Multiple sequence alignment - TraesCS3D01G099200

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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 TraesCS3D01G099200 chr3D 100.000 2168 0 0 1 2168 50881615 50879448 0.000000e+00 4004.0
1 TraesCS3D01G099200 chr3D 89.796 98 8 2 1948 2044 12459652 12459748 9.420000e-25 124.0
2 TraesCS3D01G099200 chr3D 100.000 67 0 0 2441 2507 50879175 50879109 9.420000e-25 124.0
3 TraesCS3D01G099200 chr3D 97.619 42 1 0 537 578 94802893 94802934 3.460000e-09 73.1
4 TraesCS3D01G099200 chr3D 95.238 42 0 2 537 578 574387765 574387804 5.790000e-07 65.8
5 TraesCS3D01G099200 chr3A 95.910 1198 30 10 580 1762 63838464 63837271 0.000000e+00 1923.0
6 TraesCS3D01G099200 chr3A 91.636 538 34 8 10 543 63838995 63838465 0.000000e+00 734.0
7 TraesCS3D01G099200 chr3A 88.636 132 13 2 2039 2168 63835535 63835404 2.580000e-35 159.0
8 TraesCS3D01G099200 chr3B 95.290 1189 27 12 580 1747 81334540 81333360 0.000000e+00 1858.0
9 TraesCS3D01G099200 chr3B 93.850 439 15 6 109 546 81334969 81334542 0.000000e+00 651.0
10 TraesCS3D01G099200 chr3B 97.119 243 5 2 1928 2168 81332764 81332522 2.320000e-110 409.0
11 TraesCS3D01G099200 chr3B 97.059 68 1 1 2441 2507 81332448 81332381 2.040000e-21 113.0
12 TraesCS3D01G099200 chr7D 91.489 94 8 0 1951 2044 62232696 62232789 2.020000e-26 130.0
13 TraesCS3D01G099200 chr7D 92.391 92 6 1 1953 2044 62255595 62255685 2.020000e-26 130.0
14 TraesCS3D01G099200 chr7D 97.436 39 0 1 536 574 18221880 18221843 5.790000e-07 65.8
15 TraesCS3D01G099200 chr6D 90.816 98 7 2 1947 2044 10745263 10745358 2.020000e-26 130.0
16 TraesCS3D01G099200 chr2D 90.816 98 5 4 1948 2044 633225330 633225236 7.280000e-26 128.0
17 TraesCS3D01G099200 chr4D 89.899 99 8 2 1946 2044 12648683 12648779 2.620000e-25 126.0
18 TraesCS3D01G099200 chr1D 91.398 93 6 2 1952 2044 315545658 315545748 2.620000e-25 126.0
19 TraesCS3D01G099200 chr1B 83.333 132 12 9 1916 2044 398381265 398381389 2.040000e-21 113.0
20 TraesCS3D01G099200 chr1B 88.235 51 2 4 526 574 16238387 16238435 9.690000e-05 58.4
21 TraesCS3D01G099200 chr1A 83.636 110 13 5 2 109 508103972 508104078 5.710000e-17 99.0
22 TraesCS3D01G099200 chr1A 82.143 84 10 4 10 91 592106039 592106119 1.610000e-07 67.6
23 TraesCS3D01G099200 chr1A 77.885 104 19 4 1 101 26590609 26590507 7.490000e-06 62.1
24 TraesCS3D01G099200 chr1A 87.037 54 3 3 523 572 539420059 539420006 9.690000e-05 58.4
25 TraesCS3D01G099200 chr2B 93.617 47 1 2 530 575 229991614 229991659 4.470000e-08 69.4
26 TraesCS3D01G099200 chr6B 100.000 36 0 0 539 574 27938515 27938480 1.610000e-07 67.6
27 TraesCS3D01G099200 chr6B 95.122 41 2 0 534 574 339371426 339371386 5.790000e-07 65.8
28 TraesCS3D01G099200 chr2A 95.238 42 1 1 537 578 162284216 162284176 5.790000e-07 65.8


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 TraesCS3D01G099200 chr3D 50879109 50881615 2506 True 2064.000000 4004 100.000000 1 2507 2 chr3D.!!$R1 2506
1 TraesCS3D01G099200 chr3A 63835404 63838995 3591 True 938.666667 1923 92.060667 10 2168 3 chr3A.!!$R1 2158
2 TraesCS3D01G099200 chr3B 81332381 81334969 2588 True 757.750000 1858 95.829500 109 2507 4 chr3B.!!$R1 2398

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
92 94 0.325272 GGCCGGATTATCCTCCTTCC 59.675 60.0 5.05 0.0 33.3 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1758 1830 0.035176 TCTTTTGGCCCATTGCTTGC 59.965 50.0 0.0 0.0 40.92 4.01 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
63 64 9.955102 AATAATATATGACTGTGTGCATCATCT 57.045 29.630 3.07 0.00 34.86 2.90
75 76 2.776312 CATCATCTTGATGCACAGGC 57.224 50.000 4.68 0.00 46.37 4.85
79 80 1.913951 ATCTTGATGCACAGGCCGGA 61.914 55.000 10.86 0.00 40.13 5.14
91 93 1.002544 CAGGCCGGATTATCCTCCTTC 59.997 57.143 15.90 0.66 35.78 3.46
92 94 0.325272 GGCCGGATTATCCTCCTTCC 59.675 60.000 5.05 0.00 33.30 3.46
93 95 1.056660 GCCGGATTATCCTCCTTCCA 58.943 55.000 5.05 0.00 33.30 3.53
94 96 1.420138 GCCGGATTATCCTCCTTCCAA 59.580 52.381 5.05 0.00 33.30 3.53
95 97 2.158667 GCCGGATTATCCTCCTTCCAAA 60.159 50.000 5.05 0.00 33.30 3.28
102 104 7.093945 CGGATTATCCTCCTTCCAAAAGAAAAA 60.094 37.037 9.78 0.00 33.30 1.94
103 105 8.253810 GGATTATCCTCCTTCCAAAAGAAAAAG 58.746 37.037 3.59 0.00 31.79 2.27
106 108 7.675161 ATCCTCCTTCCAAAAGAAAAAGAAA 57.325 32.000 0.00 0.00 34.14 2.52
112 114 9.382275 TCCTTCCAAAAGAAAAAGAAAAATCAG 57.618 29.630 0.00 0.00 34.14 2.90
137 140 3.749088 CCGCACTAAAAACATGTACTCCA 59.251 43.478 0.00 0.00 0.00 3.86
141 144 6.348132 CGCACTAAAAACATGTACTCCAATGA 60.348 38.462 0.00 0.00 0.00 2.57
152 155 6.109156 TGTACTCCAATGACTGTTGTACAT 57.891 37.500 0.00 0.00 37.13 2.29
159 162 3.207265 TGACTGTTGTACATGTGGCTT 57.793 42.857 9.11 0.00 0.00 4.35
473 477 2.865308 CGCATCAGTGTGCTGTGG 59.135 61.111 13.40 0.00 42.88 4.17
485 489 2.133281 TGCTGTGGCATTATTGAGCT 57.867 45.000 0.00 0.00 44.28 4.09
486 490 2.449464 TGCTGTGGCATTATTGAGCTT 58.551 42.857 0.00 0.00 44.28 3.74
488 492 2.223665 GCTGTGGCATTATTGAGCTTCC 60.224 50.000 0.00 0.00 38.54 3.46
490 494 1.683385 GTGGCATTATTGAGCTTCCCC 59.317 52.381 0.00 0.00 0.00 4.81
491 495 1.332195 GGCATTATTGAGCTTCCCCC 58.668 55.000 0.00 0.00 0.00 5.40
536 544 7.373493 GGTCGACCGAGGAGAAAAATATATAA 58.627 38.462 20.85 0.00 0.00 0.98
539 547 9.991906 TCGACCGAGGAGAAAAATATATAAAAT 57.008 29.630 0.00 0.00 0.00 1.82
555 563 5.952347 ATAAAATCAACTACTCCCTCCGT 57.048 39.130 0.00 0.00 0.00 4.69
556 564 4.635699 AAAATCAACTACTCCCTCCGTT 57.364 40.909 0.00 0.00 0.00 4.44
557 565 3.889520 AATCAACTACTCCCTCCGTTC 57.110 47.619 0.00 0.00 0.00 3.95
558 566 1.553706 TCAACTACTCCCTCCGTTCC 58.446 55.000 0.00 0.00 0.00 3.62
559 567 1.203087 TCAACTACTCCCTCCGTTCCA 60.203 52.381 0.00 0.00 0.00 3.53
560 568 1.621814 CAACTACTCCCTCCGTTCCAA 59.378 52.381 0.00 0.00 0.00 3.53
561 569 2.019807 ACTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
562 570 2.547990 ACTACTCCCTCCGTTCCAAAT 58.452 47.619 0.00 0.00 0.00 2.32
563 571 2.910977 ACTACTCCCTCCGTTCCAAATT 59.089 45.455 0.00 0.00 0.00 1.82
564 572 4.098894 ACTACTCCCTCCGTTCCAAATTA 58.901 43.478 0.00 0.00 0.00 1.40
565 573 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
566 574 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
567 575 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
568 576 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
569 577 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
570 578 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
571 579 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
572 580 2.030007 TCCGTTCCAAATTACTCGTCGT 60.030 45.455 0.00 0.00 0.00 4.34
573 581 2.091588 CCGTTCCAAATTACTCGTCGTG 59.908 50.000 0.00 0.00 0.00 4.35
574 582 2.981805 CGTTCCAAATTACTCGTCGTGA 59.018 45.455 0.56 0.00 0.00 4.35
666 677 6.463049 GCTCCTTCCTTATGCACTGATTAGTA 60.463 42.308 0.00 0.00 34.74 1.82
1623 1664 9.793252 GCATGTCTCACATTTATTATTGTCTTT 57.207 29.630 0.00 0.00 36.53 2.52
1756 1828 5.356751 TGCTTTGTGACACTTCTGTTGTAAT 59.643 36.000 7.20 0.00 0.00 1.89
1758 1830 6.197096 GCTTTGTGACACTTCTGTTGTAATTG 59.803 38.462 7.20 0.00 0.00 2.32
1788 3768 1.419762 GGCCAAAAGACCCAAACCAAT 59.580 47.619 0.00 0.00 0.00 3.16
1789 3769 2.158682 GGCCAAAAGACCCAAACCAATT 60.159 45.455 0.00 0.00 0.00 2.32
1790 3770 3.550820 GCCAAAAGACCCAAACCAATTT 58.449 40.909 0.00 0.00 0.00 1.82
1791 3771 3.951037 GCCAAAAGACCCAAACCAATTTT 59.049 39.130 0.00 0.00 0.00 1.82
1792 3772 4.400884 GCCAAAAGACCCAAACCAATTTTT 59.599 37.500 0.00 0.00 0.00 1.94
1816 3796 1.305201 TGCAACCAAGACCGAAGAAC 58.695 50.000 0.00 0.00 0.00 3.01
1817 3797 0.591659 GCAACCAAGACCGAAGAACC 59.408 55.000 0.00 0.00 0.00 3.62
1824 3804 3.072211 CAAGACCGAAGAACCCCTTAAC 58.928 50.000 0.00 0.00 34.68 2.01
1835 3815 2.807676 ACCCCTTAACTTTGATGCCAG 58.192 47.619 0.00 0.00 0.00 4.85
1840 3820 4.156008 CCCTTAACTTTGATGCCAGTGTAC 59.844 45.833 0.00 0.00 0.00 2.90
1842 3822 2.543777 ACTTTGATGCCAGTGTACGT 57.456 45.000 0.00 0.00 0.00 3.57
1843 3823 2.413837 ACTTTGATGCCAGTGTACGTC 58.586 47.619 0.00 0.00 0.00 4.34
1844 3824 2.224185 ACTTTGATGCCAGTGTACGTCA 60.224 45.455 0.00 2.09 0.00 4.35
1845 3825 1.790755 TTGATGCCAGTGTACGTCAC 58.209 50.000 0.00 0.00 46.46 3.67
1858 3838 6.187125 GTGTACGTCACCAGTCTATTAAGA 57.813 41.667 0.00 0.00 40.84 2.10
1859 3839 6.793349 GTGTACGTCACCAGTCTATTAAGAT 58.207 40.000 0.00 0.00 40.84 2.40
1860 3840 6.691818 GTGTACGTCACCAGTCTATTAAGATG 59.308 42.308 0.00 0.00 40.84 2.90
1861 3841 4.683832 ACGTCACCAGTCTATTAAGATGC 58.316 43.478 0.00 0.00 33.30 3.91
1862 3842 4.159693 ACGTCACCAGTCTATTAAGATGCA 59.840 41.667 0.00 0.00 33.30 3.96
1863 3843 4.504461 CGTCACCAGTCTATTAAGATGCAC 59.496 45.833 0.00 0.00 33.30 4.57
1864 3844 5.665459 GTCACCAGTCTATTAAGATGCACT 58.335 41.667 0.00 0.00 33.30 4.40
1865 3845 6.459710 CGTCACCAGTCTATTAAGATGCACTA 60.460 42.308 0.00 0.00 33.30 2.74
1866 3846 7.265673 GTCACCAGTCTATTAAGATGCACTAA 58.734 38.462 0.00 0.00 33.30 2.24
1867 3847 7.436673 GTCACCAGTCTATTAAGATGCACTAAG 59.563 40.741 0.00 0.00 33.30 2.18
1868 3848 7.342026 TCACCAGTCTATTAAGATGCACTAAGA 59.658 37.037 0.00 0.00 33.30 2.10
1869 3849 7.981789 CACCAGTCTATTAAGATGCACTAAGAA 59.018 37.037 0.00 0.00 33.30 2.52
1870 3850 8.200792 ACCAGTCTATTAAGATGCACTAAGAAG 58.799 37.037 0.00 0.00 33.30 2.85
1871 3851 8.417106 CCAGTCTATTAAGATGCACTAAGAAGA 58.583 37.037 0.00 0.00 33.30 2.87
1872 3852 9.809096 CAGTCTATTAAGATGCACTAAGAAGAA 57.191 33.333 0.00 0.00 33.30 2.52
1873 3853 9.810545 AGTCTATTAAGATGCACTAAGAAGAAC 57.189 33.333 0.00 0.00 33.30 3.01
1874 3854 9.587772 GTCTATTAAGATGCACTAAGAAGAACA 57.412 33.333 0.00 0.00 33.30 3.18
1896 3876 9.448294 GAACATACGAAGACGAGTATAAGAAAT 57.552 33.333 0.00 0.00 42.66 2.17
1903 3883 8.686418 CGAAGACGAGTATAAGAAATGAGATTG 58.314 37.037 0.00 0.00 42.66 2.67
1906 3886 9.953697 AGACGAGTATAAGAAATGAGATTGTAC 57.046 33.333 0.00 0.00 0.00 2.90
1907 3887 8.783999 ACGAGTATAAGAAATGAGATTGTACG 57.216 34.615 0.00 0.00 0.00 3.67
1908 3888 8.404000 ACGAGTATAAGAAATGAGATTGTACGT 58.596 33.333 0.00 0.00 0.00 3.57
1909 3889 8.893884 CGAGTATAAGAAATGAGATTGTACGTC 58.106 37.037 0.00 0.00 0.00 4.34
1910 3890 9.731819 GAGTATAAGAAATGAGATTGTACGTCA 57.268 33.333 0.00 0.00 0.00 4.35
1911 3891 9.517609 AGTATAAGAAATGAGATTGTACGTCAC 57.482 33.333 0.00 0.00 0.00 3.67
1912 3892 7.772332 ATAAGAAATGAGATTGTACGTCACC 57.228 36.000 0.00 0.00 0.00 4.02
1913 3893 5.147330 AGAAATGAGATTGTACGTCACCA 57.853 39.130 0.00 0.00 0.00 4.17
1914 3894 5.171476 AGAAATGAGATTGTACGTCACCAG 58.829 41.667 0.00 0.00 0.00 4.00
1916 3896 3.570926 TGAGATTGTACGTCACCAGTC 57.429 47.619 0.00 0.00 0.00 3.51
1917 3897 3.154710 TGAGATTGTACGTCACCAGTCT 58.845 45.455 0.00 0.00 31.25 3.24
1919 3899 4.155462 TGAGATTGTACGTCACCAGTCTAC 59.845 45.833 0.00 0.00 29.05 2.59
1921 3901 2.574006 TGTACGTCACCAGTCTACCT 57.426 50.000 0.00 0.00 0.00 3.08
1922 3902 2.430465 TGTACGTCACCAGTCTACCTC 58.570 52.381 0.00 0.00 0.00 3.85
1924 3904 0.959372 ACGTCACCAGTCTACCTCCG 60.959 60.000 0.00 0.00 0.00 4.63
1925 3905 0.959372 CGTCACCAGTCTACCTCCGT 60.959 60.000 0.00 0.00 0.00 4.69
1926 3906 1.254954 GTCACCAGTCTACCTCCGTT 58.745 55.000 0.00 0.00 0.00 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 7.487829 TGCAAAATTCAATAGCCGAATAACTTC 59.512 33.333 0.00 0.00 32.79 3.01
6 7 7.319646 TGCAAAATTCAATAGCCGAATAACTT 58.680 30.769 0.00 0.00 32.79 2.66
7 8 6.862209 TGCAAAATTCAATAGCCGAATAACT 58.138 32.000 0.00 0.00 32.79 2.24
8 9 7.698836 ATGCAAAATTCAATAGCCGAATAAC 57.301 32.000 0.00 0.00 32.79 1.89
57 58 1.688772 GGCCTGTGCATCAAGATGAT 58.311 50.000 13.93 0.00 41.20 2.45
63 64 0.254462 TAATCCGGCCTGTGCATCAA 59.746 50.000 0.00 0.00 40.13 2.57
71 72 1.002544 GAAGGAGGATAATCCGGCCTG 59.997 57.143 0.00 0.00 42.63 4.85
74 75 1.056660 TGGAAGGAGGATAATCCGGC 58.943 55.000 0.00 0.00 44.65 6.13
75 76 3.857157 TTTGGAAGGAGGATAATCCGG 57.143 47.619 0.00 0.00 44.65 5.14
79 80 8.956446 TCTTTTTCTTTTGGAAGGAGGATAAT 57.044 30.769 0.00 0.00 35.16 1.28
91 93 8.116136 CGGTTCTGATTTTTCTTTTTCTTTTGG 58.884 33.333 0.00 0.00 0.00 3.28
92 94 7.635973 GCGGTTCTGATTTTTCTTTTTCTTTTG 59.364 33.333 0.00 0.00 0.00 2.44
93 95 7.333174 TGCGGTTCTGATTTTTCTTTTTCTTTT 59.667 29.630 0.00 0.00 0.00 2.27
94 96 6.816140 TGCGGTTCTGATTTTTCTTTTTCTTT 59.184 30.769 0.00 0.00 0.00 2.52
95 97 6.255670 GTGCGGTTCTGATTTTTCTTTTTCTT 59.744 34.615 0.00 0.00 0.00 2.52
102 104 6.385649 TTTTAGTGCGGTTCTGATTTTTCT 57.614 33.333 0.00 0.00 0.00 2.52
103 105 6.474102 TGTTTTTAGTGCGGTTCTGATTTTTC 59.526 34.615 0.00 0.00 0.00 2.29
106 108 5.508200 TGTTTTTAGTGCGGTTCTGATTT 57.492 34.783 0.00 0.00 0.00 2.17
112 114 5.352643 AGTACATGTTTTTAGTGCGGTTC 57.647 39.130 2.30 0.00 0.00 3.62
137 140 3.754965 AGCCACATGTACAACAGTCATT 58.245 40.909 0.00 0.00 0.00 2.57
141 144 3.815401 GAGAAAGCCACATGTACAACAGT 59.185 43.478 0.00 0.00 0.00 3.55
152 155 0.178992 CCCAACCAGAGAAAGCCACA 60.179 55.000 0.00 0.00 0.00 4.17
159 162 2.637872 CAAGACCTACCCAACCAGAGAA 59.362 50.000 0.00 0.00 0.00 2.87
488 492 1.227556 GATCGATCCACGTTGGGGG 60.228 63.158 14.76 0.00 43.13 5.40
490 494 4.438346 GGATCGATCCACGTTGGG 57.562 61.111 34.65 0.00 46.38 4.12
536 544 3.055312 GGAACGGAGGGAGTAGTTGATTT 60.055 47.826 0.00 0.00 0.00 2.17
539 547 1.203087 TGGAACGGAGGGAGTAGTTGA 60.203 52.381 0.00 0.00 0.00 3.18
540 548 1.263356 TGGAACGGAGGGAGTAGTTG 58.737 55.000 0.00 0.00 0.00 3.16
543 551 3.629142 AATTTGGAACGGAGGGAGTAG 57.371 47.619 0.00 0.00 0.00 2.57
544 552 4.098894 AGTAATTTGGAACGGAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
545 553 2.910977 AGTAATTTGGAACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
546 554 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
547 555 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
548 556 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
549 557 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
550 558 2.597305 CGACGAGTAATTTGGAACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
551 559 2.030007 ACGACGAGTAATTTGGAACGGA 60.030 45.455 0.00 0.00 0.00 4.69
552 560 2.091588 CACGACGAGTAATTTGGAACGG 59.908 50.000 0.00 0.00 0.00 4.44
553 561 2.981805 TCACGACGAGTAATTTGGAACG 59.018 45.455 0.00 0.00 0.00 3.95
554 562 4.563524 CTCACGACGAGTAATTTGGAAC 57.436 45.455 0.00 0.00 36.94 3.62
566 574 1.068748 GTTGCCTTCTACTCACGACGA 60.069 52.381 0.00 0.00 0.00 4.20
567 575 1.068472 AGTTGCCTTCTACTCACGACG 60.068 52.381 0.00 0.00 0.00 5.12
568 576 2.726832 AGTTGCCTTCTACTCACGAC 57.273 50.000 0.00 0.00 0.00 4.34
569 577 3.418995 ACTAGTTGCCTTCTACTCACGA 58.581 45.455 0.00 0.00 31.09 4.35
570 578 3.851976 ACTAGTTGCCTTCTACTCACG 57.148 47.619 0.00 0.00 31.09 4.35
571 579 5.785243 AGAAACTAGTTGCCTTCTACTCAC 58.215 41.667 9.34 0.00 31.09 3.51
572 580 6.350277 GCTAGAAACTAGTTGCCTTCTACTCA 60.350 42.308 9.34 0.00 31.09 3.41
573 581 6.037726 GCTAGAAACTAGTTGCCTTCTACTC 58.962 44.000 9.34 0.00 31.09 2.59
574 582 5.717654 AGCTAGAAACTAGTTGCCTTCTACT 59.282 40.000 9.34 9.26 33.12 2.57
575 583 5.968254 AGCTAGAAACTAGTTGCCTTCTAC 58.032 41.667 9.34 7.45 30.90 2.59
576 584 6.607004 AAGCTAGAAACTAGTTGCCTTCTA 57.393 37.500 9.34 11.13 30.90 2.10
577 585 5.491323 AAGCTAGAAACTAGTTGCCTTCT 57.509 39.130 9.34 10.55 32.95 2.85
578 586 6.631962 TCTAAGCTAGAAACTAGTTGCCTTC 58.368 40.000 9.34 2.77 0.00 3.46
637 648 2.103941 AGTGCATAAGGAAGGAGCTAGC 59.896 50.000 6.62 6.62 0.00 3.42
666 677 1.290203 CTCACGCTTACGCATCCAAT 58.710 50.000 0.00 0.00 45.53 3.16
1227 1253 1.355916 GAAGTAGATCTCGCCGCGT 59.644 57.895 13.39 0.00 0.00 6.01
1623 1664 4.845225 TGTACACTTGGGGGTAGATTAACA 59.155 41.667 0.00 0.00 0.00 2.41
1756 1828 0.182061 TTTTGGCCCATTGCTTGCAA 59.818 45.000 10.57 10.57 40.92 4.08
1758 1830 0.035176 TCTTTTGGCCCATTGCTTGC 59.965 50.000 0.00 0.00 40.92 4.01
1793 3773 2.755655 TCTTCGGTCTTGGTTGCAAAAA 59.244 40.909 0.00 0.00 0.00 1.94
1794 3774 2.370349 TCTTCGGTCTTGGTTGCAAAA 58.630 42.857 0.00 0.00 0.00 2.44
1802 3782 0.400594 AAGGGGTTCTTCGGTCTTGG 59.599 55.000 0.00 0.00 0.00 3.61
1816 3796 2.493278 CACTGGCATCAAAGTTAAGGGG 59.507 50.000 0.00 0.00 0.00 4.79
1817 3797 3.157087 ACACTGGCATCAAAGTTAAGGG 58.843 45.455 0.00 0.00 0.00 3.95
1824 3804 2.157668 GTGACGTACACTGGCATCAAAG 59.842 50.000 9.86 0.00 45.13 2.77
1835 3815 6.691818 CATCTTAATAGACTGGTGACGTACAC 59.308 42.308 8.94 8.94 39.84 2.90
1840 3820 4.504461 GTGCATCTTAATAGACTGGTGACG 59.496 45.833 0.00 0.00 31.99 4.35
1842 3822 5.939764 AGTGCATCTTAATAGACTGGTGA 57.060 39.130 0.00 0.00 31.99 4.02
1843 3823 7.492524 TCTTAGTGCATCTTAATAGACTGGTG 58.507 38.462 0.00 0.00 31.99 4.17
1844 3824 7.661536 TCTTAGTGCATCTTAATAGACTGGT 57.338 36.000 0.00 0.00 31.99 4.00
1845 3825 8.417106 TCTTCTTAGTGCATCTTAATAGACTGG 58.583 37.037 0.00 0.00 31.99 4.00
1846 3826 9.809096 TTCTTCTTAGTGCATCTTAATAGACTG 57.191 33.333 0.00 0.00 31.99 3.51
1847 3827 9.810545 GTTCTTCTTAGTGCATCTTAATAGACT 57.189 33.333 0.00 0.00 31.99 3.24
1848 3828 9.587772 TGTTCTTCTTAGTGCATCTTAATAGAC 57.412 33.333 0.00 0.00 31.99 2.59
1852 3832 9.035607 CGTATGTTCTTCTTAGTGCATCTTAAT 57.964 33.333 0.00 0.00 0.00 1.40
1853 3833 8.248253 TCGTATGTTCTTCTTAGTGCATCTTAA 58.752 33.333 0.00 0.00 0.00 1.85
1854 3834 7.768240 TCGTATGTTCTTCTTAGTGCATCTTA 58.232 34.615 0.00 0.00 0.00 2.10
1855 3835 6.631016 TCGTATGTTCTTCTTAGTGCATCTT 58.369 36.000 0.00 0.00 0.00 2.40
1856 3836 6.208988 TCGTATGTTCTTCTTAGTGCATCT 57.791 37.500 0.00 0.00 0.00 2.90
1857 3837 6.752351 TCTTCGTATGTTCTTCTTAGTGCATC 59.248 38.462 0.00 0.00 0.00 3.91
1858 3838 6.531948 GTCTTCGTATGTTCTTCTTAGTGCAT 59.468 38.462 0.00 0.00 0.00 3.96
1859 3839 5.862323 GTCTTCGTATGTTCTTCTTAGTGCA 59.138 40.000 0.00 0.00 0.00 4.57
1860 3840 5.003590 CGTCTTCGTATGTTCTTCTTAGTGC 59.996 44.000 0.00 0.00 0.00 4.40
1861 3841 6.312487 TCGTCTTCGTATGTTCTTCTTAGTG 58.688 40.000 0.00 0.00 38.33 2.74
1862 3842 6.149142 ACTCGTCTTCGTATGTTCTTCTTAGT 59.851 38.462 0.00 0.00 38.33 2.24
1863 3843 6.544622 ACTCGTCTTCGTATGTTCTTCTTAG 58.455 40.000 0.00 0.00 38.33 2.18
1864 3844 6.492007 ACTCGTCTTCGTATGTTCTTCTTA 57.508 37.500 0.00 0.00 38.33 2.10
1865 3845 5.373981 ACTCGTCTTCGTATGTTCTTCTT 57.626 39.130 0.00 0.00 38.33 2.52
1866 3846 6.680874 ATACTCGTCTTCGTATGTTCTTCT 57.319 37.500 0.00 0.00 38.33 2.85
1867 3847 8.333908 TCTTATACTCGTCTTCGTATGTTCTTC 58.666 37.037 0.00 0.00 38.33 2.87
1868 3848 8.206325 TCTTATACTCGTCTTCGTATGTTCTT 57.794 34.615 0.00 0.00 38.33 2.52
1869 3849 7.783090 TCTTATACTCGTCTTCGTATGTTCT 57.217 36.000 0.00 0.00 38.33 3.01
1870 3850 8.832487 TTTCTTATACTCGTCTTCGTATGTTC 57.168 34.615 0.00 0.00 38.33 3.18
1871 3851 9.234384 CATTTCTTATACTCGTCTTCGTATGTT 57.766 33.333 0.00 0.00 38.33 2.71
1872 3852 8.618677 TCATTTCTTATACTCGTCTTCGTATGT 58.381 33.333 0.00 0.00 38.33 2.29
1873 3853 9.108449 CTCATTTCTTATACTCGTCTTCGTATG 57.892 37.037 0.00 0.00 38.33 2.39
1874 3854 9.053840 TCTCATTTCTTATACTCGTCTTCGTAT 57.946 33.333 0.00 0.00 38.33 3.06
1877 3857 8.686418 CAATCTCATTTCTTATACTCGTCTTCG 58.314 37.037 0.00 0.00 38.55 3.79
1896 3876 3.154710 AGACTGGTGACGTACAATCTCA 58.845 45.455 0.00 0.00 0.00 3.27
1903 3883 1.742268 GGAGGTAGACTGGTGACGTAC 59.258 57.143 0.00 0.00 0.00 3.67
1906 3886 0.959372 ACGGAGGTAGACTGGTGACG 60.959 60.000 0.00 0.00 0.00 4.35
1907 3887 1.067776 CAACGGAGGTAGACTGGTGAC 60.068 57.143 0.00 0.00 33.67 3.67
1908 3888 1.202964 TCAACGGAGGTAGACTGGTGA 60.203 52.381 0.00 0.00 37.91 4.02
1909 3889 1.254026 TCAACGGAGGTAGACTGGTG 58.746 55.000 0.00 0.00 33.18 4.17
1910 3890 2.005370 TTCAACGGAGGTAGACTGGT 57.995 50.000 0.00 0.00 0.00 4.00
1911 3891 3.611766 ATTTCAACGGAGGTAGACTGG 57.388 47.619 0.00 0.00 0.00 4.00
1912 3892 4.863131 GTGTATTTCAACGGAGGTAGACTG 59.137 45.833 0.00 0.00 0.00 3.51
1913 3893 4.525487 TGTGTATTTCAACGGAGGTAGACT 59.475 41.667 0.00 0.00 0.00 3.24
1914 3894 4.813027 TGTGTATTTCAACGGAGGTAGAC 58.187 43.478 0.00 0.00 0.00 2.59
1916 3896 5.121768 CCTTTGTGTATTTCAACGGAGGTAG 59.878 44.000 0.00 0.00 36.66 3.18
1917 3897 4.998672 CCTTTGTGTATTTCAACGGAGGTA 59.001 41.667 0.00 0.00 36.66 3.08
1919 3899 3.365969 GCCTTTGTGTATTTCAACGGAGG 60.366 47.826 5.58 0.00 36.66 4.30
1921 3901 2.554893 GGCCTTTGTGTATTTCAACGGA 59.445 45.455 0.00 0.00 36.66 4.69
1922 3902 2.352323 GGGCCTTTGTGTATTTCAACGG 60.352 50.000 0.84 0.00 37.30 4.44
1924 3904 2.630580 TGGGGCCTTTGTGTATTTCAAC 59.369 45.455 0.84 0.00 0.00 3.18
1925 3905 2.964209 TGGGGCCTTTGTGTATTTCAA 58.036 42.857 0.84 0.00 0.00 2.69
1926 3906 2.685106 TGGGGCCTTTGTGTATTTCA 57.315 45.000 0.84 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.