Multiple sequence alignment - TraesCS1A01G295900

Loading Multiple Alignment...

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 TraesCS1A01G295900 chr1A 100.000 2582 0 0 1 2582 490892890 490895471 0.000000e+00 4769.0
1 TraesCS1A01G295900 chr4B 91.681 2296 94 39 345 2577 326093577 326095838 0.000000e+00 3092.0
2 TraesCS1A01G295900 chr4B 86.726 226 21 3 119 344 326093328 326093544 2.570000e-60 243.0
3 TraesCS1A01G295900 chr1D 89.717 2295 102 48 345 2579 394410075 394407855 0.000000e+00 2808.0
4 TraesCS1A01G295900 chr1D 92.888 1167 49 15 580 1742 394452584 394451448 0.000000e+00 1664.0
5 TraesCS1A01G295900 chr1D 83.388 307 24 10 57 344 394410406 394410108 2.550000e-65 259.0
6 TraesCS1A01G295900 chr1D 87.391 230 17 6 119 344 394452999 394452778 1.190000e-63 254.0
7 TraesCS1A01G295900 chr1D 87.500 104 8 4 345 446 394452745 394452645 5.840000e-22 115.0
8 TraesCS1A01G295900 chr1D 89.091 55 1 3 64 113 394453076 394453022 2.140000e-06 63.9


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 TraesCS1A01G295900 chr1A 490892890 490895471 2581 False 4769.000 4769 100.0000 1 2582 1 chr1A.!!$F1 2581
1 TraesCS1A01G295900 chr4B 326093328 326095838 2510 False 1667.500 3092 89.2035 119 2577 2 chr4B.!!$F1 2458
2 TraesCS1A01G295900 chr1D 394407855 394410406 2551 True 1533.500 2808 86.5525 57 2579 2 chr1D.!!$R1 2522
3 TraesCS1A01G295900 chr1D 394451448 394453076 1628 True 524.225 1664 89.2175 64 1742 4 chr1D.!!$R2 1678

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
144 169 0.031178 GCATGGATAAGCGGCAAAGG 59.969 55.0 1.45 0.0 0.0 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2020 2171 1.130561 GGCGATCAGTGCTGTTAAACC 59.869 52.381 0.0 0.0 0.0 3.27 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 4.735662 GTTATAACACACGTTTCCTGCA 57.264 40.909 10.81 0.00 36.52 4.41
22 23 5.291293 GTTATAACACACGTTTCCTGCAT 57.709 39.130 10.81 0.00 36.52 3.96
23 24 5.695818 GTTATAACACACGTTTCCTGCATT 58.304 37.500 10.81 0.00 36.52 3.56
24 25 4.846779 ATAACACACGTTTCCTGCATTT 57.153 36.364 0.00 0.00 36.52 2.32
25 26 5.950758 ATAACACACGTTTCCTGCATTTA 57.049 34.783 0.00 0.00 36.52 1.40
26 27 3.619233 ACACACGTTTCCTGCATTTAC 57.381 42.857 0.00 0.00 0.00 2.01
27 28 2.946329 ACACACGTTTCCTGCATTTACA 59.054 40.909 0.00 0.00 0.00 2.41
28 29 3.242936 ACACACGTTTCCTGCATTTACAC 60.243 43.478 0.00 0.00 0.00 2.90
29 30 2.946329 ACACGTTTCCTGCATTTACACA 59.054 40.909 0.00 0.00 0.00 3.72
30 31 3.378742 ACACGTTTCCTGCATTTACACAA 59.621 39.130 0.00 0.00 0.00 3.33
31 32 4.142359 ACACGTTTCCTGCATTTACACAAA 60.142 37.500 0.00 0.00 0.00 2.83
32 33 4.981674 CACGTTTCCTGCATTTACACAAAT 59.018 37.500 0.00 0.00 34.60 2.32
33 34 5.461737 CACGTTTCCTGCATTTACACAAATT 59.538 36.000 0.00 0.00 31.82 1.82
34 35 6.019156 CACGTTTCCTGCATTTACACAAATTT 60.019 34.615 0.00 0.00 31.82 1.82
35 36 7.168302 CACGTTTCCTGCATTTACACAAATTTA 59.832 33.333 0.00 0.00 31.82 1.40
36 37 7.707035 ACGTTTCCTGCATTTACACAAATTTAA 59.293 29.630 0.00 0.00 31.82 1.52
37 38 8.707839 CGTTTCCTGCATTTACACAAATTTAAT 58.292 29.630 0.00 0.00 31.82 1.40
109 114 3.955101 CCCTAGGAGCGCGTCGAG 61.955 72.222 11.48 3.91 0.00 4.04
141 166 0.819259 GGAGCATGGATAAGCGGCAA 60.819 55.000 1.45 0.00 35.48 4.52
144 169 0.031178 GCATGGATAAGCGGCAAAGG 59.969 55.000 1.45 0.00 0.00 3.11
170 195 6.197364 AGGTTGTAGTCTTGTAGATTCTCG 57.803 41.667 0.00 0.00 0.00 4.04
225 250 1.220206 CTCGAAGCAGATGGCCACT 59.780 57.895 8.16 4.50 46.50 4.00
226 251 0.461548 CTCGAAGCAGATGGCCACTA 59.538 55.000 8.16 0.00 46.50 2.74
227 252 0.461548 TCGAAGCAGATGGCCACTAG 59.538 55.000 8.16 0.65 46.50 2.57
228 253 1.156645 CGAAGCAGATGGCCACTAGC 61.157 60.000 8.16 12.83 46.50 3.42
248 273 1.734748 GTCTAGCCGGCAGGAGTAC 59.265 63.158 31.54 16.86 41.02 2.73
277 307 1.816074 TTCACCCTTGGCGATGTAAC 58.184 50.000 0.00 0.00 0.00 2.50
301 331 2.622942 TCACAAGTTCCAGCCACAAATC 59.377 45.455 0.00 0.00 0.00 2.17
308 338 1.213537 CAGCCACAAATCCGCCAAG 59.786 57.895 0.00 0.00 0.00 3.61
314 344 3.663025 CCACAAATCCGCCAAGAAAAAT 58.337 40.909 0.00 0.00 0.00 1.82
317 347 5.698545 CCACAAATCCGCCAAGAAAAATAAA 59.301 36.000 0.00 0.00 0.00 1.40
318 348 6.347321 CCACAAATCCGCCAAGAAAAATAAAC 60.347 38.462 0.00 0.00 0.00 2.01
319 349 6.423604 CACAAATCCGCCAAGAAAAATAAACT 59.576 34.615 0.00 0.00 0.00 2.66
322 352 8.807581 CAAATCCGCCAAGAAAAATAAACTATC 58.192 33.333 0.00 0.00 0.00 2.08
410 488 1.486211 CTACAAGTCGTCCATCCCCT 58.514 55.000 0.00 0.00 0.00 4.79
456 534 3.240302 CCGGAGAATATTACACCTCCCT 58.760 50.000 12.88 0.00 41.54 4.20
482 560 8.623903 TGCAAATTAAGAAGAAGAATATCGCAT 58.376 29.630 0.00 0.00 0.00 4.73
484 562 9.310971 CAAATTAAGAAGAAGAATATCGCATCG 57.689 33.333 0.00 0.00 0.00 3.84
576 661 2.110967 CAGTTGCCCATCAGCTCGG 61.111 63.158 0.00 0.00 33.73 4.63
682 775 0.953003 TTTTAAAACCACGCTCCCCG 59.047 50.000 0.00 0.00 44.21 5.73
850 967 2.594303 CGCTGCCTTTGACCACCA 60.594 61.111 0.00 0.00 0.00 4.17
851 968 2.620112 CGCTGCCTTTGACCACCAG 61.620 63.158 0.00 0.00 0.00 4.00
860 977 1.053835 TTGACCACCAGAGCTCCACA 61.054 55.000 10.93 0.00 0.00 4.17
901 1029 1.687146 TGAGAGGGTGGGCTAGCTG 60.687 63.158 15.72 0.00 0.00 4.24
902 1030 3.086600 AGAGGGTGGGCTAGCTGC 61.087 66.667 15.72 4.98 41.94 5.25
903 1031 3.086600 GAGGGTGGGCTAGCTGCT 61.087 66.667 15.72 7.57 42.39 4.24
904 1032 1.762460 GAGGGTGGGCTAGCTGCTA 60.762 63.158 15.72 9.34 42.39 3.49
905 1033 2.034048 GAGGGTGGGCTAGCTGCTAC 62.034 65.000 15.72 6.81 42.39 3.58
906 1034 2.066999 GGGTGGGCTAGCTGCTACT 61.067 63.158 15.72 0.00 42.39 2.57
907 1035 0.759436 GGGTGGGCTAGCTGCTACTA 60.759 60.000 15.72 0.00 42.39 1.82
908 1036 0.676736 GGTGGGCTAGCTGCTACTAG 59.323 60.000 15.72 8.68 42.20 2.57
951 1079 3.767230 CGTGCACGTCGAGGCTTG 61.767 66.667 30.50 0.00 34.11 4.01
952 1080 4.077188 GTGCACGTCGAGGCTTGC 62.077 66.667 12.29 12.29 34.71 4.01
955 1083 3.767230 CACGTCGAGGCTTGCGTG 61.767 66.667 25.82 25.82 46.28 5.34
982 1114 4.069232 CTGCAGAGTTCGCGGGGA 62.069 66.667 8.42 0.00 31.83 4.81
987 1119 1.304217 AGAGTTCGCGGGGAGAAGA 60.304 57.895 6.13 0.00 0.00 2.87
988 1120 0.898789 AGAGTTCGCGGGGAGAAGAA 60.899 55.000 6.13 0.00 0.00 2.52
989 1121 0.458716 GAGTTCGCGGGGAGAAGAAG 60.459 60.000 6.13 0.00 0.00 2.85
990 1122 1.448013 GTTCGCGGGGAGAAGAAGG 60.448 63.158 6.13 0.00 0.00 3.46
991 1123 1.608336 TTCGCGGGGAGAAGAAGGA 60.608 57.895 6.13 0.00 0.00 3.36
994 1126 1.819905 GCGGGGAGAAGAAGGAGAG 59.180 63.158 0.00 0.00 0.00 3.20
995 1127 0.684805 GCGGGGAGAAGAAGGAGAGA 60.685 60.000 0.00 0.00 0.00 3.10
1043 1180 2.567497 GGACGACGAACCAGGTGGA 61.567 63.158 0.00 0.00 38.94 4.02
1332 1469 4.821589 CGCTCCCCTTCTCGGCAC 62.822 72.222 0.00 0.00 0.00 5.01
1357 1494 2.361357 ACGGTGGAGACGAGGAGG 60.361 66.667 0.00 0.00 34.93 4.30
1360 1497 2.419739 GGTGGAGACGAGGAGGAGC 61.420 68.421 0.00 0.00 0.00 4.70
1361 1498 1.679305 GTGGAGACGAGGAGGAGCA 60.679 63.158 0.00 0.00 0.00 4.26
1636 1787 1.081892 CTCACCGAAGCATGACAAGG 58.918 55.000 0.00 0.00 0.00 3.61
1670 1821 5.661458 TGTAAGCCACTTACTGCTATCTTC 58.339 41.667 16.16 0.00 44.49 2.87
1690 1841 2.358737 CGCAAGAAAGCCCGTCCT 60.359 61.111 0.00 0.00 43.02 3.85
1881 2032 6.872020 GGCCACTTTTCTACCTTAAATTTTCC 59.128 38.462 0.00 0.00 0.00 3.13
1891 2042 4.242475 CCTTAAATTTTCCGTTCAAGCCC 58.758 43.478 0.00 0.00 0.00 5.19
1929 2080 3.063045 GCGGTGTAGGCTGTACATTAAAC 59.937 47.826 0.00 0.00 0.00 2.01
1931 2082 5.653507 CGGTGTAGGCTGTACATTAAACTA 58.346 41.667 0.00 0.00 0.00 2.24
1932 2083 6.278363 CGGTGTAGGCTGTACATTAAACTAT 58.722 40.000 0.00 0.00 0.00 2.12
1933 2084 6.420008 CGGTGTAGGCTGTACATTAAACTATC 59.580 42.308 0.00 0.00 0.00 2.08
1935 2086 8.636213 GGTGTAGGCTGTACATTAAACTATCTA 58.364 37.037 0.00 0.00 0.00 1.98
1942 2093 7.384115 GCTGTACATTAAACTATCTATCGCCAA 59.616 37.037 0.00 0.00 0.00 4.52
1954 2105 5.122512 TCTATCGCCAAGAGTATTGTAGC 57.877 43.478 0.00 0.00 0.00 3.58
2020 2171 1.200483 GGCATCTCGATGTGTACGTG 58.800 55.000 0.00 0.00 40.80 4.49
2039 2190 1.804151 TGGTTTAACAGCACTGATCGC 59.196 47.619 4.31 0.00 0.00 4.58
2040 2191 1.130561 GGTTTAACAGCACTGATCGCC 59.869 52.381 4.31 0.00 0.00 5.54
2041 2192 2.076863 GTTTAACAGCACTGATCGCCT 58.923 47.619 4.31 0.00 0.00 5.52
2042 2193 2.472695 TTAACAGCACTGATCGCCTT 57.527 45.000 4.31 0.00 0.00 4.35
2043 2194 2.472695 TAACAGCACTGATCGCCTTT 57.527 45.000 4.31 0.00 0.00 3.11
2044 2195 2.472695 AACAGCACTGATCGCCTTTA 57.527 45.000 4.31 0.00 0.00 1.85
2045 2196 2.472695 ACAGCACTGATCGCCTTTAA 57.527 45.000 4.31 0.00 0.00 1.52
2063 2223 7.287810 GCCTTTAATTTAAGTCCCAGGATCTA 58.712 38.462 7.67 0.00 0.00 1.98
2108 2268 3.658342 GCGTTTGCGTATAGTAATCTGCG 60.658 47.826 0.00 0.00 40.81 5.18
2135 2295 2.391389 GCAGCTCCCGTAAGTGTGC 61.391 63.158 0.00 0.00 0.00 4.57
2137 2297 2.048503 GCTCCCGTAAGTGTGCGT 60.049 61.111 0.00 0.00 0.00 5.24
2138 2298 2.380410 GCTCCCGTAAGTGTGCGTG 61.380 63.158 0.00 0.00 0.00 5.34
2183 2343 0.248702 TTTGCGAAAAGGTTGCGTCC 60.249 50.000 0.00 0.00 0.00 4.79
2268 2436 3.459232 TTAGTGCGATGGAGGATTGAG 57.541 47.619 0.00 0.00 0.00 3.02
2330 2503 1.433879 CCCGTCTTCGTCTGGCTAG 59.566 63.158 0.00 0.00 35.01 3.42
2347 2520 2.548875 CTAGGCTAGCTGTGCTTCTTG 58.451 52.381 15.72 0.00 40.44 3.02
2364 2537 0.735978 TTGCTCCATCGCACTACGTG 60.736 55.000 0.00 0.00 44.19 4.49
2365 2538 1.153823 GCTCCATCGCACTACGTGT 60.154 57.895 0.00 0.00 44.19 4.49
2366 2539 0.099968 GCTCCATCGCACTACGTGTA 59.900 55.000 0.00 0.00 44.19 2.90
2415 2593 1.543802 TGGGTTCGATTGATTGTTGGC 59.456 47.619 0.00 0.00 0.00 4.52
2458 2636 3.699894 CCACGGCTGGAGCACTCT 61.700 66.667 0.00 0.00 44.36 3.24
2468 2646 3.269178 CTGGAGCACTCTTGGATCTTTC 58.731 50.000 0.00 0.00 0.00 2.62
2470 2648 3.269178 GGAGCACTCTTGGATCTTTCTG 58.731 50.000 0.00 0.00 0.00 3.02
2530 2708 1.730064 CAACCGGACGTCTTAACATGG 59.270 52.381 16.46 8.51 0.00 3.66
2579 2761 3.621715 GCTTAATGCACCACCACTACTAC 59.378 47.826 0.00 0.00 42.31 2.73
2580 2762 4.623171 GCTTAATGCACCACCACTACTACT 60.623 45.833 0.00 0.00 42.31 2.57
2581 2763 5.394883 GCTTAATGCACCACCACTACTACTA 60.395 44.000 0.00 0.00 42.31 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.735662 TGCAGGAAACGTGTGTTATAAC 57.264 40.909 8.75 8.75 37.31 1.89
1 2 5.950758 AATGCAGGAAACGTGTGTTATAA 57.049 34.783 0.00 0.00 37.31 0.98
2 3 5.950758 AAATGCAGGAAACGTGTGTTATA 57.049 34.783 0.00 0.00 37.31 0.98
3 4 4.846779 AAATGCAGGAAACGTGTGTTAT 57.153 36.364 0.00 0.00 37.31 1.89
4 5 4.575236 TGTAAATGCAGGAAACGTGTGTTA 59.425 37.500 0.00 0.00 37.31 2.41
6 7 2.946329 TGTAAATGCAGGAAACGTGTGT 59.054 40.909 0.00 0.00 0.00 3.72
7 8 3.242903 TGTGTAAATGCAGGAAACGTGTG 60.243 43.478 0.00 0.00 0.00 3.82
8 9 2.946329 TGTGTAAATGCAGGAAACGTGT 59.054 40.909 0.00 0.00 0.00 4.49
9 10 3.617540 TGTGTAAATGCAGGAAACGTG 57.382 42.857 0.00 0.00 0.00 4.49
10 11 4.640789 TTTGTGTAAATGCAGGAAACGT 57.359 36.364 0.00 0.00 0.00 3.99
11 12 6.523676 AAATTTGTGTAAATGCAGGAAACG 57.476 33.333 0.00 0.00 36.65 3.60
36 37 9.466497 TCTCTTGCCTGAGTTATTTTCATAAAT 57.534 29.630 3.51 0.00 35.65 1.40
37 38 8.862325 TCTCTTGCCTGAGTTATTTTCATAAA 57.138 30.769 3.51 0.00 35.68 1.40
38 39 8.862325 TTCTCTTGCCTGAGTTATTTTCATAA 57.138 30.769 3.51 0.00 35.68 1.90
39 40 8.862325 TTTCTCTTGCCTGAGTTATTTTCATA 57.138 30.769 3.51 0.00 35.68 2.15
40 41 7.765695 TTTCTCTTGCCTGAGTTATTTTCAT 57.234 32.000 3.51 0.00 35.68 2.57
41 42 7.255590 CCTTTTCTCTTGCCTGAGTTATTTTCA 60.256 37.037 3.51 0.00 35.68 2.69
42 43 7.040409 TCCTTTTCTCTTGCCTGAGTTATTTTC 60.040 37.037 3.51 0.00 35.68 2.29
43 44 6.777580 TCCTTTTCTCTTGCCTGAGTTATTTT 59.222 34.615 3.51 0.00 35.68 1.82
44 45 6.306987 TCCTTTTCTCTTGCCTGAGTTATTT 58.693 36.000 3.51 0.00 35.68 1.40
45 46 5.880901 TCCTTTTCTCTTGCCTGAGTTATT 58.119 37.500 3.51 0.00 35.68 1.40
46 47 5.505181 TCCTTTTCTCTTGCCTGAGTTAT 57.495 39.130 3.51 0.00 35.68 1.89
47 48 4.974645 TCCTTTTCTCTTGCCTGAGTTA 57.025 40.909 3.51 0.00 35.68 2.24
48 49 3.864789 TCCTTTTCTCTTGCCTGAGTT 57.135 42.857 3.51 0.00 35.68 3.01
49 50 3.392616 TCTTCCTTTTCTCTTGCCTGAGT 59.607 43.478 3.51 0.00 35.68 3.41
50 51 4.013267 TCTTCCTTTTCTCTTGCCTGAG 57.987 45.455 0.00 0.00 35.52 3.35
51 52 4.042062 TGATCTTCCTTTTCTCTTGCCTGA 59.958 41.667 0.00 0.00 0.00 3.86
52 53 4.330250 TGATCTTCCTTTTCTCTTGCCTG 58.670 43.478 0.00 0.00 0.00 4.85
53 54 4.647564 TGATCTTCCTTTTCTCTTGCCT 57.352 40.909 0.00 0.00 0.00 4.75
54 55 5.184671 ACATTGATCTTCCTTTTCTCTTGCC 59.815 40.000 0.00 0.00 0.00 4.52
55 56 6.072286 TCACATTGATCTTCCTTTTCTCTTGC 60.072 38.462 0.00 0.00 0.00 4.01
56 57 7.389884 TCTCACATTGATCTTCCTTTTCTCTTG 59.610 37.037 0.00 0.00 0.00 3.02
57 58 7.456725 TCTCACATTGATCTTCCTTTTCTCTT 58.543 34.615 0.00 0.00 0.00 2.85
58 59 7.013823 TCTCACATTGATCTTCCTTTTCTCT 57.986 36.000 0.00 0.00 0.00 3.10
59 60 6.878389 ACTCTCACATTGATCTTCCTTTTCTC 59.122 38.462 0.00 0.00 0.00 2.87
60 61 6.654161 CACTCTCACATTGATCTTCCTTTTCT 59.346 38.462 0.00 0.00 0.00 2.52
61 62 6.128063 CCACTCTCACATTGATCTTCCTTTTC 60.128 42.308 0.00 0.00 0.00 2.29
109 114 0.820871 ATGCTCCTCTCTTCGTGGTC 59.179 55.000 0.00 0.00 0.00 4.02
141 166 6.742559 TCTACAAGACTACAACCTTTCCTT 57.257 37.500 0.00 0.00 0.00 3.36
144 169 7.273815 CGAGAATCTACAAGACTACAACCTTTC 59.726 40.741 0.00 0.00 0.00 2.62
229 254 1.822613 TACTCCTGCCGGCTAGACG 60.823 63.158 29.70 12.22 0.00 4.18
230 255 1.734748 GTACTCCTGCCGGCTAGAC 59.265 63.158 29.70 16.44 0.00 2.59
231 256 1.822613 CGTACTCCTGCCGGCTAGA 60.823 63.158 29.70 22.22 0.00 2.43
232 257 1.822613 TCGTACTCCTGCCGGCTAG 60.823 63.158 29.70 23.14 0.00 3.42
233 258 2.117156 GTCGTACTCCTGCCGGCTA 61.117 63.158 29.70 13.31 0.00 3.93
248 273 1.674322 AAGGGTGAATTGGCCGTCG 60.674 57.895 0.00 0.00 0.00 5.12
277 307 0.947244 GTGGCTGGAACTTGTGACAG 59.053 55.000 0.00 0.00 0.00 3.51
301 331 4.733405 GCGATAGTTTATTTTTCTTGGCGG 59.267 41.667 0.00 0.00 39.35 6.13
308 338 8.234546 TCTTTGACTGGCGATAGTTTATTTTTC 58.765 33.333 0.00 0.00 39.35 2.29
314 344 5.357257 GGATCTTTGACTGGCGATAGTTTA 58.643 41.667 0.00 0.00 39.35 2.01
317 347 2.103263 GGGATCTTTGACTGGCGATAGT 59.897 50.000 0.00 0.00 39.35 2.12
318 348 2.548920 GGGGATCTTTGACTGGCGATAG 60.549 54.545 0.00 0.00 0.00 2.08
319 349 1.416401 GGGGATCTTTGACTGGCGATA 59.584 52.381 0.00 0.00 0.00 2.92
322 352 1.815421 CGGGGATCTTTGACTGGCG 60.815 63.158 0.00 0.00 0.00 5.69
410 488 1.604147 ATCGCTGGTCACGATCCACA 61.604 55.000 0.00 0.00 46.80 4.17
456 534 7.984391 TGCGATATTCTTCTTCTTAATTTGCA 58.016 30.769 0.00 0.00 0.00 4.08
694 787 1.357334 GATCGACCGGAGAGTGAGC 59.643 63.158 9.46 0.00 0.00 4.26
850 967 2.210013 TGCGGACTTGTGGAGCTCT 61.210 57.895 14.64 0.00 0.00 4.09
851 968 2.029844 GTGCGGACTTGTGGAGCTC 61.030 63.158 4.71 4.71 0.00 4.09
901 1029 5.776173 TCTTGGACTTATCAGCTAGTAGC 57.224 43.478 14.62 14.62 42.84 3.58
902 1030 7.341445 ACTTCTTGGACTTATCAGCTAGTAG 57.659 40.000 0.00 0.00 0.00 2.57
903 1031 6.321690 GGACTTCTTGGACTTATCAGCTAGTA 59.678 42.308 0.00 0.00 0.00 1.82
904 1032 5.128008 GGACTTCTTGGACTTATCAGCTAGT 59.872 44.000 0.00 0.00 0.00 2.57
905 1033 5.127845 TGGACTTCTTGGACTTATCAGCTAG 59.872 44.000 0.00 0.00 0.00 3.42
906 1034 5.023452 TGGACTTCTTGGACTTATCAGCTA 58.977 41.667 0.00 0.00 0.00 3.32
907 1035 3.840666 TGGACTTCTTGGACTTATCAGCT 59.159 43.478 0.00 0.00 0.00 4.24
908 1036 4.207891 TGGACTTCTTGGACTTATCAGC 57.792 45.455 0.00 0.00 0.00 4.26
909 1037 4.633565 GCTTGGACTTCTTGGACTTATCAG 59.366 45.833 0.00 0.00 0.00 2.90
910 1038 4.287067 AGCTTGGACTTCTTGGACTTATCA 59.713 41.667 0.00 0.00 0.00 2.15
957 1085 2.959357 GAACTCTGCAGGCACGCAC 61.959 63.158 15.13 0.00 36.86 5.34
958 1086 2.666190 GAACTCTGCAGGCACGCA 60.666 61.111 15.13 1.53 40.32 5.24
965 1097 3.997064 CTCCCCGCGAACTCTGCAG 62.997 68.421 8.23 7.63 0.00 4.41
980 1112 2.448453 TCGGTTCTCTCCTTCTTCTCC 58.552 52.381 0.00 0.00 0.00 3.71
982 1114 2.763448 CCATCGGTTCTCTCCTTCTTCT 59.237 50.000 0.00 0.00 0.00 2.85
987 1119 1.908483 GGCCATCGGTTCTCTCCTT 59.092 57.895 0.00 0.00 0.00 3.36
988 1120 2.427245 CGGCCATCGGTTCTCTCCT 61.427 63.158 2.24 0.00 34.75 3.69
989 1121 2.107141 CGGCCATCGGTTCTCTCC 59.893 66.667 2.24 0.00 34.75 3.71
990 1122 2.586357 GCGGCCATCGGTTCTCTC 60.586 66.667 2.24 0.00 39.69 3.20
991 1123 4.514577 CGCGGCCATCGGTTCTCT 62.515 66.667 2.24 0.00 39.69 3.10
1030 1167 1.913762 CCCTCTCCACCTGGTTCGT 60.914 63.158 0.00 0.00 36.34 3.85
1332 1469 3.691342 TCTCCACCGTCGCCCTTG 61.691 66.667 0.00 0.00 0.00 3.61
1636 1787 2.272471 GCTTACAGGTGGGGCCTC 59.728 66.667 0.84 0.00 46.96 4.70
1670 1821 2.966309 GACGGGCTTTCTTGCGGTG 61.966 63.158 0.00 0.00 0.00 4.94
1690 1841 4.646945 TCATTTGGCTCTGTTGTTAAACCA 59.353 37.500 0.00 0.00 35.25 3.67
1881 2032 3.365535 CCTTTGGGGGCTTGAACG 58.634 61.111 0.00 0.00 0.00 3.95
1891 2042 1.675641 CGCTGTCCTTCCCTTTGGG 60.676 63.158 0.00 0.00 46.11 4.12
1929 2080 6.970043 GCTACAATACTCTTGGCGATAGATAG 59.030 42.308 0.00 0.00 39.76 2.08
1931 2082 5.243954 TGCTACAATACTCTTGGCGATAGAT 59.756 40.000 0.00 0.00 39.76 1.98
1932 2083 4.583073 TGCTACAATACTCTTGGCGATAGA 59.417 41.667 0.00 0.00 39.76 1.98
1933 2084 4.681942 GTGCTACAATACTCTTGGCGATAG 59.318 45.833 0.00 0.00 0.00 2.08
1935 2086 3.458189 GTGCTACAATACTCTTGGCGAT 58.542 45.455 0.00 0.00 0.00 4.58
1936 2087 2.418197 GGTGCTACAATACTCTTGGCGA 60.418 50.000 0.00 0.00 0.00 5.54
1937 2088 1.933853 GGTGCTACAATACTCTTGGCG 59.066 52.381 0.00 0.00 0.00 5.69
1942 2093 3.090037 AGTGACGGTGCTACAATACTCT 58.910 45.455 0.00 0.00 0.00 3.24
1954 2105 3.467119 GCGTACGCAGTGACGGTG 61.467 66.667 33.90 0.00 45.73 4.94
1994 2145 1.802960 CACATCGAGATGCCATTAGCC 59.197 52.381 12.54 0.00 42.39 3.93
2020 2171 1.130561 GGCGATCAGTGCTGTTAAACC 59.869 52.381 0.00 0.00 0.00 3.27
2036 2187 4.019141 TCCTGGGACTTAAATTAAAGGCGA 60.019 41.667 0.00 0.00 35.13 5.54
2037 2188 4.266714 TCCTGGGACTTAAATTAAAGGCG 58.733 43.478 0.00 0.00 35.13 5.52
2038 2189 6.129874 AGATCCTGGGACTTAAATTAAAGGC 58.870 40.000 0.00 0.00 33.39 4.35
2039 2190 9.508642 GATAGATCCTGGGACTTAAATTAAAGG 57.491 37.037 0.00 0.00 0.00 3.11
2042 2193 8.157476 GCAGATAGATCCTGGGACTTAAATTAA 58.843 37.037 0.00 0.00 32.51 1.40
2043 2194 7.514127 AGCAGATAGATCCTGGGACTTAAATTA 59.486 37.037 0.00 0.00 32.51 1.40
2044 2195 6.331307 AGCAGATAGATCCTGGGACTTAAATT 59.669 38.462 0.00 0.00 32.51 1.82
2045 2196 5.848921 AGCAGATAGATCCTGGGACTTAAAT 59.151 40.000 0.00 0.00 32.51 1.40
2135 2295 5.864474 GGCTCCATTAGTCATTAGATACACG 59.136 44.000 0.00 0.00 0.00 4.49
2137 2297 5.566826 GCGGCTCCATTAGTCATTAGATACA 60.567 44.000 0.00 0.00 0.00 2.29
2138 2298 4.865365 GCGGCTCCATTAGTCATTAGATAC 59.135 45.833 0.00 0.00 0.00 2.24
2183 2343 2.358737 GGTGAGGTGTTGCTCGGG 60.359 66.667 0.00 0.00 0.00 5.14
2268 2436 4.107622 TCGCACTAATTTTAGTCGCCTAC 58.892 43.478 13.97 0.00 41.82 3.18
2330 2503 1.799383 GCAAGAAGCACAGCTAGCC 59.201 57.895 12.13 0.00 44.79 3.93
2374 2547 1.274167 ACCCAAACAGCATTGCTCATG 59.726 47.619 8.54 7.91 36.40 3.07
2375 2548 1.636148 ACCCAAACAGCATTGCTCAT 58.364 45.000 8.54 0.00 36.40 2.90
2376 2549 1.068895 CAACCCAAACAGCATTGCTCA 59.931 47.619 8.54 0.00 36.40 4.26
2415 2593 2.095853 GCCACTGGTGTTCATGATAACG 59.904 50.000 0.00 0.00 31.76 3.18
2449 2627 3.269178 CAGAAAGATCCAAGAGTGCTCC 58.731 50.000 0.00 0.00 0.00 4.70
2458 2636 0.392998 GCCGCTCCAGAAAGATCCAA 60.393 55.000 0.00 0.00 0.00 3.53
2468 2646 1.815421 ACTAATTGCGCCGCTCCAG 60.815 57.895 11.67 4.84 0.00 3.86
2470 2648 2.709475 CACTAATTGCGCCGCTCC 59.291 61.111 11.67 0.00 0.00 4.70
2530 2708 6.077838 GGCAAACTAATATAGCATTGCGTAC 58.922 40.000 15.97 0.00 45.38 3.67


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

AutoCloner maintained by Alex Coulton.