Multiple sequence alignment - TraesCS6B01G218200

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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 TraesCS6B01G218200 chr6B 100.000 2304 0 0 1 2304 300936378 300938681 0.000000e+00 4255.0
1 TraesCS6B01G218200 chr6D 93.120 1933 77 23 412 2304 193574460 193572544 0.000000e+00 2782.0
2 TraesCS6B01G218200 chr6A 96.777 1272 30 3 1036 2304 268588080 268586817 0.000000e+00 2111.0
3 TraesCS6B01G218200 chrUn 86.108 943 104 18 412 1331 21283659 21282721 0.000000e+00 990.0
4 TraesCS6B01G218200 chr5D 85.288 938 110 13 413 1326 324982113 324983046 0.000000e+00 942.0
5 TraesCS6B01G218200 chr5D 81.866 943 144 14 412 1330 502650138 502649199 0.000000e+00 769.0
6 TraesCS6B01G218200 chr3D 85.135 888 101 19 464 1329 537040008 537040886 0.000000e+00 880.0
7 TraesCS6B01G218200 chr5B 83.944 928 121 14 413 1317 377481240 377482162 0.000000e+00 863.0
8 TraesCS6B01G218200 chr5B 79.644 393 60 7 1 376 197126178 197125789 4.880000e-67 265.0
9 TraesCS6B01G218200 chr2B 82.109 939 139 19 412 1326 542235040 542235973 0.000000e+00 776.0
10 TraesCS6B01G218200 chr2B 81.830 776 111 20 412 1162 540310674 540309904 1.940000e-175 625.0
11 TraesCS6B01G218200 chr1A 82.239 929 132 22 414 1316 502817311 502816390 0.000000e+00 771.0
12 TraesCS6B01G218200 chr1A 88.889 630 47 13 719 1327 561332902 561333529 0.000000e+00 754.0
13 TraesCS6B01G218200 chr3B 81.462 944 146 20 410 1327 252244955 252244015 0.000000e+00 747.0
14 TraesCS6B01G218200 chr3B 94.872 39 2 0 135 173 489371489 489371451 6.870000e-06 62.1
15 TraesCS6B01G218200 chr5A 81.728 903 135 21 412 1289 608984407 608983510 0.000000e+00 726.0
16 TraesCS6B01G218200 chr2A 85.441 680 66 19 413 1062 456500942 456501618 0.000000e+00 676.0
17 TraesCS6B01G218200 chr7D 86.828 577 53 12 770 1327 124606290 124605718 6.990000e-175 623.0
18 TraesCS6B01G218200 chr1D 82.265 733 106 19 618 1331 142333984 142333257 1.510000e-171 612.0
19 TraesCS6B01G218200 chr7B 82.315 622 89 10 725 1327 442357081 442356462 9.430000e-144 520.0
20 TraesCS6B01G218200 chr4D 84.240 533 68 11 412 930 372343122 372342592 2.640000e-139 505.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G218200 chr6B 300936378 300938681 2303 False 4255 4255 100.000 1 2304 1 chr6B.!!$F1 2303
1 TraesCS6B01G218200 chr6D 193572544 193574460 1916 True 2782 2782 93.120 412 2304 1 chr6D.!!$R1 1892
2 TraesCS6B01G218200 chr6A 268586817 268588080 1263 True 2111 2111 96.777 1036 2304 1 chr6A.!!$R1 1268
3 TraesCS6B01G218200 chrUn 21282721 21283659 938 True 990 990 86.108 412 1331 1 chrUn.!!$R1 919
4 TraesCS6B01G218200 chr5D 324982113 324983046 933 False 942 942 85.288 413 1326 1 chr5D.!!$F1 913
5 TraesCS6B01G218200 chr5D 502649199 502650138 939 True 769 769 81.866 412 1330 1 chr5D.!!$R1 918
6 TraesCS6B01G218200 chr3D 537040008 537040886 878 False 880 880 85.135 464 1329 1 chr3D.!!$F1 865
7 TraesCS6B01G218200 chr5B 377481240 377482162 922 False 863 863 83.944 413 1317 1 chr5B.!!$F1 904
8 TraesCS6B01G218200 chr2B 542235040 542235973 933 False 776 776 82.109 412 1326 1 chr2B.!!$F1 914
9 TraesCS6B01G218200 chr2B 540309904 540310674 770 True 625 625 81.830 412 1162 1 chr2B.!!$R1 750
10 TraesCS6B01G218200 chr1A 502816390 502817311 921 True 771 771 82.239 414 1316 1 chr1A.!!$R1 902
11 TraesCS6B01G218200 chr1A 561332902 561333529 627 False 754 754 88.889 719 1327 1 chr1A.!!$F1 608
12 TraesCS6B01G218200 chr3B 252244015 252244955 940 True 747 747 81.462 410 1327 1 chr3B.!!$R1 917
13 TraesCS6B01G218200 chr5A 608983510 608984407 897 True 726 726 81.728 412 1289 1 chr5A.!!$R1 877
14 TraesCS6B01G218200 chr2A 456500942 456501618 676 False 676 676 85.441 413 1062 1 chr2A.!!$F1 649
15 TraesCS6B01G218200 chr7D 124605718 124606290 572 True 623 623 86.828 770 1327 1 chr7D.!!$R1 557
16 TraesCS6B01G218200 chr1D 142333257 142333984 727 True 612 612 82.265 618 1331 1 chr1D.!!$R1 713
17 TraesCS6B01G218200 chr7B 442356462 442357081 619 True 520 520 82.315 725 1327 1 chr7B.!!$R1 602
18 TraesCS6B01G218200 chr4D 372342592 372343122 530 True 505 505 84.240 412 930 1 chr4D.!!$R1 518

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
601 612 0.03582 TATGTTGGTGAGGCGGTTCC 60.036 55.0 0.0 0.0 0.0 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1680 1754 1.153005 GAGAGCTGATTGCCAGGGG 60.153 63.158 0.0 0.0 43.13 4.79 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
17 18 3.564474 ATCCCTCCTCCCCTCCAA 58.436 61.111 0.00 0.00 0.00 3.53
18 19 1.804502 ATCCCTCCTCCCCTCCAAA 59.195 57.895 0.00 0.00 0.00 3.28
19 20 0.327964 ATCCCTCCTCCCCTCCAAAG 60.328 60.000 0.00 0.00 0.00 2.77
20 21 2.003548 CCCTCCTCCCCTCCAAAGG 61.004 68.421 0.00 0.00 42.95 3.11
31 32 2.562953 TCCAAAGGGGAAAGGCAGA 58.437 52.632 0.00 0.00 44.80 4.26
32 33 0.405585 TCCAAAGGGGAAAGGCAGAG 59.594 55.000 0.00 0.00 44.80 3.35
33 34 1.253593 CCAAAGGGGAAAGGCAGAGC 61.254 60.000 0.00 0.00 40.01 4.09
34 35 0.251519 CAAAGGGGAAAGGCAGAGCT 60.252 55.000 0.00 0.00 0.00 4.09
35 36 0.251519 AAAGGGGAAAGGCAGAGCTG 60.252 55.000 0.00 0.00 0.00 4.24
36 37 1.136329 AAGGGGAAAGGCAGAGCTGA 61.136 55.000 0.85 0.00 0.00 4.26
37 38 1.377856 GGGGAAAGGCAGAGCTGAC 60.378 63.158 0.85 0.00 39.43 3.51
45 46 2.307934 GGCAGAGCTGACTTTCTAGG 57.692 55.000 0.85 0.00 35.21 3.02
46 47 1.134551 GGCAGAGCTGACTTTCTAGGG 60.135 57.143 0.85 0.00 35.21 3.53
47 48 1.742071 GCAGAGCTGACTTTCTAGGGC 60.742 57.143 0.85 0.00 0.00 5.19
48 49 0.820871 AGAGCTGACTTTCTAGGGCG 59.179 55.000 0.00 0.00 0.00 6.13
49 50 0.818296 GAGCTGACTTTCTAGGGCGA 59.182 55.000 0.00 0.00 0.00 5.54
50 51 0.533032 AGCTGACTTTCTAGGGCGAC 59.467 55.000 0.00 0.00 0.00 5.19
65 66 3.354089 GGCGACCACAATGGATTTATG 57.646 47.619 0.84 0.00 40.96 1.90
66 67 2.034558 GGCGACCACAATGGATTTATGG 59.965 50.000 0.84 0.00 40.96 2.74
67 68 2.543653 GCGACCACAATGGATTTATGGC 60.544 50.000 0.84 0.00 40.96 4.40
68 69 2.286950 CGACCACAATGGATTTATGGCG 60.287 50.000 0.84 0.00 40.96 5.69
69 70 1.408702 ACCACAATGGATTTATGGCGC 59.591 47.619 0.00 0.00 40.96 6.53
70 71 1.682854 CCACAATGGATTTATGGCGCT 59.317 47.619 7.64 0.00 40.96 5.92
71 72 2.544277 CCACAATGGATTTATGGCGCTG 60.544 50.000 7.64 0.00 40.96 5.18
72 73 1.067516 ACAATGGATTTATGGCGCTGC 59.932 47.619 7.64 0.00 0.00 5.25
73 74 1.338973 CAATGGATTTATGGCGCTGCT 59.661 47.619 7.64 0.00 0.00 4.24
74 75 0.956633 ATGGATTTATGGCGCTGCTG 59.043 50.000 7.64 0.00 0.00 4.41
75 76 1.008079 GGATTTATGGCGCTGCTGC 60.008 57.895 7.64 5.34 0.00 5.25
115 116 4.493747 GACCCGCGGTCCGAAGAG 62.494 72.222 26.12 8.44 46.19 2.85
119 120 4.194720 CGCGGTCCGAAGAGGGAG 62.195 72.222 17.49 0.00 41.52 4.30
120 121 3.839432 GCGGTCCGAAGAGGGAGG 61.839 72.222 17.49 0.00 41.52 4.30
121 122 3.148279 CGGTCCGAAGAGGGAGGG 61.148 72.222 4.91 0.00 41.52 4.30
122 123 2.363361 GGTCCGAAGAGGGAGGGA 59.637 66.667 0.00 0.00 41.52 4.20
123 124 1.758906 GGTCCGAAGAGGGAGGGAG 60.759 68.421 0.00 0.00 41.52 4.30
124 125 1.758906 GTCCGAAGAGGGAGGGAGG 60.759 68.421 0.00 0.00 41.52 4.30
125 126 2.444895 CCGAAGAGGGAGGGAGGG 60.445 72.222 0.00 0.00 35.97 4.30
126 127 2.364961 CGAAGAGGGAGGGAGGGT 59.635 66.667 0.00 0.00 0.00 4.34
127 128 1.306226 CGAAGAGGGAGGGAGGGTT 60.306 63.158 0.00 0.00 0.00 4.11
128 129 1.617947 CGAAGAGGGAGGGAGGGTTG 61.618 65.000 0.00 0.00 0.00 3.77
129 130 1.229984 AAGAGGGAGGGAGGGTTGG 60.230 63.158 0.00 0.00 0.00 3.77
130 131 1.761780 AAGAGGGAGGGAGGGTTGGA 61.762 60.000 0.00 0.00 0.00 3.53
131 132 1.004891 GAGGGAGGGAGGGTTGGAT 59.995 63.158 0.00 0.00 0.00 3.41
132 133 1.308216 AGGGAGGGAGGGTTGGATG 60.308 63.158 0.00 0.00 0.00 3.51
133 134 1.619669 GGGAGGGAGGGTTGGATGT 60.620 63.158 0.00 0.00 0.00 3.06
134 135 1.636769 GGGAGGGAGGGTTGGATGTC 61.637 65.000 0.00 0.00 0.00 3.06
135 136 0.621862 GGAGGGAGGGTTGGATGTCT 60.622 60.000 0.00 0.00 0.00 3.41
136 137 0.833949 GAGGGAGGGTTGGATGTCTC 59.166 60.000 0.00 0.00 0.00 3.36
137 138 0.419459 AGGGAGGGTTGGATGTCTCT 59.581 55.000 0.00 0.00 0.00 3.10
138 139 0.833949 GGGAGGGTTGGATGTCTCTC 59.166 60.000 0.00 0.00 0.00 3.20
139 140 0.833949 GGAGGGTTGGATGTCTCTCC 59.166 60.000 0.00 0.00 34.78 3.71
140 141 0.833949 GAGGGTTGGATGTCTCTCCC 59.166 60.000 0.00 0.00 34.12 4.30
141 142 0.621862 AGGGTTGGATGTCTCTCCCC 60.622 60.000 0.00 0.00 35.90 4.81
142 143 1.522569 GGTTGGATGTCTCTCCCCG 59.477 63.158 0.00 0.00 34.12 5.73
143 144 1.522569 GTTGGATGTCTCTCCCCGG 59.477 63.158 0.00 0.00 34.12 5.73
144 145 0.976073 GTTGGATGTCTCTCCCCGGA 60.976 60.000 0.73 0.00 34.12 5.14
145 146 0.687757 TTGGATGTCTCTCCCCGGAG 60.688 60.000 0.73 4.21 43.21 4.63
146 147 2.503382 GGATGTCTCTCCCCGGAGC 61.503 68.421 0.73 0.00 41.71 4.70
147 148 1.758514 GATGTCTCTCCCCGGAGCA 60.759 63.158 0.73 0.00 41.71 4.26
148 149 1.743321 GATGTCTCTCCCCGGAGCAG 61.743 65.000 0.73 5.13 41.71 4.24
149 150 3.151022 GTCTCTCCCCGGAGCAGG 61.151 72.222 0.73 0.00 41.71 4.85
150 151 3.347590 TCTCTCCCCGGAGCAGGA 61.348 66.667 0.73 0.00 41.71 3.86
151 152 2.123077 CTCTCCCCGGAGCAGGAT 60.123 66.667 0.73 0.00 41.71 3.24
152 153 1.764054 CTCTCCCCGGAGCAGGATT 60.764 63.158 0.73 0.00 41.71 3.01
153 154 1.753368 CTCTCCCCGGAGCAGGATTC 61.753 65.000 0.73 0.00 41.71 2.52
154 155 3.154473 TCCCCGGAGCAGGATTCG 61.154 66.667 0.73 0.00 0.00 3.34
155 156 3.470888 CCCCGGAGCAGGATTCGT 61.471 66.667 0.73 0.00 0.00 3.85
156 157 2.202932 CCCGGAGCAGGATTCGTG 60.203 66.667 0.73 1.98 0.00 4.35
157 158 2.202932 CCGGAGCAGGATTCGTGG 60.203 66.667 0.00 0.00 0.00 4.94
158 159 2.892425 CGGAGCAGGATTCGTGGC 60.892 66.667 8.33 1.54 0.00 5.01
159 160 2.892425 GGAGCAGGATTCGTGGCG 60.892 66.667 8.33 0.00 0.00 5.69
160 161 2.892425 GAGCAGGATTCGTGGCGG 60.892 66.667 8.33 0.00 0.00 6.13
161 162 3.371097 GAGCAGGATTCGTGGCGGA 62.371 63.158 8.33 0.00 0.00 5.54
162 163 2.892425 GCAGGATTCGTGGCGGAG 60.892 66.667 8.33 0.00 0.00 4.63
163 164 2.202932 CAGGATTCGTGGCGGAGG 60.203 66.667 0.00 0.00 0.00 4.30
175 176 4.598894 CGGAGGCGCTGGATCTGG 62.599 72.222 7.64 0.00 0.00 3.86
176 177 3.157252 GGAGGCGCTGGATCTGGA 61.157 66.667 7.64 0.00 0.00 3.86
177 178 2.420890 GAGGCGCTGGATCTGGAG 59.579 66.667 7.64 0.00 0.00 3.86
178 179 2.042537 AGGCGCTGGATCTGGAGA 60.043 61.111 7.64 0.00 0.00 3.71
179 180 2.107953 GGCGCTGGATCTGGAGAC 59.892 66.667 7.64 0.00 0.00 3.36
180 181 2.107953 GCGCTGGATCTGGAGACC 59.892 66.667 0.00 0.00 0.00 3.85
181 182 2.415010 CGCTGGATCTGGAGACCG 59.585 66.667 0.00 0.00 0.00 4.79
182 183 2.107953 GCTGGATCTGGAGACCGC 59.892 66.667 0.00 0.00 0.00 5.68
183 184 2.415010 CTGGATCTGGAGACCGCG 59.585 66.667 0.00 0.00 0.00 6.46
184 185 2.362503 TGGATCTGGAGACCGCGT 60.363 61.111 4.92 0.00 0.00 6.01
185 186 2.105128 GGATCTGGAGACCGCGTG 59.895 66.667 4.92 0.00 0.00 5.34
186 187 2.583593 GATCTGGAGACCGCGTGC 60.584 66.667 4.92 0.00 0.00 5.34
187 188 4.148825 ATCTGGAGACCGCGTGCC 62.149 66.667 4.92 0.65 0.00 5.01
200 201 4.704833 GTGCCCGAAGCCTGCAGA 62.705 66.667 17.39 0.00 42.71 4.26
201 202 4.704833 TGCCCGAAGCCTGCAGAC 62.705 66.667 17.39 2.52 42.71 3.51
205 206 4.069232 CGAAGCCTGCAGACCGGA 62.069 66.667 17.39 0.00 0.00 5.14
206 207 2.125350 GAAGCCTGCAGACCGGAG 60.125 66.667 17.39 0.00 0.00 4.63
207 208 4.400961 AAGCCTGCAGACCGGAGC 62.401 66.667 17.39 8.93 0.00 4.70
214 215 4.803426 CAGACCGGAGCAGGCGAC 62.803 72.222 9.46 0.00 33.69 5.19
258 259 3.680786 GCCGGGCAAAGGGTTGTC 61.681 66.667 15.62 0.00 38.72 3.18
259 260 3.361977 CCGGGCAAAGGGTTGTCG 61.362 66.667 0.00 0.00 40.46 4.35
260 261 2.593436 CGGGCAAAGGGTTGTCGT 60.593 61.111 0.00 0.00 40.46 4.34
261 262 2.613506 CGGGCAAAGGGTTGTCGTC 61.614 63.158 0.00 0.00 40.46 4.20
262 263 2.265904 GGGCAAAGGGTTGTCGTCC 61.266 63.158 0.00 0.00 40.46 4.79
263 264 2.265904 GGCAAAGGGTTGTCGTCCC 61.266 63.158 0.00 0.00 44.90 4.46
270 271 0.820226 GGGTTGTCGTCCCTACTACC 59.180 60.000 0.00 0.00 41.58 3.18
271 272 0.453390 GGTTGTCGTCCCTACTACCG 59.547 60.000 0.00 0.00 34.02 4.02
272 273 1.168714 GTTGTCGTCCCTACTACCGT 58.831 55.000 0.00 0.00 0.00 4.83
273 274 1.541588 GTTGTCGTCCCTACTACCGTT 59.458 52.381 0.00 0.00 0.00 4.44
274 275 1.167851 TGTCGTCCCTACTACCGTTG 58.832 55.000 0.00 0.00 0.00 4.10
275 276 0.453390 GTCGTCCCTACTACCGTTGG 59.547 60.000 0.00 0.00 36.04 3.77
276 277 0.327924 TCGTCCCTACTACCGTTGGA 59.672 55.000 0.00 0.00 38.14 3.53
277 278 1.064463 TCGTCCCTACTACCGTTGGAT 60.064 52.381 0.00 0.00 38.14 3.41
278 279 1.336125 CGTCCCTACTACCGTTGGATC 59.664 57.143 0.00 0.00 38.14 3.36
279 280 1.685517 GTCCCTACTACCGTTGGATCC 59.314 57.143 4.20 4.20 38.14 3.36
280 281 1.288633 TCCCTACTACCGTTGGATCCA 59.711 52.381 11.44 11.44 38.14 3.41
281 282 1.411612 CCCTACTACCGTTGGATCCAC 59.588 57.143 15.91 9.07 38.14 4.02
282 283 1.066605 CCTACTACCGTTGGATCCACG 59.933 57.143 15.91 20.04 38.14 4.94
286 287 2.819595 CCGTTGGATCCACGGCTG 60.820 66.667 30.00 15.47 40.25 4.85
287 288 3.499737 CGTTGGATCCACGGCTGC 61.500 66.667 15.91 0.00 0.00 5.25
288 289 3.499737 GTTGGATCCACGGCTGCG 61.500 66.667 15.91 0.00 0.00 5.18
289 290 3.700970 TTGGATCCACGGCTGCGA 61.701 61.111 15.91 0.00 0.00 5.10
290 291 3.664025 TTGGATCCACGGCTGCGAG 62.664 63.158 15.91 0.00 0.00 5.03
356 357 4.559063 CAGCGGCATGGGGAGGAG 62.559 72.222 1.45 0.00 0.00 3.69
360 361 4.864334 GGCATGGGGAGGAGCGTG 62.864 72.222 0.00 0.00 0.00 5.34
361 362 4.864334 GCATGGGGAGGAGCGTGG 62.864 72.222 0.00 0.00 0.00 4.94
362 363 4.864334 CATGGGGAGGAGCGTGGC 62.864 72.222 0.00 0.00 0.00 5.01
364 365 3.696518 ATGGGGAGGAGCGTGGCTA 62.697 63.158 0.00 0.00 39.88 3.93
365 366 3.081409 GGGGAGGAGCGTGGCTAA 61.081 66.667 0.00 0.00 39.88 3.09
366 367 2.187163 GGGAGGAGCGTGGCTAAC 59.813 66.667 0.00 0.00 39.88 2.34
367 368 2.187163 GGAGGAGCGTGGCTAACC 59.813 66.667 0.00 0.00 39.88 2.85
368 369 2.359967 GGAGGAGCGTGGCTAACCT 61.360 63.158 0.00 0.00 39.88 3.50
369 370 1.041447 GGAGGAGCGTGGCTAACCTA 61.041 60.000 0.00 0.00 39.88 3.08
370 371 0.386113 GAGGAGCGTGGCTAACCTAG 59.614 60.000 0.00 0.00 39.88 3.02
371 372 1.043673 AGGAGCGTGGCTAACCTAGG 61.044 60.000 7.41 7.41 39.88 3.02
372 373 1.041447 GGAGCGTGGCTAACCTAGGA 61.041 60.000 17.98 0.00 39.88 2.94
373 374 0.386113 GAGCGTGGCTAACCTAGGAG 59.614 60.000 17.98 4.16 39.88 3.69
374 375 1.227292 GCGTGGCTAACCTAGGAGC 60.227 63.158 17.98 15.06 38.00 4.70
375 376 1.065928 CGTGGCTAACCTAGGAGCG 59.934 63.158 17.98 3.62 39.72 5.03
376 377 1.664321 CGTGGCTAACCTAGGAGCGT 61.664 60.000 17.98 0.00 39.72 5.07
377 378 0.535797 GTGGCTAACCTAGGAGCGTT 59.464 55.000 17.98 1.06 39.72 4.84
378 379 0.822164 TGGCTAACCTAGGAGCGTTC 59.178 55.000 17.98 3.13 39.72 3.95
379 380 1.112950 GGCTAACCTAGGAGCGTTCT 58.887 55.000 17.98 0.00 39.72 3.01
380 381 1.481363 GGCTAACCTAGGAGCGTTCTT 59.519 52.381 17.98 0.00 39.72 2.52
381 382 2.481622 GGCTAACCTAGGAGCGTTCTTC 60.482 54.545 17.98 0.00 39.72 2.87
382 383 2.427812 GCTAACCTAGGAGCGTTCTTCT 59.572 50.000 17.98 0.00 31.67 2.85
383 384 3.735514 GCTAACCTAGGAGCGTTCTTCTG 60.736 52.174 17.98 0.00 29.02 3.02
384 385 1.187087 ACCTAGGAGCGTTCTTCTGG 58.813 55.000 17.98 0.76 29.02 3.86
385 386 1.272536 ACCTAGGAGCGTTCTTCTGGA 60.273 52.381 17.98 0.00 28.35 3.86
386 387 1.825474 CCTAGGAGCGTTCTTCTGGAA 59.175 52.381 1.05 0.00 28.35 3.53
387 388 2.432510 CCTAGGAGCGTTCTTCTGGAAT 59.567 50.000 1.05 0.00 36.24 3.01
388 389 3.118592 CCTAGGAGCGTTCTTCTGGAATT 60.119 47.826 1.05 0.00 36.24 2.17
389 390 4.099573 CCTAGGAGCGTTCTTCTGGAATTA 59.900 45.833 1.05 0.00 36.24 1.40
390 391 4.553330 AGGAGCGTTCTTCTGGAATTAA 57.447 40.909 0.00 0.00 36.24 1.40
391 392 5.104259 AGGAGCGTTCTTCTGGAATTAAT 57.896 39.130 0.00 0.00 36.24 1.40
392 393 4.878397 AGGAGCGTTCTTCTGGAATTAATG 59.122 41.667 0.00 0.00 36.24 1.90
393 394 4.035675 GGAGCGTTCTTCTGGAATTAATGG 59.964 45.833 0.00 0.00 36.24 3.16
394 395 3.378427 AGCGTTCTTCTGGAATTAATGGC 59.622 43.478 0.00 0.00 36.24 4.40
395 396 3.378427 GCGTTCTTCTGGAATTAATGGCT 59.622 43.478 0.00 0.00 36.24 4.75
396 397 4.496507 GCGTTCTTCTGGAATTAATGGCTC 60.497 45.833 0.00 0.00 36.24 4.70
397 398 4.035675 CGTTCTTCTGGAATTAATGGCTCC 59.964 45.833 0.00 0.00 36.24 4.70
398 399 4.170468 TCTTCTGGAATTAATGGCTCCC 57.830 45.455 2.82 0.00 0.00 4.30
399 400 3.117512 TCTTCTGGAATTAATGGCTCCCC 60.118 47.826 2.82 0.00 0.00 4.81
400 401 2.502745 TCTGGAATTAATGGCTCCCCT 58.497 47.619 2.82 0.00 0.00 4.79
401 402 2.175499 TCTGGAATTAATGGCTCCCCTG 59.825 50.000 2.82 0.00 0.00 4.45
402 403 1.929494 TGGAATTAATGGCTCCCCTGT 59.071 47.619 2.82 0.00 0.00 4.00
403 404 2.314549 TGGAATTAATGGCTCCCCTGTT 59.685 45.455 2.82 0.00 0.00 3.16
404 405 3.245948 TGGAATTAATGGCTCCCCTGTTT 60.246 43.478 2.82 0.00 0.00 2.83
405 406 4.017037 TGGAATTAATGGCTCCCCTGTTTA 60.017 41.667 2.82 0.00 0.00 2.01
406 407 4.341235 GGAATTAATGGCTCCCCTGTTTAC 59.659 45.833 0.00 0.00 0.00 2.01
407 408 4.881157 ATTAATGGCTCCCCTGTTTACT 57.119 40.909 0.00 0.00 0.00 2.24
408 409 2.514458 AATGGCTCCCCTGTTTACTG 57.486 50.000 0.00 0.00 0.00 2.74
409 410 1.668826 ATGGCTCCCCTGTTTACTGA 58.331 50.000 0.00 0.00 0.00 3.41
410 411 1.668826 TGGCTCCCCTGTTTACTGAT 58.331 50.000 0.00 0.00 0.00 2.90
419 420 2.236395 CCTGTTTACTGATCCTCCCGTT 59.764 50.000 0.00 0.00 0.00 4.44
457 458 8.863872 AGCAAATAGACACATAAAAGTTACCT 57.136 30.769 0.00 0.00 0.00 3.08
480 484 3.053826 AGTTCCTACTTGTCCCTTTGGT 58.946 45.455 0.00 0.00 0.00 3.67
487 491 3.976015 ACTTGTCCCTTTGGTTCAGAAA 58.024 40.909 0.00 0.00 0.00 2.52
498 503 6.200854 CCTTTGGTTCAGAAAATACAAAGCAC 59.799 38.462 17.31 0.00 41.87 4.40
532 537 2.951642 TGTGAGAAAGCAAAGGAGGTTG 59.048 45.455 0.00 0.00 0.00 3.77
554 561 0.835941 GAGTGCTGGGACTGGATCAT 59.164 55.000 0.00 0.00 0.00 2.45
601 612 0.035820 TATGTTGGTGAGGCGGTTCC 60.036 55.000 0.00 0.00 0.00 3.62
699 727 7.094549 GCAATTACAACTTGGTACTTATGGTGA 60.095 37.037 8.01 0.00 0.00 4.02
819 851 9.969001 ACATACCAAAGGCTACTATAAAAAGAA 57.031 29.630 0.00 0.00 0.00 2.52
827 859 7.696017 AGGCTACTATAAAAAGAAAGGGTTGA 58.304 34.615 0.00 0.00 0.00 3.18
829 861 8.799367 GGCTACTATAAAAAGAAAGGGTTGAAA 58.201 33.333 0.00 0.00 0.00 2.69
919 965 5.402398 GTGCTGTTTTGAGGGATGATAAAC 58.598 41.667 0.00 0.00 0.00 2.01
1079 1144 7.872993 GGTCATCGAAACCATGAATAATAGAGA 59.127 37.037 13.84 0.00 36.75 3.10
1087 1152 6.884832 ACCATGAATAATAGAGAACGGTTGA 58.115 36.000 0.00 0.00 0.00 3.18
1102 1167 1.497991 GTTGACAAGTACAGCAGCGA 58.502 50.000 0.00 0.00 0.00 4.93
1350 1418 2.747396 AAAACCTACATGCGTACCGA 57.253 45.000 0.00 0.00 0.00 4.69
1820 1894 4.452114 TCTGTCGTGGTGAAATCATCAAAG 59.548 41.667 0.00 0.00 38.92 2.77
1987 2061 4.447290 TCCTTATCATCCGATTTTTGCGA 58.553 39.130 0.00 0.00 32.73 5.10
2110 2184 6.566753 GCAGAGAGAAAACACCACTAAACATC 60.567 42.308 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.003548 CCTTTGGAGGGGAGGAGGG 61.004 68.421 0.00 0.00 39.55 4.30
3 4 3.746957 CCTTTGGAGGGGAGGAGG 58.253 66.667 0.00 0.00 39.55 4.30
11 12 0.613012 CTGCCTTTCCCCTTTGGAGG 60.613 60.000 0.00 0.00 46.24 4.30
12 13 0.405585 TCTGCCTTTCCCCTTTGGAG 59.594 55.000 0.00 0.00 46.24 3.86
13 14 0.405585 CTCTGCCTTTCCCCTTTGGA 59.594 55.000 0.00 0.00 43.18 3.53
14 15 1.253593 GCTCTGCCTTTCCCCTTTGG 61.254 60.000 0.00 0.00 0.00 3.28
15 16 0.251519 AGCTCTGCCTTTCCCCTTTG 60.252 55.000 0.00 0.00 0.00 2.77
16 17 0.251519 CAGCTCTGCCTTTCCCCTTT 60.252 55.000 0.00 0.00 0.00 3.11
17 18 1.136329 TCAGCTCTGCCTTTCCCCTT 61.136 55.000 0.00 0.00 0.00 3.95
18 19 1.539869 TCAGCTCTGCCTTTCCCCT 60.540 57.895 0.00 0.00 0.00 4.79
19 20 1.377856 GTCAGCTCTGCCTTTCCCC 60.378 63.158 0.00 0.00 0.00 4.81
20 21 0.037447 AAGTCAGCTCTGCCTTTCCC 59.963 55.000 0.00 0.00 0.00 3.97
21 22 1.809547 GAAAGTCAGCTCTGCCTTTCC 59.190 52.381 17.72 5.21 44.89 3.13
23 24 2.947127 AGAAAGTCAGCTCTGCCTTT 57.053 45.000 5.71 5.71 40.87 3.11
24 25 2.235898 CCTAGAAAGTCAGCTCTGCCTT 59.764 50.000 0.00 0.00 29.04 4.35
25 26 1.830477 CCTAGAAAGTCAGCTCTGCCT 59.170 52.381 0.00 0.00 0.00 4.75
26 27 1.134551 CCCTAGAAAGTCAGCTCTGCC 60.135 57.143 0.00 0.00 0.00 4.85
27 28 1.742071 GCCCTAGAAAGTCAGCTCTGC 60.742 57.143 0.00 0.00 0.00 4.26
28 29 1.470632 CGCCCTAGAAAGTCAGCTCTG 60.471 57.143 0.00 0.00 0.00 3.35
29 30 0.820871 CGCCCTAGAAAGTCAGCTCT 59.179 55.000 0.00 0.00 0.00 4.09
30 31 0.818296 TCGCCCTAGAAAGTCAGCTC 59.182 55.000 0.00 0.00 0.00 4.09
31 32 0.533032 GTCGCCCTAGAAAGTCAGCT 59.467 55.000 0.00 0.00 0.00 4.24
32 33 0.460459 GGTCGCCCTAGAAAGTCAGC 60.460 60.000 0.00 0.00 0.00 4.26
33 34 0.895530 TGGTCGCCCTAGAAAGTCAG 59.104 55.000 0.00 0.00 0.00 3.51
34 35 0.606604 GTGGTCGCCCTAGAAAGTCA 59.393 55.000 0.00 0.00 0.00 3.41
35 36 0.606604 TGTGGTCGCCCTAGAAAGTC 59.393 55.000 0.00 0.00 0.00 3.01
36 37 1.053424 TTGTGGTCGCCCTAGAAAGT 58.947 50.000 0.00 0.00 0.00 2.66
37 38 2.009774 CATTGTGGTCGCCCTAGAAAG 58.990 52.381 0.00 0.00 0.00 2.62
38 39 1.339631 CCATTGTGGTCGCCCTAGAAA 60.340 52.381 0.00 0.00 31.35 2.52
39 40 0.251916 CCATTGTGGTCGCCCTAGAA 59.748 55.000 0.00 0.00 31.35 2.10
40 41 0.616395 TCCATTGTGGTCGCCCTAGA 60.616 55.000 0.00 0.00 39.03 2.43
41 42 0.469917 ATCCATTGTGGTCGCCCTAG 59.530 55.000 0.00 0.00 39.03 3.02
42 43 0.916086 AATCCATTGTGGTCGCCCTA 59.084 50.000 0.00 0.00 39.03 3.53
43 44 0.039618 AAATCCATTGTGGTCGCCCT 59.960 50.000 0.00 0.00 39.03 5.19
44 45 1.757682 TAAATCCATTGTGGTCGCCC 58.242 50.000 0.00 0.00 39.03 6.13
45 46 2.034558 CCATAAATCCATTGTGGTCGCC 59.965 50.000 0.00 0.00 43.36 5.54
46 47 3.354089 CCATAAATCCATTGTGGTCGC 57.646 47.619 0.00 0.00 43.36 5.19
51 52 2.734670 CAGCGCCATAAATCCATTGTG 58.265 47.619 2.29 0.00 0.00 3.33
52 53 1.067516 GCAGCGCCATAAATCCATTGT 59.932 47.619 2.29 0.00 0.00 2.71
53 54 1.338973 AGCAGCGCCATAAATCCATTG 59.661 47.619 2.29 0.00 0.00 2.82
54 55 1.338973 CAGCAGCGCCATAAATCCATT 59.661 47.619 2.29 0.00 0.00 3.16
55 56 0.956633 CAGCAGCGCCATAAATCCAT 59.043 50.000 2.29 0.00 0.00 3.41
56 57 1.727511 GCAGCAGCGCCATAAATCCA 61.728 55.000 2.29 0.00 0.00 3.41
57 58 1.008079 GCAGCAGCGCCATAAATCC 60.008 57.895 2.29 0.00 0.00 3.01
58 59 4.622364 GCAGCAGCGCCATAAATC 57.378 55.556 2.29 0.00 0.00 2.17
102 103 4.194720 CTCCCTCTTCGGACCGCG 62.195 72.222 9.66 0.00 33.16 6.46
103 104 3.839432 CCTCCCTCTTCGGACCGC 61.839 72.222 9.66 0.00 33.16 5.68
104 105 3.148279 CCCTCCCTCTTCGGACCG 61.148 72.222 7.84 7.84 33.16 4.79
105 106 1.758906 CTCCCTCCCTCTTCGGACC 60.759 68.421 0.00 0.00 33.16 4.46
106 107 1.758906 CCTCCCTCCCTCTTCGGAC 60.759 68.421 0.00 0.00 33.16 4.79
107 108 2.690452 CCTCCCTCCCTCTTCGGA 59.310 66.667 0.00 0.00 33.16 4.55
108 109 2.444895 CCCTCCCTCCCTCTTCGG 60.445 72.222 0.00 0.00 0.00 4.30
109 110 1.306226 AACCCTCCCTCCCTCTTCG 60.306 63.158 0.00 0.00 0.00 3.79
110 111 1.275421 CCAACCCTCCCTCCCTCTTC 61.275 65.000 0.00 0.00 0.00 2.87
111 112 1.229984 CCAACCCTCCCTCCCTCTT 60.230 63.158 0.00 0.00 0.00 2.85
112 113 1.541168 ATCCAACCCTCCCTCCCTCT 61.541 60.000 0.00 0.00 0.00 3.69
113 114 1.004891 ATCCAACCCTCCCTCCCTC 59.995 63.158 0.00 0.00 0.00 4.30
114 115 1.308216 CATCCAACCCTCCCTCCCT 60.308 63.158 0.00 0.00 0.00 4.20
115 116 1.619669 ACATCCAACCCTCCCTCCC 60.620 63.158 0.00 0.00 0.00 4.30
116 117 0.621862 AGACATCCAACCCTCCCTCC 60.622 60.000 0.00 0.00 0.00 4.30
117 118 0.833949 GAGACATCCAACCCTCCCTC 59.166 60.000 0.00 0.00 0.00 4.30
118 119 0.419459 AGAGACATCCAACCCTCCCT 59.581 55.000 0.00 0.00 0.00 4.20
119 120 0.833949 GAGAGACATCCAACCCTCCC 59.166 60.000 0.00 0.00 0.00 4.30
120 121 0.833949 GGAGAGACATCCAACCCTCC 59.166 60.000 0.00 0.00 39.34 4.30
121 122 0.833949 GGGAGAGACATCCAACCCTC 59.166 60.000 0.00 0.00 41.52 4.30
122 123 0.621862 GGGGAGAGACATCCAACCCT 60.622 60.000 0.00 0.00 41.52 4.34
123 124 1.915983 GGGGAGAGACATCCAACCC 59.084 63.158 0.00 0.00 41.52 4.11
124 125 1.522569 CGGGGAGAGACATCCAACC 59.477 63.158 0.00 0.00 41.52 3.77
125 126 0.976073 TCCGGGGAGAGACATCCAAC 60.976 60.000 0.00 0.00 41.52 3.77
126 127 0.687757 CTCCGGGGAGAGACATCCAA 60.688 60.000 9.15 0.00 44.53 3.53
127 128 1.075970 CTCCGGGGAGAGACATCCA 60.076 63.158 9.15 0.00 44.53 3.41
128 129 2.503382 GCTCCGGGGAGAGACATCC 61.503 68.421 18.75 0.00 44.53 3.51
129 130 1.743321 CTGCTCCGGGGAGAGACATC 61.743 65.000 18.75 0.17 44.53 3.06
130 131 1.760086 CTGCTCCGGGGAGAGACAT 60.760 63.158 18.75 0.00 44.53 3.06
131 132 2.363018 CTGCTCCGGGGAGAGACA 60.363 66.667 18.75 6.18 44.53 3.41
132 133 2.937959 ATCCTGCTCCGGGGAGAGAC 62.938 65.000 18.75 1.60 44.53 3.36
133 134 2.243774 AATCCTGCTCCGGGGAGAGA 62.244 60.000 18.75 11.18 44.53 3.10
134 135 1.753368 GAATCCTGCTCCGGGGAGAG 61.753 65.000 18.75 11.84 44.53 3.20
135 136 1.762460 GAATCCTGCTCCGGGGAGA 60.762 63.158 18.75 0.00 44.53 3.71
136 137 2.825264 GAATCCTGCTCCGGGGAG 59.175 66.667 4.80 10.44 44.56 4.30
137 138 3.154473 CGAATCCTGCTCCGGGGA 61.154 66.667 4.80 1.38 35.96 4.81
138 139 3.470888 ACGAATCCTGCTCCGGGG 61.471 66.667 0.00 0.00 0.00 5.73
139 140 2.202932 CACGAATCCTGCTCCGGG 60.203 66.667 0.00 0.00 0.00 5.73
140 141 2.202932 CCACGAATCCTGCTCCGG 60.203 66.667 0.00 0.00 0.00 5.14
141 142 2.892425 GCCACGAATCCTGCTCCG 60.892 66.667 0.00 0.00 0.00 4.63
142 143 2.892425 CGCCACGAATCCTGCTCC 60.892 66.667 0.00 0.00 0.00 4.70
143 144 2.892425 CCGCCACGAATCCTGCTC 60.892 66.667 0.00 0.00 0.00 4.26
144 145 3.376935 CTCCGCCACGAATCCTGCT 62.377 63.158 0.00 0.00 0.00 4.24
145 146 2.892425 CTCCGCCACGAATCCTGC 60.892 66.667 0.00 0.00 0.00 4.85
146 147 2.202932 CCTCCGCCACGAATCCTG 60.203 66.667 0.00 0.00 0.00 3.86
147 148 4.162690 GCCTCCGCCACGAATCCT 62.163 66.667 0.00 0.00 0.00 3.24
158 159 4.598894 CCAGATCCAGCGCCTCCG 62.599 72.222 2.29 0.00 37.57 4.63
159 160 3.157252 TCCAGATCCAGCGCCTCC 61.157 66.667 2.29 0.00 0.00 4.30
160 161 2.130426 TCTCCAGATCCAGCGCCTC 61.130 63.158 2.29 0.00 0.00 4.70
161 162 2.042537 TCTCCAGATCCAGCGCCT 60.043 61.111 2.29 0.00 0.00 5.52
162 163 2.107953 GTCTCCAGATCCAGCGCC 59.892 66.667 2.29 0.00 0.00 6.53
163 164 2.107953 GGTCTCCAGATCCAGCGC 59.892 66.667 0.00 0.00 0.00 5.92
164 165 2.415010 CGGTCTCCAGATCCAGCG 59.585 66.667 0.00 0.00 0.00 5.18
165 166 2.107953 GCGGTCTCCAGATCCAGC 59.892 66.667 0.00 0.00 0.00 4.85
166 167 2.415010 CGCGGTCTCCAGATCCAG 59.585 66.667 0.00 0.00 0.00 3.86
167 168 2.362503 ACGCGGTCTCCAGATCCA 60.363 61.111 12.47 0.00 0.00 3.41
168 169 2.105128 CACGCGGTCTCCAGATCC 59.895 66.667 12.47 0.00 0.00 3.36
169 170 2.583593 GCACGCGGTCTCCAGATC 60.584 66.667 12.47 0.00 0.00 2.75
170 171 4.148825 GGCACGCGGTCTCCAGAT 62.149 66.667 12.47 0.00 0.00 2.90
183 184 4.704833 TCTGCAGGCTTCGGGCAC 62.705 66.667 15.13 0.00 44.01 5.01
184 185 4.704833 GTCTGCAGGCTTCGGGCA 62.705 66.667 12.09 0.00 44.01 5.36
188 189 3.997064 CTCCGGTCTGCAGGCTTCG 62.997 68.421 19.48 14.06 0.00 3.79
189 190 2.125350 CTCCGGTCTGCAGGCTTC 60.125 66.667 19.48 0.74 0.00 3.86
190 191 4.400961 GCTCCGGTCTGCAGGCTT 62.401 66.667 19.48 0.00 0.00 4.35
193 194 4.463879 CCTGCTCCGGTCTGCAGG 62.464 72.222 33.31 33.31 45.89 4.85
197 198 4.803426 GTCGCCTGCTCCGGTCTG 62.803 72.222 0.00 0.00 0.00 3.51
241 242 3.680786 GACAACCCTTTGCCCGGC 61.681 66.667 1.04 1.04 36.00 6.13
242 243 3.361977 CGACAACCCTTTGCCCGG 61.362 66.667 0.00 0.00 36.00 5.73
243 244 2.593436 ACGACAACCCTTTGCCCG 60.593 61.111 0.00 0.00 37.80 6.13
244 245 2.265904 GGACGACAACCCTTTGCCC 61.266 63.158 0.00 0.00 36.00 5.36
245 246 2.265904 GGGACGACAACCCTTTGCC 61.266 63.158 0.00 0.00 43.65 4.52
246 247 3.351450 GGGACGACAACCCTTTGC 58.649 61.111 0.00 0.00 43.65 3.68
252 253 0.453390 CGGTAGTAGGGACGACAACC 59.547 60.000 0.00 0.00 36.07 3.77
253 254 1.168714 ACGGTAGTAGGGACGACAAC 58.831 55.000 0.00 0.00 36.07 3.32
254 255 1.541147 CAACGGTAGTAGGGACGACAA 59.459 52.381 0.00 0.00 36.07 3.18
255 256 1.167851 CAACGGTAGTAGGGACGACA 58.832 55.000 0.00 0.00 36.07 4.35
256 257 0.453390 CCAACGGTAGTAGGGACGAC 59.547 60.000 0.00 0.00 0.00 4.34
257 258 0.327924 TCCAACGGTAGTAGGGACGA 59.672 55.000 0.00 0.00 31.53 4.20
258 259 1.336125 GATCCAACGGTAGTAGGGACG 59.664 57.143 0.00 0.00 36.97 4.79
259 260 1.685517 GGATCCAACGGTAGTAGGGAC 59.314 57.143 6.95 0.00 36.97 4.46
260 261 1.288633 TGGATCCAACGGTAGTAGGGA 59.711 52.381 13.46 0.00 38.02 4.20
261 262 1.411612 GTGGATCCAACGGTAGTAGGG 59.588 57.143 18.20 0.00 0.00 3.53
262 263 1.066605 CGTGGATCCAACGGTAGTAGG 59.933 57.143 18.20 0.00 0.00 3.18
263 264 1.066605 CCGTGGATCCAACGGTAGTAG 59.933 57.143 31.32 15.67 41.62 2.57
264 265 1.105457 CCGTGGATCCAACGGTAGTA 58.895 55.000 31.32 3.52 41.62 1.82
265 266 1.895238 CCGTGGATCCAACGGTAGT 59.105 57.895 31.32 0.00 41.62 2.73
266 267 4.827481 CCGTGGATCCAACGGTAG 57.173 61.111 31.32 16.68 41.62 3.18
270 271 3.499737 GCAGCCGTGGATCCAACG 61.500 66.667 18.20 20.81 0.00 4.10
271 272 3.499737 CGCAGCCGTGGATCCAAC 61.500 66.667 18.20 9.37 0.00 3.77
272 273 3.664025 CTCGCAGCCGTGGATCCAA 62.664 63.158 18.20 0.00 35.54 3.53
273 274 4.147449 CTCGCAGCCGTGGATCCA 62.147 66.667 11.44 11.44 35.54 3.41
339 340 4.559063 CTCCTCCCCATGCCGCTG 62.559 72.222 0.00 0.00 0.00 5.18
343 344 4.864334 CACGCTCCTCCCCATGCC 62.864 72.222 0.00 0.00 0.00 4.40
344 345 4.864334 CCACGCTCCTCCCCATGC 62.864 72.222 0.00 0.00 0.00 4.06
345 346 4.864334 GCCACGCTCCTCCCCATG 62.864 72.222 0.00 0.00 0.00 3.66
346 347 3.696518 TAGCCACGCTCCTCCCCAT 62.697 63.158 0.00 0.00 40.44 4.00
347 348 3.916438 TTAGCCACGCTCCTCCCCA 62.916 63.158 0.00 0.00 40.44 4.96
348 349 3.081409 TTAGCCACGCTCCTCCCC 61.081 66.667 0.00 0.00 40.44 4.81
349 350 2.187163 GTTAGCCACGCTCCTCCC 59.813 66.667 0.00 0.00 40.44 4.30
350 351 1.041447 TAGGTTAGCCACGCTCCTCC 61.041 60.000 0.00 0.00 40.44 4.30
351 352 0.386113 CTAGGTTAGCCACGCTCCTC 59.614 60.000 0.00 0.00 40.44 3.71
352 353 1.043673 CCTAGGTTAGCCACGCTCCT 61.044 60.000 0.00 0.00 40.44 3.69
353 354 1.041447 TCCTAGGTTAGCCACGCTCC 61.041 60.000 9.08 0.00 40.44 4.70
354 355 0.386113 CTCCTAGGTTAGCCACGCTC 59.614 60.000 9.08 0.00 40.44 5.03
355 356 1.677637 GCTCCTAGGTTAGCCACGCT 61.678 60.000 9.08 0.00 43.41 5.07
356 357 1.227292 GCTCCTAGGTTAGCCACGC 60.227 63.158 9.08 0.00 37.19 5.34
357 358 1.065928 CGCTCCTAGGTTAGCCACG 59.934 63.158 15.07 4.24 35.22 4.94
358 359 0.535797 AACGCTCCTAGGTTAGCCAC 59.464 55.000 15.07 0.00 35.22 5.01
359 360 0.822164 GAACGCTCCTAGGTTAGCCA 59.178 55.000 15.07 0.00 35.22 4.75
360 361 1.112950 AGAACGCTCCTAGGTTAGCC 58.887 55.000 15.07 3.64 35.22 3.93
361 362 2.427812 AGAAGAACGCTCCTAGGTTAGC 59.572 50.000 9.08 10.57 35.33 3.09
362 363 3.181485 CCAGAAGAACGCTCCTAGGTTAG 60.181 52.174 9.08 0.22 0.00 2.34
363 364 2.758979 CCAGAAGAACGCTCCTAGGTTA 59.241 50.000 9.08 0.00 0.00 2.85
364 365 1.550976 CCAGAAGAACGCTCCTAGGTT 59.449 52.381 9.08 0.00 0.00 3.50
365 366 1.187087 CCAGAAGAACGCTCCTAGGT 58.813 55.000 9.08 0.00 0.00 3.08
366 367 1.475403 TCCAGAAGAACGCTCCTAGG 58.525 55.000 0.82 0.82 0.00 3.02
367 368 3.810310 ATTCCAGAAGAACGCTCCTAG 57.190 47.619 0.00 0.00 37.29 3.02
368 369 5.670792 TTAATTCCAGAAGAACGCTCCTA 57.329 39.130 0.00 0.00 37.29 2.94
369 370 4.553330 TTAATTCCAGAAGAACGCTCCT 57.447 40.909 0.00 0.00 37.29 3.69
370 371 4.035675 CCATTAATTCCAGAAGAACGCTCC 59.964 45.833 0.00 0.00 37.29 4.70
371 372 4.496507 GCCATTAATTCCAGAAGAACGCTC 60.497 45.833 0.00 0.00 37.29 5.03
372 373 3.378427 GCCATTAATTCCAGAAGAACGCT 59.622 43.478 0.00 0.00 37.29 5.07
373 374 3.378427 AGCCATTAATTCCAGAAGAACGC 59.622 43.478 0.00 0.00 37.29 4.84
374 375 4.035675 GGAGCCATTAATTCCAGAAGAACG 59.964 45.833 0.54 0.00 37.29 3.95
375 376 4.339530 GGGAGCCATTAATTCCAGAAGAAC 59.660 45.833 6.93 0.00 37.29 3.01
376 377 4.536765 GGGAGCCATTAATTCCAGAAGAA 58.463 43.478 6.93 0.00 39.32 2.52
377 378 3.117512 GGGGAGCCATTAATTCCAGAAGA 60.118 47.826 6.93 0.00 32.50 2.87
378 379 3.117360 AGGGGAGCCATTAATTCCAGAAG 60.117 47.826 6.93 0.00 32.50 2.85
379 380 2.858768 AGGGGAGCCATTAATTCCAGAA 59.141 45.455 6.93 0.00 32.50 3.02
380 381 2.175499 CAGGGGAGCCATTAATTCCAGA 59.825 50.000 6.93 0.00 32.50 3.86
381 382 2.091665 ACAGGGGAGCCATTAATTCCAG 60.092 50.000 6.93 0.25 32.50 3.86
382 383 1.929494 ACAGGGGAGCCATTAATTCCA 59.071 47.619 6.93 0.00 32.50 3.53
383 384 2.755952 ACAGGGGAGCCATTAATTCC 57.244 50.000 0.00 0.00 0.00 3.01
384 385 5.067805 CAGTAAACAGGGGAGCCATTAATTC 59.932 44.000 0.00 0.00 0.00 2.17
385 386 4.956075 CAGTAAACAGGGGAGCCATTAATT 59.044 41.667 0.00 0.00 0.00 1.40
386 387 4.229582 TCAGTAAACAGGGGAGCCATTAAT 59.770 41.667 0.00 0.00 0.00 1.40
387 388 3.589735 TCAGTAAACAGGGGAGCCATTAA 59.410 43.478 0.00 0.00 0.00 1.40
388 389 3.186283 TCAGTAAACAGGGGAGCCATTA 58.814 45.455 0.00 0.00 0.00 1.90
389 390 1.992557 TCAGTAAACAGGGGAGCCATT 59.007 47.619 0.00 0.00 0.00 3.16
390 391 1.668826 TCAGTAAACAGGGGAGCCAT 58.331 50.000 0.00 0.00 0.00 4.40
391 392 1.559682 GATCAGTAAACAGGGGAGCCA 59.440 52.381 0.00 0.00 0.00 4.75
392 393 1.134068 GGATCAGTAAACAGGGGAGCC 60.134 57.143 0.00 0.00 0.00 4.70
393 394 1.840635 AGGATCAGTAAACAGGGGAGC 59.159 52.381 0.00 0.00 0.00 4.70
394 395 2.436173 GGAGGATCAGTAAACAGGGGAG 59.564 54.545 0.00 0.00 36.25 4.30
395 396 2.478292 GGAGGATCAGTAAACAGGGGA 58.522 52.381 0.00 0.00 36.25 4.81
396 397 1.490910 GGGAGGATCAGTAAACAGGGG 59.509 57.143 0.00 0.00 36.25 4.79
397 398 1.139058 CGGGAGGATCAGTAAACAGGG 59.861 57.143 0.00 0.00 36.25 4.45
398 399 1.831736 ACGGGAGGATCAGTAAACAGG 59.168 52.381 0.00 0.00 36.25 4.00
399 400 3.611766 AACGGGAGGATCAGTAAACAG 57.388 47.619 0.00 0.00 36.25 3.16
400 401 4.773674 TCTAAACGGGAGGATCAGTAAACA 59.226 41.667 0.00 0.00 36.25 2.83
401 402 5.105432 ACTCTAAACGGGAGGATCAGTAAAC 60.105 44.000 0.00 0.00 36.25 2.01
402 403 5.021458 ACTCTAAACGGGAGGATCAGTAAA 58.979 41.667 0.00 0.00 36.25 2.01
403 404 4.607239 ACTCTAAACGGGAGGATCAGTAA 58.393 43.478 0.00 0.00 36.25 2.24
404 405 4.246712 ACTCTAAACGGGAGGATCAGTA 57.753 45.455 0.00 0.00 36.25 2.74
405 406 3.103080 ACTCTAAACGGGAGGATCAGT 57.897 47.619 0.00 0.00 36.25 3.41
406 407 4.645588 AGTAACTCTAAACGGGAGGATCAG 59.354 45.833 0.00 0.00 36.25 2.90
407 408 4.607239 AGTAACTCTAAACGGGAGGATCA 58.393 43.478 0.00 0.00 36.25 2.92
408 409 5.595257 AAGTAACTCTAAACGGGAGGATC 57.405 43.478 0.00 0.00 35.34 3.36
409 410 6.406737 GCTAAAGTAACTCTAAACGGGAGGAT 60.407 42.308 0.00 0.00 35.34 3.24
410 411 5.105595 GCTAAAGTAACTCTAAACGGGAGGA 60.106 44.000 0.00 0.00 35.34 3.71
457 458 3.072476 CCAAAGGGACAAGTAGGAACTGA 59.928 47.826 0.00 0.00 35.73 3.41
480 484 9.979578 AATAACATGTGCTTTGTATTTTCTGAA 57.020 25.926 0.00 0.00 0.00 3.02
487 491 9.709495 ACATTGAAATAACATGTGCTTTGTATT 57.291 25.926 0.00 0.00 0.00 1.89
498 503 8.523523 TTGCTTTCTCACATTGAAATAACATG 57.476 30.769 0.00 0.00 33.65 3.21
532 537 0.908198 ATCCAGTCCCAGCACTCTTC 59.092 55.000 0.00 0.00 0.00 2.87
554 561 3.374988 CCTCGCATGCTCTTTTAATGACA 59.625 43.478 17.13 0.00 0.00 3.58
613 628 0.250295 CCCGTTCAGGCACAGAAAGA 60.250 55.000 0.00 0.00 35.64 2.52
614 629 0.250295 TCCCGTTCAGGCACAGAAAG 60.250 55.000 0.00 0.00 35.14 2.62
615 630 0.250295 CTCCCGTTCAGGCACAGAAA 60.250 55.000 0.00 0.00 35.14 2.52
616 631 1.371183 CTCCCGTTCAGGCACAGAA 59.629 57.895 0.00 0.00 39.21 3.02
699 727 1.902508 TGGACTGATTTTCGCCTCTCT 59.097 47.619 0.00 0.00 0.00 3.10
827 859 0.554305 AACCCCTTCGAGGTTGGTTT 59.446 50.000 11.47 0.00 45.93 3.27
829 861 3.997196 AACCCCTTCGAGGTTGGT 58.003 55.556 6.76 3.70 45.93 3.67
838 870 6.452242 CACATTAAGTTTTACCAACCCCTTC 58.548 40.000 0.00 0.00 0.00 3.46
919 965 6.017605 CAGTTCCCCTCTATGATGAATTTTCG 60.018 42.308 0.00 0.00 0.00 3.46
1079 1144 2.210116 CTGCTGTACTTGTCAACCGTT 58.790 47.619 0.00 0.00 0.00 4.44
1087 1152 0.668706 CTGCTCGCTGCTGTACTTGT 60.669 55.000 0.00 0.00 43.37 3.16
1349 1417 2.810852 GCCCTTCTGCAATAGTAGCATC 59.189 50.000 0.00 0.00 41.82 3.91
1350 1418 2.173356 TGCCCTTCTGCAATAGTAGCAT 59.827 45.455 0.00 0.00 41.82 3.79
1422 1490 6.881065 TCAGGAGTTTTGATAGAAGTGATTGG 59.119 38.462 0.00 0.00 0.00 3.16
1425 1493 6.881602 GGTTCAGGAGTTTTGATAGAAGTGAT 59.118 38.462 0.00 0.00 0.00 3.06
1680 1754 1.153005 GAGAGCTGATTGCCAGGGG 60.153 63.158 0.00 0.00 43.13 4.79
1820 1894 2.737252 GAGGGTCACGATGTTCTTTGAC 59.263 50.000 0.00 0.00 38.11 3.18
2110 2184 4.580580 GCTTTTCCCCTCCATAGTGTTATG 59.419 45.833 0.00 0.00 37.09 1.90


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

AutoCloner maintained by Alex Coulton.