Multiple sequence alignment - TraesCS5A01G432300

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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 TraesCS5A01G432300 chr5A 100.000 2590 0 0 1 2590 616647730 616650319 0.000000e+00 4783.0
1 TraesCS5A01G432300 chr5D 92.880 1573 81 11 276 1819 493521835 493523405 0.000000e+00 2255.0
2 TraesCS5A01G432300 chr5D 80.559 715 95 24 916 1592 493777421 493778129 6.390000e-141 510.0
3 TraesCS5A01G432300 chr5D 81.237 485 90 1 1109 1592 493688301 493688785 8.690000e-105 390.0
4 TraesCS5A01G432300 chr5D 90.204 245 20 3 1837 2081 493523388 493523628 1.500000e-82 316.0
5 TraesCS5A01G432300 chr5B 91.170 1359 86 13 471 1811 609258671 609260013 0.000000e+00 1814.0
6 TraesCS5A01G432300 chr5B 90.741 324 28 2 150 473 609258116 609258437 5.120000e-117 431.0
7 TraesCS5A01G432300 chr5B 78.103 717 104 29 918 1592 609529098 609529803 3.100000e-109 405.0
8 TraesCS5A01G432300 chr5B 77.871 714 112 24 918 1592 609499436 609500142 4.010000e-108 401.0
9 TraesCS5A01G432300 chr1A 88.091 529 42 12 2080 2590 371256260 371256785 2.200000e-170 608.0
10 TraesCS5A01G432300 chr7B 82.520 635 90 13 978 1592 584186052 584185419 2.930000e-149 538.0
11 TraesCS5A01G432300 chr3A 86.508 504 40 14 2100 2590 696404326 696403838 1.770000e-146 529.0
12 TraesCS5A01G432300 chr3A 86.398 397 32 11 2100 2484 696409797 696409411 5.160000e-112 414.0
13 TraesCS5A01G432300 chr3A 85.294 408 34 10 2100 2494 696411871 696411477 5.190000e-107 398.0
14 TraesCS5A01G432300 chr3A 85.149 404 41 11 2100 2494 696405575 696405182 1.870000e-106 396.0
15 TraesCS5A01G432300 chr3A 85.012 407 37 11 2100 2494 696414795 696414401 2.420000e-105 392.0
16 TraesCS5A01G432300 chr3A 85.176 398 36 9 2100 2484 696406409 696406022 1.120000e-103 387.0
17 TraesCS5A01G432300 chr3A 84.767 407 38 10 2100 2494 696413125 696412731 1.120000e-103 387.0
18 TraesCS5A01G432300 chr3A 84.804 408 36 12 2100 2494 696413543 696413149 1.120000e-103 387.0
19 TraesCS5A01G432300 chr3A 84.767 407 37 10 2100 2494 696414377 696413984 4.040000e-103 385.0
20 TraesCS5A01G432300 chr3A 84.029 407 41 10 2100 2494 696412289 696411895 1.130000e-98 370.0
21 TraesCS5A01G432300 chr3A 84.759 374 33 11 2133 2494 696409363 696409002 1.140000e-93 353.0
22 TraesCS5A01G432300 chr3A 80.786 229 20 12 2278 2494 696415434 696415218 9.590000e-35 158.0
23 TraesCS5A01G432300 chr7A 82.222 630 93 9 982 1592 622742224 622741595 2.280000e-145 525.0
24 TraesCS5A01G432300 chr7A 83.964 449 66 4 1146 1592 624772635 624773079 2.380000e-115 425.0
25 TraesCS5A01G432300 chr7A 87.500 80 9 1 1847 1925 421785120 421785041 9.870000e-15 91.6
26 TraesCS5A01G432300 chr4D 90.351 342 23 8 2256 2590 124265360 124265698 8.510000e-120 440.0
27 TraesCS5A01G432300 chr1D 76.539 601 129 8 1000 1592 247507649 247507053 4.160000e-83 318.0
28 TraesCS5A01G432300 chr1D 86.076 79 9 1 1847 1925 203749955 203750031 1.650000e-12 84.2
29 TraesCS5A01G432300 chr6D 85.542 83 10 2 1845 1925 429020957 429020875 4.590000e-13 86.1
30 TraesCS5A01G432300 chr6A 85.542 83 10 2 1845 1925 574263757 574263675 4.590000e-13 86.1
31 TraesCS5A01G432300 chr6A 85.000 80 11 1 1847 1925 166989421 166989500 2.140000e-11 80.5
32 TraesCS5A01G432300 chr2D 85.057 87 9 4 1845 1929 645824164 645824248 4.590000e-13 86.1
33 TraesCS5A01G432300 chr4A 79.464 112 17 5 1845 1950 38364851 38364740 9.940000e-10 75.0
34 TraesCS5A01G432300 chr1B 84.848 66 10 0 1847 1912 50815877 50815942 1.660000e-07 67.6


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 TraesCS5A01G432300 chr5A 616647730 616650319 2589 False 4783.000000 4783 100.000000 1 2590 1 chr5A.!!$F1 2589
1 TraesCS5A01G432300 chr5D 493521835 493523628 1793 False 1285.500000 2255 91.542000 276 2081 2 chr5D.!!$F3 1805
2 TraesCS5A01G432300 chr5D 493777421 493778129 708 False 510.000000 510 80.559000 916 1592 1 chr5D.!!$F2 676
3 TraesCS5A01G432300 chr5B 609258116 609260013 1897 False 1122.500000 1814 90.955500 150 1811 2 chr5B.!!$F3 1661
4 TraesCS5A01G432300 chr5B 609529098 609529803 705 False 405.000000 405 78.103000 918 1592 1 chr5B.!!$F2 674
5 TraesCS5A01G432300 chr5B 609499436 609500142 706 False 401.000000 401 77.871000 918 1592 1 chr5B.!!$F1 674
6 TraesCS5A01G432300 chr1A 371256260 371256785 525 False 608.000000 608 88.091000 2080 2590 1 chr1A.!!$F1 510
7 TraesCS5A01G432300 chr7B 584185419 584186052 633 True 538.000000 538 82.520000 978 1592 1 chr7B.!!$R1 614
8 TraesCS5A01G432300 chr3A 696403838 696415434 11596 True 379.666667 529 84.787417 2100 2590 12 chr3A.!!$R1 490
9 TraesCS5A01G432300 chr7A 622741595 622742224 629 True 525.000000 525 82.222000 982 1592 1 chr7A.!!$R2 610
10 TraesCS5A01G432300 chr1D 247507053 247507649 596 True 318.000000 318 76.539000 1000 1592 1 chr1D.!!$R1 592

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 0.109597 GTTGCCGTCATGAAAGCTGG 60.110 55.0 16.68 7.16 0.0 4.85 F
339 340 0.321564 TTTGTGGATCTGGCGGTGAG 60.322 55.0 0.00 0.00 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1413 1701 1.069765 CTTGGCTGTCACGGACTGT 59.930 57.895 0.0 0.0 34.68 3.55 R
2092 2405 0.464452 GTACCAGGCTACCGCTTCAT 59.536 55.000 0.0 0.0 36.09 2.57 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
17 18 4.440214 GCGTTGCCGTCATGAAAG 57.560 55.556 0.00 0.00 36.15 2.62
18 19 1.797537 GCGTTGCCGTCATGAAAGC 60.798 57.895 10.56 10.56 36.15 3.51
19 20 1.868997 CGTTGCCGTCATGAAAGCT 59.131 52.632 16.68 0.00 0.00 3.74
20 21 0.453282 CGTTGCCGTCATGAAAGCTG 60.453 55.000 16.68 5.82 0.00 4.24
21 22 0.109597 GTTGCCGTCATGAAAGCTGG 60.110 55.000 16.68 7.16 0.00 4.85
22 23 1.865788 TTGCCGTCATGAAAGCTGGC 61.866 55.000 16.68 15.29 42.76 4.85
23 24 2.334946 GCCGTCATGAAAGCTGGCA 61.335 57.895 15.32 0.00 42.03 4.92
24 25 1.865788 GCCGTCATGAAAGCTGGCAA 61.866 55.000 15.32 0.00 42.03 4.52
25 26 0.597568 CCGTCATGAAAGCTGGCAAA 59.402 50.000 0.00 0.00 0.00 3.68
28 29 2.664568 CGTCATGAAAGCTGGCAAAATG 59.335 45.455 0.00 0.00 0.00 2.32
29 30 2.997986 GTCATGAAAGCTGGCAAAATGG 59.002 45.455 0.00 0.00 0.00 3.16
30 31 2.898612 TCATGAAAGCTGGCAAAATGGA 59.101 40.909 0.00 0.00 0.00 3.41
31 32 2.818130 TGAAAGCTGGCAAAATGGAC 57.182 45.000 0.00 0.00 0.00 4.02
32 33 2.037901 TGAAAGCTGGCAAAATGGACA 58.962 42.857 0.00 0.00 0.00 4.02
33 34 2.433604 TGAAAGCTGGCAAAATGGACAA 59.566 40.909 0.00 0.00 0.00 3.18
36 37 3.557228 AGCTGGCAAAATGGACAAAAA 57.443 38.095 0.00 0.00 0.00 1.94
38 39 5.226194 AGCTGGCAAAATGGACAAAAATA 57.774 34.783 0.00 0.00 0.00 1.40
39 40 5.619220 AGCTGGCAAAATGGACAAAAATAA 58.381 33.333 0.00 0.00 0.00 1.40
41 42 5.334802 GCTGGCAAAATGGACAAAAATAACC 60.335 40.000 0.00 0.00 0.00 2.85
46 47 7.138081 GCAAAATGGACAAAAATAACCCAAAG 58.862 34.615 0.00 0.00 0.00 2.77
47 48 6.875948 AAATGGACAAAAATAACCCAAAGC 57.124 33.333 0.00 0.00 0.00 3.51
48 49 4.344359 TGGACAAAAATAACCCAAAGCC 57.656 40.909 0.00 0.00 0.00 4.35
49 50 3.243907 TGGACAAAAATAACCCAAAGCCG 60.244 43.478 0.00 0.00 0.00 5.52
50 51 3.006003 GGACAAAAATAACCCAAAGCCGA 59.994 43.478 0.00 0.00 0.00 5.54
52 53 5.024785 ACAAAAATAACCCAAAGCCGAAA 57.975 34.783 0.00 0.00 0.00 3.46
53 54 5.053811 ACAAAAATAACCCAAAGCCGAAAG 58.946 37.500 0.00 0.00 0.00 2.62
55 56 6.183360 ACAAAAATAACCCAAAGCCGAAAGTA 60.183 34.615 0.00 0.00 0.00 2.24
57 58 6.408107 AAATAACCCAAAGCCGAAAGTAAA 57.592 33.333 0.00 0.00 0.00 2.01
58 59 6.599356 AATAACCCAAAGCCGAAAGTAAAT 57.401 33.333 0.00 0.00 0.00 1.40
59 60 4.948341 AACCCAAAGCCGAAAGTAAATT 57.052 36.364 0.00 0.00 0.00 1.82
62 63 6.408107 ACCCAAAGCCGAAAGTAAATTAAA 57.592 33.333 0.00 0.00 0.00 1.52
93 94 7.962964 ACTCTCAACGAAATTATTTCACAGA 57.037 32.000 16.57 10.20 39.63 3.41
94 95 8.378172 ACTCTCAACGAAATTATTTCACAGAA 57.622 30.769 16.57 0.00 39.63 3.02
95 96 8.836413 ACTCTCAACGAAATTATTTCACAGAAA 58.164 29.630 16.57 0.00 39.63 2.52
112 113 8.709386 TCACAGAAATAACTCTTTCAGATAGC 57.291 34.615 0.00 0.00 37.55 2.97
113 114 7.489435 TCACAGAAATAACTCTTTCAGATAGCG 59.511 37.037 0.00 0.00 37.55 4.26
115 116 5.755861 AGAAATAACTCTTTCAGATAGCGCC 59.244 40.000 2.29 0.00 37.55 6.53
116 117 2.317530 AACTCTTTCAGATAGCGCCC 57.682 50.000 2.29 0.00 0.00 6.13
117 118 1.195115 ACTCTTTCAGATAGCGCCCA 58.805 50.000 2.29 0.00 0.00 5.36
118 119 1.555075 ACTCTTTCAGATAGCGCCCAA 59.445 47.619 2.29 0.00 0.00 4.12
140 141 1.766069 CGTATGCGCTATGCTACACA 58.234 50.000 9.73 0.00 46.63 3.72
141 142 2.124122 CGTATGCGCTATGCTACACAA 58.876 47.619 9.73 0.00 46.63 3.33
143 144 3.422214 CGTATGCGCTATGCTACACAATG 60.422 47.826 9.73 0.00 46.63 2.82
144 145 2.022764 TGCGCTATGCTACACAATGT 57.977 45.000 9.73 0.00 46.63 2.71
145 146 3.172229 TGCGCTATGCTACACAATGTA 57.828 42.857 9.73 0.00 46.63 2.29
196 197 8.585018 CAAAAGGGGTTAGATTTGTGAAATACT 58.415 33.333 0.00 0.00 0.00 2.12
203 204 9.406828 GGTTAGATTTGTGAAATACTTTTGTCC 57.593 33.333 0.00 0.00 0.00 4.02
257 258 3.924073 GGATTATTTGTGTCCGTTTTGCC 59.076 43.478 0.00 0.00 0.00 4.52
273 274 0.394762 TGCCATGAAAGCCTAGCTGG 60.395 55.000 0.00 0.00 39.62 4.85
274 275 0.394899 GCCATGAAAGCCTAGCTGGT 60.395 55.000 0.00 0.00 39.62 4.00
339 340 0.321564 TTTGTGGATCTGGCGGTGAG 60.322 55.000 0.00 0.00 0.00 3.51
389 390 3.053291 GGCGGCGGACATGTTTCA 61.053 61.111 9.78 0.00 0.00 2.69
426 427 4.094911 TGAAATTATAAAGCGCTTGCACG 58.905 39.130 25.80 0.00 42.66 5.34
466 467 7.461107 ACAAATGACGACGGAAATTACATAAG 58.539 34.615 0.00 0.00 0.00 1.73
516 753 6.038356 TCCGTCTGTATATTTTTCTCGAACC 58.962 40.000 0.00 0.00 0.00 3.62
587 828 3.917988 ACGGTAAGAAAGTAGGAAACGG 58.082 45.455 0.00 0.00 0.00 4.44
607 848 1.996292 CACACCTGATACGGACAGTG 58.004 55.000 0.00 0.00 34.04 3.66
702 953 3.195610 TGTCTGCACCTCGACTATCAAAT 59.804 43.478 5.54 0.00 0.00 2.32
703 954 4.184629 GTCTGCACCTCGACTATCAAATT 58.815 43.478 0.00 0.00 0.00 1.82
704 955 5.105513 TGTCTGCACCTCGACTATCAAATTA 60.106 40.000 5.54 0.00 0.00 1.40
705 956 5.986135 GTCTGCACCTCGACTATCAAATTAT 59.014 40.000 0.00 0.00 0.00 1.28
707 958 4.982295 TGCACCTCGACTATCAAATTATCG 59.018 41.667 0.00 0.00 0.00 2.92
708 959 5.220381 GCACCTCGACTATCAAATTATCGA 58.780 41.667 0.00 0.00 39.35 3.59
719 970 6.798315 ATCAAATTATCGATGGAAGCTCTG 57.202 37.500 8.54 0.00 0.00 3.35
767 1018 3.253432 AGGAAGAAGCGGCTGTTTAAAAG 59.747 43.478 1.81 0.00 0.00 2.27
887 1138 5.536916 CCAAGTTAACATCCCCAGTTAAACA 59.463 40.000 8.61 0.00 41.51 2.83
892 1143 7.289084 AGTTAACATCCCCAGTTAAACAAACAT 59.711 33.333 8.61 0.00 41.51 2.71
1005 1266 1.748122 CAGCCTGACAGACATGGCC 60.748 63.158 3.32 0.00 40.81 5.36
1323 1611 2.223971 CGACAACCGCTACCATAAGGAT 60.224 50.000 0.00 0.00 38.69 3.24
1620 1909 1.266446 GTACGGGATAGTTCGCTCCTC 59.734 57.143 0.00 0.00 32.83 3.71
1629 1918 0.172352 GTTCGCTCCTCAGTCCTCAG 59.828 60.000 0.00 0.00 0.00 3.35
1635 1924 2.183811 CTCAGTCCTCAGCTGCCG 59.816 66.667 9.47 2.02 34.21 5.69
1637 1926 2.433838 CAGTCCTCAGCTGCCGTG 60.434 66.667 9.47 0.00 0.00 4.94
1638 1927 3.699894 AGTCCTCAGCTGCCGTGG 61.700 66.667 9.47 8.59 0.00 4.94
1639 1928 4.767255 GTCCTCAGCTGCCGTGGG 62.767 72.222 9.47 6.04 0.00 4.61
1774 2087 3.788227 TGGGTGATATATGTTGCTCCC 57.212 47.619 0.00 0.00 35.24 4.30
1816 2129 8.800332 AAGCTGTTTTCAGATATTTCATTCAGT 58.200 29.630 0.00 0.00 46.45 3.41
1824 2137 8.593492 TCAGATATTTCATTCAGTATCAACCG 57.407 34.615 0.00 0.00 0.00 4.44
1825 2138 7.171508 TCAGATATTTCATTCAGTATCAACCGC 59.828 37.037 0.00 0.00 0.00 5.68
1826 2139 6.992123 AGATATTTCATTCAGTATCAACCGCA 59.008 34.615 0.00 0.00 0.00 5.69
1828 2141 5.697473 TTTCATTCAGTATCAACCGCAAA 57.303 34.783 0.00 0.00 0.00 3.68
1830 2143 5.697473 TCATTCAGTATCAACCGCAAAAA 57.303 34.783 0.00 0.00 0.00 1.94
1831 2144 5.698832 TCATTCAGTATCAACCGCAAAAAG 58.301 37.500 0.00 0.00 0.00 2.27
1832 2145 5.471797 TCATTCAGTATCAACCGCAAAAAGA 59.528 36.000 0.00 0.00 0.00 2.52
1834 2147 5.759506 TCAGTATCAACCGCAAAAAGAAA 57.240 34.783 0.00 0.00 0.00 2.52
1837 2150 6.695278 TCAGTATCAACCGCAAAAAGAAAAAG 59.305 34.615 0.00 0.00 0.00 2.27
1839 2152 7.382218 CAGTATCAACCGCAAAAAGAAAAAGAT 59.618 33.333 0.00 0.00 0.00 2.40
1841 2154 9.353999 GTATCAACCGCAAAAAGAAAAAGATAT 57.646 29.630 0.00 0.00 0.00 1.63
1842 2155 8.831715 ATCAACCGCAAAAAGAAAAAGATATT 57.168 26.923 0.00 0.00 0.00 1.28
1844 2157 9.103861 TCAACCGCAAAAAGAAAAAGATATTTT 57.896 25.926 0.00 0.00 0.00 1.82
1988 2301 2.290287 CCCTCCACCACCATCGACA 61.290 63.158 0.00 0.00 0.00 4.35
1994 2307 1.002659 CCACCACCATCGACAGGTTTA 59.997 52.381 8.58 0.00 37.23 2.01
2029 2342 4.876679 GGCTAAAAGTTAGTAGAGGGCTTG 59.123 45.833 0.00 0.00 0.00 4.01
2044 2357 3.266772 AGGGCTTGGTCTTCATTGACATA 59.733 43.478 0.00 0.00 38.61 2.29
2081 2394 8.256611 TGATAGTTCTGTGTTTTTAGAGCATC 57.743 34.615 0.00 0.00 0.00 3.91
2100 2413 6.963796 AGCATCTCTATTTTTAATGAAGCGG 58.036 36.000 0.00 0.00 0.00 5.52
2101 2414 6.543831 AGCATCTCTATTTTTAATGAAGCGGT 59.456 34.615 0.00 0.00 0.00 5.68
2102 2415 7.715249 AGCATCTCTATTTTTAATGAAGCGGTA 59.285 33.333 0.00 0.00 0.00 4.02
2103 2416 8.012241 GCATCTCTATTTTTAATGAAGCGGTAG 58.988 37.037 0.00 0.00 0.00 3.18
2113 3160 0.535797 GAAGCGGTAGCCTGGTACTT 59.464 55.000 6.48 0.00 46.67 2.24
2129 4012 6.293571 CCTGGTACTTCGGTTTTATTTTCGTT 60.294 38.462 0.00 0.00 0.00 3.85
2131 4014 6.482973 TGGTACTTCGGTTTTATTTTCGTTCT 59.517 34.615 0.00 0.00 0.00 3.01
2158 4041 0.120377 TTACTCCCACCTCCCACCAT 59.880 55.000 0.00 0.00 0.00 3.55
2259 5798 8.665685 ACATACAAAAATCACGGATCTAACTTC 58.334 33.333 0.00 0.00 0.00 3.01
2298 8406 4.338118 TCAACCGATCCTTTCATTAATGCC 59.662 41.667 10.76 0.00 0.00 4.40
2303 8411 5.693104 CCGATCCTTTCATTAATGCCATTTG 59.307 40.000 10.76 0.00 0.00 2.32
2308 8416 8.688747 TCCTTTCATTAATGCCATTTGTTTTT 57.311 26.923 10.76 0.00 0.00 1.94
2310 8418 8.566260 CCTTTCATTAATGCCATTTGTTTTTGA 58.434 29.630 10.76 0.00 0.00 2.69
2416 10186 2.163815 TCGTTTGTCTCCCTCTTCGATC 59.836 50.000 0.00 0.00 0.00 3.69
2424 10194 2.621055 CTCCCTCTTCGATCGATTGTCT 59.379 50.000 20.18 0.00 0.00 3.41
2428 10198 3.367607 CTCTTCGATCGATTGTCTCACC 58.632 50.000 20.18 0.00 0.00 4.02
2482 11087 1.280998 CCTTCCACACCTCCGGTTTAT 59.719 52.381 0.00 0.00 31.02 1.40
2484 11089 3.528532 CTTCCACACCTCCGGTTTATAC 58.471 50.000 0.00 0.00 31.02 1.47
2486 11091 2.498481 TCCACACCTCCGGTTTATACAG 59.502 50.000 0.00 0.00 31.02 2.74
2489 11094 4.181578 CACACCTCCGGTTTATACAGAAG 58.818 47.826 0.00 0.00 31.02 2.85
2543 11560 0.391661 ATGCACACCTCACGATCCAC 60.392 55.000 0.00 0.00 0.00 4.02
2569 11586 4.996976 CTAGACCAGCACGCACTT 57.003 55.556 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 0.109597 CCAGCTTTCATGACGGCAAC 60.110 55.000 17.72 0.00 0.00 4.17
4 5 2.334946 GCCAGCTTTCATGACGGCA 61.335 57.895 17.72 0.00 39.38 5.69
5 6 1.865788 TTGCCAGCTTTCATGACGGC 61.866 55.000 10.15 10.15 40.02 5.68
6 7 0.597568 TTTGCCAGCTTTCATGACGG 59.402 50.000 0.00 0.00 0.00 4.79
8 9 2.997986 CCATTTTGCCAGCTTTCATGAC 59.002 45.455 0.00 0.00 0.00 3.06
10 11 2.997986 GTCCATTTTGCCAGCTTTCATG 59.002 45.455 0.00 0.00 0.00 3.07
11 12 2.633967 TGTCCATTTTGCCAGCTTTCAT 59.366 40.909 0.00 0.00 0.00 2.57
12 13 2.037901 TGTCCATTTTGCCAGCTTTCA 58.962 42.857 0.00 0.00 0.00 2.69
13 14 2.818130 TGTCCATTTTGCCAGCTTTC 57.182 45.000 0.00 0.00 0.00 2.62
14 15 3.557228 TTTGTCCATTTTGCCAGCTTT 57.443 38.095 0.00 0.00 0.00 3.51
15 16 3.557228 TTTTGTCCATTTTGCCAGCTT 57.443 38.095 0.00 0.00 0.00 3.74
17 18 5.334802 GGTTATTTTTGTCCATTTTGCCAGC 60.335 40.000 0.00 0.00 0.00 4.85
18 19 5.181056 GGGTTATTTTTGTCCATTTTGCCAG 59.819 40.000 0.00 0.00 0.00 4.85
19 20 5.066593 GGGTTATTTTTGTCCATTTTGCCA 58.933 37.500 0.00 0.00 0.00 4.92
20 21 5.066593 TGGGTTATTTTTGTCCATTTTGCC 58.933 37.500 0.00 0.00 0.00 4.52
21 22 6.625873 TTGGGTTATTTTTGTCCATTTTGC 57.374 33.333 0.00 0.00 0.00 3.68
22 23 7.138081 GCTTTGGGTTATTTTTGTCCATTTTG 58.862 34.615 0.00 0.00 0.00 2.44
23 24 6.264292 GGCTTTGGGTTATTTTTGTCCATTTT 59.736 34.615 0.00 0.00 0.00 1.82
24 25 5.767665 GGCTTTGGGTTATTTTTGTCCATTT 59.232 36.000 0.00 0.00 0.00 2.32
25 26 5.312895 GGCTTTGGGTTATTTTTGTCCATT 58.687 37.500 0.00 0.00 0.00 3.16
28 29 3.006003 TCGGCTTTGGGTTATTTTTGTCC 59.994 43.478 0.00 0.00 0.00 4.02
29 30 4.245845 TCGGCTTTGGGTTATTTTTGTC 57.754 40.909 0.00 0.00 0.00 3.18
30 31 4.674281 TTCGGCTTTGGGTTATTTTTGT 57.326 36.364 0.00 0.00 0.00 2.83
31 32 5.053811 ACTTTCGGCTTTGGGTTATTTTTG 58.946 37.500 0.00 0.00 0.00 2.44
32 33 5.284861 ACTTTCGGCTTTGGGTTATTTTT 57.715 34.783 0.00 0.00 0.00 1.94
33 34 4.948341 ACTTTCGGCTTTGGGTTATTTT 57.052 36.364 0.00 0.00 0.00 1.82
36 37 6.599356 AATTTACTTTCGGCTTTGGGTTAT 57.401 33.333 0.00 0.00 0.00 1.89
38 39 4.948341 AATTTACTTTCGGCTTTGGGTT 57.052 36.364 0.00 0.00 0.00 4.11
39 40 6.408107 TTTAATTTACTTTCGGCTTTGGGT 57.592 33.333 0.00 0.00 0.00 4.51
69 70 7.962964 TCTGTGAAATAATTTCGTTGAGAGT 57.037 32.000 0.00 0.00 42.55 3.24
70 71 9.831737 ATTTCTGTGAAATAATTTCGTTGAGAG 57.168 29.630 3.99 0.00 42.55 3.20
101 102 0.652592 CGTTGGGCGCTATCTGAAAG 59.347 55.000 7.64 0.00 0.00 2.62
102 103 2.762360 CGTTGGGCGCTATCTGAAA 58.238 52.632 7.64 0.00 0.00 2.69
103 104 4.513519 CGTTGGGCGCTATCTGAA 57.486 55.556 7.64 0.00 0.00 3.02
121 122 1.766069 TGTGTAGCATAGCGCATACG 58.234 50.000 11.47 0.00 46.13 3.06
122 123 3.494626 ACATTGTGTAGCATAGCGCATAC 59.505 43.478 11.47 5.01 46.13 2.39
123 124 3.727726 ACATTGTGTAGCATAGCGCATA 58.272 40.909 11.47 0.00 46.13 3.14
124 125 2.564771 ACATTGTGTAGCATAGCGCAT 58.435 42.857 11.47 0.00 46.13 4.73
126 127 3.777807 CTACATTGTGTAGCATAGCGC 57.222 47.619 0.00 0.00 43.11 5.92
135 136 4.168014 CGCGTTAGGAACTACATTGTGTA 58.832 43.478 0.00 0.00 42.67 2.90
136 137 2.991190 CGCGTTAGGAACTACATTGTGT 59.009 45.455 0.00 0.00 42.67 3.72
138 139 3.308438 ACGCGTTAGGAACTACATTGT 57.692 42.857 5.58 0.00 42.67 2.71
140 141 2.997986 CCAACGCGTTAGGAACTACATT 59.002 45.455 26.11 0.00 42.67 2.71
141 142 2.613691 CCAACGCGTTAGGAACTACAT 58.386 47.619 26.11 0.00 42.67 2.29
143 144 1.353076 CCCAACGCGTTAGGAACTAC 58.647 55.000 29.27 0.00 42.67 2.73
144 145 0.390209 GCCCAACGCGTTAGGAACTA 60.390 55.000 35.50 0.00 41.75 2.24
145 146 1.670083 GCCCAACGCGTTAGGAACT 60.670 57.895 35.50 6.03 46.37 3.01
146 147 2.865308 GCCCAACGCGTTAGGAAC 59.135 61.111 35.50 22.46 0.00 3.62
171 172 8.721133 AGTATTTCACAAATCTAACCCCTTTT 57.279 30.769 0.00 0.00 32.38 2.27
227 228 5.048991 ACGGACACAAATAATCCAAAGACAC 60.049 40.000 0.00 0.00 32.35 3.67
228 229 5.067273 ACGGACACAAATAATCCAAAGACA 58.933 37.500 0.00 0.00 32.35 3.41
237 238 4.592485 TGGCAAAACGGACACAAATAAT 57.408 36.364 0.00 0.00 0.00 1.28
257 258 0.737219 GCACCAGCTAGGCTTTCATG 59.263 55.000 0.00 0.00 43.14 3.07
273 274 1.965930 TCTGCCGTCACCAATGCAC 60.966 57.895 0.00 0.00 0.00 4.57
274 275 1.965930 GTCTGCCGTCACCAATGCA 60.966 57.895 0.00 0.00 0.00 3.96
339 340 3.899395 GGCACAATACCGACACCC 58.101 61.111 0.00 0.00 0.00 4.61
417 418 3.475774 GTACCCGACGTGCAAGCG 61.476 66.667 0.00 4.57 37.94 4.68
426 427 0.318120 TTTGTTCCGAGGTACCCGAC 59.682 55.000 20.26 13.33 0.00 4.79
466 467 0.949105 CTGTGCACGACAGTTACCCC 60.949 60.000 13.13 0.00 46.30 4.95
587 828 0.246635 ACTGTCCGTATCAGGTGTGC 59.753 55.000 0.00 0.00 37.25 4.57
607 848 1.419107 GCACGGCGGCTAACTAGTTC 61.419 60.000 12.39 0.00 0.00 3.01
702 953 3.447229 TGTCACAGAGCTTCCATCGATAA 59.553 43.478 0.00 0.00 0.00 1.75
703 954 3.023832 TGTCACAGAGCTTCCATCGATA 58.976 45.455 0.00 0.00 0.00 2.92
704 955 1.827344 TGTCACAGAGCTTCCATCGAT 59.173 47.619 0.00 0.00 0.00 3.59
705 956 1.256812 TGTCACAGAGCTTCCATCGA 58.743 50.000 0.00 0.00 0.00 3.59
707 958 5.382618 AATTTTGTCACAGAGCTTCCATC 57.617 39.130 0.00 0.00 0.00 3.51
708 959 5.302568 TGAAATTTTGTCACAGAGCTTCCAT 59.697 36.000 0.00 0.00 0.00 3.41
949 1202 5.651576 TGCAATTATATTTGTGGCTGTGAGA 59.348 36.000 8.68 0.00 0.00 3.27
956 1209 4.935702 TCAGCTGCAATTATATTTGTGGC 58.064 39.130 9.47 11.48 0.00 5.01
1323 1611 4.082523 GCCACCACCAGCTCGCTA 62.083 66.667 0.00 0.00 0.00 4.26
1362 1650 1.532604 ATCTGTTCGTGCCGTCCAGA 61.533 55.000 15.15 15.15 38.29 3.86
1413 1701 1.069765 CTTGGCTGTCACGGACTGT 59.930 57.895 0.00 0.00 34.68 3.55
1620 1909 2.433838 CACGGCAGCTGAGGACTG 60.434 66.667 20.43 7.15 38.22 3.51
1774 2087 9.294030 GAAAACAGCTTATATTTGTGAATGGAG 57.706 33.333 0.00 0.00 0.00 3.86
1816 2129 9.921637 AATATCTTTTTCTTTTTGCGGTTGATA 57.078 25.926 0.00 0.00 0.00 2.15
1818 2131 8.655651 AAATATCTTTTTCTTTTTGCGGTTGA 57.344 26.923 0.00 0.00 0.00 3.18
1936 2249 9.472361 GCCAATTAACGAGTATAAGATGTTCTA 57.528 33.333 0.00 0.00 0.00 2.10
1937 2250 7.441458 GGCCAATTAACGAGTATAAGATGTTCT 59.559 37.037 0.00 0.00 0.00 3.01
1938 2251 7.307811 GGGCCAATTAACGAGTATAAGATGTTC 60.308 40.741 4.39 0.00 0.00 3.18
1953 2266 3.449737 GGAGGGTTTAAGGGCCAATTAAC 59.550 47.826 6.18 4.46 0.00 2.01
2063 2376 9.507329 AAAATAGAGATGCTCTAAAAACACAGA 57.493 29.630 8.11 0.00 44.76 3.41
2076 2389 6.543831 ACCGCTTCATTAAAAATAGAGATGCT 59.456 34.615 0.00 0.00 0.00 3.79
2081 2394 6.483640 AGGCTACCGCTTCATTAAAAATAGAG 59.516 38.462 0.00 0.00 36.09 2.43
2082 2395 6.260050 CAGGCTACCGCTTCATTAAAAATAGA 59.740 38.462 0.00 0.00 36.09 1.98
2083 2396 6.430451 CAGGCTACCGCTTCATTAAAAATAG 58.570 40.000 0.00 0.00 36.09 1.73
2084 2397 5.298276 CCAGGCTACCGCTTCATTAAAAATA 59.702 40.000 0.00 0.00 36.09 1.40
2085 2398 4.097892 CCAGGCTACCGCTTCATTAAAAAT 59.902 41.667 0.00 0.00 36.09 1.82
2086 2399 3.442273 CCAGGCTACCGCTTCATTAAAAA 59.558 43.478 0.00 0.00 36.09 1.94
2089 2402 1.557832 ACCAGGCTACCGCTTCATTAA 59.442 47.619 0.00 0.00 36.09 1.40
2091 2404 1.134491 GTACCAGGCTACCGCTTCATT 60.134 52.381 0.00 0.00 36.09 2.57
2092 2405 0.464452 GTACCAGGCTACCGCTTCAT 59.536 55.000 0.00 0.00 36.09 2.57
2094 2407 0.535797 AAGTACCAGGCTACCGCTTC 59.464 55.000 0.00 0.00 36.09 3.86
2095 2408 0.535797 GAAGTACCAGGCTACCGCTT 59.464 55.000 0.00 0.00 36.09 4.68
2096 2409 1.664321 CGAAGTACCAGGCTACCGCT 61.664 60.000 0.00 0.00 36.09 5.52
2097 2410 1.226888 CGAAGTACCAGGCTACCGC 60.227 63.158 0.00 0.00 0.00 5.68
2098 2411 1.318158 ACCGAAGTACCAGGCTACCG 61.318 60.000 0.00 0.00 0.00 4.02
2099 2412 0.900421 AACCGAAGTACCAGGCTACC 59.100 55.000 0.00 0.00 0.00 3.18
2100 2413 2.756840 AAACCGAAGTACCAGGCTAC 57.243 50.000 0.00 0.00 0.00 3.58
2101 2414 5.425196 AATAAAACCGAAGTACCAGGCTA 57.575 39.130 0.00 0.00 0.00 3.93
2102 2415 3.994931 ATAAAACCGAAGTACCAGGCT 57.005 42.857 0.00 0.00 0.00 4.58
2103 2416 5.381174 AAAATAAAACCGAAGTACCAGGC 57.619 39.130 0.00 0.00 0.00 4.85
2113 3160 9.733219 AATAAAACAGAACGAAAATAAAACCGA 57.267 25.926 0.00 0.00 0.00 4.69
2129 4012 5.280830 GGGAGGTGGGAGTAAATAAAACAGA 60.281 44.000 0.00 0.00 0.00 3.41
2131 4014 4.354387 TGGGAGGTGGGAGTAAATAAAACA 59.646 41.667 0.00 0.00 0.00 2.83
2141 4024 1.616628 GATGGTGGGAGGTGGGAGT 60.617 63.158 0.00 0.00 0.00 3.85
2158 4041 0.476771 GAAAACCAGTGTGGGAGGGA 59.523 55.000 0.00 0.00 43.37 4.20
2223 5343 8.723311 CCGTGATTTTTGTATGTTAGGAAAGTA 58.277 33.333 0.00 0.00 0.00 2.24
2259 5798 6.952773 TCGGTTGATTTGGATAAATTAGGG 57.047 37.500 0.00 0.00 36.66 3.53
2370 9712 1.153901 CGACGTACGGTCCAAGCAT 60.154 57.895 21.06 0.00 42.99 3.79
2416 10186 1.374125 TGGCACGGTGAGACAATCG 60.374 57.895 13.29 0.00 0.00 3.34
2424 10194 1.228003 AAAATCGGTGGCACGGTGA 60.228 52.632 22.32 15.16 0.00 4.02
2428 10198 1.265635 TGAAAGAAAATCGGTGGCACG 59.734 47.619 12.17 7.33 0.00 5.34


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

AutoCloner maintained by Alex Coulton.