Multiple sequence alignment - TraesCS2B01G055500

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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 TraesCS2B01G055500 chr2B 100.000 2584 0 0 1 2584 27016450 27019033 0.000000e+00 4772
1 TraesCS2B01G055500 chr2B 88.344 1304 74 37 499 1774 27029641 27030894 0.000000e+00 1495
2 TraesCS2B01G055500 chr2B 89.110 854 60 14 1250 2097 27070937 27071763 0.000000e+00 1031
3 TraesCS2B01G055500 chr2B 85.881 772 55 24 493 1249 27070172 27070904 0.000000e+00 773
4 TraesCS2B01G055500 chr2B 94.706 340 15 3 1574 1910 27031483 27031822 2.280000e-145 525
5 TraesCS2B01G055500 chr2B 85.911 291 18 6 1499 1774 27031851 27032133 3.250000e-74 289
6 TraesCS2B01G055500 chr2B 82.857 175 24 6 2 174 27052458 27052628 4.450000e-33 152
7 TraesCS2B01G055500 chr2D 93.830 778 39 5 1812 2584 14985379 14986152 0.000000e+00 1162
8 TraesCS2B01G055500 chr2D 93.702 778 40 5 1812 2584 15019348 15020121 0.000000e+00 1157
9 TraesCS2B01G055500 chr2D 88.590 780 50 20 492 1249 14976271 14977033 0.000000e+00 911
10 TraesCS2B01G055500 chr2D 91.714 531 35 7 1250 1776 14977066 14977591 0.000000e+00 728
11 TraesCS2B01G055500 chr2D 90.909 418 31 1 1250 1667 15016140 15016550 2.910000e-154 555
12 TraesCS2B01G055500 chr2D 91.667 384 24 4 868 1247 15015726 15016105 2.280000e-145 525
13 TraesCS2B01G055500 chr2D 84.735 321 28 8 1779 2097 15010325 15010626 4.180000e-78 302
14 TraesCS2B01G055500 chr2D 85.911 291 25 9 1317 1595 15583542 15583828 1.940000e-76 296
15 TraesCS2B01G055500 chr2D 92.903 155 7 3 1664 1816 15018677 15018829 3.350000e-54 222
16 TraesCS2B01G055500 chr2D 92.258 155 7 2 1664 1816 14984707 14984858 5.600000e-52 215
17 TraesCS2B01G055500 chr2D 83.957 187 20 6 1 187 14975865 14976041 1.230000e-38 171
18 TraesCS2B01G055500 chr2D 93.458 107 5 1 2113 2219 15010612 15010716 9.570000e-35 158
19 TraesCS2B01G055500 chr2A 91.057 615 43 8 1250 1859 17133696 17134303 0.000000e+00 821
20 TraesCS2B01G055500 chr2A 87.032 694 44 22 587 1249 17132985 17133663 0.000000e+00 741
21 TraesCS2B01G055500 chr2A 86.066 244 32 2 1337 1579 17610815 17611057 7.090000e-66 261


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 TraesCS2B01G055500 chr2B 27016450 27019033 2583 False 4772.000000 4772 100.000000 1 2584 1 chr2B.!!$F1 2583
1 TraesCS2B01G055500 chr2B 27070172 27071763 1591 False 902.000000 1031 87.495500 493 2097 2 chr2B.!!$F4 1604
2 TraesCS2B01G055500 chr2B 27029641 27032133 2492 False 769.666667 1495 89.653667 499 1910 3 chr2B.!!$F3 1411
3 TraesCS2B01G055500 chr2D 14984707 14986152 1445 False 688.500000 1162 93.044000 1664 2584 2 chr2D.!!$F3 920
4 TraesCS2B01G055500 chr2D 15015726 15020121 4395 False 614.750000 1157 92.295250 868 2584 4 chr2D.!!$F5 1716
5 TraesCS2B01G055500 chr2D 14975865 14977591 1726 False 603.333333 911 88.087000 1 1776 3 chr2D.!!$F2 1775
6 TraesCS2B01G055500 chr2A 17132985 17134303 1318 False 781.000000 821 89.044500 587 1859 2 chr2A.!!$F2 1272

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
660 732 0.028902 TGGTATCGTGATCTCGTGCG 59.971 55.0 16.03 3.07 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1915 6070 0.690762 AGCGGCCCAACTTTCTAGAA 59.309 50.0 0.0 0.0 0.0 2.1 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
217 236 8.528044 TTTTTAACTACTTGAACAGATGGGTT 57.472 30.769 0.00 0.00 0.00 4.11
218 237 8.528044 TTTTAACTACTTGAACAGATGGGTTT 57.472 30.769 0.00 0.00 0.00 3.27
219 238 9.629878 TTTTAACTACTTGAACAGATGGGTTTA 57.370 29.630 0.00 0.00 0.00 2.01
220 239 8.842358 TTAACTACTTGAACAGATGGGTTTAG 57.158 34.615 0.00 0.00 0.00 1.85
221 240 6.435292 ACTACTTGAACAGATGGGTTTAGT 57.565 37.500 0.00 0.00 33.45 2.24
222 241 6.465084 ACTACTTGAACAGATGGGTTTAGTC 58.535 40.000 0.00 0.00 32.15 2.59
223 242 4.652822 ACTTGAACAGATGGGTTTAGTCC 58.347 43.478 0.00 0.00 0.00 3.85
224 243 4.351111 ACTTGAACAGATGGGTTTAGTCCT 59.649 41.667 0.00 0.00 0.00 3.85
225 244 4.993705 TGAACAGATGGGTTTAGTCCTT 57.006 40.909 0.00 0.00 0.00 3.36
226 245 5.319043 TGAACAGATGGGTTTAGTCCTTT 57.681 39.130 0.00 0.00 0.00 3.11
227 246 5.313712 TGAACAGATGGGTTTAGTCCTTTC 58.686 41.667 0.00 0.00 0.00 2.62
228 247 4.302559 ACAGATGGGTTTAGTCCTTTCC 57.697 45.455 0.00 0.00 0.00 3.13
229 248 3.916989 ACAGATGGGTTTAGTCCTTTCCT 59.083 43.478 0.00 0.00 0.00 3.36
230 249 4.354087 ACAGATGGGTTTAGTCCTTTCCTT 59.646 41.667 0.00 0.00 0.00 3.36
231 250 4.944317 CAGATGGGTTTAGTCCTTTCCTTC 59.056 45.833 0.00 0.00 0.00 3.46
232 251 3.412237 TGGGTTTAGTCCTTTCCTTCG 57.588 47.619 0.00 0.00 0.00 3.79
233 252 2.039348 TGGGTTTAGTCCTTTCCTTCGG 59.961 50.000 0.00 0.00 0.00 4.30
234 253 2.617276 GGGTTTAGTCCTTTCCTTCGGG 60.617 54.545 0.00 0.00 0.00 5.14
235 254 2.039480 GGTTTAGTCCTTTCCTTCGGGT 59.961 50.000 0.00 0.00 36.28 5.28
236 255 3.261643 GGTTTAGTCCTTTCCTTCGGGTA 59.738 47.826 0.00 0.00 36.28 3.69
237 256 4.263025 GGTTTAGTCCTTTCCTTCGGGTAA 60.263 45.833 0.00 0.00 36.28 2.85
238 257 4.541973 TTAGTCCTTTCCTTCGGGTAAC 57.458 45.455 0.00 0.00 36.28 2.50
239 258 2.332117 AGTCCTTTCCTTCGGGTAACA 58.668 47.619 0.00 0.00 39.74 2.41
240 259 2.910977 AGTCCTTTCCTTCGGGTAACAT 59.089 45.455 0.00 0.00 39.74 2.71
241 260 3.329814 AGTCCTTTCCTTCGGGTAACATT 59.670 43.478 0.00 0.00 39.74 2.71
242 261 4.077108 GTCCTTTCCTTCGGGTAACATTT 58.923 43.478 0.00 0.00 39.74 2.32
243 262 4.521639 GTCCTTTCCTTCGGGTAACATTTT 59.478 41.667 0.00 0.00 39.74 1.82
244 263 4.763279 TCCTTTCCTTCGGGTAACATTTTC 59.237 41.667 0.00 0.00 39.74 2.29
245 264 4.765339 CCTTTCCTTCGGGTAACATTTTCT 59.235 41.667 0.00 0.00 39.74 2.52
246 265 5.106277 CCTTTCCTTCGGGTAACATTTTCTC 60.106 44.000 0.00 0.00 39.74 2.87
247 266 3.946606 TCCTTCGGGTAACATTTTCTCC 58.053 45.455 0.00 0.00 39.74 3.71
248 267 2.676342 CCTTCGGGTAACATTTTCTCCG 59.324 50.000 0.00 0.00 38.92 4.63
249 268 2.389962 TCGGGTAACATTTTCTCCGG 57.610 50.000 0.00 0.00 38.21 5.14
250 269 1.065998 TCGGGTAACATTTTCTCCGGG 60.066 52.381 0.00 0.00 38.21 5.73
251 270 1.339342 CGGGTAACATTTTCTCCGGGT 60.339 52.381 0.00 0.00 39.74 5.28
252 271 2.093553 CGGGTAACATTTTCTCCGGGTA 60.094 50.000 0.00 0.00 39.74 3.69
253 272 3.273434 GGGTAACATTTTCTCCGGGTAC 58.727 50.000 0.00 0.00 39.74 3.34
254 273 3.932638 GGGTAACATTTTCTCCGGGTACC 60.933 52.174 2.17 2.17 43.85 3.34
266 285 4.459199 GGTACCACCGGTCCCTAA 57.541 61.111 2.59 0.00 37.09 2.69
267 286 2.682631 GGTACCACCGGTCCCTAAA 58.317 57.895 2.59 0.00 37.09 1.85
268 287 1.206878 GGTACCACCGGTCCCTAAAT 58.793 55.000 2.59 0.00 37.09 1.40
269 288 2.397597 GGTACCACCGGTCCCTAAATA 58.602 52.381 2.59 0.00 37.09 1.40
270 289 2.974794 GGTACCACCGGTCCCTAAATAT 59.025 50.000 2.59 0.00 37.09 1.28
271 290 3.392285 GGTACCACCGGTCCCTAAATATT 59.608 47.826 2.59 0.00 37.09 1.28
272 291 4.141413 GGTACCACCGGTCCCTAAATATTT 60.141 45.833 2.59 5.89 37.09 1.40
273 292 4.596354 ACCACCGGTCCCTAAATATTTT 57.404 40.909 2.59 0.00 0.00 1.82
274 293 4.938028 ACCACCGGTCCCTAAATATTTTT 58.062 39.130 2.59 0.00 0.00 1.94
304 323 2.815478 TGAACAAAATGTGGAAACGGC 58.185 42.857 0.00 0.00 0.00 5.68
307 326 1.405821 ACAAAATGTGGAAACGGCGAA 59.594 42.857 16.62 0.00 0.00 4.70
312 331 4.506886 AATGTGGAAACGGCGAATTTTA 57.493 36.364 16.62 0.00 0.00 1.52
313 332 3.984508 TGTGGAAACGGCGAATTTTAA 57.015 38.095 16.62 0.00 0.00 1.52
314 333 4.303086 TGTGGAAACGGCGAATTTTAAA 57.697 36.364 16.62 0.00 0.00 1.52
341 361 7.850268 AACACAAACACTTTTTCAATTTTGC 57.150 28.000 0.00 0.00 0.00 3.68
344 364 7.917505 ACACAAACACTTTTTCAATTTTGCAAA 59.082 25.926 8.05 8.05 0.00 3.68
345 365 8.418681 CACAAACACTTTTTCAATTTTGCAAAG 58.581 29.630 12.41 1.05 35.76 2.77
380 400 9.918630 ATAACAGGAACATTTTCTGAAATTCAG 57.081 29.630 16.39 16.39 45.59 3.02
422 442 7.585286 ACATGAACATTCATTGAAATTTCCG 57.415 32.000 15.48 4.58 45.13 4.30
423 443 7.377398 ACATGAACATTCATTGAAATTTCCGA 58.623 30.769 15.48 6.82 45.13 4.55
424 444 7.871973 ACATGAACATTCATTGAAATTTCCGAA 59.128 29.630 15.48 14.49 45.13 4.30
425 445 7.636259 TGAACATTCATTGAAATTTCCGAAC 57.364 32.000 15.48 5.10 31.01 3.95
426 446 7.205992 TGAACATTCATTGAAATTTCCGAACA 58.794 30.769 15.48 7.18 31.01 3.18
427 447 7.871973 TGAACATTCATTGAAATTTCCGAACAT 59.128 29.630 15.48 5.31 31.01 2.71
428 448 8.606040 AACATTCATTGAAATTTCCGAACATT 57.394 26.923 15.48 9.94 0.00 2.71
429 449 8.606040 ACATTCATTGAAATTTCCGAACATTT 57.394 26.923 15.48 0.00 0.00 2.32
430 450 9.703892 ACATTCATTGAAATTTCCGAACATTTA 57.296 25.926 15.48 0.00 0.00 1.40
434 454 9.920133 TCATTGAAATTTCCGAACATTTATTGA 57.080 25.926 15.48 3.50 0.00 2.57
438 458 9.973450 TGAAATTTCCGAACATTTATTGAAAGA 57.027 25.926 15.48 0.00 0.00 2.52
440 460 9.757227 AAATTTCCGAACATTTATTGAAAGACA 57.243 25.926 0.00 0.00 0.00 3.41
441 461 9.757227 AATTTCCGAACATTTATTGAAAGACAA 57.243 25.926 0.00 0.00 42.95 3.18
442 462 9.757227 ATTTCCGAACATTTATTGAAAGACAAA 57.243 25.926 0.00 0.00 42.03 2.83
443 463 9.587772 TTTCCGAACATTTATTGAAAGACAAAA 57.412 25.926 0.00 0.00 42.03 2.44
444 464 9.757227 TTCCGAACATTTATTGAAAGACAAAAT 57.243 25.926 0.00 0.00 42.03 1.82
445 465 9.757227 TCCGAACATTTATTGAAAGACAAAATT 57.243 25.926 0.00 0.00 42.03 1.82
477 497 7.720515 TGGAAAAGAAAAGGTATTAAGGAACGA 59.279 33.333 0.00 0.00 0.00 3.85
483 503 8.810041 AGAAAAGGTATTAAGGAACGAGTAGAA 58.190 33.333 0.00 0.00 0.00 2.10
512 570 5.720202 TGGATGATGTGTACAACTGTAGAC 58.280 41.667 9.58 9.58 42.89 2.59
593 664 2.202703 CCTGTACGTACCAGCCGC 60.203 66.667 22.43 0.00 0.00 6.53
596 667 4.860261 GTACGTACCAGCCGCCGG 62.860 72.222 15.00 0.00 0.00 6.13
619 691 1.807226 GGGCGCCAGGATTACAAAC 59.193 57.895 30.85 1.22 0.00 2.93
644 716 0.822164 ATCCTACGTTAAGCGCTGGT 59.178 50.000 12.58 9.88 46.11 4.00
660 732 0.028902 TGGTATCGTGATCTCGTGCG 59.971 55.000 16.03 3.07 0.00 5.34
746 822 6.884295 GGAAATCCCGTATGAATCCATAATGA 59.116 38.462 0.00 0.00 37.04 2.57
805 900 6.838198 CCATGATAAGGCATTGACATTTTG 57.162 37.500 0.00 0.00 0.00 2.44
806 901 6.342906 CCATGATAAGGCATTGACATTTTGT 58.657 36.000 0.00 0.00 0.00 2.83
808 903 7.010738 CCATGATAAGGCATTGACATTTTGTTC 59.989 37.037 0.00 0.00 0.00 3.18
809 904 7.230849 TGATAAGGCATTGACATTTTGTTCT 57.769 32.000 0.00 0.00 0.00 3.01
810 905 7.669427 TGATAAGGCATTGACATTTTGTTCTT 58.331 30.769 0.00 0.00 0.00 2.52
811 906 8.149647 TGATAAGGCATTGACATTTTGTTCTTT 58.850 29.630 0.00 0.00 0.00 2.52
812 907 8.907222 ATAAGGCATTGACATTTTGTTCTTTT 57.093 26.923 0.00 0.00 0.00 2.27
813 908 6.607735 AGGCATTGACATTTTGTTCTTTTG 57.392 33.333 0.00 0.00 0.00 2.44
815 910 6.598850 AGGCATTGACATTTTGTTCTTTTGTT 59.401 30.769 0.00 0.00 0.00 2.83
850 964 6.374333 GGTTGATAAAGGCATTGACTTGACTA 59.626 38.462 5.29 0.00 32.32 2.59
860 980 2.047061 TGACTTGACTAGCACACCCTT 58.953 47.619 0.00 0.00 0.00 3.95
887 1011 9.877178 CTGGATTGTGTCTATAAATATAGTCCC 57.123 37.037 7.21 0.00 37.51 4.46
908 1033 3.498481 CCCATGTTTGTTCTTGGAGGAGA 60.498 47.826 0.00 0.00 35.49 3.71
916 1041 5.110814 TGTTCTTGGAGGAGAAAAACAGA 57.889 39.130 0.00 0.00 37.40 3.41
944 1069 1.396653 CATAGCCTTCCCTGCAAAGG 58.603 55.000 10.77 10.77 45.12 3.11
945 1070 1.002857 ATAGCCTTCCCTGCAAAGGT 58.997 50.000 15.44 6.72 44.34 3.50
986 1121 2.957006 CCAACTAGCTACGTACCCATCT 59.043 50.000 0.00 0.00 0.00 2.90
990 1125 1.984066 AGCTACGTACCCATCTCTCC 58.016 55.000 0.00 0.00 0.00 3.71
1077 1213 2.028130 ACCGGATTGTCAAGTTTTGCA 58.972 42.857 9.46 0.00 0.00 4.08
1119 1255 2.035626 ATTTGGAGCACACCGGGG 59.964 61.111 0.00 0.00 0.00 5.73
1176 1312 2.792890 CGTCGACACCAAAAACAATGCA 60.793 45.455 17.16 0.00 0.00 3.96
1297 1468 4.142049 CCAATGTACATTGCGGGGTTAATT 60.142 41.667 33.78 3.60 45.06 1.40
1310 1481 5.591099 CGGGGTTAATTTCTTCATTCATGG 58.409 41.667 0.00 0.00 0.00 3.66
1335 1508 7.417116 GGGTGAATTATTTCTTGTGATCATGCT 60.417 37.037 0.00 0.00 32.78 3.79
1627 1804 1.762957 GCCTGGCTGGTCACTCTATAA 59.237 52.381 12.43 0.00 38.35 0.98
1628 1805 2.370189 GCCTGGCTGGTCACTCTATAAT 59.630 50.000 12.43 0.00 38.35 1.28
1629 1806 3.805108 GCCTGGCTGGTCACTCTATAATG 60.805 52.174 12.43 0.00 38.35 1.90
1808 4914 9.667989 GTTAAGCTTGTAATAAAAAGTTTCGGA 57.332 29.630 9.86 0.00 30.71 4.55
1844 5999 1.815003 GGACAACAAGGAATCCTGCTG 59.185 52.381 0.90 0.15 32.13 4.41
1915 6070 2.118679 TGAATGGAGATCCGACCACAT 58.881 47.619 6.12 0.19 39.06 3.21
1934 6089 0.690762 TTCTAGAAAGTTGGGCCGCT 59.309 50.000 1.68 0.00 0.00 5.52
1943 6098 1.280998 AGTTGGGCCGCTTATGTACTT 59.719 47.619 0.00 0.00 0.00 2.24
1944 6099 2.502538 AGTTGGGCCGCTTATGTACTTA 59.497 45.455 0.00 0.00 0.00 2.24
1945 6100 2.870411 GTTGGGCCGCTTATGTACTTAG 59.130 50.000 0.00 0.00 0.00 2.18
1975 6130 5.728471 TCTTCTTGGAGACTTCATAAGCTG 58.272 41.667 0.00 0.00 0.00 4.24
2037 6192 0.899720 CCCTTTGGTCTACCTACGCA 59.100 55.000 0.02 0.00 36.82 5.24
2061 6216 1.159713 AGCATGTGTGACACCGTGTG 61.160 55.000 13.85 8.02 39.75 3.82
2064 6219 3.276846 GTGTGACACCGTGTGGCC 61.277 66.667 9.42 0.00 41.60 5.36
2089 6244 3.181465 ACATTTGCACGCTATAGCTAGGT 60.181 43.478 21.98 10.27 39.32 3.08
2117 6272 4.741676 CCTGTTGCTCAAAACAAAAGCTAG 59.258 41.667 0.00 0.00 39.47 3.42
2178 6333 9.838339 AAGAAAATCTACACCGATTGATAAGAT 57.162 29.630 0.00 0.00 34.07 2.40
2480 6640 0.238289 CAACGTTGACAGCCCACATC 59.762 55.000 23.90 0.00 0.00 3.06
2498 6658 2.401583 TCGGCAGCTGACACATTTAT 57.598 45.000 22.03 0.00 0.00 1.40
2536 6696 6.042666 TGGAGCATACCTATTGCACACTATAA 59.957 38.462 0.00 0.00 42.62 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 0.459759 GCTACAGTAACCAGACCGCC 60.460 60.000 0.00 0.00 0.00 6.13
32 33 0.806868 TCGCTACAGTAACCAGACCG 59.193 55.000 0.00 0.00 0.00 4.79
42 43 1.177256 AGTGAACGGGTCGCTACAGT 61.177 55.000 7.46 0.00 45.52 3.55
43 44 0.732880 CAGTGAACGGGTCGCTACAG 60.733 60.000 9.07 0.00 45.61 2.74
199 218 5.875359 GGACTAAACCCATCTGTTCAAGTAG 59.125 44.000 0.00 0.00 29.52 2.57
200 219 5.546499 AGGACTAAACCCATCTGTTCAAGTA 59.454 40.000 0.00 0.00 29.52 2.24
201 220 4.351111 AGGACTAAACCCATCTGTTCAAGT 59.649 41.667 0.00 0.00 31.06 3.16
203 222 4.993705 AGGACTAAACCCATCTGTTCAA 57.006 40.909 0.00 0.00 0.00 2.69
204 223 4.993705 AAGGACTAAACCCATCTGTTCA 57.006 40.909 0.00 0.00 0.00 3.18
205 224 4.700692 GGAAAGGACTAAACCCATCTGTTC 59.299 45.833 0.00 0.00 0.00 3.18
206 225 4.354087 AGGAAAGGACTAAACCCATCTGTT 59.646 41.667 0.00 0.00 0.00 3.16
207 226 3.916989 AGGAAAGGACTAAACCCATCTGT 59.083 43.478 0.00 0.00 0.00 3.41
208 227 4.576330 AGGAAAGGACTAAACCCATCTG 57.424 45.455 0.00 0.00 0.00 2.90
209 228 4.323562 CGAAGGAAAGGACTAAACCCATCT 60.324 45.833 0.00 0.00 0.00 2.90
210 229 3.939592 CGAAGGAAAGGACTAAACCCATC 59.060 47.826 0.00 0.00 0.00 3.51
211 230 3.951663 CGAAGGAAAGGACTAAACCCAT 58.048 45.455 0.00 0.00 0.00 4.00
212 231 3.412237 CGAAGGAAAGGACTAAACCCA 57.588 47.619 0.00 0.00 0.00 4.51
228 247 2.676342 CCGGAGAAAATGTTACCCGAAG 59.324 50.000 0.00 0.00 39.31 3.79
229 248 2.616001 CCCGGAGAAAATGTTACCCGAA 60.616 50.000 0.73 0.00 39.31 4.30
230 249 1.065998 CCCGGAGAAAATGTTACCCGA 60.066 52.381 0.73 0.00 39.31 5.14
231 250 1.339342 ACCCGGAGAAAATGTTACCCG 60.339 52.381 0.73 0.00 36.98 5.28
232 251 2.502142 ACCCGGAGAAAATGTTACCC 57.498 50.000 0.73 0.00 0.00 3.69
233 252 3.273434 GGTACCCGGAGAAAATGTTACC 58.727 50.000 0.73 0.00 0.00 2.85
234 253 3.686241 GTGGTACCCGGAGAAAATGTTAC 59.314 47.826 10.07 0.00 0.00 2.50
235 254 3.307621 GGTGGTACCCGGAGAAAATGTTA 60.308 47.826 10.07 0.00 30.04 2.41
236 255 2.553685 GGTGGTACCCGGAGAAAATGTT 60.554 50.000 10.07 0.00 30.04 2.71
237 256 1.003928 GGTGGTACCCGGAGAAAATGT 59.996 52.381 10.07 0.00 30.04 2.71
238 257 1.746470 GGTGGTACCCGGAGAAAATG 58.254 55.000 10.07 0.00 30.04 2.32
239 258 0.251073 CGGTGGTACCCGGAGAAAAT 59.749 55.000 10.07 0.00 44.32 1.82
240 259 1.672898 CGGTGGTACCCGGAGAAAA 59.327 57.895 10.07 0.00 44.32 2.29
241 260 3.379880 CGGTGGTACCCGGAGAAA 58.620 61.111 10.07 0.00 44.32 2.52
250 269 4.694760 AATATTTAGGGACCGGTGGTAC 57.305 45.455 14.63 0.00 35.25 3.34
251 270 5.713760 AAAATATTTAGGGACCGGTGGTA 57.286 39.130 14.63 0.00 35.25 3.25
252 271 4.596354 AAAATATTTAGGGACCGGTGGT 57.404 40.909 14.63 0.00 39.44 4.16
276 295 8.759641 CGTTTCCACATTTTGTTCATAAAATCA 58.240 29.630 0.00 0.00 37.97 2.57
277 296 8.220434 CCGTTTCCACATTTTGTTCATAAAATC 58.780 33.333 0.00 0.00 37.97 2.17
278 297 7.307692 GCCGTTTCCACATTTTGTTCATAAAAT 60.308 33.333 0.00 0.00 40.00 1.82
283 302 3.389221 GCCGTTTCCACATTTTGTTCAT 58.611 40.909 0.00 0.00 0.00 2.57
286 305 1.405821 TCGCCGTTTCCACATTTTGTT 59.594 42.857 0.00 0.00 0.00 2.83
322 342 9.741647 TTTCTTTGCAAAATTGAAAAAGTGTTT 57.258 22.222 17.78 0.00 35.38 2.83
339 359 9.823647 TGTTCCTGTTATTAAATTTTCTTTGCA 57.176 25.926 0.00 0.00 0.00 4.08
396 416 8.497554 CGGAAATTTCAATGAATGTTCATGTTT 58.502 29.630 19.49 6.18 46.60 2.83
397 417 7.871973 TCGGAAATTTCAATGAATGTTCATGTT 59.128 29.630 19.49 0.00 46.60 2.71
398 418 7.377398 TCGGAAATTTCAATGAATGTTCATGT 58.623 30.769 19.49 0.00 46.60 3.21
401 421 7.205992 TGTTCGGAAATTTCAATGAATGTTCA 58.794 30.769 19.49 10.69 42.14 3.18
402 422 7.636259 TGTTCGGAAATTTCAATGAATGTTC 57.364 32.000 19.49 3.81 0.00 3.18
403 423 8.606040 AATGTTCGGAAATTTCAATGAATGTT 57.394 26.923 19.49 13.75 0.00 2.71
404 424 8.606040 AAATGTTCGGAAATTTCAATGAATGT 57.394 26.923 19.49 9.69 0.00 2.71
408 428 9.920133 TCAATAAATGTTCGGAAATTTCAATGA 57.080 25.926 19.49 10.97 0.00 2.57
412 432 9.973450 TCTTTCAATAAATGTTCGGAAATTTCA 57.027 25.926 19.49 0.00 0.00 2.69
414 434 9.757227 TGTCTTTCAATAAATGTTCGGAAATTT 57.243 25.926 0.00 0.00 0.00 1.82
415 435 9.757227 TTGTCTTTCAATAAATGTTCGGAAATT 57.243 25.926 0.00 0.00 0.00 1.82
416 436 9.757227 TTTGTCTTTCAATAAATGTTCGGAAAT 57.243 25.926 0.00 0.00 35.84 2.17
417 437 9.587772 TTTTGTCTTTCAATAAATGTTCGGAAA 57.412 25.926 0.00 0.00 35.84 3.13
418 438 9.757227 ATTTTGTCTTTCAATAAATGTTCGGAA 57.243 25.926 0.00 0.00 35.84 4.30
419 439 9.757227 AATTTTGTCTTTCAATAAATGTTCGGA 57.243 25.926 0.00 0.00 35.84 4.55
447 467 9.429109 TCCTTAATACCTTTTCTTTTCCAAGTT 57.571 29.630 0.00 0.00 0.00 2.66
448 468 9.429109 TTCCTTAATACCTTTTCTTTTCCAAGT 57.571 29.630 0.00 0.00 0.00 3.16
449 469 9.692749 GTTCCTTAATACCTTTTCTTTTCCAAG 57.307 33.333 0.00 0.00 0.00 3.61
450 470 8.354426 CGTTCCTTAATACCTTTTCTTTTCCAA 58.646 33.333 0.00 0.00 0.00 3.53
451 471 7.720515 TCGTTCCTTAATACCTTTTCTTTTCCA 59.279 33.333 0.00 0.00 0.00 3.53
452 472 8.102800 TCGTTCCTTAATACCTTTTCTTTTCC 57.897 34.615 0.00 0.00 0.00 3.13
453 473 8.781196 ACTCGTTCCTTAATACCTTTTCTTTTC 58.219 33.333 0.00 0.00 0.00 2.29
454 474 8.687292 ACTCGTTCCTTAATACCTTTTCTTTT 57.313 30.769 0.00 0.00 0.00 2.27
455 475 9.433153 CTACTCGTTCCTTAATACCTTTTCTTT 57.567 33.333 0.00 0.00 0.00 2.52
456 476 8.810041 TCTACTCGTTCCTTAATACCTTTTCTT 58.190 33.333 0.00 0.00 0.00 2.52
457 477 8.358582 TCTACTCGTTCCTTAATACCTTTTCT 57.641 34.615 0.00 0.00 0.00 2.52
458 478 8.992835 TTCTACTCGTTCCTTAATACCTTTTC 57.007 34.615 0.00 0.00 0.00 2.29
459 479 7.548427 GCTTCTACTCGTTCCTTAATACCTTTT 59.452 37.037 0.00 0.00 0.00 2.27
460 480 7.040494 GCTTCTACTCGTTCCTTAATACCTTT 58.960 38.462 0.00 0.00 0.00 3.11
461 481 6.406737 GGCTTCTACTCGTTCCTTAATACCTT 60.407 42.308 0.00 0.00 0.00 3.50
462 482 5.068855 GGCTTCTACTCGTTCCTTAATACCT 59.931 44.000 0.00 0.00 0.00 3.08
463 483 5.163478 TGGCTTCTACTCGTTCCTTAATACC 60.163 44.000 0.00 0.00 0.00 2.73
466 486 5.615925 ATGGCTTCTACTCGTTCCTTAAT 57.384 39.130 0.00 0.00 0.00 1.40
477 497 4.080129 ACACATCATCCAATGGCTTCTACT 60.080 41.667 0.00 0.00 0.00 2.57
483 503 3.650281 TGTACACATCATCCAATGGCT 57.350 42.857 0.00 0.00 0.00 4.75
512 570 1.069022 CAGTTGGACGCCAAAGTGATG 60.069 52.381 12.01 4.57 45.73 3.07
619 691 4.383052 CAGCGCTTAACGTAGGATTATGAG 59.617 45.833 7.50 0.00 46.11 2.90
644 716 0.306840 GGACGCACGAGATCACGATA 59.693 55.000 19.57 0.00 37.03 2.92
660 732 2.050985 GCGTGCACTGCTTTGGAC 60.051 61.111 21.16 0.60 34.65 4.02
719 795 7.562259 TTATGGATTCATACGGGATTTCCTA 57.438 36.000 0.00 0.00 35.75 2.94
720 796 6.448369 TTATGGATTCATACGGGATTTCCT 57.552 37.500 0.00 0.00 35.75 3.36
815 910 2.300437 CCTTTATCAACCCCCGCAAAAA 59.700 45.455 0.00 0.00 0.00 1.94
830 925 5.355350 GTGCTAGTCAAGTCAATGCCTTTAT 59.645 40.000 0.00 0.00 0.00 1.40
831 944 4.695455 GTGCTAGTCAAGTCAATGCCTTTA 59.305 41.667 0.00 0.00 0.00 1.85
832 945 3.503748 GTGCTAGTCAAGTCAATGCCTTT 59.496 43.478 0.00 0.00 0.00 3.11
850 964 0.773644 ACAATCCAGAAGGGTGTGCT 59.226 50.000 0.00 0.00 38.11 4.40
882 1006 2.176798 TCCAAGAACAAACATGGGGACT 59.823 45.455 0.00 0.00 33.66 3.85
887 1011 3.754965 TCTCCTCCAAGAACAAACATGG 58.245 45.455 0.00 0.00 0.00 3.66
899 1024 3.632145 GCTTGTCTGTTTTTCTCCTCCAA 59.368 43.478 0.00 0.00 0.00 3.53
908 1033 3.305608 GCTATGGCTGCTTGTCTGTTTTT 60.306 43.478 0.00 0.00 35.22 1.94
916 1041 0.394899 GGAAGGCTATGGCTGCTTGT 60.395 55.000 0.00 0.00 38.81 3.16
944 1069 4.251268 GGGAGTATGTTTGTGTGGTAGAC 58.749 47.826 0.00 0.00 0.00 2.59
945 1070 3.904965 TGGGAGTATGTTTGTGTGGTAGA 59.095 43.478 0.00 0.00 0.00 2.59
986 1121 3.399330 GTCGACATCTTGTTTTGGGAGA 58.601 45.455 11.55 0.00 0.00 3.71
990 1125 1.871039 ACCGTCGACATCTTGTTTTGG 59.129 47.619 17.16 6.81 0.00 3.28
1077 1213 2.948720 GCTCCTCAGGCTTGACGGT 61.949 63.158 11.99 0.00 0.00 4.83
1119 1255 0.734889 CGTTGATGACCCCTTCATGC 59.265 55.000 0.00 0.00 45.67 4.06
1272 1443 1.181786 CCCCGCAATGTACATTGGTT 58.818 50.000 37.08 11.61 46.14 3.67
1285 1456 4.082845 TGAATGAAGAAATTAACCCCGCA 58.917 39.130 0.00 0.00 0.00 5.69
1286 1457 4.712122 TGAATGAAGAAATTAACCCCGC 57.288 40.909 0.00 0.00 0.00 6.13
1310 1481 7.486647 AGCATGATCACAAGAAATAATTCACC 58.513 34.615 0.00 0.00 38.06 4.02
1335 1508 6.262944 ACATTTGTCAAGTGAATAGTCTGCAA 59.737 34.615 14.40 0.00 0.00 4.08
1478 1651 1.134907 ACGCGGAAATAAGTGTCGGAT 60.135 47.619 12.47 0.00 0.00 4.18
1627 1804 3.312146 CACACATGTACACACACACACAT 59.688 43.478 0.00 0.00 37.54 3.21
1628 1805 2.675348 CACACATGTACACACACACACA 59.325 45.455 0.00 0.00 37.54 3.72
1629 1806 2.675844 ACACACATGTACACACACACAC 59.324 45.455 0.00 0.00 37.26 3.82
1808 4914 7.282450 CCTTGTTGTCCAGAAGTTACTTAGTTT 59.718 37.037 0.00 0.00 0.00 2.66
1823 5978 1.425066 AGCAGGATTCCTTGTTGTCCA 59.575 47.619 1.28 0.00 33.12 4.02
1915 6070 0.690762 AGCGGCCCAACTTTCTAGAA 59.309 50.000 0.00 0.00 0.00 2.10
1958 6113 5.046376 TCAATGTCAGCTTATGAAGTCTCCA 60.046 40.000 0.00 0.00 40.43 3.86
1975 6130 3.426159 CCCACATAACTTGCGTCAATGTC 60.426 47.826 0.00 0.00 31.20 3.06
2037 6192 1.536766 CGGTGTCACACATGCTTGATT 59.463 47.619 10.85 0.00 35.86 2.57
2061 6216 1.305219 TAGCGTGCAAATGTCAGGCC 61.305 55.000 0.00 0.00 43.86 5.19
2064 6219 3.244670 GCTATAGCGTGCAAATGTCAG 57.755 47.619 9.40 0.00 0.00 3.51
2089 6244 4.998671 TTGTTTTGAGCAACAGGATTCA 57.001 36.364 0.00 0.00 37.93 2.57
2117 6272 9.920946 TTATATGAGCATAAAATAGGATTCCCC 57.079 33.333 0.00 0.00 0.00 4.81
2146 6301 8.181573 TCAATCGGTGTAGATTTTCTTATTTGC 58.818 33.333 0.00 0.00 38.66 3.68
2157 6312 8.424918 AGACAATCTTATCAATCGGTGTAGATT 58.575 33.333 0.00 0.00 41.12 2.40
2444 6604 8.230486 GTCAACGTTGATTCTTCAGAAATACAT 58.770 33.333 31.81 0.00 39.73 2.29
2452 6612 3.364366 GGCTGTCAACGTTGATTCTTCAG 60.364 47.826 31.81 29.67 39.73 3.02
2480 6640 4.818534 ATTATAAATGTGTCAGCTGCCG 57.181 40.909 9.47 0.00 0.00 5.69
2487 6647 7.975058 CCACATGAAGCAATTATAAATGTGTCA 59.025 33.333 16.97 13.33 41.00 3.58
2498 6658 4.580167 GGTATGCTCCACATGAAGCAATTA 59.420 41.667 20.23 10.58 40.06 1.40
2536 6696 0.983378 AGGGAGTTCCTATTGCCGCT 60.983 55.000 0.00 0.00 45.98 5.52


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

AutoCloner maintained by Alex Coulton.