6.349611 CCAATCTGAAACCAGTTAGTCCATTG 60.350 42.308 0.00 0.00 33.49 2.82
5095 8316 4.072131 TCTGAAACCAGTTAGTCCATTGC 58.928 43.478 0.00 0.00 33.49 3.56
5096 8317 3.820467 CTGAAACCAGTTAGTCCATTGCA 59.180 43.478 0.00 0.00 0.00 4.08
5097 8318 4.211125 TGAAACCAGTTAGTCCATTGCAA 58.789 39.130 0.00 0.00 0.00 4.08
5098 8319 4.037446 TGAAACCAGTTAGTCCATTGCAAC 59.963 41.667 0.00 0.00 0.00 4.17
5099 8320 2.514803 ACCAGTTAGTCCATTGCAACC 58.485 47.619 0.00 0.00 0.00 3.77
5100 8321 2.158534 ACCAGTTAGTCCATTGCAACCA 60.159 45.455 0.00 0.00 0.00 3.67
5101 8322 2.228822 CCAGTTAGTCCATTGCAACCAC 59.771 50.000 0.00 0.00 0.00 4.16
5102 8323 3.149196 CAGTTAGTCCATTGCAACCACT 58.851 45.455 0.00 6.64 0.00 4.00
5103 8324 3.058016 CAGTTAGTCCATTGCAACCACTG 60.058 47.826 0.00 1.65 0.00 3.66
5111 8332 2.985847 GCAACCACTGCCACCTCC 60.986 66.667 0.00 0.00 46.13 4.30
5112 8333 2.839098 CAACCACTGCCACCTCCT 59.161 61.111 0.00 0.00 0.00 3.69
5113 8334 1.151450 CAACCACTGCCACCTCCTT 59.849 57.895 0.00 0.00 0.00 3.36
5114 8335 0.400213 CAACCACTGCCACCTCCTTA 59.600 55.000 0.00 0.00 0.00 2.69
5115 8336 1.145571 AACCACTGCCACCTCCTTAA 58.854 50.000 0.00 0.00 0.00 1.85
5116 8337 0.693049 ACCACTGCCACCTCCTTAAG 59.307 55.000 0.00 0.00 0.00 1.85
5117 8338 0.678048 CCACTGCCACCTCCTTAAGC 60.678 60.000 0.00 0.00 0.00 3.09
5118 8339 0.326264 CACTGCCACCTCCTTAAGCT 59.674 55.000 0.00 0.00 0.00 3.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 7.990541 TTTGTGAACAAATTCTGAGAACATG 57.009 32.000 0.00 2.19 40.55 3.21
97 103 9.985318 GAACAAAAATTCACAATCATGAACAAA 57.015 25.926 0.00 0.00 41.29 2.83
146 152 5.772825 TTTGTGACCAGATCCTGAAAAAG 57.227 39.130 0.00 0.00 32.44 2.27
158 165 8.090214 AGGAACATATTTTGAATTTGTGACCAG 58.910 33.333 15.32 0.00 0.00 4.00
161 168 8.816640 ACAGGAACATATTTTGAATTTGTGAC 57.183 30.769 0.00 0.00 0.00 3.67
356 375 7.637132 ACGAACACACACGAGTTTTAAATTTAG 59.363 33.333 0.00 0.00 0.00 1.85
559 589 5.979288 AGCTTCAGCAAAGAATCAATCTT 57.021 34.783 0.75 0.00 43.93 2.40
570 600 5.663456 AGAAAAACATGAAGCTTCAGCAAA 58.337 33.333 31.14 10.46 45.16 3.68
616 651 3.222855 CTTGGCGGCCCACACAAA 61.223 61.111 17.97 1.44 41.97 2.83
617 652 4.514585 ACTTGGCGGCCCACACAA 62.515 61.111 17.97 2.24 41.97 3.33
709 757 1.522580 GGTCGATTCCTGCAGGAGC 60.523 63.158 33.16 26.65 46.36 4.70
710 758 1.144936 GGGTCGATTCCTGCAGGAG 59.855 63.158 33.16 22.84 46.36 3.69
711 759 2.721167 CGGGTCGATTCCTGCAGGA 61.721 63.158 32.00 32.00 43.73 3.86
712 760 2.202932 CGGGTCGATTCCTGCAGG 60.203 66.667 27.87 27.87 0.00 4.85
716 764 2.107141 GAGGCGGGTCGATTCCTG 59.893 66.667 6.27 1.81 36.96 3.86
717 765 1.338136 ATTGAGGCGGGTCGATTCCT 61.338 55.000 6.27 2.52 0.00 3.36
718 766 1.146263 ATTGAGGCGGGTCGATTCC 59.854 57.895 0.00 0.00 0.00 3.01
719 767 1.776034 GCATTGAGGCGGGTCGATTC 61.776 60.000 0.00 0.00 0.00 2.52
720 768 1.819632 GCATTGAGGCGGGTCGATT 60.820 57.895 0.00 0.00 0.00 3.34
721 769 2.203070 GCATTGAGGCGGGTCGAT 60.203 61.111 0.00 0.00 0.00 3.59
722 770 2.739849 TTTGCATTGAGGCGGGTCGA 62.740 55.000 0.00 0.00 36.28 4.20
723 771 1.861542 TTTTGCATTGAGGCGGGTCG 61.862 55.000 0.00 0.00 36.28 4.79
724 772 0.532115 ATTTTGCATTGAGGCGGGTC 59.468 50.000 0.00 0.00 36.28 4.46
725 773 1.846007 TATTTTGCATTGAGGCGGGT 58.154 45.000 0.00 0.00 36.28 5.28
726 774 2.546373 CCATATTTTGCATTGAGGCGGG 60.546 50.000 0.00 0.00 36.28 6.13
727 775 2.101249 ACCATATTTTGCATTGAGGCGG 59.899 45.455 0.00 0.00 36.28 6.13
728 776 3.441496 ACCATATTTTGCATTGAGGCG 57.559 42.857 0.00 0.00 36.28 5.52
729 777 7.608308 TTTAAACCATATTTTGCATTGAGGC 57.392 32.000 0.00 0.00 0.00 4.70
753 801 9.270640 TGGTTTTGATTCATTTTCGATTCAAAT 57.729 25.926 10.18 0.00 41.35 2.32
754 802 8.654230 TGGTTTTGATTCATTTTCGATTCAAA 57.346 26.923 6.81 6.81 40.66 2.69
755 803 8.654230 TTGGTTTTGATTCATTTTCGATTCAA 57.346 26.923 0.00 0.00 34.90 2.69
756 804 8.654230 TTTGGTTTTGATTCATTTTCGATTCA 57.346 26.923 0.00 0.00 0.00 2.57
757 805 9.584839 CTTTTGGTTTTGATTCATTTTCGATTC 57.415 29.630 0.00 0.00 0.00 2.52
758 806 9.323985 TCTTTTGGTTTTGATTCATTTTCGATT 57.676 25.926 0.00 0.00 0.00 3.34
759 807 8.885494 TCTTTTGGTTTTGATTCATTTTCGAT 57.115 26.923 0.00 0.00 0.00 3.59
760 808 8.709386 TTCTTTTGGTTTTGATTCATTTTCGA 57.291 26.923 0.00 0.00 0.00 3.71
761 809 9.766277 TTTTCTTTTGGTTTTGATTCATTTTCG 57.234 25.926 0.00 0.00 0.00 3.46
807 855 2.660552 ACGGTCCAACACGCGAAG 60.661 61.111 15.93 7.57 0.00 3.79
808 856 2.962786 CACGGTCCAACACGCGAA 60.963 61.111 15.93 0.00 0.00 4.70
809 857 3.719883 AACACGGTCCAACACGCGA 62.720 57.895 15.93 0.00 0.00 5.87
810 858 2.312398 AAAACACGGTCCAACACGCG 62.312 55.000 3.53 3.53 0.00 6.01
811 859 0.863957 CAAAACACGGTCCAACACGC 60.864 55.000 0.00 0.00 0.00 5.34
812 860 0.863957 GCAAAACACGGTCCAACACG 60.864 55.000 0.00 0.00 0.00 4.49
813 861 0.863957 CGCAAAACACGGTCCAACAC 60.864 55.000 0.00 0.00 0.00 3.32
814 862 1.306642 ACGCAAAACACGGTCCAACA 61.307 50.000 0.00 0.00 34.00 3.33
815 863 0.590481 GACGCAAAACACGGTCCAAC 60.590 55.000 0.00 0.00 34.00 3.77
816 864 1.716826 GGACGCAAAACACGGTCCAA 61.717 55.000 4.29 0.00 33.65 3.53
817 865 2.181521 GGACGCAAAACACGGTCCA 61.182 57.895 4.29 0.00 33.65 4.02
818 866 2.635338 GGACGCAAAACACGGTCC 59.365 61.111 0.00 0.00 34.00 4.46
819 867 1.441732 AAGGGACGCAAAACACGGTC 61.442 55.000 0.00 0.00 34.00 4.79
820 868 0.179051 TAAGGGACGCAAAACACGGT 60.179 50.000 0.00 0.00 34.00 4.83
821 869 0.515564 CTAAGGGACGCAAAACACGG 59.484 55.000 0.00 0.00 34.00 4.94
822 870 0.110373 GCTAAGGGACGCAAAACACG 60.110 55.000 0.00 0.00 0.00 4.49
823 871 1.235724 AGCTAAGGGACGCAAAACAC 58.764 50.000 0.00 0.00 0.00 3.32
824 872 1.877443 GAAGCTAAGGGACGCAAAACA 59.123 47.619 0.00 0.00 0.00 2.83
825 873 1.136057 CGAAGCTAAGGGACGCAAAAC 60.136 52.381 0.00 0.00 0.00 2.43
826 874 1.153353 CGAAGCTAAGGGACGCAAAA 58.847 50.000 0.00 0.00 0.00 2.44
827 875 0.319083 TCGAAGCTAAGGGACGCAAA 59.681 50.000 0.00 0.00 0.00 3.68
828 876 0.319083 TTCGAAGCTAAGGGACGCAA 59.681 50.000 0.00 0.00 0.00 4.85
829 877 0.108804 CTTCGAAGCTAAGGGACGCA 60.109 55.000 13.09 0.00 0.00 5.24
830 878 0.172803 TCTTCGAAGCTAAGGGACGC 59.827 55.000 20.56 0.00 0.00 5.19
831 879 2.531206 CTTCTTCGAAGCTAAGGGACG 58.469 52.381 20.56 0.00 0.00 4.79
832 880 2.894902 CCTTCTTCGAAGCTAAGGGAC 58.105 52.381 26.84 0.00 35.80 4.46
835 883 2.735762 CGTCCCTTCTTCGAAGCTAAGG 60.736 54.545 27.28 27.28 38.58 2.69
836 884 2.531206 CGTCCCTTCTTCGAAGCTAAG 58.469 52.381 20.56 17.94 0.00 2.18
837 885 1.403780 GCGTCCCTTCTTCGAAGCTAA 60.404 52.381 20.56 9.53 31.77 3.09
838 886 0.172803 GCGTCCCTTCTTCGAAGCTA 59.827 55.000 20.56 9.67 31.77 3.32
839 887 1.079750 GCGTCCCTTCTTCGAAGCT 60.080 57.895 20.56 0.00 31.77 3.74
840 888 2.445438 CGCGTCCCTTCTTCGAAGC 61.445 63.158 20.56 6.00 0.00 3.86
841 889 1.805945 CCGCGTCCCTTCTTCGAAG 60.806 63.158 19.35 19.35 0.00 3.79
842 890 2.260434 CCGCGTCCCTTCTTCGAA 59.740 61.111 4.92 0.00 0.00 3.71
843 891 4.430765 GCCGCGTCCCTTCTTCGA 62.431 66.667 4.92 0.00 0.00 3.71
857 905 3.411351 CAAGTCGTGGTTCGGCCG 61.411 66.667 22.12 22.12 46.16 6.13
858 906 3.047877 CCAAGTCGTGGTTCGGCC 61.048 66.667 0.00 0.00 46.16 6.13
866 914 3.070446 TGGGTATATTAGGCCAAGTCGTG 59.930 47.826 5.01 0.00 0.00 4.35
867 915 3.311091 TGGGTATATTAGGCCAAGTCGT 58.689 45.455 5.01 0.00 0.00 4.34
868 916 3.306780 CCTGGGTATATTAGGCCAAGTCG 60.307 52.174 5.01 0.00 0.00 4.18
869 917 3.651423 ACCTGGGTATATTAGGCCAAGTC 59.349 47.826 5.01 0.00 34.93 3.01
870 918 3.676750 ACCTGGGTATATTAGGCCAAGT 58.323 45.455 5.01 0.00 34.93 3.16
871 919 4.844655 AGTACCTGGGTATATTAGGCCAAG 59.155 45.833 5.01 0.00 34.93 3.61
872 920 4.595781 CAGTACCTGGGTATATTAGGCCAA 59.404 45.833 5.01 0.00 34.93 4.52
873 921 4.164981 CAGTACCTGGGTATATTAGGCCA 58.835 47.826 5.01 0.00 34.93 5.36
874 922 4.820894 CAGTACCTGGGTATATTAGGCC 57.179 50.000 0.00 0.00 34.93 5.19
875 923 5.487845 AATCCAGTACCTGGGTATATTAGGC 59.512 44.000 10.26 0.00 45.38 3.93
876 924 6.729100 TCAATCCAGTACCTGGGTATATTAGG 59.271 42.308 10.26 0.00 45.38 2.69
877 925 7.674348 TCTCAATCCAGTACCTGGGTATATTAG 59.326 40.741 10.26 0.00 45.38 1.73
878 926 7.541074 TCTCAATCCAGTACCTGGGTATATTA 58.459 38.462 10.26 0.00 45.38 0.98
879 927 6.390504 TCTCAATCCAGTACCTGGGTATATT 58.609 40.000 10.26 0.56 45.38 1.28
880 928 5.977533 TCTCAATCCAGTACCTGGGTATAT 58.022 41.667 10.26 0.00 45.38 0.86
881 929 5.412617 TCTCAATCCAGTACCTGGGTATA 57.587 43.478 10.26 0.00 45.38 1.47
882 930 4.280789 TCTCAATCCAGTACCTGGGTAT 57.719 45.455 10.26 0.00 45.38 2.73
883 931 3.769189 TCTCAATCCAGTACCTGGGTA 57.231 47.619 10.26 0.00 45.38 3.69
907 955 6.362016 CACAACATTGCGTTTCATTTAAGCTA 59.638 34.615 0.00 0.00 34.86 3.32
947 995 2.487762 GGAAGAATGGATGTTTGCACGA 59.512 45.455 0.00 0.00 0.00 4.35
1068 1116 2.355615 GCCTCTTCTTCTTCTTGGAGGG 60.356 54.545 0.00 0.00 40.24 4.30
1368 1416 1.280421 GGGGACAATCTTCAGAGTGCT 59.720 52.381 4.19 0.00 43.21 4.40
1437 1485 5.758924 AGAATTGCTTAAACAAGACCGAAC 58.241 37.500 0.00 0.00 31.96 3.95
1440 1488 6.236017 TGTAGAATTGCTTAAACAAGACCG 57.764 37.500 0.00 0.00 31.96 4.79
2010 2060 4.141390 CCATAAGCCTGGGTAAGATCTTGT 60.141 45.833 18.47 0.00 32.28 3.16
2115 2165 9.748708 GGCTCACAGCATGAAATAAAATAATAA 57.251 29.630 0.00 0.00 44.75 1.40
2116 2166 9.135189 AGGCTCACAGCATGAAATAAAATAATA 57.865 29.630 0.00 0.00 44.75 0.98
2175 2225 2.785562 TGGGACACTTATTTTGGGACG 58.214 47.619 0.00 0.00 0.00 4.79
2176 2226 5.538849 TTTTGGGACACTTATTTTGGGAC 57.461 39.130 0.00 0.00 39.29 4.46
2177 2227 7.511028 ACTTATTTTGGGACACTTATTTTGGGA 59.489 33.333 0.00 0.00 39.29 4.37
2178 2228 7.602265 CACTTATTTTGGGACACTTATTTTGGG 59.398 37.037 0.00 0.00 39.29 4.12
2179 2229 8.147704 ACACTTATTTTGGGACACTTATTTTGG 58.852 33.333 0.00 0.00 39.29 3.28
2180 2230 9.191995 GACACTTATTTTGGGACACTTATTTTG 57.808 33.333 0.00 0.00 39.29 2.44
2181 2231 8.919145 TGACACTTATTTTGGGACACTTATTTT 58.081 29.630 0.00 0.00 39.29 1.82
2182 2232 8.357402 GTGACACTTATTTTGGGACACTTATTT 58.643 33.333 0.00 0.00 39.29 1.40
2183 2233 7.724061 AGTGACACTTATTTTGGGACACTTATT 59.276 33.333 1.07 0.00 39.29 1.40
2184 2234 7.231467 AGTGACACTTATTTTGGGACACTTAT 58.769 34.615 1.07 0.00 39.29 1.73
2185 2235 6.597562 AGTGACACTTATTTTGGGACACTTA 58.402 36.000 1.07 0.00 39.29 2.24
2186 2236 5.445964 AGTGACACTTATTTTGGGACACTT 58.554 37.500 1.07 0.00 39.29 3.16
2187 2237 5.048846 AGTGACACTTATTTTGGGACACT 57.951 39.130 1.07 0.00 39.29 3.55
2188 2238 5.767816 AAGTGACACTTATTTTGGGACAC 57.232 39.130 19.28 0.00 35.22 3.67
2282 2332 9.455847 GACAGTTCATGCTAAATATTTTCCATC 57.544 33.333 5.91 0.00 0.00 3.51
2496 2547 4.746729 TGTAACATCATGAAAATGGCTGC 58.253 39.130 0.00 0.00 0.00 5.25
2522 2573 8.103935 GGGAGAAGAGGAGAAGAAGAAAAATAA 58.896 37.037 0.00 0.00 0.00 1.40
2754 2805 2.228822 GTGGAATGTTGCGAACTTCCAT 59.771 45.455 17.36 0.00 43.66 3.41
2858 2909 5.353956 CGATTCAAAGTGTCCCACAATATCA 59.646 40.000 0.00 0.00 36.74 2.15
2939 2990 5.488341 TCACTATTTACCTGAAGTTCCTGC 58.512 41.667 0.00 0.00 0.00 4.85
2945 2996 8.164070 AGAAAACCATCACTATTTACCTGAAGT 58.836 33.333 0.00 0.00 0.00 3.01
2995 3046 4.688413 TGAAACAAAACAAGGTCTTGCAAC 59.312 37.500 10.31 0.00 44.03 4.17
3004 3055 5.355596 TGCTGGTATTGAAACAAAACAAGG 58.644 37.500 0.00 0.00 0.00 3.61
3086 3137 9.959749 AACGTAAAAATATCAGCTTTTCTCAAA 57.040 25.926 0.00 0.00 0.00 2.69
3183 3237 1.133513 ACAGAAAGAATGTGTGCCCCA 60.134 47.619 0.00 0.00 33.59 4.96
3266 3655 7.275123 GGGCAGCATAACTACGTAAATATCTAC 59.725 40.741 0.00 0.00 0.00 2.59
3347 3917 9.952188 AAGTGAAGCAACTCTTTCTAAATTAAC 57.048 29.630 0.00 0.00 34.56 2.01
3359 3929 7.831193 ACATGGAATAATAAGTGAAGCAACTCT 59.169 33.333 0.00 0.00 0.00 3.24
3383 3953 9.979578 AACAAAAGCTAATGATTTTACATCACA 57.020 25.926 5.73 0.00 39.41 3.58
3409 3979 5.534654 CCTGATCTTCACCCTACAAAACAAA 59.465 40.000 0.00 0.00 0.00 2.83
3790 4360 4.546570 GGTGCTGGAAGTGTCATAAAAAC 58.453 43.478 0.00 0.00 35.30 2.43
3801 4371 1.062488 ACTTGAGGGGTGCTGGAAGT 61.062 55.000 0.00 0.00 35.30 3.01
3865 4435 9.707957 ACCATATCAAATGGAAACCAATAACTA 57.292 29.630 10.90 0.00 41.64 2.24
3868 4438 8.820831 ACAACCATATCAAATGGAAACCAATAA 58.179 29.630 10.90 0.00 41.64 1.40
4007 4582 2.093447 CCTCTCGTAGCAATTCCCAAGT 60.093 50.000 0.00 0.00 0.00 3.16
4103 4681 5.050634 CCAAAAATTACGACTCAACTCACGA 60.051 40.000 0.00 0.00 0.00 4.35
4104 4682 5.137403 CCAAAAATTACGACTCAACTCACG 58.863 41.667 0.00 0.00 0.00 4.35
4127 4707 9.617975 CATCTCTTTCCAGAAGAAAAATACAAC 57.382 33.333 0.00 0.00 43.84 3.32
4128 4708 8.299570 GCATCTCTTTCCAGAAGAAAAATACAA 58.700 33.333 0.00 0.00 43.84 2.41
4130 4710 7.094205 TGGCATCTCTTTCCAGAAGAAAAATAC 60.094 37.037 0.00 0.00 43.84 1.89
4134 4714 4.520492 GTGGCATCTCTTTCCAGAAGAAAA 59.480 41.667 0.00 0.00 43.84 2.29
4141 4721 2.092538 AGGATGTGGCATCTCTTTCCAG 60.093 50.000 8.72 0.00 0.00 3.86
4142 4722 1.918262 AGGATGTGGCATCTCTTTCCA 59.082 47.619 8.72 0.00 0.00 3.53
4153 4733 1.718757 GACGATGGCAAGGATGTGGC 61.719 60.000 0.00 0.00 44.09 5.01
4154 4734 0.107508 AGACGATGGCAAGGATGTGG 60.108 55.000 0.00 0.00 0.00 4.17
4155 4735 2.159043 AGTAGACGATGGCAAGGATGTG 60.159 50.000 0.00 0.00 0.00 3.21
4156 4736 2.111384 AGTAGACGATGGCAAGGATGT 58.889 47.619 0.00 0.00 0.00 3.06
4157 4737 2.159043 ACAGTAGACGATGGCAAGGATG 60.159 50.000 0.00 0.00 0.00 3.51
4158 4738 2.111384 ACAGTAGACGATGGCAAGGAT 58.889 47.619 0.00 0.00 0.00 3.24
4159 4739 1.204704 CACAGTAGACGATGGCAAGGA 59.795 52.381 0.00 0.00 0.00 3.36
4160 4740 1.204704 TCACAGTAGACGATGGCAAGG 59.795 52.381 0.00 0.00 0.00 3.61
4161 4741 2.654749 TCACAGTAGACGATGGCAAG 57.345 50.000 0.00 0.00 0.00 4.01
4162 4742 2.892374 CATCACAGTAGACGATGGCAA 58.108 47.619 0.00 0.00 34.24 4.52
4210 4794 1.722852 CTTCGTCGCTCGGCTATCG 60.723 63.158 0.00 0.00 40.32 2.92
4224 4808 3.710722 AGACAGCTGGGCCCTTCG 61.711 66.667 25.70 12.70 0.00 3.79
4261 4845 0.605319 CGCTTACAAGTGGCCCTGAA 60.605 55.000 0.00 0.00 33.00 3.02
4272 4856 1.864711 GCAGAGAACACACGCTTACAA 59.135 47.619 0.00 0.00 0.00 2.41
4292 4876 1.302033 CCTGGCGCTTATAGCAGGG 60.302 63.158 17.42 2.74 42.58 4.45
4331 4915 9.319143 AGAGATATTCAGAATTCACCTTTTACG 57.681 33.333 8.44 0.00 0.00 3.18
4335 4919 8.991275 AGAGAGAGATATTCAGAATTCACCTTT 58.009 33.333 8.44 0.00 0.00 3.11
4352 4936 1.499007 GGAGAGTGGGGAGAGAGAGAT 59.501 57.143 0.00 0.00 0.00 2.75
4353 4937 0.923358 GGAGAGTGGGGAGAGAGAGA 59.077 60.000 0.00 0.00 0.00 3.10
4363 4947 0.326264 CCACTTCAAGGGAGAGTGGG 59.674 60.000 12.71 0.00 44.41 4.61
4365 4949 3.492102 TTTCCACTTCAAGGGAGAGTG 57.508 47.619 0.00 0.00 34.02 3.51
4366 4950 3.744530 CGTTTTCCACTTCAAGGGAGAGT 60.745 47.826 0.00 0.00 34.02 3.24
4368 4952 2.436542 TCGTTTTCCACTTCAAGGGAGA 59.563 45.455 0.00 0.00 34.02 3.71
4395 4996 2.555547 GCCCTCACACCAGTGTTGC 61.556 63.158 0.00 0.00 46.01 4.17
4418 5019 2.827190 ATGGCCACGCTGCATGAG 60.827 61.111 8.16 0.00 0.00 2.90
4465 5066 2.038164 AGAGAGCTTGCAGTTCATGACA 59.962 45.455 0.00 0.00 0.00 3.58
4489 5090 4.574674 TGCCATGAACTCCTTTCTGTAT 57.425 40.909 0.00 0.00 34.97 2.29
4492 5093 3.760151 TGATTGCCATGAACTCCTTTCTG 59.240 43.478 0.00 0.00 34.97 3.02
4493 5094 4.038271 TGATTGCCATGAACTCCTTTCT 57.962 40.909 0.00 0.00 34.97 2.52
4494 5095 4.996788 ATGATTGCCATGAACTCCTTTC 57.003 40.909 0.00 0.00 33.39 2.62
4508 5109 1.102809 TCCACCGCCATCATGATTGC 61.103 55.000 19.31 19.31 0.00 3.56
4511 5112 3.507162 TTTATCCACCGCCATCATGAT 57.493 42.857 1.18 1.18 0.00 2.45
4546 5147 3.902881 ATAGTGAAAGCACCTCTCTGG 57.097 47.619 0.00 0.00 46.32 3.86
4556 5157 5.446473 CGTGATCAGTCCAAATAGTGAAAGC 60.446 44.000 0.00 0.00 32.71 3.51
4580 5181 3.377346 TCAGAAAGAGAGCACACACTC 57.623 47.619 0.00 0.00 36.91 3.51
4584 5185 2.672381 GCTGATCAGAAAGAGAGCACAC 59.328 50.000 27.04 0.00 36.27 3.82
4608 5209 0.777631 CGCTGCAAATTTGTTGTCGG 59.222 50.000 19.03 8.69 0.00 4.79
4616 5217 1.337703 TGTTCTCTGCGCTGCAAATTT 59.662 42.857 9.73 0.00 38.41 1.82
4630 5231 5.507077 TGAAATTGTAAGCGTTGTGTTCTC 58.493 37.500 0.00 0.00 0.00 2.87
4633 5234 5.243426 ACTGAAATTGTAAGCGTTGTGTT 57.757 34.783 0.00 0.00 0.00 3.32
4634 5235 4.893424 ACTGAAATTGTAAGCGTTGTGT 57.107 36.364 0.00 0.00 0.00 3.72
4635 5236 5.270083 TGAACTGAAATTGTAAGCGTTGTG 58.730 37.500 0.00 0.00 0.00 3.33
4636 5237 5.493133 TGAACTGAAATTGTAAGCGTTGT 57.507 34.783 0.00 0.00 0.00 3.32
4637 5238 6.804534 TTTGAACTGAAATTGTAAGCGTTG 57.195 33.333 0.00 0.00 0.00 4.10
4638 5239 8.132362 TGTATTTGAACTGAAATTGTAAGCGTT 58.868 29.630 0.00 0.00 0.00 4.84
4639 5240 7.644490 TGTATTTGAACTGAAATTGTAAGCGT 58.356 30.769 0.00 0.00 0.00 5.07
4640 5241 8.500837 TTGTATTTGAACTGAAATTGTAAGCG 57.499 30.769 0.00 0.00 0.00 4.68
4754 5365 4.624913 ACCTCTTGTATCCAATCTCAGGA 58.375 43.478 0.00 0.00 39.97 3.86
4849 5460 4.010349 CCATGTTCCAAAGAGTAACCCTC 58.990 47.826 0.00 0.00 40.80 4.30
4850 5461 3.655777 TCCATGTTCCAAAGAGTAACCCT 59.344 43.478 0.00 0.00 0.00 4.34
4851 5462 3.756963 GTCCATGTTCCAAAGAGTAACCC 59.243 47.826 0.00 0.00 0.00 4.11
4852 5463 4.455877 CAGTCCATGTTCCAAAGAGTAACC 59.544 45.833 0.00 0.00 0.00 2.85
4853 5464 5.305585 TCAGTCCATGTTCCAAAGAGTAAC 58.694 41.667 0.00 0.00 0.00 2.50
4854 5465 5.560722 TCAGTCCATGTTCCAAAGAGTAA 57.439 39.130 0.00 0.00 0.00 2.24
4855 5466 5.762179 ATCAGTCCATGTTCCAAAGAGTA 57.238 39.130 0.00 0.00 0.00 2.59
4856 5467 4.647564 ATCAGTCCATGTTCCAAAGAGT 57.352 40.909 0.00 0.00 0.00 3.24
4857 5468 7.452880 TTTTATCAGTCCATGTTCCAAAGAG 57.547 36.000 0.00 0.00 0.00 2.85
4871 5482 7.254795 CCAATCGTCCTTGGTATTTTATCAGTC 60.255 40.741 6.15 0.00 40.72 3.51
4872 5483 6.542370 CCAATCGTCCTTGGTATTTTATCAGT 59.458 38.462 6.15 0.00 40.72 3.41
4956 5567 4.287552 TCCCTGGTAAGTAGGAGTGATTC 58.712 47.826 0.00 0.00 37.52 2.52
4958 5569 3.917300 CTCCCTGGTAAGTAGGAGTGAT 58.083 50.000 0.00 0.00 40.91 3.06
4976 5601 4.691216 CCAGTAGTACAACTTCTTTGCTCC 59.309 45.833 2.52 0.00 39.01 4.70
4991 5616 1.555075 CTTCAAGCCTGGCCAGTAGTA 59.445 52.381 30.63 9.81 0.00 1.82
4996 5621 0.747283 CTAGCTTCAAGCCTGGCCAG 60.747 60.000 26.87 26.87 43.77 4.85
5002 5627 4.230455 ACTCCATATCTAGCTTCAAGCCT 58.770 43.478 5.53 0.00 43.77 4.58
5032 5657 3.240069 GACAAATGCTGCATTGTCTGAC 58.760 45.455 29.57 21.41 34.04 3.51
5033 5658 2.885894 TGACAAATGCTGCATTGTCTGA 59.114 40.909 32.57 22.45 35.30 3.27
5095 8316 0.400213 TAAGGAGGTGGCAGTGGTTG 59.600 55.000 0.00 0.00 0.00 3.77
5096 8317 1.073923 CTTAAGGAGGTGGCAGTGGTT 59.926 52.381 0.00 0.00 0.00 3.67
5097 8318 0.693049 CTTAAGGAGGTGGCAGTGGT 59.307 55.000 0.00 0.00 0.00 4.16
5098 8319 0.678048 GCTTAAGGAGGTGGCAGTGG 60.678 60.000 4.29 0.00 0.00 4.00
5099 8320 0.326264 AGCTTAAGGAGGTGGCAGTG 59.674 55.000 4.29 0.00 34.08 3.66
5100 8321 2.778899 AGCTTAAGGAGGTGGCAGT 58.221 52.632 4.29 0.00 34.08 4.40


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

AutoCloner maintained by Alex Coulton.