Multiple sequence alignment - TraesCS6A01G133700

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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 TraesCS6A01G133700 chr6A 100.000 3630 0 0 1 3630 105870047 105873676 0.000000e+00 6704
1 TraesCS6A01G133700 chr6A 96.904 323 8 2 122 444 129352665 129352985 1.150000e-149 540
2 TraesCS6A01G133700 chr6A 94.671 319 16 1 120 438 5603767 5604084 9.050000e-136 494
3 TraesCS6A01G133700 chr6D 93.727 2758 81 36 447 3158 87595888 87598599 0.000000e+00 4050
4 TraesCS6A01G133700 chr6D 94.328 476 27 0 3155 3630 87598709 87599184 0.000000e+00 730
5 TraesCS6A01G133700 chr6D 91.129 124 8 1 2 122 87595759 87595882 8.060000e-37 165
6 TraesCS6A01G133700 chr6B 93.782 2557 68 22 642 3158 166593201 166595706 0.000000e+00 3757
7 TraesCS6A01G133700 chr6B 94.178 292 10 4 3155 3440 166595815 166596105 4.300000e-119 438
8 TraesCS6A01G133700 chr6B 86.667 210 9 11 447 637 166591648 166591857 7.890000e-52 215
9 TraesCS6A01G133700 chr6B 95.122 123 5 1 1 122 166591520 166591642 3.700000e-45 193
10 TraesCS6A01G133700 chr6B 96.667 90 3 0 3540 3629 166596099 166596188 2.260000e-32 150
11 TraesCS6A01G133700 chr5A 94.393 321 17 1 120 440 228894950 228895269 3.260000e-135 492
12 TraesCS6A01G133700 chr2D 94.081 321 17 2 122 442 42524538 42524856 1.520000e-133 486
13 TraesCS6A01G133700 chr2D 94.586 314 15 2 124 437 36275114 36275425 5.450000e-133 484
14 TraesCS6A01G133700 chr4A 94.062 320 16 3 122 440 689623991 689623674 1.960000e-132 483
15 TraesCS6A01G133700 chr4A 93.750 320 19 1 121 440 162418924 162419242 2.540000e-131 479
16 TraesCS6A01G133700 chr4A 86.230 305 33 2 2727 3023 611226706 611226403 4.520000e-84 322
17 TraesCS6A01G133700 chr1A 93.750 320 18 2 121 440 121359818 121360135 2.540000e-131 479
18 TraesCS6A01G133700 chr1A 93.478 322 20 1 121 442 189532860 189532540 9.120000e-131 477
19 TraesCS6A01G133700 chrUn 85.804 317 37 1 2715 3023 243363640 243363956 2.700000e-86 329
20 TraesCS6A01G133700 chr5D 86.557 305 33 1 2727 3023 552097010 552096706 2.700000e-86 329
21 TraesCS6A01G133700 chr5D 86.557 305 33 1 2727 3023 552097567 552097263 2.700000e-86 329
22 TraesCS6A01G133700 chr3D 85.804 317 37 1 2715 3023 561758416 561758732 2.700000e-86 329
23 TraesCS6A01G133700 chr7B 88.626 211 22 1 2815 3023 211940711 211940921 4.650000e-64 255
24 TraesCS6A01G133700 chr1B 89.412 170 18 0 2854 3023 36351745 36351914 7.890000e-52 215


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 TraesCS6A01G133700 chr6A 105870047 105873676 3629 False 6704.000000 6704 100.000000 1 3630 1 chr6A.!!$F2 3629
1 TraesCS6A01G133700 chr6D 87595759 87599184 3425 False 1648.333333 4050 93.061333 2 3630 3 chr6D.!!$F1 3628
2 TraesCS6A01G133700 chr6B 166591520 166596188 4668 False 950.600000 3757 93.283200 1 3629 5 chr6B.!!$F1 3628
3 TraesCS6A01G133700 chr5D 552096706 552097567 861 True 329.000000 329 86.557000 2727 3023 2 chr5D.!!$R1 296

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
142 147 0.190815 AGGGCCTGTTTGGTTCCAAT 59.809 50.0 4.50 0.00 38.35 3.16 F
289 294 0.251742 TGGGACCCATGCAAAAGGAG 60.252 55.0 9.95 0.02 0.00 3.69 F
291 296 0.251787 GGACCCATGCAAAAGGAGGT 60.252 55.0 7.00 0.23 0.00 3.85 F
325 330 0.261696 AAGTTGGGGTGGAGCAACTT 59.738 50.0 0.00 0.00 41.36 2.66 F
607 627 0.537371 ACGAGGCCAGAACCAAAAGG 60.537 55.0 5.01 0.00 0.00 3.11 F
2517 3944 0.112995 TCAGATGTGCTGCCCCTTTT 59.887 50.0 0.00 0.00 44.52 2.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2012 3439 0.904865 TCTCCTTGACGATGGTGGCT 60.905 55.000 0.00 0.0 0.00 4.75 R
2212 3639 6.038936 TCAAAACATCCAGACATCATGCATAG 59.961 38.462 0.00 0.0 0.00 2.23 R
2290 3717 3.612860 CGTCCAAGTAATTCCTCGTGAAG 59.387 47.826 0.00 0.0 36.14 3.02 R
2329 3756 6.394345 AGGTTTTCTAATCCATCTTCAGGT 57.606 37.500 0.00 0.0 0.00 4.00 R
2577 4004 1.419387 GCTGGGCCTGAGAACTATCAT 59.581 52.381 15.36 0.0 0.00 2.45 R
3505 5071 3.445096 ACAAGATAGCATTGCAAAGGGAC 59.555 43.478 11.91 0.0 0.00 4.46 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
122 127 2.743183 CGGAGGCGGAGAGAAATGATTT 60.743 50.000 0.00 0.00 0.00 2.17
124 129 4.061596 GGAGGCGGAGAGAAATGATTTAG 58.938 47.826 0.00 0.00 0.00 1.85
126 131 3.142174 GGCGGAGAGAAATGATTTAGGG 58.858 50.000 0.00 0.00 0.00 3.53
127 132 2.550180 GCGGAGAGAAATGATTTAGGGC 59.450 50.000 0.00 0.00 0.00 5.19
128 133 3.142174 CGGAGAGAAATGATTTAGGGCC 58.858 50.000 0.00 0.00 0.00 5.80
129 134 3.181450 CGGAGAGAAATGATTTAGGGCCT 60.181 47.826 12.58 12.58 0.00 5.19
131 136 4.385754 GGAGAGAAATGATTTAGGGCCTGT 60.386 45.833 18.53 1.24 0.00 4.00
134 139 5.420104 AGAGAAATGATTTAGGGCCTGTTTG 59.580 40.000 18.53 0.00 0.00 2.93
136 141 2.990740 TGATTTAGGGCCTGTTTGGT 57.009 45.000 18.53 0.00 38.35 3.67
137 142 3.252554 TGATTTAGGGCCTGTTTGGTT 57.747 42.857 18.53 0.00 38.35 3.67
138 143 3.161866 TGATTTAGGGCCTGTTTGGTTC 58.838 45.455 18.53 4.05 38.35 3.62
139 144 2.003937 TTTAGGGCCTGTTTGGTTCC 57.996 50.000 18.53 0.00 38.35 3.62
140 145 0.854218 TTAGGGCCTGTTTGGTTCCA 59.146 50.000 18.53 0.00 38.35 3.53
142 147 0.190815 AGGGCCTGTTTGGTTCCAAT 59.809 50.000 4.50 0.00 38.35 3.16
143 148 1.431243 AGGGCCTGTTTGGTTCCAATA 59.569 47.619 4.50 0.00 38.35 1.90
144 149 2.158234 AGGGCCTGTTTGGTTCCAATAA 60.158 45.455 4.50 0.00 38.35 1.40
145 150 2.233676 GGGCCTGTTTGGTTCCAATAAG 59.766 50.000 0.84 6.17 38.35 1.73
146 151 2.897326 GGCCTGTTTGGTTCCAATAAGT 59.103 45.455 5.06 0.00 38.35 2.24
147 152 3.056821 GGCCTGTTTGGTTCCAATAAGTC 60.057 47.826 5.06 0.00 38.35 3.01
148 153 3.572255 GCCTGTTTGGTTCCAATAAGTCA 59.428 43.478 5.06 1.06 38.35 3.41
150 155 4.022329 CCTGTTTGGTTCCAATAAGTCACC 60.022 45.833 5.06 0.00 0.00 4.02
151 156 4.798882 TGTTTGGTTCCAATAAGTCACCT 58.201 39.130 5.06 0.00 0.00 4.00
152 157 4.582656 TGTTTGGTTCCAATAAGTCACCTG 59.417 41.667 5.06 0.00 0.00 4.00
153 158 4.715534 TTGGTTCCAATAAGTCACCTGA 57.284 40.909 0.00 0.00 0.00 3.86
154 159 4.015872 TGGTTCCAATAAGTCACCTGAC 57.984 45.455 0.00 0.00 45.08 3.51
177 182 7.683437 ACTTATAAGTCAGGTGGCTTAAAAC 57.317 36.000 12.50 0.00 44.29 2.43
178 183 6.657966 ACTTATAAGTCAGGTGGCTTAAAACC 59.342 38.462 12.50 0.00 44.29 3.27
180 185 2.863809 AGTCAGGTGGCTTAAAACCAG 58.136 47.619 0.00 0.00 38.04 4.00
181 186 2.174854 AGTCAGGTGGCTTAAAACCAGT 59.825 45.455 0.00 0.00 38.04 4.00
182 187 3.393278 AGTCAGGTGGCTTAAAACCAGTA 59.607 43.478 0.00 0.00 38.04 2.74
183 188 4.139038 GTCAGGTGGCTTAAAACCAGTAA 58.861 43.478 0.00 0.00 38.04 2.24
184 189 4.023450 GTCAGGTGGCTTAAAACCAGTAAC 60.023 45.833 0.00 0.00 38.04 2.50
185 190 4.141344 TCAGGTGGCTTAAAACCAGTAACT 60.141 41.667 0.00 0.00 38.04 2.24
187 192 5.766174 CAGGTGGCTTAAAACCAGTAACTTA 59.234 40.000 0.00 0.00 38.04 2.24
188 193 6.433093 CAGGTGGCTTAAAACCAGTAACTTAT 59.567 38.462 0.00 0.00 38.04 1.73
189 194 7.608761 CAGGTGGCTTAAAACCAGTAACTTATA 59.391 37.037 0.00 0.00 38.04 0.98
190 195 8.165397 AGGTGGCTTAAAACCAGTAACTTATAA 58.835 33.333 0.00 0.00 38.04 0.98
192 197 9.006839 GTGGCTTAAAACCAGTAACTTATAAGT 57.993 33.333 12.50 12.50 38.30 2.24
193 198 9.223099 TGGCTTAAAACCAGTAACTTATAAGTC 57.777 33.333 18.28 7.34 33.50 3.01
198 203 4.752146 ACCAGTAACTTATAAGTCACGCC 58.248 43.478 18.28 5.45 38.57 5.68
202 207 5.867716 CAGTAACTTATAAGTCACGCCTGTT 59.132 40.000 18.28 2.57 38.57 3.16
204 209 5.607119 AACTTATAAGTCACGCCTGTTTG 57.393 39.130 18.28 0.00 38.57 2.93
205 210 4.890088 ACTTATAAGTCACGCCTGTTTGA 58.110 39.130 12.50 0.00 32.86 2.69
206 211 5.488341 ACTTATAAGTCACGCCTGTTTGAT 58.512 37.500 12.50 0.00 32.86 2.57
207 212 5.938125 ACTTATAAGTCACGCCTGTTTGATT 59.062 36.000 12.50 0.00 32.86 2.57
208 213 4.685169 ATAAGTCACGCCTGTTTGATTG 57.315 40.909 0.00 0.00 0.00 2.67
209 214 1.967319 AGTCACGCCTGTTTGATTGT 58.033 45.000 0.00 0.00 0.00 2.71
211 216 1.601903 GTCACGCCTGTTTGATTGTCA 59.398 47.619 0.00 0.00 0.00 3.58
212 217 2.226437 GTCACGCCTGTTTGATTGTCAT 59.774 45.455 0.00 0.00 0.00 3.06
213 218 2.483877 TCACGCCTGTTTGATTGTCATC 59.516 45.455 0.00 0.00 0.00 2.92
216 221 2.743664 CGCCTGTTTGATTGTCATCTGA 59.256 45.455 0.00 0.00 0.00 3.27
218 223 3.755378 GCCTGTTTGATTGTCATCTGACT 59.245 43.478 11.35 0.00 44.99 3.41
220 225 5.412594 GCCTGTTTGATTGTCATCTGACTTA 59.587 40.000 11.35 0.91 44.99 2.24
221 226 6.094603 GCCTGTTTGATTGTCATCTGACTTAT 59.905 38.462 11.35 5.33 44.99 1.73
222 227 7.280876 GCCTGTTTGATTGTCATCTGACTTATA 59.719 37.037 11.35 0.00 44.99 0.98
225 230 9.725019 TGTTTGATTGTCATCTGACTTATAAGT 57.275 29.630 18.05 18.05 44.99 2.24
239 244 2.770164 ATAAGTCACCTGAGCACACC 57.230 50.000 0.00 0.00 0.00 4.16
240 245 1.717032 TAAGTCACCTGAGCACACCT 58.283 50.000 0.00 0.00 0.00 4.00
241 246 0.839946 AAGTCACCTGAGCACACCTT 59.160 50.000 0.00 0.00 0.00 3.50
243 248 0.603975 GTCACCTGAGCACACCTTCC 60.604 60.000 0.00 0.00 0.00 3.46
244 249 1.302832 CACCTGAGCACACCTTCCC 60.303 63.158 0.00 0.00 0.00 3.97
245 250 1.770110 ACCTGAGCACACCTTCCCA 60.770 57.895 0.00 0.00 0.00 4.37
246 251 1.136329 ACCTGAGCACACCTTCCCAT 61.136 55.000 0.00 0.00 0.00 4.00
247 252 0.393537 CCTGAGCACACCTTCCCATC 60.394 60.000 0.00 0.00 0.00 3.51
249 254 1.004044 CTGAGCACACCTTCCCATCTT 59.996 52.381 0.00 0.00 0.00 2.40
250 255 1.271543 TGAGCACACCTTCCCATCTTG 60.272 52.381 0.00 0.00 0.00 3.02
253 258 1.963515 GCACACCTTCCCATCTTGTTT 59.036 47.619 0.00 0.00 0.00 2.83
254 259 2.365293 GCACACCTTCCCATCTTGTTTT 59.635 45.455 0.00 0.00 0.00 2.43
255 260 3.181466 GCACACCTTCCCATCTTGTTTTT 60.181 43.478 0.00 0.00 0.00 1.94
276 281 3.724732 TTATGTAAAGGTGGTGGGACC 57.275 47.619 0.00 0.00 39.22 4.46
277 282 0.702316 ATGTAAAGGTGGTGGGACCC 59.298 55.000 2.45 2.45 37.50 4.46
278 283 0.698198 TGTAAAGGTGGTGGGACCCA 60.698 55.000 9.95 9.95 37.50 4.51
279 284 0.702316 GTAAAGGTGGTGGGACCCAT 59.298 55.000 18.51 0.32 37.50 4.00
281 286 2.730129 AAAGGTGGTGGGACCCATGC 62.730 60.000 18.51 9.82 37.50 4.06
282 287 3.978193 GGTGGTGGGACCCATGCA 61.978 66.667 18.51 0.00 37.50 3.96
283 288 2.117206 GTGGTGGGACCCATGCAA 59.883 61.111 18.51 0.00 37.50 4.08
284 289 1.532794 GTGGTGGGACCCATGCAAA 60.533 57.895 18.51 0.00 37.50 3.68
285 290 1.118356 GTGGTGGGACCCATGCAAAA 61.118 55.000 18.51 0.00 37.50 2.44
286 291 0.831288 TGGTGGGACCCATGCAAAAG 60.831 55.000 18.51 0.00 37.50 2.27
289 294 0.251742 TGGGACCCATGCAAAAGGAG 60.252 55.000 9.95 0.02 0.00 3.69
291 296 0.251787 GGACCCATGCAAAAGGAGGT 60.252 55.000 7.00 0.23 0.00 3.85
292 297 0.890683 GACCCATGCAAAAGGAGGTG 59.109 55.000 7.00 0.00 0.00 4.00
293 298 0.482446 ACCCATGCAAAAGGAGGTGA 59.518 50.000 7.00 0.00 0.00 4.02
298 303 4.019174 CCATGCAAAAGGAGGTGACTTAT 58.981 43.478 0.00 0.00 44.43 1.73
300 305 5.652014 CCATGCAAAAGGAGGTGACTTATAA 59.348 40.000 0.00 0.00 44.43 0.98
301 306 6.183360 CCATGCAAAAGGAGGTGACTTATAAG 60.183 42.308 11.05 11.05 44.43 1.73
303 308 6.303839 TGCAAAAGGAGGTGACTTATAAGTT 58.696 36.000 18.96 3.42 44.43 2.66
304 309 6.775629 TGCAAAAGGAGGTGACTTATAAGTTT 59.224 34.615 18.96 5.24 44.43 2.66
305 310 7.286775 TGCAAAAGGAGGTGACTTATAAGTTTT 59.713 33.333 18.96 10.67 44.43 2.43
313 318 8.631480 AGGTGACTTATAAGTTTTAAGTTGGG 57.369 34.615 18.96 0.00 39.40 4.12
314 319 7.668469 AGGTGACTTATAAGTTTTAAGTTGGGG 59.332 37.037 18.96 0.00 39.40 4.96
316 321 8.294577 GTGACTTATAAGTTTTAAGTTGGGGTG 58.705 37.037 18.96 0.00 39.40 4.61
317 322 7.449086 TGACTTATAAGTTTTAAGTTGGGGTGG 59.551 37.037 18.96 0.00 39.40 4.61
318 323 7.528675 ACTTATAAGTTTTAAGTTGGGGTGGA 58.471 34.615 12.50 0.00 36.70 4.02
319 324 7.668469 ACTTATAAGTTTTAAGTTGGGGTGGAG 59.332 37.037 12.50 0.00 36.70 3.86
320 325 2.594131 AGTTTTAAGTTGGGGTGGAGC 58.406 47.619 0.00 0.00 0.00 4.70
324 329 1.145571 TAAGTTGGGGTGGAGCAACT 58.854 50.000 0.00 0.00 39.27 3.16
325 330 0.261696 AAGTTGGGGTGGAGCAACTT 59.738 50.000 0.00 0.00 41.36 2.66
326 331 1.145571 AGTTGGGGTGGAGCAACTTA 58.854 50.000 0.00 0.00 34.63 2.24
329 334 1.367346 TGGGGTGGAGCAACTTATGA 58.633 50.000 0.00 0.00 0.00 2.15
330 335 1.004277 TGGGGTGGAGCAACTTATGAC 59.996 52.381 0.00 0.00 0.00 3.06
331 336 1.282157 GGGGTGGAGCAACTTATGACT 59.718 52.381 0.00 0.00 0.00 3.41
332 337 2.290960 GGGGTGGAGCAACTTATGACTT 60.291 50.000 0.00 0.00 0.00 3.01
333 338 3.054655 GGGGTGGAGCAACTTATGACTTA 60.055 47.826 0.00 0.00 0.00 2.24
334 339 4.385310 GGGGTGGAGCAACTTATGACTTAT 60.385 45.833 0.00 0.00 0.00 1.73
335 340 5.163237 GGGGTGGAGCAACTTATGACTTATA 60.163 44.000 0.00 0.00 0.00 0.98
336 341 6.354130 GGGTGGAGCAACTTATGACTTATAA 58.646 40.000 0.00 0.00 0.00 0.98
349 354 5.836024 TGACTTATAAGTTGGGGTGACTT 57.164 39.130 18.96 0.00 39.88 3.01
350 355 6.938698 TGACTTATAAGTTGGGGTGACTTA 57.061 37.500 18.96 0.00 42.07 2.24
351 356 7.504926 TGACTTATAAGTTGGGGTGACTTAT 57.495 36.000 18.96 12.48 46.52 1.73
359 364 5.321927 AGTTGGGGTGACTTATAAGTTTGG 58.678 41.667 18.96 0.00 39.88 3.28
360 365 5.074804 GTTGGGGTGACTTATAAGTTTGGT 58.925 41.667 18.96 0.00 39.88 3.67
361 366 4.913784 TGGGGTGACTTATAAGTTTGGTC 58.086 43.478 18.96 7.15 39.88 4.02
362 367 4.600111 TGGGGTGACTTATAAGTTTGGTCT 59.400 41.667 18.96 0.00 39.88 3.85
363 368 4.941873 GGGGTGACTTATAAGTTTGGTCTG 59.058 45.833 18.96 0.00 39.88 3.51
365 370 6.002082 GGGTGACTTATAAGTTTGGTCTGTT 58.998 40.000 18.96 0.00 39.88 3.16
366 371 6.489022 GGGTGACTTATAAGTTTGGTCTGTTT 59.511 38.462 18.96 0.00 39.88 2.83
367 372 7.360361 GGTGACTTATAAGTTTGGTCTGTTTG 58.640 38.462 18.96 0.00 39.88 2.93
368 373 7.360361 GTGACTTATAAGTTTGGTCTGTTTGG 58.640 38.462 18.96 0.00 39.88 3.28
369 374 6.016610 TGACTTATAAGTTTGGTCTGTTTGGC 60.017 38.462 18.96 2.46 39.88 4.52
370 375 5.830991 ACTTATAAGTTTGGTCTGTTTGGCA 59.169 36.000 12.50 0.00 35.21 4.92
372 377 3.971245 AAGTTTGGTCTGTTTGGCAAA 57.029 38.095 8.93 8.93 0.00 3.68
373 378 3.971245 AGTTTGGTCTGTTTGGCAAAA 57.029 38.095 15.29 4.59 0.00 2.44
374 379 4.486125 AGTTTGGTCTGTTTGGCAAAAT 57.514 36.364 15.29 0.00 0.00 1.82
375 380 5.606348 AGTTTGGTCTGTTTGGCAAAATA 57.394 34.783 15.29 6.13 0.00 1.40
376 381 5.983540 AGTTTGGTCTGTTTGGCAAAATAA 58.016 33.333 15.29 2.73 0.00 1.40
377 382 6.048509 AGTTTGGTCTGTTTGGCAAAATAAG 58.951 36.000 15.29 12.47 0.00 1.73
378 383 5.606348 TTGGTCTGTTTGGCAAAATAAGT 57.394 34.783 15.29 0.00 0.00 2.24
379 384 5.195001 TGGTCTGTTTGGCAAAATAAGTC 57.805 39.130 15.29 10.05 0.00 3.01
380 385 4.646945 TGGTCTGTTTGGCAAAATAAGTCA 59.353 37.500 15.29 6.39 0.00 3.41
381 386 4.982295 GGTCTGTTTGGCAAAATAAGTCAC 59.018 41.667 15.29 7.77 0.00 3.67
382 387 5.221244 GGTCTGTTTGGCAAAATAAGTCACT 60.221 40.000 15.29 0.00 0.00 3.41
383 388 6.273071 GTCTGTTTGGCAAAATAAGTCACTT 58.727 36.000 15.29 0.00 0.00 3.16
384 389 6.756542 GTCTGTTTGGCAAAATAAGTCACTTT 59.243 34.615 15.29 0.00 0.00 2.66
385 390 7.277760 GTCTGTTTGGCAAAATAAGTCACTTTT 59.722 33.333 15.29 0.00 0.00 2.27
386 391 7.821846 TCTGTTTGGCAAAATAAGTCACTTTTT 59.178 29.630 15.29 0.00 0.00 1.94
410 415 9.724839 TTTTTCACTTTTCGACTTATAAGTTGG 57.275 29.630 25.99 17.93 39.88 3.77
411 416 8.441312 TTTCACTTTTCGACTTATAAGTTGGT 57.559 30.769 25.99 16.17 39.88 3.67
412 417 7.416154 TCACTTTTCGACTTATAAGTTGGTG 57.584 36.000 25.99 23.76 39.88 4.17
413 418 7.211573 TCACTTTTCGACTTATAAGTTGGTGA 58.788 34.615 25.99 25.09 39.88 4.02
414 419 7.170320 TCACTTTTCGACTTATAAGTTGGTGAC 59.830 37.037 25.99 10.35 39.88 3.67
415 420 6.987992 ACTTTTCGACTTATAAGTTGGTGACA 59.012 34.615 25.99 9.35 39.88 3.58
416 421 7.660208 ACTTTTCGACTTATAAGTTGGTGACAT 59.340 33.333 25.99 10.33 42.32 3.06
417 422 9.146984 CTTTTCGACTTATAAGTTGGTGACATA 57.853 33.333 25.99 8.14 42.32 2.29
418 423 9.661563 TTTTCGACTTATAAGTTGGTGACATAT 57.338 29.630 25.99 0.00 42.32 1.78
419 424 9.661563 TTTCGACTTATAAGTTGGTGACATATT 57.338 29.630 25.99 0.00 42.32 1.28
420 425 9.661563 TTCGACTTATAAGTTGGTGACATATTT 57.338 29.630 25.99 0.00 42.32 1.40
421 426 9.093970 TCGACTTATAAGTTGGTGACATATTTG 57.906 33.333 25.99 3.25 42.32 2.32
422 427 9.093970 CGACTTATAAGTTGGTGACATATTTGA 57.906 33.333 21.06 0.00 42.32 2.69
427 432 6.723298 AAGTTGGTGACATATTTGAAACCA 57.277 33.333 9.41 9.41 42.32 3.67
428 433 6.723298 AGTTGGTGACATATTTGAAACCAA 57.277 33.333 16.93 16.93 43.30 3.67
429 434 7.118496 AGTTGGTGACATATTTGAAACCAAA 57.882 32.000 20.12 0.00 45.05 3.28
430 435 7.209475 AGTTGGTGACATATTTGAAACCAAAG 58.791 34.615 20.12 0.00 45.05 2.77
431 436 6.968263 TGGTGACATATTTGAAACCAAAGA 57.032 33.333 10.53 0.00 38.24 2.52
432 437 7.353414 TGGTGACATATTTGAAACCAAAGAA 57.647 32.000 10.53 0.00 38.24 2.52
433 438 7.432869 TGGTGACATATTTGAAACCAAAGAAG 58.567 34.615 10.53 0.00 38.24 2.85
434 439 6.868339 GGTGACATATTTGAAACCAAAGAAGG 59.132 38.462 0.00 0.00 37.01 3.46
435 440 6.366061 GTGACATATTTGAAACCAAAGAAGGC 59.634 38.462 0.00 0.00 37.01 4.35
436 441 5.793817 ACATATTTGAAACCAAAGAAGGCC 58.206 37.500 0.00 0.00 37.01 5.19
437 442 5.543790 ACATATTTGAAACCAAAGAAGGCCT 59.456 36.000 0.00 0.00 37.01 5.19
438 443 6.043127 ACATATTTGAAACCAAAGAAGGCCTT 59.957 34.615 20.65 20.65 37.01 4.35
439 444 7.234577 ACATATTTGAAACCAAAGAAGGCCTTA 59.765 33.333 20.54 0.00 37.01 2.69
440 445 4.929819 TTGAAACCAAAGAAGGCCTTAC 57.070 40.909 20.54 12.29 34.00 2.34
441 446 4.178956 TGAAACCAAAGAAGGCCTTACT 57.821 40.909 20.54 14.49 34.00 2.24
442 447 5.313280 TGAAACCAAAGAAGGCCTTACTA 57.687 39.130 20.54 0.00 34.00 1.82
443 448 5.067954 TGAAACCAAAGAAGGCCTTACTAC 58.932 41.667 20.54 5.80 34.00 2.73
444 449 4.995624 AACCAAAGAAGGCCTTACTACT 57.004 40.909 20.54 8.47 34.00 2.57
445 450 4.554960 ACCAAAGAAGGCCTTACTACTC 57.445 45.455 20.54 4.59 34.00 2.59
454 460 2.170817 GGCCTTACTACTCCTCCCAAAG 59.829 54.545 0.00 0.00 0.00 2.77
462 468 3.510531 ACTCCTCCCAAAGTTCCTTTC 57.489 47.619 0.00 0.00 30.60 2.62
477 483 2.289547 TCCTTTCGGAAAAGAAGCAACG 59.710 45.455 4.53 0.00 43.90 4.10
522 528 1.658686 GAGCGCGAGAGAAGGAGGAA 61.659 60.000 12.10 0.00 0.00 3.36
523 529 1.215647 GCGCGAGAGAAGGAGGAAA 59.784 57.895 12.10 0.00 0.00 3.13
606 626 0.593128 CACGAGGCCAGAACCAAAAG 59.407 55.000 5.01 0.00 0.00 2.27
607 627 0.537371 ACGAGGCCAGAACCAAAAGG 60.537 55.000 5.01 0.00 0.00 3.11
609 629 1.533994 AGGCCAGAACCAAAAGGGC 60.534 57.895 5.01 0.00 46.14 5.19
610 630 3.059982 GCCAGAACCAAAAGGGCC 58.940 61.111 0.00 0.00 42.05 5.80
611 631 2.583441 GCCAGAACCAAAAGGGCCC 61.583 63.158 16.46 16.46 42.05 5.80
613 633 1.228429 CAGAACCAAAAGGGCCCGA 60.228 57.895 18.44 0.00 42.05 5.14
614 634 1.228459 AGAACCAAAAGGGCCCGAC 60.228 57.895 18.44 2.86 42.05 4.79
615 635 2.596338 AACCAAAAGGGCCCGACG 60.596 61.111 18.44 6.33 42.05 5.12
689 2072 4.500826 GGGGAGGGAGGGAGGGAC 62.501 77.778 0.00 0.00 0.00 4.46
979 2395 0.930726 GAAGAGGAGGAGGAGGAGGA 59.069 60.000 0.00 0.00 0.00 3.71
980 2396 0.933700 AAGAGGAGGAGGAGGAGGAG 59.066 60.000 0.00 0.00 0.00 3.69
981 2397 0.998945 AGAGGAGGAGGAGGAGGAGG 60.999 65.000 0.00 0.00 0.00 4.30
982 2398 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
983 2399 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
984 2400 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
985 2401 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
986 2402 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
987 2403 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
988 2404 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
989 2405 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
990 2406 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
991 2407 2.123033 GGAGGAGGAGGAGGAGGC 60.123 72.222 0.00 0.00 0.00 4.70
992 2408 2.123033 GAGGAGGAGGAGGAGGCC 60.123 72.222 0.00 0.00 0.00 5.19
1270 2695 0.959372 GGTCGACGTCTTCTCCCTCA 60.959 60.000 14.70 0.00 0.00 3.86
1677 3102 3.063084 AGGAGCCTCACCGTCGTC 61.063 66.667 0.00 0.00 0.00 4.20
1746 3171 2.211410 TTCCTTCCGGTTCAGCGGA 61.211 57.895 15.99 15.99 0.00 5.54
1955 3381 1.593196 TCCTTGTGAAGCACTTTCCG 58.407 50.000 0.00 0.00 35.11 4.30
2012 3439 1.516161 AGTACGTGTCTGCGTCACTA 58.484 50.000 0.00 0.00 44.55 2.74
2168 3595 3.994392 TCTTCGTGCAGGTTGTTATCTTC 59.006 43.478 6.26 0.00 0.00 2.87
2290 3717 2.632512 ACCAACAAACACCCATGATTCC 59.367 45.455 0.00 0.00 0.00 3.01
2329 3756 0.468226 ACGTGGCAGAGGAAGAACAA 59.532 50.000 0.00 0.00 0.00 2.83
2338 3765 4.805609 GCAGAGGAAGAACAACCTGAAGAT 60.806 45.833 0.00 0.00 36.57 2.40
2356 3783 5.354234 TGAAGATGGATTAGAAAACCTTCGC 59.646 40.000 0.00 0.00 36.61 4.70
2428 3855 2.225467 GACTTTCTGCTGACAAAGGCT 58.775 47.619 9.13 0.00 35.11 4.58
2517 3944 0.112995 TCAGATGTGCTGCCCCTTTT 59.887 50.000 0.00 0.00 44.52 2.27
2577 4004 2.290896 CCCAGATAGTTTTCAGTGGGCA 60.291 50.000 0.00 0.00 38.38 5.36
2590 4017 3.133542 TCAGTGGGCATGATAGTTCTCAG 59.866 47.826 0.00 0.00 0.00 3.35
2811 4247 1.693606 TGTGAGGTGTCAAGATCTGCA 59.306 47.619 0.00 0.00 33.27 4.41
2834 4270 3.195825 TCTTTGCCTCTTCTACTGCTACC 59.804 47.826 0.00 0.00 0.00 3.18
2913 4355 5.674525 AGCTTATGTATAAGTTGCTGCTGA 58.325 37.500 11.95 0.00 41.34 4.26
2927 4369 6.996879 AGTTGCTGCTGAGAAATCATGTATAT 59.003 34.615 0.00 0.00 0.00 0.86
2974 4416 5.046950 AGGAACAGGACTGACTACATTCTTC 60.047 44.000 6.29 0.00 0.00 2.87
3027 4469 1.742831 TGGACCGTGCATAGATTTTGC 59.257 47.619 0.00 0.00 40.55 3.68
3060 4502 5.193679 GGATTGGTAAGTTACTGCCTGATT 58.806 41.667 12.65 0.00 0.00 2.57
3082 4524 8.768397 TGATTATAAGATACCTTGGTGTTGTCT 58.232 33.333 2.03 0.00 33.94 3.41
3085 4527 2.371841 AGATACCTTGGTGTTGTCTGCA 59.628 45.455 2.03 0.00 0.00 4.41
3091 4533 0.890542 TGGTGTTGTCTGCATGAGGC 60.891 55.000 0.00 0.00 45.13 4.70
3104 4551 3.077556 GAGGCGAGCTCCCTTGGA 61.078 66.667 20.63 0.00 31.41 3.53
3112 4559 2.672098 GAGCTCCCTTGGATAGTCTCA 58.328 52.381 0.87 0.00 0.00 3.27
3149 4596 5.642491 GCCTTATTTCGTCTAGGTTTCTTGT 59.358 40.000 0.00 0.00 0.00 3.16
3202 4762 3.830755 AGCATTCTGATGAAGCAAGGTTT 59.169 39.130 0.00 0.00 35.16 3.27
3436 5002 2.600731 CCACTCTTTCAGACTGTAGCG 58.399 52.381 1.59 0.00 0.00 4.26
3459 5025 4.880886 TGATGTATGTGCAATCTTTCGG 57.119 40.909 0.00 0.00 0.00 4.30
3470 5036 4.095334 TGCAATCTTTCGGAGATGATGTTG 59.905 41.667 3.48 1.08 44.41 3.33
3477 5043 5.400066 TTCGGAGATGATGTTGTCTTGTA 57.600 39.130 0.00 0.00 35.04 2.41
3481 5047 5.431765 GGAGATGATGTTGTCTTGTATGGT 58.568 41.667 0.00 0.00 0.00 3.55
3505 5071 7.301054 GTGAATCTTCCTTCAAGTATGTGTTG 58.699 38.462 0.00 0.00 36.92 3.33
3530 5096 5.714333 TCCCTTTGCAATGCTATCTTGTTTA 59.286 36.000 6.82 0.00 0.00 2.01
3598 5164 9.322773 GAAGTGGTACTAACTTTTACAGAAACT 57.677 33.333 13.41 0.00 37.98 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.153147 GGGGGAGATCCTTTCGTGC 60.153 63.158 0.00 0.00 35.95 5.34
26 27 8.472007 TTTCTATGTTTTTCTTGCCCTTTCTA 57.528 30.769 0.00 0.00 0.00 2.10
122 127 0.854218 TTGGAACCAAACAGGCCCTA 59.146 50.000 0.00 0.00 43.14 3.53
124 129 1.931635 TATTGGAACCAAACAGGCCC 58.068 50.000 10.36 0.00 43.14 5.80
126 131 3.572255 TGACTTATTGGAACCAAACAGGC 59.428 43.478 10.36 11.26 43.14 4.85
127 132 4.022329 GGTGACTTATTGGAACCAAACAGG 60.022 45.833 10.36 5.07 45.67 4.00
128 133 4.827284 AGGTGACTTATTGGAACCAAACAG 59.173 41.667 10.36 11.01 37.44 3.16
129 134 4.582656 CAGGTGACTTATTGGAACCAAACA 59.417 41.667 10.36 0.00 40.21 2.83
131 136 4.825085 GTCAGGTGACTTATTGGAACCAAA 59.175 41.667 10.36 0.00 41.65 3.28
153 158 6.657966 GGTTTTAAGCCACCTGACTTATAAGT 59.342 38.462 18.05 18.05 43.16 2.24
154 159 6.657541 TGGTTTTAAGCCACCTGACTTATAAG 59.342 38.462 11.05 11.05 33.76 1.73
156 161 6.129414 TGGTTTTAAGCCACCTGACTTATA 57.871 37.500 0.00 0.00 33.76 0.98
157 162 4.993028 TGGTTTTAAGCCACCTGACTTAT 58.007 39.130 0.00 0.00 33.76 1.73
158 163 4.141344 ACTGGTTTTAAGCCACCTGACTTA 60.141 41.667 0.00 0.00 35.95 2.24
159 164 3.222603 CTGGTTTTAAGCCACCTGACTT 58.777 45.455 0.00 0.00 34.68 3.01
160 165 2.174854 ACTGGTTTTAAGCCACCTGACT 59.825 45.455 0.00 0.00 35.95 3.41
161 166 2.583143 ACTGGTTTTAAGCCACCTGAC 58.417 47.619 0.00 0.00 35.95 3.51
162 167 4.139038 GTTACTGGTTTTAAGCCACCTGA 58.861 43.478 0.00 0.00 35.95 3.86
163 168 4.142038 AGTTACTGGTTTTAAGCCACCTG 58.858 43.478 0.00 0.00 37.86 4.00
166 171 9.006839 ACTTATAAGTTACTGGTTTTAAGCCAC 57.993 33.333 12.50 0.00 35.21 5.01
168 173 9.223099 TGACTTATAAGTTACTGGTTTTAAGCC 57.777 33.333 18.96 1.86 39.88 4.35
173 178 6.148315 GGCGTGACTTATAAGTTACTGGTTTT 59.852 38.462 27.98 2.53 41.71 2.43
174 179 5.640783 GGCGTGACTTATAAGTTACTGGTTT 59.359 40.000 27.98 3.18 41.71 3.27
175 180 5.046807 AGGCGTGACTTATAAGTTACTGGTT 60.047 40.000 27.98 14.37 41.71 3.67
176 181 4.465305 AGGCGTGACTTATAAGTTACTGGT 59.535 41.667 27.98 15.12 41.71 4.00
177 182 4.804139 CAGGCGTGACTTATAAGTTACTGG 59.196 45.833 27.98 18.87 41.71 4.00
178 183 5.408356 ACAGGCGTGACTTATAAGTTACTG 58.592 41.667 27.98 23.14 41.71 2.74
180 185 6.366877 TCAAACAGGCGTGACTTATAAGTTAC 59.633 38.462 23.81 23.81 40.82 2.50
181 186 6.457355 TCAAACAGGCGTGACTTATAAGTTA 58.543 36.000 18.96 12.54 39.88 2.24
182 187 5.302360 TCAAACAGGCGTGACTTATAAGTT 58.698 37.500 18.96 3.63 39.88 2.66
183 188 4.890088 TCAAACAGGCGTGACTTATAAGT 58.110 39.130 18.05 18.05 43.16 2.24
184 189 6.128282 ACAATCAAACAGGCGTGACTTATAAG 60.128 38.462 14.38 11.05 0.00 1.73
185 190 5.703592 ACAATCAAACAGGCGTGACTTATAA 59.296 36.000 14.38 0.00 0.00 0.98
187 192 4.072131 ACAATCAAACAGGCGTGACTTAT 58.928 39.130 14.38 0.00 0.00 1.73
188 193 3.472652 ACAATCAAACAGGCGTGACTTA 58.527 40.909 14.38 0.00 0.00 2.24
189 194 2.290641 GACAATCAAACAGGCGTGACTT 59.709 45.455 14.38 3.10 0.00 3.01
190 195 1.873591 GACAATCAAACAGGCGTGACT 59.126 47.619 14.38 0.00 0.00 3.41
192 197 1.960417 TGACAATCAAACAGGCGTGA 58.040 45.000 14.38 0.00 0.00 4.35
193 198 2.485426 AGATGACAATCAAACAGGCGTG 59.515 45.455 4.53 4.53 35.03 5.34
195 200 2.743664 TCAGATGACAATCAAACAGGCG 59.256 45.455 0.00 0.00 35.03 5.52
196 201 4.088823 GTCAGATGACAATCAAACAGGC 57.911 45.455 8.09 0.00 44.18 4.85
216 221 4.322801 GGTGTGCTCAGGTGACTTATAAGT 60.323 45.833 18.05 18.05 43.16 2.24
218 223 3.838317 AGGTGTGCTCAGGTGACTTATAA 59.162 43.478 0.00 0.00 40.21 0.98
220 225 2.260822 AGGTGTGCTCAGGTGACTTAT 58.739 47.619 0.00 0.00 40.21 1.73
221 226 1.717032 AGGTGTGCTCAGGTGACTTA 58.283 50.000 0.00 0.00 40.21 2.24
222 227 0.839946 AAGGTGTGCTCAGGTGACTT 59.160 50.000 0.00 0.00 40.21 3.01
224 229 0.603975 GGAAGGTGTGCTCAGGTGAC 60.604 60.000 0.00 0.00 0.00 3.67
225 230 1.754745 GGAAGGTGTGCTCAGGTGA 59.245 57.895 0.00 0.00 0.00 4.02
226 231 1.302832 GGGAAGGTGTGCTCAGGTG 60.303 63.158 0.00 0.00 0.00 4.00
227 232 1.136329 ATGGGAAGGTGTGCTCAGGT 61.136 55.000 0.00 0.00 0.00 4.00
228 233 0.393537 GATGGGAAGGTGTGCTCAGG 60.394 60.000 0.00 0.00 0.00 3.86
229 234 0.617413 AGATGGGAAGGTGTGCTCAG 59.383 55.000 0.00 0.00 0.00 3.35
230 235 1.067295 AAGATGGGAAGGTGTGCTCA 58.933 50.000 0.00 0.00 0.00 4.26
231 236 1.271597 ACAAGATGGGAAGGTGTGCTC 60.272 52.381 0.00 0.00 0.00 4.26
233 238 1.620822 AACAAGATGGGAAGGTGTGC 58.379 50.000 0.00 0.00 0.00 4.57
234 239 4.670896 AAAAACAAGATGGGAAGGTGTG 57.329 40.909 0.00 0.00 0.00 3.82
253 258 4.833938 GGTCCCACCACCTTTACATAAAAA 59.166 41.667 0.00 0.00 38.42 1.94
254 259 4.409187 GGTCCCACCACCTTTACATAAAA 58.591 43.478 0.00 0.00 38.42 1.52
255 260 3.245336 GGGTCCCACCACCTTTACATAAA 60.245 47.826 1.78 0.00 41.02 1.40
256 261 2.309458 GGGTCCCACCACCTTTACATAA 59.691 50.000 1.78 0.00 41.02 1.90
257 262 1.917568 GGGTCCCACCACCTTTACATA 59.082 52.381 1.78 0.00 41.02 2.29
259 264 0.698198 TGGGTCCCACCACCTTTACA 60.698 55.000 6.47 0.00 41.02 2.41
260 265 0.702316 ATGGGTCCCACCACCTTTAC 59.298 55.000 14.57 0.00 44.72 2.01
261 266 0.701731 CATGGGTCCCACCACCTTTA 59.298 55.000 14.57 0.00 44.72 1.85
263 268 3.180282 CATGGGTCCCACCACCTT 58.820 61.111 14.57 0.00 44.72 3.50
264 269 3.661648 GCATGGGTCCCACCACCT 61.662 66.667 14.57 0.00 44.72 4.00
267 272 0.831288 CTTTTGCATGGGTCCCACCA 60.831 55.000 14.57 11.02 46.24 4.17
268 273 1.543944 CCTTTTGCATGGGTCCCACC 61.544 60.000 14.57 8.17 35.80 4.61
269 274 0.541764 TCCTTTTGCATGGGTCCCAC 60.542 55.000 14.57 1.42 35.80 4.61
270 275 0.251742 CTCCTTTTGCATGGGTCCCA 60.252 55.000 14.64 14.64 38.19 4.37
271 276 0.972471 CCTCCTTTTGCATGGGTCCC 60.972 60.000 0.00 0.00 0.00 4.46
272 277 0.251787 ACCTCCTTTTGCATGGGTCC 60.252 55.000 0.00 0.00 0.00 4.46
275 280 0.890683 GTCACCTCCTTTTGCATGGG 59.109 55.000 0.00 0.00 0.00 4.00
276 281 1.915141 AGTCACCTCCTTTTGCATGG 58.085 50.000 0.00 0.00 0.00 3.66
277 282 6.375455 ACTTATAAGTCACCTCCTTTTGCATG 59.625 38.462 12.50 0.00 32.86 4.06
278 283 6.485171 ACTTATAAGTCACCTCCTTTTGCAT 58.515 36.000 12.50 0.00 32.86 3.96
279 284 5.876357 ACTTATAAGTCACCTCCTTTTGCA 58.124 37.500 12.50 0.00 32.86 4.08
285 290 9.503399 CAACTTAAAACTTATAAGTCACCTCCT 57.497 33.333 18.28 0.00 41.49 3.69
286 291 8.727910 CCAACTTAAAACTTATAAGTCACCTCC 58.272 37.037 18.28 0.00 41.49 4.30
289 294 7.449395 ACCCCAACTTAAAACTTATAAGTCACC 59.551 37.037 18.28 0.00 41.49 4.02
291 296 7.449086 CCACCCCAACTTAAAACTTATAAGTCA 59.551 37.037 18.28 4.72 41.49 3.41
292 297 7.666804 TCCACCCCAACTTAAAACTTATAAGTC 59.333 37.037 18.28 0.00 41.49 3.01
293 298 7.528675 TCCACCCCAACTTAAAACTTATAAGT 58.471 34.615 12.50 12.50 43.57 2.24
295 300 6.434965 GCTCCACCCCAACTTAAAACTTATAA 59.565 38.462 0.00 0.00 0.00 0.98
298 303 4.146564 GCTCCACCCCAACTTAAAACTTA 58.853 43.478 0.00 0.00 0.00 2.24
300 305 2.091555 TGCTCCACCCCAACTTAAAACT 60.092 45.455 0.00 0.00 0.00 2.66
301 306 2.312390 TGCTCCACCCCAACTTAAAAC 58.688 47.619 0.00 0.00 0.00 2.43
303 308 2.091555 AGTTGCTCCACCCCAACTTAAA 60.092 45.455 0.56 0.00 46.86 1.52
304 309 1.497286 AGTTGCTCCACCCCAACTTAA 59.503 47.619 0.56 0.00 46.86 1.85
305 310 1.145571 AGTTGCTCCACCCCAACTTA 58.854 50.000 0.56 0.00 46.86 2.24
307 312 3.674278 AGTTGCTCCACCCCAACT 58.326 55.556 0.56 0.56 44.86 3.16
310 315 1.004277 GTCATAAGTTGCTCCACCCCA 59.996 52.381 0.00 0.00 0.00 4.96
313 318 7.484035 CTTATAAGTCATAAGTTGCTCCACC 57.516 40.000 4.18 0.00 40.84 4.61
324 329 7.504926 AGTCACCCCAACTTATAAGTCATAA 57.495 36.000 18.28 0.00 38.57 1.90
325 330 7.504926 AAGTCACCCCAACTTATAAGTCATA 57.495 36.000 18.28 0.00 38.57 2.15
326 331 6.388619 AAGTCACCCCAACTTATAAGTCAT 57.611 37.500 18.28 1.19 38.57 3.06
332 337 9.675464 CAAACTTATAAGTCACCCCAACTTATA 57.325 33.333 18.28 10.26 44.28 0.98
333 338 7.614192 CCAAACTTATAAGTCACCCCAACTTAT 59.386 37.037 18.28 11.86 46.48 1.73
334 339 6.943718 CCAAACTTATAAGTCACCCCAACTTA 59.056 38.462 18.28 0.00 41.91 2.24
335 340 5.773176 CCAAACTTATAAGTCACCCCAACTT 59.227 40.000 18.28 3.39 38.57 2.66
336 341 5.163023 ACCAAACTTATAAGTCACCCCAACT 60.163 40.000 18.28 0.00 38.57 3.16
337 342 5.074804 ACCAAACTTATAAGTCACCCCAAC 58.925 41.667 18.28 0.00 38.57 3.77
338 343 5.073965 AGACCAAACTTATAAGTCACCCCAA 59.926 40.000 18.28 0.00 38.57 4.12
339 344 4.600111 AGACCAAACTTATAAGTCACCCCA 59.400 41.667 18.28 0.00 38.57 4.96
341 346 5.557866 ACAGACCAAACTTATAAGTCACCC 58.442 41.667 18.28 7.52 38.57 4.61
343 348 7.360361 CCAAACAGACCAAACTTATAAGTCAC 58.640 38.462 18.28 8.47 38.57 3.67
344 349 6.016610 GCCAAACAGACCAAACTTATAAGTCA 60.017 38.462 18.28 0.00 38.57 3.41
349 354 6.716934 TTTGCCAAACAGACCAAACTTATA 57.283 33.333 0.00 0.00 0.00 0.98
350 355 5.606348 TTTGCCAAACAGACCAAACTTAT 57.394 34.783 0.00 0.00 0.00 1.73
351 356 5.407407 TTTTGCCAAACAGACCAAACTTA 57.593 34.783 0.00 0.00 0.00 2.24
353 358 3.971245 TTTTGCCAAACAGACCAAACT 57.029 38.095 0.00 0.00 0.00 2.66
354 359 5.815222 ACTTATTTTGCCAAACAGACCAAAC 59.185 36.000 0.00 0.00 0.00 2.93
356 361 5.127845 TGACTTATTTTGCCAAACAGACCAA 59.872 36.000 0.00 0.00 0.00 3.67
357 362 4.646945 TGACTTATTTTGCCAAACAGACCA 59.353 37.500 0.00 0.00 0.00 4.02
359 364 5.831997 AGTGACTTATTTTGCCAAACAGAC 58.168 37.500 0.00 0.00 0.00 3.51
360 365 6.463995 AAGTGACTTATTTTGCCAAACAGA 57.536 33.333 0.00 0.00 0.00 3.41
361 366 7.538303 AAAAGTGACTTATTTTGCCAAACAG 57.462 32.000 0.00 0.00 0.00 3.16
362 367 7.913674 AAAAAGTGACTTATTTTGCCAAACA 57.086 28.000 0.00 0.00 0.00 2.83
384 389 9.724839 CCAACTTATAAGTCGAAAAGTGAAAAA 57.275 29.630 18.28 0.00 38.57 1.94
385 390 8.895737 ACCAACTTATAAGTCGAAAAGTGAAAA 58.104 29.630 18.28 0.00 38.57 2.29
386 391 8.339714 CACCAACTTATAAGTCGAAAAGTGAAA 58.660 33.333 18.28 0.00 38.57 2.69
387 392 7.711772 TCACCAACTTATAAGTCGAAAAGTGAA 59.288 33.333 18.28 7.64 38.57 3.18
388 393 7.170320 GTCACCAACTTATAAGTCGAAAAGTGA 59.830 37.037 18.28 18.36 38.57 3.41
389 394 7.042321 TGTCACCAACTTATAAGTCGAAAAGTG 60.042 37.037 18.28 16.78 38.57 3.16
390 395 6.987992 TGTCACCAACTTATAAGTCGAAAAGT 59.012 34.615 18.28 7.29 38.57 2.66
391 396 7.416154 TGTCACCAACTTATAAGTCGAAAAG 57.584 36.000 18.28 7.33 38.57 2.27
392 397 7.972832 ATGTCACCAACTTATAAGTCGAAAA 57.027 32.000 18.28 2.72 38.57 2.29
393 398 9.661563 AATATGTCACCAACTTATAAGTCGAAA 57.338 29.630 18.28 8.64 38.57 3.46
394 399 9.661563 AAATATGTCACCAACTTATAAGTCGAA 57.338 29.630 18.28 1.05 38.57 3.71
395 400 9.093970 CAAATATGTCACCAACTTATAAGTCGA 57.906 33.333 18.28 10.00 38.57 4.20
396 401 9.093970 TCAAATATGTCACCAACTTATAAGTCG 57.906 33.333 18.28 13.48 38.57 4.18
401 406 9.521841 TGGTTTCAAATATGTCACCAACTTATA 57.478 29.630 0.00 0.00 37.03 0.98
402 407 8.415950 TGGTTTCAAATATGTCACCAACTTAT 57.584 30.769 0.00 0.00 37.03 1.73
403 408 7.825331 TGGTTTCAAATATGTCACCAACTTA 57.175 32.000 0.00 0.00 37.03 2.24
404 409 6.723298 TGGTTTCAAATATGTCACCAACTT 57.277 33.333 0.00 0.00 37.03 2.66
405 410 6.723298 TTGGTTTCAAATATGTCACCAACT 57.277 33.333 9.20 0.00 41.08 3.16
406 411 7.206687 TCTTTGGTTTCAAATATGTCACCAAC 58.793 34.615 11.54 0.00 43.34 3.77
407 412 7.353414 TCTTTGGTTTCAAATATGTCACCAA 57.647 32.000 9.20 9.20 42.66 3.67
408 413 6.968263 TCTTTGGTTTCAAATATGTCACCA 57.032 33.333 0.00 0.00 41.45 4.17
409 414 6.868339 CCTTCTTTGGTTTCAAATATGTCACC 59.132 38.462 0.00 0.00 41.45 4.02
410 415 6.366061 GCCTTCTTTGGTTTCAAATATGTCAC 59.634 38.462 0.00 0.00 41.45 3.67
411 416 6.454795 GCCTTCTTTGGTTTCAAATATGTCA 58.545 36.000 0.00 0.00 41.45 3.58
412 417 5.869344 GGCCTTCTTTGGTTTCAAATATGTC 59.131 40.000 0.00 0.00 41.45 3.06
413 418 5.543790 AGGCCTTCTTTGGTTTCAAATATGT 59.456 36.000 0.00 0.00 41.45 2.29
414 419 6.041423 AGGCCTTCTTTGGTTTCAAATATG 57.959 37.500 0.00 0.00 41.45 1.78
415 420 6.686484 AAGGCCTTCTTTGGTTTCAAATAT 57.314 33.333 13.78 0.00 41.45 1.28
416 421 6.780522 AGTAAGGCCTTCTTTGGTTTCAAATA 59.219 34.615 24.49 0.00 41.45 1.40
417 422 5.602561 AGTAAGGCCTTCTTTGGTTTCAAAT 59.397 36.000 24.49 0.00 41.45 2.32
418 423 4.959839 AGTAAGGCCTTCTTTGGTTTCAAA 59.040 37.500 24.49 0.00 40.23 2.69
419 424 4.542697 AGTAAGGCCTTCTTTGGTTTCAA 58.457 39.130 24.49 0.00 36.93 2.69
420 425 4.178956 AGTAAGGCCTTCTTTGGTTTCA 57.821 40.909 24.49 0.00 36.93 2.69
421 426 5.314529 AGTAGTAAGGCCTTCTTTGGTTTC 58.685 41.667 24.49 4.37 36.93 2.78
422 427 5.314529 GAGTAGTAAGGCCTTCTTTGGTTT 58.685 41.667 24.49 0.00 36.93 3.27
423 428 4.263374 GGAGTAGTAAGGCCTTCTTTGGTT 60.263 45.833 24.49 2.72 36.93 3.67
424 429 3.263681 GGAGTAGTAAGGCCTTCTTTGGT 59.736 47.826 24.49 3.30 36.93 3.67
425 430 3.519913 AGGAGTAGTAAGGCCTTCTTTGG 59.480 47.826 24.49 0.00 36.93 3.28
426 431 4.383226 GGAGGAGTAGTAAGGCCTTCTTTG 60.383 50.000 24.49 0.00 36.93 2.77
427 432 3.775866 GGAGGAGTAGTAAGGCCTTCTTT 59.224 47.826 24.49 11.37 36.93 2.52
428 433 3.376636 GGAGGAGTAGTAAGGCCTTCTT 58.623 50.000 24.49 14.09 39.40 2.52
429 434 2.359461 GGGAGGAGTAGTAAGGCCTTCT 60.359 54.545 24.49 20.26 0.00 2.85
430 435 2.040939 GGGAGGAGTAGTAAGGCCTTC 58.959 57.143 24.49 13.89 0.00 3.46
431 436 1.365028 TGGGAGGAGTAGTAAGGCCTT 59.635 52.381 24.18 24.18 0.00 4.35
432 437 1.016415 TGGGAGGAGTAGTAAGGCCT 58.984 55.000 0.00 0.00 0.00 5.19
433 438 1.875488 TTGGGAGGAGTAGTAAGGCC 58.125 55.000 0.00 0.00 0.00 5.19
434 439 2.838813 ACTTTGGGAGGAGTAGTAAGGC 59.161 50.000 0.00 0.00 0.00 4.35
435 440 4.081031 GGAACTTTGGGAGGAGTAGTAAGG 60.081 50.000 0.00 0.00 0.00 2.69
436 441 4.778427 AGGAACTTTGGGAGGAGTAGTAAG 59.222 45.833 0.00 0.00 27.25 2.34
437 442 4.759953 AGGAACTTTGGGAGGAGTAGTAA 58.240 43.478 0.00 0.00 27.25 2.24
438 443 4.415224 AGGAACTTTGGGAGGAGTAGTA 57.585 45.455 0.00 0.00 27.25 1.82
439 444 3.277416 AGGAACTTTGGGAGGAGTAGT 57.723 47.619 0.00 0.00 27.25 2.73
462 468 0.110192 GCCTCGTTGCTTCTTTTCCG 60.110 55.000 0.00 0.00 0.00 4.30
640 669 3.587342 TTGCCGTTGCGTTCGCATC 62.587 57.895 20.02 17.42 41.05 3.91
672 2045 4.500826 GTCCCTCCCTCCCTCCCC 62.501 77.778 0.00 0.00 0.00 4.81
673 2046 4.862823 CGTCCCTCCCTCCCTCCC 62.863 77.778 0.00 0.00 0.00 4.30
675 2048 3.742248 CTCCGTCCCTCCCTCCCTC 62.742 73.684 0.00 0.00 0.00 4.30
676 2049 3.756783 CTCCGTCCCTCCCTCCCT 61.757 72.222 0.00 0.00 0.00 4.20
689 2072 4.135153 CAGCAGTCCGTCCCTCCG 62.135 72.222 0.00 0.00 0.00 4.63
979 2395 4.150454 CCTCGGCCTCCTCCTCCT 62.150 72.222 0.00 0.00 0.00 3.69
980 2396 4.144727 TCCTCGGCCTCCTCCTCC 62.145 72.222 0.00 0.00 0.00 4.30
981 2397 2.520741 CTCCTCGGCCTCCTCCTC 60.521 72.222 0.00 0.00 0.00 3.71
982 2398 4.150454 CCTCCTCGGCCTCCTCCT 62.150 72.222 0.00 0.00 0.00 3.69
983 2399 3.460478 ATCCTCCTCGGCCTCCTCC 62.460 68.421 0.00 0.00 0.00 4.30
984 2400 2.200092 ATCCTCCTCGGCCTCCTC 59.800 66.667 0.00 0.00 0.00 3.71
985 2401 2.123077 CATCCTCCTCGGCCTCCT 60.123 66.667 0.00 0.00 0.00 3.69
986 2402 3.237741 CCATCCTCCTCGGCCTCC 61.238 72.222 0.00 0.00 0.00 4.30
987 2403 2.123251 TCCATCCTCCTCGGCCTC 60.123 66.667 0.00 0.00 0.00 4.70
988 2404 2.123077 CTCCATCCTCCTCGGCCT 60.123 66.667 0.00 0.00 0.00 5.19
989 2405 3.934962 GCTCCATCCTCCTCGGCC 61.935 72.222 0.00 0.00 0.00 6.13
990 2406 4.292178 CGCTCCATCCTCCTCGGC 62.292 72.222 0.00 0.00 0.00 5.54
991 2407 3.610669 CCGCTCCATCCTCCTCGG 61.611 72.222 0.00 0.00 0.00 4.63
992 2408 3.610669 CCCGCTCCATCCTCCTCG 61.611 72.222 0.00 0.00 0.00 4.63
1620 3045 3.554692 GTGAAGTCGATGCGGCGG 61.555 66.667 9.78 0.00 36.23 6.13
1746 3171 1.073897 GTTGCTGCAGAGGAAGGGT 59.926 57.895 20.43 0.00 28.76 4.34
1955 3381 6.700520 AGAACAAGTATAAGCGTATAGGCAAC 59.299 38.462 18.89 10.96 34.64 4.17
2012 3439 0.904865 TCTCCTTGACGATGGTGGCT 60.905 55.000 0.00 0.00 0.00 4.75
2168 3595 7.189693 ACTATGACCAAATACATTGCGTATG 57.810 36.000 0.00 0.00 40.04 2.39
2212 3639 6.038936 TCAAAACATCCAGACATCATGCATAG 59.961 38.462 0.00 0.00 0.00 2.23
2290 3717 3.612860 CGTCCAAGTAATTCCTCGTGAAG 59.387 47.826 0.00 0.00 36.14 3.02
2329 3756 6.394345 AGGTTTTCTAATCCATCTTCAGGT 57.606 37.500 0.00 0.00 0.00 4.00
2356 3783 3.318839 TGAAGTTTGTCATCTTGGCCAAG 59.681 43.478 35.52 35.52 39.71 3.61
2428 3855 6.208599 CCAGGAACAATTTCTTAAGGCAACTA 59.791 38.462 1.85 0.00 37.74 2.24
2517 3944 5.766150 TTCAAGAATTTCTGCCTTTCGAA 57.234 34.783 0.00 0.00 0.00 3.71
2577 4004 1.419387 GCTGGGCCTGAGAACTATCAT 59.581 52.381 15.36 0.00 0.00 2.45
2811 4247 4.141824 GGTAGCAGTAGAAGAGGCAAAGAT 60.142 45.833 0.00 0.00 0.00 2.40
2829 4265 5.992829 GCTATTTAGGGAGAAAAGAGGTAGC 59.007 44.000 0.00 0.00 0.00 3.58
2834 4270 7.607991 TCACAAAGCTATTTAGGGAGAAAAGAG 59.392 37.037 0.00 0.00 0.00 2.85
2866 4308 7.761704 GCTAACTACAAAGAGATGACTGATCAA 59.238 37.037 0.00 0.00 38.69 2.57
2974 4416 1.202651 AGTTGTCCAGTTTGTCCCTCG 60.203 52.381 0.00 0.00 0.00 4.63
3027 4469 7.119262 CAGTAACTTACCAATCCAAAGGTACAG 59.881 40.741 10.99 1.11 43.00 2.74
3060 4502 6.070481 TGCAGACAACACCAAGGTATCTTATA 60.070 38.462 0.00 0.00 0.00 0.98
3082 4524 4.166888 GGGAGCTCGCCTCATGCA 62.167 66.667 19.61 0.00 42.62 3.96
3085 4527 2.739996 CCAAGGGAGCTCGCCTCAT 61.740 63.158 25.68 5.79 42.62 2.90
3091 4533 1.611491 GAGACTATCCAAGGGAGCTCG 59.389 57.143 7.83 0.00 34.05 5.03
3104 4551 6.058183 AGGCAATAGCGATTTTTGAGACTAT 58.942 36.000 0.83 0.00 43.41 2.12
3112 4559 6.560711 ACGAAATAAGGCAATAGCGATTTTT 58.439 32.000 0.00 0.00 43.41 1.94
3171 4731 4.397481 TCATCAGAATGCTCCTGTACAG 57.603 45.455 16.34 16.34 34.76 2.74
3202 4762 9.784376 ATGGTAGGGCAATAGTAGATTATAGAA 57.216 33.333 0.00 0.00 0.00 2.10
3335 4901 5.135383 ACATTTCCATGCTGCATGTAGTAT 58.865 37.500 33.35 20.65 39.94 2.12
3436 5002 5.237127 TCCGAAAGATTGCACATACATCATC 59.763 40.000 0.00 0.00 0.00 2.92
3459 5025 6.108687 TCACCATACAAGACAACATCATCTC 58.891 40.000 0.00 0.00 0.00 2.75
3470 5036 6.173339 TGAAGGAAGATTCACCATACAAGAC 58.827 40.000 0.00 0.00 34.31 3.01
3477 5043 6.600822 CACATACTTGAAGGAAGATTCACCAT 59.399 38.462 0.00 0.00 38.87 3.55
3481 5047 6.998074 ACAACACATACTTGAAGGAAGATTCA 59.002 34.615 0.00 0.00 37.41 2.57
3505 5071 3.445096 ACAAGATAGCATTGCAAAGGGAC 59.555 43.478 11.91 0.00 0.00 4.46
3530 5096 4.970860 ATCTAACATGCTATGCTGAGGT 57.029 40.909 0.00 0.00 0.00 3.85
3570 5136 6.762333 TCTGTAAAAGTTAGTACCACTTCCC 58.238 40.000 8.19 2.06 33.12 3.97
3598 5164 9.147732 ACACAGAATATGACCATGAAGATAGTA 57.852 33.333 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.