Multiple sequence alignment - TraesCS5A01G492500

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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 TraesCS5A01G492500 chr5A 100.000 2236 0 0 1 2236 661241379 661243614 0.000000e+00 4130.0
1 TraesCS5A01G492500 chr5A 100.000 352 0 0 2612 2963 661243990 661244341 0.000000e+00 651.0
2 TraesCS5A01G492500 chr4B 94.773 1167 46 4 923 2074 610408326 610407160 0.000000e+00 1803.0
3 TraesCS5A01G492500 chr4B 95.600 750 30 2 923 1669 610426136 610425387 0.000000e+00 1199.0
4 TraesCS5A01G492500 chr4B 91.354 879 63 7 1 876 610409399 610408531 0.000000e+00 1190.0
5 TraesCS5A01G492500 chr4B 91.354 879 63 7 1 876 610427209 610426341 0.000000e+00 1190.0
6 TraesCS5A01G492500 chr4B 97.143 280 8 0 2684 2963 22439637 22439358 9.610000e-130 473.0
7 TraesCS5A01G492500 chr4B 97.143 280 8 0 2684 2963 166832907 166833186 9.610000e-130 473.0
8 TraesCS5A01G492500 chr4B 96.181 288 10 1 2677 2963 637287480 637287193 1.240000e-128 470.0
9 TraesCS5A01G492500 chr4B 92.515 334 13 2 1753 2074 610424839 610424506 4.470000e-128 468.0
10 TraesCS5A01G492500 chr4D 95.698 1046 45 0 919 1964 481415697 481414652 0.000000e+00 1683.0
11 TraesCS5A01G492500 chr4D 94.142 478 24 3 1 476 481416609 481416134 0.000000e+00 725.0
12 TraesCS5A01G492500 chr4D 90.284 422 29 9 492 910 481416150 481415738 2.600000e-150 542.0
13 TraesCS5A01G492500 chr3D 82.025 1057 139 35 943 1960 28547825 28546781 0.000000e+00 852.0
14 TraesCS5A01G492500 chr3D 81.549 1046 154 25 951 1960 28592155 28591113 0.000000e+00 826.0
15 TraesCS5A01G492500 chr3D 83.382 680 90 16 1294 1960 28944884 28945553 2.530000e-170 608.0
16 TraesCS5A01G492500 chr3D 84.590 305 47 0 956 1260 28944519 28944823 1.330000e-78 303.0
17 TraesCS5A01G492500 chr3B 81.166 1046 142 38 956 1957 49152125 49153159 0.000000e+00 789.0
18 TraesCS5A01G492500 chr3B 81.684 677 104 17 1297 1960 47476596 47475927 2.010000e-151 545.0
19 TraesCS5A01G492500 chr3B 97.143 280 8 0 2684 2963 734139954 734139675 9.610000e-130 473.0
20 TraesCS5A01G492500 chr6B 83.111 675 92 13 1294 1960 131694281 131694941 1.970000e-166 595.0
21 TraesCS5A01G492500 chr3A 82.941 680 96 17 1294 1960 38281258 38280586 1.970000e-166 595.0
22 TraesCS5A01G492500 chr3A 82.622 679 100 13 1294 1960 38300940 38301612 4.260000e-163 584.0
23 TraesCS5A01G492500 chr3A 88.172 279 33 0 955 1233 38281624 38281346 1.700000e-87 333.0
24 TraesCS5A01G492500 chr3A 86.926 283 37 0 951 1233 38300570 38300852 4.770000e-83 318.0
25 TraesCS5A01G492500 chr2B 98.214 280 5 0 2684 2963 793364327 793364048 9.540000e-135 490.0
26 TraesCS5A01G492500 chr2B 97.143 280 7 1 2684 2963 87756065 87756343 3.460000e-129 472.0
27 TraesCS5A01G492500 chr4A 97.518 282 6 1 2683 2963 683421102 683420821 5.740000e-132 481.0
28 TraesCS5A01G492500 chr2D 97.143 280 8 0 2684 2963 308681373 308681652 9.610000e-130 473.0
29 TraesCS5A01G492500 chr2A 96.809 282 9 0 2682 2963 7741066 7741347 3.460000e-129 472.0
30 TraesCS5A01G492500 chr7D 88.506 174 10 2 2072 2236 454142484 454142656 5.010000e-48 202.0
31 TraesCS5A01G492500 chr7D 96.154 52 2 0 2642 2693 454142883 454142934 5.260000e-13 86.1
32 TraesCS5A01G492500 chr6D 86.667 165 21 1 2072 2236 263042334 263042497 6.520000e-42 182.0
33 TraesCS5A01G492500 chr6D 97.436 78 2 0 2612 2689 263042540 263042617 1.850000e-27 134.0


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 TraesCS5A01G492500 chr5A 661241379 661244341 2962 False 2390.500000 4130 100.000000 1 2963 2 chr5A.!!$F1 2962
1 TraesCS5A01G492500 chr4B 610407160 610409399 2239 True 1496.500000 1803 93.063500 1 2074 2 chr4B.!!$R3 2073
2 TraesCS5A01G492500 chr4B 610424506 610427209 2703 True 952.333333 1199 93.156333 1 2074 3 chr4B.!!$R4 2073
3 TraesCS5A01G492500 chr4D 481414652 481416609 1957 True 983.333333 1683 93.374667 1 1964 3 chr4D.!!$R1 1963
4 TraesCS5A01G492500 chr3D 28546781 28547825 1044 True 852.000000 852 82.025000 943 1960 1 chr3D.!!$R1 1017
5 TraesCS5A01G492500 chr3D 28591113 28592155 1042 True 826.000000 826 81.549000 951 1960 1 chr3D.!!$R2 1009
6 TraesCS5A01G492500 chr3D 28944519 28945553 1034 False 455.500000 608 83.986000 956 1960 2 chr3D.!!$F1 1004
7 TraesCS5A01G492500 chr3B 49152125 49153159 1034 False 789.000000 789 81.166000 956 1957 1 chr3B.!!$F1 1001
8 TraesCS5A01G492500 chr3B 47475927 47476596 669 True 545.000000 545 81.684000 1297 1960 1 chr3B.!!$R1 663
9 TraesCS5A01G492500 chr6B 131694281 131694941 660 False 595.000000 595 83.111000 1294 1960 1 chr6B.!!$F1 666
10 TraesCS5A01G492500 chr3A 38280586 38281624 1038 True 464.000000 595 85.556500 955 1960 2 chr3A.!!$R1 1005
11 TraesCS5A01G492500 chr3A 38300570 38301612 1042 False 451.000000 584 84.774000 951 1960 2 chr3A.!!$F1 1009

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
632 635 0.034337 GATAAATAGCCGCCCGTCCA 59.966 55.0 0.00 0.0 0.0 4.02 F
850 858 0.384309 TATAGGCTGCAGTCGGTTCG 59.616 55.0 16.64 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1679 1886 1.703438 CGAGTTGCTCATCAGCCTGC 61.703 60.000 0.0 0.0 46.26 4.85 R
2833 3528 3.636764 TCGAGCATTGTAATAGAGAGGCA 59.363 43.478 0.0 0.0 0.00 4.75 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
29 30 7.581213 TTTGTCCACTGAAGAAAACATATGT 57.419 32.000 1.41 1.41 0.00 2.29
81 82 2.095718 GCTTGAACAAGATCCGTCCAAC 60.096 50.000 17.19 0.00 40.79 3.77
221 222 2.251893 GAGAACGAGATGACAACGTCC 58.748 52.381 0.00 0.00 39.31 4.79
242 243 1.888512 CCAAAAGCAAAGCTAGCTCCA 59.111 47.619 19.65 0.00 42.53 3.86
245 246 2.867109 AAGCAAAGCTAGCTCCAGAA 57.133 45.000 19.65 0.00 42.53 3.02
286 287 1.152673 GGTTGGATCCATGGCCCTC 60.153 63.158 17.06 11.06 0.00 4.30
349 350 7.613022 GCCAATGATAGGATAATCTTTCCATCA 59.387 37.037 0.00 0.00 36.32 3.07
367 368 4.508861 CCATCAGTTTGTTCTTGCCTTTTG 59.491 41.667 0.00 0.00 0.00 2.44
437 440 7.099764 TCTCTTTTCCTTTCTACATACAGCAG 58.900 38.462 0.00 0.00 0.00 4.24
478 481 5.277828 GCGTTCTGGTGTCTATGTTCTTTTT 60.278 40.000 0.00 0.00 0.00 1.94
528 531 4.564782 TGATGCTCCAAGAAAGATGAGT 57.435 40.909 0.00 0.00 0.00 3.41
548 551 2.949451 ACATCTTGTCGCCTCTGTAG 57.051 50.000 0.00 0.00 0.00 2.74
550 553 3.353557 ACATCTTGTCGCCTCTGTAGTA 58.646 45.455 0.00 0.00 0.00 1.82
551 554 3.762288 ACATCTTGTCGCCTCTGTAGTAA 59.238 43.478 0.00 0.00 0.00 2.24
552 555 4.402793 ACATCTTGTCGCCTCTGTAGTAAT 59.597 41.667 0.00 0.00 0.00 1.89
553 556 5.593095 ACATCTTGTCGCCTCTGTAGTAATA 59.407 40.000 0.00 0.00 0.00 0.98
554 557 6.096423 ACATCTTGTCGCCTCTGTAGTAATAA 59.904 38.462 0.00 0.00 0.00 1.40
599 602 3.855895 GCCATCAAGAATCGAATGCCATG 60.856 47.826 0.00 0.00 0.00 3.66
632 635 0.034337 GATAAATAGCCGCCCGTCCA 59.966 55.000 0.00 0.00 0.00 4.02
650 653 3.062639 GTCCATGTGCACAGATTCTTACG 59.937 47.826 25.84 4.38 0.00 3.18
709 712 3.691118 CCTGCACTGCTTATTTGCTTAGA 59.309 43.478 1.98 0.00 37.16 2.10
732 735 1.209019 AGGTGACTGAGTGATCATGGC 59.791 52.381 0.00 0.00 41.13 4.40
782 785 3.056328 GGCCACCTGCTCCGTTTC 61.056 66.667 0.00 0.00 40.92 2.78
797 801 5.335191 GCTCCGTTTCATTTGTCTTCTCATT 60.335 40.000 0.00 0.00 0.00 2.57
810 814 7.218228 TGTCTTCTCATTACACATTTTGCAT 57.782 32.000 0.00 0.00 0.00 3.96
811 815 7.085746 TGTCTTCTCATTACACATTTTGCATG 58.914 34.615 0.00 0.00 0.00 4.06
813 817 5.388408 TCTCATTACACATTTTGCATGCA 57.612 34.783 18.46 18.46 0.00 3.96
814 818 5.404096 TCTCATTACACATTTTGCATGCAG 58.596 37.500 21.50 11.84 0.00 4.41
815 819 5.047872 TCTCATTACACATTTTGCATGCAGT 60.048 36.000 21.50 16.12 0.00 4.40
816 820 5.539979 TCATTACACATTTTGCATGCAGTT 58.460 33.333 21.50 6.88 0.00 3.16
817 821 5.405873 TCATTACACATTTTGCATGCAGTTG 59.594 36.000 21.50 20.06 0.00 3.16
819 823 3.794717 ACACATTTTGCATGCAGTTGAA 58.205 36.364 21.50 14.25 0.00 2.69
820 824 4.382291 ACACATTTTGCATGCAGTTGAAT 58.618 34.783 21.50 15.76 0.00 2.57
821 825 5.539979 ACACATTTTGCATGCAGTTGAATA 58.460 33.333 21.50 0.37 0.00 1.75
822 826 5.990386 ACACATTTTGCATGCAGTTGAATAA 59.010 32.000 21.50 7.58 0.00 1.40
823 827 6.073657 ACACATTTTGCATGCAGTTGAATAAC 60.074 34.615 21.50 0.00 37.06 1.89
828 832 5.801350 TGCATGCAGTTGAATAACTCTAC 57.199 39.130 18.46 0.00 45.12 2.59
844 852 3.886505 ACTCTACTGTATAGGCTGCAGTC 59.113 47.826 11.28 11.28 46.48 3.51
845 853 2.879026 TCTACTGTATAGGCTGCAGTCG 59.121 50.000 16.64 15.08 46.48 4.18
850 858 0.384309 TATAGGCTGCAGTCGGTTCG 59.616 55.000 16.64 0.00 0.00 3.95
863 871 3.063045 AGTCGGTTCGAAAGTTTTGTGAC 59.937 43.478 0.00 7.25 37.72 3.67
883 891 5.577945 GTGACATCATGCCACCAAATTTTAG 59.422 40.000 0.00 0.00 0.00 1.85
886 894 6.532826 ACATCATGCCACCAAATTTTAGTTT 58.467 32.000 0.00 0.00 0.00 2.66
887 895 6.997476 ACATCATGCCACCAAATTTTAGTTTT 59.003 30.769 0.00 0.00 0.00 2.43
905 913 6.687653 AGTTTTTGCACATTTTGTTTTTGC 57.312 29.167 0.00 0.00 0.00 3.68
906 914 6.445475 AGTTTTTGCACATTTTGTTTTTGCT 58.555 28.000 0.00 0.00 34.18 3.91
907 915 6.581919 AGTTTTTGCACATTTTGTTTTTGCTC 59.418 30.769 0.00 0.00 34.18 4.26
908 916 5.876612 TTTGCACATTTTGTTTTTGCTCT 57.123 30.435 0.00 0.00 34.18 4.09
909 917 6.974932 TTTGCACATTTTGTTTTTGCTCTA 57.025 29.167 0.00 0.00 34.18 2.43
911 919 6.528014 TGCACATTTTGTTTTTGCTCTATG 57.472 33.333 0.00 0.00 34.18 2.23
912 920 6.047870 TGCACATTTTGTTTTTGCTCTATGT 58.952 32.000 0.00 0.00 34.18 2.29
913 921 6.538021 TGCACATTTTGTTTTTGCTCTATGTT 59.462 30.769 0.00 0.00 34.18 2.71
914 922 7.065563 TGCACATTTTGTTTTTGCTCTATGTTT 59.934 29.630 0.00 0.00 34.18 2.83
941 1118 5.193663 AGTAGTGACGATGGATGATTCAG 57.806 43.478 0.00 0.00 0.00 3.02
949 1126 3.001634 CGATGGATGATTCAGTTCGTTGG 59.998 47.826 0.00 0.00 0.00 3.77
1287 1491 4.003788 CCAAGAGTGCCCGTCGGT 62.004 66.667 11.06 0.00 0.00 4.69
1492 1696 2.180769 CGCCGACGGTGAAGATGA 59.819 61.111 22.98 0.00 34.74 2.92
1546 1750 3.240134 GAGCAGCCGTGGAAGGTCA 62.240 63.158 0.00 0.00 0.00 4.02
1679 1886 3.698382 GCTGATGAAGACGAGCGG 58.302 61.111 0.00 0.00 0.00 5.52
1801 2472 1.275010 TGCGGCTGTACAAGAGAATGA 59.725 47.619 0.00 0.00 0.00 2.57
1804 2475 2.417924 CGGCTGTACAAGAGAATGAGCT 60.418 50.000 0.00 0.00 0.00 4.09
1977 2660 1.226435 CTAGCCTCGACGACTGCAC 60.226 63.158 14.88 0.00 0.00 4.57
1978 2661 1.649390 CTAGCCTCGACGACTGCACT 61.649 60.000 14.88 2.53 0.00 4.40
2006 2697 0.454600 CATGTCCAAGCATGAGCCAC 59.545 55.000 0.00 0.00 46.65 5.01
2011 2702 4.349503 AAGCATGAGCCACGGCCA 62.350 61.111 2.24 3.01 43.56 5.36
2074 2769 5.510430 ACTTACTGATCAAAGGGGAATTCC 58.490 41.667 16.74 16.74 0.00 3.01
2075 2770 5.015178 ACTTACTGATCAAAGGGGAATTCCA 59.985 40.000 25.67 4.55 37.91 3.53
2076 2771 4.402616 ACTGATCAAAGGGGAATTCCAA 57.597 40.909 25.67 4.34 37.91 3.53
2077 2772 4.951603 ACTGATCAAAGGGGAATTCCAAT 58.048 39.130 25.67 10.70 37.91 3.16
2078 2773 6.091076 ACTGATCAAAGGGGAATTCCAATA 57.909 37.500 25.67 5.36 37.91 1.90
2079 2774 6.502138 ACTGATCAAAGGGGAATTCCAATAA 58.498 36.000 25.67 6.42 37.91 1.40
2080 2775 7.134842 ACTGATCAAAGGGGAATTCCAATAAT 58.865 34.615 25.67 10.76 37.91 1.28
2081 2776 8.288812 ACTGATCAAAGGGGAATTCCAATAATA 58.711 33.333 25.67 7.45 37.91 0.98
2082 2777 8.710749 TGATCAAAGGGGAATTCCAATAATAG 57.289 34.615 25.67 9.14 37.91 1.73
2083 2778 8.510283 TGATCAAAGGGGAATTCCAATAATAGA 58.490 33.333 25.67 13.76 37.91 1.98
2084 2779 9.539194 GATCAAAGGGGAATTCCAATAATAGAT 57.461 33.333 25.67 17.34 37.91 1.98
2085 2780 9.903190 ATCAAAGGGGAATTCCAATAATAGATT 57.097 29.630 25.67 4.83 37.91 2.40
2086 2781 9.728100 TCAAAGGGGAATTCCAATAATAGATTT 57.272 29.630 25.67 9.29 37.91 2.17
2087 2782 9.987272 CAAAGGGGAATTCCAATAATAGATTTC 57.013 33.333 25.67 3.57 37.91 2.17
2088 2783 9.728100 AAAGGGGAATTCCAATAATAGATTTCA 57.272 29.630 25.67 0.00 37.91 2.69
2089 2784 8.712228 AGGGGAATTCCAATAATAGATTTCAC 57.288 34.615 25.67 2.50 37.91 3.18
2090 2785 8.514504 AGGGGAATTCCAATAATAGATTTCACT 58.485 33.333 25.67 0.00 37.91 3.41
2091 2786 8.797438 GGGGAATTCCAATAATAGATTTCACTC 58.203 37.037 25.67 1.78 37.91 3.51
2092 2787 9.354673 GGGAATTCCAATAATAGATTTCACTCA 57.645 33.333 25.67 0.00 37.91 3.41
2142 2837 9.796120 TTAAAAATTGATTTCACTCGTTTCAGT 57.204 25.926 0.00 0.00 0.00 3.41
2144 2839 9.796120 AAAAATTGATTTCACTCGTTTCAGTAA 57.204 25.926 0.00 0.00 0.00 2.24
2145 2840 8.782533 AAATTGATTTCACTCGTTTCAGTAAC 57.217 30.769 0.00 0.00 0.00 2.50
2146 2841 6.912203 TTGATTTCACTCGTTTCAGTAACA 57.088 33.333 0.00 0.00 36.50 2.41
2147 2842 7.490962 TTGATTTCACTCGTTTCAGTAACAT 57.509 32.000 0.00 0.00 36.50 2.71
2148 2843 8.596271 TTGATTTCACTCGTTTCAGTAACATA 57.404 30.769 0.00 0.00 36.50 2.29
2149 2844 8.771920 TGATTTCACTCGTTTCAGTAACATAT 57.228 30.769 0.00 0.00 36.50 1.78
2150 2845 9.214957 TGATTTCACTCGTTTCAGTAACATATT 57.785 29.630 0.00 0.00 36.50 1.28
2153 2848 8.596271 TTCACTCGTTTCAGTAACATATTTCA 57.404 30.769 0.00 0.00 36.50 2.69
2154 2849 8.014322 TCACTCGTTTCAGTAACATATTTCAC 57.986 34.615 0.00 0.00 36.50 3.18
2155 2850 7.870954 TCACTCGTTTCAGTAACATATTTCACT 59.129 33.333 0.00 0.00 36.50 3.41
2156 2851 8.162880 CACTCGTTTCAGTAACATATTTCACTC 58.837 37.037 0.00 0.00 36.50 3.51
2157 2852 7.061905 ACTCGTTTCAGTAACATATTTCACTCG 59.938 37.037 0.00 0.00 36.50 4.18
2158 2853 6.864685 TCGTTTCAGTAACATATTTCACTCGT 59.135 34.615 0.00 0.00 36.50 4.18
2159 2854 7.383029 TCGTTTCAGTAACATATTTCACTCGTT 59.617 33.333 0.00 0.00 36.50 3.85
2160 2855 8.641155 CGTTTCAGTAACATATTTCACTCGTTA 58.359 33.333 0.00 0.00 36.50 3.18
2161 2856 9.737025 GTTTCAGTAACATATTTCACTCGTTAC 57.263 33.333 0.00 0.00 41.29 2.50
2162 2857 9.478768 TTTCAGTAACATATTTCACTCGTTACA 57.521 29.630 11.89 0.00 42.68 2.41
2163 2858 9.478768 TTCAGTAACATATTTCACTCGTTACAA 57.521 29.630 11.89 0.00 42.68 2.41
2164 2859 9.647797 TCAGTAACATATTTCACTCGTTACAAT 57.352 29.630 11.89 0.00 42.68 2.71
2170 2865 9.647797 ACATATTTCACTCGTTACAATAACAGA 57.352 29.630 0.11 0.00 0.00 3.41
2175 2870 8.596271 TTCACTCGTTACAATAACAGATTTCA 57.404 30.769 0.11 0.00 0.00 2.69
2176 2871 8.014322 TCACTCGTTACAATAACAGATTTCAC 57.986 34.615 0.11 0.00 0.00 3.18
2177 2872 7.870954 TCACTCGTTACAATAACAGATTTCACT 59.129 33.333 0.11 0.00 0.00 3.41
2178 2873 9.135843 CACTCGTTACAATAACAGATTTCACTA 57.864 33.333 0.11 0.00 0.00 2.74
2179 2874 9.701098 ACTCGTTACAATAACAGATTTCACTAA 57.299 29.630 0.11 0.00 0.00 2.24
2681 3376 8.491045 AGAAAAAGTTGAATAAAAGGGATGGA 57.509 30.769 0.00 0.00 0.00 3.41
2682 3377 8.588472 AGAAAAAGTTGAATAAAAGGGATGGAG 58.412 33.333 0.00 0.00 0.00 3.86
2683 3378 7.855784 AAAAGTTGAATAAAAGGGATGGAGT 57.144 32.000 0.00 0.00 0.00 3.85
2684 3379 7.855784 AAAGTTGAATAAAAGGGATGGAGTT 57.144 32.000 0.00 0.00 0.00 3.01
2685 3380 7.855784 AAGTTGAATAAAAGGGATGGAGTTT 57.144 32.000 0.00 0.00 0.00 2.66
2686 3381 7.855784 AGTTGAATAAAAGGGATGGAGTTTT 57.144 32.000 0.00 0.00 0.00 2.43
2687 3382 8.262601 AGTTGAATAAAAGGGATGGAGTTTTT 57.737 30.769 0.00 0.00 0.00 1.94
2711 3406 9.581099 TTTTTGAAAGAAAGTTCGAGCTTTATT 57.419 25.926 24.65 24.01 40.32 1.40
2712 3407 8.782533 TTTGAAAGAAAGTTCGAGCTTTATTC 57.217 30.769 27.30 27.43 38.46 1.75
2713 3408 7.490962 TGAAAGAAAGTTCGAGCTTTATTCA 57.509 32.000 30.20 30.20 38.46 2.57
2714 3409 8.099364 TGAAAGAAAGTTCGAGCTTTATTCAT 57.901 30.769 30.20 20.43 38.46 2.57
2715 3410 8.567948 TGAAAGAAAGTTCGAGCTTTATTCATT 58.432 29.630 30.20 19.93 38.46 2.57
2718 3413 9.436957 AAGAAAGTTCGAGCTTTATTCATTAGA 57.563 29.630 24.65 0.00 35.72 2.10
2719 3414 9.436957 AGAAAGTTCGAGCTTTATTCATTAGAA 57.563 29.630 24.65 0.00 38.64 2.10
2748 3443 7.728847 TCATTACATCGTTTATGAGGATTGG 57.271 36.000 0.00 0.00 39.07 3.16
2749 3444 7.279615 TCATTACATCGTTTATGAGGATTGGT 58.720 34.615 0.00 0.00 39.07 3.67
2750 3445 8.425703 TCATTACATCGTTTATGAGGATTGGTA 58.574 33.333 0.00 0.00 39.07 3.25
2751 3446 8.495949 CATTACATCGTTTATGAGGATTGGTAC 58.504 37.037 0.00 0.00 39.07 3.34
2752 3447 5.984725 ACATCGTTTATGAGGATTGGTACA 58.015 37.500 0.00 0.00 39.07 2.90
2753 3448 6.411376 ACATCGTTTATGAGGATTGGTACAA 58.589 36.000 0.00 0.00 40.85 2.41
2754 3449 7.054124 ACATCGTTTATGAGGATTGGTACAAT 58.946 34.615 0.00 0.00 40.85 2.71
2755 3450 7.556275 ACATCGTTTATGAGGATTGGTACAATT 59.444 33.333 0.00 0.00 40.85 2.32
2756 3451 7.857389 CATCGTTTATGAGGATTGGTACAATTG 59.143 37.037 3.24 3.24 40.33 2.32
2768 3463 5.991933 TGGTACAATTGCATTATGTGGTT 57.008 34.783 5.05 0.00 31.92 3.67
2769 3464 5.960113 TGGTACAATTGCATTATGTGGTTC 58.040 37.500 5.05 0.15 31.92 3.62
2770 3465 5.105554 TGGTACAATTGCATTATGTGGTTCC 60.106 40.000 5.05 7.26 31.92 3.62
2771 3466 5.127031 GGTACAATTGCATTATGTGGTTCCT 59.873 40.000 5.05 0.00 0.00 3.36
2772 3467 5.743636 ACAATTGCATTATGTGGTTCCTT 57.256 34.783 5.05 0.00 0.00 3.36
2773 3468 6.849085 ACAATTGCATTATGTGGTTCCTTA 57.151 33.333 5.05 0.00 0.00 2.69
2774 3469 7.238486 ACAATTGCATTATGTGGTTCCTTAA 57.762 32.000 5.05 0.00 0.00 1.85
2775 3470 7.675062 ACAATTGCATTATGTGGTTCCTTAAA 58.325 30.769 5.05 0.00 0.00 1.52
2776 3471 7.602265 ACAATTGCATTATGTGGTTCCTTAAAC 59.398 33.333 5.05 0.00 37.12 2.01
2792 3487 9.143631 GTTCCTTAAACCAATCAGAAATGAATG 57.856 33.333 0.00 0.00 31.20 2.67
2793 3488 8.648698 TCCTTAAACCAATCAGAAATGAATGA 57.351 30.769 0.00 0.00 0.00 2.57
2794 3489 9.087871 TCCTTAAACCAATCAGAAATGAATGAA 57.912 29.630 0.00 0.00 0.00 2.57
2795 3490 9.709495 CCTTAAACCAATCAGAAATGAATGAAA 57.291 29.630 0.00 0.00 0.00 2.69
2802 3497 9.245962 CCAATCAGAAATGAATGAAAATCTAGC 57.754 33.333 0.00 0.00 0.00 3.42
2803 3498 9.245962 CAATCAGAAATGAATGAAAATCTAGCC 57.754 33.333 0.00 0.00 0.00 3.93
2804 3499 7.943079 TCAGAAATGAATGAAAATCTAGCCA 57.057 32.000 0.00 0.00 0.00 4.75
2805 3500 8.352137 TCAGAAATGAATGAAAATCTAGCCAA 57.648 30.769 0.00 0.00 0.00 4.52
2806 3501 8.246180 TCAGAAATGAATGAAAATCTAGCCAAC 58.754 33.333 0.00 0.00 0.00 3.77
2807 3502 8.248945 CAGAAATGAATGAAAATCTAGCCAACT 58.751 33.333 0.00 0.00 0.00 3.16
2808 3503 8.810041 AGAAATGAATGAAAATCTAGCCAACTT 58.190 29.630 0.00 0.00 0.00 2.66
2809 3504 8.767478 AAATGAATGAAAATCTAGCCAACTTG 57.233 30.769 0.00 0.00 0.00 3.16
2810 3505 6.271488 TGAATGAAAATCTAGCCAACTTGG 57.729 37.500 3.10 3.10 41.55 3.61
2826 3521 4.243007 ACTTGGCAAGTTCATAAGCAAC 57.757 40.909 26.54 0.00 39.04 4.17
2827 3522 3.891366 ACTTGGCAAGTTCATAAGCAACT 59.109 39.130 26.54 0.00 39.04 3.16
2828 3523 4.342092 ACTTGGCAAGTTCATAAGCAACTT 59.658 37.500 26.54 0.00 43.46 2.66
2829 3524 4.935352 TGGCAAGTTCATAAGCAACTTT 57.065 36.364 0.00 0.00 41.25 2.66
2830 3525 6.040391 ACTTGGCAAGTTCATAAGCAACTTTA 59.960 34.615 26.54 0.00 41.25 1.85
2831 3526 6.588719 TGGCAAGTTCATAAGCAACTTTAT 57.411 33.333 0.00 0.00 41.25 1.40
2832 3527 6.991938 TGGCAAGTTCATAAGCAACTTTATT 58.008 32.000 0.00 0.00 41.25 1.40
2833 3528 7.441017 TGGCAAGTTCATAAGCAACTTTATTT 58.559 30.769 0.00 0.00 41.25 1.40
2834 3529 7.384660 TGGCAAGTTCATAAGCAACTTTATTTG 59.615 33.333 0.00 0.00 41.25 2.32
2847 3542 7.985476 GCAACTTTATTTGCCTCTCTATTACA 58.015 34.615 0.00 0.00 45.22 2.41
2848 3543 8.458843 GCAACTTTATTTGCCTCTCTATTACAA 58.541 33.333 0.00 0.00 45.22 2.41
2851 3546 8.624776 ACTTTATTTGCCTCTCTATTACAATGC 58.375 33.333 0.00 0.00 0.00 3.56
2852 3547 8.752005 TTTATTTGCCTCTCTATTACAATGCT 57.248 30.769 0.00 0.00 0.00 3.79
2853 3548 6.874288 ATTTGCCTCTCTATTACAATGCTC 57.126 37.500 0.00 0.00 0.00 4.26
2854 3549 3.982475 TGCCTCTCTATTACAATGCTCG 58.018 45.455 0.00 0.00 0.00 5.03
2855 3550 3.636764 TGCCTCTCTATTACAATGCTCGA 59.363 43.478 0.00 0.00 0.00 4.04
2856 3551 4.099419 TGCCTCTCTATTACAATGCTCGAA 59.901 41.667 0.00 0.00 0.00 3.71
2857 3552 5.221521 TGCCTCTCTATTACAATGCTCGAAT 60.222 40.000 0.00 0.00 0.00 3.34
2858 3553 5.347364 GCCTCTCTATTACAATGCTCGAATC 59.653 44.000 0.00 0.00 0.00 2.52
2859 3554 6.686630 CCTCTCTATTACAATGCTCGAATCT 58.313 40.000 0.00 0.00 0.00 2.40
2860 3555 7.575909 GCCTCTCTATTACAATGCTCGAATCTA 60.576 40.741 0.00 0.00 0.00 1.98
2861 3556 7.967854 CCTCTCTATTACAATGCTCGAATCTAG 59.032 40.741 0.00 0.00 0.00 2.43
2862 3557 8.622948 TCTCTATTACAATGCTCGAATCTAGA 57.377 34.615 0.00 0.00 0.00 2.43
2863 3558 9.067986 TCTCTATTACAATGCTCGAATCTAGAA 57.932 33.333 0.00 0.00 0.00 2.10
2864 3559 9.684448 CTCTATTACAATGCTCGAATCTAGAAA 57.316 33.333 0.00 0.00 0.00 2.52
2870 3565 8.948631 ACAATGCTCGAATCTAGAAATAGAAA 57.051 30.769 0.00 0.00 0.00 2.52
2871 3566 9.383519 ACAATGCTCGAATCTAGAAATAGAAAA 57.616 29.630 0.00 0.00 0.00 2.29
2875 3570 8.755941 TGCTCGAATCTAGAAATAGAAAAATCG 58.244 33.333 0.00 0.00 0.00 3.34
2876 3571 7.738176 GCTCGAATCTAGAAATAGAAAAATCGC 59.262 37.037 0.00 0.00 0.00 4.58
2877 3572 8.642908 TCGAATCTAGAAATAGAAAAATCGCA 57.357 30.769 0.00 0.00 0.00 5.10
2878 3573 9.093970 TCGAATCTAGAAATAGAAAAATCGCAA 57.906 29.630 0.00 0.00 0.00 4.85
2879 3574 9.362911 CGAATCTAGAAATAGAAAAATCGCAAG 57.637 33.333 0.00 0.00 0.00 4.01
2880 3575 9.163903 GAATCTAGAAATAGAAAAATCGCAAGC 57.836 33.333 0.00 0.00 37.18 4.01
2881 3576 7.849804 TCTAGAAATAGAAAAATCGCAAGCT 57.150 32.000 0.00 0.00 37.18 3.74
2882 3577 8.942338 TCTAGAAATAGAAAAATCGCAAGCTA 57.058 30.769 0.00 0.00 37.18 3.32
2883 3578 9.378551 TCTAGAAATAGAAAAATCGCAAGCTAA 57.621 29.630 0.00 0.00 37.18 3.09
2884 3579 9.643652 CTAGAAATAGAAAAATCGCAAGCTAAG 57.356 33.333 0.00 0.00 37.18 2.18
2885 3580 8.045176 AGAAATAGAAAAATCGCAAGCTAAGT 57.955 30.769 0.00 0.00 37.18 2.24
2886 3581 7.965107 AGAAATAGAAAAATCGCAAGCTAAGTG 59.035 33.333 0.00 0.00 37.18 3.16
2887 3582 6.985188 ATAGAAAAATCGCAAGCTAAGTGA 57.015 33.333 5.00 5.00 37.18 3.41
2888 3583 5.689383 AGAAAAATCGCAAGCTAAGTGAA 57.311 34.783 6.45 0.00 37.18 3.18
2889 3584 6.072112 AGAAAAATCGCAAGCTAAGTGAAA 57.928 33.333 6.45 0.00 37.18 2.69
2890 3585 6.503524 AGAAAAATCGCAAGCTAAGTGAAAA 58.496 32.000 6.45 0.00 37.18 2.29
2891 3586 6.417930 AGAAAAATCGCAAGCTAAGTGAAAAC 59.582 34.615 6.45 0.00 37.18 2.43
2892 3587 4.829064 AATCGCAAGCTAAGTGAAAACA 57.171 36.364 6.45 0.00 37.18 2.83
2893 3588 3.878086 TCGCAAGCTAAGTGAAAACAG 57.122 42.857 0.29 0.00 37.18 3.16
2894 3589 3.202906 TCGCAAGCTAAGTGAAAACAGT 58.797 40.909 0.29 0.00 37.18 3.55
2895 3590 3.247648 TCGCAAGCTAAGTGAAAACAGTC 59.752 43.478 0.29 0.00 37.18 3.51
2896 3591 3.002246 CGCAAGCTAAGTGAAAACAGTCA 59.998 43.478 0.00 0.00 0.00 3.41
2897 3592 4.319766 CGCAAGCTAAGTGAAAACAGTCAT 60.320 41.667 0.00 0.00 0.00 3.06
2898 3593 5.107104 CGCAAGCTAAGTGAAAACAGTCATA 60.107 40.000 0.00 0.00 0.00 2.15
2899 3594 6.565811 CGCAAGCTAAGTGAAAACAGTCATAA 60.566 38.462 0.00 0.00 0.00 1.90
2900 3595 7.138736 GCAAGCTAAGTGAAAACAGTCATAAA 58.861 34.615 0.00 0.00 0.00 1.40
2901 3596 7.647715 GCAAGCTAAGTGAAAACAGTCATAAAA 59.352 33.333 0.00 0.00 0.00 1.52
2902 3597 9.515020 CAAGCTAAGTGAAAACAGTCATAAAAA 57.485 29.630 0.00 0.00 0.00 1.94
2927 3622 4.899239 CTGCTGCCCCCGACGATC 62.899 72.222 0.00 0.00 0.00 3.69
2930 3625 4.570663 CTGCCCCCGACGATCGTC 62.571 72.222 33.22 33.22 38.40 4.20
2933 3628 3.593794 CCCCCGACGATCGTCCTC 61.594 72.222 35.48 17.52 41.76 3.71
2934 3629 3.593794 CCCCGACGATCGTCCTCC 61.594 72.222 35.48 17.18 41.76 4.30
2935 3630 2.516460 CCCGACGATCGTCCTCCT 60.516 66.667 35.48 8.06 41.76 3.69
2936 3631 2.119655 CCCGACGATCGTCCTCCTT 61.120 63.158 35.48 7.28 41.76 3.36
2937 3632 1.355916 CCGACGATCGTCCTCCTTC 59.644 63.158 35.48 15.45 41.76 3.46
2938 3633 1.011019 CGACGATCGTCCTCCTTCG 60.011 63.158 35.48 22.41 41.76 3.79
2939 3634 1.703438 CGACGATCGTCCTCCTTCGT 61.703 60.000 35.48 6.53 46.50 3.85
2940 3635 0.450983 GACGATCGTCCTCCTTCGTT 59.549 55.000 33.06 1.22 44.13 3.85
2941 3636 0.450983 ACGATCGTCCTCCTTCGTTC 59.549 55.000 16.60 0.00 41.65 3.95
2942 3637 0.450583 CGATCGTCCTCCTTCGTTCA 59.549 55.000 7.03 0.00 0.00 3.18
2943 3638 1.065701 CGATCGTCCTCCTTCGTTCAT 59.934 52.381 7.03 0.00 0.00 2.57
2944 3639 2.464865 GATCGTCCTCCTTCGTTCATG 58.535 52.381 0.00 0.00 0.00 3.07
2945 3640 0.530744 TCGTCCTCCTTCGTTCATGG 59.469 55.000 0.00 0.00 0.00 3.66
2946 3641 0.246635 CGTCCTCCTTCGTTCATGGT 59.753 55.000 0.00 0.00 0.00 3.55
2947 3642 1.736032 CGTCCTCCTTCGTTCATGGTC 60.736 57.143 0.00 0.00 0.00 4.02
2948 3643 1.550976 GTCCTCCTTCGTTCATGGTCT 59.449 52.381 0.00 0.00 0.00 3.85
2949 3644 1.825474 TCCTCCTTCGTTCATGGTCTC 59.175 52.381 0.00 0.00 0.00 3.36
2950 3645 1.469940 CCTCCTTCGTTCATGGTCTCG 60.470 57.143 0.00 0.00 0.00 4.04
2951 3646 1.472878 CTCCTTCGTTCATGGTCTCGA 59.527 52.381 0.00 0.00 0.00 4.04
2952 3647 2.099921 CTCCTTCGTTCATGGTCTCGAT 59.900 50.000 0.00 0.00 32.54 3.59
2953 3648 2.099263 TCCTTCGTTCATGGTCTCGATC 59.901 50.000 0.00 0.00 32.54 3.69
2954 3649 2.159240 CCTTCGTTCATGGTCTCGATCA 60.159 50.000 0.00 0.00 32.54 2.92
2955 3650 2.561733 TCGTTCATGGTCTCGATCAC 57.438 50.000 0.00 0.00 0.00 3.06
2956 3651 1.134367 TCGTTCATGGTCTCGATCACC 59.866 52.381 6.72 6.72 0.00 4.02
2957 3652 1.135139 CGTTCATGGTCTCGATCACCT 59.865 52.381 13.42 0.00 34.66 4.00
2958 3653 2.796383 CGTTCATGGTCTCGATCACCTC 60.796 54.545 13.42 1.52 34.66 3.85
2959 3654 1.403814 TCATGGTCTCGATCACCTCC 58.596 55.000 13.42 0.00 34.66 4.30
2960 3655 1.114627 CATGGTCTCGATCACCTCCA 58.885 55.000 13.42 1.50 34.66 3.86
2961 3656 1.690893 CATGGTCTCGATCACCTCCAT 59.309 52.381 13.42 3.60 36.30 3.41
2962 3657 2.748209 TGGTCTCGATCACCTCCATA 57.252 50.000 13.42 0.00 34.66 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 4.382901 GGCATGTCATGAGGCCAAAAATAA 60.383 41.667 21.91 0.00 45.70 1.40
221 222 1.203287 GGAGCTAGCTTTGCTTTTGGG 59.797 52.381 20.42 0.00 41.30 4.12
242 243 6.875469 TGGATATCCTAGGAACATACCTTCT 58.125 40.000 22.35 0.00 41.00 2.85
245 246 5.966935 CCATGGATATCCTAGGAACATACCT 59.033 44.000 22.35 3.35 43.32 3.08
349 350 4.020662 TGAACCAAAAGGCAAGAACAAACT 60.021 37.500 0.00 0.00 0.00 2.66
367 368 2.225727 GTCAACAGATCCGGTTTGAACC 59.774 50.000 0.00 2.75 45.76 3.62
437 440 0.882042 CGCCCTCATGATACACCAGC 60.882 60.000 0.00 0.00 0.00 4.85
482 485 0.912487 ATAGACACCAGCCCCCGAAA 60.912 55.000 0.00 0.00 0.00 3.46
483 486 1.306654 ATAGACACCAGCCCCCGAA 60.307 57.895 0.00 0.00 0.00 4.30
484 487 2.063979 CATAGACACCAGCCCCCGA 61.064 63.158 0.00 0.00 0.00 5.14
485 488 1.910580 AACATAGACACCAGCCCCCG 61.911 60.000 0.00 0.00 0.00 5.73
486 489 0.107165 GAACATAGACACCAGCCCCC 60.107 60.000 0.00 0.00 0.00 5.40
487 490 0.912486 AGAACATAGACACCAGCCCC 59.088 55.000 0.00 0.00 0.00 5.80
528 531 3.353557 ACTACAGAGGCGACAAGATGTA 58.646 45.455 0.00 0.00 0.00 2.29
548 551 4.095036 GCCTTCTTCACCAGTGCTTATTAC 59.905 45.833 0.00 0.00 0.00 1.89
550 553 3.084786 GCCTTCTTCACCAGTGCTTATT 58.915 45.455 0.00 0.00 0.00 1.40
551 554 2.040278 TGCCTTCTTCACCAGTGCTTAT 59.960 45.455 0.00 0.00 0.00 1.73
552 555 1.419762 TGCCTTCTTCACCAGTGCTTA 59.580 47.619 0.00 0.00 0.00 3.09
553 556 0.183492 TGCCTTCTTCACCAGTGCTT 59.817 50.000 0.00 0.00 0.00 3.91
554 557 0.183492 TTGCCTTCTTCACCAGTGCT 59.817 50.000 0.00 0.00 0.00 4.40
599 602 3.893326 ATTTATCTGCCTGCAAAACCC 57.107 42.857 0.00 0.00 0.00 4.11
625 628 0.677731 AATCTGTGCACATGGACGGG 60.678 55.000 22.00 6.84 42.18 5.28
650 653 2.755103 GTTGAGATTGGTTGGGTGGATC 59.245 50.000 0.00 0.00 0.00 3.36
709 712 4.330250 CCATGATCACTCAGTCACCTTTT 58.670 43.478 0.00 0.00 34.12 2.27
732 735 1.483827 TGTGGGCATCTGAAGAGCTAG 59.516 52.381 0.00 0.00 0.00 3.42
782 785 8.430063 GCAAAATGTGTAATGAGAAGACAAATG 58.570 33.333 0.00 0.00 0.00 2.32
797 801 4.581077 TCAACTGCATGCAAAATGTGTA 57.419 36.364 22.88 5.18 0.00 2.90
810 814 8.414003 CCTATACAGTAGAGTTATTCAACTGCA 58.586 37.037 1.56 0.00 45.18 4.41
811 815 7.382759 GCCTATACAGTAGAGTTATTCAACTGC 59.617 40.741 1.56 0.00 45.18 4.40
814 818 7.382759 GCAGCCTATACAGTAGAGTTATTCAAC 59.617 40.741 1.56 0.00 34.67 3.18
815 819 7.069455 TGCAGCCTATACAGTAGAGTTATTCAA 59.931 37.037 1.56 0.00 0.00 2.69
816 820 6.549736 TGCAGCCTATACAGTAGAGTTATTCA 59.450 38.462 1.56 0.00 0.00 2.57
817 821 6.982852 TGCAGCCTATACAGTAGAGTTATTC 58.017 40.000 1.56 0.00 0.00 1.75
819 823 6.071984 ACTGCAGCCTATACAGTAGAGTTAT 58.928 40.000 15.27 0.00 42.65 1.89
820 824 5.446860 ACTGCAGCCTATACAGTAGAGTTA 58.553 41.667 15.27 0.00 42.65 2.24
821 825 4.282496 ACTGCAGCCTATACAGTAGAGTT 58.718 43.478 15.27 0.00 42.65 3.01
822 826 3.886505 GACTGCAGCCTATACAGTAGAGT 59.113 47.826 15.27 0.00 44.40 3.24
823 827 3.058570 CGACTGCAGCCTATACAGTAGAG 60.059 52.174 15.27 0.00 44.40 2.43
824 828 2.879026 CGACTGCAGCCTATACAGTAGA 59.121 50.000 15.27 0.00 44.40 2.59
828 832 0.747255 ACCGACTGCAGCCTATACAG 59.253 55.000 15.27 0.00 37.45 2.74
835 839 1.901650 CTTTCGAACCGACTGCAGCC 61.902 60.000 15.27 0.16 34.89 4.85
844 852 3.392769 TGTCACAAAACTTTCGAACCG 57.607 42.857 0.00 0.00 0.00 4.44
845 853 4.915704 TGATGTCACAAAACTTTCGAACC 58.084 39.130 0.00 0.00 0.00 3.62
850 858 4.619973 TGGCATGATGTCACAAAACTTTC 58.380 39.130 0.00 0.00 0.00 2.62
863 871 7.437793 AAAACTAAAATTTGGTGGCATGATG 57.562 32.000 0.00 0.00 0.00 3.07
883 891 6.581919 AGAGCAAAAACAAAATGTGCAAAAAC 59.418 30.769 0.00 0.00 37.68 2.43
886 894 5.876612 AGAGCAAAAACAAAATGTGCAAA 57.123 30.435 0.00 0.00 37.68 3.68
887 895 6.538021 ACATAGAGCAAAAACAAAATGTGCAA 59.462 30.769 0.00 0.00 37.68 4.08
902 910 7.966753 CGTCACTACTAGTAAAACATAGAGCAA 59.033 37.037 3.76 0.00 0.00 3.91
904 912 7.692088 TCGTCACTACTAGTAAAACATAGAGC 58.308 38.462 3.76 0.00 0.00 4.09
905 913 9.653067 CATCGTCACTACTAGTAAAACATAGAG 57.347 37.037 3.76 0.00 0.00 2.43
906 914 8.618677 CCATCGTCACTACTAGTAAAACATAGA 58.381 37.037 3.76 0.00 0.00 1.98
907 915 8.618677 TCCATCGTCACTACTAGTAAAACATAG 58.381 37.037 3.76 0.00 0.00 2.23
908 916 8.510243 TCCATCGTCACTACTAGTAAAACATA 57.490 34.615 3.76 0.00 0.00 2.29
909 917 7.400599 TCCATCGTCACTACTAGTAAAACAT 57.599 36.000 3.76 0.00 0.00 2.71
911 919 7.478322 TCATCCATCGTCACTACTAGTAAAAC 58.522 38.462 3.76 2.04 0.00 2.43
912 920 7.634671 TCATCCATCGTCACTACTAGTAAAA 57.365 36.000 3.76 0.00 0.00 1.52
913 921 7.818997 ATCATCCATCGTCACTACTAGTAAA 57.181 36.000 3.76 0.00 0.00 2.01
914 922 7.501225 TGAATCATCCATCGTCACTACTAGTAA 59.499 37.037 3.76 0.00 0.00 2.24
917 925 6.016693 ACTGAATCATCCATCGTCACTACTAG 60.017 42.308 0.00 0.00 0.00 2.57
941 1118 1.081242 CTGCATGCACCCAACGAAC 60.081 57.895 18.46 0.00 0.00 3.95
949 1126 4.120331 GTTCCGGCTGCATGCACC 62.120 66.667 18.46 20.83 45.15 5.01
1305 1509 3.136123 CCGCCCACCATCTTGCAG 61.136 66.667 0.00 0.00 0.00 4.41
1509 1713 3.036429 GCCGTTGAGGAGGATGGCT 62.036 63.158 0.00 0.00 43.17 4.75
1511 1715 2.202932 CGCCGTTGAGGAGGATGG 60.203 66.667 0.00 0.00 45.00 3.51
1679 1886 1.703438 CGAGTTGCTCATCAGCCTGC 61.703 60.000 0.00 0.00 46.26 4.85
1801 2472 4.521062 GCCGTGCCTCATCGAGCT 62.521 66.667 0.00 0.00 0.00 4.09
2011 2702 3.715097 GCAGGGCAGCCTCTCAGT 61.715 66.667 12.43 0.00 0.00 3.41
2045 2740 4.640647 CCCCTTTGATCAGTAAGTAAAGCC 59.359 45.833 6.44 0.00 0.00 4.35
2116 2811 9.796120 ACTGAAACGAGTGAAATCAATTTTTAA 57.204 25.926 0.00 0.00 0.00 1.52
2118 2813 9.796120 TTACTGAAACGAGTGAAATCAATTTTT 57.204 25.926 0.00 0.00 0.00 1.94
2119 2814 9.233232 GTTACTGAAACGAGTGAAATCAATTTT 57.767 29.630 0.00 0.00 0.00 1.82
2120 2815 8.402472 TGTTACTGAAACGAGTGAAATCAATTT 58.598 29.630 0.00 0.00 41.30 1.82
2121 2816 7.925993 TGTTACTGAAACGAGTGAAATCAATT 58.074 30.769 0.00 0.00 41.30 2.32
2122 2817 7.490962 TGTTACTGAAACGAGTGAAATCAAT 57.509 32.000 0.00 0.00 41.30 2.57
2123 2818 6.912203 TGTTACTGAAACGAGTGAAATCAA 57.088 33.333 0.00 0.00 41.30 2.57
2124 2819 8.771920 ATATGTTACTGAAACGAGTGAAATCA 57.228 30.769 0.00 0.00 41.30 2.57
2127 2822 9.047371 TGAAATATGTTACTGAAACGAGTGAAA 57.953 29.630 0.00 0.00 41.30 2.69
2128 2823 8.492748 GTGAAATATGTTACTGAAACGAGTGAA 58.507 33.333 0.00 0.00 41.30 3.18
2129 2824 7.870954 AGTGAAATATGTTACTGAAACGAGTGA 59.129 33.333 0.00 0.00 41.30 3.41
2130 2825 8.018677 AGTGAAATATGTTACTGAAACGAGTG 57.981 34.615 0.00 0.00 41.30 3.51
2131 2826 7.061905 CGAGTGAAATATGTTACTGAAACGAGT 59.938 37.037 0.00 0.00 41.30 4.18
2132 2827 7.061905 ACGAGTGAAATATGTTACTGAAACGAG 59.938 37.037 0.00 0.00 41.30 4.18
2133 2828 6.864685 ACGAGTGAAATATGTTACTGAAACGA 59.135 34.615 0.00 0.00 41.30 3.85
2134 2829 7.045725 ACGAGTGAAATATGTTACTGAAACG 57.954 36.000 0.00 0.00 41.30 3.60
2135 2830 9.737025 GTAACGAGTGAAATATGTTACTGAAAC 57.263 33.333 0.00 0.00 40.86 2.78
2136 2831 9.478768 TGTAACGAGTGAAATATGTTACTGAAA 57.521 29.630 12.89 0.00 43.15 2.69
2137 2832 9.478768 TTGTAACGAGTGAAATATGTTACTGAA 57.521 29.630 12.89 0.56 43.15 3.02
2138 2833 9.647797 ATTGTAACGAGTGAAATATGTTACTGA 57.352 29.630 12.89 4.66 43.15 3.41
2144 2839 9.647797 TCTGTTATTGTAACGAGTGAAATATGT 57.352 29.630 0.00 0.00 0.00 2.29
2149 2844 9.047371 TGAAATCTGTTATTGTAACGAGTGAAA 57.953 29.630 0.00 0.00 0.00 2.69
2150 2845 8.492748 GTGAAATCTGTTATTGTAACGAGTGAA 58.507 33.333 0.00 0.00 0.00 3.18
2151 2846 7.870954 AGTGAAATCTGTTATTGTAACGAGTGA 59.129 33.333 0.00 0.00 0.00 3.41
2152 2847 8.018677 AGTGAAATCTGTTATTGTAACGAGTG 57.981 34.615 0.00 0.00 0.00 3.51
2153 2848 9.701098 TTAGTGAAATCTGTTATTGTAACGAGT 57.299 29.630 0.00 0.00 0.00 4.18
2655 3350 9.594936 TCCATCCCTTTTATTCAACTTTTTCTA 57.405 29.630 0.00 0.00 0.00 2.10
2656 3351 8.491045 TCCATCCCTTTTATTCAACTTTTTCT 57.509 30.769 0.00 0.00 0.00 2.52
2657 3352 8.367911 ACTCCATCCCTTTTATTCAACTTTTTC 58.632 33.333 0.00 0.00 0.00 2.29
2658 3353 8.262601 ACTCCATCCCTTTTATTCAACTTTTT 57.737 30.769 0.00 0.00 0.00 1.94
2659 3354 7.855784 ACTCCATCCCTTTTATTCAACTTTT 57.144 32.000 0.00 0.00 0.00 2.27
2660 3355 7.855784 AACTCCATCCCTTTTATTCAACTTT 57.144 32.000 0.00 0.00 0.00 2.66
2661 3356 7.855784 AAACTCCATCCCTTTTATTCAACTT 57.144 32.000 0.00 0.00 0.00 2.66
2662 3357 7.855784 AAAACTCCATCCCTTTTATTCAACT 57.144 32.000 0.00 0.00 0.00 3.16
2685 3380 9.581099 AATAAAGCTCGAACTTTCTTTCAAAAA 57.419 25.926 16.64 0.00 40.32 1.94
2686 3381 9.233232 GAATAAAGCTCGAACTTTCTTTCAAAA 57.767 29.630 16.64 0.00 40.32 2.44
2687 3382 8.402472 TGAATAAAGCTCGAACTTTCTTTCAAA 58.598 29.630 23.52 11.50 40.32 2.69
2688 3383 7.925993 TGAATAAAGCTCGAACTTTCTTTCAA 58.074 30.769 23.52 14.39 40.32 2.69
2689 3384 7.490962 TGAATAAAGCTCGAACTTTCTTTCA 57.509 32.000 22.70 22.70 40.32 2.69
2690 3385 8.956617 AATGAATAAAGCTCGAACTTTCTTTC 57.043 30.769 16.64 18.62 40.32 2.62
2692 3387 9.436957 TCTAATGAATAAAGCTCGAACTTTCTT 57.563 29.630 16.64 13.34 40.32 2.52
2693 3388 9.436957 TTCTAATGAATAAAGCTCGAACTTTCT 57.563 29.630 16.64 5.29 40.32 2.52
2722 3417 8.786898 CCAATCCTCATAAACGATGTAATGATT 58.213 33.333 0.00 0.00 36.84 2.57
2723 3418 7.939039 ACCAATCCTCATAAACGATGTAATGAT 59.061 33.333 0.00 0.00 36.84 2.45
2724 3419 7.279615 ACCAATCCTCATAAACGATGTAATGA 58.720 34.615 0.00 0.00 36.84 2.57
2725 3420 7.496529 ACCAATCCTCATAAACGATGTAATG 57.503 36.000 0.00 0.00 36.84 1.90
2726 3421 8.208224 TGTACCAATCCTCATAAACGATGTAAT 58.792 33.333 0.00 0.00 36.84 1.89
2727 3422 7.557724 TGTACCAATCCTCATAAACGATGTAA 58.442 34.615 0.00 0.00 36.84 2.41
2728 3423 7.114866 TGTACCAATCCTCATAAACGATGTA 57.885 36.000 0.00 0.00 36.84 2.29
2729 3424 5.984725 TGTACCAATCCTCATAAACGATGT 58.015 37.500 0.00 0.00 36.84 3.06
2730 3425 6.918892 TTGTACCAATCCTCATAAACGATG 57.081 37.500 0.00 0.00 36.82 3.84
2731 3426 7.468631 GCAATTGTACCAATCCTCATAAACGAT 60.469 37.037 7.40 0.00 0.00 3.73
2732 3427 6.183360 GCAATTGTACCAATCCTCATAAACGA 60.183 38.462 7.40 0.00 0.00 3.85
2733 3428 5.971202 GCAATTGTACCAATCCTCATAAACG 59.029 40.000 7.40 0.00 0.00 3.60
2734 3429 6.862209 TGCAATTGTACCAATCCTCATAAAC 58.138 36.000 7.40 0.00 0.00 2.01
2735 3430 7.658525 ATGCAATTGTACCAATCCTCATAAA 57.341 32.000 7.40 0.00 0.00 1.40
2736 3431 7.658525 AATGCAATTGTACCAATCCTCATAA 57.341 32.000 7.40 0.00 33.44 1.90
2737 3432 8.795513 CATAATGCAATTGTACCAATCCTCATA 58.204 33.333 7.40 0.00 36.99 2.15
2738 3433 7.288389 ACATAATGCAATTGTACCAATCCTCAT 59.712 33.333 7.40 0.00 36.99 2.90
2739 3434 6.606796 ACATAATGCAATTGTACCAATCCTCA 59.393 34.615 7.40 0.00 36.99 3.86
2740 3435 6.919662 CACATAATGCAATTGTACCAATCCTC 59.080 38.462 7.40 0.00 36.99 3.71
2741 3436 6.183360 CCACATAATGCAATTGTACCAATCCT 60.183 38.462 7.40 0.00 36.99 3.24
2742 3437 5.984926 CCACATAATGCAATTGTACCAATCC 59.015 40.000 7.40 0.00 36.99 3.01
2743 3438 6.572519 ACCACATAATGCAATTGTACCAATC 58.427 36.000 7.40 0.00 36.99 2.67
2744 3439 6.543430 ACCACATAATGCAATTGTACCAAT 57.457 33.333 7.40 0.00 36.99 3.16
2745 3440 5.991933 ACCACATAATGCAATTGTACCAA 57.008 34.783 7.40 0.00 36.99 3.67
2746 3441 5.105554 GGAACCACATAATGCAATTGTACCA 60.106 40.000 7.40 0.00 36.99 3.25
2747 3442 5.127031 AGGAACCACATAATGCAATTGTACC 59.873 40.000 7.40 0.00 36.99 3.34
2748 3443 6.207691 AGGAACCACATAATGCAATTGTAC 57.792 37.500 7.40 0.00 36.99 2.90
2749 3444 6.849085 AAGGAACCACATAATGCAATTGTA 57.151 33.333 7.40 2.30 36.99 2.41
2750 3445 5.743636 AAGGAACCACATAATGCAATTGT 57.256 34.783 7.40 0.00 36.99 2.71
2751 3446 7.962917 GTTTAAGGAACCACATAATGCAATTG 58.037 34.615 0.00 0.00 33.07 2.32
2766 3461 9.143631 CATTCATTTCTGATTGGTTTAAGGAAC 57.856 33.333 0.00 0.00 37.53 3.62
2767 3462 9.087871 TCATTCATTTCTGATTGGTTTAAGGAA 57.912 29.630 0.00 0.00 34.81 3.36
2768 3463 8.648698 TCATTCATTTCTGATTGGTTTAAGGA 57.351 30.769 0.00 0.00 34.81 3.36
2769 3464 9.709495 TTTCATTCATTTCTGATTGGTTTAAGG 57.291 29.630 0.00 0.00 34.81 2.69
2776 3471 9.245962 GCTAGATTTTCATTCATTTCTGATTGG 57.754 33.333 0.00 0.00 34.81 3.16
2777 3472 9.245962 GGCTAGATTTTCATTCATTTCTGATTG 57.754 33.333 0.00 0.00 35.18 2.67
2778 3473 8.974238 TGGCTAGATTTTCATTCATTTCTGATT 58.026 29.630 0.00 0.00 0.00 2.57
2779 3474 8.529424 TGGCTAGATTTTCATTCATTTCTGAT 57.471 30.769 0.00 0.00 0.00 2.90
2780 3475 7.943079 TGGCTAGATTTTCATTCATTTCTGA 57.057 32.000 0.00 0.00 0.00 3.27
2781 3476 8.248945 AGTTGGCTAGATTTTCATTCATTTCTG 58.751 33.333 0.00 0.00 0.00 3.02
2782 3477 8.358582 AGTTGGCTAGATTTTCATTCATTTCT 57.641 30.769 0.00 0.00 0.00 2.52
2783 3478 8.866956 CAAGTTGGCTAGATTTTCATTCATTTC 58.133 33.333 0.00 0.00 0.00 2.17
2784 3479 7.820872 CCAAGTTGGCTAGATTTTCATTCATTT 59.179 33.333 9.46 0.00 0.00 2.32
2785 3480 7.325694 CCAAGTTGGCTAGATTTTCATTCATT 58.674 34.615 9.46 0.00 0.00 2.57
2786 3481 6.870769 CCAAGTTGGCTAGATTTTCATTCAT 58.129 36.000 9.46 0.00 0.00 2.57
2787 3482 6.271488 CCAAGTTGGCTAGATTTTCATTCA 57.729 37.500 9.46 0.00 0.00 2.57
2805 3500 3.891366 AGTTGCTTATGAACTTGCCAAGT 59.109 39.130 3.74 3.74 45.46 3.16
2806 3501 4.510038 AGTTGCTTATGAACTTGCCAAG 57.490 40.909 2.11 2.11 28.94 3.61
2807 3502 4.935352 AAGTTGCTTATGAACTTGCCAA 57.065 36.364 0.00 0.00 41.16 4.52
2808 3503 4.935352 AAAGTTGCTTATGAACTTGCCA 57.065 36.364 0.00 0.00 41.71 4.92
2809 3504 7.732664 CAAATAAAGTTGCTTATGAACTTGCC 58.267 34.615 0.00 0.00 41.71 4.52
2825 3520 8.624776 GCATTGTAATAGAGAGGCAAATAAAGT 58.375 33.333 0.00 0.00 0.00 2.66
2826 3521 8.844244 AGCATTGTAATAGAGAGGCAAATAAAG 58.156 33.333 0.00 0.00 0.00 1.85
2827 3522 8.752005 AGCATTGTAATAGAGAGGCAAATAAA 57.248 30.769 0.00 0.00 0.00 1.40
2828 3523 7.171508 CGAGCATTGTAATAGAGAGGCAAATAA 59.828 37.037 0.00 0.00 0.00 1.40
2829 3524 6.646653 CGAGCATTGTAATAGAGAGGCAAATA 59.353 38.462 0.00 0.00 0.00 1.40
2830 3525 5.468072 CGAGCATTGTAATAGAGAGGCAAAT 59.532 40.000 0.00 0.00 0.00 2.32
2831 3526 4.811024 CGAGCATTGTAATAGAGAGGCAAA 59.189 41.667 0.00 0.00 0.00 3.68
2832 3527 4.099419 TCGAGCATTGTAATAGAGAGGCAA 59.901 41.667 0.00 0.00 0.00 4.52
2833 3528 3.636764 TCGAGCATTGTAATAGAGAGGCA 59.363 43.478 0.00 0.00 0.00 4.75
2834 3529 4.244425 TCGAGCATTGTAATAGAGAGGC 57.756 45.455 0.00 0.00 0.00 4.70
2835 3530 6.686630 AGATTCGAGCATTGTAATAGAGAGG 58.313 40.000 0.00 0.00 0.00 3.69
2836 3531 8.726068 TCTAGATTCGAGCATTGTAATAGAGAG 58.274 37.037 0.00 0.00 0.00 3.20
2837 3532 8.622948 TCTAGATTCGAGCATTGTAATAGAGA 57.377 34.615 0.00 0.00 0.00 3.10
2838 3533 9.684448 TTTCTAGATTCGAGCATTGTAATAGAG 57.316 33.333 0.00 0.00 0.00 2.43
2845 3540 8.948631 TTTCTATTTCTAGATTCGAGCATTGT 57.051 30.769 0.00 0.00 33.98 2.71
2849 3544 8.755941 CGATTTTTCTATTTCTAGATTCGAGCA 58.244 33.333 0.00 0.00 33.98 4.26
2850 3545 7.738176 GCGATTTTTCTATTTCTAGATTCGAGC 59.262 37.037 0.00 0.00 33.98 5.03
2851 3546 8.755941 TGCGATTTTTCTATTTCTAGATTCGAG 58.244 33.333 0.00 0.00 33.98 4.04
2852 3547 8.642908 TGCGATTTTTCTATTTCTAGATTCGA 57.357 30.769 0.00 0.00 33.98 3.71
2853 3548 9.362911 CTTGCGATTTTTCTATTTCTAGATTCG 57.637 33.333 0.00 0.00 33.98 3.34
2854 3549 9.163903 GCTTGCGATTTTTCTATTTCTAGATTC 57.836 33.333 0.00 0.00 33.98 2.52
2855 3550 8.897752 AGCTTGCGATTTTTCTATTTCTAGATT 58.102 29.630 0.00 0.00 33.98 2.40
2856 3551 8.443953 AGCTTGCGATTTTTCTATTTCTAGAT 57.556 30.769 0.00 0.00 33.98 1.98
2857 3552 7.849804 AGCTTGCGATTTTTCTATTTCTAGA 57.150 32.000 0.00 0.00 32.00 2.43
2858 3553 9.643652 CTTAGCTTGCGATTTTTCTATTTCTAG 57.356 33.333 0.00 0.00 0.00 2.43
2859 3554 9.162764 ACTTAGCTTGCGATTTTTCTATTTCTA 57.837 29.630 0.00 0.00 0.00 2.10
2860 3555 7.965107 CACTTAGCTTGCGATTTTTCTATTTCT 59.035 33.333 0.00 0.00 0.00 2.52
2861 3556 7.962918 TCACTTAGCTTGCGATTTTTCTATTTC 59.037 33.333 0.00 0.00 0.00 2.17
2862 3557 7.816640 TCACTTAGCTTGCGATTTTTCTATTT 58.183 30.769 0.00 0.00 0.00 1.40
2863 3558 7.377766 TCACTTAGCTTGCGATTTTTCTATT 57.622 32.000 0.00 0.00 0.00 1.73
2864 3559 6.985188 TCACTTAGCTTGCGATTTTTCTAT 57.015 33.333 0.00 0.00 0.00 1.98
2865 3560 6.795098 TTCACTTAGCTTGCGATTTTTCTA 57.205 33.333 0.00 0.00 0.00 2.10
2866 3561 5.689383 TTCACTTAGCTTGCGATTTTTCT 57.311 34.783 0.00 0.00 0.00 2.52
2867 3562 6.198216 TGTTTTCACTTAGCTTGCGATTTTTC 59.802 34.615 0.00 0.00 0.00 2.29
2868 3563 6.039616 TGTTTTCACTTAGCTTGCGATTTTT 58.960 32.000 0.00 0.00 0.00 1.94
2869 3564 5.587289 TGTTTTCACTTAGCTTGCGATTTT 58.413 33.333 0.00 0.00 0.00 1.82
2870 3565 5.181690 TGTTTTCACTTAGCTTGCGATTT 57.818 34.783 0.00 0.00 0.00 2.17
2871 3566 4.275936 ACTGTTTTCACTTAGCTTGCGATT 59.724 37.500 0.00 0.00 0.00 3.34
2872 3567 3.815401 ACTGTTTTCACTTAGCTTGCGAT 59.185 39.130 0.00 0.00 0.00 4.58
2873 3568 3.202906 ACTGTTTTCACTTAGCTTGCGA 58.797 40.909 0.00 0.00 0.00 5.10
2874 3569 3.002246 TGACTGTTTTCACTTAGCTTGCG 59.998 43.478 0.00 0.00 0.00 4.85
2875 3570 4.552166 TGACTGTTTTCACTTAGCTTGC 57.448 40.909 0.00 0.00 0.00 4.01
2876 3571 9.515020 TTTTTATGACTGTTTTCACTTAGCTTG 57.485 29.630 0.00 0.00 0.00 4.01
2910 3605 4.899239 GATCGTCGGGGGCAGCAG 62.899 72.222 0.00 0.00 0.00 4.24
2913 3608 4.570663 GACGATCGTCGGGGGCAG 62.571 72.222 30.46 0.00 45.59 4.85
2916 3611 3.593794 GAGGACGATCGTCGGGGG 61.594 72.222 34.69 1.01 45.59 5.40
2917 3612 3.593794 GGAGGACGATCGTCGGGG 61.594 72.222 34.69 1.76 45.59 5.73
2918 3613 2.061182 GAAGGAGGACGATCGTCGGG 62.061 65.000 34.69 2.52 45.59 5.14
2919 3614 1.355916 GAAGGAGGACGATCGTCGG 59.644 63.158 34.69 2.91 45.59 4.79
2920 3615 1.011019 CGAAGGAGGACGATCGTCG 60.011 63.158 34.69 22.09 45.41 5.12
2921 3616 0.450983 AACGAAGGAGGACGATCGTC 59.549 55.000 34.70 34.70 42.73 4.20
2922 3617 0.450983 GAACGAAGGAGGACGATCGT 59.549 55.000 22.97 22.97 44.47 3.73
2923 3618 0.450583 TGAACGAAGGAGGACGATCG 59.549 55.000 14.88 14.88 38.63 3.69
2924 3619 2.464865 CATGAACGAAGGAGGACGATC 58.535 52.381 0.00 0.00 33.30 3.69
2925 3620 1.137086 CCATGAACGAAGGAGGACGAT 59.863 52.381 0.00 0.00 0.00 3.73
2926 3621 0.530744 CCATGAACGAAGGAGGACGA 59.469 55.000 0.00 0.00 0.00 4.20
2927 3622 0.246635 ACCATGAACGAAGGAGGACG 59.753 55.000 0.00 0.00 0.00 4.79
2928 3623 1.550976 AGACCATGAACGAAGGAGGAC 59.449 52.381 0.00 0.00 0.00 3.85
2929 3624 1.825474 GAGACCATGAACGAAGGAGGA 59.175 52.381 0.00 0.00 0.00 3.71
2930 3625 1.469940 CGAGACCATGAACGAAGGAGG 60.470 57.143 0.00 0.00 0.00 4.30
2931 3626 1.472878 TCGAGACCATGAACGAAGGAG 59.527 52.381 0.00 0.00 0.00 3.69
2932 3627 1.541379 TCGAGACCATGAACGAAGGA 58.459 50.000 0.00 0.00 0.00 3.36
2933 3628 2.159240 TGATCGAGACCATGAACGAAGG 60.159 50.000 0.00 0.00 38.22 3.46
2934 3629 2.854777 GTGATCGAGACCATGAACGAAG 59.145 50.000 0.00 0.00 38.22 3.79
2935 3630 2.416836 GGTGATCGAGACCATGAACGAA 60.417 50.000 10.80 0.00 38.22 3.85
2936 3631 1.134367 GGTGATCGAGACCATGAACGA 59.866 52.381 10.80 0.00 39.01 3.85
2937 3632 1.135139 AGGTGATCGAGACCATGAACG 59.865 52.381 16.60 0.00 35.76 3.95
2938 3633 2.482142 GGAGGTGATCGAGACCATGAAC 60.482 54.545 16.60 4.83 35.76 3.18
2939 3634 1.757118 GGAGGTGATCGAGACCATGAA 59.243 52.381 16.60 0.00 35.76 2.57
2940 3635 1.341976 TGGAGGTGATCGAGACCATGA 60.342 52.381 16.60 0.00 35.76 3.07
2941 3636 1.114627 TGGAGGTGATCGAGACCATG 58.885 55.000 16.60 0.00 35.76 3.66
2942 3637 2.094100 ATGGAGGTGATCGAGACCAT 57.906 50.000 16.60 9.61 35.76 3.55
2943 3638 2.748209 TATGGAGGTGATCGAGACCA 57.252 50.000 16.60 7.96 35.76 4.02


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

AutoCloner maintained by Alex Coulton.