Multiple sequence alignment - TraesCS6B01G272200

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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 TraesCS6B01G272200 chr6B 100.000 2384 0 0 1 2384 491605755 491603372 0.000000e+00 4403
1 TraesCS6B01G272200 chr6D 93.014 1460 70 11 117 1549 327600853 327599399 0.000000e+00 2102
2 TraesCS6B01G272200 chr6D 94.421 233 12 1 2040 2271 327598860 327598628 8.100000e-95 357
3 TraesCS6B01G272200 chr6D 93.627 204 12 1 1836 2039 327599109 327598907 1.070000e-78 303
4 TraesCS6B01G272200 chr6D 92.035 113 9 0 2272 2384 327598555 327598443 2.450000e-35 159
5 TraesCS6B01G272200 chr6D 89.565 115 4 1 1614 1728 327599243 327599137 3.200000e-29 139
6 TraesCS6B01G272200 chr6A 91.520 1309 53 16 758 2039 466655415 466654138 0.000000e+00 1749
7 TraesCS6B01G272200 chr6A 89.589 365 18 7 2040 2384 466654052 466653688 1.680000e-121 446
8 TraesCS6B01G272200 chr6A 87.003 377 29 7 2027 2384 466653064 466652689 7.930000e-110 407
9 TraesCS6B01G272200 chr6A 90.698 258 16 2 320 571 466657691 466657436 1.060000e-88 337
10 TraesCS6B01G272200 chr6A 94.366 213 7 1 119 331 466659228 466659021 2.960000e-84 322
11 TraesCS6B01G272200 chr6A 92.417 211 14 2 2040 2250 466630224 466630016 1.390000e-77 300
12 TraesCS6B01G272200 chr6A 92.994 157 6 1 599 755 466657138 466656987 8.580000e-55 224
13 TraesCS6B01G272200 chr6A 95.690 116 5 0 2269 2384 466628144 466628029 1.130000e-43 187
14 TraesCS6B01G272200 chr6A 93.204 103 7 0 2269 2371 466649110 466649008 4.100000e-33 152
15 TraesCS6B01G272200 chr3D 79.211 380 49 22 963 1340 152815776 152816127 1.100000e-58 237
16 TraesCS6B01G272200 chr3A 78.788 363 57 16 980 1340 177710508 177710164 2.380000e-55 226


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 TraesCS6B01G272200 chr6B 491603372 491605755 2383 True 4403.000000 4403 100.000000 1 2384 1 chr6B.!!$R1 2383
1 TraesCS6B01G272200 chr6D 327598443 327600853 2410 True 612.000000 2102 92.532400 117 2384 5 chr6D.!!$R1 2267
2 TraesCS6B01G272200 chr6A 466649008 466659228 10220 True 519.571429 1749 91.339143 119 2384 7 chr6A.!!$R2 2265
3 TraesCS6B01G272200 chr6A 466628029 466630224 2195 True 243.500000 300 94.053500 2040 2384 2 chr6A.!!$R1 344

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
81 82 0.037232 AGAACCCGCTGCTCTAACAC 60.037 55.0 0.0 0.0 0.0 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1974 5332 0.626382 TGTTGTTCCACTGGACCCAA 59.374 50.0 0.0 1.37 0.0 4.12 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
21 22 3.514645 CAGTCCCACAAATTAATGCAGC 58.485 45.455 0.00 0.00 0.00 5.25
22 23 3.056678 CAGTCCCACAAATTAATGCAGCA 60.057 43.478 0.00 0.00 0.00 4.41
23 24 3.194116 AGTCCCACAAATTAATGCAGCAG 59.806 43.478 0.00 0.00 0.00 4.24
24 25 3.193267 GTCCCACAAATTAATGCAGCAGA 59.807 43.478 0.00 0.00 0.00 4.26
25 26 3.831333 TCCCACAAATTAATGCAGCAGAA 59.169 39.130 0.00 0.00 0.00 3.02
26 27 4.282957 TCCCACAAATTAATGCAGCAGAAA 59.717 37.500 0.00 0.00 0.00 2.52
27 28 4.389687 CCCACAAATTAATGCAGCAGAAAC 59.610 41.667 0.00 0.00 0.00 2.78
28 29 4.389687 CCACAAATTAATGCAGCAGAAACC 59.610 41.667 0.00 0.00 0.00 3.27
29 30 4.989797 CACAAATTAATGCAGCAGAAACCA 59.010 37.500 0.00 0.00 0.00 3.67
30 31 5.466058 CACAAATTAATGCAGCAGAAACCAA 59.534 36.000 0.00 0.00 0.00 3.67
31 32 6.018098 CACAAATTAATGCAGCAGAAACCAAA 60.018 34.615 0.00 0.00 0.00 3.28
32 33 6.018016 ACAAATTAATGCAGCAGAAACCAAAC 60.018 34.615 0.00 0.00 0.00 2.93
33 34 4.662468 TTAATGCAGCAGAAACCAAACA 57.338 36.364 0.00 0.00 0.00 2.83
34 35 2.514205 ATGCAGCAGAAACCAAACAC 57.486 45.000 0.00 0.00 0.00 3.32
35 36 1.473258 TGCAGCAGAAACCAAACACT 58.527 45.000 0.00 0.00 0.00 3.55
36 37 1.134753 TGCAGCAGAAACCAAACACTG 59.865 47.619 0.00 0.00 0.00 3.66
42 43 4.739046 CAGAAACCAAACACTGCTCTAG 57.261 45.455 0.00 0.00 0.00 2.43
43 44 3.058639 CAGAAACCAAACACTGCTCTAGC 60.059 47.826 0.00 0.00 42.50 3.42
44 45 1.512926 AACCAAACACTGCTCTAGCG 58.487 50.000 0.00 0.00 45.83 4.26
45 46 0.951040 ACCAAACACTGCTCTAGCGC 60.951 55.000 0.00 0.00 45.83 5.92
46 47 1.639298 CCAAACACTGCTCTAGCGCC 61.639 60.000 2.29 0.00 45.83 6.53
47 48 1.376037 AAACACTGCTCTAGCGCCC 60.376 57.895 2.29 0.00 45.83 6.13
48 49 1.831652 AAACACTGCTCTAGCGCCCT 61.832 55.000 2.29 0.00 45.83 5.19
49 50 2.105930 CACTGCTCTAGCGCCCTC 59.894 66.667 2.29 0.00 45.83 4.30
50 51 2.363018 ACTGCTCTAGCGCCCTCA 60.363 61.111 2.29 0.00 45.83 3.86
51 52 2.105930 CTGCTCTAGCGCCCTCAC 59.894 66.667 2.29 0.00 45.83 3.51
52 53 2.679996 TGCTCTAGCGCCCTCACA 60.680 61.111 2.29 0.00 45.83 3.58
53 54 2.202810 GCTCTAGCGCCCTCACAC 60.203 66.667 2.29 0.00 0.00 3.82
54 55 3.006756 GCTCTAGCGCCCTCACACA 62.007 63.158 2.29 0.00 0.00 3.72
55 56 1.153745 CTCTAGCGCCCTCACACAC 60.154 63.158 2.29 0.00 0.00 3.82
56 57 1.877576 CTCTAGCGCCCTCACACACA 61.878 60.000 2.29 0.00 0.00 3.72
57 58 1.005037 CTAGCGCCCTCACACACAA 60.005 57.895 2.29 0.00 0.00 3.33
58 59 0.602638 CTAGCGCCCTCACACACAAA 60.603 55.000 2.29 0.00 0.00 2.83
59 60 0.179043 TAGCGCCCTCACACACAAAA 60.179 50.000 2.29 0.00 0.00 2.44
60 61 1.034838 AGCGCCCTCACACACAAAAA 61.035 50.000 2.29 0.00 0.00 1.94
76 77 3.421567 AAAAAGAACCCGCTGCTCT 57.578 47.368 0.00 0.00 0.00 4.09
77 78 2.561478 AAAAAGAACCCGCTGCTCTA 57.439 45.000 0.00 0.00 0.00 2.43
78 79 2.561478 AAAAGAACCCGCTGCTCTAA 57.439 45.000 0.00 0.00 0.00 2.10
79 80 1.809684 AAAGAACCCGCTGCTCTAAC 58.190 50.000 0.00 0.00 0.00 2.34
80 81 0.685097 AAGAACCCGCTGCTCTAACA 59.315 50.000 0.00 0.00 0.00 2.41
81 82 0.037232 AGAACCCGCTGCTCTAACAC 60.037 55.000 0.00 0.00 0.00 3.32
82 83 1.003718 AACCCGCTGCTCTAACACC 60.004 57.895 0.00 0.00 0.00 4.16
83 84 1.764571 AACCCGCTGCTCTAACACCA 61.765 55.000 0.00 0.00 0.00 4.17
84 85 1.003839 CCCGCTGCTCTAACACCAA 60.004 57.895 0.00 0.00 0.00 3.67
85 86 1.298859 CCCGCTGCTCTAACACCAAC 61.299 60.000 0.00 0.00 0.00 3.77
86 87 0.602638 CCGCTGCTCTAACACCAACA 60.603 55.000 0.00 0.00 0.00 3.33
87 88 0.512952 CGCTGCTCTAACACCAACAC 59.487 55.000 0.00 0.00 0.00 3.32
88 89 0.512952 GCTGCTCTAACACCAACACG 59.487 55.000 0.00 0.00 0.00 4.49
89 90 1.865865 CTGCTCTAACACCAACACGT 58.134 50.000 0.00 0.00 0.00 4.49
90 91 2.864882 GCTGCTCTAACACCAACACGTA 60.865 50.000 0.00 0.00 0.00 3.57
91 92 2.729882 CTGCTCTAACACCAACACGTAC 59.270 50.000 0.00 0.00 0.00 3.67
92 93 2.363038 TGCTCTAACACCAACACGTACT 59.637 45.455 0.00 0.00 0.00 2.73
93 94 2.729882 GCTCTAACACCAACACGTACTG 59.270 50.000 0.00 0.00 0.00 2.74
94 95 3.797865 GCTCTAACACCAACACGTACTGT 60.798 47.826 0.00 0.00 32.89 3.55
95 96 4.557296 GCTCTAACACCAACACGTACTGTA 60.557 45.833 0.00 0.00 30.51 2.74
96 97 4.858935 TCTAACACCAACACGTACTGTAC 58.141 43.478 7.90 7.90 30.51 2.90
110 111 6.887376 CGTACTGTACGTACCTAACTCTAA 57.113 41.667 27.27 0.00 44.52 2.10
111 112 7.470289 CGTACTGTACGTACCTAACTCTAAT 57.530 40.000 27.27 0.00 44.52 1.73
112 113 7.340699 CGTACTGTACGTACCTAACTCTAATG 58.659 42.308 27.27 1.50 44.52 1.90
113 114 6.690194 ACTGTACGTACCTAACTCTAATGG 57.310 41.667 22.43 0.00 0.00 3.16
114 115 5.067023 ACTGTACGTACCTAACTCTAATGGC 59.933 44.000 22.43 0.00 0.00 4.40
115 116 4.949238 TGTACGTACCTAACTCTAATGGCA 59.051 41.667 22.43 0.00 0.00 4.92
116 117 4.382345 ACGTACCTAACTCTAATGGCAC 57.618 45.455 0.00 0.00 0.00 5.01
117 118 3.131755 ACGTACCTAACTCTAATGGCACC 59.868 47.826 0.00 0.00 0.00 5.01
195 198 1.761784 TGCCAAAATGAACAACCTGCT 59.238 42.857 0.00 0.00 0.00 4.24
198 201 1.788308 CAAAATGAACAACCTGCTGCG 59.212 47.619 0.00 0.00 0.00 5.18
378 1728 2.571653 CCTGCCGATATATTCCTTCCCA 59.428 50.000 0.00 0.00 0.00 4.37
379 1729 3.009033 CCTGCCGATATATTCCTTCCCAA 59.991 47.826 0.00 0.00 0.00 4.12
384 1734 5.125578 GCCGATATATTCCTTCCCAATTTCC 59.874 44.000 0.00 0.00 0.00 3.13
387 1737 7.553044 CCGATATATTCCTTCCCAATTTCCTAC 59.447 40.741 0.00 0.00 0.00 3.18
413 1763 6.986424 TTATCGCGAATAATCTGTACTGTG 57.014 37.500 15.24 0.00 0.00 3.66
508 1858 5.300752 CAACAAGGCCTCACCATATACTAG 58.699 45.833 5.23 0.00 43.14 2.57
548 1898 5.523552 TCAGAATAACATTACTGGTGCATCG 59.476 40.000 0.00 0.00 0.00 3.84
590 1940 5.975693 TTGTGGGCGAAATATTTTCTCTT 57.024 34.783 1.43 0.00 0.00 2.85
595 1945 5.357032 TGGGCGAAATATTTTCTCTTTCTCC 59.643 40.000 1.43 0.00 34.51 3.71
597 1947 5.357032 GGCGAAATATTTTCTCTTTCTCCCA 59.643 40.000 1.43 0.00 30.91 4.37
637 2257 1.268992 AAACCTGCATGGCATGGCAT 61.269 50.000 27.75 27.75 39.65 4.40
638 2258 1.966901 AACCTGCATGGCATGGCATG 61.967 55.000 42.44 42.44 39.65 4.06
639 2259 2.421314 CTGCATGGCATGGCATGG 59.579 61.111 44.47 32.36 39.65 3.66
789 3983 0.838987 ACCTAAGCCGTCCCTTTCCA 60.839 55.000 0.00 0.00 0.00 3.53
798 3992 3.681593 CCGTCCCTTTCCAATCTTTACA 58.318 45.455 0.00 0.00 0.00 2.41
809 4003 3.813166 CCAATCTTTACACGGACAGTTGT 59.187 43.478 0.00 0.00 0.00 3.32
911 4107 3.711059 CTCCAGCCACTGCCCATCC 62.711 68.421 0.00 0.00 38.69 3.51
1415 4630 0.731855 GCTTCGTGGTGTAGTCGGTC 60.732 60.000 0.00 0.00 0.00 4.79
1440 4655 2.029623 TGTATAGCTTCGGTGGTCTCC 58.970 52.381 0.00 0.00 0.00 3.71
1451 4666 2.026636 CGGTGGTCTCCCTCCATTTTTA 60.027 50.000 0.00 0.00 43.41 1.52
1452 4667 3.353557 GGTGGTCTCCCTCCATTTTTAC 58.646 50.000 0.00 0.00 42.87 2.01
1453 4668 3.010250 GGTGGTCTCCCTCCATTTTTACT 59.990 47.826 0.00 0.00 42.87 2.24
1469 4684 3.764237 TTACTTTGCCTCTTCGTCCTT 57.236 42.857 0.00 0.00 0.00 3.36
1528 4748 3.814268 CAATGGCCCGCGTTCCAG 61.814 66.667 19.07 5.90 35.57 3.86
1533 4753 2.744709 GCCCGCGTTCCAGCTTTA 60.745 61.111 4.92 0.00 34.40 1.85
1549 4769 7.665690 TCCAGCTTTAAAATGTCAGCAATTTA 58.334 30.769 0.00 0.00 34.49 1.40
1606 4961 3.911365 GCTCAAGATCGATCGATGTACAG 59.089 47.826 33.86 25.91 34.60 2.74
1611 4966 6.205658 TCAAGATCGATCGATGTACAGATTCT 59.794 38.462 33.86 19.15 34.60 2.40
1682 5037 2.437343 CGAACCTGCGCGTCTCTTC 61.437 63.158 8.43 3.37 0.00 2.87
1688 5043 2.433318 GCGCGTCTCTTCCTTGCT 60.433 61.111 8.43 0.00 0.00 3.91
1689 5044 2.029844 GCGCGTCTCTTCCTTGCTT 61.030 57.895 8.43 0.00 0.00 3.91
1690 5045 1.569479 GCGCGTCTCTTCCTTGCTTT 61.569 55.000 8.43 0.00 0.00 3.51
1691 5046 0.164647 CGCGTCTCTTCCTTGCTTTG 59.835 55.000 0.00 0.00 0.00 2.77
1692 5047 1.512926 GCGTCTCTTCCTTGCTTTGA 58.487 50.000 0.00 0.00 0.00 2.69
1693 5048 1.873591 GCGTCTCTTCCTTGCTTTGAA 59.126 47.619 0.00 0.00 0.00 2.69
1694 5049 2.290641 GCGTCTCTTCCTTGCTTTGAAA 59.709 45.455 0.00 0.00 0.00 2.69
1695 5050 3.608008 GCGTCTCTTCCTTGCTTTGAAAG 60.608 47.826 0.00 0.00 0.00 2.62
1696 5051 3.561725 CGTCTCTTCCTTGCTTTGAAAGT 59.438 43.478 6.81 0.00 0.00 2.66
1736 5091 4.293648 TAGCCACTGCGTGCGTGT 62.294 61.111 13.03 1.44 44.33 4.49
1740 5095 4.943591 CACTGCGTGCGTGTGTGC 62.944 66.667 8.86 0.00 0.00 4.57
1857 5215 4.813296 AGGCGAAAAGAGTTTACAGTTG 57.187 40.909 0.00 0.00 0.00 3.16
1860 5218 6.228258 AGGCGAAAAGAGTTTACAGTTGATA 58.772 36.000 0.00 0.00 0.00 2.15
1887 5245 1.745115 GGCGCAACAGTGGCAGATA 60.745 57.895 10.83 0.00 38.13 1.98
1917 5275 0.306840 CATGCATGCCAGCGTCTTAG 59.693 55.000 14.93 0.00 37.31 2.18
1941 5299 2.350772 GGATTCGCTTCAGTGTTGGTTG 60.351 50.000 0.00 0.00 0.00 3.77
1946 5304 4.323417 TCGCTTCAGTGTTGGTTGATAAT 58.677 39.130 0.00 0.00 0.00 1.28
1971 5329 5.147330 TGAGATCGAGTGTGGTTAATGTT 57.853 39.130 0.00 0.00 0.00 2.71
1974 5332 3.374220 TCGAGTGTGGTTAATGTTCGT 57.626 42.857 0.00 0.00 0.00 3.85
1975 5333 3.719924 TCGAGTGTGGTTAATGTTCGTT 58.280 40.909 0.00 0.00 0.00 3.85
2022 5380 1.810606 CGATAGTGGCTGCCGGATCT 61.811 60.000 14.98 11.71 0.00 2.75
2028 5386 1.048160 TGGCTGCCGGATCTATGTCA 61.048 55.000 14.98 0.00 0.00 3.58
2117 5560 0.685097 AAGTAGACGGGCACACACAT 59.315 50.000 0.00 0.00 0.00 3.21
2159 5603 5.935789 TGGTGGCTTACAGTGAAAAGTATAC 59.064 40.000 0.00 0.00 0.00 1.47
2319 7696 6.909550 AAAGGTTTGGTGCAATATACTGAA 57.090 33.333 0.00 0.00 0.00 3.02
2323 7700 5.163652 GGTTTGGTGCAATATACTGAAGACC 60.164 44.000 0.00 0.00 0.00 3.85
2337 12407 5.738909 ACTGAAGACCACTGGATAATTCTG 58.261 41.667 0.71 6.81 0.00 3.02
2376 12446 5.398603 TTTACCCCATAGTTGTGCATTTG 57.601 39.130 0.00 0.00 0.00 2.32
2380 12450 3.367292 CCCCATAGTTGTGCATTTGTGAC 60.367 47.826 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.193267 TCTGCTGCATTAATTTGTGGGAC 59.807 43.478 1.31 0.00 0.00 4.46
3 4 3.429492 TCTGCTGCATTAATTTGTGGGA 58.571 40.909 1.31 0.00 0.00 4.37
4 5 3.872511 TCTGCTGCATTAATTTGTGGG 57.127 42.857 1.31 0.00 0.00 4.61
5 6 4.389687 GGTTTCTGCTGCATTAATTTGTGG 59.610 41.667 1.31 0.00 0.00 4.17
6 7 4.989797 TGGTTTCTGCTGCATTAATTTGTG 59.010 37.500 1.31 0.00 0.00 3.33
7 8 5.212532 TGGTTTCTGCTGCATTAATTTGT 57.787 34.783 1.31 0.00 0.00 2.83
8 9 6.018098 TGTTTGGTTTCTGCTGCATTAATTTG 60.018 34.615 1.31 0.00 0.00 2.32
9 10 6.018016 GTGTTTGGTTTCTGCTGCATTAATTT 60.018 34.615 1.31 0.00 0.00 1.82
10 11 5.466393 GTGTTTGGTTTCTGCTGCATTAATT 59.534 36.000 1.31 0.00 0.00 1.40
11 12 4.990426 GTGTTTGGTTTCTGCTGCATTAAT 59.010 37.500 1.31 0.00 0.00 1.40
12 13 4.099266 AGTGTTTGGTTTCTGCTGCATTAA 59.901 37.500 1.31 0.00 0.00 1.40
13 14 3.636300 AGTGTTTGGTTTCTGCTGCATTA 59.364 39.130 1.31 0.00 0.00 1.90
14 15 2.431782 AGTGTTTGGTTTCTGCTGCATT 59.568 40.909 1.31 0.00 0.00 3.56
15 16 2.034124 AGTGTTTGGTTTCTGCTGCAT 58.966 42.857 1.31 0.00 0.00 3.96
16 17 1.134753 CAGTGTTTGGTTTCTGCTGCA 59.865 47.619 0.88 0.88 0.00 4.41
17 18 1.843992 CAGTGTTTGGTTTCTGCTGC 58.156 50.000 0.00 0.00 0.00 5.25
18 19 1.843992 GCAGTGTTTGGTTTCTGCTG 58.156 50.000 8.46 0.00 46.35 4.41
21 22 3.058639 GCTAGAGCAGTGTTTGGTTTCTG 60.059 47.826 0.00 0.00 41.59 3.02
22 23 3.142174 GCTAGAGCAGTGTTTGGTTTCT 58.858 45.455 0.00 0.00 41.59 2.52
23 24 2.096218 CGCTAGAGCAGTGTTTGGTTTC 60.096 50.000 1.89 0.00 42.21 2.78
24 25 1.873591 CGCTAGAGCAGTGTTTGGTTT 59.126 47.619 1.89 0.00 42.21 3.27
25 26 1.512926 CGCTAGAGCAGTGTTTGGTT 58.487 50.000 1.89 0.00 42.21 3.67
26 27 0.951040 GCGCTAGAGCAGTGTTTGGT 60.951 55.000 14.09 0.00 42.21 3.67
27 28 1.639298 GGCGCTAGAGCAGTGTTTGG 61.639 60.000 20.45 0.00 42.21 3.28
28 29 1.639298 GGGCGCTAGAGCAGTGTTTG 61.639 60.000 20.45 0.00 42.21 2.93
29 30 1.376037 GGGCGCTAGAGCAGTGTTT 60.376 57.895 20.45 0.00 42.21 2.83
30 31 2.232298 GAGGGCGCTAGAGCAGTGTT 62.232 60.000 20.45 0.22 42.21 3.32
31 32 2.681778 AGGGCGCTAGAGCAGTGT 60.682 61.111 20.45 0.00 42.21 3.55
32 33 2.105930 GAGGGCGCTAGAGCAGTG 59.894 66.667 20.45 0.00 42.21 3.66
33 34 2.363018 TGAGGGCGCTAGAGCAGT 60.363 61.111 20.45 6.14 42.21 4.40
34 35 2.105930 GTGAGGGCGCTAGAGCAG 59.894 66.667 20.45 0.00 42.21 4.24
35 36 2.679996 TGTGAGGGCGCTAGAGCA 60.680 61.111 20.45 0.00 42.21 4.26
36 37 2.202810 GTGTGAGGGCGCTAGAGC 60.203 66.667 10.35 10.35 37.78 4.09
37 38 1.153745 GTGTGTGAGGGCGCTAGAG 60.154 63.158 7.64 0.00 0.00 2.43
38 39 1.468506 TTGTGTGTGAGGGCGCTAGA 61.469 55.000 7.64 0.00 0.00 2.43
39 40 0.602638 TTTGTGTGTGAGGGCGCTAG 60.603 55.000 7.64 0.00 0.00 3.42
40 41 0.179043 TTTTGTGTGTGAGGGCGCTA 60.179 50.000 7.64 0.00 0.00 4.26
41 42 1.034838 TTTTTGTGTGTGAGGGCGCT 61.035 50.000 7.64 1.38 0.00 5.92
42 43 1.435515 TTTTTGTGTGTGAGGGCGC 59.564 52.632 0.00 0.00 0.00 6.53
58 59 2.552743 GTTAGAGCAGCGGGTTCTTTTT 59.447 45.455 3.42 0.00 38.18 1.94
59 60 2.152016 GTTAGAGCAGCGGGTTCTTTT 58.848 47.619 3.42 0.00 38.18 2.27
60 61 1.071699 TGTTAGAGCAGCGGGTTCTTT 59.928 47.619 3.42 0.00 38.18 2.52
61 62 0.685097 TGTTAGAGCAGCGGGTTCTT 59.315 50.000 3.42 0.00 38.18 2.52
62 63 0.037232 GTGTTAGAGCAGCGGGTTCT 60.037 55.000 3.59 3.59 40.50 3.01
63 64 1.019805 GGTGTTAGAGCAGCGGGTTC 61.020 60.000 0.00 0.00 0.00 3.62
64 65 1.003718 GGTGTTAGAGCAGCGGGTT 60.004 57.895 0.00 0.00 0.00 4.11
65 66 1.764571 TTGGTGTTAGAGCAGCGGGT 61.765 55.000 0.00 0.00 39.49 5.28
66 67 1.003839 TTGGTGTTAGAGCAGCGGG 60.004 57.895 0.00 0.00 39.49 6.13
67 68 0.602638 TGTTGGTGTTAGAGCAGCGG 60.603 55.000 0.00 0.00 39.49 5.52
68 69 0.512952 GTGTTGGTGTTAGAGCAGCG 59.487 55.000 0.00 0.00 39.49 5.18
69 70 0.512952 CGTGTTGGTGTTAGAGCAGC 59.487 55.000 0.00 0.00 37.38 5.25
70 71 1.865865 ACGTGTTGGTGTTAGAGCAG 58.134 50.000 0.00 0.00 32.41 4.24
71 72 2.363038 AGTACGTGTTGGTGTTAGAGCA 59.637 45.455 0.00 0.00 0.00 4.26
72 73 2.729882 CAGTACGTGTTGGTGTTAGAGC 59.270 50.000 0.00 0.00 0.00 4.09
73 74 3.973657 ACAGTACGTGTTGGTGTTAGAG 58.026 45.455 0.00 0.00 34.94 2.43
74 75 4.554526 CGTACAGTACGTGTTGGTGTTAGA 60.555 45.833 22.70 0.00 46.41 2.10
75 76 3.665409 CGTACAGTACGTGTTGGTGTTAG 59.335 47.826 22.70 0.00 46.41 2.34
76 77 3.626977 CGTACAGTACGTGTTGGTGTTA 58.373 45.455 22.70 0.00 46.41 2.41
77 78 2.462889 CGTACAGTACGTGTTGGTGTT 58.537 47.619 22.70 0.00 46.41 3.32
78 79 2.124011 CGTACAGTACGTGTTGGTGT 57.876 50.000 22.70 0.00 46.41 4.16
89 90 6.260936 GCCATTAGAGTTAGGTACGTACAGTA 59.739 42.308 26.02 14.32 0.00 2.74
90 91 5.067023 GCCATTAGAGTTAGGTACGTACAGT 59.933 44.000 26.02 15.30 0.00 3.55
91 92 5.066893 TGCCATTAGAGTTAGGTACGTACAG 59.933 44.000 26.02 2.32 0.00 2.74
92 93 4.949238 TGCCATTAGAGTTAGGTACGTACA 59.051 41.667 26.02 4.80 0.00 2.90
93 94 5.277047 GTGCCATTAGAGTTAGGTACGTAC 58.723 45.833 17.56 17.56 0.00 3.67
94 95 4.339247 GGTGCCATTAGAGTTAGGTACGTA 59.661 45.833 0.00 0.00 37.59 3.57
95 96 3.131755 GGTGCCATTAGAGTTAGGTACGT 59.868 47.826 0.00 0.00 37.59 3.57
96 97 3.383825 AGGTGCCATTAGAGTTAGGTACG 59.616 47.826 0.00 0.00 37.59 3.67
97 98 4.443034 CCAGGTGCCATTAGAGTTAGGTAC 60.443 50.000 0.00 0.00 36.22 3.34
98 99 3.709653 CCAGGTGCCATTAGAGTTAGGTA 59.290 47.826 0.00 0.00 0.00 3.08
99 100 2.505819 CCAGGTGCCATTAGAGTTAGGT 59.494 50.000 0.00 0.00 0.00 3.08
100 101 2.505819 ACCAGGTGCCATTAGAGTTAGG 59.494 50.000 0.00 0.00 0.00 2.69
101 102 3.432326 GGACCAGGTGCCATTAGAGTTAG 60.432 52.174 0.00 0.00 0.00 2.34
102 103 2.504175 GGACCAGGTGCCATTAGAGTTA 59.496 50.000 0.00 0.00 0.00 2.24
103 104 1.282157 GGACCAGGTGCCATTAGAGTT 59.718 52.381 0.00 0.00 0.00 3.01
104 105 0.912486 GGACCAGGTGCCATTAGAGT 59.088 55.000 0.00 0.00 0.00 3.24
105 106 0.911769 TGGACCAGGTGCCATTAGAG 59.088 55.000 8.93 0.00 0.00 2.43
106 107 0.618458 GTGGACCAGGTGCCATTAGA 59.382 55.000 8.93 0.00 36.41 2.10
107 108 0.394352 GGTGGACCAGGTGCCATTAG 60.394 60.000 8.93 0.00 36.41 1.73
108 109 1.688811 GGTGGACCAGGTGCCATTA 59.311 57.895 8.93 0.00 36.41 1.90
109 110 2.440599 GGTGGACCAGGTGCCATT 59.559 61.111 8.93 0.00 36.41 3.16
110 111 3.661648 GGGTGGACCAGGTGCCAT 61.662 66.667 8.93 0.00 39.85 4.40
145 146 3.002791 CCACCGTCACATATGATATGCC 58.997 50.000 10.38 0.64 37.14 4.40
146 147 3.925379 TCCACCGTCACATATGATATGC 58.075 45.455 10.38 0.00 37.14 3.14
150 151 2.034685 CGTCTCCACCGTCACATATGAT 59.965 50.000 10.38 0.00 37.14 2.45
151 152 1.404035 CGTCTCCACCGTCACATATGA 59.596 52.381 10.38 0.00 0.00 2.15
260 263 1.539388 TGGTTGCGATGAATTGTCACC 59.461 47.619 0.00 0.00 36.31 4.02
387 1737 8.789743 CACAGTACAGATTATTCGCGATAATAG 58.210 37.037 10.88 13.45 40.26 1.73
394 1744 2.097877 CGCACAGTACAGATTATTCGCG 60.098 50.000 0.00 0.00 0.00 5.87
413 1763 1.291877 ATGAAGGACGCAACAGACGC 61.292 55.000 0.00 0.00 0.00 5.19
523 1873 6.037062 CGATGCACCAGTAATGTTATTCTGAA 59.963 38.462 0.00 0.00 0.00 3.02
529 1879 5.914033 AGTACGATGCACCAGTAATGTTAT 58.086 37.500 0.00 0.00 0.00 1.89
530 1880 5.333299 AGTACGATGCACCAGTAATGTTA 57.667 39.130 0.00 0.00 0.00 2.41
535 1885 5.648178 TTCTAAGTACGATGCACCAGTAA 57.352 39.130 0.00 0.00 0.00 2.24
548 1898 7.915397 CCCACAATGCATACATTTTCTAAGTAC 59.085 37.037 0.00 0.00 44.21 2.73
590 1940 4.019174 GGATTTCATCAGCTTTGGGAGAA 58.981 43.478 0.00 0.00 0.00 2.87
595 1945 4.643334 TGATCTGGATTTCATCAGCTTTGG 59.357 41.667 0.00 0.00 0.00 3.28
597 1947 6.350780 GGTTTGATCTGGATTTCATCAGCTTT 60.351 38.462 0.00 0.00 0.00 3.51
638 2258 4.537433 CTAGTGCCGCTCCCTGCC 62.537 72.222 0.00 0.00 38.78 4.85
639 2259 3.775654 ACTAGTGCCGCTCCCTGC 61.776 66.667 0.00 0.00 38.57 4.85
640 2260 2.185350 CACTAGTGCCGCTCCCTG 59.815 66.667 10.54 0.00 0.00 4.45
763 3957 0.179054 GGACGGCTTAGGTGGAATCC 60.179 60.000 0.00 0.00 0.00 3.01
789 3983 4.957296 AGACAACTGTCCGTGTAAAGATT 58.043 39.130 6.23 0.00 45.85 2.40
798 3992 2.094494 CAGCTCATAGACAACTGTCCGT 60.094 50.000 6.23 0.00 45.85 4.69
828 4022 9.401058 GGTTTTATATCATATGCAGAGGCTTAT 57.599 33.333 0.00 0.00 40.01 1.73
911 4107 3.520290 TGGACTTATGGTAACTGCTCG 57.480 47.619 0.00 0.00 37.61 5.03
918 4114 6.778834 TCTCGTGTTATGGACTTATGGTAA 57.221 37.500 0.00 0.00 0.00 2.85
1415 4630 2.138320 CCACCGAAGCTATACATGCAG 58.862 52.381 0.00 0.00 0.00 4.41
1440 4655 5.619981 CGAAGAGGCAAAGTAAAAATGGAGG 60.620 44.000 0.00 0.00 0.00 4.30
1451 4666 3.764237 TTAAGGACGAAGAGGCAAAGT 57.236 42.857 0.00 0.00 0.00 2.66
1452 4667 4.095036 GGAATTAAGGACGAAGAGGCAAAG 59.905 45.833 0.00 0.00 0.00 2.77
1453 4668 4.007659 GGAATTAAGGACGAAGAGGCAAA 58.992 43.478 0.00 0.00 0.00 3.68
1469 4684 1.153449 CGCTGCGACCCAGGAATTA 60.153 57.895 18.66 0.00 42.03 1.40
1518 4733 2.250188 CATTTTAAAGCTGGAACGCGG 58.750 47.619 12.47 0.00 33.54 6.46
1525 4740 6.790285 AAATTGCTGACATTTTAAAGCTGG 57.210 33.333 0.00 0.00 36.60 4.85
1549 4769 7.037438 CGAATTGGATCCAAAATGTCAGATTT 58.963 34.615 30.28 15.78 39.55 2.17
1611 4966 7.555965 TCATTCTCTTTATTGATTCGTCCAGA 58.444 34.615 0.00 0.00 0.00 3.86
1674 5029 3.561725 ACTTTCAAAGCAAGGAAGAGACG 59.438 43.478 0.00 0.00 0.00 4.18
1682 5037 6.536224 ACAAGATTCAAACTTTCAAAGCAAGG 59.464 34.615 0.00 0.00 0.00 3.61
1688 5043 6.042143 GCTGGACAAGATTCAAACTTTCAAA 58.958 36.000 0.00 0.00 0.00 2.69
1689 5044 5.591099 GCTGGACAAGATTCAAACTTTCAA 58.409 37.500 0.00 0.00 0.00 2.69
1690 5045 4.261155 CGCTGGACAAGATTCAAACTTTCA 60.261 41.667 0.00 0.00 0.00 2.69
1691 5046 4.222114 CGCTGGACAAGATTCAAACTTTC 58.778 43.478 0.00 0.00 0.00 2.62
1692 5047 3.550842 GCGCTGGACAAGATTCAAACTTT 60.551 43.478 0.00 0.00 0.00 2.66
1693 5048 2.030805 GCGCTGGACAAGATTCAAACTT 60.031 45.455 0.00 0.00 0.00 2.66
1694 5049 1.537202 GCGCTGGACAAGATTCAAACT 59.463 47.619 0.00 0.00 0.00 2.66
1695 5050 1.401539 GGCGCTGGACAAGATTCAAAC 60.402 52.381 7.64 0.00 0.00 2.93
1696 5051 0.881118 GGCGCTGGACAAGATTCAAA 59.119 50.000 7.64 0.00 0.00 2.69
1755 5110 1.303155 GCAAAGAGCTCCACCTGCT 60.303 57.895 10.93 0.00 44.24 4.24
1825 5180 7.642082 AACTCTTTTCGCCTAGTAGATCTTA 57.358 36.000 0.00 0.00 0.00 2.10
1887 5245 1.645034 GCATGCATGTGACGAGTACT 58.355 50.000 26.79 0.00 0.00 2.73
1917 5275 1.126846 CAACACTGAAGCGAATCCGAC 59.873 52.381 0.00 0.00 38.22 4.79
1941 5299 5.777802 ACCACACTCGATCTCATCATTATC 58.222 41.667 0.00 0.00 0.00 1.75
1946 5304 5.105351 ACATTAACCACACTCGATCTCATCA 60.105 40.000 0.00 0.00 0.00 3.07
1971 5329 1.338890 TGTTCCACTGGACCCAACGA 61.339 55.000 0.00 0.00 0.00 3.85
1974 5332 0.626382 TGTTGTTCCACTGGACCCAA 59.374 50.000 0.00 1.37 0.00 4.12
1975 5333 0.850100 ATGTTGTTCCACTGGACCCA 59.150 50.000 0.00 0.00 0.00 4.51
2022 5380 2.368548 AGGTGCCTATGCGAATGACATA 59.631 45.455 0.00 0.00 41.78 2.29
2028 5386 2.128771 ACAAAGGTGCCTATGCGAAT 57.871 45.000 0.00 0.00 41.78 3.34
2117 5560 3.248125 CACCACTTTACGTTCGGCTTTTA 59.752 43.478 0.00 0.00 0.00 1.52
2159 5603 4.320690 CACTTGAAACCAAATTATCACGCG 59.679 41.667 3.53 3.53 0.00 6.01
2308 7685 9.784531 AATTATCCAGTGGTCTTCAGTATATTG 57.215 33.333 9.54 0.00 0.00 1.90
2319 7696 4.780021 ACTCACAGAATTATCCAGTGGTCT 59.220 41.667 9.54 0.72 34.55 3.85
2323 7700 7.201679 GGAATTCACTCACAGAATTATCCAGTG 60.202 40.741 7.93 0.00 43.60 3.66


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

AutoCloner maintained by Alex Coulton.