Multiple sequence alignment - TraesCS2D01G161900

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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 TraesCS2D01G161900 chr2D 100.000 3953 0 0 1 3953 106629014 106625062 0.000000e+00 7300.0
1 TraesCS2D01G161900 chr2D 94.737 190 10 0 1622 1811 106627247 106627058 2.990000e-76 296.0
2 TraesCS2D01G161900 chr2D 94.737 190 10 0 1768 1957 106627393 106627204 2.990000e-76 296.0
3 TraesCS2D01G161900 chr2D 91.146 192 16 1 1768 1959 622712366 622712556 3.920000e-65 259.0
4 TraesCS2D01G161900 chr2D 87.730 163 20 0 191 353 35507244 35507082 1.450000e-44 191.0
5 TraesCS2D01G161900 chr2B 92.906 2904 117 42 354 3205 156593751 156590885 0.000000e+00 4139.0
6 TraesCS2D01G161900 chr2B 90.436 711 38 13 3260 3953 156590659 156589962 0.000000e+00 909.0
7 TraesCS2D01G161900 chr2B 94.271 192 10 1 1 191 156593935 156593744 3.860000e-75 292.0
8 TraesCS2D01G161900 chr2B 92.784 194 13 1 1619 1811 156592301 156592108 3.010000e-71 279.0
9 TraesCS2D01G161900 chr2B 86.503 163 22 0 191 353 58670921 58670759 3.140000e-41 180.0
10 TraesCS2D01G161900 chr2A 91.936 1761 86 27 2226 3953 103099731 103097994 0.000000e+00 2414.0
11 TraesCS2D01G161900 chr2A 90.726 1585 108 24 633 2195 103101291 103099724 0.000000e+00 2076.0
12 TraesCS2D01G161900 chr2A 84.051 627 72 15 1007 1627 251390719 251391323 2.650000e-161 579.0
13 TraesCS2D01G161900 chr2A 92.670 191 12 2 1622 1811 103100151 103099962 1.400000e-69 274.0
14 TraesCS2D01G161900 chr2A 91.053 190 17 0 1768 1957 103100297 103100108 1.410000e-64 257.0
15 TraesCS2D01G161900 chr2A 83.590 195 21 8 8 191 103101715 103101521 5.250000e-39 172.0
16 TraesCS2D01G161900 chr2A 85.366 164 23 1 191 353 38596864 38596701 6.790000e-38 169.0
17 TraesCS2D01G161900 chr2A 94.737 57 3 0 355 411 103101527 103101471 5.440000e-14 89.8
18 TraesCS2D01G161900 chr4D 90.872 1227 85 17 1005 2227 46139925 46138722 0.000000e+00 1620.0
19 TraesCS2D01G161900 chr4D 86.422 626 64 13 1006 1627 45005469 45004861 0.000000e+00 665.0
20 TraesCS2D01G161900 chr4D 92.708 192 13 1 1622 1813 46139180 46138990 3.890000e-70 276.0
21 TraesCS2D01G161900 chr4D 90.625 192 17 1 1768 1959 46139326 46139136 1.820000e-63 254.0
22 TraesCS2D01G161900 chr4D 90.361 166 11 2 190 355 133486801 133486641 3.090000e-51 213.0
23 TraesCS2D01G161900 chr7D 92.574 781 56 2 1448 2227 475097436 475096657 0.000000e+00 1120.0
24 TraesCS2D01G161900 chr7D 93.229 192 12 1 1622 1813 475097115 475096925 8.360000e-72 281.0
25 TraesCS2D01G161900 chr7D 90.625 192 17 1 1768 1959 475097261 475097071 1.820000e-63 254.0
26 TraesCS2D01G161900 chr5B 84.906 636 70 16 1005 1633 236414536 236415152 1.560000e-173 619.0
27 TraesCS2D01G161900 chr5B 84.748 636 71 16 1005 1633 236737069 236737685 7.260000e-172 614.0
28 TraesCS2D01G161900 chr5A 84.385 634 71 16 1005 1633 669523780 669523170 7.310000e-167 597.0
29 TraesCS2D01G161900 chr5A 89.937 159 15 1 195 353 26520944 26520787 1.860000e-48 204.0
30 TraesCS2D01G161900 chr1A 84.579 629 58 19 1006 1627 570975257 570974661 4.400000e-164 588.0
31 TraesCS2D01G161900 chr1A 91.599 369 22 1 1859 2227 570974433 570974074 5.900000e-138 501.0
32 TraesCS2D01G161900 chr1A 87.117 163 21 0 191 353 558542948 558543110 6.750000e-43 185.0
33 TraesCS2D01G161900 chr1A 84.000 175 27 1 175 349 262830267 262830440 2.440000e-37 167.0
34 TraesCS2D01G161900 chr6B 92.593 162 12 0 192 353 636320638 636320477 2.380000e-57 233.0
35 TraesCS2D01G161900 chr5D 91.358 162 13 1 192 353 37647727 37647567 1.850000e-53 220.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G161900 chr2D 106625062 106629014 3952 True 2630.666667 7300 96.491333 1 3953 3 chr2D.!!$R2 3952
1 TraesCS2D01G161900 chr2B 156589962 156593935 3973 True 1404.750000 4139 92.599250 1 3953 4 chr2B.!!$R2 3952
2 TraesCS2D01G161900 chr2A 103097994 103101715 3721 True 880.466667 2414 90.785333 8 3953 6 chr2A.!!$R2 3945
3 TraesCS2D01G161900 chr2A 251390719 251391323 604 False 579.000000 579 84.051000 1007 1627 1 chr2A.!!$F1 620
4 TraesCS2D01G161900 chr4D 46138722 46139925 1203 True 716.666667 1620 91.401667 1005 2227 3 chr4D.!!$R3 1222
5 TraesCS2D01G161900 chr4D 45004861 45005469 608 True 665.000000 665 86.422000 1006 1627 1 chr4D.!!$R1 621
6 TraesCS2D01G161900 chr7D 475096657 475097436 779 True 551.666667 1120 92.142667 1448 2227 3 chr7D.!!$R1 779
7 TraesCS2D01G161900 chr5B 236414536 236415152 616 False 619.000000 619 84.906000 1005 1633 1 chr5B.!!$F1 628
8 TraesCS2D01G161900 chr5B 236737069 236737685 616 False 614.000000 614 84.748000 1005 1633 1 chr5B.!!$F2 628
9 TraesCS2D01G161900 chr5A 669523170 669523780 610 True 597.000000 597 84.385000 1005 1633 1 chr5A.!!$R2 628
10 TraesCS2D01G161900 chr1A 570974074 570975257 1183 True 544.500000 588 88.089000 1006 2227 2 chr1A.!!$R1 1221

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
326 338 0.032714 AGGTAGGGTCGGAGGTTACC 60.033 60.000 0.0 0.0 35.18 2.85 F
947 1027 0.035056 CATTCCCACACTCACCCCTC 60.035 60.000 0.0 0.0 0.00 4.30 F
2113 2379 1.470098 GCTGTCGAGCAATTCAATGGT 59.530 47.619 0.0 0.0 45.46 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1431 1550 0.248498 CATGCAATGCCGAGCAGAAG 60.248 55.0 1.53 0.0 43.65 2.85 R
2461 2730 0.535797 GTCCGGAGTTAACCCTGAGG 59.464 60.0 3.06 0.0 40.04 3.86 R
3361 3807 0.034186 GGATGCAGGGACCAATGACA 60.034 55.0 0.00 0.0 0.00 3.58 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
127 133 6.014156 AGAGAAAATCTTGTAGGTGTGCTAGT 60.014 38.462 0.00 0.00 32.99 2.57
136 142 4.283467 TGTAGGTGTGCTAGTCATGTCTTT 59.717 41.667 0.00 0.00 0.00 2.52
148 159 8.616076 GCTAGTCATGTCTTTTAGTATGCATTT 58.384 33.333 3.54 0.00 0.00 2.32
183 195 7.444183 AGACTTTTCGGAACTTTGTATCATTCA 59.556 33.333 0.00 0.00 0.00 2.57
184 196 7.936584 ACTTTTCGGAACTTTGTATCATTCAA 58.063 30.769 0.00 0.00 0.00 2.69
185 197 8.576442 ACTTTTCGGAACTTTGTATCATTCAAT 58.424 29.630 0.00 0.00 0.00 2.57
186 198 8.741101 TTTTCGGAACTTTGTATCATTCAATG 57.259 30.769 0.00 0.00 0.00 2.82
187 199 6.435430 TCGGAACTTTGTATCATTCAATGG 57.565 37.500 0.00 0.00 0.00 3.16
188 200 6.176896 TCGGAACTTTGTATCATTCAATGGA 58.823 36.000 0.00 0.00 0.00 3.41
189 201 6.828273 TCGGAACTTTGTATCATTCAATGGAT 59.172 34.615 0.00 0.00 0.00 3.41
190 202 7.339212 TCGGAACTTTGTATCATTCAATGGATT 59.661 33.333 0.00 0.00 0.00 3.01
191 203 7.975616 CGGAACTTTGTATCATTCAATGGATTT 59.024 33.333 0.00 0.00 0.00 2.17
195 207 8.917088 ACTTTGTATCATTCAATGGATTTAGGG 58.083 33.333 0.00 0.00 0.00 3.53
196 208 9.135189 CTTTGTATCATTCAATGGATTTAGGGA 57.865 33.333 0.00 0.00 0.00 4.20
197 209 9.659135 TTTGTATCATTCAATGGATTTAGGGAT 57.341 29.630 0.00 0.00 0.00 3.85
198 210 8.640063 TGTATCATTCAATGGATTTAGGGATG 57.360 34.615 0.00 0.00 0.00 3.51
199 211 6.600882 ATCATTCAATGGATTTAGGGATGC 57.399 37.500 0.00 0.00 0.00 3.91
200 212 5.456779 TCATTCAATGGATTTAGGGATGCA 58.543 37.500 0.00 0.00 0.00 3.96
201 213 5.898397 TCATTCAATGGATTTAGGGATGCAA 59.102 36.000 0.00 0.00 30.98 4.08
202 214 6.383436 TCATTCAATGGATTTAGGGATGCAAA 59.617 34.615 0.00 0.00 30.98 3.68
203 215 6.811634 TTCAATGGATTTAGGGATGCAAAT 57.188 33.333 0.00 0.00 30.98 2.32
204 216 6.811634 TCAATGGATTTAGGGATGCAAATT 57.188 33.333 0.00 0.00 30.98 1.82
205 217 7.197901 TCAATGGATTTAGGGATGCAAATTT 57.802 32.000 0.00 0.00 30.98 1.82
206 218 7.049133 TCAATGGATTTAGGGATGCAAATTTG 58.951 34.615 14.03 14.03 30.98 2.32
207 219 5.356291 TGGATTTAGGGATGCAAATTTGG 57.644 39.130 19.47 2.11 0.00 3.28
208 220 5.028802 TGGATTTAGGGATGCAAATTTGGA 58.971 37.500 19.47 17.40 0.00 3.53
209 221 5.486775 TGGATTTAGGGATGCAAATTTGGAA 59.513 36.000 16.71 0.00 30.51 3.53
210 222 5.817296 GGATTTAGGGATGCAAATTTGGAAC 59.183 40.000 16.71 13.58 30.51 3.62
211 223 4.817318 TTAGGGATGCAAATTTGGAACC 57.183 40.909 24.91 24.91 40.04 3.62
212 224 2.906568 AGGGATGCAAATTTGGAACCT 58.093 42.857 29.24 26.66 40.49 3.50
213 225 4.059773 AGGGATGCAAATTTGGAACCTA 57.940 40.909 29.24 4.32 40.49 3.08
214 226 4.623863 AGGGATGCAAATTTGGAACCTAT 58.376 39.130 29.24 19.47 40.49 2.57
215 227 5.776358 AGGGATGCAAATTTGGAACCTATA 58.224 37.500 29.24 0.00 40.49 1.31
216 228 5.835280 AGGGATGCAAATTTGGAACCTATAG 59.165 40.000 29.24 0.00 40.49 1.31
217 229 5.011023 GGGATGCAAATTTGGAACCTATAGG 59.989 44.000 29.24 17.73 40.49 2.57
218 230 5.011023 GGATGCAAATTTGGAACCTATAGGG 59.989 44.000 25.41 5.28 38.21 3.53
239 251 4.554683 GGTATCCTCCAACCCTACTTAGT 58.445 47.826 0.00 0.00 0.00 2.24
240 252 4.967442 GGTATCCTCCAACCCTACTTAGTT 59.033 45.833 0.00 0.00 0.00 2.24
241 253 5.070180 GGTATCCTCCAACCCTACTTAGTTC 59.930 48.000 0.00 0.00 0.00 3.01
242 254 4.136341 TCCTCCAACCCTACTTAGTTCA 57.864 45.455 0.00 0.00 0.00 3.18
243 255 4.495565 TCCTCCAACCCTACTTAGTTCAA 58.504 43.478 0.00 0.00 0.00 2.69
244 256 4.285260 TCCTCCAACCCTACTTAGTTCAAC 59.715 45.833 0.00 0.00 0.00 3.18
245 257 4.565028 CCTCCAACCCTACTTAGTTCAACC 60.565 50.000 0.00 0.00 0.00 3.77
246 258 3.975312 TCCAACCCTACTTAGTTCAACCA 59.025 43.478 0.00 0.00 0.00 3.67
247 259 4.412858 TCCAACCCTACTTAGTTCAACCAA 59.587 41.667 0.00 0.00 0.00 3.67
248 260 5.104024 TCCAACCCTACTTAGTTCAACCAAA 60.104 40.000 0.00 0.00 0.00 3.28
249 261 5.773176 CCAACCCTACTTAGTTCAACCAAAT 59.227 40.000 0.00 0.00 0.00 2.32
250 262 6.294508 CCAACCCTACTTAGTTCAACCAAATG 60.295 42.308 0.00 0.00 0.00 2.32
251 263 6.195600 ACCCTACTTAGTTCAACCAAATGA 57.804 37.500 0.00 0.00 0.00 2.57
252 264 6.607019 ACCCTACTTAGTTCAACCAAATGAA 58.393 36.000 0.00 0.00 36.99 2.57
264 276 8.925161 TTCAACCAAATGAACTAAGTTTTCAG 57.075 30.769 0.00 0.00 36.44 3.02
265 277 8.287439 TCAACCAAATGAACTAAGTTTTCAGA 57.713 30.769 0.00 0.00 36.44 3.27
266 278 8.744652 TCAACCAAATGAACTAAGTTTTCAGAA 58.255 29.630 0.00 0.00 36.44 3.02
267 279 9.364989 CAACCAAATGAACTAAGTTTTCAGAAA 57.635 29.630 0.00 0.00 36.44 2.52
269 281 9.533253 ACCAAATGAACTAAGTTTTCAGAAATG 57.467 29.630 0.00 0.00 36.44 2.32
270 282 8.981647 CCAAATGAACTAAGTTTTCAGAAATGG 58.018 33.333 0.00 0.00 36.44 3.16
271 283 8.981647 CAAATGAACTAAGTTTTCAGAAATGGG 58.018 33.333 0.00 0.00 36.44 4.00
272 284 6.648879 TGAACTAAGTTTTCAGAAATGGGG 57.351 37.500 0.00 0.00 0.00 4.96
273 285 6.133356 TGAACTAAGTTTTCAGAAATGGGGT 58.867 36.000 0.00 0.00 0.00 4.95
274 286 7.291566 TGAACTAAGTTTTCAGAAATGGGGTA 58.708 34.615 0.00 0.00 0.00 3.69
275 287 7.780745 TGAACTAAGTTTTCAGAAATGGGGTAA 59.219 33.333 0.00 0.00 0.00 2.85
276 288 8.541899 AACTAAGTTTTCAGAAATGGGGTAAA 57.458 30.769 0.00 0.00 0.00 2.01
277 289 8.721133 ACTAAGTTTTCAGAAATGGGGTAAAT 57.279 30.769 0.00 0.00 0.00 1.40
278 290 9.154632 ACTAAGTTTTCAGAAATGGGGTAAATT 57.845 29.630 0.00 0.00 0.00 1.82
279 291 9.639601 CTAAGTTTTCAGAAATGGGGTAAATTC 57.360 33.333 0.00 0.00 0.00 2.17
280 292 7.855784 AGTTTTCAGAAATGGGGTAAATTCT 57.144 32.000 0.00 0.00 32.55 2.40
281 293 7.670364 AGTTTTCAGAAATGGGGTAAATTCTG 58.330 34.615 7.80 7.80 46.36 3.02
291 303 9.448438 AAATGGGGTAAATTCTGAAAATTTAGC 57.552 29.630 17.67 17.67 43.95 3.09
292 304 7.790782 TGGGGTAAATTCTGAAAATTTAGCT 57.209 32.000 21.86 0.00 44.05 3.32
293 305 7.836842 TGGGGTAAATTCTGAAAATTTAGCTC 58.163 34.615 21.86 20.26 44.80 4.09
294 306 7.836842 GGGGTAAATTCTGAAAATTTAGCTCA 58.163 34.615 21.86 0.00 44.35 4.26
295 307 8.478066 GGGGTAAATTCTGAAAATTTAGCTCAT 58.522 33.333 21.86 0.00 44.35 2.90
296 308 9.875691 GGGTAAATTCTGAAAATTTAGCTCATT 57.124 29.630 21.86 0.00 44.05 2.57
310 322 9.740710 AATTTAGCTCATTTAGTTGAACTAGGT 57.259 29.630 5.10 3.82 31.47 3.08
312 324 9.871238 TTTAGCTCATTTAGTTGAACTAGGTAG 57.129 33.333 5.10 4.01 31.47 3.18
313 325 6.879400 AGCTCATTTAGTTGAACTAGGTAGG 58.121 40.000 5.10 0.00 31.47 3.18
314 326 6.049790 GCTCATTTAGTTGAACTAGGTAGGG 58.950 44.000 5.10 0.00 31.47 3.53
315 327 6.351966 GCTCATTTAGTTGAACTAGGTAGGGT 60.352 42.308 5.10 0.00 31.47 4.34
316 328 7.179076 TCATTTAGTTGAACTAGGTAGGGTC 57.821 40.000 5.10 0.00 31.47 4.46
317 329 5.649782 TTTAGTTGAACTAGGTAGGGTCG 57.350 43.478 5.10 0.00 31.47 4.79
318 330 2.454538 AGTTGAACTAGGTAGGGTCGG 58.545 52.381 0.00 0.00 0.00 4.79
319 331 2.042162 AGTTGAACTAGGTAGGGTCGGA 59.958 50.000 0.00 0.00 0.00 4.55
320 332 2.426381 GTTGAACTAGGTAGGGTCGGAG 59.574 54.545 0.00 0.00 0.00 4.63
321 333 1.064166 TGAACTAGGTAGGGTCGGAGG 60.064 57.143 0.00 0.00 0.00 4.30
322 334 1.006020 AACTAGGTAGGGTCGGAGGT 58.994 55.000 0.00 0.00 0.00 3.85
323 335 1.006020 ACTAGGTAGGGTCGGAGGTT 58.994 55.000 0.00 0.00 0.00 3.50
324 336 2.208872 ACTAGGTAGGGTCGGAGGTTA 58.791 52.381 0.00 0.00 0.00 2.85
325 337 2.092158 ACTAGGTAGGGTCGGAGGTTAC 60.092 54.545 0.00 0.00 0.00 2.50
326 338 0.032714 AGGTAGGGTCGGAGGTTACC 60.033 60.000 0.00 0.00 35.18 2.85
332 344 2.975732 GGTCGGAGGTTACCCTTTAG 57.024 55.000 0.00 0.00 42.86 1.85
333 345 1.483827 GGTCGGAGGTTACCCTTTAGG 59.516 57.143 0.00 0.00 42.86 2.69
346 358 4.615588 CCCTTTAGGTTCCAAATTTGCA 57.384 40.909 12.92 0.00 0.00 4.08
347 359 5.164620 CCCTTTAGGTTCCAAATTTGCAT 57.835 39.130 12.92 0.00 0.00 3.96
348 360 5.178061 CCCTTTAGGTTCCAAATTTGCATC 58.822 41.667 12.92 1.91 0.00 3.91
349 361 5.178061 CCTTTAGGTTCCAAATTTGCATCC 58.822 41.667 12.92 6.88 0.00 3.51
350 362 4.817318 TTAGGTTCCAAATTTGCATCCC 57.183 40.909 12.92 9.03 0.00 3.85
351 363 2.906568 AGGTTCCAAATTTGCATCCCT 58.093 42.857 12.92 10.99 0.00 4.20
352 364 4.059773 AGGTTCCAAATTTGCATCCCTA 57.940 40.909 12.92 0.00 0.00 3.53
510 551 8.539674 GTTTTTACCACTTTCAACAAGCTAATG 58.460 33.333 0.00 0.00 0.00 1.90
515 556 4.217118 CACTTTCAACAAGCTAATGCCTCT 59.783 41.667 0.00 0.00 40.80 3.69
519 560 6.500684 TTCAACAAGCTAATGCCTCTAAAG 57.499 37.500 0.00 0.00 40.80 1.85
590 631 3.955551 TCCCTTTTGTTTACCACTTCACC 59.044 43.478 0.00 0.00 0.00 4.02
613 654 1.895131 CCAGTTGCAGTGGGCTTTATT 59.105 47.619 8.95 0.00 45.15 1.40
644 718 8.458212 CAAGAATGCCTCTAAAAGAAACATTC 57.542 34.615 16.42 16.42 41.80 2.67
697 772 5.922053 TGCTAGTGCATTATCATGAAGTCT 58.078 37.500 0.00 0.00 45.31 3.24
698 773 7.054491 TGCTAGTGCATTATCATGAAGTCTA 57.946 36.000 0.00 0.00 45.31 2.59
780 858 3.006859 AGTTTCCAGCTAAACATTTGGCC 59.993 43.478 13.26 0.00 44.55 5.36
827 906 1.619363 CCCCTCTCATCCCAACCCA 60.619 63.158 0.00 0.00 0.00 4.51
930 1010 0.776080 AAACCCCCTCCACAGTCCAT 60.776 55.000 0.00 0.00 0.00 3.41
947 1027 0.035056 CATTCCCACACTCACCCCTC 60.035 60.000 0.00 0.00 0.00 4.30
1361 1455 6.516718 AGATGGTCGAGGTATAAATTGACAG 58.483 40.000 7.70 0.00 32.37 3.51
1367 1461 6.913673 GTCGAGGTATAAATTGACAGTCTCTC 59.086 42.308 1.31 0.00 31.29 3.20
1374 1468 2.423926 TTGACAGTCTCTCGTCTTGC 57.576 50.000 1.31 0.00 33.18 4.01
1393 1512 3.761897 TGCTACAAGTTGTAATGGGCTT 58.238 40.909 16.26 0.00 31.67 4.35
1402 1521 8.866093 ACAAGTTGTAATGGGCTTAAGTTAAAT 58.134 29.630 6.75 0.00 0.00 1.40
1454 1573 1.517694 GCTCGGCATTGCATGGTTG 60.518 57.895 11.39 0.00 0.00 3.77
1463 1591 3.559069 CATTGCATGGTTGGGATAGAGT 58.441 45.455 0.00 0.00 0.00 3.24
1470 1598 3.107601 TGGTTGGGATAGAGTCTTCAGG 58.892 50.000 0.00 0.00 0.00 3.86
1537 1665 3.563808 TGTGGAATTGTTGCTGTGTAGAC 59.436 43.478 0.00 0.00 0.00 2.59
1581 1716 5.813080 AGATACTGTAAATTGTTTCGGCC 57.187 39.130 0.00 0.00 0.00 6.13
1692 1958 5.106038 TGGACGTGGAGTTGTTATACTAGTG 60.106 44.000 5.39 0.00 0.00 2.74
1698 1964 7.479150 GTGGAGTTGTTATACTAGTGTAGGTC 58.521 42.308 5.39 0.00 31.51 3.85
1752 2018 5.453567 AAATGGTCTTGGCTTGAACTAAC 57.546 39.130 0.00 0.00 0.00 2.34
1773 2039 9.063615 ACTAACTTCGAATTGGTTCAGTAAATT 57.936 29.630 0.00 0.00 33.86 1.82
1786 2052 8.726988 TGGTTCAGTAAATTACTACAGCAAATC 58.273 33.333 5.23 0.00 37.23 2.17
2029 2295 5.196341 TCTTGCAGGTTGTATACGATAGG 57.804 43.478 0.00 0.00 43.77 2.57
2095 2361 2.359230 GAGGAAGTTGCTGCCGCT 60.359 61.111 0.00 0.00 33.44 5.52
2113 2379 1.470098 GCTGTCGAGCAATTCAATGGT 59.530 47.619 0.00 0.00 45.46 3.55
2294 2560 8.719560 ATGATGCTCATATATGTTCAGCTTAG 57.280 34.615 19.83 7.60 34.88 2.18
2332 2600 6.639632 TCTGATTTCCAGCATAATTAAGCC 57.360 37.500 8.99 0.00 42.62 4.35
2374 2643 7.014711 TGCTGATTGTTGGGACTATTTGTTTTA 59.985 33.333 0.00 0.00 0.00 1.52
2375 2644 7.542130 GCTGATTGTTGGGACTATTTGTTTTAG 59.458 37.037 0.00 0.00 0.00 1.85
2377 2646 8.573035 TGATTGTTGGGACTATTTGTTTTAGTC 58.427 33.333 2.90 2.90 43.11 2.59
2379 2648 7.504924 TGTTGGGACTATTTGTTTTAGTCTG 57.495 36.000 9.87 0.00 43.29 3.51
2380 2649 6.016610 TGTTGGGACTATTTGTTTTAGTCTGC 60.017 38.462 9.87 0.00 43.29 4.26
2461 2730 0.685660 AGACGTTCCAAGGAAGACCC 59.314 55.000 0.88 0.00 34.49 4.46
2698 2967 4.035102 GGCAGGTCGAGGGGCTTT 62.035 66.667 0.00 0.00 0.00 3.51
2707 2976 1.170290 CGAGGGGCTTTGGTTTCGTT 61.170 55.000 0.00 0.00 0.00 3.85
2725 2994 2.036475 CGTTACCTATGGCTCTGCTGAT 59.964 50.000 0.00 0.00 0.00 2.90
2740 3009 1.814394 GCTGATGAGGTCAACAATGCA 59.186 47.619 0.00 0.00 36.14 3.96
2746 3015 2.743664 TGAGGTCAACAATGCAATCTCG 59.256 45.455 0.00 0.00 0.00 4.04
2777 3046 3.795101 CGGCGTGGTAAGTTCTTGTATAG 59.205 47.826 0.00 0.00 0.00 1.31
2780 3049 6.510536 GGCGTGGTAAGTTCTTGTATAGTAT 58.489 40.000 0.00 0.00 0.00 2.12
2782 3051 8.137437 GGCGTGGTAAGTTCTTGTATAGTATTA 58.863 37.037 0.00 0.00 0.00 0.98
2794 3065 9.946165 TCTTGTATAGTATTATGTTCAGTGTCG 57.054 33.333 0.00 0.00 0.00 4.35
2804 3075 7.490962 TTATGTTCAGTGTCGAGTTTGAATT 57.509 32.000 8.19 3.84 32.76 2.17
2805 3076 5.155509 TGTTCAGTGTCGAGTTTGAATTG 57.844 39.130 8.19 0.00 32.76 2.32
2809 3080 6.912203 TCAGTGTCGAGTTTGAATTGTTTA 57.088 33.333 0.00 0.00 0.00 2.01
2835 3106 6.061441 TGTGAATTGTACAGTTCCTTCACAT 58.939 36.000 23.57 0.00 44.29 3.21
2864 3135 9.618890 TTTTCTGAATAGCTATGCTAATTCAGT 57.381 29.630 24.04 1.71 44.62 3.41
2870 3141 4.711399 AGCTATGCTAATTCAGTGCATGA 58.289 39.130 9.55 0.00 45.52 3.07
3046 3318 1.532921 CGCGGTTGATGAGAGAGACTC 60.533 57.143 0.00 0.00 45.11 3.36
3221 3495 1.753649 TGCTGTGTATGGCTCTCTCTC 59.246 52.381 0.00 0.00 0.00 3.20
3222 3496 2.031120 GCTGTGTATGGCTCTCTCTCT 58.969 52.381 0.00 0.00 0.00 3.10
3223 3497 3.218453 GCTGTGTATGGCTCTCTCTCTA 58.782 50.000 0.00 0.00 0.00 2.43
3224 3498 3.826157 GCTGTGTATGGCTCTCTCTCTAT 59.174 47.826 0.00 0.00 0.00 1.98
3228 3502 2.621556 ATGGCTCTCTCTCTATCCCC 57.378 55.000 0.00 0.00 0.00 4.81
3247 3521 2.559705 CCCCCTGGAAACTAAAATGCCT 60.560 50.000 0.00 0.00 0.00 4.75
3287 3732 7.612677 TGTCTTTTTCTAGATGAAGTCCCTAC 58.387 38.462 12.66 6.52 35.89 3.18
3293 3738 8.848474 TTTCTAGATGAAGTCCCTACTTTTTG 57.152 34.615 0.00 0.00 46.09 2.44
3294 3739 6.407202 TCTAGATGAAGTCCCTACTTTTTGC 58.593 40.000 0.00 0.00 46.09 3.68
3295 3740 4.985538 AGATGAAGTCCCTACTTTTTGCA 58.014 39.130 0.00 0.00 46.09 4.08
3299 3744 5.656480 TGAAGTCCCTACTTTTTGCAAAAC 58.344 37.500 23.79 10.84 46.09 2.43
3318 3764 7.011857 TGCAAAACAAAAACTCATAAATCCACC 59.988 33.333 0.00 0.00 0.00 4.61
3319 3765 7.563270 CAAAACAAAAACTCATAAATCCACCG 58.437 34.615 0.00 0.00 0.00 4.94
3326 3772 6.834168 AACTCATAAATCCACCGTGAATTT 57.166 33.333 1.10 1.10 0.00 1.82
3330 3776 5.356751 TCATAAATCCACCGTGAATTTCTGG 59.643 40.000 0.00 6.69 0.00 3.86
3335 3781 2.484264 CCACCGTGAATTTCTGGACTTC 59.516 50.000 13.10 0.00 0.00 3.01
3368 3814 8.519492 AAAATCTTAAATCCACGTTGTCATTG 57.481 30.769 0.00 0.00 0.00 2.82
3375 3829 0.874390 CACGTTGTCATTGGTCCCTG 59.126 55.000 0.00 0.00 0.00 4.45
3377 3831 0.888736 CGTTGTCATTGGTCCCTGCA 60.889 55.000 0.00 0.00 0.00 4.41
3409 3863 2.602738 GCGGTCAGCTCTGATGATG 58.397 57.895 2.62 0.00 42.18 3.07
3412 3866 0.103755 GGTCAGCTCTGATGATGCGA 59.896 55.000 2.62 0.00 42.18 5.10
3446 3900 3.570550 CGATGGTCTAACCCTCTTCCTAG 59.429 52.174 0.00 0.00 37.50 3.02
3580 4034 1.378514 AAGCGTCGCCATGGGAATT 60.379 52.632 15.13 0.00 0.00 2.17
3584 4038 0.461870 CGTCGCCATGGGAATTCAGA 60.462 55.000 15.13 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
127 133 7.936496 TCCAAATGCATACTAAAAGACATGA 57.064 32.000 0.00 0.00 0.00 3.07
136 142 5.880332 GTCTCAGGTTCCAAATGCATACTAA 59.120 40.000 0.00 0.00 0.00 2.24
148 159 2.043992 TCCGAAAAGTCTCAGGTTCCA 58.956 47.619 0.00 0.00 0.00 3.53
183 195 6.158344 TCCAAATTTGCATCCCTAAATCCATT 59.842 34.615 12.92 0.00 0.00 3.16
184 196 5.666718 TCCAAATTTGCATCCCTAAATCCAT 59.333 36.000 12.92 0.00 0.00 3.41
185 197 5.028802 TCCAAATTTGCATCCCTAAATCCA 58.971 37.500 12.92 0.00 0.00 3.41
186 198 5.612725 TCCAAATTTGCATCCCTAAATCC 57.387 39.130 12.92 0.00 0.00 3.01
187 199 5.817296 GGTTCCAAATTTGCATCCCTAAATC 59.183 40.000 12.92 0.00 0.00 2.17
188 200 5.488561 AGGTTCCAAATTTGCATCCCTAAAT 59.511 36.000 12.92 0.00 0.00 1.40
189 201 4.843516 AGGTTCCAAATTTGCATCCCTAAA 59.156 37.500 12.92 0.00 0.00 1.85
190 202 4.424842 AGGTTCCAAATTTGCATCCCTAA 58.575 39.130 12.92 0.00 0.00 2.69
191 203 4.059773 AGGTTCCAAATTTGCATCCCTA 57.940 40.909 12.92 0.00 0.00 3.53
192 204 2.906568 AGGTTCCAAATTTGCATCCCT 58.093 42.857 12.92 10.99 0.00 4.20
193 205 5.011023 CCTATAGGTTCCAAATTTGCATCCC 59.989 44.000 12.92 9.03 0.00 3.85
194 206 5.011023 CCCTATAGGTTCCAAATTTGCATCC 59.989 44.000 17.72 6.88 0.00 3.51
195 207 6.089249 CCCTATAGGTTCCAAATTTGCATC 57.911 41.667 17.72 1.91 0.00 3.91
217 229 4.554683 ACTAAGTAGGGTTGGAGGATACC 58.445 47.826 0.00 0.00 37.17 2.73
218 230 5.659971 TGAACTAAGTAGGGTTGGAGGATAC 59.340 44.000 0.00 0.00 0.00 2.24
219 231 5.845734 TGAACTAAGTAGGGTTGGAGGATA 58.154 41.667 0.00 0.00 0.00 2.59
220 232 4.695606 TGAACTAAGTAGGGTTGGAGGAT 58.304 43.478 0.00 0.00 0.00 3.24
221 233 4.136341 TGAACTAAGTAGGGTTGGAGGA 57.864 45.455 0.00 0.00 0.00 3.71
222 234 4.565028 GGTTGAACTAAGTAGGGTTGGAGG 60.565 50.000 0.00 0.00 0.00 4.30
223 235 4.041198 TGGTTGAACTAAGTAGGGTTGGAG 59.959 45.833 0.00 0.00 0.00 3.86
224 236 3.975312 TGGTTGAACTAAGTAGGGTTGGA 59.025 43.478 0.00 0.00 0.00 3.53
225 237 4.360951 TGGTTGAACTAAGTAGGGTTGG 57.639 45.455 0.00 0.00 0.00 3.77
226 238 6.488683 TCATTTGGTTGAACTAAGTAGGGTTG 59.511 38.462 0.00 0.00 0.00 3.77
227 239 6.607019 TCATTTGGTTGAACTAAGTAGGGTT 58.393 36.000 0.00 0.00 0.00 4.11
228 240 6.195600 TCATTTGGTTGAACTAAGTAGGGT 57.804 37.500 0.00 0.00 0.00 4.34
239 251 8.744652 TCTGAAAACTTAGTTCATTTGGTTGAA 58.255 29.630 0.00 0.00 34.59 2.69
240 252 8.287439 TCTGAAAACTTAGTTCATTTGGTTGA 57.713 30.769 0.00 0.00 34.59 3.18
241 253 8.925161 TTCTGAAAACTTAGTTCATTTGGTTG 57.075 30.769 0.00 0.00 34.59 3.77
243 255 9.533253 CATTTCTGAAAACTTAGTTCATTTGGT 57.467 29.630 6.95 0.00 34.59 3.67
244 256 8.981647 CCATTTCTGAAAACTTAGTTCATTTGG 58.018 33.333 6.95 1.98 34.59 3.28
245 257 8.981647 CCCATTTCTGAAAACTTAGTTCATTTG 58.018 33.333 6.95 0.00 34.59 2.32
246 258 8.150296 CCCCATTTCTGAAAACTTAGTTCATTT 58.850 33.333 6.95 0.00 34.59 2.32
247 259 7.290014 ACCCCATTTCTGAAAACTTAGTTCATT 59.710 33.333 6.95 0.00 34.59 2.57
248 260 6.782494 ACCCCATTTCTGAAAACTTAGTTCAT 59.218 34.615 6.95 0.00 34.59 2.57
249 261 6.133356 ACCCCATTTCTGAAAACTTAGTTCA 58.867 36.000 6.95 0.00 33.97 3.18
250 262 6.650427 ACCCCATTTCTGAAAACTTAGTTC 57.350 37.500 6.95 0.00 0.00 3.01
251 263 8.541899 TTTACCCCATTTCTGAAAACTTAGTT 57.458 30.769 6.95 0.00 0.00 2.24
252 264 8.721133 ATTTACCCCATTTCTGAAAACTTAGT 57.279 30.769 6.95 4.56 0.00 2.24
253 265 9.639601 GAATTTACCCCATTTCTGAAAACTTAG 57.360 33.333 6.95 0.00 0.00 2.18
254 266 9.374711 AGAATTTACCCCATTTCTGAAAACTTA 57.625 29.630 6.95 0.00 0.00 2.24
255 267 8.150296 CAGAATTTACCCCATTTCTGAAAACTT 58.850 33.333 6.95 0.00 44.97 2.66
256 268 7.508977 TCAGAATTTACCCCATTTCTGAAAACT 59.491 33.333 6.95 0.00 46.61 2.66
257 269 7.666623 TCAGAATTTACCCCATTTCTGAAAAC 58.333 34.615 6.95 0.00 46.61 2.43
258 270 7.847711 TCAGAATTTACCCCATTTCTGAAAA 57.152 32.000 6.95 0.00 46.61 2.29
262 274 9.506018 AAATTTTCAGAATTTACCCCATTTCTG 57.494 29.630 5.39 5.39 44.03 3.02
265 277 9.448438 GCTAAATTTTCAGAATTTACCCCATTT 57.552 29.630 0.00 0.00 32.64 2.32
266 278 8.825774 AGCTAAATTTTCAGAATTTACCCCATT 58.174 29.630 0.00 0.00 32.64 3.16
267 279 8.379428 AGCTAAATTTTCAGAATTTACCCCAT 57.621 30.769 0.00 0.00 32.64 4.00
268 280 7.453126 TGAGCTAAATTTTCAGAATTTACCCCA 59.547 33.333 0.00 0.00 32.64 4.96
269 281 7.836842 TGAGCTAAATTTTCAGAATTTACCCC 58.163 34.615 0.00 0.00 32.64 4.95
270 282 9.875691 AATGAGCTAAATTTTCAGAATTTACCC 57.124 29.630 0.00 0.00 32.64 3.69
284 296 9.740710 ACCTAGTTCAACTAAATGAGCTAAATT 57.259 29.630 0.00 0.00 40.92 1.82
286 298 9.871238 CTACCTAGTTCAACTAAATGAGCTAAA 57.129 33.333 0.00 0.00 40.92 1.85
287 299 8.475639 CCTACCTAGTTCAACTAAATGAGCTAA 58.524 37.037 0.00 0.00 40.92 3.09
288 300 7.069578 CCCTACCTAGTTCAACTAAATGAGCTA 59.930 40.741 0.00 1.82 40.69 3.32
289 301 6.127026 CCCTACCTAGTTCAACTAAATGAGCT 60.127 42.308 0.00 0.00 42.54 4.09
290 302 6.049790 CCCTACCTAGTTCAACTAAATGAGC 58.950 44.000 0.00 0.00 29.00 4.26
291 303 7.184067 ACCCTACCTAGTTCAACTAAATGAG 57.816 40.000 0.00 0.00 29.00 2.90
292 304 6.127535 CGACCCTACCTAGTTCAACTAAATGA 60.128 42.308 0.00 0.00 29.00 2.57
293 305 6.040878 CGACCCTACCTAGTTCAACTAAATG 58.959 44.000 0.00 0.00 29.00 2.32
294 306 5.128335 CCGACCCTACCTAGTTCAACTAAAT 59.872 44.000 0.00 0.00 29.00 1.40
295 307 4.463891 CCGACCCTACCTAGTTCAACTAAA 59.536 45.833 0.00 0.00 29.00 1.85
296 308 4.019174 CCGACCCTACCTAGTTCAACTAA 58.981 47.826 0.00 0.00 29.00 2.24
297 309 3.266772 TCCGACCCTACCTAGTTCAACTA 59.733 47.826 0.00 0.00 0.00 2.24
298 310 2.042162 TCCGACCCTACCTAGTTCAACT 59.958 50.000 0.00 0.00 0.00 3.16
299 311 2.426381 CTCCGACCCTACCTAGTTCAAC 59.574 54.545 0.00 0.00 0.00 3.18
300 312 2.622452 CCTCCGACCCTACCTAGTTCAA 60.622 54.545 0.00 0.00 0.00 2.69
301 313 1.064166 CCTCCGACCCTACCTAGTTCA 60.064 57.143 0.00 0.00 0.00 3.18
302 314 1.064091 ACCTCCGACCCTACCTAGTTC 60.064 57.143 0.00 0.00 0.00 3.01
303 315 1.006020 ACCTCCGACCCTACCTAGTT 58.994 55.000 0.00 0.00 0.00 2.24
304 316 1.006020 AACCTCCGACCCTACCTAGT 58.994 55.000 0.00 0.00 0.00 2.57
305 317 2.580962 GTAACCTCCGACCCTACCTAG 58.419 57.143 0.00 0.00 0.00 3.02
306 318 1.215423 GGTAACCTCCGACCCTACCTA 59.785 57.143 0.00 0.00 31.19 3.08
307 319 0.032714 GGTAACCTCCGACCCTACCT 60.033 60.000 0.00 0.00 31.19 3.08
308 320 2.509512 GGTAACCTCCGACCCTACC 58.490 63.158 0.00 0.00 0.00 3.18
325 337 4.615588 TGCAAATTTGGAACCTAAAGGG 57.384 40.909 19.47 0.00 40.27 3.95
326 338 5.178061 GGATGCAAATTTGGAACCTAAAGG 58.822 41.667 25.41 0.00 38.21 3.11
327 339 5.046376 AGGGATGCAAATTTGGAACCTAAAG 60.046 40.000 29.24 0.52 40.49 1.85
328 340 4.843516 AGGGATGCAAATTTGGAACCTAAA 59.156 37.500 29.24 0.00 40.49 1.85
329 341 4.424842 AGGGATGCAAATTTGGAACCTAA 58.575 39.130 29.24 0.00 40.49 2.69
330 342 4.059773 AGGGATGCAAATTTGGAACCTA 57.940 40.909 29.24 4.32 40.49 3.08
331 343 2.906568 AGGGATGCAAATTTGGAACCT 58.093 42.857 29.24 26.66 40.49 3.50
332 344 6.458210 CATATAGGGATGCAAATTTGGAACC 58.542 40.000 24.91 24.91 40.04 3.62
333 345 6.267471 TCCATATAGGGATGCAAATTTGGAAC 59.733 38.462 16.71 13.58 38.24 3.62
334 346 6.380414 TCCATATAGGGATGCAAATTTGGAA 58.620 36.000 16.71 0.00 38.24 3.53
335 347 5.963092 TCCATATAGGGATGCAAATTTGGA 58.037 37.500 19.47 17.40 38.24 3.53
336 348 6.862469 ATCCATATAGGGATGCAAATTTGG 57.138 37.500 17.94 0.00 45.90 3.28
337 349 7.673180 ACAATCCATATAGGGATGCAAATTTG 58.327 34.615 19.25 14.03 46.96 2.32
338 350 7.860649 ACAATCCATATAGGGATGCAAATTT 57.139 32.000 19.25 0.11 46.96 1.82
339 351 7.860649 AACAATCCATATAGGGATGCAAATT 57.139 32.000 19.25 7.23 46.96 1.82
340 352 7.860649 AAACAATCCATATAGGGATGCAAAT 57.139 32.000 19.25 0.71 46.96 2.32
341 353 8.805175 CATAAACAATCCATATAGGGATGCAAA 58.195 33.333 19.25 5.61 46.96 3.68
342 354 8.169393 TCATAAACAATCCATATAGGGATGCAA 58.831 33.333 19.25 4.96 46.96 4.08
343 355 7.697946 TCATAAACAATCCATATAGGGATGCA 58.302 34.615 19.25 4.30 46.96 3.96
344 356 8.627403 CATCATAAACAATCCATATAGGGATGC 58.373 37.037 19.25 0.00 46.96 3.91
345 357 9.690913 ACATCATAAACAATCCATATAGGGATG 57.309 33.333 19.25 14.82 46.96 3.51
347 359 8.889445 TGACATCATAAACAATCCATATAGGGA 58.111 33.333 8.88 8.88 42.21 4.20
348 360 9.519191 TTGACATCATAAACAATCCATATAGGG 57.481 33.333 0.00 0.00 38.24 3.53
352 364 9.139734 AGCTTTGACATCATAAACAATCCATAT 57.860 29.630 0.00 0.00 0.00 1.78
426 464 4.458397 AGATACATAGCAGCAGCACAAAT 58.542 39.130 3.17 0.00 45.49 2.32
510 551 6.387041 AGGTAAACACAAAACTTTAGAGGC 57.613 37.500 0.00 0.00 0.00 4.70
574 615 4.204012 CTGGAAGGTGAAGTGGTAAACAA 58.796 43.478 0.00 0.00 0.00 2.83
590 631 0.825010 AAGCCCACTGCAACTGGAAG 60.825 55.000 11.06 0.00 44.83 3.46
644 718 2.699954 AGCACCGGTATTCTTGTTGAG 58.300 47.619 6.87 0.00 0.00 3.02
657 731 1.715585 CAAGCATCGTTAGCACCGG 59.284 57.895 0.00 0.00 0.00 5.28
715 792 6.408434 GGAATTGGATGGGATAATGCAAACTT 60.408 38.462 0.00 0.00 40.63 2.66
718 795 4.967442 TGGAATTGGATGGGATAATGCAAA 59.033 37.500 0.00 0.00 40.63 3.68
719 796 4.554683 TGGAATTGGATGGGATAATGCAA 58.445 39.130 0.00 0.00 41.35 4.08
930 1010 1.846124 GGAGGGGTGAGTGTGGGAA 60.846 63.158 0.00 0.00 0.00 3.97
1361 1455 3.562567 ACTTGTAGCAAGACGAGAGAC 57.437 47.619 14.81 0.00 35.18 3.36
1367 1461 4.142902 CCCATTACAACTTGTAGCAAGACG 60.143 45.833 14.81 7.93 33.92 4.18
1374 1468 7.448748 AACTTAAGCCCATTACAACTTGTAG 57.551 36.000 1.29 0.00 33.92 2.74
1421 1540 4.320023 TGCCGAGCAGAAGTTTACAATTA 58.680 39.130 0.00 0.00 33.32 1.40
1423 1542 2.778299 TGCCGAGCAGAAGTTTACAAT 58.222 42.857 0.00 0.00 33.32 2.71
1425 1544 2.472695 ATGCCGAGCAGAAGTTTACA 57.527 45.000 4.90 0.00 43.65 2.41
1431 1550 0.248498 CATGCAATGCCGAGCAGAAG 60.248 55.000 1.53 0.00 43.65 2.85
1454 1573 2.962421 CTGACCCTGAAGACTCTATCCC 59.038 54.545 0.00 0.00 0.00 3.85
1463 1591 3.138283 ACAAAATGTCCTGACCCTGAAGA 59.862 43.478 0.00 0.00 0.00 2.87
1470 1598 4.097892 ACACTGAAACAAAATGTCCTGACC 59.902 41.667 0.00 0.00 0.00 4.02
1581 1716 7.091443 ACTGAACCAATTCGAACTTACTCTAG 58.909 38.462 0.00 0.00 37.69 2.43
1692 1958 7.095270 TCTTATCCTGAAGAAAAACGACCTAC 58.905 38.462 0.00 0.00 32.46 3.18
1752 2018 9.968743 GTAGTAATTTACTGAACCAATTCGAAG 57.031 33.333 17.47 0.00 39.81 3.79
1881 2147 3.192844 TCGAACTTAGTTCAAGCCGAGAT 59.807 43.478 22.70 0.00 42.05 2.75
2029 2295 4.570663 CGGCTCCGTCCGGTCATC 62.571 72.222 0.00 0.00 45.38 2.92
2095 2361 4.699735 ACATAACCATTGAATTGCTCGACA 59.300 37.500 0.00 0.00 0.00 4.35
2332 2600 2.543848 TCAGCAAAGTTCGCACTACAAG 59.456 45.455 0.00 0.00 30.68 3.16
2379 2648 3.689161 TCCAACAACTGCACTACATATGC 59.311 43.478 1.58 0.00 43.68 3.14
2380 2649 4.937620 ACTCCAACAACTGCACTACATATG 59.062 41.667 0.00 0.00 0.00 1.78
2438 2707 3.933332 GGTCTTCCTTGGAACGTCTAATG 59.067 47.826 0.00 0.00 0.00 1.90
2461 2730 0.535797 GTCCGGAGTTAACCCTGAGG 59.464 60.000 3.06 0.00 40.04 3.86
2695 2964 4.007659 AGCCATAGGTAACGAAACCAAAG 58.992 43.478 12.35 2.87 42.40 2.77
2698 2967 2.835764 AGAGCCATAGGTAACGAAACCA 59.164 45.455 12.35 1.16 42.40 3.67
2707 2976 2.896044 CTCATCAGCAGAGCCATAGGTA 59.104 50.000 0.00 0.00 0.00 3.08
2725 2994 2.743664 CGAGATTGCATTGTTGACCTCA 59.256 45.455 0.00 0.00 0.00 3.86
2777 3046 7.576750 TCAAACTCGACACTGAACATAATAC 57.423 36.000 0.00 0.00 0.00 1.89
2780 3049 7.011950 ACAATTCAAACTCGACACTGAACATAA 59.988 33.333 1.54 0.00 31.00 1.90
2782 3051 5.296780 ACAATTCAAACTCGACACTGAACAT 59.703 36.000 1.54 0.00 31.00 2.71
2804 3075 8.458573 AGGAACTGTACAATTCACATTAAACA 57.541 30.769 17.95 0.00 37.18 2.83
2805 3076 9.394477 GAAGGAACTGTACAATTCACATTAAAC 57.606 33.333 17.95 0.00 40.86 2.01
2809 3080 6.545666 TGTGAAGGAACTGTACAATTCACATT 59.454 34.615 22.78 14.31 46.79 2.71
2861 3132 5.181811 TCCTACAGAACAAAATCATGCACTG 59.818 40.000 0.00 0.00 34.88 3.66
2864 3135 4.458989 GGTCCTACAGAACAAAATCATGCA 59.541 41.667 0.00 0.00 29.87 3.96
2870 3141 4.566987 GTCGAGGTCCTACAGAACAAAAT 58.433 43.478 0.00 0.00 33.03 1.82
3046 3318 4.435425 TCCGGTATACAAATTCACTTCCG 58.565 43.478 0.00 0.00 36.00 4.30
3228 3502 4.399303 CAGTAGGCATTTTAGTTTCCAGGG 59.601 45.833 0.00 0.00 0.00 4.45
3230 3504 6.575162 AACAGTAGGCATTTTAGTTTCCAG 57.425 37.500 0.00 0.00 0.00 3.86
3231 3505 6.775629 AGAAACAGTAGGCATTTTAGTTTCCA 59.224 34.615 0.00 0.00 42.40 3.53
3232 3506 7.175119 AGAGAAACAGTAGGCATTTTAGTTTCC 59.825 37.037 0.00 0.00 42.40 3.13
3233 3507 8.017946 CAGAGAAACAGTAGGCATTTTAGTTTC 58.982 37.037 0.00 0.00 41.99 2.78
3234 3508 7.719633 TCAGAGAAACAGTAGGCATTTTAGTTT 59.280 33.333 0.00 0.00 0.00 2.66
3235 3509 7.224297 TCAGAGAAACAGTAGGCATTTTAGTT 58.776 34.615 0.00 0.00 0.00 2.24
3236 3510 6.769512 TCAGAGAAACAGTAGGCATTTTAGT 58.230 36.000 0.00 0.00 0.00 2.24
3237 3511 7.672983 TTCAGAGAAACAGTAGGCATTTTAG 57.327 36.000 0.00 0.00 0.00 1.85
3238 3512 7.665559 ACATTCAGAGAAACAGTAGGCATTTTA 59.334 33.333 0.00 0.00 0.00 1.52
3239 3513 6.491403 ACATTCAGAGAAACAGTAGGCATTTT 59.509 34.615 0.00 0.00 0.00 1.82
3240 3514 6.006449 ACATTCAGAGAAACAGTAGGCATTT 58.994 36.000 0.00 0.00 0.00 2.32
3247 3521 8.964476 AGAAAAAGACATTCAGAGAAACAGTA 57.036 30.769 0.00 0.00 0.00 2.74
3293 3738 7.351981 GGTGGATTTATGAGTTTTTGTTTTGC 58.648 34.615 0.00 0.00 0.00 3.68
3294 3739 7.223777 ACGGTGGATTTATGAGTTTTTGTTTTG 59.776 33.333 0.00 0.00 0.00 2.44
3295 3740 7.223777 CACGGTGGATTTATGAGTTTTTGTTTT 59.776 33.333 0.00 0.00 0.00 2.43
3299 3744 6.007936 TCACGGTGGATTTATGAGTTTTTG 57.992 37.500 8.50 0.00 0.00 2.44
3308 3754 5.357032 GTCCAGAAATTCACGGTGGATTTAT 59.643 40.000 23.73 19.23 39.47 1.40
3318 3764 4.222114 GCAAAGAAGTCCAGAAATTCACG 58.778 43.478 0.00 0.00 0.00 4.35
3319 3765 5.186996 TGCAAAGAAGTCCAGAAATTCAC 57.813 39.130 0.00 0.00 0.00 3.18
3346 3792 5.710099 ACCAATGACAACGTGGATTTAAGAT 59.290 36.000 0.00 0.00 0.00 2.40
3347 3793 5.067273 ACCAATGACAACGTGGATTTAAGA 58.933 37.500 0.00 0.00 0.00 2.10
3348 3794 5.371115 ACCAATGACAACGTGGATTTAAG 57.629 39.130 0.00 0.00 0.00 1.85
3349 3795 4.216687 GGACCAATGACAACGTGGATTTAA 59.783 41.667 0.00 0.00 0.00 1.52
3350 3796 3.754323 GGACCAATGACAACGTGGATTTA 59.246 43.478 0.00 0.00 0.00 1.40
3351 3797 2.556622 GGACCAATGACAACGTGGATTT 59.443 45.455 0.00 0.00 0.00 2.17
3355 3801 0.250727 AGGGACCAATGACAACGTGG 60.251 55.000 0.00 0.00 0.00 4.94
3356 3802 0.874390 CAGGGACCAATGACAACGTG 59.126 55.000 0.00 0.00 0.00 4.49
3358 3804 0.888736 TGCAGGGACCAATGACAACG 60.889 55.000 0.00 0.00 0.00 4.10
3359 3805 1.474077 GATGCAGGGACCAATGACAAC 59.526 52.381 0.00 0.00 0.00 3.32
3360 3806 1.616725 GGATGCAGGGACCAATGACAA 60.617 52.381 0.00 0.00 0.00 3.18
3361 3807 0.034186 GGATGCAGGGACCAATGACA 60.034 55.000 0.00 0.00 0.00 3.58
3362 3808 0.753111 GGGATGCAGGGACCAATGAC 60.753 60.000 0.00 0.00 0.00 3.06
3364 3810 1.825191 CGGGATGCAGGGACCAATG 60.825 63.158 0.00 0.00 0.00 2.82
3366 3812 2.933287 ACGGGATGCAGGGACCAA 60.933 61.111 0.00 0.00 0.00 3.67
3401 3855 1.325647 CGACTCGATCGCATCATCAG 58.674 55.000 11.09 3.00 45.52 2.90
3404 3858 1.135546 GATCCGACTCGATCGCATCAT 60.136 52.381 11.09 0.92 45.76 2.45
3446 3900 1.927895 AGAAGCGTTGATGATCGGAC 58.072 50.000 0.00 0.00 0.00 4.79
3529 3983 2.601314 CCAATGTCATGTACGTACACGG 59.399 50.000 29.54 23.22 44.95 4.94
3584 4038 2.765689 ATGCCCTAGACTAGCAGAGT 57.234 50.000 3.76 0.00 42.90 3.24
3729 4200 1.381056 AGAGGCGAGCTGATGGTCT 60.381 57.895 0.00 0.00 38.45 3.85


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

AutoCloner maintained by Alex Coulton.