Multiple sequence alignment - TraesCS5A01G488000

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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 TraesCS5A01G488000 chr5A 100.000 1767 0 0 594 2360 657779307 657777541 0.000000e+00 3264
1 TraesCS5A01G488000 chr5A 100.000 69 0 0 1 69 657779900 657779832 6.850000e-26 128
2 TraesCS5A01G488000 chr5D 88.030 1746 92 48 702 2360 530055253 530053538 0.000000e+00 1958
3 TraesCS5A01G488000 chr5D 96.190 105 1 1 594 695 530055521 530055417 4.030000e-38 169
4 TraesCS5A01G488000 chr5B 86.764 1783 114 55 662 2360 669233327 669231583 0.000000e+00 1873


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 TraesCS5A01G488000 chr5A 657777541 657779900 2359 True 1696.0 3264 100.000 1 2360 2 chr5A.!!$R1 2359
1 TraesCS5A01G488000 chr5D 530053538 530055521 1983 True 1063.5 1958 92.110 594 2360 2 chr5D.!!$R1 1766
2 TraesCS5A01G488000 chr5B 669231583 669233327 1744 True 1873.0 1873 86.764 662 2360 1 chr5B.!!$R1 1698

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
988 1218 0.250513 AGAAATCCACGAGAGCCACC 59.749 55.0 0.0 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1871 2146 0.181114 TTGCAGGACTTGTCACAGCT 59.819 50.0 3.08 0.0 0.0 4.24 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
22 23 5.247507 TGTGTTTTTGGTTCATGAGTCAG 57.752 39.130 0.00 0.00 0.00 3.51
23 24 4.704540 TGTGTTTTTGGTTCATGAGTCAGT 59.295 37.500 0.00 0.00 0.00 3.41
24 25 5.163663 TGTGTTTTTGGTTCATGAGTCAGTC 60.164 40.000 0.00 0.00 0.00 3.51
25 26 4.338118 TGTTTTTGGTTCATGAGTCAGTCC 59.662 41.667 0.00 0.00 0.00 3.85
26 27 4.437682 TTTTGGTTCATGAGTCAGTCCT 57.562 40.909 0.00 0.00 0.00 3.85
27 28 3.407424 TTGGTTCATGAGTCAGTCCTG 57.593 47.619 0.00 0.00 0.00 3.86
28 29 2.329267 TGGTTCATGAGTCAGTCCTGT 58.671 47.619 0.00 0.00 0.00 4.00
29 30 2.705658 TGGTTCATGAGTCAGTCCTGTT 59.294 45.455 0.00 0.00 0.00 3.16
30 31 3.136443 TGGTTCATGAGTCAGTCCTGTTT 59.864 43.478 0.00 0.00 0.00 2.83
31 32 4.137543 GGTTCATGAGTCAGTCCTGTTTT 58.862 43.478 0.00 0.00 0.00 2.43
32 33 5.163248 TGGTTCATGAGTCAGTCCTGTTTTA 60.163 40.000 0.00 0.00 0.00 1.52
33 34 5.763204 GGTTCATGAGTCAGTCCTGTTTTAA 59.237 40.000 0.00 0.00 0.00 1.52
34 35 6.262273 GGTTCATGAGTCAGTCCTGTTTTAAA 59.738 38.462 0.00 0.00 0.00 1.52
35 36 6.861065 TCATGAGTCAGTCCTGTTTTAAAC 57.139 37.500 0.00 0.20 0.00 2.01
36 37 6.591935 TCATGAGTCAGTCCTGTTTTAAACT 58.408 36.000 9.33 0.00 0.00 2.66
37 38 7.054124 TCATGAGTCAGTCCTGTTTTAAACTT 58.946 34.615 9.33 0.00 0.00 2.66
38 39 7.556275 TCATGAGTCAGTCCTGTTTTAAACTTT 59.444 33.333 9.33 0.00 0.00 2.66
39 40 7.083875 TGAGTCAGTCCTGTTTTAAACTTTG 57.916 36.000 9.33 0.22 0.00 2.77
40 41 6.094881 TGAGTCAGTCCTGTTTTAAACTTTGG 59.905 38.462 9.33 8.61 0.00 3.28
41 42 6.184789 AGTCAGTCCTGTTTTAAACTTTGGA 58.815 36.000 9.33 10.54 0.00 3.53
42 43 6.833933 AGTCAGTCCTGTTTTAAACTTTGGAT 59.166 34.615 15.81 7.23 32.23 3.41
43 44 7.013369 AGTCAGTCCTGTTTTAAACTTTGGATC 59.987 37.037 15.81 11.57 32.23 3.36
44 45 7.013369 GTCAGTCCTGTTTTAAACTTTGGATCT 59.987 37.037 15.81 12.87 32.23 2.75
45 46 7.013274 TCAGTCCTGTTTTAAACTTTGGATCTG 59.987 37.037 21.52 21.52 33.56 2.90
46 47 6.833933 AGTCCTGTTTTAAACTTTGGATCTGT 59.166 34.615 15.81 4.87 32.23 3.41
47 48 6.918022 GTCCTGTTTTAAACTTTGGATCTGTG 59.082 38.462 15.81 0.00 32.23 3.66
48 49 6.040391 TCCTGTTTTAAACTTTGGATCTGTGG 59.960 38.462 9.33 0.00 0.00 4.17
49 50 6.040391 CCTGTTTTAAACTTTGGATCTGTGGA 59.960 38.462 9.33 0.00 0.00 4.02
50 51 7.255942 CCTGTTTTAAACTTTGGATCTGTGGAT 60.256 37.037 9.33 0.00 34.45 3.41
51 52 8.017418 TGTTTTAAACTTTGGATCTGTGGATT 57.983 30.769 9.33 0.00 31.46 3.01
52 53 7.925483 TGTTTTAAACTTTGGATCTGTGGATTG 59.075 33.333 9.33 0.00 31.46 2.67
53 54 7.595819 TTTAAACTTTGGATCTGTGGATTGT 57.404 32.000 0.00 0.00 31.46 2.71
54 55 7.595819 TTAAACTTTGGATCTGTGGATTGTT 57.404 32.000 0.00 0.00 31.46 2.83
55 56 6.484364 AAACTTTGGATCTGTGGATTGTTT 57.516 33.333 0.00 0.00 31.46 2.83
56 57 5.458041 ACTTTGGATCTGTGGATTGTTTG 57.542 39.130 0.00 0.00 31.46 2.93
57 58 4.895297 ACTTTGGATCTGTGGATTGTTTGT 59.105 37.500 0.00 0.00 31.46 2.83
58 59 6.068010 ACTTTGGATCTGTGGATTGTTTGTA 58.932 36.000 0.00 0.00 31.46 2.41
59 60 6.721208 ACTTTGGATCTGTGGATTGTTTGTAT 59.279 34.615 0.00 0.00 31.46 2.29
60 61 7.233348 ACTTTGGATCTGTGGATTGTTTGTATT 59.767 33.333 0.00 0.00 31.46 1.89
61 62 6.513806 TGGATCTGTGGATTGTTTGTATTG 57.486 37.500 0.00 0.00 31.46 1.90
62 63 5.105797 TGGATCTGTGGATTGTTTGTATTGC 60.106 40.000 0.00 0.00 31.46 3.56
63 64 5.105797 GGATCTGTGGATTGTTTGTATTGCA 60.106 40.000 0.00 0.00 31.46 4.08
64 65 5.981088 TCTGTGGATTGTTTGTATTGCAT 57.019 34.783 0.00 0.00 0.00 3.96
65 66 7.201812 GGATCTGTGGATTGTTTGTATTGCATA 60.202 37.037 0.00 0.00 31.46 3.14
66 67 7.643569 TCTGTGGATTGTTTGTATTGCATAT 57.356 32.000 0.00 0.00 0.00 1.78
67 68 8.744568 TCTGTGGATTGTTTGTATTGCATATA 57.255 30.769 0.00 0.00 0.00 0.86
68 69 9.353431 TCTGTGGATTGTTTGTATTGCATATAT 57.647 29.630 0.00 0.00 0.00 0.86
638 642 6.039829 GTCTTGGGATCTTTCTGTGAGTTTTT 59.960 38.462 0.00 0.00 0.00 1.94
671 675 7.115095 GGTATAAGAGTCTGTATCGTCATTTGC 59.885 40.741 0.00 0.00 0.00 3.68
899 1110 0.740868 CTCCCACGCATATATGGCCG 60.741 60.000 14.51 12.10 34.37 6.13
929 1151 1.676006 CACCCTCACCAAGTTCAACAC 59.324 52.381 0.00 0.00 0.00 3.32
930 1152 1.283613 ACCCTCACCAAGTTCAACACA 59.716 47.619 0.00 0.00 0.00 3.72
978 1204 3.428045 CCAAGAATCGCCAAGAAATCCAC 60.428 47.826 0.00 0.00 0.00 4.02
987 1217 1.734465 CAAGAAATCCACGAGAGCCAC 59.266 52.381 0.00 0.00 0.00 5.01
988 1218 0.250513 AGAAATCCACGAGAGCCACC 59.749 55.000 0.00 0.00 0.00 4.61
989 1219 0.250513 GAAATCCACGAGAGCCACCT 59.749 55.000 0.00 0.00 0.00 4.00
990 1220 1.480954 GAAATCCACGAGAGCCACCTA 59.519 52.381 0.00 0.00 0.00 3.08
991 1221 1.115467 AATCCACGAGAGCCACCTAG 58.885 55.000 0.00 0.00 0.00 3.02
992 1222 1.395826 ATCCACGAGAGCCACCTAGC 61.396 60.000 0.00 0.00 0.00 3.42
1008 1238 4.595629 GCGTTAGCAATGGCATCG 57.404 55.556 0.00 0.00 44.61 3.84
1152 1394 3.432046 CCAAGAAGGAGAAGAGCATCCTC 60.432 52.174 0.00 0.00 45.39 3.71
1371 1613 5.165961 AGAAAGGCTGAACTACATAAGCA 57.834 39.130 0.00 0.00 37.40 3.91
1374 1616 2.233922 AGGCTGAACTACATAAGCACGT 59.766 45.455 0.00 0.00 37.40 4.49
1433 1686 5.527214 TCGATTTATTGCTGTAACTCCATGG 59.473 40.000 4.97 4.97 0.00 3.66
1473 1730 3.004524 TGCATATATGTACACGCGGTGTA 59.995 43.478 12.47 13.87 45.56 2.90
1566 1823 4.727507 TCTCTCAAAGGCTCAGTATGTC 57.272 45.455 0.00 0.00 37.40 3.06
1569 1835 5.893824 TCTCTCAAAGGCTCAGTATGTCATA 59.106 40.000 0.00 0.00 37.40 2.15
1584 1850 8.097038 CAGTATGTCATATACCCATGTTAAGCT 58.903 37.037 0.00 0.00 0.00 3.74
1650 1916 6.919721 TGGGACTGCTGATTTTAAACATAAC 58.080 36.000 0.00 0.00 0.00 1.89
1653 1919 8.398665 GGGACTGCTGATTTTAAACATAACTAG 58.601 37.037 0.00 0.00 0.00 2.57
1654 1920 8.947115 GGACTGCTGATTTTAAACATAACTAGT 58.053 33.333 0.00 0.00 0.00 2.57
1765 2036 0.695347 AACAGAGGAAGCTCTTGGGG 59.305 55.000 0.00 0.00 0.00 4.96
1831 2106 9.554395 CTTTTCCCTTTATTTTGTATGGTTGTT 57.446 29.630 0.00 0.00 0.00 2.83
1871 2146 6.656902 AGCAGAGATCAACAATTGGATAGAA 58.343 36.000 10.83 0.00 0.00 2.10
1872 2147 6.766944 AGCAGAGATCAACAATTGGATAGAAG 59.233 38.462 10.83 0.00 0.00 2.85
1878 2153 5.559770 TCAACAATTGGATAGAAGCTGTGA 58.440 37.500 10.83 0.00 0.00 3.58
1923 2209 5.170021 TGCATGCAGTTATGAAACAAATCC 58.830 37.500 18.46 0.00 38.12 3.01
1958 2244 4.764679 CAGAATGTTTCACGAAATCCCA 57.235 40.909 0.00 0.00 32.36 4.37
2031 2321 2.822255 GGCCTTGCCGTGCGAATA 60.822 61.111 0.00 0.00 39.62 1.75
2059 2349 1.934220 TTACAGTCGCGCCAGGAGAG 61.934 60.000 0.00 0.00 0.00 3.20
2133 2423 5.426689 AAGACCTGCAGATGTTAAGATCA 57.573 39.130 17.39 0.00 0.00 2.92
2138 2428 6.109359 ACCTGCAGATGTTAAGATCAAGTAC 58.891 40.000 17.39 0.67 0.00 2.73
2140 2430 6.257411 CCTGCAGATGTTAAGATCAAGTACAG 59.743 42.308 17.39 12.15 0.00 2.74
2142 2432 7.038048 TGCAGATGTTAAGATCAAGTACAGAG 58.962 38.462 14.46 0.00 0.00 3.35
2145 2435 9.247126 CAGATGTTAAGATCAAGTACAGAGATG 57.753 37.037 14.46 0.00 0.00 2.90
2146 2436 7.925483 AGATGTTAAGATCAAGTACAGAGATGC 59.075 37.037 14.46 0.00 0.00 3.91
2151 2441 5.845103 AGATCAAGTACAGAGATGCATCAG 58.155 41.667 27.81 18.60 0.00 2.90
2152 2442 5.597594 AGATCAAGTACAGAGATGCATCAGA 59.402 40.000 27.81 11.19 0.00 3.27
2153 2443 5.259832 TCAAGTACAGAGATGCATCAGAG 57.740 43.478 27.81 17.93 0.00 3.35
2154 2444 4.099113 TCAAGTACAGAGATGCATCAGAGG 59.901 45.833 27.81 15.98 0.00 3.69
2155 2445 3.641046 AGTACAGAGATGCATCAGAGGT 58.359 45.455 27.81 20.25 0.00 3.85
2156 2446 4.029520 AGTACAGAGATGCATCAGAGGTT 58.970 43.478 27.81 6.52 0.00 3.50
2158 2448 1.941294 CAGAGATGCATCAGAGGTTGC 59.059 52.381 27.81 7.01 39.62 4.17
2163 2454 0.397564 TGCATCAGAGGTTGCACTCA 59.602 50.000 7.05 0.00 43.01 3.41
2165 2456 2.236893 TGCATCAGAGGTTGCACTCATA 59.763 45.455 7.05 0.00 43.01 2.15
2173 2464 1.209504 GGTTGCACTCATAGGGTAGCA 59.790 52.381 0.00 0.00 0.00 3.49
2177 2468 1.811941 GCACTCATAGGGTAGCAAGGC 60.812 57.143 0.00 0.00 0.00 4.35
2179 2470 1.765314 ACTCATAGGGTAGCAAGGCAG 59.235 52.381 0.00 0.00 0.00 4.85
2184 2475 1.379044 GGGTAGCAAGGCAGCATGT 60.379 57.895 4.78 0.00 39.31 3.21
2185 2476 0.967380 GGGTAGCAAGGCAGCATGTT 60.967 55.000 4.78 0.00 39.31 2.71
2186 2477 0.453390 GGTAGCAAGGCAGCATGTTC 59.547 55.000 4.78 0.00 39.31 3.18
2187 2478 1.167851 GTAGCAAGGCAGCATGTTCA 58.832 50.000 4.78 0.00 39.31 3.18
2188 2479 1.747355 GTAGCAAGGCAGCATGTTCAT 59.253 47.619 4.78 0.00 39.31 2.57
2189 2480 2.133281 AGCAAGGCAGCATGTTCATA 57.867 45.000 4.78 0.00 39.31 2.15
2191 2482 2.165030 AGCAAGGCAGCATGTTCATAAC 59.835 45.455 4.78 0.00 39.31 1.89
2193 2484 1.767759 AGGCAGCATGTTCATAACCC 58.232 50.000 0.00 0.00 39.31 4.11
2194 2485 1.005805 AGGCAGCATGTTCATAACCCA 59.994 47.619 0.00 0.00 39.31 4.51
2195 2486 1.406539 GGCAGCATGTTCATAACCCAG 59.593 52.381 0.00 0.00 39.31 4.45
2196 2487 2.094675 GCAGCATGTTCATAACCCAGT 58.905 47.619 0.00 0.00 39.31 4.00
2197 2488 2.159338 GCAGCATGTTCATAACCCAGTG 60.159 50.000 0.00 0.00 39.31 3.66
2198 2489 2.424601 CAGCATGTTCATAACCCAGTGG 59.575 50.000 0.63 0.63 37.80 4.00
2209 2502 2.276732 ACCCAGTGGTGATGAAACAG 57.723 50.000 8.74 0.00 45.58 3.16
2211 2504 2.376518 ACCCAGTGGTGATGAAACAGAT 59.623 45.455 8.74 0.00 45.58 2.90
2216 2509 5.707298 CCAGTGGTGATGAAACAGATTACTT 59.293 40.000 0.00 0.00 0.00 2.24
2220 2513 6.653320 GTGGTGATGAAACAGATTACTTACCA 59.347 38.462 0.00 0.00 0.00 3.25
2247 2540 6.403866 ACTATGCTGAACAAATTTTCCACA 57.596 33.333 0.00 0.00 0.00 4.17
2256 2549 6.378564 TGAACAAATTTTCCACACTAACAGGA 59.621 34.615 0.00 0.00 0.00 3.86
2259 2552 6.153680 ACAAATTTTCCACACTAACAGGAACA 59.846 34.615 0.00 0.00 40.88 3.18
2280 2573 2.857186 TGAATAGCAAGACACCAGCA 57.143 45.000 0.00 0.00 0.00 4.41
2323 2616 3.209410 AGTGAGCCAACAAGACTGAAAG 58.791 45.455 0.00 0.00 42.29 2.62
2332 2626 5.221126 CCAACAAGACTGAAAGGGAGAAAAG 60.221 44.000 0.00 0.00 39.30 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.704540 ACTGACTCATGAACCAAAAACACA 59.295 37.500 0.00 0.00 0.00 3.72
1 2 5.248870 ACTGACTCATGAACCAAAAACAC 57.751 39.130 0.00 0.00 0.00 3.32
2 3 4.338118 GGACTGACTCATGAACCAAAAACA 59.662 41.667 0.00 0.00 0.00 2.83
3 4 4.580580 AGGACTGACTCATGAACCAAAAAC 59.419 41.667 0.00 0.00 0.00 2.43
4 5 4.580167 CAGGACTGACTCATGAACCAAAAA 59.420 41.667 0.00 0.00 31.94 1.94
5 6 4.136796 CAGGACTGACTCATGAACCAAAA 58.863 43.478 0.00 0.00 31.94 2.44
6 7 3.136443 ACAGGACTGACTCATGAACCAAA 59.864 43.478 6.29 0.00 34.11 3.28
7 8 2.705658 ACAGGACTGACTCATGAACCAA 59.294 45.455 6.29 0.00 34.11 3.67
8 9 2.329267 ACAGGACTGACTCATGAACCA 58.671 47.619 6.29 0.00 34.11 3.67
9 10 3.409026 AACAGGACTGACTCATGAACC 57.591 47.619 6.29 0.00 34.11 3.62
10 11 6.861065 TTAAAACAGGACTGACTCATGAAC 57.139 37.500 6.29 0.00 34.11 3.18
11 12 7.054124 AGTTTAAAACAGGACTGACTCATGAA 58.946 34.615 6.29 0.00 34.11 2.57
12 13 6.591935 AGTTTAAAACAGGACTGACTCATGA 58.408 36.000 6.29 0.00 34.11 3.07
13 14 6.867662 AGTTTAAAACAGGACTGACTCATG 57.132 37.500 6.29 0.00 36.70 3.07
14 15 7.201821 CCAAAGTTTAAAACAGGACTGACTCAT 60.202 37.037 6.29 0.00 0.00 2.90
15 16 6.094881 CCAAAGTTTAAAACAGGACTGACTCA 59.905 38.462 6.29 0.00 0.00 3.41
16 17 6.317893 TCCAAAGTTTAAAACAGGACTGACTC 59.682 38.462 6.29 0.00 0.00 3.36
17 18 6.184789 TCCAAAGTTTAAAACAGGACTGACT 58.815 36.000 6.29 0.00 0.00 3.41
18 19 6.445357 TCCAAAGTTTAAAACAGGACTGAC 57.555 37.500 6.29 0.00 0.00 3.51
19 20 7.013274 CAGATCCAAAGTTTAAAACAGGACTGA 59.987 37.037 6.29 0.00 34.73 3.41
20 21 7.141363 CAGATCCAAAGTTTAAAACAGGACTG 58.859 38.462 0.00 0.00 33.82 3.51
21 22 6.833933 ACAGATCCAAAGTTTAAAACAGGACT 59.166 34.615 0.00 0.00 33.82 3.85
22 23 6.918022 CACAGATCCAAAGTTTAAAACAGGAC 59.082 38.462 0.00 0.00 33.82 3.85
23 24 6.040391 CCACAGATCCAAAGTTTAAAACAGGA 59.960 38.462 0.00 0.00 34.92 3.86
24 25 6.040391 TCCACAGATCCAAAGTTTAAAACAGG 59.960 38.462 0.00 0.00 0.00 4.00
25 26 7.038154 TCCACAGATCCAAAGTTTAAAACAG 57.962 36.000 0.00 0.00 0.00 3.16
26 27 7.595819 ATCCACAGATCCAAAGTTTAAAACA 57.404 32.000 0.00 0.00 0.00 2.83
27 28 7.926018 ACAATCCACAGATCCAAAGTTTAAAAC 59.074 33.333 0.00 0.00 0.00 2.43
28 29 8.017418 ACAATCCACAGATCCAAAGTTTAAAA 57.983 30.769 0.00 0.00 0.00 1.52
29 30 7.595819 ACAATCCACAGATCCAAAGTTTAAA 57.404 32.000 0.00 0.00 0.00 1.52
30 31 7.595819 AACAATCCACAGATCCAAAGTTTAA 57.404 32.000 0.00 0.00 0.00 1.52
31 32 7.069331 ACAAACAATCCACAGATCCAAAGTTTA 59.931 33.333 0.00 0.00 0.00 2.01
32 33 6.127083 ACAAACAATCCACAGATCCAAAGTTT 60.127 34.615 0.00 0.00 0.00 2.66
33 34 5.363580 ACAAACAATCCACAGATCCAAAGTT 59.636 36.000 0.00 0.00 0.00 2.66
34 35 4.895297 ACAAACAATCCACAGATCCAAAGT 59.105 37.500 0.00 0.00 0.00 2.66
35 36 5.458041 ACAAACAATCCACAGATCCAAAG 57.542 39.130 0.00 0.00 0.00 2.77
36 37 7.377398 CAATACAAACAATCCACAGATCCAAA 58.623 34.615 0.00 0.00 0.00 3.28
37 38 6.572119 GCAATACAAACAATCCACAGATCCAA 60.572 38.462 0.00 0.00 0.00 3.53
38 39 5.105797 GCAATACAAACAATCCACAGATCCA 60.106 40.000 0.00 0.00 0.00 3.41
39 40 5.105797 TGCAATACAAACAATCCACAGATCC 60.106 40.000 0.00 0.00 0.00 3.36
40 41 5.953183 TGCAATACAAACAATCCACAGATC 58.047 37.500 0.00 0.00 0.00 2.75
41 42 5.981088 TGCAATACAAACAATCCACAGAT 57.019 34.783 0.00 0.00 0.00 2.90
42 43 5.981088 ATGCAATACAAACAATCCACAGA 57.019 34.783 0.00 0.00 0.00 3.41
638 642 8.677300 ACGATACAGACTCTTATACCGTAAAAA 58.323 33.333 0.00 0.00 0.00 1.94
695 699 0.664767 GCGTTGCTTCGTCTGTCTCT 60.665 55.000 3.52 0.00 0.00 3.10
696 700 0.664767 AGCGTTGCTTCGTCTGTCTC 60.665 55.000 3.52 0.00 33.89 3.36
698 702 1.488957 CAGCGTTGCTTCGTCTGTC 59.511 57.895 12.73 0.00 36.40 3.51
699 703 1.956170 CCAGCGTTGCTTCGTCTGT 60.956 57.895 16.35 0.00 36.40 3.41
700 704 2.856032 CCAGCGTTGCTTCGTCTG 59.144 61.111 0.00 13.42 36.40 3.51
821 1032 1.148157 CTTATCCTCACCACGCGCAG 61.148 60.000 5.73 0.00 0.00 5.18
929 1151 4.511454 CGAAATGTATGTATGGTGGGACTG 59.489 45.833 0.00 0.00 0.00 3.51
930 1152 4.703897 CGAAATGTATGTATGGTGGGACT 58.296 43.478 0.00 0.00 0.00 3.85
978 1204 0.029567 CTAACGCTAGGTGGCTCTCG 59.970 60.000 0.00 0.00 0.00 4.04
987 1217 1.532868 GATGCCATTGCTAACGCTAGG 59.467 52.381 0.00 0.00 38.71 3.02
988 1218 1.193203 CGATGCCATTGCTAACGCTAG 59.807 52.381 0.00 0.00 38.71 3.42
989 1219 1.217001 CGATGCCATTGCTAACGCTA 58.783 50.000 0.00 0.00 38.71 4.26
990 1220 1.439353 CCGATGCCATTGCTAACGCT 61.439 55.000 0.00 0.00 38.71 5.07
991 1221 1.009675 CCGATGCCATTGCTAACGC 60.010 57.895 0.00 0.00 38.71 4.84
992 1222 0.027979 CACCGATGCCATTGCTAACG 59.972 55.000 0.00 0.00 38.71 3.18
1005 1235 4.096003 CTGCCGAACCCCACCGAT 62.096 66.667 0.00 0.00 0.00 4.18
1050 1292 3.217743 CTACTCCTCCCCGCCGAC 61.218 72.222 0.00 0.00 0.00 4.79
1053 1295 4.862823 AGGCTACTCCTCCCCGCC 62.863 72.222 0.00 0.00 43.20 6.13
1054 1296 2.764547 AAGGCTACTCCTCCCCGC 60.765 66.667 0.00 0.00 46.94 6.13
1055 1297 2.491022 CGAAGGCTACTCCTCCCCG 61.491 68.421 0.00 0.00 46.94 5.73
1056 1298 2.798364 GCGAAGGCTACTCCTCCCC 61.798 68.421 0.00 0.00 46.94 4.81
1358 1600 1.266891 GCGCACGTGCTTATGTAGTTC 60.267 52.381 35.27 5.18 39.32 3.01
1359 1601 0.719465 GCGCACGTGCTTATGTAGTT 59.281 50.000 35.27 0.00 39.32 2.24
1360 1602 1.410737 CGCGCACGTGCTTATGTAGT 61.411 55.000 35.27 0.00 39.32 2.73
1363 1605 4.147322 GCGCGCACGTGCTTATGT 62.147 61.111 35.27 0.00 46.85 2.29
1473 1730 6.712095 TCACAGCAAGAATCATTTGAGTAGTT 59.288 34.615 0.00 0.00 0.00 2.24
1566 1823 6.639632 AGCAAAGCTTAACATGGGTATATG 57.360 37.500 0.00 0.00 33.89 1.78
1584 1850 5.127031 GGTATTGGGATCTTAGCAAAGCAAA 59.873 40.000 0.00 0.00 32.36 3.68
1656 1922 9.862149 TTTGGCTATGATCTAGATATCCGTATA 57.138 33.333 4.89 0.00 0.00 1.47
1657 1923 8.768501 TTTGGCTATGATCTAGATATCCGTAT 57.231 34.615 4.89 0.00 0.00 3.06
1658 1924 8.053355 TCTTTGGCTATGATCTAGATATCCGTA 58.947 37.037 4.89 0.00 0.00 4.02
1659 1925 6.892456 TCTTTGGCTATGATCTAGATATCCGT 59.108 38.462 4.89 0.00 0.00 4.69
1660 1926 7.340122 TCTTTGGCTATGATCTAGATATCCG 57.660 40.000 4.89 0.00 0.00 4.18
1661 1927 9.545105 CAATCTTTGGCTATGATCTAGATATCC 57.455 37.037 4.89 3.59 0.00 2.59
1662 1928 9.545105 CCAATCTTTGGCTATGATCTAGATATC 57.455 37.037 4.89 0.00 45.17 1.63
1725 1992 9.003658 TCTGTTCCTCTGATATTTTTCAGTTTC 57.996 33.333 1.76 0.00 43.02 2.78
1729 1996 7.334090 TCCTCTGTTCCTCTGATATTTTTCAG 58.666 38.462 0.00 0.00 43.70 3.02
1730 1997 7.257790 TCCTCTGTTCCTCTGATATTTTTCA 57.742 36.000 0.00 0.00 0.00 2.69
1731 1998 7.201688 GCTTCCTCTGTTCCTCTGATATTTTTC 60.202 40.741 0.00 0.00 0.00 2.29
1732 1999 6.601217 GCTTCCTCTGTTCCTCTGATATTTTT 59.399 38.462 0.00 0.00 0.00 1.94
1765 2036 1.142474 GGAATTTGCTGTTGCTGTGC 58.858 50.000 0.00 0.00 40.48 4.57
1871 2146 0.181114 TTGCAGGACTTGTCACAGCT 59.819 50.000 3.08 0.00 0.00 4.24
1872 2147 1.024271 TTTGCAGGACTTGTCACAGC 58.976 50.000 3.08 4.19 0.00 4.40
1958 2244 3.181774 CGTTTGAACTTGTCGAGTCGATT 59.818 43.478 19.75 8.75 37.72 3.34
2031 2321 1.136446 GCGCGACTGTAACACGAAAAT 60.136 47.619 12.10 0.00 0.00 1.82
2048 2338 0.674895 AATGTTCACTCTCCTGGCGC 60.675 55.000 0.00 0.00 0.00 6.53
2059 2349 5.491982 AGATGTCCAAGTCCTAATGTTCAC 58.508 41.667 0.00 0.00 0.00 3.18
2133 2423 4.029520 ACCTCTGATGCATCTCTGTACTT 58.970 43.478 26.32 2.03 0.00 2.24
2138 2428 1.941294 GCAACCTCTGATGCATCTCTG 59.059 52.381 26.32 16.25 42.12 3.35
2140 2430 2.034104 TGCAACCTCTGATGCATCTC 57.966 50.000 26.32 4.13 46.87 2.75
2145 2435 1.747709 ATGAGTGCAACCTCTGATGC 58.252 50.000 5.97 0.00 42.86 3.91
2146 2436 3.464907 CCTATGAGTGCAACCTCTGATG 58.535 50.000 5.97 0.00 37.80 3.07
2151 2441 2.483889 GCTACCCTATGAGTGCAACCTC 60.484 54.545 0.00 0.00 37.80 3.85
2152 2442 1.486726 GCTACCCTATGAGTGCAACCT 59.513 52.381 0.00 0.00 37.80 3.50
2153 2443 1.209504 TGCTACCCTATGAGTGCAACC 59.790 52.381 0.00 0.00 37.80 3.77
2154 2444 2.691409 TGCTACCCTATGAGTGCAAC 57.309 50.000 0.00 0.00 0.00 4.17
2155 2445 2.092968 CCTTGCTACCCTATGAGTGCAA 60.093 50.000 0.00 0.00 37.96 4.08
2156 2446 1.486310 CCTTGCTACCCTATGAGTGCA 59.514 52.381 0.00 0.00 0.00 4.57
2158 2448 1.486310 TGCCTTGCTACCCTATGAGTG 59.514 52.381 0.00 0.00 0.00 3.51
2163 2454 1.143813 ATGCTGCCTTGCTACCCTAT 58.856 50.000 0.00 0.00 0.00 2.57
2165 2456 1.077212 CATGCTGCCTTGCTACCCT 60.077 57.895 0.00 0.00 0.00 4.34
2173 2464 2.102578 GGGTTATGAACATGCTGCCTT 58.897 47.619 0.00 0.00 0.00 4.35
2177 2468 2.424601 CCACTGGGTTATGAACATGCTG 59.575 50.000 0.00 0.00 0.00 4.41
2191 2482 2.566833 TCTGTTTCATCACCACTGGG 57.433 50.000 0.00 0.00 41.29 4.45
2193 2484 6.808008 AAGTAATCTGTTTCATCACCACTG 57.192 37.500 0.00 0.00 0.00 3.66
2194 2485 6.879458 GGTAAGTAATCTGTTTCATCACCACT 59.121 38.462 0.00 0.00 0.00 4.00
2195 2486 6.653320 TGGTAAGTAATCTGTTTCATCACCAC 59.347 38.462 0.00 0.00 0.00 4.16
2196 2487 6.774673 TGGTAAGTAATCTGTTTCATCACCA 58.225 36.000 0.00 0.00 0.00 4.17
2197 2488 7.681939 TTGGTAAGTAATCTGTTTCATCACC 57.318 36.000 0.00 0.00 0.00 4.02
2198 2489 9.959749 TTTTTGGTAAGTAATCTGTTTCATCAC 57.040 29.630 0.00 0.00 0.00 3.06
2207 2500 8.946085 TCAGCATAGTTTTTGGTAAGTAATCTG 58.054 33.333 0.00 0.00 0.00 2.90
2209 2502 9.556030 GTTCAGCATAGTTTTTGGTAAGTAATC 57.444 33.333 0.00 0.00 0.00 1.75
2211 2504 8.453238 TGTTCAGCATAGTTTTTGGTAAGTAA 57.547 30.769 0.00 0.00 0.00 2.24
2216 2509 9.606631 AAAATTTGTTCAGCATAGTTTTTGGTA 57.393 25.926 0.00 0.00 0.00 3.25
2220 2513 8.611757 GTGGAAAATTTGTTCAGCATAGTTTTT 58.388 29.630 0.00 0.00 29.33 1.94
2247 2540 7.119846 GTCTTGCTATTCAATGTTCCTGTTAGT 59.880 37.037 0.00 0.00 33.57 2.24
2256 2549 4.082571 GCTGGTGTCTTGCTATTCAATGTT 60.083 41.667 0.00 0.00 33.57 2.71
2259 2552 3.689347 TGCTGGTGTCTTGCTATTCAAT 58.311 40.909 0.00 0.00 33.57 2.57
2280 2573 6.150474 CACTAAACAAGATACCCATTTCGGTT 59.850 38.462 0.00 0.00 37.34 4.44
2323 2616 7.121168 TCACATGTTGATAATCACTTTTCTCCC 59.879 37.037 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.