Multiple sequence alignment - TraesCS2D01G226800

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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 TraesCS2D01G226800 chr2D 100.000 2555 0 0 1 2555 194808382 194805828 0.000000e+00 4719.0
1 TraesCS2D01G226800 chr2B 93.942 1172 32 10 688 1828 250903275 250902112 0.000000e+00 1735.0
2 TraesCS2D01G226800 chr2B 93.076 621 23 6 72 691 250903906 250903305 0.000000e+00 891.0
3 TraesCS2D01G226800 chr2A 93.130 1179 38 12 688 1828 209583947 209582774 0.000000e+00 1688.0
4 TraesCS2D01G226800 chr2A 92.122 622 19 9 72 691 209584570 209583977 0.000000e+00 850.0
5 TraesCS2D01G226800 chr2A 87.106 698 70 11 1869 2555 5386032 5385344 0.000000e+00 773.0
6 TraesCS2D01G226800 chr2A 86.506 704 82 9 1862 2555 431082372 431081672 0.000000e+00 761.0
7 TraesCS2D01G226800 chr2A 93.617 47 3 0 30 76 755989462 755989508 1.270000e-08 71.3
8 TraesCS2D01G226800 chr1A 88.571 700 67 6 1867 2555 557890797 557890100 0.000000e+00 837.0
9 TraesCS2D01G226800 chr1A 87.143 700 76 10 1866 2555 337815393 337814698 0.000000e+00 782.0
10 TraesCS2D01G226800 chr3D 87.500 696 70 7 1869 2555 467734429 467735116 0.000000e+00 787.0
11 TraesCS2D01G226800 chr1D 87.055 703 81 4 1862 2555 383180910 383180209 0.000000e+00 785.0
12 TraesCS2D01G226800 chr1D 100.000 30 0 0 2 31 31090145 31090174 3.550000e-04 56.5
13 TraesCS2D01G226800 chr1D 100.000 30 0 0 2 31 34301770 34301741 3.550000e-04 56.5
14 TraesCS2D01G226800 chr5B 86.338 710 84 7 1855 2555 361014176 361013471 0.000000e+00 761.0
15 TraesCS2D01G226800 chr5B 86.552 699 71 15 1869 2555 421455136 421454449 0.000000e+00 749.0
16 TraesCS2D01G226800 chr5B 93.750 48 3 0 30 77 434989316 434989363 3.530000e-09 73.1
17 TraesCS2D01G226800 chr7D 87.538 666 64 14 1903 2555 168500392 168501051 0.000000e+00 752.0
18 TraesCS2D01G226800 chr7D 97.778 45 1 0 30 74 90575161 90575205 7.580000e-11 78.7
19 TraesCS2D01G226800 chrUn 97.143 35 0 1 2 36 331357194 331357227 9.870000e-05 58.4
20 TraesCS2D01G226800 chr6B 100.000 31 0 0 1 31 654646291 654646261 9.870000e-05 58.4
21 TraesCS2D01G226800 chr3B 100.000 31 0 0 1 31 581090093 581090063 9.870000e-05 58.4
22 TraesCS2D01G226800 chr6D 100.000 30 0 0 2 31 402318040 402318069 3.550000e-04 56.5
23 TraesCS2D01G226800 chr1B 100.000 30 0 0 2 31 177489292 177489321 3.550000e-04 56.5
24 TraesCS2D01G226800 chr1B 100.000 30 0 0 2 31 353970732 353970703 3.550000e-04 56.5
25 TraesCS2D01G226800 chr1B 100.000 30 0 0 2 31 676679317 676679346 3.550000e-04 56.5


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 TraesCS2D01G226800 chr2D 194805828 194808382 2554 True 4719 4719 100.000 1 2555 1 chr2D.!!$R1 2554
1 TraesCS2D01G226800 chr2B 250902112 250903906 1794 True 1313 1735 93.509 72 1828 2 chr2B.!!$R1 1756
2 TraesCS2D01G226800 chr2A 209582774 209584570 1796 True 1269 1688 92.626 72 1828 2 chr2A.!!$R3 1756
3 TraesCS2D01G226800 chr2A 5385344 5386032 688 True 773 773 87.106 1869 2555 1 chr2A.!!$R1 686
4 TraesCS2D01G226800 chr2A 431081672 431082372 700 True 761 761 86.506 1862 2555 1 chr2A.!!$R2 693
5 TraesCS2D01G226800 chr1A 557890100 557890797 697 True 837 837 88.571 1867 2555 1 chr1A.!!$R2 688
6 TraesCS2D01G226800 chr1A 337814698 337815393 695 True 782 782 87.143 1866 2555 1 chr1A.!!$R1 689
7 TraesCS2D01G226800 chr3D 467734429 467735116 687 False 787 787 87.500 1869 2555 1 chr3D.!!$F1 686
8 TraesCS2D01G226800 chr1D 383180209 383180910 701 True 785 785 87.055 1862 2555 1 chr1D.!!$R2 693
9 TraesCS2D01G226800 chr5B 361013471 361014176 705 True 761 761 86.338 1855 2555 1 chr5B.!!$R1 700
10 TraesCS2D01G226800 chr5B 421454449 421455136 687 True 749 749 86.552 1869 2555 1 chr5B.!!$R2 686
11 TraesCS2D01G226800 chr7D 168500392 168501051 659 False 752 752 87.538 1903 2555 1 chr7D.!!$F2 652

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
21 22 0.042131 ACTCCCTCCGTCCCATAACA 59.958 55.0 0.0 0.0 0.0 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1898 1993 0.032815 AATCCAAACAAAACGGGCGG 59.967 50.0 0.0 0.0 0.0 6.13 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
19 20 2.852714 TTACTCCCTCCGTCCCATAA 57.147 50.000 0.00 0.00 0.00 1.90
20 21 2.077687 TACTCCCTCCGTCCCATAAC 57.922 55.000 0.00 0.00 0.00 1.89
21 22 0.042131 ACTCCCTCCGTCCCATAACA 59.958 55.000 0.00 0.00 0.00 2.41
22 23 1.344087 ACTCCCTCCGTCCCATAACAT 60.344 52.381 0.00 0.00 0.00 2.71
23 24 2.090943 ACTCCCTCCGTCCCATAACATA 60.091 50.000 0.00 0.00 0.00 2.29
24 25 2.969950 CTCCCTCCGTCCCATAACATAA 59.030 50.000 0.00 0.00 0.00 1.90
25 26 2.969950 TCCCTCCGTCCCATAACATAAG 59.030 50.000 0.00 0.00 0.00 1.73
26 27 2.969950 CCCTCCGTCCCATAACATAAGA 59.030 50.000 0.00 0.00 0.00 2.10
27 28 3.389983 CCCTCCGTCCCATAACATAAGAA 59.610 47.826 0.00 0.00 0.00 2.52
28 29 4.377897 CCTCCGTCCCATAACATAAGAAC 58.622 47.826 0.00 0.00 0.00 3.01
29 30 4.049186 CTCCGTCCCATAACATAAGAACG 58.951 47.826 0.00 0.00 0.00 3.95
30 31 3.448301 TCCGTCCCATAACATAAGAACGT 59.552 43.478 0.00 0.00 0.00 3.99
31 32 3.554324 CCGTCCCATAACATAAGAACGTG 59.446 47.826 0.00 0.00 0.00 4.49
32 33 4.178540 CGTCCCATAACATAAGAACGTGT 58.821 43.478 0.00 0.00 0.00 4.49
33 34 5.342433 CGTCCCATAACATAAGAACGTGTA 58.658 41.667 0.00 0.00 0.00 2.90
34 35 5.457799 CGTCCCATAACATAAGAACGTGTAG 59.542 44.000 0.00 0.00 0.00 2.74
35 36 6.335777 GTCCCATAACATAAGAACGTGTAGT 58.664 40.000 0.00 0.00 0.00 2.73
36 37 6.255020 GTCCCATAACATAAGAACGTGTAGTG 59.745 42.308 0.00 0.00 0.00 2.74
37 38 6.071221 TCCCATAACATAAGAACGTGTAGTGT 60.071 38.462 0.00 0.00 0.00 3.55
38 39 6.255020 CCCATAACATAAGAACGTGTAGTGTC 59.745 42.308 0.00 0.00 0.00 3.67
39 40 6.809689 CCATAACATAAGAACGTGTAGTGTCA 59.190 38.462 0.00 0.00 0.00 3.58
40 41 7.329962 CCATAACATAAGAACGTGTAGTGTCAA 59.670 37.037 0.00 0.00 0.00 3.18
41 42 8.705134 CATAACATAAGAACGTGTAGTGTCAAA 58.295 33.333 0.00 0.00 0.00 2.69
42 43 7.542534 AACATAAGAACGTGTAGTGTCAAAA 57.457 32.000 0.00 0.00 0.00 2.44
43 44 7.542534 ACATAAGAACGTGTAGTGTCAAAAA 57.457 32.000 0.00 0.00 0.00 1.94
44 45 7.404203 ACATAAGAACGTGTAGTGTCAAAAAC 58.596 34.615 0.00 0.00 0.00 2.43
45 46 4.509915 AGAACGTGTAGTGTCAAAAACG 57.490 40.909 0.00 0.00 37.09 3.60
46 47 3.928375 AGAACGTGTAGTGTCAAAAACGT 59.072 39.130 0.00 0.10 45.26 3.99
47 48 3.912708 ACGTGTAGTGTCAAAAACGTC 57.087 42.857 0.00 0.00 39.87 4.34
48 49 2.604462 ACGTGTAGTGTCAAAAACGTCC 59.396 45.455 0.00 0.00 39.87 4.79
49 50 2.861935 CGTGTAGTGTCAAAAACGTCCT 59.138 45.455 0.00 0.00 0.00 3.85
50 51 3.307782 CGTGTAGTGTCAAAAACGTCCTT 59.692 43.478 0.00 0.00 0.00 3.36
51 52 4.503734 CGTGTAGTGTCAAAAACGTCCTTA 59.496 41.667 0.00 0.00 0.00 2.69
52 53 5.176223 CGTGTAGTGTCAAAAACGTCCTTAT 59.824 40.000 0.00 0.00 0.00 1.73
53 54 6.363088 CGTGTAGTGTCAAAAACGTCCTTATA 59.637 38.462 0.00 0.00 0.00 0.98
54 55 7.062605 CGTGTAGTGTCAAAAACGTCCTTATAT 59.937 37.037 0.00 0.00 0.00 0.86
55 56 8.715088 GTGTAGTGTCAAAAACGTCCTTATATT 58.285 33.333 0.00 0.00 0.00 1.28
56 57 9.275398 TGTAGTGTCAAAAACGTCCTTATATTT 57.725 29.630 0.00 0.00 0.00 1.40
60 61 9.550811 GTGTCAAAAACGTCCTTATATTTTAGG 57.449 33.333 0.00 0.00 0.00 2.69
61 62 9.504708 TGTCAAAAACGTCCTTATATTTTAGGA 57.495 29.630 0.00 0.00 38.22 2.94
70 71 7.857404 TCCTTATATTTTAGGACAGAGGGAG 57.143 40.000 0.00 0.00 35.66 4.30
227 230 7.714813 AGAAAAGGGGATAAAAATGTTTGTGTG 59.285 33.333 0.00 0.00 0.00 3.82
228 231 6.493189 AAGGGGATAAAAATGTTTGTGTGT 57.507 33.333 0.00 0.00 0.00 3.72
309 312 7.394016 TCAGAGGCTTAGATAACATGAACAAA 58.606 34.615 0.00 0.00 0.00 2.83
323 326 6.830736 ACATGAACAAAACTTTTGAAAGCAC 58.169 32.000 19.07 5.97 39.63 4.40
389 392 0.313987 GGTTGTAGCAACAGGTTGGC 59.686 55.000 13.52 6.42 40.74 4.52
422 425 3.383698 TCCTCCTTCTGGTACTAGTGG 57.616 52.381 5.39 9.82 34.23 4.00
429 432 5.655532 TCCTTCTGGTACTAGTGGAATGTAC 59.344 44.000 16.51 0.00 36.70 2.90
431 434 6.405953 CCTTCTGGTACTAGTGGAATGTACTG 60.406 46.154 5.39 0.00 37.35 2.74
432 435 5.577100 TCTGGTACTAGTGGAATGTACTGT 58.423 41.667 5.39 0.00 37.35 3.55
433 436 6.724351 TCTGGTACTAGTGGAATGTACTGTA 58.276 40.000 5.39 0.00 37.35 2.74
434 437 7.351952 TCTGGTACTAGTGGAATGTACTGTAT 58.648 38.462 5.39 0.00 37.35 2.29
435 438 7.837689 TCTGGTACTAGTGGAATGTACTGTATT 59.162 37.037 5.39 0.00 37.35 1.89
436 439 9.128404 CTGGTACTAGTGGAATGTACTGTATTA 57.872 37.037 5.39 0.00 37.35 0.98
437 440 9.650714 TGGTACTAGTGGAATGTACTGTATTAT 57.349 33.333 5.39 0.00 37.35 1.28
481 490 2.434185 GGTGCTCGGTCGCATCAA 60.434 61.111 0.00 0.00 42.62 2.57
511 520 5.831786 CAACTCAACGTTGTGAACAAAAAG 58.168 37.500 30.80 18.59 46.23 2.27
662 671 4.553429 GCAATGACTCGGTTAAATTTGTCG 59.447 41.667 0.00 2.39 0.00 4.35
694 737 8.936070 TTGCATTAGGAGAATGAATTGAATTG 57.064 30.769 0.00 0.00 0.00 2.32
696 739 6.927381 GCATTAGGAGAATGAATTGAATTGGG 59.073 38.462 0.00 0.00 0.00 4.12
711 754 4.039852 TGAATTGGGAAAACAAACTAGGCC 59.960 41.667 0.00 0.00 33.48 5.19
765 808 1.202770 CGGAACAGAAAGGGGTTGACT 60.203 52.381 0.00 0.00 0.00 3.41
766 809 2.230660 GGAACAGAAAGGGGTTGACTG 58.769 52.381 0.00 0.00 35.14 3.51
767 810 1.609072 GAACAGAAAGGGGTTGACTGC 59.391 52.381 0.00 0.00 32.67 4.40
768 811 0.178990 ACAGAAAGGGGTTGACTGCC 60.179 55.000 0.00 0.00 32.67 4.85
769 812 0.178992 CAGAAAGGGGTTGACTGCCA 60.179 55.000 0.00 0.00 0.00 4.92
793 836 2.779282 TGCCATGCATGTTACTCCG 58.221 52.632 24.58 9.02 31.71 4.63
833 883 3.461085 ACAGCCCTATCATTCTCCATGTT 59.539 43.478 0.00 0.00 34.06 2.71
867 917 0.321919 TCATGGAGGCAAGTGTCTGC 60.322 55.000 0.00 0.00 41.85 4.26
882 932 7.268586 CAAGTGTCTGCTATTATACACCTCTT 58.731 38.462 0.00 0.00 42.50 2.85
992 1071 7.810658 TCTCTTGTCAATAAATCTTGCTTCAC 58.189 34.615 0.00 0.00 0.00 3.18
1354 1436 1.347817 GCTCTCAGCGGAACAAGTCG 61.348 60.000 0.00 0.00 0.00 4.18
1584 1675 1.075482 CTGCTGCCCTTTCCTGGAA 59.925 57.895 4.68 4.68 0.00 3.53
1654 1746 5.678107 GCCATCTTTGGTGAGACAATCATTC 60.678 44.000 0.00 0.00 45.57 2.67
1672 1764 0.994247 TCCATCCACCTGACTGCATT 59.006 50.000 0.00 0.00 0.00 3.56
1681 1773 0.520404 CTGACTGCATTCCTGTGTGC 59.480 55.000 1.11 0.00 41.61 4.57
1718 1810 1.348696 TCAGCTTTCCTGCTCATGTGA 59.651 47.619 0.00 0.00 41.98 3.58
1828 1923 1.187087 AACCTCGCCTTCTGGAGTAG 58.813 55.000 0.00 0.00 34.59 2.57
1829 1924 1.324005 ACCTCGCCTTCTGGAGTAGC 61.324 60.000 0.00 0.00 34.59 3.58
1830 1925 1.323271 CCTCGCCTTCTGGAGTAGCA 61.323 60.000 0.00 0.00 34.59 3.49
1831 1926 0.102120 CTCGCCTTCTGGAGTAGCAG 59.898 60.000 0.00 0.00 34.59 4.24
1832 1927 0.323451 TCGCCTTCTGGAGTAGCAGA 60.323 55.000 0.00 0.00 34.59 4.26
1833 1928 0.749649 CGCCTTCTGGAGTAGCAGAT 59.250 55.000 0.00 0.00 34.57 2.90
1834 1929 1.957177 CGCCTTCTGGAGTAGCAGATA 59.043 52.381 0.00 0.00 34.57 1.98
1835 1930 2.362397 CGCCTTCTGGAGTAGCAGATAA 59.638 50.000 0.00 0.00 34.57 1.75
1836 1931 3.551863 CGCCTTCTGGAGTAGCAGATAAG 60.552 52.174 0.00 0.00 34.57 1.73
1837 1932 3.639094 GCCTTCTGGAGTAGCAGATAAGA 59.361 47.826 0.00 0.00 34.57 2.10
1838 1933 4.283212 GCCTTCTGGAGTAGCAGATAAGAT 59.717 45.833 0.00 0.00 34.57 2.40
1839 1934 5.221621 GCCTTCTGGAGTAGCAGATAAGATT 60.222 44.000 0.00 0.00 34.57 2.40
1840 1935 6.454795 CCTTCTGGAGTAGCAGATAAGATTC 58.545 44.000 0.00 0.00 34.57 2.52
1841 1936 6.041409 CCTTCTGGAGTAGCAGATAAGATTCA 59.959 42.308 0.00 0.00 34.57 2.57
1842 1937 7.256261 CCTTCTGGAGTAGCAGATAAGATTCAT 60.256 40.741 0.00 0.00 34.57 2.57
1843 1938 8.712228 TTCTGGAGTAGCAGATAAGATTCATA 57.288 34.615 0.00 0.00 0.00 2.15
1844 1939 8.116651 TCTGGAGTAGCAGATAAGATTCATAC 57.883 38.462 0.00 0.00 0.00 2.39
1845 1940 7.947332 TCTGGAGTAGCAGATAAGATTCATACT 59.053 37.037 0.00 0.00 0.00 2.12
1846 1941 8.116651 TGGAGTAGCAGATAAGATTCATACTC 57.883 38.462 0.00 0.00 37.98 2.59
1847 1942 7.947332 TGGAGTAGCAGATAAGATTCATACTCT 59.053 37.037 8.45 0.00 38.48 3.24
1848 1943 8.802267 GGAGTAGCAGATAAGATTCATACTCTT 58.198 37.037 8.45 0.00 38.48 2.85
1849 1944 9.624697 GAGTAGCAGATAAGATTCATACTCTTG 57.375 37.037 0.00 0.00 36.54 3.02
1850 1945 9.360901 AGTAGCAGATAAGATTCATACTCTTGA 57.639 33.333 0.00 0.00 34.81 3.02
1851 1946 9.973450 GTAGCAGATAAGATTCATACTCTTGAA 57.027 33.333 0.00 0.00 39.77 2.69
1860 1955 9.730705 AAGATTCATACTCTTGAATTGAGTTGA 57.269 29.630 2.59 4.53 44.35 3.18
1877 1972 3.084786 GTTGATGCTCTTAGGCCAACTT 58.915 45.455 5.01 0.00 34.20 2.66
1886 1981 0.887387 TAGGCCAACTTCAACGCACC 60.887 55.000 5.01 0.00 0.00 5.01
1888 1983 1.659794 GCCAACTTCAACGCACCAT 59.340 52.632 0.00 0.00 0.00 3.55
1898 1993 0.598065 AACGCACCATCTCAAAAGGC 59.402 50.000 0.00 0.00 0.00 4.35
1901 1996 1.508088 CACCATCTCAAAAGGCCGC 59.492 57.895 0.00 0.00 0.00 6.53
1954 2053 1.377202 CAATGGGACCGTGTCTGGG 60.377 63.158 4.41 0.00 32.47 4.45
1972 2071 2.103143 TTTGTGTTTGTGCCGGCG 59.897 55.556 23.90 0.00 0.00 6.46
2016 2115 0.395311 TTCTGCCCTATCTCGTCCGT 60.395 55.000 0.00 0.00 0.00 4.69
2019 2118 1.890979 GCCCTATCTCGTCCGTCGA 60.891 63.158 0.00 0.53 46.83 4.20
2167 2270 4.854291 CACTTAAAGTTTGTGCACACGAAA 59.146 37.500 21.56 8.90 36.54 3.46
2243 2346 1.166129 CAAGTCATCTTGCAGCTGCT 58.834 50.000 36.61 16.43 43.34 4.24
2246 2354 1.277273 AGTCATCTTGCAGCTGCTGTA 59.723 47.619 36.61 23.01 42.66 2.74
2257 2365 1.482182 AGCTGCTGTATTCCGATCACA 59.518 47.619 0.00 0.00 0.00 3.58
2258 2366 2.103771 AGCTGCTGTATTCCGATCACAT 59.896 45.455 0.00 0.00 0.00 3.21
2265 2373 6.159293 GCTGTATTCCGATCACATATCTCAA 58.841 40.000 0.00 0.00 0.00 3.02
2317 2425 1.990060 GAGGTGGGTGCTCAGGCTA 60.990 63.158 0.00 0.00 39.59 3.93
2332 2440 4.101114 TCAGGCTAAACATTCTCACCCTA 58.899 43.478 0.00 0.00 0.00 3.53
2421 2529 1.002888 CACAAGCAGTCATCACCTCCT 59.997 52.381 0.00 0.00 0.00 3.69
2489 2597 1.067283 CATCGAGACTGAAGCACACCT 60.067 52.381 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.288633 TGTTATGGGACGGAGGGAGTA 59.711 52.381 0.00 0.00 0.00 2.59
2 3 0.042131 TGTTATGGGACGGAGGGAGT 59.958 55.000 0.00 0.00 0.00 3.85
5 6 2.969950 TCTTATGTTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
6 7 4.377897 GTTCTTATGTTATGGGACGGAGG 58.622 47.826 0.00 0.00 0.00 4.30
8 9 3.448301 ACGTTCTTATGTTATGGGACGGA 59.552 43.478 0.00 0.00 0.00 4.69
9 10 3.554324 CACGTTCTTATGTTATGGGACGG 59.446 47.826 0.00 0.00 0.00 4.79
10 11 4.178540 ACACGTTCTTATGTTATGGGACG 58.821 43.478 0.00 0.00 0.00 4.79
11 12 6.255020 CACTACACGTTCTTATGTTATGGGAC 59.745 42.308 0.00 0.00 0.00 4.46
12 13 6.071221 ACACTACACGTTCTTATGTTATGGGA 60.071 38.462 0.00 0.00 0.00 4.37
13 14 6.103997 ACACTACACGTTCTTATGTTATGGG 58.896 40.000 0.00 0.00 0.00 4.00
14 15 6.809689 TGACACTACACGTTCTTATGTTATGG 59.190 38.462 0.00 0.00 0.00 2.74
15 16 7.806149 TGACACTACACGTTCTTATGTTATG 57.194 36.000 0.00 0.00 0.00 1.90
16 17 8.821147 TTTGACACTACACGTTCTTATGTTAT 57.179 30.769 0.00 0.00 0.00 1.89
17 18 8.645730 TTTTGACACTACACGTTCTTATGTTA 57.354 30.769 0.00 0.00 0.00 2.41
18 19 7.542534 TTTTGACACTACACGTTCTTATGTT 57.457 32.000 0.00 0.00 0.00 2.71
19 20 7.404203 GTTTTTGACACTACACGTTCTTATGT 58.596 34.615 0.00 0.00 0.00 2.29
20 21 6.568601 CGTTTTTGACACTACACGTTCTTATG 59.431 38.462 0.00 0.00 0.00 1.90
21 22 6.256321 ACGTTTTTGACACTACACGTTCTTAT 59.744 34.615 0.00 0.00 0.00 1.73
22 23 5.576384 ACGTTTTTGACACTACACGTTCTTA 59.424 36.000 0.00 0.00 0.00 2.10
23 24 4.389687 ACGTTTTTGACACTACACGTTCTT 59.610 37.500 0.00 0.00 0.00 2.52
24 25 3.928375 ACGTTTTTGACACTACACGTTCT 59.072 39.130 0.00 0.00 0.00 3.01
25 26 4.249181 ACGTTTTTGACACTACACGTTC 57.751 40.909 0.00 0.00 0.00 3.95
26 27 3.062504 GGACGTTTTTGACACTACACGTT 59.937 43.478 0.00 0.00 32.59 3.99
27 28 2.604462 GGACGTTTTTGACACTACACGT 59.396 45.455 0.00 0.00 35.21 4.49
28 29 2.861935 AGGACGTTTTTGACACTACACG 59.138 45.455 0.00 0.00 0.00 4.49
29 30 4.870221 AAGGACGTTTTTGACACTACAC 57.130 40.909 0.00 0.00 0.00 2.90
30 31 8.836268 AATATAAGGACGTTTTTGACACTACA 57.164 30.769 0.00 0.00 0.00 2.74
34 35 9.550811 CCTAAAATATAAGGACGTTTTTGACAC 57.449 33.333 0.00 0.00 34.58 3.67
35 36 9.504708 TCCTAAAATATAAGGACGTTTTTGACA 57.495 29.630 0.00 0.00 36.97 3.58
46 47 7.371043 ACTCCCTCTGTCCTAAAATATAAGGA 58.629 38.462 0.00 0.00 39.63 3.36
47 48 7.619512 ACTCCCTCTGTCCTAAAATATAAGG 57.380 40.000 0.00 0.00 0.00 2.69
48 49 9.369672 ACTACTCCCTCTGTCCTAAAATATAAG 57.630 37.037 0.00 0.00 0.00 1.73
49 50 9.725206 AACTACTCCCTCTGTCCTAAAATATAA 57.275 33.333 0.00 0.00 0.00 0.98
50 51 9.725206 AAACTACTCCCTCTGTCCTAAAATATA 57.275 33.333 0.00 0.00 0.00 0.86
51 52 8.625467 AAACTACTCCCTCTGTCCTAAAATAT 57.375 34.615 0.00 0.00 0.00 1.28
52 53 8.445361 AAAACTACTCCCTCTGTCCTAAAATA 57.555 34.615 0.00 0.00 0.00 1.40
53 54 6.954352 AAACTACTCCCTCTGTCCTAAAAT 57.046 37.500 0.00 0.00 0.00 1.82
54 55 6.758806 AAAACTACTCCCTCTGTCCTAAAA 57.241 37.500 0.00 0.00 0.00 1.52
55 56 6.758806 AAAAACTACTCCCTCTGTCCTAAA 57.241 37.500 0.00 0.00 0.00 1.85
92 93 4.390264 AGGCCTACTTCTCAGACAAAAAC 58.610 43.478 1.29 0.00 0.00 2.43
227 230 5.073311 TGAGGTGTAAAGATGCACTAGAC 57.927 43.478 0.00 0.00 41.38 2.59
228 231 5.016831 TCTGAGGTGTAAAGATGCACTAGA 58.983 41.667 0.00 0.00 41.38 2.43
309 312 2.682856 TCTCAGCGTGCTTTCAAAAGTT 59.317 40.909 4.54 0.00 38.28 2.66
389 392 2.503895 AGGAGGAAGCAAATGGACAG 57.496 50.000 0.00 0.00 0.00 3.51
436 439 8.550585 ACAGTCTGAAACTAGTAGTAGGAGTAT 58.449 37.037 6.91 0.00 36.07 2.12
437 440 7.915930 ACAGTCTGAAACTAGTAGTAGGAGTA 58.084 38.462 6.91 0.00 36.07 2.59
438 441 6.781943 ACAGTCTGAAACTAGTAGTAGGAGT 58.218 40.000 6.91 0.65 36.07 3.85
439 442 6.036300 CGACAGTCTGAAACTAGTAGTAGGAG 59.964 46.154 6.91 0.05 36.07 3.69
440 443 5.873712 CGACAGTCTGAAACTAGTAGTAGGA 59.126 44.000 6.91 0.00 36.07 2.94
441 444 5.064962 CCGACAGTCTGAAACTAGTAGTAGG 59.935 48.000 6.91 0.00 36.07 3.18
442 445 5.642919 ACCGACAGTCTGAAACTAGTAGTAG 59.357 44.000 6.91 2.87 36.07 2.57
443 446 5.410746 CACCGACAGTCTGAAACTAGTAGTA 59.589 44.000 6.91 0.00 36.07 1.82
444 447 4.215827 CACCGACAGTCTGAAACTAGTAGT 59.784 45.833 6.91 0.00 36.07 2.73
445 448 4.724303 CACCGACAGTCTGAAACTAGTAG 58.276 47.826 6.91 0.00 36.07 2.57
646 655 6.701432 AGAGTTACGACAAATTTAACCGAG 57.299 37.500 11.35 0.00 0.00 4.63
662 671 7.849804 TTCATTCTCCTAATGCAAGAGTTAC 57.150 36.000 0.00 0.00 0.00 2.50
694 737 1.900245 TCGGCCTAGTTTGTTTTCCC 58.100 50.000 0.00 0.00 0.00 3.97
696 739 4.866921 ACAAATCGGCCTAGTTTGTTTTC 58.133 39.130 18.54 0.00 41.75 2.29
793 836 4.932200 GGCTGTCATGATTATACCACTAGC 59.068 45.833 0.00 0.00 0.00 3.42
833 883 5.005740 CCTCCATGATTGTCACTTGAGAAA 58.994 41.667 0.00 0.00 30.91 2.52
867 917 9.376075 CCATGCAAGATAAGAGGTGTATAATAG 57.624 37.037 0.00 0.00 0.00 1.73
882 932 3.010027 TGGTGTTTCCTCCATGCAAGATA 59.990 43.478 0.00 0.00 37.07 1.98
992 1071 2.862541 TGTCACAAATGAGGAAGGTGG 58.137 47.619 0.00 0.00 34.75 4.61
1093 1172 0.322098 CGGTTGTGCCCACCTTGATA 60.322 55.000 0.00 0.00 0.00 2.15
1354 1436 2.044650 TGCAGCATTGGGGAGCTC 60.045 61.111 4.71 4.71 39.50 4.09
1584 1675 2.629617 CACAAAGAAACCCAAGATGCCT 59.370 45.455 0.00 0.00 0.00 4.75
1654 1746 1.386533 GAATGCAGTCAGGTGGATGG 58.613 55.000 9.72 0.00 0.00 3.51
1672 1764 4.451150 GGATCGCGGCACACAGGA 62.451 66.667 6.13 0.00 0.00 3.86
1681 1773 1.590792 GACCTAAACCGGATCGCGG 60.591 63.158 9.46 17.75 0.00 6.46
1690 1782 1.813178 GCAGGAAAGCTGACCTAAACC 59.187 52.381 10.94 0.00 34.87 3.27
1718 1810 2.501723 AGACTACCTTTCCACGCATCAT 59.498 45.455 0.00 0.00 0.00 2.45
1834 1929 9.730705 TCAACTCAATTCAAGAGTATGAATCTT 57.269 29.630 3.26 0.00 46.57 2.40
1835 1930 9.902684 ATCAACTCAATTCAAGAGTATGAATCT 57.097 29.630 3.26 0.00 46.57 2.40
1836 1931 9.932699 CATCAACTCAATTCAAGAGTATGAATC 57.067 33.333 3.26 0.00 46.57 2.52
1838 1933 7.609146 AGCATCAACTCAATTCAAGAGTATGAA 59.391 33.333 9.65 0.00 45.11 2.57
1839 1934 7.108194 AGCATCAACTCAATTCAAGAGTATGA 58.892 34.615 9.65 9.58 45.11 2.15
1840 1935 7.280428 AGAGCATCAACTCAATTCAAGAGTATG 59.720 37.037 0.00 0.00 45.11 2.39
1841 1936 7.337167 AGAGCATCAACTCAATTCAAGAGTAT 58.663 34.615 0.00 0.00 45.11 2.12
1842 1937 6.705302 AGAGCATCAACTCAATTCAAGAGTA 58.295 36.000 0.00 0.00 45.11 2.59
1844 1939 6.497785 AAGAGCATCAACTCAATTCAAGAG 57.502 37.500 0.00 0.00 39.26 2.85
1845 1940 6.596888 CCTAAGAGCATCAACTCAATTCAAGA 59.403 38.462 0.00 0.00 39.26 3.02
1846 1941 6.677431 GCCTAAGAGCATCAACTCAATTCAAG 60.677 42.308 0.00 0.00 39.26 3.02
1847 1942 5.124457 GCCTAAGAGCATCAACTCAATTCAA 59.876 40.000 0.00 0.00 39.26 2.69
1848 1943 4.637534 GCCTAAGAGCATCAACTCAATTCA 59.362 41.667 0.00 0.00 39.26 2.57
1849 1944 4.036144 GGCCTAAGAGCATCAACTCAATTC 59.964 45.833 0.00 0.00 39.26 2.17
1850 1945 3.950395 GGCCTAAGAGCATCAACTCAATT 59.050 43.478 0.00 0.00 39.26 2.32
1851 1946 3.054139 TGGCCTAAGAGCATCAACTCAAT 60.054 43.478 3.32 0.00 39.26 2.57
1852 1947 2.305635 TGGCCTAAGAGCATCAACTCAA 59.694 45.455 3.32 0.00 39.26 3.02
1853 1948 1.908619 TGGCCTAAGAGCATCAACTCA 59.091 47.619 3.32 0.00 39.26 3.41
1854 1949 2.680339 GTTGGCCTAAGAGCATCAACTC 59.320 50.000 3.32 0.00 37.82 3.01
1855 1950 2.307098 AGTTGGCCTAAGAGCATCAACT 59.693 45.455 3.32 0.00 39.15 3.16
1856 1951 2.716217 AGTTGGCCTAAGAGCATCAAC 58.284 47.619 3.32 0.00 37.82 3.18
1857 1952 3.244875 TGAAGTTGGCCTAAGAGCATCAA 60.245 43.478 3.32 0.00 37.82 2.57
1858 1953 2.305635 TGAAGTTGGCCTAAGAGCATCA 59.694 45.455 3.32 0.00 37.82 3.07
1859 1954 2.991250 TGAAGTTGGCCTAAGAGCATC 58.009 47.619 3.32 0.00 0.00 3.91
1860 1955 3.084786 GTTGAAGTTGGCCTAAGAGCAT 58.915 45.455 3.32 0.00 0.00 3.79
1877 1972 1.879380 CCTTTTGAGATGGTGCGTTGA 59.121 47.619 0.00 0.00 0.00 3.18
1886 1981 2.764314 CGGGCGGCCTTTTGAGATG 61.764 63.158 27.04 2.56 0.00 2.90
1888 1983 2.969300 AAACGGGCGGCCTTTTGAGA 62.969 55.000 28.26 0.00 0.00 3.27
1898 1993 0.032815 AATCCAAACAAAACGGGCGG 59.967 50.000 0.00 0.00 0.00 6.13
1901 1996 3.047093 GACGAAATCCAAACAAAACGGG 58.953 45.455 0.00 0.00 0.00 5.28
1930 2025 2.034066 ACGGTCCCATTGCCACTG 59.966 61.111 0.00 0.00 0.00 3.66
1931 2026 2.034066 CACGGTCCCATTGCCACT 59.966 61.111 0.00 0.00 0.00 4.00
1954 2053 2.227568 CGCCGGCACAAACACAAAC 61.228 57.895 28.98 0.00 0.00 2.93
2016 2115 5.941058 TGATTTTATTGTACTTGGCCTTCGA 59.059 36.000 3.32 0.00 0.00 3.71
2019 2118 6.014669 TGCTTGATTTTATTGTACTTGGCCTT 60.015 34.615 3.32 0.00 0.00 4.35
2138 2241 5.992217 TGTGCACAAACTTTAAGTGGTTTTT 59.008 32.000 19.28 0.00 34.01 1.94
2148 2251 5.700846 TCTTTTTCGTGTGCACAAACTTTA 58.299 33.333 23.59 5.45 0.00 1.85
2243 2346 7.524717 TCTTGAGATATGTGATCGGAATACA 57.475 36.000 1.05 1.05 0.00 2.29
2246 2354 7.237209 TCATCTTGAGATATGTGATCGGAAT 57.763 36.000 0.00 0.00 32.63 3.01
2257 2365 9.471702 AGTTTGTCCAATTTCATCTTGAGATAT 57.528 29.630 0.00 0.00 32.63 1.63
2258 2366 8.733458 CAGTTTGTCCAATTTCATCTTGAGATA 58.267 33.333 0.00 0.00 32.63 1.98
2265 2373 6.713762 TGAACAGTTTGTCCAATTTCATCT 57.286 33.333 0.00 0.00 0.00 2.90
2317 2425 7.039714 GGTTTGATTTCTAGGGTGAGAATGTTT 60.040 37.037 0.00 0.00 35.41 2.83
2332 2440 3.223674 ACGACCAAGGGTTTGATTTCT 57.776 42.857 0.00 0.00 35.25 2.52
2421 2529 3.008375 ACATGGAGCACTCAGAAGCTTTA 59.992 43.478 0.00 0.00 42.04 1.85
2489 2597 2.401583 AAGATGTGGAGCGTGCATTA 57.598 45.000 0.00 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.