Multiple sequence alignment - TraesCS1D01G171100

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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 TraesCS1D01G171100 chr1D 100.000 2132 0 0 1 2132 244481858 244483989 0.000000e+00 3938
1 TraesCS1D01G171100 chr1D 92.416 2057 105 31 120 2132 254500106 254498057 0.000000e+00 2887
2 TraesCS1D01G171100 chr1D 98.667 150 2 0 1 150 33225446 33225297 1.250000e-67 267
3 TraesCS1D01G171100 chr1D 96.203 158 5 1 1 157 125476092 125476249 7.550000e-65 257
4 TraesCS1D01G171100 chr5D 93.097 2028 90 30 120 2104 560874576 560872556 0.000000e+00 2924
5 TraesCS1D01G171100 chr5D 92.562 2057 100 26 120 2132 6199174 6201221 0.000000e+00 2902
6 TraesCS1D01G171100 chr5D 92.364 2056 104 34 120 2132 329164282 329162237 0.000000e+00 2878
7 TraesCS1D01G171100 chr5D 98.039 153 2 1 1 152 242862383 242862231 4.510000e-67 265
8 TraesCS1D01G171100 chr5D 99.315 146 1 0 2 147 500770261 500770116 4.510000e-67 265
9 TraesCS1D01G171100 chr5D 96.795 156 3 2 1 154 474680441 474680596 2.100000e-65 259
10 TraesCS1D01G171100 chr1A 91.870 2054 115 31 120 2132 168448465 168450507 0.000000e+00 2820
11 TraesCS1D01G171100 chr4D 91.334 2054 127 29 120 2131 19918600 19916556 0.000000e+00 2760
12 TraesCS1D01G171100 chr7A 90.940 2053 140 27 120 2132 352191918 352193964 0.000000e+00 2719
13 TraesCS1D01G171100 chr6B 93.460 1422 79 10 723 2132 22427423 22426004 0.000000e+00 2098
14 TraesCS1D01G171100 chr3D 95.390 1063 45 4 1072 2132 21905747 21904687 0.000000e+00 1688
15 TraesCS1D01G171100 chr3D 89.560 364 26 6 685 1037 10747953 10748315 3.230000e-123 451
16 TraesCS1D01G171100 chr3D 95.652 161 6 1 1 160 477769065 477768905 7.550000e-65 257
17 TraesCS1D01G171100 chr3B 91.344 1213 59 25 120 1291 201516787 201515580 0.000000e+00 1616
18 TraesCS1D01G171100 chr3B 93.112 813 44 6 685 1486 201515155 201514344 0.000000e+00 1181
19 TraesCS1D01G171100 chrUn 93.662 994 51 8 685 1667 445811546 445812538 0.000000e+00 1476
20 TraesCS1D01G171100 chrUn 88.792 687 42 15 610 1263 30305738 30306422 0.000000e+00 809
21 TraesCS1D01G171100 chr7B 92.226 566 32 10 129 685 102631530 102632092 0.000000e+00 791
22 TraesCS1D01G171100 chr7B 93.976 166 8 2 1 164 731263193 731263028 1.260000e-62 250
23 TraesCS1D01G171100 chr2A 88.492 252 7 8 535 764 677893170 677892919 3.460000e-73 285
24 TraesCS1D01G171100 chr2D 98.658 149 1 1 1 149 175700486 175700633 1.620000e-66 263
25 TraesCS1D01G171100 chr6D 99.296 142 1 0 1 142 169862055 169862196 7.550000e-65 257
26 TraesCS1D01G171100 chr5B 86.636 217 6 9 570 764 185297045 185297260 3.560000e-53 219


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 TraesCS1D01G171100 chr1D 244481858 244483989 2131 False 3938.0 3938 100.000 1 2132 1 chr1D.!!$F2 2131
1 TraesCS1D01G171100 chr1D 254498057 254500106 2049 True 2887.0 2887 92.416 120 2132 1 chr1D.!!$R2 2012
2 TraesCS1D01G171100 chr5D 560872556 560874576 2020 True 2924.0 2924 93.097 120 2104 1 chr5D.!!$R4 1984
3 TraesCS1D01G171100 chr5D 6199174 6201221 2047 False 2902.0 2902 92.562 120 2132 1 chr5D.!!$F1 2012
4 TraesCS1D01G171100 chr5D 329162237 329164282 2045 True 2878.0 2878 92.364 120 2132 1 chr5D.!!$R2 2012
5 TraesCS1D01G171100 chr1A 168448465 168450507 2042 False 2820.0 2820 91.870 120 2132 1 chr1A.!!$F1 2012
6 TraesCS1D01G171100 chr4D 19916556 19918600 2044 True 2760.0 2760 91.334 120 2131 1 chr4D.!!$R1 2011
7 TraesCS1D01G171100 chr7A 352191918 352193964 2046 False 2719.0 2719 90.940 120 2132 1 chr7A.!!$F1 2012
8 TraesCS1D01G171100 chr6B 22426004 22427423 1419 True 2098.0 2098 93.460 723 2132 1 chr6B.!!$R1 1409
9 TraesCS1D01G171100 chr3D 21904687 21905747 1060 True 1688.0 1688 95.390 1072 2132 1 chr3D.!!$R1 1060
10 TraesCS1D01G171100 chr3B 201514344 201516787 2443 True 1398.5 1616 92.228 120 1486 2 chr3B.!!$R1 1366
11 TraesCS1D01G171100 chrUn 445811546 445812538 992 False 1476.0 1476 93.662 685 1667 1 chrUn.!!$F2 982
12 TraesCS1D01G171100 chrUn 30305738 30306422 684 False 809.0 809 88.792 610 1263 1 chrUn.!!$F1 653
13 TraesCS1D01G171100 chr7B 102631530 102632092 562 False 791.0 791 92.226 129 685 1 chr7B.!!$F1 556

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
31 32 0.043334 AGTAGGAGCCCACCACATCT 59.957 55.0 0.0 0.0 0.0 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1634 2721 0.75906 GCAGTCCAAGGGGTTGGTTT 60.759 55.0 4.14 0.0 42.62 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
22 23 4.755266 TTTGTCATAGAAGTAGGAGCCC 57.245 45.455 0.00 0.00 0.00 5.19
23 24 3.398318 TGTCATAGAAGTAGGAGCCCA 57.602 47.619 0.00 0.00 0.00 5.36
24 25 3.031736 TGTCATAGAAGTAGGAGCCCAC 58.968 50.000 0.00 0.00 0.00 4.61
25 26 2.365941 GTCATAGAAGTAGGAGCCCACC 59.634 54.545 0.00 0.00 0.00 4.61
26 27 2.023404 TCATAGAAGTAGGAGCCCACCA 60.023 50.000 0.00 0.00 0.00 4.17
27 28 1.861982 TAGAAGTAGGAGCCCACCAC 58.138 55.000 0.00 0.00 0.00 4.16
28 29 0.178903 AGAAGTAGGAGCCCACCACA 60.179 55.000 0.00 0.00 0.00 4.17
29 30 0.912486 GAAGTAGGAGCCCACCACAT 59.088 55.000 0.00 0.00 0.00 3.21
30 31 0.912486 AAGTAGGAGCCCACCACATC 59.088 55.000 0.00 0.00 0.00 3.06
31 32 0.043334 AGTAGGAGCCCACCACATCT 59.957 55.000 0.00 0.00 0.00 2.90
32 33 1.291033 AGTAGGAGCCCACCACATCTA 59.709 52.381 0.00 0.00 0.00 1.98
33 34 2.090494 AGTAGGAGCCCACCACATCTAT 60.090 50.000 0.00 0.00 0.00 1.98
34 35 1.135094 AGGAGCCCACCACATCTATG 58.865 55.000 0.00 0.00 0.00 2.23
35 36 1.131638 GGAGCCCACCACATCTATGA 58.868 55.000 0.00 0.00 0.00 2.15
36 37 1.701847 GGAGCCCACCACATCTATGAT 59.298 52.381 0.00 0.00 0.00 2.45
37 38 2.551721 GGAGCCCACCACATCTATGATG 60.552 54.545 6.06 6.06 0.00 3.07
38 39 2.369860 GAGCCCACCACATCTATGATGA 59.630 50.000 13.63 0.00 0.00 2.92
39 40 2.984604 AGCCCACCACATCTATGATGAT 59.015 45.455 13.63 0.00 0.00 2.45
40 41 4.170449 AGCCCACCACATCTATGATGATA 58.830 43.478 13.63 0.00 0.00 2.15
41 42 4.019860 AGCCCACCACATCTATGATGATAC 60.020 45.833 13.63 0.00 0.00 2.24
42 43 4.836825 CCCACCACATCTATGATGATACC 58.163 47.826 13.63 0.00 0.00 2.73
43 44 4.498241 CCACCACATCTATGATGATACCG 58.502 47.826 13.63 0.06 0.00 4.02
44 45 4.498241 CACCACATCTATGATGATACCGG 58.502 47.826 13.63 0.00 0.00 5.28
45 46 3.515502 ACCACATCTATGATGATACCGGG 59.484 47.826 6.32 0.00 0.00 5.73
46 47 3.515502 CCACATCTATGATGATACCGGGT 59.484 47.826 6.32 4.46 0.00 5.28
47 48 4.020218 CCACATCTATGATGATACCGGGTT 60.020 45.833 4.31 0.00 0.00 4.11
48 49 5.513094 CCACATCTATGATGATACCGGGTTT 60.513 44.000 4.31 0.00 0.00 3.27
49 50 5.997746 CACATCTATGATGATACCGGGTTTT 59.002 40.000 4.31 0.00 0.00 2.43
50 51 5.997746 ACATCTATGATGATACCGGGTTTTG 59.002 40.000 4.31 0.00 0.00 2.44
51 52 5.623956 TCTATGATGATACCGGGTTTTGT 57.376 39.130 4.31 0.00 0.00 2.83
52 53 5.607477 TCTATGATGATACCGGGTTTTGTC 58.393 41.667 4.31 0.82 0.00 3.18
53 54 3.704800 TGATGATACCGGGTTTTGTCA 57.295 42.857 4.31 5.88 0.00 3.58
54 55 3.340034 TGATGATACCGGGTTTTGTCAC 58.660 45.455 4.31 2.17 0.00 3.67
55 56 2.932855 TGATACCGGGTTTTGTCACA 57.067 45.000 4.31 0.00 0.00 3.58
56 57 3.210232 TGATACCGGGTTTTGTCACAA 57.790 42.857 4.31 0.00 0.00 3.33
57 58 3.757270 TGATACCGGGTTTTGTCACAAT 58.243 40.909 4.31 0.00 0.00 2.71
58 59 4.145807 TGATACCGGGTTTTGTCACAATT 58.854 39.130 4.31 0.00 0.00 2.32
59 60 5.314529 TGATACCGGGTTTTGTCACAATTA 58.685 37.500 4.31 0.00 0.00 1.40
60 61 5.946972 TGATACCGGGTTTTGTCACAATTAT 59.053 36.000 4.31 0.00 0.00 1.28
61 62 4.776795 ACCGGGTTTTGTCACAATTATC 57.223 40.909 6.32 0.00 0.00 1.75
62 63 3.189702 ACCGGGTTTTGTCACAATTATCG 59.810 43.478 6.32 0.00 0.00 2.92
63 64 3.189702 CCGGGTTTTGTCACAATTATCGT 59.810 43.478 0.00 0.00 0.00 3.73
64 65 4.399978 CGGGTTTTGTCACAATTATCGTC 58.600 43.478 0.00 0.00 0.00 4.20
65 66 4.083749 CGGGTTTTGTCACAATTATCGTCA 60.084 41.667 0.00 0.00 0.00 4.35
66 67 5.391523 CGGGTTTTGTCACAATTATCGTCAT 60.392 40.000 0.00 0.00 0.00 3.06
67 68 6.183360 CGGGTTTTGTCACAATTATCGTCATA 60.183 38.462 0.00 0.00 0.00 2.15
68 69 7.186804 GGGTTTTGTCACAATTATCGTCATAG 58.813 38.462 0.00 0.00 0.00 2.23
69 70 7.065324 GGGTTTTGTCACAATTATCGTCATAGA 59.935 37.037 0.00 0.00 0.00 1.98
70 71 8.447833 GGTTTTGTCACAATTATCGTCATAGAA 58.552 33.333 0.00 0.00 0.00 2.10
71 72 9.478019 GTTTTGTCACAATTATCGTCATAGAAG 57.522 33.333 0.00 0.00 0.00 2.85
72 73 8.771920 TTTGTCACAATTATCGTCATAGAAGT 57.228 30.769 0.00 0.00 0.00 3.01
73 74 7.755582 TGTCACAATTATCGTCATAGAAGTG 57.244 36.000 0.00 0.00 0.00 3.16
74 75 7.320399 TGTCACAATTATCGTCATAGAAGTGT 58.680 34.615 0.00 0.00 0.00 3.55
75 76 7.488150 TGTCACAATTATCGTCATAGAAGTGTC 59.512 37.037 0.00 0.00 0.00 3.67
76 77 7.488150 GTCACAATTATCGTCATAGAAGTGTCA 59.512 37.037 0.00 0.00 0.00 3.58
77 78 8.197439 TCACAATTATCGTCATAGAAGTGTCAT 58.803 33.333 0.00 0.00 0.00 3.06
78 79 9.463443 CACAATTATCGTCATAGAAGTGTCATA 57.537 33.333 0.00 0.00 0.00 2.15
85 86 8.391075 TCGTCATAGAAGTGTCATATGTATGA 57.609 34.615 1.90 4.48 40.19 2.15
110 111 2.892784 AAAAATTTCGTTCGCCCCAA 57.107 40.000 0.00 0.00 0.00 4.12
111 112 2.892784 AAAATTTCGTTCGCCCCAAA 57.107 40.000 0.00 0.00 0.00 3.28
112 113 2.892784 AAATTTCGTTCGCCCCAAAA 57.107 40.000 0.00 0.00 0.00 2.44
113 114 3.394674 AAATTTCGTTCGCCCCAAAAT 57.605 38.095 0.00 0.00 0.00 1.82
114 115 2.362169 ATTTCGTTCGCCCCAAAATG 57.638 45.000 0.00 0.00 0.00 2.32
115 116 1.033574 TTTCGTTCGCCCCAAAATGT 58.966 45.000 0.00 0.00 0.00 2.71
116 117 0.594110 TTCGTTCGCCCCAAAATGTC 59.406 50.000 0.00 0.00 0.00 3.06
117 118 0.535328 TCGTTCGCCCCAAAATGTCA 60.535 50.000 0.00 0.00 0.00 3.58
118 119 0.386731 CGTTCGCCCCAAAATGTCAC 60.387 55.000 0.00 0.00 0.00 3.67
119 120 0.386731 GTTCGCCCCAAAATGTCACG 60.387 55.000 0.00 0.00 0.00 4.35
120 121 1.519751 TTCGCCCCAAAATGTCACGG 61.520 55.000 0.00 0.00 0.00 4.94
121 122 1.969064 CGCCCCAAAATGTCACGGA 60.969 57.895 0.00 0.00 0.00 4.69
122 123 1.312371 CGCCCCAAAATGTCACGGAT 61.312 55.000 0.00 0.00 0.00 4.18
123 124 0.173255 GCCCCAAAATGTCACGGATG 59.827 55.000 0.00 0.00 0.00 3.51
124 125 1.544724 CCCCAAAATGTCACGGATGT 58.455 50.000 0.00 0.00 0.00 3.06
126 127 1.885887 CCCAAAATGTCACGGATGTGT 59.114 47.619 0.00 0.00 46.49 3.72
127 128 2.095263 CCCAAAATGTCACGGATGTGTC 60.095 50.000 0.00 0.00 46.49 3.67
128 129 2.813754 CCAAAATGTCACGGATGTGTCT 59.186 45.455 0.00 0.00 46.49 3.41
129 130 3.253188 CCAAAATGTCACGGATGTGTCTT 59.747 43.478 0.00 0.00 46.49 3.01
130 131 4.261572 CCAAAATGTCACGGATGTGTCTTT 60.262 41.667 0.00 0.00 46.49 2.52
131 132 5.280945 CAAAATGTCACGGATGTGTCTTTT 58.719 37.500 0.00 0.00 46.49 2.27
132 133 5.514274 AAATGTCACGGATGTGTCTTTTT 57.486 34.783 0.00 0.00 46.49 1.94
245 246 5.127031 AGTCTCAAGCTAAACAAAAGGCAAA 59.873 36.000 0.00 0.00 0.00 3.68
288 289 9.467258 AACCGCTTGATAATCATTTATTGAATG 57.533 29.630 0.00 0.00 45.31 2.67
305 306 4.744570 TGAATGAGTGTAATGACTCGACC 58.255 43.478 0.00 0.00 44.68 4.79
398 405 6.787085 AGAACTACTTGAATTTTCCAGTCG 57.213 37.500 0.74 0.00 35.19 4.18
552 562 9.384764 GCCCTTTCTATGTATTATCAATAGGAC 57.615 37.037 0.00 0.00 0.00 3.85
572 582 4.084013 GGACCAATTCTAACAAGTCACACG 60.084 45.833 0.00 0.00 0.00 4.49
587 597 2.101415 TCACACGCTCATATTCCAGAGG 59.899 50.000 0.00 0.00 32.54 3.69
708 740 6.720288 TCCTAATTGGTTAAAATTCCGTCCAA 59.280 34.615 0.00 0.00 38.90 3.53
767 1841 8.928270 AGATAGGAATATAGCGAATAAAACGG 57.072 34.615 0.00 0.00 0.00 4.44
768 1842 8.746530 AGATAGGAATATAGCGAATAAAACGGA 58.253 33.333 0.00 0.00 0.00 4.69
769 1843 9.362539 GATAGGAATATAGCGAATAAAACGGAA 57.637 33.333 0.00 0.00 0.00 4.30
771 1845 7.439381 AGGAATATAGCGAATAAAACGGAAGA 58.561 34.615 0.00 0.00 0.00 2.87
772 1846 7.929785 AGGAATATAGCGAATAAAACGGAAGAA 59.070 33.333 0.00 0.00 0.00 2.52
773 1847 8.718734 GGAATATAGCGAATAAAACGGAAGAAT 58.281 33.333 0.00 0.00 0.00 2.40
786 1860 8.973835 AAAACGGAAGAATTATAATTTCGCAA 57.026 26.923 11.92 0.00 0.00 4.85
787 1861 9.581099 AAAACGGAAGAATTATAATTTCGCAAT 57.419 25.926 11.92 3.39 0.00 3.56
800 1884 2.438795 GCAATAACCCGGGGCGAA 60.439 61.111 27.92 7.17 0.00 4.70
841 1925 6.999705 TCAAGGGTTTCAGTAAACTACCTA 57.000 37.500 0.00 0.00 43.76 3.08
847 1931 6.470278 GGTTTCAGTAAACTACCTACACCAT 58.530 40.000 0.00 0.00 43.76 3.55
888 1972 6.476243 TTAGAACTATCTTCAACGGTTTGC 57.524 37.500 0.00 0.00 37.10 3.68
889 1973 4.385825 AGAACTATCTTCAACGGTTTGCA 58.614 39.130 0.00 0.00 29.15 4.08
895 1979 1.812571 CTTCAACGGTTTGCATAGCCT 59.187 47.619 0.62 0.00 32.17 4.58
940 2024 8.773404 AGTGTTGACTTTGTATACTATTCCAC 57.227 34.615 4.17 1.85 0.00 4.02
977 2061 6.910536 ACACGATCTTTTTGTAGATCCATC 57.089 37.500 7.77 0.00 45.00 3.51
1036 2120 6.010850 ACTTTAGTCGCCATCTCCATATCTA 58.989 40.000 0.00 0.00 0.00 1.98
1107 2191 5.106515 GCAACCCTCTCAACAATTAAGAGAC 60.107 44.000 0.31 0.00 39.09 3.36
1121 2205 2.656560 AGAGACCCATTCGAAGAACG 57.343 50.000 3.35 0.00 45.90 3.95
1139 2223 7.148787 CGAAGAACGCAGAGACTAATTTAAGTT 60.149 37.037 0.00 0.00 34.51 2.66
1231 2315 4.141688 GGAACCTTAGGTGATTCTCGGAAT 60.142 45.833 3.99 0.00 35.34 3.01
1302 2388 8.567948 CGTATAAACCAATGCTTCCATAGATTT 58.432 33.333 0.00 0.00 0.00 2.17
1404 2491 5.252630 AGAAGAGTCAAAGAAAGGATGGGAT 59.747 40.000 0.00 0.00 0.00 3.85
1471 2558 5.420725 AACAATGTGTATCTGACTGCCTA 57.579 39.130 0.00 0.00 0.00 3.93
1479 2566 6.382859 TGTGTATCTGACTGCCTATTTCCTTA 59.617 38.462 0.00 0.00 0.00 2.69
1502 2589 4.453480 AGTTGGATCTCCCACTTTTTGA 57.547 40.909 0.00 0.00 46.62 2.69
1521 2608 7.784633 TTTTGAAATGTTCCAAATTCCACTC 57.215 32.000 0.00 0.00 33.00 3.51
1534 2621 2.787473 TCCACTCGAGCATCCAAATT 57.213 45.000 13.61 0.00 0.00 1.82
1561 2648 7.828717 TGGATCAATACTAGCAAAAACATCTCA 59.171 33.333 0.00 0.00 0.00 3.27
1634 2721 4.217550 GCAAAGGTAGCATGACCAAAAGTA 59.782 41.667 6.37 0.00 42.47 2.24
1701 2788 5.112129 AGTAGCCCGGTCTAATTCAAAAT 57.888 39.130 0.00 0.00 0.00 1.82
1722 2809 3.713826 TTTCCCCTAATTGAGAACGCT 57.286 42.857 0.00 0.00 0.00 5.07
1723 2810 2.981859 TCCCCTAATTGAGAACGCTC 57.018 50.000 0.00 0.00 41.67 5.03
1791 2879 1.207329 GTTCGCCACCATAGAACTCCT 59.793 52.381 0.88 0.00 40.57 3.69
1794 2882 1.204146 GCCACCATAGAACTCCTCCA 58.796 55.000 0.00 0.00 0.00 3.86
1798 2886 4.042187 GCCACCATAGAACTCCTCCATTAT 59.958 45.833 0.00 0.00 0.00 1.28
1876 2964 6.518200 GCTCTAACAATTCCCTCCTCATCTAG 60.518 46.154 0.00 0.00 0.00 2.43
1886 2974 4.566488 CCCTCCTCATCTAGCAAAACAACT 60.566 45.833 0.00 0.00 0.00 3.16
2022 3111 2.371510 GAGCCTGCTCTGAATAATCCCT 59.628 50.000 11.82 0.00 39.80 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.534500 TGGGCTCCTACTTCTATGACAAAA 59.466 41.667 0.00 0.00 0.00 2.44
1 2 4.081087 GTGGGCTCCTACTTCTATGACAAA 60.081 45.833 0.00 0.00 0.00 2.83
2 3 3.451178 GTGGGCTCCTACTTCTATGACAA 59.549 47.826 0.00 0.00 0.00 3.18
4 5 2.365941 GGTGGGCTCCTACTTCTATGAC 59.634 54.545 2.46 0.00 0.00 3.06
6 7 2.103263 GTGGTGGGCTCCTACTTCTATG 59.897 54.545 2.46 0.00 0.00 2.23
7 8 2.292918 TGTGGTGGGCTCCTACTTCTAT 60.293 50.000 2.46 0.00 0.00 1.98
9 10 0.178903 TGTGGTGGGCTCCTACTTCT 60.179 55.000 2.46 0.00 0.00 2.85
10 11 0.912486 ATGTGGTGGGCTCCTACTTC 59.088 55.000 2.46 0.00 0.00 3.01
11 12 0.912486 GATGTGGTGGGCTCCTACTT 59.088 55.000 2.46 0.00 0.00 2.24
12 13 0.043334 AGATGTGGTGGGCTCCTACT 59.957 55.000 2.46 0.00 0.00 2.57
13 14 1.789523 TAGATGTGGTGGGCTCCTAC 58.210 55.000 0.00 0.00 0.00 3.18
14 15 2.090775 TCATAGATGTGGTGGGCTCCTA 60.091 50.000 0.00 0.00 0.00 2.94
15 16 1.135094 CATAGATGTGGTGGGCTCCT 58.865 55.000 0.00 0.00 0.00 3.69
17 18 2.369860 TCATCATAGATGTGGTGGGCTC 59.630 50.000 6.86 0.00 0.00 4.70
19 20 2.936919 TCATCATAGATGTGGTGGGC 57.063 50.000 6.86 0.00 0.00 5.36
20 21 4.621510 CGGTATCATCATAGATGTGGTGGG 60.622 50.000 6.86 0.00 0.00 4.61
21 22 4.498241 CGGTATCATCATAGATGTGGTGG 58.502 47.826 6.86 0.00 0.00 4.61
22 23 4.498241 CCGGTATCATCATAGATGTGGTG 58.502 47.826 6.86 0.00 0.00 4.17
23 24 3.515502 CCCGGTATCATCATAGATGTGGT 59.484 47.826 0.00 0.00 0.00 4.16
24 25 3.515502 ACCCGGTATCATCATAGATGTGG 59.484 47.826 0.00 3.53 0.00 4.17
25 26 4.808414 ACCCGGTATCATCATAGATGTG 57.192 45.455 0.00 0.00 0.00 3.21
26 27 5.825593 AAACCCGGTATCATCATAGATGT 57.174 39.130 0.00 0.00 0.00 3.06
27 28 5.997746 ACAAAACCCGGTATCATCATAGATG 59.002 40.000 0.00 0.62 0.00 2.90
28 29 6.183361 TGACAAAACCCGGTATCATCATAGAT 60.183 38.462 0.00 0.00 0.00 1.98
29 30 5.129650 TGACAAAACCCGGTATCATCATAGA 59.870 40.000 0.00 0.00 0.00 1.98
30 31 5.236478 GTGACAAAACCCGGTATCATCATAG 59.764 44.000 0.00 0.00 0.00 2.23
31 32 5.120399 GTGACAAAACCCGGTATCATCATA 58.880 41.667 0.00 0.00 0.00 2.15
32 33 3.945285 GTGACAAAACCCGGTATCATCAT 59.055 43.478 0.00 0.00 0.00 2.45
33 34 3.244596 TGTGACAAAACCCGGTATCATCA 60.245 43.478 0.00 0.00 0.00 3.07
34 35 3.340034 TGTGACAAAACCCGGTATCATC 58.660 45.455 0.00 0.00 0.00 2.92
35 36 3.426787 TGTGACAAAACCCGGTATCAT 57.573 42.857 0.00 0.00 0.00 2.45
36 37 2.932855 TGTGACAAAACCCGGTATCA 57.067 45.000 0.00 0.00 0.00 2.15
37 38 4.776795 AATTGTGACAAAACCCGGTATC 57.223 40.909 0.62 0.00 0.00 2.24
38 39 5.065474 CGATAATTGTGACAAAACCCGGTAT 59.935 40.000 0.62 0.00 0.00 2.73
39 40 4.392445 CGATAATTGTGACAAAACCCGGTA 59.608 41.667 0.62 0.00 0.00 4.02
40 41 3.189702 CGATAATTGTGACAAAACCCGGT 59.810 43.478 0.62 0.00 0.00 5.28
41 42 3.189702 ACGATAATTGTGACAAAACCCGG 59.810 43.478 0.62 0.00 0.00 5.73
42 43 4.083749 TGACGATAATTGTGACAAAACCCG 60.084 41.667 0.62 7.01 0.00 5.28
43 44 5.365403 TGACGATAATTGTGACAAAACCC 57.635 39.130 0.62 0.00 0.00 4.11
44 45 7.970384 TCTATGACGATAATTGTGACAAAACC 58.030 34.615 0.62 0.00 0.00 3.27
45 46 9.478019 CTTCTATGACGATAATTGTGACAAAAC 57.522 33.333 0.62 0.00 0.00 2.43
46 47 9.214957 ACTTCTATGACGATAATTGTGACAAAA 57.785 29.630 0.62 0.00 0.00 2.44
47 48 8.655970 CACTTCTATGACGATAATTGTGACAAA 58.344 33.333 0.62 0.00 0.00 2.83
48 49 7.817478 ACACTTCTATGACGATAATTGTGACAA 59.183 33.333 0.00 0.00 0.00 3.18
49 50 7.320399 ACACTTCTATGACGATAATTGTGACA 58.680 34.615 0.00 0.00 0.00 3.58
50 51 7.488150 TGACACTTCTATGACGATAATTGTGAC 59.512 37.037 0.00 0.00 0.00 3.67
51 52 7.543756 TGACACTTCTATGACGATAATTGTGA 58.456 34.615 0.00 0.00 0.00 3.58
52 53 7.755582 TGACACTTCTATGACGATAATTGTG 57.244 36.000 0.00 0.00 0.00 3.33
59 60 9.014297 TCATACATATGACACTTCTATGACGAT 57.986 33.333 10.38 0.00 37.76 3.73
60 61 8.391075 TCATACATATGACACTTCTATGACGA 57.609 34.615 10.38 0.00 37.76 4.20
91 92 2.892784 TTGGGGCGAACGAAATTTTT 57.107 40.000 0.00 0.00 0.00 1.94
92 93 2.892784 TTTGGGGCGAACGAAATTTT 57.107 40.000 0.00 0.00 0.00 1.82
93 94 2.892784 TTTTGGGGCGAACGAAATTT 57.107 40.000 0.00 0.00 0.00 1.82
94 95 2.036604 ACATTTTGGGGCGAACGAAATT 59.963 40.909 0.00 0.00 31.28 1.82
95 96 1.616374 ACATTTTGGGGCGAACGAAAT 59.384 42.857 0.00 0.00 33.33 2.17
96 97 1.001158 GACATTTTGGGGCGAACGAAA 60.001 47.619 0.00 0.00 0.00 3.46
97 98 0.594110 GACATTTTGGGGCGAACGAA 59.406 50.000 0.00 0.00 0.00 3.85
98 99 0.535328 TGACATTTTGGGGCGAACGA 60.535 50.000 0.00 0.00 0.00 3.85
99 100 0.386731 GTGACATTTTGGGGCGAACG 60.387 55.000 0.00 0.00 0.00 3.95
100 101 0.386731 CGTGACATTTTGGGGCGAAC 60.387 55.000 0.00 0.00 0.00 3.95
101 102 1.519751 CCGTGACATTTTGGGGCGAA 61.520 55.000 0.00 0.00 0.00 4.70
102 103 1.969064 CCGTGACATTTTGGGGCGA 60.969 57.895 0.00 0.00 0.00 5.54
103 104 1.312371 ATCCGTGACATTTTGGGGCG 61.312 55.000 0.00 0.00 0.00 6.13
104 105 0.173255 CATCCGTGACATTTTGGGGC 59.827 55.000 0.00 0.00 0.00 5.80
105 106 1.202114 CACATCCGTGACATTTTGGGG 59.798 52.381 0.00 0.00 46.80 4.96
106 107 1.885887 ACACATCCGTGACATTTTGGG 59.114 47.619 0.00 0.00 46.80 4.12
107 108 2.813754 AGACACATCCGTGACATTTTGG 59.186 45.455 0.00 0.00 46.80 3.28
108 109 4.488126 AAGACACATCCGTGACATTTTG 57.512 40.909 0.00 0.00 46.80 2.44
109 110 5.514274 AAAAGACACATCCGTGACATTTT 57.486 34.783 0.00 1.58 46.80 1.82
110 111 5.514274 AAAAAGACACATCCGTGACATTT 57.486 34.783 0.00 0.00 46.80 2.32
288 289 5.704217 GATTTGGTCGAGTCATTACACTC 57.296 43.478 0.00 0.00 39.68 3.51
324 327 5.256474 TCCAATTTTGTTTGCCCAAAAGAA 58.744 33.333 10.49 0.00 44.80 2.52
392 399 1.966451 GACCTTGCAACCCGACTGG 60.966 63.158 0.00 0.00 41.37 4.00
398 405 4.585879 TCACTATTAAGACCTTGCAACCC 58.414 43.478 0.00 0.00 0.00 4.11
449 459 5.833082 TCTGGAACACGAAATAGATAGAGC 58.167 41.667 0.00 0.00 0.00 4.09
552 562 3.498397 AGCGTGTGACTTGTTAGAATTGG 59.502 43.478 0.00 0.00 0.00 3.16
572 582 2.891580 TCGGTACCTCTGGAATATGAGC 59.108 50.000 10.90 0.00 0.00 4.26
677 688 8.466798 CGGAATTTTAACCAATTAGGAAGTCAT 58.533 33.333 1.54 0.00 41.22 3.06
764 1838 9.659830 GTTATTGCGAAATTATAATTCTTCCGT 57.340 29.630 11.08 0.00 0.00 4.69
766 1840 9.406828 GGGTTATTGCGAAATTATAATTCTTCC 57.593 33.333 11.08 2.15 0.00 3.46
767 1841 9.113876 CGGGTTATTGCGAAATTATAATTCTTC 57.886 33.333 11.08 5.64 0.00 2.87
768 1842 8.079809 CCGGGTTATTGCGAAATTATAATTCTT 58.920 33.333 11.08 0.00 0.00 2.52
769 1843 7.308951 CCCGGGTTATTGCGAAATTATAATTCT 60.309 37.037 14.18 2.49 0.00 2.40
771 1845 6.294843 CCCCGGGTTATTGCGAAATTATAATT 60.295 38.462 21.85 4.81 0.00 1.40
772 1846 5.184287 CCCCGGGTTATTGCGAAATTATAAT 59.816 40.000 21.85 0.00 0.00 1.28
773 1847 4.519730 CCCCGGGTTATTGCGAAATTATAA 59.480 41.667 21.85 0.00 0.00 0.98
775 1849 2.888414 CCCCGGGTTATTGCGAAATTAT 59.112 45.455 21.85 0.00 0.00 1.28
776 1850 2.299521 CCCCGGGTTATTGCGAAATTA 58.700 47.619 21.85 0.00 0.00 1.40
777 1851 1.107945 CCCCGGGTTATTGCGAAATT 58.892 50.000 21.85 0.00 0.00 1.82
778 1852 1.388837 GCCCCGGGTTATTGCGAAAT 61.389 55.000 21.85 0.00 0.00 2.17
779 1853 2.047443 GCCCCGGGTTATTGCGAAA 61.047 57.895 21.85 0.00 0.00 3.46
782 1856 4.841861 TCGCCCCGGGTTATTGCG 62.842 66.667 28.57 28.57 46.09 4.85
783 1857 1.388837 AATTCGCCCCGGGTTATTGC 61.389 55.000 21.85 14.51 0.00 3.56
784 1858 1.066454 GAAATTCGCCCCGGGTTATTG 59.934 52.381 21.85 4.20 0.00 1.90
785 1859 1.395635 GAAATTCGCCCCGGGTTATT 58.604 50.000 21.85 10.09 0.00 1.40
786 1860 0.466739 GGAAATTCGCCCCGGGTTAT 60.467 55.000 21.85 3.77 0.00 1.89
787 1861 1.077572 GGAAATTCGCCCCGGGTTA 60.078 57.895 21.85 0.15 0.00 2.85
800 1884 5.539955 CCCTTGAATTCGGAATATGGGAAAT 59.460 40.000 14.85 0.00 34.34 2.17
841 1925 1.408969 AGGCCAAAACGAAATGGTGT 58.591 45.000 5.01 0.00 39.00 4.16
847 1931 4.716794 TCTAAACCTAGGCCAAAACGAAA 58.283 39.130 9.30 0.00 0.00 3.46
915 1999 8.594550 AGTGGAATAGTATACAAAGTCAACACT 58.405 33.333 5.50 8.22 0.00 3.55
939 2023 9.485206 AAAAGATCGTGTATTTACAACTACAGT 57.515 29.630 0.00 0.00 38.04 3.55
1036 2120 9.749340 ATACCCATTAAAGCTTACAAGTAAACT 57.251 29.630 0.00 0.00 0.00 2.66
1055 2139 3.181469 CGCGGTATATAAGGCATACCCAT 60.181 47.826 0.00 0.00 43.39 4.00
1107 2191 1.002366 CTCTGCGTTCTTCGAATGGG 58.998 55.000 0.00 0.00 42.86 4.00
1121 2205 9.089601 GGACTTCTAACTTAAATTAGTCTCTGC 57.910 37.037 3.79 0.00 34.36 4.26
1248 2333 8.255905 TCCTTTTAGTTTCGACTTTAGGGATAG 58.744 37.037 0.00 0.00 0.00 2.08
1378 2465 6.272324 TCCCATCCTTTCTTTGACTCTTCTTA 59.728 38.462 0.00 0.00 0.00 2.10
1381 2468 4.911390 TCCCATCCTTTCTTTGACTCTTC 58.089 43.478 0.00 0.00 0.00 2.87
1462 2549 6.385759 TCCAACTATAAGGAAATAGGCAGTCA 59.614 38.462 0.00 0.00 34.34 3.41
1502 2589 4.321230 GCTCGAGTGGAATTTGGAACATTT 60.321 41.667 15.13 0.00 39.30 2.32
1534 2621 8.579850 AGATGTTTTTGCTAGTATTGATCCAA 57.420 30.769 0.00 0.00 0.00 3.53
1546 2633 7.275888 ACATTGTTCTGAGATGTTTTTGCTA 57.724 32.000 0.00 0.00 30.22 3.49
1561 2648 2.472695 TGGCGCTAGAACATTGTTCT 57.527 45.000 29.38 29.38 0.00 3.01
1634 2721 0.759060 GCAGTCCAAGGGGTTGGTTT 60.759 55.000 4.14 0.00 42.62 3.27
1701 2788 4.007659 GAGCGTTCTCAATTAGGGGAAAA 58.992 43.478 0.00 0.00 39.16 2.29
1791 2879 5.414454 GTGTTGAACAAGTAGGCATAATGGA 59.586 40.000 0.00 0.00 0.00 3.41
1798 2886 7.120579 CCAAATATAGTGTTGAACAAGTAGGCA 59.879 37.037 0.00 0.00 0.00 4.75
1876 2964 5.793026 TGAAACATTTCCAGTTGTTTTGC 57.207 34.783 2.00 0.00 43.95 3.68
2022 3111 9.575868 TTATATTGGTAATAATCCGGCAAAAGA 57.424 29.630 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.