Multiple sequence alignment - TraesCS3A01G350000

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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 TraesCS3A01G350000 chr3A 100.000 3704 0 0 1 3704 598567291 598563588 0.000000e+00 6841
1 TraesCS3A01G350000 chr3D 95.621 3334 113 15 395 3704 455882858 455879534 0.000000e+00 5317
2 TraesCS3A01G350000 chr3D 89.141 396 39 3 1 393 455931752 455931358 1.200000e-134 490
3 TraesCS3A01G350000 chr3B 93.267 3416 129 39 314 3704 602367332 602363993 0.000000e+00 4940
4 TraesCS3A01G350000 chr3B 87.970 266 30 1 2 265 602367599 602367334 2.780000e-81 313


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 TraesCS3A01G350000 chr3A 598563588 598567291 3703 True 6841.0 6841 100.0000 1 3704 1 chr3A.!!$R1 3703
1 TraesCS3A01G350000 chr3D 455879534 455882858 3324 True 5317.0 5317 95.6210 395 3704 1 chr3D.!!$R1 3309
2 TraesCS3A01G350000 chr3B 602363993 602367599 3606 True 2626.5 4940 90.6185 2 3704 2 chr3B.!!$R1 3702

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
501 504 0.031178 GGAGTGTGTTTGCAAGCCTG 59.969 55.0 11.02 0.0 0.00 4.85 F
636 640 0.031585 TGCGCGGTAGGCAATACTAG 59.968 55.0 8.83 0.0 43.84 2.57 F
1644 1664 0.173708 GAGTGGAAGTAGGTGCCTCG 59.826 60.0 0.00 0.0 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1671 1691 0.817229 TGCACTCAAATGTGGCGACA 60.817 50.000 3.31 3.31 38.31 4.35 R
2484 2504 1.302192 ACCAACATGGGTTCCGTCG 60.302 57.895 0.00 0.00 43.37 5.12 R
2908 2931 0.036164 TCATCCCACAACAACCCTCG 59.964 55.000 0.00 0.00 0.00 4.63 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
31 32 5.715070 TCAGCTCAAAAGTAGAGTTCTAGC 58.285 41.667 0.00 0.00 35.55 3.42
72 73 9.686683 AAATTGCTCATACTAAATAAGACACCT 57.313 29.630 0.00 0.00 0.00 4.00
171 172 5.387113 AACCTGGCCAAGAATGATACATA 57.613 39.130 8.77 0.00 0.00 2.29
172 173 5.589367 ACCTGGCCAAGAATGATACATAT 57.411 39.130 8.77 0.00 0.00 1.78
176 177 6.596888 CCTGGCCAAGAATGATACATATACAG 59.403 42.308 7.01 0.00 0.00 2.74
179 180 7.161404 GGCCAAGAATGATACATATACAGTGA 58.839 38.462 0.00 0.00 0.00 3.41
182 183 8.982685 CCAAGAATGATACATATACAGTGACAC 58.017 37.037 0.00 0.00 0.00 3.67
190 191 4.688879 ACATATACAGTGACACAAACACGG 59.311 41.667 8.59 0.00 42.25 4.94
200 203 0.961019 ACAAACACGGCTCATGCAAT 59.039 45.000 0.00 0.00 41.91 3.56
203 206 1.246649 AACACGGCTCATGCAATTGA 58.753 45.000 10.34 0.00 41.91 2.57
245 248 3.791973 AAGATGCCACAAAACGACAAA 57.208 38.095 0.00 0.00 0.00 2.83
259 262 7.165154 ACAAAACGACAAATTGACAAGAATACG 59.835 33.333 0.00 0.27 0.00 3.06
265 268 7.393551 ACAAATTGACAAGAATACGCAAAAG 57.606 32.000 0.00 0.00 0.00 2.27
266 269 6.978080 ACAAATTGACAAGAATACGCAAAAGT 59.022 30.769 0.00 0.00 0.00 2.66
267 270 6.991485 AATTGACAAGAATACGCAAAAGTG 57.009 33.333 0.00 0.00 0.00 3.16
285 288 3.340337 GTGCCAAAACACTCTCTTGAC 57.660 47.619 0.00 0.00 37.58 3.18
286 289 2.033424 GTGCCAAAACACTCTCTTGACC 59.967 50.000 0.00 0.00 37.58 4.02
287 290 2.297701 GCCAAAACACTCTCTTGACCA 58.702 47.619 0.00 0.00 0.00 4.02
288 291 2.033424 GCCAAAACACTCTCTTGACCAC 59.967 50.000 0.00 0.00 0.00 4.16
289 292 2.618709 CCAAAACACTCTCTTGACCACC 59.381 50.000 0.00 0.00 0.00 4.61
290 293 2.618709 CAAAACACTCTCTTGACCACCC 59.381 50.000 0.00 0.00 0.00 4.61
291 294 0.765510 AACACTCTCTTGACCACCCC 59.234 55.000 0.00 0.00 0.00 4.95
292 295 0.104934 ACACTCTCTTGACCACCCCT 60.105 55.000 0.00 0.00 0.00 4.79
293 296 0.610687 CACTCTCTTGACCACCCCTC 59.389 60.000 0.00 0.00 0.00 4.30
294 297 0.900647 ACTCTCTTGACCACCCCTCG 60.901 60.000 0.00 0.00 0.00 4.63
295 298 2.232298 CTCTCTTGACCACCCCTCGC 62.232 65.000 0.00 0.00 0.00 5.03
296 299 3.316573 CTCTTGACCACCCCTCGCC 62.317 68.421 0.00 0.00 0.00 5.54
297 300 4.760047 CTTGACCACCCCTCGCCG 62.760 72.222 0.00 0.00 0.00 6.46
300 303 4.754667 GACCACCCCTCGCCGTTC 62.755 72.222 0.00 0.00 0.00 3.95
302 305 4.016706 CCACCCCTCGCCGTTCTT 62.017 66.667 0.00 0.00 0.00 2.52
303 306 2.434359 CACCCCTCGCCGTTCTTC 60.434 66.667 0.00 0.00 0.00 2.87
304 307 2.603776 ACCCCTCGCCGTTCTTCT 60.604 61.111 0.00 0.00 0.00 2.85
305 308 2.214920 ACCCCTCGCCGTTCTTCTT 61.215 57.895 0.00 0.00 0.00 2.52
306 309 1.448013 CCCCTCGCCGTTCTTCTTC 60.448 63.158 0.00 0.00 0.00 2.87
307 310 1.448013 CCCTCGCCGTTCTTCTTCC 60.448 63.158 0.00 0.00 0.00 3.46
308 311 1.448013 CCTCGCCGTTCTTCTTCCC 60.448 63.158 0.00 0.00 0.00 3.97
309 312 1.448013 CTCGCCGTTCTTCTTCCCC 60.448 63.158 0.00 0.00 0.00 4.81
310 313 2.436115 CGCCGTTCTTCTTCCCCC 60.436 66.667 0.00 0.00 0.00 5.40
332 335 0.105778 CTTCTTCTCCGATGCCTCCC 59.894 60.000 0.00 0.00 0.00 4.30
351 354 1.615883 CCATCTCTCACCATCTACCGG 59.384 57.143 0.00 0.00 0.00 5.28
378 381 4.779733 GCCCCTCCTCCCTCGACA 62.780 72.222 0.00 0.00 0.00 4.35
418 421 2.359478 TCGCGGCCTTCCTTTTCC 60.359 61.111 6.13 0.00 0.00 3.13
433 436 3.574396 CCTTTTCCACTCCCCTTTTCTTC 59.426 47.826 0.00 0.00 0.00 2.87
442 445 9.064602 TCCACTCCCCTTTTCTTCTTTATTATA 57.935 33.333 0.00 0.00 0.00 0.98
501 504 0.031178 GGAGTGTGTTTGCAAGCCTG 59.969 55.000 11.02 0.00 0.00 4.85
516 519 2.977772 GCCTGGCTAGATGGCTATAG 57.022 55.000 12.43 0.00 43.05 1.31
539 542 3.328382 TCCACTCGAGGTAAATTGGTG 57.672 47.619 18.41 2.96 0.00 4.17
580 583 2.446435 AGGTCTACGGTTAAGCGGTTA 58.554 47.619 28.51 13.44 32.68 2.85
633 637 3.802507 TTGCGCGGTAGGCAATAC 58.197 55.556 8.83 0.00 44.79 1.89
634 638 1.219664 TTGCGCGGTAGGCAATACT 59.780 52.632 8.83 0.00 44.79 2.12
635 639 0.460722 TTGCGCGGTAGGCAATACTA 59.539 50.000 8.83 0.00 44.79 1.82
636 640 0.031585 TGCGCGGTAGGCAATACTAG 59.968 55.000 8.83 0.00 43.84 2.57
659 667 3.763897 ACGGCAATAGAAAGGCAATTCTT 59.236 39.130 10.27 0.00 40.13 2.52
695 706 1.210722 CTGCTACCTTTTCCCTCTCCC 59.789 57.143 0.00 0.00 0.00 4.30
1254 1274 1.742268 GAGGTGTACTCCTCGTACCAC 59.258 57.143 24.21 4.81 46.36 4.16
1371 1391 3.482783 GTGCGAGCCAGCGAGTTC 61.483 66.667 0.00 0.00 40.67 3.01
1422 1442 0.692756 CCTCCTCCTCCTTTCTCCCC 60.693 65.000 0.00 0.00 0.00 4.81
1540 1560 3.394836 GCTCCGAGGCTCAACCCT 61.395 66.667 15.95 0.00 40.58 4.34
1582 1602 2.475466 CCGGTGCCACATCATGAGC 61.475 63.158 0.09 0.00 0.00 4.26
1644 1664 0.173708 GAGTGGAAGTAGGTGCCTCG 59.826 60.000 0.00 0.00 0.00 4.63
1671 1691 3.394836 GAGGAGCGGGGCAAGAGT 61.395 66.667 0.00 0.00 0.00 3.24
1755 1775 1.153005 CCATCTCTTCTGCTGGCCC 60.153 63.158 0.00 0.00 0.00 5.80
1886 1906 1.273759 TCAGATGCAGAGAAGGCTGT 58.726 50.000 0.00 0.00 38.17 4.40
2046 2066 0.881118 GGCGCCTTCTTGATCAACAA 59.119 50.000 22.15 0.00 36.97 2.83
2170 2190 1.338200 GGATGAGAGCAAGACGGTTGT 60.338 52.381 2.22 0.00 0.00 3.32
2481 2501 0.811281 CTTTGAATCCCGAGGCAACC 59.189 55.000 0.00 0.00 37.17 3.77
2484 2504 1.814169 GAATCCCGAGGCAACCGTC 60.814 63.158 0.00 0.00 37.17 4.79
2626 2649 0.408309 TTCGAGAACCCTGAGGAGGA 59.592 55.000 0.00 0.00 42.93 3.71
2627 2650 0.033991 TCGAGAACCCTGAGGAGGAG 60.034 60.000 0.00 0.00 42.93 3.69
2628 2651 1.040339 CGAGAACCCTGAGGAGGAGG 61.040 65.000 0.00 0.00 42.93 4.30
2670 2693 4.521146 CTTCTTTAGATGTGGATGGTGCT 58.479 43.478 0.00 0.00 0.00 4.40
2826 2849 6.899089 ACAATGTTCTTTCCCTTTCCATTTT 58.101 32.000 0.00 0.00 0.00 1.82
3131 3154 9.578576 AAGCCTGATCTTTTATGCTCATTTATA 57.421 29.630 0.00 0.00 0.00 0.98
3266 3289 6.204495 AGTTCTTTTTCTCATGAGAGCAAGTC 59.796 38.462 28.37 23.94 41.81 3.01
3272 3295 4.965814 TCTCATGAGAGCAAGTCAAAACT 58.034 39.130 21.67 0.00 41.81 2.66
3290 3313 6.320164 TCAAAACTTGGTACACTATTGCAAGT 59.680 34.615 4.94 0.00 39.29 3.16
3301 3324 6.427150 ACACTATTGCAAGTAGAAAACAACG 58.573 36.000 17.40 0.00 0.00 4.10
3332 3355 7.309012 GGAAATGTAACCTCTAAAGAAACACCC 60.309 40.741 0.00 0.00 0.00 4.61
3333 3356 5.633655 TGTAACCTCTAAAGAAACACCCA 57.366 39.130 0.00 0.00 0.00 4.51
3372 3395 5.637810 TCATTTGATGGTTCGTGTAGTCTTC 59.362 40.000 0.00 0.00 0.00 2.87
3383 3406 7.595502 GGTTCGTGTAGTCTTCCTGATATTATG 59.404 40.741 0.00 0.00 0.00 1.90
3466 3489 1.069358 GGAGACCGATCACTCATTCCC 59.931 57.143 11.70 0.00 35.17 3.97
3505 3528 6.037172 ACAGTTGCATAAGTATTCAATCGTCC 59.963 38.462 0.00 0.00 0.00 4.79
3594 3618 1.333619 GTGCATTTGGAACTCACGTGT 59.666 47.619 16.51 0.00 0.00 4.49
3599 3623 2.971660 TTGGAACTCACGTGTCTGAA 57.028 45.000 16.51 1.11 0.00 3.02
3600 3624 2.509052 TGGAACTCACGTGTCTGAAG 57.491 50.000 16.51 7.58 0.00 3.02
3601 3625 1.068588 TGGAACTCACGTGTCTGAAGG 59.931 52.381 16.51 1.40 0.00 3.46
3603 3627 0.393077 AACTCACGTGTCTGAAGGGG 59.607 55.000 16.51 0.00 0.00 4.79
3604 3628 0.469331 ACTCACGTGTCTGAAGGGGA 60.469 55.000 16.51 0.00 0.00 4.81
3606 3630 2.100197 CTCACGTGTCTGAAGGGGATA 58.900 52.381 16.51 0.00 0.00 2.59
3607 3631 1.822990 TCACGTGTCTGAAGGGGATAC 59.177 52.381 16.51 0.00 0.00 2.24
3653 3695 9.790344 AAAGATGATCTAGACCCATATTTCTTG 57.210 33.333 17.16 0.00 29.09 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.344950 ACTTTTGAGCTGATCTGAGCG 58.655 47.619 3.42 0.00 44.24 5.03
16 17 7.048512 ACACAACAAAGCTAGAACTCTACTTT 58.951 34.615 0.00 7.76 33.89 2.66
31 32 7.697352 TGAGCAATTTTATGACACAACAAAG 57.303 32.000 0.00 0.00 0.00 2.77
149 150 3.737559 TGTATCATTCTTGGCCAGGTT 57.262 42.857 15.41 0.78 0.00 3.50
153 154 6.936335 CACTGTATATGTATCATTCTTGGCCA 59.064 38.462 0.00 0.00 0.00 5.36
155 156 7.657354 TGTCACTGTATATGTATCATTCTTGGC 59.343 37.037 0.00 0.00 0.00 4.52
157 158 9.533253 TGTGTCACTGTATATGTATCATTCTTG 57.467 33.333 4.27 0.00 0.00 3.02
171 172 1.871039 GCCGTGTTTGTGTCACTGTAT 59.129 47.619 4.27 0.00 34.14 2.29
172 173 1.134640 AGCCGTGTTTGTGTCACTGTA 60.135 47.619 4.27 0.00 34.14 2.74
176 177 0.944386 ATGAGCCGTGTTTGTGTCAC 59.056 50.000 0.00 0.00 0.00 3.67
179 180 1.100463 TGCATGAGCCGTGTTTGTGT 61.100 50.000 0.00 0.00 41.13 3.72
182 183 1.722464 CAATTGCATGAGCCGTGTTTG 59.278 47.619 0.00 0.00 41.13 2.93
190 191 5.177725 TCATACATGTCAATTGCATGAGC 57.822 39.130 31.57 9.90 44.60 4.26
245 248 4.917415 GCACTTTTGCGTATTCTTGTCAAT 59.083 37.500 0.00 0.00 39.50 2.57
265 268 2.033424 GGTCAAGAGAGTGTTTTGGCAC 59.967 50.000 0.00 0.00 39.51 5.01
266 269 2.297701 GGTCAAGAGAGTGTTTTGGCA 58.702 47.619 0.00 0.00 0.00 4.92
267 270 2.033424 GTGGTCAAGAGAGTGTTTTGGC 59.967 50.000 0.00 0.00 0.00 4.52
268 271 2.618709 GGTGGTCAAGAGAGTGTTTTGG 59.381 50.000 0.00 0.00 0.00 3.28
269 272 2.618709 GGGTGGTCAAGAGAGTGTTTTG 59.381 50.000 0.00 0.00 0.00 2.44
270 273 2.422945 GGGGTGGTCAAGAGAGTGTTTT 60.423 50.000 0.00 0.00 0.00 2.43
271 274 1.143073 GGGGTGGTCAAGAGAGTGTTT 59.857 52.381 0.00 0.00 0.00 2.83
272 275 0.765510 GGGGTGGTCAAGAGAGTGTT 59.234 55.000 0.00 0.00 0.00 3.32
273 276 0.104934 AGGGGTGGTCAAGAGAGTGT 60.105 55.000 0.00 0.00 0.00 3.55
274 277 0.610687 GAGGGGTGGTCAAGAGAGTG 59.389 60.000 0.00 0.00 0.00 3.51
275 278 0.900647 CGAGGGGTGGTCAAGAGAGT 60.901 60.000 0.00 0.00 0.00 3.24
276 279 1.893786 CGAGGGGTGGTCAAGAGAG 59.106 63.158 0.00 0.00 0.00 3.20
277 280 2.283529 GCGAGGGGTGGTCAAGAGA 61.284 63.158 0.00 0.00 0.00 3.10
278 281 2.266055 GCGAGGGGTGGTCAAGAG 59.734 66.667 0.00 0.00 0.00 2.85
279 282 3.319198 GGCGAGGGGTGGTCAAGA 61.319 66.667 0.00 0.00 0.00 3.02
280 283 4.760047 CGGCGAGGGGTGGTCAAG 62.760 72.222 0.00 0.00 0.00 3.02
283 286 4.754667 GAACGGCGAGGGGTGGTC 62.755 72.222 16.62 0.00 0.00 4.02
285 288 3.952628 GAAGAACGGCGAGGGGTGG 62.953 68.421 16.62 0.00 0.00 4.61
286 289 2.434359 GAAGAACGGCGAGGGGTG 60.434 66.667 16.62 0.00 0.00 4.61
287 290 2.168666 GAAGAAGAACGGCGAGGGGT 62.169 60.000 16.62 0.00 0.00 4.95
288 291 1.448013 GAAGAAGAACGGCGAGGGG 60.448 63.158 16.62 0.00 0.00 4.79
289 292 1.448013 GGAAGAAGAACGGCGAGGG 60.448 63.158 16.62 0.00 0.00 4.30
290 293 1.448013 GGGAAGAAGAACGGCGAGG 60.448 63.158 16.62 0.00 0.00 4.63
291 294 1.448013 GGGGAAGAAGAACGGCGAG 60.448 63.158 16.62 0.00 0.00 5.03
292 295 2.660802 GGGGAAGAAGAACGGCGA 59.339 61.111 16.62 0.00 0.00 5.54
293 296 2.436115 GGGGGAAGAAGAACGGCG 60.436 66.667 4.80 4.80 0.00 6.46
307 310 0.755686 CATCGGAGAAGAAGAGGGGG 59.244 60.000 0.00 0.00 43.58 5.40
308 311 0.105778 GCATCGGAGAAGAAGAGGGG 59.894 60.000 0.00 0.00 43.58 4.79
309 312 0.105778 GGCATCGGAGAAGAAGAGGG 59.894 60.000 0.00 0.00 43.58 4.30
310 313 1.068434 GAGGCATCGGAGAAGAAGAGG 59.932 57.143 0.00 0.00 43.58 3.69
311 314 1.068434 GGAGGCATCGGAGAAGAAGAG 59.932 57.143 0.00 0.00 43.58 2.85
312 315 1.115467 GGAGGCATCGGAGAAGAAGA 58.885 55.000 0.00 0.00 43.58 2.87
332 335 1.000283 GCCGGTAGATGGTGAGAGATG 60.000 57.143 1.90 0.00 0.00 2.90
378 381 2.657237 CACGAGGAGAAGGCGGTT 59.343 61.111 0.00 0.00 0.00 4.44
442 445 6.205658 CACGAAGAGGAAGAAGAAAGGAAAAT 59.794 38.462 0.00 0.00 0.00 1.82
474 477 1.518325 CAAACACACTCCATGGCGTA 58.482 50.000 7.14 0.00 0.00 4.42
501 504 4.284746 AGTGGAAACTATAGCCATCTAGCC 59.715 45.833 0.00 0.00 33.66 3.93
516 519 4.070009 ACCAATTTACCTCGAGTGGAAAC 58.930 43.478 20.75 0.00 0.00 2.78
553 556 3.869832 GCTTAACCGTAGACCTTTCATCC 59.130 47.826 0.00 0.00 0.00 3.51
583 586 0.782384 CGTCACGTTAACAGCTGGTC 59.218 55.000 19.93 0.00 0.00 4.02
597 600 3.651480 GAACGGCATGCTGCGTCAC 62.651 63.158 26.52 16.09 46.21 3.67
611 614 3.849953 GCCTACCGCGCAAGAACG 61.850 66.667 8.75 0.00 43.02 3.95
618 621 0.313043 TCTAGTATTGCCTACCGCGC 59.687 55.000 0.00 0.00 42.08 6.86
633 637 3.179443 TGCCTTTCTATTGCCGTCTAG 57.821 47.619 0.00 0.00 0.00 2.43
634 638 3.620427 TTGCCTTTCTATTGCCGTCTA 57.380 42.857 0.00 0.00 0.00 2.59
635 639 2.489938 TTGCCTTTCTATTGCCGTCT 57.510 45.000 0.00 0.00 0.00 4.18
636 640 3.378427 AGAATTGCCTTTCTATTGCCGTC 59.622 43.478 0.00 0.00 34.21 4.79
853 873 1.051008 CTCGTCATGGATGGGATGGA 58.949 55.000 0.00 0.00 0.00 3.41
854 874 0.604780 GCTCGTCATGGATGGGATGG 60.605 60.000 0.00 0.00 0.00 3.51
855 875 0.604780 GGCTCGTCATGGATGGGATG 60.605 60.000 0.00 0.00 0.00 3.51
856 876 1.757306 GGCTCGTCATGGATGGGAT 59.243 57.895 0.00 0.00 0.00 3.85
857 877 2.796193 CGGCTCGTCATGGATGGGA 61.796 63.158 0.00 0.00 0.00 4.37
1422 1442 1.218875 TGTACCTTGTTGCAGCGTCG 61.219 55.000 0.00 0.00 0.00 5.12
1644 1664 3.213402 CGCTCCTCCGACTCCTCC 61.213 72.222 0.00 0.00 0.00 4.30
1671 1691 0.817229 TGCACTCAAATGTGGCGACA 60.817 50.000 3.31 3.31 38.31 4.35
1755 1775 6.639632 ACATTAAGCCATTGGTATAAGCAG 57.360 37.500 4.26 2.51 0.00 4.24
1886 1906 4.007457 GCTGCTTGCCTTCATCCA 57.993 55.556 0.00 0.00 35.15 3.41
2046 2066 7.283354 TCGAATCTACTCACACTACTCATGATT 59.717 37.037 0.00 0.00 0.00 2.57
2170 2190 3.884091 GGAGAGTTATCTACCTCGCTCAA 59.116 47.826 0.00 0.00 35.30 3.02
2453 2473 1.609580 CGGGATTCAAAGGGTTCGACA 60.610 52.381 0.00 0.00 0.00 4.35
2481 2501 1.373748 AACATGGGTTCCGTCGACG 60.374 57.895 30.33 30.33 39.44 5.12
2484 2504 1.302192 ACCAACATGGGTTCCGTCG 60.302 57.895 0.00 0.00 43.37 5.12
2628 2651 4.021925 AACGCACTGCTCCTCCCC 62.022 66.667 0.00 0.00 0.00 4.81
2670 2693 4.196778 TTGTTGCGCTGTGGGGGA 62.197 61.111 9.73 0.00 0.00 4.81
2826 2849 9.498176 GGACTAAACAGAACCATTCTAGTAAAA 57.502 33.333 0.00 0.00 38.11 1.52
2908 2931 0.036164 TCATCCCACAACAACCCTCG 59.964 55.000 0.00 0.00 0.00 4.63
3131 3154 7.173390 GCTTTTGAGAGTAACTTATGTTGGAGT 59.827 37.037 4.33 0.00 37.59 3.85
3219 3242 6.824553 ACTTCTATTTCATCATCTGCTAGCA 58.175 36.000 18.22 18.22 0.00 3.49
3266 3289 6.503524 ACTTGCAATAGTGTACCAAGTTTTG 58.496 36.000 0.00 0.00 42.26 2.44
3272 3295 7.499563 TGTTTTCTACTTGCAATAGTGTACCAA 59.500 33.333 0.00 0.00 0.00 3.67
3278 3301 6.655062 TCGTTGTTTTCTACTTGCAATAGTG 58.345 36.000 0.00 0.00 0.00 2.74
3290 3313 6.687081 ACATTTCCAGTTCGTTGTTTTCTA 57.313 33.333 0.00 0.00 0.00 2.10
3301 3324 8.617290 TTCTTTAGAGGTTACATTTCCAGTTC 57.383 34.615 0.00 0.00 0.00 3.01
3332 3355 7.201574 CCATCAAATGAAACAATGCCATAGTTG 60.202 37.037 0.00 0.00 0.00 3.16
3333 3356 6.819649 CCATCAAATGAAACAATGCCATAGTT 59.180 34.615 0.00 0.00 0.00 2.24
3383 3406 7.671495 AAATGCAAAACCAAGATAATGGAAC 57.329 32.000 0.00 0.00 43.54 3.62
3466 3489 3.002246 TGCAACTGTAGTTTCTTTGCTCG 59.998 43.478 6.22 0.00 42.48 5.03
3505 3528 5.527214 TGATCTTCAAGTTACTTGGTGTGTG 59.473 40.000 22.82 8.73 41.33 3.82
3566 3589 6.193761 GTGAGTTCCAAATGCACAATTTTTG 58.806 36.000 0.00 0.00 36.28 2.44
3570 3594 3.068024 ACGTGAGTTCCAAATGCACAATT 59.932 39.130 0.00 0.00 46.40 2.32
3594 3618 2.691241 GCTCCTCTGTATCCCCTTCAGA 60.691 54.545 0.00 0.00 36.85 3.27
3599 3623 0.105246 CCTGCTCCTCTGTATCCCCT 60.105 60.000 0.00 0.00 0.00 4.79
3600 3624 0.105453 TCCTGCTCCTCTGTATCCCC 60.105 60.000 0.00 0.00 0.00 4.81
3601 3625 1.337118 CTCCTGCTCCTCTGTATCCC 58.663 60.000 0.00 0.00 0.00 3.85
3603 3627 1.337118 CCCTCCTGCTCCTCTGTATC 58.663 60.000 0.00 0.00 0.00 2.24
3604 3628 0.105246 CCCCTCCTGCTCCTCTGTAT 60.105 60.000 0.00 0.00 0.00 2.29
3606 3630 2.040278 CCCCTCCTGCTCCTCTGT 59.960 66.667 0.00 0.00 0.00 3.41
3607 3631 0.911525 TTTCCCCTCCTGCTCCTCTG 60.912 60.000 0.00 0.00 0.00 3.35
3637 3679 7.093640 ACGAACACTACAAGAAATATGGGTCTA 60.094 37.037 0.00 0.00 0.00 2.59
3643 3685 5.447279 GGCCACGAACACTACAAGAAATATG 60.447 44.000 0.00 0.00 0.00 1.78
3653 3695 6.453092 ACAATATATAGGCCACGAACACTAC 58.547 40.000 5.01 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.