Multiple sequence alignment - TraesCS2B01G504100

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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 TraesCS2B01G504100 chr2B 100.000 3780 0 0 1 3780 698297747 698293968 0.000000e+00 6981
1 TraesCS2B01G504100 chr2B 98.438 192 3 0 742 933 677333038 677332847 4.680000e-89 339
2 TraesCS2B01G504100 chr2B 82.206 281 46 3 1375 1655 698306307 698306031 4.880000e-59 239
3 TraesCS2B01G504100 chr2B 83.051 236 38 2 1421 1655 698954509 698954275 2.960000e-51 213
4 TraesCS2B01G504100 chr2D 94.970 2465 96 11 1287 3733 579996238 579993784 0.000000e+00 3840
5 TraesCS2B01G504100 chr2D 92.999 757 35 13 1 741 579997292 579996538 0.000000e+00 1088
6 TraesCS2B01G504100 chr2D 92.628 312 13 3 934 1236 579996546 579996236 1.250000e-119 440
7 TraesCS2B01G504100 chr2D 80.496 282 49 3 1375 1655 580007169 580006893 1.060000e-50 211
8 TraesCS2B01G504100 chr2A 92.194 2037 91 21 934 2916 717858551 717856529 0.000000e+00 2819
9 TraesCS2B01G504100 chr2A 90.621 757 51 14 1 741 717859295 717858543 0.000000e+00 987
10 TraesCS2B01G504100 chr2A 92.361 576 33 7 2914 3482 717845128 717844557 0.000000e+00 809
11 TraesCS2B01G504100 chr2A 93.399 303 19 1 3478 3780 717838173 717837872 7.450000e-122 448
12 TraesCS2B01G504100 chr2A 98.469 196 3 0 741 936 725722309 725722114 2.790000e-91 346
13 TraesCS2B01G504100 chr2A 81.139 281 49 1 1375 1655 717882219 717881943 4.910000e-54 222
14 TraesCS2B01G504100 chr1B 98.469 196 3 0 740 935 680813721 680813916 2.790000e-91 346
15 TraesCS2B01G504100 chr3B 98.446 193 3 0 741 933 7286285 7286477 1.300000e-89 340
16 TraesCS2B01G504100 chr6A 96.939 196 6 0 740 935 11011656 11011851 2.810000e-86 329
17 TraesCS2B01G504100 chr4A 94.686 207 11 0 730 936 691684648 691684854 4.710000e-84 322
18 TraesCS2B01G504100 chr7B 93.868 212 13 0 729 940 624145963 624146174 1.690000e-83 320
19 TraesCS2B01G504100 chr3A 94.258 209 12 0 730 938 740691904 740692112 1.690000e-83 320
20 TraesCS2B01G504100 chr3A 94.258 209 12 0 730 938 740723498 740723706 1.690000e-83 320


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 TraesCS2B01G504100 chr2B 698293968 698297747 3779 True 6981.000000 6981 100.000000 1 3780 1 chr2B.!!$R2 3779
1 TraesCS2B01G504100 chr2D 579993784 579997292 3508 True 1789.333333 3840 93.532333 1 3733 3 chr2D.!!$R2 3732
2 TraesCS2B01G504100 chr2A 717856529 717859295 2766 True 1903.000000 2819 91.407500 1 2916 2 chr2A.!!$R5 2915
3 TraesCS2B01G504100 chr2A 717844557 717845128 571 True 809.000000 809 92.361000 2914 3482 1 chr2A.!!$R2 568

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
783 802 0.171455 GCTCCGCTATAGCACGCTAT 59.829 55.0 23.99 15.45 42.21 2.97 F
878 897 0.171455 GCTCCGCTATAGCACGCTAT 59.829 55.0 23.99 15.45 42.21 2.97 F
1443 1479 0.314302 GCGTCTATACCACCGATGCT 59.686 55.0 0.00 0.00 36.89 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1734 1795 0.336048 ATGCCATAAACCCTGCCAGT 59.664 50.0 0.00 0.0 0.00 4.00 R
2571 2635 0.371989 CACAGAAACAACACGACGCA 59.628 50.0 0.00 0.0 0.00 5.24 R
3238 3315 0.178918 CTGGGGTCCCTATCCTCTCC 60.179 65.0 8.15 0.0 36.94 3.71 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
61 62 6.577103 AGTAGTGAGTCATGTATGGTTCATG 58.423 40.000 0.00 0.00 42.53 3.07
63 64 3.940852 GTGAGTCATGTATGGTTCATGCA 59.059 43.478 0.00 0.00 40.36 3.96
80 81 3.724508 TGCAATGTGGTTTTCGTTGAT 57.275 38.095 0.00 0.00 34.80 2.57
85 86 5.901336 GCAATGTGGTTTTCGTTGATTTTTC 59.099 36.000 0.00 0.00 34.80 2.29
104 105 5.730296 TTTCTCTCCAGTTCTTCTACCTG 57.270 43.478 0.00 0.00 0.00 4.00
118 119 9.327628 GTTCTTCTACCTGTTTTCTTTCTAACT 57.672 33.333 0.00 0.00 0.00 2.24
119 120 9.543783 TTCTTCTACCTGTTTTCTTTCTAACTC 57.456 33.333 0.00 0.00 0.00 3.01
120 121 8.701895 TCTTCTACCTGTTTTCTTTCTAACTCA 58.298 33.333 0.00 0.00 0.00 3.41
122 123 8.833231 TCTACCTGTTTTCTTTCTAACTCATG 57.167 34.615 0.00 0.00 0.00 3.07
123 124 8.429641 TCTACCTGTTTTCTTTCTAACTCATGT 58.570 33.333 0.00 0.00 0.00 3.21
124 125 7.497925 ACCTGTTTTCTTTCTAACTCATGTC 57.502 36.000 0.00 0.00 0.00 3.06
125 126 6.202954 ACCTGTTTTCTTTCTAACTCATGTCG 59.797 38.462 0.00 0.00 0.00 4.35
126 127 6.202954 CCTGTTTTCTTTCTAACTCATGTCGT 59.797 38.462 0.00 0.00 0.00 4.34
127 128 6.943981 TGTTTTCTTTCTAACTCATGTCGTG 58.056 36.000 0.00 0.00 0.00 4.35
132 138 7.173863 TCTTTCTAACTCATGTCGTGTTTTC 57.826 36.000 0.00 0.00 33.51 2.29
143 149 8.610248 TCATGTCGTGTTTTCTTTTCCTTATA 57.390 30.769 0.00 0.00 0.00 0.98
379 388 5.767269 TGTGAGCATTTCTTTAAATTGCGA 58.233 33.333 0.00 0.00 35.79 5.10
384 393 5.512788 AGCATTTCTTTAAATTGCGACATCG 59.487 36.000 0.00 0.00 35.79 3.84
608 626 4.083696 GGAAAAGAAACGCGGAAGTGAATA 60.084 41.667 12.47 0.00 46.66 1.75
615 633 1.480219 GCGGAAGTGAATAGGTCGCG 61.480 60.000 0.00 0.00 41.95 5.87
656 674 3.119849 GCCGTTTGCTCATTATTCAGTGT 60.120 43.478 0.00 0.00 36.87 3.55
712 731 3.024217 GAGGCCCTCTCCCTCTCT 58.976 66.667 2.64 0.00 44.40 3.10
741 760 3.582647 TCCTAACTGTTGCATCTTCTCCA 59.417 43.478 2.69 0.00 0.00 3.86
742 761 3.686726 CCTAACTGTTGCATCTTCTCCAC 59.313 47.826 2.69 0.00 0.00 4.02
743 762 3.498774 AACTGTTGCATCTTCTCCACT 57.501 42.857 0.00 0.00 0.00 4.00
745 764 2.105477 ACTGTTGCATCTTCTCCACTGT 59.895 45.455 0.00 0.00 0.00 3.55
747 766 3.554934 TGTTGCATCTTCTCCACTGTTT 58.445 40.909 0.00 0.00 0.00 2.83
748 767 3.953612 TGTTGCATCTTCTCCACTGTTTT 59.046 39.130 0.00 0.00 0.00 2.43
749 768 5.129634 TGTTGCATCTTCTCCACTGTTTTA 58.870 37.500 0.00 0.00 0.00 1.52
750 769 5.592282 TGTTGCATCTTCTCCACTGTTTTAA 59.408 36.000 0.00 0.00 0.00 1.52
751 770 6.096141 TGTTGCATCTTCTCCACTGTTTTAAA 59.904 34.615 0.00 0.00 0.00 1.52
752 771 6.899393 TGCATCTTCTCCACTGTTTTAAAT 57.101 33.333 0.00 0.00 0.00 1.40
753 772 7.994425 TGCATCTTCTCCACTGTTTTAAATA 57.006 32.000 0.00 0.00 0.00 1.40
754 773 8.044060 TGCATCTTCTCCACTGTTTTAAATAG 57.956 34.615 0.00 0.00 0.00 1.73
755 774 6.969473 GCATCTTCTCCACTGTTTTAAATAGC 59.031 38.462 1.36 0.00 0.00 2.97
756 775 7.475840 CATCTTCTCCACTGTTTTAAATAGCC 58.524 38.462 1.36 0.00 0.00 3.93
757 776 5.944007 TCTTCTCCACTGTTTTAAATAGCCC 59.056 40.000 1.36 0.00 0.00 5.19
758 777 4.258543 TCTCCACTGTTTTAAATAGCCCG 58.741 43.478 1.36 0.00 0.00 6.13
759 778 2.750712 TCCACTGTTTTAAATAGCCCGC 59.249 45.455 1.36 0.00 0.00 6.13
760 779 2.752903 CCACTGTTTTAAATAGCCCGCT 59.247 45.455 1.36 0.00 0.00 5.52
761 780 3.942748 CCACTGTTTTAAATAGCCCGCTA 59.057 43.478 0.00 0.00 0.00 4.26
762 781 4.578928 CCACTGTTTTAAATAGCCCGCTAT 59.421 41.667 3.31 3.31 40.63 2.97
763 782 5.761234 CCACTGTTTTAAATAGCCCGCTATA 59.239 40.000 9.56 0.00 38.20 1.31
764 783 6.073222 CCACTGTTTTAAATAGCCCGCTATAG 60.073 42.308 9.56 4.62 38.20 1.31
765 784 5.469084 ACTGTTTTAAATAGCCCGCTATAGC 59.531 40.000 15.09 15.09 38.20 2.97
766 785 5.617252 TGTTTTAAATAGCCCGCTATAGCT 58.383 37.500 21.98 6.31 43.20 3.32
767 786 5.699458 TGTTTTAAATAGCCCGCTATAGCTC 59.301 40.000 21.98 11.04 40.56 4.09
768 787 4.467198 TTAAATAGCCCGCTATAGCTCC 57.533 45.455 21.98 10.06 40.56 4.70
769 788 0.818296 AATAGCCCGCTATAGCTCCG 59.182 55.000 21.98 10.15 40.56 4.63
770 789 1.668101 ATAGCCCGCTATAGCTCCGC 61.668 60.000 21.98 18.46 40.56 5.54
771 790 2.766306 TAGCCCGCTATAGCTCCGCT 62.766 60.000 24.41 24.41 43.41 5.52
772 791 2.341101 GCCCGCTATAGCTCCGCTA 61.341 63.158 21.98 0.00 45.55 4.26
780 799 1.579932 TAGCTCCGCTATAGCACGC 59.420 57.895 23.99 20.26 42.62 5.34
781 800 0.889638 TAGCTCCGCTATAGCACGCT 60.890 55.000 25.78 25.78 42.62 5.07
782 801 0.889638 AGCTCCGCTATAGCACGCTA 60.890 55.000 23.99 0.39 42.62 4.26
783 802 0.171455 GCTCCGCTATAGCACGCTAT 59.829 55.000 23.99 15.45 42.21 2.97
784 803 1.400846 GCTCCGCTATAGCACGCTATA 59.599 52.381 23.99 15.99 42.21 1.31
800 819 3.948851 GCTATAGCGTTTACAAAAGGGC 58.051 45.455 9.40 0.00 0.00 5.19
801 820 3.626217 GCTATAGCGTTTACAAAAGGGCT 59.374 43.478 9.40 4.09 34.69 5.19
802 821 4.095932 GCTATAGCGTTTACAAAAGGGCTT 59.904 41.667 9.40 0.00 32.29 4.35
803 822 2.793278 AGCGTTTACAAAAGGGCTTG 57.207 45.000 0.00 0.00 0.00 4.01
804 823 1.136690 GCGTTTACAAAAGGGCTTGC 58.863 50.000 0.00 0.00 0.00 4.01
805 824 1.404477 CGTTTACAAAAGGGCTTGCG 58.596 50.000 0.00 0.00 0.00 4.85
806 825 1.136690 GTTTACAAAAGGGCTTGCGC 58.863 50.000 0.00 0.00 0.00 6.09
807 826 1.036707 TTTACAAAAGGGCTTGCGCT 58.963 45.000 9.73 6.36 36.09 5.92
808 827 1.898902 TTACAAAAGGGCTTGCGCTA 58.101 45.000 9.73 0.00 36.09 4.26
809 828 1.898902 TACAAAAGGGCTTGCGCTAA 58.101 45.000 9.73 0.00 36.09 3.09
810 829 0.598065 ACAAAAGGGCTTGCGCTAAG 59.402 50.000 9.73 11.92 39.49 2.18
811 830 0.881118 CAAAAGGGCTTGCGCTAAGA 59.119 50.000 19.38 0.00 38.76 2.10
812 831 1.135575 CAAAAGGGCTTGCGCTAAGAG 60.136 52.381 19.38 9.33 38.76 2.85
813 832 0.324943 AAAGGGCTTGCGCTAAGAGA 59.675 50.000 19.38 0.00 38.76 3.10
814 833 0.391793 AAGGGCTTGCGCTAAGAGAC 60.392 55.000 19.38 10.04 38.76 3.36
815 834 1.219393 GGGCTTGCGCTAAGAGACT 59.781 57.895 19.38 0.00 38.76 3.24
816 835 0.391793 GGGCTTGCGCTAAGAGACTT 60.392 55.000 19.38 0.00 38.76 3.01
817 836 1.443802 GGCTTGCGCTAAGAGACTTT 58.556 50.000 19.38 0.00 38.76 2.66
818 837 1.129437 GGCTTGCGCTAAGAGACTTTG 59.871 52.381 19.38 0.00 38.76 2.77
819 838 2.069273 GCTTGCGCTAAGAGACTTTGA 58.931 47.619 19.38 0.00 38.76 2.69
820 839 2.675348 GCTTGCGCTAAGAGACTTTGAT 59.325 45.455 19.38 0.00 38.76 2.57
821 840 3.242252 GCTTGCGCTAAGAGACTTTGATC 60.242 47.826 19.38 0.00 38.76 2.92
822 841 2.893637 TGCGCTAAGAGACTTTGATCC 58.106 47.619 9.73 0.00 0.00 3.36
823 842 2.233676 TGCGCTAAGAGACTTTGATCCA 59.766 45.455 9.73 0.00 0.00 3.41
824 843 3.262420 GCGCTAAGAGACTTTGATCCAA 58.738 45.455 0.00 0.00 0.00 3.53
825 844 3.684788 GCGCTAAGAGACTTTGATCCAAA 59.315 43.478 0.00 0.00 0.00 3.28
826 845 4.436183 GCGCTAAGAGACTTTGATCCAAAC 60.436 45.833 0.00 0.00 0.00 2.93
827 846 4.690748 CGCTAAGAGACTTTGATCCAAACA 59.309 41.667 0.00 0.00 0.00 2.83
828 847 5.179368 CGCTAAGAGACTTTGATCCAAACAA 59.821 40.000 0.00 0.00 0.00 2.83
829 848 6.293407 CGCTAAGAGACTTTGATCCAAACAAA 60.293 38.462 0.00 0.00 36.15 2.83
830 849 7.573843 CGCTAAGAGACTTTGATCCAAACAAAT 60.574 37.037 0.00 0.00 36.79 2.32
831 850 7.540055 GCTAAGAGACTTTGATCCAAACAAATG 59.460 37.037 0.00 0.00 36.79 2.32
832 851 7.587037 AAGAGACTTTGATCCAAACAAATGA 57.413 32.000 0.00 0.00 36.79 2.57
833 852 7.587037 AGAGACTTTGATCCAAACAAATGAA 57.413 32.000 0.00 0.00 36.79 2.57
834 853 7.428826 AGAGACTTTGATCCAAACAAATGAAC 58.571 34.615 0.00 0.00 36.79 3.18
835 854 7.068593 AGAGACTTTGATCCAAACAAATGAACA 59.931 33.333 0.00 0.00 36.79 3.18
836 855 7.555087 AGACTTTGATCCAAACAAATGAACAA 58.445 30.769 0.00 0.00 36.79 2.83
837 856 8.040132 AGACTTTGATCCAAACAAATGAACAAA 58.960 29.630 0.00 0.00 36.79 2.83
838 857 7.973601 ACTTTGATCCAAACAAATGAACAAAC 58.026 30.769 0.00 0.00 36.79 2.93
839 858 7.605691 ACTTTGATCCAAACAAATGAACAAACA 59.394 29.630 0.00 0.00 36.79 2.83
840 859 8.503458 TTTGATCCAAACAAATGAACAAACAT 57.497 26.923 0.00 0.00 33.25 2.71
841 860 8.503458 TTGATCCAAACAAATGAACAAACATT 57.497 26.923 0.00 0.00 41.43 2.71
842 861 8.503458 TGATCCAAACAAATGAACAAACATTT 57.497 26.923 0.00 0.00 46.85 2.32
843 862 8.610896 TGATCCAAACAAATGAACAAACATTTC 58.389 29.630 0.00 0.00 45.00 2.17
844 863 7.912056 TCCAAACAAATGAACAAACATTTCA 57.088 28.000 0.00 0.00 45.00 2.69
845 864 8.327941 TCCAAACAAATGAACAAACATTTCAA 57.672 26.923 0.00 0.00 45.00 2.69
846 865 8.786898 TCCAAACAAATGAACAAACATTTCAAA 58.213 25.926 0.00 0.00 45.00 2.69
847 866 9.570488 CCAAACAAATGAACAAACATTTCAAAT 57.430 25.926 0.00 0.00 45.00 2.32
850 869 9.934190 AACAAATGAACAAACATTTCAAATAGC 57.066 25.926 0.00 0.00 45.00 2.97
851 870 8.274939 ACAAATGAACAAACATTTCAAATAGCG 58.725 29.630 0.00 0.00 45.00 4.26
852 871 5.820926 TGAACAAACATTTCAAATAGCGC 57.179 34.783 0.00 0.00 29.89 5.92
853 872 4.381270 TGAACAAACATTTCAAATAGCGCG 59.619 37.500 0.00 0.00 29.89 6.86
854 873 2.661195 ACAAACATTTCAAATAGCGCGC 59.339 40.909 26.66 26.66 0.00 6.86
855 874 2.916716 CAAACATTTCAAATAGCGCGCT 59.083 40.909 38.01 38.01 0.00 5.92
856 875 4.094911 CAAACATTTCAAATAGCGCGCTA 58.905 39.130 39.72 39.72 0.00 4.26
857 876 4.552166 AACATTTCAAATAGCGCGCTAT 57.448 36.364 40.32 40.32 40.63 2.97
858 877 5.666969 AACATTTCAAATAGCGCGCTATA 57.333 34.783 43.81 31.73 38.20 1.31
859 878 5.269459 ACATTTCAAATAGCGCGCTATAG 57.731 39.130 43.81 37.02 38.20 1.31
860 879 3.788434 TTTCAAATAGCGCGCTATAGC 57.212 42.857 43.81 15.09 38.20 2.97
861 880 2.724977 TCAAATAGCGCGCTATAGCT 57.275 45.000 43.81 30.41 46.53 3.32
862 881 2.596452 TCAAATAGCGCGCTATAGCTC 58.404 47.619 43.81 13.77 43.44 4.09
863 882 1.656095 CAAATAGCGCGCTATAGCTCC 59.344 52.381 43.81 10.26 43.44 4.70
864 883 0.179161 AATAGCGCGCTATAGCTCCG 60.179 55.000 43.81 22.32 43.44 4.63
867 886 2.868196 CGCGCTATAGCTCCGCTA 59.132 61.111 21.98 0.00 45.55 4.26
875 894 1.579932 TAGCTCCGCTATAGCACGC 59.420 57.895 23.99 20.26 42.62 5.34
876 895 0.889638 TAGCTCCGCTATAGCACGCT 60.890 55.000 25.78 25.78 42.62 5.07
877 896 0.889638 AGCTCCGCTATAGCACGCTA 60.890 55.000 23.99 0.39 42.62 4.26
878 897 0.171455 GCTCCGCTATAGCACGCTAT 59.829 55.000 23.99 15.45 42.21 2.97
879 898 1.400846 GCTCCGCTATAGCACGCTATA 59.599 52.381 23.99 15.99 42.21 1.31
887 906 5.709011 CTATAGCACGCTATAGCATTTGG 57.291 43.478 25.42 9.98 46.26 3.28
888 907 2.620251 AGCACGCTATAGCATTTGGA 57.380 45.000 23.99 0.00 42.21 3.53
889 908 2.917933 AGCACGCTATAGCATTTGGAA 58.082 42.857 23.99 0.00 42.21 3.53
890 909 2.874701 AGCACGCTATAGCATTTGGAAG 59.125 45.455 23.99 7.87 42.21 3.46
891 910 2.872245 GCACGCTATAGCATTTGGAAGA 59.128 45.455 23.99 0.00 42.21 2.87
892 911 3.059325 GCACGCTATAGCATTTGGAAGAG 60.059 47.826 23.99 6.48 42.21 2.85
893 912 3.496130 CACGCTATAGCATTTGGAAGAGG 59.504 47.826 23.99 5.98 42.21 3.69
894 913 3.134804 ACGCTATAGCATTTGGAAGAGGT 59.865 43.478 23.99 6.60 42.21 3.85
895 914 3.743396 CGCTATAGCATTTGGAAGAGGTC 59.257 47.826 23.99 0.00 42.21 3.85
896 915 4.068599 GCTATAGCATTTGGAAGAGGTCC 58.931 47.826 20.01 0.00 43.38 4.46
897 916 5.330561 GCTATAGCATTTGGAAGAGGTCCG 61.331 50.000 20.01 0.00 44.91 4.79
903 922 3.291611 GGAAGAGGTCCGCCGTTA 58.708 61.111 0.00 0.00 40.50 3.18
904 923 1.593265 GGAAGAGGTCCGCCGTTAA 59.407 57.895 0.00 0.00 40.50 2.01
905 924 0.459759 GGAAGAGGTCCGCCGTTAAG 60.460 60.000 0.00 0.00 40.50 1.85
906 925 0.529378 GAAGAGGTCCGCCGTTAAGA 59.471 55.000 0.00 0.00 40.50 2.10
907 926 1.136500 GAAGAGGTCCGCCGTTAAGAT 59.864 52.381 0.00 0.00 40.50 2.40
908 927 0.460311 AGAGGTCCGCCGTTAAGATG 59.540 55.000 0.00 0.00 40.50 2.90
909 928 1.152383 GAGGTCCGCCGTTAAGATGC 61.152 60.000 0.00 0.00 40.50 3.91
910 929 1.153429 GGTCCGCCGTTAAGATGCT 60.153 57.895 0.00 0.00 0.00 3.79
911 930 0.743345 GGTCCGCCGTTAAGATGCTT 60.743 55.000 0.00 0.00 0.00 3.91
912 931 1.472026 GGTCCGCCGTTAAGATGCTTA 60.472 52.381 0.00 0.00 0.00 3.09
913 932 1.859080 GTCCGCCGTTAAGATGCTTAG 59.141 52.381 0.00 0.00 0.00 2.18
914 933 0.582005 CCGCCGTTAAGATGCTTAGC 59.418 55.000 0.00 0.00 0.00 3.09
915 934 1.286501 CGCCGTTAAGATGCTTAGCA 58.713 50.000 10.09 10.09 44.86 3.49
916 935 1.004927 CGCCGTTAAGATGCTTAGCAC 60.005 52.381 9.82 3.78 43.04 4.40
917 936 1.004927 GCCGTTAAGATGCTTAGCACG 60.005 52.381 9.82 7.39 43.04 5.34
918 937 1.004927 CCGTTAAGATGCTTAGCACGC 60.005 52.381 9.82 4.80 43.04 5.34
919 938 1.927174 CGTTAAGATGCTTAGCACGCT 59.073 47.619 9.82 7.37 43.04 5.07
920 939 3.113322 CGTTAAGATGCTTAGCACGCTA 58.887 45.455 9.82 0.00 43.04 4.26
921 940 3.736252 CGTTAAGATGCTTAGCACGCTAT 59.264 43.478 9.82 0.00 43.04 2.97
922 941 4.209288 CGTTAAGATGCTTAGCACGCTATT 59.791 41.667 9.82 0.00 43.04 1.73
923 942 5.276868 CGTTAAGATGCTTAGCACGCTATTT 60.277 40.000 9.82 0.85 43.04 1.40
924 943 6.074516 CGTTAAGATGCTTAGCACGCTATTTA 60.075 38.462 9.82 0.00 43.04 1.40
925 944 7.516155 CGTTAAGATGCTTAGCACGCTATTTAA 60.516 37.037 9.82 5.91 43.04 1.52
926 945 6.677781 AAGATGCTTAGCACGCTATTTAAA 57.322 33.333 9.82 0.00 43.04 1.52
927 946 6.677781 AGATGCTTAGCACGCTATTTAAAA 57.322 33.333 9.82 0.00 43.04 1.52
928 947 6.487103 AGATGCTTAGCACGCTATTTAAAAC 58.513 36.000 9.82 0.00 43.04 2.43
929 948 5.873179 TGCTTAGCACGCTATTTAAAACT 57.127 34.783 1.39 0.00 31.71 2.66
930 949 6.971527 TGCTTAGCACGCTATTTAAAACTA 57.028 33.333 1.39 0.00 31.71 2.24
931 950 7.548196 TGCTTAGCACGCTATTTAAAACTAT 57.452 32.000 1.39 0.00 31.71 2.12
932 951 7.406553 TGCTTAGCACGCTATTTAAAACTATG 58.593 34.615 1.39 0.00 31.71 2.23
933 952 7.279090 TGCTTAGCACGCTATTTAAAACTATGA 59.721 33.333 1.39 0.00 31.71 2.15
934 953 8.283291 GCTTAGCACGCTATTTAAAACTATGAT 58.717 33.333 0.00 0.00 0.00 2.45
935 954 9.798885 CTTAGCACGCTATTTAAAACTATGATC 57.201 33.333 0.00 0.00 0.00 2.92
936 955 9.542462 TTAGCACGCTATTTAAAACTATGATCT 57.458 29.630 0.00 0.00 0.00 2.75
937 956 8.438676 AGCACGCTATTTAAAACTATGATCTT 57.561 30.769 0.00 0.00 0.00 2.40
938 957 8.552034 AGCACGCTATTTAAAACTATGATCTTC 58.448 33.333 0.00 0.00 0.00 2.87
939 958 8.552034 GCACGCTATTTAAAACTATGATCTTCT 58.448 33.333 0.00 0.00 0.00 2.85
941 960 9.262358 ACGCTATTTAAAACTATGATCTTCTCC 57.738 33.333 0.00 0.00 0.00 3.71
942 961 8.428536 CGCTATTTAAAACTATGATCTTCTCCG 58.571 37.037 0.00 0.00 0.00 4.63
943 962 9.477484 GCTATTTAAAACTATGATCTTCTCCGA 57.523 33.333 0.00 0.00 0.00 4.55
945 964 7.751047 TTTAAAACTATGATCTTCTCCGACG 57.249 36.000 0.00 0.00 0.00 5.12
946 965 3.357166 AACTATGATCTTCTCCGACGC 57.643 47.619 0.00 0.00 0.00 5.19
947 966 2.577700 ACTATGATCTTCTCCGACGCT 58.422 47.619 0.00 0.00 0.00 5.07
948 967 2.292016 ACTATGATCTTCTCCGACGCTG 59.708 50.000 0.00 0.00 0.00 5.18
949 968 0.387202 ATGATCTTCTCCGACGCTGG 59.613 55.000 0.00 0.00 0.00 4.85
950 969 0.679960 TGATCTTCTCCGACGCTGGA 60.680 55.000 0.00 0.00 36.37 3.86
983 1002 1.905922 GCAGACAGCCACGAAGAAGC 61.906 60.000 0.00 0.00 37.23 3.86
1044 1066 1.515954 GATGGAGAACCGAGGCGAA 59.484 57.895 0.00 0.00 39.42 4.70
1142 1167 1.539124 AGGAGGAACCAGTGGACCC 60.539 63.158 18.40 15.80 42.04 4.46
1157 1182 1.615424 ACCCGATGGCCTTAGTGGT 60.615 57.895 3.32 5.26 38.35 4.16
1160 1185 0.469917 CCGATGGCCTTAGTGGTGAT 59.530 55.000 3.32 0.00 38.35 3.06
1239 1264 2.713011 GCAAGTAAGCAAGCATCGATG 58.287 47.619 21.27 21.27 0.00 3.84
1240 1265 2.352651 GCAAGTAAGCAAGCATCGATGA 59.647 45.455 29.20 2.86 0.00 2.92
1241 1266 3.003068 GCAAGTAAGCAAGCATCGATGAT 59.997 43.478 29.20 20.98 0.00 2.45
1276 1301 1.414158 CCGATCTTCTTCTAGCCCCA 58.586 55.000 0.00 0.00 0.00 4.96
1304 1329 0.530650 CATCTCCACCATTCCCGTCG 60.531 60.000 0.00 0.00 0.00 5.12
1443 1479 0.314302 GCGTCTATACCACCGATGCT 59.686 55.000 0.00 0.00 36.89 3.79
1454 1490 1.066454 CACCGATGCTATACACCGACA 59.934 52.381 0.00 0.00 0.00 4.35
1567 1603 2.452813 GCTGGATGTGTACGGCGTG 61.453 63.158 24.86 2.98 29.03 5.34
1733 1794 1.679977 GCATGGCCGCATGGGATAT 60.680 57.895 12.02 0.00 38.47 1.63
1734 1795 0.394216 GCATGGCCGCATGGGATATA 60.394 55.000 12.02 0.00 38.47 0.86
1760 1821 2.830923 CAGGGTTTATGGCATGGTTTCA 59.169 45.455 10.98 0.00 0.00 2.69
1834 1895 2.094390 GTCACAGTTACCTATGCCGTCA 60.094 50.000 0.00 0.00 0.00 4.35
1937 2000 6.376299 TCTGCATAGCTGAAAGATGAATTTGT 59.624 34.615 0.00 0.00 33.82 2.83
2149 2213 4.340617 TGATATGGGGCCGAATTTAATCC 58.659 43.478 0.00 0.00 0.00 3.01
2428 2492 2.357154 GGTGGAGGCTACCATGACAATT 60.357 50.000 8.58 0.00 42.17 2.32
2461 2525 0.318762 GATCCTGGCCCACTCGATAC 59.681 60.000 0.00 0.00 0.00 2.24
2474 2538 2.956333 ACTCGATACCATGGACGATTCA 59.044 45.455 21.47 4.51 34.41 2.57
2477 2541 3.004419 TCGATACCATGGACGATTCACTC 59.996 47.826 21.47 0.54 0.00 3.51
2479 2543 1.275666 ACCATGGACGATTCACTCCA 58.724 50.000 21.47 3.19 40.92 3.86
2487 2551 3.364062 GACGATTCACTCCACGTATCTG 58.636 50.000 0.00 0.00 39.04 2.90
2571 2635 0.105593 AATGGCACGATCGAGCTCAT 59.894 50.000 31.26 27.37 32.43 2.90
2587 2651 1.526887 CTCATGCGTCGTGTTGTTTCT 59.473 47.619 0.00 0.00 0.00 2.52
2612 2676 0.610687 AGAAAACGGAGAGCTGAGGG 59.389 55.000 0.00 0.00 0.00 4.30
2667 2731 2.676471 GGCTGGTTCGGTTGCCAT 60.676 61.111 0.00 0.00 44.34 4.40
2699 2763 1.992557 TGTTTGCCCCTAGAAGGTCAT 59.007 47.619 0.00 0.00 31.93 3.06
2790 2854 2.135933 GAACCGGTGACATATGCTAGC 58.864 52.381 8.52 8.10 0.00 3.42
2792 2856 0.313987 CCGGTGACATATGCTAGCGA 59.686 55.000 24.23 0.15 36.26 4.93
2853 2923 6.985059 AGCGTAGTTAATCAAATAAGGAGGAC 59.015 38.462 0.00 0.00 0.00 3.85
3118 3195 3.290710 CTGGGTTCGATGAATCCCAATT 58.709 45.455 15.73 0.00 41.79 2.32
3183 3260 2.608988 CCACCAGGGCTCCTCTGT 60.609 66.667 0.00 0.00 0.00 3.41
3209 3286 2.390599 CGACAAGGCCATGTGTCCG 61.391 63.158 20.20 12.29 40.91 4.79
3213 3290 2.596851 AAGGCCATGTGTCCGCTCT 61.597 57.895 5.01 0.00 0.00 4.09
3262 3339 3.174779 GAGGATAGGGACCCCAGATAAC 58.825 54.545 7.00 0.00 38.92 1.89
3351 3430 1.276421 CGACTCTTGGTCCACCTCATT 59.724 52.381 0.00 0.00 41.64 2.57
3362 3441 2.308570 TCCACCTCATTGGCATTGTAGT 59.691 45.455 9.03 5.51 40.22 2.73
3372 3451 1.376609 GCATTGTAGTGGAAGGCCGG 61.377 60.000 0.00 0.00 36.79 6.13
3508 3587 0.968393 GACTCCTTCTCCGACCAGCT 60.968 60.000 0.00 0.00 0.00 4.24
3510 3589 0.610687 CTCCTTCTCCGACCAGCTTT 59.389 55.000 0.00 0.00 0.00 3.51
3542 3621 4.158764 CGAGGAGTTTGAGGTTATGTCTCT 59.841 45.833 0.00 0.00 32.78 3.10
3593 3672 2.028385 GTCCAACCCACTACATCGTCTT 60.028 50.000 0.00 0.00 0.00 3.01
3594 3673 2.028476 TCCAACCCACTACATCGTCTTG 60.028 50.000 0.00 0.00 0.00 3.02
3622 3701 2.339728 GACGACAGTCTGTCTTCCAG 57.660 55.000 26.46 15.16 44.85 3.86
3655 3734 2.423892 TGACATCTTCTAGCTCCGACAC 59.576 50.000 0.00 0.00 0.00 3.67
3662 3741 1.066645 TCTAGCTCCGACACGTGACTA 60.067 52.381 25.01 11.75 0.00 2.59
3717 3796 3.830178 TCGATGGTGTTTCAGAGGTCTAA 59.170 43.478 0.00 0.00 0.00 2.10
3733 3812 3.751698 GGTCTAAAGACGGCATCAAGTTT 59.248 43.478 4.13 0.00 45.65 2.66
3734 3813 4.142881 GGTCTAAAGACGGCATCAAGTTTC 60.143 45.833 4.13 0.00 45.65 2.78
3735 3814 2.969443 AAAGACGGCATCAAGTTTCG 57.031 45.000 0.00 0.00 0.00 3.46
3736 3815 1.156736 AAGACGGCATCAAGTTTCGG 58.843 50.000 0.00 0.00 0.00 4.30
3737 3816 0.034896 AGACGGCATCAAGTTTCGGT 59.965 50.000 0.00 0.00 0.00 4.69
3738 3817 1.274167 AGACGGCATCAAGTTTCGGTA 59.726 47.619 0.00 0.00 0.00 4.02
3739 3818 2.070783 GACGGCATCAAGTTTCGGTAA 58.929 47.619 0.00 0.00 0.00 2.85
3740 3819 2.073816 ACGGCATCAAGTTTCGGTAAG 58.926 47.619 0.00 0.00 0.00 2.34
3741 3820 1.396996 CGGCATCAAGTTTCGGTAAGG 59.603 52.381 0.00 0.00 0.00 2.69
3742 3821 2.706890 GGCATCAAGTTTCGGTAAGGA 58.293 47.619 0.00 0.00 0.00 3.36
3743 3822 2.418976 GGCATCAAGTTTCGGTAAGGAC 59.581 50.000 0.00 0.00 0.00 3.85
3744 3823 3.071479 GCATCAAGTTTCGGTAAGGACA 58.929 45.455 0.00 0.00 0.00 4.02
3745 3824 3.689649 GCATCAAGTTTCGGTAAGGACAT 59.310 43.478 0.00 0.00 0.00 3.06
3746 3825 4.437390 GCATCAAGTTTCGGTAAGGACATG 60.437 45.833 0.00 0.00 0.00 3.21
3747 3826 3.071479 TCAAGTTTCGGTAAGGACATGC 58.929 45.455 0.00 0.00 0.00 4.06
3748 3827 2.109425 AGTTTCGGTAAGGACATGCC 57.891 50.000 0.00 0.00 0.00 4.40
3750 3829 1.022451 TTTCGGTAAGGACATGCCGC 61.022 55.000 2.67 0.00 46.52 6.53
3751 3830 2.862674 TTCGGTAAGGACATGCCGCC 62.863 60.000 2.67 5.32 46.52 6.13
3752 3831 2.895372 GGTAAGGACATGCCGCCG 60.895 66.667 0.00 0.00 43.43 6.46
3753 3832 2.185867 GTAAGGACATGCCGCCGA 59.814 61.111 0.00 0.00 43.43 5.54
3754 3833 2.171725 GTAAGGACATGCCGCCGAC 61.172 63.158 0.00 0.00 43.43 4.79
3755 3834 3.709880 TAAGGACATGCCGCCGACG 62.710 63.158 0.00 0.00 43.43 5.12
3758 3837 4.796231 GACATGCCGCCGACGAGT 62.796 66.667 0.00 0.00 43.93 4.18
3765 3844 4.778415 CGCCGACGAGTGTGGGAG 62.778 72.222 0.00 0.00 46.14 4.30
3766 3845 4.436998 GCCGACGAGTGTGGGAGG 62.437 72.222 0.00 0.00 46.14 4.30
3767 3846 2.675423 CCGACGAGTGTGGGAGGA 60.675 66.667 0.00 0.00 46.14 3.71
3768 3847 2.273179 CCGACGAGTGTGGGAGGAA 61.273 63.158 0.00 0.00 46.14 3.36
3769 3848 1.213013 CGACGAGTGTGGGAGGAAG 59.787 63.158 0.00 0.00 0.00 3.46
3770 3849 1.241990 CGACGAGTGTGGGAGGAAGA 61.242 60.000 0.00 0.00 0.00 2.87
3771 3850 1.187087 GACGAGTGTGGGAGGAAGAT 58.813 55.000 0.00 0.00 0.00 2.40
3772 3851 0.898320 ACGAGTGTGGGAGGAAGATG 59.102 55.000 0.00 0.00 0.00 2.90
3773 3852 0.176680 CGAGTGTGGGAGGAAGATGG 59.823 60.000 0.00 0.00 0.00 3.51
3774 3853 1.280457 GAGTGTGGGAGGAAGATGGT 58.720 55.000 0.00 0.00 0.00 3.55
3775 3854 0.987294 AGTGTGGGAGGAAGATGGTG 59.013 55.000 0.00 0.00 0.00 4.17
3776 3855 0.693049 GTGTGGGAGGAAGATGGTGT 59.307 55.000 0.00 0.00 0.00 4.16
3777 3856 1.906574 GTGTGGGAGGAAGATGGTGTA 59.093 52.381 0.00 0.00 0.00 2.90
3778 3857 2.093447 GTGTGGGAGGAAGATGGTGTAG 60.093 54.545 0.00 0.00 0.00 2.74
3779 3858 2.225522 TGTGGGAGGAAGATGGTGTAGA 60.226 50.000 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 5.757099 TCATGAGGATGCATATCTCACAT 57.243 39.130 25.31 13.83 33.68 3.21
36 37 6.605471 TGAACCATACATGACTCACTACTT 57.395 37.500 0.00 0.00 0.00 2.24
61 62 5.402464 AAAATCAACGAAAACCACATTGC 57.598 34.783 0.00 0.00 0.00 3.56
63 64 7.264947 AGAGAAAAATCAACGAAAACCACATT 58.735 30.769 0.00 0.00 0.00 2.71
80 81 6.099845 ACAGGTAGAAGAACTGGAGAGAAAAA 59.900 38.462 0.00 0.00 36.57 1.94
85 86 5.476091 AAACAGGTAGAAGAACTGGAGAG 57.524 43.478 0.00 0.00 36.57 3.20
104 105 6.945072 ACACGACATGAGTTAGAAAGAAAAC 58.055 36.000 0.00 0.00 0.00 2.43
118 119 5.828299 AAGGAAAAGAAAACACGACATGA 57.172 34.783 0.00 0.00 0.00 3.07
157 163 9.758651 TCTTAAAAAGGGAAAACATAGAAAAGC 57.241 29.630 0.00 0.00 0.00 3.51
355 364 6.143758 GTCGCAATTTAAAGAAATGCTCACAA 59.856 34.615 12.98 0.00 35.38 3.33
410 419 9.241919 TGTAATGTATCAAAAGATGTTCACCAT 57.758 29.630 0.00 0.00 36.13 3.55
608 626 3.771160 CTACTTGGGCCGCGACCT 61.771 66.667 12.39 0.00 0.00 3.85
615 633 1.153549 CACGAGAGCTACTTGGGCC 60.154 63.158 0.00 0.00 34.46 5.80
656 674 5.198965 AGTCCTCCTACTCAACGCTATAAA 58.801 41.667 0.00 0.00 0.00 1.40
712 731 2.181125 TGCAACAGTTAGGATCCGGTA 58.819 47.619 5.98 0.00 0.00 4.02
741 760 5.469084 GCTATAGCGGGCTATTTAAAACAGT 59.531 40.000 17.49 0.00 39.65 3.55
742 761 5.928153 GCTATAGCGGGCTATTTAAAACAG 58.072 41.667 17.49 8.76 39.65 3.16
743 762 5.934935 GCTATAGCGGGCTATTTAAAACA 57.065 39.130 17.49 0.00 39.65 2.83
764 783 0.171455 ATAGCGTGCTATAGCGGAGC 59.829 55.000 22.98 22.98 45.83 4.70
765 784 3.326733 CTATAGCGTGCTATAGCGGAG 57.673 52.381 27.04 13.65 46.26 4.63
779 798 3.626217 AGCCCTTTTGTAAACGCTATAGC 59.374 43.478 15.09 15.09 37.78 2.97
780 799 5.569413 CAAGCCCTTTTGTAAACGCTATAG 58.431 41.667 0.00 0.00 0.00 1.31
781 800 4.142556 GCAAGCCCTTTTGTAAACGCTATA 60.143 41.667 0.00 0.00 0.00 1.31
782 801 3.366985 GCAAGCCCTTTTGTAAACGCTAT 60.367 43.478 0.00 0.00 0.00 2.97
783 802 2.030628 GCAAGCCCTTTTGTAAACGCTA 60.031 45.455 0.00 0.00 0.00 4.26
784 803 1.269569 GCAAGCCCTTTTGTAAACGCT 60.270 47.619 0.00 0.00 0.00 5.07
785 804 1.136690 GCAAGCCCTTTTGTAAACGC 58.863 50.000 0.00 0.00 0.00 4.84
786 805 1.404477 CGCAAGCCCTTTTGTAAACG 58.596 50.000 0.00 0.00 0.00 3.60
800 819 3.308323 GGATCAAAGTCTCTTAGCGCAAG 59.692 47.826 11.47 11.67 35.38 4.01
801 820 3.262420 GGATCAAAGTCTCTTAGCGCAA 58.738 45.455 11.47 0.50 0.00 4.85
802 821 2.233676 TGGATCAAAGTCTCTTAGCGCA 59.766 45.455 11.47 0.00 0.00 6.09
803 822 2.893637 TGGATCAAAGTCTCTTAGCGC 58.106 47.619 0.00 0.00 0.00 5.92
804 823 4.690748 TGTTTGGATCAAAGTCTCTTAGCG 59.309 41.667 0.00 0.00 33.82 4.26
805 824 6.560253 TTGTTTGGATCAAAGTCTCTTAGC 57.440 37.500 0.00 0.00 33.82 3.09
806 825 8.786898 TCATTTGTTTGGATCAAAGTCTCTTAG 58.213 33.333 0.00 0.00 38.02 2.18
807 826 8.690203 TCATTTGTTTGGATCAAAGTCTCTTA 57.310 30.769 0.00 0.00 38.02 2.10
808 827 7.587037 TCATTTGTTTGGATCAAAGTCTCTT 57.413 32.000 0.00 0.00 38.02 2.85
809 828 7.068593 TGTTCATTTGTTTGGATCAAAGTCTCT 59.931 33.333 0.00 0.00 38.02 3.10
810 829 7.202526 TGTTCATTTGTTTGGATCAAAGTCTC 58.797 34.615 0.00 0.00 38.02 3.36
811 830 7.111247 TGTTCATTTGTTTGGATCAAAGTCT 57.889 32.000 0.00 0.00 38.02 3.24
812 831 7.769272 TTGTTCATTTGTTTGGATCAAAGTC 57.231 32.000 0.00 0.00 38.02 3.01
813 832 7.605691 TGTTTGTTCATTTGTTTGGATCAAAGT 59.394 29.630 0.00 0.00 38.02 2.66
814 833 7.972527 TGTTTGTTCATTTGTTTGGATCAAAG 58.027 30.769 0.00 0.00 38.02 2.77
815 834 7.912056 TGTTTGTTCATTTGTTTGGATCAAA 57.088 28.000 0.00 0.00 38.77 2.69
816 835 8.503458 AATGTTTGTTCATTTGTTTGGATCAA 57.497 26.923 0.00 0.00 34.86 2.57
817 836 8.503458 AAATGTTTGTTCATTTGTTTGGATCA 57.497 26.923 0.00 0.00 43.50 2.92
818 837 8.610896 TGAAATGTTTGTTCATTTGTTTGGATC 58.389 29.630 8.96 0.00 44.62 3.36
819 838 8.503458 TGAAATGTTTGTTCATTTGTTTGGAT 57.497 26.923 8.96 0.00 44.62 3.41
820 839 7.912056 TGAAATGTTTGTTCATTTGTTTGGA 57.088 28.000 8.96 0.00 44.62 3.53
821 840 8.961294 TTTGAAATGTTTGTTCATTTGTTTGG 57.039 26.923 8.96 0.00 44.62 3.28
824 843 9.934190 GCTATTTGAAATGTTTGTTCATTTGTT 57.066 25.926 8.96 0.00 44.62 2.83
825 844 8.274939 CGCTATTTGAAATGTTTGTTCATTTGT 58.725 29.630 8.96 0.00 44.62 2.83
826 845 7.266756 GCGCTATTTGAAATGTTTGTTCATTTG 59.733 33.333 0.00 0.00 44.62 2.32
827 846 7.290118 GCGCTATTTGAAATGTTTGTTCATTT 58.710 30.769 0.00 4.66 46.41 2.32
828 847 6.399880 CGCGCTATTTGAAATGTTTGTTCATT 60.400 34.615 5.56 0.00 39.35 2.57
829 848 5.060816 CGCGCTATTTGAAATGTTTGTTCAT 59.939 36.000 5.56 0.00 35.03 2.57
830 849 4.381270 CGCGCTATTTGAAATGTTTGTTCA 59.619 37.500 5.56 0.00 33.21 3.18
831 850 4.718168 GCGCGCTATTTGAAATGTTTGTTC 60.718 41.667 26.67 0.00 0.00 3.18
832 851 3.121113 GCGCGCTATTTGAAATGTTTGTT 59.879 39.130 26.67 0.00 0.00 2.83
833 852 2.661195 GCGCGCTATTTGAAATGTTTGT 59.339 40.909 26.67 0.00 0.00 2.83
834 853 2.916716 AGCGCGCTATTTGAAATGTTTG 59.083 40.909 35.79 0.00 0.00 2.93
835 854 3.216147 AGCGCGCTATTTGAAATGTTT 57.784 38.095 35.79 1.95 0.00 2.83
836 855 2.919666 AGCGCGCTATTTGAAATGTT 57.080 40.000 35.79 2.52 0.00 2.71
837 856 4.377431 GCTATAGCGCGCTATTTGAAATGT 60.377 41.667 46.76 28.88 39.65 2.71
838 857 4.084507 GCTATAGCGCGCTATTTGAAATG 58.915 43.478 46.76 29.61 39.65 2.32
839 858 4.327854 GCTATAGCGCGCTATTTGAAAT 57.672 40.909 46.76 31.12 39.65 2.17
840 859 3.788434 GCTATAGCGCGCTATTTGAAA 57.212 42.857 46.76 31.88 39.65 2.69
859 878 0.171455 ATAGCGTGCTATAGCGGAGC 59.829 55.000 22.98 22.98 45.83 4.70
860 879 3.326733 CTATAGCGTGCTATAGCGGAG 57.673 52.381 27.04 13.65 46.26 4.63
866 885 5.400066 TCCAAATGCTATAGCGTGCTATA 57.600 39.130 20.02 17.96 45.83 1.31
867 886 4.271696 TCCAAATGCTATAGCGTGCTAT 57.728 40.909 20.02 17.65 45.83 2.97
868 887 3.744238 TCCAAATGCTATAGCGTGCTA 57.256 42.857 20.02 3.73 45.83 3.49
869 888 2.620251 TCCAAATGCTATAGCGTGCT 57.380 45.000 20.02 7.98 45.83 4.40
870 889 2.872245 TCTTCCAAATGCTATAGCGTGC 59.128 45.455 20.02 0.00 45.83 5.34
871 890 3.496130 CCTCTTCCAAATGCTATAGCGTG 59.504 47.826 20.02 16.14 45.83 5.34
872 891 3.134804 ACCTCTTCCAAATGCTATAGCGT 59.865 43.478 19.55 16.84 45.83 5.07
873 892 3.733337 ACCTCTTCCAAATGCTATAGCG 58.267 45.455 19.55 5.29 45.83 4.26
874 893 4.068599 GGACCTCTTCCAAATGCTATAGC 58.931 47.826 18.18 18.18 45.10 2.97
875 894 4.310769 CGGACCTCTTCCAAATGCTATAG 58.689 47.826 0.00 0.00 46.29 1.31
876 895 3.494398 GCGGACCTCTTCCAAATGCTATA 60.494 47.826 0.00 0.00 46.29 1.31
877 896 2.746472 GCGGACCTCTTCCAAATGCTAT 60.746 50.000 0.00 0.00 46.29 2.97
878 897 1.406887 GCGGACCTCTTCCAAATGCTA 60.407 52.381 0.00 0.00 46.29 3.49
879 898 0.678048 GCGGACCTCTTCCAAATGCT 60.678 55.000 0.00 0.00 46.29 3.79
880 899 1.657751 GGCGGACCTCTTCCAAATGC 61.658 60.000 0.00 0.00 46.29 3.56
881 900 1.369091 CGGCGGACCTCTTCCAAATG 61.369 60.000 0.00 0.00 46.29 2.32
882 901 1.078426 CGGCGGACCTCTTCCAAAT 60.078 57.895 0.00 0.00 46.29 2.32
883 902 2.047213 AACGGCGGACCTCTTCCAAA 62.047 55.000 13.24 0.00 46.29 3.28
884 903 1.186917 TAACGGCGGACCTCTTCCAA 61.187 55.000 13.24 0.00 46.29 3.53
885 904 1.186917 TTAACGGCGGACCTCTTCCA 61.187 55.000 13.24 0.00 46.29 3.53
886 905 0.459759 CTTAACGGCGGACCTCTTCC 60.460 60.000 13.24 0.00 41.75 3.46
887 906 0.529378 TCTTAACGGCGGACCTCTTC 59.471 55.000 13.24 0.00 0.00 2.87
888 907 1.134788 CATCTTAACGGCGGACCTCTT 60.135 52.381 13.24 0.00 0.00 2.85
889 908 0.460311 CATCTTAACGGCGGACCTCT 59.540 55.000 13.24 0.00 0.00 3.69
890 909 1.152383 GCATCTTAACGGCGGACCTC 61.152 60.000 13.24 0.00 0.00 3.85
891 910 1.153429 GCATCTTAACGGCGGACCT 60.153 57.895 13.24 0.00 0.00 3.85
892 911 0.743345 AAGCATCTTAACGGCGGACC 60.743 55.000 13.24 0.00 0.00 4.46
893 912 1.859080 CTAAGCATCTTAACGGCGGAC 59.141 52.381 13.24 0.00 0.00 4.79
894 913 1.805120 GCTAAGCATCTTAACGGCGGA 60.805 52.381 13.24 0.00 0.00 5.54
895 914 0.582005 GCTAAGCATCTTAACGGCGG 59.418 55.000 13.24 0.00 0.00 6.13
896 915 1.004927 GTGCTAAGCATCTTAACGGCG 60.005 52.381 4.80 4.80 41.91 6.46
897 916 1.004927 CGTGCTAAGCATCTTAACGGC 60.005 52.381 0.00 0.00 41.91 5.68
898 917 1.004927 GCGTGCTAAGCATCTTAACGG 60.005 52.381 10.75 0.00 41.91 4.44
899 918 1.927174 AGCGTGCTAAGCATCTTAACG 59.073 47.619 0.00 6.50 41.91 3.18
900 919 5.659048 AATAGCGTGCTAAGCATCTTAAC 57.341 39.130 5.56 0.00 41.91 2.01
901 920 7.780008 TTAAATAGCGTGCTAAGCATCTTAA 57.220 32.000 5.56 1.95 41.91 1.85
902 921 7.780008 TTTAAATAGCGTGCTAAGCATCTTA 57.220 32.000 5.56 0.00 41.91 2.10
903 922 6.677781 TTTAAATAGCGTGCTAAGCATCTT 57.322 33.333 5.56 0.00 41.91 2.40
904 923 6.316390 AGTTTTAAATAGCGTGCTAAGCATCT 59.684 34.615 5.56 0.00 41.91 2.90
905 924 6.487103 AGTTTTAAATAGCGTGCTAAGCATC 58.513 36.000 5.56 0.00 41.91 3.91
906 925 6.436843 AGTTTTAAATAGCGTGCTAAGCAT 57.563 33.333 5.56 0.00 41.91 3.79
907 926 5.873179 AGTTTTAAATAGCGTGCTAAGCA 57.127 34.783 5.56 0.00 37.01 3.91
908 927 7.627340 TCATAGTTTTAAATAGCGTGCTAAGC 58.373 34.615 5.56 0.00 31.73 3.09
909 928 9.798885 GATCATAGTTTTAAATAGCGTGCTAAG 57.201 33.333 5.56 0.00 31.73 2.18
910 929 9.542462 AGATCATAGTTTTAAATAGCGTGCTAA 57.458 29.630 5.56 0.00 31.73 3.09
911 930 9.542462 AAGATCATAGTTTTAAATAGCGTGCTA 57.458 29.630 3.73 3.73 0.00 3.49
912 931 8.438676 AAGATCATAGTTTTAAATAGCGTGCT 57.561 30.769 0.00 0.00 0.00 4.40
913 932 8.552034 AGAAGATCATAGTTTTAAATAGCGTGC 58.448 33.333 0.00 0.00 0.00 5.34
915 934 9.262358 GGAGAAGATCATAGTTTTAAATAGCGT 57.738 33.333 0.00 0.00 0.00 5.07
916 935 8.428536 CGGAGAAGATCATAGTTTTAAATAGCG 58.571 37.037 0.00 0.00 0.00 4.26
917 936 9.477484 TCGGAGAAGATCATAGTTTTAAATAGC 57.523 33.333 0.00 0.00 0.00 2.97
919 938 9.459640 CGTCGGAGAAGATCATAGTTTTAAATA 57.540 33.333 0.00 0.00 38.59 1.40
920 939 7.042658 GCGTCGGAGAAGATCATAGTTTTAAAT 60.043 37.037 0.00 0.00 38.59 1.40
921 940 6.255020 GCGTCGGAGAAGATCATAGTTTTAAA 59.745 38.462 0.00 0.00 38.59 1.52
922 941 5.747197 GCGTCGGAGAAGATCATAGTTTTAA 59.253 40.000 0.00 0.00 38.59 1.52
923 942 5.067413 AGCGTCGGAGAAGATCATAGTTTTA 59.933 40.000 0.00 0.00 38.59 1.52
924 943 4.113354 GCGTCGGAGAAGATCATAGTTTT 58.887 43.478 0.00 0.00 38.59 2.43
925 944 3.381908 AGCGTCGGAGAAGATCATAGTTT 59.618 43.478 0.00 0.00 38.59 2.66
926 945 2.952978 AGCGTCGGAGAAGATCATAGTT 59.047 45.455 0.00 0.00 38.59 2.24
927 946 2.292016 CAGCGTCGGAGAAGATCATAGT 59.708 50.000 0.00 0.00 38.59 2.12
928 947 2.351253 CCAGCGTCGGAGAAGATCATAG 60.351 54.545 0.00 0.00 38.59 2.23
929 948 1.609072 CCAGCGTCGGAGAAGATCATA 59.391 52.381 0.00 0.00 38.59 2.15
930 949 0.387202 CCAGCGTCGGAGAAGATCAT 59.613 55.000 0.00 0.00 38.59 2.45
931 950 0.679960 TCCAGCGTCGGAGAAGATCA 60.680 55.000 0.00 0.00 38.59 2.92
932 951 2.107705 TCCAGCGTCGGAGAAGATC 58.892 57.895 0.00 0.00 38.59 2.75
933 952 4.338815 TCCAGCGTCGGAGAAGAT 57.661 55.556 0.00 0.00 38.59 2.40
1028 1050 1.595993 CTCTTCGCCTCGGTTCTCCA 61.596 60.000 0.00 0.00 0.00 3.86
1044 1066 1.545706 GCTTCCCCGTCCACTTCTCT 61.546 60.000 0.00 0.00 0.00 3.10
1142 1167 1.586422 CATCACCACTAAGGCCATCG 58.414 55.000 5.01 0.00 43.14 3.84
1157 1182 1.029947 TCTCTCGCGGTACTGCATCA 61.030 55.000 25.74 8.48 34.15 3.07
1160 1185 1.433471 CATCTCTCGCGGTACTGCA 59.567 57.895 25.74 12.22 34.15 4.41
1253 1278 1.341852 GGCTAGAAGAAGATCGGGGAC 59.658 57.143 0.00 0.00 0.00 4.46
1254 1279 1.705873 GGCTAGAAGAAGATCGGGGA 58.294 55.000 0.00 0.00 0.00 4.81
1257 1282 1.342819 CTGGGGCTAGAAGAAGATCGG 59.657 57.143 0.00 0.00 0.00 4.18
1270 1295 3.092511 ATGGTGATCGCTGGGGCT 61.093 61.111 6.18 0.00 36.09 5.19
1276 1301 0.977627 TGGTGGAGATGGTGATCGCT 60.978 55.000 6.18 0.00 33.34 4.93
1304 1329 5.774498 AGAATGAAAAATAGGAATCGGCC 57.226 39.130 0.00 0.00 0.00 6.13
1443 1479 1.142314 GGCGGCTTGTCGGTGTATA 59.858 57.895 0.00 0.00 0.00 1.47
1495 1531 1.442184 CACCGAGAAGACGACCACG 60.442 63.158 0.00 0.00 45.75 4.94
1576 1612 4.467084 TGGTCCGCTGAATCCCGC 62.467 66.667 0.00 0.00 0.00 6.13
1733 1794 0.995803 TGCCATAAACCCTGCCAGTA 59.004 50.000 0.00 0.00 0.00 2.74
1734 1795 0.336048 ATGCCATAAACCCTGCCAGT 59.664 50.000 0.00 0.00 0.00 4.00
1760 1821 9.095065 GTCGAATTAACCTATGAATACAACAGT 57.905 33.333 0.00 0.00 0.00 3.55
2149 2213 4.124238 GCATGGGATGATGTTGGAAAATG 58.876 43.478 0.00 0.00 0.00 2.32
2335 2399 3.050275 GTGTGGCAGCGAACTCCC 61.050 66.667 0.00 0.00 0.00 4.30
2428 2492 1.453379 GGATCCCTCGGTGACTCGA 60.453 63.158 0.00 0.00 37.60 4.04
2461 2525 1.656652 GTGGAGTGAATCGTCCATGG 58.343 55.000 4.97 4.97 44.71 3.66
2474 2538 1.267121 AGGTTGCAGATACGTGGAGT 58.733 50.000 0.00 0.00 0.00 3.85
2477 2541 2.093306 TCAAGGTTGCAGATACGTGG 57.907 50.000 0.00 0.00 0.00 4.94
2479 2543 3.262420 GTCATCAAGGTTGCAGATACGT 58.738 45.455 0.00 0.00 0.00 3.57
2487 2551 1.168714 GTCCCTGTCATCAAGGTTGC 58.831 55.000 0.00 0.00 0.00 4.17
2571 2635 0.371989 CACAGAAACAACACGACGCA 59.628 50.000 0.00 0.00 0.00 5.24
2587 2651 1.416401 AGCTCTCCGTTTTCTTCCACA 59.584 47.619 0.00 0.00 0.00 4.17
2612 2676 1.372872 GCCATGCGTCCACCAAAAC 60.373 57.895 0.00 0.00 0.00 2.43
2667 2731 1.205893 GGGCAAACAACACTTCACCAA 59.794 47.619 0.00 0.00 0.00 3.67
2699 2763 1.488812 ACACACACCCTTGCTTCTACA 59.511 47.619 0.00 0.00 0.00 2.74
2790 2854 3.961477 TGATGTGGTCAAACAAACTCG 57.039 42.857 0.00 0.00 32.78 4.18
2980 3052 7.875327 ATTTGACTAATAAAATGTACGGCCT 57.125 32.000 0.00 0.00 0.00 5.19
3209 3286 1.217779 GTGGCAGACAGAGGAGAGC 59.782 63.158 0.00 0.00 0.00 4.09
3213 3290 1.475169 CCAGTGTGGCAGACAGAGGA 61.475 60.000 17.69 0.00 34.28 3.71
3238 3315 0.178918 CTGGGGTCCCTATCCTCTCC 60.179 65.000 8.15 0.00 36.94 3.71
3262 3339 9.372369 AGGAATGAAACTCTAATTAAAGAGACG 57.628 33.333 11.44 0.00 44.93 4.18
3290 3367 3.096852 ACTGCACTATGCCACTACTGTA 58.903 45.455 0.00 0.00 44.23 2.74
3351 3430 0.323360 GGCCTTCCACTACAATGCCA 60.323 55.000 0.00 0.00 35.30 4.92
3362 3441 3.833645 CGATCGACCGGCCTTCCA 61.834 66.667 10.26 0.00 0.00 3.53
3372 3451 2.924290 CCAAAAGAGAAGGACGATCGAC 59.076 50.000 24.34 16.38 0.00 4.20
3508 3587 0.984230 AACTCCTCGAGGGCATCAAA 59.016 50.000 30.80 9.13 33.35 2.69
3510 3589 0.250234 CAAACTCCTCGAGGGCATCA 59.750 55.000 30.80 10.69 33.35 3.07
3593 3672 0.959553 GACTGTCGTCCCAGAGAACA 59.040 55.000 6.53 0.00 36.30 3.18
3594 3673 1.068194 CAGACTGTCGTCCCAGAGAAC 60.068 57.143 1.52 0.00 41.16 3.01
3622 3701 8.293867 AGCTAGAAGATGTCAACGATAACTATC 58.706 37.037 0.00 0.00 0.00 2.08
3625 3704 6.458232 AGCTAGAAGATGTCAACGATAACT 57.542 37.500 0.00 0.00 0.00 2.24
3634 3713 2.423892 GTGTCGGAGCTAGAAGATGTCA 59.576 50.000 0.00 0.00 0.00 3.58
3655 3734 2.126071 CAGCGGTGGGTAGTCACG 60.126 66.667 6.74 0.00 38.46 4.35
3717 3796 1.156736 CCGAAACTTGATGCCGTCTT 58.843 50.000 0.00 0.00 0.00 3.01
3735 3814 2.895372 CGGCGGCATGTCCTTACC 60.895 66.667 10.53 0.00 0.00 2.85
3736 3815 2.171725 GTCGGCGGCATGTCCTTAC 61.172 63.158 6.63 0.00 0.00 2.34
3737 3816 2.185867 GTCGGCGGCATGTCCTTA 59.814 61.111 6.63 0.00 0.00 2.69
3741 3820 4.796231 ACTCGTCGGCGGCATGTC 62.796 66.667 13.62 0.00 38.89 3.06
3748 3827 4.778415 CTCCCACACTCGTCGGCG 62.778 72.222 1.15 1.15 39.92 6.46
3749 3828 4.436998 CCTCCCACACTCGTCGGC 62.437 72.222 0.00 0.00 0.00 5.54
3750 3829 2.214181 CTTCCTCCCACACTCGTCGG 62.214 65.000 0.00 0.00 0.00 4.79
3751 3830 1.213013 CTTCCTCCCACACTCGTCG 59.787 63.158 0.00 0.00 0.00 5.12
3752 3831 1.134965 CATCTTCCTCCCACACTCGTC 60.135 57.143 0.00 0.00 0.00 4.20
3753 3832 0.898320 CATCTTCCTCCCACACTCGT 59.102 55.000 0.00 0.00 0.00 4.18
3754 3833 0.176680 CCATCTTCCTCCCACACTCG 59.823 60.000 0.00 0.00 0.00 4.18
3755 3834 1.065854 CACCATCTTCCTCCCACACTC 60.066 57.143 0.00 0.00 0.00 3.51
3756 3835 0.987294 CACCATCTTCCTCCCACACT 59.013 55.000 0.00 0.00 0.00 3.55
3757 3836 0.693049 ACACCATCTTCCTCCCACAC 59.307 55.000 0.00 0.00 0.00 3.82
3758 3837 2.187958 CTACACCATCTTCCTCCCACA 58.812 52.381 0.00 0.00 0.00 4.17
3759 3838 2.467880 TCTACACCATCTTCCTCCCAC 58.532 52.381 0.00 0.00 0.00 4.61
3760 3839 2.940514 TCTACACCATCTTCCTCCCA 57.059 50.000 0.00 0.00 0.00 4.37


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

AutoCloner maintained by Alex Coulton.