Multiple sequence alignment - TraesCS5A01G537500

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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 TraesCS5A01G537500 chr5A 100.000 2195 0 0 1 2195 693882303 693880109 0.000000e+00 4054
1 TraesCS5A01G537500 chr6B 94.828 1218 56 4 886 2099 648850269 648851483 0.000000e+00 1893
2 TraesCS5A01G537500 chr6B 94.745 1218 58 3 886 2099 648886317 648887532 0.000000e+00 1890
3 TraesCS5A01G537500 chr6B 91.720 471 27 4 418 887 648849771 648850230 0.000000e+00 643
4 TraesCS5A01G537500 chr6B 91.083 471 30 4 418 887 648885819 648886278 5.140000e-176 627
5 TraesCS5A01G537500 chr6B 93.780 209 13 0 1 209 648849570 648849778 4.550000e-82 315
6 TraesCS5A01G537500 chr6B 93.780 209 12 1 1 209 648885619 648885826 1.640000e-81 313
7 TraesCS5A01G537500 chr5B 92.852 1315 71 7 885 2195 10496765 10498060 0.000000e+00 1886
8 TraesCS5A01G537500 chr5B 92.434 1282 89 4 886 2160 49392848 49394128 0.000000e+00 1823
9 TraesCS5A01G537500 chr5B 89.384 471 47 3 418 887 49392340 49392808 6.750000e-165 590
10 TraesCS5A01G537500 chr5B 89.362 470 41 3 418 887 10496267 10496727 1.130000e-162 582
11 TraesCS5A01G537500 chr5B 94.258 209 12 0 1 209 49392139 49392347 9.780000e-84 320
12 TraesCS5A01G537500 chr5B 93.301 209 12 1 1 209 10496068 10496274 7.610000e-80 307
13 TraesCS5A01G537500 chr3B 92.846 1314 69 7 886 2195 436377948 436376656 0.000000e+00 1882
14 TraesCS5A01G537500 chr3B 94.499 1218 62 3 886 2099 21575111 21573895 0.000000e+00 1873
15 TraesCS5A01G537500 chr3B 90.506 474 33 5 421 893 21575606 21575144 1.110000e-172 616
16 TraesCS5A01G537500 chr3B 94.521 219 11 1 205 422 456109560 456109778 9.710000e-89 337
17 TraesCS5A01G537500 chr3B 93.780 209 12 1 1 209 21575809 21575602 1.640000e-81 313
18 TraesCS5A01G537500 chr4B 92.471 1315 65 14 886 2195 560024090 560022805 0.000000e+00 1849
19 TraesCS5A01G537500 chr4B 93.837 1217 72 2 886 2099 108080007 108081223 0.000000e+00 1829
20 TraesCS5A01G537500 chr4B 91.144 1276 104 5 886 2156 222963441 222964712 0.000000e+00 1722
21 TraesCS5A01G537500 chr4B 90.446 471 33 4 418 887 108079509 108079968 5.180000e-171 610
22 TraesCS5A01G537500 chr4B 93.780 209 13 0 1 209 108079308 108079516 4.550000e-82 315
23 TraesCS5A01G537500 chr2B 91.933 1314 83 6 886 2195 22381139 22382433 0.000000e+00 1818
24 TraesCS5A01G537500 chr2B 90.105 475 41 3 418 887 311834326 311834799 1.440000e-171 612
25 TraesCS5A01G537500 chr2B 93.301 209 13 1 1 209 22380456 22380663 7.610000e-80 307
26 TraesCS5A01G537500 chr1B 90.486 473 45 0 421 893 92853599 92853127 1.850000e-175 625
27 TraesCS5A01G537500 chr1B 92.823 209 13 2 1 209 92853801 92853595 3.540000e-78 302
28 TraesCS5A01G537500 chr1B 92.823 209 14 1 1 209 678498973 678499180 3.540000e-78 302
29 TraesCS5A01G537500 chr7B 89.384 471 44 2 418 887 101714846 101715311 2.430000e-164 588
30 TraesCS5A01G537500 chr7B 94.170 223 12 1 203 424 648055895 648055673 2.700000e-89 339
31 TraesCS5A01G537500 chr6D 94.273 227 12 1 203 428 469559270 469559044 1.610000e-91 346
32 TraesCS5A01G537500 chr4D 94.595 222 10 2 202 422 87544255 87544035 2.090000e-90 342
33 TraesCS5A01G537500 chr3D 93.860 228 13 1 205 431 554681772 554681545 2.090000e-90 342
34 TraesCS5A01G537500 chr5D 93.363 226 14 1 205 429 439659561 439659336 1.260000e-87 333
35 TraesCS5A01G537500 chr2A 93.013 229 13 3 201 427 141901025 141901252 4.520000e-87 331
36 TraesCS5A01G537500 chrUn 91.176 238 20 1 201 437 192573083 192573320 2.720000e-84 322
37 TraesCS5A01G537500 chrUn 91.489 235 19 1 204 437 339572351 339572117 2.720000e-84 322


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 TraesCS5A01G537500 chr5A 693880109 693882303 2194 True 4054.000000 4054 100.000000 1 2195 1 chr5A.!!$R1 2194
1 TraesCS5A01G537500 chr6B 648849570 648851483 1913 False 950.333333 1893 93.442667 1 2099 3 chr6B.!!$F1 2098
2 TraesCS5A01G537500 chr6B 648885619 648887532 1913 False 943.333333 1890 93.202667 1 2099 3 chr6B.!!$F2 2098
3 TraesCS5A01G537500 chr5B 10496068 10498060 1992 False 925.000000 1886 91.838333 1 2195 3 chr5B.!!$F1 2194
4 TraesCS5A01G537500 chr5B 49392139 49394128 1989 False 911.000000 1823 92.025333 1 2160 3 chr5B.!!$F2 2159
5 TraesCS5A01G537500 chr3B 436376656 436377948 1292 True 1882.000000 1882 92.846000 886 2195 1 chr3B.!!$R1 1309
6 TraesCS5A01G537500 chr3B 21573895 21575809 1914 True 934.000000 1873 92.928333 1 2099 3 chr3B.!!$R2 2098
7 TraesCS5A01G537500 chr4B 560022805 560024090 1285 True 1849.000000 1849 92.471000 886 2195 1 chr4B.!!$R1 1309
8 TraesCS5A01G537500 chr4B 222963441 222964712 1271 False 1722.000000 1722 91.144000 886 2156 1 chr4B.!!$F1 1270
9 TraesCS5A01G537500 chr4B 108079308 108081223 1915 False 918.000000 1829 92.687667 1 2099 3 chr4B.!!$F2 2098
10 TraesCS5A01G537500 chr2B 22380456 22382433 1977 False 1062.500000 1818 92.617000 1 2195 2 chr2B.!!$F2 2194
11 TraesCS5A01G537500 chr1B 92853127 92853801 674 True 463.500000 625 91.654500 1 893 2 chr1B.!!$R1 892

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
244 247 0.102481 CAAGTCCTGCGCGTATACCT 59.898 55.0 8.43 0.00 0.0 3.08 F
248 251 0.179009 TCCTGCGCGTATACCTAGGT 60.179 55.0 20.57 20.57 0.0 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1121 1176 0.540133 GGAGGAGGGATAGGACGACC 60.540 65.0 0.0 0.0 0.00 4.79 R
1669 1731 1.225376 ACGAAATTCTGCGTTGCCGA 61.225 50.0 0.0 0.0 37.48 5.54 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
53 54 1.377725 CAGCGTGGGAATGGAAGCT 60.378 57.895 0.00 0.00 35.06 3.74
55 56 2.409870 GCGTGGGAATGGAAGCTGG 61.410 63.158 0.00 0.00 0.00 4.85
156 158 7.014038 CGTTCCCACACTACTACTAAATATCCT 59.986 40.741 0.00 0.00 0.00 3.24
196 199 6.063404 AGTAGTAGCGAGGAGTATAAAAGCT 58.937 40.000 0.00 0.00 37.27 3.74
204 207 3.385111 AGGAGTATAAAAGCTGCGCTACT 59.615 43.478 9.73 5.05 38.25 2.57
205 208 4.583489 AGGAGTATAAAAGCTGCGCTACTA 59.417 41.667 9.73 0.00 38.25 1.82
206 209 4.680567 GGAGTATAAAAGCTGCGCTACTAC 59.319 45.833 9.73 1.96 38.25 2.73
207 210 5.507650 GGAGTATAAAAGCTGCGCTACTACT 60.508 44.000 9.73 5.67 38.25 2.57
208 211 6.293845 GGAGTATAAAAGCTGCGCTACTACTA 60.294 42.308 9.73 1.65 38.25 1.82
209 212 6.437094 AGTATAAAAGCTGCGCTACTACTAC 58.563 40.000 9.73 6.23 38.25 2.73
210 213 2.580966 AAAGCTGCGCTACTACTACC 57.419 50.000 9.73 0.00 38.25 3.18
211 214 1.765230 AAGCTGCGCTACTACTACCT 58.235 50.000 9.73 0.00 38.25 3.08
212 215 1.310904 AGCTGCGCTACTACTACCTC 58.689 55.000 9.73 0.00 36.99 3.85
213 216 0.311477 GCTGCGCTACTACTACCTCC 59.689 60.000 9.73 0.00 0.00 4.30
214 217 0.587285 CTGCGCTACTACTACCTCCG 59.413 60.000 9.73 0.00 0.00 4.63
215 218 0.107508 TGCGCTACTACTACCTCCGT 60.108 55.000 9.73 0.00 0.00 4.69
216 219 1.020437 GCGCTACTACTACCTCCGTT 58.980 55.000 0.00 0.00 0.00 4.44
217 220 1.403323 GCGCTACTACTACCTCCGTTT 59.597 52.381 0.00 0.00 0.00 3.60
218 221 2.540565 GCGCTACTACTACCTCCGTTTC 60.541 54.545 0.00 0.00 0.00 2.78
219 222 2.679837 CGCTACTACTACCTCCGTTTCA 59.320 50.000 0.00 0.00 0.00 2.69
220 223 3.242673 CGCTACTACTACCTCCGTTTCAG 60.243 52.174 0.00 0.00 0.00 3.02
221 224 3.693578 GCTACTACTACCTCCGTTTCAGT 59.306 47.826 0.00 0.00 0.00 3.41
222 225 4.157472 GCTACTACTACCTCCGTTTCAGTT 59.843 45.833 0.00 0.00 0.00 3.16
223 226 5.336293 GCTACTACTACCTCCGTTTCAGTTT 60.336 44.000 0.00 0.00 0.00 2.66
224 227 6.127897 GCTACTACTACCTCCGTTTCAGTTTA 60.128 42.308 0.00 0.00 0.00 2.01
225 228 6.018589 ACTACTACCTCCGTTTCAGTTTAC 57.981 41.667 0.00 0.00 0.00 2.01
226 229 4.942761 ACTACCTCCGTTTCAGTTTACA 57.057 40.909 0.00 0.00 0.00 2.41
227 230 5.280654 ACTACCTCCGTTTCAGTTTACAA 57.719 39.130 0.00 0.00 0.00 2.41
228 231 5.295152 ACTACCTCCGTTTCAGTTTACAAG 58.705 41.667 0.00 0.00 0.00 3.16
229 232 4.146745 ACCTCCGTTTCAGTTTACAAGT 57.853 40.909 0.00 0.00 0.00 3.16
230 233 4.124970 ACCTCCGTTTCAGTTTACAAGTC 58.875 43.478 0.00 0.00 0.00 3.01
231 234 3.497262 CCTCCGTTTCAGTTTACAAGTCC 59.503 47.826 0.00 0.00 0.00 3.85
232 235 4.377897 CTCCGTTTCAGTTTACAAGTCCT 58.622 43.478 0.00 0.00 0.00 3.85
233 236 4.124238 TCCGTTTCAGTTTACAAGTCCTG 58.876 43.478 0.00 0.00 0.00 3.86
234 237 3.303791 CCGTTTCAGTTTACAAGTCCTGC 60.304 47.826 0.00 0.00 0.00 4.85
235 238 3.603857 CGTTTCAGTTTACAAGTCCTGCG 60.604 47.826 0.00 0.00 0.00 5.18
236 239 1.508632 TCAGTTTACAAGTCCTGCGC 58.491 50.000 0.00 0.00 0.00 6.09
237 240 0.163788 CAGTTTACAAGTCCTGCGCG 59.836 55.000 0.00 0.00 0.00 6.86
238 241 0.249741 AGTTTACAAGTCCTGCGCGT 60.250 50.000 8.43 0.00 0.00 6.01
239 242 1.000060 AGTTTACAAGTCCTGCGCGTA 60.000 47.619 8.43 0.71 0.00 4.42
240 243 1.997606 GTTTACAAGTCCTGCGCGTAT 59.002 47.619 8.43 0.00 0.00 3.06
241 244 3.119388 AGTTTACAAGTCCTGCGCGTATA 60.119 43.478 8.43 0.00 0.00 1.47
242 245 2.480224 TACAAGTCCTGCGCGTATAC 57.520 50.000 8.43 4.74 0.00 1.47
243 246 0.179119 ACAAGTCCTGCGCGTATACC 60.179 55.000 8.43 0.00 0.00 2.73
244 247 0.102481 CAAGTCCTGCGCGTATACCT 59.898 55.000 8.43 0.00 0.00 3.08
245 248 1.335810 CAAGTCCTGCGCGTATACCTA 59.664 52.381 8.43 0.00 0.00 3.08
246 249 1.236628 AGTCCTGCGCGTATACCTAG 58.763 55.000 8.43 0.00 0.00 3.02
247 250 0.240411 GTCCTGCGCGTATACCTAGG 59.760 60.000 7.41 7.41 0.00 3.02
248 251 0.179009 TCCTGCGCGTATACCTAGGT 60.179 55.000 20.57 20.57 0.00 3.08
249 252 0.672342 CCTGCGCGTATACCTAGGTT 59.328 55.000 22.11 10.62 0.00 3.50
250 253 1.602165 CCTGCGCGTATACCTAGGTTG 60.602 57.143 22.11 9.15 0.00 3.77
251 254 0.249155 TGCGCGTATACCTAGGTTGC 60.249 55.000 22.11 17.41 0.00 4.17
252 255 0.249155 GCGCGTATACCTAGGTTGCA 60.249 55.000 22.11 1.66 0.00 4.08
253 256 1.803625 GCGCGTATACCTAGGTTGCAA 60.804 52.381 22.11 1.21 0.00 4.08
254 257 2.750948 CGCGTATACCTAGGTTGCAAT 58.249 47.619 22.11 10.05 0.00 3.56
255 258 3.128349 CGCGTATACCTAGGTTGCAATT 58.872 45.455 22.11 0.00 0.00 2.32
256 259 3.558418 CGCGTATACCTAGGTTGCAATTT 59.442 43.478 22.11 0.00 0.00 1.82
257 260 4.034742 CGCGTATACCTAGGTTGCAATTTT 59.965 41.667 22.11 0.00 0.00 1.82
258 261 5.234757 CGCGTATACCTAGGTTGCAATTTTA 59.765 40.000 22.11 0.00 0.00 1.52
259 262 6.073440 CGCGTATACCTAGGTTGCAATTTTAT 60.073 38.462 22.11 6.50 0.00 1.40
260 263 7.116662 CGCGTATACCTAGGTTGCAATTTTATA 59.883 37.037 22.11 5.43 0.00 0.98
261 264 8.776470 GCGTATACCTAGGTTGCAATTTTATAA 58.224 33.333 22.11 0.00 0.00 0.98
264 267 6.785337 ACCTAGGTTGCAATTTTATAACCC 57.215 37.500 9.21 0.00 42.71 4.11
265 268 6.499436 ACCTAGGTTGCAATTTTATAACCCT 58.501 36.000 9.21 3.39 42.71 4.34
266 269 7.645002 ACCTAGGTTGCAATTTTATAACCCTA 58.355 34.615 9.21 4.48 42.71 3.53
267 270 8.117312 ACCTAGGTTGCAATTTTATAACCCTAA 58.883 33.333 9.21 0.00 42.71 2.69
268 271 9.143155 CCTAGGTTGCAATTTTATAACCCTAAT 57.857 33.333 0.59 0.00 42.71 1.73
318 321 9.720769 ATATCTTTTGAAAGTAGAAACTCCGAA 57.279 29.630 3.63 0.00 37.31 4.30
319 322 7.478520 TCTTTTGAAAGTAGAAACTCCGAAG 57.521 36.000 3.63 0.00 37.31 3.79
320 323 7.046033 TCTTTTGAAAGTAGAAACTCCGAAGT 58.954 34.615 3.63 0.00 37.31 3.01
321 324 7.551617 TCTTTTGAAAGTAGAAACTCCGAAGTT 59.448 33.333 3.63 0.00 40.87 2.66
336 339 9.457436 AACTCCGAAGTTTATGTTGGTATATTT 57.543 29.630 0.00 0.00 43.28 1.40
337 340 9.457436 ACTCCGAAGTTTATGTTGGTATATTTT 57.543 29.630 0.00 0.00 28.74 1.82
390 393 7.174082 GTCAAATTGACAATCTAGAAGTACGC 58.826 38.462 20.08 0.00 46.22 4.42
391 394 5.950965 AATTGACAATCTAGAAGTACGCG 57.049 39.130 3.53 3.53 0.00 6.01
392 395 2.793933 TGACAATCTAGAAGTACGCGC 58.206 47.619 5.73 0.00 0.00 6.86
393 396 2.162809 TGACAATCTAGAAGTACGCGCA 59.837 45.455 5.73 0.00 0.00 6.09
394 397 3.181490 TGACAATCTAGAAGTACGCGCAT 60.181 43.478 5.73 0.00 0.00 4.73
395 398 3.116300 ACAATCTAGAAGTACGCGCATG 58.884 45.455 5.73 0.00 0.00 4.06
396 399 1.772182 ATCTAGAAGTACGCGCATGC 58.228 50.000 5.73 7.91 37.91 4.06
397 400 0.248907 TCTAGAAGTACGCGCATGCC 60.249 55.000 13.15 3.98 38.08 4.40
398 401 1.215655 CTAGAAGTACGCGCATGCCC 61.216 60.000 13.15 1.12 38.08 5.36
399 402 1.672854 TAGAAGTACGCGCATGCCCT 61.673 55.000 13.15 0.00 38.08 5.19
400 403 2.813179 GAAGTACGCGCATGCCCTG 61.813 63.158 13.15 4.41 38.08 4.45
401 404 3.605749 AAGTACGCGCATGCCCTGT 62.606 57.895 13.15 10.60 38.08 4.00
402 405 2.202824 GTACGCGCATGCCCTGTA 60.203 61.111 13.15 9.55 38.08 2.74
403 406 1.812093 GTACGCGCATGCCCTGTAA 60.812 57.895 13.15 0.00 38.08 2.41
404 407 1.079057 TACGCGCATGCCCTGTAAA 60.079 52.632 13.15 0.00 38.08 2.01
405 408 1.363145 TACGCGCATGCCCTGTAAAC 61.363 55.000 13.15 0.00 38.08 2.01
406 409 2.398554 CGCGCATGCCCTGTAAACT 61.399 57.895 13.15 0.00 38.08 2.66
407 410 1.087202 CGCGCATGCCCTGTAAACTA 61.087 55.000 13.15 0.00 38.08 2.24
408 411 1.091537 GCGCATGCCCTGTAAACTAA 58.908 50.000 13.15 0.00 33.98 2.24
409 412 1.202143 GCGCATGCCCTGTAAACTAAC 60.202 52.381 13.15 0.00 33.98 2.34
410 413 2.080693 CGCATGCCCTGTAAACTAACA 58.919 47.619 13.15 0.00 0.00 2.41
411 414 2.095853 CGCATGCCCTGTAAACTAACAG 59.904 50.000 13.15 0.00 45.33 3.16
567 570 1.282157 GCACCACAACCTTATCTCCCT 59.718 52.381 0.00 0.00 0.00 4.20
585 588 4.938756 TGTCCCTTGCCCCACCCT 62.939 66.667 0.00 0.00 0.00 4.34
647 650 3.420482 CCTCCTCCGCCCCCAAAT 61.420 66.667 0.00 0.00 0.00 2.32
653 656 4.418328 CCGCCCCCAAATGACGGA 62.418 66.667 0.00 0.00 46.71 4.69
717 720 0.453793 CCAGCTCATCTTCTCGTCGT 59.546 55.000 0.00 0.00 0.00 4.34
863 868 4.853142 TCCATCCCTAGCCGCGGT 62.853 66.667 28.70 16.08 0.00 5.68
919 965 5.351948 AAGTAGCATCTTCTTCTTCCTCC 57.648 43.478 0.00 0.00 0.00 4.30
977 1031 3.209097 GCGTGGTTGTGTGCAGGT 61.209 61.111 0.00 0.00 0.00 4.00
991 1045 2.054799 TGCAGGTAGTTGAAGGAAGGT 58.945 47.619 0.00 0.00 0.00 3.50
994 1049 2.372172 CAGGTAGTTGAAGGAAGGTGGT 59.628 50.000 0.00 0.00 0.00 4.16
1166 1221 1.132640 GTTACTGGAAGCAAGCGCG 59.867 57.895 0.00 0.00 45.49 6.86
1261 1317 2.546778 GTTTCTCTGTTCACCGACACA 58.453 47.619 0.00 0.00 0.00 3.72
1271 1328 4.920112 CCGACACACCCACGGCAA 62.920 66.667 0.00 0.00 40.19 4.52
1457 1514 7.154656 TGCTTCAAGTACTAGCATATGTATGG 58.845 38.462 13.61 0.00 39.79 2.74
1573 1632 5.072040 ACGTAGTGACATGTGATTCATCA 57.928 39.130 1.15 0.00 42.51 3.07
1624 1686 4.027674 ACTCTAAGTGACTCTGCTCTCA 57.972 45.455 0.00 0.00 0.00 3.27
1631 1693 1.228583 ACTCTGCTCTCACCGTCCA 60.229 57.895 0.00 0.00 0.00 4.02
1756 1818 2.839486 AGTAGCAGCAGCACAAGTAA 57.161 45.000 3.17 0.00 45.49 2.24
1794 1856 7.749570 CAGATTTCTCACTTGTGCAAAGAATAG 59.250 37.037 13.35 8.43 0.00 1.73
2052 2115 4.754618 GCCTGAATTTAAAGTGGTTTTGGG 59.245 41.667 0.00 0.00 0.00 4.12
2053 2116 5.686387 GCCTGAATTTAAAGTGGTTTTGGGT 60.686 40.000 0.00 0.00 0.00 4.51
2156 2219 5.464030 AGTTCAGTAAATGTGTACGTCCT 57.536 39.130 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 79 0.816421 AGCGCACTGTTTTTACCCGT 60.816 50.000 11.47 0.00 0.00 5.28
156 158 4.537945 ACTACTATAAGCTGTCCTGGGA 57.462 45.455 0.00 0.00 0.00 4.37
196 199 0.107508 ACGGAGGTAGTAGTAGCGCA 60.108 55.000 11.47 0.00 0.00 6.09
204 207 6.040842 ACTTGTAAACTGAAACGGAGGTAGTA 59.959 38.462 0.00 0.00 0.00 1.82
205 208 4.942761 TGTAAACTGAAACGGAGGTAGT 57.057 40.909 0.00 0.00 0.00 2.73
206 209 5.295152 ACTTGTAAACTGAAACGGAGGTAG 58.705 41.667 0.00 0.00 0.00 3.18
207 210 5.280654 ACTTGTAAACTGAAACGGAGGTA 57.719 39.130 0.00 0.00 0.00 3.08
208 211 4.124970 GACTTGTAAACTGAAACGGAGGT 58.875 43.478 0.00 0.00 0.00 3.85
209 212 3.497262 GGACTTGTAAACTGAAACGGAGG 59.503 47.826 0.00 0.00 0.00 4.30
210 213 4.211374 CAGGACTTGTAAACTGAAACGGAG 59.789 45.833 0.00 0.00 32.86 4.63
211 214 4.124238 CAGGACTTGTAAACTGAAACGGA 58.876 43.478 0.00 0.00 32.86 4.69
212 215 3.303791 GCAGGACTTGTAAACTGAAACGG 60.304 47.826 0.00 0.00 32.86 4.44
213 216 3.603857 CGCAGGACTTGTAAACTGAAACG 60.604 47.826 0.00 0.00 32.86 3.60
214 217 3.848554 GCGCAGGACTTGTAAACTGAAAC 60.849 47.826 0.30 0.00 32.86 2.78
215 218 2.289547 GCGCAGGACTTGTAAACTGAAA 59.710 45.455 0.30 0.00 32.86 2.69
216 219 1.871039 GCGCAGGACTTGTAAACTGAA 59.129 47.619 0.30 0.00 32.86 3.02
217 220 1.508632 GCGCAGGACTTGTAAACTGA 58.491 50.000 0.30 0.00 32.86 3.41
218 221 0.163788 CGCGCAGGACTTGTAAACTG 59.836 55.000 8.75 0.00 0.00 3.16
219 222 0.249741 ACGCGCAGGACTTGTAAACT 60.250 50.000 5.73 0.00 0.00 2.66
220 223 1.421382 TACGCGCAGGACTTGTAAAC 58.579 50.000 5.73 0.00 0.00 2.01
221 224 2.373540 ATACGCGCAGGACTTGTAAA 57.626 45.000 5.73 0.00 0.00 2.01
222 225 2.480073 GGTATACGCGCAGGACTTGTAA 60.480 50.000 5.73 0.00 0.00 2.41
223 226 1.066002 GGTATACGCGCAGGACTTGTA 59.934 52.381 5.73 0.00 0.00 2.41
224 227 0.179119 GGTATACGCGCAGGACTTGT 60.179 55.000 5.73 0.00 0.00 3.16
225 228 0.102481 AGGTATACGCGCAGGACTTG 59.898 55.000 5.73 0.00 0.00 3.16
226 229 1.607628 CTAGGTATACGCGCAGGACTT 59.392 52.381 5.73 0.00 0.00 3.01
227 230 1.236628 CTAGGTATACGCGCAGGACT 58.763 55.000 5.73 1.68 0.00 3.85
228 231 0.240411 CCTAGGTATACGCGCAGGAC 59.760 60.000 5.73 0.00 0.00 3.85
229 232 0.179009 ACCTAGGTATACGCGCAGGA 60.179 55.000 14.41 0.00 0.00 3.86
230 233 0.672342 AACCTAGGTATACGCGCAGG 59.328 55.000 16.67 6.39 0.00 4.85
231 234 1.767289 CAACCTAGGTATACGCGCAG 58.233 55.000 16.67 2.42 0.00 5.18
232 235 0.249155 GCAACCTAGGTATACGCGCA 60.249 55.000 16.67 0.00 0.00 6.09
233 236 0.249155 TGCAACCTAGGTATACGCGC 60.249 55.000 16.67 11.52 0.00 6.86
234 237 2.212869 TTGCAACCTAGGTATACGCG 57.787 50.000 16.67 3.53 0.00 6.01
235 238 5.494632 AAAATTGCAACCTAGGTATACGC 57.505 39.130 16.67 15.74 0.00 4.42
238 241 9.577222 GGGTTATAAAATTGCAACCTAGGTATA 57.423 33.333 16.67 2.90 40.27 1.47
239 242 8.286620 AGGGTTATAAAATTGCAACCTAGGTAT 58.713 33.333 16.67 1.27 40.27 2.73
240 243 7.645002 AGGGTTATAAAATTGCAACCTAGGTA 58.355 34.615 16.67 0.00 40.27 3.08
241 244 6.499436 AGGGTTATAAAATTGCAACCTAGGT 58.501 36.000 9.21 9.21 40.27 3.08
242 245 8.528044 TTAGGGTTATAAAATTGCAACCTAGG 57.472 34.615 7.41 7.41 40.27 3.02
292 295 9.720769 TTCGGAGTTTCTACTTTCAAAAGATAT 57.279 29.630 9.39 0.00 39.31 1.63
293 296 9.204570 CTTCGGAGTTTCTACTTTCAAAAGATA 57.795 33.333 9.39 0.00 39.31 1.98
294 297 7.715686 ACTTCGGAGTTTCTACTTTCAAAAGAT 59.284 33.333 9.39 0.00 34.40 2.40
295 298 7.046033 ACTTCGGAGTTTCTACTTTCAAAAGA 58.954 34.615 9.39 0.00 34.40 2.52
296 299 7.247929 ACTTCGGAGTTTCTACTTTCAAAAG 57.752 36.000 0.00 0.97 35.92 2.27
297 300 7.619964 AACTTCGGAGTTTCTACTTTCAAAA 57.380 32.000 2.29 0.00 43.48 2.44
311 314 9.457436 AAAATATACCAACATAAACTTCGGAGT 57.543 29.630 0.00 0.00 37.87 3.85
357 360 9.958180 TCTAGATTGTCAATTTGACCAATCTAA 57.042 29.630 31.76 26.05 46.40 2.10
358 361 9.958180 TTCTAGATTGTCAATTTGACCAATCTA 57.042 29.630 31.17 31.17 46.40 1.98
359 362 8.868522 TTCTAGATTGTCAATTTGACCAATCT 57.131 30.769 31.76 31.76 46.40 2.40
360 363 8.734386 ACTTCTAGATTGTCAATTTGACCAATC 58.266 33.333 26.50 26.50 46.40 2.67
361 364 8.641498 ACTTCTAGATTGTCAATTTGACCAAT 57.359 30.769 23.22 20.57 46.40 3.16
362 365 8.999431 GTACTTCTAGATTGTCAATTTGACCAA 58.001 33.333 23.22 17.62 46.40 3.67
363 366 7.330946 CGTACTTCTAGATTGTCAATTTGACCA 59.669 37.037 23.22 15.04 46.40 4.02
364 367 7.674240 GCGTACTTCTAGATTGTCAATTTGACC 60.674 40.741 23.22 10.69 46.40 4.02
366 369 6.034577 CGCGTACTTCTAGATTGTCAATTTGA 59.965 38.462 0.00 0.00 0.00 2.69
367 370 6.178507 CGCGTACTTCTAGATTGTCAATTTG 58.821 40.000 0.00 0.00 0.00 2.32
368 371 5.220416 GCGCGTACTTCTAGATTGTCAATTT 60.220 40.000 8.43 0.00 0.00 1.82
369 372 4.267928 GCGCGTACTTCTAGATTGTCAATT 59.732 41.667 8.43 0.00 0.00 2.32
370 373 3.797256 GCGCGTACTTCTAGATTGTCAAT 59.203 43.478 8.43 0.00 0.00 2.57
371 374 3.176708 GCGCGTACTTCTAGATTGTCAA 58.823 45.455 8.43 0.00 0.00 3.18
372 375 2.162809 TGCGCGTACTTCTAGATTGTCA 59.837 45.455 8.43 0.00 0.00 3.58
373 376 2.793933 TGCGCGTACTTCTAGATTGTC 58.206 47.619 8.43 0.00 0.00 3.18
374 377 2.933495 TGCGCGTACTTCTAGATTGT 57.067 45.000 8.43 0.00 0.00 2.71
375 378 2.097202 GCATGCGCGTACTTCTAGATTG 60.097 50.000 8.43 0.00 0.00 2.67
376 379 2.128035 GCATGCGCGTACTTCTAGATT 58.872 47.619 8.43 0.00 0.00 2.40
377 380 1.603172 GGCATGCGCGTACTTCTAGAT 60.603 52.381 12.44 0.00 39.92 1.98
378 381 0.248907 GGCATGCGCGTACTTCTAGA 60.249 55.000 12.44 0.00 39.92 2.43
379 382 1.215655 GGGCATGCGCGTACTTCTAG 61.216 60.000 19.70 0.00 39.92 2.43
380 383 1.227147 GGGCATGCGCGTACTTCTA 60.227 57.895 19.70 0.00 39.92 2.10
381 384 2.511600 GGGCATGCGCGTACTTCT 60.512 61.111 19.70 0.00 39.92 2.85
382 385 2.511600 AGGGCATGCGCGTACTTC 60.512 61.111 26.71 3.44 39.92 3.01
383 386 2.233605 TACAGGGCATGCGCGTACTT 62.234 55.000 26.71 13.77 39.92 2.24
384 387 2.233605 TTACAGGGCATGCGCGTACT 62.234 55.000 26.71 13.80 39.92 2.73
385 388 1.363145 TTTACAGGGCATGCGCGTAC 61.363 55.000 26.71 5.72 39.92 3.67
386 389 1.079057 TTTACAGGGCATGCGCGTA 60.079 52.632 26.71 25.35 39.92 4.42
387 390 2.359354 TTTACAGGGCATGCGCGT 60.359 55.556 26.71 26.25 39.92 6.01
388 391 1.087202 TAGTTTACAGGGCATGCGCG 61.087 55.000 26.71 22.63 39.92 6.86
389 392 1.091537 TTAGTTTACAGGGCATGCGC 58.908 50.000 26.04 26.04 37.44 6.09
390 393 2.080693 TGTTAGTTTACAGGGCATGCG 58.919 47.619 12.44 0.00 0.00 4.73
391 394 3.343617 TCTGTTAGTTTACAGGGCATGC 58.656 45.455 9.90 9.90 44.47 4.06
392 395 4.832248 TCTCTGTTAGTTTACAGGGCATG 58.168 43.478 0.00 0.00 44.60 4.06
393 396 4.080863 CCTCTCTGTTAGTTTACAGGGCAT 60.081 45.833 0.00 0.00 44.60 4.40
394 397 3.260884 CCTCTCTGTTAGTTTACAGGGCA 59.739 47.826 0.00 0.00 44.60 5.36
395 398 3.261137 ACCTCTCTGTTAGTTTACAGGGC 59.739 47.826 0.00 0.00 44.60 5.19
396 399 5.715753 ACTACCTCTCTGTTAGTTTACAGGG 59.284 44.000 0.00 0.00 46.00 4.45
397 400 6.837471 ACTACCTCTCTGTTAGTTTACAGG 57.163 41.667 0.00 0.00 44.47 4.00
398 401 8.564509 AGTACTACCTCTCTGTTAGTTTACAG 57.435 38.462 0.00 0.00 45.46 2.74
404 407 9.978336 AGAAAATAGTACTACCTCTCTGTTAGT 57.022 33.333 4.31 0.00 0.00 2.24
407 410 9.978336 ACTAGAAAATAGTACTACCTCTCTGTT 57.022 33.333 4.31 0.00 0.00 3.16
419 422 6.076557 CCGCGCTAGTACTAGAAAATAGTAC 58.923 44.000 30.09 14.50 46.16 2.73
435 438 1.638467 GAATTGCAGACCGCGCTAG 59.362 57.895 5.56 0.00 46.97 3.42
506 509 2.186903 CCACGGGTGCTTCGCTAT 59.813 61.111 0.00 0.00 0.00 2.97
507 510 4.752879 GCCACGGGTGCTTCGCTA 62.753 66.667 0.00 0.00 0.00 4.26
567 570 3.909651 GGGTGGGGCAAGGGACAA 61.910 66.667 0.00 0.00 0.00 3.18
647 650 3.371063 GCGTCCCTGTCTCCGTCA 61.371 66.667 0.00 0.00 0.00 4.35
717 720 2.607750 AGGCTCCTCCAAAGCGGA 60.608 61.111 0.00 0.00 43.61 5.54
791 796 0.692419 TGGAGAAGGATGGAGCTCCC 60.692 60.000 29.95 15.27 44.95 4.30
800 805 1.342076 TGCCTCGTAGTGGAGAAGGAT 60.342 52.381 0.00 0.00 45.27 3.24
863 868 1.180456 TCGGCGTTAGAGGTTGGACA 61.180 55.000 6.85 0.00 0.00 4.02
919 965 0.391263 CCGGGGAAGAAGAAGAACCG 60.391 60.000 0.00 0.00 39.54 4.44
977 1031 1.702957 CCCACCACCTTCCTTCAACTA 59.297 52.381 0.00 0.00 0.00 2.24
994 1049 2.679092 CAGCTTCTCCATGGCCCA 59.321 61.111 6.96 0.00 0.00 5.36
1121 1176 0.540133 GGAGGAGGGATAGGACGACC 60.540 65.000 0.00 0.00 0.00 4.79
1166 1221 3.305676 CGTGGATGAGATGAGATGGTACC 60.306 52.174 4.43 4.43 0.00 3.34
1220 1275 3.882888 ACGATATGGGCATAAACACAAGG 59.117 43.478 0.00 0.00 0.00 3.61
1261 1317 2.747686 CTGTAGGTTGCCGTGGGT 59.252 61.111 0.00 0.00 0.00 4.51
1271 1328 2.122729 TGGGCAGAGGCTGTAGGT 59.877 61.111 0.00 0.00 40.87 3.08
1573 1632 3.266510 TGTGTCTTGCTTGACTTGACT 57.733 42.857 10.14 0.00 37.79 3.41
1669 1731 1.225376 ACGAAATTCTGCGTTGCCGA 61.225 50.000 0.00 0.00 37.48 5.54
1682 1744 6.238484 GCAAGAAATATAGTGCAGGACGAAAT 60.238 38.462 0.00 0.00 36.97 2.17
1756 1818 6.368805 AGTGAGAAATCTGAAACCCTTCTTT 58.631 36.000 0.00 0.00 32.33 2.52
2052 2115 9.730420 AAGTGACACATTACTGAAAATTACAAC 57.270 29.630 8.59 0.00 0.00 3.32
2053 2116 9.944663 GAAGTGACACATTACTGAAAATTACAA 57.055 29.630 8.59 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.