Multiple sequence alignment - TraesCS4D01G250200

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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 TraesCS4D01G250200 chr4D 100.000 2542 0 0 1 2542 419136189 419138730 0.000000e+00 4695.0
1 TraesCS4D01G250200 chr4D 99.366 631 4 0 1 631 419140401 419139771 0.000000e+00 1144.0
2 TraesCS4D01G250200 chr4D 92.598 635 39 5 1 631 46046614 46045984 0.000000e+00 905.0
3 TraesCS4D01G250200 chr4D 95.302 149 7 0 1237 1385 477749909 477750057 1.180000e-58 237.0
4 TraesCS4D01G250200 chr4D 94.937 79 4 0 1053 1131 477749833 477749911 9.550000e-25 124.0
5 TraesCS4D01G250200 chr4B 91.736 968 44 15 992 1927 516952398 516951435 0.000000e+00 1312.0
6 TraesCS4D01G250200 chr4B 93.919 148 9 0 1237 1384 603520189 603520336 9.150000e-55 224.0
7 TraesCS4D01G250200 chr4B 94.937 79 4 0 1053 1131 603520113 603520191 9.550000e-25 124.0
8 TraesCS4D01G250200 chr4B 92.537 67 0 2 865 926 516952571 516952505 9.680000e-15 91.6
9 TraesCS4D01G250200 chr4A 83.709 1197 71 49 872 1986 45858600 45859754 0.000000e+00 1016.0
10 TraesCS4D01G250200 chr4A 93.158 190 13 0 658 847 736464881 736465070 1.930000e-71 279.0
11 TraesCS4D01G250200 chr4A 94.771 153 8 0 1233 1385 684536232 684536384 3.270000e-59 239.0
12 TraesCS4D01G250200 chr4A 88.021 192 22 1 1461 1652 684536512 684536702 2.540000e-55 226.0
13 TraesCS4D01G250200 chr4A 94.118 85 5 0 1053 1137 684536084 684536168 2.050000e-26 130.0
14 TraesCS4D01G250200 chr2B 92.756 635 38 6 1 631 206284450 206283820 0.000000e+00 911.0
15 TraesCS4D01G250200 chr2B 85.047 214 27 4 424 635 579662267 579662477 1.980000e-51 213.0
16 TraesCS4D01G250200 chr7D 92.733 633 37 8 1 631 228280277 228279652 0.000000e+00 905.0
17 TraesCS4D01G250200 chr7D 82.219 658 74 27 1 635 146087367 146086730 6.230000e-146 527.0
18 TraesCS4D01G250200 chr7D 95.213 188 9 0 660 847 104080391 104080578 5.320000e-77 298.0
19 TraesCS4D01G250200 chr7D 94.624 186 10 0 660 845 17827664 17827849 3.200000e-74 289.0
20 TraesCS4D01G250200 chr7D 94.149 188 11 0 660 847 9084902 9085089 1.150000e-73 287.0
21 TraesCS4D01G250200 chr3A 92.441 635 39 8 1 631 88875429 88876058 0.000000e+00 898.0
22 TraesCS4D01G250200 chr3A 91.935 186 15 0 663 848 31546007 31546192 6.980000e-66 261.0
23 TraesCS4D01G250200 chr7A 92.114 634 42 5 1 631 323510269 323510897 0.000000e+00 887.0
24 TraesCS4D01G250200 chr7A 93.407 182 12 0 666 847 149551948 149552129 1.160000e-68 270.0
25 TraesCS4D01G250200 chr7A 78.238 193 26 11 460 650 466015758 466015936 2.670000e-20 110.0
26 TraesCS4D01G250200 chr7A 81.203 133 15 8 508 638 231257627 231257503 5.790000e-17 99.0
27 TraesCS4D01G250200 chr7A 100.000 28 0 0 2213 2240 113368761 113368734 5.000000e-03 52.8
28 TraesCS4D01G250200 chr5A 92.089 632 42 5 1 631 525083837 525083213 0.000000e+00 883.0
29 TraesCS4D01G250200 chr5A 79.298 285 34 13 1492 1755 703409173 703408893 2.600000e-40 176.0
30 TraesCS4D01G250200 chr5A 86.525 141 13 5 496 632 133903725 133903863 1.580000e-32 150.0
31 TraesCS4D01G250200 chr2D 91.969 635 42 9 1 631 133214339 133214968 0.000000e+00 881.0
32 TraesCS4D01G250200 chr2D 87.326 647 60 20 1 639 500786079 500785447 0.000000e+00 721.0
33 TraesCS4D01G250200 chr1D 94.681 188 10 0 660 847 4666477 4666664 2.470000e-75 292.0
34 TraesCS4D01G250200 chr1D 86.022 93 6 5 540 632 275417706 275417791 2.690000e-15 93.5
35 TraesCS4D01G250200 chr7B 91.351 185 16 0 663 847 642535951 642535767 1.170000e-63 254.0
36 TraesCS4D01G250200 chr7B 89.011 182 13 4 630 810 58873088 58873263 4.260000e-53 219.0
37 TraesCS4D01G250200 chr5D 74.925 670 107 50 1 643 361139562 361140197 1.510000e-62 250.0
38 TraesCS4D01G250200 chr5D 89.855 69 7 0 1064 1132 565702679 565702611 3.480000e-14 89.8
39 TraesCS4D01G250200 chr5D 79.310 116 21 3 1244 1358 565702607 565702494 7.540000e-11 78.7
40 TraesCS4D01G250200 chr6A 90.476 189 17 1 663 850 453879217 453879029 5.430000e-62 248.0
41 TraesCS4D01G250200 chr5B 87.500 80 10 0 1236 1315 529988417 529988496 2.690000e-15 93.5
42 TraesCS4D01G250200 chr5B 79.508 122 22 3 1238 1358 707440484 707440603 1.620000e-12 84.2
43 TraesCS4D01G250200 chr2A 76.503 183 30 11 457 638 271313220 271313050 1.250000e-13 87.9


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G250200 chr4D 419136189 419138730 2541 False 4695.0 4695 100.0000 1 2542 1 chr4D.!!$F1 2541
1 TraesCS4D01G250200 chr4D 419139771 419140401 630 True 1144.0 1144 99.3660 1 631 1 chr4D.!!$R2 630
2 TraesCS4D01G250200 chr4D 46045984 46046614 630 True 905.0 905 92.5980 1 631 1 chr4D.!!$R1 630
3 TraesCS4D01G250200 chr4B 516951435 516952571 1136 True 701.8 1312 92.1365 865 1927 2 chr4B.!!$R1 1062
4 TraesCS4D01G250200 chr4A 45858600 45859754 1154 False 1016.0 1016 83.7090 872 1986 1 chr4A.!!$F1 1114
5 TraesCS4D01G250200 chr2B 206283820 206284450 630 True 911.0 911 92.7560 1 631 1 chr2B.!!$R1 630
6 TraesCS4D01G250200 chr7D 228279652 228280277 625 True 905.0 905 92.7330 1 631 1 chr7D.!!$R2 630
7 TraesCS4D01G250200 chr7D 146086730 146087367 637 True 527.0 527 82.2190 1 635 1 chr7D.!!$R1 634
8 TraesCS4D01G250200 chr3A 88875429 88876058 629 False 898.0 898 92.4410 1 631 1 chr3A.!!$F2 630
9 TraesCS4D01G250200 chr7A 323510269 323510897 628 False 887.0 887 92.1140 1 631 1 chr7A.!!$F2 630
10 TraesCS4D01G250200 chr5A 525083213 525083837 624 True 883.0 883 92.0890 1 631 1 chr5A.!!$R1 630
11 TraesCS4D01G250200 chr2D 133214339 133214968 629 False 881.0 881 91.9690 1 631 1 chr2D.!!$F1 630
12 TraesCS4D01G250200 chr2D 500785447 500786079 632 True 721.0 721 87.3260 1 639 1 chr2D.!!$R1 638
13 TraesCS4D01G250200 chr5D 361139562 361140197 635 False 250.0 250 74.9250 1 643 1 chr5D.!!$F1 642

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
859 921 0.950836 TTTTACACGTGCTGCATGCT 59.049 45.0 21.11 9.5 43.37 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1989 2179 0.106015 AGTGGCATAATTGGGAGGCC 60.106 55.0 0.0 0.0 44.82 5.19 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
631 693 2.716244 CGAGGGACGTCATCGAGG 59.284 66.667 28.32 7.52 38.72 4.63
632 694 2.835705 CGAGGGACGTCATCGAGGG 61.836 68.421 28.32 7.22 38.72 4.30
633 695 1.753463 GAGGGACGTCATCGAGGGT 60.753 63.158 18.91 0.00 40.62 4.34
634 696 2.005960 GAGGGACGTCATCGAGGGTG 62.006 65.000 18.91 0.00 40.62 4.61
635 697 2.494918 GGACGTCATCGAGGGTGG 59.505 66.667 18.91 0.00 40.62 4.61
636 698 2.202756 GACGTCATCGAGGGTGGC 60.203 66.667 11.55 0.00 40.62 5.01
638 700 4.873129 CGTCATCGAGGGTGGCGG 62.873 72.222 3.65 0.00 40.71 6.13
649 711 4.545706 GTGGCGGCGGATGATGGA 62.546 66.667 9.78 0.00 0.00 3.41
650 712 3.559263 TGGCGGCGGATGATGGAT 61.559 61.111 9.78 0.00 0.00 3.41
651 713 2.743928 GGCGGCGGATGATGGATC 60.744 66.667 9.78 0.00 0.00 3.36
652 714 3.114616 GCGGCGGATGATGGATCG 61.115 66.667 9.78 0.00 30.87 3.69
657 719 2.046892 GGATGATGGATCGGGCGG 60.047 66.667 0.00 0.00 30.87 6.13
686 748 3.177249 GCGTAGGGTTCGCGTGAC 61.177 66.667 5.77 6.41 43.94 3.67
687 749 2.872925 CGTAGGGTTCGCGTGACG 60.873 66.667 5.77 0.00 45.62 4.35
688 750 2.505557 GTAGGGTTCGCGTGACGG 60.506 66.667 7.25 0.00 43.89 4.79
689 751 4.424566 TAGGGTTCGCGTGACGGC 62.425 66.667 7.25 0.00 43.89 5.68
710 772 4.897509 CCTGGTGGCTATCTGATATCAA 57.102 45.455 6.90 0.00 0.00 2.57
711 773 4.829968 CCTGGTGGCTATCTGATATCAAG 58.170 47.826 6.90 2.73 0.00 3.02
712 774 4.285517 CCTGGTGGCTATCTGATATCAAGT 59.714 45.833 6.90 1.00 0.00 3.16
713 775 5.221803 CCTGGTGGCTATCTGATATCAAGTT 60.222 44.000 6.90 0.00 0.00 2.66
714 776 5.614308 TGGTGGCTATCTGATATCAAGTTG 58.386 41.667 6.90 0.00 0.00 3.16
715 777 5.366477 TGGTGGCTATCTGATATCAAGTTGA 59.634 40.000 8.27 8.27 0.00 3.18
716 778 6.126796 TGGTGGCTATCTGATATCAAGTTGAA 60.127 38.462 10.14 0.00 0.00 2.69
717 779 6.426328 GGTGGCTATCTGATATCAAGTTGAAG 59.574 42.308 10.14 2.73 0.00 3.02
718 780 7.212976 GTGGCTATCTGATATCAAGTTGAAGA 58.787 38.462 10.14 8.49 0.00 2.87
719 781 7.384660 GTGGCTATCTGATATCAAGTTGAAGAG 59.615 40.741 10.14 0.00 0.00 2.85
720 782 6.873076 GGCTATCTGATATCAAGTTGAAGAGG 59.127 42.308 10.14 6.66 0.00 3.69
721 783 7.441017 GCTATCTGATATCAAGTTGAAGAGGT 58.559 38.462 10.14 2.66 0.00 3.85
722 784 8.580720 GCTATCTGATATCAAGTTGAAGAGGTA 58.419 37.037 10.14 3.65 0.00 3.08
724 786 7.353414 TCTGATATCAAGTTGAAGAGGTAGG 57.647 40.000 10.14 0.00 0.00 3.18
725 787 6.897966 TCTGATATCAAGTTGAAGAGGTAGGT 59.102 38.462 10.14 0.00 0.00 3.08
726 788 7.400339 TCTGATATCAAGTTGAAGAGGTAGGTT 59.600 37.037 10.14 0.00 0.00 3.50
727 789 7.918076 TGATATCAAGTTGAAGAGGTAGGTTT 58.082 34.615 10.14 0.00 0.00 3.27
728 790 9.042450 TGATATCAAGTTGAAGAGGTAGGTTTA 57.958 33.333 10.14 0.00 0.00 2.01
729 791 9.535878 GATATCAAGTTGAAGAGGTAGGTTTAG 57.464 37.037 10.14 0.00 0.00 1.85
730 792 6.110411 TCAAGTTGAAGAGGTAGGTTTAGG 57.890 41.667 2.20 0.00 0.00 2.69
731 793 5.012768 TCAAGTTGAAGAGGTAGGTTTAGGG 59.987 44.000 2.20 0.00 0.00 3.53
732 794 4.500452 AGTTGAAGAGGTAGGTTTAGGGT 58.500 43.478 0.00 0.00 0.00 4.34
733 795 4.912133 AGTTGAAGAGGTAGGTTTAGGGTT 59.088 41.667 0.00 0.00 0.00 4.11
734 796 5.371769 AGTTGAAGAGGTAGGTTTAGGGTTT 59.628 40.000 0.00 0.00 0.00 3.27
735 797 5.917545 TGAAGAGGTAGGTTTAGGGTTTT 57.082 39.130 0.00 0.00 0.00 2.43
736 798 5.627135 TGAAGAGGTAGGTTTAGGGTTTTG 58.373 41.667 0.00 0.00 0.00 2.44
737 799 4.030314 AGAGGTAGGTTTAGGGTTTTGC 57.970 45.455 0.00 0.00 0.00 3.68
738 800 3.396611 AGAGGTAGGTTTAGGGTTTTGCA 59.603 43.478 0.00 0.00 0.00 4.08
739 801 4.044191 AGAGGTAGGTTTAGGGTTTTGCAT 59.956 41.667 0.00 0.00 0.00 3.96
740 802 4.086457 AGGTAGGTTTAGGGTTTTGCATG 58.914 43.478 0.00 0.00 0.00 4.06
741 803 3.194755 GGTAGGTTTAGGGTTTTGCATGG 59.805 47.826 0.00 0.00 0.00 3.66
742 804 2.256306 AGGTTTAGGGTTTTGCATGGG 58.744 47.619 0.00 0.00 0.00 4.00
743 805 1.974957 GGTTTAGGGTTTTGCATGGGT 59.025 47.619 0.00 0.00 0.00 4.51
744 806 2.370519 GGTTTAGGGTTTTGCATGGGTT 59.629 45.455 0.00 0.00 0.00 4.11
745 807 3.398406 GTTTAGGGTTTTGCATGGGTTG 58.602 45.455 0.00 0.00 0.00 3.77
757 819 3.155093 CATGGGTTGCTAACATTCAGC 57.845 47.619 0.00 0.00 39.56 4.26
758 820 1.544724 TGGGTTGCTAACATTCAGCC 58.455 50.000 0.00 0.00 38.29 4.85
759 821 1.075374 TGGGTTGCTAACATTCAGCCT 59.925 47.619 0.00 0.00 38.29 4.58
760 822 1.745653 GGGTTGCTAACATTCAGCCTC 59.254 52.381 0.00 0.00 38.29 4.70
761 823 2.436417 GGTTGCTAACATTCAGCCTCA 58.564 47.619 0.00 0.00 38.29 3.86
762 824 2.162408 GGTTGCTAACATTCAGCCTCAC 59.838 50.000 0.00 0.00 38.29 3.51
763 825 1.725641 TGCTAACATTCAGCCTCACG 58.274 50.000 0.00 0.00 38.29 4.35
764 826 1.001974 TGCTAACATTCAGCCTCACGT 59.998 47.619 0.00 0.00 38.29 4.49
765 827 1.661112 GCTAACATTCAGCCTCACGTC 59.339 52.381 0.00 0.00 32.68 4.34
766 828 2.675317 GCTAACATTCAGCCTCACGTCT 60.675 50.000 0.00 0.00 32.68 4.18
767 829 2.086054 AACATTCAGCCTCACGTCTC 57.914 50.000 0.00 0.00 0.00 3.36
768 830 1.261480 ACATTCAGCCTCACGTCTCT 58.739 50.000 0.00 0.00 0.00 3.10
769 831 1.620819 ACATTCAGCCTCACGTCTCTT 59.379 47.619 0.00 0.00 0.00 2.85
770 832 2.037772 ACATTCAGCCTCACGTCTCTTT 59.962 45.455 0.00 0.00 0.00 2.52
771 833 3.258372 ACATTCAGCCTCACGTCTCTTTA 59.742 43.478 0.00 0.00 0.00 1.85
772 834 4.081420 ACATTCAGCCTCACGTCTCTTTAT 60.081 41.667 0.00 0.00 0.00 1.40
773 835 5.127194 ACATTCAGCCTCACGTCTCTTTATA 59.873 40.000 0.00 0.00 0.00 0.98
774 836 5.854010 TTCAGCCTCACGTCTCTTTATAT 57.146 39.130 0.00 0.00 0.00 0.86
775 837 6.954487 TTCAGCCTCACGTCTCTTTATATA 57.046 37.500 0.00 0.00 0.00 0.86
776 838 6.561737 TCAGCCTCACGTCTCTTTATATAG 57.438 41.667 0.00 0.00 0.00 1.31
777 839 6.296803 TCAGCCTCACGTCTCTTTATATAGA 58.703 40.000 0.00 0.00 0.00 1.98
778 840 6.943146 TCAGCCTCACGTCTCTTTATATAGAT 59.057 38.462 0.00 0.00 0.00 1.98
779 841 7.026562 CAGCCTCACGTCTCTTTATATAGATG 58.973 42.308 0.00 0.00 35.32 2.90
780 842 6.943146 AGCCTCACGTCTCTTTATATAGATGA 59.057 38.462 0.00 2.03 33.74 2.92
781 843 7.613801 AGCCTCACGTCTCTTTATATAGATGAT 59.386 37.037 0.00 0.00 33.74 2.45
782 844 7.913297 GCCTCACGTCTCTTTATATAGATGATC 59.087 40.741 0.00 0.00 33.74 2.92
783 845 8.951243 CCTCACGTCTCTTTATATAGATGATCA 58.049 37.037 0.00 0.00 33.74 2.92
836 898 8.242053 ACGTGTACATATACAATATGCTAGACC 58.758 37.037 0.00 0.00 42.99 3.85
837 899 7.701078 CGTGTACATATACAATATGCTAGACCC 59.299 40.741 0.00 0.00 42.99 4.46
838 900 8.750298 GTGTACATATACAATATGCTAGACCCT 58.250 37.037 0.00 0.00 42.99 4.34
839 901 9.984590 TGTACATATACAATATGCTAGACCCTA 57.015 33.333 6.79 0.00 38.40 3.53
847 909 8.904099 ACAATATGCTAGACCCTATTTTACAC 57.096 34.615 0.00 0.00 0.00 2.90
848 910 7.656137 ACAATATGCTAGACCCTATTTTACACG 59.344 37.037 0.00 0.00 0.00 4.49
849 911 5.609533 ATGCTAGACCCTATTTTACACGT 57.390 39.130 0.00 0.00 0.00 4.49
850 912 4.751060 TGCTAGACCCTATTTTACACGTG 58.249 43.478 15.48 15.48 0.00 4.49
851 913 3.554731 GCTAGACCCTATTTTACACGTGC 59.445 47.826 17.22 0.00 0.00 5.34
852 914 3.975168 AGACCCTATTTTACACGTGCT 57.025 42.857 17.22 5.64 0.00 4.40
853 915 3.596214 AGACCCTATTTTACACGTGCTG 58.404 45.455 17.22 0.00 0.00 4.41
854 916 2.081462 ACCCTATTTTACACGTGCTGC 58.919 47.619 17.22 0.00 0.00 5.25
855 917 2.080693 CCCTATTTTACACGTGCTGCA 58.919 47.619 17.22 0.00 0.00 4.41
856 918 2.682856 CCCTATTTTACACGTGCTGCAT 59.317 45.455 17.22 5.80 0.00 3.96
857 919 3.487376 CCCTATTTTACACGTGCTGCATG 60.487 47.826 19.72 19.72 0.00 4.06
858 920 1.981254 ATTTTACACGTGCTGCATGC 58.019 45.000 21.11 11.82 43.25 4.06
859 921 0.950836 TTTTACACGTGCTGCATGCT 59.049 45.000 21.11 9.50 43.37 3.79
860 922 1.802069 TTTACACGTGCTGCATGCTA 58.198 45.000 21.11 8.53 43.37 3.49
861 923 2.022764 TTACACGTGCTGCATGCTAT 57.977 45.000 21.11 9.64 43.37 2.97
862 924 1.289276 TACACGTGCTGCATGCTATG 58.711 50.000 21.11 14.35 43.37 2.23
946 1031 1.134610 CCCCAAAATTCATGGCTCTGC 60.135 52.381 4.98 0.00 36.58 4.26
969 1058 5.049818 GCAATACTGCTCTAGTAAATGCCTG 60.050 44.000 13.05 0.00 44.59 4.85
971 1060 6.978674 ATACTGCTCTAGTAAATGCCTGTA 57.021 37.500 0.00 0.00 44.64 2.74
974 1063 4.960938 TGCTCTAGTAAATGCCTGTATGG 58.039 43.478 0.00 0.00 39.35 2.74
1438 1585 7.500720 TGCCATGATAATCTGTGATTACTTG 57.499 36.000 0.00 5.88 0.00 3.16
1463 1610 6.563398 TTAATTAACTCGTGTGCGTCTATG 57.437 37.500 0.00 0.00 39.49 2.23
1550 1705 3.818210 GCCTAGAGTTCTGATCATCGAGA 59.182 47.826 0.00 0.00 0.00 4.04
1555 1710 5.192927 AGAGTTCTGATCATCGAGAAGACT 58.807 41.667 0.00 0.00 0.00 3.24
1841 2031 3.238441 GACTGAAGCGAGTACAGTTCTG 58.762 50.000 0.00 0.00 43.49 3.02
1844 2034 1.544691 GAAGCGAGTACAGTTCTGGGA 59.455 52.381 4.82 0.00 0.00 4.37
1867 2057 8.398665 GGGAAATGAATAATTATCTGTATCGGC 58.601 37.037 0.00 0.00 0.00 5.54
1882 2072 0.899720 TCGGCAGTTATTCGAGGGTT 59.100 50.000 0.00 0.00 0.00 4.11
1927 2117 8.046294 TCAAGTTTCAAGTTGTAAGTTTGCTA 57.954 30.769 11.38 0.00 39.69 3.49
1934 2124 3.252458 AGTTGTAAGTTTGCTAAAGCCGG 59.748 43.478 0.00 0.00 41.18 6.13
1953 2143 2.615493 CGGTGTAGCCCAAAACAGATCT 60.615 50.000 0.00 0.00 0.00 2.75
1964 2154 5.188434 CCAAAACAGATCTGAGATGGCTTA 58.812 41.667 29.27 0.00 0.00 3.09
1986 2176 1.094785 CGGGCCAGTTTTATCAGTGG 58.905 55.000 4.39 0.00 39.96 4.00
1990 2180 1.094785 CCAGTTTTATCAGTGGCGGG 58.905 55.000 0.00 0.00 30.24 6.13
1991 2181 0.451783 CAGTTTTATCAGTGGCGGGC 59.548 55.000 0.00 0.00 0.00 6.13
1992 2182 0.679960 AGTTTTATCAGTGGCGGGCC 60.680 55.000 1.86 1.86 0.00 5.80
1993 2183 0.679960 GTTTTATCAGTGGCGGGCCT 60.680 55.000 11.55 0.00 36.94 5.19
1994 2184 0.393808 TTTTATCAGTGGCGGGCCTC 60.394 55.000 11.55 7.48 36.94 4.70
1995 2185 2.265467 TTTATCAGTGGCGGGCCTCC 62.265 60.000 5.34 5.34 36.94 4.30
2000 2190 4.759205 GTGGCGGGCCTCCCAATT 62.759 66.667 10.69 0.00 45.83 2.32
2001 2191 3.018193 TGGCGGGCCTCCCAATTA 61.018 61.111 10.69 0.00 45.83 1.40
2002 2192 2.391130 TGGCGGGCCTCCCAATTAT 61.391 57.895 10.69 0.00 45.83 1.28
2003 2193 1.903404 GGCGGGCCTCCCAATTATG 60.903 63.158 0.00 0.00 45.83 1.90
2004 2194 2.564721 GCGGGCCTCCCAATTATGC 61.565 63.158 0.84 0.00 45.83 3.14
2005 2195 1.903404 CGGGCCTCCCAATTATGCC 60.903 63.158 0.84 0.00 45.83 4.40
2006 2196 1.232792 GGGCCTCCCAATTATGCCA 59.767 57.895 0.84 0.00 44.65 4.92
2007 2197 1.115326 GGGCCTCCCAATTATGCCAC 61.115 60.000 0.84 0.00 44.65 5.01
2008 2198 0.106015 GGCCTCCCAATTATGCCACT 60.106 55.000 0.00 0.00 41.76 4.00
2009 2199 1.035139 GCCTCCCAATTATGCCACTG 58.965 55.000 0.00 0.00 0.00 3.66
2010 2200 1.410083 GCCTCCCAATTATGCCACTGA 60.410 52.381 0.00 0.00 0.00 3.41
2011 2201 2.754186 GCCTCCCAATTATGCCACTGAT 60.754 50.000 0.00 0.00 0.00 2.90
2012 2202 3.498481 GCCTCCCAATTATGCCACTGATA 60.498 47.826 0.00 0.00 0.00 2.15
2013 2203 4.728772 CCTCCCAATTATGCCACTGATAA 58.271 43.478 0.00 0.00 0.00 1.75
2014 2204 5.139727 CCTCCCAATTATGCCACTGATAAA 58.860 41.667 0.00 0.00 0.00 1.40
2015 2205 5.598005 CCTCCCAATTATGCCACTGATAAAA 59.402 40.000 0.00 0.00 0.00 1.52
2016 2206 6.461509 CCTCCCAATTATGCCACTGATAAAAC 60.462 42.308 0.00 0.00 0.00 2.43
2017 2207 6.194235 TCCCAATTATGCCACTGATAAAACT 58.806 36.000 0.00 0.00 0.00 2.66
2018 2208 6.096705 TCCCAATTATGCCACTGATAAAACTG 59.903 38.462 0.00 0.00 0.00 3.16
2019 2209 6.275335 CCAATTATGCCACTGATAAAACTGG 58.725 40.000 0.00 0.00 0.00 4.00
2022 2212 1.544724 GCCACTGATAAAACTGGCCA 58.455 50.000 4.71 4.71 43.01 5.36
2023 2213 1.202348 GCCACTGATAAAACTGGCCAC 59.798 52.381 0.00 0.00 43.01 5.01
2024 2214 1.468520 CCACTGATAAAACTGGCCACG 59.531 52.381 0.00 0.00 0.00 4.94
2025 2215 1.468520 CACTGATAAAACTGGCCACGG 59.531 52.381 0.00 0.00 0.00 4.94
2026 2216 0.451783 CTGATAAAACTGGCCACGGC 59.548 55.000 0.00 0.00 41.06 5.68
2027 2217 1.302383 TGATAAAACTGGCCACGGCG 61.302 55.000 0.00 4.80 43.06 6.46
2028 2218 2.592623 GATAAAACTGGCCACGGCGC 62.593 60.000 6.90 0.00 43.06 6.53
2029 2219 3.835790 TAAAACTGGCCACGGCGCT 62.836 57.895 6.90 0.00 43.06 5.92
2048 2238 6.675515 GCGCTGCCAAAATAAATATAACTC 57.324 37.500 0.00 0.00 0.00 3.01
2049 2239 5.629435 GCGCTGCCAAAATAAATATAACTCC 59.371 40.000 0.00 0.00 0.00 3.85
2050 2240 6.515035 GCGCTGCCAAAATAAATATAACTCCT 60.515 38.462 0.00 0.00 0.00 3.69
2051 2241 7.425606 CGCTGCCAAAATAAATATAACTCCTT 58.574 34.615 0.00 0.00 0.00 3.36
2052 2242 7.920682 CGCTGCCAAAATAAATATAACTCCTTT 59.079 33.333 0.00 0.00 0.00 3.11
2053 2243 9.599866 GCTGCCAAAATAAATATAACTCCTTTT 57.400 29.630 0.00 0.00 0.00 2.27
2077 2267 2.812664 GCCAGGGAAAATAGGCTGG 58.187 57.895 0.00 0.00 43.70 4.85
2078 2268 2.812664 CCAGGGAAAATAGGCTGGC 58.187 57.895 0.00 0.00 0.00 4.85
2079 2269 0.756815 CCAGGGAAAATAGGCTGGCC 60.757 60.000 3.00 3.00 0.00 5.36
2080 2270 0.756815 CAGGGAAAATAGGCTGGCCC 60.757 60.000 8.11 0.28 36.58 5.80
2081 2271 1.221213 AGGGAAAATAGGCTGGCCCA 61.221 55.000 8.11 0.00 38.04 5.36
2082 2272 1.043116 GGGAAAATAGGCTGGCCCAC 61.043 60.000 8.11 0.00 35.63 4.61
2083 2273 1.043116 GGAAAATAGGCTGGCCCACC 61.043 60.000 8.11 0.37 36.58 4.61
2084 2274 1.001631 AAAATAGGCTGGCCCACCC 59.998 57.895 8.11 0.00 36.58 4.61
2085 2275 1.518431 AAAATAGGCTGGCCCACCCT 61.518 55.000 2.47 2.47 36.58 4.34
2086 2276 2.228841 AAATAGGCTGGCCCACCCTG 62.229 60.000 7.93 0.00 36.58 4.45
2100 2290 2.047655 CCTGCCAGCGAACGGTTA 60.048 61.111 0.00 0.00 0.00 2.85
2101 2291 2.388232 CCTGCCAGCGAACGGTTAC 61.388 63.158 0.00 0.00 0.00 2.50
2102 2292 1.374252 CTGCCAGCGAACGGTTACT 60.374 57.895 0.00 0.00 0.00 2.24
2103 2293 0.949105 CTGCCAGCGAACGGTTACTT 60.949 55.000 0.00 0.00 0.00 2.24
2104 2294 0.533308 TGCCAGCGAACGGTTACTTT 60.533 50.000 0.00 0.00 0.00 2.66
2105 2295 0.589708 GCCAGCGAACGGTTACTTTT 59.410 50.000 0.00 0.00 0.00 2.27
2106 2296 1.002142 GCCAGCGAACGGTTACTTTTT 60.002 47.619 0.00 0.00 0.00 1.94
2168 2358 9.492973 TTTTTACGAGCTAGGTGTTTAATAACT 57.507 29.630 0.00 0.00 35.24 2.24
2169 2359 9.492973 TTTTACGAGCTAGGTGTTTAATAACTT 57.507 29.630 0.00 0.00 35.24 2.66
2171 2361 9.573133 TTACGAGCTAGGTGTTTAATAACTTAC 57.427 33.333 0.00 0.00 35.24 2.34
2172 2362 7.038048 ACGAGCTAGGTGTTTAATAACTTACC 58.962 38.462 0.00 0.00 35.24 2.85
2173 2363 7.037438 CGAGCTAGGTGTTTAATAACTTACCA 58.963 38.462 0.00 0.00 34.40 3.25
2174 2364 7.546667 CGAGCTAGGTGTTTAATAACTTACCAA 59.453 37.037 0.00 0.00 34.40 3.67
2175 2365 9.223099 GAGCTAGGTGTTTAATAACTTACCAAA 57.777 33.333 0.00 0.00 34.40 3.28
2176 2366 9.577222 AGCTAGGTGTTTAATAACTTACCAAAA 57.423 29.630 0.00 0.00 34.40 2.44
2180 2370 8.644216 AGGTGTTTAATAACTTACCAAAAAGGG 58.356 33.333 0.00 0.00 37.11 3.95
2181 2371 8.640651 GGTGTTTAATAACTTACCAAAAAGGGA 58.359 33.333 0.00 0.00 37.11 4.20
2196 2386 9.871175 ACCAAAAAGGGAAGTAGTATTAGAAAA 57.129 29.630 0.00 0.00 43.89 2.29
2391 2581 9.658475 TTGTAGTGTATTTGAAAAATGTCTTCG 57.342 29.630 0.00 0.00 0.00 3.79
2392 2582 7.801315 TGTAGTGTATTTGAAAAATGTCTTCGC 59.199 33.333 0.00 0.00 0.00 4.70
2393 2583 6.734137 AGTGTATTTGAAAAATGTCTTCGCA 58.266 32.000 0.00 0.00 0.00 5.10
2394 2584 7.370383 AGTGTATTTGAAAAATGTCTTCGCAT 58.630 30.769 0.00 0.00 0.00 4.73
2395 2585 7.867403 AGTGTATTTGAAAAATGTCTTCGCATT 59.133 29.630 0.00 0.00 40.43 3.56
2397 2587 9.684448 TGTATTTGAAAAATGTCTTCGCATTTA 57.316 25.926 4.74 0.00 45.17 1.40
2399 2589 8.816640 ATTTGAAAAATGTCTTCGCATTTAGT 57.183 26.923 4.74 0.00 45.17 2.24
2400 2590 9.906660 ATTTGAAAAATGTCTTCGCATTTAGTA 57.093 25.926 4.74 0.00 45.17 1.82
2401 2591 9.737427 TTTGAAAAATGTCTTCGCATTTAGTAA 57.263 25.926 4.74 0.00 45.17 2.24
2402 2592 9.737427 TTGAAAAATGTCTTCGCATTTAGTAAA 57.263 25.926 0.00 0.00 45.17 2.01
2403 2593 9.737427 TGAAAAATGTCTTCGCATTTAGTAAAA 57.263 25.926 0.00 0.00 45.17 1.52
2410 2600 9.982291 TGTCTTCGCATTTAGTAAAATATTCAC 57.018 29.630 0.00 0.00 33.45 3.18
2411 2601 9.982291 GTCTTCGCATTTAGTAAAATATTCACA 57.018 29.630 0.00 0.00 33.45 3.58
2413 2603 9.988350 CTTCGCATTTAGTAAAATATTCACAGT 57.012 29.630 0.00 0.00 33.45 3.55
2481 2671 3.502123 AAAACCAATCTGGAAGGACGA 57.498 42.857 0.00 0.00 40.96 4.20
2482 2672 2.770164 AACCAATCTGGAAGGACGAG 57.230 50.000 0.00 0.00 40.96 4.18
2483 2673 0.250513 ACCAATCTGGAAGGACGAGC 59.749 55.000 0.00 0.00 40.96 5.03
2484 2674 0.250234 CCAATCTGGAAGGACGAGCA 59.750 55.000 0.00 0.00 40.96 4.26
2485 2675 1.134280 CCAATCTGGAAGGACGAGCAT 60.134 52.381 0.00 0.00 40.96 3.79
2486 2676 2.103094 CCAATCTGGAAGGACGAGCATA 59.897 50.000 0.00 0.00 40.96 3.14
2487 2677 3.432186 CCAATCTGGAAGGACGAGCATAA 60.432 47.826 0.00 0.00 40.96 1.90
2488 2678 4.191544 CAATCTGGAAGGACGAGCATAAA 58.808 43.478 0.00 0.00 0.00 1.40
2489 2679 3.973206 TCTGGAAGGACGAGCATAAAA 57.027 42.857 0.00 0.00 0.00 1.52
2490 2680 4.280436 TCTGGAAGGACGAGCATAAAAA 57.720 40.909 0.00 0.00 0.00 1.94
2525 2715 8.989653 AAAAACAAGAATAACACCGAAAGAAA 57.010 26.923 0.00 0.00 0.00 2.52
2526 2716 8.989653 AAAACAAGAATAACACCGAAAGAAAA 57.010 26.923 0.00 0.00 0.00 2.29
2527 2717 8.989653 AAACAAGAATAACACCGAAAGAAAAA 57.010 26.923 0.00 0.00 0.00 1.94
2528 2718 7.980742 ACAAGAATAACACCGAAAGAAAAAC 57.019 32.000 0.00 0.00 0.00 2.43
2529 2719 7.540299 ACAAGAATAACACCGAAAGAAAAACA 58.460 30.769 0.00 0.00 0.00 2.83
2530 2720 8.194769 ACAAGAATAACACCGAAAGAAAAACAT 58.805 29.630 0.00 0.00 0.00 2.71
2531 2721 9.672086 CAAGAATAACACCGAAAGAAAAACATA 57.328 29.630 0.00 0.00 0.00 2.29
2537 2727 8.989653 AACACCGAAAGAAAAACATAAAAGAA 57.010 26.923 0.00 0.00 0.00 2.52
2538 2728 8.989653 ACACCGAAAGAAAAACATAAAAGAAA 57.010 26.923 0.00 0.00 0.00 2.52
2539 2729 9.425577 ACACCGAAAGAAAAACATAAAAGAAAA 57.574 25.926 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
475 534 0.459063 CGGGGTGTAAACGGTAGAGC 60.459 60.000 0.00 0.00 0.00 4.09
632 694 3.832237 ATCCATCATCCGCCGCCAC 62.832 63.158 0.00 0.00 0.00 5.01
633 695 3.535629 GATCCATCATCCGCCGCCA 62.536 63.158 0.00 0.00 0.00 5.69
634 696 2.743928 GATCCATCATCCGCCGCC 60.744 66.667 0.00 0.00 0.00 6.13
635 697 3.114616 CGATCCATCATCCGCCGC 61.115 66.667 0.00 0.00 0.00 6.53
636 698 2.433145 CCGATCCATCATCCGCCG 60.433 66.667 0.00 0.00 0.00 6.46
638 700 2.743928 GCCCGATCCATCATCCGC 60.744 66.667 0.00 0.00 0.00 5.54
639 701 2.433145 CGCCCGATCCATCATCCG 60.433 66.667 0.00 0.00 0.00 4.18
640 702 2.046892 CCGCCCGATCCATCATCC 60.047 66.667 0.00 0.00 0.00 3.51
641 703 2.743928 GCCGCCCGATCCATCATC 60.744 66.667 0.00 0.00 0.00 2.92
642 704 4.687215 CGCCGCCCGATCCATCAT 62.687 66.667 0.00 0.00 40.02 2.45
670 732 2.872925 CGTCACGCGAACCCTACG 60.873 66.667 15.93 9.11 44.77 3.51
671 733 2.505557 CCGTCACGCGAACCCTAC 60.506 66.667 15.93 0.00 44.77 3.18
672 734 4.424566 GCCGTCACGCGAACCCTA 62.425 66.667 15.93 0.00 44.77 3.53
689 751 4.285517 ACTTGATATCAGATAGCCACCAGG 59.714 45.833 5.39 0.00 38.23 4.45
690 752 5.480642 ACTTGATATCAGATAGCCACCAG 57.519 43.478 5.39 0.00 0.00 4.00
691 753 5.366477 TCAACTTGATATCAGATAGCCACCA 59.634 40.000 5.39 0.00 0.00 4.17
692 754 5.858381 TCAACTTGATATCAGATAGCCACC 58.142 41.667 5.39 0.00 0.00 4.61
693 755 7.212976 TCTTCAACTTGATATCAGATAGCCAC 58.787 38.462 5.39 0.00 0.00 5.01
694 756 7.365497 TCTTCAACTTGATATCAGATAGCCA 57.635 36.000 5.39 0.00 0.00 4.75
695 757 6.873076 CCTCTTCAACTTGATATCAGATAGCC 59.127 42.308 5.39 0.00 0.00 3.93
696 758 7.441017 ACCTCTTCAACTTGATATCAGATAGC 58.559 38.462 5.39 0.00 0.00 2.97
698 760 9.083422 CCTACCTCTTCAACTTGATATCAGATA 57.917 37.037 5.39 0.00 0.00 1.98
699 761 7.566879 ACCTACCTCTTCAACTTGATATCAGAT 59.433 37.037 5.39 0.00 0.00 2.90
700 762 6.897966 ACCTACCTCTTCAACTTGATATCAGA 59.102 38.462 5.39 0.00 0.00 3.27
701 763 7.118496 ACCTACCTCTTCAACTTGATATCAG 57.882 40.000 5.39 3.35 0.00 2.90
702 764 7.496346 AACCTACCTCTTCAACTTGATATCA 57.504 36.000 0.00 0.00 0.00 2.15
703 765 9.535878 CTAAACCTACCTCTTCAACTTGATATC 57.464 37.037 0.00 0.00 0.00 1.63
704 766 8.487028 CCTAAACCTACCTCTTCAACTTGATAT 58.513 37.037 0.00 0.00 0.00 1.63
705 767 7.093024 CCCTAAACCTACCTCTTCAACTTGATA 60.093 40.741 0.00 0.00 0.00 2.15
706 768 6.296489 CCCTAAACCTACCTCTTCAACTTGAT 60.296 42.308 0.00 0.00 0.00 2.57
707 769 5.012768 CCCTAAACCTACCTCTTCAACTTGA 59.987 44.000 0.00 0.00 0.00 3.02
708 770 5.221864 ACCCTAAACCTACCTCTTCAACTTG 60.222 44.000 0.00 0.00 0.00 3.16
709 771 4.912133 ACCCTAAACCTACCTCTTCAACTT 59.088 41.667 0.00 0.00 0.00 2.66
710 772 4.500452 ACCCTAAACCTACCTCTTCAACT 58.500 43.478 0.00 0.00 0.00 3.16
711 773 4.904895 ACCCTAAACCTACCTCTTCAAC 57.095 45.455 0.00 0.00 0.00 3.18
712 774 5.917545 AAACCCTAAACCTACCTCTTCAA 57.082 39.130 0.00 0.00 0.00 2.69
713 775 5.627135 CAAAACCCTAAACCTACCTCTTCA 58.373 41.667 0.00 0.00 0.00 3.02
714 776 4.458295 GCAAAACCCTAAACCTACCTCTTC 59.542 45.833 0.00 0.00 0.00 2.87
715 777 4.141111 TGCAAAACCCTAAACCTACCTCTT 60.141 41.667 0.00 0.00 0.00 2.85
716 778 3.396611 TGCAAAACCCTAAACCTACCTCT 59.603 43.478 0.00 0.00 0.00 3.69
717 779 3.758425 TGCAAAACCCTAAACCTACCTC 58.242 45.455 0.00 0.00 0.00 3.85
718 780 3.887916 TGCAAAACCCTAAACCTACCT 57.112 42.857 0.00 0.00 0.00 3.08
719 781 3.194755 CCATGCAAAACCCTAAACCTACC 59.805 47.826 0.00 0.00 0.00 3.18
720 782 3.194755 CCCATGCAAAACCCTAAACCTAC 59.805 47.826 0.00 0.00 0.00 3.18
721 783 3.181416 ACCCATGCAAAACCCTAAACCTA 60.181 43.478 0.00 0.00 0.00 3.08
722 784 2.256306 CCCATGCAAAACCCTAAACCT 58.744 47.619 0.00 0.00 0.00 3.50
723 785 1.974957 ACCCATGCAAAACCCTAAACC 59.025 47.619 0.00 0.00 0.00 3.27
724 786 3.398406 CAACCCATGCAAAACCCTAAAC 58.602 45.455 0.00 0.00 0.00 2.01
725 787 3.760580 CAACCCATGCAAAACCCTAAA 57.239 42.857 0.00 0.00 0.00 1.85
737 799 2.159198 GGCTGAATGTTAGCAACCCATG 60.159 50.000 0.00 0.00 42.88 3.66
738 800 2.102578 GGCTGAATGTTAGCAACCCAT 58.897 47.619 0.00 0.00 42.88 4.00
739 801 1.075374 AGGCTGAATGTTAGCAACCCA 59.925 47.619 0.00 0.00 42.88 4.51
740 802 1.745653 GAGGCTGAATGTTAGCAACCC 59.254 52.381 0.00 0.00 42.88 4.11
741 803 2.162408 GTGAGGCTGAATGTTAGCAACC 59.838 50.000 0.00 0.00 42.88 3.77
742 804 2.159653 CGTGAGGCTGAATGTTAGCAAC 60.160 50.000 0.00 0.00 42.88 4.17
743 805 2.076100 CGTGAGGCTGAATGTTAGCAA 58.924 47.619 0.00 0.00 42.88 3.91
744 806 1.001974 ACGTGAGGCTGAATGTTAGCA 59.998 47.619 0.00 0.00 42.88 3.49
745 807 1.661112 GACGTGAGGCTGAATGTTAGC 59.339 52.381 0.00 0.00 40.41 3.09
756 818 7.147143 TCATCTATATAAAGAGACGTGAGGC 57.853 40.000 0.00 0.00 42.06 4.70
757 819 8.951243 TGATCATCTATATAAAGAGACGTGAGG 58.049 37.037 0.00 0.00 0.00 3.86
810 872 8.242053 GGTCTAGCATATTGTATATGTACACGT 58.758 37.037 0.00 0.00 40.40 4.49
811 873 7.701078 GGGTCTAGCATATTGTATATGTACACG 59.299 40.741 0.00 0.00 40.40 4.49
812 874 8.750298 AGGGTCTAGCATATTGTATATGTACAC 58.250 37.037 0.00 0.00 40.40 2.90
813 875 8.895141 AGGGTCTAGCATATTGTATATGTACA 57.105 34.615 0.00 0.00 39.00 2.90
821 883 9.991906 GTGTAAAATAGGGTCTAGCATATTGTA 57.008 33.333 0.44 0.00 0.00 2.41
822 884 7.656137 CGTGTAAAATAGGGTCTAGCATATTGT 59.344 37.037 0.44 0.00 0.00 2.71
823 885 7.656137 ACGTGTAAAATAGGGTCTAGCATATTG 59.344 37.037 0.44 0.00 0.00 1.90
824 886 7.656137 CACGTGTAAAATAGGGTCTAGCATATT 59.344 37.037 7.58 0.00 0.00 1.28
825 887 7.152645 CACGTGTAAAATAGGGTCTAGCATAT 58.847 38.462 7.58 0.00 0.00 1.78
826 888 6.509656 CACGTGTAAAATAGGGTCTAGCATA 58.490 40.000 7.58 0.00 0.00 3.14
827 889 5.357257 CACGTGTAAAATAGGGTCTAGCAT 58.643 41.667 7.58 0.00 0.00 3.79
828 890 4.751060 CACGTGTAAAATAGGGTCTAGCA 58.249 43.478 7.58 0.00 0.00 3.49
829 891 3.554731 GCACGTGTAAAATAGGGTCTAGC 59.445 47.826 18.38 0.00 0.00 3.42
830 892 4.804139 CAGCACGTGTAAAATAGGGTCTAG 59.196 45.833 18.38 0.00 0.00 2.43
831 893 4.751060 CAGCACGTGTAAAATAGGGTCTA 58.249 43.478 18.38 0.00 0.00 2.59
832 894 3.596214 CAGCACGTGTAAAATAGGGTCT 58.404 45.455 18.38 0.00 0.00 3.85
833 895 2.095372 GCAGCACGTGTAAAATAGGGTC 59.905 50.000 18.38 0.00 0.00 4.46
834 896 2.081462 GCAGCACGTGTAAAATAGGGT 58.919 47.619 18.38 0.00 0.00 4.34
835 897 2.080693 TGCAGCACGTGTAAAATAGGG 58.919 47.619 18.38 0.00 0.00 3.53
836 898 3.683989 CATGCAGCACGTGTAAAATAGG 58.316 45.455 18.38 0.00 0.00 2.57
837 899 3.100817 GCATGCAGCACGTGTAAAATAG 58.899 45.455 18.38 3.65 44.79 1.73
838 900 3.129852 GCATGCAGCACGTGTAAAATA 57.870 42.857 18.38 0.00 44.79 1.40
839 901 1.981254 GCATGCAGCACGTGTAAAAT 58.019 45.000 18.38 3.83 44.79 1.82
840 902 3.470520 GCATGCAGCACGTGTAAAA 57.529 47.368 18.38 1.34 44.79 1.52
854 916 1.602888 GCAGGGGGAGCATAGCATG 60.603 63.158 0.00 0.00 0.00 4.06
855 917 2.080536 TGCAGGGGGAGCATAGCAT 61.081 57.895 0.00 0.00 37.02 3.79
856 918 2.691996 TGCAGGGGGAGCATAGCA 60.692 61.111 0.00 0.00 37.02 3.49
862 924 3.851955 CAATGATGCAGGGGGAGC 58.148 61.111 0.00 0.00 0.00 4.70
946 1031 6.051717 ACAGGCATTTACTAGAGCAGTATTG 58.948 40.000 0.00 0.00 39.51 1.90
969 1058 1.355971 ACGACGACAACATGCCATAC 58.644 50.000 0.00 0.00 0.00 2.39
971 1060 1.067142 ACTACGACGACAACATGCCAT 60.067 47.619 0.00 0.00 0.00 4.40
974 1063 0.093026 GCACTACGACGACAACATGC 59.907 55.000 0.00 0.00 0.00 4.06
1014 1121 4.756084 ACTAAGTACGTACAGTTTCGCT 57.244 40.909 26.55 1.16 0.00 4.93
1360 1483 1.136695 CTCGAGCTTCTCCATGAGCTT 59.863 52.381 7.95 0.00 37.79 3.74
1411 1541 2.486918 TCACAGATTATCATGGCAGCG 58.513 47.619 0.00 0.00 0.00 5.18
1438 1585 5.697848 AGACGCACACGAGTTAATTAATC 57.302 39.130 0.31 0.28 43.93 1.75
1463 1610 1.653151 GCACGTACTTCTGGGGATTC 58.347 55.000 0.00 0.00 0.00 2.52
1550 1705 2.303022 TGAGAGAAATGGCGGAAGTCTT 59.697 45.455 0.00 0.00 36.07 3.01
1555 1710 0.740868 CGCTGAGAGAAATGGCGGAA 60.741 55.000 0.00 0.00 41.77 4.30
1589 1744 4.526970 TCAGCAAACTATTCCTTCCATCC 58.473 43.478 0.00 0.00 0.00 3.51
1593 1756 6.765915 AATCTTCAGCAAACTATTCCTTCC 57.234 37.500 0.00 0.00 0.00 3.46
1645 1808 4.005650 AGACCGATCGAGTACAAGTACAA 58.994 43.478 18.66 0.00 38.48 2.41
1646 1809 3.603532 AGACCGATCGAGTACAAGTACA 58.396 45.455 18.66 0.00 38.48 2.90
1647 1810 3.302350 CGAGACCGATCGAGTACAAGTAC 60.302 52.174 18.66 2.18 45.56 2.73
1648 1811 2.862536 CGAGACCGATCGAGTACAAGTA 59.137 50.000 18.66 0.00 45.56 2.24
1649 1812 1.664659 CGAGACCGATCGAGTACAAGT 59.335 52.381 18.66 3.31 45.56 3.16
1650 1813 1.003759 CCGAGACCGATCGAGTACAAG 60.004 57.143 18.66 0.00 45.56 3.16
1841 2031 8.398665 GCCGATACAGATAATTATTCATTTCCC 58.601 37.037 0.00 0.00 0.00 3.97
1844 2034 9.507329 ACTGCCGATACAGATAATTATTCATTT 57.493 29.630 0.00 0.00 40.25 2.32
1867 2057 4.062293 TCACAACAACCCTCGAATAACTG 58.938 43.478 0.00 0.00 0.00 3.16
1927 2117 0.468400 TTTTGGGCTACACCGGCTTT 60.468 50.000 0.00 0.00 40.62 3.51
1934 2124 3.674997 TCAGATCTGTTTTGGGCTACAC 58.325 45.455 21.92 0.00 0.00 2.90
1953 2143 1.223487 GCCCGGTTAAGCCATCTCA 59.777 57.895 0.00 0.00 36.97 3.27
1964 2154 1.074889 ACTGATAAAACTGGCCCGGTT 59.925 47.619 0.88 0.88 34.04 4.44
1988 2178 1.115326 GTGGCATAATTGGGAGGCCC 61.115 60.000 0.00 0.00 43.96 5.80
1989 2179 0.106015 AGTGGCATAATTGGGAGGCC 60.106 55.000 0.00 0.00 44.82 5.19
1990 2180 1.035139 CAGTGGCATAATTGGGAGGC 58.965 55.000 0.00 0.00 0.00 4.70
1991 2181 2.734755 TCAGTGGCATAATTGGGAGG 57.265 50.000 0.00 0.00 0.00 4.30
1992 2182 6.322201 AGTTTTATCAGTGGCATAATTGGGAG 59.678 38.462 0.00 0.00 0.00 4.30
1993 2183 6.096705 CAGTTTTATCAGTGGCATAATTGGGA 59.903 38.462 0.00 0.00 0.00 4.37
1994 2184 6.275335 CAGTTTTATCAGTGGCATAATTGGG 58.725 40.000 0.00 0.00 0.00 4.12
1995 2185 6.275335 CCAGTTTTATCAGTGGCATAATTGG 58.725 40.000 0.00 0.00 30.24 3.16
2004 2194 1.468520 CGTGGCCAGTTTTATCAGTGG 59.531 52.381 5.11 0.00 39.96 4.00
2005 2195 1.468520 CCGTGGCCAGTTTTATCAGTG 59.531 52.381 5.11 0.00 0.00 3.66
2006 2196 1.821216 CCGTGGCCAGTTTTATCAGT 58.179 50.000 5.11 0.00 0.00 3.41
2007 2197 0.451783 GCCGTGGCCAGTTTTATCAG 59.548 55.000 5.11 0.00 34.56 2.90
2008 2198 1.302383 CGCCGTGGCCAGTTTTATCA 61.302 55.000 5.11 0.00 37.98 2.15
2009 2199 1.427819 CGCCGTGGCCAGTTTTATC 59.572 57.895 5.11 0.00 37.98 1.75
2010 2200 2.696759 GCGCCGTGGCCAGTTTTAT 61.697 57.895 5.11 0.00 37.98 1.40
2011 2201 3.358707 GCGCCGTGGCCAGTTTTA 61.359 61.111 5.11 0.00 37.98 1.52
2025 2215 5.629435 GGAGTTATATTTATTTTGGCAGCGC 59.371 40.000 0.00 0.00 0.00 5.92
2026 2216 6.970484 AGGAGTTATATTTATTTTGGCAGCG 58.030 36.000 0.00 0.00 0.00 5.18
2027 2217 9.599866 AAAAGGAGTTATATTTATTTTGGCAGC 57.400 29.630 0.00 0.00 0.00 5.25
2052 2242 5.414789 GCCTATTTTCCCTGGCTTAAAAA 57.585 39.130 0.00 0.00 41.92 1.94
2059 2249 2.812664 CCAGCCTATTTTCCCTGGC 58.187 57.895 0.00 0.00 45.21 4.85
2060 2250 0.756815 GGCCAGCCTATTTTCCCTGG 60.757 60.000 0.00 0.00 45.93 4.45
2061 2251 0.756815 GGGCCAGCCTATTTTCCCTG 60.757 60.000 4.39 0.00 36.10 4.45
2062 2252 1.221213 TGGGCCAGCCTATTTTCCCT 61.221 55.000 0.00 0.00 34.89 4.20
2063 2253 1.043116 GTGGGCCAGCCTATTTTCCC 61.043 60.000 6.40 0.00 36.10 3.97
2064 2254 1.043116 GGTGGGCCAGCCTATTTTCC 61.043 60.000 25.03 6.35 36.10 3.13
2065 2255 2.504920 GGTGGGCCAGCCTATTTTC 58.495 57.895 25.03 0.00 36.10 2.29
2066 2256 4.785575 GGTGGGCCAGCCTATTTT 57.214 55.556 25.03 0.00 36.10 1.82
2082 2272 3.599285 TAACCGTTCGCTGGCAGGG 62.599 63.158 24.22 24.22 0.00 4.45
2083 2273 2.047655 TAACCGTTCGCTGGCAGG 60.048 61.111 17.64 6.64 0.00 4.85
2084 2274 0.949105 AAGTAACCGTTCGCTGGCAG 60.949 55.000 10.94 10.94 0.00 4.85
2085 2275 0.533308 AAAGTAACCGTTCGCTGGCA 60.533 50.000 0.00 0.00 0.00 4.92
2086 2276 0.589708 AAAAGTAACCGTTCGCTGGC 59.410 50.000 0.00 0.00 0.00 4.85
2142 2332 9.492973 AGTTATTAAACACCTAGCTCGTAAAAA 57.507 29.630 0.00 0.00 38.12 1.94
2143 2333 9.492973 AAGTTATTAAACACCTAGCTCGTAAAA 57.507 29.630 0.00 0.00 38.12 1.52
2145 2335 9.573133 GTAAGTTATTAAACACCTAGCTCGTAA 57.427 33.333 0.00 0.00 38.12 3.18
2146 2336 8.190784 GGTAAGTTATTAAACACCTAGCTCGTA 58.809 37.037 0.00 0.00 38.12 3.43
2147 2337 7.038048 GGTAAGTTATTAAACACCTAGCTCGT 58.962 38.462 0.00 0.00 38.12 4.18
2148 2338 7.037438 TGGTAAGTTATTAAACACCTAGCTCG 58.963 38.462 0.00 0.00 38.12 5.03
2149 2339 8.782339 TTGGTAAGTTATTAAACACCTAGCTC 57.218 34.615 0.00 0.00 38.12 4.09
2150 2340 9.577222 TTTTGGTAAGTTATTAAACACCTAGCT 57.423 29.630 0.00 0.00 38.12 3.32
2154 2344 8.644216 CCCTTTTTGGTAAGTTATTAAACACCT 58.356 33.333 0.00 0.00 38.12 4.00
2155 2345 8.640651 TCCCTTTTTGGTAAGTTATTAAACACC 58.359 33.333 0.00 0.00 38.12 4.16
2166 2356 9.955102 CTAATACTACTTCCCTTTTTGGTAAGT 57.045 33.333 0.00 0.00 33.38 2.24
2170 2360 9.871175 TTTTCTAATACTACTTCCCTTTTTGGT 57.129 29.630 0.00 0.00 0.00 3.67
2365 2555 9.658475 CGAAGACATTTTTCAAATACACTACAA 57.342 29.630 0.00 0.00 0.00 2.41
2366 2556 7.801315 GCGAAGACATTTTTCAAATACACTACA 59.199 33.333 0.00 0.00 0.00 2.74
2367 2557 7.801315 TGCGAAGACATTTTTCAAATACACTAC 59.199 33.333 0.00 0.00 0.00 2.73
2368 2558 7.866729 TGCGAAGACATTTTTCAAATACACTA 58.133 30.769 0.00 0.00 0.00 2.74
2369 2559 6.734137 TGCGAAGACATTTTTCAAATACACT 58.266 32.000 0.00 0.00 0.00 3.55
2370 2560 6.984740 TGCGAAGACATTTTTCAAATACAC 57.015 33.333 0.00 0.00 0.00 2.90
2371 2561 8.586570 AAATGCGAAGACATTTTTCAAATACA 57.413 26.923 0.00 0.00 45.63 2.29
2373 2563 9.906660 ACTAAATGCGAAGACATTTTTCAAATA 57.093 25.926 7.70 0.00 45.63 1.40
2374 2564 8.816640 ACTAAATGCGAAGACATTTTTCAAAT 57.183 26.923 7.70 0.00 45.63 2.32
2375 2565 9.737427 TTACTAAATGCGAAGACATTTTTCAAA 57.263 25.926 7.70 0.00 45.63 2.69
2376 2566 9.737427 TTTACTAAATGCGAAGACATTTTTCAA 57.263 25.926 7.70 0.00 45.63 2.69
2377 2567 9.737427 TTTTACTAAATGCGAAGACATTTTTCA 57.263 25.926 7.70 0.00 45.63 2.69
2384 2574 9.982291 GTGAATATTTTACTAAATGCGAAGACA 57.018 29.630 0.00 0.00 35.61 3.41
2385 2575 9.982291 TGTGAATATTTTACTAAATGCGAAGAC 57.018 29.630 0.00 0.00 35.61 3.01
2387 2577 9.988350 ACTGTGAATATTTTACTAAATGCGAAG 57.012 29.630 0.00 0.00 35.61 3.79
2460 2650 3.821033 CTCGTCCTTCCAGATTGGTTTTT 59.179 43.478 0.00 0.00 39.03 1.94
2461 2651 3.412386 CTCGTCCTTCCAGATTGGTTTT 58.588 45.455 0.00 0.00 39.03 2.43
2462 2652 2.876079 GCTCGTCCTTCCAGATTGGTTT 60.876 50.000 0.00 0.00 39.03 3.27
2463 2653 1.339151 GCTCGTCCTTCCAGATTGGTT 60.339 52.381 0.00 0.00 39.03 3.67
2464 2654 0.250513 GCTCGTCCTTCCAGATTGGT 59.749 55.000 0.00 0.00 39.03 3.67
2465 2655 0.250234 TGCTCGTCCTTCCAGATTGG 59.750 55.000 0.00 0.00 39.43 3.16
2466 2656 2.322355 ATGCTCGTCCTTCCAGATTG 57.678 50.000 0.00 0.00 0.00 2.67
2467 2657 4.487714 TTTATGCTCGTCCTTCCAGATT 57.512 40.909 0.00 0.00 0.00 2.40
2468 2658 4.487714 TTTTATGCTCGTCCTTCCAGAT 57.512 40.909 0.00 0.00 0.00 2.90
2469 2659 3.973206 TTTTATGCTCGTCCTTCCAGA 57.027 42.857 0.00 0.00 0.00 3.86
2500 2690 8.989653 TTTCTTTCGGTGTTATTCTTGTTTTT 57.010 26.923 0.00 0.00 0.00 1.94
2501 2691 8.989653 TTTTCTTTCGGTGTTATTCTTGTTTT 57.010 26.923 0.00 0.00 0.00 2.43
2502 2692 8.865978 GTTTTTCTTTCGGTGTTATTCTTGTTT 58.134 29.630 0.00 0.00 0.00 2.83
2503 2693 8.030106 TGTTTTTCTTTCGGTGTTATTCTTGTT 58.970 29.630 0.00 0.00 0.00 2.83
2504 2694 7.540299 TGTTTTTCTTTCGGTGTTATTCTTGT 58.460 30.769 0.00 0.00 0.00 3.16
2505 2695 7.979115 TGTTTTTCTTTCGGTGTTATTCTTG 57.021 32.000 0.00 0.00 0.00 3.02
2512 2702 8.989653 TTCTTTTATGTTTTTCTTTCGGTGTT 57.010 26.923 0.00 0.00 0.00 3.32
2513 2703 8.989653 TTTCTTTTATGTTTTTCTTTCGGTGT 57.010 26.923 0.00 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.