Multiple sequence alignment - TraesCS5B01G072600

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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 TraesCS5B01G072600 chr5B 100.000 3775 0 0 1 3775 84927705 84923931 0.000000e+00 6972.0
1 TraesCS5B01G072600 chr5B 91.018 501 42 3 1 500 280034954 280035452 0.000000e+00 673.0
2 TraesCS5B01G072600 chr5B 85.669 314 34 3 3121 3431 86173244 86172939 1.690000e-83 320.0
3 TraesCS5B01G072600 chr5B 77.874 461 77 18 2299 2757 86173753 86173316 2.890000e-66 263.0
4 TraesCS5B01G072600 chr5A 93.173 2739 123 21 62 2757 71481163 71478446 0.000000e+00 3964.0
5 TraesCS5B01G072600 chr5A 91.176 748 27 15 3054 3773 71478462 71477726 0.000000e+00 979.0
6 TraesCS5B01G072600 chr5A 91.018 501 42 3 1 500 170842434 170842932 0.000000e+00 673.0
7 TraesCS5B01G072600 chr5A 85.371 458 42 15 2300 2738 71471455 71471004 5.750000e-123 451.0
8 TraesCS5B01G072600 chr5D 95.966 1983 53 10 799 2757 76216252 76214273 0.000000e+00 3193.0
9 TraesCS5B01G072600 chr5D 93.984 748 17 8 3054 3774 76214289 76213543 0.000000e+00 1107.0
10 TraesCS5B01G072600 chr5D 89.352 648 38 7 1 645 76216872 76216253 0.000000e+00 785.0
11 TraesCS5B01G072600 chr5D 86.214 457 42 10 2300 2738 76102049 76101596 3.410000e-130 475.0
12 TraesCS5B01G072600 chr2D 91.218 501 41 3 1 500 418069273 418068775 0.000000e+00 678.0
13 TraesCS5B01G072600 chr2D 91.218 501 41 3 1 500 453734668 453735166 0.000000e+00 678.0
14 TraesCS5B01G072600 chr6A 91.018 501 42 3 1 500 178521575 178522073 0.000000e+00 673.0
15 TraesCS5B01G072600 chr6A 91.018 501 42 3 1 500 234188370 234188868 0.000000e+00 673.0
16 TraesCS5B01G072600 chr4D 91.018 501 42 3 1 500 248939745 248940243 0.000000e+00 673.0
17 TraesCS5B01G072600 chr4A 91.018 501 42 3 1 500 624980664 624981162 0.000000e+00 673.0
18 TraesCS5B01G072600 chr4B 97.810 274 3 2 2750 3023 462230612 462230882 1.590000e-128 470.0
19 TraesCS5B01G072600 chr7A 97.674 258 3 2 2766 3023 271626834 271626580 1.240000e-119 440.0
20 TraesCS5B01G072600 chr2B 96.241 266 6 2 2758 3023 591261840 591262101 2.080000e-117 433.0
21 TraesCS5B01G072600 chr6D 95.896 268 7 2 2756 3023 44244579 44244316 7.490000e-117 431.0
22 TraesCS5B01G072600 chr6B 95.255 274 6 5 2750 3023 227272766 227273032 9.690000e-116 427.0
23 TraesCS5B01G072600 chr1B 94.891 274 9 4 2750 3023 304518263 304518531 1.250000e-114 424.0
24 TraesCS5B01G072600 chr3B 94.161 274 12 3 2750 3023 820904053 820904322 7.540000e-112 414.0
25 TraesCS5B01G072600 chr3B 94.776 268 9 3 2756 3023 265849871 265849609 2.710000e-111 412.0
26 TraesCS5B01G072600 chr3B 94.161 274 11 3 2750 3023 820903871 820904139 2.710000e-111 412.0
27 TraesCS5B01G072600 chr3A 94.340 53 2 1 783 835 683535125 683535176 3.130000e-11 80.5
28 TraesCS5B01G072600 chr3A 89.474 57 6 0 678 734 7796001 7796057 5.230000e-09 73.1
29 TraesCS5B01G072600 chr1A 90.909 55 2 2 782 835 582274922 582274870 1.880000e-08 71.3
30 TraesCS5B01G072600 chr1A 90.196 51 4 1 782 832 364938843 364938794 8.750000e-07 65.8
31 TraesCS5B01G072600 chr1A 97.059 34 1 0 677 710 248620047 248620014 1.460000e-04 58.4


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 TraesCS5B01G072600 chr5B 84923931 84927705 3774 True 6972.0 6972 100.000000 1 3775 1 chr5B.!!$R1 3774
1 TraesCS5B01G072600 chr5B 86172939 86173753 814 True 291.5 320 81.771500 2299 3431 2 chr5B.!!$R2 1132
2 TraesCS5B01G072600 chr5A 71477726 71481163 3437 True 2471.5 3964 92.174500 62 3773 2 chr5A.!!$R2 3711
3 TraesCS5B01G072600 chr5D 76213543 76216872 3329 True 1695.0 3193 93.100667 1 3774 3 chr5D.!!$R2 3773

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
144 146 0.321346 CCATGCACCCCTTCAAAACC 59.679 55.0 0.00 0.00 0.00 3.27 F
455 457 0.392998 ACCATAGCTTGAAGCCGGTG 60.393 55.0 18.99 12.99 43.77 4.94 F
2056 2085 0.110486 GAAGTTCAGGTGGCCTTCCA 59.890 55.0 17.31 0.00 40.85 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2038 2067 0.111253 CTGGAAGGCCACCTGAACTT 59.889 55.0 17.68 0.0 39.92 2.66 R
2348 2392 1.118965 TCTGGTCTTGGTGCGGAAGA 61.119 55.0 0.00 0.0 0.00 2.87 R
3054 3104 0.033920 TGGCACGGCTGCTATAGATG 59.966 55.0 3.21 0.0 43.66 2.90 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
44 45 7.038017 TGTGATTCTCTCTCTTTAATCAGGGTT 60.038 37.037 0.00 0.00 38.61 4.11
52 53 8.258708 TCTCTCTTTAATCAGGGTTTTAGCTAC 58.741 37.037 0.00 0.00 0.00 3.58
53 54 7.913789 TCTCTTTAATCAGGGTTTTAGCTACA 58.086 34.615 0.00 0.00 0.00 2.74
57 58 7.548196 TTAATCAGGGTTTTAGCTACAATCG 57.452 36.000 0.00 0.00 0.00 3.34
96 97 7.505258 AGCAAAGGTTAAGATATCTTCTCCTC 58.495 38.462 27.14 19.73 37.82 3.71
144 146 0.321346 CCATGCACCCCTTCAAAACC 59.679 55.000 0.00 0.00 0.00 3.27
152 154 3.702045 CACCCCTTCAAAACCTGTGTTAA 59.298 43.478 0.00 0.00 33.30 2.01
236 238 0.693049 AACCATGTCCTCCAGACCAC 59.307 55.000 0.00 0.00 45.68 4.16
238 240 0.911525 CCATGTCCTCCAGACCACCT 60.912 60.000 0.00 0.00 45.68 4.00
278 280 1.350684 TCTCATTGTGGCCTACTTGCA 59.649 47.619 3.32 0.00 0.00 4.08
340 342 4.475016 ACTACCAGCTTGACCAGGATAATT 59.525 41.667 0.00 0.00 0.00 1.40
352 354 0.466963 GGATAATTCGGTCCCCACGT 59.533 55.000 0.00 0.00 0.00 4.49
390 392 2.771943 CTCCATACTTGAGGCCCTTGTA 59.228 50.000 0.00 0.00 0.00 2.41
430 432 2.031258 TTTCTGTTTGCAGTCGTCCA 57.969 45.000 0.00 0.00 43.05 4.02
431 433 2.254546 TTCTGTTTGCAGTCGTCCAT 57.745 45.000 0.00 0.00 43.05 3.41
455 457 0.392998 ACCATAGCTTGAAGCCGGTG 60.393 55.000 18.99 12.99 43.77 4.94
480 482 1.760613 CCACCTCCTTCGCCTTATGTA 59.239 52.381 0.00 0.00 0.00 2.29
498 500 2.714250 TGTACCCTCCATTTGGTTGTCT 59.286 45.455 0.00 0.00 36.04 3.41
499 501 3.139397 TGTACCCTCCATTTGGTTGTCTT 59.861 43.478 0.00 0.00 36.04 3.01
508 512 6.349300 TCCATTTGGTTGTCTTCTCTATAGC 58.651 40.000 0.00 0.00 36.34 2.97
638 644 6.591935 TGAGAACAACAGAAGTAATGGAGTT 58.408 36.000 0.00 0.00 0.00 3.01
648 654 7.066284 ACAGAAGTAATGGAGTTATGCATGTTC 59.934 37.037 10.16 3.96 37.57 3.18
710 716 2.434336 GGTGAGGTAGGATGTGTGCATA 59.566 50.000 0.00 0.00 35.07 3.14
715 721 5.104569 TGAGGTAGGATGTGTGCATATTGAA 60.105 40.000 0.00 0.00 35.07 2.69
730 736 9.846248 GTGCATATTGAAAGAAATGAAAGTAGT 57.154 29.630 0.00 0.00 0.00 2.73
748 755 8.980832 AAAGTAGTGGGGATCAAGATATAGAT 57.019 34.615 0.00 0.00 0.00 1.98
821 828 7.069877 ACCAACACCTATCTTACAACTGTTA 57.930 36.000 0.00 0.00 0.00 2.41
882 889 2.014574 GCTTGGGTGTGTGTGTGTGTA 61.015 52.381 0.00 0.00 0.00 2.90
1269 1286 5.600669 ACCAAAATTTTCTACTCCCTCCT 57.399 39.130 0.00 0.00 0.00 3.69
1391 1420 6.145535 GTGCTCTTAATTTTTCTCACAGTGG 58.854 40.000 0.00 0.00 0.00 4.00
1406 1435 5.977533 TCACAGTGGATTATAGGTAGGGAT 58.022 41.667 0.00 0.00 0.00 3.85
1609 1638 7.048512 AGGAACAGGATAAGTTTATTCTTCGG 58.951 38.462 0.00 0.00 26.14 4.30
1615 1644 6.383147 AGGATAAGTTTATTCTTCGGTCAGGA 59.617 38.462 0.00 0.00 0.00 3.86
1926 1955 2.033299 ACAGTTGAGTGTGCAATTTCCG 59.967 45.455 0.00 0.00 0.00 4.30
2038 2067 8.050325 TCTTCAAAATATATTCCGGAACCAAGA 58.950 33.333 21.56 12.45 0.00 3.02
2056 2085 0.110486 GAAGTTCAGGTGGCCTTCCA 59.890 55.000 17.31 0.00 40.85 3.53
2074 2103 0.391661 CAGGGTCCACTGAATCACGG 60.392 60.000 0.00 0.00 40.97 4.94
2075 2104 1.745489 GGGTCCACTGAATCACGGC 60.745 63.158 0.00 0.00 0.00 5.68
2117 2146 1.827681 ACTGACTAGCGCTCAGAAGA 58.172 50.000 26.36 3.67 37.90 2.87
2348 2392 3.404899 CAAGGATTTTGCAGCCAAACAT 58.595 40.909 0.00 0.00 40.45 2.71
2413 2457 0.899720 AGCAAAACATGGGATGCCAG 59.100 50.000 12.95 6.63 39.59 4.85
2586 2630 5.512082 CACCTCTTAAAGAATGTCGTCGTAG 59.488 44.000 0.00 0.00 0.00 3.51
2750 2800 9.664332 AGAATATTTGTGTCCATCATCTATAGC 57.336 33.333 0.00 0.00 0.00 2.97
2751 2801 9.440773 GAATATTTGTGTCCATCATCTATAGCA 57.559 33.333 0.00 0.00 0.00 3.49
2752 2802 9.445878 AATATTTGTGTCCATCATCTATAGCAG 57.554 33.333 0.00 0.00 0.00 4.24
2753 2803 4.263018 TGTGTCCATCATCTATAGCAGC 57.737 45.455 0.00 0.00 0.00 5.25
2754 2804 3.007290 TGTGTCCATCATCTATAGCAGCC 59.993 47.826 0.00 0.00 0.00 4.85
2755 2805 2.232208 TGTCCATCATCTATAGCAGCCG 59.768 50.000 0.00 0.00 0.00 5.52
2756 2806 2.232452 GTCCATCATCTATAGCAGCCGT 59.768 50.000 0.00 0.00 0.00 5.68
2757 2807 3.444034 GTCCATCATCTATAGCAGCCGTA 59.556 47.826 0.00 0.00 0.00 4.02
2758 2808 4.082190 GTCCATCATCTATAGCAGCCGTAA 60.082 45.833 0.00 0.00 0.00 3.18
2759 2809 4.526650 TCCATCATCTATAGCAGCCGTAAA 59.473 41.667 0.00 0.00 0.00 2.01
2760 2810 4.867047 CCATCATCTATAGCAGCCGTAAAG 59.133 45.833 0.00 0.00 0.00 1.85
2761 2811 3.914312 TCATCTATAGCAGCCGTAAAGC 58.086 45.455 0.00 0.00 0.00 3.51
2762 2812 3.574396 TCATCTATAGCAGCCGTAAAGCT 59.426 43.478 0.00 0.00 46.45 3.74
2768 2818 2.747855 AGCCGTAAAGCTGCTGCC 60.748 61.111 12.44 0.00 42.95 4.85
2769 2819 2.747855 GCCGTAAAGCTGCTGCCT 60.748 61.111 12.44 2.45 40.80 4.75
2770 2820 2.335712 GCCGTAAAGCTGCTGCCTT 61.336 57.895 12.44 8.34 40.80 4.35
2771 2821 1.503542 CCGTAAAGCTGCTGCCTTG 59.496 57.895 12.44 0.00 40.80 3.61
2772 2822 1.237285 CCGTAAAGCTGCTGCCTTGT 61.237 55.000 12.44 0.00 40.80 3.16
2773 2823 0.110056 CGTAAAGCTGCTGCCTTGTG 60.110 55.000 12.44 0.00 40.80 3.33
2774 2824 1.238439 GTAAAGCTGCTGCCTTGTGA 58.762 50.000 12.44 0.00 40.80 3.58
2775 2825 1.068954 GTAAAGCTGCTGCCTTGTGAC 60.069 52.381 12.44 0.00 40.80 3.67
2776 2826 1.458639 AAAGCTGCTGCCTTGTGACC 61.459 55.000 12.44 0.00 40.80 4.02
2777 2827 2.595463 GCTGCTGCCTTGTGACCA 60.595 61.111 3.85 0.00 0.00 4.02
2778 2828 1.975407 GCTGCTGCCTTGTGACCAT 60.975 57.895 3.85 0.00 0.00 3.55
2779 2829 1.880894 CTGCTGCCTTGTGACCATG 59.119 57.895 0.00 0.00 0.00 3.66
2780 2830 0.607217 CTGCTGCCTTGTGACCATGA 60.607 55.000 0.00 0.00 0.00 3.07
2781 2831 0.607217 TGCTGCCTTGTGACCATGAG 60.607 55.000 0.00 0.00 0.00 2.90
2782 2832 1.310933 GCTGCCTTGTGACCATGAGG 61.311 60.000 0.00 0.00 42.21 3.86
2792 2842 4.617875 CCATGAGGTCACGGGTTC 57.382 61.111 0.00 0.00 0.00 3.62
2793 2843 1.676968 CCATGAGGTCACGGGTTCA 59.323 57.895 0.00 0.00 0.00 3.18
2794 2844 0.036164 CCATGAGGTCACGGGTTCAA 59.964 55.000 0.00 0.00 0.00 2.69
2795 2845 1.442769 CATGAGGTCACGGGTTCAAG 58.557 55.000 0.00 0.00 0.00 3.02
2796 2846 1.056660 ATGAGGTCACGGGTTCAAGT 58.943 50.000 0.00 0.00 0.00 3.16
2797 2847 0.391597 TGAGGTCACGGGTTCAAGTC 59.608 55.000 0.00 0.00 0.00 3.01
2798 2848 0.320508 GAGGTCACGGGTTCAAGTCC 60.321 60.000 0.00 0.00 0.00 3.85
2799 2849 0.763223 AGGTCACGGGTTCAAGTCCT 60.763 55.000 0.00 0.00 0.00 3.85
2800 2850 0.602905 GGTCACGGGTTCAAGTCCTG 60.603 60.000 0.00 0.00 37.36 3.86
2801 2851 0.602905 GTCACGGGTTCAAGTCCTGG 60.603 60.000 0.00 0.00 35.79 4.45
2802 2852 0.761323 TCACGGGTTCAAGTCCTGGA 60.761 55.000 0.00 0.00 35.79 3.86
2803 2853 0.107831 CACGGGTTCAAGTCCTGGAA 59.892 55.000 0.00 0.00 35.79 3.53
2804 2854 0.841289 ACGGGTTCAAGTCCTGGAAA 59.159 50.000 0.00 0.00 35.79 3.13
2805 2855 1.423921 ACGGGTTCAAGTCCTGGAAAT 59.576 47.619 0.00 0.00 35.79 2.17
2806 2856 2.640826 ACGGGTTCAAGTCCTGGAAATA 59.359 45.455 0.00 0.00 35.79 1.40
2807 2857 3.270877 CGGGTTCAAGTCCTGGAAATAG 58.729 50.000 0.00 0.00 0.00 1.73
2808 2858 3.017442 GGGTTCAAGTCCTGGAAATAGC 58.983 50.000 0.00 0.00 0.00 2.97
2809 2859 3.017442 GGTTCAAGTCCTGGAAATAGCC 58.983 50.000 0.00 0.00 0.00 3.93
2810 2860 3.308473 GGTTCAAGTCCTGGAAATAGCCT 60.308 47.826 0.00 0.00 0.00 4.58
2811 2861 3.914426 TCAAGTCCTGGAAATAGCCTC 57.086 47.619 0.00 0.00 0.00 4.70
2812 2862 3.454858 TCAAGTCCTGGAAATAGCCTCT 58.545 45.455 0.00 0.00 0.00 3.69
2813 2863 3.846588 TCAAGTCCTGGAAATAGCCTCTT 59.153 43.478 0.00 0.00 0.00 2.85
2814 2864 3.922171 AGTCCTGGAAATAGCCTCTTG 57.078 47.619 0.00 0.00 0.00 3.02
2815 2865 2.092699 AGTCCTGGAAATAGCCTCTTGC 60.093 50.000 0.00 0.00 41.71 4.01
2816 2866 1.915489 TCCTGGAAATAGCCTCTTGCA 59.085 47.619 0.00 0.00 44.83 4.08
2817 2867 2.092753 TCCTGGAAATAGCCTCTTGCAG 60.093 50.000 0.00 4.42 44.83 4.41
2818 2868 2.092753 CCTGGAAATAGCCTCTTGCAGA 60.093 50.000 10.96 0.00 41.90 4.26
2819 2869 3.614092 CTGGAAATAGCCTCTTGCAGAA 58.386 45.455 5.23 0.00 41.90 3.02
2820 2870 4.012374 CTGGAAATAGCCTCTTGCAGAAA 58.988 43.478 5.23 0.00 41.90 2.52
2821 2871 4.603131 TGGAAATAGCCTCTTGCAGAAAT 58.397 39.130 0.00 0.00 44.83 2.17
2822 2872 4.400251 TGGAAATAGCCTCTTGCAGAAATG 59.600 41.667 0.00 0.00 44.83 2.32
2823 2873 4.400567 GGAAATAGCCTCTTGCAGAAATGT 59.599 41.667 0.00 0.00 44.83 2.71
2824 2874 5.590259 GGAAATAGCCTCTTGCAGAAATGTA 59.410 40.000 0.00 0.00 44.83 2.29
2825 2875 6.238593 GGAAATAGCCTCTTGCAGAAATGTAG 60.239 42.308 0.00 0.00 44.83 2.74
2826 2876 2.996631 AGCCTCTTGCAGAAATGTAGG 58.003 47.619 0.00 0.00 44.83 3.18
2827 2877 2.019984 GCCTCTTGCAGAAATGTAGGG 58.980 52.381 0.00 0.00 40.77 3.53
2828 2878 2.356125 GCCTCTTGCAGAAATGTAGGGA 60.356 50.000 0.00 0.00 40.77 4.20
2829 2879 3.873801 GCCTCTTGCAGAAATGTAGGGAA 60.874 47.826 0.00 0.00 40.77 3.97
2830 2880 4.335416 CCTCTTGCAGAAATGTAGGGAAA 58.665 43.478 0.00 0.00 0.00 3.13
2831 2881 4.397417 CCTCTTGCAGAAATGTAGGGAAAG 59.603 45.833 0.00 0.00 0.00 2.62
2832 2882 4.335416 TCTTGCAGAAATGTAGGGAAAGG 58.665 43.478 0.00 0.00 0.00 3.11
2833 2883 2.446435 TGCAGAAATGTAGGGAAAGGC 58.554 47.619 0.00 0.00 0.00 4.35
2834 2884 2.041620 TGCAGAAATGTAGGGAAAGGCT 59.958 45.455 0.00 0.00 0.00 4.58
2835 2885 2.424956 GCAGAAATGTAGGGAAAGGCTG 59.575 50.000 0.00 0.00 0.00 4.85
2836 2886 2.424956 CAGAAATGTAGGGAAAGGCTGC 59.575 50.000 0.00 0.00 0.00 5.25
2837 2887 1.401905 GAAATGTAGGGAAAGGCTGCG 59.598 52.381 0.00 0.00 0.00 5.18
2838 2888 0.328258 AATGTAGGGAAAGGCTGCGT 59.672 50.000 0.00 0.00 0.00 5.24
2839 2889 1.200519 ATGTAGGGAAAGGCTGCGTA 58.799 50.000 0.00 0.00 0.00 4.42
2840 2890 0.248289 TGTAGGGAAAGGCTGCGTAC 59.752 55.000 0.00 0.00 37.28 3.67
2841 2891 0.248289 GTAGGGAAAGGCTGCGTACA 59.752 55.000 0.00 0.00 36.89 2.90
2842 2892 0.978151 TAGGGAAAGGCTGCGTACAA 59.022 50.000 0.00 0.00 0.00 2.41
2843 2893 0.328258 AGGGAAAGGCTGCGTACAAT 59.672 50.000 0.00 0.00 0.00 2.71
2844 2894 1.557832 AGGGAAAGGCTGCGTACAATA 59.442 47.619 0.00 0.00 0.00 1.90
2845 2895 1.940613 GGGAAAGGCTGCGTACAATAG 59.059 52.381 0.00 0.00 0.00 1.73
2846 2896 2.419574 GGGAAAGGCTGCGTACAATAGA 60.420 50.000 0.00 0.00 0.00 1.98
2847 2897 2.608090 GGAAAGGCTGCGTACAATAGAC 59.392 50.000 0.00 0.00 0.00 2.59
2848 2898 2.311124 AAGGCTGCGTACAATAGACC 57.689 50.000 0.00 0.00 0.00 3.85
2849 2899 0.464452 AGGCTGCGTACAATAGACCC 59.536 55.000 0.00 0.00 0.00 4.46
2850 2900 0.177141 GGCTGCGTACAATAGACCCA 59.823 55.000 0.00 0.00 0.00 4.51
2851 2901 1.406341 GGCTGCGTACAATAGACCCAA 60.406 52.381 0.00 0.00 0.00 4.12
2852 2902 2.352388 GCTGCGTACAATAGACCCAAA 58.648 47.619 0.00 0.00 0.00 3.28
2853 2903 2.351726 GCTGCGTACAATAGACCCAAAG 59.648 50.000 0.00 0.00 0.00 2.77
2854 2904 3.596214 CTGCGTACAATAGACCCAAAGT 58.404 45.455 0.00 0.00 0.00 2.66
2855 2905 3.331150 TGCGTACAATAGACCCAAAGTG 58.669 45.455 0.00 0.00 0.00 3.16
2856 2906 2.676342 GCGTACAATAGACCCAAAGTGG 59.324 50.000 0.00 0.00 37.25 4.00
2857 2907 3.867216 GCGTACAATAGACCCAAAGTGGT 60.867 47.826 0.00 0.00 42.79 4.16
2862 2912 4.373771 GACCCAAAGTGGTCGGAC 57.626 61.111 0.00 0.00 44.98 4.79
2863 2913 1.302271 GACCCAAAGTGGTCGGACC 60.302 63.158 20.36 20.36 44.98 4.46
2864 2914 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
2865 2915 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
2866 2916 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
2867 2917 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.000 23.81 13.97 37.50 3.46
2868 2918 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
2869 2919 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
2870 2920 3.714001 GTGGTCGGACCCTTCCCC 61.714 72.222 23.81 0.00 38.99 4.81
2871 2921 4.257810 TGGTCGGACCCTTCCCCA 62.258 66.667 23.81 0.69 38.99 4.96
2872 2922 3.400054 GGTCGGACCCTTCCCCAG 61.400 72.222 16.55 0.00 38.99 4.45
2873 2923 2.284405 GTCGGACCCTTCCCCAGA 60.284 66.667 0.00 0.00 38.99 3.86
2874 2924 2.284405 TCGGACCCTTCCCCAGAC 60.284 66.667 0.00 0.00 38.99 3.51
2875 2925 3.400054 CGGACCCTTCCCCAGACC 61.400 72.222 0.00 0.00 38.99 3.85
2876 2926 3.015753 GGACCCTTCCCCAGACCC 61.016 72.222 0.00 0.00 35.57 4.46
2877 2927 2.125225 GACCCTTCCCCAGACCCT 59.875 66.667 0.00 0.00 0.00 4.34
2878 2928 2.204151 ACCCTTCCCCAGACCCTG 60.204 66.667 0.00 0.00 0.00 4.45
2879 2929 3.732849 CCCTTCCCCAGACCCTGC 61.733 72.222 0.00 0.00 0.00 4.85
2880 2930 4.101448 CCTTCCCCAGACCCTGCG 62.101 72.222 0.00 0.00 0.00 5.18
2881 2931 4.785453 CTTCCCCAGACCCTGCGC 62.785 72.222 0.00 0.00 0.00 6.09
2902 2952 4.115279 CGGGAGCTACATGCACTG 57.885 61.111 0.00 0.00 45.94 3.66
2903 2953 1.522355 CGGGAGCTACATGCACTGG 60.522 63.158 0.00 0.00 45.94 4.00
2904 2954 1.153086 GGGAGCTACATGCACTGGG 60.153 63.158 0.00 0.00 45.94 4.45
2905 2955 1.153086 GGAGCTACATGCACTGGGG 60.153 63.158 0.00 0.00 45.94 4.96
2906 2956 1.821332 GAGCTACATGCACTGGGGC 60.821 63.158 0.00 0.00 45.94 5.80
2907 2957 2.262774 GAGCTACATGCACTGGGGCT 62.263 60.000 13.29 13.29 45.94 5.19
2908 2958 2.117156 GCTACATGCACTGGGGCTG 61.117 63.158 0.00 0.00 42.31 4.85
2909 2959 2.045045 TACATGCACTGGGGCTGC 60.045 61.111 0.00 0.00 35.03 5.25
2910 2960 3.643595 TACATGCACTGGGGCTGCC 62.644 63.158 11.05 11.05 33.36 4.85
2922 2972 3.374318 GGCTGCCCCCTTTTAAGAA 57.626 52.632 7.66 0.00 0.00 2.52
2923 2973 1.186200 GGCTGCCCCCTTTTAAGAAG 58.814 55.000 7.66 0.00 0.00 2.85
2924 2974 1.186200 GCTGCCCCCTTTTAAGAAGG 58.814 55.000 8.60 8.60 37.17 3.46
2932 2982 3.458044 CCTTTTAAGAAGGGGAGCCTT 57.542 47.619 0.00 0.00 33.79 4.35
2933 2983 3.092301 CCTTTTAAGAAGGGGAGCCTTG 58.908 50.000 0.00 0.00 33.79 3.61
2934 2984 2.899303 TTTAAGAAGGGGAGCCTTGG 57.101 50.000 0.00 0.00 0.00 3.61
2935 2985 0.331616 TTAAGAAGGGGAGCCTTGGC 59.668 55.000 2.97 2.97 0.00 4.52
2936 2986 1.910580 TAAGAAGGGGAGCCTTGGCG 61.911 60.000 5.95 0.00 0.00 5.69
2944 2994 3.605749 GAGCCTTGGCGCAGTGGTA 62.606 63.158 10.83 0.00 0.00 3.25
2945 2995 2.671619 GCCTTGGCGCAGTGGTAA 60.672 61.111 10.83 0.00 0.00 2.85
2946 2996 2.265182 GCCTTGGCGCAGTGGTAAA 61.265 57.895 10.83 0.00 0.00 2.01
2947 2997 1.875963 CCTTGGCGCAGTGGTAAAG 59.124 57.895 10.83 0.71 0.00 1.85
2948 2998 1.210155 CTTGGCGCAGTGGTAAAGC 59.790 57.895 10.83 0.00 0.00 3.51
2949 2999 1.228124 TTGGCGCAGTGGTAAAGCT 60.228 52.632 10.83 0.00 0.00 3.74
2950 3000 1.514678 TTGGCGCAGTGGTAAAGCTG 61.515 55.000 10.83 0.00 35.93 4.24
2955 3005 1.878775 CAGTGGTAAAGCTGCTGCC 59.121 57.895 12.44 7.07 40.80 4.85
2956 3006 0.607489 CAGTGGTAAAGCTGCTGCCT 60.607 55.000 12.44 2.45 40.80 4.75
2957 3007 0.111253 AGTGGTAAAGCTGCTGCCTT 59.889 50.000 12.44 8.34 40.80 4.35
2958 3008 0.242017 GTGGTAAAGCTGCTGCCTTG 59.758 55.000 12.44 0.00 40.80 3.61
2959 3009 0.178992 TGGTAAAGCTGCTGCCTTGT 60.179 50.000 12.44 0.00 40.80 3.16
2960 3010 0.242017 GGTAAAGCTGCTGCCTTGTG 59.758 55.000 12.44 0.00 40.80 3.33
2961 3011 1.238439 GTAAAGCTGCTGCCTTGTGA 58.762 50.000 12.44 0.00 40.80 3.58
2962 3012 1.068954 GTAAAGCTGCTGCCTTGTGAC 60.069 52.381 12.44 0.00 40.80 3.67
2963 3013 1.458639 AAAGCTGCTGCCTTGTGACC 61.459 55.000 12.44 0.00 40.80 4.02
2964 3014 2.595463 GCTGCTGCCTTGTGACCA 60.595 61.111 3.85 0.00 0.00 4.02
2965 3015 1.975407 GCTGCTGCCTTGTGACCAT 60.975 57.895 3.85 0.00 0.00 3.55
2966 3016 1.880894 CTGCTGCCTTGTGACCATG 59.119 57.895 0.00 0.00 0.00 3.66
2967 3017 0.607217 CTGCTGCCTTGTGACCATGA 60.607 55.000 0.00 0.00 0.00 3.07
2968 3018 0.607217 TGCTGCCTTGTGACCATGAG 60.607 55.000 0.00 0.00 0.00 2.90
2969 3019 1.310933 GCTGCCTTGTGACCATGAGG 61.311 60.000 0.00 0.00 42.21 3.86
2984 3034 2.859165 TGAGGTCATGGGTTCAAGTC 57.141 50.000 0.00 0.00 0.00 3.01
2985 3035 1.351017 TGAGGTCATGGGTTCAAGTCC 59.649 52.381 0.00 0.00 0.00 3.85
2986 3036 1.630878 GAGGTCATGGGTTCAAGTCCT 59.369 52.381 0.00 0.00 0.00 3.85
2987 3037 1.352352 AGGTCATGGGTTCAAGTCCTG 59.648 52.381 0.00 0.00 0.00 3.86
2988 3038 1.614317 GGTCATGGGTTCAAGTCCTGG 60.614 57.143 0.00 0.00 0.00 4.45
2989 3039 1.351017 GTCATGGGTTCAAGTCCTGGA 59.649 52.381 0.00 0.00 0.00 3.86
2990 3040 2.061848 TCATGGGTTCAAGTCCTGGAA 58.938 47.619 0.00 0.00 0.00 3.53
2991 3041 2.445145 TCATGGGTTCAAGTCCTGGAAA 59.555 45.455 0.00 0.00 0.00 3.13
2992 3042 2.358322 TGGGTTCAAGTCCTGGAAAC 57.642 50.000 0.00 0.00 0.00 2.78
2993 3043 1.566703 TGGGTTCAAGTCCTGGAAACA 59.433 47.619 0.00 0.00 32.36 2.83
3007 3057 4.431416 TGGAAACAGCCTCTTACAGAAA 57.569 40.909 0.00 0.00 35.01 2.52
3008 3058 4.985538 TGGAAACAGCCTCTTACAGAAAT 58.014 39.130 0.00 0.00 35.01 2.17
3009 3059 4.761739 TGGAAACAGCCTCTTACAGAAATG 59.238 41.667 0.00 0.00 35.01 2.32
3010 3060 4.762251 GGAAACAGCCTCTTACAGAAATGT 59.238 41.667 0.00 0.00 0.00 2.71
3011 3061 5.938125 GGAAACAGCCTCTTACAGAAATGTA 59.062 40.000 0.00 0.00 0.00 2.29
3012 3062 6.092807 GGAAACAGCCTCTTACAGAAATGTAG 59.907 42.308 0.00 0.00 0.00 2.74
3013 3063 5.091261 ACAGCCTCTTACAGAAATGTAGG 57.909 43.478 0.00 0.00 0.00 3.18
3014 3064 4.080863 ACAGCCTCTTACAGAAATGTAGGG 60.081 45.833 0.00 0.66 0.00 3.53
3015 3065 4.162320 CAGCCTCTTACAGAAATGTAGGGA 59.838 45.833 0.00 0.00 0.00 4.20
3016 3066 4.783227 AGCCTCTTACAGAAATGTAGGGAA 59.217 41.667 0.00 0.00 0.00 3.97
3017 3067 5.250774 AGCCTCTTACAGAAATGTAGGGAAA 59.749 40.000 0.00 0.00 0.00 3.13
3018 3068 5.586643 GCCTCTTACAGAAATGTAGGGAAAG 59.413 44.000 0.00 0.00 0.00 2.62
3019 3069 6.116126 CCTCTTACAGAAATGTAGGGAAAGG 58.884 44.000 0.00 0.00 0.00 3.11
3020 3070 5.497474 TCTTACAGAAATGTAGGGAAAGGC 58.503 41.667 0.00 0.00 0.00 4.35
3021 3071 5.250774 TCTTACAGAAATGTAGGGAAAGGCT 59.749 40.000 0.00 0.00 0.00 4.58
3022 3072 3.690460 ACAGAAATGTAGGGAAAGGCTG 58.310 45.455 0.00 0.00 0.00 4.85
3023 3073 3.019564 CAGAAATGTAGGGAAAGGCTGG 58.980 50.000 0.00 0.00 0.00 4.85
3024 3074 2.024941 AGAAATGTAGGGAAAGGCTGGG 60.025 50.000 0.00 0.00 0.00 4.45
3025 3075 1.681229 AATGTAGGGAAAGGCTGGGA 58.319 50.000 0.00 0.00 0.00 4.37
3026 3076 1.216990 ATGTAGGGAAAGGCTGGGAG 58.783 55.000 0.00 0.00 0.00 4.30
3027 3077 1.224870 GTAGGGAAAGGCTGGGAGC 59.775 63.158 0.00 0.00 41.46 4.70
3028 3078 1.082954 TAGGGAAAGGCTGGGAGCT 59.917 57.895 0.00 0.00 41.99 4.09
3029 3079 0.341961 TAGGGAAAGGCTGGGAGCTA 59.658 55.000 0.00 0.00 41.99 3.32
3030 3080 1.224870 GGGAAAGGCTGGGAGCTAC 59.775 63.158 0.00 0.00 41.99 3.58
3031 3081 1.562672 GGGAAAGGCTGGGAGCTACA 61.563 60.000 0.00 0.00 41.99 2.74
3032 3082 0.548510 GGAAAGGCTGGGAGCTACAT 59.451 55.000 0.00 0.00 41.99 2.29
3033 3083 1.673168 GAAAGGCTGGGAGCTACATG 58.327 55.000 0.00 0.00 41.99 3.21
3034 3084 0.394899 AAAGGCTGGGAGCTACATGC 60.395 55.000 0.00 0.25 41.99 4.06
3035 3085 1.565390 AAGGCTGGGAGCTACATGCA 61.565 55.000 13.31 0.00 45.94 3.96
3036 3086 1.821332 GGCTGGGAGCTACATGCAC 60.821 63.158 13.31 1.22 45.94 4.57
3042 3092 3.558674 GAGCTACATGCACCAGGTT 57.441 52.632 0.00 0.00 45.94 3.50
3043 3093 1.089920 GAGCTACATGCACCAGGTTG 58.910 55.000 0.00 0.00 45.94 3.77
3044 3094 0.962356 AGCTACATGCACCAGGTTGC 60.962 55.000 8.03 8.03 44.17 4.17
3045 3095 1.937546 GCTACATGCACCAGGTTGCC 61.938 60.000 10.46 0.00 39.88 4.52
3046 3096 1.304052 TACATGCACCAGGTTGCCC 60.304 57.895 10.46 0.00 42.25 5.36
3047 3097 1.788518 TACATGCACCAGGTTGCCCT 61.789 55.000 10.46 0.00 42.25 5.19
3048 3098 1.909781 CATGCACCAGGTTGCCCTT 60.910 57.895 10.46 0.00 42.25 3.95
3049 3099 1.152269 ATGCACCAGGTTGCCCTTT 60.152 52.632 10.46 0.00 42.25 3.11
3050 3100 0.763986 ATGCACCAGGTTGCCCTTTT 60.764 50.000 10.46 0.00 42.25 2.27
3051 3101 0.980231 TGCACCAGGTTGCCCTTTTT 60.980 50.000 10.46 0.00 42.25 1.94
3132 3203 4.699735 TCTGTTGTTTCTTGCTCTGTTGAA 59.300 37.500 0.00 0.00 0.00 2.69
3166 3237 2.874086 TGCCTTATGAATGTGCATCGAG 59.126 45.455 0.00 0.00 0.00 4.04
3310 3381 2.233431 GGACAAGGGCAAATGTTATGCA 59.767 45.455 0.00 0.00 45.60 3.96
3532 3609 9.883142 TTTTGTATCAGAAATCCACAAACTTTT 57.117 25.926 0.00 0.00 38.45 2.27
3571 3648 5.222631 CAAATACTTGCAAGAAACCCTGTC 58.777 41.667 32.50 0.00 0.00 3.51
3654 3736 8.232913 TGTTTCAAAGCTACTGGTTAGATTTT 57.767 30.769 0.00 0.00 42.57 1.82
3739 3833 4.853924 ATTGATATTGCCGAACCAATCC 57.146 40.909 0.00 0.00 36.80 3.01
3774 3868 2.044650 GCCTGGCCTCTGCATCAA 60.045 61.111 7.66 0.00 40.13 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 8.646004 CCCTGATTAAAGAGAGAGAATCACATA 58.354 37.037 0.00 0.00 37.82 2.29
31 32 8.122952 CGATTGTAGCTAAAACCCTGATTAAAG 58.877 37.037 0.00 0.00 0.00 1.85
38 39 4.000988 ACACGATTGTAGCTAAAACCCTG 58.999 43.478 0.00 0.00 32.60 4.45
44 45 4.665212 CCTACGACACGATTGTAGCTAAA 58.335 43.478 0.00 0.00 42.20 1.85
52 53 2.855187 GCTCTAGCCTACGACACGATTG 60.855 54.545 0.00 0.00 34.31 2.67
53 54 1.334243 GCTCTAGCCTACGACACGATT 59.666 52.381 0.00 0.00 34.31 3.34
57 58 2.531206 CTTTGCTCTAGCCTACGACAC 58.469 52.381 0.00 0.00 41.18 3.67
96 97 3.255149 GGCTATGGCATCAAGAATCAAGG 59.745 47.826 1.65 0.00 40.87 3.61
144 146 3.187637 CCACGTGGGTACATTTAACACAG 59.812 47.826 27.57 0.00 28.96 3.66
152 154 2.046700 CGGCCACGTGGGTACATT 60.047 61.111 34.58 0.00 39.65 2.71
236 238 1.277557 CACCAAGAGGGAGTTCTGAGG 59.722 57.143 0.00 0.00 41.15 3.86
238 240 2.103153 ACACCAAGAGGGAGTTCTGA 57.897 50.000 0.00 0.00 37.12 3.27
278 280 0.462047 GTTAGCAGCGTGTATGCCCT 60.462 55.000 0.00 0.00 44.97 5.19
352 354 4.047627 TGGAGTGGTAGATGTCAAGAGA 57.952 45.455 0.00 0.00 0.00 3.10
390 392 1.562942 TGGAGCAGGCATCTTTGATCT 59.437 47.619 0.00 0.00 30.82 2.75
430 432 3.545703 GGCTTCAAGCTATGGTACACAT 58.454 45.455 9.83 0.00 41.49 3.21
431 433 2.676750 CGGCTTCAAGCTATGGTACACA 60.677 50.000 9.83 0.00 41.49 3.72
455 457 2.579738 GCGAAGGAGGTGGAGGAC 59.420 66.667 0.00 0.00 0.00 3.85
480 482 2.447047 AGAAGACAACCAAATGGAGGGT 59.553 45.455 6.42 0.95 39.65 4.34
674 680 0.106268 TCACCACACATGCCACCTTT 60.106 50.000 0.00 0.00 0.00 3.11
675 681 0.538057 CTCACCACACATGCCACCTT 60.538 55.000 0.00 0.00 0.00 3.50
710 716 7.010160 TCCCCACTACTTTCATTTCTTTCAAT 58.990 34.615 0.00 0.00 0.00 2.57
715 721 6.139679 TGATCCCCACTACTTTCATTTCTT 57.860 37.500 0.00 0.00 0.00 2.52
748 755 7.396055 TGATCATGTGACACGGAATCCTATATA 59.604 37.037 0.22 0.00 0.00 0.86
761 768 7.596621 CACCTAGTATGTATGATCATGTGACAC 59.403 40.741 18.72 8.43 0.00 3.67
821 828 9.420118 CAGATATATCTTACTAAGGGCATCTCT 57.580 37.037 12.75 0.00 34.22 3.10
882 889 1.485480 CCACTGAGAGGACATGCTCAT 59.515 52.381 3.08 0.00 40.11 2.90
1357 1386 9.598517 AGAAAAATTAAGAGCACATGTTTTCAA 57.401 25.926 12.37 0.57 36.60 2.69
1391 1420 5.308237 CCAGCCCATATCCCTACCTATAATC 59.692 48.000 0.00 0.00 0.00 1.75
1406 1435 4.229582 AGGTTAAGTGATTTCCAGCCCATA 59.770 41.667 0.00 0.00 0.00 2.74
1609 1638 0.984230 TGAAGTCCACCCATCCTGAC 59.016 55.000 0.00 0.00 0.00 3.51
1926 1955 7.482654 AAAAGAAATCCTAAAAAGCAGCAAC 57.517 32.000 0.00 0.00 0.00 4.17
1957 1986 7.711772 TCATGAAAGCAACAATGAGAACAAAAT 59.288 29.630 0.00 0.00 0.00 1.82
1972 2001 4.687018 GTGCAACATCAATCATGAAAGCAA 59.313 37.500 0.00 0.00 39.49 3.91
2038 2067 0.111253 CTGGAAGGCCACCTGAACTT 59.889 55.000 17.68 0.00 39.92 2.66
2056 2085 1.983224 CCGTGATTCAGTGGACCCT 59.017 57.895 0.00 0.00 0.00 4.34
2074 2103 3.084786 ACAGCCCTTTTCTAAGATGTGC 58.915 45.455 0.00 0.00 32.92 4.57
2075 2104 7.225538 CAGTATACAGCCCTTTTCTAAGATGTG 59.774 40.741 5.50 0.00 32.92 3.21
2117 2146 3.792401 TCACAAATGTGTCGACTCTTGT 58.208 40.909 17.92 16.41 45.76 3.16
2348 2392 1.118965 TCTGGTCTTGGTGCGGAAGA 61.119 55.000 0.00 0.00 0.00 2.87
2413 2457 5.163713 GCTCCATCAGTGATAACCTTCAAAC 60.164 44.000 5.03 0.00 0.00 2.93
2586 2630 3.088532 TGGTTGATTTGGTATGTCCTGC 58.911 45.455 0.00 0.00 37.07 4.85
2732 2782 3.007290 GGCTGCTATAGATGATGGACACA 59.993 47.826 3.21 0.00 0.00 3.72
2752 2802 2.335712 AAGGCAGCAGCTTTACGGC 61.336 57.895 0.00 0.00 38.40 5.68
2753 2803 1.237285 ACAAGGCAGCAGCTTTACGG 61.237 55.000 0.00 0.00 38.07 4.02
2754 2804 0.110056 CACAAGGCAGCAGCTTTACG 60.110 55.000 0.00 0.00 38.07 3.18
2755 2805 1.068954 GTCACAAGGCAGCAGCTTTAC 60.069 52.381 0.00 0.00 38.07 2.01
2756 2806 1.238439 GTCACAAGGCAGCAGCTTTA 58.762 50.000 0.00 0.00 38.07 1.85
2757 2807 1.458639 GGTCACAAGGCAGCAGCTTT 61.459 55.000 0.00 0.00 41.17 3.51
2758 2808 1.900498 GGTCACAAGGCAGCAGCTT 60.900 57.895 0.00 0.00 41.70 3.74
2759 2809 2.282040 GGTCACAAGGCAGCAGCT 60.282 61.111 0.00 0.00 41.70 4.24
2760 2810 1.975407 ATGGTCACAAGGCAGCAGC 60.975 57.895 0.00 0.00 41.10 5.25
2761 2811 0.607217 TCATGGTCACAAGGCAGCAG 60.607 55.000 0.00 0.00 0.00 4.24
2762 2812 0.607217 CTCATGGTCACAAGGCAGCA 60.607 55.000 0.00 0.00 0.00 4.41
2763 2813 1.310933 CCTCATGGTCACAAGGCAGC 61.311 60.000 0.00 0.00 0.00 5.25
2764 2814 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.000 0.00 0.00 44.78 4.85
2765 2815 2.154139 ACCTCATGGTCACAAGGCA 58.846 52.632 0.00 0.00 44.78 4.75
2776 2826 1.270839 ACTTGAACCCGTGACCTCATG 60.271 52.381 0.00 0.00 0.00 3.07
2777 2827 1.002087 GACTTGAACCCGTGACCTCAT 59.998 52.381 0.00 0.00 0.00 2.90
2778 2828 0.391597 GACTTGAACCCGTGACCTCA 59.608 55.000 0.00 0.00 0.00 3.86
2779 2829 0.320508 GGACTTGAACCCGTGACCTC 60.321 60.000 0.00 0.00 0.00 3.85
2780 2830 0.763223 AGGACTTGAACCCGTGACCT 60.763 55.000 0.00 0.00 0.00 3.85
2781 2831 0.602905 CAGGACTTGAACCCGTGACC 60.603 60.000 0.00 0.00 0.00 4.02
2782 2832 0.602905 CCAGGACTTGAACCCGTGAC 60.603 60.000 0.00 0.00 0.00 3.67
2783 2833 0.761323 TCCAGGACTTGAACCCGTGA 60.761 55.000 0.00 0.00 0.00 4.35
2784 2834 0.107831 TTCCAGGACTTGAACCCGTG 59.892 55.000 0.00 0.00 0.00 4.94
2785 2835 0.841289 TTTCCAGGACTTGAACCCGT 59.159 50.000 0.00 0.00 0.00 5.28
2786 2836 2.200373 ATTTCCAGGACTTGAACCCG 57.800 50.000 0.00 0.00 0.00 5.28
2787 2837 3.017442 GCTATTTCCAGGACTTGAACCC 58.983 50.000 0.00 0.00 0.00 4.11
2788 2838 3.017442 GGCTATTTCCAGGACTTGAACC 58.983 50.000 0.00 0.00 0.00 3.62
2789 2839 3.942115 GAGGCTATTTCCAGGACTTGAAC 59.058 47.826 0.00 0.00 0.00 3.18
2790 2840 3.846588 AGAGGCTATTTCCAGGACTTGAA 59.153 43.478 0.00 0.00 0.00 2.69
2791 2841 3.454858 AGAGGCTATTTCCAGGACTTGA 58.545 45.455 0.00 0.00 0.00 3.02
2792 2842 3.922171 AGAGGCTATTTCCAGGACTTG 57.078 47.619 0.00 0.00 0.00 3.16
2793 2843 3.623453 GCAAGAGGCTATTTCCAGGACTT 60.623 47.826 0.00 0.00 40.25 3.01
2794 2844 2.092699 GCAAGAGGCTATTTCCAGGACT 60.093 50.000 0.00 0.00 40.25 3.85
2795 2845 2.293170 GCAAGAGGCTATTTCCAGGAC 58.707 52.381 0.00 0.00 40.25 3.85
2796 2846 1.915489 TGCAAGAGGCTATTTCCAGGA 59.085 47.619 0.00 0.00 45.15 3.86
2797 2847 2.092753 TCTGCAAGAGGCTATTTCCAGG 60.093 50.000 15.29 0.00 38.67 4.45
2798 2848 3.272574 TCTGCAAGAGGCTATTTCCAG 57.727 47.619 11.19 11.19 38.67 3.86
2810 2860 4.335416 CCTTTCCCTACATTTCTGCAAGA 58.665 43.478 0.00 0.00 44.68 3.02
2811 2861 3.119352 GCCTTTCCCTACATTTCTGCAAG 60.119 47.826 0.00 0.00 0.00 4.01
2812 2862 2.825532 GCCTTTCCCTACATTTCTGCAA 59.174 45.455 0.00 0.00 0.00 4.08
2813 2863 2.041620 AGCCTTTCCCTACATTTCTGCA 59.958 45.455 0.00 0.00 0.00 4.41
2814 2864 2.424956 CAGCCTTTCCCTACATTTCTGC 59.575 50.000 0.00 0.00 0.00 4.26
2815 2865 2.424956 GCAGCCTTTCCCTACATTTCTG 59.575 50.000 0.00 0.00 0.00 3.02
2816 2866 2.728007 GCAGCCTTTCCCTACATTTCT 58.272 47.619 0.00 0.00 0.00 2.52
2817 2867 1.401905 CGCAGCCTTTCCCTACATTTC 59.598 52.381 0.00 0.00 0.00 2.17
2818 2868 1.271926 ACGCAGCCTTTCCCTACATTT 60.272 47.619 0.00 0.00 0.00 2.32
2819 2869 0.328258 ACGCAGCCTTTCCCTACATT 59.672 50.000 0.00 0.00 0.00 2.71
2820 2870 1.134491 GTACGCAGCCTTTCCCTACAT 60.134 52.381 0.00 0.00 0.00 2.29
2821 2871 0.248289 GTACGCAGCCTTTCCCTACA 59.752 55.000 0.00 0.00 0.00 2.74
2822 2872 0.248289 TGTACGCAGCCTTTCCCTAC 59.752 55.000 0.00 0.00 0.00 3.18
2823 2873 0.978151 TTGTACGCAGCCTTTCCCTA 59.022 50.000 0.00 0.00 0.00 3.53
2824 2874 0.328258 ATTGTACGCAGCCTTTCCCT 59.672 50.000 0.00 0.00 0.00 4.20
2825 2875 1.940613 CTATTGTACGCAGCCTTTCCC 59.059 52.381 0.00 0.00 0.00 3.97
2826 2876 2.608090 GTCTATTGTACGCAGCCTTTCC 59.392 50.000 0.00 0.00 0.00 3.13
2827 2877 2.608090 GGTCTATTGTACGCAGCCTTTC 59.392 50.000 0.00 0.00 0.00 2.62
2828 2878 2.629051 GGTCTATTGTACGCAGCCTTT 58.371 47.619 0.00 0.00 0.00 3.11
2829 2879 1.134491 GGGTCTATTGTACGCAGCCTT 60.134 52.381 0.00 0.00 0.00 4.35
2830 2880 0.464452 GGGTCTATTGTACGCAGCCT 59.536 55.000 0.00 0.00 0.00 4.58
2831 2881 0.177141 TGGGTCTATTGTACGCAGCC 59.823 55.000 0.00 0.00 35.18 4.85
2832 2882 2.018542 TTGGGTCTATTGTACGCAGC 57.981 50.000 0.00 0.00 40.36 5.25
2833 2883 3.370978 CACTTTGGGTCTATTGTACGCAG 59.629 47.826 0.00 0.00 40.36 5.18
2834 2884 3.331150 CACTTTGGGTCTATTGTACGCA 58.669 45.455 0.00 0.00 37.94 5.24
2835 2885 2.676342 CCACTTTGGGTCTATTGTACGC 59.324 50.000 0.00 0.00 32.67 4.42
2836 2886 3.934068 ACCACTTTGGGTCTATTGTACG 58.066 45.455 0.00 0.00 43.37 3.67
2846 2896 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
2847 2897 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
2848 2898 0.605589 GAAGGGTCCGACCACTTTGG 60.606 60.000 19.43 0.00 41.02 3.28
2849 2899 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.000 19.43 0.00 41.02 2.77
2850 2900 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
2851 2901 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
2852 2902 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
2853 2903 3.714001 GGGGAAGGGTCCGACCAC 61.714 72.222 19.43 8.70 46.04 4.16
2854 2904 4.257810 TGGGGAAGGGTCCGACCA 62.258 66.667 19.43 0.00 46.04 4.02
2855 2905 3.400054 CTGGGGAAGGGTCCGACC 61.400 72.222 9.30 9.30 46.04 4.79
2856 2906 2.284405 TCTGGGGAAGGGTCCGAC 60.284 66.667 0.00 0.00 46.04 4.79
2857 2907 2.284405 GTCTGGGGAAGGGTCCGA 60.284 66.667 0.00 0.00 46.04 4.55
2858 2908 3.400054 GGTCTGGGGAAGGGTCCG 61.400 72.222 0.00 0.00 46.04 4.79
2859 2909 3.015753 GGGTCTGGGGAAGGGTCC 61.016 72.222 0.00 0.00 44.10 4.46
2860 2910 2.125225 AGGGTCTGGGGAAGGGTC 59.875 66.667 0.00 0.00 0.00 4.46
2861 2911 2.204151 CAGGGTCTGGGGAAGGGT 60.204 66.667 0.00 0.00 0.00 4.34
2862 2912 3.732849 GCAGGGTCTGGGGAAGGG 61.733 72.222 0.00 0.00 31.21 3.95
2863 2913 4.101448 CGCAGGGTCTGGGGAAGG 62.101 72.222 4.35 0.00 40.11 3.46
2864 2914 4.785453 GCGCAGGGTCTGGGGAAG 62.785 72.222 0.30 0.00 43.28 3.46
2876 2926 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
2879 2929 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
2880 2930 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
2881 2931 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
2882 2932 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
2884 2934 2.176273 CAGTGCATGTAGCTCCCGC 61.176 63.158 0.00 0.00 45.94 6.13
2885 2935 1.522355 CCAGTGCATGTAGCTCCCG 60.522 63.158 0.00 0.00 45.94 5.14
2886 2936 1.153086 CCCAGTGCATGTAGCTCCC 60.153 63.158 0.00 0.00 45.94 4.30
2887 2937 1.153086 CCCCAGTGCATGTAGCTCC 60.153 63.158 0.00 0.00 45.94 4.70
2888 2938 1.821332 GCCCCAGTGCATGTAGCTC 60.821 63.158 0.00 0.00 45.94 4.09
2889 2939 2.273449 GCCCCAGTGCATGTAGCT 59.727 61.111 0.00 0.00 45.94 3.32
2890 2940 2.117156 CAGCCCCAGTGCATGTAGC 61.117 63.158 0.00 0.00 45.96 3.58
2891 2941 2.117156 GCAGCCCCAGTGCATGTAG 61.117 63.158 0.00 0.00 40.86 2.74
2892 2942 2.045045 GCAGCCCCAGTGCATGTA 60.045 61.111 0.00 0.00 40.86 2.29
2903 2953 0.252057 TTCTTAAAAGGGGGCAGCCC 60.252 55.000 24.23 24.23 44.51 5.19
2904 2954 1.186200 CTTCTTAAAAGGGGGCAGCC 58.814 55.000 1.26 1.26 0.00 4.85
2905 2955 1.186200 CCTTCTTAAAAGGGGGCAGC 58.814 55.000 7.97 0.00 33.79 5.25
2926 2976 3.605749 TACCACTGCGCCAAGGCTC 62.606 63.158 4.18 1.20 39.32 4.70
2927 2977 2.690653 TTTACCACTGCGCCAAGGCT 62.691 55.000 4.18 0.00 39.32 4.58
2928 2978 2.200170 CTTTACCACTGCGCCAAGGC 62.200 60.000 4.18 0.00 37.85 4.35
2929 2979 1.875963 CTTTACCACTGCGCCAAGG 59.124 57.895 4.18 6.21 0.00 3.61
2930 2980 1.210155 GCTTTACCACTGCGCCAAG 59.790 57.895 4.18 0.00 0.00 3.61
2931 2981 1.228124 AGCTTTACCACTGCGCCAA 60.228 52.632 4.18 0.00 0.00 4.52
2932 2982 1.965930 CAGCTTTACCACTGCGCCA 60.966 57.895 4.18 0.00 0.00 5.69
2933 2983 2.870372 CAGCTTTACCACTGCGCC 59.130 61.111 4.18 0.00 0.00 6.53
2937 2987 0.607489 AGGCAGCAGCTTTACCACTG 60.607 55.000 0.00 0.00 41.70 3.66
2938 2988 0.111253 AAGGCAGCAGCTTTACCACT 59.889 50.000 0.00 0.00 38.40 4.00
2939 2989 0.242017 CAAGGCAGCAGCTTTACCAC 59.758 55.000 0.00 0.00 38.07 4.16
2940 2990 0.178992 ACAAGGCAGCAGCTTTACCA 60.179 50.000 0.00 0.00 38.07 3.25
2941 2991 0.242017 CACAAGGCAGCAGCTTTACC 59.758 55.000 0.00 0.00 38.07 2.85
2942 2992 1.068954 GTCACAAGGCAGCAGCTTTAC 60.069 52.381 0.00 0.00 38.07 2.01
2943 2993 1.238439 GTCACAAGGCAGCAGCTTTA 58.762 50.000 0.00 0.00 38.07 1.85
2944 2994 1.458639 GGTCACAAGGCAGCAGCTTT 61.459 55.000 0.00 0.00 41.17 3.51
2945 2995 1.900498 GGTCACAAGGCAGCAGCTT 60.900 57.895 0.00 0.00 41.70 3.74
2946 2996 2.282040 GGTCACAAGGCAGCAGCT 60.282 61.111 0.00 0.00 41.70 4.24
2947 2997 1.975407 ATGGTCACAAGGCAGCAGC 60.975 57.895 0.00 0.00 41.10 5.25
2948 2998 0.607217 TCATGGTCACAAGGCAGCAG 60.607 55.000 0.00 0.00 0.00 4.24
2949 2999 0.607217 CTCATGGTCACAAGGCAGCA 60.607 55.000 0.00 0.00 0.00 4.41
2950 3000 1.310933 CCTCATGGTCACAAGGCAGC 61.311 60.000 0.00 0.00 0.00 5.25
2951 3001 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.000 0.00 0.00 44.78 4.85
2952 3002 2.154139 ACCTCATGGTCACAAGGCA 58.846 52.632 0.00 0.00 44.78 4.75
2964 3014 2.025887 GGACTTGAACCCATGACCTCAT 60.026 50.000 0.00 0.00 36.96 2.90
2965 3015 1.351017 GGACTTGAACCCATGACCTCA 59.649 52.381 0.00 0.00 32.45 3.86
2966 3016 1.630878 AGGACTTGAACCCATGACCTC 59.369 52.381 0.00 0.00 37.82 3.85
2967 3017 1.352352 CAGGACTTGAACCCATGACCT 59.648 52.381 0.00 0.00 40.96 3.85
2968 3018 1.614317 CCAGGACTTGAACCCATGACC 60.614 57.143 0.00 0.00 34.29 4.02
2969 3019 1.351017 TCCAGGACTTGAACCCATGAC 59.649 52.381 0.00 0.00 0.00 3.06
2970 3020 1.741028 TCCAGGACTTGAACCCATGA 58.259 50.000 0.00 0.00 0.00 3.07
2971 3021 2.558359 GTTTCCAGGACTTGAACCCATG 59.442 50.000 0.00 0.00 0.00 3.66
2972 3022 2.176798 TGTTTCCAGGACTTGAACCCAT 59.823 45.455 0.00 0.00 0.00 4.00
2973 3023 1.566703 TGTTTCCAGGACTTGAACCCA 59.433 47.619 0.00 0.00 0.00 4.51
2974 3024 2.230660 CTGTTTCCAGGACTTGAACCC 58.769 52.381 0.00 0.00 34.90 4.11
2975 3025 1.609072 GCTGTTTCCAGGACTTGAACC 59.391 52.381 0.00 0.00 39.22 3.62
2976 3026 1.609072 GGCTGTTTCCAGGACTTGAAC 59.391 52.381 0.00 0.00 39.22 3.18
2977 3027 1.494721 AGGCTGTTTCCAGGACTTGAA 59.505 47.619 0.00 0.00 39.22 2.69
2978 3028 1.072331 GAGGCTGTTTCCAGGACTTGA 59.928 52.381 0.00 0.00 39.22 3.02
2979 3029 1.072965 AGAGGCTGTTTCCAGGACTTG 59.927 52.381 0.00 0.00 39.22 3.16
2980 3030 1.439543 AGAGGCTGTTTCCAGGACTT 58.560 50.000 0.00 0.00 39.22 3.01
2981 3031 1.439543 AAGAGGCTGTTTCCAGGACT 58.560 50.000 0.00 0.00 39.22 3.85
2982 3032 2.038557 TGTAAGAGGCTGTTTCCAGGAC 59.961 50.000 0.90 0.00 39.22 3.85
2983 3033 2.303022 CTGTAAGAGGCTGTTTCCAGGA 59.697 50.000 0.90 0.00 35.89 3.86
2984 3034 2.303022 TCTGTAAGAGGCTGTTTCCAGG 59.697 50.000 17.71 5.83 38.67 4.45
2985 3035 3.685139 TCTGTAAGAGGCTGTTTCCAG 57.315 47.619 0.90 9.48 38.67 3.86
2997 3047 5.250774 AGCCTTTCCCTACATTTCTGTAAGA 59.749 40.000 0.00 0.00 44.68 2.10
2998 3048 5.355350 CAGCCTTTCCCTACATTTCTGTAAG 59.645 44.000 0.00 0.00 37.41 2.34
2999 3049 5.253330 CAGCCTTTCCCTACATTTCTGTAA 58.747 41.667 0.00 0.00 37.41 2.41
3000 3050 4.324254 CCAGCCTTTCCCTACATTTCTGTA 60.324 45.833 0.00 0.00 36.79 2.74
3001 3051 3.562176 CCAGCCTTTCCCTACATTTCTGT 60.562 47.826 0.00 0.00 39.49 3.41
3002 3052 3.019564 CCAGCCTTTCCCTACATTTCTG 58.980 50.000 0.00 0.00 0.00 3.02
3003 3053 2.024941 CCCAGCCTTTCCCTACATTTCT 60.025 50.000 0.00 0.00 0.00 2.52
3004 3054 2.025321 TCCCAGCCTTTCCCTACATTTC 60.025 50.000 0.00 0.00 0.00 2.17
3005 3055 2.000048 TCCCAGCCTTTCCCTACATTT 59.000 47.619 0.00 0.00 0.00 2.32
3006 3056 1.566231 CTCCCAGCCTTTCCCTACATT 59.434 52.381 0.00 0.00 0.00 2.71
3007 3057 1.216990 CTCCCAGCCTTTCCCTACAT 58.783 55.000 0.00 0.00 0.00 2.29
3008 3058 1.562672 GCTCCCAGCCTTTCCCTACA 61.563 60.000 0.00 0.00 34.48 2.74
3009 3059 1.224870 GCTCCCAGCCTTTCCCTAC 59.775 63.158 0.00 0.00 34.48 3.18
3010 3060 0.341961 TAGCTCCCAGCCTTTCCCTA 59.658 55.000 0.00 0.00 43.77 3.53
3011 3061 1.082954 TAGCTCCCAGCCTTTCCCT 59.917 57.895 0.00 0.00 43.77 4.20
3012 3062 1.224870 GTAGCTCCCAGCCTTTCCC 59.775 63.158 0.00 0.00 43.77 3.97
3013 3063 0.548510 ATGTAGCTCCCAGCCTTTCC 59.451 55.000 0.00 0.00 43.77 3.13
3014 3064 1.673168 CATGTAGCTCCCAGCCTTTC 58.327 55.000 0.00 0.00 43.77 2.62
3015 3065 0.394899 GCATGTAGCTCCCAGCCTTT 60.395 55.000 0.00 0.00 43.77 3.11
3016 3066 1.225704 GCATGTAGCTCCCAGCCTT 59.774 57.895 0.00 0.00 43.77 4.35
3017 3067 1.997311 TGCATGTAGCTCCCAGCCT 60.997 57.895 0.00 0.00 43.77 4.58
3018 3068 1.821332 GTGCATGTAGCTCCCAGCC 60.821 63.158 0.00 0.00 43.77 4.85
3019 3069 3.819188 GTGCATGTAGCTCCCAGC 58.181 61.111 0.00 0.00 45.94 4.85
3024 3074 1.089920 CAACCTGGTGCATGTAGCTC 58.910 55.000 14.15 0.00 45.94 4.09
3025 3075 0.962356 GCAACCTGGTGCATGTAGCT 60.962 55.000 14.15 0.00 44.29 3.32
3026 3076 1.508088 GCAACCTGGTGCATGTAGC 59.492 57.895 6.00 6.00 44.29 3.58
3027 3077 2.183409 GGCAACCTGGTGCATGTAG 58.817 57.895 18.44 0.00 46.81 2.74
3028 3078 4.413928 GGCAACCTGGTGCATGTA 57.586 55.556 18.44 0.00 46.81 2.29
3049 3099 3.312421 GCACGGCTGCTATAGATGAAAAA 59.688 43.478 3.21 0.00 40.63 1.94
3050 3100 2.872245 GCACGGCTGCTATAGATGAAAA 59.128 45.455 3.21 0.00 40.63 2.29
3051 3101 2.483876 GCACGGCTGCTATAGATGAAA 58.516 47.619 3.21 0.00 40.63 2.69
3052 3102 1.270305 GGCACGGCTGCTATAGATGAA 60.270 52.381 3.21 0.00 43.66 2.57
3053 3103 0.318441 GGCACGGCTGCTATAGATGA 59.682 55.000 3.21 0.00 43.66 2.92
3054 3104 0.033920 TGGCACGGCTGCTATAGATG 59.966 55.000 3.21 0.00 43.66 2.90
3055 3105 0.758734 TTGGCACGGCTGCTATAGAT 59.241 50.000 3.21 0.00 43.66 1.98
3056 3106 0.104855 CTTGGCACGGCTGCTATAGA 59.895 55.000 3.21 0.00 43.66 1.98
3057 3107 1.502163 GCTTGGCACGGCTGCTATAG 61.502 60.000 0.00 0.00 43.66 1.31
3058 3108 1.523711 GCTTGGCACGGCTGCTATA 60.524 57.895 0.00 0.00 43.66 1.31
3059 3109 2.825836 GCTTGGCACGGCTGCTAT 60.826 61.111 0.00 0.00 43.66 2.97
3060 3110 4.020617 AGCTTGGCACGGCTGCTA 62.021 61.111 12.45 0.72 43.66 3.49
3132 3203 7.775120 CATTCATAAGGCAGAATGGTAAGTTT 58.225 34.615 7.14 0.00 44.51 2.66
3166 3237 3.126000 GCACTTCTATGGACTGAGTTTGC 59.874 47.826 0.00 0.00 0.00 3.68
3267 3338 2.227194 TGTCGCCGATATAGAGCTTGA 58.773 47.619 0.00 0.00 0.00 3.02
3310 3381 3.136626 ACTTCTTCCAGCCTGTTTGTAGT 59.863 43.478 0.00 0.00 0.00 2.73
3392 3463 0.687354 ACGTTCATGGTGAGCTCCTT 59.313 50.000 12.15 0.00 0.00 3.36
3571 3648 2.515926 AACCCATCTCATCGACATCG 57.484 50.000 0.00 0.00 41.45 3.84
3677 3759 2.423892 TCACTCGGTGTAGAGATTGAGC 59.576 50.000 0.62 0.00 40.57 4.26


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

AutoCloner maintained by Alex Coulton.