Multiple sequence alignment - TraesCS4A01G242400

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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 TraesCS4A01G242400 chr4A 100.000 3451 0 0 1 3451 552406850 552410300 0.000000e+00 6373.0
1 TraesCS4A01G242400 chr4A 95.000 40 2 0 2839 2878 201708362 201708401 2.880000e-06 63.9
2 TraesCS4A01G242400 chr4B 89.953 2150 156 27 611 2715 68097150 68095016 0.000000e+00 2719.0
3 TraesCS4A01G242400 chr4B 90.388 541 38 11 2906 3442 68094976 68094446 0.000000e+00 699.0
4 TraesCS4A01G242400 chr4B 79.104 134 18 7 2751 2881 286072561 286072435 2.210000e-12 84.2
5 TraesCS4A01G242400 chr4D 93.220 885 44 7 1847 2715 46597119 46596235 0.000000e+00 1288.0
6 TraesCS4A01G242400 chr4D 90.508 885 62 10 938 1809 46598001 46597126 0.000000e+00 1149.0
7 TraesCS4A01G242400 chr4D 90.121 577 29 14 2874 3442 46596238 46595682 0.000000e+00 725.0
8 TraesCS4A01G242400 chr4D 90.214 327 13 10 593 903 46598324 46598001 3.210000e-110 409.0
9 TraesCS4A01G242400 chr7A 97.808 593 12 1 1 592 23150231 23150823 0.000000e+00 1022.0
10 TraesCS4A01G242400 chr7A 97.114 589 16 1 1 588 490172350 490172938 0.000000e+00 992.0
11 TraesCS4A01G242400 chr7A 97.297 37 1 0 2839 2875 32527977 32527941 2.880000e-06 63.9
12 TraesCS4A01G242400 chr2A 93.467 597 25 5 1 594 775553845 775554430 0.000000e+00 874.0
13 TraesCS4A01G242400 chr2A 91.429 105 3 3 2711 2815 186403776 186403678 4.640000e-29 139.0
14 TraesCS4A01G242400 chr6A 80.769 208 29 3 216 413 426965493 426965699 5.970000e-33 152.0
15 TraesCS4A01G242400 chr6A 88.496 113 7 5 2711 2823 474880232 474880338 7.770000e-27 132.0
16 TraesCS4A01G242400 chr6A 97.297 37 1 0 2843 2879 97593958 97593994 2.880000e-06 63.9
17 TraesCS4A01G242400 chr6B 90.826 109 7 2 2710 2815 712570157 712570265 3.590000e-30 143.0
18 TraesCS4A01G242400 chr6B 91.262 103 3 3 2712 2814 613115862 613115958 6.010000e-28 135.0
19 TraesCS4A01G242400 chr6B 90.196 51 4 1 542 592 450630542 450630493 7.990000e-07 65.8
20 TraesCS4A01G242400 chr1A 74.266 443 67 21 196 599 328839177 328839611 3.590000e-30 143.0
21 TraesCS4A01G242400 chr1A 100.000 36 0 0 2843 2878 374579455 374579420 2.220000e-07 67.6
22 TraesCS4A01G242400 chr1D 89.815 108 7 3 2711 2814 52665817 52665924 6.010000e-28 135.0
23 TraesCS4A01G242400 chr1D 89.720 107 7 3 2712 2818 302346047 302346149 2.160000e-27 134.0
24 TraesCS4A01G242400 chr2D 89.815 108 5 3 2711 2818 532305901 532306002 2.160000e-27 134.0
25 TraesCS4A01G242400 chr3A 88.496 113 7 5 2711 2823 511210404 511210510 7.770000e-27 132.0
26 TraesCS4A01G242400 chr3A 89.091 110 6 3 2712 2821 572598542 572598439 7.770000e-27 132.0
27 TraesCS4A01G242400 chr3A 95.000 40 2 0 2839 2878 652030475 652030436 2.880000e-06 63.9
28 TraesCS4A01G242400 chr2B 90.110 91 9 0 499 589 139364446 139364536 6.050000e-23 119.0
29 TraesCS4A01G242400 chr2B 92.727 55 2 2 542 595 74404277 74404330 1.030000e-10 78.7
30 TraesCS4A01G242400 chr2B 97.297 37 1 0 2839 2875 690207349 690207313 2.880000e-06 63.9
31 TraesCS4A01G242400 chr3B 93.750 48 2 1 2836 2882 189492713 189492760 1.720000e-08 71.3
32 TraesCS4A01G242400 chr7B 91.304 46 4 0 2839 2884 746337326 746337281 2.880000e-06 63.9


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 TraesCS4A01G242400 chr4A 552406850 552410300 3450 False 6373.00 6373 100.00000 1 3451 1 chr4A.!!$F2 3450
1 TraesCS4A01G242400 chr4B 68094446 68097150 2704 True 1709.00 2719 90.17050 611 3442 2 chr4B.!!$R2 2831
2 TraesCS4A01G242400 chr4D 46595682 46598324 2642 True 892.75 1288 91.01575 593 3442 4 chr4D.!!$R1 2849
3 TraesCS4A01G242400 chr7A 23150231 23150823 592 False 1022.00 1022 97.80800 1 592 1 chr7A.!!$F1 591
4 TraesCS4A01G242400 chr7A 490172350 490172938 588 False 992.00 992 97.11400 1 588 1 chr7A.!!$F2 587
5 TraesCS4A01G242400 chr2A 775553845 775554430 585 False 874.00 874 93.46700 1 594 1 chr2A.!!$F1 593

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
967 990 1.142936 CACCTCCATCCATCCATCCA 58.857 55.0 0.00 0.0 0.00 3.41 F
1683 1719 0.177604 CTGGCCTGGAGATGACACTC 59.822 60.0 3.32 0.0 36.31 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1850 1898 0.110295 CCGCCCCACCATGATTCATA 59.89 55.0 0.00 0.00 0.00 2.15 R
3077 3165 0.110056 ACTCGCAGCGAATTTGCAAG 60.11 50.0 20.04 12.34 41.59 4.01 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
122 123 3.043635 GACTGTTTCGTCGACGCTATA 57.956 47.619 32.19 18.43 39.60 1.31
290 292 4.766891 CCCACAGTCAAGAATATGGTGTTT 59.233 41.667 0.00 0.00 0.00 2.83
348 350 7.285629 TCCTCTTGAGAATACTTCATCACGTAT 59.714 37.037 0.00 0.00 0.00 3.06
596 600 9.030301 CGACTGATTTTAAACATTTTCCTTTGT 57.970 29.630 0.00 0.00 0.00 2.83
609 613 8.646900 ACATTTTCCTTTGTCTAGGCATAAAAA 58.353 29.630 0.00 3.77 35.15 1.94
639 643 5.321102 TGACAGGCAAAAATACAGTATGGT 58.679 37.500 0.00 0.00 43.62 3.55
768 779 2.218759 CGAACAGACAGGTGAAGAAACG 59.781 50.000 0.00 0.00 0.00 3.60
847 870 5.105554 ACACATTGCCTTAGACTAGAGTGAG 60.106 44.000 0.00 0.00 0.00 3.51
904 927 2.297895 TGCCCATAGGAAGCACCGT 61.298 57.895 0.00 0.00 44.74 4.83
940 963 1.577736 CCAGGTGGGTTCTCATCTCT 58.422 55.000 0.00 0.00 0.00 3.10
967 990 1.142936 CACCTCCATCCATCCATCCA 58.857 55.000 0.00 0.00 0.00 3.41
968 991 1.709115 CACCTCCATCCATCCATCCAT 59.291 52.381 0.00 0.00 0.00 3.41
969 992 1.991070 ACCTCCATCCATCCATCCATC 59.009 52.381 0.00 0.00 0.00 3.51
970 993 1.284198 CCTCCATCCATCCATCCATCC 59.716 57.143 0.00 0.00 0.00 3.51
986 1009 2.507058 CCATCCTCTGTGATCTTTCCCA 59.493 50.000 0.00 0.00 0.00 4.37
1103 1126 1.135460 GCACTTCTTCAAGCTCATGGC 60.135 52.381 0.00 0.00 42.19 4.40
1114 1137 1.153289 CTCATGGCTGGGGACTTCG 60.153 63.158 0.00 0.00 0.00 3.79
1151 1174 0.618968 AATCTTCCGTCTGCCTCCCT 60.619 55.000 0.00 0.00 0.00 4.20
1169 1197 1.675415 CCTCACTGCAGAGCTTTCTCC 60.675 57.143 23.35 0.00 40.22 3.71
1204 1232 8.244113 GCTTATATTGCCTTTGTAAACTCAAGT 58.756 33.333 0.00 0.00 0.00 3.16
1221 1249 7.348080 ACTCAAGTGTGGATCTCGATTTATA 57.652 36.000 0.00 0.00 0.00 0.98
1223 1251 8.085296 ACTCAAGTGTGGATCTCGATTTATATC 58.915 37.037 0.00 0.00 0.00 1.63
1227 1255 8.127150 AGTGTGGATCTCGATTTATATCATCA 57.873 34.615 0.00 0.00 0.00 3.07
1328 1364 1.064463 GGTCATCAATCTGAAGCCCCA 60.064 52.381 0.00 0.00 0.00 4.96
1351 1387 1.097232 TGGCAAATCTTGGAGCATCG 58.903 50.000 0.00 0.00 34.37 3.84
1410 1446 1.003233 GGGTGGAAGGAGTTTGTCGAT 59.997 52.381 0.00 0.00 0.00 3.59
1412 1448 2.289444 GGTGGAAGGAGTTTGTCGATGA 60.289 50.000 0.00 0.00 0.00 2.92
1413 1449 2.737252 GTGGAAGGAGTTTGTCGATGAC 59.263 50.000 0.00 0.00 0.00 3.06
1419 1455 0.949105 AGTTTGTCGATGACCACGGC 60.949 55.000 0.00 0.00 35.87 5.68
1448 1484 1.153667 GAGACCGCCTGCTCTTCAG 60.154 63.158 0.00 0.00 42.49 3.02
1492 1528 0.526211 TGTCCTGATGTTCGACTCGG 59.474 55.000 0.00 0.00 0.00 4.63
1512 1548 3.365265 GGCTGCCAGAAACCACCG 61.365 66.667 15.17 0.00 0.00 4.94
1513 1549 2.594592 GCTGCCAGAAACCACCGT 60.595 61.111 0.00 0.00 0.00 4.83
1521 1557 1.737008 GAAACCACCGTCTCCTCGC 60.737 63.158 0.00 0.00 0.00 5.03
1584 1620 2.031495 ACTCTGCCAGAGGTAAAGGT 57.969 50.000 24.79 0.59 46.45 3.50
1614 1650 0.517316 GCTACCACGCTTCCAACAAG 59.483 55.000 0.00 0.00 0.00 3.16
1645 1681 3.499737 CACCGCATCCGCCTTCAC 61.500 66.667 0.00 0.00 33.11 3.18
1680 1716 1.919816 TGCTGGCCTGGAGATGACA 60.920 57.895 12.06 0.00 0.00 3.58
1683 1719 0.177604 CTGGCCTGGAGATGACACTC 59.822 60.000 3.32 0.00 36.31 3.51
1744 1792 4.445453 ACATGATATAGGCATGCCATACG 58.555 43.478 37.18 20.59 45.32 3.06
1781 1829 3.679502 GCACCAGTTGGAATTTTATGTGC 59.320 43.478 4.92 0.00 39.61 4.57
1834 1882 1.302271 CTGTTGAGCCTGCTGCAGA 60.302 57.895 30.10 7.99 44.83 4.26
1840 1888 3.138798 GCCTGCTGCAGACCATGG 61.139 66.667 30.10 11.19 40.77 3.66
1850 1898 2.240414 TGCAGACCATGGAGATGTTGAT 59.760 45.455 21.47 0.00 0.00 2.57
1854 1902 5.744007 GCAGACCATGGAGATGTTGATATGA 60.744 44.000 21.47 0.00 0.00 2.15
1864 1912 6.150641 GGAGATGTTGATATGAATCATGGTGG 59.849 42.308 5.91 0.00 41.73 4.61
1886 1934 1.543429 GCGGCTGCCAAGAATAGGTAT 60.543 52.381 20.29 0.00 33.98 2.73
2113 2166 6.425417 TGCAATGCCAATATATTCAGCAAATG 59.575 34.615 18.75 19.20 36.95 2.32
2114 2167 6.619874 GCAATGCCAATATATTCAGCAAATGC 60.620 38.462 25.59 25.59 40.58 3.56
2126 2179 1.617740 GCAAATGCGGTGTTAAGAGC 58.382 50.000 0.00 0.00 0.00 4.09
2156 2224 1.059369 CTTTGTTCGGATCGCGCTG 59.941 57.895 5.56 0.00 0.00 5.18
2167 2235 3.648982 CGCGCTGTGTTGCTTCCA 61.649 61.111 5.56 0.00 0.00 3.53
2189 2257 3.461773 CAGGGCGTGTCCTCGGAT 61.462 66.667 0.00 0.00 34.31 4.18
2494 2562 1.842052 TATGTGCTCGACTGTACCCA 58.158 50.000 0.00 0.00 0.00 4.51
2503 2571 4.337555 GCTCGACTGTACCCATAGAACTTA 59.662 45.833 0.00 0.00 0.00 2.24
2539 2607 6.558775 ACTGGAATAATAATAGAGGCTGGTGA 59.441 38.462 0.00 0.00 0.00 4.02
2559 2627 5.221130 GTGATACGAGCTTATCCCAGTAAC 58.779 45.833 3.50 0.00 0.00 2.50
2715 2788 6.206634 TGTGGAAACATGAGAAAACCATACTC 59.793 38.462 0.00 0.00 46.14 2.59
2716 2789 5.710099 TGGAAACATGAGAAAACCATACTCC 59.290 40.000 0.00 0.00 33.40 3.85
2717 2790 5.125578 GGAAACATGAGAAAACCATACTCCC 59.874 44.000 0.00 0.00 0.00 4.30
2718 2791 5.520748 AACATGAGAAAACCATACTCCCT 57.479 39.130 0.00 0.00 0.00 4.20
2719 2792 5.104259 ACATGAGAAAACCATACTCCCTC 57.896 43.478 0.00 0.00 0.00 4.30
2720 2793 4.080299 ACATGAGAAAACCATACTCCCTCC 60.080 45.833 0.00 0.00 0.00 4.30
2721 2794 2.500098 TGAGAAAACCATACTCCCTCCG 59.500 50.000 0.00 0.00 0.00 4.63
2722 2795 2.500504 GAGAAAACCATACTCCCTCCGT 59.499 50.000 0.00 0.00 0.00 4.69
2723 2796 2.910977 AGAAAACCATACTCCCTCCGTT 59.089 45.455 0.00 0.00 0.00 4.44
2724 2797 3.329814 AGAAAACCATACTCCCTCCGTTT 59.670 43.478 0.00 0.00 0.00 3.60
2725 2798 3.345508 AAACCATACTCCCTCCGTTTC 57.654 47.619 0.00 0.00 0.00 2.78
2726 2799 1.946984 ACCATACTCCCTCCGTTTCA 58.053 50.000 0.00 0.00 0.00 2.69
2727 2800 2.262637 ACCATACTCCCTCCGTTTCAA 58.737 47.619 0.00 0.00 0.00 2.69
2728 2801 2.640826 ACCATACTCCCTCCGTTTCAAA 59.359 45.455 0.00 0.00 0.00 2.69
2729 2802 3.073356 ACCATACTCCCTCCGTTTCAAAA 59.927 43.478 0.00 0.00 0.00 2.44
2730 2803 4.263771 ACCATACTCCCTCCGTTTCAAAAT 60.264 41.667 0.00 0.00 0.00 1.82
2731 2804 5.045432 ACCATACTCCCTCCGTTTCAAAATA 60.045 40.000 0.00 0.00 0.00 1.40
2732 2805 5.527582 CCATACTCCCTCCGTTTCAAAATAG 59.472 44.000 0.00 0.00 0.00 1.73
2733 2806 4.903045 ACTCCCTCCGTTTCAAAATAGA 57.097 40.909 0.00 0.00 0.00 1.98
2734 2807 5.437191 ACTCCCTCCGTTTCAAAATAGAT 57.563 39.130 0.00 0.00 0.00 1.98
2735 2808 5.186198 ACTCCCTCCGTTTCAAAATAGATG 58.814 41.667 0.00 0.00 0.00 2.90
2736 2809 5.045869 ACTCCCTCCGTTTCAAAATAGATGA 60.046 40.000 0.00 0.00 0.00 2.92
2737 2810 6.001449 TCCCTCCGTTTCAAAATAGATGAT 57.999 37.500 0.00 0.00 0.00 2.45
2738 2811 6.055588 TCCCTCCGTTTCAAAATAGATGATC 58.944 40.000 0.00 0.00 0.00 2.92
2739 2812 5.239525 CCCTCCGTTTCAAAATAGATGATCC 59.760 44.000 0.00 0.00 0.00 3.36
2740 2813 5.822519 CCTCCGTTTCAAAATAGATGATCCA 59.177 40.000 0.00 0.00 0.00 3.41
2741 2814 6.318648 CCTCCGTTTCAAAATAGATGATCCAA 59.681 38.462 0.00 0.00 0.00 3.53
2742 2815 7.083875 TCCGTTTCAAAATAGATGATCCAAC 57.916 36.000 0.00 0.00 0.00 3.77
2743 2816 6.884295 TCCGTTTCAAAATAGATGATCCAACT 59.116 34.615 0.00 0.00 0.00 3.16
2744 2817 7.393234 TCCGTTTCAAAATAGATGATCCAACTT 59.607 33.333 0.00 0.00 0.00 2.66
2745 2818 8.028938 CCGTTTCAAAATAGATGATCCAACTTT 58.971 33.333 0.00 0.00 0.00 2.66
2746 2819 8.853345 CGTTTCAAAATAGATGATCCAACTTTG 58.147 33.333 0.00 0.00 0.00 2.77
2747 2820 9.696917 GTTTCAAAATAGATGATCCAACTTTGT 57.303 29.630 0.00 0.00 0.00 2.83
2756 2829 8.230472 AGATGATCCAACTTTGTAAATGATCC 57.770 34.615 0.00 0.00 0.00 3.36
2757 2830 7.835682 AGATGATCCAACTTTGTAAATGATCCA 59.164 33.333 0.00 0.00 0.00 3.41
2758 2831 7.773489 TGATCCAACTTTGTAAATGATCCAA 57.227 32.000 0.00 0.00 0.00 3.53
2759 2832 7.601856 TGATCCAACTTTGTAAATGATCCAAC 58.398 34.615 0.00 0.00 0.00 3.77
2760 2833 7.451255 TGATCCAACTTTGTAAATGATCCAACT 59.549 33.333 0.00 0.00 0.00 3.16
2761 2834 7.595819 TCCAACTTTGTAAATGATCCAACTT 57.404 32.000 0.00 0.00 0.00 2.66
2762 2835 8.017418 TCCAACTTTGTAAATGATCCAACTTT 57.983 30.769 0.00 0.00 0.00 2.66
2763 2836 7.925483 TCCAACTTTGTAAATGATCCAACTTTG 59.075 33.333 0.00 0.00 0.00 2.77
2764 2837 7.710475 CCAACTTTGTAAATGATCCAACTTTGT 59.290 33.333 0.00 0.00 0.00 2.83
2765 2838 8.542132 CAACTTTGTAAATGATCCAACTTTGTG 58.458 33.333 0.00 0.00 0.00 3.33
2766 2839 7.781056 ACTTTGTAAATGATCCAACTTTGTGT 58.219 30.769 0.00 0.00 0.00 3.72
2767 2840 8.257306 ACTTTGTAAATGATCCAACTTTGTGTT 58.743 29.630 0.00 0.00 39.92 3.32
2768 2841 9.743057 CTTTGTAAATGATCCAACTTTGTGTTA 57.257 29.630 0.00 0.00 37.07 2.41
2771 2844 9.743057 TGTAAATGATCCAACTTTGTGTTAAAG 57.257 29.630 0.00 0.00 37.07 1.85
2772 2845 9.744468 GTAAATGATCCAACTTTGTGTTAAAGT 57.256 29.630 0.00 0.00 41.82 2.66
2775 2848 9.965824 AATGATCCAACTTTGTGTTAAAGTTAG 57.034 29.630 15.03 9.89 45.57 2.34
2776 2849 8.514330 TGATCCAACTTTGTGTTAAAGTTAGT 57.486 30.769 15.03 6.67 45.57 2.24
2777 2850 9.616156 TGATCCAACTTTGTGTTAAAGTTAGTA 57.384 29.630 15.03 6.64 45.57 1.82
2778 2851 9.874215 GATCCAACTTTGTGTTAAAGTTAGTAC 57.126 33.333 15.03 6.67 45.57 2.73
2779 2852 8.789825 TCCAACTTTGTGTTAAAGTTAGTACA 57.210 30.769 15.03 0.00 45.57 2.90
2780 2853 9.228949 TCCAACTTTGTGTTAAAGTTAGTACAA 57.771 29.630 15.03 0.00 45.57 2.41
2781 2854 9.843334 CCAACTTTGTGTTAAAGTTAGTACAAA 57.157 29.630 15.03 0.00 45.57 2.83
2788 2861 9.439500 TGTGTTAAAGTTAGTACAAAGTTGAGT 57.561 29.630 0.00 0.00 0.00 3.41
2789 2862 9.911980 GTGTTAAAGTTAGTACAAAGTTGAGTC 57.088 33.333 0.00 0.00 0.00 3.36
2790 2863 9.656040 TGTTAAAGTTAGTACAAAGTTGAGTCA 57.344 29.630 0.00 0.00 0.00 3.41
2800 2873 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
2801 2874 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
2802 2875 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
2803 2876 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
2804 2877 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
2805 2878 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
2806 2879 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
2807 2880 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
2808 2881 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
2809 2882 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
2810 2883 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
2811 2884 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
2812 2885 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
2813 2886 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
2814 2887 2.845363 TTTTGGAACGGAGGGAGTAC 57.155 50.000 0.00 0.00 0.00 2.73
2815 2888 2.019807 TTTGGAACGGAGGGAGTACT 57.980 50.000 0.00 0.00 0.00 2.73
2816 2889 2.019807 TTGGAACGGAGGGAGTACTT 57.980 50.000 0.00 0.00 0.00 2.24
2817 2890 1.263356 TGGAACGGAGGGAGTACTTG 58.737 55.000 0.00 0.00 0.00 3.16
2818 2891 1.203087 TGGAACGGAGGGAGTACTTGA 60.203 52.381 0.00 0.00 0.00 3.02
2819 2892 2.108970 GGAACGGAGGGAGTACTTGAT 58.891 52.381 0.00 0.00 0.00 2.57
2820 2893 3.294214 GGAACGGAGGGAGTACTTGATA 58.706 50.000 0.00 0.00 0.00 2.15
2821 2894 3.703052 GGAACGGAGGGAGTACTTGATAA 59.297 47.826 0.00 0.00 0.00 1.75
2822 2895 4.202131 GGAACGGAGGGAGTACTTGATAAG 60.202 50.000 0.00 0.00 0.00 1.73
2823 2896 3.297736 ACGGAGGGAGTACTTGATAAGG 58.702 50.000 0.00 0.00 0.00 2.69
2824 2897 2.628657 CGGAGGGAGTACTTGATAAGGG 59.371 54.545 0.00 0.00 0.00 3.95
2825 2898 3.690438 CGGAGGGAGTACTTGATAAGGGA 60.690 52.174 0.00 0.00 0.00 4.20
2826 2899 4.296056 GGAGGGAGTACTTGATAAGGGAA 58.704 47.826 0.00 0.00 0.00 3.97
2827 2900 4.720273 GGAGGGAGTACTTGATAAGGGAAA 59.280 45.833 0.00 0.00 0.00 3.13
2828 2901 5.191124 GGAGGGAGTACTTGATAAGGGAAAA 59.809 44.000 0.00 0.00 0.00 2.29
2829 2902 6.314899 AGGGAGTACTTGATAAGGGAAAAG 57.685 41.667 0.00 0.00 0.00 2.27
2830 2903 5.191921 AGGGAGTACTTGATAAGGGAAAAGG 59.808 44.000 0.00 0.00 0.00 3.11
2831 2904 5.437946 GGAGTACTTGATAAGGGAAAAGGG 58.562 45.833 0.00 0.00 0.00 3.95
2832 2905 5.191124 GGAGTACTTGATAAGGGAAAAGGGA 59.809 44.000 0.00 0.00 0.00 4.20
2833 2906 6.296836 GGAGTACTTGATAAGGGAAAAGGGAA 60.297 42.308 0.00 0.00 0.00 3.97
2834 2907 7.098845 AGTACTTGATAAGGGAAAAGGGAAA 57.901 36.000 0.00 0.00 0.00 3.13
2835 2908 7.532199 AGTACTTGATAAGGGAAAAGGGAAAA 58.468 34.615 0.00 0.00 0.00 2.29
2836 2909 6.918067 ACTTGATAAGGGAAAAGGGAAAAG 57.082 37.500 0.00 0.00 0.00 2.27
2837 2910 5.780282 ACTTGATAAGGGAAAAGGGAAAAGG 59.220 40.000 0.00 0.00 0.00 3.11
2838 2911 5.608798 TGATAAGGGAAAAGGGAAAAGGA 57.391 39.130 0.00 0.00 0.00 3.36
2839 2912 6.165742 TGATAAGGGAAAAGGGAAAAGGAT 57.834 37.500 0.00 0.00 0.00 3.24
2840 2913 7.291991 TGATAAGGGAAAAGGGAAAAGGATA 57.708 36.000 0.00 0.00 0.00 2.59
2841 2914 7.893482 TGATAAGGGAAAAGGGAAAAGGATAT 58.107 34.615 0.00 0.00 0.00 1.63
2842 2915 9.020644 TGATAAGGGAAAAGGGAAAAGGATATA 57.979 33.333 0.00 0.00 0.00 0.86
2843 2916 9.521841 GATAAGGGAAAAGGGAAAAGGATATAG 57.478 37.037 0.00 0.00 0.00 1.31
2844 2917 6.927691 AGGGAAAAGGGAAAAGGATATAGT 57.072 37.500 0.00 0.00 0.00 2.12
2845 2918 7.298678 AGGGAAAAGGGAAAAGGATATAGTT 57.701 36.000 0.00 0.00 0.00 2.24
2846 2919 7.126061 AGGGAAAAGGGAAAAGGATATAGTTG 58.874 38.462 0.00 0.00 0.00 3.16
2847 2920 7.036132 AGGGAAAAGGGAAAAGGATATAGTTGA 60.036 37.037 0.00 0.00 0.00 3.18
2848 2921 7.285629 GGGAAAAGGGAAAAGGATATAGTTGAG 59.714 40.741 0.00 0.00 0.00 3.02
2849 2922 7.834681 GGAAAAGGGAAAAGGATATAGTTGAGT 59.165 37.037 0.00 0.00 0.00 3.41
2850 2923 8.809468 AAAAGGGAAAAGGATATAGTTGAGTC 57.191 34.615 0.00 0.00 0.00 3.36
2851 2924 7.510675 AAGGGAAAAGGATATAGTTGAGTCA 57.489 36.000 0.00 0.00 0.00 3.41
2852 2925 7.698163 AGGGAAAAGGATATAGTTGAGTCAT 57.302 36.000 0.00 0.00 0.00 3.06
2853 2926 7.740805 AGGGAAAAGGATATAGTTGAGTCATC 58.259 38.462 0.00 0.00 0.00 2.92
2854 2927 7.570607 AGGGAAAAGGATATAGTTGAGTCATCT 59.429 37.037 8.71 8.71 0.00 2.90
2855 2928 8.871125 GGGAAAAGGATATAGTTGAGTCATCTA 58.129 37.037 12.28 12.28 0.00 1.98
2867 2940 8.868522 AGTTGAGTCATCTATTTTGAAATGGA 57.131 30.769 1.70 5.21 39.67 3.41
2868 2941 8.954350 AGTTGAGTCATCTATTTTGAAATGGAG 58.046 33.333 1.70 2.49 38.91 3.86
2869 2942 7.870509 TGAGTCATCTATTTTGAAATGGAGG 57.129 36.000 7.79 7.79 38.91 4.30
2870 2943 6.830324 TGAGTCATCTATTTTGAAATGGAGGG 59.170 38.462 12.38 6.38 38.91 4.30
2871 2944 6.973642 AGTCATCTATTTTGAAATGGAGGGA 58.026 36.000 12.38 8.08 38.91 4.20
2872 2945 7.059156 AGTCATCTATTTTGAAATGGAGGGAG 58.941 38.462 12.38 3.00 38.91 4.30
2873 2946 6.830838 GTCATCTATTTTGAAATGGAGGGAGT 59.169 38.462 12.38 0.00 38.91 3.85
2874 2947 7.993183 GTCATCTATTTTGAAATGGAGGGAGTA 59.007 37.037 12.38 0.00 38.91 2.59
2875 2948 7.993183 TCATCTATTTTGAAATGGAGGGAGTAC 59.007 37.037 12.38 0.00 38.91 2.73
2876 2949 7.510675 TCTATTTTGAAATGGAGGGAGTACT 57.489 36.000 0.00 0.00 31.98 2.73
3014 3102 4.036734 CACAACACAATCTACAGTTTGGCT 59.963 41.667 5.32 0.00 0.00 4.75
3051 3139 1.382522 ATCGACAATCACATGTGGGC 58.617 50.000 25.16 11.00 32.57 5.36
3063 3151 4.022068 TCACATGTGGGCTTTCTTTGATTC 60.022 41.667 25.16 0.00 0.00 2.52
3077 3165 2.859165 TGATTCCACTGAACTCCCAC 57.141 50.000 0.00 0.00 32.13 4.61
3080 3168 2.638480 TTCCACTGAACTCCCACTTG 57.362 50.000 0.00 0.00 0.00 3.16
3099 3187 0.442310 GCAAATTCGCTGCGAGTGTA 59.558 50.000 24.61 10.83 37.14 2.90
3131 3219 5.986135 AGAGAAACAGCATGATACCGATTAC 59.014 40.000 0.00 0.00 39.69 1.89
3150 3238 9.716507 CCGATTACGAATTAAAGATTTCAACAT 57.283 29.630 0.00 0.00 42.66 2.71
3153 3241 8.682128 TTACGAATTAAAGATTTCAACATGCC 57.318 30.769 0.00 0.00 0.00 4.40
3178 3266 4.240096 GCAAACAAGAACCATCCAATGAG 58.760 43.478 0.00 0.00 0.00 2.90
3265 3354 1.197036 GAGACAAAAACTAGCACCGGC 59.803 52.381 0.00 0.00 41.61 6.13
3278 3367 2.115266 CCGGCAGTGGGGAGTTTT 59.885 61.111 0.00 0.00 0.00 2.43
3329 3420 2.224621 TGAACCCAGAAGAGCTTCCAAG 60.225 50.000 6.61 0.00 40.33 3.61
3358 3449 4.037446 GCACCCAAAAGAACTGTTGTATCA 59.963 41.667 0.00 0.00 0.00 2.15
3399 3490 4.512571 TCGTCCTTTAAGTACCTGCAAAAC 59.487 41.667 0.00 0.00 0.00 2.43
3438 3529 6.761714 AGGTAGGTTCGACATGAAAATCATAC 59.238 38.462 0.00 0.00 38.60 2.39
3441 3532 7.447374 AGGTTCGACATGAAAATCATACAAA 57.553 32.000 0.00 0.00 38.60 2.83
3442 3533 7.881142 AGGTTCGACATGAAAATCATACAAAA 58.119 30.769 0.00 0.00 38.60 2.44
3443 3534 8.522830 AGGTTCGACATGAAAATCATACAAAAT 58.477 29.630 0.00 0.00 38.60 1.82
3444 3535 9.781834 GGTTCGACATGAAAATCATACAAAATA 57.218 29.630 0.00 0.00 38.60 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.808202 GCCTTCATCATAGCATCACCGT 60.808 50.000 0.00 0.00 0.00 4.83
62 63 0.744874 TCGTAGCAGGGTAGCATGTC 59.255 55.000 8.51 0.96 36.85 3.06
144 145 2.417933 GCATAGAACCATCGCATCATCC 59.582 50.000 0.00 0.00 0.00 3.51
185 187 2.547218 GGTAGTGTTCTTGACGCCTTCA 60.547 50.000 0.00 0.00 39.64 3.02
290 292 5.288804 GCAAGTAGCAAACAAAGATTCCAA 58.711 37.500 0.00 0.00 44.79 3.53
462 464 3.006217 CCATCTATCTGATTCTGACCGCA 59.994 47.826 0.00 0.00 32.05 5.69
662 667 5.847670 ATTGAGACGAGCTTAGAACAAAC 57.152 39.130 0.00 0.00 0.00 2.93
664 669 6.093404 CAGTATTGAGACGAGCTTAGAACAA 58.907 40.000 0.00 0.00 0.00 2.83
666 671 5.038033 CCAGTATTGAGACGAGCTTAGAAC 58.962 45.833 0.00 0.00 0.00 3.01
667 672 4.705507 ACCAGTATTGAGACGAGCTTAGAA 59.294 41.667 0.00 0.00 0.00 2.10
669 674 4.142359 ACACCAGTATTGAGACGAGCTTAG 60.142 45.833 0.00 0.00 0.00 2.18
670 675 3.762288 ACACCAGTATTGAGACGAGCTTA 59.238 43.478 0.00 0.00 0.00 3.09
714 725 6.560711 ACGAAAATGCAACCAGGATTATTAC 58.439 36.000 0.00 0.00 37.28 1.89
768 779 2.410939 GGTAACAACTGTCGGAAGGTC 58.589 52.381 0.00 0.00 0.00 3.85
847 870 2.452813 CGGCATGTCGGCACACTAC 61.453 63.158 12.98 0.00 41.26 2.73
904 927 2.234661 CCTGGTGTTCTGATAGCACAGA 59.765 50.000 0.00 0.00 40.83 3.41
932 955 1.549620 AGGTGTGCAGTCAGAGATGAG 59.450 52.381 0.00 0.00 0.00 2.90
940 963 1.126948 TGGATGGAGGTGTGCAGTCA 61.127 55.000 0.00 0.00 0.00 3.41
986 1009 1.221523 TCTGCATCTGGGAGGGTATCT 59.778 52.381 0.00 0.00 35.32 1.98
1140 1163 2.267324 GCAGTGAGGGAGGCAGAC 59.733 66.667 0.00 0.00 0.00 3.51
1151 1174 1.346062 AGGAGAAAGCTCTGCAGTGA 58.654 50.000 19.61 0.00 42.28 3.41
1169 1197 6.314400 ACAAAGGCAATATAAGCAAATGCAAG 59.686 34.615 8.28 0.00 45.16 4.01
1240 1276 4.641094 GCTCTACAGGAAGAACAGCTAGTA 59.359 45.833 0.00 0.00 0.00 1.82
1245 1281 3.326836 AAGCTCTACAGGAAGAACAGC 57.673 47.619 0.00 0.00 0.00 4.40
1328 1364 3.370840 TGCTCCAAGATTTGCCACTAT 57.629 42.857 0.00 0.00 0.00 2.12
1351 1387 2.508663 GGTGTCGCCGGCTACTTC 60.509 66.667 28.82 21.03 0.00 3.01
1412 1448 4.096003 CTTCCCCGATGCCGTGGT 62.096 66.667 0.00 0.00 34.80 4.16
1413 1449 4.856801 CCTTCCCCGATGCCGTGG 62.857 72.222 0.00 0.00 34.50 4.94
1419 1455 2.815308 CGGTCTCCTTCCCCGATG 59.185 66.667 0.00 0.00 44.41 3.84
1448 1484 0.386113 GGAGGACGCTCCACTGTATC 59.614 60.000 4.37 0.00 42.86 2.24
1512 1548 2.939261 TTTGACGGGGCGAGGAGAC 61.939 63.158 0.00 0.00 0.00 3.36
1513 1549 2.602267 TTTGACGGGGCGAGGAGA 60.602 61.111 0.00 0.00 0.00 3.71
1602 1638 0.239347 CTTCAGCCTTGTTGGAAGCG 59.761 55.000 0.00 0.00 38.35 4.68
1614 1650 4.090057 GGTGCGCGTTCTTCAGCC 62.090 66.667 8.43 0.00 0.00 4.85
1641 1677 4.302509 TCGCCTTTCGCCGGTGAA 62.303 61.111 26.19 26.19 38.06 3.18
1659 1695 3.790437 ATCTCCAGGCCAGCACCG 61.790 66.667 5.01 0.00 33.69 4.94
1680 1716 2.352032 GCCGGTGCCTCTGTAGAGT 61.352 63.158 1.90 0.00 40.48 3.24
1683 1719 1.448540 CTTGCCGGTGCCTCTGTAG 60.449 63.158 1.90 0.00 36.33 2.74
1711 1747 4.589908 CCTATATCATGTTTACCTGCCCC 58.410 47.826 0.00 0.00 0.00 5.80
1744 1792 4.189231 ACTGGTGCATTCGAATTAGTACC 58.811 43.478 21.41 21.41 0.00 3.34
1809 1857 3.488721 GCAGCAGGCTCAACAGATAAATG 60.489 47.826 0.00 0.00 40.25 2.32
1815 1863 1.302271 CTGCAGCAGGCTCAACAGA 60.302 57.895 15.35 0.00 45.15 3.41
1817 1865 1.598962 GTCTGCAGCAGGCTCAACA 60.599 57.895 20.33 0.00 45.15 3.33
1834 1882 6.844829 TGATTCATATCAACATCTCCATGGT 58.155 36.000 12.58 0.00 37.83 3.55
1840 1888 6.150641 CCCACCATGATTCATATCAACATCTC 59.849 42.308 0.00 0.00 43.67 2.75
1850 1898 0.110295 CCGCCCCACCATGATTCATA 59.890 55.000 0.00 0.00 0.00 2.15
1854 1902 3.743017 AGCCGCCCCACCATGATT 61.743 61.111 0.00 0.00 0.00 2.57
1886 1934 2.446435 GGCCCATTCTTGCAGAAGTAA 58.554 47.619 0.00 0.00 37.69 2.24
2113 2166 0.373716 CATTCCGCTCTTAACACCGC 59.626 55.000 0.00 0.00 0.00 5.68
2114 2167 0.373716 GCATTCCGCTCTTAACACCG 59.626 55.000 0.00 0.00 37.77 4.94
2126 2179 2.476185 CCGAACAAAGCTTAGCATTCCG 60.476 50.000 7.07 4.32 0.00 4.30
2156 2224 1.503542 CTGCGGATGGAAGCAACAC 59.496 57.895 0.00 0.00 43.31 3.32
2212 2280 2.562298 AGAATGATCTCTCTGCCGATCC 59.438 50.000 0.00 0.00 36.15 3.36
2494 2562 5.473931 CAGTGACACAGCTGTAAGTTCTAT 58.526 41.667 21.20 4.26 35.30 1.98
2503 2571 3.769739 TTATTCCAGTGACACAGCTGT 57.230 42.857 15.25 15.25 0.00 4.40
2539 2607 3.255149 CGGTTACTGGGATAAGCTCGTAT 59.745 47.826 0.00 0.00 31.68 3.06
2626 2694 0.964358 AGCTTCTTCCATGCACCTGC 60.964 55.000 0.00 0.00 42.50 4.85
2635 2703 2.884639 GGTTAACAGCAAGCTTCTTCCA 59.115 45.455 8.10 0.00 0.00 3.53
2681 2754 3.758554 CTCATGTTTCCACAGTTAAGGGG 59.241 47.826 0.00 0.00 35.94 4.79
2715 2788 5.239525 GGATCATCTATTTTGAAACGGAGGG 59.760 44.000 0.00 0.00 0.00 4.30
2716 2789 5.822519 TGGATCATCTATTTTGAAACGGAGG 59.177 40.000 0.00 0.00 0.00 4.30
2717 2790 6.925610 TGGATCATCTATTTTGAAACGGAG 57.074 37.500 0.00 0.00 0.00 4.63
2718 2791 6.884295 AGTTGGATCATCTATTTTGAAACGGA 59.116 34.615 0.00 0.00 0.00 4.69
2719 2792 7.088589 AGTTGGATCATCTATTTTGAAACGG 57.911 36.000 0.00 0.00 0.00 4.44
2720 2793 8.853345 CAAAGTTGGATCATCTATTTTGAAACG 58.147 33.333 0.00 0.00 0.00 3.60
2721 2794 9.696917 ACAAAGTTGGATCATCTATTTTGAAAC 57.303 29.630 12.56 0.00 0.00 2.78
2730 2803 9.342308 GGATCATTTACAAAGTTGGATCATCTA 57.658 33.333 0.00 0.00 33.20 1.98
2731 2804 7.835682 TGGATCATTTACAAAGTTGGATCATCT 59.164 33.333 0.00 0.00 33.20 2.90
2732 2805 7.999679 TGGATCATTTACAAAGTTGGATCATC 58.000 34.615 0.00 0.00 33.20 2.92
2733 2806 7.959658 TGGATCATTTACAAAGTTGGATCAT 57.040 32.000 0.00 0.00 33.20 2.45
2734 2807 7.451255 AGTTGGATCATTTACAAAGTTGGATCA 59.549 33.333 0.00 0.00 33.20 2.92
2735 2808 7.830739 AGTTGGATCATTTACAAAGTTGGATC 58.169 34.615 0.00 0.00 0.00 3.36
2736 2809 7.781324 AGTTGGATCATTTACAAAGTTGGAT 57.219 32.000 0.00 0.00 0.00 3.41
2737 2810 7.595819 AAGTTGGATCATTTACAAAGTTGGA 57.404 32.000 0.00 0.00 0.00 3.53
2738 2811 7.710475 ACAAAGTTGGATCATTTACAAAGTTGG 59.290 33.333 0.00 0.00 30.51 3.77
2739 2812 8.542132 CACAAAGTTGGATCATTTACAAAGTTG 58.458 33.333 0.00 0.60 0.00 3.16
2740 2813 8.257306 ACACAAAGTTGGATCATTTACAAAGTT 58.743 29.630 0.00 0.00 0.00 2.66
2741 2814 7.781056 ACACAAAGTTGGATCATTTACAAAGT 58.219 30.769 0.00 0.00 0.00 2.66
2742 2815 8.647143 AACACAAAGTTGGATCATTTACAAAG 57.353 30.769 0.00 0.00 39.49 2.77
2745 2818 9.743057 CTTTAACACAAAGTTGGATCATTTACA 57.257 29.630 0.00 0.00 41.50 2.41
2746 2819 9.744468 ACTTTAACACAAAGTTGGATCATTTAC 57.256 29.630 0.00 0.00 41.50 2.01
2749 2822 9.965824 CTAACTTTAACACAAAGTTGGATCATT 57.034 29.630 20.03 0.32 45.59 2.57
2750 2823 9.131791 ACTAACTTTAACACAAAGTTGGATCAT 57.868 29.630 23.92 6.88 45.59 2.45
2751 2824 8.514330 ACTAACTTTAACACAAAGTTGGATCA 57.486 30.769 23.92 7.19 45.59 2.92
2752 2825 9.874215 GTACTAACTTTAACACAAAGTTGGATC 57.126 33.333 23.92 15.34 45.59 3.36
2753 2826 9.398538 TGTACTAACTTTAACACAAAGTTGGAT 57.601 29.630 23.92 14.55 45.59 3.41
2754 2827 8.789825 TGTACTAACTTTAACACAAAGTTGGA 57.210 30.769 23.92 10.82 45.59 3.53
2755 2828 9.843334 TTTGTACTAACTTTAACACAAAGTTGG 57.157 29.630 20.03 19.28 46.41 3.77
2762 2835 9.439500 ACTCAACTTTGTACTAACTTTAACACA 57.561 29.630 0.00 0.00 0.00 3.72
2763 2836 9.911980 GACTCAACTTTGTACTAACTTTAACAC 57.088 33.333 0.00 0.00 0.00 3.32
2764 2837 9.656040 TGACTCAACTTTGTACTAACTTTAACA 57.344 29.630 0.00 0.00 0.00 2.41
2774 2847 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
2775 2848 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
2776 2849 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
2777 2850 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
2778 2851 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
2779 2852 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
2780 2853 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
2781 2854 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
2782 2855 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
2783 2856 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
2784 2857 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
2785 2858 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
2786 2859 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
2787 2860 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
2788 2861 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
2789 2862 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
2790 2863 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
2791 2864 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
2792 2865 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
2793 2866 4.098894 AGTACTCCCTCCGTTCCAAAATA 58.901 43.478 0.00 0.00 0.00 1.40
2794 2867 2.910977 AGTACTCCCTCCGTTCCAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
2795 2868 2.332117 AGTACTCCCTCCGTTCCAAAA 58.668 47.619 0.00 0.00 0.00 2.44
2796 2869 2.019807 AGTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
2797 2870 1.621814 CAAGTACTCCCTCCGTTCCAA 59.378 52.381 0.00 0.00 0.00 3.53
2798 2871 1.203087 TCAAGTACTCCCTCCGTTCCA 60.203 52.381 0.00 0.00 0.00 3.53
2799 2872 1.553706 TCAAGTACTCCCTCCGTTCC 58.446 55.000 0.00 0.00 0.00 3.62
2800 2873 4.202131 CCTTATCAAGTACTCCCTCCGTTC 60.202 50.000 0.00 0.00 0.00 3.95
2801 2874 3.705072 CCTTATCAAGTACTCCCTCCGTT 59.295 47.826 0.00 0.00 0.00 4.44
2802 2875 3.297736 CCTTATCAAGTACTCCCTCCGT 58.702 50.000 0.00 0.00 0.00 4.69
2803 2876 2.628657 CCCTTATCAAGTACTCCCTCCG 59.371 54.545 0.00 0.00 0.00 4.63
2804 2877 3.924922 TCCCTTATCAAGTACTCCCTCC 58.075 50.000 0.00 0.00 0.00 4.30
2805 2878 5.952347 TTTCCCTTATCAAGTACTCCCTC 57.048 43.478 0.00 0.00 0.00 4.30
2806 2879 5.191921 CCTTTTCCCTTATCAAGTACTCCCT 59.808 44.000 0.00 0.00 0.00 4.20
2807 2880 5.437946 CCTTTTCCCTTATCAAGTACTCCC 58.562 45.833 0.00 0.00 0.00 4.30
2808 2881 5.191124 TCCCTTTTCCCTTATCAAGTACTCC 59.809 44.000 0.00 0.00 0.00 3.85
2809 2882 6.309389 TCCCTTTTCCCTTATCAAGTACTC 57.691 41.667 0.00 0.00 0.00 2.59
2810 2883 6.713731 TTCCCTTTTCCCTTATCAAGTACT 57.286 37.500 0.00 0.00 0.00 2.73
2811 2884 7.093902 CCTTTTCCCTTTTCCCTTATCAAGTAC 60.094 40.741 0.00 0.00 0.00 2.73
2812 2885 6.951778 CCTTTTCCCTTTTCCCTTATCAAGTA 59.048 38.462 0.00 0.00 0.00 2.24
2813 2886 5.780282 CCTTTTCCCTTTTCCCTTATCAAGT 59.220 40.000 0.00 0.00 0.00 3.16
2814 2887 6.016555 TCCTTTTCCCTTTTCCCTTATCAAG 58.983 40.000 0.00 0.00 0.00 3.02
2815 2888 5.971493 TCCTTTTCCCTTTTCCCTTATCAA 58.029 37.500 0.00 0.00 0.00 2.57
2816 2889 5.608798 TCCTTTTCCCTTTTCCCTTATCA 57.391 39.130 0.00 0.00 0.00 2.15
2817 2890 9.521841 CTATATCCTTTTCCCTTTTCCCTTATC 57.478 37.037 0.00 0.00 0.00 1.75
2818 2891 9.026170 ACTATATCCTTTTCCCTTTTCCCTTAT 57.974 33.333 0.00 0.00 0.00 1.73
2819 2892 8.415392 ACTATATCCTTTTCCCTTTTCCCTTA 57.585 34.615 0.00 0.00 0.00 2.69
2820 2893 7.298678 ACTATATCCTTTTCCCTTTTCCCTT 57.701 36.000 0.00 0.00 0.00 3.95
2821 2894 6.927691 ACTATATCCTTTTCCCTTTTCCCT 57.072 37.500 0.00 0.00 0.00 4.20
2822 2895 7.123383 TCAACTATATCCTTTTCCCTTTTCCC 58.877 38.462 0.00 0.00 0.00 3.97
2823 2896 7.834681 ACTCAACTATATCCTTTTCCCTTTTCC 59.165 37.037 0.00 0.00 0.00 3.13
2824 2897 8.809468 ACTCAACTATATCCTTTTCCCTTTTC 57.191 34.615 0.00 0.00 0.00 2.29
2825 2898 8.390921 TGACTCAACTATATCCTTTTCCCTTTT 58.609 33.333 0.00 0.00 0.00 2.27
2826 2899 7.928873 TGACTCAACTATATCCTTTTCCCTTT 58.071 34.615 0.00 0.00 0.00 3.11
2827 2900 7.510675 TGACTCAACTATATCCTTTTCCCTT 57.489 36.000 0.00 0.00 0.00 3.95
2828 2901 7.570607 AGATGACTCAACTATATCCTTTTCCCT 59.429 37.037 0.00 0.00 0.00 4.20
2829 2902 7.740805 AGATGACTCAACTATATCCTTTTCCC 58.259 38.462 0.00 0.00 0.00 3.97
2841 2914 9.958180 TCCATTTCAAAATAGATGACTCAACTA 57.042 29.630 0.00 0.00 0.00 2.24
2842 2915 8.868522 TCCATTTCAAAATAGATGACTCAACT 57.131 30.769 0.00 0.00 0.00 3.16
2843 2916 8.186821 CCTCCATTTCAAAATAGATGACTCAAC 58.813 37.037 0.00 0.00 0.00 3.18
2844 2917 7.340232 CCCTCCATTTCAAAATAGATGACTCAA 59.660 37.037 0.00 0.00 0.00 3.02
2845 2918 6.830324 CCCTCCATTTCAAAATAGATGACTCA 59.170 38.462 0.00 0.00 0.00 3.41
2846 2919 7.056635 TCCCTCCATTTCAAAATAGATGACTC 58.943 38.462 0.00 0.00 0.00 3.36
2847 2920 6.973642 TCCCTCCATTTCAAAATAGATGACT 58.026 36.000 0.00 0.00 0.00 3.41
2848 2921 6.830838 ACTCCCTCCATTTCAAAATAGATGAC 59.169 38.462 0.00 0.00 0.00 3.06
2849 2922 6.973642 ACTCCCTCCATTTCAAAATAGATGA 58.026 36.000 0.00 0.00 0.00 2.92
2850 2923 7.995488 AGTACTCCCTCCATTTCAAAATAGATG 59.005 37.037 0.00 0.00 0.00 2.90
2851 2924 8.107196 AGTACTCCCTCCATTTCAAAATAGAT 57.893 34.615 0.00 0.00 0.00 1.98
2852 2925 7.510675 AGTACTCCCTCCATTTCAAAATAGA 57.489 36.000 0.00 0.00 0.00 1.98
2853 2926 7.829211 TCAAGTACTCCCTCCATTTCAAAATAG 59.171 37.037 0.00 0.00 0.00 1.73
2854 2927 7.695055 TCAAGTACTCCCTCCATTTCAAAATA 58.305 34.615 0.00 0.00 0.00 1.40
2855 2928 6.552008 TCAAGTACTCCCTCCATTTCAAAAT 58.448 36.000 0.00 0.00 0.00 1.82
2856 2929 5.947663 TCAAGTACTCCCTCCATTTCAAAA 58.052 37.500 0.00 0.00 0.00 2.44
2857 2930 5.576563 TCAAGTACTCCCTCCATTTCAAA 57.423 39.130 0.00 0.00 0.00 2.69
2858 2931 5.779241 ATCAAGTACTCCCTCCATTTCAA 57.221 39.130 0.00 0.00 0.00 2.69
2859 2932 6.126768 CCTTATCAAGTACTCCCTCCATTTCA 60.127 42.308 0.00 0.00 0.00 2.69
2860 2933 6.292150 CCTTATCAAGTACTCCCTCCATTTC 58.708 44.000 0.00 0.00 0.00 2.17
2861 2934 5.132816 CCCTTATCAAGTACTCCCTCCATTT 59.867 44.000 0.00 0.00 0.00 2.32
2862 2935 4.660771 CCCTTATCAAGTACTCCCTCCATT 59.339 45.833 0.00 0.00 0.00 3.16
2863 2936 4.077982 TCCCTTATCAAGTACTCCCTCCAT 60.078 45.833 0.00 0.00 0.00 3.41
2864 2937 3.273886 TCCCTTATCAAGTACTCCCTCCA 59.726 47.826 0.00 0.00 0.00 3.86
2865 2938 3.924922 TCCCTTATCAAGTACTCCCTCC 58.075 50.000 0.00 0.00 0.00 4.30
2866 2939 5.952347 TTTCCCTTATCAAGTACTCCCTC 57.048 43.478 0.00 0.00 0.00 4.30
2867 2940 5.191921 CCTTTTCCCTTATCAAGTACTCCCT 59.808 44.000 0.00 0.00 0.00 4.20
2868 2941 5.191124 TCCTTTTCCCTTATCAAGTACTCCC 59.809 44.000 0.00 0.00 0.00 4.30
2869 2942 6.309389 TCCTTTTCCCTTATCAAGTACTCC 57.691 41.667 0.00 0.00 0.00 3.85
2990 3074 4.202010 GCCAAACTGTAGATTGTGTTGTGT 60.202 41.667 1.99 0.00 0.00 3.72
2999 3087 7.985184 TCGTTATTGATAGCCAAACTGTAGATT 59.015 33.333 0.00 0.00 38.43 2.40
3031 3119 2.170397 AGCCCACATGTGATTGTCGATA 59.830 45.455 27.46 0.00 0.00 2.92
3032 3120 1.065199 AGCCCACATGTGATTGTCGAT 60.065 47.619 27.46 2.97 0.00 3.59
3033 3121 0.324614 AGCCCACATGTGATTGTCGA 59.675 50.000 27.46 0.00 0.00 4.20
3034 3122 1.167851 AAGCCCACATGTGATTGTCG 58.832 50.000 27.46 8.91 0.00 4.35
3035 3123 2.821969 AGAAAGCCCACATGTGATTGTC 59.178 45.455 27.46 15.10 0.00 3.18
3037 3125 3.947910 AAGAAAGCCCACATGTGATTG 57.052 42.857 27.46 15.30 0.00 2.67
3038 3126 3.896888 TCAAAGAAAGCCCACATGTGATT 59.103 39.130 27.46 15.07 0.00 2.57
3051 3139 5.048434 GGGAGTTCAGTGGAATCAAAGAAAG 60.048 44.000 0.55 0.00 35.05 2.62
3063 3151 0.179020 TGCAAGTGGGAGTTCAGTGG 60.179 55.000 0.00 0.00 0.00 4.00
3077 3165 0.110056 ACTCGCAGCGAATTTGCAAG 60.110 50.000 20.04 12.34 41.59 4.01
3080 3168 0.442310 TACACTCGCAGCGAATTTGC 59.558 50.000 20.04 9.87 34.74 3.68
3099 3187 5.929058 TCATGCTGTTTCTCTATGAGTCT 57.071 39.130 0.00 0.00 0.00 3.24
3107 3195 4.679373 ATCGGTATCATGCTGTTTCTCT 57.321 40.909 0.00 0.00 0.00 3.10
3131 3219 6.195244 CGAGGCATGTTGAAATCTTTAATTCG 59.805 38.462 0.00 0.00 0.00 3.34
3150 3238 0.749818 TGGTTCTTGTTTGCGAGGCA 60.750 50.000 0.00 0.00 36.47 4.75
3153 3241 1.879380 TGGATGGTTCTTGTTTGCGAG 59.121 47.619 0.00 0.00 0.00 5.03
3178 3266 3.425359 CGTCCTTTTGATCAGCACATGTC 60.425 47.826 0.00 0.00 0.00 3.06
3214 3303 9.010029 ACAAACGGACATTCTACTTGATATTTT 57.990 29.630 0.00 0.00 0.00 1.82
3254 3343 3.706373 CCCACTGCCGGTGCTAGT 61.706 66.667 1.90 0.00 44.08 2.57
3278 3367 6.723298 TTTCCTGGATTCTGCAAAGTTAAA 57.277 33.333 0.00 0.00 0.00 1.52
3329 3420 2.229784 CAGTTCTTTTGGGTGCATCTCC 59.770 50.000 0.00 0.00 0.00 3.71
3399 3490 0.813184 CTACCTGGCATGCAACCTTG 59.187 55.000 21.36 3.74 0.00 3.61


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

AutoCloner maintained by Alex Coulton.