Multiple sequence alignment - TraesCS5D01G474700

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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 TraesCS5D01G474700 chr5D 100.000 2702 0 0 1 2702 514514231 514516932 0.000000e+00 4990
1 TraesCS5D01G474700 chr5D 86.796 977 118 8 993 1966 514412816 514411848 0.000000e+00 1079
2 TraesCS5D01G474700 chr5D 84.007 1088 163 10 883 1963 514294519 514295602 0.000000e+00 1035
3 TraesCS5D01G474700 chr5D 86.126 728 64 20 1955 2675 514295624 514296321 0.000000e+00 750
4 TraesCS5D01G474700 chr5D 95.714 70 3 0 1 70 84221096 84221165 2.200000e-21 113
5 TraesCS5D01G474700 chr5A 94.625 2028 88 12 679 2702 642905327 642907337 0.000000e+00 3121
6 TraesCS5D01G474700 chr5A 85.805 1726 202 13 954 2675 641781629 641779943 0.000000e+00 1790
7 TraesCS5D01G474700 chr5A 83.640 1088 164 12 883 1963 642502635 642503715 0.000000e+00 1011
8 TraesCS5D01G474700 chr5A 89.408 321 33 1 1955 2274 642503737 642504057 1.170000e-108 403
9 TraesCS5D01G474700 chr5A 84.434 424 21 20 61 441 642904190 642904611 2.540000e-100 375
10 TraesCS5D01G474700 chr5A 87.712 236 14 7 456 680 642905062 642905293 7.420000e-66 261
11 TraesCS5D01G474700 chr5A 90.217 184 18 0 1986 2169 642695536 642695719 9.670000e-60 241
12 TraesCS5D01G474700 chr5A 93.168 161 9 2 2219 2379 642695720 642695878 4.500000e-58 235
13 TraesCS5D01G474700 chr5A 90.244 82 6 2 1 81 145840278 145840198 3.680000e-19 106
14 TraesCS5D01G474700 chr5B 96.142 1633 57 5 1074 2702 646627111 646628741 0.000000e+00 2662
15 TraesCS5D01G474700 chr5B 84.777 1859 232 22 830 2675 645063175 645061355 0.000000e+00 1818
16 TraesCS5D01G474700 chr5B 86.063 983 136 1 985 1966 646376141 646377123 0.000000e+00 1055
17 TraesCS5D01G474700 chr5B 84.303 1083 159 10 889 1963 645993287 645992208 0.000000e+00 1048
18 TraesCS5D01G474700 chr5B 85.185 729 70 22 1955 2675 646267715 646268413 0.000000e+00 713
19 TraesCS5D01G474700 chr5B 85.121 578 39 19 495 1029 646626539 646627112 5.090000e-152 547
20 TraesCS5D01G474700 chr5B 88.372 344 40 0 1958 2301 645992183 645991840 5.380000e-112 414
21 TraesCS5D01G474700 chr5B 88.281 256 29 1 1958 2213 645980524 645980270 3.380000e-79 305
22 TraesCS5D01G474700 chr3D 97.183 71 2 0 1 71 527509736 527509666 1.310000e-23 121
23 TraesCS5D01G474700 chr2A 95.946 74 3 0 1 74 738190100 738190173 1.310000e-23 121
24 TraesCS5D01G474700 chr7B 97.143 70 1 1 1 70 552932084 552932152 1.700000e-22 117
25 TraesCS5D01G474700 chr7B 95.714 70 3 0 1 70 1768414 1768345 2.200000e-21 113
26 TraesCS5D01G474700 chr6B 95.833 72 2 1 2 73 492188371 492188441 6.110000e-22 115
27 TraesCS5D01G474700 chr2D 95.775 71 2 1 1 71 238966761 238966830 2.200000e-21 113
28 TraesCS5D01G474700 chr3A 93.421 76 4 1 1 75 719863080 719863155 7.910000e-21 111


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 TraesCS5D01G474700 chr5D 514514231 514516932 2701 False 4990.000000 4990 100.000000 1 2702 1 chr5D.!!$F2 2701
1 TraesCS5D01G474700 chr5D 514411848 514412816 968 True 1079.000000 1079 86.796000 993 1966 1 chr5D.!!$R1 973
2 TraesCS5D01G474700 chr5D 514294519 514296321 1802 False 892.500000 1035 85.066500 883 2675 2 chr5D.!!$F3 1792
3 TraesCS5D01G474700 chr5A 641779943 641781629 1686 True 1790.000000 1790 85.805000 954 2675 1 chr5A.!!$R2 1721
4 TraesCS5D01G474700 chr5A 642904190 642907337 3147 False 1252.333333 3121 88.923667 61 2702 3 chr5A.!!$F3 2641
5 TraesCS5D01G474700 chr5A 642502635 642504057 1422 False 707.000000 1011 86.524000 883 2274 2 chr5A.!!$F1 1391
6 TraesCS5D01G474700 chr5B 645061355 645063175 1820 True 1818.000000 1818 84.777000 830 2675 1 chr5B.!!$R1 1845
7 TraesCS5D01G474700 chr5B 646626539 646628741 2202 False 1604.500000 2662 90.631500 495 2702 2 chr5B.!!$F3 2207
8 TraesCS5D01G474700 chr5B 646376141 646377123 982 False 1055.000000 1055 86.063000 985 1966 1 chr5B.!!$F2 981
9 TraesCS5D01G474700 chr5B 645991840 645993287 1447 True 731.000000 1048 86.337500 889 2301 2 chr5B.!!$R3 1412
10 TraesCS5D01G474700 chr5B 646267715 646268413 698 False 713.000000 713 85.185000 1955 2675 1 chr5B.!!$F1 720

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
38 39 0.035317 GAGCACATGGACACCACTGA 59.965 55.0 0.0 0.0 35.8 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1968 2558 0.036732 TGAAAGATGGGCAAGTCGCT 59.963 50.0 0.0 0.0 41.91 4.93 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 1.973138 CGCATCTGAAGGCAAAACTG 58.027 50.000 5.68 0.00 30.94 3.16
20 21 1.536766 CGCATCTGAAGGCAAAACTGA 59.463 47.619 5.68 0.00 30.94 3.41
21 22 2.413765 CGCATCTGAAGGCAAAACTGAG 60.414 50.000 5.68 0.00 30.94 3.35
22 23 2.670509 GCATCTGAAGGCAAAACTGAGC 60.671 50.000 0.47 0.00 30.94 4.26
23 24 2.346766 TCTGAAGGCAAAACTGAGCA 57.653 45.000 0.00 0.00 0.00 4.26
24 25 1.949525 TCTGAAGGCAAAACTGAGCAC 59.050 47.619 0.00 0.00 0.00 4.40
25 26 1.677576 CTGAAGGCAAAACTGAGCACA 59.322 47.619 0.00 0.00 0.00 4.57
26 27 2.295349 CTGAAGGCAAAACTGAGCACAT 59.705 45.455 0.00 0.00 0.00 3.21
27 28 2.034939 TGAAGGCAAAACTGAGCACATG 59.965 45.455 0.00 0.00 0.00 3.21
28 29 0.963962 AGGCAAAACTGAGCACATGG 59.036 50.000 0.00 0.00 0.00 3.66
29 30 0.961019 GGCAAAACTGAGCACATGGA 59.039 50.000 0.00 0.00 0.00 3.41
30 31 1.336240 GGCAAAACTGAGCACATGGAC 60.336 52.381 0.00 0.00 0.00 4.02
31 32 1.337703 GCAAAACTGAGCACATGGACA 59.662 47.619 0.00 0.00 0.00 4.02
32 33 2.859806 GCAAAACTGAGCACATGGACAC 60.860 50.000 0.00 0.00 0.00 3.67
33 34 1.609208 AAACTGAGCACATGGACACC 58.391 50.000 0.00 0.00 0.00 4.16
34 35 0.473755 AACTGAGCACATGGACACCA 59.526 50.000 0.00 0.00 38.19 4.17
35 36 0.250467 ACTGAGCACATGGACACCAC 60.250 55.000 0.00 0.00 35.80 4.16
36 37 0.035881 CTGAGCACATGGACACCACT 59.964 55.000 0.00 0.00 35.80 4.00
37 38 0.250424 TGAGCACATGGACACCACTG 60.250 55.000 0.00 0.00 35.80 3.66
38 39 0.035317 GAGCACATGGACACCACTGA 59.965 55.000 0.00 0.00 35.80 3.41
39 40 0.035881 AGCACATGGACACCACTGAG 59.964 55.000 0.00 0.00 35.80 3.35
40 41 0.957395 GCACATGGACACCACTGAGG 60.957 60.000 0.00 0.00 45.67 3.86
41 42 0.321919 CACATGGACACCACTGAGGG 60.322 60.000 0.00 0.00 43.89 4.30
42 43 1.377725 CATGGACACCACTGAGGGC 60.378 63.158 0.00 0.00 43.89 5.19
43 44 1.847506 ATGGACACCACTGAGGGCA 60.848 57.895 0.00 0.00 43.89 5.36
44 45 1.426251 ATGGACACCACTGAGGGCAA 61.426 55.000 0.00 0.00 43.89 4.52
45 46 1.150536 GGACACCACTGAGGGCAAA 59.849 57.895 0.00 0.00 43.89 3.68
46 47 0.467290 GGACACCACTGAGGGCAAAA 60.467 55.000 0.00 0.00 43.89 2.44
47 48 0.954452 GACACCACTGAGGGCAAAAG 59.046 55.000 0.00 0.00 43.89 2.27
48 49 0.468029 ACACCACTGAGGGCAAAAGG 60.468 55.000 0.00 0.00 43.89 3.11
49 50 0.178992 CACCACTGAGGGCAAAAGGA 60.179 55.000 0.00 0.00 43.89 3.36
50 51 0.779997 ACCACTGAGGGCAAAAGGAT 59.220 50.000 0.00 0.00 43.89 3.24
51 52 1.992557 ACCACTGAGGGCAAAAGGATA 59.007 47.619 0.00 0.00 43.89 2.59
52 53 2.378547 ACCACTGAGGGCAAAAGGATAA 59.621 45.455 0.00 0.00 43.89 1.75
53 54 3.011708 ACCACTGAGGGCAAAAGGATAAT 59.988 43.478 0.00 0.00 43.89 1.28
54 55 4.026052 CCACTGAGGGCAAAAGGATAATT 58.974 43.478 0.00 0.00 0.00 1.40
55 56 5.200483 CCACTGAGGGCAAAAGGATAATTA 58.800 41.667 0.00 0.00 0.00 1.40
56 57 5.656416 CCACTGAGGGCAAAAGGATAATTAA 59.344 40.000 0.00 0.00 0.00 1.40
57 58 6.405842 CCACTGAGGGCAAAAGGATAATTAAC 60.406 42.308 0.00 0.00 0.00 2.01
58 59 5.656859 ACTGAGGGCAAAAGGATAATTAACC 59.343 40.000 3.60 3.60 0.00 2.85
59 60 4.959839 TGAGGGCAAAAGGATAATTAACCC 59.040 41.667 8.09 3.96 34.91 4.11
60 61 5.220872 AGGGCAAAAGGATAATTAACCCT 57.779 39.130 8.09 6.12 40.37 4.34
61 62 5.599751 AGGGCAAAAGGATAATTAACCCTT 58.400 37.500 13.69 13.69 42.56 3.95
158 159 4.511826 CCCTAAGGTGAATTGCGATAGTTC 59.488 45.833 0.00 0.00 39.35 3.01
162 163 6.851222 AAGGTGAATTGCGATAGTTCTATG 57.149 37.500 0.00 0.00 39.35 2.23
172 173 6.749139 TGCGATAGTTCTATGCTATTCACTT 58.251 36.000 0.00 0.00 39.35 3.16
177 178 9.418045 GATAGTTCTATGCTATTCACTTCCTTC 57.582 37.037 0.00 0.00 30.09 3.46
182 183 4.623932 TGCTATTCACTTCCTTCTGTGT 57.376 40.909 0.00 0.00 35.82 3.72
206 207 2.701073 TTTCCGACTCTCTCAACGAC 57.299 50.000 0.00 0.00 0.00 4.34
214 215 0.539669 TCTCTCAACGACAGGGAGCA 60.540 55.000 0.00 0.00 0.00 4.26
219 220 0.443869 CAACGACAGGGAGCAAATCG 59.556 55.000 0.00 0.00 38.71 3.34
227 228 1.084370 GGGAGCAAATCGTCTCACCG 61.084 60.000 0.00 0.00 0.00 4.94
233 234 0.999406 AAATCGTCTCACCGCATTCG 59.001 50.000 0.00 0.00 0.00 3.34
262 292 0.107508 CTCATGTTGAGCCGTCCCAT 60.108 55.000 0.00 0.00 37.72 4.00
273 303 1.595093 CCGTCCCATGGGCAAGTTTC 61.595 60.000 27.41 8.64 34.68 2.78
311 341 7.181569 GGATCACATTCCCCTCAAAATTAAA 57.818 36.000 0.00 0.00 0.00 1.52
328 358 9.667989 CAAAATTAAAATCTTTCTTTGGCAAGG 57.332 29.630 2.45 2.45 0.00 3.61
372 414 1.593006 GTGATCTTGGAACGTATGCCG 59.407 52.381 0.00 0.00 44.03 5.69
417 459 4.282195 AGATTGAGGACTCGGAACATATCC 59.718 45.833 0.00 0.00 45.57 2.59
436 478 7.278646 ACATATCCTGCATATATAGCAAACACG 59.721 37.037 9.93 0.00 42.17 4.49
437 479 4.956085 TCCTGCATATATAGCAAACACGT 58.044 39.130 9.93 0.00 42.17 4.49
438 480 4.988540 TCCTGCATATATAGCAAACACGTC 59.011 41.667 9.93 0.00 42.17 4.34
439 481 4.991056 CCTGCATATATAGCAAACACGTCT 59.009 41.667 9.93 0.00 42.17 4.18
440 482 5.107337 CCTGCATATATAGCAAACACGTCTG 60.107 44.000 9.93 0.00 42.17 3.51
441 483 4.211164 TGCATATATAGCAAACACGTCTGC 59.789 41.667 5.81 5.81 39.39 4.26
442 484 4.664139 GCATATATAGCAAACACGTCTGCG 60.664 45.833 7.85 0.00 43.51 5.18
443 485 0.996462 TATAGCAAACACGTCTGCGC 59.004 50.000 0.00 0.00 43.51 6.09
444 486 0.670546 ATAGCAAACACGTCTGCGCT 60.671 50.000 9.73 6.29 43.51 5.92
445 487 0.878523 TAGCAAACACGTCTGCGCTT 60.879 50.000 9.73 0.00 43.51 4.68
462 949 4.699735 TGCGCTTTCTGGAAAAATGATCTA 59.300 37.500 9.73 0.00 0.00 1.98
463 950 5.030936 GCGCTTTCTGGAAAAATGATCTAC 58.969 41.667 0.00 0.00 0.00 2.59
473 960 5.066505 GGAAAAATGATCTACGTGATGGCTT 59.933 40.000 0.00 0.00 35.14 4.35
480 969 1.860950 CTACGTGATGGCTTTGGATCG 59.139 52.381 0.00 0.00 0.00 3.69
488 977 2.147958 TGGCTTTGGATCGTGTTACAC 58.852 47.619 5.27 5.27 0.00 2.90
489 978 1.467342 GGCTTTGGATCGTGTTACACC 59.533 52.381 10.10 0.00 0.00 4.16
491 980 1.730064 CTTTGGATCGTGTTACACCGG 59.270 52.381 10.10 0.00 0.00 5.28
492 981 0.967662 TTGGATCGTGTTACACCGGA 59.032 50.000 9.46 2.75 0.00 5.14
493 982 0.244450 TGGATCGTGTTACACCGGAC 59.756 55.000 9.46 0.00 0.00 4.79
538 1027 3.211045 GTGCACCACTTTAGAGGAACAA 58.789 45.455 5.22 0.00 0.00 2.83
625 1114 4.175489 CGTCGGCGATGGTCGTCT 62.175 66.667 21.01 0.00 43.21 4.18
632 1121 3.188786 GATGGTCGTCTGTGCCGC 61.189 66.667 0.00 0.00 0.00 6.53
680 1178 6.128117 CCGATATCCTTTTCCGTTTTTGAAGA 60.128 38.462 0.00 0.00 0.00 2.87
682 1180 7.806014 CGATATCCTTTTCCGTTTTTGAAGAAA 59.194 33.333 0.00 0.00 0.00 2.52
683 1181 8.812147 ATATCCTTTTCCGTTTTTGAAGAAAC 57.188 30.769 0.00 0.00 36.43 2.78
991 1551 0.694196 TCCGTCCGGGAATTTTCCTT 59.306 50.000 0.00 0.00 46.72 3.36
1060 1620 0.253044 GGAGGCTCAAGGCACACATA 59.747 55.000 17.69 0.00 44.01 2.29
1469 2029 4.756642 TGTCTTCAAGAAGCCACATGTTAG 59.243 41.667 0.00 0.00 38.28 2.34
1487 2047 1.018910 AGTGAAACCAAACCGTTCCG 58.981 50.000 0.00 0.00 37.80 4.30
1583 2143 3.503748 GTCAGTTTCATTGTTGGAGGAGG 59.496 47.826 0.00 0.00 0.00 4.30
1619 2179 2.472695 AGGTTTGTTCTCGCTATGCA 57.527 45.000 0.00 0.00 0.00 3.96
1620 2180 2.778299 AGGTTTGTTCTCGCTATGCAA 58.222 42.857 0.00 0.00 0.00 4.08
1699 2259 3.696051 GTGCATAACCATCAAGGACATGT 59.304 43.478 0.00 0.00 41.22 3.21
1968 2558 3.780804 TCGGGTTTCAAGGATCTCAAA 57.219 42.857 0.00 0.00 0.00 2.69
2076 2666 7.031226 TGCTAAATTTCTCATACCAATCTGC 57.969 36.000 0.00 0.00 0.00 4.26
2099 2689 3.681897 CGTAGGGATAATCAGCTCAATGC 59.318 47.826 0.00 0.00 43.29 3.56
2114 2704 4.746089 GCTCAATGCTAGATGGATCCAAGT 60.746 45.833 20.67 11.54 38.95 3.16
2379 2974 9.862149 TCTCCCTTTCACTTTCTATAAAAGTTT 57.138 29.630 0.58 0.00 38.32 2.66
2414 3009 1.375908 GTGTGATTGCCCTCTCGCA 60.376 57.895 0.00 0.00 36.85 5.10
2559 3155 7.505923 GGCAGGGGTAAGAAATGTAATTCTATT 59.494 37.037 0.00 0.00 38.69 1.73
2639 3237 3.530149 CCTTCCCAGGGATAAAAAGGGTA 59.470 47.826 9.80 0.00 40.48 3.69
2683 3288 9.878599 AGACATTTTCACTTCTTTAAATGTACG 57.121 29.630 10.85 0.00 45.86 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.536766 TCAGTTTTGCCTTCAGATGCG 59.463 47.619 0.00 0.00 0.00 4.73
1 2 2.670509 GCTCAGTTTTGCCTTCAGATGC 60.671 50.000 0.00 0.00 0.00 3.91
3 4 2.555757 GTGCTCAGTTTTGCCTTCAGAT 59.444 45.455 0.00 0.00 0.00 2.90
4 5 1.949525 GTGCTCAGTTTTGCCTTCAGA 59.050 47.619 0.00 0.00 0.00 3.27
6 7 1.761449 TGTGCTCAGTTTTGCCTTCA 58.239 45.000 0.00 0.00 0.00 3.02
7 8 2.608752 CCATGTGCTCAGTTTTGCCTTC 60.609 50.000 0.00 0.00 0.00 3.46
8 9 1.342174 CCATGTGCTCAGTTTTGCCTT 59.658 47.619 0.00 0.00 0.00 4.35
9 10 0.963962 CCATGTGCTCAGTTTTGCCT 59.036 50.000 0.00 0.00 0.00 4.75
10 11 0.961019 TCCATGTGCTCAGTTTTGCC 59.039 50.000 0.00 0.00 0.00 4.52
11 12 1.337703 TGTCCATGTGCTCAGTTTTGC 59.662 47.619 0.00 0.00 0.00 3.68
12 13 2.287788 GGTGTCCATGTGCTCAGTTTTG 60.288 50.000 0.00 0.00 0.00 2.44
13 14 1.956477 GGTGTCCATGTGCTCAGTTTT 59.044 47.619 0.00 0.00 0.00 2.43
14 15 1.133823 TGGTGTCCATGTGCTCAGTTT 60.134 47.619 0.00 0.00 0.00 2.66
15 16 0.473755 TGGTGTCCATGTGCTCAGTT 59.526 50.000 0.00 0.00 0.00 3.16
16 17 0.250467 GTGGTGTCCATGTGCTCAGT 60.250 55.000 0.00 0.00 35.28 3.41
17 18 0.035881 AGTGGTGTCCATGTGCTCAG 59.964 55.000 0.00 0.00 35.28 3.35
18 19 0.250424 CAGTGGTGTCCATGTGCTCA 60.250 55.000 0.00 0.00 35.28 4.26
19 20 0.035317 TCAGTGGTGTCCATGTGCTC 59.965 55.000 0.00 0.00 35.28 4.26
20 21 0.035881 CTCAGTGGTGTCCATGTGCT 59.964 55.000 0.00 0.00 35.28 4.40
21 22 0.957395 CCTCAGTGGTGTCCATGTGC 60.957 60.000 0.00 0.00 35.28 4.57
22 23 0.321919 CCCTCAGTGGTGTCCATGTG 60.322 60.000 0.00 0.00 35.28 3.21
23 24 2.069776 CCCTCAGTGGTGTCCATGT 58.930 57.895 0.00 0.00 35.28 3.21
24 25 1.377725 GCCCTCAGTGGTGTCCATG 60.378 63.158 0.00 0.00 35.28 3.66
25 26 1.426251 TTGCCCTCAGTGGTGTCCAT 61.426 55.000 0.00 0.00 35.28 3.41
26 27 1.640593 TTTGCCCTCAGTGGTGTCCA 61.641 55.000 0.00 0.00 0.00 4.02
27 28 0.467290 TTTTGCCCTCAGTGGTGTCC 60.467 55.000 0.00 0.00 0.00 4.02
28 29 0.954452 CTTTTGCCCTCAGTGGTGTC 59.046 55.000 0.00 0.00 0.00 3.67
29 30 0.468029 CCTTTTGCCCTCAGTGGTGT 60.468 55.000 0.00 0.00 0.00 4.16
30 31 0.178992 TCCTTTTGCCCTCAGTGGTG 60.179 55.000 0.00 0.00 0.00 4.17
31 32 0.779997 ATCCTTTTGCCCTCAGTGGT 59.220 50.000 0.00 0.00 0.00 4.16
32 33 2.806945 TATCCTTTTGCCCTCAGTGG 57.193 50.000 0.00 0.00 0.00 4.00
33 34 6.405842 GGTTAATTATCCTTTTGCCCTCAGTG 60.406 42.308 5.46 0.00 0.00 3.66
34 35 5.656859 GGTTAATTATCCTTTTGCCCTCAGT 59.343 40.000 5.46 0.00 0.00 3.41
35 36 5.069119 GGGTTAATTATCCTTTTGCCCTCAG 59.931 44.000 11.51 0.00 0.00 3.35
36 37 4.959839 GGGTTAATTATCCTTTTGCCCTCA 59.040 41.667 11.51 0.00 0.00 3.86
37 38 5.208890 AGGGTTAATTATCCTTTTGCCCTC 58.791 41.667 11.51 0.00 39.57 4.30
38 39 5.220872 AGGGTTAATTATCCTTTTGCCCT 57.779 39.130 11.51 0.00 38.99 5.19
39 40 5.950544 AAGGGTTAATTATCCTTTTGCCC 57.049 39.130 11.51 0.00 37.60 5.36
132 133 3.149005 TCGCAATTCACCTTAGGGTTT 57.851 42.857 2.32 0.00 44.73 3.27
152 153 9.153479 AGAAGGAAGTGAATAGCATAGAACTAT 57.847 33.333 0.00 0.00 31.60 2.12
158 159 6.344500 ACACAGAAGGAAGTGAATAGCATAG 58.656 40.000 0.00 0.00 39.03 2.23
162 163 3.935828 GGACACAGAAGGAAGTGAATAGC 59.064 47.826 0.00 0.00 39.03 2.97
172 173 3.194968 GTCGGAAATAGGACACAGAAGGA 59.805 47.826 0.00 0.00 33.41 3.36
177 178 3.697045 AGAGAGTCGGAAATAGGACACAG 59.303 47.826 0.00 0.00 35.63 3.66
182 183 3.377485 CGTTGAGAGAGTCGGAAATAGGA 59.623 47.826 0.00 0.00 0.00 2.94
206 207 1.363744 GTGAGACGATTTGCTCCCTG 58.636 55.000 0.00 0.00 0.00 4.45
214 215 0.999406 CGAATGCGGTGAGACGATTT 59.001 50.000 0.00 0.00 35.47 2.17
227 228 2.010145 TGAGTCTACAAGCCGAATGC 57.990 50.000 0.00 0.00 41.71 3.56
233 234 2.675348 GCTCAACATGAGTCTACAAGCC 59.325 50.000 0.00 0.00 45.94 4.35
238 239 2.531206 GACGGCTCAACATGAGTCTAC 58.469 52.381 9.96 1.11 46.36 2.59
262 292 2.434331 CCCTCGGAAACTTGCCCA 59.566 61.111 0.00 0.00 0.00 5.36
273 303 1.264749 TGATCCCTTCACACCCTCGG 61.265 60.000 0.00 0.00 0.00 4.63
311 341 6.153510 GTCTAATCCCTTGCCAAAGAAAGATT 59.846 38.462 0.00 0.00 35.19 2.40
328 358 1.594564 GGAAGGCGCCGTCTAATCC 60.595 63.158 35.60 24.63 0.00 3.01
372 414 2.805099 CTCCACAAAGAGAACTGCAGAC 59.195 50.000 23.35 13.87 35.82 3.51
374 416 3.065655 CTCTCCACAAAGAGAACTGCAG 58.934 50.000 13.48 13.48 44.67 4.41
417 459 5.613360 GCAGACGTGTTTGCTATATATGCAG 60.613 44.000 8.14 0.00 41.71 4.41
436 478 2.774439 TTTTTCCAGAAAGCGCAGAC 57.226 45.000 11.47 0.00 0.00 3.51
437 479 2.884012 TCATTTTTCCAGAAAGCGCAGA 59.116 40.909 11.47 0.00 0.00 4.26
438 480 3.287312 TCATTTTTCCAGAAAGCGCAG 57.713 42.857 11.47 0.00 0.00 5.18
439 481 3.507233 AGATCATTTTTCCAGAAAGCGCA 59.493 39.130 11.47 0.00 0.00 6.09
440 482 4.102035 AGATCATTTTTCCAGAAAGCGC 57.898 40.909 0.00 0.00 0.00 5.92
441 483 5.163854 ACGTAGATCATTTTTCCAGAAAGCG 60.164 40.000 0.00 0.00 0.00 4.68
442 484 6.024049 CACGTAGATCATTTTTCCAGAAAGC 58.976 40.000 0.00 0.00 0.00 3.51
443 485 7.364522 TCACGTAGATCATTTTTCCAGAAAG 57.635 36.000 0.00 0.00 0.00 2.62
444 486 7.148255 CCATCACGTAGATCATTTTTCCAGAAA 60.148 37.037 0.00 0.00 33.72 2.52
445 487 6.316140 CCATCACGTAGATCATTTTTCCAGAA 59.684 38.462 0.00 0.00 33.72 3.02
462 949 0.036388 ACGATCCAAAGCCATCACGT 60.036 50.000 0.00 0.00 0.00 4.49
463 950 0.374758 CACGATCCAAAGCCATCACG 59.625 55.000 0.00 0.00 0.00 4.35
473 960 0.967662 TCCGGTGTAACACGATCCAA 59.032 50.000 0.00 0.00 39.98 3.53
480 969 2.967362 TGATGATGTCCGGTGTAACAC 58.033 47.619 0.00 0.00 39.98 3.32
488 977 1.600957 GCACAAGATGATGATGTCCGG 59.399 52.381 0.00 0.00 0.00 5.14
489 978 1.600957 GGCACAAGATGATGATGTCCG 59.399 52.381 0.00 0.00 0.00 4.79
491 980 2.617308 CCAGGCACAAGATGATGATGTC 59.383 50.000 0.00 0.00 0.00 3.06
492 981 2.240414 TCCAGGCACAAGATGATGATGT 59.760 45.455 0.00 0.00 0.00 3.06
493 982 2.879026 CTCCAGGCACAAGATGATGATG 59.121 50.000 0.00 0.00 0.00 3.07
538 1027 2.362503 TCGATGTCCCGAGCCAGT 60.363 61.111 0.00 0.00 34.19 4.00
637 1126 0.733150 GGAAGCCATCAAACGCTACC 59.267 55.000 0.00 0.00 34.11 3.18
649 1147 2.484770 CGGAAAAGGATATCGGAAGCCA 60.485 50.000 0.00 0.00 0.00 4.75
680 1178 2.325484 CTGGGCTTGGGGTTTAAGTTT 58.675 47.619 0.00 0.00 0.00 2.66
682 1180 0.541998 GCTGGGCTTGGGGTTTAAGT 60.542 55.000 0.00 0.00 0.00 2.24
683 1181 1.257750 GGCTGGGCTTGGGGTTTAAG 61.258 60.000 0.00 0.00 0.00 1.85
991 1551 3.942130 ACATGTCTTCATCTCGTGACA 57.058 42.857 0.00 0.00 42.50 3.58
1060 1620 6.186957 TGCTGTAACCCAAGATATCAAACAT 58.813 36.000 5.32 0.00 0.00 2.71
1187 1747 5.886960 GATGTAATCTTGGCCATATCCAC 57.113 43.478 6.09 3.07 41.17 4.02
1487 2047 1.087202 TGGTGGCATGTCGATTACGC 61.087 55.000 0.00 0.00 39.58 4.42
1583 2143 0.947244 CCTATGCGCTTCAATGGTCC 59.053 55.000 9.73 0.00 0.00 4.46
1619 2179 4.798574 CTCTGCTTTAAAAACAGGCGATT 58.201 39.130 14.66 0.00 32.19 3.34
1620 2180 3.366374 GCTCTGCTTTAAAAACAGGCGAT 60.366 43.478 14.66 0.00 32.19 4.58
1699 2259 1.960689 GGCCTTGAAAACAGCAGGTTA 59.039 47.619 0.00 0.00 39.29 2.85
1848 2408 2.303022 GGTGTCCTTGTTCAGATCCTCA 59.697 50.000 0.00 0.00 0.00 3.86
1950 2510 2.162408 CGCTTTGAGATCCTTGAAACCC 59.838 50.000 0.00 0.00 0.00 4.11
1968 2558 0.036732 TGAAAGATGGGCAAGTCGCT 59.963 50.000 0.00 0.00 41.91 4.93
2073 2663 1.620819 AGCTGATTATCCCTACGGCAG 59.379 52.381 0.00 0.00 37.14 4.85
2076 2666 4.248859 CATTGAGCTGATTATCCCTACGG 58.751 47.826 0.00 0.00 0.00 4.02
2114 2704 6.833041 TCACTTGAGAATTAACCTAACCACA 58.167 36.000 0.00 0.00 0.00 4.17
2379 2974 3.901222 TCACACAAATCTGAGAGGGTACA 59.099 43.478 0.00 0.00 0.00 2.90
2382 2977 4.330250 CAATCACACAAATCTGAGAGGGT 58.670 43.478 0.00 0.00 0.00 4.34
2383 2978 3.128242 GCAATCACACAAATCTGAGAGGG 59.872 47.826 0.00 0.00 0.00 4.30
2442 3037 0.908198 CTTGGGAAGACCTGAGGGAG 59.092 60.000 2.38 0.00 41.11 4.30
2443 3038 0.491823 TCTTGGGAAGACCTGAGGGA 59.508 55.000 2.38 0.00 41.11 4.20
2559 3155 5.290493 ACTCTCAACAACCAACTCACATA 57.710 39.130 0.00 0.00 0.00 2.29
2654 3256 8.196771 ACATTTAAAGAAGTGAAAATGTCTGCA 58.803 29.630 6.48 0.00 44.91 4.41
2655 3257 8.579682 ACATTTAAAGAAGTGAAAATGTCTGC 57.420 30.769 6.48 0.00 44.91 4.26


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

AutoCloner maintained by Alex Coulton.