Multiple sequence alignment - TraesCS2D01G166400

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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 TraesCS2D01G166400 chr2D 100.000 2885 0 0 1 2885 110631366 110628482 0.000000e+00 5328.0
1 TraesCS2D01G166400 chr2D 91.853 1031 51 12 918 1925 110403221 110404241 0.000000e+00 1408.0
2 TraesCS2D01G166400 chr2D 92.713 494 21 4 1441 1925 109913688 109914175 0.000000e+00 699.0
3 TraesCS2D01G166400 chr2D 92.994 471 25 3 969 1438 109906394 109906857 0.000000e+00 680.0
4 TraesCS2D01G166400 chr2D 84.765 617 72 12 1 601 303359458 303360068 1.480000e-167 599.0
5 TraesCS2D01G166400 chr2D 84.578 616 71 13 1 598 303340267 303340876 8.900000e-165 590.0
6 TraesCS2D01G166400 chr2D 89.655 87 9 0 2003 2089 109914212 109914298 8.450000e-21 111.0
7 TraesCS2D01G166400 chr2D 86.275 102 6 5 818 914 110403074 110403172 1.410000e-18 104.0
8 TraesCS2D01G166400 chr2B 92.875 1207 58 9 728 1925 159602637 159601450 0.000000e+00 1727.0
9 TraesCS2D01G166400 chr2B 93.019 1017 51 8 918 1925 159573295 159574300 0.000000e+00 1467.0
10 TraesCS2D01G166400 chr2B 84.384 698 83 10 9 694 159603416 159602733 0.000000e+00 662.0
11 TraesCS2D01G166400 chr2B 86.154 130 13 2 1797 1925 159326521 159326646 5.010000e-28 135.0
12 TraesCS2D01G166400 chr2B 91.045 67 4 2 857 923 159573192 159573256 3.960000e-14 89.8
13 TraesCS2D01G166400 chr2A 92.681 1175 59 12 768 1925 105682014 105683178 0.000000e+00 1668.0
14 TraesCS2D01G166400 chr2A 92.761 1119 57 9 821 1925 106654018 106652910 0.000000e+00 1596.0
15 TraesCS2D01G166400 chr2A 89.645 647 54 4 1 636 106655901 106655257 0.000000e+00 811.0
16 TraesCS2D01G166400 chr2A 94.794 461 20 3 2425 2885 106650493 106650037 0.000000e+00 715.0
17 TraesCS2D01G166400 chr2A 89.216 408 38 3 1672 2073 105592054 105592461 3.320000e-139 505.0
18 TraesCS2D01G166400 chr2A 98.062 258 5 0 2213 2470 106650751 106650494 1.580000e-122 449.0
19 TraesCS2D01G166400 chr2A 90.196 204 14 3 628 831 106655148 106654951 7.930000e-66 261.0
20 TraesCS2D01G166400 chr4D 84.967 612 72 10 1 597 437594878 437594272 1.140000e-168 603.0
21 TraesCS2D01G166400 chr7D 84.853 614 72 12 1 598 540994317 540993709 1.480000e-167 599.0
22 TraesCS2D01G166400 chr3D 84.853 614 72 11 1 598 501024760 501025368 1.480000e-167 599.0
23 TraesCS2D01G166400 chr4A 84.502 613 75 11 1 598 535559598 535560205 3.200000e-164 588.0
24 TraesCS2D01G166400 chr5D 84.437 604 73 11 30 617 563631156 563631754 2.490000e-160 575.0
25 TraesCS2D01G166400 chr3B 100.000 29 0 0 2110 2138 58858849 58858821 1.000000e-03 54.7


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 TraesCS2D01G166400 chr2D 110628482 110631366 2884 True 5328.0 5328 100.0000 1 2885 1 chr2D.!!$R1 2884
1 TraesCS2D01G166400 chr2D 110403074 110404241 1167 False 756.0 1408 89.0640 818 1925 2 chr2D.!!$F5 1107
2 TraesCS2D01G166400 chr2D 303359458 303360068 610 False 599.0 599 84.7650 1 601 1 chr2D.!!$F3 600
3 TraesCS2D01G166400 chr2D 303340267 303340876 609 False 590.0 590 84.5780 1 598 1 chr2D.!!$F2 597
4 TraesCS2D01G166400 chr2D 109913688 109914298 610 False 405.0 699 91.1840 1441 2089 2 chr2D.!!$F4 648
5 TraesCS2D01G166400 chr2B 159601450 159603416 1966 True 1194.5 1727 88.6295 9 1925 2 chr2B.!!$R1 1916
6 TraesCS2D01G166400 chr2B 159573192 159574300 1108 False 778.4 1467 92.0320 857 1925 2 chr2B.!!$F2 1068
7 TraesCS2D01G166400 chr2A 105682014 105683178 1164 False 1668.0 1668 92.6810 768 1925 1 chr2A.!!$F2 1157
8 TraesCS2D01G166400 chr2A 106650037 106655901 5864 True 766.4 1596 93.0916 1 2885 5 chr2A.!!$R1 2884
9 TraesCS2D01G166400 chr4D 437594272 437594878 606 True 603.0 603 84.9670 1 597 1 chr4D.!!$R1 596
10 TraesCS2D01G166400 chr7D 540993709 540994317 608 True 599.0 599 84.8530 1 598 1 chr7D.!!$R1 597
11 TraesCS2D01G166400 chr3D 501024760 501025368 608 False 599.0 599 84.8530 1 598 1 chr3D.!!$F1 597
12 TraesCS2D01G166400 chr4A 535559598 535560205 607 False 588.0 588 84.5020 1 598 1 chr4A.!!$F1 597
13 TraesCS2D01G166400 chr5D 563631156 563631754 598 False 575.0 575 84.4370 30 617 1 chr5D.!!$F1 587

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
694 830 0.262876 TCAGAGCAGAGGGGCTGATA 59.737 55.0 0.0 0.0 44.71 2.15 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1892 3128 0.321346 TGCTTTGATCCTGCTGTCGA 59.679 50.0 0.0 0.0 0.0 4.2 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
41 42 7.933577 TGTCAATCAAACAGTCTAGTCATTCTT 59.066 33.333 0.00 0.00 0.00 2.52
61 62 1.230324 GTGGAAGGTGTTCAGACTGC 58.770 55.000 0.00 0.00 33.93 4.40
79 87 0.889186 GCCAAGGCTTCACGAAGGAA 60.889 55.000 3.29 0.00 38.80 3.36
83 91 0.321996 AGGCTTCACGAAGGAACTCC 59.678 55.000 8.78 1.32 38.49 3.85
201 212 5.974370 TGTCCCTACTATAAAACCCCATCTT 59.026 40.000 0.00 0.00 0.00 2.40
302 319 6.428159 CCTTACTACATTTGCTCTTGTGAGTT 59.572 38.462 0.00 0.00 42.13 3.01
303 320 5.931441 ACTACATTTGCTCTTGTGAGTTC 57.069 39.130 0.00 0.00 42.13 3.01
348 365 3.134458 CCTCTGGTTCCTCATAATTCGC 58.866 50.000 0.00 0.00 0.00 4.70
349 366 3.432186 CCTCTGGTTCCTCATAATTCGCA 60.432 47.826 0.00 0.00 0.00 5.10
437 454 4.101114 TGGGTTGGAGTTCTTATAGCTCA 58.899 43.478 0.00 0.00 37.18 4.26
454 472 2.862541 CTCAAGTCAACCATCCCAACA 58.137 47.619 0.00 0.00 0.00 3.33
504 522 7.789831 AGGTATAAATCTAGTTGTCCTGGATGA 59.210 37.037 0.00 0.00 40.22 2.92
533 551 1.962100 AGTTATCCCTCCCGATTCGAC 59.038 52.381 7.83 0.00 0.00 4.20
538 556 1.179814 CCCTCCCGATTCGACCCTAG 61.180 65.000 7.83 0.00 0.00 3.02
547 565 1.619654 TTCGACCCTAGGACGTGAAA 58.380 50.000 11.48 3.88 41.15 2.69
554 572 2.481449 CCCTAGGACGTGAAAATCGAGG 60.481 54.545 11.48 0.00 0.00 4.63
678 814 1.662629 CTTGCGGTGTTGCTAGATCAG 59.337 52.381 0.00 0.00 39.60 2.90
694 830 0.262876 TCAGAGCAGAGGGGCTGATA 59.737 55.000 0.00 0.00 44.71 2.15
695 831 1.126488 CAGAGCAGAGGGGCTGATAA 58.874 55.000 0.00 0.00 44.71 1.75
696 832 1.698532 CAGAGCAGAGGGGCTGATAAT 59.301 52.381 0.00 0.00 44.71 1.28
697 833 2.106166 CAGAGCAGAGGGGCTGATAATT 59.894 50.000 0.00 0.00 44.71 1.40
698 834 2.106166 AGAGCAGAGGGGCTGATAATTG 59.894 50.000 0.00 0.00 44.71 2.32
699 835 2.105477 GAGCAGAGGGGCTGATAATTGA 59.895 50.000 0.00 0.00 44.71 2.57
700 836 3.434167 GAGCAGAGGGGCTGATAATTGAA 60.434 47.826 0.00 0.00 44.71 2.69
701 837 4.749166 GAGCAGAGGGGCTGATAATTGAAT 60.749 45.833 0.00 0.00 44.71 2.57
702 838 6.546615 GAGCAGAGGGGCTGATAATTGAATC 61.547 48.000 0.00 0.00 44.71 2.52
704 840 3.077359 GAGGGGCTGATAATTGAATCCG 58.923 50.000 0.00 0.00 0.00 4.18
705 841 2.162681 GGGGCTGATAATTGAATCCGG 58.837 52.381 0.00 0.00 0.00 5.14
706 842 2.162681 GGGCTGATAATTGAATCCGGG 58.837 52.381 0.00 0.00 0.00 5.73
772 973 3.108521 GAATGGATCGATCGGACGG 57.891 57.895 18.81 0.00 0.00 4.79
808 1009 3.586100 TTGATTTCGTCGGATGACTCA 57.414 42.857 0.00 3.78 43.21 3.41
928 2125 8.597167 CAACTCCCCTACATATATTTCAGATCA 58.403 37.037 0.00 0.00 0.00 2.92
975 2181 5.139435 TGAGATTCAGATCAACGACACTT 57.861 39.130 0.00 0.00 34.60 3.16
989 2196 7.129622 TCAACGACACTTAAACAGCAAATTAG 58.870 34.615 0.00 0.00 0.00 1.73
1433 2640 2.781681 ACGTGCTTGGCTAGGTAAAT 57.218 45.000 0.00 0.00 0.00 1.40
1439 2664 4.009675 TGCTTGGCTAGGTAAATCTGTTG 58.990 43.478 0.00 0.00 0.00 3.33
1456 2681 5.188434 TCTGTTGATCAAATCTGGGCTAAG 58.812 41.667 10.35 0.00 0.00 2.18
1809 3043 2.872858 ACGAGTCAAGCAAGAAGAAACC 59.127 45.455 0.00 0.00 0.00 3.27
1860 3096 2.469024 CGAACCGCTCGTTTACGTTAAC 60.469 50.000 7.36 7.36 42.89 2.01
1863 3099 1.791785 CCGCTCGTTTACGTTAACCAA 59.208 47.619 11.49 0.20 40.80 3.67
1889 3125 1.064952 GCGTGCACCTGTTTAGTGTTT 59.935 47.619 12.15 0.00 37.56 2.83
1890 3126 2.715268 CGTGCACCTGTTTAGTGTTTG 58.285 47.619 12.15 0.00 37.56 2.93
1892 3128 3.426963 CGTGCACCTGTTTAGTGTTTGTT 60.427 43.478 12.15 0.00 37.56 2.83
1908 3144 2.542020 TGTTCGACAGCAGGATCAAA 57.458 45.000 0.00 0.00 0.00 2.69
1910 3146 1.129437 GTTCGACAGCAGGATCAAAGC 59.871 52.381 0.00 0.00 0.00 3.51
1911 3147 0.321346 TCGACAGCAGGATCAAAGCA 59.679 50.000 0.00 0.00 0.00 3.91
1912 3148 0.725686 CGACAGCAGGATCAAAGCAG 59.274 55.000 0.00 0.00 0.00 4.24
1913 3149 1.673923 CGACAGCAGGATCAAAGCAGA 60.674 52.381 0.00 0.00 0.00 4.26
1914 3150 2.430465 GACAGCAGGATCAAAGCAGAA 58.570 47.619 0.00 0.00 0.00 3.02
1915 3151 3.015327 GACAGCAGGATCAAAGCAGAAT 58.985 45.455 0.00 0.00 0.00 2.40
1916 3152 3.015327 ACAGCAGGATCAAAGCAGAATC 58.985 45.455 0.00 0.00 0.00 2.52
1917 3153 3.280295 CAGCAGGATCAAAGCAGAATCT 58.720 45.455 0.00 0.00 0.00 2.40
1918 3154 3.695060 CAGCAGGATCAAAGCAGAATCTT 59.305 43.478 0.00 0.00 0.00 2.40
1919 3155 3.946558 AGCAGGATCAAAGCAGAATCTTC 59.053 43.478 0.00 0.00 0.00 2.87
1920 3156 3.946558 GCAGGATCAAAGCAGAATCTTCT 59.053 43.478 0.00 0.00 38.25 2.85
1953 3193 1.407989 GGGCAGAATCTTCAGGTCCTG 60.408 57.143 13.21 13.21 0.00 3.86
1977 3217 1.659098 GCCGATGAACTTGTAAGGACG 59.341 52.381 0.00 0.00 0.00 4.79
1981 3221 3.608506 CGATGAACTTGTAAGGACGACTG 59.391 47.826 0.00 0.00 0.00 3.51
1982 3222 3.380479 TGAACTTGTAAGGACGACTGG 57.620 47.619 0.00 0.00 0.00 4.00
1983 3223 2.036733 TGAACTTGTAAGGACGACTGGG 59.963 50.000 0.00 0.00 0.00 4.45
1984 3224 1.713297 ACTTGTAAGGACGACTGGGT 58.287 50.000 0.00 0.00 0.00 4.51
1986 3226 3.233507 ACTTGTAAGGACGACTGGGTTA 58.766 45.455 0.00 0.00 0.00 2.85
1987 3227 3.836562 ACTTGTAAGGACGACTGGGTTAT 59.163 43.478 0.00 0.00 0.00 1.89
1988 3228 3.880047 TGTAAGGACGACTGGGTTATG 57.120 47.619 0.00 0.00 0.00 1.90
1989 3229 3.167485 TGTAAGGACGACTGGGTTATGT 58.833 45.455 0.00 0.00 0.00 2.29
1990 3230 3.579586 TGTAAGGACGACTGGGTTATGTT 59.420 43.478 0.00 0.00 0.00 2.71
1991 3231 3.329929 AAGGACGACTGGGTTATGTTC 57.670 47.619 0.00 0.00 0.00 3.18
1992 3232 2.537143 AGGACGACTGGGTTATGTTCT 58.463 47.619 0.00 0.00 0.00 3.01
2006 3246 8.164733 TGGGTTATGTTCTTGTTTAGGTTATGA 58.835 33.333 0.00 0.00 0.00 2.15
2030 3509 7.450014 TGATGTTTGGGTTATGTTGACTACATT 59.550 33.333 7.83 0.00 45.19 2.71
2071 3550 8.603898 TTAAGGGTTTGTCTAGATCACATCTA 57.396 34.615 0.00 0.00 40.76 1.98
2104 3583 9.797642 ACATAATTATGAACAGAATATCCTGCA 57.202 29.630 28.13 0.00 36.16 4.41
2148 3640 6.961554 GGCTGAACAGTAAAACAGAATATTCG 59.038 38.462 9.78 7.61 32.90 3.34
2149 3641 6.466097 GCTGAACAGTAAAACAGAATATTCGC 59.534 38.462 9.78 0.00 32.90 4.70
2187 3679 0.679960 GCCCGTGTCAGCCCTTAAAT 60.680 55.000 0.00 0.00 0.00 1.40
2254 5396 5.437191 ACTTTTCCTCGATGGACCTTAAT 57.563 39.130 3.44 0.00 46.14 1.40
2279 5421 0.753848 GCGGTTCTCTCCCTCTAGCT 60.754 60.000 0.00 0.00 0.00 3.32
2328 5470 4.245251 AGTGTTTCCACCACCTTTTACT 57.755 40.909 0.00 0.00 42.88 2.24
2478 5666 6.546972 TTGTTTAATCAGTGCATTCGTACA 57.453 33.333 0.00 0.00 0.00 2.90
2490 5678 9.244799 CAGTGCATTCGTACAGTTAAATCTATA 57.755 33.333 0.00 0.00 0.00 1.31
2522 5710 9.102453 AGGGTTTCCTATCTTCACTAATATACC 57.898 37.037 0.00 0.00 42.75 2.73
2532 5720 7.788026 TCTTCACTAATATACCACGGAATTGT 58.212 34.615 0.00 0.00 0.00 2.71
2534 5722 7.780008 TCACTAATATACCACGGAATTGTTG 57.220 36.000 0.00 0.00 0.00 3.33
2536 5724 6.037720 CACTAATATACCACGGAATTGTTGCA 59.962 38.462 0.00 0.00 0.00 4.08
2537 5725 5.906113 AATATACCACGGAATTGTTGCAA 57.094 34.783 0.00 0.00 0.00 4.08
2538 5726 5.906113 ATATACCACGGAATTGTTGCAAA 57.094 34.783 0.00 0.00 0.00 3.68
2539 5727 2.969628 ACCACGGAATTGTTGCAAAA 57.030 40.000 0.00 0.00 0.00 2.44
2561 5749 3.141409 AAAAACCATGGAAGGGCGT 57.859 47.368 21.47 0.00 45.79 5.68
2593 5781 7.887996 AATGCCACAAATATAAAACACACAG 57.112 32.000 0.00 0.00 0.00 3.66
2609 5797 5.686753 ACACACAGGTAATTGGTCTAAACA 58.313 37.500 0.00 0.00 0.00 2.83
2695 5883 3.054139 TCCTCCAGTCCATTGGATTTCTG 60.054 47.826 9.01 11.24 45.80 3.02
2702 5890 4.533311 AGTCCATTGGATTTCTGGCATTTT 59.467 37.500 9.01 0.00 32.73 1.82
2728 5916 6.155475 AGTAATGAGTCTGATTACTCCAGC 57.845 41.667 16.37 0.00 44.40 4.85
2770 5958 8.928733 AGCATGCTTATTTCATGTTGTTAAAAG 58.071 29.630 16.30 0.00 42.34 2.27
2783 5971 4.718858 TGTTAAAAGTTGTCATCCGACG 57.281 40.909 0.00 0.00 45.80 5.12
2785 5973 0.511221 AAAAGTTGTCATCCGACGCG 59.489 50.000 3.53 3.53 45.80 6.01
2831 6019 6.739112 TCAGTGTATAGATGAATCTTCCACG 58.261 40.000 0.00 0.00 38.32 4.94
2856 6044 1.002659 CCGTGACCACATTACCCTTGA 59.997 52.381 0.85 0.00 0.00 3.02
2880 6068 6.267500 GTTTGCATAAACGTGAATTTGTGT 57.733 33.333 0.00 0.00 37.08 3.72
2881 6069 5.879948 TTGCATAAACGTGAATTTGTGTG 57.120 34.783 0.00 0.00 34.26 3.82
2882 6070 3.733224 TGCATAAACGTGAATTTGTGTGC 59.267 39.130 0.00 0.00 34.26 4.57
2884 6072 4.208047 GCATAAACGTGAATTTGTGTGCAA 59.792 37.500 0.00 0.00 34.26 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 7.047891 TGACTAGACTGTTTGATTGACAAGTT 58.952 34.615 0.00 0.00 39.77 2.66
20 21 6.652481 CCACAAGAATGACTAGACTGTTTGAT 59.348 38.462 0.00 0.00 0.00 2.57
41 42 1.475034 GCAGTCTGAACACCTTCCACA 60.475 52.381 3.32 0.00 0.00 4.17
61 62 0.875059 GTTCCTTCGTGAAGCCTTGG 59.125 55.000 4.05 0.00 37.11 3.61
79 87 1.057851 TTCGGAAGTTGTGGGGGAGT 61.058 55.000 0.00 0.00 0.00 3.85
201 212 5.348259 AAAGGTTTCTAAAAGGATGGGGA 57.652 39.130 0.00 0.00 0.00 4.81
286 303 4.699257 GGATGAGAACTCACAAGAGCAAAT 59.301 41.667 6.67 0.00 46.09 2.32
302 319 1.111277 TCTCGCAAATCCGGATGAGA 58.889 50.000 22.09 22.09 0.00 3.27
303 320 1.863454 CTTCTCGCAAATCCGGATGAG 59.137 52.381 19.95 19.31 0.00 2.90
437 454 3.343617 CGTATGTTGGGATGGTTGACTT 58.656 45.455 0.00 0.00 0.00 3.01
454 472 3.184736 GGTTGGATGCAACCCGTAT 57.815 52.632 32.66 0.00 46.62 3.06
504 522 3.833070 CGGGAGGGATAACTAGCTGTAAT 59.167 47.826 0.00 0.00 0.00 1.89
533 551 2.481449 CCTCGATTTTCACGTCCTAGGG 60.481 54.545 9.46 0.00 0.00 3.53
538 556 0.442699 GTGCCTCGATTTTCACGTCC 59.557 55.000 0.00 0.00 0.00 4.79
554 572 3.134127 GTTCATGCCCGAGGGTGC 61.134 66.667 10.26 0.00 37.65 5.01
678 814 2.105477 TCAATTATCAGCCCCTCTGCTC 59.895 50.000 0.00 0.00 40.32 4.26
694 830 0.179045 CTCTCGCCCCGGATTCAATT 60.179 55.000 0.73 0.00 0.00 2.32
695 831 1.048724 TCTCTCGCCCCGGATTCAAT 61.049 55.000 0.73 0.00 0.00 2.57
696 832 1.676678 CTCTCTCGCCCCGGATTCAA 61.677 60.000 0.73 0.00 0.00 2.69
697 833 2.043349 TCTCTCGCCCCGGATTCA 60.043 61.111 0.73 0.00 0.00 2.57
698 834 1.392710 TTCTCTCTCGCCCCGGATTC 61.393 60.000 0.73 0.00 0.00 2.52
699 835 1.381327 TTCTCTCTCGCCCCGGATT 60.381 57.895 0.73 0.00 0.00 3.01
700 836 1.830408 CTTCTCTCTCGCCCCGGAT 60.830 63.158 0.73 0.00 0.00 4.18
701 837 2.440430 CTTCTCTCTCGCCCCGGA 60.440 66.667 0.73 0.00 0.00 5.14
702 838 3.532155 CCTTCTCTCTCGCCCCGG 61.532 72.222 0.00 0.00 0.00 5.73
704 840 2.364448 ACCCTTCTCTCTCGCCCC 60.364 66.667 0.00 0.00 0.00 5.80
705 841 1.671901 CTGACCCTTCTCTCTCGCCC 61.672 65.000 0.00 0.00 0.00 6.13
706 842 1.813192 CTGACCCTTCTCTCTCGCC 59.187 63.158 0.00 0.00 0.00 5.54
808 1009 4.803098 AACAGACAAAGGCGACTACTAT 57.197 40.909 0.00 0.00 42.68 2.12
928 2125 4.100373 ACTAAGATCTGGGTGCTTCTCTT 58.900 43.478 0.00 0.00 0.00 2.85
967 2173 5.449304 GCTAATTTGCTGTTTAAGTGTCGT 58.551 37.500 4.53 0.00 0.00 4.34
969 2175 5.858581 CAGGCTAATTTGCTGTTTAAGTGTC 59.141 40.000 11.61 0.00 0.00 3.67
973 2179 7.433425 GCTAATCAGGCTAATTTGCTGTTTAAG 59.567 37.037 9.22 5.04 33.78 1.85
975 2181 6.376864 TGCTAATCAGGCTAATTTGCTGTTTA 59.623 34.615 16.05 11.10 36.33 2.01
989 2196 2.617532 GGGATCTCCATGCTAATCAGGC 60.618 54.545 0.00 0.00 37.91 4.85
1069 2276 3.755628 GAGGCTGCGTACCACGGA 61.756 66.667 0.00 0.00 42.82 4.69
1070 2277 4.814294 GGAGGCTGCGTACCACGG 62.814 72.222 0.00 0.00 42.82 4.94
1338 2545 4.530857 CCGGCGGCCAAGTCTAGG 62.531 72.222 20.71 6.13 0.00 3.02
1397 2604 4.748102 AGCACGTAAAGTTTGAGATTTCGA 59.252 37.500 0.00 0.00 0.00 3.71
1433 2640 3.726557 AGCCCAGATTTGATCAACAGA 57.273 42.857 7.89 0.00 0.00 3.41
1439 2664 4.273318 ACCAACTTAGCCCAGATTTGATC 58.727 43.478 0.00 0.00 0.00 2.92
1456 2681 6.512297 ACACCTGATTAAATCACAAACCAAC 58.488 36.000 0.00 0.00 35.06 3.77
1661 2895 1.004320 CCGTGGACCAACGAATCCA 60.004 57.895 15.29 0.00 46.49 3.41
1809 3043 1.271163 ACACGTATCTTGGTTGGGTGG 60.271 52.381 0.00 0.00 0.00 4.61
1860 3096 4.114997 GGTGCACGCCCGAATTGG 62.115 66.667 11.45 0.00 37.55 3.16
1863 3099 3.842925 AACAGGTGCACGCCCGAAT 62.843 57.895 11.45 0.00 0.00 3.34
1889 3125 2.416747 CTTTGATCCTGCTGTCGAACA 58.583 47.619 0.00 0.00 0.00 3.18
1890 3126 1.129437 GCTTTGATCCTGCTGTCGAAC 59.871 52.381 0.00 0.00 0.00 3.95
1892 3128 0.321346 TGCTTTGATCCTGCTGTCGA 59.679 50.000 0.00 0.00 0.00 4.20
1927 3163 4.998051 ACCTGAAGATTCTGCCCTAAAAA 58.002 39.130 0.00 0.00 0.00 1.94
1928 3164 4.567747 GGACCTGAAGATTCTGCCCTAAAA 60.568 45.833 0.00 0.00 0.00 1.52
1929 3165 3.054361 GGACCTGAAGATTCTGCCCTAAA 60.054 47.826 0.00 0.00 0.00 1.85
1930 3166 2.505819 GGACCTGAAGATTCTGCCCTAA 59.494 50.000 0.00 0.00 0.00 2.69
1931 3167 2.119495 GGACCTGAAGATTCTGCCCTA 58.881 52.381 0.00 0.00 0.00 3.53
1932 3168 0.915364 GGACCTGAAGATTCTGCCCT 59.085 55.000 0.00 0.00 0.00 5.19
1933 3169 0.915364 AGGACCTGAAGATTCTGCCC 59.085 55.000 0.00 0.00 0.00 5.36
1934 3170 1.407989 CCAGGACCTGAAGATTCTGCC 60.408 57.143 23.77 0.00 32.44 4.85
1935 3171 1.280421 ACCAGGACCTGAAGATTCTGC 59.720 52.381 23.77 0.00 32.44 4.26
1936 3172 3.431486 GCTACCAGGACCTGAAGATTCTG 60.431 52.174 23.77 5.83 32.44 3.02
1953 3193 3.118884 TCCTTACAAGTTCATCGGCTACC 60.119 47.826 0.00 0.00 0.00 3.18
1977 3217 6.002082 ACCTAAACAAGAACATAACCCAGTC 58.998 40.000 0.00 0.00 0.00 3.51
1981 3221 8.570068 TCATAACCTAAACAAGAACATAACCC 57.430 34.615 0.00 0.00 0.00 4.11
1986 3226 9.912634 CAAACATCATAACCTAAACAAGAACAT 57.087 29.630 0.00 0.00 0.00 2.71
1987 3227 8.356657 CCAAACATCATAACCTAAACAAGAACA 58.643 33.333 0.00 0.00 0.00 3.18
1988 3228 7.812669 CCCAAACATCATAACCTAAACAAGAAC 59.187 37.037 0.00 0.00 0.00 3.01
1989 3229 7.507616 ACCCAAACATCATAACCTAAACAAGAA 59.492 33.333 0.00 0.00 0.00 2.52
1990 3230 7.007723 ACCCAAACATCATAACCTAAACAAGA 58.992 34.615 0.00 0.00 0.00 3.02
1991 3231 7.227049 ACCCAAACATCATAACCTAAACAAG 57.773 36.000 0.00 0.00 0.00 3.16
1992 3232 7.604657 AACCCAAACATCATAACCTAAACAA 57.395 32.000 0.00 0.00 0.00 2.83
2089 3568 6.660521 TCTGTTTCATTGCAGGATATTCTGTT 59.339 34.615 12.74 0.00 37.12 3.16
2090 3569 6.094603 GTCTGTTTCATTGCAGGATATTCTGT 59.905 38.462 12.74 0.00 37.12 3.41
2091 3570 6.459298 GGTCTGTTTCATTGCAGGATATTCTG 60.459 42.308 6.65 6.65 37.79 3.02
2092 3571 5.591877 GGTCTGTTTCATTGCAGGATATTCT 59.408 40.000 0.00 0.00 33.81 2.40
2093 3572 5.221126 GGGTCTGTTTCATTGCAGGATATTC 60.221 44.000 0.00 0.00 33.81 1.75
2094 3573 4.646492 GGGTCTGTTTCATTGCAGGATATT 59.354 41.667 0.00 0.00 33.81 1.28
2097 3576 2.450476 GGGTCTGTTTCATTGCAGGAT 58.550 47.619 0.00 0.00 33.81 3.24
2098 3577 1.547675 GGGGTCTGTTTCATTGCAGGA 60.548 52.381 0.00 0.00 33.81 3.86
2099 3578 0.890683 GGGGTCTGTTTCATTGCAGG 59.109 55.000 0.00 0.00 33.81 4.85
2100 3579 0.523072 CGGGGTCTGTTTCATTGCAG 59.477 55.000 0.00 0.00 0.00 4.41
2101 3580 1.523154 GCGGGGTCTGTTTCATTGCA 61.523 55.000 0.00 0.00 0.00 4.08
2102 3581 1.212751 GCGGGGTCTGTTTCATTGC 59.787 57.895 0.00 0.00 0.00 3.56
2103 3582 0.958091 TTGCGGGGTCTGTTTCATTG 59.042 50.000 0.00 0.00 0.00 2.82
2104 3583 1.247567 CTTGCGGGGTCTGTTTCATT 58.752 50.000 0.00 0.00 0.00 2.57
2128 3620 6.183360 CCTCGCGAATATTCTGTTTTACTGTT 60.183 38.462 11.33 0.00 0.00 3.16
2131 3623 5.416947 ACCTCGCGAATATTCTGTTTTACT 58.583 37.500 11.33 0.00 0.00 2.24
2133 3625 6.148150 ACAAACCTCGCGAATATTCTGTTTTA 59.852 34.615 11.33 0.00 0.00 1.52
2137 3629 3.596214 ACAAACCTCGCGAATATTCTGT 58.404 40.909 11.33 6.34 0.00 3.41
2148 3640 4.084888 CGGCGGAACAAACCTCGC 62.085 66.667 0.00 0.00 46.35 5.03
2149 3641 4.084888 GCGGCGGAACAAACCTCG 62.085 66.667 9.78 0.00 0.00 4.63
2171 3663 2.004583 TCGATTTAAGGGCTGACACG 57.995 50.000 0.00 0.00 0.00 4.49
2195 3688 8.877864 TGGTTCTTTAGTATTTGGATGATTGT 57.122 30.769 0.00 0.00 0.00 2.71
2209 3702 8.706322 AGTACAATTTCCATTGGTTCTTTAGT 57.294 30.769 1.86 0.00 43.82 2.24
2210 3703 9.981114 AAAGTACAATTTCCATTGGTTCTTTAG 57.019 29.630 1.86 0.00 43.82 1.85
2279 5421 0.322456 GGTGGTGCCAGCATGTAGAA 60.322 55.000 14.75 0.00 43.20 2.10
2344 5486 8.023128 CGAGAAACTTTAACCAATCATCAACAT 58.977 33.333 0.00 0.00 0.00 2.71
2460 5648 7.892778 TTTAACTGTACGAATGCACTGATTA 57.107 32.000 0.00 0.00 0.00 1.75
2546 5734 1.002134 CTGACGCCCTTCCATGGTT 60.002 57.895 12.58 0.00 0.00 3.67
2593 5781 7.708998 TGTCACTTTTGTTTAGACCAATTACC 58.291 34.615 0.00 0.00 0.00 2.85
2702 5890 8.198109 GCTGGAGTAATCAGACTCATTACTAAA 58.802 37.037 11.29 3.21 46.51 1.85
2770 5958 0.364515 GTAACGCGTCGGATGACAAC 59.635 55.000 14.44 0.00 45.80 3.32
2783 5971 5.804979 AGTTTATGCAAATTCCATGTAACGC 59.195 36.000 0.00 0.00 0.00 4.84
2785 5973 8.028938 ACTGAGTTTATGCAAATTCCATGTAAC 58.971 33.333 0.00 6.40 31.24 2.50
2831 6019 1.802365 GGTAATGTGGTCACGGTCAAC 59.198 52.381 0.00 0.00 0.00 3.18
2856 6044 6.019961 CACACAAATTCACGTTTATGCAAACT 60.020 34.615 0.00 0.00 41.62 2.66


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

AutoCloner maintained by Alex Coulton.