Multiple sequence alignment - TraesCS4D01G260300

Loading Multiple Alignment...

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 TraesCS4D01G260300 chr4D 100.000 5555 0 0 1 5555 429477173 429482727 0.000000e+00 10259.0
1 TraesCS4D01G260300 chr4A 98.407 3766 50 7 4 3764 37052294 37048534 0.000000e+00 6613.0
2 TraesCS4D01G260300 chr4A 95.041 1089 26 13 3810 4870 37048549 37047461 0.000000e+00 1687.0
3 TraesCS4D01G260300 chr4A 90.835 491 17 10 5005 5494 37047437 37046974 2.820000e-177 632.0
4 TraesCS4D01G260300 chr4A 92.000 125 9 1 3146 3270 67512883 67512760 2.060000e-39 174.0
5 TraesCS4D01G260300 chr4A 90.588 85 5 3 5470 5552 617363069 617362986 5.880000e-20 110.0
6 TraesCS4D01G260300 chr4B 97.889 3505 57 10 265 3764 527291604 527295096 0.000000e+00 6047.0
7 TraesCS4D01G260300 chr4B 99.210 886 7 0 3810 4695 527295081 527295966 0.000000e+00 1598.0
8 TraesCS4D01G260300 chr4B 95.304 724 25 5 4687 5408 527295985 527296701 0.000000e+00 1140.0
9 TraesCS4D01G260300 chr4B 96.698 212 7 0 1 212 527291388 527291599 2.460000e-93 353.0
10 TraesCS4D01G260300 chr7B 92.000 125 9 1 3146 3270 52981939 52981816 2.060000e-39 174.0
11 TraesCS4D01G260300 chr7B 91.200 125 10 1 3146 3270 52947760 52947883 9.570000e-38 169.0
12 TraesCS4D01G260300 chr7A 96.923 65 2 0 5488 5552 33365898 33365962 5.880000e-20 110.0
13 TraesCS4D01G260300 chr7A 100.000 47 0 0 3763 3809 688882459 688882505 2.760000e-13 87.9
14 TraesCS4D01G260300 chr1A 96.875 64 2 0 5489 5552 134973599 134973536 2.120000e-19 108.0
15 TraesCS4D01G260300 chr1A 96.774 62 2 0 5488 5549 518077197 518077258 2.740000e-18 104.0
16 TraesCS4D01G260300 chr5D 96.774 62 2 0 5488 5549 380324356 380324417 2.740000e-18 104.0
17 TraesCS4D01G260300 chr5D 87.879 66 6 2 3761 3824 539483082 539483017 5.970000e-10 76.8
18 TraesCS4D01G260300 chr1D 94.118 68 2 1 5485 5552 11489666 11489731 9.850000e-18 102.0
19 TraesCS4D01G260300 chr1B 92.857 70 5 0 5483 5552 675878683 675878752 9.850000e-18 102.0
20 TraesCS4D01G260300 chr1B 91.667 72 6 0 5481 5552 350969106 350969177 3.540000e-17 100.0
21 TraesCS4D01G260300 chr1B 100.000 29 0 0 5258 5286 258502335 258502307 3.000000e-03 54.7
22 TraesCS4D01G260300 chr2B 89.873 79 6 1 5474 5552 123063433 123063357 3.540000e-17 100.0
23 TraesCS4D01G260300 chr2A 100.000 48 0 0 3763 3810 57868017 57868064 7.660000e-14 89.8
24 TraesCS4D01G260300 chr2A 91.379 58 3 2 3761 3816 18173312 18173369 1.660000e-10 78.7
25 TraesCS4D01G260300 chr2A 87.692 65 5 3 3762 3825 551501232 551501294 7.720000e-09 73.1
26 TraesCS4D01G260300 chr7D 94.643 56 2 1 3763 3818 510440743 510440797 9.920000e-13 86.1
27 TraesCS4D01G260300 chr7D 89.231 65 4 3 3762 3824 95086331 95086394 1.660000e-10 78.7
28 TraesCS4D01G260300 chr3A 97.917 48 1 0 3763 3810 512321506 512321459 3.570000e-12 84.2
29 TraesCS4D01G260300 chr2D 96.154 52 1 1 3760 3810 198461087 198461138 3.570000e-12 84.2


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 TraesCS4D01G260300 chr4D 429477173 429482727 5554 False 10259.000000 10259 100.00000 1 5555 1 chr4D.!!$F1 5554
1 TraesCS4D01G260300 chr4A 37046974 37052294 5320 True 2977.333333 6613 94.76100 4 5494 3 chr4A.!!$R3 5490
2 TraesCS4D01G260300 chr4B 527291388 527296701 5313 False 2284.500000 6047 97.27525 1 5408 4 chr4B.!!$F1 5407

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
435 439 1.066430 GCCAGTAGGAATTCGGTGTCA 60.066 52.381 0.00 0.0 36.89 3.58 F
1083 1092 1.084370 CACCGGAATCTCTCGCAACC 61.084 60.000 9.46 0.0 0.00 3.77 F
1137 1146 1.946768 CCAGGAAAACGAGAAGCAACA 59.053 47.619 0.00 0.0 0.00 3.33 F
2047 2056 2.697751 ACTGCATATCGGAGAGCTCTTT 59.302 45.455 19.36 6.2 43.63 2.52 F
2945 2954 3.882444 CTGAGCAAGAGGATCAAATGGA 58.118 45.455 0.00 0.0 42.23 3.41 F
3100 3109 5.217978 ACGACCACTTACATTTCTTACCA 57.782 39.130 0.00 0.0 0.00 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2047 2056 0.783206 TCCAAATTCCAGGGCCTTGA 59.217 50.000 18.01 2.06 0.00 3.02 R
2236 2245 5.591877 CAGGATCCCACTTTATTTCTTGGAG 59.408 44.000 8.55 0.00 0.00 3.86 R
3100 3109 7.833786 ACACATGCTATCATCATTTGAGTTTT 58.166 30.769 0.00 0.00 37.89 2.43 R
3786 3795 1.956297 TTCGAAACGGAGGCAAAAGA 58.044 45.000 0.00 0.00 0.00 2.52 R
3787 3796 2.766970 TTTCGAAACGGAGGCAAAAG 57.233 45.000 6.47 0.00 0.00 2.27 R
4630 4640 5.278364 GCCAAGGATGCAATGAGATTTCTAG 60.278 44.000 0.00 0.00 0.00 2.43 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
133 134 5.221126 GCATAAGGAGAATGTCATTGGGTTC 60.221 44.000 1.88 0.00 30.09 3.62
238 241 9.961265 GTTAGTTGTTTCCTTATTTTAGCAGTT 57.039 29.630 0.00 0.00 0.00 3.16
241 244 8.793592 AGTTGTTTCCTTATTTTAGCAGTTAGG 58.206 33.333 0.00 0.00 0.00 2.69
247 250 6.027749 CCTTATTTTAGCAGTTAGGTTTGCG 58.972 40.000 0.00 0.00 44.80 4.85
256 259 4.558860 GCAGTTAGGTTTGCGAAATCAATC 59.441 41.667 0.00 0.00 0.00 2.67
263 266 1.164411 TGCGAAATCAATCGTGCCTT 58.836 45.000 0.00 0.00 44.49 4.35
280 283 3.328931 TGCCTTCTCTTCTCAGGATTGTT 59.671 43.478 0.00 0.00 0.00 2.83
435 439 1.066430 GCCAGTAGGAATTCGGTGTCA 60.066 52.381 0.00 0.00 36.89 3.58
588 592 9.237187 TGCTGATTACTTGTTTTGTATATCCAA 57.763 29.630 0.00 0.00 0.00 3.53
596 600 9.174166 ACTTGTTTTGTATATCCAATCCTGTAC 57.826 33.333 0.00 0.00 0.00 2.90
673 679 4.567971 ACCATGCAATTACCAATGTTGTG 58.432 39.130 0.00 0.00 0.00 3.33
683 689 2.223144 ACCAATGTTGTGTGATTCGTCG 59.777 45.455 0.00 0.00 0.00 5.12
690 696 4.508492 TGTTGTGTGATTCGTCGTGTTTAT 59.492 37.500 0.00 0.00 0.00 1.40
835 841 4.514441 ACTTGCTATATGCTTGCTCATGTC 59.486 41.667 0.00 0.00 43.37 3.06
1083 1092 1.084370 CACCGGAATCTCTCGCAACC 61.084 60.000 9.46 0.00 0.00 3.77
1137 1146 1.946768 CCAGGAAAACGAGAAGCAACA 59.053 47.619 0.00 0.00 0.00 3.33
1737 1746 8.462016 AGAAACAGAAACCTATGTAATTGCATC 58.538 33.333 12.62 0.00 0.00 3.91
1787 1796 8.326680 TGTCCATCATACAAGTTATATGCATG 57.673 34.615 10.16 0.00 31.26 4.06
2047 2056 2.697751 ACTGCATATCGGAGAGCTCTTT 59.302 45.455 19.36 6.20 43.63 2.52
2236 2245 7.389607 TGTTTGTACTTATCAGAAAGCTAACCC 59.610 37.037 0.00 0.00 0.00 4.11
2622 2631 4.448732 GTGAATCATTTCCTTGGTGTTTGC 59.551 41.667 0.00 0.00 0.00 3.68
2945 2954 3.882444 CTGAGCAAGAGGATCAAATGGA 58.118 45.455 0.00 0.00 42.23 3.41
3100 3109 5.217978 ACGACCACTTACATTTCTTACCA 57.782 39.130 0.00 0.00 0.00 3.25
3760 3769 9.764363 TGTATTTATTTGCTATCATCTTCGAGT 57.236 29.630 0.00 0.00 0.00 4.18
3763 3772 8.948631 TTTATTTGCTATCATCTTCGAGTTCT 57.051 30.769 0.00 0.00 0.00 3.01
3764 3773 8.581057 TTATTTGCTATCATCTTCGAGTTCTC 57.419 34.615 0.00 0.00 0.00 2.87
3765 3774 5.843673 TTGCTATCATCTTCGAGTTCTCT 57.156 39.130 0.00 0.00 0.00 3.10
3766 3775 5.843673 TGCTATCATCTTCGAGTTCTCTT 57.156 39.130 0.00 0.00 0.00 2.85
3767 3776 6.944234 TGCTATCATCTTCGAGTTCTCTTA 57.056 37.500 0.00 0.00 0.00 2.10
3768 3777 7.334844 TGCTATCATCTTCGAGTTCTCTTAA 57.665 36.000 0.00 0.00 0.00 1.85
3769 3778 7.946207 TGCTATCATCTTCGAGTTCTCTTAAT 58.054 34.615 0.00 0.00 0.00 1.40
3770 3779 8.417106 TGCTATCATCTTCGAGTTCTCTTAATT 58.583 33.333 0.00 0.00 0.00 1.40
3771 3780 9.900710 GCTATCATCTTCGAGTTCTCTTAATTA 57.099 33.333 0.00 0.00 0.00 1.40
3781 3790 9.534565 TCGAGTTCTCTTAATTAAATGATGAGG 57.465 33.333 10.05 0.00 0.00 3.86
3782 3791 8.279103 CGAGTTCTCTTAATTAAATGATGAGGC 58.721 37.037 10.05 5.70 0.00 4.70
3783 3792 9.113838 GAGTTCTCTTAATTAAATGATGAGGCA 57.886 33.333 10.05 0.00 0.00 4.75
3784 3793 9.466497 AGTTCTCTTAATTAAATGATGAGGCAA 57.534 29.630 10.05 0.00 0.00 4.52
3793 3802 7.599630 TTAAATGATGAGGCAAATCTTTTGC 57.400 32.000 14.88 14.88 44.22 3.68
3800 3809 2.438868 GCAAATCTTTTGCCTCCGTT 57.561 45.000 12.74 0.00 39.38 4.44
3801 3810 2.754472 GCAAATCTTTTGCCTCCGTTT 58.246 42.857 12.74 0.00 39.38 3.60
3802 3811 2.731451 GCAAATCTTTTGCCTCCGTTTC 59.269 45.455 12.74 0.00 39.38 2.78
3803 3812 2.979813 CAAATCTTTTGCCTCCGTTTCG 59.020 45.455 0.00 0.00 0.00 3.46
3804 3813 2.178912 ATCTTTTGCCTCCGTTTCGA 57.821 45.000 0.00 0.00 0.00 3.71
3805 3814 1.956297 TCTTTTGCCTCCGTTTCGAA 58.044 45.000 0.00 0.00 0.00 3.71
3806 3815 2.290464 TCTTTTGCCTCCGTTTCGAAA 58.710 42.857 6.47 6.47 0.00 3.46
3807 3816 2.683867 TCTTTTGCCTCCGTTTCGAAAA 59.316 40.909 13.10 0.00 0.00 2.29
3808 3817 3.128938 TCTTTTGCCTCCGTTTCGAAAAA 59.871 39.130 13.10 0.00 0.00 1.94
3840 3849 2.000447 GTTCTGGCTCGGTCATACAAC 59.000 52.381 0.00 0.00 0.00 3.32
4341 4350 5.420725 TGGCAAGCATTCTAAGAACTCTA 57.579 39.130 0.00 0.00 0.00 2.43
4827 4864 5.605534 TGAAAGAGATATGCTTGGTAGAGC 58.394 41.667 0.00 0.00 43.00 4.09
4926 4963 8.108999 TCAGAAATCAATGAAATCCAGTCCTAA 58.891 33.333 0.00 0.00 0.00 2.69
4997 5034 3.058016 CGCCATTAGATGAAAATGCCGAT 60.058 43.478 0.00 0.00 37.36 4.18
5002 5039 7.517259 GCCATTAGATGAAAATGCCGATTTTTC 60.517 37.037 9.22 9.22 41.06 2.29
5003 5040 7.707893 CCATTAGATGAAAATGCCGATTTTTCT 59.292 33.333 14.29 9.00 41.06 2.52
5004 5041 9.090692 CATTAGATGAAAATGCCGATTTTTCTT 57.909 29.630 14.29 10.18 41.06 2.52
5005 5042 9.657419 ATTAGATGAAAATGCCGATTTTTCTTT 57.343 25.926 14.29 6.27 41.06 2.52
5186 5223 7.602645 CACTTAACCCGAAAAGTTTTAAAACG 58.397 34.615 22.04 11.96 43.51 3.60
5254 5292 3.492102 TCTGTTCAGTTGAGGAAAGGG 57.508 47.619 0.00 0.00 0.00 3.95
5288 5326 6.872628 TCATGATAGATTGGTGAATGAAGC 57.127 37.500 0.00 0.00 0.00 3.86
5319 5357 2.698855 AGGATATGCACCACACTGAC 57.301 50.000 0.00 0.00 0.00 3.51
5321 5359 2.093288 AGGATATGCACCACACTGACTG 60.093 50.000 0.00 0.00 0.00 3.51
5344 5382 1.937108 GCCGTGGACAAGTGAAGAGAG 60.937 57.143 0.00 0.00 0.00 3.20
5375 5414 5.594725 GTGATGTCTCCATCTTACCAGAGTA 59.405 44.000 4.51 0.00 46.38 2.59
5494 5533 9.699703 GGAGTAAAGATTTCCACAGATATCTAC 57.300 37.037 4.54 0.00 39.16 2.59
5497 5536 9.699703 GTAAAGATTTCCACAGATATCTACTCC 57.300 37.037 4.54 0.00 39.16 3.85
5498 5537 6.926630 AGATTTCCACAGATATCTACTCCC 57.073 41.667 4.54 0.00 38.55 4.30
5499 5538 6.629156 AGATTTCCACAGATATCTACTCCCT 58.371 40.000 4.54 0.00 38.55 4.20
5500 5539 6.723977 AGATTTCCACAGATATCTACTCCCTC 59.276 42.308 4.54 0.00 38.55 4.30
5501 5540 4.390129 TCCACAGATATCTACTCCCTCC 57.610 50.000 4.54 0.00 0.00 4.30
5502 5541 3.085533 CCACAGATATCTACTCCCTCCG 58.914 54.545 4.54 0.00 0.00 4.63
5503 5542 3.498841 CCACAGATATCTACTCCCTCCGT 60.499 52.174 4.54 0.00 0.00 4.69
5504 5543 4.145807 CACAGATATCTACTCCCTCCGTT 58.854 47.826 4.54 0.00 0.00 4.44
5505 5544 4.216687 CACAGATATCTACTCCCTCCGTTC 59.783 50.000 4.54 0.00 0.00 3.95
5506 5545 4.105057 ACAGATATCTACTCCCTCCGTTCT 59.895 45.833 4.54 0.00 0.00 3.01
5507 5546 4.457603 CAGATATCTACTCCCTCCGTTCTG 59.542 50.000 4.54 0.00 0.00 3.02
5508 5547 4.351407 AGATATCTACTCCCTCCGTTCTGA 59.649 45.833 2.53 0.00 0.00 3.27
5509 5548 2.893215 TCTACTCCCTCCGTTCTGAA 57.107 50.000 0.00 0.00 0.00 3.02
5510 5549 3.383698 TCTACTCCCTCCGTTCTGAAT 57.616 47.619 0.00 0.00 0.00 2.57
5511 5550 3.709587 TCTACTCCCTCCGTTCTGAATT 58.290 45.455 0.00 0.00 0.00 2.17
5512 5551 4.863548 TCTACTCCCTCCGTTCTGAATTA 58.136 43.478 0.00 0.00 0.00 1.40
5513 5552 3.889520 ACTCCCTCCGTTCTGAATTAC 57.110 47.619 0.00 0.00 0.00 1.89
5514 5553 3.442076 ACTCCCTCCGTTCTGAATTACT 58.558 45.455 0.00 0.00 0.00 2.24
5515 5554 3.838903 ACTCCCTCCGTTCTGAATTACTT 59.161 43.478 0.00 0.00 0.00 2.24
5516 5555 4.184629 CTCCCTCCGTTCTGAATTACTTG 58.815 47.826 0.00 0.00 0.00 3.16
5517 5556 3.581332 TCCCTCCGTTCTGAATTACTTGT 59.419 43.478 0.00 0.00 0.00 3.16
5518 5557 3.933332 CCCTCCGTTCTGAATTACTTGTC 59.067 47.826 0.00 0.00 0.00 3.18
5519 5558 4.322801 CCCTCCGTTCTGAATTACTTGTCT 60.323 45.833 0.00 0.00 0.00 3.41
5520 5559 4.865365 CCTCCGTTCTGAATTACTTGTCTC 59.135 45.833 0.00 0.00 0.00 3.36
5521 5560 4.482386 TCCGTTCTGAATTACTTGTCTCG 58.518 43.478 0.00 0.00 0.00 4.04
5522 5561 3.612860 CCGTTCTGAATTACTTGTCTCGG 59.387 47.826 0.00 0.00 0.00 4.63
5523 5562 4.482386 CGTTCTGAATTACTTGTCTCGGA 58.518 43.478 0.00 0.00 0.00 4.55
5524 5563 4.921515 CGTTCTGAATTACTTGTCTCGGAA 59.078 41.667 0.00 0.00 32.16 4.30
5525 5564 5.404366 CGTTCTGAATTACTTGTCTCGGAAA 59.596 40.000 0.00 0.00 35.51 3.13
5526 5565 6.090898 CGTTCTGAATTACTTGTCTCGGAAAT 59.909 38.462 0.00 0.00 35.51 2.17
5527 5566 6.968131 TCTGAATTACTTGTCTCGGAAATG 57.032 37.500 0.00 0.00 0.00 2.32
5528 5567 5.874810 TCTGAATTACTTGTCTCGGAAATGG 59.125 40.000 0.00 0.00 0.00 3.16
5529 5568 5.800296 TGAATTACTTGTCTCGGAAATGGA 58.200 37.500 0.00 0.00 0.00 3.41
5530 5569 6.414732 TGAATTACTTGTCTCGGAAATGGAT 58.585 36.000 0.00 0.00 0.00 3.41
5531 5570 6.316140 TGAATTACTTGTCTCGGAAATGGATG 59.684 38.462 0.00 0.00 0.00 3.51
5532 5571 3.703001 ACTTGTCTCGGAAATGGATGT 57.297 42.857 0.00 0.00 0.00 3.06
5533 5572 4.819105 ACTTGTCTCGGAAATGGATGTA 57.181 40.909 0.00 0.00 0.00 2.29
5534 5573 5.359194 ACTTGTCTCGGAAATGGATGTAT 57.641 39.130 0.00 0.00 0.00 2.29
5535 5574 5.360591 ACTTGTCTCGGAAATGGATGTATC 58.639 41.667 0.00 0.00 0.00 2.24
5536 5575 5.129485 ACTTGTCTCGGAAATGGATGTATCT 59.871 40.000 0.00 0.00 0.00 1.98
5537 5576 6.323996 ACTTGTCTCGGAAATGGATGTATCTA 59.676 38.462 0.00 0.00 0.00 1.98
5538 5577 6.724893 TGTCTCGGAAATGGATGTATCTAA 57.275 37.500 0.00 0.00 0.00 2.10
5539 5578 7.119709 TGTCTCGGAAATGGATGTATCTAAA 57.880 36.000 0.00 0.00 0.00 1.85
5540 5579 7.561251 TGTCTCGGAAATGGATGTATCTAAAA 58.439 34.615 0.00 0.00 0.00 1.52
5541 5580 7.494625 TGTCTCGGAAATGGATGTATCTAAAAC 59.505 37.037 0.00 0.00 0.00 2.43
5542 5581 7.711339 GTCTCGGAAATGGATGTATCTAAAACT 59.289 37.037 0.00 0.00 0.00 2.66
5543 5582 8.920174 TCTCGGAAATGGATGTATCTAAAACTA 58.080 33.333 0.00 0.00 0.00 2.24
5544 5583 9.542462 CTCGGAAATGGATGTATCTAAAACTAA 57.458 33.333 0.00 0.00 0.00 2.24
5545 5584 9.893634 TCGGAAATGGATGTATCTAAAACTAAA 57.106 29.630 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
133 134 2.095768 CGCACATCAAAGTACCAACTGG 60.096 50.000 0.00 0.00 35.62 4.00
238 241 3.425625 GCACGATTGATTTCGCAAACCTA 60.426 43.478 0.00 0.00 42.82 3.08
241 244 1.648681 GGCACGATTGATTTCGCAAAC 59.351 47.619 0.00 0.00 42.82 2.93
247 250 4.633565 AGAAGAGAAGGCACGATTGATTTC 59.366 41.667 0.00 0.00 0.00 2.17
256 259 0.891373 TCCTGAGAAGAGAAGGCACG 59.109 55.000 0.00 0.00 0.00 5.34
263 266 3.517100 CCTCCAACAATCCTGAGAAGAGA 59.483 47.826 0.00 0.00 0.00 3.10
280 283 6.349280 CGAAAATAATTTCAGCAGTTCCTCCA 60.349 38.462 4.24 0.00 44.24 3.86
588 592 7.624549 ACAGACATAGAACAATTGTACAGGAT 58.375 34.615 12.39 0.00 0.00 3.24
596 600 8.763049 TCAGAGTTACAGACATAGAACAATTG 57.237 34.615 3.24 3.24 0.00 2.32
673 679 3.173599 TCGGATAAACACGACGAATCAC 58.826 45.455 0.00 0.00 33.69 3.06
683 689 6.541111 AAGTTTCACTTCTCGGATAAACAC 57.459 37.500 0.00 0.00 31.77 3.32
690 696 4.186159 ACGAAAAAGTTTCACTTCTCGGA 58.814 39.130 18.12 0.00 42.67 4.55
1083 1092 1.089920 CACTTGCTGAGAAATCCCGG 58.910 55.000 0.00 0.00 0.00 5.73
1137 1146 4.164796 TCATTCACTTGGCTATCATCAGGT 59.835 41.667 0.00 0.00 0.00 4.00
1787 1796 5.314923 TGCAGAGATTTTAATTGAGGCAC 57.685 39.130 0.00 0.00 0.00 5.01
2047 2056 0.783206 TCCAAATTCCAGGGCCTTGA 59.217 50.000 18.01 2.06 0.00 3.02
2236 2245 5.591877 CAGGATCCCACTTTATTTCTTGGAG 59.408 44.000 8.55 0.00 0.00 3.86
3100 3109 7.833786 ACACATGCTATCATCATTTGAGTTTT 58.166 30.769 0.00 0.00 37.89 2.43
3755 3764 9.534565 CCTCATCATTTAATTAAGAGAACTCGA 57.465 33.333 11.18 0.00 34.09 4.04
3756 3765 8.279103 GCCTCATCATTTAATTAAGAGAACTCG 58.721 37.037 11.18 0.00 34.09 4.18
3757 3766 9.113838 TGCCTCATCATTTAATTAAGAGAACTC 57.886 33.333 11.18 0.00 0.00 3.01
3758 3767 9.466497 TTGCCTCATCATTTAATTAAGAGAACT 57.534 29.630 11.18 0.00 0.00 3.01
3767 3776 8.671028 GCAAAAGATTTGCCTCATCATTTAATT 58.329 29.630 15.12 0.00 39.38 1.40
3768 3777 8.205131 GCAAAAGATTTGCCTCATCATTTAAT 57.795 30.769 15.12 0.00 39.38 1.40
3769 3778 7.599630 GCAAAAGATTTGCCTCATCATTTAA 57.400 32.000 15.12 0.00 39.38 1.52
3781 3790 2.438868 AACGGAGGCAAAAGATTTGC 57.561 45.000 17.18 17.18 44.22 3.68
3782 3791 2.979813 CGAAACGGAGGCAAAAGATTTG 59.020 45.455 0.00 0.00 0.00 2.32
3783 3792 2.882137 TCGAAACGGAGGCAAAAGATTT 59.118 40.909 0.00 0.00 0.00 2.17
3784 3793 2.500229 TCGAAACGGAGGCAAAAGATT 58.500 42.857 0.00 0.00 0.00 2.40
3785 3794 2.178912 TCGAAACGGAGGCAAAAGAT 57.821 45.000 0.00 0.00 0.00 2.40
3786 3795 1.956297 TTCGAAACGGAGGCAAAAGA 58.044 45.000 0.00 0.00 0.00 2.52
3787 3796 2.766970 TTTCGAAACGGAGGCAAAAG 57.233 45.000 6.47 0.00 0.00 2.27
3788 3797 3.505464 TTTTTCGAAACGGAGGCAAAA 57.495 38.095 10.79 0.00 0.00 2.44
3805 3814 5.006386 AGCCAGAACTCGAAGATGATTTTT 58.994 37.500 0.00 0.00 33.89 1.94
3806 3815 4.583871 AGCCAGAACTCGAAGATGATTTT 58.416 39.130 0.00 0.00 33.89 1.82
3807 3816 4.187694 GAGCCAGAACTCGAAGATGATTT 58.812 43.478 0.00 0.00 33.89 2.17
3808 3817 3.791245 GAGCCAGAACTCGAAGATGATT 58.209 45.455 0.00 0.00 33.89 2.57
3809 3818 3.451141 GAGCCAGAACTCGAAGATGAT 57.549 47.619 0.00 0.00 33.89 2.45
3840 3849 5.237996 CACATGCAGGTAATATCAACCTCAG 59.762 44.000 2.51 0.17 44.20 3.35
4630 4640 5.278364 GCCAAGGATGCAATGAGATTTCTAG 60.278 44.000 0.00 0.00 0.00 2.43
4997 5034 7.495901 TGGATGCAGTGATGTAAAAAGAAAAA 58.504 30.769 0.00 0.00 0.00 1.94
5002 5039 8.461222 TCTTTATGGATGCAGTGATGTAAAAAG 58.539 33.333 0.00 0.00 0.00 2.27
5003 5040 8.347004 TCTTTATGGATGCAGTGATGTAAAAA 57.653 30.769 0.00 0.00 0.00 1.94
5004 5041 7.936496 TCTTTATGGATGCAGTGATGTAAAA 57.064 32.000 0.00 0.00 0.00 1.52
5005 5042 7.774625 TGATCTTTATGGATGCAGTGATGTAAA 59.225 33.333 0.00 0.00 0.00 2.01
5128 5165 7.495606 ACCAATGAAATGTTCCTCAAAGAAAAC 59.504 33.333 0.00 0.00 0.00 2.43
5186 5223 1.615883 TCACTTCACAGAGCAGGTCTC 59.384 52.381 0.00 0.00 42.21 3.36
5254 5292 6.098679 CCAATCTATCATGATCGTCTTCCTC 58.901 44.000 12.53 0.00 0.00 3.71
5288 5326 4.217118 GGTGCATATCCTTTGCTTGGATAG 59.783 45.833 14.68 9.91 46.08 2.08
5319 5357 3.953775 ACTTGTCCACGGCCCCAG 61.954 66.667 0.00 0.00 0.00 4.45
5321 5359 3.485346 TTCACTTGTCCACGGCCCC 62.485 63.158 0.00 0.00 0.00 5.80
5326 5364 2.223829 ACACTCTCTTCACTTGTCCACG 60.224 50.000 0.00 0.00 0.00 4.94
5375 5414 4.649674 ACGTCACTGGGATACTGATTGTAT 59.350 41.667 0.00 0.00 43.94 2.29
5438 5477 3.009723 TGAAGCACTTTATGTGGCTAGC 58.990 45.455 6.04 6.04 46.27 3.42
5474 5513 7.079048 AGGGAGTAGATATCTGTGGAAATCTT 58.921 38.462 15.79 0.00 31.38 2.40
5494 5533 4.184629 CAAGTAATTCAGAACGGAGGGAG 58.815 47.826 0.00 0.00 0.00 4.30
5495 5534 3.581332 ACAAGTAATTCAGAACGGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
5496 5535 3.933332 GACAAGTAATTCAGAACGGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
5497 5536 4.822026 AGACAAGTAATTCAGAACGGAGG 58.178 43.478 0.00 0.00 0.00 4.30
5498 5537 4.559251 CGAGACAAGTAATTCAGAACGGAG 59.441 45.833 0.00 0.00 0.00 4.63
5499 5538 4.482386 CGAGACAAGTAATTCAGAACGGA 58.518 43.478 0.00 0.00 0.00 4.69
5500 5539 3.612860 CCGAGACAAGTAATTCAGAACGG 59.387 47.826 0.00 0.00 0.00 4.44
5501 5540 4.482386 TCCGAGACAAGTAATTCAGAACG 58.518 43.478 0.00 0.00 0.00 3.95
5502 5541 6.780706 TTTCCGAGACAAGTAATTCAGAAC 57.219 37.500 0.00 0.00 0.00 3.01
5503 5542 6.371548 CCATTTCCGAGACAAGTAATTCAGAA 59.628 38.462 0.00 0.00 0.00 3.02
5504 5543 5.874810 CCATTTCCGAGACAAGTAATTCAGA 59.125 40.000 0.00 0.00 0.00 3.27
5505 5544 5.874810 TCCATTTCCGAGACAAGTAATTCAG 59.125 40.000 0.00 0.00 0.00 3.02
5506 5545 5.800296 TCCATTTCCGAGACAAGTAATTCA 58.200 37.500 0.00 0.00 0.00 2.57
5507 5546 6.316390 ACATCCATTTCCGAGACAAGTAATTC 59.684 38.462 0.00 0.00 0.00 2.17
5508 5547 6.180472 ACATCCATTTCCGAGACAAGTAATT 58.820 36.000 0.00 0.00 0.00 1.40
5509 5548 5.745227 ACATCCATTTCCGAGACAAGTAAT 58.255 37.500 0.00 0.00 0.00 1.89
5510 5549 5.160607 ACATCCATTTCCGAGACAAGTAA 57.839 39.130 0.00 0.00 0.00 2.24
5511 5550 4.819105 ACATCCATTTCCGAGACAAGTA 57.181 40.909 0.00 0.00 0.00 2.24
5512 5551 3.703001 ACATCCATTTCCGAGACAAGT 57.297 42.857 0.00 0.00 0.00 3.16
5513 5552 5.605534 AGATACATCCATTTCCGAGACAAG 58.394 41.667 0.00 0.00 0.00 3.16
5514 5553 5.614324 AGATACATCCATTTCCGAGACAA 57.386 39.130 0.00 0.00 0.00 3.18
5515 5554 6.724893 TTAGATACATCCATTTCCGAGACA 57.275 37.500 0.00 0.00 0.00 3.41
5516 5555 7.711339 AGTTTTAGATACATCCATTTCCGAGAC 59.289 37.037 0.00 0.00 0.00 3.36
5517 5556 7.792032 AGTTTTAGATACATCCATTTCCGAGA 58.208 34.615 0.00 0.00 0.00 4.04
5518 5557 9.542462 TTAGTTTTAGATACATCCATTTCCGAG 57.458 33.333 0.00 0.00 0.00 4.63
5519 5558 9.893634 TTTAGTTTTAGATACATCCATTTCCGA 57.106 29.630 0.00 0.00 0.00 4.55


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

AutoCloner maintained by Alex Coulton.