Multiple sequence alignment - TraesCS1D01G399300

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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 TraesCS1D01G399300 chr1D 100.000 2374 0 0 1 2374 465944465 465942092 0.000000e+00 4385
1 TraesCS1D01G399300 chr1D 95.192 104 3 2 2185 2286 362603727 362603830 1.890000e-36 163
2 TraesCS1D01G399300 chr1D 95.192 104 3 2 2183 2286 465890070 465889969 1.890000e-36 163
3 TraesCS1D01G399300 chr1B 92.116 1484 67 17 11 1454 642737575 642736102 0.000000e+00 2047
4 TraesCS1D01G399300 chr1B 91.613 310 18 6 2070 2374 642735076 642734770 2.820000e-114 422
5 TraesCS1D01G399300 chr1B 84.527 433 31 16 1455 1868 642736024 642735609 1.710000e-106 396
6 TraesCS1D01G399300 chr1B 95.968 124 5 0 1866 1989 642735469 642735346 4.000000e-48 202
7 TraesCS1D01G399300 chr1B 96.000 100 3 1 2187 2286 642679660 642679562 6.790000e-36 161
8 TraesCS1D01G399300 chr2A 82.343 572 70 15 103 658 141160049 141160605 3.570000e-128 468
9 TraesCS1D01G399300 chr2A 81.919 542 79 13 926 1453 141166447 141166983 7.790000e-120 440
10 TraesCS1D01G399300 chr2D 82.689 543 72 16 926 1453 133241311 133241846 1.660000e-126 462
11 TraesCS1D01G399300 chr2D 81.411 581 70 24 103 667 133237239 133237797 7.790000e-120 440
12 TraesCS1D01G399300 chr2B 81.239 581 76 17 103 667 189598941 189599504 2.800000e-119 438
13 TraesCS1D01G399300 chr1A 91.186 295 21 5 2067 2358 558194662 558194370 1.710000e-106 396
14 TraesCS1D01G399300 chr1A 89.590 317 19 4 1703 2008 558195062 558194749 7.960000e-105 390
15 TraesCS1D01G399300 chr1A 87.037 216 19 5 1461 1673 558195423 558195214 3.940000e-58 235
16 TraesCS1D01G399300 chr1A 95.283 106 2 3 2181 2286 462119951 462120053 5.250000e-37 165
17 TraesCS1D01G399300 chr3A 84.422 199 20 5 103 290 543728025 543727827 4.030000e-43 185
18 TraesCS1D01G399300 chr3A 93.396 106 4 3 2194 2297 497631374 497631270 1.140000e-33 154
19 TraesCS1D01G399300 chr4A 94.393 107 1 3 2184 2285 625489933 625489827 2.440000e-35 159
20 TraesCS1D01G399300 chr3B 93.396 106 5 2 2181 2286 683342465 683342568 3.160000e-34 156


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 TraesCS1D01G399300 chr1D 465942092 465944465 2373 True 4385.000000 4385 100.000 1 2374 1 chr1D.!!$R2 2373
1 TraesCS1D01G399300 chr1B 642734770 642737575 2805 True 766.750000 2047 91.056 11 2374 4 chr1B.!!$R2 2363
2 TraesCS1D01G399300 chr2A 141160049 141160605 556 False 468.000000 468 82.343 103 658 1 chr2A.!!$F1 555
3 TraesCS1D01G399300 chr2A 141166447 141166983 536 False 440.000000 440 81.919 926 1453 1 chr2A.!!$F2 527
4 TraesCS1D01G399300 chr2D 133237239 133241846 4607 False 451.000000 462 82.050 103 1453 2 chr2D.!!$F1 1350
5 TraesCS1D01G399300 chr2B 189598941 189599504 563 False 438.000000 438 81.239 103 667 1 chr2B.!!$F1 564
6 TraesCS1D01G399300 chr1A 558194370 558195423 1053 True 340.333333 396 89.271 1461 2358 3 chr1A.!!$R1 897

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
826 4129 0.397941 CTCTTCAGGTTGCCCAGTGA 59.602 55.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2201 6134 0.456142 CGAATCCTGCTGTCGACGAA 60.456 55.0 11.62 0.0 36.92 3.85 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
134 136 7.889873 AATATGGGAGTATCGAGGATCTTAG 57.110 40.000 0.00 0.00 34.37 2.18
198 205 5.586643 GGTTATGAACTCTTTTCAGGCTAGG 59.413 44.000 0.00 0.00 0.00 3.02
243 261 9.495754 GATCAGTTTTATTCTAAGTCATTGCAC 57.504 33.333 0.00 0.00 0.00 4.57
463 493 6.764560 GTGGTAGTTACTTTCAGGTTTCAAGA 59.235 38.462 0.00 0.00 0.00 3.02
474 504 2.296190 AGGTTTCAAGATTTTCCCGTGC 59.704 45.455 0.00 0.00 0.00 5.34
498 528 1.831580 ATCACTTCTTCCTTGGCTGC 58.168 50.000 0.00 0.00 0.00 5.25
502 532 1.593296 CTTCTTCCTTGGCTGCTGGC 61.593 60.000 10.40 10.40 40.90 4.85
591 626 9.743057 TTTTTATCATTGGAGGCATAAATAACG 57.257 29.630 0.00 0.00 0.00 3.18
616 651 7.201741 CGAAGTTCAGACTGATATTCCTAGTGA 60.202 40.741 17.85 0.00 35.91 3.41
689 3949 5.437289 TCTAACCAGAACACTTTGCATTG 57.563 39.130 0.00 0.00 0.00 2.82
753 4017 2.436469 TGGCGCTGGCATAGTGTG 60.436 61.111 7.64 0.00 42.47 3.82
754 4018 2.436646 GGCGCTGGCATAGTGTGT 60.437 61.111 7.64 0.00 42.47 3.72
755 4019 2.753966 GGCGCTGGCATAGTGTGTG 61.754 63.158 7.64 0.00 42.47 3.82
756 4020 2.034879 GCGCTGGCATAGTGTGTGT 61.035 57.895 0.00 0.00 39.16 3.72
757 4021 1.577328 GCGCTGGCATAGTGTGTGTT 61.577 55.000 0.00 0.00 39.16 3.32
758 4022 0.443869 CGCTGGCATAGTGTGTGTTC 59.556 55.000 0.00 0.00 32.17 3.18
785 4084 3.428870 CGATGGTCGGCTATGATGTTTAC 59.571 47.826 0.00 0.00 36.00 2.01
786 4085 4.632153 GATGGTCGGCTATGATGTTTACT 58.368 43.478 0.00 0.00 0.00 2.24
787 4086 3.792401 TGGTCGGCTATGATGTTTACTG 58.208 45.455 0.00 0.00 0.00 2.74
826 4129 0.397941 CTCTTCAGGTTGCCCAGTGA 59.602 55.000 0.00 0.00 0.00 3.41
843 4146 4.080863 CCAGTGAAAGGGAGCAGTACTAAT 60.081 45.833 0.00 0.00 0.00 1.73
850 4153 2.288273 GGGAGCAGTACTAATGGCGTAG 60.288 54.545 0.00 0.00 0.00 3.51
851 4154 2.361438 GGAGCAGTACTAATGGCGTAGT 59.639 50.000 0.00 6.03 37.98 2.73
852 4155 3.181478 GGAGCAGTACTAATGGCGTAGTT 60.181 47.826 0.00 0.00 35.85 2.24
853 4156 4.430908 GAGCAGTACTAATGGCGTAGTTT 58.569 43.478 0.00 0.00 35.85 2.66
854 4157 4.828829 AGCAGTACTAATGGCGTAGTTTT 58.171 39.130 0.00 0.00 35.85 2.43
855 4158 5.969423 AGCAGTACTAATGGCGTAGTTTTA 58.031 37.500 0.00 0.00 35.85 1.52
868 4182 8.156994 TGGCGTAGTTTTAGTCAAATTTTAGT 57.843 30.769 0.00 0.00 0.00 2.24
881 4195 9.768662 AGTCAAATTTTAGTCAAGCATTTTCAT 57.231 25.926 0.00 0.00 0.00 2.57
957 4288 5.553123 TCGGCTACTTTTCTTTGTTCCATA 58.447 37.500 0.00 0.00 0.00 2.74
980 4311 3.278574 CGGGGAATCAAGCAGTTATTCA 58.721 45.455 0.00 0.00 32.42 2.57
1010 4341 0.251922 AGCCCCACAATGCTTCACAT 60.252 50.000 0.00 0.00 42.30 3.21
1039 4370 5.288804 ACATTTGTTTTGTGTAGCCATGTC 58.711 37.500 0.00 0.00 0.00 3.06
1057 4388 5.870978 CCATGTCTTTTCTTAAATTGCTGGG 59.129 40.000 0.00 0.00 0.00 4.45
1058 4389 4.881920 TGTCTTTTCTTAAATTGCTGGGC 58.118 39.130 0.00 0.00 0.00 5.36
1156 4487 1.077930 TCATCTTGGCTGCTGCTCC 60.078 57.895 15.64 2.78 39.59 4.70
1190 4521 0.615331 ATGGCAGTGATCGGAACAGT 59.385 50.000 0.00 0.00 0.00 3.55
1200 4531 4.021229 TGATCGGAACAGTAGTGTGGTAT 58.979 43.478 3.39 0.00 36.84 2.73
1252 4587 2.996249 TTGCTTAGATCCTGCAGAGG 57.004 50.000 17.39 0.00 41.39 3.69
1331 4667 0.104855 GTGACAGCACACAGGTCTCA 59.895 55.000 0.00 0.00 44.51 3.27
1339 4675 1.135083 CACACAGGTCTCACCGGATAC 60.135 57.143 9.46 0.00 44.90 2.24
1355 4691 2.159028 GGATACCAGAAGCTCACTGTCC 60.159 54.545 16.14 13.29 34.04 4.02
1379 4728 2.760634 TCTCAATGCTGTAAAGCCGA 57.239 45.000 1.45 0.00 0.00 5.54
1457 4806 6.857437 CCAAAAGGATGGTAGAGGAATTTT 57.143 37.500 0.00 0.00 35.65 1.82
1458 4807 7.244886 CCAAAAGGATGGTAGAGGAATTTTT 57.755 36.000 0.00 0.00 35.65 1.94
1459 4808 7.099120 CCAAAAGGATGGTAGAGGAATTTTTG 58.901 38.462 0.00 0.00 35.65 2.44
1479 4906 5.596836 TTGTTGACAAGGCAGAAGAATTT 57.403 34.783 0.00 0.00 0.00 1.82
1597 5025 3.068165 TCTGACTAATGTACCATGAGGCG 59.932 47.826 0.00 0.00 39.06 5.52
1607 5038 5.478407 TGTACCATGAGGCGACATATTATG 58.522 41.667 0.00 2.03 39.06 1.90
1628 5059 2.289195 GGTGGCGATTACGGGATATGAA 60.289 50.000 0.00 0.00 40.15 2.57
1629 5060 3.596214 GTGGCGATTACGGGATATGAAT 58.404 45.455 0.00 0.00 40.15 2.57
1630 5061 4.382254 GGTGGCGATTACGGGATATGAATA 60.382 45.833 0.00 0.00 40.15 1.75
1631 5062 5.357257 GTGGCGATTACGGGATATGAATAT 58.643 41.667 0.00 0.00 40.15 1.28
1632 5063 5.234329 GTGGCGATTACGGGATATGAATATG 59.766 44.000 0.00 0.00 40.15 1.78
1633 5064 5.128008 TGGCGATTACGGGATATGAATATGA 59.872 40.000 0.00 0.00 40.15 2.15
1634 5065 6.183360 TGGCGATTACGGGATATGAATATGAT 60.183 38.462 0.00 0.00 40.15 2.45
1635 5066 6.706270 GGCGATTACGGGATATGAATATGATT 59.294 38.462 0.00 0.00 40.15 2.57
1673 5104 1.475280 CCGACCTGTTATCTTCGGTGA 59.525 52.381 0.66 0.00 44.90 4.02
1674 5105 2.100916 CCGACCTGTTATCTTCGGTGAT 59.899 50.000 0.66 0.00 44.90 3.06
1675 5106 3.116300 CGACCTGTTATCTTCGGTGATG 58.884 50.000 0.00 0.00 0.00 3.07
1677 5108 4.113354 GACCTGTTATCTTCGGTGATGTC 58.887 47.826 0.00 0.00 0.00 3.06
1679 5110 4.115516 CCTGTTATCTTCGGTGATGTCAG 58.884 47.826 2.18 8.53 33.17 3.51
1681 5112 3.513912 TGTTATCTTCGGTGATGTCAGGT 59.486 43.478 2.18 0.00 0.00 4.00
1694 5135 4.219725 TGATGTCAGGTTTGAGTCGTCATA 59.780 41.667 0.00 0.00 32.98 2.15
1713 5266 7.590322 TCGTCATATAGAGAATAAGTTTGCGAC 59.410 37.037 0.00 0.00 0.00 5.19
1715 5268 7.590322 GTCATATAGAGAATAAGTTTGCGACGA 59.410 37.037 0.00 0.00 0.00 4.20
1716 5269 8.132995 TCATATAGAGAATAAGTTTGCGACGAA 58.867 33.333 0.00 0.00 0.00 3.85
1745 5298 6.736110 ATATATGCCTCAAATTTGCCTGTT 57.264 33.333 13.54 1.29 0.00 3.16
1751 5308 4.747810 CCTCAAATTTGCCTGTTCATACC 58.252 43.478 13.54 0.00 0.00 2.73
1761 5318 3.193479 GCCTGTTCATACCCCAAAAGAAG 59.807 47.826 0.00 0.00 0.00 2.85
1762 5319 4.407365 CCTGTTCATACCCCAAAAGAAGT 58.593 43.478 0.00 0.00 0.00 3.01
1767 5324 5.570205 TCATACCCCAAAAGAAGTGTGTA 57.430 39.130 0.00 0.00 0.00 2.90
1878 5577 6.374333 ACTTTCAGTTCAAAGTCTGCTACAAA 59.626 34.615 0.00 0.00 41.87 2.83
1974 5683 4.605183 TCAGAAACCAAGAAACTTGGGAA 58.395 39.130 26.94 9.03 43.71 3.97
1977 5686 5.023452 AGAAACCAAGAAACTTGGGAAACT 58.977 37.500 26.94 18.74 43.71 2.66
1989 5698 5.063880 ACTTGGGAAACTGCAACTTAGTAG 58.936 41.667 0.00 0.00 0.00 2.57
1990 5699 3.408634 TGGGAAACTGCAACTTAGTAGC 58.591 45.455 0.00 0.00 0.00 3.58
1991 5700 3.181449 TGGGAAACTGCAACTTAGTAGCA 60.181 43.478 0.00 0.00 36.72 3.49
1992 5701 3.818773 GGGAAACTGCAACTTAGTAGCAA 59.181 43.478 0.00 0.00 37.89 3.91
1993 5702 4.277423 GGGAAACTGCAACTTAGTAGCAAA 59.723 41.667 0.00 0.00 37.89 3.68
1994 5703 5.048013 GGGAAACTGCAACTTAGTAGCAAAT 60.048 40.000 0.00 0.00 37.89 2.32
1995 5704 6.150474 GGGAAACTGCAACTTAGTAGCAAATA 59.850 38.462 0.00 0.00 37.89 1.40
1996 5705 7.244192 GGAAACTGCAACTTAGTAGCAAATAG 58.756 38.462 0.00 0.00 37.89 1.73
1997 5706 7.094762 GGAAACTGCAACTTAGTAGCAAATAGT 60.095 37.037 0.00 0.00 37.89 2.12
1998 5707 7.745620 AACTGCAACTTAGTAGCAAATAGTT 57.254 32.000 0.00 0.00 37.89 2.24
1999 5708 7.133891 ACTGCAACTTAGTAGCAAATAGTTG 57.866 36.000 0.00 0.00 45.17 3.16
2000 5709 6.934645 ACTGCAACTTAGTAGCAAATAGTTGA 59.065 34.615 7.18 2.75 45.20 3.18
2001 5710 7.118390 ACTGCAACTTAGTAGCAAATAGTTGAG 59.882 37.037 7.18 11.75 45.20 3.02
2002 5711 6.371548 TGCAACTTAGTAGCAAATAGTTGAGG 59.628 38.462 7.18 0.00 45.20 3.86
2003 5712 6.183360 GCAACTTAGTAGCAAATAGTTGAGGG 60.183 42.308 7.18 0.00 45.20 4.30
2004 5713 5.990668 ACTTAGTAGCAAATAGTTGAGGGG 58.009 41.667 7.18 0.00 36.83 4.79
2005 5714 3.283259 AGTAGCAAATAGTTGAGGGGC 57.717 47.619 7.18 0.00 36.83 5.80
2006 5715 2.576191 AGTAGCAAATAGTTGAGGGGCA 59.424 45.455 7.18 0.00 36.83 5.36
2007 5716 2.603075 AGCAAATAGTTGAGGGGCAA 57.397 45.000 7.18 0.00 36.83 4.52
2008 5717 2.888212 AGCAAATAGTTGAGGGGCAAA 58.112 42.857 7.18 0.00 38.44 3.68
2009 5718 3.238597 AGCAAATAGTTGAGGGGCAAAA 58.761 40.909 7.18 0.00 38.44 2.44
2010 5719 3.840078 AGCAAATAGTTGAGGGGCAAAAT 59.160 39.130 7.18 0.00 38.44 1.82
2011 5720 4.286808 AGCAAATAGTTGAGGGGCAAAATT 59.713 37.500 7.18 0.00 38.44 1.82
2012 5721 5.003160 GCAAATAGTTGAGGGGCAAAATTT 58.997 37.500 7.18 0.00 38.44 1.82
2013 5722 5.122239 GCAAATAGTTGAGGGGCAAAATTTC 59.878 40.000 7.18 0.00 38.44 2.17
2014 5723 6.229733 CAAATAGTTGAGGGGCAAAATTTCA 58.770 36.000 0.00 0.00 38.44 2.69
2015 5724 6.432403 AATAGTTGAGGGGCAAAATTTCAA 57.568 33.333 0.00 0.00 38.44 2.69
2016 5725 4.769345 AGTTGAGGGGCAAAATTTCAAA 57.231 36.364 0.00 0.00 38.44 2.69
2017 5726 5.109500 AGTTGAGGGGCAAAATTTCAAAA 57.891 34.783 0.00 0.00 38.44 2.44
2018 5727 5.504853 AGTTGAGGGGCAAAATTTCAAAAA 58.495 33.333 0.00 0.00 38.44 1.94
2039 5913 0.686789 AAAAGTTGAGGGGCAATGGC 59.313 50.000 0.00 0.00 39.03 4.40
2040 5914 0.471591 AAAGTTGAGGGGCAATGGCA 60.472 50.000 9.51 0.00 43.71 4.92
2043 5917 1.304381 TTGAGGGGCAATGGCAGTC 60.304 57.895 9.51 4.93 43.71 3.51
2052 5931 1.171308 CAATGGCAGTCAGTTCAGGG 58.829 55.000 0.00 0.00 0.00 4.45
2056 5935 1.376553 GCAGTCAGTTCAGGGAGCC 60.377 63.158 0.00 0.00 0.00 4.70
2125 6057 7.058354 CGTCAACAAAATATTATCGCAGCATAC 59.942 37.037 0.00 0.00 0.00 2.39
2304 6237 5.758296 TCGACTGCTCTGACAAAAGTTTTAT 59.242 36.000 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.244113 GCTACAGTTTGCAGTTAATTAGGAAAT 58.756 33.333 0.00 0.00 0.00 2.17
1 2 7.308951 GGCTACAGTTTGCAGTTAATTAGGAAA 60.309 37.037 0.00 0.00 0.00 3.13
2 3 6.150474 GGCTACAGTTTGCAGTTAATTAGGAA 59.850 38.462 0.00 0.00 0.00 3.36
3 4 5.646360 GGCTACAGTTTGCAGTTAATTAGGA 59.354 40.000 0.00 0.00 0.00 2.94
4 5 5.648092 AGGCTACAGTTTGCAGTTAATTAGG 59.352 40.000 0.00 0.00 0.00 2.69
5 6 6.743575 AGGCTACAGTTTGCAGTTAATTAG 57.256 37.500 0.00 0.00 0.00 1.73
6 7 6.072175 CCAAGGCTACAGTTTGCAGTTAATTA 60.072 38.462 0.00 0.00 0.00 1.40
7 8 5.278957 CCAAGGCTACAGTTTGCAGTTAATT 60.279 40.000 0.00 0.00 0.00 1.40
8 9 4.218417 CCAAGGCTACAGTTTGCAGTTAAT 59.782 41.667 0.00 0.00 0.00 1.40
9 10 3.568007 CCAAGGCTACAGTTTGCAGTTAA 59.432 43.478 0.00 0.00 0.00 2.01
20 21 2.839486 TGTGTCTTCCAAGGCTACAG 57.161 50.000 0.00 0.00 0.00 2.74
134 136 4.122046 GCATAGGTGGAAAAATGGATTGC 58.878 43.478 0.00 0.00 0.00 3.56
198 205 7.769220 ACTGATCAAATGAAAGAATCCATGAC 58.231 34.615 0.00 0.00 0.00 3.06
232 250 5.647658 TCTCCATTTATTCGTGCAATGACTT 59.352 36.000 0.00 0.00 30.66 3.01
243 261 5.808540 TCGTTTGGTACTCTCCATTTATTCG 59.191 40.000 0.00 0.00 37.33 3.34
369 395 2.011617 GCACCATGGATAGGGCCCTT 62.012 60.000 34.04 18.42 0.00 3.95
440 470 7.981102 ATCTTGAAACCTGAAAGTAACTACC 57.019 36.000 0.00 0.00 0.00 3.18
463 493 3.078837 AGTGATTTACGCACGGGAAAAT 58.921 40.909 0.00 0.00 41.04 1.82
474 504 4.003648 AGCCAAGGAAGAAGTGATTTACG 58.996 43.478 0.00 0.00 0.00 3.18
498 528 1.741706 CCAGATGTTAGTTGCTGCCAG 59.258 52.381 0.00 0.00 0.00 4.85
502 532 2.935201 GAGCTCCAGATGTTAGTTGCTG 59.065 50.000 0.87 0.00 0.00 4.41
508 538 7.095910 CAGGTAATATGAGCTCCAGATGTTAG 58.904 42.308 12.15 0.00 0.00 2.34
570 603 6.772716 ACTTCGTTATTTATGCCTCCAATGAT 59.227 34.615 0.00 0.00 0.00 2.45
591 626 8.001881 TCACTAGGAATATCAGTCTGAACTTC 57.998 38.462 6.64 11.93 31.71 3.01
680 3940 5.969423 AGAATGGGTTGATACAATGCAAAG 58.031 37.500 0.00 0.00 0.00 2.77
689 3949 6.149807 TCGGTTTTTGTAGAATGGGTTGATAC 59.850 38.462 0.00 0.00 0.00 2.24
753 4017 1.859080 GCCGACCATCGAATAGAACAC 59.141 52.381 0.00 0.00 43.74 3.32
754 4018 1.754803 AGCCGACCATCGAATAGAACA 59.245 47.619 0.00 0.00 43.74 3.18
755 4019 2.510768 AGCCGACCATCGAATAGAAC 57.489 50.000 0.00 0.00 43.74 3.01
756 4020 3.824443 TCATAGCCGACCATCGAATAGAA 59.176 43.478 0.00 0.00 43.74 2.10
757 4021 3.418047 TCATAGCCGACCATCGAATAGA 58.582 45.455 0.00 0.00 43.74 1.98
758 4022 3.850122 TCATAGCCGACCATCGAATAG 57.150 47.619 0.00 0.00 43.74 1.73
785 4084 1.613836 AAGAAAAGGAGCCACTGCAG 58.386 50.000 13.48 13.48 41.13 4.41
786 4085 2.071778 AAAGAAAAGGAGCCACTGCA 57.928 45.000 0.00 0.00 41.13 4.41
787 4086 2.625314 AGAAAAGAAAAGGAGCCACTGC 59.375 45.455 0.00 0.00 37.95 4.40
826 4129 2.420129 CGCCATTAGTACTGCTCCCTTT 60.420 50.000 5.39 0.00 0.00 3.11
843 4146 8.156994 ACTAAAATTTGACTAAAACTACGCCA 57.843 30.769 0.00 0.00 0.00 5.69
855 4158 9.768662 ATGAAAATGCTTGACTAAAATTTGACT 57.231 25.926 0.00 0.00 0.00 3.41
881 4195 9.098355 GAGCACACTCTTACAACATGAATTATA 57.902 33.333 0.00 0.00 40.03 0.98
923 4237 6.583562 AGAAAAGTAGCCGATAAGCAGTAAT 58.416 36.000 0.00 0.00 34.23 1.89
957 4288 0.988832 TAACTGCTTGATTCCCCGGT 59.011 50.000 0.00 0.00 0.00 5.28
1010 4341 6.043411 GGCTACACAAAACAAATGTTTACCA 58.957 36.000 11.60 0.00 46.47 3.25
1039 4370 5.702209 ACAATGCCCAGCAATTTAAGAAAAG 59.298 36.000 0.00 0.00 43.62 2.27
1156 4487 1.639280 GCCATAACAAACGGCAATGG 58.361 50.000 0.00 0.00 45.52 3.16
1331 4667 0.824759 GTGAGCTTCTGGTATCCGGT 59.175 55.000 0.00 0.00 0.00 5.28
1339 4675 0.389166 GTCGGACAGTGAGCTTCTGG 60.389 60.000 19.14 6.56 37.25 3.86
1355 4691 3.242543 GGCTTTACAGCATTGAGATGTCG 60.243 47.826 2.81 0.00 45.25 4.35
1379 4728 1.628846 ACCGCCTTTTCCTGATACTGT 59.371 47.619 0.00 0.00 0.00 3.55
1454 4803 5.398603 TTCTTCTGCCTTGTCAACAAAAA 57.601 34.783 0.00 0.00 35.15 1.94
1455 4804 5.596836 ATTCTTCTGCCTTGTCAACAAAA 57.403 34.783 0.00 0.00 35.15 2.44
1456 4805 5.596836 AATTCTTCTGCCTTGTCAACAAA 57.403 34.783 0.00 0.00 35.15 2.83
1457 4806 5.596836 AAATTCTTCTGCCTTGTCAACAA 57.403 34.783 0.00 0.00 0.00 2.83
1458 4807 5.596836 AAAATTCTTCTGCCTTGTCAACA 57.403 34.783 0.00 0.00 0.00 3.33
1459 4808 5.812127 ACAAAAATTCTTCTGCCTTGTCAAC 59.188 36.000 0.00 0.00 0.00 3.18
1597 5025 4.328983 CCGTAATCGCCACCATAATATGTC 59.671 45.833 0.00 0.00 35.54 3.06
1607 5038 1.274167 TCATATCCCGTAATCGCCACC 59.726 52.381 0.00 0.00 35.54 4.61
1628 5059 8.098912 GGGTAAACCGGAACTATACAATCATAT 58.901 37.037 9.46 0.00 36.71 1.78
1629 5060 7.444299 GGGTAAACCGGAACTATACAATCATA 58.556 38.462 9.46 0.00 36.71 2.15
1630 5061 6.293698 GGGTAAACCGGAACTATACAATCAT 58.706 40.000 9.46 0.00 36.71 2.45
1631 5062 5.673514 GGGTAAACCGGAACTATACAATCA 58.326 41.667 9.46 0.00 36.71 2.57
1646 5077 3.900966 AGATAACAGGTCGGGTAAACC 57.099 47.619 0.00 0.00 37.03 3.27
1658 5089 4.115516 CCTGACATCACCGAAGATAACAG 58.884 47.826 0.00 0.00 33.84 3.16
1665 5096 2.738846 CTCAAACCTGACATCACCGAAG 59.261 50.000 0.00 0.00 0.00 3.79
1673 5104 3.685139 ATGACGACTCAAACCTGACAT 57.315 42.857 0.00 0.00 0.00 3.06
1674 5105 4.801330 ATATGACGACTCAAACCTGACA 57.199 40.909 0.00 0.00 0.00 3.58
1675 5106 6.038382 TCTCTATATGACGACTCAAACCTGAC 59.962 42.308 0.00 0.00 0.00 3.51
1677 5108 6.378710 TCTCTATATGACGACTCAAACCTG 57.621 41.667 0.00 0.00 0.00 4.00
1679 5110 9.400638 CTTATTCTCTATATGACGACTCAAACC 57.599 37.037 0.00 0.00 0.00 3.27
1694 5135 6.253727 CACTTCGTCGCAAACTTATTCTCTAT 59.746 38.462 0.00 0.00 0.00 1.98
1713 5266 9.385902 CAAATTTGAGGCATATATAACACTTCG 57.614 33.333 13.08 0.00 0.00 3.79
1715 5268 8.143835 GGCAAATTTGAGGCATATATAACACTT 58.856 33.333 22.31 0.00 0.00 3.16
1716 5269 7.506938 AGGCAAATTTGAGGCATATATAACACT 59.493 33.333 22.31 0.00 0.00 3.55
1724 5277 4.467082 TGAACAGGCAAATTTGAGGCATAT 59.533 37.500 22.31 1.08 0.00 1.78
1745 5298 4.447138 ACACACTTCTTTTGGGGTATGA 57.553 40.909 0.00 0.00 0.00 2.15
1751 5308 7.095695 TCTTCTTTTACACACTTCTTTTGGG 57.904 36.000 0.00 0.00 0.00 4.12
1761 5318 8.545420 TGATCGTTACTTTCTTCTTTTACACAC 58.455 33.333 0.00 0.00 0.00 3.82
1762 5319 8.651391 TGATCGTTACTTTCTTCTTTTACACA 57.349 30.769 0.00 0.00 0.00 3.72
1767 5324 8.209917 ACAGTTGATCGTTACTTTCTTCTTTT 57.790 30.769 0.00 0.00 0.00 2.27
1878 5577 7.151999 TCACAGTTTAACAGTTTTGTGTGAT 57.848 32.000 12.05 0.00 37.67 3.06
1974 5683 7.444183 TCAACTATTTGCTACTAAGTTGCAGTT 59.556 33.333 8.30 0.00 43.79 3.16
1977 5686 6.371548 CCTCAACTATTTGCTACTAAGTTGCA 59.628 38.462 8.30 0.00 44.18 4.08
1989 5698 3.676291 TTTTGCCCCTCAACTATTTGC 57.324 42.857 0.00 0.00 33.73 3.68
1990 5699 6.229733 TGAAATTTTGCCCCTCAACTATTTG 58.770 36.000 0.00 0.00 33.17 2.32
1991 5700 6.432403 TGAAATTTTGCCCCTCAACTATTT 57.568 33.333 0.00 0.00 34.50 1.40
1992 5701 6.432403 TTGAAATTTTGCCCCTCAACTATT 57.568 33.333 0.00 0.00 33.73 1.73
1993 5702 6.432403 TTTGAAATTTTGCCCCTCAACTAT 57.568 33.333 0.00 0.00 33.73 2.12
1994 5703 5.878406 TTTGAAATTTTGCCCCTCAACTA 57.122 34.783 0.00 0.00 33.73 2.24
1995 5704 4.769345 TTTGAAATTTTGCCCCTCAACT 57.231 36.364 0.00 0.00 33.73 3.16
1996 5705 5.826601 TTTTTGAAATTTTGCCCCTCAAC 57.173 34.783 0.00 0.00 33.73 3.18
2019 5728 1.072173 GCCATTGCCCCTCAACTTTTT 59.928 47.619 0.00 0.00 37.53 1.94
2022 5896 0.901580 CTGCCATTGCCCCTCAACTT 60.902 55.000 0.00 0.00 37.53 2.66
2039 5913 1.079543 CGGCTCCCTGAACTGACTG 60.080 63.158 0.00 0.00 0.00 3.51
2040 5914 0.616111 ATCGGCTCCCTGAACTGACT 60.616 55.000 0.00 0.00 0.00 3.41
2043 5917 1.817099 GCATCGGCTCCCTGAACTG 60.817 63.158 0.00 0.00 36.96 3.16
2052 5931 1.153086 ATGAACAGGGCATCGGCTC 60.153 57.895 0.00 0.00 42.47 4.70
2056 5935 1.452110 TGTTCATGAACAGGGCATCG 58.548 50.000 32.36 0.00 45.42 3.84
2093 6024 6.413526 GCGATAATATTTTGTTGACGCAATCA 59.586 34.615 0.00 0.00 42.39 2.57
2125 6057 8.863049 CGTTTGAGATTTGAGGGAATATTTTTG 58.137 33.333 0.00 0.00 0.00 2.44
2135 6067 3.129287 CCCATTCGTTTGAGATTTGAGGG 59.871 47.826 0.00 0.00 0.00 4.30
2201 6134 0.456142 CGAATCCTGCTGTCGACGAA 60.456 55.000 11.62 0.00 36.92 3.85
2310 6243 9.661563 CAGGGTACATAGTTTCTAACATTTACA 57.338 33.333 0.00 0.00 0.00 2.41
2317 6250 7.201617 GCAATGACAGGGTACATAGTTTCTAAC 60.202 40.741 0.00 0.00 0.00 2.34
2323 6256 4.568072 TGCAATGACAGGGTACATAGTT 57.432 40.909 0.00 0.00 0.00 2.24
2325 6258 4.883585 ACAATGCAATGACAGGGTACATAG 59.116 41.667 9.20 0.00 0.00 2.23
2326 6259 4.639755 CACAATGCAATGACAGGGTACATA 59.360 41.667 9.20 0.00 0.00 2.29
2327 6260 3.444742 CACAATGCAATGACAGGGTACAT 59.555 43.478 9.20 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.