Multiple sequence alignment - TraesCS3B01G123200

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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 TraesCS3B01G123200 chr3B 100.000 2507 0 0 1 2507 94864798 94867304 0.000000e+00 4630
1 TraesCS3B01G123200 chr3D 87.971 2494 143 75 103 2505 59261177 59263604 0.000000e+00 2798
2 TraesCS3B01G123200 chr3A 84.968 1876 113 71 103 1898 68126911 68128697 0.000000e+00 1746
3 TraesCS3B01G123200 chr3A 85.987 471 32 10 2060 2507 68128822 68129281 8.120000e-130 473
4 TraesCS3B01G123200 chr3A 86.111 72 7 1 1949 2020 68128757 68128825 9.620000e-10 75


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 TraesCS3B01G123200 chr3B 94864798 94867304 2506 False 4630.000000 4630 100.000000 1 2507 1 chr3B.!!$F1 2506
1 TraesCS3B01G123200 chr3D 59261177 59263604 2427 False 2798.000000 2798 87.971000 103 2505 1 chr3D.!!$F1 2402
2 TraesCS3B01G123200 chr3A 68126911 68129281 2370 False 764.666667 1746 85.688667 103 2507 3 chr3A.!!$F1 2404

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
70 71 0.107945 CTTGCTCCCTTCCTTCTCCG 60.108 60.0 0.0 0.0 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1638 1739 0.026803 GCGAAAGAAAGCGATGCGAT 59.973 50.0 0.0 0.0 0.0 4.58 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
21 22 3.274288 CAGTTGCCTCAGAGAAATACCC 58.726 50.000 0.00 0.00 0.00 3.69
22 23 3.054802 CAGTTGCCTCAGAGAAATACCCT 60.055 47.826 0.00 0.00 0.00 4.34
23 24 4.162320 CAGTTGCCTCAGAGAAATACCCTA 59.838 45.833 0.00 0.00 0.00 3.53
24 25 4.783227 AGTTGCCTCAGAGAAATACCCTAA 59.217 41.667 0.00 0.00 0.00 2.69
25 26 5.250774 AGTTGCCTCAGAGAAATACCCTAAA 59.749 40.000 0.00 0.00 0.00 1.85
26 27 5.772393 TGCCTCAGAGAAATACCCTAAAA 57.228 39.130 0.00 0.00 0.00 1.52
27 28 6.134535 TGCCTCAGAGAAATACCCTAAAAA 57.865 37.500 0.00 0.00 0.00 1.94
48 49 5.921962 AAAAAGTTGCCTCAGAGAAACTT 57.078 34.783 18.58 18.58 42.97 2.66
50 51 5.921962 AAAGTTGCCTCAGAGAAACTTTT 57.078 34.783 24.49 15.55 45.73 2.27
51 52 5.506686 AAGTTGCCTCAGAGAAACTTTTC 57.493 39.130 18.58 0.00 39.24 2.29
52 53 5.654209 AAAGTTGCCTCAGAGAAACTTTTCT 59.346 36.000 24.49 3.83 45.73 2.52
53 54 5.196695 AGTTGCCTCAGAGAAACTTTTCTT 58.803 37.500 11.01 0.00 46.84 2.52
54 55 5.067023 AGTTGCCTCAGAGAAACTTTTCTTG 59.933 40.000 11.01 6.62 46.84 3.02
55 56 3.316308 TGCCTCAGAGAAACTTTTCTTGC 59.684 43.478 5.71 5.35 46.84 4.01
56 57 3.567585 GCCTCAGAGAAACTTTTCTTGCT 59.432 43.478 5.71 0.00 46.84 3.91
57 58 4.320129 GCCTCAGAGAAACTTTTCTTGCTC 60.320 45.833 5.71 0.00 46.84 4.26
58 59 4.215185 CCTCAGAGAAACTTTTCTTGCTCC 59.785 45.833 5.71 0.00 46.84 4.70
59 60 4.137543 TCAGAGAAACTTTTCTTGCTCCC 58.862 43.478 5.71 0.00 46.84 4.30
60 61 4.140536 CAGAGAAACTTTTCTTGCTCCCT 58.859 43.478 5.71 0.00 46.84 4.20
61 62 4.582240 CAGAGAAACTTTTCTTGCTCCCTT 59.418 41.667 5.71 0.00 46.84 3.95
62 63 4.824537 AGAGAAACTTTTCTTGCTCCCTTC 59.175 41.667 5.71 0.00 46.84 3.46
63 64 3.891977 AGAAACTTTTCTTGCTCCCTTCC 59.108 43.478 0.00 0.00 44.70 3.46
64 65 3.602205 AACTTTTCTTGCTCCCTTCCT 57.398 42.857 0.00 0.00 0.00 3.36
65 66 3.602205 ACTTTTCTTGCTCCCTTCCTT 57.398 42.857 0.00 0.00 0.00 3.36
66 67 3.491342 ACTTTTCTTGCTCCCTTCCTTC 58.509 45.455 0.00 0.00 0.00 3.46
67 68 3.139211 ACTTTTCTTGCTCCCTTCCTTCT 59.861 43.478 0.00 0.00 0.00 2.85
68 69 3.425162 TTTCTTGCTCCCTTCCTTCTC 57.575 47.619 0.00 0.00 0.00 2.87
69 70 1.280457 TCTTGCTCCCTTCCTTCTCC 58.720 55.000 0.00 0.00 0.00 3.71
70 71 0.107945 CTTGCTCCCTTCCTTCTCCG 60.108 60.000 0.00 0.00 0.00 4.63
71 72 1.553690 TTGCTCCCTTCCTTCTCCGG 61.554 60.000 0.00 0.00 0.00 5.14
72 73 1.990614 GCTCCCTTCCTTCTCCGGT 60.991 63.158 0.00 0.00 0.00 5.28
73 74 1.901085 CTCCCTTCCTTCTCCGGTG 59.099 63.158 0.00 0.00 0.00 4.94
74 75 0.905337 CTCCCTTCCTTCTCCGGTGT 60.905 60.000 0.00 0.00 0.00 4.16
75 76 1.192146 TCCCTTCCTTCTCCGGTGTG 61.192 60.000 0.00 0.00 0.00 3.82
76 77 1.481056 CCCTTCCTTCTCCGGTGTGT 61.481 60.000 0.00 0.00 0.00 3.72
77 78 1.263356 CCTTCCTTCTCCGGTGTGTA 58.737 55.000 0.00 0.00 0.00 2.90
78 79 1.204941 CCTTCCTTCTCCGGTGTGTAG 59.795 57.143 0.00 0.00 0.00 2.74
79 80 0.606604 TTCCTTCTCCGGTGTGTAGC 59.393 55.000 0.00 0.00 0.00 3.58
80 81 0.251653 TCCTTCTCCGGTGTGTAGCT 60.252 55.000 0.00 0.00 0.00 3.32
81 82 0.608640 CCTTCTCCGGTGTGTAGCTT 59.391 55.000 0.00 0.00 0.00 3.74
82 83 1.404315 CCTTCTCCGGTGTGTAGCTTC 60.404 57.143 0.00 0.00 0.00 3.86
83 84 1.546476 CTTCTCCGGTGTGTAGCTTCT 59.454 52.381 0.00 0.00 0.00 2.85
84 85 1.629043 TCTCCGGTGTGTAGCTTCTT 58.371 50.000 0.00 0.00 0.00 2.52
85 86 1.968493 TCTCCGGTGTGTAGCTTCTTT 59.032 47.619 0.00 0.00 0.00 2.52
86 87 2.029290 TCTCCGGTGTGTAGCTTCTTTC 60.029 50.000 0.00 0.00 0.00 2.62
87 88 1.001633 TCCGGTGTGTAGCTTCTTTCC 59.998 52.381 0.00 0.00 0.00 3.13
88 89 1.002087 CCGGTGTGTAGCTTCTTTCCT 59.998 52.381 0.00 0.00 0.00 3.36
89 90 2.232941 CCGGTGTGTAGCTTCTTTCCTA 59.767 50.000 0.00 0.00 0.00 2.94
90 91 3.251571 CGGTGTGTAGCTTCTTTCCTAC 58.748 50.000 0.00 0.00 35.60 3.18
91 92 3.597255 GGTGTGTAGCTTCTTTCCTACC 58.403 50.000 0.00 0.00 34.44 3.18
92 93 3.597255 GTGTGTAGCTTCTTTCCTACCC 58.403 50.000 0.00 0.00 34.44 3.69
93 94 3.007614 GTGTGTAGCTTCTTTCCTACCCA 59.992 47.826 0.00 0.00 34.44 4.51
94 95 3.649023 TGTGTAGCTTCTTTCCTACCCAA 59.351 43.478 0.00 0.00 34.44 4.12
95 96 4.103469 TGTGTAGCTTCTTTCCTACCCAAA 59.897 41.667 0.00 0.00 34.44 3.28
96 97 5.067954 GTGTAGCTTCTTTCCTACCCAAAA 58.932 41.667 0.00 0.00 34.44 2.44
97 98 5.533528 GTGTAGCTTCTTTCCTACCCAAAAA 59.466 40.000 0.00 0.00 34.44 1.94
293 301 2.190578 CGGATCAGAACAGCCCCC 59.809 66.667 0.00 0.00 0.00 5.40
298 306 4.020617 CAGAACAGCCCCCGCAGA 62.021 66.667 0.00 0.00 37.52 4.26
356 364 3.499918 GCAGATAGAGCAAAACACACACT 59.500 43.478 0.00 0.00 0.00 3.55
365 379 0.466189 AAACACACACTCCAGCTGGG 60.466 55.000 32.23 23.77 35.41 4.45
371 385 2.113986 ACTCCAGCTGGGCACAAC 59.886 61.111 32.23 0.00 36.21 3.32
394 413 3.543680 ATACACGACCCAGAGAAATGG 57.456 47.619 0.00 0.00 40.29 3.16
497 539 3.013990 CGTCACGAGCGCGAGATC 61.014 66.667 19.05 8.17 44.53 2.75
525 567 2.354560 GCGTTTCGTTTTCTGGCGC 61.355 57.895 0.00 0.00 36.75 6.53
698 743 0.178990 GAGGAGAGGAGAGGAGAGGC 60.179 65.000 0.00 0.00 0.00 4.70
999 1064 4.840005 GGAGCGCTGGTAGGGTGC 62.840 72.222 18.48 0.00 40.08 5.01
1517 1606 0.178995 GTAGAGTAGGGTAGGGCGCT 60.179 60.000 7.64 8.86 43.25 5.92
1518 1607 0.110104 TAGAGTAGGGTAGGGCGCTC 59.890 60.000 6.54 1.48 40.99 5.03
1519 1608 2.518825 AGTAGGGTAGGGCGCTCG 60.519 66.667 6.54 0.00 40.99 5.03
1521 1610 4.908487 TAGGGTAGGGCGCTCGGG 62.908 72.222 6.54 0.00 40.99 5.14
1526 1615 4.772231 TAGGGCGCTCGGGGAGTT 62.772 66.667 6.54 0.00 31.39 3.01
1579 1679 0.104487 TTTCGGACGGTTGTACAGCA 59.896 50.000 12.05 0.00 0.00 4.41
1587 1687 0.250727 GGTTGTACAGCAGGCAAGGA 60.251 55.000 12.05 0.00 0.00 3.36
1626 1727 2.483197 GGGTGGTTCGTTTTGGCGT 61.483 57.895 0.00 0.00 0.00 5.68
1630 1731 2.719354 GTTCGTTTTGGCGTGGCT 59.281 55.556 0.00 0.00 0.00 4.75
1706 1813 1.369091 ATCAATGCGGTCGGTCTTGC 61.369 55.000 0.00 0.00 0.00 4.01
1707 1814 2.034879 CAATGCGGTCGGTCTTGCT 61.035 57.895 0.00 0.00 0.00 3.91
1719 1830 0.937304 GTCTTGCTTGTGCGTTGAGA 59.063 50.000 0.00 0.00 43.34 3.27
1748 1859 3.358111 TGCGAGGAAATGGAAATGGTA 57.642 42.857 0.00 0.00 0.00 3.25
1757 1868 2.969821 TGGAAATGGTACTTGCTGGT 57.030 45.000 0.00 0.00 0.00 4.00
1759 1870 2.107378 TGGAAATGGTACTTGCTGGTGA 59.893 45.455 0.00 0.00 0.00 4.02
1767 1878 0.667487 ACTTGCTGGTGACACGATCG 60.667 55.000 14.88 14.88 35.60 3.69
1816 1927 1.136057 GCTTTTGCGTCCGGTTTCTAG 60.136 52.381 0.00 0.00 34.86 2.43
1844 1964 1.134220 TCAGTTTTCCTGTTCCGTGCT 60.134 47.619 0.00 0.00 42.19 4.40
1846 1966 2.480419 CAGTTTTCCTGTTCCGTGCTAG 59.520 50.000 0.00 0.00 36.37 3.42
1847 1967 2.367567 AGTTTTCCTGTTCCGTGCTAGA 59.632 45.455 0.00 0.00 0.00 2.43
1848 1968 3.135994 GTTTTCCTGTTCCGTGCTAGAA 58.864 45.455 0.00 0.00 0.00 2.10
1849 1969 2.450609 TTCCTGTTCCGTGCTAGAAC 57.549 50.000 0.00 0.00 43.20 3.01
1850 1970 0.606604 TCCTGTTCCGTGCTAGAACC 59.393 55.000 0.00 0.00 42.41 3.62
1851 1971 0.391263 CCTGTTCCGTGCTAGAACCC 60.391 60.000 0.00 0.00 42.41 4.11
1898 2018 1.591158 GAGCGGCGTTTGAATTCGATA 59.409 47.619 9.37 0.00 0.00 2.92
1917 2037 5.146482 GATATCGATCGTACTACTCCTGC 57.854 47.826 15.94 0.00 0.00 4.85
1918 2038 1.215244 TCGATCGTACTACTCCTGCG 58.785 55.000 15.94 0.00 0.00 5.18
1921 2041 2.223203 CGATCGTACTACTCCTGCGTTT 60.223 50.000 7.03 0.00 0.00 3.60
1922 2042 3.730061 CGATCGTACTACTCCTGCGTTTT 60.730 47.826 7.03 0.00 0.00 2.43
1923 2043 2.937591 TCGTACTACTCCTGCGTTTTG 58.062 47.619 0.00 0.00 0.00 2.44
1924 2044 2.294233 TCGTACTACTCCTGCGTTTTGT 59.706 45.455 0.00 0.00 0.00 2.83
1925 2045 3.054878 CGTACTACTCCTGCGTTTTGTT 58.945 45.455 0.00 0.00 0.00 2.83
1926 2046 3.492011 CGTACTACTCCTGCGTTTTGTTT 59.508 43.478 0.00 0.00 0.00 2.83
1965 2085 2.381961 ACCTACCCAACCCACATTCAAT 59.618 45.455 0.00 0.00 0.00 2.57
1966 2086 3.023832 CCTACCCAACCCACATTCAATC 58.976 50.000 0.00 0.00 0.00 2.67
1974 2106 1.600957 CCCACATTCAATCAGCTAGCG 59.399 52.381 9.55 4.60 0.00 4.26
2031 2177 3.032459 GTCCCGAGGAAAGAAGACCTAT 58.968 50.000 0.00 0.00 36.57 2.57
2039 2185 7.120138 CCGAGGAAAGAAGACCTATCTATCTAC 59.880 44.444 0.00 0.00 36.57 2.59
2040 2186 7.662258 CGAGGAAAGAAGACCTATCTATCTACA 59.338 40.741 0.00 0.00 36.57 2.74
2041 2187 8.934023 AGGAAAGAAGACCTATCTATCTACAG 57.066 38.462 0.00 0.00 33.57 2.74
2042 2188 8.507761 AGGAAAGAAGACCTATCTATCTACAGT 58.492 37.037 0.00 0.00 33.57 3.55
2043 2189 9.796180 GGAAAGAAGACCTATCTATCTACAGTA 57.204 37.037 0.00 0.00 33.57 2.74
2046 2192 8.857694 AGAAGACCTATCTATCTACAGTAAGC 57.142 38.462 0.00 0.00 33.57 3.09
2047 2193 8.441572 AGAAGACCTATCTATCTACAGTAAGCA 58.558 37.037 0.00 0.00 33.57 3.91
2048 2194 8.630054 AAGACCTATCTATCTACAGTAAGCAG 57.370 38.462 0.00 0.00 33.57 4.24
2049 2195 7.172342 AGACCTATCTATCTACAGTAAGCAGG 58.828 42.308 0.00 0.00 31.46 4.85
2050 2196 7.017750 AGACCTATCTATCTACAGTAAGCAGGA 59.982 40.741 0.00 0.00 31.46 3.86
2051 2197 6.943718 ACCTATCTATCTACAGTAAGCAGGAC 59.056 42.308 0.00 0.00 0.00 3.85
2052 2198 7.172342 CCTATCTATCTACAGTAAGCAGGACT 58.828 42.308 0.00 0.00 0.00 3.85
2053 2199 8.322828 CCTATCTATCTACAGTAAGCAGGACTA 58.677 40.741 0.00 0.00 0.00 2.59
2054 2200 9.378551 CTATCTATCTACAGTAAGCAGGACTAG 57.621 40.741 0.00 0.00 0.00 2.57
2055 2201 7.139287 TCTATCTACAGTAAGCAGGACTAGT 57.861 40.000 0.00 0.00 0.00 2.57
2056 2202 8.260099 TCTATCTACAGTAAGCAGGACTAGTA 57.740 38.462 0.00 0.00 0.00 1.82
2057 2203 8.369424 TCTATCTACAGTAAGCAGGACTAGTAG 58.631 40.741 0.00 0.00 33.96 2.57
2058 2204 6.310764 TCTACAGTAAGCAGGACTAGTAGT 57.689 41.667 1.37 1.37 34.13 2.73
2059 2205 7.429374 TCTACAGTAAGCAGGACTAGTAGTA 57.571 40.000 1.88 0.00 34.13 1.82
2060 2206 7.499292 TCTACAGTAAGCAGGACTAGTAGTAG 58.501 42.308 1.88 2.87 34.13 2.57
2061 2207 5.438833 ACAGTAAGCAGGACTAGTAGTAGG 58.561 45.833 1.88 0.00 0.00 3.18
2062 2208 5.191323 ACAGTAAGCAGGACTAGTAGTAGGA 59.809 44.000 1.88 0.00 0.00 2.94
2122 2282 2.287915 CCGGAGCATGAACTAATTTCCG 59.712 50.000 0.00 3.22 44.10 4.30
2123 2283 2.936498 CGGAGCATGAACTAATTTCCGT 59.064 45.455 0.00 0.00 40.73 4.69
2168 2331 0.250124 TTCGTGGTCTGGACGCATTT 60.250 50.000 0.00 0.00 36.75 2.32
2169 2332 0.250124 TCGTGGTCTGGACGCATTTT 60.250 50.000 0.00 0.00 36.75 1.82
2170 2333 0.591170 CGTGGTCTGGACGCATTTTT 59.409 50.000 0.00 0.00 0.00 1.94
2239 2402 0.681733 ATAGCCATGAATCCGCGAGT 59.318 50.000 8.23 0.00 0.00 4.18
2251 2414 2.734723 GCGAGTGAGCGAGCACAA 60.735 61.111 10.13 0.00 41.19 3.33
2338 2505 3.360340 GCAGCCTGCTGTGTGGAC 61.360 66.667 19.45 0.00 45.24 4.02
2391 2563 4.883083 TCACTGTAGTAGTTTCAGGCTTG 58.117 43.478 0.00 0.00 37.60 4.01
2419 2601 4.678269 CGCAGCACAGCACAGCAC 62.678 66.667 0.00 0.00 0.00 4.40
2420 2602 3.588906 GCAGCACAGCACAGCACA 61.589 61.111 0.00 0.00 0.00 4.57
2429 2611 0.181114 AGCACAGCACAGGTCAAAGA 59.819 50.000 0.00 0.00 0.00 2.52
2473 2659 2.124983 AGGCATGCAGCTACCACG 60.125 61.111 21.36 0.00 44.79 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.636153 AGGGTATTTCTCTGAGGCAAC 57.364 47.619 4.59 0.00 0.00 4.17
4 5 5.772393 TTTTAGGGTATTTCTCTGAGGCA 57.228 39.130 4.59 0.00 0.00 4.75
28 29 5.654209 AGAAAAGTTTCTCTGAGGCAACTTT 59.346 36.000 26.30 26.30 46.59 2.66
29 30 5.196695 AGAAAAGTTTCTCTGAGGCAACTT 58.803 37.500 20.88 20.88 46.59 2.66
31 32 5.277047 CAAGAAAAGTTTCTCTGAGGCAAC 58.723 41.667 6.76 8.43 46.22 4.17
32 33 4.202050 GCAAGAAAAGTTTCTCTGAGGCAA 60.202 41.667 6.76 0.00 46.22 4.52
33 34 3.316308 GCAAGAAAAGTTTCTCTGAGGCA 59.684 43.478 6.76 0.00 46.22 4.75
34 35 3.567585 AGCAAGAAAAGTTTCTCTGAGGC 59.432 43.478 6.76 6.53 46.22 4.70
35 36 4.215185 GGAGCAAGAAAAGTTTCTCTGAGG 59.785 45.833 6.76 0.00 46.22 3.86
36 37 4.215185 GGGAGCAAGAAAAGTTTCTCTGAG 59.785 45.833 6.76 0.00 46.22 3.35
37 38 4.137543 GGGAGCAAGAAAAGTTTCTCTGA 58.862 43.478 6.76 0.00 46.22 3.27
38 39 4.140536 AGGGAGCAAGAAAAGTTTCTCTG 58.859 43.478 6.76 8.53 46.22 3.35
39 40 4.445557 AGGGAGCAAGAAAAGTTTCTCT 57.554 40.909 6.76 1.34 46.22 3.10
40 41 4.022762 GGAAGGGAGCAAGAAAAGTTTCTC 60.023 45.833 6.76 0.00 46.22 2.87
42 43 3.891977 AGGAAGGGAGCAAGAAAAGTTTC 59.108 43.478 0.00 0.00 37.45 2.78
43 44 3.916035 AGGAAGGGAGCAAGAAAAGTTT 58.084 40.909 0.00 0.00 0.00 2.66
44 45 3.602205 AGGAAGGGAGCAAGAAAAGTT 57.398 42.857 0.00 0.00 0.00 2.66
45 46 3.139211 AGAAGGAAGGGAGCAAGAAAAGT 59.861 43.478 0.00 0.00 0.00 2.66
46 47 3.755905 GAGAAGGAAGGGAGCAAGAAAAG 59.244 47.826 0.00 0.00 0.00 2.27
47 48 3.498661 GGAGAAGGAAGGGAGCAAGAAAA 60.499 47.826 0.00 0.00 0.00 2.29
48 49 2.040412 GGAGAAGGAAGGGAGCAAGAAA 59.960 50.000 0.00 0.00 0.00 2.52
49 50 1.630878 GGAGAAGGAAGGGAGCAAGAA 59.369 52.381 0.00 0.00 0.00 2.52
50 51 1.280457 GGAGAAGGAAGGGAGCAAGA 58.720 55.000 0.00 0.00 0.00 3.02
51 52 0.107945 CGGAGAAGGAAGGGAGCAAG 60.108 60.000 0.00 0.00 0.00 4.01
52 53 1.553690 CCGGAGAAGGAAGGGAGCAA 61.554 60.000 0.00 0.00 0.00 3.91
53 54 1.990060 CCGGAGAAGGAAGGGAGCA 60.990 63.158 0.00 0.00 0.00 4.26
54 55 1.990614 ACCGGAGAAGGAAGGGAGC 60.991 63.158 9.46 0.00 34.73 4.70
55 56 0.905337 ACACCGGAGAAGGAAGGGAG 60.905 60.000 9.46 0.00 34.73 4.30
56 57 1.157751 ACACCGGAGAAGGAAGGGA 59.842 57.895 9.46 0.00 34.73 4.20
57 58 1.296715 CACACCGGAGAAGGAAGGG 59.703 63.158 9.46 0.00 34.73 3.95
58 59 1.204941 CTACACACCGGAGAAGGAAGG 59.795 57.143 9.46 0.00 34.73 3.46
59 60 1.404315 GCTACACACCGGAGAAGGAAG 60.404 57.143 9.46 2.75 34.73 3.46
60 61 0.606604 GCTACACACCGGAGAAGGAA 59.393 55.000 9.46 0.00 34.73 3.36
61 62 0.251653 AGCTACACACCGGAGAAGGA 60.252 55.000 9.46 0.00 34.73 3.36
62 63 0.608640 AAGCTACACACCGGAGAAGG 59.391 55.000 9.46 0.00 37.30 3.46
63 64 1.546476 AGAAGCTACACACCGGAGAAG 59.454 52.381 9.46 0.84 0.00 2.85
64 65 1.629043 AGAAGCTACACACCGGAGAA 58.371 50.000 9.46 0.00 0.00 2.87
65 66 1.629043 AAGAAGCTACACACCGGAGA 58.371 50.000 9.46 0.00 0.00 3.71
66 67 2.338500 GAAAGAAGCTACACACCGGAG 58.662 52.381 9.46 1.26 0.00 4.63
67 68 1.001633 GGAAAGAAGCTACACACCGGA 59.998 52.381 9.46 0.00 0.00 5.14
68 69 1.002087 AGGAAAGAAGCTACACACCGG 59.998 52.381 0.00 0.00 0.00 5.28
69 70 2.457366 AGGAAAGAAGCTACACACCG 57.543 50.000 0.00 0.00 0.00 4.94
70 71 3.597255 GGTAGGAAAGAAGCTACACACC 58.403 50.000 0.00 0.00 0.00 4.16
71 72 3.007614 TGGGTAGGAAAGAAGCTACACAC 59.992 47.826 0.00 0.00 31.65 3.82
72 73 3.244582 TGGGTAGGAAAGAAGCTACACA 58.755 45.455 0.00 0.00 33.86 3.72
73 74 3.975168 TGGGTAGGAAAGAAGCTACAC 57.025 47.619 0.00 0.00 0.00 2.90
74 75 4.986054 TTTGGGTAGGAAAGAAGCTACA 57.014 40.909 0.00 0.00 0.00 2.74
143 144 1.219646 GGTTTTACACCAGCGTCGAA 58.780 50.000 0.00 0.00 46.42 3.71
152 154 5.747483 CCTTCCGGGAGAGGTTTTACACC 62.747 56.522 12.85 0.00 41.24 4.16
201 205 2.009774 CGGATTAACCTTGTGAGCTGG 58.990 52.381 0.00 0.00 36.31 4.85
280 288 4.020617 CTGCGGGGGCTGTTCTGA 62.021 66.667 0.00 0.00 0.00 3.27
283 291 1.250840 AAAATCTGCGGGGGCTGTTC 61.251 55.000 0.00 0.00 0.00 3.18
293 301 1.850377 TGTTGTTGCCAAAATCTGCG 58.150 45.000 0.00 0.00 30.94 5.18
298 306 1.939255 CGCCTTTGTTGTTGCCAAAAT 59.061 42.857 0.00 0.00 31.86 1.82
356 364 2.370459 ATTGGTTGTGCCCAGCTGGA 62.370 55.000 34.91 12.85 35.49 3.86
365 379 0.519961 GGGTCGTGTATTGGTTGTGC 59.480 55.000 0.00 0.00 0.00 4.57
371 385 3.328382 TTTCTCTGGGTCGTGTATTGG 57.672 47.619 0.00 0.00 0.00 3.16
502 544 0.721483 CAGAAAACGAAACGCTCCGC 60.721 55.000 0.00 0.00 0.00 5.54
503 545 0.110823 CCAGAAAACGAAACGCTCCG 60.111 55.000 0.00 0.00 0.00 4.63
504 546 0.385598 GCCAGAAAACGAAACGCTCC 60.386 55.000 0.00 0.00 0.00 4.70
505 547 0.721483 CGCCAGAAAACGAAACGCTC 60.721 55.000 0.00 0.00 0.00 5.03
506 548 1.278637 CGCCAGAAAACGAAACGCT 59.721 52.632 0.00 0.00 0.00 5.07
507 549 2.354560 GCGCCAGAAAACGAAACGC 61.355 57.895 0.00 0.00 37.93 4.84
508 550 2.067039 CGCGCCAGAAAACGAAACG 61.067 57.895 0.00 0.00 0.00 3.60
509 551 0.721483 CTCGCGCCAGAAAACGAAAC 60.721 55.000 0.00 0.00 33.61 2.78
510 552 1.567537 CTCGCGCCAGAAAACGAAA 59.432 52.632 0.00 0.00 33.61 3.46
677 719 1.421646 CCTCTCCTCTCCTCTCCTCTC 59.578 61.905 0.00 0.00 0.00 3.20
850 895 2.618241 TCCACGTCGGTTTATATAGCGT 59.382 45.455 13.21 0.00 39.80 5.07
987 1052 1.153086 CTCCATGCACCCTACCAGC 60.153 63.158 0.00 0.00 0.00 4.85
999 1064 2.146061 GGCCTCCTCCTCCTCCATG 61.146 68.421 0.00 0.00 0.00 3.66
1236 1313 0.948623 TGCCGTTGATGGTCACGAAG 60.949 55.000 0.00 0.00 0.00 3.79
1368 1445 3.934391 CTTGGTGTCGTCGGGCTCC 62.934 68.421 0.00 0.00 0.00 4.70
1497 1580 0.178995 GCGCCCTACCCTACTCTACT 60.179 60.000 0.00 0.00 0.00 2.57
1517 1606 1.550130 CCTTGCCTACAACTCCCCGA 61.550 60.000 0.00 0.00 0.00 5.14
1518 1607 1.078426 CCTTGCCTACAACTCCCCG 60.078 63.158 0.00 0.00 0.00 5.73
1519 1608 1.378646 GCCTTGCCTACAACTCCCC 60.379 63.158 0.00 0.00 0.00 4.81
1521 1610 0.248289 TACGCCTTGCCTACAACTCC 59.752 55.000 0.00 0.00 0.00 3.85
1523 1612 1.944430 GCTTACGCCTTGCCTACAACT 60.944 52.381 0.00 0.00 0.00 3.16
1525 1614 1.017177 CGCTTACGCCTTGCCTACAA 61.017 55.000 0.00 0.00 0.00 2.41
1526 1615 1.447140 CGCTTACGCCTTGCCTACA 60.447 57.895 0.00 0.00 0.00 2.74
1528 1617 0.179129 GTACGCTTACGCCTTGCCTA 60.179 55.000 0.00 0.00 45.53 3.93
1579 1679 0.188342 TCCTGGCTTTTTCCTTGCCT 59.812 50.000 0.00 0.00 46.23 4.75
1608 1709 2.333581 CGCCAAAACGAACCACCC 59.666 61.111 0.00 0.00 34.06 4.61
1638 1739 0.026803 GCGAAAGAAAGCGATGCGAT 59.973 50.000 0.00 0.00 0.00 4.58
1672 1773 4.482386 GCATTGATGAATGAATCCATCGG 58.518 43.478 9.25 0.00 41.49 4.18
1677 1784 3.607775 CGACCGCATTGATGAATGAATCC 60.608 47.826 9.25 0.00 41.49 3.01
1679 1786 2.291465 CCGACCGCATTGATGAATGAAT 59.709 45.455 9.25 0.00 41.49 2.57
1681 1788 1.298602 CCGACCGCATTGATGAATGA 58.701 50.000 9.25 0.00 41.49 2.57
1683 1790 1.134401 AGACCGACCGCATTGATGAAT 60.134 47.619 0.00 0.00 0.00 2.57
1706 1813 1.143305 CTCACCTCTCAACGCACAAG 58.857 55.000 0.00 0.00 0.00 3.16
1707 1814 0.249868 CCTCACCTCTCAACGCACAA 60.250 55.000 0.00 0.00 0.00 3.33
1719 1830 0.693049 ATTTCCTCGCAACCTCACCT 59.307 50.000 0.00 0.00 0.00 4.00
1748 1859 0.667487 CGATCGTGTCACCAGCAAGT 60.667 55.000 7.03 0.00 0.00 3.16
1757 1868 4.451150 GCCAGCCCGATCGTGTCA 62.451 66.667 15.09 0.00 0.00 3.58
1759 1870 4.457496 CAGCCAGCCCGATCGTGT 62.457 66.667 15.09 0.00 0.00 4.49
1767 1878 3.066814 CAAAGAGCCAGCCAGCCC 61.067 66.667 0.00 0.00 0.00 5.19
1779 1890 2.892334 GCAGGCAACGCGACAAAGA 61.892 57.895 15.93 0.00 46.39 2.52
1781 1892 1.999071 AAAGCAGGCAACGCGACAAA 61.999 50.000 15.93 0.00 46.39 2.83
1844 1964 2.635915 TCAAGGCGAGAAAAGGGTTCTA 59.364 45.455 0.00 0.00 0.00 2.10
1846 1966 1.535896 GTCAAGGCGAGAAAAGGGTTC 59.464 52.381 0.00 0.00 0.00 3.62
1847 1967 1.143073 AGTCAAGGCGAGAAAAGGGTT 59.857 47.619 0.00 0.00 0.00 4.11
1848 1968 0.765510 AGTCAAGGCGAGAAAAGGGT 59.234 50.000 0.00 0.00 0.00 4.34
1849 1969 1.160137 CAGTCAAGGCGAGAAAAGGG 58.840 55.000 0.00 0.00 0.00 3.95
1850 1970 1.160137 CCAGTCAAGGCGAGAAAAGG 58.840 55.000 0.00 0.00 0.00 3.11
1851 1971 0.519077 GCCAGTCAAGGCGAGAAAAG 59.481 55.000 0.00 0.00 46.12 2.27
1898 2018 1.799403 CGCAGGAGTAGTACGATCGAT 59.201 52.381 24.34 9.73 0.00 3.59
1910 2030 4.450082 AAGAAAAACAAAACGCAGGAGT 57.550 36.364 0.00 0.00 0.00 3.85
1915 2035 6.183359 CGAAAGAGAAAGAAAAACAAAACGCA 60.183 34.615 0.00 0.00 0.00 5.24
1916 2036 6.168975 CGAAAGAGAAAGAAAAACAAAACGC 58.831 36.000 0.00 0.00 0.00 4.84
1917 2037 6.168975 GCGAAAGAGAAAGAAAAACAAAACG 58.831 36.000 0.00 0.00 0.00 3.60
1918 2038 6.090223 TGGCGAAAGAGAAAGAAAAACAAAAC 59.910 34.615 0.00 0.00 0.00 2.43
1921 2041 5.317733 TGGCGAAAGAGAAAGAAAAACAA 57.682 34.783 0.00 0.00 0.00 2.83
1922 2042 4.974368 TGGCGAAAGAGAAAGAAAAACA 57.026 36.364 0.00 0.00 0.00 2.83
1923 2043 4.503007 GGTTGGCGAAAGAGAAAGAAAAAC 59.497 41.667 0.00 0.00 0.00 2.43
1924 2044 4.401202 AGGTTGGCGAAAGAGAAAGAAAAA 59.599 37.500 0.00 0.00 0.00 1.94
1925 2045 3.951680 AGGTTGGCGAAAGAGAAAGAAAA 59.048 39.130 0.00 0.00 0.00 2.29
1926 2046 3.551846 AGGTTGGCGAAAGAGAAAGAAA 58.448 40.909 0.00 0.00 0.00 2.52
1965 2085 2.488355 GTACACGCCGCTAGCTGA 59.512 61.111 13.93 0.00 40.39 4.26
1966 2086 2.663630 ATCGTACACGCCGCTAGCTG 62.664 60.000 13.93 7.58 40.39 4.24
1974 2106 0.733729 AGAGACTGATCGTACACGCC 59.266 55.000 0.00 0.00 39.60 5.68
1983 2129 6.634805 TGAGATTGGTTAACAGAGACTGATC 58.365 40.000 8.10 0.00 35.18 2.92
2031 2177 7.139287 ACTAGTCCTGCTTACTGTAGATAGA 57.861 40.000 0.00 0.00 0.00 1.98
2039 2185 5.682659 TCCTACTACTAGTCCTGCTTACTG 58.317 45.833 0.00 0.00 0.00 2.74
2040 2186 5.429435 ACTCCTACTACTAGTCCTGCTTACT 59.571 44.000 0.00 0.00 0.00 2.24
2041 2187 5.683681 ACTCCTACTACTAGTCCTGCTTAC 58.316 45.833 0.00 0.00 0.00 2.34
2042 2188 5.972327 ACTCCTACTACTAGTCCTGCTTA 57.028 43.478 0.00 0.00 0.00 3.09
2043 2189 4.866327 ACTCCTACTACTAGTCCTGCTT 57.134 45.455 0.00 0.00 0.00 3.91
2044 2190 4.970640 ACTACTCCTACTACTAGTCCTGCT 59.029 45.833 0.00 0.00 0.00 4.24
2045 2191 5.294734 ACTACTCCTACTACTAGTCCTGC 57.705 47.826 0.00 0.00 0.00 4.85
2046 2192 7.601705 AGTACTACTCCTACTACTAGTCCTG 57.398 44.000 0.00 0.00 0.00 3.86
2047 2193 9.722317 TTTAGTACTACTCCTACTACTAGTCCT 57.278 37.037 0.91 0.00 0.00 3.85
2056 2202 9.710818 TGGATTCATTTTAGTACTACTCCTACT 57.289 33.333 0.91 0.00 0.00 2.57
2059 2205 9.047947 ACTTGGATTCATTTTAGTACTACTCCT 57.952 33.333 0.91 0.00 0.00 3.69
2060 2206 9.668497 AACTTGGATTCATTTTAGTACTACTCC 57.332 33.333 0.91 0.00 0.00 3.85
2062 2208 9.449719 CCAACTTGGATTCATTTTAGTACTACT 57.550 33.333 0.91 0.00 40.96 2.57
2122 2282 1.916000 GAACGCACTACATGTACCGAC 59.084 52.381 17.61 10.19 0.00 4.79
2123 2283 1.466192 CGAACGCACTACATGTACCGA 60.466 52.381 17.61 0.00 0.00 4.69
2168 2331 4.573201 CCGTCGCCTCTTTGGAATATAAAA 59.427 41.667 0.00 0.00 38.35 1.52
2169 2332 4.124238 CCGTCGCCTCTTTGGAATATAAA 58.876 43.478 0.00 0.00 38.35 1.40
2170 2333 3.133362 ACCGTCGCCTCTTTGGAATATAA 59.867 43.478 0.00 0.00 38.35 0.98
2172 2335 1.485066 ACCGTCGCCTCTTTGGAATAT 59.515 47.619 0.00 0.00 38.35 1.28
2173 2336 0.899720 ACCGTCGCCTCTTTGGAATA 59.100 50.000 0.00 0.00 38.35 1.75
2174 2337 0.899720 TACCGTCGCCTCTTTGGAAT 59.100 50.000 0.00 0.00 38.35 3.01
2175 2338 0.037975 GTACCGTCGCCTCTTTGGAA 60.038 55.000 0.00 0.00 38.35 3.53
2176 2339 1.588082 GTACCGTCGCCTCTTTGGA 59.412 57.895 0.00 0.00 38.35 3.53
2177 2340 1.804326 CGTACCGTCGCCTCTTTGG 60.804 63.158 0.00 0.00 39.35 3.28
2178 2341 0.387622 TTCGTACCGTCGCCTCTTTG 60.388 55.000 0.00 0.00 0.00 2.77
2179 2342 0.314935 TTTCGTACCGTCGCCTCTTT 59.685 50.000 0.00 0.00 0.00 2.52
2187 2350 1.654105 CTGCATCTGTTTCGTACCGTC 59.346 52.381 0.00 0.00 0.00 4.79
2239 2402 1.669115 GCTCCTTTGTGCTCGCTCA 60.669 57.895 0.00 0.00 0.00 4.26
2338 2505 4.385093 CTGCACTGCGCTGCACTG 62.385 66.667 19.17 9.33 42.36 3.66
2416 2598 0.308993 GTGCTGTCTTTGACCTGTGC 59.691 55.000 0.00 0.00 0.00 4.57
2417 2599 0.583438 CGTGCTGTCTTTGACCTGTG 59.417 55.000 0.00 0.00 0.00 3.66
2418 2600 0.178068 ACGTGCTGTCTTTGACCTGT 59.822 50.000 0.00 0.00 0.00 4.00
2419 2601 1.299541 AACGTGCTGTCTTTGACCTG 58.700 50.000 0.00 0.00 0.00 4.00
2420 2602 1.940613 GAAACGTGCTGTCTTTGACCT 59.059 47.619 0.00 0.00 0.00 3.85
2429 2611 1.222300 TGCGTAATGAAACGTGCTGT 58.778 45.000 0.00 0.00 44.64 4.40
2455 2641 2.466982 CGTGGTAGCTGCATGCCTG 61.467 63.158 16.68 9.38 44.23 4.85
2456 2642 2.124983 CGTGGTAGCTGCATGCCT 60.125 61.111 16.68 8.55 44.23 4.75
2457 2643 2.125147 TCGTGGTAGCTGCATGCC 60.125 61.111 16.68 0.00 44.23 4.40
2458 2644 0.179111 TAGTCGTGGTAGCTGCATGC 60.179 55.000 11.82 11.82 43.29 4.06
2473 2659 1.616374 GCTAGACCTGGCCTGATAGTC 59.384 57.143 11.88 10.02 0.00 2.59


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

AutoCloner maintained by Alex Coulton.