Multiple sequence alignment - TraesCS1B01G051000

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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 TraesCS1B01G051000 chr1B 100.000 2492 0 0 1 2492 30848674 30846183 0.000000e+00 4602.0
1 TraesCS1B01G051000 chr1A 93.490 891 58 0 1512 2402 18085259 18084369 0.000000e+00 1325.0
2 TraesCS1B01G051000 chr1A 90.048 623 53 4 900 1513 18086114 18085492 0.000000e+00 798.0
3 TraesCS1B01G051000 chr1A 88.750 80 6 2 1 80 18086933 18086857 7.340000e-16 95.3
4 TraesCS1B01G051000 chr1A 93.548 62 4 0 2431 2492 18084306 18084245 2.640000e-15 93.5
5 TraesCS1B01G051000 chr1A 87.500 72 8 1 2422 2492 18102351 18102280 5.710000e-12 82.4
6 TraesCS1B01G051000 chr1D 91.461 890 62 9 1514 2403 16897709 16896834 0.000000e+00 1210.0
7 TraesCS1B01G051000 chr1D 93.120 814 48 6 702 1513 16898747 16897940 0.000000e+00 1186.0
8 TraesCS1B01G051000 chr1D 93.548 93 6 0 614 706 16899108 16899016 3.340000e-29 139.0
9 TraesCS1B01G051000 chr1D 94.521 73 2 2 2422 2492 16896780 16896708 7.290000e-21 111.0
10 TraesCS1B01G051000 chr2D 91.234 867 73 1 1512 2375 174457646 174456780 0.000000e+00 1177.0
11 TraesCS1B01G051000 chr2D 88.926 894 84 7 1512 2390 30328067 30327174 0.000000e+00 1088.0
12 TraesCS1B01G051000 chr2D 84.722 504 77 0 985 1488 174458363 174457860 2.860000e-139 505.0
13 TraesCS1B01G051000 chr2B 90.487 862 79 1 1512 2370 222235343 222234482 0.000000e+00 1134.0
14 TraesCS1B01G051000 chr3A 90.369 841 73 4 1512 2351 13536169 13535336 0.000000e+00 1098.0
15 TraesCS1B01G051000 chr3B 89.405 840 83 6 1512 2351 8074065 8074898 0.000000e+00 1053.0
16 TraesCS1B01G051000 chr2A 87.912 910 78 7 1512 2403 3539141 3540036 0.000000e+00 1042.0
17 TraesCS1B01G051000 chr2A 91.495 729 59 1 1512 2237 174445657 174444929 0.000000e+00 1000.0
18 TraesCS1B01G051000 chr3D 88.333 840 92 6 1512 2351 6677245 6678078 0.000000e+00 1003.0


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 TraesCS1B01G051000 chr1B 30846183 30848674 2491 True 4602.00 4602 100.0000 1 2492 1 chr1B.!!$R1 2491
1 TraesCS1B01G051000 chr1A 18084245 18086933 2688 True 577.95 1325 91.4590 1 2492 4 chr1A.!!$R2 2491
2 TraesCS1B01G051000 chr1D 16896708 16899108 2400 True 661.50 1210 93.1625 614 2492 4 chr1D.!!$R1 1878
3 TraesCS1B01G051000 chr2D 30327174 30328067 893 True 1088.00 1088 88.9260 1512 2390 1 chr2D.!!$R1 878
4 TraesCS1B01G051000 chr2D 174456780 174458363 1583 True 841.00 1177 87.9780 985 2375 2 chr2D.!!$R2 1390
5 TraesCS1B01G051000 chr2B 222234482 222235343 861 True 1134.00 1134 90.4870 1512 2370 1 chr2B.!!$R1 858
6 TraesCS1B01G051000 chr3A 13535336 13536169 833 True 1098.00 1098 90.3690 1512 2351 1 chr3A.!!$R1 839
7 TraesCS1B01G051000 chr3B 8074065 8074898 833 False 1053.00 1053 89.4050 1512 2351 1 chr3B.!!$F1 839
8 TraesCS1B01G051000 chr2A 3539141 3540036 895 False 1042.00 1042 87.9120 1512 2403 1 chr2A.!!$F1 891
9 TraesCS1B01G051000 chr2A 174444929 174445657 728 True 1000.00 1000 91.4950 1512 2237 1 chr2A.!!$R1 725
10 TraesCS1B01G051000 chr3D 6677245 6678078 833 False 1003.00 1003 88.3330 1512 2351 1 chr3D.!!$F1 839

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
979 1346 0.181824 TTACAGAATTAGCCCCGGCC 59.818 55.0 1.02 0.0 43.17 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1989 2613 2.680707 TCCATGGTCCGCACGGTA 60.681 61.111 12.58 0.0 36.47 4.02 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
111 112 5.066968 AGCTTTCTTCTCTTCGGAACTAG 57.933 43.478 0.00 0.00 0.00 2.57
124 125 7.217200 TCTTCGGAACTAGCAAGCATTAATAT 58.783 34.615 0.00 0.00 0.00 1.28
125 126 7.385205 TCTTCGGAACTAGCAAGCATTAATATC 59.615 37.037 0.00 0.00 0.00 1.63
126 127 5.932303 TCGGAACTAGCAAGCATTAATATCC 59.068 40.000 0.00 0.00 0.00 2.59
127 128 5.934625 CGGAACTAGCAAGCATTAATATCCT 59.065 40.000 0.00 0.00 0.00 3.24
153 165 2.857186 TGCTCTTAGAATGTGCCACA 57.143 45.000 0.00 0.00 0.00 4.17
156 168 3.273434 GCTCTTAGAATGTGCCACATCA 58.727 45.455 11.38 0.00 37.97 3.07
168 180 5.366460 TGTGCCACATCATCAAAATTGTTT 58.634 33.333 0.00 0.00 0.00 2.83
170 182 7.520776 ATGTGCCACATCATCAAAATTGTTTTG 60.521 33.333 4.03 8.47 42.00 2.44
183 195 7.842484 CAAAATTGTTTTGGCCATTGATTTTG 58.158 30.769 23.57 23.57 44.75 2.44
184 196 6.712179 AATTGTTTTGGCCATTGATTTTGT 57.288 29.167 6.09 0.00 0.00 2.83
185 197 6.712179 ATTGTTTTGGCCATTGATTTTGTT 57.288 29.167 6.09 0.00 0.00 2.83
186 198 5.496133 TGTTTTGGCCATTGATTTTGTTG 57.504 34.783 6.09 0.00 0.00 3.33
187 199 4.337555 TGTTTTGGCCATTGATTTTGTTGG 59.662 37.500 6.09 0.00 0.00 3.77
188 200 3.853355 TTGGCCATTGATTTTGTTGGT 57.147 38.095 6.09 0.00 0.00 3.67
189 201 3.853355 TGGCCATTGATTTTGTTGGTT 57.147 38.095 0.00 0.00 0.00 3.67
190 202 4.162040 TGGCCATTGATTTTGTTGGTTT 57.838 36.364 0.00 0.00 0.00 3.27
191 203 3.881688 TGGCCATTGATTTTGTTGGTTTG 59.118 39.130 0.00 0.00 0.00 2.93
192 204 4.133078 GGCCATTGATTTTGTTGGTTTGA 58.867 39.130 0.00 0.00 0.00 2.69
193 205 4.761227 GGCCATTGATTTTGTTGGTTTGAT 59.239 37.500 0.00 0.00 0.00 2.57
194 206 5.106594 GGCCATTGATTTTGTTGGTTTGATC 60.107 40.000 0.00 0.00 0.00 2.92
195 207 5.702209 GCCATTGATTTTGTTGGTTTGATCT 59.298 36.000 0.00 0.00 0.00 2.75
196 208 6.873076 GCCATTGATTTTGTTGGTTTGATCTA 59.127 34.615 0.00 0.00 0.00 1.98
197 209 7.148590 GCCATTGATTTTGTTGGTTTGATCTAC 60.149 37.037 0.00 0.00 0.00 2.59
198 210 7.871973 CCATTGATTTTGTTGGTTTGATCTACA 59.128 33.333 0.00 0.00 0.00 2.74
199 211 9.258826 CATTGATTTTGTTGGTTTGATCTACAA 57.741 29.630 0.00 0.00 36.65 2.41
200 212 9.829507 ATTGATTTTGTTGGTTTGATCTACAAA 57.170 25.926 0.00 0.00 44.79 2.83
212 224 7.984422 TTTGATCTACAAACATCAGTGTGAT 57.016 32.000 0.00 0.00 42.57 3.06
213 225 7.601073 TTGATCTACAAACATCAGTGTGATC 57.399 36.000 0.00 0.00 38.92 2.92
214 226 6.939622 TGATCTACAAACATCAGTGTGATCT 58.060 36.000 0.00 0.00 38.92 2.75
215 227 8.066612 TGATCTACAAACATCAGTGTGATCTA 57.933 34.615 0.00 0.00 38.92 1.98
216 228 8.531146 TGATCTACAAACATCAGTGTGATCTAA 58.469 33.333 0.00 0.00 38.92 2.10
217 229 9.371136 GATCTACAAACATCAGTGTGATCTAAA 57.629 33.333 0.00 0.00 38.92 1.85
218 230 9.896645 ATCTACAAACATCAGTGTGATCTAAAT 57.103 29.630 0.00 0.00 38.92 1.40
219 231 9.154847 TCTACAAACATCAGTGTGATCTAAATG 57.845 33.333 0.00 0.00 38.92 2.32
220 232 7.149569 ACAAACATCAGTGTGATCTAAATGG 57.850 36.000 0.00 0.00 38.92 3.16
221 233 6.942005 ACAAACATCAGTGTGATCTAAATGGA 59.058 34.615 0.00 0.00 38.92 3.41
222 234 7.448161 ACAAACATCAGTGTGATCTAAATGGAA 59.552 33.333 0.00 0.00 38.92 3.53
223 235 8.464404 CAAACATCAGTGTGATCTAAATGGAAT 58.536 33.333 0.00 0.00 38.92 3.01
224 236 7.798596 ACATCAGTGTGATCTAAATGGAATC 57.201 36.000 0.00 0.00 34.28 2.52
225 237 6.769822 ACATCAGTGTGATCTAAATGGAATCC 59.230 38.462 0.00 0.00 34.28 3.01
226 238 5.684704 TCAGTGTGATCTAAATGGAATCCC 58.315 41.667 0.00 0.00 0.00 3.85
227 239 5.429762 TCAGTGTGATCTAAATGGAATCCCT 59.570 40.000 0.00 0.00 0.00 4.20
228 240 5.762218 CAGTGTGATCTAAATGGAATCCCTC 59.238 44.000 0.00 0.00 0.00 4.30
229 241 5.669447 AGTGTGATCTAAATGGAATCCCTCT 59.331 40.000 0.00 0.00 0.00 3.69
230 242 5.994668 GTGTGATCTAAATGGAATCCCTCTC 59.005 44.000 0.00 0.00 0.00 3.20
235 247 1.600058 AATGGAATCCCTCTCTGCCA 58.400 50.000 0.00 0.00 0.00 4.92
266 278 4.741321 CATGAATGCATTTAAGTGGGGT 57.259 40.909 14.33 0.00 30.68 4.95
268 280 6.219417 CATGAATGCATTTAAGTGGGGTTA 57.781 37.500 14.33 0.00 30.68 2.85
269 281 6.638610 CATGAATGCATTTAAGTGGGGTTAA 58.361 36.000 14.33 0.00 30.68 2.01
271 283 7.251321 TGAATGCATTTAAGTGGGGTTAAAT 57.749 32.000 14.33 0.00 41.31 1.40
272 284 7.327214 TGAATGCATTTAAGTGGGGTTAAATC 58.673 34.615 14.33 0.00 39.52 2.17
273 285 7.180051 TGAATGCATTTAAGTGGGGTTAAATCT 59.820 33.333 14.33 0.00 39.52 2.40
274 286 6.926630 TGCATTTAAGTGGGGTTAAATCTT 57.073 33.333 0.00 0.00 39.52 2.40
275 287 6.696411 TGCATTTAAGTGGGGTTAAATCTTG 58.304 36.000 0.00 0.00 39.52 3.02
276 288 5.580691 GCATTTAAGTGGGGTTAAATCTTGC 59.419 40.000 0.00 0.00 39.52 4.01
277 289 6.696411 CATTTAAGTGGGGTTAAATCTTGCA 58.304 36.000 0.00 0.00 39.52 4.08
278 290 6.926630 TTTAAGTGGGGTTAAATCTTGCAT 57.073 33.333 0.00 0.00 28.92 3.96
279 291 6.926630 TTAAGTGGGGTTAAATCTTGCATT 57.073 33.333 0.00 0.00 0.00 3.56
280 292 5.823861 AAGTGGGGTTAAATCTTGCATTT 57.176 34.783 0.00 0.00 0.00 2.32
281 293 6.926630 AAGTGGGGTTAAATCTTGCATTTA 57.073 33.333 0.00 0.00 0.00 1.40
282 294 6.530019 AGTGGGGTTAAATCTTGCATTTAG 57.470 37.500 0.00 0.00 0.00 1.85
283 295 6.016555 AGTGGGGTTAAATCTTGCATTTAGT 58.983 36.000 0.00 0.00 0.00 2.24
284 296 6.496911 AGTGGGGTTAAATCTTGCATTTAGTT 59.503 34.615 0.00 0.00 0.00 2.24
285 297 7.672239 AGTGGGGTTAAATCTTGCATTTAGTTA 59.328 33.333 0.00 0.00 0.00 2.24
286 298 8.474831 GTGGGGTTAAATCTTGCATTTAGTTAT 58.525 33.333 0.00 0.00 0.00 1.89
287 299 8.474025 TGGGGTTAAATCTTGCATTTAGTTATG 58.526 33.333 0.00 0.00 0.00 1.90
288 300 7.926018 GGGGTTAAATCTTGCATTTAGTTATGG 59.074 37.037 0.00 0.00 0.00 2.74
289 301 7.438160 GGGTTAAATCTTGCATTTAGTTATGGC 59.562 37.037 0.00 0.00 0.00 4.40
290 302 7.978975 GGTTAAATCTTGCATTTAGTTATGGCA 59.021 33.333 0.00 0.00 0.00 4.92
291 303 9.533253 GTTAAATCTTGCATTTAGTTATGGCAT 57.467 29.630 4.88 4.88 0.00 4.40
292 304 9.531942 TTAAATCTTGCATTTAGTTATGGCATG 57.468 29.630 10.98 0.00 0.00 4.06
293 305 6.720112 ATCTTGCATTTAGTTATGGCATGT 57.280 33.333 10.98 0.00 0.00 3.21
294 306 6.528537 TCTTGCATTTAGTTATGGCATGTT 57.471 33.333 10.98 0.00 0.00 2.71
295 307 6.934056 TCTTGCATTTAGTTATGGCATGTTT 58.066 32.000 10.98 0.00 0.00 2.83
296 308 8.060931 TCTTGCATTTAGTTATGGCATGTTTA 57.939 30.769 10.98 0.00 0.00 2.01
297 309 8.526978 TCTTGCATTTAGTTATGGCATGTTTAA 58.473 29.630 10.98 3.01 0.00 1.52
298 310 8.472683 TTGCATTTAGTTATGGCATGTTTAAC 57.527 30.769 10.98 6.49 0.00 2.01
299 311 7.835822 TGCATTTAGTTATGGCATGTTTAACT 58.164 30.769 10.98 13.77 39.05 2.24
300 312 8.310382 TGCATTTAGTTATGGCATGTTTAACTT 58.690 29.630 16.17 0.00 37.37 2.66
301 313 9.150348 GCATTTAGTTATGGCATGTTTAACTTT 57.850 29.630 16.17 3.01 37.37 2.66
306 318 8.761575 AGTTATGGCATGTTTAACTTTTCATG 57.238 30.769 10.98 0.00 40.09 3.07
307 319 8.367156 AGTTATGGCATGTTTAACTTTTCATGT 58.633 29.630 10.98 0.00 39.54 3.21
308 320 8.987890 GTTATGGCATGTTTAACTTTTCATGTT 58.012 29.630 10.98 0.00 39.54 2.71
311 323 9.723601 ATGGCATGTTTAACTTTTCATGTTAAT 57.276 25.926 0.00 0.00 38.93 1.40
426 440 3.319137 TTTCAATCCTGTGTCGAGAGG 57.681 47.619 0.00 0.00 33.65 3.69
486 501 5.728471 AGCAGATCCATCTCAAATATACCG 58.272 41.667 0.00 0.00 34.22 4.02
487 502 5.481824 AGCAGATCCATCTCAAATATACCGA 59.518 40.000 0.00 0.00 34.22 4.69
488 503 6.155910 AGCAGATCCATCTCAAATATACCGAT 59.844 38.462 0.00 0.00 34.22 4.18
489 504 7.343057 AGCAGATCCATCTCAAATATACCGATA 59.657 37.037 0.00 0.00 34.22 2.92
490 505 7.981789 GCAGATCCATCTCAAATATACCGATAA 59.018 37.037 0.00 0.00 34.22 1.75
509 524 6.959311 CCGATAATTAAGTTCACGTTTTGGAG 59.041 38.462 0.00 0.00 0.00 3.86
513 528 9.840427 ATAATTAAGTTCACGTTTTGGAGAATG 57.160 29.630 0.00 0.00 0.00 2.67
514 529 6.687081 TTAAGTTCACGTTTTGGAGAATGT 57.313 33.333 0.00 0.00 0.00 2.71
515 530 5.576447 AAGTTCACGTTTTGGAGAATGTT 57.424 34.783 0.00 0.00 0.00 2.71
516 531 6.687081 AAGTTCACGTTTTGGAGAATGTTA 57.313 33.333 0.00 0.00 0.00 2.41
521 536 5.079406 CACGTTTTGGAGAATGTTATGTCG 58.921 41.667 0.00 0.00 0.00 4.35
523 538 5.107220 ACGTTTTGGAGAATGTTATGTCGAC 60.107 40.000 9.11 9.11 0.00 4.20
540 555 4.822350 TGTCGACAAAACATTACCATGGAA 59.178 37.500 21.47 8.96 34.27 3.53
546 561 5.957774 ACAAAACATTACCATGGAAGCCTAT 59.042 36.000 21.47 0.00 34.27 2.57
547 562 6.127366 ACAAAACATTACCATGGAAGCCTATG 60.127 38.462 21.47 13.44 34.27 2.23
550 565 4.079787 ACATTACCATGGAAGCCTATGTGT 60.080 41.667 21.47 5.53 34.27 3.72
564 579 4.766375 CCTATGTGTAAGACCCGACAAAT 58.234 43.478 0.00 0.00 0.00 2.32
575 590 6.131544 AGACCCGACAAATTGCAATATTAC 57.868 37.500 13.39 4.63 0.00 1.89
576 591 5.650266 AGACCCGACAAATTGCAATATTACA 59.350 36.000 13.39 0.00 0.00 2.41
612 627 8.481974 TCTTGAGACATCTCTACGTATATAGC 57.518 38.462 10.18 0.00 43.25 2.97
613 628 8.095169 TCTTGAGACATCTCTACGTATATAGCA 58.905 37.037 10.18 0.00 43.25 3.49
619 634 8.392372 ACATCTCTACGTATATAGCAGACAAA 57.608 34.615 0.00 0.00 0.00 2.83
703 719 5.213891 ACCTTAGCAATTTTTGGGTCAAG 57.786 39.130 0.00 0.00 0.00 3.02
712 1002 6.316140 GCAATTTTTGGGTCAAGAAGAAAACT 59.684 34.615 0.00 0.00 0.00 2.66
718 1008 6.353404 TGGGTCAAGAAGAAAACTTTGTTT 57.647 33.333 0.00 0.00 0.00 2.83
828 1120 4.520111 GGGCAAGGAAAATTTGAGCAAAAT 59.480 37.500 0.00 0.00 40.32 1.82
866 1158 6.578163 TTTTTACCCTATTTGTGTGGTAGC 57.422 37.500 0.00 0.00 34.96 3.58
898 1262 8.978874 TTTAGGAGCACATGTGATTACATTAT 57.021 30.769 29.80 7.15 45.01 1.28
955 1319 8.429493 ACTCAGTTACTAACTTGTTTTACCAC 57.571 34.615 0.00 0.00 40.46 4.16
966 1330 6.108015 ACTTGTTTTACCACGTTCTTACAGA 58.892 36.000 0.00 0.00 0.00 3.41
971 1335 8.767085 TGTTTTACCACGTTCTTACAGAATTAG 58.233 33.333 0.00 0.00 36.50 1.73
979 1346 0.181824 TTACAGAATTAGCCCCGGCC 59.818 55.000 1.02 0.00 43.17 6.13
980 1347 2.035237 TACAGAATTAGCCCCGGCCG 62.035 60.000 21.04 21.04 43.17 6.13
999 1366 1.689959 GTCGCATTTGGAGTGCAAAG 58.310 50.000 15.33 8.63 42.62 2.77
1076 1449 1.752498 GTTGATCAGAATGGCATGGCA 59.248 47.619 25.52 25.52 36.16 4.92
1172 1545 3.854669 CCTCCCGGCGCTTCTCAT 61.855 66.667 7.64 0.00 0.00 2.90
1173 1546 2.187946 CTCCCGGCGCTTCTCATT 59.812 61.111 7.64 0.00 0.00 2.57
1191 1564 1.843462 TTAAGGGCCCGCTGCAAGTA 61.843 55.000 18.44 0.00 43.89 2.24
1231 1604 0.605319 GATGGGGAGCGTGTTCACAA 60.605 55.000 3.87 0.00 0.00 3.33
1245 1618 3.693578 TGTTCACAATGAGACTGTTGCAA 59.306 39.130 0.00 0.00 0.00 4.08
1281 1654 1.074775 GGTTGGGCCAGATGTGTCA 59.925 57.895 6.23 0.00 37.17 3.58
1701 2322 1.005394 CAGGTACAAAGACGGCCGT 60.005 57.895 34.89 34.89 0.00 5.68
1732 2353 3.900892 CGGAGGTCGTCGGGATGG 61.901 72.222 0.00 0.00 0.00 3.51
1944 2568 1.302832 CAAGGAGGTTCTGCGGCTT 60.303 57.895 0.00 0.00 0.00 4.35
2003 2627 1.743995 GCTTTACCGTGCGGACCAT 60.744 57.895 18.16 0.00 38.96 3.55
2104 2728 0.613853 CAAGGACCCGGAGAGGTACA 60.614 60.000 0.73 0.00 44.05 2.90
2169 2793 0.179134 GAGCATTCTCGTACACGGCT 60.179 55.000 1.39 2.17 40.29 5.52
2375 3008 4.034048 GTCAACGACCGCTTAAATCATGAT 59.966 41.667 1.18 1.18 0.00 2.45
2405 3038 9.563593 TCAGAGACCCTACATATATCTACTACT 57.436 37.037 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 7.877003 TCCGAAGAGAAGAAAGCTATATGTAG 58.123 38.462 0.00 0.00 0.00 2.74
82 83 7.818997 TCCGAAGAGAAGAAAGCTATATGTA 57.181 36.000 0.00 0.00 0.00 2.29
84 85 7.206687 AGTTCCGAAGAGAAGAAAGCTATATG 58.793 38.462 0.00 0.00 0.00 1.78
86 87 6.777213 AGTTCCGAAGAGAAGAAAGCTATA 57.223 37.500 0.00 0.00 0.00 1.31
88 89 5.393243 GCTAGTTCCGAAGAGAAGAAAGCTA 60.393 44.000 0.00 0.00 0.00 3.32
89 90 4.619628 GCTAGTTCCGAAGAGAAGAAAGCT 60.620 45.833 0.00 0.00 0.00 3.74
90 91 3.615056 GCTAGTTCCGAAGAGAAGAAAGC 59.385 47.826 0.00 0.00 0.00 3.51
91 92 4.810790 TGCTAGTTCCGAAGAGAAGAAAG 58.189 43.478 0.00 0.00 0.00 2.62
92 93 4.866508 TGCTAGTTCCGAAGAGAAGAAA 57.133 40.909 0.00 0.00 0.00 2.52
93 94 4.810790 CTTGCTAGTTCCGAAGAGAAGAA 58.189 43.478 0.00 0.00 0.00 2.52
94 95 3.367498 GCTTGCTAGTTCCGAAGAGAAGA 60.367 47.826 0.00 0.00 0.00 2.87
95 96 2.926838 GCTTGCTAGTTCCGAAGAGAAG 59.073 50.000 0.00 0.00 0.00 2.85
96 97 2.299013 TGCTTGCTAGTTCCGAAGAGAA 59.701 45.455 0.00 0.00 0.00 2.87
97 98 1.893137 TGCTTGCTAGTTCCGAAGAGA 59.107 47.619 0.00 0.00 0.00 3.10
98 99 2.370281 TGCTTGCTAGTTCCGAAGAG 57.630 50.000 0.00 0.00 0.00 2.85
99 100 3.334583 AATGCTTGCTAGTTCCGAAGA 57.665 42.857 0.00 0.00 0.00 2.87
100 101 5.741388 ATTAATGCTTGCTAGTTCCGAAG 57.259 39.130 0.00 0.00 0.00 3.79
101 102 6.426937 GGATATTAATGCTTGCTAGTTCCGAA 59.573 38.462 0.00 0.00 0.00 4.30
102 103 5.932303 GGATATTAATGCTTGCTAGTTCCGA 59.068 40.000 0.00 0.00 0.00 4.55
103 104 5.934625 AGGATATTAATGCTTGCTAGTTCCG 59.065 40.000 0.00 0.00 27.51 4.30
104 105 7.751768 AAGGATATTAATGCTTGCTAGTTCC 57.248 36.000 0.00 0.00 41.70 3.62
140 152 6.778834 ATTTTGATGATGTGGCACATTCTA 57.221 33.333 31.83 20.38 44.52 2.10
142 154 5.640357 ACAATTTTGATGATGTGGCACATTC 59.360 36.000 31.83 25.51 44.52 2.67
144 156 5.155278 ACAATTTTGATGATGTGGCACAT 57.845 34.783 31.84 31.84 44.52 3.21
168 180 3.853355 ACCAACAAAATCAATGGCCAA 57.147 38.095 10.96 0.00 36.37 4.52
170 182 4.133078 TCAAACCAACAAAATCAATGGCC 58.867 39.130 0.00 0.00 36.37 5.36
171 183 5.702209 AGATCAAACCAACAAAATCAATGGC 59.298 36.000 0.00 0.00 36.37 4.40
172 184 7.871973 TGTAGATCAAACCAACAAAATCAATGG 59.128 33.333 0.00 0.00 38.91 3.16
173 185 8.815141 TGTAGATCAAACCAACAAAATCAATG 57.185 30.769 0.00 0.00 0.00 2.82
174 186 9.829507 TTTGTAGATCAAACCAACAAAATCAAT 57.170 25.926 0.00 0.00 40.56 2.57
188 200 7.879677 AGATCACACTGATGTTTGTAGATCAAA 59.120 33.333 0.00 0.00 39.17 2.69
189 201 7.389232 AGATCACACTGATGTTTGTAGATCAA 58.611 34.615 0.00 0.00 37.20 2.57
190 202 6.939622 AGATCACACTGATGTTTGTAGATCA 58.060 36.000 0.00 0.00 37.20 2.92
191 203 8.932945 TTAGATCACACTGATGTTTGTAGATC 57.067 34.615 0.00 0.00 37.20 2.75
192 204 9.896645 ATTTAGATCACACTGATGTTTGTAGAT 57.103 29.630 0.00 0.00 37.20 1.98
193 205 9.154847 CATTTAGATCACACTGATGTTTGTAGA 57.845 33.333 0.00 0.00 37.20 2.59
194 206 8.393366 CCATTTAGATCACACTGATGTTTGTAG 58.607 37.037 0.00 0.00 37.20 2.74
195 207 8.100164 TCCATTTAGATCACACTGATGTTTGTA 58.900 33.333 0.00 0.00 37.20 2.41
196 208 6.942005 TCCATTTAGATCACACTGATGTTTGT 59.058 34.615 0.00 0.00 37.20 2.83
197 209 7.381766 TCCATTTAGATCACACTGATGTTTG 57.618 36.000 0.00 0.00 37.20 2.93
198 210 8.585471 ATTCCATTTAGATCACACTGATGTTT 57.415 30.769 0.00 0.00 37.20 2.83
199 211 7.284034 GGATTCCATTTAGATCACACTGATGTT 59.716 37.037 0.00 0.00 37.20 2.71
200 212 6.769822 GGATTCCATTTAGATCACACTGATGT 59.230 38.462 0.00 0.00 37.20 3.06
201 213 6.206243 GGGATTCCATTTAGATCACACTGATG 59.794 42.308 4.80 0.00 37.20 3.07
202 214 6.102321 AGGGATTCCATTTAGATCACACTGAT 59.898 38.462 4.80 0.00 36.09 2.90
203 215 5.429762 AGGGATTCCATTTAGATCACACTGA 59.570 40.000 4.80 0.00 34.83 3.41
204 216 5.688807 AGGGATTCCATTTAGATCACACTG 58.311 41.667 4.80 0.00 34.83 3.66
205 217 5.669447 AGAGGGATTCCATTTAGATCACACT 59.331 40.000 4.80 0.00 34.83 3.55
206 218 5.934781 AGAGGGATTCCATTTAGATCACAC 58.065 41.667 4.80 0.00 34.83 3.82
207 219 5.907662 AGAGAGGGATTCCATTTAGATCACA 59.092 40.000 4.80 0.00 34.83 3.58
208 220 6.229733 CAGAGAGGGATTCCATTTAGATCAC 58.770 44.000 4.80 0.00 34.83 3.06
209 221 5.221803 GCAGAGAGGGATTCCATTTAGATCA 60.222 44.000 4.80 0.00 34.83 2.92
210 222 5.244755 GCAGAGAGGGATTCCATTTAGATC 58.755 45.833 4.80 0.00 34.83 2.75
211 223 4.042684 GGCAGAGAGGGATTCCATTTAGAT 59.957 45.833 4.80 0.00 34.83 1.98
212 224 3.392616 GGCAGAGAGGGATTCCATTTAGA 59.607 47.826 4.80 0.00 34.83 2.10
213 225 3.137176 TGGCAGAGAGGGATTCCATTTAG 59.863 47.826 4.80 0.00 34.83 1.85
214 226 3.122480 TGGCAGAGAGGGATTCCATTTA 58.878 45.455 4.80 0.00 34.83 1.40
215 227 1.925255 TGGCAGAGAGGGATTCCATTT 59.075 47.619 4.80 0.00 34.83 2.32
216 228 1.600058 TGGCAGAGAGGGATTCCATT 58.400 50.000 4.80 0.00 34.83 3.16
217 229 1.424302 CATGGCAGAGAGGGATTCCAT 59.576 52.381 4.80 0.00 34.90 3.41
218 230 0.841961 CATGGCAGAGAGGGATTCCA 59.158 55.000 4.80 0.00 34.83 3.53
219 231 0.536915 GCATGGCAGAGAGGGATTCC 60.537 60.000 0.00 0.00 0.00 3.01
220 232 0.182061 TGCATGGCAGAGAGGGATTC 59.818 55.000 0.00 0.00 33.32 2.52
221 233 2.314402 TGCATGGCAGAGAGGGATT 58.686 52.632 0.00 0.00 33.32 3.01
222 234 4.078167 TGCATGGCAGAGAGGGAT 57.922 55.556 0.00 0.00 33.32 3.85
248 260 7.555965 AGATTTAACCCCACTTAAATGCATTC 58.444 34.615 13.38 0.00 36.74 2.67
266 278 9.531942 CATGCCATAACTAAATGCAAGATTTAA 57.468 29.630 0.00 0.00 0.00 1.52
268 280 7.558604 ACATGCCATAACTAAATGCAAGATTT 58.441 30.769 0.00 0.00 0.00 2.17
269 281 7.116075 ACATGCCATAACTAAATGCAAGATT 57.884 32.000 0.00 0.00 0.00 2.40
271 283 6.528537 AACATGCCATAACTAAATGCAAGA 57.471 33.333 0.00 0.00 0.00 3.02
272 284 8.594687 GTTAAACATGCCATAACTAAATGCAAG 58.405 33.333 0.00 0.00 0.00 4.01
273 285 8.310382 AGTTAAACATGCCATAACTAAATGCAA 58.690 29.630 13.65 0.00 37.92 4.08
274 286 7.835822 AGTTAAACATGCCATAACTAAATGCA 58.164 30.769 13.65 0.00 37.92 3.96
275 287 8.702163 AAGTTAAACATGCCATAACTAAATGC 57.298 30.769 14.93 0.00 38.55 3.56
280 292 9.853555 CATGAAAAGTTAAACATGCCATAACTA 57.146 29.630 14.93 4.61 38.55 2.24
281 293 8.367156 ACATGAAAAGTTAAACATGCCATAACT 58.633 29.630 0.00 10.83 42.28 2.24
282 294 8.532977 ACATGAAAAGTTAAACATGCCATAAC 57.467 30.769 0.00 0.15 42.28 1.89
285 297 9.723601 ATTAACATGAAAAGTTAAACATGCCAT 57.276 25.926 0.00 0.00 42.63 4.40
337 349 9.690913 AGATTGAAATCATGTGAGAAATTCCTA 57.309 29.630 5.86 0.00 37.89 2.94
338 350 8.591114 AGATTGAAATCATGTGAGAAATTCCT 57.409 30.769 5.86 0.00 37.89 3.36
396 408 8.073768 TCGACACAGGATTGAAAAGTAATTTTC 58.926 33.333 18.90 18.90 40.39 2.29
400 412 6.464222 TCTCGACACAGGATTGAAAAGTAAT 58.536 36.000 0.00 0.00 0.00 1.89
404 416 3.681897 CCTCTCGACACAGGATTGAAAAG 59.318 47.826 0.00 0.00 30.32 2.27
413 425 2.644676 TGATACTCCTCTCGACACAGG 58.355 52.381 0.00 0.00 0.00 4.00
414 426 4.133820 AGATGATACTCCTCTCGACACAG 58.866 47.826 0.00 0.00 0.00 3.66
415 427 4.157849 AGATGATACTCCTCTCGACACA 57.842 45.455 0.00 0.00 0.00 3.72
416 428 6.811253 AATAGATGATACTCCTCTCGACAC 57.189 41.667 0.00 0.00 0.00 3.67
453 468 6.465084 TGAGATGGATCTGCTTATTGAGATG 58.535 40.000 0.00 0.00 37.25 2.90
459 474 9.678260 GGTATATTTGAGATGGATCTGCTTATT 57.322 33.333 0.00 0.00 37.25 1.40
460 475 7.984050 CGGTATATTTGAGATGGATCTGCTTAT 59.016 37.037 0.00 0.00 37.25 1.73
461 476 7.178451 TCGGTATATTTGAGATGGATCTGCTTA 59.822 37.037 0.00 0.00 37.25 3.09
462 477 6.014242 TCGGTATATTTGAGATGGATCTGCTT 60.014 38.462 0.00 0.00 37.25 3.91
463 478 5.481824 TCGGTATATTTGAGATGGATCTGCT 59.518 40.000 0.00 0.00 37.25 4.24
464 479 5.724328 TCGGTATATTTGAGATGGATCTGC 58.276 41.667 0.00 0.00 37.25 4.26
487 502 9.840427 CATTCTCCAAAACGTGAACTTAATTAT 57.160 29.630 0.00 0.00 0.00 1.28
488 503 8.842280 ACATTCTCCAAAACGTGAACTTAATTA 58.158 29.630 0.00 0.00 0.00 1.40
489 504 7.712797 ACATTCTCCAAAACGTGAACTTAATT 58.287 30.769 0.00 0.00 0.00 1.40
490 505 7.272037 ACATTCTCCAAAACGTGAACTTAAT 57.728 32.000 0.00 0.00 0.00 1.40
491 506 6.687081 ACATTCTCCAAAACGTGAACTTAA 57.313 33.333 0.00 0.00 0.00 1.85
492 507 6.687081 AACATTCTCCAAAACGTGAACTTA 57.313 33.333 0.00 0.00 0.00 2.24
498 513 5.079406 CGACATAACATTCTCCAAAACGTG 58.921 41.667 0.00 0.00 0.00 4.49
512 527 6.862711 TGGTAATGTTTTGTCGACATAACA 57.137 33.333 38.41 38.41 46.30 2.41
513 528 6.745450 CCATGGTAATGTTTTGTCGACATAAC 59.255 38.462 32.18 32.18 36.76 1.89
514 529 6.655425 TCCATGGTAATGTTTTGTCGACATAA 59.345 34.615 20.80 18.17 36.76 1.90
515 530 6.174049 TCCATGGTAATGTTTTGTCGACATA 58.826 36.000 20.80 12.38 36.76 2.29
516 531 5.007034 TCCATGGTAATGTTTTGTCGACAT 58.993 37.500 20.80 5.63 39.31 3.06
521 536 4.220602 AGGCTTCCATGGTAATGTTTTGTC 59.779 41.667 12.58 0.00 31.27 3.18
523 538 4.806640 AGGCTTCCATGGTAATGTTTTG 57.193 40.909 12.58 0.00 31.27 2.44
531 546 4.966168 TCTTACACATAGGCTTCCATGGTA 59.034 41.667 12.58 0.02 0.00 3.25
540 555 1.755380 GTCGGGTCTTACACATAGGCT 59.245 52.381 0.00 0.00 0.00 4.58
546 561 2.550606 GCAATTTGTCGGGTCTTACACA 59.449 45.455 0.00 0.00 0.00 3.72
547 562 2.550606 TGCAATTTGTCGGGTCTTACAC 59.449 45.455 0.00 0.00 0.00 2.90
550 565 6.767524 AATATTGCAATTTGTCGGGTCTTA 57.232 33.333 18.75 0.00 0.00 2.10
589 604 8.095169 TCTGCTATATACGTAGAGATGTCTCAA 58.905 37.037 12.21 0.00 45.21 3.02
631 646 8.217111 TGTCCATATCATTGCTGGTATTTAGAA 58.783 33.333 0.00 0.00 0.00 2.10
647 662 3.975982 ACCATCCAGACATGTCCATATCA 59.024 43.478 22.21 1.34 0.00 2.15
718 1008 1.189752 TGGCAGCCACTCAAACAAAA 58.810 45.000 11.22 0.00 0.00 2.44
721 1011 2.284754 TATTGGCAGCCACTCAAACA 57.715 45.000 15.89 0.00 30.78 2.83
723 1014 4.567971 CAAAATATTGGCAGCCACTCAAA 58.432 39.130 15.89 0.00 30.78 2.69
876 1168 7.056006 TCAATAATGTAATCACATGTGCTCCT 58.944 34.615 21.38 7.41 44.83 3.69
898 1262 0.108992 GTACGCGAGACACCCATCAA 60.109 55.000 15.93 0.00 0.00 2.57
966 1330 4.540735 CGACGGCCGGGGCTAATT 62.541 66.667 31.76 4.91 41.60 1.40
979 1346 0.040514 TTTGCACTCCAAATGCGACG 60.041 50.000 0.00 0.00 46.49 5.12
980 1347 1.266718 TCTTTGCACTCCAAATGCGAC 59.733 47.619 0.00 0.00 46.49 5.19
999 1366 5.105997 CCAAAGGACTCTTGTCAATTCCATC 60.106 44.000 9.54 0.00 44.61 3.51
1094 1467 2.225727 GGAGGTGATCGTTTGGTTGTTC 59.774 50.000 0.00 0.00 0.00 3.18
1172 1545 1.843462 TACTTGCAGCGGGCCCTTAA 61.843 55.000 22.43 6.54 43.89 1.85
1173 1546 1.843462 TTACTTGCAGCGGGCCCTTA 61.843 55.000 22.43 0.00 43.89 2.69
1231 1604 1.265095 CTTGCGTTGCAACAGTCTCAT 59.735 47.619 28.01 0.00 43.99 2.90
1281 1654 1.203225 AGCCCTTGGAAGAAATGGCTT 60.203 47.619 0.00 0.00 45.55 4.35
1305 1678 1.101635 CGTCCTGGCTGATCTCCGTA 61.102 60.000 0.00 0.00 0.00 4.02
1365 1738 1.904144 CGAAATCTACGTCGAAGGCA 58.096 50.000 0.00 0.00 39.64 4.75
1444 1817 2.125326 CCATGAGTCGGGCGTAGGA 61.125 63.158 0.00 0.00 0.00 2.94
1594 2203 0.969149 ATGCCGGAGAATATCTCGCA 59.031 50.000 5.05 10.81 44.28 5.10
1732 2353 3.112709 GAACAGCGCCGAGACCAC 61.113 66.667 2.29 0.00 0.00 4.16
1752 2376 2.282040 GAGCTTGTGTGCTGCCCT 60.282 61.111 0.00 0.00 44.17 5.19
1809 2433 4.892965 AGGTGCTTGGCGTTGGCA 62.893 61.111 0.00 0.00 42.47 4.92
1989 2613 2.680707 TCCATGGTCCGCACGGTA 60.681 61.111 12.58 0.00 36.47 4.02
2003 2627 2.753043 GGTACTCGTCGCCCTCCA 60.753 66.667 0.00 0.00 0.00 3.86
2244 2868 4.163427 TCTCCATCTCAAAGTTCCTCAGT 58.837 43.478 0.00 0.00 0.00 3.41
2375 3008 7.350044 AGATATATGTAGGGTCTCTGAAGGA 57.650 40.000 0.00 0.00 0.00 3.36
2410 3043 7.648142 CGCAACTGTAATTTATTGGTCCATAT 58.352 34.615 0.00 0.00 0.00 1.78
2411 3044 6.459024 GCGCAACTGTAATTTATTGGTCCATA 60.459 38.462 0.30 0.00 0.00 2.74
2414 3047 4.102649 GCGCAACTGTAATTTATTGGTCC 58.897 43.478 0.30 0.00 0.00 4.46
2415 3048 4.102649 GGCGCAACTGTAATTTATTGGTC 58.897 43.478 10.83 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.