Multiple sequence alignment - TraesCS3D01G475400

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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 TraesCS3D01G475400 chr3D 100.000 5382 0 0 799 6180 575848672 575854053 0.000000e+00 9939
1 TraesCS3D01G475400 chr3D 100.000 535 0 0 1 535 575847874 575848408 0.000000e+00 989
2 TraesCS3D01G475400 chr3A 95.194 5451 181 39 799 6180 711402776 711408214 0.000000e+00 8540
3 TraesCS3D01G475400 chr3A 95.500 200 9 0 185 384 711402369 711402568 2.780000e-83 320
4 TraesCS3D01G475400 chr3A 86.301 219 19 5 18 227 711402154 711402370 1.730000e-55 228
5 TraesCS3D01G475400 chr3B 97.156 2567 72 1 799 3365 768255141 768252576 0.000000e+00 4335
6 TraesCS3D01G475400 chr3B 94.793 2151 84 16 3418 5551 768252578 768250439 0.000000e+00 3326
7 TraesCS3D01G475400 chr3B 88.852 601 36 19 5606 6180 768250141 768249546 0.000000e+00 710
8 TraesCS3D01G475400 chr3B 94.340 159 9 0 225 383 768255511 768255353 1.720000e-60 244
9 TraesCS3D01G475400 chr3B 91.558 154 11 2 383 535 768255317 768255165 1.750000e-50 211


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 TraesCS3D01G475400 chr3D 575847874 575854053 6179 False 5464.000000 9939 100.000000 1 6180 2 chr3D.!!$F1 6179
1 TraesCS3D01G475400 chr3A 711402154 711408214 6060 False 3029.333333 8540 92.331667 18 6180 3 chr3A.!!$F1 6162
2 TraesCS3D01G475400 chr3B 768249546 768255511 5965 True 1765.200000 4335 93.339800 225 6180 5 chr3B.!!$R1 5955

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
170 179 0.249447 GTTTGTTGAGGTGCCAAGCC 60.249 55.000 0.00 0.0 0.00 4.35 F
1506 1593 0.598065 AAAACAGCATCCGTTGGAGC 59.402 50.000 0.00 0.0 34.05 4.70 F
3205 3292 1.149174 CACCTCCCACAAGTGCAGT 59.851 57.895 0.00 0.0 0.00 4.40 F
3826 3924 0.891373 TCTTTGGAGAGAGGCTCACG 59.109 55.000 18.26 0.0 45.81 4.35 F
4459 4557 2.701951 AGTAACTCGGGTTTTCAGTGGA 59.298 45.455 5.71 0.0 36.92 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1908 1995 1.180029 GCAGTGAATCCAGTTGCCAT 58.820 50.000 0.0 0.0 31.53 4.40 R
3424 3511 1.996291 TCACCATCCATACCCAACCAA 59.004 47.619 0.0 0.0 0.00 3.67 R
4490 4588 0.034337 AATTTGGGCTGCTTGCTGTG 59.966 50.000 0.0 0.0 42.39 3.66 R
4633 4731 0.914644 CCCCTGATGTCATGTGTCCT 59.085 55.000 0.0 0.0 0.00 3.85 R
5767 6173 1.009829 GATGTGTCCGTCAATCAGCC 58.990 55.000 0.0 0.0 0.00 4.85 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
36 37 2.955342 TGCTCTTGCATATATGGCCA 57.045 45.000 8.56 8.56 45.31 5.36
41 42 5.188434 GCTCTTGCATATATGGCCAGAATA 58.812 41.667 13.05 12.30 39.41 1.75
56 57 4.444876 GCCAGAATAGAATCTGCCCTTGTA 60.445 45.833 0.00 0.00 44.43 2.41
58 59 5.704515 CCAGAATAGAATCTGCCCTTGTATG 59.295 44.000 0.00 0.00 44.43 2.39
66 67 4.150897 TCTGCCCTTGTATGTTACCATC 57.849 45.455 0.00 0.00 32.29 3.51
71 72 4.705023 GCCCTTGTATGTTACCATCAACTT 59.295 41.667 0.00 0.00 32.29 2.66
89 90 7.517614 TCAACTTGCTATTGGTGTCAATTTA 57.482 32.000 0.00 0.00 42.90 1.40
101 102 7.764695 TGGTGTCAATTTATATGTACACGAG 57.235 36.000 0.00 0.00 38.43 4.18
112 121 1.071605 GTACACGAGCTTGCTCTTGG 58.928 55.000 25.47 15.13 0.00 3.61
119 128 2.157738 GAGCTTGCTCTTGGTGTCAAT 58.842 47.619 14.65 0.00 31.75 2.57
121 130 2.961062 AGCTTGCTCTTGGTGTCAATTT 59.039 40.909 0.00 0.00 31.75 1.82
143 152 0.994995 GCGTACTCTGTGTGAGCATG 59.005 55.000 0.00 0.00 46.41 4.06
148 157 1.690893 ACTCTGTGTGAGCATGTGTCT 59.309 47.619 0.00 0.00 46.41 3.41
165 174 1.604278 GTCTGAGTTTGTTGAGGTGCC 59.396 52.381 0.00 0.00 0.00 5.01
170 179 0.249447 GTTTGTTGAGGTGCCAAGCC 60.249 55.000 0.00 0.00 0.00 4.35
206 257 9.202273 GAGATAAAATGTATGATCACTCCAGTC 57.798 37.037 0.00 0.00 0.00 3.51
230 281 0.808755 GTCTGCCCATTTGTTACCGG 59.191 55.000 0.00 0.00 0.00 5.28
293 344 4.216472 CCTTTCTCAGTTAGGCAAGAAACC 59.784 45.833 0.00 0.00 34.82 3.27
384 435 4.073425 AGGCCAAAAATAATCCAAGGGA 57.927 40.909 5.01 0.00 35.55 4.20
385 436 4.434195 AGGCCAAAAATAATCCAAGGGAA 58.566 39.130 5.01 0.00 34.34 3.97
387 438 4.225042 GGCCAAAAATAATCCAAGGGAAGT 59.775 41.667 0.00 0.00 34.34 3.01
388 439 5.178061 GCCAAAAATAATCCAAGGGAAGTG 58.822 41.667 0.00 0.00 34.34 3.16
392 478 4.591321 AATAATCCAAGGGAAGTGCAGA 57.409 40.909 0.00 0.00 34.34 4.26
425 511 8.113062 CGTTTCTTGCTCATATTCTTCAGTAAG 58.887 37.037 0.00 0.00 31.81 2.34
448 534 4.181578 ACAGTAAGCGATAACACATGTCC 58.818 43.478 0.00 0.00 0.00 4.02
482 568 6.326843 GGATATGGTTACAGTCTAGGGTTTCT 59.673 42.308 0.00 0.00 0.00 2.52
503 590 2.038659 CAGGGGCTTTCTTTTCACCAA 58.961 47.619 0.00 0.00 0.00 3.67
523 610 5.111989 CCAATGTTTCTATGCGAAGAGAGA 58.888 41.667 0.00 0.00 32.21 3.10
899 986 4.661240 TCTGACTGGCTACTACTCTCCTAT 59.339 45.833 0.00 0.00 0.00 2.57
907 994 8.235359 TGGCTACTACTCTCCTATTTTTCTAC 57.765 38.462 0.00 0.00 0.00 2.59
930 1017 4.023450 CCTATATTGTGCATCCACTTGCTG 60.023 45.833 0.00 0.00 43.18 4.41
951 1038 5.431420 TGTTGTTATTTGTGGTGCTACTG 57.569 39.130 0.00 0.00 0.00 2.74
1011 1098 3.999001 CTGCTTGCACAATGAGAGTAGAA 59.001 43.478 0.00 0.00 0.00 2.10
1075 1162 1.740664 GGCGAGGAGTTCCGGTTTC 60.741 63.158 0.00 0.00 42.08 2.78
1083 1170 2.033194 GTTCCGGTTTCTGGAGGCG 61.033 63.158 0.00 0.00 36.72 5.52
1188 1275 2.095059 CCACTACAAAATGGACAGCAGC 60.095 50.000 0.00 0.00 38.34 5.25
1398 1485 2.583441 CCAGTGGCTCGACCCTGAA 61.583 63.158 16.47 0.00 38.39 3.02
1506 1593 0.598065 AAAACAGCATCCGTTGGAGC 59.402 50.000 0.00 0.00 34.05 4.70
1530 1617 6.147581 CCAAATTGAGTATGCATATGCTGAC 58.852 40.000 27.13 22.61 42.66 3.51
1813 1900 3.097614 GGGTCTACTCAGGTAAGCTTCA 58.902 50.000 0.00 0.00 0.00 3.02
2102 2189 1.528129 CCTTTCAAGGCTCCAGTGAC 58.472 55.000 0.00 0.00 39.76 3.67
2199 2286 1.953686 GTTGCCAAGGCTCACAAACTA 59.046 47.619 12.96 0.00 42.51 2.24
2323 2410 3.511856 GCATAGTGCATCGAACTTAGC 57.488 47.619 0.00 0.00 44.26 3.09
2337 2424 8.752254 CATCGAACTTAGCGTAATCAAAGATAA 58.248 33.333 0.00 0.00 0.00 1.75
2685 2772 1.971695 GGGCCTGTGCTGGTTGTAC 60.972 63.158 0.84 0.00 37.74 2.90
2793 2880 8.691661 TGTTCTACTGGAAGAAGCTTATTTTT 57.308 30.769 7.91 0.00 36.19 1.94
2794 2881 8.784043 TGTTCTACTGGAAGAAGCTTATTTTTC 58.216 33.333 7.91 5.95 36.19 2.29
2918 3005 9.049523 CAGTATTACAAGCAGTGTCATCAATAT 57.950 33.333 0.00 0.00 41.98 1.28
3022 3109 1.394917 GTGCTGTTAGATGAGGCAACG 59.605 52.381 0.00 0.00 46.39 4.10
3100 3187 2.223340 GCAGTCAGGCCAAATACGAATG 60.223 50.000 5.01 1.97 0.00 2.67
3205 3292 1.149174 CACCTCCCACAAGTGCAGT 59.851 57.895 0.00 0.00 0.00 4.40
3267 3354 9.133627 GTTGATAAAGCTCTTCAAAAGAAATCC 57.866 33.333 7.32 0.00 37.02 3.01
3397 3484 1.956477 GTTGATCAACCTGCACCTGTT 59.044 47.619 25.26 0.00 35.36 3.16
3423 3510 9.393249 TGAAACAGAATAAAAACGAATGTCATC 57.607 29.630 0.00 0.00 0.00 2.92
3424 3511 9.612620 GAAACAGAATAAAAACGAATGTCATCT 57.387 29.630 0.00 0.00 0.00 2.90
3461 3548 8.055181 TGGATGGTGAAAGCTCTCTTTTATTAT 58.945 33.333 0.00 0.00 42.24 1.28
3502 3589 4.637091 CCAACATATGCTGAACATCAGTGA 59.363 41.667 7.70 0.00 45.94 3.41
3593 3691 2.495409 TGCGAAATGGCATGCATAAG 57.505 45.000 21.36 6.40 38.17 1.73
3632 3730 1.801178 GCGTTGCTGAGAAGTTTAGCT 59.199 47.619 0.00 0.00 38.25 3.32
3826 3924 0.891373 TCTTTGGAGAGAGGCTCACG 59.109 55.000 18.26 0.00 45.81 4.35
4020 4118 6.743575 AAAGTAACCTAGCAAAGCACATAG 57.256 37.500 0.00 0.00 0.00 2.23
4025 4123 5.677319 ACCTAGCAAAGCACATAGAACTA 57.323 39.130 0.00 0.00 0.00 2.24
4117 4215 5.934625 AGGAACTGTACAGCTGATTTACTTG 59.065 40.000 23.35 11.71 37.18 3.16
4225 4323 5.957842 TGCATTTACCAAGTTCAGTAAGG 57.042 39.130 0.00 0.00 30.57 2.69
4459 4557 2.701951 AGTAACTCGGGTTTTCAGTGGA 59.298 45.455 5.71 0.00 36.92 4.02
4490 4588 3.119291 CTGCGACCAGAATATCACTGTC 58.881 50.000 8.41 0.00 41.77 3.51
4493 4591 3.676049 GCGACCAGAATATCACTGTCACA 60.676 47.826 8.41 0.00 34.04 3.58
4575 4673 6.375174 CCAGGTATTGATGTTGTTGAGAATGA 59.625 38.462 0.00 0.00 0.00 2.57
4633 4731 5.948758 TGCATGGGATAAAGTTGACATGTTA 59.051 36.000 0.00 0.00 38.29 2.41
4798 4896 7.349711 TGATTTGAGCAAAGACGTTAAGTTAC 58.650 34.615 1.92 0.00 33.32 2.50
4854 4952 1.198759 ACACGGTAAGGCAGGATGGT 61.199 55.000 0.00 0.00 35.86 3.55
4917 5015 4.351192 TCTTTCTTTGCTTTGCGTTTCTC 58.649 39.130 0.00 0.00 0.00 2.87
5038 5142 2.681064 GCCATTTGCCAGCCAGGA 60.681 61.111 0.00 0.00 41.22 3.86
5194 5298 1.465794 GCTAGACGGAGACAGGTCTT 58.534 55.000 3.07 0.00 43.02 3.01
5218 5323 5.960683 TGTGTAAGATGTTTTCGTCGTTTTG 59.039 36.000 0.00 0.00 40.47 2.44
5222 5327 6.790336 AAGATGTTTTCGTCGTTTTGAAAG 57.210 33.333 0.00 0.00 40.47 2.62
5225 5330 7.465989 AGATGTTTTCGTCGTTTTGAAAGTTA 58.534 30.769 0.00 0.00 40.47 2.24
5226 5331 8.126700 AGATGTTTTCGTCGTTTTGAAAGTTAT 58.873 29.630 0.00 0.00 40.47 1.89
5253 5358 5.072741 ACTGCACCAGATGTTACAAAGAAT 58.927 37.500 0.00 0.00 35.18 2.40
5257 5362 5.621422 CACCAGATGTTACAAAGAATGACG 58.379 41.667 0.00 0.00 0.00 4.35
5307 5412 2.796032 GCACAAACACCTCTTGCTTGAC 60.796 50.000 0.00 0.00 35.23 3.18
5308 5413 2.423185 CACAAACACCTCTTGCTTGACA 59.577 45.455 0.00 0.00 35.23 3.58
5384 5495 8.752005 TGTAATAAGCTGGAATAAATGCTTCT 57.248 30.769 2.24 0.00 43.55 2.85
5439 5550 7.040686 TGTTTATTTTGCTTCTCCCTAGTTGTC 60.041 37.037 0.00 0.00 0.00 3.18
5441 5552 1.629043 TGCTTCTCCCTAGTTGTCGT 58.371 50.000 0.00 0.00 0.00 4.34
5442 5553 1.272490 TGCTTCTCCCTAGTTGTCGTG 59.728 52.381 0.00 0.00 0.00 4.35
5443 5554 1.404315 GCTTCTCCCTAGTTGTCGTGG 60.404 57.143 0.00 0.00 0.00 4.94
5445 5556 1.254026 TCTCCCTAGTTGTCGTGGTG 58.746 55.000 0.00 0.00 0.00 4.17
5446 5557 1.202964 TCTCCCTAGTTGTCGTGGTGA 60.203 52.381 0.00 0.00 0.00 4.02
5448 5559 2.036733 CTCCCTAGTTGTCGTGGTGAAA 59.963 50.000 0.00 0.00 0.00 2.69
5449 5560 2.036733 TCCCTAGTTGTCGTGGTGAAAG 59.963 50.000 0.00 0.00 0.00 2.62
5450 5561 2.224209 CCCTAGTTGTCGTGGTGAAAGT 60.224 50.000 0.00 0.00 0.00 2.66
5453 5564 2.980568 AGTTGTCGTGGTGAAAGTTGA 58.019 42.857 0.00 0.00 0.00 3.18
5454 5565 3.340034 AGTTGTCGTGGTGAAAGTTGAA 58.660 40.909 0.00 0.00 0.00 2.69
5455 5566 3.945285 AGTTGTCGTGGTGAAAGTTGAAT 59.055 39.130 0.00 0.00 0.00 2.57
5457 5568 4.285807 TGTCGTGGTGAAAGTTGAATTG 57.714 40.909 0.00 0.00 0.00 2.32
5459 5570 4.876679 TGTCGTGGTGAAAGTTGAATTGTA 59.123 37.500 0.00 0.00 0.00 2.41
5463 5574 6.748198 TCGTGGTGAAAGTTGAATTGTAAAAC 59.252 34.615 0.00 0.00 0.00 2.43
5464 5575 6.020201 CGTGGTGAAAGTTGAATTGTAAAACC 60.020 38.462 0.00 0.00 0.00 3.27
5466 5577 7.010091 GTGGTGAAAGTTGAATTGTAAAACCTG 59.990 37.037 0.00 0.00 0.00 4.00
5467 5578 7.093727 TGGTGAAAGTTGAATTGTAAAACCTGA 60.094 33.333 0.00 0.00 0.00 3.86
5468 5579 7.762159 GGTGAAAGTTGAATTGTAAAACCTGAA 59.238 33.333 0.00 0.00 0.00 3.02
5470 5581 9.712305 TGAAAGTTGAATTGTAAAACCTGAAAA 57.288 25.926 0.00 0.00 0.00 2.29
5473 5584 9.665719 AAGTTGAATTGTAAAACCTGAAAATGT 57.334 25.926 0.00 0.00 0.00 2.71
5481 5609 8.611654 TGTAAAACCTGAAAATGTAGTACCTC 57.388 34.615 0.00 0.00 0.00 3.85
5503 5631 5.511571 TCGCTTCATCAGTATCTCTTTACG 58.488 41.667 0.00 0.00 0.00 3.18
5557 5685 5.673337 TGCACAACTTTCTCATTAGTCAC 57.327 39.130 0.00 0.00 0.00 3.67
5567 5695 7.450634 ACTTTCTCATTAGTCACTACACCACTA 59.549 37.037 0.00 0.00 0.00 2.74
5569 5697 7.334844 TCTCATTAGTCACTACACCACTATG 57.665 40.000 0.00 0.00 0.00 2.23
5570 5698 5.902681 TCATTAGTCACTACACCACTATGC 58.097 41.667 0.00 0.00 0.00 3.14
5571 5699 5.420739 TCATTAGTCACTACACCACTATGCA 59.579 40.000 0.00 0.00 0.00 3.96
5572 5700 5.932619 TTAGTCACTACACCACTATGCAT 57.067 39.130 3.79 3.79 0.00 3.96
5573 5701 4.128925 AGTCACTACACCACTATGCATG 57.871 45.455 10.16 1.82 0.00 4.06
5574 5702 3.515502 AGTCACTACACCACTATGCATGT 59.484 43.478 10.16 0.88 0.00 3.21
5575 5703 3.618594 GTCACTACACCACTATGCATGTG 59.381 47.826 10.16 14.78 35.39 3.21
5577 5705 4.162131 TCACTACACCACTATGCATGTGAT 59.838 41.667 22.76 9.70 37.60 3.06
5578 5706 5.362430 TCACTACACCACTATGCATGTGATA 59.638 40.000 22.76 14.12 37.60 2.15
5579 5707 6.041979 TCACTACACCACTATGCATGTGATAT 59.958 38.462 22.76 13.38 37.60 1.63
5681 6086 6.946229 ACATACATATATTCGTTCTTCGGC 57.054 37.500 0.00 0.00 40.32 5.54
5767 6173 8.819974 ACTGAAACATTTGCAAAAGATTTACAG 58.180 29.630 20.40 22.07 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 6.393171 GCAAGAGCAAATTCCTTTTGTAGAT 58.607 36.000 9.56 0.00 45.41 1.98
2 3 5.772521 GCAAGAGCAAATTCCTTTTGTAGA 58.227 37.500 9.56 0.00 45.41 2.59
18 19 3.063510 TCTGGCCATATATGCAAGAGC 57.936 47.619 5.51 4.92 33.86 4.09
19 20 6.647229 TCTATTCTGGCCATATATGCAAGAG 58.353 40.000 5.51 0.00 39.84 2.85
20 21 6.625532 TCTATTCTGGCCATATATGCAAGA 57.374 37.500 5.51 8.35 37.01 3.02
21 22 7.774157 AGATTCTATTCTGGCCATATATGCAAG 59.226 37.037 5.51 6.26 0.00 4.01
22 23 7.555195 CAGATTCTATTCTGGCCATATATGCAA 59.445 37.037 5.51 1.94 39.58 4.08
23 24 7.052248 CAGATTCTATTCTGGCCATATATGCA 58.948 38.462 5.51 0.00 39.58 3.96
24 25 6.017275 GCAGATTCTATTCTGGCCATATATGC 60.017 42.308 5.51 9.87 42.78 3.14
25 26 7.493743 GCAGATTCTATTCTGGCCATATATG 57.506 40.000 5.51 5.68 42.78 1.78
35 36 6.294473 ACATACAAGGGCAGATTCTATTCTG 58.706 40.000 0.00 0.00 44.87 3.02
36 37 6.506538 ACATACAAGGGCAGATTCTATTCT 57.493 37.500 0.00 0.00 0.00 2.40
41 42 4.227300 TGGTAACATACAAGGGCAGATTCT 59.773 41.667 0.00 0.00 46.17 2.40
58 59 5.183140 ACACCAATAGCAAGTTGATGGTAAC 59.817 40.000 17.29 0.00 39.05 2.50
71 72 9.620259 TGTACATATAAATTGACACCAATAGCA 57.380 29.630 0.00 0.00 41.84 3.49
89 90 4.115516 CAAGAGCAAGCTCGTGTACATAT 58.884 43.478 23.74 0.19 46.90 1.78
93 94 1.071605 CCAAGAGCAAGCTCGTGTAC 58.928 55.000 27.56 3.19 46.18 2.90
99 100 1.597742 TTGACACCAAGAGCAAGCTC 58.402 50.000 14.00 14.00 43.03 4.09
101 102 3.054878 CAAATTGACACCAAGAGCAAGC 58.945 45.455 0.00 0.00 35.48 4.01
112 121 3.247648 ACAGAGTACGCACAAATTGACAC 59.752 43.478 0.00 0.00 0.00 3.67
119 128 2.469826 CTCACACAGAGTACGCACAAA 58.530 47.619 0.00 0.00 39.62 2.83
121 130 0.318699 GCTCACACAGAGTACGCACA 60.319 55.000 0.00 0.00 46.47 4.57
143 152 2.032178 GCACCTCAACAAACTCAGACAC 59.968 50.000 0.00 0.00 0.00 3.67
148 157 2.023673 CTTGGCACCTCAACAAACTCA 58.976 47.619 0.00 0.00 0.00 3.41
165 174 6.773976 TTTTATCTCCTGTATTTGGGCTTG 57.226 37.500 0.00 0.00 0.00 4.01
206 257 1.269012 AACAAATGGGCAGACATGGG 58.731 50.000 0.00 0.00 0.00 4.00
384 435 3.744660 AGAAACGAATTCCTCTGCACTT 58.255 40.909 0.00 0.00 38.94 3.16
385 436 3.409026 AGAAACGAATTCCTCTGCACT 57.591 42.857 0.00 0.00 38.94 4.40
387 438 2.226437 GCAAGAAACGAATTCCTCTGCA 59.774 45.455 0.00 0.00 38.94 4.41
388 439 2.485814 AGCAAGAAACGAATTCCTCTGC 59.514 45.455 0.00 3.51 38.94 4.26
392 478 6.825721 AGAATATGAGCAAGAAACGAATTCCT 59.174 34.615 0.00 0.00 38.94 3.36
425 511 4.267928 GGACATGTGTTATCGCTTACTGTC 59.732 45.833 1.15 0.00 0.00 3.51
462 548 4.485875 TGAGAAACCCTAGACTGTAACCA 58.514 43.478 0.00 0.00 0.00 3.67
482 568 1.216678 TGGTGAAAAGAAAGCCCCTGA 59.783 47.619 0.00 0.00 0.00 3.86
503 590 5.590530 AGTCTCTCTTCGCATAGAAACAT 57.409 39.130 0.00 0.00 38.57 2.71
812 899 5.854010 TCATATCAGACACAGAAGGGTAC 57.146 43.478 0.00 0.00 0.00 3.34
813 900 7.345653 AGAAATCATATCAGACACAGAAGGGTA 59.654 37.037 0.00 0.00 0.00 3.69
899 986 8.052748 AGTGGATGCACAATATAGGTAGAAAAA 58.947 33.333 20.21 0.00 0.00 1.94
907 994 4.494350 GCAAGTGGATGCACAATATAGG 57.506 45.455 20.21 1.87 45.70 2.57
930 1017 5.682943 TCAGTAGCACCACAAATAACAAC 57.317 39.130 0.00 0.00 0.00 3.32
951 1038 1.135689 GGACAACAACACGCCATGATC 60.136 52.381 0.00 0.00 0.00 2.92
1089 1176 1.526575 CCTCAAACGCAATGCACCCT 61.527 55.000 5.91 0.00 0.00 4.34
1188 1275 3.365453 CAGGATGACAGCGTAATGACGG 61.365 54.545 4.40 0.00 44.81 4.79
1207 1294 3.644966 TTTGTTCCTATGGCTACCCAG 57.355 47.619 0.00 0.00 46.24 4.45
1398 1485 2.358322 ACTGAACATTTCGGTTGGGT 57.642 45.000 0.00 0.00 46.80 4.51
1506 1593 6.147581 GTCAGCATATGCATACTCAATTTGG 58.852 40.000 28.62 3.00 45.16 3.28
1908 1995 1.180029 GCAGTGAATCCAGTTGCCAT 58.820 50.000 0.00 0.00 31.53 4.40
2102 2189 5.987347 AGGAATTGTTTGATTTTCTGCACAG 59.013 36.000 0.00 0.00 0.00 3.66
2286 2373 6.201425 GCACTATGCCAAAATGTGAATATTGG 59.799 38.462 0.00 0.00 44.09 3.16
2793 2880 4.993705 AGCCATATCCCTTAAATTCGGA 57.006 40.909 0.00 0.00 0.00 4.55
2794 2881 4.827284 ACAAGCCATATCCCTTAAATTCGG 59.173 41.667 0.00 0.00 0.00 4.30
2918 3005 7.566760 TTTCTTCAAGCAGTTTACAAGATGA 57.433 32.000 0.00 0.00 0.00 2.92
3022 3109 7.631717 ACTTGCCTGAAGAATATCCTTAAAC 57.368 36.000 0.00 0.00 35.42 2.01
3100 3187 9.360093 CCTTATATCTATTTTCTCATGGACGTC 57.640 37.037 7.13 7.13 0.00 4.34
3340 3427 9.396022 CAACAATTGTAGGATTGGATTACTACT 57.604 33.333 12.39 0.00 40.50 2.57
3397 3484 9.393249 GATGACATTCGTTTTTATTCTGTTTCA 57.607 29.630 0.00 0.00 0.00 2.69
3413 3500 2.436417 ACCCAACCAAGATGACATTCG 58.564 47.619 0.00 0.00 0.00 3.34
3423 3510 2.025416 TCACCATCCATACCCAACCAAG 60.025 50.000 0.00 0.00 0.00 3.61
3424 3511 1.996291 TCACCATCCATACCCAACCAA 59.004 47.619 0.00 0.00 0.00 3.67
3632 3730 5.818336 TGACCAATGTCGACAAGAAAAACTA 59.182 36.000 24.13 1.12 44.86 2.24
3826 3924 7.068226 ACAAATGGTAGTAAAGTATTGATGGCC 59.932 37.037 0.00 0.00 0.00 5.36
4020 4118 9.654663 ATTACTAACCAACTGTCTGAATAGTTC 57.345 33.333 5.81 0.00 34.92 3.01
4117 4215 3.366374 GCTTCTGCAACCTGTTATCCAAC 60.366 47.826 0.00 0.00 39.41 3.77
4209 4307 3.717913 ACCAACCCTTACTGAACTTGGTA 59.282 43.478 0.00 0.00 39.65 3.25
4211 4309 3.223674 ACCAACCCTTACTGAACTTGG 57.776 47.619 0.00 0.00 35.31 3.61
4225 4323 7.759489 TCATAAATATTCAGGCATACCAACC 57.241 36.000 0.00 0.00 39.06 3.77
4459 4557 5.543507 ATTCTGGTCGCAGAGAATTAGAT 57.456 39.130 0.00 0.00 35.78 1.98
4490 4588 0.034337 AATTTGGGCTGCTTGCTGTG 59.966 50.000 0.00 0.00 42.39 3.66
4493 4591 0.895100 TCGAATTTGGGCTGCTTGCT 60.895 50.000 0.00 0.00 42.39 3.91
4633 4731 0.914644 CCCCTGATGTCATGTGTCCT 59.085 55.000 0.00 0.00 0.00 3.85
4759 4857 6.405538 TGCTCAAATCAAACAAAAGAACCTT 58.594 32.000 0.00 0.00 0.00 3.50
4760 4858 5.976458 TGCTCAAATCAAACAAAAGAACCT 58.024 33.333 0.00 0.00 0.00 3.50
4798 4896 2.708514 CTGCACGAAAACAGAACACAG 58.291 47.619 0.00 0.00 35.90 3.66
4854 4952 5.116180 CAAGACCTCATAAATGCCGTAGAA 58.884 41.667 0.00 0.00 0.00 2.10
4917 5015 2.289882 TGTCAACCATTCAGCTCTCAGG 60.290 50.000 0.00 0.00 0.00 3.86
5038 5142 3.276846 GGCCACGACGCAAACTGT 61.277 61.111 0.00 0.00 0.00 3.55
5194 5298 5.721876 AAACGACGAAAACATCTTACACA 57.278 34.783 0.00 0.00 0.00 3.72
5218 5323 7.593825 ACATCTGGTGCAGTTTTATAACTTTC 58.406 34.615 0.00 0.00 41.85 2.62
5222 5327 7.812648 TGTAACATCTGGTGCAGTTTTATAAC 58.187 34.615 0.00 0.00 32.61 1.89
5225 5330 6.892658 TTGTAACATCTGGTGCAGTTTTAT 57.107 33.333 0.00 0.00 32.61 1.40
5226 5331 6.544197 TCTTTGTAACATCTGGTGCAGTTTTA 59.456 34.615 0.00 0.00 32.61 1.52
5253 5358 4.457949 ACAGTGATACATACAGTGTCGTCA 59.542 41.667 0.00 0.00 45.07 4.35
5257 5362 7.597369 TGTGTAAACAGTGATACATACAGTGTC 59.403 37.037 0.00 0.00 46.71 3.67
5307 5412 5.048782 ACATGCTTGTACCAGTTTGTGTATG 60.049 40.000 2.92 0.00 33.16 2.39
5308 5413 5.048782 CACATGCTTGTACCAGTTTGTGTAT 60.049 40.000 16.48 0.00 33.76 2.29
5439 5550 6.020201 GGTTTTACAATTCAACTTTCACCACG 60.020 38.462 0.00 0.00 0.00 4.94
5441 5552 7.038659 CAGGTTTTACAATTCAACTTTCACCA 58.961 34.615 0.00 0.00 0.00 4.17
5442 5553 7.262048 TCAGGTTTTACAATTCAACTTTCACC 58.738 34.615 0.00 0.00 0.00 4.02
5443 5554 8.696410 TTCAGGTTTTACAATTCAACTTTCAC 57.304 30.769 0.00 0.00 0.00 3.18
5454 5565 9.582648 AGGTACTACATTTTCAGGTTTTACAAT 57.417 29.630 0.00 0.00 36.02 2.71
5455 5566 8.983702 AGGTACTACATTTTCAGGTTTTACAA 57.016 30.769 0.00 0.00 36.02 2.41
5457 5568 7.622880 GCGAGGTACTACATTTTCAGGTTTTAC 60.623 40.741 0.00 0.00 41.55 2.01
5459 5570 5.180680 GCGAGGTACTACATTTTCAGGTTTT 59.819 40.000 0.00 0.00 41.55 2.43
5463 5574 4.124851 AGCGAGGTACTACATTTTCAGG 57.875 45.455 0.00 0.00 41.55 3.86
5464 5575 5.168569 TGAAGCGAGGTACTACATTTTCAG 58.831 41.667 0.00 0.00 41.55 3.02
5466 5577 5.810587 TGATGAAGCGAGGTACTACATTTTC 59.189 40.000 0.00 0.00 41.55 2.29
5467 5578 5.730550 TGATGAAGCGAGGTACTACATTTT 58.269 37.500 0.00 0.00 41.55 1.82
5468 5579 5.105310 ACTGATGAAGCGAGGTACTACATTT 60.105 40.000 0.00 0.00 41.55 2.32
5470 5581 3.954904 ACTGATGAAGCGAGGTACTACAT 59.045 43.478 0.00 0.00 41.55 2.29
5471 5582 3.353557 ACTGATGAAGCGAGGTACTACA 58.646 45.455 0.00 0.00 41.55 2.74
5473 5584 5.622180 AGATACTGATGAAGCGAGGTACTA 58.378 41.667 0.00 0.00 41.55 1.82
5475 5586 4.517453 AGAGATACTGATGAAGCGAGGTAC 59.483 45.833 0.00 0.00 0.00 3.34
5476 5587 4.720046 AGAGATACTGATGAAGCGAGGTA 58.280 43.478 0.00 0.00 0.00 3.08
5481 5609 5.511571 TCGTAAAGAGATACTGATGAAGCG 58.488 41.667 0.00 0.00 0.00 4.68
5519 5647 2.094494 TGTGCAACGGTGAAATTTGTGT 60.094 40.909 3.55 0.00 42.39 3.72
5557 5685 6.458210 TCATATCACATGCATAGTGGTGTAG 58.542 40.000 21.35 12.86 37.58 2.74
5567 5695 3.683340 GCTGTCGATCATATCACATGCAT 59.317 43.478 0.00 0.00 0.00 3.96
5569 5697 3.062042 TGCTGTCGATCATATCACATGC 58.938 45.455 0.00 0.00 0.00 4.06
5570 5698 4.092968 CCATGCTGTCGATCATATCACATG 59.907 45.833 0.00 0.00 0.00 3.21
5571 5699 4.020839 TCCATGCTGTCGATCATATCACAT 60.021 41.667 0.00 0.00 0.00 3.21
5572 5700 3.321682 TCCATGCTGTCGATCATATCACA 59.678 43.478 0.00 0.00 0.00 3.58
5573 5701 3.917988 TCCATGCTGTCGATCATATCAC 58.082 45.455 0.00 0.00 0.00 3.06
5574 5702 4.020839 ACATCCATGCTGTCGATCATATCA 60.021 41.667 0.00 0.00 0.00 2.15
5575 5703 4.502016 ACATCCATGCTGTCGATCATATC 58.498 43.478 0.00 0.00 0.00 1.63
5577 5705 5.413499 CATACATCCATGCTGTCGATCATA 58.587 41.667 2.76 0.00 0.00 2.15
5578 5706 2.924757 ACATCCATGCTGTCGATCAT 57.075 45.000 0.00 0.00 0.00 2.45
5579 5707 3.555586 CCATACATCCATGCTGTCGATCA 60.556 47.826 2.76 0.00 0.00 2.92
5615 6016 3.686622 TGAAGCGCTTCAGAACTGT 57.313 47.368 41.19 10.73 43.90 3.55
5659 6060 5.004440 CGGCCGAAGAACGAATATATGTATG 59.996 44.000 24.07 0.00 45.77 2.39
5663 6064 2.092211 GCGGCCGAAGAACGAATATATG 59.908 50.000 33.48 0.00 45.77 1.78
5667 6068 1.519898 GGCGGCCGAAGAACGAATA 60.520 57.895 33.48 0.00 45.77 1.75
5668 6069 2.818274 GGCGGCCGAAGAACGAAT 60.818 61.111 33.48 0.00 45.77 3.34
5703 6108 9.071221 CATATACAAGTTAATGCGCTTTCAAAA 57.929 29.630 12.27 0.00 0.00 2.44
5706 6111 6.198687 GCATATACAAGTTAATGCGCTTTCA 58.801 36.000 12.27 0.00 35.81 2.69
5740 6145 9.809096 TGTAAATCTTTTGCAAATGTTTCAGTA 57.191 25.926 20.69 8.84 0.00 2.74
5767 6173 1.009829 GATGTGTCCGTCAATCAGCC 58.990 55.000 0.00 0.00 0.00 4.85
6057 6466 4.161377 TGCTGATTGGCATGTACTGTAGTA 59.839 41.667 0.00 0.00 37.29 1.82
6058 6467 3.055167 TGCTGATTGGCATGTACTGTAGT 60.055 43.478 0.00 0.00 37.29 2.73
6059 6468 3.534554 TGCTGATTGGCATGTACTGTAG 58.465 45.455 0.00 0.00 37.29 2.74
6060 6469 3.197549 TCTGCTGATTGGCATGTACTGTA 59.802 43.478 0.00 0.00 41.63 2.74


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

AutoCloner maintained by Alex Coulton.