Multiple sequence alignment - TraesCS6A01G142200

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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 TraesCS6A01G142200 chr6A 100.000 2765 0 0 341 3105 116913712 116910948 0.000000e+00 5107
1 TraesCS6A01G142200 chr6A 100.000 278 0 0 1 278 116914052 116913775 5.940000e-142 514
2 TraesCS6A01G142200 chr6B 95.884 1409 52 2 857 2261 182586041 182584635 0.000000e+00 2276
3 TraesCS6A01G142200 chr6B 96.749 646 17 2 2464 3105 182584365 182583720 0.000000e+00 1074
4 TraesCS6A01G142200 chr6D 94.725 872 33 5 826 1687 97914714 97913846 0.000000e+00 1343
5 TraesCS6A01G142200 chr6D 97.508 642 16 0 2464 3105 97912870 97912229 0.000000e+00 1098
6 TraesCS6A01G142200 chr2B 98.357 487 8 0 341 827 39435518 39436004 0.000000e+00 856
7 TraesCS6A01G142200 chr2B 97.737 486 11 0 341 826 461110710 461111195 0.000000e+00 837
8 TraesCS6A01G142200 chr2B 97.541 488 12 0 341 828 689370012 689369525 0.000000e+00 835
9 TraesCS6A01G142200 chr2B 99.640 278 1 0 1 278 461110597 461110874 2.760000e-140 508
10 TraesCS6A01G142200 chr2B 99.640 278 1 0 1 278 689370125 689369848 2.760000e-140 508
11 TraesCS6A01G142200 chr2A 98.156 488 9 0 341 828 145431942 145431455 0.000000e+00 852
12 TraesCS6A01G142200 chr2A 97.737 486 11 0 341 826 100136130 100136615 0.000000e+00 837
13 TraesCS6A01G142200 chr2A 99.640 278 1 0 1 278 100136017 100136294 2.760000e-140 508
14 TraesCS6A01G142200 chr4A 98.148 486 9 0 341 826 152589592 152590077 0.000000e+00 848
15 TraesCS6A01G142200 chr7A 97.737 486 11 0 341 826 22970069 22970554 0.000000e+00 837
16 TraesCS6A01G142200 chr7A 97.737 486 11 0 341 826 105254232 105253747 0.000000e+00 837
17 TraesCS6A01G142200 chr7A 100.000 278 0 0 1 278 333077140 333077417 5.940000e-142 514
18 TraesCS6A01G142200 chr7A 99.281 278 2 0 1 278 121055163 121055440 1.290000e-138 503
19 TraesCS6A01G142200 chr1A 97.531 486 12 0 341 826 552383595 552384080 0.000000e+00 832
20 TraesCS6A01G142200 chr1A 99.640 278 1 0 1 278 449188366 449188643 2.760000e-140 508
21 TraesCS6A01G142200 chr1A 99.281 278 2 0 1 278 552383482 552383759 1.290000e-138 503
22 TraesCS6A01G142200 chr1A 72.008 518 122 17 1414 1916 39871420 39870911 6.990000e-27 132
23 TraesCS6A01G142200 chr5A 99.640 278 1 0 1 278 403302487 403302764 2.760000e-140 508
24 TraesCS6A01G142200 chr1B 99.281 278 2 0 1 278 364307884 364307607 1.290000e-138 503
25 TraesCS6A01G142200 chr1B 72.340 517 122 16 1414 1916 60108386 60107877 3.230000e-30 143
26 TraesCS6A01G142200 chr4D 82.927 369 61 2 915 1282 456047317 456047684 6.420000e-87 331
27 TraesCS6A01G142200 chr4B 82.609 368 64 0 915 1282 570138765 570139132 2.990000e-85 326


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 TraesCS6A01G142200 chr6A 116910948 116914052 3104 True 2810.5 5107 100.0000 1 3105 2 chr6A.!!$R1 3104
1 TraesCS6A01G142200 chr6B 182583720 182586041 2321 True 1675.0 2276 96.3165 857 3105 2 chr6B.!!$R1 2248
2 TraesCS6A01G142200 chr6D 97912229 97914714 2485 True 1220.5 1343 96.1165 826 3105 2 chr6D.!!$R1 2279
3 TraesCS6A01G142200 chr2B 461110597 461111195 598 False 672.5 837 98.6885 1 826 2 chr2B.!!$F2 825
4 TraesCS6A01G142200 chr2B 689369525 689370125 600 True 671.5 835 98.5905 1 828 2 chr2B.!!$R1 827
5 TraesCS6A01G142200 chr2A 100136017 100136615 598 False 672.5 837 98.6885 1 826 2 chr2A.!!$F1 825
6 TraesCS6A01G142200 chr1A 552383482 552384080 598 False 667.5 832 98.4060 1 826 2 chr1A.!!$F2 825

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
266 267 0.035725 GTCTAAGGGTTTGGGTCGGG 60.036 60.0 0.00 0.0 0.00 5.14 F
268 269 0.322187 CTAAGGGTTTGGGTCGGGTG 60.322 60.0 0.00 0.0 0.00 4.61 F
2048 2063 0.040067 GATCCATTTCGCCCGAATGC 60.040 55.0 3.77 0.0 33.79 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1768 1783 0.386478 GAGCGCTTGCCTGACAAAAG 60.386 55.000 13.26 0.0 37.96 2.27 R
2065 2080 1.076024 TGCTTCTTTTGGAGCCTGGAT 59.924 47.619 0.00 0.0 0.00 3.41 R
2997 3695 3.682696 TCTCTTCAGTTAGTAGCGGTGA 58.317 45.455 0.00 0.0 0.00 4.02 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
160 161 4.045736 GAGATTACCTTAAGGGAGGGGTT 58.954 47.826 25.31 5.15 41.31 4.11
161 162 3.786450 AGATTACCTTAAGGGAGGGGTTG 59.214 47.826 25.31 0.00 41.31 3.77
162 163 1.975471 TACCTTAAGGGAGGGGTTGG 58.025 55.000 25.31 0.00 41.31 3.77
163 164 1.306633 CCTTAAGGGAGGGGTTGGC 59.693 63.158 14.25 0.00 37.23 4.52
164 165 1.214992 CCTTAAGGGAGGGGTTGGCT 61.215 60.000 14.25 0.00 37.23 4.75
165 166 0.704664 CTTAAGGGAGGGGTTGGCTT 59.295 55.000 0.00 0.00 0.00 4.35
166 167 0.702316 TTAAGGGAGGGGTTGGCTTC 59.298 55.000 0.00 0.00 0.00 3.86
167 168 0.476808 TAAGGGAGGGGTTGGCTTCA 60.477 55.000 0.00 0.00 0.00 3.02
168 169 1.368268 AAGGGAGGGGTTGGCTTCAA 61.368 55.000 0.00 0.00 0.00 2.69
169 170 1.155155 GGGAGGGGTTGGCTTCAAA 59.845 57.895 0.00 0.00 31.46 2.69
170 171 0.471022 GGGAGGGGTTGGCTTCAAAA 60.471 55.000 0.00 0.00 31.46 2.44
171 172 1.644509 GGAGGGGTTGGCTTCAAAAT 58.355 50.000 0.00 0.00 31.46 1.82
172 173 1.550524 GGAGGGGTTGGCTTCAAAATC 59.449 52.381 0.00 0.00 31.46 2.17
173 174 1.550524 GAGGGGTTGGCTTCAAAATCC 59.449 52.381 0.00 0.00 31.46 3.01
174 175 1.132881 AGGGGTTGGCTTCAAAATCCA 60.133 47.619 0.00 0.00 31.46 3.41
175 176 1.001974 GGGGTTGGCTTCAAAATCCAC 59.998 52.381 0.00 0.00 31.46 4.02
176 177 1.336795 GGGTTGGCTTCAAAATCCACG 60.337 52.381 0.00 0.00 31.46 4.94
177 178 1.336795 GGTTGGCTTCAAAATCCACGG 60.337 52.381 0.00 0.00 31.46 4.94
178 179 1.339929 GTTGGCTTCAAAATCCACGGT 59.660 47.619 0.00 0.00 31.46 4.83
179 180 0.958091 TGGCTTCAAAATCCACGGTG 59.042 50.000 0.00 0.00 0.00 4.94
180 181 0.958822 GGCTTCAAAATCCACGGTGT 59.041 50.000 7.45 0.00 0.00 4.16
181 182 1.335872 GGCTTCAAAATCCACGGTGTG 60.336 52.381 7.45 0.00 0.00 3.82
182 183 1.336755 GCTTCAAAATCCACGGTGTGT 59.663 47.619 7.45 0.00 0.00 3.72
190 191 2.668212 CACGGTGTGTGGCGGATT 60.668 61.111 0.00 0.00 45.21 3.01
191 192 2.112297 ACGGTGTGTGGCGGATTT 59.888 55.556 0.00 0.00 0.00 2.17
192 193 2.258013 ACGGTGTGTGGCGGATTTG 61.258 57.895 0.00 0.00 0.00 2.32
193 194 2.258286 GGTGTGTGGCGGATTTGC 59.742 61.111 0.00 0.00 0.00 3.68
194 195 2.560119 GGTGTGTGGCGGATTTGCA 61.560 57.895 0.00 0.00 36.28 4.08
195 196 1.361993 GTGTGTGGCGGATTTGCAA 59.638 52.632 0.00 0.00 36.28 4.08
196 197 0.664166 GTGTGTGGCGGATTTGCAAG 60.664 55.000 0.00 0.00 36.28 4.01
197 198 0.821301 TGTGTGGCGGATTTGCAAGA 60.821 50.000 0.00 0.00 36.28 3.02
198 199 0.527565 GTGTGGCGGATTTGCAAGAT 59.472 50.000 0.00 0.00 36.28 2.40
199 200 1.067635 GTGTGGCGGATTTGCAAGATT 60.068 47.619 0.00 0.00 36.28 2.40
200 201 1.617850 TGTGGCGGATTTGCAAGATTT 59.382 42.857 0.00 0.00 36.28 2.17
201 202 1.994779 GTGGCGGATTTGCAAGATTTG 59.005 47.619 0.00 0.00 36.28 2.32
202 203 1.891811 TGGCGGATTTGCAAGATTTGA 59.108 42.857 0.00 0.00 36.28 2.69
203 204 2.094597 TGGCGGATTTGCAAGATTTGAG 60.095 45.455 0.00 0.00 36.28 3.02
204 205 2.164219 GGCGGATTTGCAAGATTTGAGA 59.836 45.455 0.00 0.00 36.28 3.27
205 206 3.367292 GGCGGATTTGCAAGATTTGAGAA 60.367 43.478 0.00 0.00 36.28 2.87
206 207 3.855950 GCGGATTTGCAAGATTTGAGAAG 59.144 43.478 0.00 0.00 34.15 2.85
207 208 4.418392 CGGATTTGCAAGATTTGAGAAGG 58.582 43.478 0.00 0.00 0.00 3.46
208 209 4.156556 CGGATTTGCAAGATTTGAGAAGGA 59.843 41.667 0.00 0.00 0.00 3.36
209 210 5.163581 CGGATTTGCAAGATTTGAGAAGGAT 60.164 40.000 0.00 0.00 0.00 3.24
210 211 6.626623 CGGATTTGCAAGATTTGAGAAGGATT 60.627 38.462 0.00 0.00 0.00 3.01
211 212 7.101700 GGATTTGCAAGATTTGAGAAGGATTT 58.898 34.615 0.00 0.00 0.00 2.17
212 213 7.064253 GGATTTGCAAGATTTGAGAAGGATTTG 59.936 37.037 0.00 0.00 0.00 2.32
213 214 6.653526 TTGCAAGATTTGAGAAGGATTTGA 57.346 33.333 0.00 0.00 0.00 2.69
214 215 6.263516 TGCAAGATTTGAGAAGGATTTGAG 57.736 37.500 0.00 0.00 0.00 3.02
215 216 6.005823 TGCAAGATTTGAGAAGGATTTGAGA 58.994 36.000 0.00 0.00 0.00 3.27
216 217 6.150641 TGCAAGATTTGAGAAGGATTTGAGAG 59.849 38.462 0.00 0.00 0.00 3.20
217 218 6.404513 GCAAGATTTGAGAAGGATTTGAGAGG 60.405 42.308 0.00 0.00 0.00 3.69
218 219 5.753716 AGATTTGAGAAGGATTTGAGAGGG 58.246 41.667 0.00 0.00 0.00 4.30
219 220 4.307032 TTTGAGAAGGATTTGAGAGGGG 57.693 45.455 0.00 0.00 0.00 4.79
220 221 2.200081 TGAGAAGGATTTGAGAGGGGG 58.800 52.381 0.00 0.00 0.00 5.40
234 235 3.120191 GGGGGAGAGGGGAAGAGA 58.880 66.667 0.00 0.00 0.00 3.10
235 236 1.074850 GGGGGAGAGGGGAAGAGAG 60.075 68.421 0.00 0.00 0.00 3.20
236 237 1.074850 GGGGAGAGGGGAAGAGAGG 60.075 68.421 0.00 0.00 0.00 3.69
237 238 1.595058 GGGGAGAGGGGAAGAGAGGA 61.595 65.000 0.00 0.00 0.00 3.71
238 239 0.105709 GGGAGAGGGGAAGAGAGGAG 60.106 65.000 0.00 0.00 0.00 3.69
239 240 0.105709 GGAGAGGGGAAGAGAGGAGG 60.106 65.000 0.00 0.00 0.00 4.30
240 241 0.105709 GAGAGGGGAAGAGAGGAGGG 60.106 65.000 0.00 0.00 0.00 4.30
241 242 1.764454 GAGGGGAAGAGAGGAGGGC 60.764 68.421 0.00 0.00 0.00 5.19
242 243 2.770475 GGGGAAGAGAGGAGGGCC 60.770 72.222 0.00 0.00 0.00 5.80
243 244 3.157949 GGGAAGAGAGGAGGGCCG 61.158 72.222 0.00 0.00 39.96 6.13
244 245 3.855853 GGAAGAGAGGAGGGCCGC 61.856 72.222 0.00 0.00 39.96 6.53
245 246 3.077556 GAAGAGAGGAGGGCCGCA 61.078 66.667 10.15 0.00 39.96 5.69
246 247 2.607750 AAGAGAGGAGGGCCGCAA 60.608 61.111 10.15 0.00 39.96 4.85
247 248 2.585791 GAAGAGAGGAGGGCCGCAAG 62.586 65.000 10.15 0.00 39.96 4.01
248 249 3.394836 GAGAGGAGGGCCGCAAGT 61.395 66.667 10.15 0.00 39.96 3.16
249 250 3.378399 GAGAGGAGGGCCGCAAGTC 62.378 68.421 10.15 2.42 39.96 3.01
250 251 3.394836 GAGGAGGGCCGCAAGTCT 61.395 66.667 10.15 0.00 39.96 3.24
251 252 2.038975 AGGAGGGCCGCAAGTCTA 59.961 61.111 10.15 0.00 39.96 2.59
252 253 1.612442 AGGAGGGCCGCAAGTCTAA 60.612 57.895 10.15 0.00 39.96 2.10
253 254 1.153349 GGAGGGCCGCAAGTCTAAG 60.153 63.158 10.15 0.00 0.00 2.18
254 255 1.153349 GAGGGCCGCAAGTCTAAGG 60.153 63.158 1.02 0.00 0.00 2.69
255 256 2.124695 GGGCCGCAAGTCTAAGGG 60.125 66.667 0.00 0.00 0.00 3.95
256 257 2.669240 GGCCGCAAGTCTAAGGGT 59.331 61.111 0.00 0.00 0.00 4.34
257 258 1.002502 GGCCGCAAGTCTAAGGGTT 60.003 57.895 0.00 0.00 0.00 4.11
258 259 0.608308 GGCCGCAAGTCTAAGGGTTT 60.608 55.000 0.00 0.00 0.00 3.27
259 260 0.521735 GCCGCAAGTCTAAGGGTTTG 59.478 55.000 0.00 0.00 0.00 2.93
260 261 1.165270 CCGCAAGTCTAAGGGTTTGG 58.835 55.000 0.00 0.00 0.00 3.28
261 262 1.165270 CGCAAGTCTAAGGGTTTGGG 58.835 55.000 0.00 0.00 0.00 4.12
262 263 1.544759 CGCAAGTCTAAGGGTTTGGGT 60.545 52.381 0.00 0.00 0.00 4.51
263 264 2.160205 GCAAGTCTAAGGGTTTGGGTC 58.840 52.381 0.00 0.00 0.00 4.46
264 265 2.423577 CAAGTCTAAGGGTTTGGGTCG 58.576 52.381 0.00 0.00 0.00 4.79
265 266 0.981943 AGTCTAAGGGTTTGGGTCGG 59.018 55.000 0.00 0.00 0.00 4.79
266 267 0.035725 GTCTAAGGGTTTGGGTCGGG 60.036 60.000 0.00 0.00 0.00 5.14
267 268 0.474273 TCTAAGGGTTTGGGTCGGGT 60.474 55.000 0.00 0.00 0.00 5.28
268 269 0.322187 CTAAGGGTTTGGGTCGGGTG 60.322 60.000 0.00 0.00 0.00 4.61
269 270 1.781153 TAAGGGTTTGGGTCGGGTGG 61.781 60.000 0.00 0.00 0.00 4.61
270 271 4.671590 GGGTTTGGGTCGGGTGGG 62.672 72.222 0.00 0.00 0.00 4.61
271 272 4.671590 GGTTTGGGTCGGGTGGGG 62.672 72.222 0.00 0.00 0.00 4.96
272 273 4.671590 GTTTGGGTCGGGTGGGGG 62.672 72.222 0.00 0.00 0.00 5.40
361 362 3.213206 TGGATGAAAATGAGGGGATCG 57.787 47.619 0.00 0.00 0.00 3.69
362 363 2.158623 TGGATGAAAATGAGGGGATCGG 60.159 50.000 0.00 0.00 0.00 4.18
363 364 2.106511 GGATGAAAATGAGGGGATCGGA 59.893 50.000 0.00 0.00 0.00 4.55
364 365 3.406764 GATGAAAATGAGGGGATCGGAG 58.593 50.000 0.00 0.00 0.00 4.63
365 366 1.490490 TGAAAATGAGGGGATCGGAGG 59.510 52.381 0.00 0.00 0.00 4.30
366 367 1.768870 GAAAATGAGGGGATCGGAGGA 59.231 52.381 0.00 0.00 0.00 3.71
367 368 1.428869 AAATGAGGGGATCGGAGGAG 58.571 55.000 0.00 0.00 0.00 3.69
368 369 0.563173 AATGAGGGGATCGGAGGAGA 59.437 55.000 0.00 0.00 0.00 3.71
369 370 0.789687 ATGAGGGGATCGGAGGAGAT 59.210 55.000 0.00 0.00 0.00 2.75
370 371 0.563173 TGAGGGGATCGGAGGAGATT 59.437 55.000 0.00 0.00 0.00 2.40
371 372 1.787058 TGAGGGGATCGGAGGAGATTA 59.213 52.381 0.00 0.00 0.00 1.75
372 373 2.172679 GAGGGGATCGGAGGAGATTAC 58.827 57.143 0.00 0.00 0.00 1.89
373 374 1.203199 AGGGGATCGGAGGAGATTACC 60.203 57.143 0.00 0.00 0.00 2.85
374 375 1.203199 GGGGATCGGAGGAGATTACCT 60.203 57.143 0.00 0.00 43.64 3.08
375 376 2.610873 GGGATCGGAGGAGATTACCTT 58.389 52.381 0.00 0.00 40.73 3.50
376 377 3.501751 GGGGATCGGAGGAGATTACCTTA 60.502 52.174 0.00 0.00 40.73 2.69
377 378 4.158015 GGGATCGGAGGAGATTACCTTAA 58.842 47.826 0.00 0.00 40.73 1.85
378 379 4.221041 GGGATCGGAGGAGATTACCTTAAG 59.779 50.000 0.00 0.00 40.73 1.85
379 380 4.221041 GGATCGGAGGAGATTACCTTAAGG 59.779 50.000 20.42 20.42 40.73 2.69
380 381 3.573695 TCGGAGGAGATTACCTTAAGGG 58.426 50.000 25.31 7.85 40.73 3.95
381 382 3.205959 TCGGAGGAGATTACCTTAAGGGA 59.794 47.826 25.31 15.27 40.73 4.20
382 383 3.574826 CGGAGGAGATTACCTTAAGGGAG 59.425 52.174 25.31 0.91 40.73 4.30
383 384 3.904965 GGAGGAGATTACCTTAAGGGAGG 59.095 52.174 25.31 1.03 40.73 4.30
384 385 3.904965 GAGGAGATTACCTTAAGGGAGGG 59.095 52.174 25.31 0.97 41.31 4.30
385 386 2.980379 GGAGATTACCTTAAGGGAGGGG 59.020 54.545 25.31 0.19 41.31 4.79
386 387 3.635531 GGAGATTACCTTAAGGGAGGGGT 60.636 52.174 25.31 6.76 41.31 4.95
629 630 1.550524 AGATCTTAGGCGTTGCACAGA 59.449 47.619 0.00 0.00 0.00 3.41
795 796 5.010012 ACCAGGTCAGTTTGTGATTTGATTC 59.990 40.000 0.00 0.00 37.56 2.52
799 800 5.464168 GTCAGTTTGTGATTTGATTCCTGG 58.536 41.667 0.00 0.00 37.56 4.45
809 810 1.361204 TGATTCCTGGCTGAGGTCAA 58.639 50.000 2.71 0.00 43.37 3.18
837 838 3.326006 TGATTTCTGCCTCTGTTCTGACT 59.674 43.478 0.00 0.00 0.00 3.41
848 849 4.009675 TCTGTTCTGACTGTTGCTGTTTT 58.990 39.130 0.00 0.00 0.00 2.43
851 852 4.458989 TGTTCTGACTGTTGCTGTTTTCTT 59.541 37.500 0.00 0.00 0.00 2.52
852 853 5.048083 TGTTCTGACTGTTGCTGTTTTCTTT 60.048 36.000 0.00 0.00 0.00 2.52
855 856 2.860136 GACTGTTGCTGTTTTCTTTGCC 59.140 45.455 0.00 0.00 0.00 4.52
882 883 1.017387 GCTTCATCCATTCCACGTCC 58.983 55.000 0.00 0.00 0.00 4.79
883 884 1.407437 GCTTCATCCATTCCACGTCCT 60.407 52.381 0.00 0.00 0.00 3.85
900 901 2.552743 GTCCTTGGTTCTAACTGTTGGC 59.447 50.000 2.69 0.00 0.00 4.52
930 931 2.426024 CTGATTGCAGGAACTTGATGGG 59.574 50.000 0.00 0.00 34.60 4.00
975 976 2.444624 CGACGTGATTGCAGGGACG 61.445 63.158 0.00 10.76 37.82 4.79
1203 1204 3.681835 GGGGAGACACGCGTGAGT 61.682 66.667 42.94 28.99 0.00 3.41
1209 1210 2.658707 GACACGCGTGAGTCAAGCC 61.659 63.158 42.94 17.34 35.58 4.35
1278 1279 5.226396 CCAATCATCTTCTCCAGATACGAC 58.774 45.833 0.00 0.00 40.67 4.34
1435 1450 3.827898 GCCCTCCTCTCCGACGTG 61.828 72.222 0.00 0.00 0.00 4.49
1497 1512 0.387367 CACTTCGAGACCACGGACAG 60.387 60.000 0.00 0.00 0.00 3.51
1502 1517 2.842462 AGACCACGGACAGGCACA 60.842 61.111 0.00 0.00 0.00 4.57
1624 1639 5.927281 ACAATGATTTCTTCCCCATCAAG 57.073 39.130 0.00 0.00 30.79 3.02
1660 1675 2.470057 AGTTCCTCATCCTCTCCCTC 57.530 55.000 0.00 0.00 0.00 4.30
1696 1711 1.805945 GCTCGCGGACAAGTTCGAT 60.806 57.895 6.13 0.00 0.00 3.59
1753 1768 2.221055 GCTCTACAACAAAGGTGTGTCG 59.779 50.000 0.00 0.00 38.27 4.35
1768 1783 2.083522 GTCGCCGCTCATCGATAGC 61.084 63.158 13.59 13.59 41.67 2.97
1858 1873 4.018609 CGCTACCTTCGCATCCAG 57.981 61.111 0.00 0.00 0.00 3.86
1882 1897 0.613777 ACGATCTCAAGGGGAACACC 59.386 55.000 0.00 0.00 39.11 4.16
1916 1931 1.301716 GCCACGCCAGAGAACTTGA 60.302 57.895 0.00 0.00 0.00 3.02
1963 1978 3.248602 CACTACTGAAGAAACAGGTGTGC 59.751 47.826 0.00 0.00 41.59 4.57
2000 2015 2.258726 GGAAAAAGCGTGCCGGACT 61.259 57.895 5.05 0.00 0.00 3.85
2031 2046 1.066573 CACCAACGAGGAAGAGCTGAT 60.067 52.381 0.00 0.00 41.22 2.90
2048 2063 0.040067 GATCCATTTCGCCCGAATGC 60.040 55.000 3.77 0.00 33.79 3.56
2065 2080 1.082169 GCTGTCGCATGAACGCAAA 60.082 52.632 0.00 0.00 35.78 3.68
2118 2133 3.165071 CAAAGTAAACCTTGGCTGGGAT 58.835 45.455 3.54 0.00 32.32 3.85
2154 2169 2.775890 AGCTAGGATGTACATGCATGC 58.224 47.619 26.61 25.94 37.45 4.06
2157 2172 1.977056 AGGATGTACATGCATGCCAG 58.023 50.000 26.61 10.19 37.84 4.85
2183 2198 5.879777 TGATATGAACTGTTGGTGTGGTATG 59.120 40.000 0.00 0.00 0.00 2.39
2274 2289 8.467963 ACATTTATCCATATGCAACTTGATGA 57.532 30.769 0.00 0.00 0.00 2.92
2275 2290 9.085645 ACATTTATCCATATGCAACTTGATGAT 57.914 29.630 0.00 0.00 0.00 2.45
2276 2291 9.353999 CATTTATCCATATGCAACTTGATGATG 57.646 33.333 0.00 0.73 0.00 3.07
2277 2292 8.694581 TTTATCCATATGCAACTTGATGATGA 57.305 30.769 0.00 0.00 0.00 2.92
2278 2293 8.694581 TTATCCATATGCAACTTGATGATGAA 57.305 30.769 0.00 0.00 0.00 2.57
2279 2294 7.776618 ATCCATATGCAACTTGATGATGAAT 57.223 32.000 0.00 0.00 0.00 2.57
2280 2295 7.591421 TCCATATGCAACTTGATGATGAATT 57.409 32.000 0.00 0.00 0.00 2.17
2281 2296 8.014070 TCCATATGCAACTTGATGATGAATTT 57.986 30.769 0.00 0.00 0.00 1.82
2283 2298 9.188588 CCATATGCAACTTGATGATGAATTTAC 57.811 33.333 0.00 0.00 0.00 2.01
2287 2302 9.715121 ATGCAACTTGATGATGAATTTACTTTT 57.285 25.926 0.00 0.00 0.00 2.27
2289 2304 9.801714 GCAACTTGATGATGAATTTACTTTTTG 57.198 29.630 0.00 0.00 0.00 2.44
2301 2316 9.849166 TGAATTTACTTTTTGAGAAAAACGAGT 57.151 25.926 0.00 0.00 35.57 4.18
2308 2323 9.338291 ACTTTTTGAGAAAAACGAGTAGAAAAC 57.662 29.630 0.00 0.00 35.57 2.43
2309 2324 9.556030 CTTTTTGAGAAAAACGAGTAGAAAACT 57.444 29.630 0.00 0.00 36.96 2.66
2312 2327 8.937634 TTGAGAAAAACGAGTAGAAAACTAGT 57.062 30.769 0.00 0.00 44.90 2.57
2313 2328 8.571461 TGAGAAAAACGAGTAGAAAACTAGTC 57.429 34.615 0.00 0.00 42.51 2.59
2314 2329 8.192774 TGAGAAAAACGAGTAGAAAACTAGTCA 58.807 33.333 0.00 0.00 42.51 3.41
2315 2330 8.937634 AGAAAAACGAGTAGAAAACTAGTCAA 57.062 30.769 0.00 0.00 42.51 3.18
2316 2331 9.543783 AGAAAAACGAGTAGAAAACTAGTCAAT 57.456 29.630 0.00 0.00 42.51 2.57
2320 2335 9.924650 AAACGAGTAGAAAACTAGTCAATATGT 57.075 29.630 0.00 0.00 42.51 2.29
2321 2336 8.912787 ACGAGTAGAAAACTAGTCAATATGTG 57.087 34.615 0.00 0.00 39.59 3.21
2322 2337 7.488471 ACGAGTAGAAAACTAGTCAATATGTGC 59.512 37.037 0.00 0.00 39.59 4.57
2323 2338 7.488150 CGAGTAGAAAACTAGTCAATATGTGCA 59.512 37.037 0.00 0.00 39.07 4.57
2324 2339 9.319143 GAGTAGAAAACTAGTCAATATGTGCAT 57.681 33.333 0.00 0.00 39.07 3.96
2325 2340 9.672673 AGTAGAAAACTAGTCAATATGTGCATT 57.327 29.630 0.00 0.00 36.36 3.56
2328 2343 9.448438 AGAAAACTAGTCAATATGTGCATTACA 57.552 29.630 0.00 0.00 44.87 2.41
2345 2360 6.073327 CATTACATTCAGAATGCATGAGCT 57.927 37.500 21.22 4.50 42.52 4.09
2346 2361 5.746307 TTACATTCAGAATGCATGAGCTC 57.254 39.130 21.22 6.82 42.52 4.09
2347 2362 3.617284 ACATTCAGAATGCATGAGCTCA 58.383 40.909 20.79 20.79 42.52 4.26
2348 2363 3.377485 ACATTCAGAATGCATGAGCTCAC 59.623 43.478 20.97 8.09 42.52 3.51
2349 2364 2.773993 TCAGAATGCATGAGCTCACA 57.226 45.000 20.97 14.32 42.74 3.58
2350 2365 3.062122 TCAGAATGCATGAGCTCACAA 57.938 42.857 20.97 7.99 42.74 3.33
2351 2366 3.007635 TCAGAATGCATGAGCTCACAAG 58.992 45.455 20.97 13.25 42.74 3.16
2352 2367 2.097629 CAGAATGCATGAGCTCACAAGG 59.902 50.000 20.97 10.24 42.74 3.61
2353 2368 2.089980 GAATGCATGAGCTCACAAGGT 58.910 47.619 20.97 4.50 42.74 3.50
2354 2369 2.211250 ATGCATGAGCTCACAAGGTT 57.789 45.000 20.97 0.00 42.74 3.50
2355 2370 1.527034 TGCATGAGCTCACAAGGTTC 58.473 50.000 20.97 0.00 42.74 3.62
2356 2371 1.202794 TGCATGAGCTCACAAGGTTCA 60.203 47.619 20.97 0.00 42.74 3.18
2357 2372 1.198637 GCATGAGCTCACAAGGTTCAC 59.801 52.381 20.97 0.00 37.91 3.18
2358 2373 2.497138 CATGAGCTCACAAGGTTCACA 58.503 47.619 20.97 0.00 32.07 3.58
2359 2374 2.708216 TGAGCTCACAAGGTTCACAA 57.292 45.000 13.74 0.00 32.07 3.33
2360 2375 2.997980 TGAGCTCACAAGGTTCACAAA 58.002 42.857 13.74 0.00 32.07 2.83
2367 2382 3.128589 TCACAAGGTTCACAAAGTTCAGC 59.871 43.478 0.00 0.00 0.00 4.26
2381 2396 3.152341 AGTTCAGCTAGTTTGCAAGCAT 58.848 40.909 16.04 3.55 41.32 3.79
2398 2413 2.466846 GCATTGAGCAATCCATTTCCG 58.533 47.619 0.00 0.00 44.79 4.30
2400 2415 3.429272 GCATTGAGCAATCCATTTCCGAA 60.429 43.478 0.00 0.00 44.79 4.30
2403 2418 2.491693 TGAGCAATCCATTTCCGAAACC 59.508 45.455 0.00 0.00 0.00 3.27
2404 2419 2.755103 GAGCAATCCATTTCCGAAACCT 59.245 45.455 0.00 0.00 0.00 3.50
2407 2422 3.056891 GCAATCCATTTCCGAAACCTTGA 60.057 43.478 0.00 0.00 0.00 3.02
2408 2423 4.485163 CAATCCATTTCCGAAACCTTGAC 58.515 43.478 0.00 0.00 0.00 3.18
2409 2424 2.510613 TCCATTTCCGAAACCTTGACC 58.489 47.619 0.00 0.00 0.00 4.02
2410 2425 2.158593 TCCATTTCCGAAACCTTGACCA 60.159 45.455 0.00 0.00 0.00 4.02
2411 2426 2.228822 CCATTTCCGAAACCTTGACCAG 59.771 50.000 0.00 0.00 0.00 4.00
2412 2427 3.146066 CATTTCCGAAACCTTGACCAGA 58.854 45.455 0.00 0.00 0.00 3.86
2413 2428 3.284793 TTTCCGAAACCTTGACCAGAA 57.715 42.857 0.00 0.00 0.00 3.02
2415 2430 3.053831 TCCGAAACCTTGACCAGAATC 57.946 47.619 0.00 0.00 0.00 2.52
2416 2431 2.370519 TCCGAAACCTTGACCAGAATCA 59.629 45.455 0.00 0.00 0.00 2.57
2417 2432 2.744202 CCGAAACCTTGACCAGAATCAG 59.256 50.000 0.00 0.00 0.00 2.90
2418 2433 3.403038 CGAAACCTTGACCAGAATCAGT 58.597 45.455 0.00 0.00 0.00 3.41
2419 2434 3.187227 CGAAACCTTGACCAGAATCAGTG 59.813 47.826 0.00 0.00 0.00 3.66
2420 2435 4.389374 GAAACCTTGACCAGAATCAGTGA 58.611 43.478 0.00 0.00 0.00 3.41
2421 2436 4.647564 AACCTTGACCAGAATCAGTGAT 57.352 40.909 0.00 0.00 0.00 3.06
2422 2437 3.947868 ACCTTGACCAGAATCAGTGATG 58.052 45.455 6.34 0.00 0.00 3.07
2423 2438 3.584406 ACCTTGACCAGAATCAGTGATGA 59.416 43.478 6.34 0.00 0.00 2.92
2424 2439 4.042062 ACCTTGACCAGAATCAGTGATGAA 59.958 41.667 6.34 0.00 0.00 2.57
2425 2440 5.005740 CCTTGACCAGAATCAGTGATGAAA 58.994 41.667 6.34 0.00 0.00 2.69
2426 2441 5.123502 CCTTGACCAGAATCAGTGATGAAAG 59.876 44.000 6.34 4.45 0.00 2.62
2428 2443 5.485620 TGACCAGAATCAGTGATGAAAGAG 58.514 41.667 6.34 0.00 0.00 2.85
2429 2444 4.841422 ACCAGAATCAGTGATGAAAGAGG 58.159 43.478 6.34 6.13 0.00 3.69
2430 2445 3.626670 CCAGAATCAGTGATGAAAGAGGC 59.373 47.826 6.34 0.00 0.00 4.70
2432 2447 3.055530 AGAATCAGTGATGAAAGAGGCGT 60.056 43.478 6.34 0.00 0.00 5.68
2433 2448 2.370281 TCAGTGATGAAAGAGGCGTC 57.630 50.000 0.00 0.00 0.00 5.19
2434 2449 0.994995 CAGTGATGAAAGAGGCGTCG 59.005 55.000 0.00 0.00 0.00 5.12
2435 2450 0.108615 AGTGATGAAAGAGGCGTCGG 60.109 55.000 0.00 0.00 0.00 4.79
2436 2451 0.389948 GTGATGAAAGAGGCGTCGGT 60.390 55.000 0.00 0.00 0.00 4.69
2437 2452 0.389817 TGATGAAAGAGGCGTCGGTG 60.390 55.000 0.00 0.00 0.00 4.94
2438 2453 0.389948 GATGAAAGAGGCGTCGGTGT 60.390 55.000 0.00 0.00 0.00 4.16
2440 2455 0.599204 TGAAAGAGGCGTCGGTGTTC 60.599 55.000 0.00 4.83 0.00 3.18
2441 2456 0.599204 GAAAGAGGCGTCGGTGTTCA 60.599 55.000 0.00 0.00 0.00 3.18
2442 2457 0.600255 AAAGAGGCGTCGGTGTTCAG 60.600 55.000 0.00 0.00 0.00 3.02
2445 2460 0.878961 GAGGCGTCGGTGTTCAGTTT 60.879 55.000 0.00 0.00 0.00 2.66
2446 2461 0.390124 AGGCGTCGGTGTTCAGTTTA 59.610 50.000 0.00 0.00 0.00 2.01
2447 2462 1.202557 AGGCGTCGGTGTTCAGTTTAA 60.203 47.619 0.00 0.00 0.00 1.52
2448 2463 1.070376 GGCGTCGGTGTTCAGTTTAAC 60.070 52.381 0.00 0.00 0.00 2.01
2449 2464 1.862827 GCGTCGGTGTTCAGTTTAACT 59.137 47.619 0.00 0.00 0.00 2.24
2450 2465 3.052036 GCGTCGGTGTTCAGTTTAACTA 58.948 45.455 0.00 0.00 0.00 2.24
2451 2466 3.490526 GCGTCGGTGTTCAGTTTAACTAA 59.509 43.478 0.00 0.00 0.00 2.24
2457 2472 7.062722 GTCGGTGTTCAGTTTAACTAACTATCC 59.937 40.741 0.00 6.92 45.29 2.59
2458 2473 6.312180 CGGTGTTCAGTTTAACTAACTATCCC 59.688 42.308 0.00 3.09 45.29 3.85
2459 2474 7.392418 GGTGTTCAGTTTAACTAACTATCCCT 58.608 38.462 0.00 0.00 45.29 4.20
2460 2475 7.333672 GGTGTTCAGTTTAACTAACTATCCCTG 59.666 40.741 0.00 0.00 45.29 4.45
2461 2476 6.877322 TGTTCAGTTTAACTAACTATCCCTGC 59.123 38.462 0.00 0.00 45.29 4.85
2476 3170 2.163412 TCCCTGCATCGTAAACAAATGC 59.837 45.455 9.41 9.41 44.72 3.56
2493 3187 3.923017 ATGCTTAGTTTCCACTGCAAC 57.077 42.857 0.00 0.00 35.99 4.17
2803 3501 7.729124 ATACTTCTAACTAAGTGGGTGCTTA 57.271 36.000 0.00 0.00 39.95 3.09
2810 3508 3.844211 ACTAAGTGGGTGCTTATCTCCAA 59.156 43.478 0.00 0.00 31.42 3.53
2919 3617 3.260483 GATCACCGCAGCTCGCTG 61.260 66.667 14.30 14.30 46.15 5.18
2935 3633 0.897401 GCTGGCTGCCTTTCCTCTTT 60.897 55.000 21.03 0.00 35.15 2.52
2997 3695 2.831770 CCGATGCCCAGCAGGTAT 59.168 61.111 0.00 0.00 44.90 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
160 161 0.958091 CACCGTGGATTTTGAAGCCA 59.042 50.000 0.00 0.00 46.37 4.75
161 162 0.958822 ACACCGTGGATTTTGAAGCC 59.041 50.000 3.03 0.00 37.50 4.35
162 163 1.336755 ACACACCGTGGATTTTGAAGC 59.663 47.619 3.03 0.00 37.94 3.86
163 164 2.998772 CACACACCGTGGATTTTGAAG 58.001 47.619 3.03 0.00 42.34 3.02
173 174 2.258013 AAATCCGCCACACACCGTG 61.258 57.895 0.00 0.00 45.92 4.94
174 175 2.112297 AAATCCGCCACACACCGT 59.888 55.556 0.00 0.00 0.00 4.83
175 176 2.560861 CAAATCCGCCACACACCG 59.439 61.111 0.00 0.00 0.00 4.94
176 177 2.081425 TTGCAAATCCGCCACACACC 62.081 55.000 0.00 0.00 0.00 4.16
177 178 0.664166 CTTGCAAATCCGCCACACAC 60.664 55.000 0.00 0.00 0.00 3.82
178 179 0.821301 TCTTGCAAATCCGCCACACA 60.821 50.000 0.00 0.00 0.00 3.72
179 180 0.527565 ATCTTGCAAATCCGCCACAC 59.472 50.000 0.00 0.00 0.00 3.82
180 181 1.255882 AATCTTGCAAATCCGCCACA 58.744 45.000 0.00 0.00 0.00 4.17
181 182 1.994779 CAAATCTTGCAAATCCGCCAC 59.005 47.619 0.00 0.00 0.00 5.01
182 183 1.891811 TCAAATCTTGCAAATCCGCCA 59.108 42.857 0.00 0.00 0.00 5.69
183 184 2.164219 TCTCAAATCTTGCAAATCCGCC 59.836 45.455 0.00 0.00 0.00 6.13
184 185 3.492421 TCTCAAATCTTGCAAATCCGC 57.508 42.857 0.00 0.00 0.00 5.54
185 186 4.156556 TCCTTCTCAAATCTTGCAAATCCG 59.843 41.667 0.00 0.00 0.00 4.18
186 187 5.649782 TCCTTCTCAAATCTTGCAAATCC 57.350 39.130 0.00 0.00 0.00 3.01
187 188 7.816031 TCAAATCCTTCTCAAATCTTGCAAATC 59.184 33.333 0.00 0.00 0.00 2.17
188 189 7.673180 TCAAATCCTTCTCAAATCTTGCAAAT 58.327 30.769 0.00 0.00 0.00 2.32
189 190 7.014518 TCTCAAATCCTTCTCAAATCTTGCAAA 59.985 33.333 0.00 0.00 0.00 3.68
190 191 6.491062 TCTCAAATCCTTCTCAAATCTTGCAA 59.509 34.615 0.00 0.00 0.00 4.08
191 192 6.005823 TCTCAAATCCTTCTCAAATCTTGCA 58.994 36.000 0.00 0.00 0.00 4.08
192 193 6.404513 CCTCTCAAATCCTTCTCAAATCTTGC 60.405 42.308 0.00 0.00 0.00 4.01
193 194 6.095160 CCCTCTCAAATCCTTCTCAAATCTTG 59.905 42.308 0.00 0.00 0.00 3.02
194 195 6.186234 CCCTCTCAAATCCTTCTCAAATCTT 58.814 40.000 0.00 0.00 0.00 2.40
195 196 5.339861 CCCCTCTCAAATCCTTCTCAAATCT 60.340 44.000 0.00 0.00 0.00 2.40
196 197 4.886489 CCCCTCTCAAATCCTTCTCAAATC 59.114 45.833 0.00 0.00 0.00 2.17
197 198 4.325658 CCCCCTCTCAAATCCTTCTCAAAT 60.326 45.833 0.00 0.00 0.00 2.32
198 199 3.010584 CCCCCTCTCAAATCCTTCTCAAA 59.989 47.826 0.00 0.00 0.00 2.69
199 200 2.578021 CCCCCTCTCAAATCCTTCTCAA 59.422 50.000 0.00 0.00 0.00 3.02
200 201 2.200081 CCCCCTCTCAAATCCTTCTCA 58.800 52.381 0.00 0.00 0.00 3.27
217 218 1.074850 CTCTCTTCCCCTCTCCCCC 60.075 68.421 0.00 0.00 0.00 5.40
218 219 1.074850 CCTCTCTTCCCCTCTCCCC 60.075 68.421 0.00 0.00 0.00 4.81
219 220 0.105709 CTCCTCTCTTCCCCTCTCCC 60.106 65.000 0.00 0.00 0.00 4.30
220 221 0.105709 CCTCCTCTCTTCCCCTCTCC 60.106 65.000 0.00 0.00 0.00 3.71
221 222 0.105709 CCCTCCTCTCTTCCCCTCTC 60.106 65.000 0.00 0.00 0.00 3.20
222 223 2.023532 CCCTCCTCTCTTCCCCTCT 58.976 63.158 0.00 0.00 0.00 3.69
223 224 1.764454 GCCCTCCTCTCTTCCCCTC 60.764 68.421 0.00 0.00 0.00 4.30
224 225 2.370633 GCCCTCCTCTCTTCCCCT 59.629 66.667 0.00 0.00 0.00 4.79
225 226 2.770475 GGCCCTCCTCTCTTCCCC 60.770 72.222 0.00 0.00 0.00 4.81
226 227 3.157949 CGGCCCTCCTCTCTTCCC 61.158 72.222 0.00 0.00 0.00 3.97
227 228 3.855853 GCGGCCCTCCTCTCTTCC 61.856 72.222 0.00 0.00 0.00 3.46
228 229 2.585791 CTTGCGGCCCTCCTCTCTTC 62.586 65.000 0.00 0.00 0.00 2.87
229 230 2.607750 TTGCGGCCCTCCTCTCTT 60.608 61.111 0.00 0.00 0.00 2.85
230 231 3.080121 CTTGCGGCCCTCCTCTCT 61.080 66.667 0.00 0.00 0.00 3.10
231 232 3.378399 GACTTGCGGCCCTCCTCTC 62.378 68.421 0.00 0.00 0.00 3.20
232 233 2.516048 TAGACTTGCGGCCCTCCTCT 62.516 60.000 0.00 0.00 0.00 3.69
233 234 1.614241 TTAGACTTGCGGCCCTCCTC 61.614 60.000 0.00 0.00 0.00 3.71
234 235 1.612442 TTAGACTTGCGGCCCTCCT 60.612 57.895 0.00 0.00 0.00 3.69
235 236 1.153349 CTTAGACTTGCGGCCCTCC 60.153 63.158 0.00 0.00 0.00 4.30
236 237 1.153349 CCTTAGACTTGCGGCCCTC 60.153 63.158 0.00 0.00 0.00 4.30
237 238 2.670148 CCCTTAGACTTGCGGCCCT 61.670 63.158 0.00 0.00 0.00 5.19
238 239 2.124695 CCCTTAGACTTGCGGCCC 60.125 66.667 0.00 0.00 0.00 5.80
239 240 0.608308 AAACCCTTAGACTTGCGGCC 60.608 55.000 0.00 0.00 0.00 6.13
240 241 0.521735 CAAACCCTTAGACTTGCGGC 59.478 55.000 0.00 0.00 0.00 6.53
241 242 1.165270 CCAAACCCTTAGACTTGCGG 58.835 55.000 0.00 0.00 0.00 5.69
242 243 1.165270 CCCAAACCCTTAGACTTGCG 58.835 55.000 0.00 0.00 0.00 4.85
243 244 2.160205 GACCCAAACCCTTAGACTTGC 58.840 52.381 0.00 0.00 0.00 4.01
244 245 2.423577 CGACCCAAACCCTTAGACTTG 58.576 52.381 0.00 0.00 0.00 3.16
245 246 1.350019 CCGACCCAAACCCTTAGACTT 59.650 52.381 0.00 0.00 0.00 3.01
246 247 0.981943 CCGACCCAAACCCTTAGACT 59.018 55.000 0.00 0.00 0.00 3.24
247 248 0.035725 CCCGACCCAAACCCTTAGAC 60.036 60.000 0.00 0.00 0.00 2.59
248 249 0.474273 ACCCGACCCAAACCCTTAGA 60.474 55.000 0.00 0.00 0.00 2.10
249 250 0.322187 CACCCGACCCAAACCCTTAG 60.322 60.000 0.00 0.00 0.00 2.18
250 251 1.762471 CACCCGACCCAAACCCTTA 59.238 57.895 0.00 0.00 0.00 2.69
251 252 2.518933 CACCCGACCCAAACCCTT 59.481 61.111 0.00 0.00 0.00 3.95
252 253 3.576259 CCACCCGACCCAAACCCT 61.576 66.667 0.00 0.00 0.00 4.34
253 254 4.671590 CCCACCCGACCCAAACCC 62.672 72.222 0.00 0.00 0.00 4.11
254 255 4.671590 CCCCACCCGACCCAAACC 62.672 72.222 0.00 0.00 0.00 3.27
255 256 4.671590 CCCCCACCCGACCCAAAC 62.672 72.222 0.00 0.00 0.00 2.93
340 341 3.499202 CCGATCCCCTCATTTTCATCCAT 60.499 47.826 0.00 0.00 0.00 3.41
341 342 2.158623 CCGATCCCCTCATTTTCATCCA 60.159 50.000 0.00 0.00 0.00 3.41
342 343 2.106511 TCCGATCCCCTCATTTTCATCC 59.893 50.000 0.00 0.00 0.00 3.51
343 344 3.406764 CTCCGATCCCCTCATTTTCATC 58.593 50.000 0.00 0.00 0.00 2.92
344 345 2.107204 CCTCCGATCCCCTCATTTTCAT 59.893 50.000 0.00 0.00 0.00 2.57
345 346 1.490490 CCTCCGATCCCCTCATTTTCA 59.510 52.381 0.00 0.00 0.00 2.69
346 347 1.768870 TCCTCCGATCCCCTCATTTTC 59.231 52.381 0.00 0.00 0.00 2.29
347 348 1.771255 CTCCTCCGATCCCCTCATTTT 59.229 52.381 0.00 0.00 0.00 1.82
348 349 1.062121 TCTCCTCCGATCCCCTCATTT 60.062 52.381 0.00 0.00 0.00 2.32
349 350 0.563173 TCTCCTCCGATCCCCTCATT 59.437 55.000 0.00 0.00 0.00 2.57
350 351 0.789687 ATCTCCTCCGATCCCCTCAT 59.210 55.000 0.00 0.00 0.00 2.90
351 352 0.563173 AATCTCCTCCGATCCCCTCA 59.437 55.000 0.00 0.00 0.00 3.86
352 353 2.172679 GTAATCTCCTCCGATCCCCTC 58.827 57.143 0.00 0.00 0.00 4.30
353 354 1.203199 GGTAATCTCCTCCGATCCCCT 60.203 57.143 0.00 0.00 0.00 4.79
354 355 1.203199 AGGTAATCTCCTCCGATCCCC 60.203 57.143 0.00 0.00 31.32 4.81
355 356 2.312424 AGGTAATCTCCTCCGATCCC 57.688 55.000 0.00 0.00 31.32 3.85
356 357 4.221041 CCTTAAGGTAATCTCCTCCGATCC 59.779 50.000 13.83 0.00 36.74 3.36
357 358 4.221041 CCCTTAAGGTAATCTCCTCCGATC 59.779 50.000 20.22 0.00 36.74 3.69
358 359 4.140758 TCCCTTAAGGTAATCTCCTCCGAT 60.141 45.833 20.22 0.00 36.74 4.18
359 360 3.205959 TCCCTTAAGGTAATCTCCTCCGA 59.794 47.826 20.22 2.91 36.74 4.55
360 361 3.573695 TCCCTTAAGGTAATCTCCTCCG 58.426 50.000 20.22 0.46 36.74 4.63
361 362 3.904965 CCTCCCTTAAGGTAATCTCCTCC 59.095 52.174 20.22 0.00 36.74 4.30
362 363 3.904965 CCCTCCCTTAAGGTAATCTCCTC 59.095 52.174 20.22 0.00 36.74 3.71
363 364 3.376555 CCCCTCCCTTAAGGTAATCTCCT 60.377 52.174 20.22 0.00 39.84 3.69
364 365 2.980379 CCCCTCCCTTAAGGTAATCTCC 59.020 54.545 20.22 0.00 36.75 3.71
365 366 3.666568 ACCCCTCCCTTAAGGTAATCTC 58.333 50.000 20.22 0.00 36.75 2.75
366 367 3.786450 CAACCCCTCCCTTAAGGTAATCT 59.214 47.826 20.22 0.00 36.75 2.40
367 368 3.117625 CCAACCCCTCCCTTAAGGTAATC 60.118 52.174 20.22 0.00 36.75 1.75
368 369 2.856864 CCAACCCCTCCCTTAAGGTAAT 59.143 50.000 20.22 0.00 36.75 1.89
369 370 2.281034 CCAACCCCTCCCTTAAGGTAA 58.719 52.381 20.22 7.17 36.75 2.85
370 371 1.975471 CCAACCCCTCCCTTAAGGTA 58.025 55.000 20.22 3.36 36.75 3.08
371 372 1.506907 GCCAACCCCTCCCTTAAGGT 61.507 60.000 20.22 0.00 36.75 3.50
372 373 1.214992 AGCCAACCCCTCCCTTAAGG 61.215 60.000 15.14 15.14 36.08 2.69
373 374 0.704664 AAGCCAACCCCTCCCTTAAG 59.295 55.000 0.00 0.00 0.00 1.85
374 375 0.702316 GAAGCCAACCCCTCCCTTAA 59.298 55.000 0.00 0.00 0.00 1.85
375 376 1.559065 CGAAGCCAACCCCTCCCTTA 61.559 60.000 0.00 0.00 0.00 2.69
376 377 2.907179 CGAAGCCAACCCCTCCCTT 61.907 63.158 0.00 0.00 0.00 3.95
377 378 3.330720 CGAAGCCAACCCCTCCCT 61.331 66.667 0.00 0.00 0.00 4.20
378 379 2.420466 TTTCGAAGCCAACCCCTCCC 62.420 60.000 0.00 0.00 0.00 4.30
379 380 0.323451 ATTTCGAAGCCAACCCCTCC 60.323 55.000 0.00 0.00 0.00 4.30
380 381 1.095600 GATTTCGAAGCCAACCCCTC 58.904 55.000 0.00 0.00 0.00 4.30
381 382 0.323451 GGATTTCGAAGCCAACCCCT 60.323 55.000 12.65 0.00 36.80 4.79
382 383 0.610785 TGGATTTCGAAGCCAACCCC 60.611 55.000 16.61 4.97 45.40 4.95
383 384 2.955609 TGGATTTCGAAGCCAACCC 58.044 52.632 16.61 6.13 45.40 4.11
684 685 2.514824 CAGCGCCCTTCCCTTAGC 60.515 66.667 2.29 0.00 0.00 3.09
743 744 2.206576 AATTTCACTCTGCTGACCCC 57.793 50.000 0.00 0.00 0.00 4.95
799 800 6.493116 CAGAAATCACATATTTGACCTCAGC 58.507 40.000 0.00 0.00 0.00 4.26
809 810 6.318144 CAGAACAGAGGCAGAAATCACATATT 59.682 38.462 0.00 0.00 0.00 1.28
837 838 2.891112 CAGGCAAAGAAAACAGCAACA 58.109 42.857 0.00 0.00 0.00 3.33
848 849 0.030638 GAAGCAAACGCAGGCAAAGA 59.969 50.000 0.00 0.00 0.00 2.52
851 852 0.039256 GATGAAGCAAACGCAGGCAA 60.039 50.000 0.00 0.00 0.00 4.52
852 853 1.580942 GATGAAGCAAACGCAGGCA 59.419 52.632 0.00 0.00 0.00 4.75
855 856 2.523015 GAATGGATGAAGCAAACGCAG 58.477 47.619 0.00 0.00 0.00 5.18
882 883 2.032030 CACGCCAACAGTTAGAACCAAG 60.032 50.000 0.00 0.00 0.00 3.61
883 884 1.944024 CACGCCAACAGTTAGAACCAA 59.056 47.619 0.00 0.00 0.00 3.67
1047 1048 2.093973 CAGGTAGAAGGCGTTGATGTCT 60.094 50.000 0.00 0.00 0.00 3.41
1122 1123 1.454663 GGGCCCCTTGATGCTCTTC 60.455 63.158 12.23 0.00 0.00 2.87
1203 1204 1.159285 CGATGTTCTGCAAGGCTTGA 58.841 50.000 30.45 14.23 0.00 3.02
1209 1210 0.716108 GGACGACGATGTTCTGCAAG 59.284 55.000 0.00 0.00 0.00 4.01
1278 1279 1.066358 GTGGAGGGGGAAGAACTTACG 60.066 57.143 0.00 0.00 0.00 3.18
1290 1291 2.290705 ACGTTTATTTGGAGTGGAGGGG 60.291 50.000 0.00 0.00 0.00 4.79
1291 1292 2.747446 CACGTTTATTTGGAGTGGAGGG 59.253 50.000 0.00 0.00 0.00 4.30
1341 1350 1.615107 GCGACGTACTCAGGCAACAC 61.615 60.000 0.00 0.00 41.41 3.32
1502 1517 4.107051 GAATGCGCGTGGCTTGCT 62.107 61.111 8.43 0.00 44.05 3.91
1624 1639 3.809374 CTTCCCATAGTCGGCCGGC 62.809 68.421 25.39 25.39 0.00 6.13
1753 1768 1.070309 CAAAAGCTATCGATGAGCGGC 60.070 52.381 8.54 4.77 44.98 6.53
1768 1783 0.386478 GAGCGCTTGCCTGACAAAAG 60.386 55.000 13.26 0.00 37.96 2.27
1858 1873 1.414158 TCCCCTTGAGATCGTCATCC 58.586 55.000 0.00 0.00 34.17 3.51
1906 1921 3.496130 CGACAAGCATGTTCAAGTTCTCT 59.504 43.478 0.00 0.00 40.74 3.10
1916 1931 1.282248 CCGACGTCGACAAGCATGTT 61.282 55.000 37.65 0.00 40.74 2.71
1963 1978 1.502640 GGTCTCGACGTCCACTCTG 59.497 63.158 10.58 0.00 0.00 3.35
2000 2015 1.228124 CGTTGGTGCCCCTCTTCAA 60.228 57.895 0.00 0.00 0.00 2.69
2031 2046 1.077787 AGCATTCGGGCGAAATGGA 60.078 52.632 11.07 0.00 37.69 3.41
2048 2063 1.527696 GATTTGCGTTCATGCGACAG 58.472 50.000 0.00 0.00 37.81 3.51
2065 2080 1.076024 TGCTTCTTTTGGAGCCTGGAT 59.924 47.619 0.00 0.00 0.00 3.41
2118 2133 4.106502 TCCTAGCTAGCCTCAAATCCTAGA 59.893 45.833 15.74 0.00 32.27 2.43
2154 2169 5.065602 CACACCAACAGTTCATATCATCTGG 59.934 44.000 0.00 0.00 32.92 3.86
2157 2172 4.943705 ACCACACCAACAGTTCATATCATC 59.056 41.667 0.00 0.00 0.00 2.92
2219 2234 1.964223 TCCAGACACACCTTCTCTGTC 59.036 52.381 0.00 0.00 35.51 3.51
2257 2272 9.188588 GTAAATTCATCATCAAGTTGCATATGG 57.811 33.333 4.56 0.00 0.00 2.74
2261 2276 9.715121 AAAAGTAAATTCATCATCAAGTTGCAT 57.285 25.926 0.00 0.00 0.00 3.96
2262 2277 9.545105 AAAAAGTAAATTCATCATCAAGTTGCA 57.455 25.926 0.00 0.00 0.00 4.08
2263 2278 9.801714 CAAAAAGTAAATTCATCATCAAGTTGC 57.198 29.630 0.00 0.00 0.00 4.17
2275 2290 9.849166 ACTCGTTTTTCTCAAAAAGTAAATTCA 57.151 25.926 0.00 0.00 40.71 2.57
2283 2298 9.556030 AGTTTTCTACTCGTTTTTCTCAAAAAG 57.444 29.630 0.00 0.00 35.07 2.27
2287 2302 8.937634 ACTAGTTTTCTACTCGTTTTTCTCAA 57.062 30.769 0.00 0.00 38.33 3.02
2289 2304 8.571461 TGACTAGTTTTCTACTCGTTTTTCTC 57.429 34.615 0.00 0.00 38.33 2.87
2290 2305 8.937634 TTGACTAGTTTTCTACTCGTTTTTCT 57.062 30.769 0.00 0.00 38.33 2.52
2294 2309 9.924650 ACATATTGACTAGTTTTCTACTCGTTT 57.075 29.630 0.00 0.00 38.33 3.60
2295 2310 9.355215 CACATATTGACTAGTTTTCTACTCGTT 57.645 33.333 0.00 0.00 38.33 3.85
2296 2311 7.488471 GCACATATTGACTAGTTTTCTACTCGT 59.512 37.037 0.00 0.00 38.33 4.18
2297 2312 7.488150 TGCACATATTGACTAGTTTTCTACTCG 59.512 37.037 0.00 0.00 38.33 4.18
2322 2337 6.073327 AGCTCATGCATTCTGAATGTAATG 57.927 37.500 26.22 25.99 42.74 1.90
2323 2338 5.826208 TGAGCTCATGCATTCTGAATGTAAT 59.174 36.000 26.22 18.75 42.74 1.89
2324 2339 5.065602 GTGAGCTCATGCATTCTGAATGTAA 59.934 40.000 26.22 17.58 42.74 2.41
2325 2340 4.573607 GTGAGCTCATGCATTCTGAATGTA 59.426 41.667 26.22 23.56 42.74 2.29
2326 2341 3.377485 GTGAGCTCATGCATTCTGAATGT 59.623 43.478 26.22 9.46 42.74 2.71
2327 2342 3.377172 TGTGAGCTCATGCATTCTGAATG 59.623 43.478 21.47 22.83 42.74 2.67
2328 2343 3.617284 TGTGAGCTCATGCATTCTGAAT 58.383 40.909 21.47 0.00 42.74 2.57
2329 2344 3.062122 TGTGAGCTCATGCATTCTGAA 57.938 42.857 21.47 0.00 42.74 3.02
2330 2345 2.773993 TGTGAGCTCATGCATTCTGA 57.226 45.000 21.47 0.00 42.74 3.27
2331 2346 2.097629 CCTTGTGAGCTCATGCATTCTG 59.902 50.000 21.47 4.79 42.74 3.02
2332 2347 2.290768 ACCTTGTGAGCTCATGCATTCT 60.291 45.455 21.47 0.00 42.74 2.40
2333 2348 2.089980 ACCTTGTGAGCTCATGCATTC 58.910 47.619 21.47 6.23 42.74 2.67
2334 2349 2.211250 ACCTTGTGAGCTCATGCATT 57.789 45.000 21.47 1.78 42.74 3.56
2335 2350 2.089980 GAACCTTGTGAGCTCATGCAT 58.910 47.619 21.47 4.54 42.74 3.96
2336 2351 1.202794 TGAACCTTGTGAGCTCATGCA 60.203 47.619 21.47 11.54 42.74 3.96
2337 2352 1.198637 GTGAACCTTGTGAGCTCATGC 59.801 52.381 21.47 8.66 40.05 4.06
2338 2353 2.497138 TGTGAACCTTGTGAGCTCATG 58.503 47.619 21.47 12.93 0.00 3.07
2339 2354 2.936919 TGTGAACCTTGTGAGCTCAT 57.063 45.000 21.47 1.50 0.00 2.90
2340 2355 2.708216 TTGTGAACCTTGTGAGCTCA 57.292 45.000 13.74 13.74 0.00 4.26
2341 2356 2.945668 ACTTTGTGAACCTTGTGAGCTC 59.054 45.455 6.82 6.82 0.00 4.09
2342 2357 3.004752 ACTTTGTGAACCTTGTGAGCT 57.995 42.857 0.00 0.00 0.00 4.09
2343 2358 3.128589 TGAACTTTGTGAACCTTGTGAGC 59.871 43.478 0.00 0.00 0.00 4.26
2344 2359 4.731773 GCTGAACTTTGTGAACCTTGTGAG 60.732 45.833 0.00 0.00 0.00 3.51
2345 2360 3.128589 GCTGAACTTTGTGAACCTTGTGA 59.871 43.478 0.00 0.00 0.00 3.58
2346 2361 3.129287 AGCTGAACTTTGTGAACCTTGTG 59.871 43.478 0.00 0.00 0.00 3.33
2347 2362 3.356290 AGCTGAACTTTGTGAACCTTGT 58.644 40.909 0.00 0.00 0.00 3.16
2348 2363 4.576463 ACTAGCTGAACTTTGTGAACCTTG 59.424 41.667 0.00 0.00 0.00 3.61
2349 2364 4.781934 ACTAGCTGAACTTTGTGAACCTT 58.218 39.130 0.00 0.00 0.00 3.50
2350 2365 4.423625 ACTAGCTGAACTTTGTGAACCT 57.576 40.909 0.00 0.00 0.00 3.50
2351 2366 5.273944 CAAACTAGCTGAACTTTGTGAACC 58.726 41.667 0.00 0.00 0.00 3.62
2352 2367 4.735338 GCAAACTAGCTGAACTTTGTGAAC 59.265 41.667 0.00 0.00 0.00 3.18
2353 2368 4.397730 TGCAAACTAGCTGAACTTTGTGAA 59.602 37.500 0.00 0.00 34.99 3.18
2354 2369 3.944650 TGCAAACTAGCTGAACTTTGTGA 59.055 39.130 0.00 0.00 34.99 3.58
2355 2370 4.291540 TGCAAACTAGCTGAACTTTGTG 57.708 40.909 0.00 0.00 34.99 3.33
2356 2371 4.734695 GCTTGCAAACTAGCTGAACTTTGT 60.735 41.667 0.00 0.00 40.89 2.83
2357 2372 3.732721 GCTTGCAAACTAGCTGAACTTTG 59.267 43.478 0.00 0.00 40.89 2.77
2358 2373 3.381272 TGCTTGCAAACTAGCTGAACTTT 59.619 39.130 9.40 0.00 43.92 2.66
2359 2374 2.951642 TGCTTGCAAACTAGCTGAACTT 59.048 40.909 9.40 0.00 43.92 2.66
2360 2375 2.575532 TGCTTGCAAACTAGCTGAACT 58.424 42.857 9.40 0.00 43.92 3.01
2367 2382 3.564235 TGCTCAATGCTTGCAAACTAG 57.436 42.857 0.00 0.00 43.37 2.57
2381 2396 3.056891 GGTTTCGGAAATGGATTGCTCAA 60.057 43.478 6.43 0.00 0.00 3.02
2398 2413 4.389374 TCACTGATTCTGGTCAAGGTTTC 58.611 43.478 0.00 0.00 0.00 2.78
2400 2415 4.042062 TCATCACTGATTCTGGTCAAGGTT 59.958 41.667 0.00 0.00 0.00 3.50
2403 2418 5.936372 TCTTTCATCACTGATTCTGGTCAAG 59.064 40.000 0.00 0.00 0.00 3.02
2404 2419 5.868454 TCTTTCATCACTGATTCTGGTCAA 58.132 37.500 0.00 0.00 0.00 3.18
2407 2422 4.841422 CCTCTTTCATCACTGATTCTGGT 58.159 43.478 0.00 0.00 0.00 4.00
2408 2423 3.626670 GCCTCTTTCATCACTGATTCTGG 59.373 47.826 0.00 0.00 0.00 3.86
2409 2424 3.309138 CGCCTCTTTCATCACTGATTCTG 59.691 47.826 0.00 0.00 0.00 3.02
2410 2425 3.055530 ACGCCTCTTTCATCACTGATTCT 60.056 43.478 0.00 0.00 0.00 2.40
2411 2426 3.265791 ACGCCTCTTTCATCACTGATTC 58.734 45.455 0.00 0.00 0.00 2.52
2412 2427 3.265791 GACGCCTCTTTCATCACTGATT 58.734 45.455 0.00 0.00 0.00 2.57
2413 2428 2.736719 CGACGCCTCTTTCATCACTGAT 60.737 50.000 0.00 0.00 0.00 2.90
2415 2430 0.994995 CGACGCCTCTTTCATCACTG 59.005 55.000 0.00 0.00 0.00 3.66
2416 2431 0.108615 CCGACGCCTCTTTCATCACT 60.109 55.000 0.00 0.00 0.00 3.41
2417 2432 0.389948 ACCGACGCCTCTTTCATCAC 60.390 55.000 0.00 0.00 0.00 3.06
2418 2433 0.389817 CACCGACGCCTCTTTCATCA 60.390 55.000 0.00 0.00 0.00 3.07
2419 2434 0.389948 ACACCGACGCCTCTTTCATC 60.390 55.000 0.00 0.00 0.00 2.92
2420 2435 0.034896 AACACCGACGCCTCTTTCAT 59.965 50.000 0.00 0.00 0.00 2.57
2421 2436 0.599204 GAACACCGACGCCTCTTTCA 60.599 55.000 0.00 0.00 0.00 2.69
2422 2437 0.599204 TGAACACCGACGCCTCTTTC 60.599 55.000 0.00 0.00 0.00 2.62
2423 2438 0.600255 CTGAACACCGACGCCTCTTT 60.600 55.000 0.00 0.00 0.00 2.52
2424 2439 1.006102 CTGAACACCGACGCCTCTT 60.006 57.895 0.00 0.00 0.00 2.85
2425 2440 1.745320 AACTGAACACCGACGCCTCT 61.745 55.000 0.00 0.00 0.00 3.69
2426 2441 0.878961 AAACTGAACACCGACGCCTC 60.879 55.000 0.00 0.00 0.00 4.70
2428 2443 1.070376 GTTAAACTGAACACCGACGCC 60.070 52.381 0.00 0.00 0.00 5.68
2429 2444 1.862827 AGTTAAACTGAACACCGACGC 59.137 47.619 0.00 0.00 0.00 5.19
2430 2445 4.741676 AGTTAGTTAAACTGAACACCGACG 59.258 41.667 0.00 0.00 46.90 5.12
2442 2457 6.047231 ACGATGCAGGGATAGTTAGTTAAAC 58.953 40.000 0.00 0.00 38.46 2.01
2445 2460 6.964807 TTACGATGCAGGGATAGTTAGTTA 57.035 37.500 0.00 0.00 0.00 2.24
2446 2461 5.864418 TTACGATGCAGGGATAGTTAGTT 57.136 39.130 0.00 0.00 0.00 2.24
2447 2462 5.128171 TGTTTACGATGCAGGGATAGTTAGT 59.872 40.000 0.00 0.00 0.00 2.24
2448 2463 5.597806 TGTTTACGATGCAGGGATAGTTAG 58.402 41.667 0.00 0.00 0.00 2.34
2449 2464 5.601583 TGTTTACGATGCAGGGATAGTTA 57.398 39.130 0.00 0.00 0.00 2.24
2450 2465 4.481368 TGTTTACGATGCAGGGATAGTT 57.519 40.909 0.00 0.00 0.00 2.24
2451 2466 4.481368 TTGTTTACGATGCAGGGATAGT 57.519 40.909 0.00 0.00 0.00 2.12
2453 2468 4.036262 GCATTTGTTTACGATGCAGGGATA 59.964 41.667 13.02 0.00 44.18 2.59
2457 2472 3.492421 AGCATTTGTTTACGATGCAGG 57.508 42.857 17.53 0.00 46.48 4.85
2458 2473 5.631026 ACTAAGCATTTGTTTACGATGCAG 58.369 37.500 17.53 11.92 46.48 4.41
2459 2474 5.621197 ACTAAGCATTTGTTTACGATGCA 57.379 34.783 17.53 0.00 46.48 3.96
2476 3170 5.743872 GTGAAAAGTTGCAGTGGAAACTAAG 59.256 40.000 0.00 0.00 42.31 2.18
2493 3187 7.175641 ACAAAAGGAGACTCCATATGTGAAAAG 59.824 37.037 23.60 3.31 42.68 2.27
2997 3695 3.682696 TCTCTTCAGTTAGTAGCGGTGA 58.317 45.455 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.