Multiple sequence alignment - TraesCS3D01G349400

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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 TraesCS3D01G349400 chr3D 100.000 2633 0 0 1 2633 460930365 460932997 0.000000e+00 4863
1 TraesCS3D01G349400 chr3B 91.111 2565 141 37 93 2633 611149956 611152457 0.000000e+00 3393
2 TraesCS3D01G349400 chr3B 82.378 471 28 22 2161 2621 611170630 611171055 2.490000e-95 359
3 TraesCS3D01G349400 chr3B 96.154 78 3 0 26 103 611145096 611145173 7.650000e-26 128
4 TraesCS3D01G349400 chr3A 90.859 1280 65 23 1380 2632 603234260 603235514 0.000000e+00 1668
5 TraesCS3D01G349400 chr3A 87.833 863 69 18 554 1383 603233367 603234226 0.000000e+00 979
6 TraesCS3D01G349400 chr3A 86.510 341 31 11 571 896 603232578 603232918 6.930000e-96 361
7 TraesCS3D01G349400 chr2D 83.516 182 18 7 1299 1478 316020249 316020078 2.710000e-35 159
8 TraesCS3D01G349400 chr2D 86.719 128 10 4 948 1071 557133174 557133050 4.570000e-28 135
9 TraesCS3D01G349400 chr6D 85.926 135 11 7 919 1046 87262717 87262584 1.270000e-28 137
10 TraesCS3D01G349400 chr6D 84.444 135 11 8 919 1046 68024604 68024735 9.900000e-25 124
11 TraesCS3D01G349400 chr1B 86.364 110 7 7 919 1021 14940800 14940908 2.140000e-21 113


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 TraesCS3D01G349400 chr3D 460930365 460932997 2632 False 4863.000000 4863 100.000000 1 2633 1 chr3D.!!$F1 2632
1 TraesCS3D01G349400 chr3B 611149956 611152457 2501 False 3393.000000 3393 91.111000 93 2633 1 chr3B.!!$F2 2540
2 TraesCS3D01G349400 chr3A 603232578 603235514 2936 False 1002.666667 1668 88.400667 554 2632 3 chr3A.!!$F1 2078

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
911 1163 0.244994 TCAGCAGGCTTCGTCTTCTC 59.755 55.0 0.0 0.0 0.0 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2016 2341 0.246635 ATCGGAACAAGACAGGACCG 59.753 55.0 0.0 0.0 41.39 4.79 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 5.813513 AGCAATGGAATTTTGAAGGAACT 57.186 34.783 0.00 0.00 34.01 3.01
25 26 5.240121 CAATGGAATTTTGAAGGAACTGGG 58.760 41.667 0.00 0.00 32.70 4.45
26 27 4.191804 TGGAATTTTGAAGGAACTGGGA 57.808 40.909 0.00 0.00 40.86 4.37
27 28 4.151883 TGGAATTTTGAAGGAACTGGGAG 58.848 43.478 0.00 0.00 40.86 4.30
28 29 4.141041 TGGAATTTTGAAGGAACTGGGAGA 60.141 41.667 0.00 0.00 40.86 3.71
29 30 4.460731 GGAATTTTGAAGGAACTGGGAGAG 59.539 45.833 0.00 0.00 40.86 3.20
31 32 2.118403 TTGAAGGAACTGGGAGAGGT 57.882 50.000 0.00 0.00 40.86 3.85
33 34 2.821437 TGAAGGAACTGGGAGAGGTAG 58.179 52.381 0.00 0.00 40.86 3.18
34 35 2.111972 TGAAGGAACTGGGAGAGGTAGT 59.888 50.000 0.00 0.00 40.86 2.73
35 36 3.335786 TGAAGGAACTGGGAGAGGTAGTA 59.664 47.826 0.00 0.00 40.86 1.82
37 38 3.199671 AGGAACTGGGAGAGGTAGTAGA 58.800 50.000 0.00 0.00 37.18 2.59
38 39 3.596956 AGGAACTGGGAGAGGTAGTAGAA 59.403 47.826 0.00 0.00 37.18 2.10
40 41 4.570292 GGAACTGGGAGAGGTAGTAGAAGT 60.570 50.000 0.00 0.00 0.00 3.01
41 42 5.339861 GGAACTGGGAGAGGTAGTAGAAGTA 60.340 48.000 0.00 0.00 0.00 2.24
42 43 5.793034 ACTGGGAGAGGTAGTAGAAGTAA 57.207 43.478 0.00 0.00 0.00 2.24
43 44 6.150034 ACTGGGAGAGGTAGTAGAAGTAAA 57.850 41.667 0.00 0.00 0.00 2.01
44 45 6.189133 ACTGGGAGAGGTAGTAGAAGTAAAG 58.811 44.000 0.00 0.00 0.00 1.85
45 46 6.150034 TGGGAGAGGTAGTAGAAGTAAAGT 57.850 41.667 0.00 0.00 0.00 2.66
46 47 5.950549 TGGGAGAGGTAGTAGAAGTAAAGTG 59.049 44.000 0.00 0.00 0.00 3.16
47 48 5.163530 GGGAGAGGTAGTAGAAGTAAAGTGC 60.164 48.000 0.00 0.00 0.00 4.40
49 50 5.008980 AGAGGTAGTAGAAGTAAAGTGCGT 58.991 41.667 0.00 0.00 0.00 5.24
51 52 4.763793 AGGTAGTAGAAGTAAAGTGCGTCA 59.236 41.667 0.00 0.00 0.00 4.35
52 53 5.242393 AGGTAGTAGAAGTAAAGTGCGTCAA 59.758 40.000 0.00 0.00 0.00 3.18
53 54 5.572126 GGTAGTAGAAGTAAAGTGCGTCAAG 59.428 44.000 0.00 0.00 0.00 3.02
54 55 5.449107 AGTAGAAGTAAAGTGCGTCAAGA 57.551 39.130 0.00 0.00 0.00 3.02
57 58 6.929606 AGTAGAAGTAAAGTGCGTCAAGATTT 59.070 34.615 0.00 0.00 0.00 2.17
58 59 8.086522 AGTAGAAGTAAAGTGCGTCAAGATTTA 58.913 33.333 0.00 0.00 0.00 1.40
59 60 7.907214 AGAAGTAAAGTGCGTCAAGATTTAT 57.093 32.000 0.00 0.00 0.00 1.40
60 61 8.997621 AGAAGTAAAGTGCGTCAAGATTTATA 57.002 30.769 0.00 0.00 0.00 0.98
61 62 8.870879 AGAAGTAAAGTGCGTCAAGATTTATAC 58.129 33.333 0.00 0.00 0.00 1.47
62 63 8.773404 AAGTAAAGTGCGTCAAGATTTATACT 57.227 30.769 0.00 0.00 0.00 2.12
63 64 8.408743 AGTAAAGTGCGTCAAGATTTATACTC 57.591 34.615 0.00 0.00 0.00 2.59
65 66 7.849804 AAAGTGCGTCAAGATTTATACTCAT 57.150 32.000 0.00 0.00 0.00 2.90
66 67 6.834959 AGTGCGTCAAGATTTATACTCATG 57.165 37.500 0.00 0.00 0.00 3.07
67 68 6.341316 AGTGCGTCAAGATTTATACTCATGT 58.659 36.000 0.00 0.00 0.00 3.21
68 69 6.818644 AGTGCGTCAAGATTTATACTCATGTT 59.181 34.615 0.00 0.00 0.00 2.71
69 70 7.979537 AGTGCGTCAAGATTTATACTCATGTTA 59.020 33.333 0.00 0.00 0.00 2.41
70 71 8.600625 GTGCGTCAAGATTTATACTCATGTTAA 58.399 33.333 0.00 0.00 0.00 2.01
71 72 9.325198 TGCGTCAAGATTTATACTCATGTTAAT 57.675 29.630 0.00 0.00 0.00 1.40
97 98 9.947433 TTAGATTTTCTTTTGAATTGGCATCAT 57.053 25.926 0.00 0.00 38.37 2.45
165 166 5.540400 CCTAAGGGGTTCGTATTACATGA 57.460 43.478 0.00 0.00 0.00 3.07
166 167 5.920903 CCTAAGGGGTTCGTATTACATGAA 58.079 41.667 0.00 0.00 0.00 2.57
246 247 7.881775 ATAATCCTCAAAAATAGCGTCCTTT 57.118 32.000 0.00 0.00 0.00 3.11
268 269 9.712305 CCTTTAAATGACATATACTAGGAGGTG 57.288 37.037 0.00 0.00 0.00 4.00
284 285 4.901250 AGGAGGTGATGGACAAACATTTTT 59.099 37.500 0.00 0.00 0.00 1.94
295 296 6.183360 TGGACAAACATTTTTAAAAAGTGCGG 60.183 34.615 17.72 10.11 0.00 5.69
304 305 1.770294 AAAAAGTGCGGTGAAAGGGA 58.230 45.000 0.00 0.00 0.00 4.20
339 340 6.491403 TCTCTTAACTTCCGTTGTTAGGTAGT 59.509 38.462 0.00 0.00 40.41 2.73
412 413 5.706916 TGCTAGACCTACAAAGAGTTTACG 58.293 41.667 0.00 0.00 0.00 3.18
420 421 7.858583 ACCTACAAAGAGTTTACGAATGTTTC 58.141 34.615 0.00 0.00 0.00 2.78
424 425 7.415229 ACAAAGAGTTTACGAATGTTTCCTTC 58.585 34.615 0.00 0.00 0.00 3.46
464 465 5.708736 TGGCACCCTTCATTTCTCTATTA 57.291 39.130 0.00 0.00 0.00 0.98
468 469 5.885912 GCACCCTTCATTTCTCTATTACCAA 59.114 40.000 0.00 0.00 0.00 3.67
681 923 2.477176 CGAGAGCCGGAGAGACAGG 61.477 68.421 5.05 0.00 36.93 4.00
905 1157 1.910772 AGGTCTCAGCAGGCTTCGT 60.911 57.895 0.00 0.00 0.00 3.85
911 1163 0.244994 TCAGCAGGCTTCGTCTTCTC 59.755 55.000 0.00 0.00 0.00 2.87
938 1191 1.488527 CGGAAGCTATACCGTTGCTC 58.511 55.000 15.59 0.00 43.53 4.26
939 1192 1.067212 CGGAAGCTATACCGTTGCTCT 59.933 52.381 15.59 0.00 43.53 4.09
942 1195 2.892784 AGCTATACCGTTGCTCTTCC 57.107 50.000 0.00 0.00 33.51 3.46
991 1262 2.591715 GTGGCTTGGTGTGCTCGT 60.592 61.111 0.00 0.00 0.00 4.18
1078 1349 5.131642 AGCAGGATAATGATCTGGTTGAGAA 59.868 40.000 0.00 0.00 33.12 2.87
1085 1356 2.833943 TGATCTGGTTGAGAAGCTAGCA 59.166 45.455 18.83 0.00 33.12 3.49
1103 1374 1.451207 AGCATGCGCCATTTCCGTA 60.451 52.632 13.01 0.00 39.83 4.02
1182 1453 3.616560 GCTACGACATGAACAAGGAGGAA 60.617 47.826 0.00 0.00 0.00 3.36
1216 1487 1.648467 GGAGAAGCACGCCAACATCC 61.648 60.000 0.00 0.00 38.35 3.51
1242 1513 1.722011 CCGTCACATCCACTGGTAAC 58.278 55.000 0.00 0.00 0.00 2.50
1633 1951 0.795085 AGACGACAACGACGACTAGG 59.205 55.000 0.00 0.00 42.66 3.02
1698 2016 6.290294 ACTAAAATATACGAGGGTGTGTGT 57.710 37.500 0.00 0.00 0.00 3.72
1758 2081 1.687493 GTACCCCTGGCTCAGCTCT 60.687 63.158 0.00 0.00 0.00 4.09
1804 2127 0.107831 TCCTTCAGTTGGTTGGTCCG 59.892 55.000 0.00 0.00 39.52 4.79
1809 2132 2.938838 TCAGTTGGTTGGTCCGAAATT 58.061 42.857 0.00 0.00 39.52 1.82
1830 2153 9.136952 GAAATTGAAAAGATTCAGAATCACCAG 57.863 33.333 22.70 0.00 45.82 4.00
1842 2165 4.394712 CACCAGTCCACCGGAGCC 62.395 72.222 9.46 0.00 29.39 4.70
2019 2344 1.674057 CTGTCAGAGGAAAGCCGGT 59.326 57.895 1.90 0.00 39.96 5.28
2049 2374 0.174845 TCCGATTCCGATCTTTGCGT 59.825 50.000 0.00 0.00 38.22 5.24
2072 2397 6.237490 CGTTGGCTTTTTCTACGTATACTCAG 60.237 42.308 0.00 0.00 0.00 3.35
2252 2585 4.891727 CCCGCCCGTTCGATCAGG 62.892 72.222 0.00 0.00 0.00 3.86
2261 2594 3.001902 TTCGATCAGGCCGCGACTT 62.002 57.895 8.23 0.00 33.33 3.01
2275 2612 1.154150 GACTTGCGCGTACGTAGGT 60.154 57.895 17.90 10.11 46.28 3.08
2310 2647 1.825474 TGGTGAGCTACTTGCCTACTC 59.175 52.381 0.00 0.00 44.23 2.59
2375 2712 1.004185 CGATGCATGCACTTGTAGAGC 60.004 52.381 25.37 0.00 32.26 4.09
2376 2713 2.286872 GATGCATGCACTTGTAGAGCT 58.713 47.619 25.37 1.94 32.86 4.09
2377 2714 3.461061 GATGCATGCACTTGTAGAGCTA 58.539 45.455 25.37 0.00 32.86 3.32
2378 2715 2.897436 TGCATGCACTTGTAGAGCTAG 58.103 47.619 18.46 0.00 32.86 3.42
2379 2716 2.497273 TGCATGCACTTGTAGAGCTAGA 59.503 45.455 18.46 0.00 32.86 2.43
2380 2717 3.122297 GCATGCACTTGTAGAGCTAGAG 58.878 50.000 14.21 0.00 32.86 2.43
2432 2770 2.662866 TGGCTTGTACTATACTCGGCT 58.337 47.619 0.00 0.00 0.00 5.52
2497 2842 5.898630 GGCACGTAGTAGTAGTAGAGTAC 57.101 47.826 0.00 0.00 41.61 2.73
2611 2956 2.192861 CGGCAGAGGATCGAGCTCT 61.193 63.158 12.85 0.00 42.67 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.511888 CCAGTTCCTTCAAAATTCCATTGCT 60.512 40.000 0.00 0.00 0.00 3.91
1 2 4.692155 CCAGTTCCTTCAAAATTCCATTGC 59.308 41.667 0.00 0.00 0.00 3.56
2 3 5.011943 TCCCAGTTCCTTCAAAATTCCATTG 59.988 40.000 0.00 0.00 0.00 2.82
3 4 5.154418 TCCCAGTTCCTTCAAAATTCCATT 58.846 37.500 0.00 0.00 0.00 3.16
6 7 4.407365 TCTCCCAGTTCCTTCAAAATTCC 58.593 43.478 0.00 0.00 0.00 3.01
7 8 4.460731 CCTCTCCCAGTTCCTTCAAAATTC 59.539 45.833 0.00 0.00 0.00 2.17
8 9 4.140924 ACCTCTCCCAGTTCCTTCAAAATT 60.141 41.667 0.00 0.00 0.00 1.82
9 10 3.399305 ACCTCTCCCAGTTCCTTCAAAAT 59.601 43.478 0.00 0.00 0.00 1.82
10 11 2.783510 ACCTCTCCCAGTTCCTTCAAAA 59.216 45.455 0.00 0.00 0.00 2.44
11 12 2.418669 ACCTCTCCCAGTTCCTTCAAA 58.581 47.619 0.00 0.00 0.00 2.69
13 14 2.111972 ACTACCTCTCCCAGTTCCTTCA 59.888 50.000 0.00 0.00 0.00 3.02
14 15 2.822697 ACTACCTCTCCCAGTTCCTTC 58.177 52.381 0.00 0.00 0.00 3.46
16 17 3.199671 TCTACTACCTCTCCCAGTTCCT 58.800 50.000 0.00 0.00 0.00 3.36
17 18 3.666345 TCTACTACCTCTCCCAGTTCC 57.334 52.381 0.00 0.00 0.00 3.62
18 19 4.602107 ACTTCTACTACCTCTCCCAGTTC 58.398 47.826 0.00 0.00 0.00 3.01
19 20 4.678538 ACTTCTACTACCTCTCCCAGTT 57.321 45.455 0.00 0.00 0.00 3.16
20 21 5.793034 TTACTTCTACTACCTCTCCCAGT 57.207 43.478 0.00 0.00 0.00 4.00
21 22 6.095720 CACTTTACTTCTACTACCTCTCCCAG 59.904 46.154 0.00 0.00 0.00 4.45
22 23 5.950549 CACTTTACTTCTACTACCTCTCCCA 59.049 44.000 0.00 0.00 0.00 4.37
25 26 5.123661 ACGCACTTTACTTCTACTACCTCTC 59.876 44.000 0.00 0.00 0.00 3.20
26 27 5.008980 ACGCACTTTACTTCTACTACCTCT 58.991 41.667 0.00 0.00 0.00 3.69
27 28 5.106396 TGACGCACTTTACTTCTACTACCTC 60.106 44.000 0.00 0.00 0.00 3.85
28 29 4.763793 TGACGCACTTTACTTCTACTACCT 59.236 41.667 0.00 0.00 0.00 3.08
29 30 5.051891 TGACGCACTTTACTTCTACTACC 57.948 43.478 0.00 0.00 0.00 3.18
31 32 6.564709 TCTTGACGCACTTTACTTCTACTA 57.435 37.500 0.00 0.00 0.00 1.82
33 34 6.707599 AATCTTGACGCACTTTACTTCTAC 57.292 37.500 0.00 0.00 0.00 2.59
34 35 8.997621 ATAAATCTTGACGCACTTTACTTCTA 57.002 30.769 0.00 0.00 0.00 2.10
35 36 7.907214 ATAAATCTTGACGCACTTTACTTCT 57.093 32.000 0.00 0.00 0.00 2.85
37 38 8.773404 AGTATAAATCTTGACGCACTTTACTT 57.227 30.769 0.00 0.00 0.00 2.24
38 39 8.033038 TGAGTATAAATCTTGACGCACTTTACT 58.967 33.333 0.00 0.00 0.00 2.24
40 41 8.817100 CATGAGTATAAATCTTGACGCACTTTA 58.183 33.333 0.00 0.00 0.00 1.85
41 42 7.334421 ACATGAGTATAAATCTTGACGCACTTT 59.666 33.333 0.00 0.00 0.00 2.66
42 43 6.818644 ACATGAGTATAAATCTTGACGCACTT 59.181 34.615 0.00 0.00 0.00 3.16
43 44 6.341316 ACATGAGTATAAATCTTGACGCACT 58.659 36.000 0.00 0.00 0.00 4.40
44 45 6.589830 ACATGAGTATAAATCTTGACGCAC 57.410 37.500 0.00 0.00 0.00 5.34
45 46 8.710835 TTAACATGAGTATAAATCTTGACGCA 57.289 30.769 0.00 0.00 0.00 5.24
70 71 9.947433 TGATGCCAATTCAAAAGAAAATCTAAT 57.053 25.926 0.00 0.00 0.00 1.73
71 72 9.947433 ATGATGCCAATTCAAAAGAAAATCTAA 57.053 25.926 0.00 0.00 0.00 2.10
73 74 9.595823 CTATGATGCCAATTCAAAAGAAAATCT 57.404 29.630 0.00 0.00 0.00 2.40
74 75 8.823818 CCTATGATGCCAATTCAAAAGAAAATC 58.176 33.333 0.00 0.00 0.00 2.17
75 76 8.323567 ACCTATGATGCCAATTCAAAAGAAAAT 58.676 29.630 0.00 0.00 0.00 1.82
76 77 7.603404 CACCTATGATGCCAATTCAAAAGAAAA 59.397 33.333 0.00 0.00 0.00 2.29
77 78 7.098477 CACCTATGATGCCAATTCAAAAGAAA 58.902 34.615 0.00 0.00 0.00 2.52
78 79 6.351202 CCACCTATGATGCCAATTCAAAAGAA 60.351 38.462 0.00 0.00 0.00 2.52
79 80 5.127519 CCACCTATGATGCCAATTCAAAAGA 59.872 40.000 0.00 0.00 0.00 2.52
80 81 5.127519 TCCACCTATGATGCCAATTCAAAAG 59.872 40.000 0.00 0.00 0.00 2.27
81 82 5.022122 TCCACCTATGATGCCAATTCAAAA 58.978 37.500 0.00 0.00 0.00 2.44
82 83 4.608269 TCCACCTATGATGCCAATTCAAA 58.392 39.130 0.00 0.00 0.00 2.69
83 84 4.248174 TCCACCTATGATGCCAATTCAA 57.752 40.909 0.00 0.00 0.00 2.69
84 85 3.949586 TCCACCTATGATGCCAATTCA 57.050 42.857 0.00 0.00 0.00 2.57
85 86 4.560108 GCATTCCACCTATGATGCCAATTC 60.560 45.833 0.00 0.00 0.00 2.17
86 87 3.322828 GCATTCCACCTATGATGCCAATT 59.677 43.478 0.00 0.00 0.00 2.32
87 88 2.895404 GCATTCCACCTATGATGCCAAT 59.105 45.455 0.00 0.00 0.00 3.16
89 90 1.214923 TGCATTCCACCTATGATGCCA 59.785 47.619 4.90 0.00 34.45 4.92
90 91 1.985473 TGCATTCCACCTATGATGCC 58.015 50.000 4.90 0.00 34.45 4.40
91 92 4.945543 TGATATGCATTCCACCTATGATGC 59.054 41.667 3.54 0.00 35.77 3.91
92 93 6.602009 ACATGATATGCATTCCACCTATGATG 59.398 38.462 3.54 2.84 34.15 3.07
93 94 6.728411 ACATGATATGCATTCCACCTATGAT 58.272 36.000 3.54 0.00 34.15 2.45
94 95 6.130692 ACATGATATGCATTCCACCTATGA 57.869 37.500 3.54 0.00 34.15 2.15
95 96 6.541278 CCTACATGATATGCATTCCACCTATG 59.459 42.308 3.54 3.66 34.15 2.23
97 98 5.784906 TCCTACATGATATGCATTCCACCTA 59.215 40.000 3.54 0.00 34.15 3.08
242 243 9.712305 CACCTCCTAGTATATGTCATTTAAAGG 57.288 37.037 0.00 0.00 0.00 3.11
246 247 9.035890 CCATCACCTCCTAGTATATGTCATTTA 57.964 37.037 0.00 0.00 0.00 1.40
268 269 7.582319 CGCACTTTTTAAAAATGTTTGTCCATC 59.418 33.333 13.55 0.20 0.00 3.51
284 285 2.933573 TCCCTTTCACCGCACTTTTTA 58.066 42.857 0.00 0.00 0.00 1.52
304 305 4.262938 CGGAAGTTAAGAGAGGGGACTTTT 60.263 45.833 0.00 0.00 44.43 2.27
339 340 9.932207 AGAGATTACAATTGCATCAAAATTCAA 57.068 25.926 16.69 0.00 0.00 2.69
445 446 7.775093 TGATTGGTAATAGAGAAATGAAGGGTG 59.225 37.037 0.00 0.00 0.00 4.61
446 447 7.872138 TGATTGGTAATAGAGAAATGAAGGGT 58.128 34.615 0.00 0.00 0.00 4.34
464 465 4.214986 TGGTGTGACGATTATGATTGGT 57.785 40.909 0.00 0.00 0.00 3.67
468 469 6.757897 ACAAATTGGTGTGACGATTATGAT 57.242 33.333 0.00 0.00 0.00 2.45
477 478 6.473397 TTTTCACAAACAAATTGGTGTGAC 57.527 33.333 24.64 0.00 42.34 3.67
513 514 5.663795 AGTCGAGCAATGCTACATTTATG 57.336 39.130 8.12 0.00 39.88 1.90
528 529 4.929808 TCTTTCACCAATTCTTAGTCGAGC 59.070 41.667 0.00 0.00 0.00 5.03
770 1022 1.142748 GGAGAGGGACATGTCAGCG 59.857 63.158 26.47 0.00 0.00 5.18
889 1141 0.037790 AAGACGAAGCCTGCTGAGAC 60.038 55.000 0.00 0.00 0.00 3.36
905 1157 1.001269 TTCCGCGGGAGAGAGAAGA 60.001 57.895 27.83 0.00 31.21 2.87
911 1163 0.241481 GTATAGCTTCCGCGGGAGAG 59.759 60.000 37.89 25.59 42.32 3.20
928 1180 1.210931 CGACGGAAGAGCAACGGTA 59.789 57.895 0.00 0.00 0.00 4.02
934 1187 0.171231 CACAGATCGACGGAAGAGCA 59.829 55.000 0.00 0.00 0.00 4.26
935 1188 1.142778 GCACAGATCGACGGAAGAGC 61.143 60.000 0.00 0.00 0.00 4.09
938 1191 2.508891 GCGCACAGATCGACGGAAG 61.509 63.158 0.30 0.00 0.00 3.46
939 1192 2.506217 GCGCACAGATCGACGGAA 60.506 61.111 0.30 0.00 0.00 4.30
1058 1329 5.619220 AGCTTCTCAACCAGATCATTATCC 58.381 41.667 0.00 0.00 31.98 2.59
1059 1330 6.368516 GCTAGCTTCTCAACCAGATCATTATC 59.631 42.308 7.70 0.00 0.00 1.75
1062 1333 4.080695 TGCTAGCTTCTCAACCAGATCATT 60.081 41.667 17.23 0.00 0.00 2.57
1078 1349 3.769369 ATGGCGCATGCTGCTAGCT 62.769 57.895 25.77 10.12 42.97 3.32
1085 1356 0.819259 ATACGGAAATGGCGCATGCT 60.819 50.000 17.13 0.00 42.25 3.79
1242 1513 1.214062 GTGAGAGTGGACGGAGCTG 59.786 63.158 0.00 0.00 0.00 4.24
1405 1717 3.883489 ACAGATTGACATGCTGATGGATG 59.117 43.478 10.90 0.00 45.75 3.51
1686 2004 0.103390 TACACACACACACACCCTCG 59.897 55.000 0.00 0.00 0.00 4.63
1698 2016 5.220586 GCTAGCTGCGATTTATTTACACACA 60.221 40.000 7.70 0.00 0.00 3.72
1732 2050 4.752879 CCAGGGGTACGTGCGTGG 62.753 72.222 7.55 0.64 0.00 4.94
1735 2053 4.814294 GAGCCAGGGGTACGTGCG 62.814 72.222 0.00 0.00 0.00 5.34
1804 2127 9.136952 CTGGTGATTCTGAATCTTTTCAATTTC 57.863 33.333 25.83 2.76 41.22 2.17
1809 2132 5.707298 GGACTGGTGATTCTGAATCTTTTCA 59.293 40.000 25.83 17.74 39.54 2.69
1830 2153 3.775654 CCAGAGGCTCCGGTGGAC 61.776 72.222 14.43 0.00 31.04 4.02
1842 2165 7.665690 ACTAGTATGCATACAAGATTCCAGAG 58.334 38.462 32.69 17.07 35.74 3.35
2016 2341 0.246635 ATCGGAACAAGACAGGACCG 59.753 55.000 0.00 0.00 41.39 4.79
2019 2344 1.067142 CGGAATCGGAACAAGACAGGA 60.067 52.381 0.00 0.00 0.00 3.86
2049 2374 6.694447 ACTGAGTATACGTAGAAAAAGCCAA 58.306 36.000 13.97 0.00 0.00 4.52
2072 2397 2.262915 CAGCCCGTGTGGAGAGAC 59.737 66.667 0.00 0.00 37.49 3.36
2155 2488 0.746563 GCCGACGGATGGGAATTTGA 60.747 55.000 20.50 0.00 0.00 2.69
2180 2513 2.651361 CCGCAGACGTCCAACTCT 59.349 61.111 13.01 0.00 37.70 3.24
2243 2576 3.001902 AAGTCGCGGCCTGATCGAA 62.002 57.895 7.31 0.00 33.81 3.71
2310 2647 1.226746 GGACGAAATAATCCTGCCCG 58.773 55.000 0.00 0.00 31.75 6.13
2362 2699 2.949451 GCTCTAGCTCTACAAGTGCA 57.051 50.000 0.00 0.00 37.20 4.57
2432 2770 0.606604 GTAGGGACTGCGACCTGAAA 59.393 55.000 0.00 0.00 41.52 2.69
2454 2792 2.182030 GTTCCTGTCCGAGCCGAG 59.818 66.667 0.00 0.00 0.00 4.63
2455 2793 3.744719 CGTTCCTGTCCGAGCCGA 61.745 66.667 0.00 0.00 0.00 5.54
2489 2834 9.535270 GTACGTAAAATATCCATCGTACTCTAC 57.465 37.037 15.14 0.00 45.16 2.59
2497 2842 5.214417 TCCGTGTACGTAAAATATCCATCG 58.786 41.667 0.00 0.00 37.74 3.84
2611 2956 2.431771 ATACGAGCACGCAACGCA 60.432 55.556 2.62 0.00 43.96 5.24


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

AutoCloner maintained by Alex Coulton.