Multiple sequence alignment - TraesCS2D01G562700

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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 TraesCS2D01G562700 chr2D 100.000 3414 0 0 1 3414 634406457 634409870 0.000000e+00 6305.0
1 TraesCS2D01G562700 chr2D 93.150 2613 134 15 818 3401 575238701 575241297 0.000000e+00 3792.0
2 TraesCS2D01G562700 chr2D 82.095 296 24 16 491 776 575230699 575230975 3.430000e-55 226.0
3 TraesCS2D01G562700 chr2D 88.827 179 18 1 92 268 106376160 106376338 5.740000e-53 219.0
4 TraesCS2D01G562700 chr2B 89.058 2239 172 24 277 2490 691418182 691415992 0.000000e+00 2710.0
5 TraesCS2D01G562700 chr2B 92.544 1435 82 14 946 2359 691270532 691271962 0.000000e+00 2034.0
6 TraesCS2D01G562700 chr2B 89.988 809 46 14 2355 3150 691282963 691283749 0.000000e+00 1013.0
7 TraesCS2D01G562700 chr2B 92.653 245 14 3 3159 3402 691307428 691307669 1.950000e-92 350.0
8 TraesCS2D01G562700 chr2B 80.290 482 31 24 489 951 691268595 691269031 4.280000e-79 305.0
9 TraesCS2D01G562700 chr2B 87.568 185 21 1 91 273 510379297 510379481 2.670000e-51 213.0
10 TraesCS2D01G562700 chr2B 93.151 73 5 0 17 89 662583364 662583436 1.300000e-19 108.0
11 TraesCS2D01G562700 chr2A 92.377 1771 91 16 652 2401 713530865 713532612 0.000000e+00 2483.0
12 TraesCS2D01G562700 chr2A 91.471 1020 66 8 2395 3401 713532776 713533787 0.000000e+00 1382.0
13 TraesCS2D01G562700 chr2A 88.043 184 20 1 92 273 410877233 410877416 2.060000e-52 217.0
14 TraesCS2D01G562700 chr2A 90.196 102 10 0 3004 3105 509936990 509937091 2.140000e-27 134.0
15 TraesCS2D01G562700 chr2A 78.090 178 28 7 3183 3355 12047097 12046926 6.030000e-18 102.0
16 TraesCS2D01G562700 chr4B 76.331 1390 277 39 1015 2382 643893565 643894924 0.000000e+00 697.0
17 TraesCS2D01G562700 chr4B 84.713 157 21 3 2946 3102 282541492 282541645 1.640000e-33 154.0
18 TraesCS2D01G562700 chr5D 89.944 179 16 2 95 273 279837361 279837537 2.650000e-56 230.0
19 TraesCS2D01G562700 chr5D 87.831 189 21 2 92 279 70202639 70202452 1.590000e-53 220.0
20 TraesCS2D01G562700 chr3D 89.503 181 18 1 94 273 136769896 136769716 9.530000e-56 228.0
21 TraesCS2D01G562700 chr3D 92.000 75 2 3 17 89 45396387 45396459 6.030000e-18 102.0
22 TraesCS2D01G562700 chr3D 90.411 73 3 3 19 89 45396451 45396521 3.630000e-15 93.5
23 TraesCS2D01G562700 chr6B 88.298 188 20 2 93 279 35007570 35007384 1.230000e-54 224.0
24 TraesCS2D01G562700 chr5B 88.525 183 19 1 93 273 181467199 181467381 1.590000e-53 220.0
25 TraesCS2D01G562700 chr5B 79.562 137 15 4 3222 3354 690707271 690707398 6.070000e-13 86.1
26 TraesCS2D01G562700 chr1D 75.930 457 86 17 1007 1445 69197741 69197291 2.670000e-51 213.0
27 TraesCS2D01G562700 chr1D 85.535 159 22 1 2945 3102 437684579 437684737 7.580000e-37 165.0
28 TraesCS2D01G562700 chr7D 86.000 200 21 5 2910 3105 528904487 528904291 1.240000e-49 207.0
29 TraesCS2D01G562700 chr1B 86.702 188 24 1 92 279 557441783 557441597 1.240000e-49 207.0
30 TraesCS2D01G562700 chr1B 96.774 31 1 0 2516 2546 547403380 547403410 6.000000e-03 52.8
31 TraesCS2D01G562700 chr3A 83.230 161 26 1 2945 3105 399605591 399605750 2.750000e-31 147.0
32 TraesCS2D01G562700 chrUn 90.816 98 9 0 3006 3103 71401020 71401117 7.690000e-27 132.0
33 TraesCS2D01G562700 chr6D 82.237 152 25 2 3204 3354 387726750 387726600 2.760000e-26 130.0
34 TraesCS2D01G562700 chr6A 81.457 151 28 0 3204 3354 532849353 532849203 1.290000e-24 124.0
35 TraesCS2D01G562700 chr6A 89.744 78 8 0 2560 2637 41232219 41232296 2.170000e-17 100.0
36 TraesCS2D01G562700 chr4D 81.618 136 18 5 3214 3343 399538157 399538291 4.660000e-19 106.0
37 TraesCS2D01G562700 chr7A 83.784 111 15 3 3180 3289 694298753 694298861 6.030000e-18 102.0
38 TraesCS2D01G562700 chr7A 85.897 78 11 0 2560 2637 735874729 735874652 2.180000e-12 84.2
39 TraesCS2D01G562700 chr1A 88.372 86 9 1 2552 2637 382743035 382743119 6.030000e-18 102.0
40 TraesCS2D01G562700 chr4A 89.744 78 8 0 2560 2637 223854265 223854342 2.170000e-17 100.0
41 TraesCS2D01G562700 chr3B 83.582 67 5 4 2560 2622 581654995 581654931 1.320000e-04 58.4


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G562700 chr2D 634406457 634409870 3413 False 6305.0 6305 100.000 1 3414 1 chr2D.!!$F4 3413
1 TraesCS2D01G562700 chr2D 575238701 575241297 2596 False 3792.0 3792 93.150 818 3401 1 chr2D.!!$F3 2583
2 TraesCS2D01G562700 chr2B 691415992 691418182 2190 True 2710.0 2710 89.058 277 2490 1 chr2B.!!$R1 2213
3 TraesCS2D01G562700 chr2B 691268595 691271962 3367 False 1169.5 2034 86.417 489 2359 2 chr2B.!!$F5 1870
4 TraesCS2D01G562700 chr2B 691282963 691283749 786 False 1013.0 1013 89.988 2355 3150 1 chr2B.!!$F3 795
5 TraesCS2D01G562700 chr2A 713530865 713533787 2922 False 1932.5 2483 91.924 652 3401 2 chr2A.!!$F3 2749
6 TraesCS2D01G562700 chr4B 643893565 643894924 1359 False 697.0 697 76.331 1015 2382 1 chr4B.!!$F2 1367

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
71 72 0.321298 GGTGCGGTTTAGAGGAGCAA 60.321 55.0 0.00 0.0 39.67 3.91 F
207 208 0.475828 ACCCTACTGGCCTGGAACTT 60.476 55.0 14.82 0.0 37.83 2.66 F
1612 3187 0.107654 CGGGGTTCATCCAGTTCCTC 60.108 60.0 0.00 0.0 38.11 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1129 2666 0.179111 CGGTAGAAGAAGATGCCGCA 60.179 55.0 0.00 0.0 37.85 5.69 R
2107 3706 0.538746 TGGAGCGCATATACTCGGGA 60.539 55.0 11.47 0.0 33.55 5.14 R
3144 4937 1.116536 TCAACCTACACCACGCTCCA 61.117 55.0 0.00 0.0 0.00 3.86 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
42 43 7.828508 TTTTACTCCTCTAACGCATATAGGA 57.171 36.000 0.00 0.00 35.20 2.94
48 49 6.358178 TCCTCTAACGCATATAGGAGATAGG 58.642 44.000 5.80 2.50 33.24 2.57
49 50 6.069556 TCCTCTAACGCATATAGGAGATAGGT 60.070 42.308 5.80 0.00 33.24 3.08
50 51 6.603997 CCTCTAACGCATATAGGAGATAGGTT 59.396 42.308 5.80 0.00 31.05 3.50
51 52 7.774157 CCTCTAACGCATATAGGAGATAGGTTA 59.226 40.741 5.80 0.00 31.05 2.85
52 53 8.734218 TCTAACGCATATAGGAGATAGGTTAG 57.266 38.462 5.80 0.00 37.00 2.34
53 54 6.777213 AACGCATATAGGAGATAGGTTAGG 57.223 41.667 0.00 0.00 0.00 2.69
54 55 5.828871 ACGCATATAGGAGATAGGTTAGGT 58.171 41.667 0.00 0.00 0.00 3.08
55 56 5.652891 ACGCATATAGGAGATAGGTTAGGTG 59.347 44.000 0.00 0.00 0.00 4.00
56 57 5.450688 CGCATATAGGAGATAGGTTAGGTGC 60.451 48.000 0.00 0.00 0.00 5.01
57 58 5.450688 GCATATAGGAGATAGGTTAGGTGCG 60.451 48.000 0.00 0.00 0.00 5.34
58 59 1.705873 AGGAGATAGGTTAGGTGCGG 58.294 55.000 0.00 0.00 0.00 5.69
59 60 1.063114 AGGAGATAGGTTAGGTGCGGT 60.063 52.381 0.00 0.00 0.00 5.68
60 61 1.761198 GGAGATAGGTTAGGTGCGGTT 59.239 52.381 0.00 0.00 0.00 4.44
61 62 2.169978 GGAGATAGGTTAGGTGCGGTTT 59.830 50.000 0.00 0.00 0.00 3.27
62 63 3.385755 GGAGATAGGTTAGGTGCGGTTTA 59.614 47.826 0.00 0.00 0.00 2.01
63 64 4.501058 GGAGATAGGTTAGGTGCGGTTTAG 60.501 50.000 0.00 0.00 0.00 1.85
64 65 4.284178 AGATAGGTTAGGTGCGGTTTAGA 58.716 43.478 0.00 0.00 0.00 2.10
65 66 4.341520 AGATAGGTTAGGTGCGGTTTAGAG 59.658 45.833 0.00 0.00 0.00 2.43
66 67 1.553704 AGGTTAGGTGCGGTTTAGAGG 59.446 52.381 0.00 0.00 0.00 3.69
67 68 1.551883 GGTTAGGTGCGGTTTAGAGGA 59.448 52.381 0.00 0.00 0.00 3.71
68 69 2.418334 GGTTAGGTGCGGTTTAGAGGAG 60.418 54.545 0.00 0.00 0.00 3.69
69 70 0.822164 TAGGTGCGGTTTAGAGGAGC 59.178 55.000 0.00 0.00 0.00 4.70
70 71 1.192146 AGGTGCGGTTTAGAGGAGCA 61.192 55.000 0.00 0.00 35.27 4.26
71 72 0.321298 GGTGCGGTTTAGAGGAGCAA 60.321 55.000 0.00 0.00 39.67 3.91
72 73 1.519408 GTGCGGTTTAGAGGAGCAAA 58.481 50.000 0.00 0.00 39.67 3.68
73 74 1.877443 GTGCGGTTTAGAGGAGCAAAA 59.123 47.619 0.00 0.00 39.67 2.44
74 75 1.877443 TGCGGTTTAGAGGAGCAAAAC 59.123 47.619 0.00 0.00 34.66 2.43
75 76 1.199327 GCGGTTTAGAGGAGCAAAACC 59.801 52.381 6.20 6.20 45.64 3.27
77 78 1.810755 GGTTTAGAGGAGCAAAACCGG 59.189 52.381 0.00 0.00 41.84 5.28
78 79 2.551504 GGTTTAGAGGAGCAAAACCGGA 60.552 50.000 9.46 0.00 41.84 5.14
79 80 3.143728 GTTTAGAGGAGCAAAACCGGAA 58.856 45.455 9.46 0.00 0.00 4.30
80 81 3.713826 TTAGAGGAGCAAAACCGGAAT 57.286 42.857 9.46 0.00 0.00 3.01
81 82 2.586648 AGAGGAGCAAAACCGGAATT 57.413 45.000 9.46 0.00 0.00 2.17
82 83 2.876581 AGAGGAGCAAAACCGGAATTT 58.123 42.857 9.46 6.28 0.00 1.82
83 84 3.230976 AGAGGAGCAAAACCGGAATTTT 58.769 40.909 9.46 1.93 31.87 1.82
84 85 4.403734 AGAGGAGCAAAACCGGAATTTTA 58.596 39.130 9.46 0.00 30.57 1.52
85 86 4.217767 AGAGGAGCAAAACCGGAATTTTAC 59.782 41.667 9.46 0.00 30.57 2.01
86 87 4.149598 AGGAGCAAAACCGGAATTTTACT 58.850 39.130 9.46 5.50 29.56 2.24
87 88 4.217767 AGGAGCAAAACCGGAATTTTACTC 59.782 41.667 9.46 14.56 39.63 2.59
88 89 4.482386 GAGCAAAACCGGAATTTTACTCC 58.518 43.478 9.46 0.00 36.54 3.85
154 155 8.941995 ATAATGCTACATAGTTCACTAGGAGA 57.058 34.615 5.67 0.00 34.61 3.71
155 156 6.892658 ATGCTACATAGTTCACTAGGAGAG 57.107 41.667 5.67 3.97 34.61 3.20
156 157 5.133941 TGCTACATAGTTCACTAGGAGAGG 58.866 45.833 5.67 0.00 34.61 3.69
157 158 5.134661 GCTACATAGTTCACTAGGAGAGGT 58.865 45.833 5.67 0.00 34.61 3.85
158 159 6.126565 TGCTACATAGTTCACTAGGAGAGGTA 60.127 42.308 5.67 0.00 34.61 3.08
159 160 6.943718 GCTACATAGTTCACTAGGAGAGGTAT 59.056 42.308 5.67 0.00 34.61 2.73
160 161 8.102047 GCTACATAGTTCACTAGGAGAGGTATA 58.898 40.741 5.67 0.00 34.61 1.47
161 162 9.661563 CTACATAGTTCACTAGGAGAGGTATAG 57.338 40.741 5.67 0.00 34.61 1.31
162 163 8.048016 ACATAGTTCACTAGGAGAGGTATAGT 57.952 38.462 5.67 0.00 34.61 2.12
163 164 9.168553 ACATAGTTCACTAGGAGAGGTATAGTA 57.831 37.037 5.67 0.00 34.61 1.82
164 165 9.661563 CATAGTTCACTAGGAGAGGTATAGTAG 57.338 40.741 0.00 0.00 32.42 2.57
165 166 7.934354 AGTTCACTAGGAGAGGTATAGTAGA 57.066 40.000 0.00 0.00 0.00 2.59
166 167 7.970102 AGTTCACTAGGAGAGGTATAGTAGAG 58.030 42.308 0.00 0.00 0.00 2.43
167 168 6.938698 TCACTAGGAGAGGTATAGTAGAGG 57.061 45.833 0.00 0.00 0.00 3.69
168 169 5.786457 TCACTAGGAGAGGTATAGTAGAGGG 59.214 48.000 0.00 0.00 0.00 4.30
169 170 5.045432 CACTAGGAGAGGTATAGTAGAGGGG 60.045 52.000 0.00 0.00 0.00 4.79
170 171 3.270812 AGGAGAGGTATAGTAGAGGGGG 58.729 54.545 0.00 0.00 0.00 5.40
171 172 2.995301 GGAGAGGTATAGTAGAGGGGGT 59.005 54.545 0.00 0.00 0.00 4.95
172 173 4.140008 AGGAGAGGTATAGTAGAGGGGGTA 60.140 50.000 0.00 0.00 0.00 3.69
173 174 4.227982 GGAGAGGTATAGTAGAGGGGGTAG 59.772 54.167 0.00 0.00 0.00 3.18
174 175 4.185518 AGAGGTATAGTAGAGGGGGTAGG 58.814 52.174 0.00 0.00 0.00 3.18
175 176 4.140008 AGAGGTATAGTAGAGGGGGTAGGA 60.140 50.000 0.00 0.00 0.00 2.94
176 177 4.795165 GAGGTATAGTAGAGGGGGTAGGAT 59.205 50.000 0.00 0.00 0.00 3.24
177 178 4.795165 AGGTATAGTAGAGGGGGTAGGATC 59.205 50.000 0.00 0.00 0.00 3.36
178 179 4.543337 GGTATAGTAGAGGGGGTAGGATCA 59.457 50.000 0.00 0.00 0.00 2.92
179 180 5.196165 GGTATAGTAGAGGGGGTAGGATCAT 59.804 48.000 0.00 0.00 0.00 2.45
180 181 3.837399 AGTAGAGGGGGTAGGATCATC 57.163 52.381 0.00 0.00 0.00 2.92
181 182 2.384029 AGTAGAGGGGGTAGGATCATCC 59.616 54.545 0.00 0.00 36.58 3.51
182 183 1.255033 AGAGGGGGTAGGATCATCCA 58.745 55.000 6.42 0.00 39.61 3.41
183 184 1.585592 AGAGGGGGTAGGATCATCCAA 59.414 52.381 6.42 0.00 39.61 3.53
184 185 1.700186 GAGGGGGTAGGATCATCCAAC 59.300 57.143 6.42 0.00 39.61 3.77
185 186 0.771755 GGGGGTAGGATCATCCAACC 59.228 60.000 6.42 4.02 39.61 3.77
186 187 1.518367 GGGGTAGGATCATCCAACCA 58.482 55.000 6.42 0.00 39.61 3.67
187 188 1.421646 GGGGTAGGATCATCCAACCAG 59.578 57.143 6.42 0.00 39.61 4.00
188 189 2.408565 GGGTAGGATCATCCAACCAGA 58.591 52.381 6.42 0.00 39.61 3.86
189 190 2.104963 GGGTAGGATCATCCAACCAGAC 59.895 54.545 6.42 0.00 39.61 3.51
190 191 2.104963 GGTAGGATCATCCAACCAGACC 59.895 54.545 6.42 0.00 39.61 3.85
191 192 1.216990 AGGATCATCCAACCAGACCC 58.783 55.000 6.42 0.00 39.61 4.46
192 193 1.216990 GGATCATCCAACCAGACCCT 58.783 55.000 0.00 0.00 36.28 4.34
193 194 2.022035 AGGATCATCCAACCAGACCCTA 60.022 50.000 6.42 0.00 39.61 3.53
194 195 2.104963 GGATCATCCAACCAGACCCTAC 59.895 54.545 0.00 0.00 36.28 3.18
195 196 2.642171 TCATCCAACCAGACCCTACT 57.358 50.000 0.00 0.00 0.00 2.57
196 197 2.187958 TCATCCAACCAGACCCTACTG 58.812 52.381 0.00 0.00 37.61 2.74
202 203 3.313874 CAGACCCTACTGGCCTGG 58.686 66.667 14.82 4.64 37.83 4.45
203 204 1.306141 CAGACCCTACTGGCCTGGA 60.306 63.158 14.82 4.14 37.83 3.86
204 205 0.909610 CAGACCCTACTGGCCTGGAA 60.910 60.000 14.82 0.69 37.83 3.53
205 206 0.910088 AGACCCTACTGGCCTGGAAC 60.910 60.000 14.82 4.35 37.83 3.62
206 207 0.910088 GACCCTACTGGCCTGGAACT 60.910 60.000 14.82 0.00 37.83 3.01
207 208 0.475828 ACCCTACTGGCCTGGAACTT 60.476 55.000 14.82 0.00 37.83 2.66
208 209 1.203389 ACCCTACTGGCCTGGAACTTA 60.203 52.381 14.82 0.00 37.83 2.24
209 210 1.486726 CCCTACTGGCCTGGAACTTAG 59.513 57.143 14.82 5.98 0.00 2.18
210 211 1.134371 CCTACTGGCCTGGAACTTAGC 60.134 57.143 14.82 0.00 0.00 3.09
211 212 0.909623 TACTGGCCTGGAACTTAGCC 59.090 55.000 14.82 0.00 45.96 3.93
218 219 1.826385 CTGGAACTTAGCCAGTTGGG 58.174 55.000 3.63 0.00 46.53 4.12
229 230 2.787473 CCAGTTGGGCTAGTTCATGA 57.213 50.000 0.00 0.00 0.00 3.07
230 231 2.636830 CCAGTTGGGCTAGTTCATGAG 58.363 52.381 0.00 0.00 0.00 2.90
231 232 2.012673 CAGTTGGGCTAGTTCATGAGC 58.987 52.381 0.50 0.50 38.00 4.26
232 233 1.912043 AGTTGGGCTAGTTCATGAGCT 59.088 47.619 16.75 16.75 38.79 4.09
233 234 2.093235 AGTTGGGCTAGTTCATGAGCTC 60.093 50.000 16.01 6.82 39.79 4.09
234 235 0.833287 TGGGCTAGTTCATGAGCTCC 59.167 55.000 16.01 11.63 38.49 4.70
235 236 0.833287 GGGCTAGTTCATGAGCTCCA 59.167 55.000 16.01 0.00 38.79 3.86
236 237 1.210478 GGGCTAGTTCATGAGCTCCAA 59.790 52.381 16.01 0.00 38.79 3.53
237 238 2.356125 GGGCTAGTTCATGAGCTCCAAA 60.356 50.000 16.01 0.00 38.79 3.28
238 239 3.347216 GGCTAGTTCATGAGCTCCAAAA 58.653 45.455 16.01 0.00 38.79 2.44
239 240 3.950395 GGCTAGTTCATGAGCTCCAAAAT 59.050 43.478 16.01 4.73 38.79 1.82
240 241 4.400567 GGCTAGTTCATGAGCTCCAAAATT 59.599 41.667 16.01 2.07 38.79 1.82
241 242 5.105595 GGCTAGTTCATGAGCTCCAAAATTT 60.106 40.000 16.01 0.00 38.79 1.82
242 243 5.803967 GCTAGTTCATGAGCTCCAAAATTTG 59.196 40.000 16.01 0.00 35.73 2.32
243 244 5.796424 AGTTCATGAGCTCCAAAATTTGT 57.204 34.783 12.15 0.00 0.00 2.83
244 245 6.165700 AGTTCATGAGCTCCAAAATTTGTT 57.834 33.333 12.15 0.00 0.00 2.83
245 246 6.585416 AGTTCATGAGCTCCAAAATTTGTTT 58.415 32.000 12.15 0.00 0.00 2.83
246 247 6.703165 AGTTCATGAGCTCCAAAATTTGTTTC 59.297 34.615 12.15 0.00 0.00 2.78
247 248 5.540911 TCATGAGCTCCAAAATTTGTTTCC 58.459 37.500 12.15 0.00 0.00 3.13
248 249 4.335400 TGAGCTCCAAAATTTGTTTCCC 57.665 40.909 12.15 0.00 0.00 3.97
249 250 3.966665 TGAGCTCCAAAATTTGTTTCCCT 59.033 39.130 12.15 0.00 0.00 4.20
250 251 5.144100 TGAGCTCCAAAATTTGTTTCCCTA 58.856 37.500 12.15 0.00 0.00 3.53
251 252 5.779771 TGAGCTCCAAAATTTGTTTCCCTAT 59.220 36.000 12.15 0.00 0.00 2.57
252 253 6.269769 TGAGCTCCAAAATTTGTTTCCCTATT 59.730 34.615 12.15 0.00 0.00 1.73
253 254 6.701340 AGCTCCAAAATTTGTTTCCCTATTC 58.299 36.000 4.92 0.00 0.00 1.75
254 255 5.576774 GCTCCAAAATTTGTTTCCCTATTCG 59.423 40.000 4.92 0.00 0.00 3.34
255 256 5.474825 TCCAAAATTTGTTTCCCTATTCGC 58.525 37.500 4.92 0.00 0.00 4.70
256 257 5.011125 TCCAAAATTTGTTTCCCTATTCGCA 59.989 36.000 4.92 0.00 0.00 5.10
257 258 5.874261 CCAAAATTTGTTTCCCTATTCGCAT 59.126 36.000 4.92 0.00 0.00 4.73
258 259 6.183360 CCAAAATTTGTTTCCCTATTCGCATG 60.183 38.462 4.92 0.00 0.00 4.06
259 260 3.502191 TTTGTTTCCCTATTCGCATGC 57.498 42.857 7.91 7.91 0.00 4.06
260 261 2.418368 TGTTTCCCTATTCGCATGCT 57.582 45.000 17.13 0.00 0.00 3.79
261 262 2.288666 TGTTTCCCTATTCGCATGCTC 58.711 47.619 17.13 0.00 0.00 4.26
262 263 2.288666 GTTTCCCTATTCGCATGCTCA 58.711 47.619 17.13 1.61 0.00 4.26
263 264 2.880890 GTTTCCCTATTCGCATGCTCAT 59.119 45.455 17.13 9.80 0.00 2.90
264 265 4.065088 GTTTCCCTATTCGCATGCTCATA 58.935 43.478 17.13 10.43 0.00 2.15
265 266 3.319137 TCCCTATTCGCATGCTCATAC 57.681 47.619 17.13 0.00 0.00 2.39
266 267 2.899900 TCCCTATTCGCATGCTCATACT 59.100 45.455 17.13 0.00 0.00 2.12
267 268 3.324846 TCCCTATTCGCATGCTCATACTT 59.675 43.478 17.13 0.00 0.00 2.24
268 269 4.526650 TCCCTATTCGCATGCTCATACTTA 59.473 41.667 17.13 0.00 0.00 2.24
269 270 5.011635 TCCCTATTCGCATGCTCATACTTAA 59.988 40.000 17.13 0.00 0.00 1.85
270 271 5.120830 CCCTATTCGCATGCTCATACTTAAC 59.879 44.000 17.13 0.00 0.00 2.01
271 272 5.120830 CCTATTCGCATGCTCATACTTAACC 59.879 44.000 17.13 0.00 0.00 2.85
272 273 2.833794 TCGCATGCTCATACTTAACCC 58.166 47.619 17.13 0.00 0.00 4.11
273 274 1.873591 CGCATGCTCATACTTAACCCC 59.126 52.381 17.13 0.00 0.00 4.95
274 275 2.485479 CGCATGCTCATACTTAACCCCT 60.485 50.000 17.13 0.00 0.00 4.79
275 276 3.244078 CGCATGCTCATACTTAACCCCTA 60.244 47.826 17.13 0.00 0.00 3.53
279 280 5.093849 TGCTCATACTTAACCCCTACAAC 57.906 43.478 0.00 0.00 0.00 3.32
289 290 1.890489 ACCCCTACAACGGCAATTTTC 59.110 47.619 0.00 0.00 0.00 2.29
301 302 7.042389 ACAACGGCAATTTTCGTGAAAAATATT 60.042 29.630 11.40 0.14 44.88 1.28
333 334 4.634184 TTTAAAACTGCAAACGCCTACA 57.366 36.364 0.00 0.00 0.00 2.74
341 342 3.207778 TGCAAACGCCTACAACTAAAGT 58.792 40.909 0.00 0.00 0.00 2.66
343 344 4.815308 TGCAAACGCCTACAACTAAAGTTA 59.185 37.500 0.00 0.00 36.32 2.24
364 365 6.044637 AGTTACCACCCCTCTACATTAAAACA 59.955 38.462 0.00 0.00 0.00 2.83
372 373 5.245531 CCTCTACATTAAAACAGCCACTCA 58.754 41.667 0.00 0.00 0.00 3.41
377 378 6.403866 ACATTAAAACAGCCACTCAAATCA 57.596 33.333 0.00 0.00 0.00 2.57
386 387 2.733227 GCCACTCAAATCATCCGCAAAG 60.733 50.000 0.00 0.00 0.00 2.77
393 395 0.749454 ATCATCCGCAAAGCCACCTC 60.749 55.000 0.00 0.00 0.00 3.85
423 427 1.670083 CCTTCCCCCAACGAACGTC 60.670 63.158 0.00 0.00 0.00 4.34
425 429 0.604578 CTTCCCCCAACGAACGTCTA 59.395 55.000 0.00 0.00 0.00 2.59
491 495 5.827797 TGGCTAAGATTATCCCACATTGTTC 59.172 40.000 0.00 0.00 0.00 3.18
502 506 3.443329 CCCACATTGTTCGATTTGATCCA 59.557 43.478 0.00 0.00 0.00 3.41
525 529 9.081204 TCCATTTATTTACATGGATCCAATGAG 57.919 33.333 20.67 11.62 43.44 2.90
549 553 7.896811 AGCATGATTATCCGTTAGAGTAATGA 58.103 34.615 0.00 0.00 0.00 2.57
633 637 6.272324 TGGAGTTATGATTGGTAATAGGGAGG 59.728 42.308 0.00 0.00 0.00 4.30
736 743 9.632807 CTCTGTAGGTCTAGCATTATTGTTATC 57.367 37.037 0.00 0.00 0.00 1.75
738 745 9.988815 CTGTAGGTCTAGCATTATTGTTATCTT 57.011 33.333 0.00 0.00 0.00 2.40
739 746 9.764363 TGTAGGTCTAGCATTATTGTTATCTTG 57.236 33.333 0.00 0.00 0.00 3.02
740 747 9.982651 GTAGGTCTAGCATTATTGTTATCTTGA 57.017 33.333 0.00 0.00 0.00 3.02
776 787 2.804527 CGATGATTACAGCACCCATGAG 59.195 50.000 0.00 0.00 32.22 2.90
785 796 1.028868 GCACCCATGAGCTTCCTGAC 61.029 60.000 0.00 0.00 0.00 3.51
835 846 3.908103 AGTGAAGGGGTGTAACAGTACAT 59.092 43.478 0.00 0.00 42.18 2.29
860 872 4.223032 ACATGGATTAGAAACGAGTGGTCT 59.777 41.667 0.00 0.00 0.00 3.85
1069 2606 4.498520 CAGCCTCGCCGACGACAT 62.499 66.667 0.00 0.00 45.12 3.06
1079 2616 1.367078 CGACGACATCGCGAGAGAG 60.367 63.158 16.66 8.91 45.52 3.20
1104 2641 2.172372 CCTCTCCGACGTCGACGAT 61.172 63.158 41.52 26.13 43.02 3.73
1340 2880 1.380403 CGACTGGCAGATCTCGAGGT 61.380 60.000 23.66 4.76 0.00 3.85
1378 2918 1.147376 CCGCCATTCCCGTGGATTA 59.853 57.895 0.00 0.00 42.02 1.75
1612 3187 0.107654 CGGGGTTCATCCAGTTCCTC 60.108 60.000 0.00 0.00 38.11 3.71
1679 3275 3.753434 CTGCCTGGTCTCGCGAGT 61.753 66.667 33.33 0.00 0.00 4.18
1680 3276 3.691744 CTGCCTGGTCTCGCGAGTC 62.692 68.421 33.33 27.89 0.00 3.36
1696 3292 2.733218 TCGCTTGACGCACGAAGG 60.733 61.111 0.00 0.00 43.23 3.46
2230 3829 4.717629 CAGCGCGTGGACTTCGGA 62.718 66.667 8.43 0.00 0.00 4.55
2417 4189 9.172060 AGGATAGTATTAAACAGCCCTAGAAAT 57.828 33.333 0.00 0.00 0.00 2.17
2476 4248 2.869801 CCTTTTCGAAACAAAAAGCCCC 59.130 45.455 10.79 0.00 40.68 5.80
2515 4287 9.178758 AGAGAGAATTTCTTGTTTAACACTGTT 57.821 29.630 0.00 0.00 35.87 3.16
2587 4364 4.407621 TCCATCCATTTAGAGCCTTAACGA 59.592 41.667 0.00 0.00 0.00 3.85
2683 4460 5.068460 CCATACAGGGAACAAACACTTTCAA 59.932 40.000 0.00 0.00 0.00 2.69
2799 4576 3.710722 CCTTGGCCTCGGCTGACT 61.711 66.667 3.32 0.00 41.60 3.41
2814 4591 2.749076 GCTGACTGTTGGATGCATGTAA 59.251 45.455 2.46 0.00 0.00 2.41
2902 4679 5.562506 TGGTACAAAATTGTGTCGAACAA 57.437 34.783 4.02 13.12 45.20 2.83
2913 4690 3.259625 TGTGTCGAACAACCATCCAGATA 59.740 43.478 0.00 0.00 35.24 1.98
2914 4691 3.865745 GTGTCGAACAACCATCCAGATAG 59.134 47.826 0.00 0.00 0.00 2.08
3007 4788 4.000325 TCAGGTATCATTTGACACCGTTG 59.000 43.478 2.50 0.00 45.92 4.10
3013 4794 1.608590 CATTTGACACCGTTGAGGCTT 59.391 47.619 0.00 0.00 46.52 4.35
3026 4807 3.426787 TGAGGCTTAAAATGGACGGAA 57.573 42.857 0.00 0.00 0.00 4.30
3072 4853 5.786264 AGACACGGTGTTATATAGGGAAG 57.214 43.478 15.94 0.00 0.00 3.46
3151 4944 1.549203 AAAAGGATGCATTGGAGCGT 58.451 45.000 0.00 0.00 37.31 5.07
3156 4949 1.303561 ATGCATTGGAGCGTGGTGT 60.304 52.632 0.00 0.00 37.31 4.16
3178 4971 6.527722 GTGTAGGTTGATGCATTGTTGTAATG 59.472 38.462 0.00 0.00 0.00 1.90
3203 4996 6.094048 GGTGTTGCTAAATCTTATTCAGCTGA 59.906 38.462 13.74 13.74 33.38 4.26
3265 5058 7.822334 AGATCTTACATTGACATCGGTGTAAAA 59.178 33.333 0.00 0.00 39.09 1.52
3266 5059 7.731882 TCTTACATTGACATCGGTGTAAAAA 57.268 32.000 0.00 0.00 39.09 1.94
3270 5063 9.751542 TTACATTGACATCGGTGTAAAAATTTT 57.248 25.926 0.00 0.00 39.09 1.82
3317 5110 8.122472 TCTTATATCACTTGACTGACACTTGA 57.878 34.615 0.00 0.00 0.00 3.02
3328 5121 9.261180 CTTGACTGACACTTGATTAAGTCTTAA 57.739 33.333 7.49 7.49 45.12 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 8.241497 TCCTATATGCGTTAGAGGAGTAAAAA 57.759 34.615 5.92 0.00 42.21 1.94
18 19 7.828508 TCCTATATGCGTTAGAGGAGTAAAA 57.171 36.000 5.92 0.00 42.21 1.52
24 25 6.069556 ACCTATCTCCTATATGCGTTAGAGGA 60.070 42.308 8.94 8.94 44.33 3.71
25 26 6.123651 ACCTATCTCCTATATGCGTTAGAGG 58.876 44.000 1.68 1.68 40.16 3.69
26 27 7.633193 AACCTATCTCCTATATGCGTTAGAG 57.367 40.000 0.00 0.00 0.00 2.43
27 28 7.774157 CCTAACCTATCTCCTATATGCGTTAGA 59.226 40.741 0.00 0.00 34.66 2.10
28 29 7.556996 ACCTAACCTATCTCCTATATGCGTTAG 59.443 40.741 0.00 0.00 33.25 2.34
29 30 7.338703 CACCTAACCTATCTCCTATATGCGTTA 59.661 40.741 0.00 0.00 0.00 3.18
30 31 6.153000 CACCTAACCTATCTCCTATATGCGTT 59.847 42.308 0.00 0.00 0.00 4.84
31 32 5.652891 CACCTAACCTATCTCCTATATGCGT 59.347 44.000 0.00 0.00 0.00 5.24
32 33 5.450688 GCACCTAACCTATCTCCTATATGCG 60.451 48.000 0.00 0.00 0.00 4.73
33 34 5.450688 CGCACCTAACCTATCTCCTATATGC 60.451 48.000 0.00 0.00 0.00 3.14
34 35 5.067936 CCGCACCTAACCTATCTCCTATATG 59.932 48.000 0.00 0.00 0.00 1.78
35 36 5.202004 CCGCACCTAACCTATCTCCTATAT 58.798 45.833 0.00 0.00 0.00 0.86
36 37 4.043812 ACCGCACCTAACCTATCTCCTATA 59.956 45.833 0.00 0.00 0.00 1.31
37 38 3.181420 ACCGCACCTAACCTATCTCCTAT 60.181 47.826 0.00 0.00 0.00 2.57
38 39 2.176364 ACCGCACCTAACCTATCTCCTA 59.824 50.000 0.00 0.00 0.00 2.94
39 40 1.063114 ACCGCACCTAACCTATCTCCT 60.063 52.381 0.00 0.00 0.00 3.69
40 41 1.411041 ACCGCACCTAACCTATCTCC 58.589 55.000 0.00 0.00 0.00 3.71
41 42 3.538634 AAACCGCACCTAACCTATCTC 57.461 47.619 0.00 0.00 0.00 2.75
42 43 4.284178 TCTAAACCGCACCTAACCTATCT 58.716 43.478 0.00 0.00 0.00 1.98
43 44 4.501058 CCTCTAAACCGCACCTAACCTATC 60.501 50.000 0.00 0.00 0.00 2.08
44 45 3.387050 CCTCTAAACCGCACCTAACCTAT 59.613 47.826 0.00 0.00 0.00 2.57
45 46 2.762327 CCTCTAAACCGCACCTAACCTA 59.238 50.000 0.00 0.00 0.00 3.08
46 47 1.553704 CCTCTAAACCGCACCTAACCT 59.446 52.381 0.00 0.00 0.00 3.50
47 48 1.551883 TCCTCTAAACCGCACCTAACC 59.448 52.381 0.00 0.00 0.00 2.85
48 49 2.889852 CTCCTCTAAACCGCACCTAAC 58.110 52.381 0.00 0.00 0.00 2.34
49 50 1.206371 GCTCCTCTAAACCGCACCTAA 59.794 52.381 0.00 0.00 0.00 2.69
50 51 0.822164 GCTCCTCTAAACCGCACCTA 59.178 55.000 0.00 0.00 0.00 3.08
51 52 1.192146 TGCTCCTCTAAACCGCACCT 61.192 55.000 0.00 0.00 0.00 4.00
52 53 0.321298 TTGCTCCTCTAAACCGCACC 60.321 55.000 0.00 0.00 0.00 5.01
53 54 1.519408 TTTGCTCCTCTAAACCGCAC 58.481 50.000 0.00 0.00 0.00 5.34
54 55 1.877443 GTTTTGCTCCTCTAAACCGCA 59.123 47.619 0.00 0.00 35.38 5.69
55 56 1.199327 GGTTTTGCTCCTCTAAACCGC 59.801 52.381 0.00 0.00 45.56 5.68
58 59 2.774687 TCCGGTTTTGCTCCTCTAAAC 58.225 47.619 0.00 0.00 38.89 2.01
59 60 3.495434 TTCCGGTTTTGCTCCTCTAAA 57.505 42.857 0.00 0.00 0.00 1.85
60 61 3.713826 ATTCCGGTTTTGCTCCTCTAA 57.286 42.857 0.00 0.00 0.00 2.10
61 62 3.713826 AATTCCGGTTTTGCTCCTCTA 57.286 42.857 0.00 0.00 0.00 2.43
62 63 2.586648 AATTCCGGTTTTGCTCCTCT 57.413 45.000 0.00 0.00 0.00 3.69
63 64 3.660501 AAAATTCCGGTTTTGCTCCTC 57.339 42.857 0.00 0.00 30.55 3.71
64 65 4.149598 AGTAAAATTCCGGTTTTGCTCCT 58.850 39.130 12.98 2.93 38.94 3.69
65 66 4.482386 GAGTAAAATTCCGGTTTTGCTCC 58.518 43.478 25.19 14.40 46.25 4.70
67 68 4.514781 GGAGTAAAATTCCGGTTTTGCT 57.485 40.909 17.04 17.04 43.54 3.91
128 129 9.368416 TCTCCTAGTGAACTATGTAGCATTATT 57.632 33.333 0.00 0.00 0.00 1.40
129 130 8.941995 TCTCCTAGTGAACTATGTAGCATTAT 57.058 34.615 0.00 0.00 0.00 1.28
130 131 7.448777 CCTCTCCTAGTGAACTATGTAGCATTA 59.551 40.741 0.00 0.00 0.00 1.90
131 132 6.266558 CCTCTCCTAGTGAACTATGTAGCATT 59.733 42.308 0.00 0.00 0.00 3.56
132 133 5.772672 CCTCTCCTAGTGAACTATGTAGCAT 59.227 44.000 0.00 0.00 0.00 3.79
133 134 5.133941 CCTCTCCTAGTGAACTATGTAGCA 58.866 45.833 0.00 0.00 0.00 3.49
134 135 5.134661 ACCTCTCCTAGTGAACTATGTAGC 58.865 45.833 0.00 0.00 0.00 3.58
135 136 9.661563 CTATACCTCTCCTAGTGAACTATGTAG 57.338 40.741 0.00 0.00 0.00 2.74
136 137 9.168553 ACTATACCTCTCCTAGTGAACTATGTA 57.831 37.037 0.00 0.00 0.00 2.29
137 138 8.048016 ACTATACCTCTCCTAGTGAACTATGT 57.952 38.462 0.00 0.00 0.00 2.29
138 139 9.661563 CTACTATACCTCTCCTAGTGAACTATG 57.338 40.741 0.00 0.00 0.00 2.23
139 140 9.618447 TCTACTATACCTCTCCTAGTGAACTAT 57.382 37.037 0.00 0.00 0.00 2.12
140 141 9.092338 CTCTACTATACCTCTCCTAGTGAACTA 57.908 40.741 0.00 0.00 0.00 2.24
141 142 7.016858 CCTCTACTATACCTCTCCTAGTGAACT 59.983 44.444 0.00 0.00 0.00 3.01
142 143 7.163441 CCTCTACTATACCTCTCCTAGTGAAC 58.837 46.154 0.00 0.00 0.00 3.18
143 144 6.272792 CCCTCTACTATACCTCTCCTAGTGAA 59.727 46.154 0.00 0.00 0.00 3.18
144 145 5.786457 CCCTCTACTATACCTCTCCTAGTGA 59.214 48.000 0.00 0.00 0.00 3.41
145 146 5.045432 CCCCTCTACTATACCTCTCCTAGTG 60.045 52.000 0.00 0.00 0.00 2.74
146 147 5.102967 CCCCTCTACTATACCTCTCCTAGT 58.897 50.000 0.00 0.00 0.00 2.57
147 148 4.475747 CCCCCTCTACTATACCTCTCCTAG 59.524 54.167 0.00 0.00 0.00 3.02
148 149 4.140008 ACCCCCTCTACTATACCTCTCCTA 60.140 50.000 0.00 0.00 0.00 2.94
149 150 3.270812 CCCCCTCTACTATACCTCTCCT 58.729 54.545 0.00 0.00 0.00 3.69
150 151 2.995301 ACCCCCTCTACTATACCTCTCC 59.005 54.545 0.00 0.00 0.00 3.71
151 152 4.227982 CCTACCCCCTCTACTATACCTCTC 59.772 54.167 0.00 0.00 0.00 3.20
152 153 4.140008 TCCTACCCCCTCTACTATACCTCT 60.140 50.000 0.00 0.00 0.00 3.69
153 154 4.182318 TCCTACCCCCTCTACTATACCTC 58.818 52.174 0.00 0.00 0.00 3.85
154 155 4.255169 TCCTACCCCCTCTACTATACCT 57.745 50.000 0.00 0.00 0.00 3.08
155 156 4.543337 TGATCCTACCCCCTCTACTATACC 59.457 50.000 0.00 0.00 0.00 2.73
156 157 5.793034 TGATCCTACCCCCTCTACTATAC 57.207 47.826 0.00 0.00 0.00 1.47
157 158 5.435707 GGATGATCCTACCCCCTCTACTATA 59.564 48.000 3.71 0.00 32.53 1.31
158 159 4.233287 GGATGATCCTACCCCCTCTACTAT 59.767 50.000 3.71 0.00 32.53 2.12
159 160 3.596956 GGATGATCCTACCCCCTCTACTA 59.403 52.174 3.71 0.00 32.53 1.82
160 161 2.384029 GGATGATCCTACCCCCTCTACT 59.616 54.545 3.71 0.00 32.53 2.57
161 162 2.111972 TGGATGATCCTACCCCCTCTAC 59.888 54.545 13.44 0.00 37.46 2.59
162 163 2.449764 TGGATGATCCTACCCCCTCTA 58.550 52.381 13.44 0.00 37.46 2.43
163 164 1.255033 TGGATGATCCTACCCCCTCT 58.745 55.000 13.44 0.00 37.46 3.69
164 165 1.700186 GTTGGATGATCCTACCCCCTC 59.300 57.143 14.00 0.00 36.48 4.30
165 166 1.821088 GTTGGATGATCCTACCCCCT 58.179 55.000 14.00 0.00 36.48 4.79
170 171 2.104963 GGGTCTGGTTGGATGATCCTAC 59.895 54.545 16.20 16.20 40.75 3.18
171 172 2.022035 AGGGTCTGGTTGGATGATCCTA 60.022 50.000 13.44 1.60 39.34 2.94
172 173 1.216990 GGGTCTGGTTGGATGATCCT 58.783 55.000 13.44 0.00 37.46 3.24
173 174 1.216990 AGGGTCTGGTTGGATGATCC 58.783 55.000 4.05 4.05 36.96 3.36
174 175 3.041946 AGTAGGGTCTGGTTGGATGATC 58.958 50.000 0.00 0.00 0.00 2.92
175 176 2.774234 CAGTAGGGTCTGGTTGGATGAT 59.226 50.000 0.00 0.00 0.00 2.45
176 177 2.187958 CAGTAGGGTCTGGTTGGATGA 58.812 52.381 0.00 0.00 0.00 2.92
177 178 1.210478 CCAGTAGGGTCTGGTTGGATG 59.790 57.143 4.75 0.00 46.92 3.51
178 179 1.584724 CCAGTAGGGTCTGGTTGGAT 58.415 55.000 4.75 0.00 46.92 3.41
179 180 3.082619 CCAGTAGGGTCTGGTTGGA 57.917 57.895 4.75 0.00 46.92 3.53
187 188 0.910088 AGTTCCAGGCCAGTAGGGTC 60.910 60.000 5.01 0.00 43.70 4.46
188 189 0.475828 AAGTTCCAGGCCAGTAGGGT 60.476 55.000 5.01 0.00 39.65 4.34
189 190 1.486726 CTAAGTTCCAGGCCAGTAGGG 59.513 57.143 5.01 0.00 40.85 3.53
190 191 1.134371 GCTAAGTTCCAGGCCAGTAGG 60.134 57.143 5.01 0.54 38.23 3.18
191 192 1.134371 GGCTAAGTTCCAGGCCAGTAG 60.134 57.143 5.01 0.00 43.59 2.57
192 193 0.909623 GGCTAAGTTCCAGGCCAGTA 59.090 55.000 5.01 0.00 43.59 2.74
193 194 1.685820 GGCTAAGTTCCAGGCCAGT 59.314 57.895 5.01 0.00 43.59 4.00
194 195 4.645809 GGCTAAGTTCCAGGCCAG 57.354 61.111 5.01 0.00 43.59 4.85
196 197 4.645809 CTGGCTAAGTTCCAGGCC 57.354 61.111 0.00 0.00 45.62 5.19
199 200 1.826385 CCCAACTGGCTAAGTTCCAG 58.174 55.000 8.69 8.69 46.60 3.86
210 211 2.636830 CTCATGAACTAGCCCAACTGG 58.363 52.381 0.00 0.00 37.09 4.00
211 212 2.012673 GCTCATGAACTAGCCCAACTG 58.987 52.381 0.00 0.00 32.40 3.16
212 213 1.912043 AGCTCATGAACTAGCCCAACT 59.088 47.619 0.00 0.00 39.64 3.16
213 214 2.284190 GAGCTCATGAACTAGCCCAAC 58.716 52.381 9.40 0.00 39.64 3.77
214 215 1.210478 GGAGCTCATGAACTAGCCCAA 59.790 52.381 17.19 0.00 39.64 4.12
215 216 0.833287 GGAGCTCATGAACTAGCCCA 59.167 55.000 17.19 0.00 39.64 5.36
216 217 0.833287 TGGAGCTCATGAACTAGCCC 59.167 55.000 17.19 2.54 39.64 5.19
217 218 2.698855 TTGGAGCTCATGAACTAGCC 57.301 50.000 17.19 0.00 39.64 3.93
218 219 5.573337 AATTTTGGAGCTCATGAACTAGC 57.427 39.130 17.19 0.00 39.08 3.42
219 220 6.917533 ACAAATTTTGGAGCTCATGAACTAG 58.082 36.000 17.19 2.00 34.12 2.57
220 221 6.899393 ACAAATTTTGGAGCTCATGAACTA 57.101 33.333 17.19 0.00 34.12 2.24
221 222 5.796424 ACAAATTTTGGAGCTCATGAACT 57.204 34.783 17.19 0.00 34.12 3.01
222 223 6.073602 GGAAACAAATTTTGGAGCTCATGAAC 60.074 38.462 17.19 0.00 34.12 3.18
223 224 5.990996 GGAAACAAATTTTGGAGCTCATGAA 59.009 36.000 17.19 6.70 34.12 2.57
224 225 5.511202 GGGAAACAAATTTTGGAGCTCATGA 60.511 40.000 17.19 0.00 34.12 3.07
225 226 4.692155 GGGAAACAAATTTTGGAGCTCATG 59.308 41.667 17.19 4.97 34.12 3.07
226 227 4.594491 AGGGAAACAAATTTTGGAGCTCAT 59.406 37.500 17.19 0.00 34.12 2.90
227 228 3.966665 AGGGAAACAAATTTTGGAGCTCA 59.033 39.130 17.19 0.00 34.12 4.26
228 229 4.607293 AGGGAAACAAATTTTGGAGCTC 57.393 40.909 13.42 4.71 34.12 4.09
229 230 6.572314 CGAATAGGGAAACAAATTTTGGAGCT 60.572 38.462 13.42 0.00 34.12 4.09
230 231 5.576774 CGAATAGGGAAACAAATTTTGGAGC 59.423 40.000 13.42 2.25 34.12 4.70
231 232 5.576774 GCGAATAGGGAAACAAATTTTGGAG 59.423 40.000 13.42 0.00 34.12 3.86
232 233 5.011125 TGCGAATAGGGAAACAAATTTTGGA 59.989 36.000 13.42 0.00 34.12 3.53
233 234 5.233988 TGCGAATAGGGAAACAAATTTTGG 58.766 37.500 13.42 0.00 34.12 3.28
234 235 6.672836 GCATGCGAATAGGGAAACAAATTTTG 60.673 38.462 0.00 7.59 0.00 2.44
235 236 5.351189 GCATGCGAATAGGGAAACAAATTTT 59.649 36.000 0.00 0.00 0.00 1.82
236 237 4.869861 GCATGCGAATAGGGAAACAAATTT 59.130 37.500 0.00 0.00 0.00 1.82
237 238 4.160252 AGCATGCGAATAGGGAAACAAATT 59.840 37.500 13.01 0.00 0.00 1.82
238 239 3.701040 AGCATGCGAATAGGGAAACAAAT 59.299 39.130 13.01 0.00 0.00 2.32
239 240 3.088532 AGCATGCGAATAGGGAAACAAA 58.911 40.909 13.01 0.00 0.00 2.83
240 241 2.682856 GAGCATGCGAATAGGGAAACAA 59.317 45.455 13.01 0.00 0.00 2.83
241 242 2.288666 GAGCATGCGAATAGGGAAACA 58.711 47.619 13.01 0.00 0.00 2.83
242 243 2.288666 TGAGCATGCGAATAGGGAAAC 58.711 47.619 13.01 0.00 0.00 2.78
243 244 2.708216 TGAGCATGCGAATAGGGAAA 57.292 45.000 13.01 0.00 0.00 3.13
244 245 2.936919 ATGAGCATGCGAATAGGGAA 57.063 45.000 13.01 0.00 0.00 3.97
245 246 2.899900 AGTATGAGCATGCGAATAGGGA 59.100 45.455 13.01 0.00 0.00 4.20
246 247 3.325293 AGTATGAGCATGCGAATAGGG 57.675 47.619 13.01 0.00 0.00 3.53
247 248 5.120830 GGTTAAGTATGAGCATGCGAATAGG 59.879 44.000 13.01 0.00 0.00 2.57
248 249 5.120830 GGGTTAAGTATGAGCATGCGAATAG 59.879 44.000 13.01 0.00 0.00 1.73
249 250 4.994852 GGGTTAAGTATGAGCATGCGAATA 59.005 41.667 13.01 11.38 0.00 1.75
250 251 3.815401 GGGTTAAGTATGAGCATGCGAAT 59.185 43.478 13.01 12.42 0.00 3.34
251 252 3.202906 GGGTTAAGTATGAGCATGCGAA 58.797 45.455 13.01 4.76 0.00 4.70
252 253 2.484770 GGGGTTAAGTATGAGCATGCGA 60.485 50.000 13.01 3.11 0.00 5.10
253 254 1.873591 GGGGTTAAGTATGAGCATGCG 59.126 52.381 13.01 0.00 0.00 4.73
254 255 3.214696 AGGGGTTAAGTATGAGCATGC 57.785 47.619 10.51 10.51 0.00 4.06
255 256 5.290493 TGTAGGGGTTAAGTATGAGCATG 57.710 43.478 0.00 0.00 0.00 4.06
256 257 5.681639 GTTGTAGGGGTTAAGTATGAGCAT 58.318 41.667 0.00 0.00 0.00 3.79
257 258 4.382254 CGTTGTAGGGGTTAAGTATGAGCA 60.382 45.833 0.00 0.00 0.00 4.26
258 259 4.117685 CGTTGTAGGGGTTAAGTATGAGC 58.882 47.826 0.00 0.00 0.00 4.26
259 260 4.690122 CCGTTGTAGGGGTTAAGTATGAG 58.310 47.826 0.00 0.00 0.00 2.90
260 261 3.118665 GCCGTTGTAGGGGTTAAGTATGA 60.119 47.826 0.00 0.00 0.00 2.15
261 262 3.200483 GCCGTTGTAGGGGTTAAGTATG 58.800 50.000 0.00 0.00 0.00 2.39
262 263 2.839425 TGCCGTTGTAGGGGTTAAGTAT 59.161 45.455 0.00 0.00 0.00 2.12
263 264 2.255406 TGCCGTTGTAGGGGTTAAGTA 58.745 47.619 0.00 0.00 0.00 2.24
264 265 1.058284 TGCCGTTGTAGGGGTTAAGT 58.942 50.000 0.00 0.00 0.00 2.24
265 266 2.188062 TTGCCGTTGTAGGGGTTAAG 57.812 50.000 0.00 0.00 0.00 1.85
266 267 2.883122 ATTGCCGTTGTAGGGGTTAA 57.117 45.000 0.00 0.00 0.00 2.01
267 268 2.883122 AATTGCCGTTGTAGGGGTTA 57.117 45.000 0.00 0.00 0.00 2.85
268 269 2.003937 AAATTGCCGTTGTAGGGGTT 57.996 45.000 0.00 0.00 0.00 4.11
269 270 1.890489 GAAAATTGCCGTTGTAGGGGT 59.110 47.619 0.00 0.00 0.00 4.95
270 271 1.135517 CGAAAATTGCCGTTGTAGGGG 60.136 52.381 0.00 0.00 0.00 4.79
271 272 1.538075 ACGAAAATTGCCGTTGTAGGG 59.462 47.619 0.00 0.00 35.21 3.53
272 273 2.224549 TCACGAAAATTGCCGTTGTAGG 59.775 45.455 3.05 0.00 36.83 3.18
273 274 3.529634 TCACGAAAATTGCCGTTGTAG 57.470 42.857 3.05 0.00 36.83 2.74
274 275 3.965292 TTCACGAAAATTGCCGTTGTA 57.035 38.095 3.05 0.00 36.83 2.41
275 276 2.853731 TTCACGAAAATTGCCGTTGT 57.146 40.000 3.05 0.00 36.83 3.32
279 280 8.706656 AAAAATATTTTTCACGAAAATTGCCG 57.293 26.923 18.40 0.00 43.65 5.69
305 306 8.819643 AGGCGTTTGCAGTTTTAAATATTTTA 57.180 26.923 5.91 0.00 45.35 1.52
310 311 6.315091 TGTAGGCGTTTGCAGTTTTAAATA 57.685 33.333 0.00 0.00 45.35 1.40
311 312 5.189659 TGTAGGCGTTTGCAGTTTTAAAT 57.810 34.783 0.00 0.00 45.35 1.40
312 313 4.634184 TGTAGGCGTTTGCAGTTTTAAA 57.366 36.364 0.00 0.00 45.35 1.52
313 314 4.096682 AGTTGTAGGCGTTTGCAGTTTTAA 59.903 37.500 0.00 0.00 45.35 1.52
314 315 3.628487 AGTTGTAGGCGTTTGCAGTTTTA 59.372 39.130 0.00 0.00 45.35 1.52
327 328 4.005650 GGGTGGTAACTTTAGTTGTAGGC 58.994 47.826 5.41 0.00 38.90 3.93
333 334 5.157395 TGTAGAGGGGTGGTAACTTTAGTT 58.843 41.667 0.29 0.29 41.73 2.24
341 342 6.451292 TGTTTTAATGTAGAGGGGTGGTAA 57.549 37.500 0.00 0.00 0.00 2.85
343 344 4.809691 GCTGTTTTAATGTAGAGGGGTGGT 60.810 45.833 0.00 0.00 0.00 4.16
364 365 0.035152 TGCGGATGATTTGAGTGGCT 60.035 50.000 0.00 0.00 0.00 4.75
372 373 0.532115 GGTGGCTTTGCGGATGATTT 59.468 50.000 0.00 0.00 0.00 2.17
377 378 2.044946 GGAGGTGGCTTTGCGGAT 60.045 61.111 0.00 0.00 0.00 4.18
404 406 2.359478 CGTTCGTTGGGGGAAGGG 60.359 66.667 0.00 0.00 0.00 3.95
407 409 0.318120 GTAGACGTTCGTTGGGGGAA 59.682 55.000 0.00 0.00 0.00 3.97
408 410 1.535204 GGTAGACGTTCGTTGGGGGA 61.535 60.000 0.00 0.00 0.00 4.81
410 412 0.389426 CTGGTAGACGTTCGTTGGGG 60.389 60.000 0.00 0.00 0.00 4.96
414 418 4.240096 CCAATAACTGGTAGACGTTCGTT 58.760 43.478 0.00 0.00 40.78 3.85
423 427 3.793559 CTTCGACCCCAATAACTGGTAG 58.206 50.000 0.00 0.00 44.76 3.18
425 429 1.339727 GCTTCGACCCCAATAACTGGT 60.340 52.381 0.00 0.00 44.76 4.00
438 442 0.804989 CTTCCATGGTTGGCTTCGAC 59.195 55.000 12.58 0.00 43.29 4.20
440 444 1.937546 GCCTTCCATGGTTGGCTTCG 61.938 60.000 29.97 8.15 43.29 3.79
502 506 8.481492 TGCTCATTGGATCCATGTAAATAAAT 57.519 30.769 17.06 0.00 0.00 1.40
525 529 8.709386 ATCATTACTCTAACGGATAATCATGC 57.291 34.615 0.00 0.00 0.00 4.06
578 582 9.982291 CAGCTTGCTCGTAAAAATATTAAGTAA 57.018 29.630 0.00 0.00 0.00 2.24
579 583 9.373603 TCAGCTTGCTCGTAAAAATATTAAGTA 57.626 29.630 0.00 0.00 0.00 2.24
580 584 8.263940 TCAGCTTGCTCGTAAAAATATTAAGT 57.736 30.769 0.00 0.00 0.00 2.24
581 585 9.162793 CATCAGCTTGCTCGTAAAAATATTAAG 57.837 33.333 0.00 0.00 0.00 1.85
582 586 8.673711 ACATCAGCTTGCTCGTAAAAATATTAA 58.326 29.630 0.00 0.00 0.00 1.40
583 587 8.122330 CACATCAGCTTGCTCGTAAAAATATTA 58.878 33.333 0.00 0.00 0.00 0.98
584 588 6.968904 CACATCAGCTTGCTCGTAAAAATATT 59.031 34.615 0.00 0.00 0.00 1.28
585 589 6.458751 CCACATCAGCTTGCTCGTAAAAATAT 60.459 38.462 0.00 0.00 0.00 1.28
586 590 5.163764 CCACATCAGCTTGCTCGTAAAAATA 60.164 40.000 0.00 0.00 0.00 1.40
595 599 1.818642 AACTCCACATCAGCTTGCTC 58.181 50.000 0.00 0.00 0.00 4.26
596 600 3.054875 TCATAACTCCACATCAGCTTGCT 60.055 43.478 0.00 0.00 0.00 3.91
649 653 3.913799 TCTCTCTCCCACCAATTTAACCA 59.086 43.478 0.00 0.00 0.00 3.67
650 654 4.225267 TCTCTCTCTCCCACCAATTTAACC 59.775 45.833 0.00 0.00 0.00 2.85
654 658 5.527026 AATTCTCTCTCTCCCACCAATTT 57.473 39.130 0.00 0.00 0.00 1.82
700 707 5.528320 GCTAGACCTACAGAGAAACTACGAT 59.472 44.000 0.00 0.00 0.00 3.73
702 709 4.634883 TGCTAGACCTACAGAGAAACTACG 59.365 45.833 0.00 0.00 0.00 3.51
736 743 5.814188 TCATCGAAACATTCTCCTCATCAAG 59.186 40.000 0.00 0.00 0.00 3.02
738 745 5.343307 TCATCGAAACATTCTCCTCATCA 57.657 39.130 0.00 0.00 0.00 3.07
739 746 6.857777 AATCATCGAAACATTCTCCTCATC 57.142 37.500 0.00 0.00 0.00 2.92
740 747 7.275183 TGTAATCATCGAAACATTCTCCTCAT 58.725 34.615 0.00 0.00 0.00 2.90
776 787 1.208293 CTCTAACCCCTGTCAGGAAGC 59.792 57.143 21.23 0.00 37.67 3.86
785 796 0.460311 CGTGTAGGCTCTAACCCCTG 59.540 60.000 0.00 0.00 32.65 4.45
835 846 6.045072 ACCACTCGTTTCTAATCCATGTAA 57.955 37.500 0.00 0.00 0.00 2.41
1079 2616 4.856607 CGTCGGAGAGGCGCTTCC 62.857 72.222 16.77 14.97 42.71 3.46
1104 2641 2.258591 GACCGCAGCTCGTCTTGA 59.741 61.111 2.90 0.00 36.19 3.02
1129 2666 0.179111 CGGTAGAAGAAGATGCCGCA 60.179 55.000 0.00 0.00 37.85 5.69
1378 2918 0.902516 ACCTCGAAGCAGAGCTCCTT 60.903 55.000 10.93 7.58 38.25 3.36
1750 3349 2.979814 TGTCATCCTCGGTTGGTATG 57.020 50.000 0.00 0.00 0.00 2.39
1752 3351 2.569853 ACAATGTCATCCTCGGTTGGTA 59.430 45.455 0.00 0.00 0.00 3.25
2107 3706 0.538746 TGGAGCGCATATACTCGGGA 60.539 55.000 11.47 0.00 33.55 5.14
2417 4189 6.071391 CCTGGCTTATTTTTCAGCTTAGGAAA 60.071 38.462 8.43 0.00 40.13 3.13
2555 4327 6.547510 GGCTCTAAATGGATGGAAGTGTTATT 59.452 38.462 0.00 0.00 0.00 1.40
2587 4364 8.237811 AGTTCTTTTCAGGTGTCATTTAACAT 57.762 30.769 0.00 0.00 0.00 2.71
2683 4460 3.349006 CGCTCCGCACAAGCTGTT 61.349 61.111 0.00 0.00 37.62 3.16
2785 4562 3.241530 AACAGTCAGCCGAGGCCA 61.242 61.111 10.95 0.00 43.17 5.36
2799 4576 2.689471 GCCTCATTACATGCATCCAACA 59.311 45.455 0.00 0.00 0.00 3.33
2814 4591 2.149973 GGGAAGGAAACATGCCTCAT 57.850 50.000 0.00 0.00 36.50 2.90
2902 4679 3.070734 GCATGTGACTCTATCTGGATGGT 59.929 47.826 0.00 0.00 0.00 3.55
2913 4690 5.799213 AGTTTAGCTTTAGCATGTGACTCT 58.201 37.500 4.33 0.00 45.16 3.24
2914 4691 6.036191 GGTAGTTTAGCTTTAGCATGTGACTC 59.964 42.308 4.33 0.00 45.16 3.36
2966 4747 4.089361 CTGAAAAGACCTATTTGCCCCTT 58.911 43.478 0.00 0.00 0.00 3.95
3007 4788 3.127030 CACTTCCGTCCATTTTAAGCCTC 59.873 47.826 0.00 0.00 0.00 4.70
3013 4794 7.747155 TTTTATGACACTTCCGTCCATTTTA 57.253 32.000 0.00 0.00 34.88 1.52
3063 4844 9.856162 ACACTGAAAAACTTTTACTTCCCTATA 57.144 29.630 0.00 0.00 0.00 1.31
3083 4864 7.581213 ACATTGTTTCCTTATTTGACACTGA 57.419 32.000 0.00 0.00 0.00 3.41
3144 4937 1.116536 TCAACCTACACCACGCTCCA 61.117 55.000 0.00 0.00 0.00 3.86
3151 4944 3.153369 ACAATGCATCAACCTACACCA 57.847 42.857 0.00 0.00 0.00 4.17
3156 4949 5.714333 ACCATTACAACAATGCATCAACCTA 59.286 36.000 0.00 0.00 0.00 3.08
3178 4971 6.094048 TCAGCTGAATAAGATTTAGCAACACC 59.906 38.462 15.67 0.00 36.87 4.16
3203 4996 6.565234 CATCGACTAAGACATAACCAAGTCT 58.435 40.000 0.00 0.00 46.45 3.24
3293 5086 8.939201 ATCAAGTGTCAGTCAAGTGATATAAG 57.061 34.615 0.00 0.00 33.10 1.73
3328 5121 3.130693 GGCGTGACTAGGTCTCAGTTAAT 59.869 47.826 0.00 0.00 33.15 1.40


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

AutoCloner maintained by Alex Coulton.