Multiple sequence alignment - TraesCS1B01G086100

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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 TraesCS1B01G086100 chr1B 100.000 2515 0 0 1 2515 70705934 70708448 0.000000e+00 4645.0
1 TraesCS1B01G086100 chr1B 100.000 1161 0 0 2766 3926 70708699 70709859 0.000000e+00 2145.0
2 TraesCS1B01G086100 chr1D 94.134 2165 93 14 336 2486 50192025 50194169 0.000000e+00 3264.0
3 TraesCS1B01G086100 chr1D 94.332 1041 53 6 2766 3803 50194255 50195292 0.000000e+00 1591.0
4 TraesCS1B01G086100 chr1D 94.712 208 5 4 1 203 50191780 50191986 6.330000e-83 318.0
5 TraesCS1B01G086100 chr1D 96.970 132 4 0 205 336 194139900 194139769 5.110000e-54 222.0
6 TraesCS1B01G086100 chr1A 92.169 2158 86 34 329 2454 49360707 49362813 0.000000e+00 2972.0
7 TraesCS1B01G086100 chr1A 93.005 1158 63 12 2781 3926 49363207 49364358 0.000000e+00 1674.0
8 TraesCS1B01G086100 chr1A 94.355 124 2 3 90 209 49360584 49360706 6.700000e-43 185.0
9 TraesCS1B01G086100 chr1A 94.737 57 2 1 3 58 49360529 49360585 1.940000e-13 87.9
10 TraesCS1B01G086100 chr6B 98.473 131 2 0 205 335 603910655 603910785 8.480000e-57 231.0
11 TraesCS1B01G086100 chr5B 96.350 137 5 0 201 337 640272734 640272870 3.950000e-55 226.0
12 TraesCS1B01G086100 chr4A 97.710 131 3 0 204 334 628200698 628200828 3.950000e-55 226.0
13 TraesCS1B01G086100 chr4A 96.269 134 5 0 202 335 729151974 729151841 1.840000e-53 220.0
14 TraesCS1B01G086100 chr7D 96.970 132 4 0 204 335 161488728 161488859 5.110000e-54 222.0
15 TraesCS1B01G086100 chr4B 96.296 135 5 0 200 334 70813975 70814109 5.110000e-54 222.0
16 TraesCS1B01G086100 chr3A 96.947 131 4 0 204 334 348834576 348834446 1.840000e-53 220.0
17 TraesCS1B01G086100 chr5D 89.937 159 14 2 198 355 241844069 241844226 1.850000e-48 204.0


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 TraesCS1B01G086100 chr1B 70705934 70709859 3925 False 3395.000000 4645 100.000000 1 3926 2 chr1B.!!$F1 3925
1 TraesCS1B01G086100 chr1D 50191780 50195292 3512 False 1724.333333 3264 94.392667 1 3803 3 chr1D.!!$F1 3802
2 TraesCS1B01G086100 chr1A 49360529 49364358 3829 False 1229.725000 2972 93.566500 3 3926 4 chr1A.!!$F1 3923

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
409 415 1.002430 TGTGGACTGGCTGAGCTTTAG 59.998 52.381 3.72 3.39 0.0 1.85 F
1520 1561 1.202114 CACGCCAATACAGGTTTGCAT 59.798 47.619 0.00 0.00 0.0 3.96 F
2036 2078 1.672363 CCAACATCATGCGCATACAGT 59.328 47.619 24.84 17.84 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2063 2105 0.114364 TCCACTGGTAGCAGTCCTCA 59.886 55.000 24.25 6.18 32.26 3.86 R
2873 2988 0.948678 TCGCCACCTGTAGCAAAAAC 59.051 50.000 0.00 0.00 0.00 2.43 R
2971 3086 2.755469 CCAACCCCTCGGCCATTG 60.755 66.667 2.24 0.00 0.00 2.82 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
26 27 8.660373 CAGACCTATCTCTTGTGTTTATGTTTC 58.340 37.037 0.00 0.00 30.42 2.78
150 152 3.164268 CAAACATGGAAATCTGTGGGGA 58.836 45.455 0.00 0.00 0.00 4.81
214 220 8.677870 ATGCTTCTCTCAAATATATACTCCCT 57.322 34.615 0.00 0.00 0.00 4.20
215 221 8.128322 TGCTTCTCTCAAATATATACTCCCTC 57.872 38.462 0.00 0.00 0.00 4.30
216 222 7.179338 TGCTTCTCTCAAATATATACTCCCTCC 59.821 40.741 0.00 0.00 0.00 4.30
218 224 6.791371 TCTCTCAAATATATACTCCCTCCGT 58.209 40.000 0.00 0.00 0.00 4.69
220 226 5.950549 TCTCAAATATATACTCCCTCCGTCC 59.049 44.000 0.00 0.00 0.00 4.79
221 227 5.021458 TCAAATATATACTCCCTCCGTCCC 58.979 45.833 0.00 0.00 0.00 4.46
222 228 4.687262 AATATATACTCCCTCCGTCCCA 57.313 45.455 0.00 0.00 0.00 4.37
225 231 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
227 233 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
228 234 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
229 235 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
230 236 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
231 237 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
232 238 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
233 239 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
234 240 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
235 241 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
236 242 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
237 243 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
239 245 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
240 246 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
241 247 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
242 248 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
243 249 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
244 250 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
245 251 7.814587 CCCAAAATTCTTGTCTTAGATTTGTCC 59.185 37.037 0.00 0.00 28.79 4.02
246 252 8.359642 CCAAAATTCTTGTCTTAGATTTGTCCA 58.640 33.333 0.00 0.00 28.79 4.02
247 253 9.748708 CAAAATTCTTGTCTTAGATTTGTCCAA 57.251 29.630 0.00 0.00 0.00 3.53
252 258 8.251750 TCTTGTCTTAGATTTGTCCAAATACG 57.748 34.615 5.29 0.00 40.77 3.06
253 259 6.978343 TGTCTTAGATTTGTCCAAATACGG 57.022 37.500 5.29 0.00 40.77 4.02
254 260 6.703319 TGTCTTAGATTTGTCCAAATACGGA 58.297 36.000 5.29 0.82 40.77 4.69
255 261 7.335627 TGTCTTAGATTTGTCCAAATACGGAT 58.664 34.615 5.29 0.00 40.77 4.18
256 262 7.279981 TGTCTTAGATTTGTCCAAATACGGATG 59.720 37.037 5.29 0.00 40.77 3.51
257 263 7.280205 GTCTTAGATTTGTCCAAATACGGATGT 59.720 37.037 5.29 0.00 40.77 3.06
258 264 8.479689 TCTTAGATTTGTCCAAATACGGATGTA 58.520 33.333 5.29 0.00 40.77 2.29
259 265 9.273016 CTTAGATTTGTCCAAATACGGATGTAT 57.727 33.333 5.29 0.00 43.14 2.29
260 266 7.730364 AGATTTGTCCAAATACGGATGTATC 57.270 36.000 5.29 0.00 40.42 2.24
261 267 7.279615 AGATTTGTCCAAATACGGATGTATCA 58.720 34.615 5.29 0.00 40.42 2.15
262 268 7.773224 AGATTTGTCCAAATACGGATGTATCAA 59.227 33.333 5.29 0.00 40.42 2.57
263 269 6.918892 TTGTCCAAATACGGATGTATCAAG 57.081 37.500 0.00 0.00 40.42 3.02
264 270 5.984725 TGTCCAAATACGGATGTATCAAGT 58.015 37.500 0.00 0.00 40.42 3.16
265 271 6.046593 TGTCCAAATACGGATGTATCAAGTC 58.953 40.000 0.00 0.00 40.42 3.01
266 272 6.046593 GTCCAAATACGGATGTATCAAGTCA 58.953 40.000 0.00 0.00 40.42 3.41
267 273 6.018994 GTCCAAATACGGATGTATCAAGTCAC 60.019 42.308 0.00 0.00 40.42 3.67
268 274 5.051039 CCAAATACGGATGTATCAAGTCACG 60.051 44.000 0.00 0.00 40.42 4.35
269 275 4.913335 ATACGGATGTATCAAGTCACGT 57.087 40.909 0.00 0.00 36.56 4.49
270 276 3.587797 ACGGATGTATCAAGTCACGTT 57.412 42.857 0.00 0.00 0.00 3.99
271 277 3.921677 ACGGATGTATCAAGTCACGTTT 58.078 40.909 0.00 0.00 0.00 3.60
272 278 4.312443 ACGGATGTATCAAGTCACGTTTT 58.688 39.130 0.00 0.00 0.00 2.43
273 279 5.472148 ACGGATGTATCAAGTCACGTTTTA 58.528 37.500 0.00 0.00 0.00 1.52
274 280 5.575606 ACGGATGTATCAAGTCACGTTTTAG 59.424 40.000 0.00 0.00 0.00 1.85
275 281 5.575606 CGGATGTATCAAGTCACGTTTTAGT 59.424 40.000 0.00 0.00 0.00 2.24
276 282 6.748658 CGGATGTATCAAGTCACGTTTTAGTA 59.251 38.462 0.00 0.00 0.00 1.82
277 283 7.434307 CGGATGTATCAAGTCACGTTTTAGTAT 59.566 37.037 0.00 0.00 0.00 2.12
278 284 9.095065 GGATGTATCAAGTCACGTTTTAGTATT 57.905 33.333 0.00 0.00 0.00 1.89
288 294 9.962783 AGTCACGTTTTAGTATTAGATACATCC 57.037 33.333 0.00 0.00 38.21 3.51
289 295 8.899776 GTCACGTTTTAGTATTAGATACATCCG 58.100 37.037 0.00 0.00 38.21 4.18
290 296 8.623903 TCACGTTTTAGTATTAGATACATCCGT 58.376 33.333 0.00 0.00 38.21 4.69
291 297 9.882996 CACGTTTTAGTATTAGATACATCCGTA 57.117 33.333 0.00 0.00 38.21 4.02
309 315 9.439500 ACATCCGTATCTAGACTAATCTAAGAC 57.561 37.037 0.00 0.00 36.98 3.01
310 316 9.438228 CATCCGTATCTAGACTAATCTAAGACA 57.562 37.037 0.00 0.00 36.98 3.41
312 318 9.491675 TCCGTATCTAGACTAATCTAAGACAAG 57.508 37.037 0.00 0.00 36.98 3.16
313 319 9.491675 CCGTATCTAGACTAATCTAAGACAAGA 57.508 37.037 0.00 0.00 36.98 3.02
321 327 9.454859 AGACTAATCTAAGACAAGAATTTTGGG 57.545 33.333 5.68 0.00 31.46 4.12
322 328 9.449719 GACTAATCTAAGACAAGAATTTTGGGA 57.550 33.333 5.68 0.00 0.00 4.37
323 329 9.232473 ACTAATCTAAGACAAGAATTTTGGGAC 57.768 33.333 5.68 0.00 0.00 4.46
324 330 9.231297 CTAATCTAAGACAAGAATTTTGGGACA 57.769 33.333 5.68 0.00 0.00 4.02
352 358 7.462571 GGAGTACATCCTTGTTTATTGGTTT 57.537 36.000 0.00 0.00 45.64 3.27
353 359 7.892609 GGAGTACATCCTTGTTTATTGGTTTT 58.107 34.615 0.00 0.00 45.64 2.43
409 415 1.002430 TGTGGACTGGCTGAGCTTTAG 59.998 52.381 3.72 3.39 0.00 1.85
419 427 3.873952 GGCTGAGCTTTAGTGGATGTAAG 59.126 47.826 3.72 0.00 0.00 2.34
434 442 5.479724 TGGATGTAAGATGTGAAAATGGCAA 59.520 36.000 0.00 0.00 0.00 4.52
435 443 5.807011 GGATGTAAGATGTGAAAATGGCAAC 59.193 40.000 0.00 0.00 0.00 4.17
452 463 2.595386 CAACGCTTCCCATTTTACTGC 58.405 47.619 0.00 0.00 0.00 4.40
482 494 7.651808 TGGTATTCTTGCAAGAAAGAAAGAAG 58.348 34.615 37.81 6.63 44.26 2.85
483 495 7.087007 GGTATTCTTGCAAGAAAGAAAGAAGG 58.913 38.462 37.81 6.56 44.26 3.46
484 496 6.966534 ATTCTTGCAAGAAAGAAAGAAGGA 57.033 33.333 37.81 17.03 44.26 3.36
485 497 6.773976 TTCTTGCAAGAAAGAAAGAAGGAA 57.226 33.333 34.01 11.48 41.92 3.36
491 503 8.103948 TGCAAGAAAGAAAGAAGGAAATAGAG 57.896 34.615 0.00 0.00 0.00 2.43
495 507 6.657117 AGAAAGAAAGAAGGAAATAGAGTGCC 59.343 38.462 0.00 0.00 0.00 5.01
496 508 4.508662 AGAAAGAAGGAAATAGAGTGCCG 58.491 43.478 0.00 0.00 0.00 5.69
512 524 4.507879 CGAGGCGGAAAATACGGT 57.492 55.556 0.00 0.00 0.00 4.83
528 540 2.641197 GGTGACGGGTTGAAAGCAT 58.359 52.632 0.00 0.00 0.00 3.79
546 558 2.678705 CATACACGTAGCGCGAAAAAG 58.321 47.619 12.10 0.00 44.77 2.27
549 561 2.097728 CGTAGCGCGAAAAAGGCC 59.902 61.111 12.10 0.00 44.77 5.19
562 574 1.770294 AAAGGCCAAAGTTCGAACCA 58.230 45.000 24.22 0.00 0.00 3.67
663 685 2.735857 GCAAAGCCAAAGCCAGCG 60.736 61.111 0.00 0.00 41.25 5.18
816 843 3.434167 CCACCATCCCAATCAGTAGAAGG 60.434 52.174 0.00 0.00 0.00 3.46
818 845 2.107204 CCATCCCAATCAGTAGAAGGGG 59.893 54.545 0.00 0.00 41.24 4.79
848 879 5.048224 AGAGTGAGACAAGCCAAATCAAATG 60.048 40.000 0.00 0.00 0.00 2.32
874 908 2.023673 CAACAAGAGCCAAGAACACCA 58.976 47.619 0.00 0.00 0.00 4.17
878 912 3.012518 CAAGAGCCAAGAACACCATAGG 58.987 50.000 0.00 0.00 0.00 2.57
915 956 1.368579 CAAACCAAAGGCCAGCAGG 59.631 57.895 5.01 3.40 38.23 4.85
987 1028 2.901813 CTGAGCAGGAGGAGCAGG 59.098 66.667 0.00 0.00 0.00 4.85
990 1031 3.082701 AGCAGGAGGAGCAGGAGC 61.083 66.667 0.00 0.00 42.56 4.70
1003 1044 1.760086 AGGAGCTGGACCGAGATGG 60.760 63.158 0.00 0.00 46.41 3.51
1194 1235 2.866726 GCTCCTCATCTCCCTCGCC 61.867 68.421 0.00 0.00 0.00 5.54
1520 1561 1.202114 CACGCCAATACAGGTTTGCAT 59.798 47.619 0.00 0.00 0.00 3.96
1525 1566 3.679502 GCCAATACAGGTTTGCATTTCAC 59.320 43.478 0.00 0.00 0.00 3.18
1527 1568 4.021192 CCAATACAGGTTTGCATTTCACCT 60.021 41.667 0.00 0.00 41.97 4.00
1530 1571 3.832527 ACAGGTTTGCATTTCACCTACT 58.167 40.909 6.99 0.00 39.01 2.57
1532 1573 2.558359 AGGTTTGCATTTCACCTACTGC 59.442 45.455 5.77 0.00 39.28 4.40
1570 1612 3.988976 TGCTCCTCTTGCTATTTGTCT 57.011 42.857 0.00 0.00 0.00 3.41
1619 1661 9.856488 TTGTAGTACAACAGAACTGATAATCTC 57.144 33.333 11.75 0.00 32.34 2.75
1628 1670 9.757227 AACAGAACTGATAATCTCAACTATAGC 57.243 33.333 8.87 0.00 32.14 2.97
1629 1671 8.364142 ACAGAACTGATAATCTCAACTATAGCC 58.636 37.037 8.87 0.00 32.14 3.93
1630 1672 7.540400 CAGAACTGATAATCTCAACTATAGCCG 59.460 40.741 0.00 0.00 32.14 5.52
1631 1673 5.715070 ACTGATAATCTCAACTATAGCCGC 58.285 41.667 0.00 0.00 32.14 6.53
1666 1708 9.829507 AACATAACAAATTGTCAAAGAAATGGA 57.170 25.926 0.00 0.00 0.00 3.41
1835 1877 2.975489 AGAGTGTGACCTCAGGACAAAT 59.025 45.455 0.00 0.00 33.75 2.32
1961 2003 9.720769 TTGTAGTTCTAACTAATAGCTTTGCTT 57.279 29.630 4.20 0.00 42.66 3.91
2036 2078 1.672363 CCAACATCATGCGCATACAGT 59.328 47.619 24.84 17.84 0.00 3.55
2102 2144 2.917713 ACAATGCCCCAAACATCCTA 57.082 45.000 0.00 0.00 0.00 2.94
2402 2445 6.095160 TGCTTTTCATTGGCATTTGTTTTCTT 59.905 30.769 0.00 0.00 0.00 2.52
2443 2490 3.075884 CCCCAAAAATGCATTTCCAGTG 58.924 45.455 24.28 18.00 0.00 3.66
2821 2936 7.967890 TGATGATACTGGCAATATAACACAG 57.032 36.000 0.00 0.00 35.40 3.66
2826 2941 8.046708 TGATACTGGCAATATAACACAGTTTCT 58.953 33.333 12.35 0.00 41.99 2.52
2848 2963 3.193267 TGTTTGTGGCCATCTATTTGCTC 59.807 43.478 9.72 0.00 0.00 4.26
2855 2970 4.581824 TGGCCATCTATTTGCTCTGATTTC 59.418 41.667 0.00 0.00 0.00 2.17
2873 2988 7.550551 TCTGATTTCTCTAACACTGCTTTATGG 59.449 37.037 0.00 0.00 0.00 2.74
2944 3059 0.530870 GGCTAGCCATCGGAACTCAC 60.531 60.000 29.33 0.00 35.81 3.51
3159 3277 9.479549 AGTTAGAGAATTCAGAAGAGAAGAGAT 57.520 33.333 8.44 0.00 0.00 2.75
3163 3281 9.039165 AGAGAATTCAGAAGAGAAGAGATTTCT 57.961 33.333 8.44 0.00 33.90 2.52
3360 3479 3.367025 GGACCGTCGTATTTTGAAGTGAG 59.633 47.826 0.00 0.00 0.00 3.51
3398 3517 3.861341 TGGATACAGCTCAGCAACC 57.139 52.632 0.00 0.00 46.17 3.77
3399 3518 0.983467 TGGATACAGCTCAGCAACCA 59.017 50.000 0.00 0.00 46.17 3.67
3463 3583 2.886913 TGGGATGCCAAACAAATGAGA 58.113 42.857 2.13 0.00 0.00 3.27
3510 3632 6.492007 AAAAAGTGCAGTGATCATCTACAG 57.508 37.500 0.00 0.00 0.00 2.74
3513 3635 5.157940 AGTGCAGTGATCATCTACAGTTT 57.842 39.130 0.00 0.00 0.00 2.66
3573 3695 2.017049 CCACTATGGTAGCCAAAGTGC 58.983 52.381 11.03 0.00 36.95 4.40
3646 3768 7.702772 AGTGATGTCATGTCTATCGAGTAAAAC 59.297 37.037 0.00 0.00 0.00 2.43
3743 3867 7.093112 GGCCTGTCTACCTTCTGATATGATTAT 60.093 40.741 0.00 0.00 0.00 1.28
3836 3962 3.815809 TGTGGTTGTCTGGTAAGGAAAG 58.184 45.455 0.00 0.00 0.00 2.62
3837 3963 3.146847 GTGGTTGTCTGGTAAGGAAAGG 58.853 50.000 0.00 0.00 0.00 3.11
3856 3982 4.162040 AGGCTTTACAGCTCAGCAATAT 57.838 40.909 0.00 0.00 46.44 1.28
3921 4047 7.043986 CGATAAGACAAACTCCTGATAAGAACG 60.044 40.741 0.00 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 7.487484 TCATGAAGCAAGAAACATAAACACAA 58.513 30.769 0.00 0.00 0.00 3.33
92 94 3.843999 TGCCAAAAAGCATCGGAATTAC 58.156 40.909 0.00 0.00 38.00 1.89
209 215 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
210 216 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
211 217 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
212 218 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
213 219 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
214 220 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
215 221 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
216 222 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
218 224 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
220 226 8.359642 TGGACAAATCTAAGACAAGAATTTTGG 58.640 33.333 0.00 0.00 33.04 3.28
221 227 9.748708 TTGGACAAATCTAAGACAAGAATTTTG 57.251 29.630 0.00 0.00 34.13 2.44
227 233 7.333423 CCGTATTTGGACAAATCTAAGACAAGA 59.667 37.037 13.07 0.00 40.99 3.02
228 234 7.333423 TCCGTATTTGGACAAATCTAAGACAAG 59.667 37.037 13.07 2.30 40.99 3.16
229 235 7.162761 TCCGTATTTGGACAAATCTAAGACAA 58.837 34.615 13.07 0.00 40.99 3.18
230 236 6.703319 TCCGTATTTGGACAAATCTAAGACA 58.297 36.000 13.07 0.00 40.99 3.41
231 237 7.280205 ACATCCGTATTTGGACAAATCTAAGAC 59.720 37.037 13.07 5.74 41.85 3.01
232 238 7.335627 ACATCCGTATTTGGACAAATCTAAGA 58.664 34.615 13.07 7.57 41.85 2.10
233 239 7.553881 ACATCCGTATTTGGACAAATCTAAG 57.446 36.000 13.07 1.07 41.85 2.18
234 240 9.268268 GATACATCCGTATTTGGACAAATCTAA 57.732 33.333 13.07 0.00 41.85 2.10
235 241 8.425703 TGATACATCCGTATTTGGACAAATCTA 58.574 33.333 13.07 0.00 41.85 1.98
236 242 7.279615 TGATACATCCGTATTTGGACAAATCT 58.720 34.615 13.07 0.00 41.85 2.40
237 243 7.490962 TGATACATCCGTATTTGGACAAATC 57.509 36.000 13.07 5.63 41.85 2.17
239 245 6.882140 ACTTGATACATCCGTATTTGGACAAA 59.118 34.615 0.00 0.00 41.85 2.83
240 246 6.411376 ACTTGATACATCCGTATTTGGACAA 58.589 36.000 0.00 0.00 41.85 3.18
241 247 5.984725 ACTTGATACATCCGTATTTGGACA 58.015 37.500 0.00 0.00 41.85 4.02
242 248 6.018994 GTGACTTGATACATCCGTATTTGGAC 60.019 42.308 0.00 0.00 41.85 4.02
243 249 6.046593 GTGACTTGATACATCCGTATTTGGA 58.953 40.000 0.00 0.00 43.58 3.53
244 250 5.051039 CGTGACTTGATACATCCGTATTTGG 60.051 44.000 0.00 0.00 38.48 3.28
245 251 5.518847 ACGTGACTTGATACATCCGTATTTG 59.481 40.000 0.00 0.00 38.48 2.32
246 252 5.657474 ACGTGACTTGATACATCCGTATTT 58.343 37.500 0.00 0.00 38.48 1.40
247 253 5.258456 ACGTGACTTGATACATCCGTATT 57.742 39.130 0.00 0.00 38.48 1.89
248 254 4.913335 ACGTGACTTGATACATCCGTAT 57.087 40.909 0.00 0.00 41.16 3.06
249 255 4.707030 AACGTGACTTGATACATCCGTA 57.293 40.909 0.00 0.00 0.00 4.02
250 256 3.587797 AACGTGACTTGATACATCCGT 57.412 42.857 0.00 0.00 0.00 4.69
251 257 4.921470 AAAACGTGACTTGATACATCCG 57.079 40.909 0.00 0.00 0.00 4.18
252 258 6.963049 ACTAAAACGTGACTTGATACATCC 57.037 37.500 0.00 0.00 0.00 3.51
262 268 9.962783 GGATGTATCTAATACTAAAACGTGACT 57.037 33.333 0.00 0.00 36.70 3.41
263 269 8.899776 CGGATGTATCTAATACTAAAACGTGAC 58.100 37.037 0.00 0.00 36.70 3.67
264 270 8.623903 ACGGATGTATCTAATACTAAAACGTGA 58.376 33.333 0.00 0.00 36.70 4.35
265 271 8.792831 ACGGATGTATCTAATACTAAAACGTG 57.207 34.615 0.00 0.00 36.70 4.49
283 289 9.439500 GTCTTAGATTAGTCTAGATACGGATGT 57.561 37.037 0.00 0.00 38.17 3.06
284 290 9.438228 TGTCTTAGATTAGTCTAGATACGGATG 57.562 37.037 0.00 0.00 38.17 3.51
286 292 9.491675 CTTGTCTTAGATTAGTCTAGATACGGA 57.508 37.037 0.00 0.00 38.17 4.69
287 293 9.491675 TCTTGTCTTAGATTAGTCTAGATACGG 57.508 37.037 0.00 0.00 38.17 4.02
295 301 9.454859 CCCAAAATTCTTGTCTTAGATTAGTCT 57.545 33.333 0.00 0.00 38.52 3.24
296 302 9.449719 TCCCAAAATTCTTGTCTTAGATTAGTC 57.550 33.333 0.00 0.00 0.00 2.59
297 303 9.232473 GTCCCAAAATTCTTGTCTTAGATTAGT 57.768 33.333 0.00 0.00 0.00 2.24
298 304 9.231297 TGTCCCAAAATTCTTGTCTTAGATTAG 57.769 33.333 0.00 0.00 0.00 1.73
299 305 9.581289 TTGTCCCAAAATTCTTGTCTTAGATTA 57.419 29.630 0.00 0.00 0.00 1.75
300 306 8.477419 TTGTCCCAAAATTCTTGTCTTAGATT 57.523 30.769 0.00 0.00 0.00 2.40
301 307 8.477419 TTTGTCCCAAAATTCTTGTCTTAGAT 57.523 30.769 0.00 0.00 0.00 1.98
302 308 7.014230 CCTTTGTCCCAAAATTCTTGTCTTAGA 59.986 37.037 0.00 0.00 0.00 2.10
303 309 7.147976 CCTTTGTCCCAAAATTCTTGTCTTAG 58.852 38.462 0.00 0.00 0.00 2.18
304 310 6.041523 CCCTTTGTCCCAAAATTCTTGTCTTA 59.958 38.462 0.00 0.00 0.00 2.10
305 311 5.163311 CCCTTTGTCCCAAAATTCTTGTCTT 60.163 40.000 0.00 0.00 0.00 3.01
306 312 4.344968 CCCTTTGTCCCAAAATTCTTGTCT 59.655 41.667 0.00 0.00 0.00 3.41
307 313 4.343814 TCCCTTTGTCCCAAAATTCTTGTC 59.656 41.667 0.00 0.00 0.00 3.18
308 314 4.294347 TCCCTTTGTCCCAAAATTCTTGT 58.706 39.130 0.00 0.00 0.00 3.16
309 315 4.344968 ACTCCCTTTGTCCCAAAATTCTTG 59.655 41.667 0.00 0.00 0.00 3.02
310 316 4.556697 ACTCCCTTTGTCCCAAAATTCTT 58.443 39.130 0.00 0.00 0.00 2.52
311 317 4.199002 ACTCCCTTTGTCCCAAAATTCT 57.801 40.909 0.00 0.00 0.00 2.40
312 318 4.830600 TGTACTCCCTTTGTCCCAAAATTC 59.169 41.667 0.00 0.00 0.00 2.17
313 319 4.810345 TGTACTCCCTTTGTCCCAAAATT 58.190 39.130 0.00 0.00 0.00 1.82
314 320 4.463050 TGTACTCCCTTTGTCCCAAAAT 57.537 40.909 0.00 0.00 0.00 1.82
315 321 3.955524 TGTACTCCCTTTGTCCCAAAA 57.044 42.857 0.00 0.00 0.00 2.44
316 322 3.245122 GGATGTACTCCCTTTGTCCCAAA 60.245 47.826 0.00 0.00 38.19 3.28
317 323 2.307686 GGATGTACTCCCTTTGTCCCAA 59.692 50.000 0.00 0.00 38.19 4.12
318 324 1.913419 GGATGTACTCCCTTTGTCCCA 59.087 52.381 0.00 0.00 38.19 4.37
319 325 2.197465 AGGATGTACTCCCTTTGTCCC 58.803 52.381 7.50 0.00 46.27 4.46
320 326 3.009143 ACAAGGATGTACTCCCTTTGTCC 59.991 47.826 14.12 0.00 46.27 4.02
321 327 4.287766 ACAAGGATGTACTCCCTTTGTC 57.712 45.455 14.12 0.00 46.27 3.18
322 328 4.724279 AACAAGGATGTACTCCCTTTGT 57.276 40.909 14.12 12.11 46.27 2.83
323 329 7.362920 CCAATAAACAAGGATGTACTCCCTTTG 60.363 40.741 14.12 11.64 46.27 2.77
324 330 6.663523 CCAATAAACAAGGATGTACTCCCTTT 59.336 38.462 14.12 9.13 46.27 3.11
325 331 6.187682 CCAATAAACAAGGATGTACTCCCTT 58.812 40.000 11.85 11.85 46.27 3.95
326 332 5.253096 ACCAATAAACAAGGATGTACTCCCT 59.747 40.000 7.50 4.66 46.27 4.20
327 333 5.506708 ACCAATAAACAAGGATGTACTCCC 58.493 41.667 7.50 2.60 46.27 4.30
351 357 8.632679 CAAGAGCATCAGGCCTTATAATAAAAA 58.367 33.333 0.00 0.00 46.50 1.94
352 358 7.998383 TCAAGAGCATCAGGCCTTATAATAAAA 59.002 33.333 0.00 0.00 46.50 1.52
353 359 7.517320 TCAAGAGCATCAGGCCTTATAATAAA 58.483 34.615 0.00 0.00 46.50 1.40
361 367 2.822707 ATTCAAGAGCATCAGGCCTT 57.177 45.000 0.00 0.00 46.50 4.35
409 415 5.105797 TGCCATTTTCACATCTTACATCCAC 60.106 40.000 0.00 0.00 0.00 4.02
419 427 2.352503 AGCGTTGCCATTTTCACATC 57.647 45.000 0.00 0.00 0.00 3.06
434 442 1.904287 TGCAGTAAAATGGGAAGCGT 58.096 45.000 0.00 0.00 0.00 5.07
435 443 3.296322 TTTGCAGTAAAATGGGAAGCG 57.704 42.857 0.00 0.00 0.00 4.68
452 463 8.592105 TTCTTTCTTGCAAGAATACCATTTTG 57.408 30.769 35.66 18.95 43.92 2.44
464 476 8.571336 TCTATTTCCTTCTTTCTTTCTTGCAAG 58.429 33.333 20.81 20.81 0.00 4.01
482 494 0.876342 CGCCTCGGCACTCTATTTCC 60.876 60.000 8.87 0.00 42.06 3.13
483 495 0.876342 CCGCCTCGGCACTCTATTTC 60.876 60.000 8.87 0.00 41.17 2.17
484 496 1.144057 CCGCCTCGGCACTCTATTT 59.856 57.895 8.87 0.00 41.17 1.40
485 497 2.815308 CCGCCTCGGCACTCTATT 59.185 61.111 8.87 0.00 41.17 1.73
495 507 0.458889 TCACCGTATTTTCCGCCTCG 60.459 55.000 0.00 0.00 0.00 4.63
496 508 1.004595 GTCACCGTATTTTCCGCCTC 58.995 55.000 0.00 0.00 0.00 4.70
507 519 0.600782 GCTTTCAACCCGTCACCGTA 60.601 55.000 0.00 0.00 0.00 4.02
512 524 2.147958 GTGTATGCTTTCAACCCGTCA 58.852 47.619 0.00 0.00 0.00 4.35
525 537 0.367548 TTTTCGCGCTACGTGTATGC 59.632 50.000 5.56 0.00 44.19 3.14
528 540 1.062258 CCTTTTTCGCGCTACGTGTA 58.938 50.000 5.56 0.00 44.19 2.90
546 558 2.198406 GTTTTGGTTCGAACTTTGGCC 58.802 47.619 26.32 10.54 0.00 5.36
549 561 7.569677 TTACTTTGTTTTGGTTCGAACTTTG 57.430 32.000 26.32 9.88 0.00 2.77
562 574 7.570132 ACCCTTGCCTTTATTTACTTTGTTTT 58.430 30.769 0.00 0.00 0.00 2.43
663 685 3.867493 GGCGTACTTGTGGGTATTCTAAC 59.133 47.826 0.00 0.00 0.00 2.34
816 843 1.548269 CTTGTCTCACTCTCACTCCCC 59.452 57.143 0.00 0.00 0.00 4.81
818 845 1.067213 GGCTTGTCTCACTCTCACTCC 60.067 57.143 0.00 0.00 0.00 3.85
878 912 8.630054 TGGTTTGGTTTATATGATATGGCTAC 57.370 34.615 0.00 0.00 0.00 3.58
915 956 0.179171 CTTATGTGCACTGCTGCTGC 60.179 55.000 19.41 8.89 44.57 5.25
916 957 1.445871 TCTTATGTGCACTGCTGCTG 58.554 50.000 19.41 4.89 44.57 4.41
917 958 1.808945 GTTCTTATGTGCACTGCTGCT 59.191 47.619 19.41 0.00 44.57 4.24
918 959 1.536766 TGTTCTTATGTGCACTGCTGC 59.463 47.619 19.41 0.00 44.52 5.25
919 960 3.069289 TCTGTTCTTATGTGCACTGCTG 58.931 45.455 19.41 6.29 0.00 4.41
920 961 3.332919 CTCTGTTCTTATGTGCACTGCT 58.667 45.455 19.41 5.41 0.00 4.24
921 962 2.159599 GCTCTGTTCTTATGTGCACTGC 60.160 50.000 19.41 0.00 0.00 4.40
984 1025 1.440893 CATCTCGGTCCAGCTCCTG 59.559 63.158 0.00 0.00 0.00 3.86
987 1028 1.439644 GTCCATCTCGGTCCAGCTC 59.560 63.158 0.00 0.00 35.57 4.09
990 1031 2.808315 CCGTCCATCTCGGTCCAG 59.192 66.667 0.00 0.00 42.62 3.86
996 1037 0.385751 AGTACATGCCGTCCATCTCG 59.614 55.000 0.00 0.00 29.71 4.04
997 1038 2.288273 GGTAGTACATGCCGTCCATCTC 60.288 54.545 2.06 0.00 29.71 2.75
1003 1044 1.067212 CTGAGGGTAGTACATGCCGTC 59.933 57.143 2.06 12.88 45.65 4.79
1134 1175 3.503363 GGCGTCTGCAGCATGGAC 61.503 66.667 9.47 0.00 45.35 4.02
1520 1561 5.473504 GGAAGAAAATGAGCAGTAGGTGAAA 59.526 40.000 0.00 0.00 0.00 2.69
1525 1566 7.814264 AATATGGAAGAAAATGAGCAGTAGG 57.186 36.000 0.00 0.00 0.00 3.18
1527 1568 7.340232 AGCAAATATGGAAGAAAATGAGCAGTA 59.660 33.333 0.00 0.00 0.00 2.74
1530 1571 6.406177 GGAGCAAATATGGAAGAAAATGAGCA 60.406 38.462 0.00 0.00 0.00 4.26
1532 1573 7.284944 AGAGGAGCAAATATGGAAGAAAATGAG 59.715 37.037 0.00 0.00 0.00 2.90
1609 1651 5.105752 GGCGGCTATAGTTGAGATTATCAG 58.894 45.833 0.00 0.00 39.68 2.90
1628 1670 2.336478 TTATGTTTGTGCCGGGCGG 61.336 57.895 15.40 0.00 38.57 6.13
1629 1671 1.154112 GTTATGTTTGTGCCGGGCG 60.154 57.895 15.40 0.00 0.00 6.13
1630 1672 0.315568 TTGTTATGTTTGTGCCGGGC 59.684 50.000 13.32 13.32 0.00 6.13
1631 1673 2.802787 TTTGTTATGTTTGTGCCGGG 57.197 45.000 2.18 0.00 0.00 5.73
1690 1732 4.616835 GCAACTGGTGAACTGGATCAATTC 60.617 45.833 0.00 0.00 0.00 2.17
1691 1733 3.256631 GCAACTGGTGAACTGGATCAATT 59.743 43.478 0.00 0.00 0.00 2.32
1733 1775 3.820467 TGAACATAAACCTGTGCTTGAGG 59.180 43.478 0.00 0.00 36.57 3.86
1789 1831 1.691434 TGGGTTTTGAATCTTGGTGGC 59.309 47.619 0.00 0.00 0.00 5.01
2015 2057 0.381445 TGTATGCGCATGATGTTGGC 59.619 50.000 32.48 11.92 0.00 4.52
2063 2105 0.114364 TCCACTGGTAGCAGTCCTCA 59.886 55.000 24.25 6.18 32.26 3.86
2102 2144 2.674177 GCACGAGTTACACTGGTAGCAT 60.674 50.000 0.00 0.00 34.88 3.79
2252 2294 1.671979 CGTATGGGTACTCGGAGACA 58.328 55.000 12.86 5.56 0.00 3.41
2354 2397 4.021719 AGCAATCAAACAGAAATGGAGTGG 60.022 41.667 0.00 0.00 0.00 4.00
2358 2401 3.575256 AGCAGCAATCAAACAGAAATGGA 59.425 39.130 0.00 0.00 0.00 3.41
2402 2445 3.069443 GGGCTGAAACCAAACATCTGAAA 59.931 43.478 0.00 0.00 0.00 2.69
2803 2918 7.165485 ACAGAAACTGTGTTATATTGCCAGTA 58.835 34.615 3.54 0.00 43.63 2.74
2821 2936 5.391312 AATAGATGGCCACAAACAGAAAC 57.609 39.130 8.16 0.00 0.00 2.78
2826 2941 3.164268 AGCAAATAGATGGCCACAAACA 58.836 40.909 8.16 0.00 0.00 2.83
2848 2963 7.335422 ACCATAAAGCAGTGTTAGAGAAATCAG 59.665 37.037 0.00 0.00 0.00 2.90
2855 2970 6.363357 GCAAAAACCATAAAGCAGTGTTAGAG 59.637 38.462 0.00 0.00 0.00 2.43
2873 2988 0.948678 TCGCCACCTGTAGCAAAAAC 59.051 50.000 0.00 0.00 0.00 2.43
2971 3086 2.755469 CCAACCCCTCGGCCATTG 60.755 66.667 2.24 0.00 0.00 2.82
3159 3277 5.222233 TGGATTTCCCACCATAGACAAGAAA 60.222 40.000 0.00 0.00 40.82 2.52
3163 3281 3.591527 ACTGGATTTCCCACCATAGACAA 59.408 43.478 0.00 0.00 40.82 3.18
3292 3411 4.714308 AGAGCCTGTCTTAGATTTAGCTGT 59.286 41.667 0.00 0.00 27.07 4.40
3360 3479 7.617041 ATCCACTATCTAAAGTGCTTTCAAC 57.383 36.000 0.00 0.00 44.56 3.18
3439 3559 5.483231 TCTCATTTGTTTGGCATCCCATTAA 59.517 36.000 0.00 0.00 41.78 1.40
3513 3635 8.100791 GGGATATATGCTCTTGTAACCAATACA 58.899 37.037 4.09 0.00 42.75 2.29
3527 3649 7.406104 AGAAAGGTTAATGGGGATATATGCTC 58.594 38.462 4.09 0.02 0.00 4.26
3537 3659 3.739401 AGTGGAGAAAGGTTAATGGGG 57.261 47.619 0.00 0.00 0.00 4.96
3618 3740 6.214191 ACTCGATAGACATGACATCACTTT 57.786 37.500 0.00 0.00 42.67 2.66
3646 3768 4.250116 GTCATATAGCTGACTCTGTGGG 57.750 50.000 0.00 0.00 41.87 4.61
3670 3794 3.076621 ACCAACAGTACATGTGCTGATG 58.923 45.455 39.60 36.02 44.51 3.07
3743 3867 3.527937 AGGTTTAGCCTCAGTTTAGGGA 58.472 45.455 0.00 0.00 46.96 4.20
3810 3936 5.942961 TCCTTACCAGACAACCACATAAAA 58.057 37.500 0.00 0.00 0.00 1.52
3811 3937 5.570205 TCCTTACCAGACAACCACATAAA 57.430 39.130 0.00 0.00 0.00 1.40
3812 3938 5.570205 TTCCTTACCAGACAACCACATAA 57.430 39.130 0.00 0.00 0.00 1.90
3813 3939 5.514136 CCTTTCCTTACCAGACAACCACATA 60.514 44.000 0.00 0.00 0.00 2.29
3814 3940 4.398319 CTTTCCTTACCAGACAACCACAT 58.602 43.478 0.00 0.00 0.00 3.21
3815 3941 3.434453 CCTTTCCTTACCAGACAACCACA 60.434 47.826 0.00 0.00 0.00 4.17
3836 3962 4.907879 AATATTGCTGAGCTGTAAAGCC 57.092 40.909 5.83 0.00 36.05 4.35
3837 3963 5.883661 TGAAATATTGCTGAGCTGTAAAGC 58.116 37.500 5.83 0.00 37.46 3.51
3874 4000 7.807977 ATCGTTACATTATTCTGCCTTGAAT 57.192 32.000 0.00 0.00 39.63 2.57


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

AutoCloner maintained by Alex Coulton.