Multiple sequence alignment - TraesCS3A01G440400

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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 TraesCS3A01G440400 chr3A 100.000 3459 0 0 1 3459 683213541 683216999 0.000000e+00 6388.0
1 TraesCS3A01G440400 chr3A 98.780 164 2 0 1 164 700884541 700884378 3.380000e-75 292.0
2 TraesCS3A01G440400 chr3B 92.872 1908 117 7 950 2839 723459509 723461415 0.000000e+00 2752.0
3 TraesCS3A01G440400 chr3B 88.846 1820 169 24 814 2615 723466232 723468035 0.000000e+00 2206.0
4 TraesCS3A01G440400 chr3B 87.634 655 66 8 167 808 723457999 723458651 0.000000e+00 747.0
5 TraesCS3A01G440400 chr3B 78.801 467 78 12 352 808 723464972 723465427 9.390000e-76 294.0
6 TraesCS3A01G440400 chr3D 88.919 1823 167 25 814 2617 546387985 546389791 0.000000e+00 2215.0
7 TraesCS3A01G440400 chr3D 95.537 605 26 1 2855 3459 403884690 403885293 0.000000e+00 966.0
8 TraesCS3A01G440400 chr3D 95.372 605 28 0 2855 3459 208875918 208876522 0.000000e+00 963.0
9 TraesCS3A01G440400 chr3D 95.380 606 26 2 2855 3459 228622650 228623254 0.000000e+00 963.0
10 TraesCS3A01G440400 chr3D 78.801 467 78 12 352 808 546386737 546387192 9.390000e-76 294.0
11 TraesCS3A01G440400 chr3D 98.160 163 3 0 3 165 578450072 578450234 5.650000e-73 285.0
12 TraesCS3A01G440400 chr2A 89.752 1249 119 5 1228 2472 619771360 619770117 0.000000e+00 1589.0
13 TraesCS3A01G440400 chr2A 98.171 164 3 0 1 164 5314632 5314795 1.570000e-73 287.0
14 TraesCS3A01G440400 chr2B 83.280 1256 179 16 1228 2469 786104803 786106041 0.000000e+00 1127.0
15 TraesCS3A01G440400 chr2B 100.000 28 0 0 268 295 19843207 19843180 6.000000e-03 52.8
16 TraesCS3A01G440400 chr1D 96.007 601 24 0 2859 3459 403244586 403245186 0.000000e+00 977.0
17 TraesCS3A01G440400 chr1D 95.702 605 24 2 2855 3459 196195053 196194451 0.000000e+00 972.0
18 TraesCS3A01G440400 chr5D 95.537 605 26 1 2855 3459 492552404 492553007 0.000000e+00 966.0
19 TraesCS3A01G440400 chr6D 95.372 605 28 0 2855 3459 88219915 88219311 0.000000e+00 963.0
20 TraesCS3A01G440400 chr6D 95.372 605 27 1 2855 3459 323928676 323928073 0.000000e+00 961.0
21 TraesCS3A01G440400 chr2D 95.372 605 28 0 2855 3459 244161848 244162452 0.000000e+00 963.0
22 TraesCS3A01G440400 chr2D 81.497 935 159 12 1229 2158 477425627 477424702 0.000000e+00 756.0
23 TraesCS3A01G440400 chr5B 80.668 988 142 19 1516 2479 7069299 7068337 0.000000e+00 721.0
24 TraesCS3A01G440400 chr7A 98.780 164 2 0 1 164 94397449 94397286 3.380000e-75 292.0
25 TraesCS3A01G440400 chr7A 98.171 164 3 0 1 164 49508352 49508189 1.570000e-73 287.0
26 TraesCS3A01G440400 chr7A 97.576 165 4 0 1 165 161209532 161209696 2.030000e-72 283.0
27 TraesCS3A01G440400 chr7A 97.561 164 4 0 1 164 28261346 28261509 7.310000e-72 281.0
28 TraesCS3A01G440400 chr4A 98.780 164 2 0 1 164 636048623 636048786 3.380000e-75 292.0
29 TraesCS3A01G440400 chr6B 95.906 171 7 0 1 171 67111577 67111407 9.450000e-71 278.0
30 TraesCS3A01G440400 chr5A 100.000 29 0 0 263 291 535614154 535614182 2.000000e-03 54.7


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 TraesCS3A01G440400 chr3A 683213541 683216999 3458 False 6388.00 6388 100.00000 1 3459 1 chr3A.!!$F1 3458
1 TraesCS3A01G440400 chr3B 723457999 723468035 10036 False 1499.75 2752 87.03825 167 2839 4 chr3B.!!$F1 2672
2 TraesCS3A01G440400 chr3D 546386737 546389791 3054 False 1254.50 2215 83.86000 352 2617 2 chr3D.!!$F5 2265
3 TraesCS3A01G440400 chr3D 403884690 403885293 603 False 966.00 966 95.53700 2855 3459 1 chr3D.!!$F3 604
4 TraesCS3A01G440400 chr3D 208875918 208876522 604 False 963.00 963 95.37200 2855 3459 1 chr3D.!!$F1 604
5 TraesCS3A01G440400 chr3D 228622650 228623254 604 False 963.00 963 95.38000 2855 3459 1 chr3D.!!$F2 604
6 TraesCS3A01G440400 chr2A 619770117 619771360 1243 True 1589.00 1589 89.75200 1228 2472 1 chr2A.!!$R1 1244
7 TraesCS3A01G440400 chr2B 786104803 786106041 1238 False 1127.00 1127 83.28000 1228 2469 1 chr2B.!!$F1 1241
8 TraesCS3A01G440400 chr1D 403244586 403245186 600 False 977.00 977 96.00700 2859 3459 1 chr1D.!!$F1 600
9 TraesCS3A01G440400 chr1D 196194451 196195053 602 True 972.00 972 95.70200 2855 3459 1 chr1D.!!$R1 604
10 TraesCS3A01G440400 chr5D 492552404 492553007 603 False 966.00 966 95.53700 2855 3459 1 chr5D.!!$F1 604
11 TraesCS3A01G440400 chr6D 88219311 88219915 604 True 963.00 963 95.37200 2855 3459 1 chr6D.!!$R1 604
12 TraesCS3A01G440400 chr6D 323928073 323928676 603 True 961.00 961 95.37200 2855 3459 1 chr6D.!!$R2 604
13 TraesCS3A01G440400 chr2D 244161848 244162452 604 False 963.00 963 95.37200 2855 3459 1 chr2D.!!$F1 604
14 TraesCS3A01G440400 chr2D 477424702 477425627 925 True 756.00 756 81.49700 1229 2158 1 chr2D.!!$R1 929
15 TraesCS3A01G440400 chr5B 7068337 7069299 962 True 721.00 721 80.66800 1516 2479 1 chr5B.!!$R1 963

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
588 600 0.245266 TGCAAGTTCGCGAGGTATCA 59.755 50.0 9.59 3.55 33.35 2.15 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2527 3446 0.316937 TTCGCAAGCACGAGCAAAAG 60.317 50.0 7.77 0.0 44.0 2.27 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
30 31 8.717821 TGTAGTTAGAATGTATTGTTGTTCTGC 58.282 33.333 0.00 0.00 33.36 4.26
31 32 7.744087 AGTTAGAATGTATTGTTGTTCTGCA 57.256 32.000 0.00 0.00 33.36 4.41
32 33 8.165239 AGTTAGAATGTATTGTTGTTCTGCAA 57.835 30.769 0.00 0.00 33.36 4.08
33 34 8.629158 AGTTAGAATGTATTGTTGTTCTGCAAA 58.371 29.630 0.00 0.00 39.03 3.68
34 35 9.243637 GTTAGAATGTATTGTTGTTCTGCAAAA 57.756 29.630 0.00 0.00 39.03 2.44
35 36 9.979578 TTAGAATGTATTGTTGTTCTGCAAAAT 57.020 25.926 0.00 0.00 39.03 1.82
36 37 8.891671 AGAATGTATTGTTGTTCTGCAAAATT 57.108 26.923 0.00 0.00 39.03 1.82
37 38 9.328845 AGAATGTATTGTTGTTCTGCAAAATTT 57.671 25.926 0.00 0.00 39.03 1.82
38 39 9.372541 GAATGTATTGTTGTTCTGCAAAATTTG 57.627 29.630 0.57 0.57 39.03 2.32
39 40 8.659925 ATGTATTGTTGTTCTGCAAAATTTGA 57.340 26.923 10.26 0.00 39.03 2.69
40 41 8.484641 TGTATTGTTGTTCTGCAAAATTTGAA 57.515 26.923 10.26 0.00 39.03 2.69
41 42 8.602328 TGTATTGTTGTTCTGCAAAATTTGAAG 58.398 29.630 10.26 8.76 39.03 3.02
42 43 7.614124 ATTGTTGTTCTGCAAAATTTGAAGT 57.386 28.000 13.03 0.00 37.59 3.01
43 44 7.432350 TTGTTGTTCTGCAAAATTTGAAGTT 57.568 28.000 13.03 0.00 37.59 2.66
44 45 7.059448 TGTTGTTCTGCAAAATTTGAAGTTC 57.941 32.000 13.03 8.30 37.59 3.01
45 46 6.648310 TGTTGTTCTGCAAAATTTGAAGTTCA 59.352 30.769 13.03 10.44 37.59 3.18
46 47 7.333921 TGTTGTTCTGCAAAATTTGAAGTTCAT 59.666 29.630 13.03 0.00 37.59 2.57
47 48 8.816144 GTTGTTCTGCAAAATTTGAAGTTCATA 58.184 29.630 13.03 1.98 37.59 2.15
48 49 9.545105 TTGTTCTGCAAAATTTGAAGTTCATAT 57.455 25.926 13.03 4.61 37.59 1.78
49 50 8.980610 TGTTCTGCAAAATTTGAAGTTCATATG 58.019 29.630 13.03 0.00 37.59 1.78
50 51 8.981647 GTTCTGCAAAATTTGAAGTTCATATGT 58.018 29.630 13.03 0.00 37.59 2.29
51 52 9.545105 TTCTGCAAAATTTGAAGTTCATATGTT 57.455 25.926 13.03 6.17 37.59 2.71
52 53 8.980610 TCTGCAAAATTTGAAGTTCATATGTTG 58.019 29.630 24.18 24.18 36.64 3.33
53 54 8.659925 TGCAAAATTTGAAGTTCATATGTTGT 57.340 26.923 26.67 6.70 36.24 3.32
54 55 8.549548 TGCAAAATTTGAAGTTCATATGTTGTG 58.450 29.630 26.67 16.78 36.24 3.33
55 56 8.550376 GCAAAATTTGAAGTTCATATGTTGTGT 58.450 29.630 26.67 5.88 36.24 3.72
57 58 8.506140 AAATTTGAAGTTCATATGTTGTGTCG 57.494 30.769 6.36 0.00 0.00 4.35
58 59 6.612247 TTTGAAGTTCATATGTTGTGTCGT 57.388 33.333 6.36 0.00 0.00 4.34
59 60 6.612247 TTGAAGTTCATATGTTGTGTCGTT 57.388 33.333 6.36 0.00 0.00 3.85
60 61 6.612247 TGAAGTTCATATGTTGTGTCGTTT 57.388 33.333 0.08 0.00 0.00 3.60
61 62 6.426327 TGAAGTTCATATGTTGTGTCGTTTG 58.574 36.000 0.08 0.00 0.00 2.93
62 63 6.258947 TGAAGTTCATATGTTGTGTCGTTTGA 59.741 34.615 0.08 0.00 0.00 2.69
63 64 6.228273 AGTTCATATGTTGTGTCGTTTGAG 57.772 37.500 1.90 0.00 0.00 3.02
64 65 5.989168 AGTTCATATGTTGTGTCGTTTGAGA 59.011 36.000 1.90 0.00 0.00 3.27
65 66 6.146184 AGTTCATATGTTGTGTCGTTTGAGAG 59.854 38.462 1.90 0.00 0.00 3.20
66 67 5.778862 TCATATGTTGTGTCGTTTGAGAGA 58.221 37.500 1.90 0.00 0.00 3.10
67 68 6.220201 TCATATGTTGTGTCGTTTGAGAGAA 58.780 36.000 1.90 0.00 0.00 2.87
68 69 6.704050 TCATATGTTGTGTCGTTTGAGAGAAA 59.296 34.615 1.90 0.00 0.00 2.52
69 70 4.593597 TGTTGTGTCGTTTGAGAGAAAC 57.406 40.909 0.00 0.00 0.00 2.78
70 71 3.997681 TGTTGTGTCGTTTGAGAGAAACA 59.002 39.130 0.00 0.00 33.19 2.83
71 72 4.452795 TGTTGTGTCGTTTGAGAGAAACAA 59.547 37.500 0.00 0.00 40.94 2.83
72 73 5.049336 TGTTGTGTCGTTTGAGAGAAACAAA 60.049 36.000 3.15 0.00 43.64 2.83
73 74 5.614923 TGTGTCGTTTGAGAGAAACAAAA 57.385 34.783 0.00 0.00 38.63 2.44
74 75 6.003234 TGTGTCGTTTGAGAGAAACAAAAA 57.997 33.333 0.00 0.00 38.63 1.94
93 94 4.838665 AAAAGACAAATGTGTTTGCACG 57.161 36.364 9.13 0.00 46.84 5.34
94 95 2.490328 AGACAAATGTGTTTGCACGG 57.510 45.000 0.00 0.00 46.84 4.94
95 96 2.020720 AGACAAATGTGTTTGCACGGA 58.979 42.857 0.00 0.00 46.84 4.69
96 97 2.622942 AGACAAATGTGTTTGCACGGAT 59.377 40.909 0.00 0.00 46.84 4.18
97 98 2.979813 GACAAATGTGTTTGCACGGATC 59.020 45.455 0.00 0.00 46.84 3.36
98 99 2.622942 ACAAATGTGTTTGCACGGATCT 59.377 40.909 0.00 0.00 46.84 2.75
99 100 3.068024 ACAAATGTGTTTGCACGGATCTT 59.932 39.130 0.00 0.00 46.84 2.40
100 101 5.028291 ACAAATGTGTTTGCACGGATCTTG 61.028 41.667 0.00 0.00 46.84 3.02
101 102 7.172943 ACAAATGTGTTTGCACGGATCTTGA 62.173 40.000 0.00 0.00 46.84 3.02
102 103 8.399304 ACAAATGTGTTTGCACGGATCTTGAT 62.399 38.462 0.00 0.00 46.84 2.57
103 104 2.855180 GTGTTTGCACGGATCTTGATG 58.145 47.619 0.00 0.00 35.75 3.07
104 105 1.199789 TGTTTGCACGGATCTTGATGC 59.800 47.619 0.00 0.00 38.59 3.91
105 106 1.199789 GTTTGCACGGATCTTGATGCA 59.800 47.619 8.86 8.86 45.94 3.96
106 107 1.753930 TTGCACGGATCTTGATGCAT 58.246 45.000 0.00 0.00 46.75 3.96
107 108 2.618442 TGCACGGATCTTGATGCATA 57.382 45.000 0.00 0.00 42.92 3.14
108 109 2.916640 TGCACGGATCTTGATGCATAA 58.083 42.857 0.00 0.00 42.92 1.90
109 110 3.277715 TGCACGGATCTTGATGCATAAA 58.722 40.909 0.00 0.00 42.92 1.40
110 111 3.884693 TGCACGGATCTTGATGCATAAAT 59.115 39.130 0.00 0.00 42.92 1.40
111 112 4.224433 GCACGGATCTTGATGCATAAATG 58.776 43.478 0.00 0.00 38.00 2.32
112 113 4.790878 CACGGATCTTGATGCATAAATGG 58.209 43.478 0.00 0.00 0.00 3.16
113 114 4.516321 CACGGATCTTGATGCATAAATGGA 59.484 41.667 0.00 0.00 0.00 3.41
114 115 5.182570 CACGGATCTTGATGCATAAATGGAT 59.817 40.000 0.00 0.00 41.76 3.41
115 116 5.182570 ACGGATCTTGATGCATAAATGGATG 59.817 40.000 0.00 0.00 39.04 3.51
116 117 5.392703 CGGATCTTGATGCATAAATGGATGG 60.393 44.000 0.00 0.00 39.04 3.51
117 118 4.859304 TCTTGATGCATAAATGGATGGC 57.141 40.909 0.00 0.00 39.04 4.40
118 119 4.216708 TCTTGATGCATAAATGGATGGCA 58.783 39.130 0.00 0.00 39.04 4.92
119 120 4.650131 TCTTGATGCATAAATGGATGGCAA 59.350 37.500 0.00 1.02 39.04 4.52
120 121 5.128991 TCTTGATGCATAAATGGATGGCAAA 59.871 36.000 0.00 0.00 39.04 3.68
121 122 4.951254 TGATGCATAAATGGATGGCAAAG 58.049 39.130 0.00 0.00 39.04 2.77
122 123 4.650131 TGATGCATAAATGGATGGCAAAGA 59.350 37.500 0.00 0.00 39.04 2.52
123 124 5.305902 TGATGCATAAATGGATGGCAAAGAT 59.694 36.000 0.00 0.00 39.04 2.40
124 125 6.494146 TGATGCATAAATGGATGGCAAAGATA 59.506 34.615 0.00 0.00 39.04 1.98
125 126 6.728089 TGCATAAATGGATGGCAAAGATAA 57.272 33.333 0.00 0.00 0.00 1.75
126 127 6.751157 TGCATAAATGGATGGCAAAGATAAG 58.249 36.000 0.00 0.00 0.00 1.73
127 128 6.161381 GCATAAATGGATGGCAAAGATAAGG 58.839 40.000 0.00 0.00 0.00 2.69
128 129 6.694447 CATAAATGGATGGCAAAGATAAGGG 58.306 40.000 0.00 0.00 0.00 3.95
129 130 2.754012 TGGATGGCAAAGATAAGGGG 57.246 50.000 0.00 0.00 0.00 4.79
130 131 1.929494 TGGATGGCAAAGATAAGGGGT 59.071 47.619 0.00 0.00 0.00 4.95
131 132 3.127250 TGGATGGCAAAGATAAGGGGTA 58.873 45.455 0.00 0.00 0.00 3.69
132 133 3.117663 TGGATGGCAAAGATAAGGGGTAC 60.118 47.826 0.00 0.00 0.00 3.34
144 145 3.277133 GGGTACCGTGTAGCGTGA 58.723 61.111 5.65 0.00 40.86 4.35
145 146 1.138247 GGGTACCGTGTAGCGTGAG 59.862 63.158 5.65 0.00 40.86 3.51
161 162 4.842139 CGTGAGCTATAGAAAACCACAC 57.158 45.455 3.21 0.00 0.00 3.82
162 163 4.495422 CGTGAGCTATAGAAAACCACACT 58.505 43.478 3.21 0.00 0.00 3.55
163 164 4.563184 CGTGAGCTATAGAAAACCACACTC 59.437 45.833 3.21 0.00 0.00 3.51
164 165 5.622460 CGTGAGCTATAGAAAACCACACTCT 60.622 44.000 3.21 0.00 0.00 3.24
165 166 5.808030 GTGAGCTATAGAAAACCACACTCTC 59.192 44.000 3.21 0.00 0.00 3.20
198 199 7.578458 TTCCTCAGTTAGTTTAGGGGTTAAT 57.422 36.000 0.00 0.00 0.00 1.40
216 217 7.363431 GGGTTAATGCAATCTTAGTTAGATGC 58.637 38.462 0.00 0.50 42.90 3.91
223 224 5.289595 CAATCTTAGTTAGATGCGCTACCA 58.710 41.667 9.73 0.00 42.90 3.25
240 241 5.389516 CGCTACCATTTTTGCGGAGTATATC 60.390 44.000 0.00 0.00 43.97 1.63
241 242 5.701290 GCTACCATTTTTGCGGAGTATATCT 59.299 40.000 0.00 0.00 0.00 1.98
291 300 7.667557 CGACAAGTAATATGGATAGGAGGAAA 58.332 38.462 0.00 0.00 0.00 3.13
312 321 9.423061 AGGAAATACACTATTTTGTTTGAATGC 57.577 29.630 0.00 0.00 38.42 3.56
379 388 5.360591 CACCTTCAACAGTATATGACTCCC 58.639 45.833 0.00 0.00 35.64 4.30
408 417 4.032900 CCAAGAACGAATTGTCCTACATCG 59.967 45.833 0.00 2.46 36.85 3.84
443 452 0.399519 ATCCCGTTCCCCTTCGGTAT 60.400 55.000 0.00 0.00 44.51 2.73
481 490 1.123928 AAAGCCCCATCTCTACCTCG 58.876 55.000 0.00 0.00 0.00 4.63
502 511 0.543410 ATGTACACCAGGGACGACCA 60.543 55.000 6.20 0.00 43.89 4.02
527 539 5.003804 TCTTCTGGTCCTTAAAATGACTGC 58.996 41.667 0.00 0.00 0.00 4.40
533 545 4.454504 GGTCCTTAAAATGACTGCTCGAAA 59.545 41.667 0.00 0.00 0.00 3.46
578 590 2.930040 ACGATGGTATCTTGCAAGTTCG 59.070 45.455 25.19 22.54 0.00 3.95
579 591 2.285834 CGATGGTATCTTGCAAGTTCGC 60.286 50.000 25.19 13.32 0.00 4.70
588 600 0.245266 TGCAAGTTCGCGAGGTATCA 59.755 50.000 9.59 3.55 33.35 2.15
614 626 2.165030 CAGGTGATTTCATGGCTGGTTC 59.835 50.000 0.00 0.00 0.00 3.62
619 631 1.974265 TTTCATGGCTGGTTCGAACA 58.026 45.000 28.24 14.13 0.00 3.18
625 637 1.300697 GCTGGTTCGAACACGGACT 60.301 57.895 28.24 0.00 36.01 3.85
628 640 1.364901 GGTTCGAACACGGACTCCA 59.635 57.895 28.24 0.00 36.01 3.86
649 661 3.898517 CGCTCTACGTATCATCTGGAA 57.101 47.619 0.00 0.00 36.87 3.53
653 665 5.343593 CGCTCTACGTATCATCTGGAAAATC 59.656 44.000 0.00 0.00 36.87 2.17
657 669 4.130118 ACGTATCATCTGGAAAATCAGGC 58.870 43.478 0.00 0.00 35.58 4.85
659 671 2.787473 TCATCTGGAAAATCAGGCGT 57.213 45.000 0.00 0.00 35.58 5.68
718 739 2.784380 GCTATGAACAAGAGCGACTACG 59.216 50.000 0.00 0.00 42.93 3.51
724 745 1.064296 AAGAGCGACTACGGATGCG 59.936 57.895 4.58 4.58 40.15 4.73
740 761 2.586079 CGTCAGCACCCATAGCGG 60.586 66.667 0.00 0.00 37.01 5.52
744 765 4.864334 AGCACCCATAGCGGCTGC 62.864 66.667 13.86 10.33 43.24 5.25
756 777 0.589729 GCGGCTGCATTGATGTAACG 60.590 55.000 14.08 0.00 42.15 3.18
764 785 3.799963 TGCATTGATGTAACGGACGATAC 59.200 43.478 0.00 1.64 0.00 2.24
780 801 5.636121 GGACGATACAACACTCAAACATGTA 59.364 40.000 0.00 0.00 0.00 2.29
802 823 0.320421 TTACCGGTGCAAGTGCTCTC 60.320 55.000 19.93 0.00 42.66 3.20
808 829 1.071987 TGCAAGTGCTCTCCTGGTG 59.928 57.895 4.69 0.00 42.66 4.17
809 830 1.372683 GCAAGTGCTCTCCTGGTGA 59.627 57.895 0.00 0.00 38.21 4.02
810 831 0.250467 GCAAGTGCTCTCCTGGTGAA 60.250 55.000 0.00 0.00 38.21 3.18
811 832 1.612726 GCAAGTGCTCTCCTGGTGAAT 60.613 52.381 0.00 0.00 38.21 2.57
816 1671 5.957771 AGTGCTCTCCTGGTGAATAAATA 57.042 39.130 0.00 0.00 0.00 1.40
823 1678 7.068716 GCTCTCCTGGTGAATAAATACCAAAAT 59.931 37.037 0.00 0.00 45.65 1.82
824 1679 8.893563 TCTCCTGGTGAATAAATACCAAAATT 57.106 30.769 0.00 0.00 45.65 1.82
845 1700 7.807977 AATTTATGAAGATCGCTAACCACAT 57.192 32.000 0.00 0.00 0.00 3.21
851 1706 5.350365 TGAAGATCGCTAACCACATAAACAC 59.650 40.000 0.00 0.00 0.00 3.32
857 1713 4.927425 CGCTAACCACATAAACACTACTGT 59.073 41.667 0.00 0.00 0.00 3.55
861 1717 6.371809 AACCACATAAACACTACTGTTGTG 57.628 37.500 18.46 18.46 39.88 3.33
872 1728 4.512944 CACTACTGTTGTGTTGAAGCTCAT 59.487 41.667 13.13 0.00 0.00 2.90
881 1737 5.771469 TGTGTTGAAGCTCATAATTTGTGG 58.229 37.500 0.00 0.00 0.00 4.17
893 1749 2.837532 ATTTGTGGCATGGGTCAAAC 57.162 45.000 2.78 0.00 33.63 2.93
896 1752 1.489481 TGTGGCATGGGTCAAACAAA 58.511 45.000 0.00 0.00 0.00 2.83
898 1754 2.224233 TGTGGCATGGGTCAAACAAATG 60.224 45.455 0.00 0.00 0.00 2.32
905 1761 5.337491 GCATGGGTCAAACAAATGGATAGTT 60.337 40.000 0.00 0.00 0.00 2.24
925 1781 4.926238 AGTTTTTGTTGTGAAAATCGCACA 59.074 33.333 0.00 0.00 43.89 4.57
929 1785 6.926280 TTTGTTGTGAAAATCGCACATATC 57.074 33.333 0.00 0.00 44.81 1.63
931 1787 5.389778 TGTTGTGAAAATCGCACATATCAC 58.610 37.500 0.00 0.00 44.81 3.06
935 1791 5.181056 TGTGAAAATCGCACATATCACTGTT 59.819 36.000 9.44 0.00 41.00 3.16
936 1792 5.509272 GTGAAAATCGCACATATCACTGTTG 59.491 40.000 0.00 0.00 35.49 3.33
939 1795 2.892374 TCGCACATATCACTGTTGGAG 58.108 47.619 0.00 0.00 0.00 3.86
942 1798 3.429410 CGCACATATCACTGTTGGAGAGA 60.429 47.826 0.00 0.00 0.00 3.10
943 1799 4.701765 GCACATATCACTGTTGGAGAGAT 58.298 43.478 0.00 0.00 36.18 2.75
966 1822 9.398170 AGATATTGCATACAAATTTCGTATTGC 57.602 29.630 16.64 16.64 39.77 3.56
967 1823 9.179552 GATATTGCATACAAATTTCGTATTGCA 57.820 29.630 19.08 19.08 39.77 4.08
1011 1869 9.547753 CTTACTGTGCTATTTACAGATACCAAT 57.452 33.333 11.65 0.00 46.52 3.16
1037 1907 2.030185 GCCATCAGCCAGATAAATGCAG 60.030 50.000 0.00 0.00 34.43 4.41
1060 1930 4.103311 GGGGTATCTGCCAGAATAGTTTCT 59.897 45.833 0.00 0.00 43.09 2.52
1088 1958 5.163447 GCTATACATGTACCAGTTGTCCTCA 60.163 44.000 7.96 0.00 0.00 3.86
1125 1995 1.010419 GCGCCACAGGAAAATGCAAG 61.010 55.000 0.00 0.00 0.00 4.01
1133 2003 3.834231 ACAGGAAAATGCAAGCCAACTAT 59.166 39.130 0.00 0.00 0.00 2.12
1219 2093 7.254692 GGAGATAAATAACTCACTTAAACGGGC 60.255 40.741 0.00 0.00 35.17 6.13
1224 2098 1.628846 ACTCACTTAAACGGGCCATCT 59.371 47.619 4.39 0.00 0.00 2.90
1250 2124 5.484715 TGCAGGTGTTACTATTGGACTAAC 58.515 41.667 0.00 0.00 0.00 2.34
1589 2466 5.036090 CAGAGAGATCGACAAGTTCATCAG 58.964 45.833 0.00 0.00 0.00 2.90
1785 2680 2.683933 AGGGTCGCCACCGAGATT 60.684 61.111 0.00 0.00 45.38 2.40
1788 2683 2.434185 GTCGCCACCGAGATTGCA 60.434 61.111 0.00 0.00 45.38 4.08
1922 2817 4.271816 CGTCGAGGCTGATCCCGG 62.272 72.222 0.00 0.00 34.51 5.73
2084 2980 1.478510 AGCCGATCATTCAGAACGAGT 59.521 47.619 0.00 0.00 44.30 4.18
2173 3075 0.466372 TGGACGCTCAGATCCTCGAT 60.466 55.000 0.00 0.00 35.86 3.59
2189 3091 0.657840 CGATGAAGCGAATGGGGAAC 59.342 55.000 0.00 0.00 0.00 3.62
2544 3463 1.727022 CCTTTTGCTCGTGCTTGCG 60.727 57.895 11.19 0.00 40.48 4.85
2547 3466 0.316937 TTTTGCTCGTGCTTGCGAAG 60.317 50.000 11.19 0.00 40.57 3.79
2548 3467 1.436195 TTTGCTCGTGCTTGCGAAGT 61.436 50.000 11.19 0.00 40.57 3.01
2561 3480 6.033513 GTGCTTGCGAAGTCCAATTTTATAAC 59.966 38.462 0.00 0.00 0.00 1.89
2569 3488 9.763465 CGAAGTCCAATTTTATAACGTGTATTT 57.237 29.630 0.00 0.00 0.00 1.40
2615 3534 7.609760 AAAAGTGATTTCTTTTTGGACCAAC 57.390 32.000 6.36 0.00 42.58 3.77
2641 3560 1.619654 CCACCAATCAGCAGAACCAA 58.380 50.000 0.00 0.00 0.00 3.67
2645 3564 1.197721 CCAATCAGCAGAACCAACGAC 59.802 52.381 0.00 0.00 0.00 4.34
2689 3608 0.603975 AACAGAGCGCAAAGGAGGAC 60.604 55.000 11.47 0.00 0.00 3.85
2737 3656 2.887152 AGTCTGGATGGTGCTGTTTTTC 59.113 45.455 0.00 0.00 0.00 2.29
2765 3684 2.098443 ACCGTGCAATGAGAAACGTTTT 59.902 40.909 15.89 5.23 34.30 2.43
2766 3685 2.467305 CCGTGCAATGAGAAACGTTTTG 59.533 45.455 15.89 10.01 34.30 2.44
2777 3696 7.605410 TGAGAAACGTTTTGAGAAGTACTTT 57.395 32.000 15.89 0.00 0.00 2.66
2922 5195 0.323629 CCCAGAAGTCCTTTACCGCA 59.676 55.000 0.00 0.00 0.00 5.69
2978 5305 1.343465 AGGGGTGTACTTCTTCACACG 59.657 52.381 0.00 0.00 44.80 4.49
3052 5379 2.930562 AAGCCTGGCGAGGGAGTT 60.931 61.111 17.33 0.00 40.19 3.01
3054 5381 3.706373 GCCTGGCGAGGGAGTTGA 61.706 66.667 17.33 0.00 40.19 3.18
3071 5398 1.991121 TGACCACGACCTGACTAACT 58.009 50.000 0.00 0.00 0.00 2.24
3073 5400 3.079578 TGACCACGACCTGACTAACTAG 58.920 50.000 0.00 0.00 0.00 2.57
3114 5441 0.106149 ATCGCCTATTCGGGTTCCAC 59.894 55.000 0.00 0.00 0.00 4.02
3302 6666 5.127031 ACAAACACCAGAAACTAGTTGCAAT 59.873 36.000 16.18 0.00 0.00 3.56
3307 6671 5.705441 CACCAGAAACTAGTTGCAATTCCTA 59.295 40.000 16.18 0.00 0.00 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 8.717821 GCAGAACAACAATACATTCTAACTACA 58.282 33.333 0.00 0.00 30.28 2.74
5 6 8.717821 TGCAGAACAACAATACATTCTAACTAC 58.282 33.333 0.00 0.00 30.28 2.73
6 7 8.840833 TGCAGAACAACAATACATTCTAACTA 57.159 30.769 0.00 0.00 30.28 2.24
7 8 7.744087 TGCAGAACAACAATACATTCTAACT 57.256 32.000 0.00 0.00 30.28 2.24
8 9 8.795786 TTTGCAGAACAACAATACATTCTAAC 57.204 30.769 0.00 0.00 38.23 2.34
9 10 9.979578 ATTTTGCAGAACAACAATACATTCTAA 57.020 25.926 0.00 0.00 38.23 2.10
10 11 9.979578 AATTTTGCAGAACAACAATACATTCTA 57.020 25.926 0.00 0.00 38.23 2.10
11 12 8.891671 AATTTTGCAGAACAACAATACATTCT 57.108 26.923 0.00 0.00 38.23 2.40
12 13 9.372541 CAAATTTTGCAGAACAACAATACATTC 57.627 29.630 0.00 0.00 38.23 2.67
13 14 9.107177 TCAAATTTTGCAGAACAACAATACATT 57.893 25.926 4.19 0.00 38.23 2.71
14 15 8.659925 TCAAATTTTGCAGAACAACAATACAT 57.340 26.923 4.19 0.00 38.23 2.29
15 16 8.484641 TTCAAATTTTGCAGAACAACAATACA 57.515 26.923 4.19 0.00 38.23 2.29
16 17 8.603181 ACTTCAAATTTTGCAGAACAACAATAC 58.397 29.630 14.44 0.00 38.23 1.89
17 18 8.715191 ACTTCAAATTTTGCAGAACAACAATA 57.285 26.923 14.44 0.00 38.23 1.90
18 19 7.614124 ACTTCAAATTTTGCAGAACAACAAT 57.386 28.000 14.44 0.00 38.23 2.71
19 20 7.172190 TGAACTTCAAATTTTGCAGAACAACAA 59.828 29.630 14.44 0.00 38.23 2.83
20 21 6.648310 TGAACTTCAAATTTTGCAGAACAACA 59.352 30.769 14.44 5.42 38.23 3.33
21 22 7.059448 TGAACTTCAAATTTTGCAGAACAAC 57.941 32.000 14.44 3.44 38.23 3.32
22 23 7.846644 ATGAACTTCAAATTTTGCAGAACAA 57.153 28.000 14.44 0.00 36.13 2.83
23 24 8.980610 CATATGAACTTCAAATTTTGCAGAACA 58.019 29.630 14.44 12.81 0.00 3.18
24 25 8.981647 ACATATGAACTTCAAATTTTGCAGAAC 58.018 29.630 14.44 8.63 0.00 3.01
25 26 9.545105 AACATATGAACTTCAAATTTTGCAGAA 57.455 25.926 14.44 0.00 0.00 3.02
26 27 8.980610 CAACATATGAACTTCAAATTTTGCAGA 58.019 29.630 14.44 0.67 0.00 4.26
27 28 8.767085 ACAACATATGAACTTCAAATTTTGCAG 58.233 29.630 10.38 7.16 0.00 4.41
28 29 8.549548 CACAACATATGAACTTCAAATTTTGCA 58.450 29.630 10.38 0.00 0.00 4.08
29 30 8.550376 ACACAACATATGAACTTCAAATTTTGC 58.450 29.630 10.38 0.00 0.00 3.68
31 32 8.967218 CGACACAACATATGAACTTCAAATTTT 58.033 29.630 10.38 0.00 0.00 1.82
32 33 8.134895 ACGACACAACATATGAACTTCAAATTT 58.865 29.630 10.38 0.00 0.00 1.82
33 34 7.648142 ACGACACAACATATGAACTTCAAATT 58.352 30.769 10.38 0.00 0.00 1.82
34 35 7.202016 ACGACACAACATATGAACTTCAAAT 57.798 32.000 10.38 0.00 0.00 2.32
35 36 6.612247 ACGACACAACATATGAACTTCAAA 57.388 33.333 10.38 0.00 0.00 2.69
36 37 6.612247 AACGACACAACATATGAACTTCAA 57.388 33.333 10.38 0.00 0.00 2.69
37 38 6.258947 TCAAACGACACAACATATGAACTTCA 59.741 34.615 10.38 0.00 0.00 3.02
38 39 6.655062 TCAAACGACACAACATATGAACTTC 58.345 36.000 10.38 0.00 0.00 3.01
39 40 6.481976 TCTCAAACGACACAACATATGAACTT 59.518 34.615 10.38 0.00 0.00 2.66
40 41 5.989168 TCTCAAACGACACAACATATGAACT 59.011 36.000 10.38 0.00 0.00 3.01
41 42 6.145534 TCTCTCAAACGACACAACATATGAAC 59.854 38.462 10.38 0.00 0.00 3.18
42 43 6.220201 TCTCTCAAACGACACAACATATGAA 58.780 36.000 10.38 0.00 0.00 2.57
43 44 5.778862 TCTCTCAAACGACACAACATATGA 58.221 37.500 10.38 0.00 0.00 2.15
44 45 6.466308 TTCTCTCAAACGACACAACATATG 57.534 37.500 0.00 0.00 0.00 1.78
45 46 6.481976 TGTTTCTCTCAAACGACACAACATAT 59.518 34.615 0.00 0.00 33.05 1.78
46 47 5.813157 TGTTTCTCTCAAACGACACAACATA 59.187 36.000 0.00 0.00 33.05 2.29
47 48 4.634004 TGTTTCTCTCAAACGACACAACAT 59.366 37.500 0.00 0.00 33.05 2.71
48 49 3.997681 TGTTTCTCTCAAACGACACAACA 59.002 39.130 0.00 0.00 33.05 3.33
49 50 4.593597 TGTTTCTCTCAAACGACACAAC 57.406 40.909 0.00 0.00 33.05 3.32
50 51 5.614923 TTTGTTTCTCTCAAACGACACAA 57.385 34.783 0.00 0.00 30.54 3.33
51 52 5.614923 TTTTGTTTCTCTCAAACGACACA 57.385 34.783 0.00 0.00 35.05 3.72
83 84 2.855180 CATCAAGATCCGTGCAAACAC 58.145 47.619 0.00 0.00 43.76 3.32
84 85 1.199789 GCATCAAGATCCGTGCAAACA 59.800 47.619 0.00 0.00 37.52 2.83
85 86 1.199789 TGCATCAAGATCCGTGCAAAC 59.800 47.619 8.80 0.00 43.83 2.93
86 87 1.532523 TGCATCAAGATCCGTGCAAA 58.467 45.000 8.80 0.00 43.83 3.68
87 88 3.246403 TGCATCAAGATCCGTGCAA 57.754 47.368 8.80 0.00 43.83 4.08
89 90 3.969117 TTTATGCATCAAGATCCGTGC 57.031 42.857 0.19 0.00 38.05 5.34
90 91 4.516321 TCCATTTATGCATCAAGATCCGTG 59.484 41.667 0.19 0.00 0.00 4.94
91 92 4.717877 TCCATTTATGCATCAAGATCCGT 58.282 39.130 0.19 0.00 0.00 4.69
92 93 5.392703 CCATCCATTTATGCATCAAGATCCG 60.393 44.000 0.19 0.00 0.00 4.18
93 94 5.623824 GCCATCCATTTATGCATCAAGATCC 60.624 44.000 0.19 0.00 0.00 3.36
94 95 5.047590 TGCCATCCATTTATGCATCAAGATC 60.048 40.000 0.19 0.00 0.00 2.75
95 96 4.836175 TGCCATCCATTTATGCATCAAGAT 59.164 37.500 0.19 0.00 0.00 2.40
96 97 4.216708 TGCCATCCATTTATGCATCAAGA 58.783 39.130 0.19 0.00 0.00 3.02
97 98 4.594123 TGCCATCCATTTATGCATCAAG 57.406 40.909 0.19 0.00 0.00 3.02
98 99 5.128991 TCTTTGCCATCCATTTATGCATCAA 59.871 36.000 0.19 0.00 0.00 2.57
99 100 4.650131 TCTTTGCCATCCATTTATGCATCA 59.350 37.500 0.19 0.00 0.00 3.07
100 101 5.204409 TCTTTGCCATCCATTTATGCATC 57.796 39.130 0.19 0.00 0.00 3.91
101 102 5.818678 ATCTTTGCCATCCATTTATGCAT 57.181 34.783 3.79 3.79 0.00 3.96
102 103 6.239373 CCTTATCTTTGCCATCCATTTATGCA 60.239 38.462 0.00 0.00 0.00 3.96
103 104 6.161381 CCTTATCTTTGCCATCCATTTATGC 58.839 40.000 0.00 0.00 0.00 3.14
104 105 6.295462 CCCCTTATCTTTGCCATCCATTTATG 60.295 42.308 0.00 0.00 0.00 1.90
105 106 5.781818 CCCCTTATCTTTGCCATCCATTTAT 59.218 40.000 0.00 0.00 0.00 1.40
106 107 5.147032 CCCCTTATCTTTGCCATCCATTTA 58.853 41.667 0.00 0.00 0.00 1.40
107 108 3.969312 CCCCTTATCTTTGCCATCCATTT 59.031 43.478 0.00 0.00 0.00 2.32
108 109 3.051880 ACCCCTTATCTTTGCCATCCATT 60.052 43.478 0.00 0.00 0.00 3.16
109 110 2.519691 ACCCCTTATCTTTGCCATCCAT 59.480 45.455 0.00 0.00 0.00 3.41
110 111 1.929494 ACCCCTTATCTTTGCCATCCA 59.071 47.619 0.00 0.00 0.00 3.41
111 112 2.755952 ACCCCTTATCTTTGCCATCC 57.244 50.000 0.00 0.00 0.00 3.51
112 113 3.487372 GGTACCCCTTATCTTTGCCATC 58.513 50.000 0.00 0.00 0.00 3.51
113 114 2.158667 CGGTACCCCTTATCTTTGCCAT 60.159 50.000 6.25 0.00 0.00 4.40
114 115 1.210967 CGGTACCCCTTATCTTTGCCA 59.789 52.381 6.25 0.00 0.00 4.92
115 116 1.211212 ACGGTACCCCTTATCTTTGCC 59.789 52.381 6.25 0.00 0.00 4.52
116 117 2.285977 CACGGTACCCCTTATCTTTGC 58.714 52.381 6.25 0.00 0.00 3.68
117 118 3.622166 ACACGGTACCCCTTATCTTTG 57.378 47.619 6.25 0.00 0.00 2.77
118 119 3.133542 GCTACACGGTACCCCTTATCTTT 59.866 47.826 6.25 0.00 0.00 2.52
119 120 2.697229 GCTACACGGTACCCCTTATCTT 59.303 50.000 6.25 0.00 0.00 2.40
120 121 2.314246 GCTACACGGTACCCCTTATCT 58.686 52.381 6.25 0.00 0.00 1.98
121 122 1.000938 CGCTACACGGTACCCCTTATC 60.001 57.143 6.25 0.00 38.44 1.75
122 123 1.035139 CGCTACACGGTACCCCTTAT 58.965 55.000 6.25 0.00 38.44 1.73
123 124 2.492418 CGCTACACGGTACCCCTTA 58.508 57.895 6.25 0.00 38.44 2.69
124 125 3.291611 CGCTACACGGTACCCCTT 58.708 61.111 6.25 0.00 38.44 3.95
128 129 1.930908 AGCTCACGCTACACGGTACC 61.931 60.000 0.16 0.16 46.79 3.34
129 130 0.729116 TAGCTCACGCTACACGGTAC 59.271 55.000 0.00 0.00 46.79 3.34
130 131 3.157727 TAGCTCACGCTACACGGTA 57.842 52.632 0.00 0.00 46.79 4.02
131 132 3.991999 TAGCTCACGCTACACGGT 58.008 55.556 0.00 0.00 46.79 4.83
139 140 3.062234 GTGTGGTTTTCTATAGCTCACGC 59.938 47.826 0.00 0.00 30.94 5.34
140 141 4.495422 AGTGTGGTTTTCTATAGCTCACG 58.505 43.478 0.00 0.00 40.45 4.35
141 142 5.725362 AGAGTGTGGTTTTCTATAGCTCAC 58.275 41.667 0.00 0.00 37.61 3.51
142 143 5.717178 AGAGAGTGTGGTTTTCTATAGCTCA 59.283 40.000 0.00 0.00 0.00 4.26
143 144 6.215495 AGAGAGTGTGGTTTTCTATAGCTC 57.785 41.667 0.00 0.00 0.00 4.09
144 145 7.906199 ATAGAGAGTGTGGTTTTCTATAGCT 57.094 36.000 0.00 0.00 31.25 3.32
145 146 9.849166 GATATAGAGAGTGTGGTTTTCTATAGC 57.151 37.037 0.00 3.55 37.00 2.97
148 149 9.440761 AAGGATATAGAGAGTGTGGTTTTCTAT 57.559 33.333 0.00 0.00 35.75 1.98
149 150 8.840200 AAGGATATAGAGAGTGTGGTTTTCTA 57.160 34.615 0.00 0.00 0.00 2.10
150 151 7.741554 AAGGATATAGAGAGTGTGGTTTTCT 57.258 36.000 0.00 0.00 0.00 2.52
151 152 7.496263 GGAAAGGATATAGAGAGTGTGGTTTTC 59.504 40.741 0.00 0.00 0.00 2.29
152 153 7.182930 AGGAAAGGATATAGAGAGTGTGGTTTT 59.817 37.037 0.00 0.00 0.00 2.43
153 154 6.674419 AGGAAAGGATATAGAGAGTGTGGTTT 59.326 38.462 0.00 0.00 0.00 3.27
154 155 6.206042 AGGAAAGGATATAGAGAGTGTGGTT 58.794 40.000 0.00 0.00 0.00 3.67
155 156 5.782925 AGGAAAGGATATAGAGAGTGTGGT 58.217 41.667 0.00 0.00 0.00 4.16
156 157 5.835819 TGAGGAAAGGATATAGAGAGTGTGG 59.164 44.000 0.00 0.00 0.00 4.17
157 158 6.549364 ACTGAGGAAAGGATATAGAGAGTGTG 59.451 42.308 0.00 0.00 0.00 3.82
158 159 6.678547 ACTGAGGAAAGGATATAGAGAGTGT 58.321 40.000 0.00 0.00 0.00 3.55
159 160 7.595819 AACTGAGGAAAGGATATAGAGAGTG 57.404 40.000 0.00 0.00 0.00 3.51
160 161 8.507761 ACTAACTGAGGAAAGGATATAGAGAGT 58.492 37.037 0.00 0.00 0.00 3.24
161 162 8.934023 ACTAACTGAGGAAAGGATATAGAGAG 57.066 38.462 0.00 0.00 0.00 3.20
162 163 9.716556 AAACTAACTGAGGAAAGGATATAGAGA 57.283 33.333 0.00 0.00 0.00 3.10
198 199 3.797039 AGCGCATCTAACTAAGATTGCA 58.203 40.909 11.47 0.00 42.62 4.08
254 263 9.909644 CCATATTACTTGTCGCTAACTTAGTAT 57.090 33.333 0.00 0.00 30.83 2.12
263 272 6.377429 CCTCCTATCCATATTACTTGTCGCTA 59.623 42.308 0.00 0.00 0.00 4.26
283 292 8.934023 TCAAACAAAATAGTGTATTTCCTCCT 57.066 30.769 0.00 0.00 37.39 3.69
291 300 9.142515 CACATGCATTCAAACAAAATAGTGTAT 57.857 29.630 0.00 0.00 0.00 2.29
348 357 8.328758 TCATATACTGTTGAAGGTGGAAAGAAT 58.671 33.333 0.00 0.00 0.00 2.40
379 388 3.365364 GGACAATTCGTTCTTGGCTGAAG 60.365 47.826 0.00 0.00 32.00 3.02
408 417 1.160137 GGATGCTCATATTCCCGCAC 58.840 55.000 0.00 0.00 34.93 5.34
443 452 0.250858 TGCAAAGCAGCCAAGCTCTA 60.251 50.000 0.00 0.00 45.89 2.43
481 490 0.739813 GTCGTCCCTGGTGTACATGC 60.740 60.000 0.00 0.00 0.00 4.06
502 511 6.151817 GCAGTCATTTTAAGGACCAGAAGAAT 59.848 38.462 3.87 0.00 40.35 2.40
520 532 0.244994 ACGAGCTTTCGAGCAGTCAT 59.755 50.000 1.98 0.00 37.25 3.06
527 539 1.332178 GTCTGTGACGAGCTTTCGAG 58.668 55.000 1.98 0.00 36.85 4.04
533 545 5.532779 TCAATAGATATGTCTGTGACGAGCT 59.467 40.000 1.62 0.00 34.95 4.09
561 573 1.075542 CGCGAACTTGCAAGATACCA 58.924 50.000 32.50 0.00 34.15 3.25
578 590 2.423446 CTGGCCCTGATACCTCGC 59.577 66.667 0.00 0.00 0.00 5.03
579 591 1.762460 ACCTGGCCCTGATACCTCG 60.762 63.158 0.00 0.00 0.00 4.63
588 600 0.032813 CCATGAAATCACCTGGCCCT 60.033 55.000 0.00 0.00 0.00 5.19
614 626 3.103911 GCGTGGAGTCCGTGTTCG 61.104 66.667 4.30 5.54 0.00 3.95
619 631 2.396955 CGTAGAGCGTGGAGTCCGT 61.397 63.158 4.30 0.00 35.54 4.69
638 650 4.129380 CACGCCTGATTTTCCAGATGATA 58.871 43.478 0.00 0.00 36.29 2.15
649 661 1.238439 CACTTCACCACGCCTGATTT 58.762 50.000 0.00 0.00 0.00 2.17
653 665 2.669569 CCCACTTCACCACGCCTG 60.670 66.667 0.00 0.00 0.00 4.85
657 669 1.086696 CAATAGCCCACTTCACCACG 58.913 55.000 0.00 0.00 0.00 4.94
659 671 4.018870 TGTTATCAATAGCCCACTTCACCA 60.019 41.667 0.00 0.00 0.00 4.17
699 717 3.011818 TCCGTAGTCGCTCTTGTTCATA 58.988 45.455 0.00 0.00 35.54 2.15
724 745 2.897350 GCCGCTATGGGTGCTGAC 60.897 66.667 0.00 0.00 38.63 3.51
735 756 1.939934 GTTACATCAATGCAGCCGCTA 59.060 47.619 0.00 0.00 39.64 4.26
740 761 1.267532 CGTCCGTTACATCAATGCAGC 60.268 52.381 0.00 0.00 0.00 5.25
744 765 5.289917 TGTTGTATCGTCCGTTACATCAATG 59.710 40.000 14.50 0.00 32.08 2.82
745 766 5.290158 GTGTTGTATCGTCCGTTACATCAAT 59.710 40.000 16.85 0.00 34.54 2.57
756 777 4.451096 ACATGTTTGAGTGTTGTATCGTCC 59.549 41.667 0.00 0.00 0.00 4.79
764 785 5.333798 CGGTAACCTACATGTTTGAGTGTTG 60.334 44.000 2.30 0.00 0.00 3.33
780 801 1.599797 GCACTTGCACCGGTAACCT 60.600 57.895 6.87 0.00 41.59 3.50
816 1671 7.122055 TGGTTAGCGATCTTCATAAATTTTGGT 59.878 33.333 0.00 0.00 0.00 3.67
823 1678 8.609176 GTTTATGTGGTTAGCGATCTTCATAAA 58.391 33.333 0.00 0.00 35.56 1.40
824 1679 7.766738 TGTTTATGTGGTTAGCGATCTTCATAA 59.233 33.333 0.00 0.00 0.00 1.90
834 1689 4.927425 ACAGTAGTGTTTATGTGGTTAGCG 59.073 41.667 0.00 0.00 30.30 4.26
851 1706 6.785488 TTATGAGCTTCAACACAACAGTAG 57.215 37.500 0.00 0.00 0.00 2.57
857 1713 6.215121 CCACAAATTATGAGCTTCAACACAA 58.785 36.000 0.00 0.00 0.00 3.33
861 1717 4.808558 TGCCACAAATTATGAGCTTCAAC 58.191 39.130 0.00 0.00 34.38 3.18
872 1728 3.643320 TGTTTGACCCATGCCACAAATTA 59.357 39.130 10.73 4.07 35.31 1.40
881 1737 3.615224 ATCCATTTGTTTGACCCATGC 57.385 42.857 0.00 0.00 0.00 4.06
896 1752 7.116233 GCGATTTTCACAACAAAAACTATCCAT 59.884 33.333 0.00 0.00 0.00 3.41
898 1754 6.419413 TGCGATTTTCACAACAAAAACTATCC 59.581 34.615 0.00 0.00 0.00 2.59
905 1761 6.920210 TGATATGTGCGATTTTCACAACAAAA 59.080 30.769 0.00 0.00 46.07 2.44
920 1776 2.862536 CTCTCCAACAGTGATATGTGCG 59.137 50.000 0.00 0.00 32.52 5.34
925 1781 7.071069 TGCAATATCTCTCCAACAGTGATAT 57.929 36.000 0.00 1.92 44.77 1.63
929 1785 6.051074 TGTATGCAATATCTCTCCAACAGTG 58.949 40.000 0.00 0.00 0.00 3.66
931 1787 7.558161 TTTGTATGCAATATCTCTCCAACAG 57.442 36.000 0.00 0.00 34.18 3.16
935 1791 7.498900 ACGAAATTTGTATGCAATATCTCTCCA 59.501 33.333 0.00 0.00 34.18 3.86
936 1792 7.865707 ACGAAATTTGTATGCAATATCTCTCC 58.134 34.615 0.00 0.00 34.18 3.71
942 1798 8.967218 GTGCAATACGAAATTTGTATGCAATAT 58.033 29.630 21.03 1.54 37.70 1.28
943 1799 7.970614 TGTGCAATACGAAATTTGTATGCAATA 59.029 29.630 21.03 14.87 37.70 1.90
964 1820 8.481314 AGTAAGATCTCTGATTATCTTTGTGCA 58.519 33.333 16.09 0.00 41.50 4.57
966 1822 9.814899 ACAGTAAGATCTCTGATTATCTTTGTG 57.185 33.333 16.22 15.23 41.50 3.33
967 1823 9.814899 CACAGTAAGATCTCTGATTATCTTTGT 57.185 33.333 16.22 13.33 41.50 2.83
1011 1869 1.499368 TATCTGGCTGATGGCACTCA 58.501 50.000 16.17 0.00 44.10 3.41
1037 1907 4.103311 AGAAACTATTCTGGCAGATACCCC 59.897 45.833 19.50 5.03 44.25 4.95
1060 1930 6.294361 ACAACTGGTACATGTATAGCTTCA 57.706 37.500 9.18 1.26 38.20 3.02
1074 1944 2.976185 TGTTCCATGAGGACAACTGGTA 59.024 45.455 0.00 0.00 45.73 3.25
1088 1958 3.316308 GGCGCTATTGAAATCTGTTCCAT 59.684 43.478 7.64 0.00 0.00 3.41
1109 1979 0.680618 TGGCTTGCATTTTCCTGTGG 59.319 50.000 0.00 0.00 0.00 4.17
1159 2029 7.769044 AGCAGAAACCATAATACGTATGAACTT 59.231 33.333 9.24 0.00 42.07 2.66
1169 2039 9.944376 TCCAAGATATAGCAGAAACCATAATAC 57.056 33.333 0.00 0.00 0.00 1.89
1175 2047 6.753913 ATCTCCAAGATATAGCAGAAACCA 57.246 37.500 0.00 0.00 32.12 3.67
1176 2048 9.732130 ATTTATCTCCAAGATATAGCAGAAACC 57.268 33.333 0.00 0.00 37.09 3.27
1192 2065 7.767198 CCCGTTTAAGTGAGTTATTTATCTCCA 59.233 37.037 0.00 0.00 0.00 3.86
1219 2093 6.205464 CCAATAGTAACACCTGCAATAGATGG 59.795 42.308 0.00 0.00 0.00 3.51
1224 2098 6.308015 AGTCCAATAGTAACACCTGCAATA 57.692 37.500 0.00 0.00 0.00 1.90
1250 2124 1.303888 AGAATGCCTGCACCACTGG 60.304 57.895 0.00 0.00 40.30 4.00
1579 2456 1.205893 GGAGACCTCGCTGATGAACTT 59.794 52.381 0.00 0.00 0.00 2.66
1589 2466 0.523966 CGATAGGATGGAGACCTCGC 59.476 60.000 0.00 0.00 38.76 5.03
1638 2515 3.252701 CAGATTCTAGGCAACATCCATGC 59.747 47.826 0.00 0.00 43.08 4.06
1827 2722 3.351794 TGACGTCTCTGTGTAGGATCT 57.648 47.619 17.92 0.00 0.00 2.75
1922 2817 1.199558 GACTAGGTGTGTCTGGTCGAC 59.800 57.143 7.13 7.13 43.14 4.20
2084 2980 1.134699 CAGGTTCTGCTTCTCGCCATA 60.135 52.381 0.00 0.00 38.05 2.74
2173 3075 1.376683 CCGTTCCCCATTCGCTTCA 60.377 57.895 0.00 0.00 0.00 3.02
2189 3091 2.360350 AGCCATGCACAGAACCCG 60.360 61.111 0.00 0.00 0.00 5.28
2407 3326 0.815734 CCTGCTCTTGGCTGAATTGG 59.184 55.000 0.00 0.00 41.52 3.16
2497 3416 6.233905 AGGATACACACAACTGTATATGCA 57.766 37.500 0.00 0.00 37.45 3.96
2527 3446 0.316937 TTCGCAAGCACGAGCAAAAG 60.317 50.000 7.77 0.00 44.00 2.27
2587 3506 8.482128 TGGTCCAAAAAGAAATCACTTTTACAT 58.518 29.630 0.00 0.00 45.43 2.29
2601 3520 2.661718 GTCCAGGTTGGTCCAAAAAGA 58.338 47.619 5.69 0.00 39.03 2.52
2645 3564 2.486472 ACAGAGGAGACAAAGGCATG 57.514 50.000 0.00 0.00 0.00 4.06
2720 3639 2.665165 ACAGAAAAACAGCACCATCCA 58.335 42.857 0.00 0.00 0.00 3.41
2724 3643 2.165437 GTGGAACAGAAAAACAGCACCA 59.835 45.455 0.00 0.00 41.80 4.17
2737 3656 0.518636 CTCATTGCACGGTGGAACAG 59.481 55.000 17.44 12.83 41.80 3.16
2765 3684 9.607988 TGTTTCTCATAACAAAAGTACTTCTCA 57.392 29.630 8.95 0.00 35.22 3.27
2839 3758 8.689061 TCTAAAATACGCTAAAGTGGATACTCA 58.311 33.333 0.00 0.00 35.69 3.41
2840 3759 9.182933 CTCTAAAATACGCTAAAGTGGATACTC 57.817 37.037 0.00 0.00 35.69 2.59
2841 3760 8.693625 ACTCTAAAATACGCTAAAGTGGATACT 58.306 33.333 0.00 0.00 39.32 2.12
2842 3761 8.868635 ACTCTAAAATACGCTAAAGTGGATAC 57.131 34.615 0.00 0.00 0.00 2.24
2844 3763 9.694137 GATACTCTAAAATACGCTAAAGTGGAT 57.306 33.333 0.00 0.00 0.00 3.41
2845 3764 8.139989 GGATACTCTAAAATACGCTAAAGTGGA 58.860 37.037 0.00 0.00 0.00 4.02
2847 3766 8.753175 GTGGATACTCTAAAATACGCTAAAGTG 58.247 37.037 0.00 0.00 37.61 3.16
2849 3768 9.530633 AAGTGGATACTCTAAAATACGCTAAAG 57.469 33.333 0.00 0.00 40.12 1.85
2850 3769 9.880157 AAAGTGGATACTCTAAAATACGCTAAA 57.120 29.630 0.00 0.00 40.12 1.85
2851 3770 9.525409 GAAAGTGGATACTCTAAAATACGCTAA 57.475 33.333 0.00 0.00 40.12 3.09
2852 3771 8.689061 TGAAAGTGGATACTCTAAAATACGCTA 58.311 33.333 0.00 0.00 40.12 4.26
2922 5195 1.878088 TCTATTCGAATAGCCGCGTCT 59.122 47.619 31.65 0.00 38.57 4.18
3052 5379 1.991121 AGTTAGTCAGGTCGTGGTCA 58.009 50.000 0.00 0.00 0.00 4.02
3054 5381 2.444421 CCTAGTTAGTCAGGTCGTGGT 58.556 52.381 0.00 0.00 0.00 4.16
3071 5398 2.312140 ACCTGGACTAGAGACTTGCCTA 59.688 50.000 0.00 0.00 0.00 3.93
3073 5400 1.562783 ACCTGGACTAGAGACTTGCC 58.437 55.000 0.00 0.00 0.00 4.52
3302 6666 2.577700 GCCTCGATCTCTGTCTAGGAA 58.422 52.381 0.00 0.00 33.98 3.36
3307 6671 1.686355 AATCGCCTCGATCTCTGTCT 58.314 50.000 2.01 0.00 46.30 3.41


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

AutoCloner maintained by Alex Coulton.