Multiple sequence alignment - TraesCS4D01G009700

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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 TraesCS4D01G009700 chr4D 100.000 4366 0 0 1 4366 4517032 4521397 0.000000e+00 8063.0
1 TraesCS4D01G009700 chr4D 74.246 2155 383 114 1125 3179 450686174 450684092 0.000000e+00 747.0
2 TraesCS4D01G009700 chr4D 81.646 158 20 3 2366 2514 4273646 4273489 5.930000e-24 122.0
3 TraesCS4D01G009700 chr4D 76.305 249 44 12 2247 2489 4663827 4664066 7.670000e-23 119.0
4 TraesCS4D01G009700 chr4D 80.690 145 26 2 3290 3433 4272666 4272523 1.280000e-20 111.0
5 TraesCS4D01G009700 chr4D 86.667 60 8 0 3293 3352 4664831 4664890 2.820000e-07 67.6
6 TraesCS4D01G009700 chr4D 100.000 33 0 0 1764 1796 4345752 4345720 1.310000e-05 62.1
7 TraesCS4D01G009700 chr4D 100.000 30 0 0 923 952 4641936 4641965 6.100000e-04 56.5
8 TraesCS4D01G009700 chrUn 91.234 4141 193 57 355 4366 47254249 47250150 0.000000e+00 5480.0
9 TraesCS4D01G009700 chrUn 91.272 3483 162 48 989 4366 294658060 294661505 0.000000e+00 4617.0
10 TraesCS4D01G009700 chrUn 91.930 1995 93 20 2432 4366 47246420 47244434 0.000000e+00 2730.0
11 TraesCS4D01G009700 chrUn 91.711 374 17 7 3 363 47255666 47255294 1.400000e-139 507.0
12 TraesCS4D01G009700 chrUn 85.473 296 24 9 2203 2493 476939070 476939351 1.540000e-74 291.0
13 TraesCS4D01G009700 chrUn 74.576 295 54 15 2250 2530 47278023 47277736 4.620000e-20 110.0
14 TraesCS4D01G009700 chrUn 94.595 37 0 1 923 959 47290802 47290768 6.100000e-04 56.5
15 TraesCS4D01G009700 chrUn 100.000 30 0 0 923 952 47313217 47313246 6.100000e-04 56.5
16 TraesCS4D01G009700 chr4A 91.272 3483 162 47 989 4366 598763517 598760072 0.000000e+00 4617.0
17 TraesCS4D01G009700 chr4A 91.711 374 17 7 3 363 598766923 598766551 1.400000e-139 507.0
18 TraesCS4D01G009700 chr4A 74.582 1196 206 48 2034 3166 16049181 16050341 6.710000e-118 435.0
19 TraesCS4D01G009700 chr4A 94.776 134 7 0 355 488 598765506 598765373 4.420000e-50 209.0
20 TraesCS4D01G009700 chr4A 89.024 82 7 1 1018 1099 16047764 16047843 2.780000e-17 100.0
21 TraesCS4D01G009700 chr4A 92.308 65 4 1 3290 3353 599354995 599355059 1.670000e-14 91.6
22 TraesCS4D01G009700 chr4A 78.906 128 24 2 1758 1884 598793303 598793178 2.800000e-12 84.2
23 TraesCS4D01G009700 chr1B 90.760 3355 198 35 1106 4366 46225625 46228961 0.000000e+00 4375.0
24 TraesCS4D01G009700 chr1B 85.424 590 36 12 565 1110 46225001 46225584 6.340000e-158 568.0
25 TraesCS4D01G009700 chr1B 74.098 471 89 17 2483 2941 371492950 371493399 3.490000e-36 163.0
26 TraesCS4D01G009700 chr4B 83.903 1112 142 23 3281 4363 7502319 7503422 0.000000e+00 1027.0
27 TraesCS4D01G009700 chr4B 84.358 1106 109 22 2203 3294 7501137 7502192 0.000000e+00 1026.0
28 TraesCS4D01G009700 chr4B 88.728 346 22 11 1124 1456 7500200 7500541 1.460000e-109 407.0
29 TraesCS4D01G009700 chr4B 76.142 591 110 17 2594 3179 564076320 564075756 9.240000e-72 281.0
30 TraesCS4D01G009700 chr4B 80.597 402 26 21 732 1112 7499770 7500140 3.350000e-66 263.0
31 TraesCS4D01G009700 chr4B 83.333 72 9 2 1752 1822 7404302 7404371 3.650000e-06 63.9
32 TraesCS4D01G009700 chr4B 100.000 33 0 0 1764 1796 7030057 7030025 1.310000e-05 62.1
33 TraesCS4D01G009700 chr3A 90.672 461 31 5 1 450 691851599 691851140 1.740000e-168 603.0
34 TraesCS4D01G009700 chr3A 89.590 317 31 2 252 567 691857325 691857010 6.800000e-108 401.0


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 TraesCS4D01G009700 chr4D 4517032 4521397 4365 False 8063.000000 8063 100.000000 1 4366 1 chr4D.!!$F1 4365
1 TraesCS4D01G009700 chr4D 450684092 450686174 2082 True 747.000000 747 74.246000 1125 3179 1 chr4D.!!$R2 2054
2 TraesCS4D01G009700 chrUn 294658060 294661505 3445 False 4617.000000 4617 91.272000 989 4366 1 chrUn.!!$F2 3377
3 TraesCS4D01G009700 chrUn 47244434 47255666 11232 True 2905.666667 5480 91.625000 3 4366 3 chrUn.!!$R3 4363
4 TraesCS4D01G009700 chr4A 598760072 598766923 6851 True 1777.666667 4617 92.586333 3 4366 3 chr4A.!!$R2 4363
5 TraesCS4D01G009700 chr4A 16047764 16050341 2577 False 267.500000 435 81.803000 1018 3166 2 chr4A.!!$F2 2148
6 TraesCS4D01G009700 chr1B 46225001 46228961 3960 False 2471.500000 4375 88.092000 565 4366 2 chr1B.!!$F2 3801
7 TraesCS4D01G009700 chr4B 7499770 7503422 3652 False 680.750000 1027 84.396500 732 4363 4 chr4B.!!$F2 3631
8 TraesCS4D01G009700 chr4B 564075756 564076320 564 True 281.000000 281 76.142000 2594 3179 1 chr4B.!!$R2 585

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
977 2112 0.390340 CAGCAGTGCTTTCTCGCCTA 60.390 55.0 16.89 0.0 36.40 3.93 F
1494 4075 0.690762 ATATCCCCGTCCATTTCCGG 59.309 55.0 0.00 0.0 43.82 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2066 5088 0.106708 AGCCGCATTCCATGACGTAT 59.893 50.0 0.0 0.0 0.0 3.06 R
3450 12446 0.464036 TCTGTGTGCTCGACCAAAGT 59.536 50.0 0.0 0.0 0.0 2.66 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
25 26 5.503002 TGGTATAGCCTTGAGTAAAAACCC 58.497 41.667 0.00 0.00 38.35 4.11
31 32 4.099419 AGCCTTGAGTAAAAACCCTGTTTG 59.901 41.667 0.00 0.00 0.00 2.93
92 93 9.599866 CATTATATACAGAACTGTGTTGAGGAA 57.400 33.333 16.37 3.72 44.63 3.36
99 100 1.490490 ACTGTGTTGAGGAAGGCAAGA 59.510 47.619 0.00 0.00 0.00 3.02
159 160 5.973565 GCGGATATTTTGACAAAATCTCTGG 59.026 40.000 30.02 23.29 39.16 3.86
163 164 8.531146 GGATATTTTGACAAAATCTCTGGGAAA 58.469 33.333 25.53 8.92 41.16 3.13
191 192 2.433970 GTTCCAGGAGATGAGGAGAAGG 59.566 54.545 0.00 0.00 32.11 3.46
202 203 3.520696 TGAGGAGAAGGATTGGAGTTCA 58.479 45.455 0.00 0.00 0.00 3.18
253 254 3.708451 GGGGGTGAATGTTAGGATTTGT 58.292 45.455 0.00 0.00 0.00 2.83
254 255 3.699538 GGGGGTGAATGTTAGGATTTGTC 59.300 47.826 0.00 0.00 0.00 3.18
255 256 3.699538 GGGGTGAATGTTAGGATTTGTCC 59.300 47.826 0.00 0.00 0.00 4.02
272 284 5.508200 TTGTCCATGTCAAAGTGTAAACC 57.492 39.130 0.00 0.00 0.00 3.27
281 293 2.144482 AAGTGTAAACCGGACTGTCG 57.856 50.000 9.46 0.00 0.00 4.35
303 315 3.114065 GTTTATAAGGCAGTCTCGGACG 58.886 50.000 0.00 0.00 37.67 4.79
328 340 6.715264 GGTCCGGTATTCAATTAGGATTCAAT 59.285 38.462 0.00 0.00 0.00 2.57
352 366 1.671845 TCGTGTGTGTTTAAACCTGGC 59.328 47.619 15.59 4.49 0.00 4.85
410 1477 3.119096 GTTGGGCGCGAACTCTCC 61.119 66.667 12.10 0.00 0.00 3.71
419 1486 1.647702 CGCGAACTCTCCGTAAAACTC 59.352 52.381 0.00 0.00 0.00 3.01
453 1520 6.882140 TCGAAGCAATAAAATGAGGAAGGTTA 59.118 34.615 0.00 0.00 0.00 2.85
463 1530 4.967084 TGAGGAAGGTTAAGCTGTTGTA 57.033 40.909 8.16 0.00 0.00 2.41
485 1552 8.911918 TGTAATAAGATTTATGGGCGTACAAT 57.088 30.769 0.00 0.00 0.00 2.71
490 1557 6.131544 AGATTTATGGGCGTACAATTGTTC 57.868 37.500 17.78 10.94 0.00 3.18
505 1572 6.935167 ACAATTGTTCTGTTTTTCTCCTGTT 58.065 32.000 4.92 0.00 0.00 3.16
509 1576 5.708948 TGTTCTGTTTTTCTCCTGTTTGTG 58.291 37.500 0.00 0.00 0.00 3.33
552 1619 2.289882 GGCCATCTGATCAATCGATCCA 60.290 50.000 0.00 0.00 46.50 3.41
581 1648 9.116067 GCTATCCTTACACCATGTGTATTTAAA 57.884 33.333 7.82 0.00 46.36 1.52
771 1841 1.377536 GCCATCTCCAAGCTCTTCAC 58.622 55.000 0.00 0.00 0.00 3.18
869 1941 2.596631 ACTTGCTGCCAGCCAGTG 60.597 61.111 21.34 8.01 44.35 3.66
892 1965 4.271291 GGAGTAAATGAGCAATCGAGAACC 59.729 45.833 0.00 0.00 0.00 3.62
894 1967 3.356529 AAATGAGCAATCGAGAACCCT 57.643 42.857 0.00 0.00 0.00 4.34
895 1968 4.487714 AAATGAGCAATCGAGAACCCTA 57.512 40.909 0.00 0.00 0.00 3.53
896 1969 4.487714 AATGAGCAATCGAGAACCCTAA 57.512 40.909 0.00 0.00 0.00 2.69
977 2112 0.390340 CAGCAGTGCTTTCTCGCCTA 60.390 55.000 16.89 0.00 36.40 3.93
1317 3882 2.317609 CCGTGGCCTTGTTGTCTCG 61.318 63.158 3.32 0.00 0.00 4.04
1318 3885 2.946762 GTGGCCTTGTTGTCTCGC 59.053 61.111 3.32 0.00 0.00 5.03
1346 3920 2.164422 TCGGATACTGACTCACTTGCTG 59.836 50.000 0.00 0.00 0.00 4.41
1393 3972 3.636231 CCCCTGCACGAGGTGGAA 61.636 66.667 0.00 0.00 40.87 3.53
1399 3978 0.976641 TGCACGAGGTGGAATTCTCT 59.023 50.000 5.23 1.03 33.64 3.10
1456 4035 3.055591 CAGCTCCACGTATGATGATGAC 58.944 50.000 0.00 0.00 0.00 3.06
1491 4072 7.553044 CCTTTTCTATATATCCCCGTCCATTTC 59.447 40.741 0.00 0.00 0.00 2.17
1492 4073 6.555463 TTCTATATATCCCCGTCCATTTCC 57.445 41.667 0.00 0.00 0.00 3.13
1493 4074 3.906720 ATATATCCCCGTCCATTTCCG 57.093 47.619 0.00 0.00 0.00 4.30
1494 4075 0.690762 ATATCCCCGTCCATTTCCGG 59.309 55.000 0.00 0.00 43.82 5.14
1496 4077 4.418328 CCCCGTCCATTTCCGGCA 62.418 66.667 0.00 0.00 42.87 5.69
1580 4225 5.386526 CGCGATAATTAGAAGAAACGAGCTC 60.387 44.000 0.00 2.73 0.00 4.09
1633 4284 2.589798 ATGCATGCCAACAGTAATGC 57.410 45.000 16.68 0.00 44.49 3.56
1746 4416 2.159653 GGATTGCAGATGTGTGTCGTTC 60.160 50.000 0.00 0.00 0.00 3.95
1823 4810 4.766375 ACCTAATTGTCGGTATTCCTGTG 58.234 43.478 0.00 0.00 0.00 3.66
1842 4830 2.287915 GTGTATGGCAATGCTTAGGTCG 59.712 50.000 4.82 0.00 0.00 4.79
1848 4836 2.414161 GGCAATGCTTAGGTCGTCAAAC 60.414 50.000 4.82 0.00 0.00 2.93
1850 4838 3.119849 GCAATGCTTAGGTCGTCAAACAT 60.120 43.478 0.00 0.00 0.00 2.71
1869 4857 2.604969 TAATTTTGCCGTCTTGCGAC 57.395 45.000 0.00 0.00 44.77 5.19
1990 5010 6.590068 ACGGTCGGCTACTCTACATATATAT 58.410 40.000 0.00 0.00 0.00 0.86
2006 5026 8.607441 ACATATATATATTATGCCAAGTGCCG 57.393 34.615 2.28 0.00 40.16 5.69
2026 5048 5.009210 TGCCGTTTTTAGTTTATTCACTGCT 59.991 36.000 0.00 0.00 0.00 4.24
2159 5210 2.643551 ACCGATGTCCATTCCAATGTC 58.356 47.619 0.00 0.00 34.60 3.06
2206 5257 8.407457 TGTCGTTTTGTAAATATCTCTAGCAG 57.593 34.615 0.00 0.00 0.00 4.24
2397 5478 3.054878 CTGACATTGCTCTTTTTGGCAC 58.945 45.455 0.00 0.00 38.23 5.01
2640 5744 8.803397 ACTAACCTACTTTTTCACTTTGTCTT 57.197 30.769 0.00 0.00 0.00 3.01
2658 5762 6.915544 TGTCTTGAATCAGCTGATTGATAC 57.084 37.500 39.54 30.08 44.14 2.24
2724 5828 4.267349 TGTAACTTGTTGGCTCTAGACC 57.733 45.455 0.00 0.00 0.00 3.85
2820 5950 9.037737 TCTACCATTTAAATTTAGTTCGATCGG 57.962 33.333 16.41 0.00 0.00 4.18
2846 5977 5.297547 TCTTCAGAATTGACAGTGTGGTAC 58.702 41.667 0.00 0.00 31.71 3.34
2859 11706 5.108517 CAGTGTGGTACTTTTGCATTGTTT 58.891 37.500 0.00 0.00 37.60 2.83
3002 11854 8.725405 TTCCAGTTTCACGCTATTATGATAAA 57.275 30.769 0.00 0.00 0.00 1.40
3116 11974 3.634910 TGGTTTTTGGAGCACTTAGGTTC 59.365 43.478 0.00 0.00 0.00 3.62
3157 12015 3.479505 TGGCCGTCGAATATTGTTTTG 57.520 42.857 0.00 0.00 0.00 2.44
3428 12424 3.325870 ACAATGGTGTGTGTGTATCTCG 58.674 45.455 0.00 0.00 36.31 4.04
3449 12445 2.490115 GGAAGTGGTTGTGTTGTGTTGA 59.510 45.455 0.00 0.00 0.00 3.18
3450 12446 3.057174 GGAAGTGGTTGTGTTGTGTTGAA 60.057 43.478 0.00 0.00 0.00 2.69
3550 12546 9.107367 GAACTTGTTGTCTTTTCTATCGAATTG 57.893 33.333 0.00 0.00 0.00 2.32
3565 12561 3.555547 TCGAATTGTGTGTCTGTCAACTG 59.444 43.478 0.00 0.00 0.00 3.16
3650 12646 0.396556 GGTTGGTGGGTGGTGACTTT 60.397 55.000 0.00 0.00 0.00 2.66
3659 12655 4.822896 GTGGGTGGTGACTTTGTTATGTTA 59.177 41.667 0.00 0.00 0.00 2.41
3726 12722 2.522367 TTTGGGTCCGGAGTGGGTC 61.522 63.158 3.06 0.00 38.76 4.46
3728 12724 4.716977 GGGTCCGGAGTGGGTCCT 62.717 72.222 3.06 0.00 44.35 3.85
3742 12738 1.757699 GGGTCCTCGTATTGAGCTCTT 59.242 52.381 16.19 5.11 43.82 2.85
3745 12741 4.039366 GGGTCCTCGTATTGAGCTCTTAAT 59.961 45.833 16.19 9.78 43.82 1.40
3754 12750 9.035607 TCGTATTGAGCTCTTAATTCTCATTTC 57.964 33.333 16.19 0.00 36.81 2.17
3848 12844 1.061131 CAAACTGTCTAATCTGCCGCG 59.939 52.381 0.00 0.00 0.00 6.46
4030 13028 6.155475 TGGAAATGTCGGAGAAAAATGTTT 57.845 33.333 0.00 0.00 39.69 2.83
4058 13056 3.053619 AGAGGTGCCAAAACTAATAGGGG 60.054 47.826 0.00 0.00 0.00 4.79
4070 13071 8.531146 CAAAACTAATAGGGGTGATGTCAAAAT 58.469 33.333 0.00 0.00 0.00 1.82
4071 13072 9.762381 AAAACTAATAGGGGTGATGTCAAAATA 57.238 29.630 0.00 0.00 0.00 1.40
4072 13073 9.762381 AAACTAATAGGGGTGATGTCAAAATAA 57.238 29.630 0.00 0.00 0.00 1.40
4120 13122 1.060713 CGTGTACAGTTCGGAAGCTG 58.939 55.000 14.57 14.57 38.58 4.24
4142 13145 0.652592 GGAACATGGTTCGCTCATCG 59.347 55.000 0.00 0.00 40.15 3.84
4164 13167 2.838202 TGGCCTACTCACTCCTAAAAGG 59.162 50.000 3.32 0.00 36.46 3.11
4166 13169 3.118702 GGCCTACTCACTCCTAAAAGGTC 60.119 52.174 0.00 0.00 36.53 3.85
4171 13174 4.660168 ACTCACTCCTAAAAGGTCGTAGA 58.340 43.478 0.00 0.00 36.53 2.59
4212 13216 6.934645 TCAGAGTAATTCGGAACTGAAACAAT 59.065 34.615 5.75 0.00 32.66 2.71
4213 13217 7.444183 TCAGAGTAATTCGGAACTGAAACAATT 59.556 33.333 5.75 0.00 32.66 2.32
4214 13218 8.076178 CAGAGTAATTCGGAACTGAAACAATTT 58.924 33.333 0.00 0.00 0.00 1.82
4215 13219 8.630037 AGAGTAATTCGGAACTGAAACAATTTT 58.370 29.630 0.00 0.00 0.00 1.82
4216 13220 9.244799 GAGTAATTCGGAACTGAAACAATTTTT 57.755 29.630 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.412214 GGTTTTTACTCAAGGCTATACCAGA 58.588 40.000 0.00 0.00 43.14 3.86
25 26 4.153117 GCTTACTCCTGTCATGACAAACAG 59.847 45.833 27.63 22.99 41.33 3.16
31 32 3.319137 TGTGCTTACTCCTGTCATGAC 57.681 47.619 19.27 19.27 0.00 3.06
76 77 1.490490 TGCCTTCCTCAACACAGTTCT 59.510 47.619 0.00 0.00 0.00 3.01
92 93 3.350833 GTGGTTGATCTTGATCTTGCCT 58.649 45.455 11.31 0.00 0.00 4.75
99 100 4.504858 GTCCTAACGTGGTTGATCTTGAT 58.495 43.478 0.00 0.00 0.00 2.57
159 160 5.711976 TCATCTCCTGGAACTTGATTTTTCC 59.288 40.000 0.00 0.00 41.62 3.13
163 164 4.537688 TCCTCATCTCCTGGAACTTGATTT 59.462 41.667 0.00 0.00 0.00 2.17
191 192 2.743636 TCACGGACTGAACTCCAATC 57.256 50.000 0.00 0.00 0.00 2.67
202 203 3.402628 AAGTGCATTACTTCACGGACT 57.597 42.857 0.00 0.00 46.55 3.85
251 252 3.562141 CGGTTTACACTTTGACATGGACA 59.438 43.478 0.00 0.00 0.00 4.02
252 253 3.058501 CCGGTTTACACTTTGACATGGAC 60.059 47.826 0.00 0.00 0.00 4.02
253 254 3.142951 CCGGTTTACACTTTGACATGGA 58.857 45.455 0.00 0.00 0.00 3.41
254 255 3.058501 GTCCGGTTTACACTTTGACATGG 60.059 47.826 0.00 0.00 0.00 3.66
255 256 3.813166 AGTCCGGTTTACACTTTGACATG 59.187 43.478 0.00 0.00 0.00 3.21
272 284 2.199236 GCCTTATAAACCGACAGTCCG 58.801 52.381 0.00 0.00 0.00 4.79
281 293 3.455327 GTCCGAGACTGCCTTATAAACC 58.545 50.000 0.00 0.00 0.00 3.27
303 315 5.617252 TGAATCCTAATTGAATACCGGACC 58.383 41.667 9.46 0.00 0.00 4.46
328 340 3.623960 CAGGTTTAAACACACACGAAGGA 59.376 43.478 19.57 0.00 0.00 3.36
352 366 1.517257 CAAGACGCGACCCTGCTAG 60.517 63.158 15.93 0.00 0.00 3.42
380 1447 1.602237 CCCAACACGGCCTACTGAT 59.398 57.895 0.00 0.00 0.00 2.90
410 1477 8.778141 TGCTTCGACTTATATAGAGTTTTACG 57.222 34.615 0.00 0.00 0.00 3.18
442 1509 3.857157 ACAACAGCTTAACCTTCCTCA 57.143 42.857 0.00 0.00 0.00 3.86
453 1520 7.468631 CGCCCATAAATCTTATTACAACAGCTT 60.469 37.037 0.00 0.00 0.00 3.74
463 1530 8.232913 ACAATTGTACGCCCATAAATCTTATT 57.767 30.769 9.97 0.00 0.00 1.40
485 1552 6.155827 CACAAACAGGAGAAAAACAGAACAA 58.844 36.000 0.00 0.00 0.00 2.83
490 1557 4.399303 AGACCACAAACAGGAGAAAAACAG 59.601 41.667 0.00 0.00 0.00 3.16
505 1572 1.208535 ACCTGACGAACAAGACCACAA 59.791 47.619 0.00 0.00 0.00 3.33
509 1576 0.531974 TGCACCTGACGAACAAGACC 60.532 55.000 0.00 0.00 0.00 3.85
552 1619 3.459598 ACACATGGTGTAAGGATAGCCAT 59.540 43.478 0.00 0.00 45.56 4.40
581 1648 9.065798 CCCACTGGTCATTGAAAATTTAAAAAT 57.934 29.630 0.00 0.00 0.00 1.82
587 1654 3.244526 GCCCCACTGGTCATTGAAAATTT 60.245 43.478 0.00 0.00 36.04 1.82
855 1925 4.340246 CTCCACTGGCTGGCAGCA 62.340 66.667 37.49 23.25 44.75 4.41
869 1941 4.271291 GGTTCTCGATTGCTCATTTACTCC 59.729 45.833 0.00 0.00 0.00 3.85
892 1965 2.087646 GGAGCCTTTTGACAGCTTAGG 58.912 52.381 0.00 0.00 36.87 2.69
894 1967 1.071699 ACGGAGCCTTTTGACAGCTTA 59.928 47.619 0.00 0.00 36.87 3.09
895 1968 0.179018 ACGGAGCCTTTTGACAGCTT 60.179 50.000 0.00 0.00 36.87 3.74
896 1969 0.603975 GACGGAGCCTTTTGACAGCT 60.604 55.000 0.00 0.00 40.24 4.24
968 2080 0.108472 TCGTCGAGAGTAGGCGAGAA 60.108 55.000 0.00 0.00 37.18 2.87
977 2112 0.526662 GATGTTGGGTCGTCGAGAGT 59.473 55.000 0.00 0.00 0.00 3.24
1083 3505 1.006102 GAGCACGGCGTGGCTATAT 60.006 57.895 37.33 15.97 41.22 0.86
1317 3882 0.308376 GTCAGTATCCGAGACGAGGC 59.692 60.000 0.00 0.00 0.00 4.70
1318 3885 1.868498 GAGTCAGTATCCGAGACGAGG 59.132 57.143 0.00 0.00 37.36 4.63
1346 3920 1.509923 GGATGGCAAAGCAGAGCAC 59.490 57.895 0.00 0.00 0.00 4.40
1393 3972 0.831307 GGGCGTCCACCTTAGAGAAT 59.169 55.000 0.00 0.00 0.00 2.40
1399 3978 2.203877 ACCAGGGCGTCCACCTTA 60.204 61.111 9.71 0.00 35.78 2.69
1456 4035 7.147461 GGGGATATATAGAAAAGGAAGGGCTAG 60.147 44.444 0.00 0.00 0.00 3.42
1491 4072 0.602106 ATCTGAATCGATGCTGCCGG 60.602 55.000 4.68 0.00 0.00 6.13
1492 4073 0.511653 CATCTGAATCGATGCTGCCG 59.488 55.000 4.68 0.00 34.92 5.69
1493 4074 1.263484 CACATCTGAATCGATGCTGCC 59.737 52.381 4.68 0.00 43.54 4.85
1494 4075 1.938577 ACACATCTGAATCGATGCTGC 59.061 47.619 4.68 0.00 43.54 5.25
1496 4077 4.005650 ACAAACACATCTGAATCGATGCT 58.994 39.130 4.68 0.00 43.54 3.79
1580 4225 5.981315 TCCGTTAGTACAAGAAACAGAACTG 59.019 40.000 0.00 0.00 0.00 3.16
1616 4261 3.996150 ATAGCATTACTGTTGGCATGC 57.004 42.857 9.90 9.90 42.05 4.06
1823 4810 2.544267 GACGACCTAAGCATTGCCATAC 59.456 50.000 4.70 0.00 0.00 2.39
1842 4830 5.388371 GCAAGACGGCAAAATTATGTTTGAC 60.388 40.000 0.00 0.00 42.19 3.18
1848 4836 3.129852 TCGCAAGACGGCAAAATTATG 57.870 42.857 0.00 0.00 45.01 1.90
1869 4857 9.778741 TGGCAGATTTAGTAATACTAGAAATGG 57.221 33.333 6.03 1.40 31.47 3.16
2006 5026 7.997071 GCTGAAGCAGTGAATAAACTAAAAAC 58.003 34.615 0.00 0.00 41.59 2.43
2026 5048 6.479990 CACATCCGAGTAGAAATAATGCTGAA 59.520 38.462 0.00 0.00 0.00 3.02
2042 5064 1.807165 CTGCACCGACACATCCGAG 60.807 63.158 0.00 0.00 0.00 4.63
2066 5088 0.106708 AGCCGCATTCCATGACGTAT 59.893 50.000 0.00 0.00 0.00 3.06
2159 5210 1.678635 TTTTCCTGCCCGAGCCATG 60.679 57.895 0.00 0.00 38.69 3.66
2270 5334 4.079269 TCAAGGGGCCATTTTCTATCATGA 60.079 41.667 4.39 0.00 0.00 3.07
2364 5433 9.507329 AAAGAGCAATGTCAGAAAACTAGAATA 57.493 29.630 0.00 0.00 0.00 1.75
2380 5449 2.138596 ACGTGCCAAAAAGAGCAATG 57.861 45.000 0.00 0.00 41.48 2.82
2381 5450 3.505680 TGATACGTGCCAAAAAGAGCAAT 59.494 39.130 0.00 0.00 41.48 3.56
2397 5478 3.845178 TCTTAGCACCAACACTGATACG 58.155 45.455 0.00 0.00 0.00 3.06
2640 5744 6.408869 TGAGTTGTATCAATCAGCTGATTCA 58.591 36.000 33.95 25.80 42.41 2.57
2724 5828 6.648725 AACTTAGTTGCGCTATAAACAGAG 57.351 37.500 9.73 8.87 0.00 3.35
2814 5944 1.863454 CAATTCTGAAGAGGCCGATCG 59.137 52.381 8.51 8.51 0.00 3.69
2819 5949 2.746362 CACTGTCAATTCTGAAGAGGCC 59.254 50.000 0.00 0.00 31.88 5.19
2820 5950 3.188048 CACACTGTCAATTCTGAAGAGGC 59.812 47.826 0.00 0.00 31.88 4.70
2913 11760 1.135460 GCATCAAAGTCTGGAGCTTGC 60.135 52.381 0.00 0.00 0.00 4.01
3116 11974 2.887151 ATGGGACCTTCAAAGACCAG 57.113 50.000 0.00 0.00 31.25 4.00
3157 12015 7.375017 CGGCCAAAACGTTATGATAAGATTAAC 59.625 37.037 2.24 0.00 0.00 2.01
3243 12101 8.079211 TGCAAGGTAGTCTGTATCTTATTCTT 57.921 34.615 0.00 0.00 0.00 2.52
3428 12424 2.490115 TCAACACAACACAACCACTTCC 59.510 45.455 0.00 0.00 0.00 3.46
3449 12445 1.134521 TCTGTGTGCTCGACCAAAGTT 60.135 47.619 0.00 0.00 0.00 2.66
3450 12446 0.464036 TCTGTGTGCTCGACCAAAGT 59.536 50.000 0.00 0.00 0.00 2.66
3550 12546 9.587772 AAAGATATATACAGTTGACAGACACAC 57.412 33.333 0.00 0.00 0.00 3.82
3565 12561 8.454106 GGCCATTCATGACACAAAGATATATAC 58.546 37.037 0.00 0.00 0.00 1.47
3650 12646 5.767665 AGAACCAGCAACACATAACATAACA 59.232 36.000 0.00 0.00 0.00 2.41
3659 12655 6.403866 TGATAAAAAGAACCAGCAACACAT 57.596 33.333 0.00 0.00 0.00 3.21
3716 12712 0.102481 CAATACGAGGACCCACTCCG 59.898 60.000 0.00 0.00 45.10 4.63
3726 12722 6.507900 TGAGAATTAAGAGCTCAATACGAGG 58.492 40.000 17.77 0.00 42.55 4.63
3728 12724 8.948631 AAATGAGAATTAAGAGCTCAATACGA 57.051 30.769 17.77 0.00 41.48 3.43
3742 12738 3.963129 ACCGGCCAAGAAATGAGAATTA 58.037 40.909 0.00 0.00 0.00 1.40
3745 12741 3.644966 ATACCGGCCAAGAAATGAGAA 57.355 42.857 0.00 0.00 0.00 2.87
3779 12775 3.155167 GGGAGGAGGCCGACGAAT 61.155 66.667 0.00 0.00 0.00 3.34
3848 12844 3.238597 ACATATCTTCTCCCTCCTCTGC 58.761 50.000 0.00 0.00 0.00 4.26
3857 12853 1.543429 CCGCCCCAACATATCTTCTCC 60.543 57.143 0.00 0.00 0.00 3.71
4030 13028 1.032014 GTTTTGGCACCTCTGAGCAA 58.968 50.000 0.00 0.00 0.00 3.91
4058 13056 7.218204 GCCGAACTATGTTTATTTTGACATCAC 59.782 37.037 0.00 0.00 37.62 3.06
4070 13071 2.028294 TGGAACCGCCGAACTATGTTTA 60.028 45.455 0.00 0.00 40.66 2.01
4071 13072 1.270947 TGGAACCGCCGAACTATGTTT 60.271 47.619 0.00 0.00 40.66 2.83
4072 13073 0.322322 TGGAACCGCCGAACTATGTT 59.678 50.000 0.00 0.00 40.66 2.71
4120 13122 2.380084 TGAGCGAACCATGTTCCTAC 57.620 50.000 1.66 0.00 0.00 3.18
4142 13145 3.369576 CCTTTTAGGAGTGAGTAGGCCAC 60.370 52.174 5.01 0.54 37.67 5.01
4216 13220 9.998106 AAGTATTTCACTCTAGCTACTCAAAAA 57.002 29.630 0.00 0.00 36.04 1.94
4217 13221 9.424319 CAAGTATTTCACTCTAGCTACTCAAAA 57.576 33.333 0.00 0.00 36.04 2.44
4218 13222 8.803235 TCAAGTATTTCACTCTAGCTACTCAAA 58.197 33.333 0.00 0.00 36.04 2.69
4225 13229 9.732130 AAAATTCTCAAGTATTTCACTCTAGCT 57.268 29.630 0.00 0.00 36.04 3.32
4253 13257 8.265764 GGAGAAAAGGAAAGTATATGTGGTACT 58.734 37.037 0.00 0.00 33.98 2.73
4254 13258 8.265764 AGGAGAAAAGGAAAGTATATGTGGTAC 58.734 37.037 0.00 0.00 0.00 3.34
4270 13296 8.017418 AGTCATACTATCAAGAGGAGAAAAGG 57.983 38.462 0.00 0.00 0.00 3.11


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

AutoCloner maintained by Alex Coulton.