Multiple sequence alignment - TraesCS6D01G059900

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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 TraesCS6D01G059900 chr6D 100.000 2357 0 0 1 2357 28035668 28033312 0.000000e+00 4353
1 TraesCS6D01G059900 chr6D 94.726 474 24 1 155 627 435992569 435992096 0.000000e+00 736
2 TraesCS6D01G059900 chr6D 96.620 355 12 0 2002 2356 435992066 435991712 7.260000e-165 590
3 TraesCS6D01G059900 chr6D 93.388 121 4 1 2037 2153 9156178 9156298 2.410000e-40 176
4 TraesCS6D01G059900 chr2D 96.649 1343 43 2 627 1967 73126872 73125530 0.000000e+00 2230
5 TraesCS6D01G059900 chr2D 95.926 1350 49 6 624 1970 621748800 621750146 0.000000e+00 2183
6 TraesCS6D01G059900 chr2D 96.901 355 11 0 2002 2356 113496227 113495873 1.560000e-166 595
7 TraesCS6D01G059900 chr1D 96.511 1347 43 4 627 1970 60171816 60170471 0.000000e+00 2224
8 TraesCS6D01G059900 chr1D 95.697 1348 52 6 627 1970 247505758 247504413 0.000000e+00 2163
9 TraesCS6D01G059900 chr1D 95.818 1339 49 7 626 1962 205134698 205133365 0.000000e+00 2156
10 TraesCS6D01G059900 chr3D 95.991 1347 51 3 623 1966 584701397 584700051 0.000000e+00 2185
11 TraesCS6D01G059900 chr7D 95.979 1343 50 4 623 1963 497560903 497562243 0.000000e+00 2178
12 TraesCS6D01G059900 chr7D 95.775 1349 54 3 627 1972 50081832 50080484 0.000000e+00 2172
13 TraesCS6D01G059900 chr7D 85.684 475 49 10 155 627 375971251 375970794 1.270000e-132 483
14 TraesCS6D01G059900 chr5D 95.899 1341 52 3 626 1964 275171749 275170410 0.000000e+00 2169
15 TraesCS6D01G059900 chr4D 95.570 474 20 1 155 627 36620511 36620038 0.000000e+00 758
16 TraesCS6D01G059900 chr4D 95.359 474 21 1 155 627 416829170 416828697 0.000000e+00 752
17 TraesCS6D01G059900 chr4D 96.620 355 12 0 2002 2356 36620008 36619654 7.260000e-165 590
18 TraesCS6D01G059900 chr4D 96.848 349 10 1 2008 2356 416828661 416828314 1.210000e-162 582
19 TraesCS6D01G059900 chr7A 95.148 474 20 2 155 627 612424512 612424041 0.000000e+00 745
20 TraesCS6D01G059900 chr7A 97.183 355 10 0 2002 2356 612424011 612423657 3.350000e-168 601
21 TraesCS6D01G059900 chr7A 87.282 401 47 4 155 553 422476917 422476519 2.760000e-124 455
22 TraesCS6D01G059900 chr7B 94.515 474 18 2 155 627 665305087 665304621 0.000000e+00 725
23 TraesCS6D01G059900 chr7B 97.746 355 8 0 2002 2356 665304591 665304237 1.550000e-171 612
24 TraesCS6D01G059900 chr7B 88.529 401 42 4 155 553 370264861 370264463 1.270000e-132 483
25 TraesCS6D01G059900 chr4B 94.816 463 23 1 166 627 399068605 399069067 0.000000e+00 721
26 TraesCS6D01G059900 chr4B 95.493 355 14 2 2002 2356 399069097 399069449 1.220000e-157 566
27 TraesCS6D01G059900 chr6B 94.872 117 6 0 2037 2153 16984056 16984172 1.440000e-42 183


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 TraesCS6D01G059900 chr6D 28033312 28035668 2356 True 4353.0 4353 100.0000 1 2357 1 chr6D.!!$R1 2356
1 TraesCS6D01G059900 chr6D 435991712 435992569 857 True 663.0 736 95.6730 155 2356 2 chr6D.!!$R2 2201
2 TraesCS6D01G059900 chr2D 73125530 73126872 1342 True 2230.0 2230 96.6490 627 1967 1 chr2D.!!$R1 1340
3 TraesCS6D01G059900 chr2D 621748800 621750146 1346 False 2183.0 2183 95.9260 624 1970 1 chr2D.!!$F1 1346
4 TraesCS6D01G059900 chr1D 60170471 60171816 1345 True 2224.0 2224 96.5110 627 1970 1 chr1D.!!$R1 1343
5 TraesCS6D01G059900 chr1D 247504413 247505758 1345 True 2163.0 2163 95.6970 627 1970 1 chr1D.!!$R3 1343
6 TraesCS6D01G059900 chr1D 205133365 205134698 1333 True 2156.0 2156 95.8180 626 1962 1 chr1D.!!$R2 1336
7 TraesCS6D01G059900 chr3D 584700051 584701397 1346 True 2185.0 2185 95.9910 623 1966 1 chr3D.!!$R1 1343
8 TraesCS6D01G059900 chr7D 497560903 497562243 1340 False 2178.0 2178 95.9790 623 1963 1 chr7D.!!$F1 1340
9 TraesCS6D01G059900 chr7D 50080484 50081832 1348 True 2172.0 2172 95.7750 627 1972 1 chr7D.!!$R1 1345
10 TraesCS6D01G059900 chr5D 275170410 275171749 1339 True 2169.0 2169 95.8990 626 1964 1 chr5D.!!$R1 1338
11 TraesCS6D01G059900 chr4D 36619654 36620511 857 True 674.0 758 96.0950 155 2356 2 chr4D.!!$R1 2201
12 TraesCS6D01G059900 chr4D 416828314 416829170 856 True 667.0 752 96.1035 155 2356 2 chr4D.!!$R2 2201
13 TraesCS6D01G059900 chr7A 612423657 612424512 855 True 673.0 745 96.1655 155 2356 2 chr7A.!!$R2 2201
14 TraesCS6D01G059900 chr7B 665304237 665305087 850 True 668.5 725 96.1305 155 2356 2 chr7B.!!$R2 2201
15 TraesCS6D01G059900 chr4B 399068605 399069449 844 False 643.5 721 95.1545 166 2356 2 chr4B.!!$F1 2190

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
688 690 0.031585 GACGATGCATACGGCCACTA 59.968 55.0 18.34 0.0 43.89 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1973 1985 1.549203 AACATTCACATGGGTCAGCC 58.451 50.0 0.0 0.0 34.27 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
24 25 4.854361 CACTGATGAGTAATGAGTGCAC 57.146 45.455 9.40 9.40 42.48 4.57
25 26 4.502016 CACTGATGAGTAATGAGTGCACT 58.498 43.478 21.88 21.88 42.48 4.40
26 27 4.565962 CACTGATGAGTAATGAGTGCACTC 59.434 45.833 35.04 35.04 42.48 3.51
27 28 4.465660 ACTGATGAGTAATGAGTGCACTCT 59.534 41.667 38.81 26.30 43.25 3.24
28 29 5.654209 ACTGATGAGTAATGAGTGCACTCTA 59.346 40.000 38.81 27.86 43.25 2.43
29 30 5.895928 TGATGAGTAATGAGTGCACTCTAC 58.104 41.667 38.81 32.39 43.25 2.59
30 31 5.418840 TGATGAGTAATGAGTGCACTCTACA 59.581 40.000 38.81 28.13 43.25 2.74
31 32 5.722021 TGAGTAATGAGTGCACTCTACAA 57.278 39.130 38.81 24.27 43.25 2.41
32 33 5.714047 TGAGTAATGAGTGCACTCTACAAG 58.286 41.667 38.81 0.00 43.25 3.16
33 34 5.078411 AGTAATGAGTGCACTCTACAAGG 57.922 43.478 38.81 0.00 43.25 3.61
34 35 4.528596 AGTAATGAGTGCACTCTACAAGGT 59.471 41.667 38.81 19.44 43.25 3.50
35 36 4.357918 AATGAGTGCACTCTACAAGGTT 57.642 40.909 38.81 21.71 43.25 3.50
36 37 5.483685 AATGAGTGCACTCTACAAGGTTA 57.516 39.130 38.81 21.25 43.25 2.85
37 38 4.521130 TGAGTGCACTCTACAAGGTTAG 57.479 45.455 38.81 0.00 43.25 2.34
38 39 3.254892 GAGTGCACTCTACAAGGTTAGC 58.745 50.000 34.54 8.49 39.81 3.09
39 40 2.028020 AGTGCACTCTACAAGGTTAGCC 60.028 50.000 15.25 0.00 0.00 3.93
40 41 1.278127 TGCACTCTACAAGGTTAGCCC 59.722 52.381 0.00 0.00 34.57 5.19
42 43 2.764572 GCACTCTACAAGGTTAGCCCTA 59.235 50.000 0.00 0.00 45.47 3.53
43 44 3.430513 GCACTCTACAAGGTTAGCCCTAC 60.431 52.174 0.00 0.00 45.47 3.18
44 45 4.024670 CACTCTACAAGGTTAGCCCTACT 58.975 47.826 0.00 0.00 45.47 2.57
45 46 4.024670 ACTCTACAAGGTTAGCCCTACTG 58.975 47.826 0.00 0.00 45.47 2.74
46 47 2.764572 TCTACAAGGTTAGCCCTACTGC 59.235 50.000 0.00 0.00 45.47 4.40
47 48 0.618981 ACAAGGTTAGCCCTACTGCC 59.381 55.000 0.00 0.00 45.47 4.85
48 49 0.618458 CAAGGTTAGCCCTACTGCCA 59.382 55.000 0.00 0.00 45.47 4.92
49 50 1.212935 CAAGGTTAGCCCTACTGCCAT 59.787 52.381 0.00 0.00 45.47 4.40
50 51 1.596496 AGGTTAGCCCTACTGCCATT 58.404 50.000 0.00 0.00 43.87 3.16
51 52 1.212935 AGGTTAGCCCTACTGCCATTG 59.787 52.381 0.00 0.00 43.87 2.82
52 53 1.680338 GTTAGCCCTACTGCCATTGG 58.320 55.000 0.00 0.00 0.00 3.16
53 54 1.064685 GTTAGCCCTACTGCCATTGGT 60.065 52.381 4.26 0.00 0.00 3.67
54 55 2.171870 GTTAGCCCTACTGCCATTGGTA 59.828 50.000 4.26 0.00 0.00 3.25
55 56 0.546598 AGCCCTACTGCCATTGGTAC 59.453 55.000 4.26 0.00 0.00 3.34
56 57 0.546598 GCCCTACTGCCATTGGTACT 59.453 55.000 4.26 0.00 0.00 2.73
57 58 1.747206 GCCCTACTGCCATTGGTACTG 60.747 57.143 4.26 0.00 0.00 2.74
58 59 1.837439 CCCTACTGCCATTGGTACTGA 59.163 52.381 4.26 0.00 0.00 3.41
59 60 2.238646 CCCTACTGCCATTGGTACTGAA 59.761 50.000 4.26 0.00 0.00 3.02
60 61 3.270877 CCTACTGCCATTGGTACTGAAC 58.729 50.000 4.26 0.00 0.00 3.18
61 62 3.055094 CCTACTGCCATTGGTACTGAACT 60.055 47.826 4.26 0.00 0.00 3.01
62 63 4.161565 CCTACTGCCATTGGTACTGAACTA 59.838 45.833 4.26 0.00 0.00 2.24
63 64 3.939066 ACTGCCATTGGTACTGAACTAC 58.061 45.455 4.26 0.00 0.00 2.73
64 65 3.583086 ACTGCCATTGGTACTGAACTACT 59.417 43.478 4.26 0.00 0.00 2.57
65 66 3.935203 CTGCCATTGGTACTGAACTACTG 59.065 47.826 4.26 0.00 0.00 2.74
66 67 3.580895 TGCCATTGGTACTGAACTACTGA 59.419 43.478 4.26 0.00 0.00 3.41
67 68 3.933332 GCCATTGGTACTGAACTACTGAC 59.067 47.826 4.26 0.00 0.00 3.51
68 69 4.562757 GCCATTGGTACTGAACTACTGACA 60.563 45.833 4.26 0.00 0.00 3.58
69 70 5.547465 CCATTGGTACTGAACTACTGACAA 58.453 41.667 0.00 0.00 0.00 3.18
70 71 6.173339 CCATTGGTACTGAACTACTGACAAT 58.827 40.000 0.00 0.00 0.00 2.71
71 72 6.655003 CCATTGGTACTGAACTACTGACAATT 59.345 38.462 0.00 0.00 0.00 2.32
72 73 7.822334 CCATTGGTACTGAACTACTGACAATTA 59.178 37.037 0.00 0.00 0.00 1.40
73 74 9.383519 CATTGGTACTGAACTACTGACAATTAT 57.616 33.333 0.00 0.00 0.00 1.28
74 75 8.997621 TTGGTACTGAACTACTGACAATTATC 57.002 34.615 0.00 0.00 0.00 1.75
75 76 8.362464 TGGTACTGAACTACTGACAATTATCT 57.638 34.615 0.00 0.00 0.00 1.98
76 77 8.812972 TGGTACTGAACTACTGACAATTATCTT 58.187 33.333 0.00 0.00 0.00 2.40
77 78 9.654663 GGTACTGAACTACTGACAATTATCTTT 57.345 33.333 0.00 0.00 0.00 2.52
80 81 9.372369 ACTGAACTACTGACAATTATCTTTAGC 57.628 33.333 0.00 0.00 0.00 3.09
81 82 9.593134 CTGAACTACTGACAATTATCTTTAGCT 57.407 33.333 0.00 0.00 0.00 3.32
108 109 7.776618 TTCTCTTTTATCTATAGCATCCCGA 57.223 36.000 0.00 0.00 0.00 5.14
109 110 7.776618 TCTCTTTTATCTATAGCATCCCGAA 57.223 36.000 0.00 0.00 0.00 4.30
110 111 7.831753 TCTCTTTTATCTATAGCATCCCGAAG 58.168 38.462 0.00 0.00 0.00 3.79
131 132 8.459521 CGAAGGTGACAAAATTTTATATTGCA 57.540 30.769 2.44 0.00 0.00 4.08
132 133 9.086336 CGAAGGTGACAAAATTTTATATTGCAT 57.914 29.630 2.44 0.00 0.00 3.96
134 135 8.721019 AGGTGACAAAATTTTATATTGCATGG 57.279 30.769 2.44 0.00 0.00 3.66
135 136 8.320617 AGGTGACAAAATTTTATATTGCATGGT 58.679 29.630 2.44 0.00 0.00 3.55
136 137 8.945057 GGTGACAAAATTTTATATTGCATGGTT 58.055 29.630 2.44 0.00 0.00 3.67
137 138 9.757859 GTGACAAAATTTTATATTGCATGGTTG 57.242 29.630 2.44 0.00 0.00 3.77
138 139 9.499479 TGACAAAATTTTATATTGCATGGTTGT 57.501 25.926 2.44 0.00 0.00 3.32
151 152 8.907222 ATTGCATGGTTGTAAATTTCTCTTTT 57.093 26.923 0.00 0.00 30.96 2.27
152 153 7.712264 TGCATGGTTGTAAATTTCTCTTTTG 57.288 32.000 0.00 0.00 0.00 2.44
153 154 7.271511 TGCATGGTTGTAAATTTCTCTTTTGT 58.728 30.769 0.00 0.00 0.00 2.83
243 244 4.463891 ACATATTTTCTCCCACAAAGGCAG 59.536 41.667 0.00 0.00 35.39 4.85
244 245 1.039856 TTTTCTCCCACAAAGGCAGC 58.960 50.000 0.00 0.00 35.39 5.25
287 288 1.000955 GATGACCGTGTCTCTGTGGTT 59.999 52.381 5.77 0.00 34.12 3.67
297 298 0.397941 CTCTGTGGTTGAGGCCTTGA 59.602 55.000 6.77 0.00 0.00 3.02
307 308 1.704628 TGAGGCCTTGATCTTGGTCAA 59.295 47.619 6.77 0.00 36.70 3.18
327 328 2.622436 AGAGTGTTTATTCGCTCAGGC 58.378 47.619 9.37 0.00 44.43 4.85
350 351 5.106277 GCCGCTTAGTGGAAGAATAACTTTT 60.106 40.000 16.92 0.00 39.13 2.27
373 374 6.486253 TGTGCAGAGTGACATTTCTATTTC 57.514 37.500 0.00 0.00 0.00 2.17
393 394 6.567687 TTTCGACTGCAAGGAATCAAAATA 57.432 33.333 0.00 0.00 39.30 1.40
454 456 9.281371 CAGGATTGAGAATAGATTATGCTTTCA 57.719 33.333 0.00 0.00 0.00 2.69
544 546 8.607713 TCCAGTAGATACCATTTTTGAGGTAAA 58.392 33.333 0.00 0.00 43.14 2.01
593 595 3.485877 GCATATTCTTTGAGACCGTGCAC 60.486 47.826 6.82 6.82 30.17 4.57
688 690 0.031585 GACGATGCATACGGCCACTA 59.968 55.000 18.34 0.00 43.89 2.74
802 804 1.725641 TGATGCAGTGGTGTCGAATC 58.274 50.000 0.00 0.00 0.00 2.52
951 953 1.696336 CTTCCACCGATCCATCTCCAT 59.304 52.381 0.00 0.00 0.00 3.41
1031 1033 4.379243 CTCGACCACCCTGCGCTT 62.379 66.667 9.73 0.00 0.00 4.68
1048 1050 1.001020 TTGTCCATCCAGCCGCATT 60.001 52.632 0.00 0.00 0.00 3.56
1112 1114 4.049186 GTCAATGACGCGGTAGATACAAT 58.951 43.478 12.47 0.00 0.00 2.71
1136 1138 2.162906 ACCACCTGGCAACCTCCAT 61.163 57.895 0.00 0.00 39.32 3.41
1149 1151 1.338107 CCTCCATACCATCGCCACTA 58.662 55.000 0.00 0.00 0.00 2.74
1309 1311 1.229853 AGGGGTTCGAGGGTGGATT 60.230 57.895 0.00 0.00 0.00 3.01
1369 1372 1.086067 CAAGTGACATCGCCGATGCT 61.086 55.000 25.90 12.87 43.15 3.79
1380 1383 2.514592 CGATGCTGGGCCGAACAT 60.515 61.111 2.96 2.96 0.00 2.71
1401 1404 0.250166 CCGACCAAAGTTTCCTCCGT 60.250 55.000 0.00 0.00 0.00 4.69
1991 2003 3.271250 GGCTGACCCATGTGAATGT 57.729 52.632 0.00 0.00 0.00 2.71
1992 2004 1.549203 GGCTGACCCATGTGAATGTT 58.451 50.000 0.00 0.00 0.00 2.71
1993 2005 2.722094 GGCTGACCCATGTGAATGTTA 58.278 47.619 0.00 0.00 0.00 2.41
1994 2006 3.290710 GGCTGACCCATGTGAATGTTAT 58.709 45.455 0.00 0.00 0.00 1.89
1995 2007 3.316308 GGCTGACCCATGTGAATGTTATC 59.684 47.826 0.00 0.00 0.00 1.75
1996 2008 3.947196 GCTGACCCATGTGAATGTTATCA 59.053 43.478 0.00 0.00 0.00 2.15
1997 2009 4.581824 GCTGACCCATGTGAATGTTATCAT 59.418 41.667 0.00 0.00 35.59 2.45
1998 2010 5.764686 GCTGACCCATGTGAATGTTATCATA 59.235 40.000 0.00 0.00 33.49 2.15
1999 2011 6.432162 GCTGACCCATGTGAATGTTATCATAT 59.568 38.462 0.00 0.00 32.13 1.78
2000 2012 7.607607 GCTGACCCATGTGAATGTTATCATATA 59.392 37.037 0.00 0.00 30.99 0.86
2091 2103 7.982354 AGCCTACTAATTAGCTAGAACAAGTTG 59.018 37.037 12.54 0.00 0.00 3.16
2156 2168 5.692115 TTGTTGATATTCAGTCCTAGCCA 57.308 39.130 0.00 0.00 0.00 4.75
2165 2177 2.438021 TCAGTCCTAGCCACACAAAACT 59.562 45.455 0.00 0.00 0.00 2.66
2332 2344 9.881529 TTTTTACCTTAACAAGTTACATTAGCG 57.118 29.630 0.00 0.00 0.00 4.26
2356 2368 6.140737 CGATGTGTAAAAGTTTGTCAAAGCTC 59.859 38.462 0.00 0.00 0.00 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.692625 GTGCACTCATTACTCATCAGTGTT 59.307 41.667 10.32 0.00 36.38 3.32
5 6 5.008619 AGAGTGCACTCATTACTCATCAG 57.991 43.478 40.25 0.00 45.21 2.90
6 7 5.418840 TGTAGAGTGCACTCATTACTCATCA 59.581 40.000 40.25 23.33 45.21 3.07
7 8 5.895928 TGTAGAGTGCACTCATTACTCATC 58.104 41.667 40.25 21.56 45.21 2.92
8 9 5.921962 TGTAGAGTGCACTCATTACTCAT 57.078 39.130 40.25 23.67 45.21 2.90
9 10 5.336770 CCTTGTAGAGTGCACTCATTACTCA 60.337 44.000 40.25 26.51 45.21 3.41
10 11 5.105752 CCTTGTAGAGTGCACTCATTACTC 58.894 45.833 40.25 24.75 45.21 2.59
11 12 4.528596 ACCTTGTAGAGTGCACTCATTACT 59.471 41.667 40.25 25.63 45.21 2.24
12 13 4.822026 ACCTTGTAGAGTGCACTCATTAC 58.178 43.478 40.25 33.11 45.21 1.89
13 14 5.483685 AACCTTGTAGAGTGCACTCATTA 57.516 39.130 40.25 25.96 45.21 1.90
14 15 4.357918 AACCTTGTAGAGTGCACTCATT 57.642 40.909 40.25 26.95 45.21 2.57
15 16 4.621747 GCTAACCTTGTAGAGTGCACTCAT 60.622 45.833 40.25 28.70 45.21 2.90
16 17 3.306088 GCTAACCTTGTAGAGTGCACTCA 60.306 47.826 40.25 26.48 45.21 3.41
17 18 3.254892 GCTAACCTTGTAGAGTGCACTC 58.745 50.000 34.82 34.82 43.17 3.51
18 19 2.028020 GGCTAACCTTGTAGAGTGCACT 60.028 50.000 21.88 21.88 0.00 4.40
19 20 2.347731 GGCTAACCTTGTAGAGTGCAC 58.652 52.381 9.40 9.40 0.00 4.57
20 21 1.278127 GGGCTAACCTTGTAGAGTGCA 59.722 52.381 0.00 0.00 35.85 4.57
21 22 2.025589 GGGCTAACCTTGTAGAGTGC 57.974 55.000 0.00 0.00 35.85 4.40
32 33 1.680338 CAATGGCAGTAGGGCTAACC 58.320 55.000 0.00 0.00 43.83 2.85
33 34 1.064685 ACCAATGGCAGTAGGGCTAAC 60.065 52.381 0.00 0.00 43.83 2.34
34 35 1.295020 ACCAATGGCAGTAGGGCTAA 58.705 50.000 0.00 0.00 43.83 3.09
35 36 1.766496 GTACCAATGGCAGTAGGGCTA 59.234 52.381 0.00 0.00 43.83 3.93
36 37 0.546598 GTACCAATGGCAGTAGGGCT 59.453 55.000 0.00 0.00 43.83 5.19
37 38 0.546598 AGTACCAATGGCAGTAGGGC 59.453 55.000 0.00 0.00 43.73 5.19
38 39 1.837439 TCAGTACCAATGGCAGTAGGG 59.163 52.381 0.00 0.00 0.00 3.53
39 40 3.055094 AGTTCAGTACCAATGGCAGTAGG 60.055 47.826 0.00 0.00 0.00 3.18
40 41 4.207891 AGTTCAGTACCAATGGCAGTAG 57.792 45.455 0.00 0.00 0.00 2.57
41 42 4.775780 AGTAGTTCAGTACCAATGGCAGTA 59.224 41.667 0.00 0.00 0.00 2.74
42 43 3.583086 AGTAGTTCAGTACCAATGGCAGT 59.417 43.478 0.00 0.00 0.00 4.40
43 44 3.935203 CAGTAGTTCAGTACCAATGGCAG 59.065 47.826 0.00 0.00 0.00 4.85
44 45 3.580895 TCAGTAGTTCAGTACCAATGGCA 59.419 43.478 0.00 0.00 0.00 4.92
45 46 3.933332 GTCAGTAGTTCAGTACCAATGGC 59.067 47.826 0.00 0.00 0.00 4.40
46 47 5.147330 TGTCAGTAGTTCAGTACCAATGG 57.853 43.478 0.00 0.00 0.00 3.16
47 48 7.672983 AATTGTCAGTAGTTCAGTACCAATG 57.327 36.000 0.00 0.00 0.00 2.82
48 49 9.601217 GATAATTGTCAGTAGTTCAGTACCAAT 57.399 33.333 0.00 0.00 0.00 3.16
49 50 8.812972 AGATAATTGTCAGTAGTTCAGTACCAA 58.187 33.333 4.92 0.00 0.00 3.67
50 51 8.362464 AGATAATTGTCAGTAGTTCAGTACCA 57.638 34.615 4.92 0.00 0.00 3.25
51 52 9.654663 AAAGATAATTGTCAGTAGTTCAGTACC 57.345 33.333 4.92 0.00 0.00 3.34
54 55 9.372369 GCTAAAGATAATTGTCAGTAGTTCAGT 57.628 33.333 4.92 0.00 0.00 3.41
55 56 9.593134 AGCTAAAGATAATTGTCAGTAGTTCAG 57.407 33.333 4.92 0.00 0.00 3.02
82 83 8.816894 TCGGGATGCTATAGATAAAAGAGAAAT 58.183 33.333 3.21 0.00 0.00 2.17
83 84 8.190326 TCGGGATGCTATAGATAAAAGAGAAA 57.810 34.615 3.21 0.00 0.00 2.52
84 85 7.776618 TCGGGATGCTATAGATAAAAGAGAA 57.223 36.000 3.21 0.00 0.00 2.87
85 86 7.093727 CCTTCGGGATGCTATAGATAAAAGAGA 60.094 40.741 3.21 0.00 37.25 3.10
86 87 7.038659 CCTTCGGGATGCTATAGATAAAAGAG 58.961 42.308 3.21 0.00 37.25 2.85
87 88 6.497259 ACCTTCGGGATGCTATAGATAAAAGA 59.503 38.462 3.21 0.00 38.77 2.52
88 89 6.591834 CACCTTCGGGATGCTATAGATAAAAG 59.408 42.308 3.21 0.00 38.77 2.27
89 90 6.269077 TCACCTTCGGGATGCTATAGATAAAA 59.731 38.462 3.21 0.00 38.77 1.52
90 91 5.778241 TCACCTTCGGGATGCTATAGATAAA 59.222 40.000 3.21 0.00 38.77 1.40
91 92 5.185249 GTCACCTTCGGGATGCTATAGATAA 59.815 44.000 3.21 0.00 38.77 1.75
92 93 4.705507 GTCACCTTCGGGATGCTATAGATA 59.294 45.833 3.21 0.00 38.77 1.98
93 94 3.511934 GTCACCTTCGGGATGCTATAGAT 59.488 47.826 3.21 0.00 38.77 1.98
94 95 2.891580 GTCACCTTCGGGATGCTATAGA 59.108 50.000 3.21 0.00 38.77 1.98
95 96 2.628178 TGTCACCTTCGGGATGCTATAG 59.372 50.000 0.00 0.00 38.77 1.31
96 97 2.673258 TGTCACCTTCGGGATGCTATA 58.327 47.619 0.00 0.00 38.77 1.31
97 98 1.496060 TGTCACCTTCGGGATGCTAT 58.504 50.000 0.00 0.00 38.77 2.97
98 99 1.271856 TTGTCACCTTCGGGATGCTA 58.728 50.000 0.00 0.00 38.77 3.49
99 100 0.400213 TTTGTCACCTTCGGGATGCT 59.600 50.000 0.00 0.00 38.77 3.79
100 101 1.243902 TTTTGTCACCTTCGGGATGC 58.756 50.000 0.00 0.00 38.77 3.91
101 102 4.519540 AAATTTTGTCACCTTCGGGATG 57.480 40.909 0.00 0.00 38.77 3.51
102 103 6.850752 ATAAAATTTTGTCACCTTCGGGAT 57.149 33.333 13.76 0.00 38.77 3.85
103 104 7.948034 ATATAAAATTTTGTCACCTTCGGGA 57.052 32.000 13.76 0.00 38.77 5.14
104 105 7.010091 GCAATATAAAATTTTGTCACCTTCGGG 59.990 37.037 13.76 0.00 41.87 5.14
105 106 7.543868 TGCAATATAAAATTTTGTCACCTTCGG 59.456 33.333 13.76 0.00 0.00 4.30
106 107 8.459521 TGCAATATAAAATTTTGTCACCTTCG 57.540 30.769 13.76 0.00 0.00 3.79
108 109 9.165035 CCATGCAATATAAAATTTTGTCACCTT 57.835 29.630 13.76 0.00 0.00 3.50
109 110 8.320617 ACCATGCAATATAAAATTTTGTCACCT 58.679 29.630 13.76 0.00 0.00 4.00
110 111 8.491331 ACCATGCAATATAAAATTTTGTCACC 57.509 30.769 13.76 0.00 0.00 4.02
111 112 9.757859 CAACCATGCAATATAAAATTTTGTCAC 57.242 29.630 13.76 0.00 0.00 3.67
112 113 9.499479 ACAACCATGCAATATAAAATTTTGTCA 57.501 25.926 13.76 1.86 0.00 3.58
125 126 9.995003 AAAAGAGAAATTTACAACCATGCAATA 57.005 25.926 0.00 0.00 0.00 1.90
126 127 8.776470 CAAAAGAGAAATTTACAACCATGCAAT 58.224 29.630 0.00 0.00 0.00 3.56
127 128 7.768120 ACAAAAGAGAAATTTACAACCATGCAA 59.232 29.630 0.00 0.00 0.00 4.08
128 129 7.271511 ACAAAAGAGAAATTTACAACCATGCA 58.728 30.769 0.00 0.00 0.00 3.96
129 130 7.653311 AGACAAAAGAGAAATTTACAACCATGC 59.347 33.333 0.00 0.00 0.00 4.06
164 165 7.496346 AAATGAGGACACCTAGAGACATAAA 57.504 36.000 0.00 0.00 31.76 1.40
287 288 1.361204 TGACCAAGATCAAGGCCTCA 58.639 50.000 5.23 0.00 0.00 3.86
297 298 5.122396 GCGAATAAACACTCTTGACCAAGAT 59.878 40.000 12.29 1.32 45.40 2.40
307 308 2.622436 GCCTGAGCGAATAAACACTCT 58.378 47.619 0.00 0.00 0.00 3.24
327 328 6.072673 ACAAAAGTTATTCTTCCACTAAGCGG 60.073 38.462 0.00 0.00 35.02 5.52
350 351 5.120674 CGAAATAGAAATGTCACTCTGCACA 59.879 40.000 0.00 0.00 0.00 4.57
373 374 4.635765 TCCTATTTTGATTCCTTGCAGTCG 59.364 41.667 0.00 0.00 0.00 4.18
393 394 2.270434 TAAAGCCTCCTGGTCATCCT 57.730 50.000 0.00 0.00 35.27 3.24
454 456 5.065914 TGCTTTCAGTAGCATGAAAACTCT 58.934 37.500 0.00 0.00 45.80 3.24
544 546 7.014230 AGCGGTAATTAATATTCACAGCCATTT 59.986 33.333 0.00 0.00 0.00 2.32
802 804 3.132289 TCTGTTTGGTATTAGGCTCGGAG 59.868 47.826 0.00 0.00 0.00 4.63
951 953 0.526211 CTGTGCGTCAGTACCTGCTA 59.474 55.000 0.00 0.00 39.17 3.49
1031 1033 1.451927 GAATGCGGCTGGATGGACA 60.452 57.895 0.00 0.00 0.00 4.02
1070 1072 4.758251 CGAGTGGTGGCGGCATGA 62.758 66.667 17.19 1.04 0.00 3.07
1136 1138 1.399714 CTCCAGTAGTGGCGATGGTA 58.600 55.000 12.14 0.00 44.60 3.25
1149 1151 1.755008 GGCTCCGAGTAGCTCCAGT 60.755 63.158 0.00 0.00 42.37 4.00
1334 1337 0.320073 CTTGACGCCGTTACCCTTCA 60.320 55.000 0.00 0.00 0.00 3.02
1380 1383 0.536460 GGAGGAAACTTTGGTCGGCA 60.536 55.000 0.00 0.00 44.43 5.69
1401 1404 1.303898 TTGGTGGCATAGGATGGGAA 58.696 50.000 0.00 0.00 0.00 3.97
1598 1602 3.583086 TCTGGATCCTTTCTTCGGACTTT 59.417 43.478 14.23 0.00 32.41 2.66
1599 1603 3.173965 TCTGGATCCTTTCTTCGGACTT 58.826 45.455 14.23 0.00 32.41 3.01
1973 1985 1.549203 AACATTCACATGGGTCAGCC 58.451 50.000 0.00 0.00 34.27 4.85
1974 1986 3.947196 TGATAACATTCACATGGGTCAGC 59.053 43.478 0.00 0.00 34.27 4.26
1975 1987 7.991084 ATATGATAACATTCACATGGGTCAG 57.009 36.000 0.00 0.00 37.87 3.51
2091 2103 8.779354 AACAAATAACATCTACCTCTTGACTC 57.221 34.615 0.00 0.00 0.00 3.36
2094 2106 9.793259 AAAGAACAAATAACATCTACCTCTTGA 57.207 29.630 0.00 0.00 0.00 3.02
2156 2168 1.663695 AGTGTAGCGCAGTTTTGTGT 58.336 45.000 11.47 0.00 37.15 3.72
2165 2177 6.103330 TCATTATAAGTGAAAGTGTAGCGCA 58.897 36.000 11.47 0.00 0.00 6.09
2273 2285 4.820716 CCATTTTTCATTGCTGGGAAACAA 59.179 37.500 0.00 0.00 33.10 2.83
2311 2323 6.877322 ACATCGCTAATGTAACTTGTTAAGGT 59.123 34.615 0.15 0.00 46.95 3.50
2332 2344 7.381744 GAGCTTTGACAAACTTTTACACATC 57.618 36.000 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.