Multiple sequence alignment - TraesCS4D01G214200

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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 TraesCS4D01G214200 chr4D 100.000 4714 0 0 1 4714 367049196 367044483 0.000000e+00 8706.0
1 TraesCS4D01G214200 chr4A 95.634 3665 88 28 1011 4663 97870264 97873868 0.000000e+00 5816.0
2 TraesCS4D01G214200 chr4A 92.213 488 27 5 429 912 97869412 97869892 0.000000e+00 680.0
3 TraesCS4D01G214200 chr4A 90.303 165 15 1 123 287 97868565 97868728 1.030000e-51 215.0
4 TraesCS4D01G214200 chr4A 92.742 124 8 1 1 123 97868190 97868313 1.350000e-40 178.0
5 TraesCS4D01G214200 chr4B 95.096 3385 103 17 1130 4502 451910851 451907518 0.000000e+00 5273.0
6 TraesCS4D01G214200 chr4B 96.296 567 9 4 538 1102 451911676 451911120 0.000000e+00 920.0
7 TraesCS4D01G214200 chr4B 87.990 383 35 10 128 506 451912356 451911981 4.330000e-120 442.0
8 TraesCS4D01G214200 chr4B 82.609 322 21 13 4368 4655 451907464 451907144 7.830000e-63 252.0
9 TraesCS4D01G214200 chr4B 92.373 118 8 1 1 117 451912787 451912670 2.920000e-37 167.0
10 TraesCS4D01G214200 chr4B 91.743 109 8 1 16 123 117067720 117067612 2.940000e-32 150.0
11 TraesCS4D01G214200 chr4B 91.743 109 8 1 16 123 117088812 117088704 2.940000e-32 150.0
12 TraesCS4D01G214200 chr5B 92.453 106 8 0 18 123 669924565 669924460 8.170000e-33 152.0
13 TraesCS4D01G214200 chrUn 91.743 109 8 1 16 123 312186073 312186181 2.940000e-32 150.0
14 TraesCS4D01G214200 chr6D 91.667 108 9 0 16 123 77826318 77826425 2.940000e-32 150.0
15 TraesCS4D01G214200 chr6A 91.589 107 9 0 17 123 522460393 522460287 1.060000e-31 148.0
16 TraesCS4D01G214200 chr7A 90.826 109 10 0 15 123 665742283 665742391 3.800000e-31 147.0
17 TraesCS4D01G214200 chr7B 86.076 79 4 3 4625 4696 332816100 332816022 1.410000e-10 78.7


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 TraesCS4D01G214200 chr4D 367044483 367049196 4713 True 8706.00 8706 100.0000 1 4714 1 chr4D.!!$R1 4713
1 TraesCS4D01G214200 chr4A 97868190 97873868 5678 False 1722.25 5816 92.7230 1 4663 4 chr4A.!!$F1 4662
2 TraesCS4D01G214200 chr4B 451907144 451912787 5643 True 1410.80 5273 90.8728 1 4655 5 chr4B.!!$R3 4654

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
263 572 0.813610 TTGCTTAGCACGTGCACACT 60.814 50.000 39.21 22.87 45.16 3.55 F
269 578 1.024046 AGCACGTGCACACTGTGAAA 61.024 50.000 39.21 0.00 45.16 2.69 F
547 1678 1.895966 CAGGCTGCAGCAGTAGAGA 59.104 57.895 37.63 0.00 44.36 3.10 F
2473 4120 2.171659 TGGTGCCACACTCAAGAAGTTA 59.828 45.455 0.00 0.00 35.45 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2224 3871 0.947960 TTCGGCAATTTCGCACAAGA 59.052 45.000 0.00 0.0 0.00 3.02 R
2392 4039 0.110192 GCAAACTCAAGCGCTGTACC 60.110 55.000 12.58 0.0 0.00 3.34 R
2488 4135 3.515901 AGTGATCCTCTGTGGTAAGGAAC 59.484 47.826 0.00 0.0 44.61 3.62 R
3834 5482 0.036164 CGTGGGTTCAGATGGTGGAA 59.964 55.000 0.00 0.0 0.00 3.53 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
30 32 1.133575 CCACTATACTCCCTCCGGTCA 60.134 57.143 0.00 0.00 0.00 4.02
124 127 8.438676 AGTATCAACATCTACAATACCAAAGC 57.561 34.615 0.00 0.00 0.00 3.51
142 450 6.775629 ACCAAAGCTTCCTTCATTTAAGTGTA 59.224 34.615 0.00 0.00 32.89 2.90
202 510 3.307339 GGTCACCAAAATGCTCTCTCTCT 60.307 47.826 0.00 0.00 0.00 3.10
217 525 6.406849 GCTCTCTCTCTTCCTAATTGATGTGT 60.407 42.308 0.00 0.00 0.00 3.72
227 535 6.816136 TCCTAATTGATGTGTCGTGTCATAT 58.184 36.000 0.00 0.00 0.00 1.78
263 572 0.813610 TTGCTTAGCACGTGCACACT 60.814 50.000 39.21 22.87 45.16 3.55
269 578 1.024046 AGCACGTGCACACTGTGAAA 61.024 50.000 39.21 0.00 45.16 2.69
304 899 4.614993 GCCTTATAGCTGACTCGACTCATC 60.615 50.000 0.00 0.00 0.00 2.92
312 907 2.628178 TGACTCGACTCATCAGGTGTTT 59.372 45.455 0.00 0.00 0.00 2.83
341 940 8.819974 AGGCAGATTTTATTGAAATAATTTGCG 58.180 29.630 0.00 0.00 38.06 4.85
343 942 8.330302 GCAGATTTTATTGAAATAATTTGCGCT 58.670 29.630 9.73 0.00 38.06 5.92
344 943 9.839589 CAGATTTTATTGAAATAATTTGCGCTC 57.160 29.630 9.73 0.00 38.06 5.03
345 944 9.585099 AGATTTTATTGAAATAATTTGCGCTCA 57.415 25.926 9.73 0.00 38.06 4.26
417 1019 6.727824 ATAGCTCATGTCACTTGTGTTTAC 57.272 37.500 0.00 0.00 0.00 2.01
427 1282 5.619607 GTCACTTGTGTTTACTATTGTTGCG 59.380 40.000 0.46 0.00 0.00 4.85
451 1306 9.632969 GCGTAGTGTGTATGTATTATTCTTTTG 57.367 33.333 0.00 0.00 0.00 2.44
467 1324 9.739276 TTATTCTTTTGTCCTTCACATATCAGT 57.261 29.630 0.00 0.00 33.90 3.41
515 1373 4.354587 CTGTACGGACCTAATAACGGAAC 58.645 47.826 0.00 0.00 0.00 3.62
547 1678 1.895966 CAGGCTGCAGCAGTAGAGA 59.104 57.895 37.63 0.00 44.36 3.10
668 1800 3.077088 CCCTATACCTAGACCTAGCCCAA 59.923 52.174 0.00 0.00 31.95 4.12
1651 3297 9.974750 CTCTTTCTTGTCCTACGAATTAATTTC 57.025 33.333 1.43 0.00 0.00 2.17
1721 3367 4.586841 TGTTCTATTTGGAAAGGGTTGGTG 59.413 41.667 0.00 0.00 0.00 4.17
1748 3394 6.046593 TGGGATGTTTGTAAAGCGAGTATAG 58.953 40.000 0.00 0.00 0.00 1.31
1809 3456 4.667519 AGTGTAACGTCTCACCTTTTCT 57.332 40.909 15.95 0.00 45.86 2.52
1990 3637 9.321590 GTTTTGAAAAGCAGATTATCAAAATGC 57.678 29.630 13.15 0.00 45.90 3.56
2040 3687 9.765795 GTAAGAGCATACATTCATAGGTTACTT 57.234 33.333 0.00 0.00 0.00 2.24
2045 3692 9.899661 AGCATACATTCATAGGTTACTTGTTTA 57.100 29.630 0.00 0.00 0.00 2.01
2219 3866 2.299326 GGCATCCCCAGCATATCTTT 57.701 50.000 0.00 0.00 0.00 2.52
2224 3871 4.477249 CATCCCCAGCATATCTTTTCCTT 58.523 43.478 0.00 0.00 0.00 3.36
2392 4039 5.068723 TGCTAACTACTATTTCCCTCCTTCG 59.931 44.000 0.00 0.00 0.00 3.79
2473 4120 2.171659 TGGTGCCACACTCAAGAAGTTA 59.828 45.455 0.00 0.00 35.45 2.24
2488 4135 6.921857 TCAAGAAGTTAGACCTTCAGTTTACG 59.078 38.462 3.99 0.00 42.68 3.18
2527 4174 2.560981 TCACTGTCAATTAGTCCAGCGA 59.439 45.455 0.00 0.00 0.00 4.93
2682 4329 2.630580 GGTGAGGGATGTGATAGGAGAC 59.369 54.545 0.00 0.00 0.00 3.36
3076 4723 4.327087 GCCTTTCTTATGTTGGCGAATTTG 59.673 41.667 0.00 0.00 33.96 2.32
3084 4731 3.034924 TGGCGAATTTGGCAAGACT 57.965 47.368 19.07 0.00 41.96 3.24
3111 4758 1.636148 ACATGTTGCTTGGGAATGCT 58.364 45.000 0.00 0.00 0.00 3.79
3276 4923 2.303311 GGGATACAAGGCATCTCCTACC 59.697 54.545 0.00 0.00 46.94 3.18
3592 5240 0.398318 ACCCACTCTGAACTGCCTTC 59.602 55.000 0.00 0.00 0.00 3.46
3614 5262 4.638421 TCGTATCTTAGGGGCAACATTTTG 59.362 41.667 0.00 0.00 39.74 2.44
3752 5400 0.890683 AGCTTTGCCCACTGTATTGC 59.109 50.000 0.00 0.00 0.00 3.56
3817 5465 6.862608 GTGAAACAATCTGCACAATGTTATGA 59.137 34.615 0.00 0.00 35.09 2.15
3820 5468 8.836268 AAACAATCTGCACAATGTTATGATTT 57.164 26.923 0.00 0.00 35.09 2.17
3821 5469 9.926158 AAACAATCTGCACAATGTTATGATTTA 57.074 25.926 0.00 0.00 35.09 1.40
3822 5470 8.915871 ACAATCTGCACAATGTTATGATTTAC 57.084 30.769 0.00 0.00 0.00 2.01
3823 5471 8.742777 ACAATCTGCACAATGTTATGATTTACT 58.257 29.630 0.00 0.00 0.00 2.24
3824 5472 9.016623 CAATCTGCACAATGTTATGATTTACTG 57.983 33.333 0.00 0.00 0.00 2.74
3825 5473 7.087409 TCTGCACAATGTTATGATTTACTGG 57.913 36.000 0.00 0.00 0.00 4.00
3826 5474 6.658816 TCTGCACAATGTTATGATTTACTGGT 59.341 34.615 0.00 0.00 0.00 4.00
3827 5475 7.176515 TCTGCACAATGTTATGATTTACTGGTT 59.823 33.333 0.00 0.00 0.00 3.67
3828 5476 7.089538 TGCACAATGTTATGATTTACTGGTTG 58.910 34.615 0.00 0.00 0.00 3.77
3829 5477 7.090173 GCACAATGTTATGATTTACTGGTTGT 58.910 34.615 0.00 0.00 0.00 3.32
3830 5478 7.062138 GCACAATGTTATGATTTACTGGTTGTG 59.938 37.037 0.00 0.00 43.13 3.33
3831 5479 8.296000 CACAATGTTATGATTTACTGGTTGTGA 58.704 33.333 0.00 0.00 43.00 3.58
3832 5480 9.023962 ACAATGTTATGATTTACTGGTTGTGAT 57.976 29.630 0.00 0.00 0.00 3.06
3833 5481 9.859427 CAATGTTATGATTTACTGGTTGTGATT 57.141 29.630 0.00 0.00 0.00 2.57
3836 5484 9.906660 TGTTATGATTTACTGGTTGTGATTTTC 57.093 29.630 0.00 0.00 0.00 2.29
3837 5485 9.353999 GTTATGATTTACTGGTTGTGATTTTCC 57.646 33.333 0.00 0.00 0.00 3.13
3838 5486 6.968263 TGATTTACTGGTTGTGATTTTCCA 57.032 33.333 0.00 0.00 0.00 3.53
3839 5487 6.744112 TGATTTACTGGTTGTGATTTTCCAC 58.256 36.000 0.00 0.00 37.55 4.02
3840 5488 5.523438 TTTACTGGTTGTGATTTTCCACC 57.477 39.130 0.00 0.00 36.26 4.61
3841 5489 3.025322 ACTGGTTGTGATTTTCCACCA 57.975 42.857 0.00 0.00 36.26 4.17
3842 5490 3.575805 ACTGGTTGTGATTTTCCACCAT 58.424 40.909 0.00 0.00 36.26 3.55
3843 5491 3.573967 ACTGGTTGTGATTTTCCACCATC 59.426 43.478 0.00 0.00 36.26 3.51
3844 5492 3.828451 CTGGTTGTGATTTTCCACCATCT 59.172 43.478 0.00 0.00 36.26 2.90
3845 5493 3.573538 TGGTTGTGATTTTCCACCATCTG 59.426 43.478 0.00 0.00 36.26 2.90
3870 5518 9.015367 TGAACCCACGAATATCTTGAAATTTTA 57.985 29.630 0.00 0.00 0.00 1.52
4045 5695 8.524870 ACTTGCTGTGAAATTTTACATGATTC 57.475 30.769 15.31 4.93 0.00 2.52
4046 5696 8.143193 ACTTGCTGTGAAATTTTACATGATTCA 58.857 29.630 15.31 7.01 0.00 2.57
4047 5697 8.523523 TTGCTGTGAAATTTTACATGATTCAG 57.476 30.769 15.31 4.48 31.24 3.02
4048 5698 7.884257 TGCTGTGAAATTTTACATGATTCAGA 58.116 30.769 15.31 0.00 31.24 3.27
4050 5700 9.362539 GCTGTGAAATTTTACATGATTCAGAAT 57.637 29.630 15.31 0.00 31.24 2.40
4130 5782 5.281037 GGAAGGAATTTAAGAGGGTTGAGGA 60.281 44.000 0.00 0.00 0.00 3.71
4250 5903 9.490379 AAAAATAGAGTGAAAGTGTATTCGACT 57.510 29.630 0.00 0.00 34.95 4.18
4254 5907 9.953697 ATAGAGTGAAAGTGTATTCGACTATTC 57.046 33.333 0.00 0.00 31.80 1.75
4255 5908 7.827701 AGAGTGAAAGTGTATTCGACTATTCA 58.172 34.615 0.00 0.00 31.80 2.57
4256 5909 8.304596 AGAGTGAAAGTGTATTCGACTATTCAA 58.695 33.333 0.00 0.00 29.93 2.69
4257 5910 8.827177 AGTGAAAGTGTATTCGACTATTCAAA 57.173 30.769 0.00 0.00 29.93 2.69
4258 5911 8.926710 AGTGAAAGTGTATTCGACTATTCAAAG 58.073 33.333 0.00 0.00 29.93 2.77
4259 5912 8.922676 GTGAAAGTGTATTCGACTATTCAAAGA 58.077 33.333 0.00 0.00 29.93 2.52
4260 5913 9.483916 TGAAAGTGTATTCGACTATTCAAAGAA 57.516 29.630 0.00 0.00 31.80 2.52
4366 6019 7.391833 CCTAATCCTATTAGGCAATGGACTTTC 59.608 40.741 11.70 0.00 35.60 2.62
4475 6326 9.866655 ATTGCAGTATTCCTATAGAAAAATCCA 57.133 29.630 0.00 0.00 38.21 3.41
4563 6436 5.422970 AGCAATCCATAGGAAAATTTCTGCA 59.577 36.000 12.52 0.00 34.34 4.41
4568 6441 8.953368 ATCCATAGGAAAATTTCTGCATTTTC 57.047 30.769 12.71 12.71 46.17 2.29
4576 6449 8.551122 GAAAATTTCTGCATTTTCCTTTGTTG 57.449 30.769 10.76 0.00 43.22 3.33
4577 6450 7.628769 AAATTTCTGCATTTTCCTTTGTTGT 57.371 28.000 0.00 0.00 0.00 3.32
4578 6451 8.729805 AAATTTCTGCATTTTCCTTTGTTGTA 57.270 26.923 0.00 0.00 0.00 2.41
4612 6489 8.674263 AATCCTCTATTCTTAAACAGATGCAG 57.326 34.615 0.00 0.00 0.00 4.41
4620 6497 2.814805 AAACAGATGCAGCCCACTAT 57.185 45.000 0.00 0.00 0.00 2.12
4656 6535 1.882912 TGGAACTATGCCGCATCATC 58.117 50.000 9.71 6.76 0.00 2.92
4658 6537 2.221169 GGAACTATGCCGCATCATCAA 58.779 47.619 9.71 0.00 0.00 2.57
4659 6538 2.225019 GGAACTATGCCGCATCATCAAG 59.775 50.000 9.71 3.77 0.00 3.02
4660 6539 2.627515 ACTATGCCGCATCATCAAGT 57.372 45.000 9.71 4.46 0.00 3.16
4661 6540 2.487934 ACTATGCCGCATCATCAAGTC 58.512 47.619 9.71 0.00 0.00 3.01
4662 6541 2.103771 ACTATGCCGCATCATCAAGTCT 59.896 45.455 9.71 0.00 0.00 3.24
4663 6542 1.306148 ATGCCGCATCATCAAGTCTG 58.694 50.000 0.00 0.00 0.00 3.51
4664 6543 0.249955 TGCCGCATCATCAAGTCTGA 59.750 50.000 0.00 0.00 35.56 3.27
4665 6544 1.134310 TGCCGCATCATCAAGTCTGAT 60.134 47.619 0.00 0.00 43.40 2.90
4666 6545 1.530293 GCCGCATCATCAAGTCTGATC 59.470 52.381 0.00 0.00 40.49 2.92
4667 6546 1.791204 CCGCATCATCAAGTCTGATCG 59.209 52.381 0.00 0.00 40.49 3.69
4668 6547 2.467838 CGCATCATCAAGTCTGATCGT 58.532 47.619 0.00 0.00 40.49 3.73
4669 6548 3.550842 CCGCATCATCAAGTCTGATCGTA 60.551 47.826 0.00 0.00 40.49 3.43
4670 6549 4.044426 CGCATCATCAAGTCTGATCGTAA 58.956 43.478 0.00 0.00 40.49 3.18
4671 6550 4.147826 CGCATCATCAAGTCTGATCGTAAG 59.852 45.833 0.00 0.00 40.49 2.34
4672 6551 5.046529 GCATCATCAAGTCTGATCGTAAGT 58.953 41.667 0.00 0.00 40.49 2.24
4673 6552 5.521735 GCATCATCAAGTCTGATCGTAAGTT 59.478 40.000 0.00 0.00 40.49 2.66
4674 6553 6.697455 GCATCATCAAGTCTGATCGTAAGTTA 59.303 38.462 0.00 0.00 40.49 2.24
4675 6554 7.306283 GCATCATCAAGTCTGATCGTAAGTTAC 60.306 40.741 2.72 2.72 40.49 2.50
4676 6555 7.153217 TCATCAAGTCTGATCGTAAGTTACA 57.847 36.000 13.33 1.33 40.49 2.41
4677 6556 7.599171 TCATCAAGTCTGATCGTAAGTTACAA 58.401 34.615 13.33 0.00 40.49 2.41
4678 6557 8.251026 TCATCAAGTCTGATCGTAAGTTACAAT 58.749 33.333 13.33 0.00 40.49 2.71
4679 6558 8.873830 CATCAAGTCTGATCGTAAGTTACAATT 58.126 33.333 13.33 0.00 40.49 2.32
4680 6559 8.827177 TCAAGTCTGATCGTAAGTTACAATTT 57.173 30.769 13.33 0.00 39.48 1.82
4681 6560 9.917129 TCAAGTCTGATCGTAAGTTACAATTTA 57.083 29.630 13.33 0.00 39.48 1.40
4684 6563 8.818057 AGTCTGATCGTAAGTTACAATTTATGC 58.182 33.333 13.33 0.00 39.48 3.14
4685 6564 8.600625 GTCTGATCGTAAGTTACAATTTATGCA 58.399 33.333 13.33 0.00 39.48 3.96
4686 6565 8.600625 TCTGATCGTAAGTTACAATTTATGCAC 58.399 33.333 13.33 0.00 39.48 4.57
4687 6566 8.487313 TGATCGTAAGTTACAATTTATGCACT 57.513 30.769 13.33 0.00 39.48 4.40
4688 6567 9.589111 TGATCGTAAGTTACAATTTATGCACTA 57.411 29.630 13.33 0.00 39.48 2.74
4704 6583 9.646427 TTTATGCACTAATTTATTTGTGGAACC 57.354 29.630 13.09 2.13 43.75 3.62
4705 6584 6.656632 TGCACTAATTTATTTGTGGAACCA 57.343 33.333 15.36 5.55 39.75 3.67
4706 6585 7.238486 TGCACTAATTTATTTGTGGAACCAT 57.762 32.000 15.36 0.00 39.75 3.55
4707 6586 7.095910 TGCACTAATTTATTTGTGGAACCATG 58.904 34.615 15.36 0.00 39.75 3.66
4708 6587 6.035975 GCACTAATTTATTTGTGGAACCATGC 59.964 38.462 15.36 0.00 41.57 4.06
4709 6588 6.534793 CACTAATTTATTTGTGGAACCATGCC 59.465 38.462 8.54 0.00 38.99 4.40
4710 6589 3.584406 TTTATTTGTGGAACCATGCCG 57.416 42.857 0.00 0.00 34.36 5.69
4711 6590 0.814457 TATTTGTGGAACCATGCCGC 59.186 50.000 0.00 0.00 34.36 6.53
4712 6591 1.887344 ATTTGTGGAACCATGCCGCC 61.887 55.000 0.00 0.00 35.05 6.13
4713 6592 3.799286 TTGTGGAACCATGCCGCCA 62.799 57.895 0.00 0.00 35.05 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
123 126 8.045176 AGACAATACACTTAAATGAAGGAAGC 57.955 34.615 0.00 0.00 39.74 3.86
142 450 0.324943 AGCACGCCAACCTAGACAAT 59.675 50.000 0.00 0.00 0.00 2.71
202 510 4.888917 TGACACGACACATCAATTAGGAA 58.111 39.130 0.00 0.00 0.00 3.36
258 567 2.036958 TCCCAGTGTTTCACAGTGTG 57.963 50.000 17.53 17.53 45.61 3.82
263 572 0.467290 GCCCTTCCCAGTGTTTCACA 60.467 55.000 2.80 0.00 36.74 3.58
269 578 2.127708 CTATAAGGCCCTTCCCAGTGT 58.872 52.381 0.00 0.00 34.51 3.55
304 899 8.087750 TCAATAAAATCTGCCTTTAAACACCTG 58.912 33.333 0.00 0.00 0.00 4.00
417 1019 7.694388 ATACATACACACTACGCAACAATAG 57.306 36.000 0.00 0.00 0.00 1.73
475 1333 2.042979 ACAGGGGTGTGGCTCAAATATT 59.957 45.455 0.00 0.00 0.00 1.28
477 1335 1.072266 ACAGGGGTGTGGCTCAAATA 58.928 50.000 0.00 0.00 0.00 1.40
479 1337 0.109723 GTACAGGGGTGTGGCTCAAA 59.890 55.000 0.00 0.00 0.00 2.69
492 1350 2.951642 TCCGTTATTAGGTCCGTACAGG 59.048 50.000 0.00 0.00 42.97 4.00
601 1732 4.899239 GACAGATCCAGCGGCGGG 62.899 72.222 13.32 13.32 0.00 6.13
668 1800 2.176148 TCGGGTTTTTCCTTCCTTTCCT 59.824 45.455 0.00 0.00 36.25 3.36
964 2096 2.003548 GGTTGGGATGAGGGAGGCT 61.004 63.158 0.00 0.00 0.00 4.58
965 2097 2.597903 GGTTGGGATGAGGGAGGC 59.402 66.667 0.00 0.00 0.00 4.70
966 2098 2.386935 GGGGTTGGGATGAGGGAGG 61.387 68.421 0.00 0.00 0.00 4.30
968 2100 1.928567 GTGGGGTTGGGATGAGGGA 60.929 63.158 0.00 0.00 0.00 4.20
969 2101 2.683475 GTGGGGTTGGGATGAGGG 59.317 66.667 0.00 0.00 0.00 4.30
993 2125 2.723464 ATTTCAACGGGGGTGTGGGG 62.723 60.000 0.00 0.00 0.00 4.96
994 2126 1.228737 ATTTCAACGGGGGTGTGGG 60.229 57.895 0.00 0.00 0.00 4.61
995 2127 1.248101 GGATTTCAACGGGGGTGTGG 61.248 60.000 0.00 0.00 0.00 4.17
996 2128 1.582610 CGGATTTCAACGGGGGTGTG 61.583 60.000 0.00 0.00 0.00 3.82
997 2129 1.302993 CGGATTTCAACGGGGGTGT 60.303 57.895 0.00 0.00 0.00 4.16
998 2130 2.696759 GCGGATTTCAACGGGGGTG 61.697 63.158 0.00 0.00 0.00 4.61
999 2131 2.360726 GCGGATTTCAACGGGGGT 60.361 61.111 0.00 0.00 0.00 4.95
1721 3367 3.013921 TCGCTTTACAAACATCCCATCC 58.986 45.455 0.00 0.00 0.00 3.51
1748 3394 9.825972 TCGAAATGAACAAAAGAACATCTTATC 57.174 29.630 0.00 0.00 35.27 1.75
1772 3419 5.333568 CGTTACACTTACTTTTCCCCTTTCG 60.334 44.000 0.00 0.00 0.00 3.46
1935 3582 8.228206 TCTCCACCAAGTATCATAGTTCTCTAT 58.772 37.037 0.00 0.00 37.35 1.98
2070 3717 2.993937 ACAACGTTTCCAGTTTCCTGA 58.006 42.857 0.00 0.00 41.50 3.86
2209 3856 4.095483 CGCACAAGAAGGAAAAGATATGCT 59.905 41.667 0.00 0.00 0.00 3.79
2219 3866 2.288152 GGCAATTTCGCACAAGAAGGAA 60.288 45.455 0.00 0.00 0.00 3.36
2224 3871 0.947960 TTCGGCAATTTCGCACAAGA 59.052 45.000 0.00 0.00 0.00 3.02
2392 4039 0.110192 GCAAACTCAAGCGCTGTACC 60.110 55.000 12.58 0.00 0.00 3.34
2473 4120 4.684484 AAGGAACGTAAACTGAAGGTCT 57.316 40.909 0.00 0.00 0.00 3.85
2488 4135 3.515901 AGTGATCCTCTGTGGTAAGGAAC 59.484 47.826 0.00 0.00 44.61 3.62
2682 4329 1.804748 GCAACAACTTCTAACCCTCGG 59.195 52.381 0.00 0.00 0.00 4.63
3076 4723 0.108138 ATGTAGCGGACAGTCTTGCC 60.108 55.000 12.84 2.52 42.79 4.52
3084 4731 1.155889 CAAGCAACATGTAGCGGACA 58.844 50.000 0.00 0.00 43.97 4.02
3111 4758 1.061111 AGTCCATCATCAGATCCCCCA 60.061 52.381 0.00 0.00 30.20 4.96
3276 4923 2.969238 GCCATGAGATCGGTGCCG 60.969 66.667 3.94 3.94 41.35 5.69
3417 5064 4.153411 ACGGATAGAGGGGAATTACTGAG 58.847 47.826 0.00 0.00 0.00 3.35
3592 5240 4.202010 CCAAAATGTTGCCCCTAAGATACG 60.202 45.833 0.00 0.00 33.01 3.06
3614 5262 2.019156 GCCAGATGAACAGCTTACCCC 61.019 57.143 0.00 0.00 0.00 4.95
3817 5465 5.600484 TGGTGGAAAATCACAACCAGTAAAT 59.400 36.000 0.00 0.00 39.27 1.40
3820 5468 4.171878 TGGTGGAAAATCACAACCAGTA 57.828 40.909 0.00 0.00 39.27 2.74
3821 5469 3.025322 TGGTGGAAAATCACAACCAGT 57.975 42.857 0.00 0.00 39.27 4.00
3822 5470 3.828451 AGATGGTGGAAAATCACAACCAG 59.172 43.478 0.00 0.00 39.27 4.00
3823 5471 3.573538 CAGATGGTGGAAAATCACAACCA 59.426 43.478 0.00 0.00 39.27 3.67
3824 5472 3.826157 TCAGATGGTGGAAAATCACAACC 59.174 43.478 0.00 0.00 39.27 3.77
3825 5473 5.222631 GTTCAGATGGTGGAAAATCACAAC 58.777 41.667 0.00 0.00 39.27 3.32
3826 5474 4.280677 GGTTCAGATGGTGGAAAATCACAA 59.719 41.667 0.00 0.00 39.27 3.33
3827 5475 3.826157 GGTTCAGATGGTGGAAAATCACA 59.174 43.478 0.00 0.00 39.27 3.58
3828 5476 3.193479 GGGTTCAGATGGTGGAAAATCAC 59.807 47.826 0.00 0.00 36.95 3.06
3829 5477 3.181424 TGGGTTCAGATGGTGGAAAATCA 60.181 43.478 0.00 0.00 0.00 2.57
3830 5478 3.193479 GTGGGTTCAGATGGTGGAAAATC 59.807 47.826 0.00 0.00 0.00 2.17
3831 5479 3.165071 GTGGGTTCAGATGGTGGAAAAT 58.835 45.455 0.00 0.00 0.00 1.82
3832 5480 2.593026 GTGGGTTCAGATGGTGGAAAA 58.407 47.619 0.00 0.00 0.00 2.29
3833 5481 1.544537 CGTGGGTTCAGATGGTGGAAA 60.545 52.381 0.00 0.00 0.00 3.13
3834 5482 0.036164 CGTGGGTTCAGATGGTGGAA 59.964 55.000 0.00 0.00 0.00 3.53
3835 5483 0.834261 TCGTGGGTTCAGATGGTGGA 60.834 55.000 0.00 0.00 0.00 4.02
3836 5484 0.036164 TTCGTGGGTTCAGATGGTGG 59.964 55.000 0.00 0.00 0.00 4.61
3837 5485 2.113860 ATTCGTGGGTTCAGATGGTG 57.886 50.000 0.00 0.00 0.00 4.17
3838 5486 3.711704 AGATATTCGTGGGTTCAGATGGT 59.288 43.478 0.00 0.00 0.00 3.55
3839 5487 4.342862 AGATATTCGTGGGTTCAGATGG 57.657 45.455 0.00 0.00 0.00 3.51
3840 5488 5.359756 TCAAGATATTCGTGGGTTCAGATG 58.640 41.667 0.00 0.00 0.00 2.90
3841 5489 5.614324 TCAAGATATTCGTGGGTTCAGAT 57.386 39.130 0.00 0.00 0.00 2.90
3842 5490 5.414789 TTCAAGATATTCGTGGGTTCAGA 57.585 39.130 0.00 0.00 0.00 3.27
3843 5491 6.683974 ATTTCAAGATATTCGTGGGTTCAG 57.316 37.500 0.00 0.00 0.00 3.02
3844 5492 7.461182 AAATTTCAAGATATTCGTGGGTTCA 57.539 32.000 0.00 0.00 0.00 3.18
3845 5493 9.285770 GTAAAATTTCAAGATATTCGTGGGTTC 57.714 33.333 0.00 0.00 0.00 3.62
4004 5654 4.694037 CAGCAAGTGACATCTCAATCTTCA 59.306 41.667 0.00 0.00 0.00 3.02
4045 5695 9.269453 TGCAGAATCTCATGATAAGTTATTCTG 57.731 33.333 21.62 21.62 45.85 3.02
4051 5701 8.834465 GTGTTATGCAGAATCTCATGATAAGTT 58.166 33.333 0.00 0.00 31.70 2.66
4055 5705 7.729116 TCTGTGTTATGCAGAATCTCATGATA 58.271 34.615 0.00 0.00 39.70 2.15
4090 5740 9.426534 AAATTCCTTCCTAGCAAAAGCTTATAT 57.573 29.630 0.00 0.00 0.00 0.86
4091 5741 8.823220 AAATTCCTTCCTAGCAAAAGCTTATA 57.177 30.769 0.00 0.00 0.00 0.98
4092 5742 7.724490 AAATTCCTTCCTAGCAAAAGCTTAT 57.276 32.000 0.00 0.00 0.00 1.73
4093 5743 8.644374 TTAAATTCCTTCCTAGCAAAAGCTTA 57.356 30.769 0.00 0.00 0.00 3.09
4094 5744 7.451566 TCTTAAATTCCTTCCTAGCAAAAGCTT 59.548 33.333 0.00 0.00 0.00 3.74
4130 5782 9.707957 TTCTGAATATCTTTCTCTACCTTCTCT 57.292 33.333 0.00 0.00 0.00 3.10
4252 5905 9.958234 TCGAACATCATTTTGTTATTCTTTGAA 57.042 25.926 0.00 0.00 39.85 2.69
4253 5906 9.611284 CTCGAACATCATTTTGTTATTCTTTGA 57.389 29.630 0.00 0.00 39.85 2.69
4254 5907 9.398170 ACTCGAACATCATTTTGTTATTCTTTG 57.602 29.630 0.00 0.00 39.85 2.77
4255 5908 9.965824 AACTCGAACATCATTTTGTTATTCTTT 57.034 25.926 0.00 0.00 39.85 2.52
4256 5909 9.612620 GAACTCGAACATCATTTTGTTATTCTT 57.387 29.630 0.00 0.00 39.85 2.52
4257 5910 8.783093 TGAACTCGAACATCATTTTGTTATTCT 58.217 29.630 0.00 0.00 39.85 2.40
4258 5911 8.948853 TGAACTCGAACATCATTTTGTTATTC 57.051 30.769 0.00 0.00 39.85 1.75
4260 5913 9.988350 GTATGAACTCGAACATCATTTTGTTAT 57.012 29.630 11.17 0.00 39.85 1.89
4261 5914 9.214957 AGTATGAACTCGAACATCATTTTGTTA 57.785 29.630 11.17 0.00 39.85 2.41
4262 5915 8.017373 CAGTATGAACTCGAACATCATTTTGTT 58.983 33.333 11.17 0.00 39.80 2.83
4263 5916 7.387673 TCAGTATGAACTCGAACATCATTTTGT 59.612 33.333 11.17 0.00 45.97 2.83
4264 5917 7.742151 TCAGTATGAACTCGAACATCATTTTG 58.258 34.615 11.17 10.18 45.97 2.44
4265 5918 7.905604 TCAGTATGAACTCGAACATCATTTT 57.094 32.000 11.17 0.94 45.97 1.82
4344 5997 6.266131 TGAAAGTCCATTGCCTAATAGGAT 57.734 37.500 11.13 0.00 37.67 3.24
4409 6255 8.554490 AATGCCCTAAGAGTCTCTTTAGATTA 57.446 34.615 20.03 0.58 37.89 1.75
4410 6256 7.444703 AATGCCCTAAGAGTCTCTTTAGATT 57.555 36.000 20.03 9.07 37.89 2.40
4475 6326 4.103153 TCTTTGTTTCAGATGACCCAGTCT 59.897 41.667 0.00 0.00 33.15 3.24
4568 6441 9.125026 AGAGGATTTATAGCAATACAACAAAGG 57.875 33.333 0.00 0.00 0.00 3.11
4604 6481 3.977134 ATAGATAGTGGGCTGCATCTG 57.023 47.619 0.50 0.00 0.00 2.90
4639 6518 2.874701 ACTTGATGATGCGGCATAGTTC 59.125 45.455 16.66 12.92 0.00 3.01
4658 6537 8.818057 GCATAAATTGTAACTTACGATCAGACT 58.182 33.333 2.62 0.00 31.61 3.24
4659 6538 8.600625 TGCATAAATTGTAACTTACGATCAGAC 58.399 33.333 2.62 0.00 31.61 3.51
4660 6539 8.600625 GTGCATAAATTGTAACTTACGATCAGA 58.399 33.333 2.62 0.00 31.61 3.27
4661 6540 8.604035 AGTGCATAAATTGTAACTTACGATCAG 58.396 33.333 2.62 0.00 31.61 2.90
4662 6541 8.487313 AGTGCATAAATTGTAACTTACGATCA 57.513 30.769 2.62 0.00 31.61 2.92
4678 6557 9.646427 GGTTCCACAAATAAATTAGTGCATAAA 57.354 29.630 0.00 0.00 0.00 1.40
4679 6558 8.807118 TGGTTCCACAAATAAATTAGTGCATAA 58.193 29.630 0.00 0.00 0.00 1.90
4680 6559 8.354711 TGGTTCCACAAATAAATTAGTGCATA 57.645 30.769 0.00 0.00 0.00 3.14
4681 6560 7.238486 TGGTTCCACAAATAAATTAGTGCAT 57.762 32.000 0.00 0.00 0.00 3.96
4682 6561 6.656632 TGGTTCCACAAATAAATTAGTGCA 57.343 33.333 0.00 0.00 0.00 4.57
4683 6562 6.035975 GCATGGTTCCACAAATAAATTAGTGC 59.964 38.462 0.00 0.00 0.00 4.40
4684 6563 6.534793 GGCATGGTTCCACAAATAAATTAGTG 59.465 38.462 0.00 0.00 0.00 2.74
4685 6564 6.627065 CGGCATGGTTCCACAAATAAATTAGT 60.627 38.462 0.00 0.00 0.00 2.24
4686 6565 5.748152 CGGCATGGTTCCACAAATAAATTAG 59.252 40.000 0.00 0.00 0.00 1.73
4687 6566 5.655488 CGGCATGGTTCCACAAATAAATTA 58.345 37.500 0.00 0.00 0.00 1.40
4688 6567 4.502962 CGGCATGGTTCCACAAATAAATT 58.497 39.130 0.00 0.00 0.00 1.82
4689 6568 3.678529 GCGGCATGGTTCCACAAATAAAT 60.679 43.478 0.00 0.00 0.00 1.40
4690 6569 2.353208 GCGGCATGGTTCCACAAATAAA 60.353 45.455 0.00 0.00 0.00 1.40
4691 6570 1.203523 GCGGCATGGTTCCACAAATAA 59.796 47.619 0.00 0.00 0.00 1.40
4692 6571 0.814457 GCGGCATGGTTCCACAAATA 59.186 50.000 0.00 0.00 0.00 1.40
4693 6572 1.591183 GCGGCATGGTTCCACAAAT 59.409 52.632 0.00 0.00 0.00 2.32
4694 6573 2.569354 GGCGGCATGGTTCCACAAA 61.569 57.895 3.07 0.00 0.00 2.83
4695 6574 2.988684 GGCGGCATGGTTCCACAA 60.989 61.111 3.07 0.00 0.00 3.33
4696 6575 4.277009 TGGCGGCATGGTTCCACA 62.277 61.111 7.97 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.