Multiple sequence alignment - TraesCS1B01G023600

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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 TraesCS1B01G023600 chr1B 100.000 3613 0 0 1 3613 10976079 10972467 0.000000e+00 6673
1 TraesCS1B01G023600 chr1B 91.259 1716 109 20 959 2665 10549875 10551558 0.000000e+00 2300
2 TraesCS1B01G023600 chr1B 89.610 1511 113 14 1095 2601 29514384 29512914 0.000000e+00 1881
3 TraesCS1B01G023600 chr1B 88.855 978 91 10 977 1942 29393664 29394635 0.000000e+00 1186
4 TraesCS1B01G023600 chr1B 89.790 666 53 7 1286 1942 29423891 29424550 0.000000e+00 839
5 TraesCS1B01G023600 chr1B 83.867 750 95 12 1748 2476 11132387 11131643 0.000000e+00 691
6 TraesCS1B01G023600 chr1B 85.185 675 69 16 1931 2601 29395101 29395748 0.000000e+00 664
7 TraesCS1B01G023600 chr1B 84.741 675 72 16 1931 2601 29424992 29425639 0.000000e+00 647
8 TraesCS1B01G023600 chr1B 91.696 289 23 1 2600 2887 29512222 29511934 2.020000e-107 399
9 TraesCS1B01G023600 chr1B 85.942 377 46 4 139 513 10548711 10549082 2.610000e-106 396
10 TraesCS1B01G023600 chr1B 77.438 523 93 18 1003 1514 29290731 29291239 4.560000e-74 289
11 TraesCS1B01G023600 chr1B 92.941 170 12 0 795 964 10549678 10549847 7.750000e-62 248
12 TraesCS1B01G023600 chr1B 91.558 154 12 1 2647 2799 10553016 10553169 1.020000e-50 211
13 TraesCS1B01G023600 chr1B 98.765 81 1 0 2719 2799 29395845 29395925 1.050000e-30 145
14 TraesCS1B01G023600 chr1B 98.765 81 1 0 2719 2799 29425736 29425816 1.050000e-30 145
15 TraesCS1B01G023600 chr1B 91.837 98 8 0 2798 2895 10553274 10553371 1.750000e-28 137
16 TraesCS1B01G023600 chr1B 83.333 156 9 4 826 964 29368419 29368574 1.050000e-25 128
17 TraesCS1B01G023600 chr1B 87.379 103 9 1 2798 2896 29396030 29396132 8.200000e-22 115
18 TraesCS1B01G023600 chr1A 90.931 1665 111 20 967 2601 9788750 9787096 0.000000e+00 2202
19 TraesCS1B01G023600 chr1A 80.787 1499 236 40 1003 2475 9772107 9773579 0.000000e+00 1125
20 TraesCS1B01G023600 chr1A 88.972 399 31 8 530 915 9790084 9789686 7.020000e-132 481
21 TraesCS1B01G023600 chr1A 91.228 228 16 2 306 529 9791404 9791177 1.260000e-79 307
22 TraesCS1B01G023600 chr1D 90.839 1037 74 11 1573 2601 8280882 8279859 0.000000e+00 1369
23 TraesCS1B01G023600 chr1D 80.504 1508 229 42 996 2475 8269621 8271091 0.000000e+00 1096
24 TraesCS1B01G023600 chr1D 93.880 719 42 2 2896 3612 5358919 5359637 0.000000e+00 1083
25 TraesCS1B01G023600 chr1D 89.878 820 62 13 159 959 8282764 8281947 0.000000e+00 1035
26 TraesCS1B01G023600 chr1D 89.779 587 56 4 964 1550 8281892 8281310 0.000000e+00 749
27 TraesCS1B01G023600 chr6B 94.150 718 41 1 2897 3613 695752783 695753500 0.000000e+00 1092
28 TraesCS1B01G023600 chr6B 97.315 149 4 0 1 149 653877215 653877067 1.670000e-63 254
29 TraesCS1B01G023600 chr6B 97.315 149 3 1 1 149 701666200 701666053 5.990000e-63 252
30 TraesCS1B01G023600 chr5D 94.036 721 39 2 2897 3613 556573082 556573802 0.000000e+00 1090
31 TraesCS1B01G023600 chr5D 93.646 724 42 3 2894 3613 563630763 563630040 0.000000e+00 1079
32 TraesCS1B01G023600 chrUn 93.750 720 42 3 2896 3613 90383127 90383845 0.000000e+00 1077
33 TraesCS1B01G023600 chr2D 93.646 724 40 3 2896 3613 625333365 625334088 0.000000e+00 1077
34 TraesCS1B01G023600 chr7B 93.602 719 44 2 2897 3613 454832814 454833532 0.000000e+00 1072
35 TraesCS1B01G023600 chr3B 93.602 719 44 2 2897 3613 402076841 402076123 0.000000e+00 1072
36 TraesCS1B01G023600 chr3B 97.315 149 3 1 1 149 50934103 50933956 5.990000e-63 252
37 TraesCS1B01G023600 chr2B 93.288 730 44 4 2888 3613 5843185 5842457 0.000000e+00 1072
38 TraesCS1B01G023600 chr2B 97.315 149 4 0 1 149 26448940 26449088 1.670000e-63 254
39 TraesCS1B01G023600 chr2B 97.315 149 4 0 1 149 147589142 147589290 1.670000e-63 254
40 TraesCS1B01G023600 chr2A 83.848 551 51 18 1618 2138 766643042 766642500 1.170000e-134 490
41 TraesCS1B01G023600 chr2A 81.277 470 76 4 1007 1476 766643556 766643099 1.580000e-98 370
42 TraesCS1B01G023600 chr5B 96.154 156 5 1 1 155 101252891 101253046 1.670000e-63 254
43 TraesCS1B01G023600 chr5B 97.315 149 3 1 1 149 457402580 457402727 5.990000e-63 252
44 TraesCS1B01G023600 chr4B 97.315 149 4 0 1 149 533505084 533505232 1.670000e-63 254
45 TraesCS1B01G023600 chr4D 95.484 155 7 0 1 155 322665753 322665599 7.750000e-62 248


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 TraesCS1B01G023600 chr1B 10972467 10976079 3612 True 6673.000000 6673 100.000000 1 3613 1 chr1B.!!$R1 3612
1 TraesCS1B01G023600 chr1B 29511934 29514384 2450 True 1140.000000 1881 90.653000 1095 2887 2 chr1B.!!$R3 1792
2 TraesCS1B01G023600 chr1B 11131643 11132387 744 True 691.000000 691 83.867000 1748 2476 1 chr1B.!!$R2 728
3 TraesCS1B01G023600 chr1B 10548711 10553371 4660 False 658.400000 2300 90.707400 139 2895 5 chr1B.!!$F3 2756
4 TraesCS1B01G023600 chr1B 29423891 29425816 1925 False 543.666667 839 91.098667 1286 2799 3 chr1B.!!$F5 1513
5 TraesCS1B01G023600 chr1B 29393664 29396132 2468 False 527.500000 1186 90.046000 977 2896 4 chr1B.!!$F4 1919
6 TraesCS1B01G023600 chr1B 29290731 29291239 508 False 289.000000 289 77.438000 1003 1514 1 chr1B.!!$F1 511
7 TraesCS1B01G023600 chr1A 9772107 9773579 1472 False 1125.000000 1125 80.787000 1003 2475 1 chr1A.!!$F1 1472
8 TraesCS1B01G023600 chr1A 9787096 9791404 4308 True 996.666667 2202 90.377000 306 2601 3 chr1A.!!$R1 2295
9 TraesCS1B01G023600 chr1D 8269621 8271091 1470 False 1096.000000 1096 80.504000 996 2475 1 chr1D.!!$F2 1479
10 TraesCS1B01G023600 chr1D 5358919 5359637 718 False 1083.000000 1083 93.880000 2896 3612 1 chr1D.!!$F1 716
11 TraesCS1B01G023600 chr1D 8279859 8282764 2905 True 1051.000000 1369 90.165333 159 2601 3 chr1D.!!$R1 2442
12 TraesCS1B01G023600 chr6B 695752783 695753500 717 False 1092.000000 1092 94.150000 2897 3613 1 chr6B.!!$F1 716
13 TraesCS1B01G023600 chr5D 556573082 556573802 720 False 1090.000000 1090 94.036000 2897 3613 1 chr5D.!!$F1 716
14 TraesCS1B01G023600 chr5D 563630040 563630763 723 True 1079.000000 1079 93.646000 2894 3613 1 chr5D.!!$R1 719
15 TraesCS1B01G023600 chrUn 90383127 90383845 718 False 1077.000000 1077 93.750000 2896 3613 1 chrUn.!!$F1 717
16 TraesCS1B01G023600 chr2D 625333365 625334088 723 False 1077.000000 1077 93.646000 2896 3613 1 chr2D.!!$F1 717
17 TraesCS1B01G023600 chr7B 454832814 454833532 718 False 1072.000000 1072 93.602000 2897 3613 1 chr7B.!!$F1 716
18 TraesCS1B01G023600 chr3B 402076123 402076841 718 True 1072.000000 1072 93.602000 2897 3613 1 chr3B.!!$R2 716
19 TraesCS1B01G023600 chr2B 5842457 5843185 728 True 1072.000000 1072 93.288000 2888 3613 1 chr2B.!!$R1 725
20 TraesCS1B01G023600 chr2A 766642500 766643556 1056 True 430.000000 490 82.562500 1007 2138 2 chr2A.!!$R1 1131

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
129 130 0.187606 GGGTTTGAGGGTTTGAGGGT 59.812 55.000 0.0 0.0 0.00 4.34 F
563 1663 1.123077 ACTCAGTGTGGCAAGACTCA 58.877 50.000 0.0 0.0 0.00 3.41 F
2510 5876 1.227823 CAGCCGTGGTGGTCTTCAA 60.228 57.895 0.0 0.0 41.21 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1242 3617 1.745890 CATATGGTTCGGCGGAGGA 59.254 57.895 7.21 0.0 0.0 3.71 R
2549 5915 0.737367 GCAGCTGAGCATGTGTCGTA 60.737 55.000 20.43 0.0 0.0 3.43 R
3525 9188 6.493458 TGATTGGTTCGATGACTATGAGGATA 59.507 38.462 0.00 0.0 0.0 2.59 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
22 23 4.981794 CCCTTAAAGCAGTTTACGGATTG 58.018 43.478 3.37 0.00 39.05 2.67
23 24 4.142469 CCCTTAAAGCAGTTTACGGATTGG 60.142 45.833 3.37 0.00 39.05 3.16
24 25 4.142469 CCTTAAAGCAGTTTACGGATTGGG 60.142 45.833 0.00 0.00 39.05 4.12
25 26 2.579410 AAGCAGTTTACGGATTGGGT 57.421 45.000 0.00 0.00 0.00 4.51
26 27 2.579410 AGCAGTTTACGGATTGGGTT 57.421 45.000 0.00 0.00 0.00 4.11
27 28 2.871453 AGCAGTTTACGGATTGGGTTT 58.129 42.857 0.00 0.00 0.00 3.27
28 29 2.556622 AGCAGTTTACGGATTGGGTTTG 59.443 45.455 0.00 0.00 0.00 2.93
29 30 2.554893 GCAGTTTACGGATTGGGTTTGA 59.445 45.455 0.00 0.00 0.00 2.69
30 31 3.365969 GCAGTTTACGGATTGGGTTTGAG 60.366 47.826 0.00 0.00 0.00 3.02
31 32 3.190535 CAGTTTACGGATTGGGTTTGAGG 59.809 47.826 0.00 0.00 0.00 3.86
32 33 2.490509 GTTTACGGATTGGGTTTGAGGG 59.509 50.000 0.00 0.00 0.00 4.30
33 34 1.364269 TACGGATTGGGTTTGAGGGT 58.636 50.000 0.00 0.00 0.00 4.34
34 35 0.481128 ACGGATTGGGTTTGAGGGTT 59.519 50.000 0.00 0.00 0.00 4.11
35 36 1.173913 CGGATTGGGTTTGAGGGTTC 58.826 55.000 0.00 0.00 0.00 3.62
36 37 1.271926 CGGATTGGGTTTGAGGGTTCT 60.272 52.381 0.00 0.00 0.00 3.01
37 38 2.026636 CGGATTGGGTTTGAGGGTTCTA 60.027 50.000 0.00 0.00 0.00 2.10
38 39 3.621558 GGATTGGGTTTGAGGGTTCTAG 58.378 50.000 0.00 0.00 0.00 2.43
39 40 3.010250 GGATTGGGTTTGAGGGTTCTAGT 59.990 47.826 0.00 0.00 0.00 2.57
40 41 3.782656 TTGGGTTTGAGGGTTCTAGTC 57.217 47.619 0.00 0.00 0.00 2.59
41 42 2.986050 TGGGTTTGAGGGTTCTAGTCT 58.014 47.619 0.00 0.00 0.00 3.24
42 43 3.323775 TGGGTTTGAGGGTTCTAGTCTT 58.676 45.455 0.00 0.00 0.00 3.01
43 44 3.720002 TGGGTTTGAGGGTTCTAGTCTTT 59.280 43.478 0.00 0.00 0.00 2.52
44 45 4.072839 GGGTTTGAGGGTTCTAGTCTTTG 58.927 47.826 0.00 0.00 0.00 2.77
45 46 4.202430 GGGTTTGAGGGTTCTAGTCTTTGA 60.202 45.833 0.00 0.00 0.00 2.69
46 47 4.755629 GGTTTGAGGGTTCTAGTCTTTGAC 59.244 45.833 0.00 0.00 0.00 3.18
47 48 4.618920 TTGAGGGTTCTAGTCTTTGACC 57.381 45.455 0.00 0.00 32.18 4.02
48 49 2.904434 TGAGGGTTCTAGTCTTTGACCC 59.096 50.000 1.63 1.63 32.18 4.46
49 50 3.277416 AGGGTTCTAGTCTTTGACCCT 57.723 47.619 6.56 6.56 41.09 4.34
50 51 2.907042 AGGGTTCTAGTCTTTGACCCTG 59.093 50.000 11.37 0.00 43.91 4.45
51 52 2.638363 GGGTTCTAGTCTTTGACCCTGT 59.362 50.000 2.68 0.00 32.18 4.00
52 53 3.072622 GGGTTCTAGTCTTTGACCCTGTT 59.927 47.826 2.68 0.00 32.18 3.16
53 54 4.445879 GGGTTCTAGTCTTTGACCCTGTTT 60.446 45.833 2.68 0.00 32.18 2.83
54 55 5.131067 GGTTCTAGTCTTTGACCCTGTTTT 58.869 41.667 0.00 0.00 32.18 2.43
55 56 5.593095 GGTTCTAGTCTTTGACCCTGTTTTT 59.407 40.000 0.00 0.00 32.18 1.94
56 57 6.238676 GGTTCTAGTCTTTGACCCTGTTTTTC 60.239 42.308 0.00 0.00 32.18 2.29
57 58 5.996644 TCTAGTCTTTGACCCTGTTTTTCA 58.003 37.500 0.00 0.00 32.18 2.69
58 59 6.419791 TCTAGTCTTTGACCCTGTTTTTCAA 58.580 36.000 0.00 0.00 32.18 2.69
59 60 5.324784 AGTCTTTGACCCTGTTTTTCAAC 57.675 39.130 0.00 0.00 32.18 3.18
60 61 4.159693 AGTCTTTGACCCTGTTTTTCAACC 59.840 41.667 0.00 0.00 32.18 3.77
61 62 3.449377 TCTTTGACCCTGTTTTTCAACCC 59.551 43.478 0.00 0.00 31.02 4.11
62 63 2.838637 TGACCCTGTTTTTCAACCCT 57.161 45.000 0.00 0.00 31.02 4.34
63 64 3.108847 TGACCCTGTTTTTCAACCCTT 57.891 42.857 0.00 0.00 31.02 3.95
64 65 4.252570 TGACCCTGTTTTTCAACCCTTA 57.747 40.909 0.00 0.00 31.02 2.69
65 66 4.611367 TGACCCTGTTTTTCAACCCTTAA 58.389 39.130 0.00 0.00 31.02 1.85
66 67 5.024118 TGACCCTGTTTTTCAACCCTTAAA 58.976 37.500 0.00 0.00 31.02 1.52
67 68 5.484290 TGACCCTGTTTTTCAACCCTTAAAA 59.516 36.000 0.00 0.00 31.02 1.52
68 69 5.984725 ACCCTGTTTTTCAACCCTTAAAAG 58.015 37.500 0.00 0.00 31.02 2.27
69 70 5.486063 ACCCTGTTTTTCAACCCTTAAAAGT 59.514 36.000 0.00 0.00 31.02 2.66
70 71 5.815222 CCCTGTTTTTCAACCCTTAAAAGTG 59.185 40.000 0.00 0.00 31.02 3.16
71 72 6.403049 CCTGTTTTTCAACCCTTAAAAGTGT 58.597 36.000 0.00 0.00 31.02 3.55
72 73 6.533723 CCTGTTTTTCAACCCTTAAAAGTGTC 59.466 38.462 0.00 0.00 31.02 3.67
73 74 6.994221 TGTTTTTCAACCCTTAAAAGTGTCA 58.006 32.000 0.00 0.00 31.02 3.58
74 75 7.442656 TGTTTTTCAACCCTTAAAAGTGTCAA 58.557 30.769 0.00 0.00 31.02 3.18
75 76 7.931948 TGTTTTTCAACCCTTAAAAGTGTCAAA 59.068 29.630 0.00 0.00 31.02 2.69
76 77 8.775527 GTTTTTCAACCCTTAAAAGTGTCAAAA 58.224 29.630 0.00 0.00 0.00 2.44
77 78 8.904099 TTTTCAACCCTTAAAAGTGTCAAAAA 57.096 26.923 0.00 0.00 0.00 1.94
78 79 7.892778 TTCAACCCTTAAAAGTGTCAAAAAC 57.107 32.000 0.00 0.00 0.00 2.43
79 80 7.234661 TCAACCCTTAAAAGTGTCAAAAACT 57.765 32.000 0.00 0.00 0.00 2.66
80 81 7.093992 TCAACCCTTAAAAGTGTCAAAAACTG 58.906 34.615 0.00 0.00 0.00 3.16
81 82 5.972935 ACCCTTAAAAGTGTCAAAAACTGG 58.027 37.500 0.00 0.00 0.00 4.00
82 83 4.808895 CCCTTAAAAGTGTCAAAAACTGGC 59.191 41.667 0.00 0.00 0.00 4.85
83 84 5.415221 CCTTAAAAGTGTCAAAAACTGGCA 58.585 37.500 0.00 0.00 37.29 4.92
84 85 6.048509 CCTTAAAAGTGTCAAAAACTGGCAT 58.951 36.000 0.00 0.00 42.94 4.40
85 86 6.538381 CCTTAAAAGTGTCAAAAACTGGCATT 59.462 34.615 0.00 0.00 42.94 3.56
86 87 7.065683 CCTTAAAAGTGTCAAAAACTGGCATTT 59.934 33.333 0.00 0.00 42.94 2.32
87 88 6.421377 AAAAGTGTCAAAAACTGGCATTTC 57.579 33.333 0.00 0.00 42.94 2.17
88 89 5.343307 AAGTGTCAAAAACTGGCATTTCT 57.657 34.783 0.00 0.00 42.94 2.52
89 90 4.936891 AGTGTCAAAAACTGGCATTTCTC 58.063 39.130 0.00 0.00 42.94 2.87
90 91 4.402155 AGTGTCAAAAACTGGCATTTCTCA 59.598 37.500 0.00 0.00 42.94 3.27
91 92 5.105392 AGTGTCAAAAACTGGCATTTCTCAA 60.105 36.000 0.00 0.00 42.94 3.02
92 93 5.005682 GTGTCAAAAACTGGCATTTCTCAAC 59.994 40.000 0.00 0.00 42.94 3.18
93 94 4.507756 GTCAAAAACTGGCATTTCTCAACC 59.492 41.667 0.00 0.00 0.00 3.77
94 95 3.751479 AAAACTGGCATTTCTCAACCC 57.249 42.857 0.00 0.00 0.00 4.11
95 96 2.683211 AACTGGCATTTCTCAACCCT 57.317 45.000 0.00 0.00 0.00 4.34
96 97 2.683211 ACTGGCATTTCTCAACCCTT 57.317 45.000 0.00 0.00 0.00 3.95
97 98 3.806949 ACTGGCATTTCTCAACCCTTA 57.193 42.857 0.00 0.00 0.00 2.69
98 99 4.112634 ACTGGCATTTCTCAACCCTTAA 57.887 40.909 0.00 0.00 0.00 1.85
99 100 4.479158 ACTGGCATTTCTCAACCCTTAAA 58.521 39.130 0.00 0.00 0.00 1.52
100 101 4.898861 ACTGGCATTTCTCAACCCTTAAAA 59.101 37.500 0.00 0.00 0.00 1.52
101 102 5.208463 TGGCATTTCTCAACCCTTAAAAC 57.792 39.130 0.00 0.00 0.00 2.43
102 103 4.898861 TGGCATTTCTCAACCCTTAAAACT 59.101 37.500 0.00 0.00 0.00 2.66
103 104 5.221422 TGGCATTTCTCAACCCTTAAAACTG 60.221 40.000 0.00 0.00 0.00 3.16
104 105 4.686091 GCATTTCTCAACCCTTAAAACTGC 59.314 41.667 0.00 0.00 0.00 4.40
105 106 5.509670 GCATTTCTCAACCCTTAAAACTGCT 60.510 40.000 0.00 0.00 0.00 4.24
106 107 6.294508 GCATTTCTCAACCCTTAAAACTGCTA 60.295 38.462 0.00 0.00 0.00 3.49
107 108 7.577616 GCATTTCTCAACCCTTAAAACTGCTAT 60.578 37.037 0.00 0.00 0.00 2.97
108 109 8.956426 CATTTCTCAACCCTTAAAACTGCTATA 58.044 33.333 0.00 0.00 0.00 1.31
109 110 8.927675 TTTCTCAACCCTTAAAACTGCTATAA 57.072 30.769 0.00 0.00 0.00 0.98
110 111 8.561738 TTCTCAACCCTTAAAACTGCTATAAG 57.438 34.615 0.00 0.00 0.00 1.73
111 112 7.110155 TCTCAACCCTTAAAACTGCTATAAGG 58.890 38.462 4.23 4.23 43.43 2.69
117 118 7.696992 CCTTAAAACTGCTATAAGGGTTTGA 57.303 36.000 3.42 0.00 41.21 2.69
118 119 7.762382 CCTTAAAACTGCTATAAGGGTTTGAG 58.238 38.462 3.42 0.00 41.21 3.02
119 120 7.148069 CCTTAAAACTGCTATAAGGGTTTGAGG 60.148 40.741 3.42 0.00 41.21 3.86
120 121 3.933861 ACTGCTATAAGGGTTTGAGGG 57.066 47.619 0.00 0.00 0.00 4.30
121 122 3.190439 ACTGCTATAAGGGTTTGAGGGT 58.810 45.455 0.00 0.00 0.00 4.34
122 123 3.591977 ACTGCTATAAGGGTTTGAGGGTT 59.408 43.478 0.00 0.00 0.00 4.11
123 124 4.044191 ACTGCTATAAGGGTTTGAGGGTTT 59.956 41.667 0.00 0.00 0.00 3.27
124 125 4.340617 TGCTATAAGGGTTTGAGGGTTTG 58.659 43.478 0.00 0.00 0.00 2.93
125 126 4.043561 TGCTATAAGGGTTTGAGGGTTTGA 59.956 41.667 0.00 0.00 0.00 2.69
126 127 4.640647 GCTATAAGGGTTTGAGGGTTTGAG 59.359 45.833 0.00 0.00 0.00 3.02
127 128 2.381752 AAGGGTTTGAGGGTTTGAGG 57.618 50.000 0.00 0.00 0.00 3.86
128 129 0.482887 AGGGTTTGAGGGTTTGAGGG 59.517 55.000 0.00 0.00 0.00 4.30
129 130 0.187606 GGGTTTGAGGGTTTGAGGGT 59.812 55.000 0.00 0.00 0.00 4.34
130 131 1.412505 GGGTTTGAGGGTTTGAGGGTT 60.413 52.381 0.00 0.00 0.00 4.11
131 132 1.961394 GGTTTGAGGGTTTGAGGGTTC 59.039 52.381 0.00 0.00 0.00 3.62
132 133 2.424379 GGTTTGAGGGTTTGAGGGTTCT 60.424 50.000 0.00 0.00 0.00 3.01
133 134 3.181437 GGTTTGAGGGTTTGAGGGTTCTA 60.181 47.826 0.00 0.00 0.00 2.10
134 135 3.782656 TTGAGGGTTTGAGGGTTCTAC 57.217 47.619 0.00 0.00 0.00 2.59
135 136 2.986050 TGAGGGTTTGAGGGTTCTACT 58.014 47.619 0.00 0.00 0.00 2.57
136 137 4.136341 TGAGGGTTTGAGGGTTCTACTA 57.864 45.455 0.00 0.00 0.00 1.82
137 138 4.094476 TGAGGGTTTGAGGGTTCTACTAG 58.906 47.826 0.00 0.00 0.00 2.57
138 139 4.095211 GAGGGTTTGAGGGTTCTACTAGT 58.905 47.826 0.00 0.00 0.00 2.57
139 140 5.222400 TGAGGGTTTGAGGGTTCTACTAGTA 60.222 44.000 1.89 1.89 0.00 1.82
140 141 5.658474 AGGGTTTGAGGGTTCTACTAGTAA 58.342 41.667 3.76 0.00 0.00 2.24
141 142 6.269974 AGGGTTTGAGGGTTCTACTAGTAAT 58.730 40.000 3.76 0.00 0.00 1.89
142 143 6.156429 AGGGTTTGAGGGTTCTACTAGTAATG 59.844 42.308 3.76 0.00 0.00 1.90
143 144 5.816258 GGTTTGAGGGTTCTACTAGTAATGC 59.184 44.000 3.76 0.00 0.00 3.56
144 145 6.351966 GGTTTGAGGGTTCTACTAGTAATGCT 60.352 42.308 3.76 0.00 0.00 3.79
145 146 6.466885 TTGAGGGTTCTACTAGTAATGCTC 57.533 41.667 3.76 0.00 0.00 4.26
154 155 9.575783 GTTCTACTAGTAATGCTCTTATATGGC 57.424 37.037 3.76 0.00 0.00 4.40
182 183 5.529581 AAGGTTGTGGTAAAAATGTGAGG 57.470 39.130 0.00 0.00 0.00 3.86
214 216 9.767684 TCGCAAAAATTGTAACATAATCTACTG 57.232 29.630 0.00 0.00 0.00 2.74
250 252 1.948145 TCGTAGGAAGAATCGAGAGGC 59.052 52.381 0.00 0.00 0.00 4.70
275 277 4.204012 TGGGTCAAGTTTGAAGACGAAAT 58.796 39.130 0.00 0.00 39.21 2.17
363 367 5.063312 CCATGTAAACATTCGGCATTTTTCC 59.937 40.000 0.00 0.00 33.61 3.13
532 1632 6.554334 TTTGTTCTTATCAAGGAAACGGAG 57.446 37.500 0.00 0.00 0.00 4.63
554 1654 3.490348 AGGAATTCCAAACTCAGTGTGG 58.510 45.455 26.22 7.87 42.04 4.17
563 1663 1.123077 ACTCAGTGTGGCAAGACTCA 58.877 50.000 0.00 0.00 0.00 3.41
564 1664 1.696336 ACTCAGTGTGGCAAGACTCAT 59.304 47.619 0.00 0.00 0.00 2.90
651 1752 5.179368 TCCTCGAACTATTCAAAGTGCAAAG 59.821 40.000 0.00 0.00 0.00 2.77
658 1759 2.849880 TCAAAGTGCAAAGAGTGTGC 57.150 45.000 0.00 0.00 42.55 4.57
662 1763 1.696063 AGTGCAAAGAGTGTGCCATT 58.304 45.000 0.00 0.00 41.49 3.16
714 1816 8.682936 AGTAATCCAAGACTATATTTTGCCTG 57.317 34.615 0.00 0.00 0.00 4.85
717 1819 5.192927 TCCAAGACTATATTTTGCCTGGTG 58.807 41.667 0.00 0.00 0.00 4.17
744 1846 5.154932 CACACTTACTCTACTTGGAGAACG 58.845 45.833 0.00 0.00 37.13 3.95
789 2226 6.573664 TGACAACCATCCTTGAAATAGTTG 57.426 37.500 0.00 0.00 39.14 3.16
809 2257 5.308237 AGTTGAAGGACCTCACTCTTTACAT 59.692 40.000 0.00 0.00 0.00 2.29
893 2341 1.355971 CAAGCTTGACATGGCATTGC 58.644 50.000 22.31 16.51 0.00 3.56
1125 3485 1.435168 ACCTTCTCCTTCCTCTCCACT 59.565 52.381 0.00 0.00 0.00 4.00
1213 3582 1.376295 GTGCCGGACGGGTTAATGT 60.376 57.895 5.05 0.00 38.44 2.71
1215 3584 2.169146 GCCGGACGGGTTAATGTCG 61.169 63.158 5.05 0.00 38.44 4.35
1595 4402 4.631377 CCTGAGACGAATGCTTGTGAAATA 59.369 41.667 0.00 0.00 0.00 1.40
1632 4439 2.202492 CGGACGAGCTTCTGACCG 60.202 66.667 9.96 9.96 34.77 4.79
1656 4463 3.148279 CGGGCCTCGGAAGCTACT 61.148 66.667 0.84 0.00 34.75 2.57
2258 5594 1.517832 CCGTCCCTTCTTCAGCGAT 59.482 57.895 0.00 0.00 0.00 4.58
2450 5816 1.360820 GCGGCAGTAGGAAGAACTTC 58.639 55.000 6.06 6.06 38.80 3.01
2453 5819 2.608268 GGCAGTAGGAAGAACTTCGAC 58.392 52.381 8.20 8.63 40.37 4.20
2477 5843 4.609301 AGCTTCTCAAGATAGTCTGTCCT 58.391 43.478 0.00 0.00 0.00 3.85
2481 5847 5.906113 TCTCAAGATAGTCTGTCCTTCAC 57.094 43.478 0.00 0.00 0.00 3.18
2510 5876 1.227823 CAGCCGTGGTGGTCTTCAA 60.228 57.895 0.00 0.00 41.21 2.69
2549 5915 3.997064 GACGAGATGCGCACCTGCT 62.997 63.158 12.71 8.08 46.04 4.24
2560 5926 1.970917 GCACCTGCTACGACACATGC 61.971 60.000 0.00 0.00 38.21 4.06
2626 6689 6.239458 CCCCAAAAATAGTGTTTTTCTGGCTA 60.239 38.462 7.31 0.00 32.00 3.93
2631 6694 6.840780 AATAGTGTTTTTCTGGCTAATGCT 57.159 33.333 0.00 0.00 39.59 3.79
2638 6701 7.114953 GTGTTTTTCTGGCTAATGCTAAAGTTC 59.885 37.037 0.00 0.00 39.59 3.01
2654 6718 6.038714 GCTAAAGTTCCCACTCAAGGAATATG 59.961 42.308 0.00 0.00 44.95 1.78
2670 8211 7.372260 AGGAATATGAGCATTTAGTCTCTGT 57.628 36.000 0.00 0.00 0.00 3.41
2680 8221 4.623932 TTTAGTCTCTGTTGTCATGGCT 57.376 40.909 0.00 0.00 0.00 4.75
2688 8229 3.441222 TCTGTTGTCATGGCTGCTATTTG 59.559 43.478 0.00 0.00 0.00 2.32
2701 8242 4.506654 GCTGCTATTTGCTGATCAATTTGG 59.493 41.667 0.00 0.00 42.27 3.28
2703 8244 6.283544 TGCTATTTGCTGATCAATTTGGAA 57.716 33.333 0.00 0.00 43.37 3.53
2799 8340 4.112634 TGGACTAGTTCTTGGGCAATTT 57.887 40.909 2.07 0.00 0.00 1.82
2876 8527 9.937175 GATACCTTTCATTAGCTGTAATCAAAC 57.063 33.333 0.00 0.00 0.00 2.93
2889 8540 9.905713 AGCTGTAATCAAACTCTATATTTTGGA 57.094 29.630 0.00 0.00 34.14 3.53
2925 8576 0.966179 AAAAGGGTCATTTGTCCCGC 59.034 50.000 7.15 0.00 46.13 6.13
2956 8607 2.341257 CCATCTGTCTCGGTTGTGAAG 58.659 52.381 0.00 0.00 0.00 3.02
2979 8630 3.576648 CGTGTCTAAAGGGTCTTCACTC 58.423 50.000 0.00 0.00 0.00 3.51
2983 8634 4.899457 TGTCTAAAGGGTCTTCACTCAAGA 59.101 41.667 0.00 0.00 38.95 3.02
2984 8635 5.544176 TGTCTAAAGGGTCTTCACTCAAGAT 59.456 40.000 0.00 0.00 43.33 2.40
3028 8679 0.541392 CATGAACCGGGACAGATGGA 59.459 55.000 6.32 0.00 0.00 3.41
3075 8726 2.118294 GCAGGAGGGCCTTTGGTT 59.882 61.111 7.89 0.00 43.90 3.67
3107 8758 0.259356 ACCAACCGGGACCAAAAGAA 59.741 50.000 6.32 0.00 41.15 2.52
3120 8771 2.287308 CCAAAAGAAATCCACGCGTCAA 60.287 45.455 9.86 0.00 0.00 3.18
3127 8778 2.434658 ATCCACGCGTCAACAGCTGA 62.435 55.000 23.35 0.00 0.00 4.26
3196 8857 8.423349 GTTTTGGGGTTAATTTAGGTTGTTAGT 58.577 33.333 0.00 0.00 0.00 2.24
3264 8925 3.385111 ACCAACTCTACTGCTATGCCTAC 59.615 47.826 0.00 0.00 0.00 3.18
3504 9167 9.731819 TCATCATACAACTTCTACTCGTTATTC 57.268 33.333 0.00 0.00 0.00 1.75
3520 9183 7.434307 ACTCGTTATTCATAACAAGTCATACGG 59.566 37.037 9.77 0.00 36.13 4.02
3525 9188 9.607988 TTATTCATAACAAGTCATACGGTCATT 57.392 29.630 0.00 0.00 0.00 2.57
3548 9211 5.815233 ATCCTCATAGTCATCGAACCAAT 57.185 39.130 0.00 0.00 0.00 3.16
3550 9213 4.649218 TCCTCATAGTCATCGAACCAATCA 59.351 41.667 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.142469 CCAATCCGTAAACTGCTTTAAGGG 60.142 45.833 9.49 2.19 40.23 3.95
1 2 4.142469 CCCAATCCGTAAACTGCTTTAAGG 60.142 45.833 4.65 4.65 40.83 2.69
2 3 4.457949 ACCCAATCCGTAAACTGCTTTAAG 59.542 41.667 0.00 0.00 0.00 1.85
6 7 2.579410 ACCCAATCCGTAAACTGCTT 57.421 45.000 0.00 0.00 0.00 3.91
7 8 2.556622 CAAACCCAATCCGTAAACTGCT 59.443 45.455 0.00 0.00 0.00 4.24
8 9 2.554893 TCAAACCCAATCCGTAAACTGC 59.445 45.455 0.00 0.00 0.00 4.40
9 10 3.190535 CCTCAAACCCAATCCGTAAACTG 59.809 47.826 0.00 0.00 0.00 3.16
10 11 3.418047 CCTCAAACCCAATCCGTAAACT 58.582 45.455 0.00 0.00 0.00 2.66
11 12 2.490509 CCCTCAAACCCAATCCGTAAAC 59.509 50.000 0.00 0.00 0.00 2.01
12 13 2.108601 ACCCTCAAACCCAATCCGTAAA 59.891 45.455 0.00 0.00 0.00 2.01
13 14 1.706305 ACCCTCAAACCCAATCCGTAA 59.294 47.619 0.00 0.00 0.00 3.18
14 15 1.364269 ACCCTCAAACCCAATCCGTA 58.636 50.000 0.00 0.00 0.00 4.02
15 16 0.481128 AACCCTCAAACCCAATCCGT 59.519 50.000 0.00 0.00 0.00 4.69
16 17 1.173913 GAACCCTCAAACCCAATCCG 58.826 55.000 0.00 0.00 0.00 4.18
17 18 2.604912 AGAACCCTCAAACCCAATCC 57.395 50.000 0.00 0.00 0.00 3.01
18 19 4.019231 AGACTAGAACCCTCAAACCCAATC 60.019 45.833 0.00 0.00 0.00 2.67
19 20 3.916989 AGACTAGAACCCTCAAACCCAAT 59.083 43.478 0.00 0.00 0.00 3.16
20 21 3.323775 AGACTAGAACCCTCAAACCCAA 58.676 45.455 0.00 0.00 0.00 4.12
21 22 2.986050 AGACTAGAACCCTCAAACCCA 58.014 47.619 0.00 0.00 0.00 4.51
22 23 4.072839 CAAAGACTAGAACCCTCAAACCC 58.927 47.826 0.00 0.00 0.00 4.11
23 24 4.755629 GTCAAAGACTAGAACCCTCAAACC 59.244 45.833 0.00 0.00 0.00 3.27
24 25 4.755629 GGTCAAAGACTAGAACCCTCAAAC 59.244 45.833 0.00 0.00 32.47 2.93
25 26 4.202430 GGGTCAAAGACTAGAACCCTCAAA 60.202 45.833 10.47 0.00 35.54 2.69
26 27 3.326880 GGGTCAAAGACTAGAACCCTCAA 59.673 47.826 10.47 0.00 35.54 3.02
27 28 2.904434 GGGTCAAAGACTAGAACCCTCA 59.096 50.000 10.47 0.00 35.54 3.86
28 29 3.055747 CAGGGTCAAAGACTAGAACCCTC 60.056 52.174 15.42 0.00 42.75 4.30
29 30 2.907042 CAGGGTCAAAGACTAGAACCCT 59.093 50.000 13.39 13.39 42.75 4.34
30 31 2.638363 ACAGGGTCAAAGACTAGAACCC 59.362 50.000 8.01 9.02 42.75 4.11
31 32 4.353383 AACAGGGTCAAAGACTAGAACC 57.647 45.455 0.00 4.16 42.06 3.62
32 33 6.317893 TGAAAAACAGGGTCAAAGACTAGAAC 59.682 38.462 0.00 0.00 32.47 3.01
33 34 6.419791 TGAAAAACAGGGTCAAAGACTAGAA 58.580 36.000 0.00 0.00 32.47 2.10
34 35 5.996644 TGAAAAACAGGGTCAAAGACTAGA 58.003 37.500 0.00 0.00 32.47 2.43
35 36 6.459710 GGTTGAAAAACAGGGTCAAAGACTAG 60.460 42.308 0.00 0.00 33.29 2.57
36 37 5.358725 GGTTGAAAAACAGGGTCAAAGACTA 59.641 40.000 0.00 0.00 33.29 2.59
37 38 4.159693 GGTTGAAAAACAGGGTCAAAGACT 59.840 41.667 0.00 0.00 33.29 3.24
38 39 4.430007 GGTTGAAAAACAGGGTCAAAGAC 58.570 43.478 0.00 0.00 33.29 3.01
39 40 3.449377 GGGTTGAAAAACAGGGTCAAAGA 59.551 43.478 0.00 0.00 32.77 2.52
40 41 3.450817 AGGGTTGAAAAACAGGGTCAAAG 59.549 43.478 0.00 0.00 32.77 2.77
41 42 3.445987 AGGGTTGAAAAACAGGGTCAAA 58.554 40.909 0.00 0.00 32.77 2.69
42 43 3.108847 AGGGTTGAAAAACAGGGTCAA 57.891 42.857 0.00 0.00 32.77 3.18
43 44 2.838637 AGGGTTGAAAAACAGGGTCA 57.161 45.000 0.00 0.00 32.77 4.02
44 45 5.601583 TTTAAGGGTTGAAAAACAGGGTC 57.398 39.130 0.00 0.00 32.77 4.46
45 46 5.486063 ACTTTTAAGGGTTGAAAAACAGGGT 59.514 36.000 0.00 0.00 32.77 4.34
46 47 5.815222 CACTTTTAAGGGTTGAAAAACAGGG 59.185 40.000 0.00 0.00 32.77 4.45
47 48 6.403049 ACACTTTTAAGGGTTGAAAAACAGG 58.597 36.000 0.00 0.00 40.45 4.00
48 49 7.093992 TGACACTTTTAAGGGTTGAAAAACAG 58.906 34.615 0.00 0.00 44.15 3.16
49 50 6.994221 TGACACTTTTAAGGGTTGAAAAACA 58.006 32.000 0.00 0.00 44.15 2.83
50 51 7.892778 TTGACACTTTTAAGGGTTGAAAAAC 57.107 32.000 0.00 0.00 44.15 2.43
51 52 8.904099 TTTTGACACTTTTAAGGGTTGAAAAA 57.096 26.923 0.00 4.88 44.15 1.94
52 53 8.775527 GTTTTTGACACTTTTAAGGGTTGAAAA 58.224 29.630 11.78 11.78 44.15 2.29
53 54 8.151596 AGTTTTTGACACTTTTAAGGGTTGAAA 58.848 29.630 0.00 1.60 44.15 2.69
54 55 7.600752 CAGTTTTTGACACTTTTAAGGGTTGAA 59.399 33.333 0.00 0.00 44.15 2.69
55 56 7.093992 CAGTTTTTGACACTTTTAAGGGTTGA 58.906 34.615 0.00 0.00 44.15 3.18
56 57 6.312672 CCAGTTTTTGACACTTTTAAGGGTTG 59.687 38.462 0.00 0.00 44.15 3.77
57 58 6.403049 CCAGTTTTTGACACTTTTAAGGGTT 58.597 36.000 0.00 0.00 44.15 4.11
59 60 4.808895 GCCAGTTTTTGACACTTTTAAGGG 59.191 41.667 0.00 0.00 34.93 3.95
60 61 5.415221 TGCCAGTTTTTGACACTTTTAAGG 58.585 37.500 0.00 0.00 0.00 2.69
61 62 7.538303 AATGCCAGTTTTTGACACTTTTAAG 57.462 32.000 0.00 0.00 0.00 1.85
62 63 7.821846 AGAAATGCCAGTTTTTGACACTTTTAA 59.178 29.630 0.00 0.00 0.00 1.52
63 64 7.327214 AGAAATGCCAGTTTTTGACACTTTTA 58.673 30.769 0.00 0.00 0.00 1.52
64 65 6.172630 AGAAATGCCAGTTTTTGACACTTTT 58.827 32.000 0.00 0.00 0.00 2.27
65 66 5.733676 AGAAATGCCAGTTTTTGACACTTT 58.266 33.333 0.00 0.00 0.00 2.66
66 67 5.105392 TGAGAAATGCCAGTTTTTGACACTT 60.105 36.000 0.00 0.00 0.00 3.16
67 68 4.402155 TGAGAAATGCCAGTTTTTGACACT 59.598 37.500 0.00 0.00 0.00 3.55
68 69 4.681744 TGAGAAATGCCAGTTTTTGACAC 58.318 39.130 0.00 0.00 0.00 3.67
69 70 4.998671 TGAGAAATGCCAGTTTTTGACA 57.001 36.364 0.00 0.00 0.00 3.58
70 71 4.507756 GGTTGAGAAATGCCAGTTTTTGAC 59.492 41.667 0.00 0.00 0.00 3.18
71 72 4.442753 GGGTTGAGAAATGCCAGTTTTTGA 60.443 41.667 0.00 0.00 0.00 2.69
72 73 3.809279 GGGTTGAGAAATGCCAGTTTTTG 59.191 43.478 0.00 0.00 0.00 2.44
73 74 3.711190 AGGGTTGAGAAATGCCAGTTTTT 59.289 39.130 0.00 0.00 0.00 1.94
74 75 3.308401 AGGGTTGAGAAATGCCAGTTTT 58.692 40.909 0.00 0.00 0.00 2.43
75 76 2.962859 AGGGTTGAGAAATGCCAGTTT 58.037 42.857 0.00 0.00 0.00 2.66
76 77 2.683211 AGGGTTGAGAAATGCCAGTT 57.317 45.000 0.00 0.00 0.00 3.16
77 78 2.683211 AAGGGTTGAGAAATGCCAGT 57.317 45.000 0.00 0.00 0.00 4.00
78 79 5.011023 AGTTTTAAGGGTTGAGAAATGCCAG 59.989 40.000 0.00 0.00 0.00 4.85
79 80 4.898861 AGTTTTAAGGGTTGAGAAATGCCA 59.101 37.500 0.00 0.00 0.00 4.92
80 81 5.230182 CAGTTTTAAGGGTTGAGAAATGCC 58.770 41.667 0.00 0.00 0.00 4.40
81 82 4.686091 GCAGTTTTAAGGGTTGAGAAATGC 59.314 41.667 0.00 0.00 0.00 3.56
82 83 6.089249 AGCAGTTTTAAGGGTTGAGAAATG 57.911 37.500 0.00 0.00 0.00 2.32
83 84 9.528489 TTATAGCAGTTTTAAGGGTTGAGAAAT 57.472 29.630 0.00 0.00 0.00 2.17
84 85 8.927675 TTATAGCAGTTTTAAGGGTTGAGAAA 57.072 30.769 0.00 0.00 0.00 2.52
85 86 7.610305 CCTTATAGCAGTTTTAAGGGTTGAGAA 59.390 37.037 5.83 0.00 38.77 2.87
86 87 7.110155 CCTTATAGCAGTTTTAAGGGTTGAGA 58.890 38.462 5.83 0.00 38.77 3.27
87 88 7.321745 CCTTATAGCAGTTTTAAGGGTTGAG 57.678 40.000 5.83 0.00 38.77 3.02
93 94 7.148069 CCTCAAACCCTTATAGCAGTTTTAAGG 60.148 40.741 6.56 6.56 41.02 2.69
94 95 7.148069 CCCTCAAACCCTTATAGCAGTTTTAAG 60.148 40.741 0.00 0.00 30.27 1.85
95 96 6.661805 CCCTCAAACCCTTATAGCAGTTTTAA 59.338 38.462 0.00 0.00 30.27 1.52
96 97 6.184789 CCCTCAAACCCTTATAGCAGTTTTA 58.815 40.000 0.00 0.00 30.27 1.52
97 98 5.016831 CCCTCAAACCCTTATAGCAGTTTT 58.983 41.667 0.00 0.00 30.27 2.43
98 99 4.044191 ACCCTCAAACCCTTATAGCAGTTT 59.956 41.667 0.00 0.00 32.84 2.66
99 100 3.591977 ACCCTCAAACCCTTATAGCAGTT 59.408 43.478 0.00 0.00 0.00 3.16
100 101 3.190439 ACCCTCAAACCCTTATAGCAGT 58.810 45.455 0.00 0.00 0.00 4.40
101 102 3.933861 ACCCTCAAACCCTTATAGCAG 57.066 47.619 0.00 0.00 0.00 4.24
102 103 4.043561 TCAAACCCTCAAACCCTTATAGCA 59.956 41.667 0.00 0.00 0.00 3.49
103 104 4.595986 TCAAACCCTCAAACCCTTATAGC 58.404 43.478 0.00 0.00 0.00 2.97
104 105 5.193679 CCTCAAACCCTCAAACCCTTATAG 58.806 45.833 0.00 0.00 0.00 1.31
105 106 4.017867 CCCTCAAACCCTCAAACCCTTATA 60.018 45.833 0.00 0.00 0.00 0.98
106 107 3.245622 CCCTCAAACCCTCAAACCCTTAT 60.246 47.826 0.00 0.00 0.00 1.73
107 108 2.109304 CCCTCAAACCCTCAAACCCTTA 59.891 50.000 0.00 0.00 0.00 2.69
108 109 1.133167 CCCTCAAACCCTCAAACCCTT 60.133 52.381 0.00 0.00 0.00 3.95
109 110 0.482887 CCCTCAAACCCTCAAACCCT 59.517 55.000 0.00 0.00 0.00 4.34
110 111 0.187606 ACCCTCAAACCCTCAAACCC 59.812 55.000 0.00 0.00 0.00 4.11
111 112 1.961394 GAACCCTCAAACCCTCAAACC 59.039 52.381 0.00 0.00 0.00 3.27
112 113 2.945456 AGAACCCTCAAACCCTCAAAC 58.055 47.619 0.00 0.00 0.00 2.93
113 114 3.720002 AGTAGAACCCTCAAACCCTCAAA 59.280 43.478 0.00 0.00 0.00 2.69
114 115 3.323775 AGTAGAACCCTCAAACCCTCAA 58.676 45.455 0.00 0.00 0.00 3.02
115 116 2.986050 AGTAGAACCCTCAAACCCTCA 58.014 47.619 0.00 0.00 0.00 3.86
116 117 4.095211 ACTAGTAGAACCCTCAAACCCTC 58.905 47.826 3.59 0.00 0.00 4.30
117 118 4.143406 ACTAGTAGAACCCTCAAACCCT 57.857 45.455 3.59 0.00 0.00 4.34
118 119 6.346896 CATTACTAGTAGAACCCTCAAACCC 58.653 44.000 3.59 0.00 0.00 4.11
119 120 5.816258 GCATTACTAGTAGAACCCTCAAACC 59.184 44.000 3.59 0.00 0.00 3.27
120 121 6.641474 AGCATTACTAGTAGAACCCTCAAAC 58.359 40.000 3.59 0.00 0.00 2.93
121 122 6.668283 AGAGCATTACTAGTAGAACCCTCAAA 59.332 38.462 3.59 0.00 0.00 2.69
122 123 6.195700 AGAGCATTACTAGTAGAACCCTCAA 58.804 40.000 3.59 0.00 0.00 3.02
123 124 5.767670 AGAGCATTACTAGTAGAACCCTCA 58.232 41.667 3.59 0.00 0.00 3.86
124 125 6.718522 AAGAGCATTACTAGTAGAACCCTC 57.281 41.667 3.59 6.41 0.00 4.30
128 129 9.575783 GCCATATAAGAGCATTACTAGTAGAAC 57.424 37.037 3.59 0.00 0.00 3.01
129 130 8.750298 GGCCATATAAGAGCATTACTAGTAGAA 58.250 37.037 3.59 0.00 0.00 2.10
130 131 7.342284 GGGCCATATAAGAGCATTACTAGTAGA 59.658 40.741 4.39 0.00 0.00 2.59
131 132 7.418025 GGGGCCATATAAGAGCATTACTAGTAG 60.418 44.444 4.39 0.00 0.00 2.57
132 133 6.383147 GGGGCCATATAAGAGCATTACTAGTA 59.617 42.308 4.39 0.00 0.00 1.82
133 134 5.189934 GGGGCCATATAAGAGCATTACTAGT 59.810 44.000 4.39 0.00 0.00 2.57
134 135 5.426833 AGGGGCCATATAAGAGCATTACTAG 59.573 44.000 4.39 0.00 0.00 2.57
135 136 5.350547 AGGGGCCATATAAGAGCATTACTA 58.649 41.667 4.39 0.00 0.00 1.82
136 137 4.179133 AGGGGCCATATAAGAGCATTACT 58.821 43.478 4.39 0.00 0.00 2.24
137 138 4.576330 AGGGGCCATATAAGAGCATTAC 57.424 45.455 4.39 0.00 0.00 1.89
138 139 6.297010 CCTTTAGGGGCCATATAAGAGCATTA 60.297 42.308 4.39 0.00 0.00 1.90
139 140 5.517299 CCTTTAGGGGCCATATAAGAGCATT 60.517 44.000 4.39 0.00 0.00 3.56
140 141 4.018050 CCTTTAGGGGCCATATAAGAGCAT 60.018 45.833 4.39 0.00 0.00 3.79
141 142 3.330701 CCTTTAGGGGCCATATAAGAGCA 59.669 47.826 4.39 0.00 0.00 4.26
142 143 3.330998 ACCTTTAGGGGCCATATAAGAGC 59.669 47.826 4.39 0.00 40.27 4.09
143 144 5.163088 ACAACCTTTAGGGGCCATATAAGAG 60.163 44.000 4.39 6.50 40.27 2.85
144 145 4.729881 ACAACCTTTAGGGGCCATATAAGA 59.270 41.667 4.39 0.00 40.27 2.10
145 146 4.827284 CACAACCTTTAGGGGCCATATAAG 59.173 45.833 4.39 9.22 40.27 1.73
154 155 5.305902 ACATTTTTACCACAACCTTTAGGGG 59.694 40.000 0.10 0.00 40.27 4.79
182 183 6.763303 ATGTTACAATTTTTGCGAAACCTC 57.237 33.333 0.00 0.00 0.00 3.85
214 216 5.833082 TCCTACGATATTGTCTGCTTTCTC 58.167 41.667 0.00 0.00 0.00 2.87
250 252 3.563808 TCGTCTTCAAACTTGACCCATTG 59.436 43.478 0.00 0.00 36.83 2.82
363 367 6.607689 TGACTTCAATATAGCAAACAAACCG 58.392 36.000 0.00 0.00 0.00 4.44
444 452 6.767423 AGCCTATTTTTGACAATTTTGCAAGT 59.233 30.769 0.00 0.00 0.00 3.16
457 465 9.734620 CAAATATGATTTCGAGCCTATTTTTGA 57.265 29.630 9.72 0.00 0.00 2.69
532 1632 3.503748 CCACACTGAGTTTGGAATTCCTC 59.496 47.826 24.73 14.33 35.60 3.71
554 1654 5.393461 CCTTTACATTTGGGATGAGTCTTGC 60.393 44.000 0.00 0.00 0.00 4.01
563 1663 4.772100 CACTTCACCCTTTACATTTGGGAT 59.228 41.667 4.11 0.00 43.47 3.85
564 1664 4.148838 CACTTCACCCTTTACATTTGGGA 58.851 43.478 4.11 0.00 43.47 4.37
658 1759 7.868922 TGTTGAACTGATTTTGAATCTGAATGG 59.131 33.333 12.53 0.00 0.00 3.16
662 1763 7.332213 TGTGTTGAACTGATTTTGAATCTGA 57.668 32.000 12.53 0.00 0.00 3.27
717 1819 5.241064 TCTCCAAGTAGAGTAAGTGTGTCAC 59.759 44.000 0.00 0.00 35.28 3.67
737 1839 8.076178 CCATGGAAATTATCATTTACGTTCTCC 58.924 37.037 5.56 0.00 36.11 3.71
744 1846 9.868277 TGTCAAACCATGGAAATTATCATTTAC 57.132 29.630 21.47 5.36 34.10 2.01
775 2212 5.309543 TGAGGTCCTTCAACTATTTCAAGGA 59.690 40.000 0.00 0.00 41.79 3.36
789 2226 5.153950 ACATGTAAAGAGTGAGGTCCTTC 57.846 43.478 0.00 0.00 0.00 3.46
893 2341 3.604667 TGGTTTGCCGCTTGCCAG 61.605 61.111 0.00 0.00 40.16 4.85
1242 3617 1.745890 CATATGGTTCGGCGGAGGA 59.254 57.895 7.21 0.00 0.00 3.71
1374 3749 2.203070 GCGGCCATCCAGACGAAT 60.203 61.111 2.24 0.00 0.00 3.34
2043 5365 4.052229 CGACCAGAGGAACGGCGT 62.052 66.667 6.77 6.77 0.00 5.68
2258 5594 2.202610 CGCGCGTTCATCCTCTGA 60.203 61.111 24.19 0.00 0.00 3.27
2297 5633 1.153823 CTCGAAGACCGTGCCGAAT 60.154 57.895 0.00 0.00 39.75 3.34
2346 5682 2.046892 GAGCAGCCATGACACCGT 60.047 61.111 0.00 0.00 0.00 4.83
2377 5713 2.446848 ATCTCCTGCATCCGGGTGG 61.447 63.158 18.38 0.00 38.71 4.61
2438 5804 4.281182 AGAAGCTTGTCGAAGTTCTTCCTA 59.719 41.667 2.10 0.00 32.65 2.94
2450 5816 4.797868 CAGACTATCTTGAGAAGCTTGTCG 59.202 45.833 17.82 5.73 0.00 4.35
2453 5819 5.105392 AGGACAGACTATCTTGAGAAGCTTG 60.105 44.000 2.10 0.00 0.00 4.01
2477 5843 0.819259 GGCTGTGCTCTTGTGGTGAA 60.819 55.000 0.00 0.00 0.00 3.18
2481 5847 2.281070 ACGGCTGTGCTCTTGTGG 60.281 61.111 0.00 0.00 0.00 4.17
2503 5869 1.716581 CTGCTTCGTCGACTTGAAGAC 59.283 52.381 27.23 20.32 43.34 3.01
2510 5876 1.211449 CTCTGCTGCTTCGTCGACT 59.789 57.895 14.70 0.00 0.00 4.18
2549 5915 0.737367 GCAGCTGAGCATGTGTCGTA 60.737 55.000 20.43 0.00 0.00 3.43
2626 6689 4.082125 CCTTGAGTGGGAACTTTAGCATT 58.918 43.478 0.00 0.00 0.00 3.56
2631 6694 7.265599 TCATATTCCTTGAGTGGGAACTTTA 57.734 36.000 0.00 0.00 44.34 1.85
2638 6701 3.565764 TGCTCATATTCCTTGAGTGGG 57.434 47.619 2.97 0.00 42.12 4.61
2654 6718 5.064452 CCATGACAACAGAGACTAAATGCTC 59.936 44.000 0.00 0.00 0.00 4.26
2670 8211 2.945447 GCAAATAGCAGCCATGACAA 57.055 45.000 0.00 0.00 44.79 3.18
2688 8229 3.935203 TCGACTCTTCCAAATTGATCAGC 59.065 43.478 0.00 0.00 0.00 4.26
2701 8242 8.443160 TGAAACATAATGTCATTTCGACTCTTC 58.557 33.333 2.79 0.32 45.60 2.87
2703 8244 7.905604 TGAAACATAATGTCATTTCGACTCT 57.094 32.000 2.79 0.00 45.60 3.24
2863 8514 9.905713 TCCAAAATATAGAGTTTGATTACAGCT 57.094 29.630 11.55 0.00 41.99 4.24
2889 8540 8.434392 TGACCCTTTTTCTACTAGTGTAACAAT 58.566 33.333 5.39 0.00 41.43 2.71
2925 8576 1.482593 AGACAGATGGGCCTTACGAAG 59.517 52.381 4.53 0.00 0.00 3.79
2956 8607 1.001633 TGAAGACCCTTTAGACACGGC 59.998 52.381 0.00 0.00 0.00 5.68
2960 8611 4.899457 TCTTGAGTGAAGACCCTTTAGACA 59.101 41.667 0.00 0.00 35.64 3.41
2962 8613 6.019748 AGATCTTGAGTGAAGACCCTTTAGA 58.980 40.000 0.00 0.00 43.71 2.10
2979 8630 3.243907 CGGGACTAAAGGCCTAGATCTTG 60.244 52.174 5.16 0.00 0.00 3.02
2983 8634 1.062352 ACCGGGACTAAAGGCCTAGAT 60.062 52.381 5.16 0.00 0.00 1.98
2984 8635 0.337428 ACCGGGACTAAAGGCCTAGA 59.663 55.000 5.16 0.00 0.00 2.43
3107 8758 1.301716 AGCTGTTGACGCGTGGATT 60.302 52.632 20.70 0.00 0.00 3.01
3127 8778 5.343307 AAAACAAAAACCTCAGCTCATGT 57.657 34.783 0.00 0.00 0.00 3.21
3248 8909 3.321968 CCATGTGTAGGCATAGCAGTAGA 59.678 47.826 0.00 0.00 0.00 2.59
3264 8925 5.163683 CCTTCACTTCAATCTAAGCCATGTG 60.164 44.000 0.00 0.00 0.00 3.21
3504 9167 7.872993 AGGATAATGACCGTATGACTTGTTATG 59.127 37.037 0.00 0.00 0.00 1.90
3520 9183 6.809196 GGTTCGATGACTATGAGGATAATGAC 59.191 42.308 0.00 0.00 0.00 3.06
3525 9188 6.493458 TGATTGGTTCGATGACTATGAGGATA 59.507 38.462 0.00 0.00 0.00 2.59
3548 9211 9.665719 TCATGTGCTAAGAACAATTAAGTATGA 57.334 29.630 0.00 0.00 0.00 2.15


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

AutoCloner maintained by Alex Coulton.