Multiple sequence alignment - TraesCS1D01G376400

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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 TraesCS1D01G376400 chr1D 100.000 4391 0 0 1 4391 453112592 453116982 0.000000e+00 8109
1 TraesCS1D01G376400 chr1B 96.094 4404 151 16 1 4391 623546773 623551168 0.000000e+00 7160
2 TraesCS1D01G376400 chr7B 84.823 2741 361 27 440 3150 724956243 724953528 0.000000e+00 2706
3 TraesCS1D01G376400 chr7B 85.532 2509 333 17 665 3163 466668807 466671295 0.000000e+00 2595
4 TraesCS1D01G376400 chr7B 81.592 2412 407 23 763 3156 723929188 723931580 0.000000e+00 1960
5 TraesCS1D01G376400 chr7D 84.458 2741 369 26 440 3150 625355708 625352995 0.000000e+00 2649
6 TraesCS1D01G376400 chr7D 84.553 2460 347 17 716 3163 448855381 448857819 0.000000e+00 2407
7 TraesCS1D01G376400 chr7D 82.268 2628 414 32 546 3150 625250328 625252926 0.000000e+00 2224
8 TraesCS1D01G376400 chr7D 82.002 2428 401 24 747 3156 625227706 625225297 0.000000e+00 2030
9 TraesCS1D01G376400 chr7A 83.340 2461 378 18 716 3163 547114175 547111734 0.000000e+00 2244
10 TraesCS1D01G376400 chr7A 82.433 2499 395 19 671 3156 720864418 720861951 0.000000e+00 2143
11 TraesCS1D01G376400 chr6A 81.579 2432 407 25 747 3156 608493799 608491387 0.000000e+00 1971
12 TraesCS1D01G376400 chr4A 85.714 168 17 6 3489 3653 731004177 731004340 2.100000e-38 171


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 TraesCS1D01G376400 chr1D 453112592 453116982 4390 False 8109 8109 100.000 1 4391 1 chr1D.!!$F1 4390
1 TraesCS1D01G376400 chr1B 623546773 623551168 4395 False 7160 7160 96.094 1 4391 1 chr1B.!!$F1 4390
2 TraesCS1D01G376400 chr7B 724953528 724956243 2715 True 2706 2706 84.823 440 3150 1 chr7B.!!$R1 2710
3 TraesCS1D01G376400 chr7B 466668807 466671295 2488 False 2595 2595 85.532 665 3163 1 chr7B.!!$F1 2498
4 TraesCS1D01G376400 chr7B 723929188 723931580 2392 False 1960 1960 81.592 763 3156 1 chr7B.!!$F2 2393
5 TraesCS1D01G376400 chr7D 625352995 625355708 2713 True 2649 2649 84.458 440 3150 1 chr7D.!!$R2 2710
6 TraesCS1D01G376400 chr7D 448855381 448857819 2438 False 2407 2407 84.553 716 3163 1 chr7D.!!$F1 2447
7 TraesCS1D01G376400 chr7D 625250328 625252926 2598 False 2224 2224 82.268 546 3150 1 chr7D.!!$F2 2604
8 TraesCS1D01G376400 chr7D 625225297 625227706 2409 True 2030 2030 82.002 747 3156 1 chr7D.!!$R1 2409
9 TraesCS1D01G376400 chr7A 547111734 547114175 2441 True 2244 2244 83.340 716 3163 1 chr7A.!!$R1 2447
10 TraesCS1D01G376400 chr7A 720861951 720864418 2467 True 2143 2143 82.433 671 3156 1 chr7A.!!$R2 2485
11 TraesCS1D01G376400 chr6A 608491387 608493799 2412 True 1971 1971 81.579 747 3156 1 chr6A.!!$R1 2409

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
427 429 0.383231 GCTGCACAATGGATGGCTAC 59.617 55.0 0.00 0.0 0.0 3.58 F
828 875 0.744874 CCTCGGCTCGTGAATTCCTA 59.255 55.0 2.27 0.0 0.0 2.94 F
1782 1832 1.349067 AGCTACCTTCCACGGACTTT 58.651 50.0 0.00 0.0 0.0 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1461 1511 0.613012 GACCCCAATCAGCAGCCTTT 60.613 55.0 0.00 0.0 0.00 3.11 R
2631 2706 1.081892 CCAAGCACTCGTGATGAAGG 58.918 55.0 0.39 0.0 0.00 3.46 R
3608 3696 0.181114 TTGCCTGTCTGTTGCAGAGT 59.819 50.0 0.00 0.0 41.46 3.24 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
50 51 8.677300 GTGTGTTCAGTTTGAATCATATACCAT 58.323 33.333 0.00 0.00 38.79 3.55
58 59 9.085645 AGTTTGAATCATATACCATGATGCATT 57.914 29.630 0.00 0.00 42.07 3.56
96 97 5.101628 TGTTTTTCTGTCTGCATGTTCAAC 58.898 37.500 0.00 0.00 0.00 3.18
99 100 2.560504 TCTGTCTGCATGTTCAACGTT 58.439 42.857 0.00 0.00 0.00 3.99
103 104 4.123506 TGTCTGCATGTTCAACGTTTAGA 58.876 39.130 0.00 0.00 0.00 2.10
111 112 7.167302 TGCATGTTCAACGTTTAGATTTTTCAG 59.833 33.333 0.00 0.00 0.00 3.02
114 115 8.211116 TGTTCAACGTTTAGATTTTTCAGGTA 57.789 30.769 0.00 0.00 0.00 3.08
143 144 1.676006 ACCAGTTGAAAGCCTGAAACG 59.324 47.619 0.00 0.00 0.00 3.60
145 146 2.357637 CCAGTTGAAAGCCTGAAACGAA 59.642 45.455 0.00 0.00 0.00 3.85
160 161 4.451096 TGAAACGAAGGACAATTCTACAGC 59.549 41.667 0.00 0.00 0.00 4.40
180 181 1.946768 CGCTGGACCTTGAAAGACAAA 59.053 47.619 0.00 0.00 38.08 2.83
197 198 9.424319 GAAAGACAAAGACATCACAGAATAGTA 57.576 33.333 0.00 0.00 0.00 1.82
291 292 3.367703 CCATGATGCAAAGTTGACCCTTC 60.368 47.826 0.00 0.00 0.00 3.46
297 298 2.959030 GCAAAGTTGACCCTTCTTTCCT 59.041 45.455 0.00 0.00 30.41 3.36
298 299 3.004839 GCAAAGTTGACCCTTCTTTCCTC 59.995 47.826 0.00 0.00 30.41 3.71
332 334 2.560981 CCCGGCAACTTTTGTAGGAAAT 59.439 45.455 0.00 0.00 33.32 2.17
334 336 4.142469 CCCGGCAACTTTTGTAGGAAATAG 60.142 45.833 0.00 0.00 33.32 1.73
335 337 4.412207 CGGCAACTTTTGTAGGAAATAGC 58.588 43.478 0.00 0.00 0.00 2.97
382 384 5.980116 CGTTTTCACCACACAATTGGAATAA 59.020 36.000 10.83 0.00 39.24 1.40
385 387 5.913137 TCACCACACAATTGGAATAATCC 57.087 39.130 10.83 0.00 46.76 3.01
409 411 8.677300 TCCAGTATATTTCTTTCACTCATTTGC 58.323 33.333 0.00 0.00 0.00 3.68
412 414 8.186821 AGTATATTTCTTTCACTCATTTGCTGC 58.813 33.333 0.00 0.00 0.00 5.25
413 415 4.652421 TTTCTTTCACTCATTTGCTGCA 57.348 36.364 0.00 0.00 0.00 4.41
414 416 3.631145 TCTTTCACTCATTTGCTGCAC 57.369 42.857 0.00 0.00 0.00 4.57
415 417 2.950975 TCTTTCACTCATTTGCTGCACA 59.049 40.909 0.00 0.00 0.00 4.57
423 425 2.093921 TCATTTGCTGCACAATGGATGG 60.094 45.455 24.03 9.62 38.31 3.51
427 429 0.383231 GCTGCACAATGGATGGCTAC 59.617 55.000 0.00 0.00 0.00 3.58
428 430 2.020694 GCTGCACAATGGATGGCTACT 61.021 52.381 0.00 0.00 0.00 2.57
430 432 3.544684 CTGCACAATGGATGGCTACTAA 58.455 45.455 0.00 0.00 0.00 2.24
455 457 1.873591 GCACGAGTGGTCAAAACTGAT 59.126 47.619 5.32 0.00 0.00 2.90
456 458 3.064207 GCACGAGTGGTCAAAACTGATA 58.936 45.455 5.32 0.00 0.00 2.15
458 460 4.154195 GCACGAGTGGTCAAAACTGATAAT 59.846 41.667 5.32 0.00 0.00 1.28
459 461 5.621422 CACGAGTGGTCAAAACTGATAATG 58.379 41.667 0.00 0.00 0.00 1.90
460 462 4.154195 ACGAGTGGTCAAAACTGATAATGC 59.846 41.667 0.00 0.00 0.00 3.56
462 464 4.666512 AGTGGTCAAAACTGATAATGCCT 58.333 39.130 0.00 0.00 0.00 4.75
469 473 5.774690 TCAAAACTGATAATGCCTTGGAGTT 59.225 36.000 0.00 0.00 0.00 3.01
487 491 6.472887 TGGAGTTTGTAGACTTATTTCAGGG 58.527 40.000 0.00 0.00 0.00 4.45
508 513 2.678336 GGTACACATCAGCCAGCTAAAC 59.322 50.000 0.00 0.00 0.00 2.01
527 532 6.426937 GCTAAACAAGAGACAATTCTACCACA 59.573 38.462 0.00 0.00 29.47 4.17
534 539 7.964604 AGAGACAATTCTACCACACTTAAAC 57.035 36.000 0.00 0.00 29.47 2.01
583 591 8.728088 ACTATTGATTGAATTGTTGACGAAAC 57.272 30.769 0.00 0.00 39.41 2.78
631 641 3.074538 AGGACAAGCACCTACCAATTTCT 59.925 43.478 0.00 0.00 35.84 2.52
755 796 2.762327 CCAAGCTTCCAGCAAATATGGT 59.238 45.455 0.00 0.00 45.56 3.55
828 875 0.744874 CCTCGGCTCGTGAATTCCTA 59.255 55.000 2.27 0.00 0.00 2.94
882 929 1.903877 CGGACAGGCTCCATTCACCT 61.904 60.000 0.00 0.00 39.39 4.00
945 992 7.765695 AAATGCCTTTGTCTTCTCTATTTGA 57.234 32.000 0.00 0.00 0.00 2.69
993 1043 2.012673 GTCTGGAGCGCAAATCATCTT 58.987 47.619 11.47 0.00 0.00 2.40
1167 1217 2.104111 CGTGAAGGGCCAAGGTGATATA 59.896 50.000 6.18 0.00 0.00 0.86
1168 1218 3.744660 GTGAAGGGCCAAGGTGATATAG 58.255 50.000 6.18 0.00 0.00 1.31
1221 1271 6.604171 TGATACATTGCTACCCAATCAGAAT 58.396 36.000 0.00 0.00 42.15 2.40
1234 1284 5.829924 CCCAATCAGAATATAACTGCTGGTT 59.170 40.000 18.24 0.00 41.54 3.67
1238 1288 7.798596 ATCAGAATATAACTGCTGGTTCAAG 57.201 36.000 0.00 0.00 39.17 3.02
1753 1803 2.599597 GGCATGGGCAGGAGATGT 59.400 61.111 0.00 0.00 43.71 3.06
1782 1832 1.349067 AGCTACCTTCCACGGACTTT 58.651 50.000 0.00 0.00 0.00 2.66
1788 1838 1.405661 CCTTCCACGGACTTTCTAGGC 60.406 57.143 0.00 0.00 0.00 3.93
1820 1873 6.309251 CGTAAGATTGAGTCAGTTTCTCTTCC 59.691 42.308 0.00 0.00 43.02 3.46
1974 2031 3.415212 TCTCAAGCTTCCCAAGACATTG 58.585 45.455 0.00 0.00 36.09 2.82
2253 2325 9.289782 GAGGTTGGCTATGAAATGATAACTAAT 57.710 33.333 0.00 0.00 0.00 1.73
2505 2577 1.556451 TCTGATGGACCACACAGGATG 59.444 52.381 22.35 6.11 46.00 3.51
3334 3421 7.056006 TGGATGCAAAACTATGATGTGTATCT 58.944 34.615 0.00 0.00 33.45 1.98
3372 3459 2.560504 CATGAGCCGCTTGTATACCAA 58.439 47.619 0.00 0.00 0.00 3.67
3479 3566 1.095228 CGGTGTGTCTGTGTGGCTTT 61.095 55.000 0.00 0.00 0.00 3.51
3506 3593 4.305989 TCCAGTTGACAGCATTGTTTTC 57.694 40.909 0.00 0.00 37.76 2.29
3532 3619 1.006922 GAAACAGTTGCCCAGCTGC 60.007 57.895 8.66 0.00 42.43 5.25
3559 3646 9.663904 CTTGAGAAATATTTCAACGAAAACTCA 57.336 29.630 26.02 15.81 39.61 3.41
3653 3743 4.594920 AGCATATACCTGGCATTACAGACT 59.405 41.667 0.00 0.00 40.97 3.24
3693 3783 4.546674 TCATATCAAGCACTAGGACTGGA 58.453 43.478 0.00 0.00 0.00 3.86
3737 3827 2.764010 ACACACAGGTTAGTCACTGACA 59.236 45.455 11.80 0.00 38.09 3.58
3841 3932 6.069029 AGGAACCCTTAGGCTGTGTATTAAAT 60.069 38.462 0.00 0.00 36.11 1.40
3842 3933 6.262496 GGAACCCTTAGGCTGTGTATTAAATC 59.738 42.308 0.00 0.00 36.11 2.17
3868 3959 8.939929 CAAAGATGTGTTGAGTTCTGTATACAT 58.060 33.333 5.91 0.00 0.00 2.29
3926 4017 6.998074 TGTCCATTTCCAATCCTACATGATAC 59.002 38.462 0.00 0.00 0.00 2.24
4015 4106 8.607713 TCAAGAGGAAAATATAACAGGGTAACA 58.392 33.333 0.00 0.00 39.74 2.41
4016 4107 8.674607 CAAGAGGAAAATATAACAGGGTAACAC 58.325 37.037 0.00 0.00 39.74 3.32
4033 4124 1.620323 ACACGTCCCTTTAGTACCCAC 59.380 52.381 0.00 0.00 0.00 4.61
4149 4240 2.745102 TCAAACATGCGTACGAGTGAA 58.255 42.857 21.65 0.00 0.00 3.18
4158 4249 1.135373 CGTACGAGTGAATGCACCTCT 60.135 52.381 10.44 0.00 46.32 3.69
4168 4259 4.342378 GTGAATGCACCTCTCTCTACCATA 59.658 45.833 0.00 0.00 39.14 2.74
4175 4266 5.380900 CACCTCTCTCTACCATATCACTCA 58.619 45.833 0.00 0.00 0.00 3.41
4178 4269 6.009589 CCTCTCTCTACCATATCACTCACAT 58.990 44.000 0.00 0.00 0.00 3.21
4180 4271 7.667635 CCTCTCTCTACCATATCACTCACATAA 59.332 40.741 0.00 0.00 0.00 1.90
4181 4272 8.628630 TCTCTCTACCATATCACTCACATAAG 57.371 38.462 0.00 0.00 0.00 1.73
4182 4273 8.440771 TCTCTCTACCATATCACTCACATAAGA 58.559 37.037 0.00 0.00 0.00 2.10
4183 4274 8.996651 TCTCTACCATATCACTCACATAAGAA 57.003 34.615 0.00 0.00 0.00 2.52
4224 4317 1.003580 TCACCAGATTCTGCCACTTCC 59.996 52.381 8.23 0.00 0.00 3.46
4234 4327 0.251297 TGCCACTTCCCCAATGACAG 60.251 55.000 0.00 0.00 0.00 3.51
4264 4357 1.100510 CTGAGGATTGCACCCACATG 58.899 55.000 7.04 0.00 0.00 3.21
4294 4387 4.631377 TCCATCGTCATCAAGATTGTCAAC 59.369 41.667 0.00 0.00 0.00 3.18
4300 4393 5.443824 CGTCATCAAGATTGTCAACTCTTCG 60.444 44.000 7.07 5.21 29.34 3.79
4317 4410 5.181433 ACTCTTCGTCCCTTGCTTTAAATTC 59.819 40.000 0.00 0.00 0.00 2.17
4349 4442 6.494835 AGTCTAAATTTTCCTTCATTGCCAGT 59.505 34.615 0.00 0.00 0.00 4.00
4354 4447 3.410631 TTCCTTCATTGCCAGTCGTTA 57.589 42.857 0.00 0.00 0.00 3.18
4355 4448 3.627395 TCCTTCATTGCCAGTCGTTAT 57.373 42.857 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.156556 CACACAACTGTCTATCCATTTGGG 59.843 45.833 0.00 0.00 35.28 4.12
50 51 5.212532 ACAGTTTTTGGCTTAATGCATCA 57.787 34.783 0.00 0.00 45.15 3.07
84 85 6.991485 AAAATCTAAACGTTGAACATGCAG 57.009 33.333 0.00 0.00 0.00 4.41
103 104 8.301252 ACTGGTTAAAACAGTACCTGAAAAAT 57.699 30.769 11.24 0.00 46.62 1.82
143 144 2.349886 CAGCGCTGTAGAATTGTCCTTC 59.650 50.000 29.24 0.00 0.00 3.46
145 146 1.406069 CCAGCGCTGTAGAATTGTCCT 60.406 52.381 33.75 0.00 0.00 3.85
160 161 1.593196 TTGTCTTTCAAGGTCCAGCG 58.407 50.000 0.00 0.00 0.00 5.18
197 198 7.453126 TGTTGGGTGGTAAATTGTTCTATTCAT 59.547 33.333 0.00 0.00 0.00 2.57
210 211 3.709587 TGTCCTTTTGTTGGGTGGTAAA 58.290 40.909 0.00 0.00 0.00 2.01
254 255 4.201940 GCATCATGGATTTCATTGTCGACA 60.202 41.667 15.76 15.76 32.92 4.35
255 256 4.201940 TGCATCATGGATTTCATTGTCGAC 60.202 41.667 9.11 9.11 32.92 4.20
256 257 3.946558 TGCATCATGGATTTCATTGTCGA 59.053 39.130 0.00 0.00 32.92 4.20
257 258 4.295857 TGCATCATGGATTTCATTGTCG 57.704 40.909 0.00 0.00 32.92 4.35
291 292 3.004419 GGGTCCAAACTTTTCGAGGAAAG 59.996 47.826 7.83 7.83 41.34 2.62
297 298 1.167781 GCCGGGTCCAAACTTTTCGA 61.168 55.000 2.18 0.00 0.00 3.71
298 299 1.284715 GCCGGGTCCAAACTTTTCG 59.715 57.895 2.18 0.00 0.00 3.46
334 336 9.777575 ACGGTATACATAAGTAACAAATTTTGC 57.222 29.630 9.04 0.00 33.13 3.68
349 351 5.791666 TGTGTGGTGAAAACGGTATACATA 58.208 37.500 5.01 0.00 0.00 2.29
357 359 2.099921 TCCAATTGTGTGGTGAAAACGG 59.900 45.455 4.43 0.00 39.88 4.44
358 360 3.428746 TCCAATTGTGTGGTGAAAACG 57.571 42.857 4.43 0.00 39.88 3.60
362 364 6.279513 GGATTATTCCAATTGTGTGGTGAA 57.720 37.500 4.43 0.00 42.12 3.18
385 387 9.499585 CAGCAAATGAGTGAAAGAAATATACTG 57.500 33.333 0.00 0.00 0.00 2.74
391 393 4.986659 GTGCAGCAAATGAGTGAAAGAAAT 59.013 37.500 0.00 0.00 0.00 2.17
397 399 3.553302 CCATTGTGCAGCAAATGAGTGAA 60.553 43.478 22.02 0.00 40.91 3.18
398 400 2.029739 CCATTGTGCAGCAAATGAGTGA 60.030 45.455 22.02 0.00 40.91 3.41
400 402 2.241160 TCCATTGTGCAGCAAATGAGT 58.759 42.857 22.02 0.00 40.91 3.41
401 403 3.186909 CATCCATTGTGCAGCAAATGAG 58.813 45.455 22.02 15.46 40.91 2.90
402 404 2.093921 CCATCCATTGTGCAGCAAATGA 60.094 45.455 22.02 13.44 40.91 2.57
403 405 2.276201 CCATCCATTGTGCAGCAAATG 58.724 47.619 17.01 17.01 40.91 2.32
404 406 1.406341 GCCATCCATTGTGCAGCAAAT 60.406 47.619 0.00 0.00 40.91 2.32
406 408 0.901114 AGCCATCCATTGTGCAGCAA 60.901 50.000 0.00 4.56 41.89 3.91
408 410 0.383231 GTAGCCATCCATTGTGCAGC 59.617 55.000 0.00 0.00 0.00 5.25
409 411 2.048444 AGTAGCCATCCATTGTGCAG 57.952 50.000 0.00 0.00 0.00 4.41
427 429 1.002366 GACCACTCGTGCATGCTTAG 58.998 55.000 20.33 15.07 0.00 2.18
428 430 0.320050 TGACCACTCGTGCATGCTTA 59.680 50.000 20.33 3.08 0.00 3.09
430 432 0.534877 TTTGACCACTCGTGCATGCT 60.535 50.000 20.33 0.00 0.00 3.79
434 436 1.013596 CAGTTTTGACCACTCGTGCA 58.986 50.000 0.00 0.00 0.00 4.57
435 437 1.295792 TCAGTTTTGACCACTCGTGC 58.704 50.000 0.00 0.00 0.00 5.34
455 457 5.499004 AGTCTACAAACTCCAAGGCATTA 57.501 39.130 0.00 0.00 0.00 1.90
456 458 4.373156 AGTCTACAAACTCCAAGGCATT 57.627 40.909 0.00 0.00 0.00 3.56
458 460 3.857157 AAGTCTACAAACTCCAAGGCA 57.143 42.857 0.00 0.00 0.00 4.75
459 461 6.430000 TGAAATAAGTCTACAAACTCCAAGGC 59.570 38.462 0.00 0.00 0.00 4.35
460 462 7.119846 CCTGAAATAAGTCTACAAACTCCAAGG 59.880 40.741 0.00 0.00 0.00 3.61
462 464 6.940298 CCCTGAAATAAGTCTACAAACTCCAA 59.060 38.462 0.00 0.00 0.00 3.53
469 473 6.270463 TGTGTACCCCTGAAATAAGTCTACAA 59.730 38.462 0.00 0.00 0.00 2.41
487 491 2.678336 GTTTAGCTGGCTGATGTGTACC 59.322 50.000 5.25 0.00 0.00 3.34
508 513 7.962964 TTAAGTGTGGTAGAATTGTCTCTTG 57.037 36.000 0.00 0.00 35.12 3.02
527 532 5.830000 AAGTCGCCTTTTCAAGTTTAAGT 57.170 34.783 0.00 0.00 0.00 2.24
534 539 3.251004 AGCTGTAAAGTCGCCTTTTCAAG 59.749 43.478 0.00 0.00 41.18 3.02
542 547 5.107133 TCAATAGTTAGCTGTAAAGTCGCC 58.893 41.667 0.00 0.00 0.00 5.54
543 548 6.830114 ATCAATAGTTAGCTGTAAAGTCGC 57.170 37.500 0.00 0.00 0.00 5.19
544 549 8.407457 TCAATCAATAGTTAGCTGTAAAGTCG 57.593 34.615 0.00 0.00 0.00 4.18
583 591 5.718146 TCTTGAGAGTGATAGTTTGCTCTG 58.282 41.667 0.00 0.00 38.31 3.35
755 796 3.636679 AGCAGAGAGGTAGAGTATGCAA 58.363 45.455 0.00 0.00 34.71 4.08
828 875 3.083997 AGAAAGGAGCCCGGCGAT 61.084 61.111 9.30 0.00 0.00 4.58
882 929 2.875672 GCCACAGCTGAAAGTACCATCA 60.876 50.000 23.35 0.00 35.30 3.07
945 992 6.426328 CAGTCTTTTCAGCTGTGTTAGAGAAT 59.574 38.462 14.67 6.53 0.00 2.40
993 1043 1.608336 CCAGGAGTACACGGGGTGA 60.608 63.158 2.29 0.00 36.96 4.02
1167 1217 5.713861 AGAATCAAAGCTTTGCCATAGAACT 59.286 36.000 30.35 17.45 38.05 3.01
1168 1218 5.958955 AGAATCAAAGCTTTGCCATAGAAC 58.041 37.500 30.35 15.89 38.05 3.01
1221 1271 4.042311 TCCAACCTTGAACCAGCAGTTATA 59.958 41.667 0.00 0.00 39.40 0.98
1234 1284 6.615726 AGCCTATTACTAGATTCCAACCTTGA 59.384 38.462 0.00 0.00 0.00 3.02
1238 1288 7.541916 AGTAGCCTATTACTAGATTCCAACC 57.458 40.000 0.00 0.00 32.25 3.77
1461 1511 0.613012 GACCCCAATCAGCAGCCTTT 60.613 55.000 0.00 0.00 0.00 3.11
1753 1803 4.753107 CGTGGAAGGTAGCTTCAAAAAGTA 59.247 41.667 30.11 9.19 35.19 2.24
1782 1832 6.943146 ACTCAATCTTACGATCATAGCCTAGA 59.057 38.462 0.00 0.00 0.00 2.43
1788 1838 8.864069 AAACTGACTCAATCTTACGATCATAG 57.136 34.615 0.00 0.00 0.00 2.23
1832 1885 2.611292 GTGCAGTCACTCAAGCATATCC 59.389 50.000 0.00 0.00 39.43 2.59
1860 1913 2.642311 TCCTTGCCAGTATGAGAAACCA 59.358 45.455 0.00 0.00 39.69 3.67
1974 2031 2.440539 TCGAGGACTTTGAGACTTGC 57.559 50.000 0.00 0.00 0.00 4.01
2253 2325 5.079689 TGTAAGTGTATCTGCGGAAATGA 57.920 39.130 0.00 0.00 0.00 2.57
2505 2577 8.237267 CCATTCTCAACATACTCTAAAACCAAC 58.763 37.037 0.00 0.00 0.00 3.77
2631 2706 1.081892 CCAAGCACTCGTGATGAAGG 58.918 55.000 0.39 0.00 0.00 3.46
2730 2805 6.128282 CGCCTCTATTTAGAAGTTTTGCAAGA 60.128 38.462 0.00 0.00 0.00 3.02
3334 3421 7.118245 CGGCTCATGCTATTCTTGATTTACATA 59.882 37.037 0.00 0.00 39.59 2.29
3341 3428 2.149578 GCGGCTCATGCTATTCTTGAT 58.850 47.619 0.00 0.00 39.59 2.57
3372 3459 9.832445 AGTGTGGTCGAATACAAAATTCTATAT 57.168 29.630 4.74 0.00 0.00 0.86
3479 3566 2.727123 TGCTGTCAACTGGAAAGGAA 57.273 45.000 0.00 0.00 30.87 3.36
3506 3593 1.269051 GGGCAACTGTTTCGTTTGGAG 60.269 52.381 0.00 0.00 0.00 3.86
3532 3619 9.118236 GAGTTTTCGTTGAAATATTTCTCAAGG 57.882 33.333 24.77 18.40 38.29 3.61
3601 3689 4.756642 CCTGTCTGTTGCAGAGTCAAAATA 59.243 41.667 0.00 0.00 41.46 1.40
3608 3696 0.181114 TTGCCTGTCTGTTGCAGAGT 59.819 50.000 0.00 0.00 41.46 3.24
3638 3728 2.009774 CCGAAAGTCTGTAATGCCAGG 58.990 52.381 0.00 0.00 33.14 4.45
3693 3783 2.957402 TTGGCTGGAAGAGTCATTGT 57.043 45.000 0.00 0.00 35.75 2.71
3841 3932 8.147704 TGTATACAGAACTCAACACATCTTTGA 58.852 33.333 0.08 0.00 0.00 2.69
3842 3933 8.310406 TGTATACAGAACTCAACACATCTTTG 57.690 34.615 0.08 0.00 0.00 2.77
3926 4017 5.250235 TCTACTCCTAGAAAACTGCATCG 57.750 43.478 0.00 0.00 0.00 3.84
3973 4064 6.899089 TCCTCTTGAATATAGTGAATTGCCA 58.101 36.000 0.00 0.00 0.00 4.92
4015 4106 2.014010 TGTGGGTACTAAAGGGACGT 57.986 50.000 0.00 0.00 0.00 4.34
4016 4107 4.262335 GGATATGTGGGTACTAAAGGGACG 60.262 50.000 0.00 0.00 0.00 4.79
4025 4116 6.203072 ACTTAGTTCTGGATATGTGGGTACT 58.797 40.000 0.00 0.00 0.00 2.73
4082 4173 4.996758 GGCTAGTAGTTTTAAACCAACCGA 59.003 41.667 4.01 0.00 0.00 4.69
4118 4209 4.478699 ACGCATGTTTGATCTCATGTTTG 58.521 39.130 19.12 14.35 42.09 2.93
4149 4240 4.526262 GTGATATGGTAGAGAGAGGTGCAT 59.474 45.833 0.00 0.00 0.00 3.96
4158 4249 8.996651 TTCTTATGTGAGTGATATGGTAGAGA 57.003 34.615 0.00 0.00 0.00 3.10
4168 4259 8.457261 GCTGATTCTTTTTCTTATGTGAGTGAT 58.543 33.333 0.00 0.00 0.00 3.06
4175 4266 7.836183 ACCATAGGCTGATTCTTTTTCTTATGT 59.164 33.333 0.00 0.00 0.00 2.29
4178 4269 7.633789 AGACCATAGGCTGATTCTTTTTCTTA 58.366 34.615 0.00 0.00 0.00 2.10
4180 4271 6.072199 AGACCATAGGCTGATTCTTTTTCT 57.928 37.500 0.00 0.00 0.00 2.52
4181 4272 6.375455 TGAAGACCATAGGCTGATTCTTTTTC 59.625 38.462 0.00 0.00 31.06 2.29
4182 4273 6.151817 GTGAAGACCATAGGCTGATTCTTTTT 59.848 38.462 0.00 0.00 31.06 1.94
4183 4274 5.649831 GTGAAGACCATAGGCTGATTCTTTT 59.350 40.000 0.00 0.00 31.06 2.27
4217 4310 1.202927 ACACTGTCATTGGGGAAGTGG 60.203 52.381 6.13 0.00 42.00 4.00
4224 4317 3.723772 TGGTGACACTGTCATTGGG 57.276 52.632 14.95 0.00 44.63 4.12
4277 4370 5.406780 ACGAAGAGTTGACAATCTTGATGAC 59.593 40.000 13.94 3.54 35.93 3.06
4294 4387 5.412904 AGAATTTAAAGCAAGGGACGAAGAG 59.587 40.000 0.00 0.00 0.00 2.85
4300 4393 6.584185 TTGGTAGAATTTAAAGCAAGGGAC 57.416 37.500 0.00 0.00 0.00 4.46
4330 4423 3.573967 ACGACTGGCAATGAAGGAAAATT 59.426 39.130 0.00 0.00 0.00 1.82
4349 4442 2.494073 GACCAAATGGCCCAAATAACGA 59.506 45.455 0.00 0.00 39.32 3.85
4354 4447 2.629017 AGAGACCAAATGGCCCAAAT 57.371 45.000 0.00 0.00 39.32 2.32
4355 4448 2.378547 AGTAGAGACCAAATGGCCCAAA 59.621 45.455 0.00 0.00 39.32 3.28


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

AutoCloner maintained by Alex Coulton.