Multiple sequence alignment - TraesCS5D01G250000

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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 TraesCS5D01G250000 chr5D 100.000 2282 0 0 1 2282 356319527 356321808 0.000000e+00 4215
1 TraesCS5D01G250000 chr5B 89.816 1247 57 25 188 1382 421274770 421275998 0.000000e+00 1535
2 TraesCS5D01G250000 chr5B 92.776 526 29 5 1325 1845 421276005 421276526 0.000000e+00 752
3 TraesCS5D01G250000 chr5B 79.424 695 68 35 844 1486 421187486 421188157 2.710000e-114 422
4 TraesCS5D01G250000 chr5B 88.630 343 34 5 1940 2281 421276580 421276918 1.630000e-111 412
5 TraesCS5D01G250000 chr5B 93.258 89 2 3 107 191 421274640 421274728 6.620000e-26 128
6 TraesCS5D01G250000 chr5B 100.000 55 0 0 8 62 421274590 421274644 4.010000e-18 102
7 TraesCS5D01G250000 chr5A 83.702 1086 114 36 766 1804 457915024 457916093 0.000000e+00 966
8 TraesCS5D01G250000 chr5A 88.390 267 23 7 2022 2282 457916341 457916605 4.730000e-82 315
9 TraesCS5D01G250000 chr5A 89.773 88 8 1 991 1078 457905820 457905906 6.660000e-21 111
10 TraesCS5D01G250000 chr2B 81.132 212 33 7 1601 1807 564821205 564821414 1.810000e-36 163
11 TraesCS5D01G250000 chr6B 82.716 162 23 5 1649 1807 623340924 623340765 3.060000e-29 139
12 TraesCS5D01G250000 chr4A 79.688 192 33 6 1623 1812 585237010 585236823 1.420000e-27 134
13 TraesCS5D01G250000 chr7D 85.567 97 12 2 1713 1808 510003940 510003845 1.440000e-17 100


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 TraesCS5D01G250000 chr5D 356319527 356321808 2281 False 4215.0 4215 100.000 1 2282 1 chr5D.!!$F1 2281
1 TraesCS5D01G250000 chr5B 421274590 421276918 2328 False 585.8 1535 92.896 8 2281 5 chr5B.!!$F2 2273
2 TraesCS5D01G250000 chr5B 421187486 421188157 671 False 422.0 422 79.424 844 1486 1 chr5B.!!$F1 642
3 TraesCS5D01G250000 chr5A 457915024 457916605 1581 False 640.5 966 86.046 766 2282 2 chr5A.!!$F2 1516

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
414 468 0.393077 ATTTAGAGATGCCCCCGTCG 59.607 55.0 0.0 0.0 32.12 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2047 2340 0.029834 CTTTGTGCTGAAAGTGCGCT 59.97 50.0 9.73 0.0 41.05 5.92 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
98 99 9.713713 AACAATAACTTAAAAATTATTGGCCGT 57.286 25.926 16.54 0.00 46.28 5.68
99 100 9.713713 ACAATAACTTAAAAATTATTGGCCGTT 57.286 25.926 16.54 0.00 46.28 4.44
103 104 8.528917 AACTTAAAAATTATTGGCCGTTCTTC 57.471 30.769 0.00 0.00 0.00 2.87
104 105 7.892609 ACTTAAAAATTATTGGCCGTTCTTCT 58.107 30.769 0.00 0.00 0.00 2.85
105 106 8.364894 ACTTAAAAATTATTGGCCGTTCTTCTT 58.635 29.630 0.00 0.00 0.00 2.52
106 107 9.203421 CTTAAAAATTATTGGCCGTTCTTCTTT 57.797 29.630 0.00 0.00 0.00 2.52
196 200 7.826260 ACAATAACTTCAAAATTATTGGCCG 57.174 32.000 16.52 0.00 46.28 6.13
215 265 2.054363 CGTTAGCTCGATCGCATTGAT 58.946 47.619 11.09 1.86 41.06 2.57
217 267 3.668656 CGTTAGCTCGATCGCATTGATAA 59.331 43.478 11.09 7.00 37.47 1.75
218 268 4.324669 CGTTAGCTCGATCGCATTGATAAT 59.675 41.667 11.09 0.00 37.47 1.28
219 269 5.497754 CGTTAGCTCGATCGCATTGATAATC 60.498 44.000 11.09 4.70 37.47 1.75
220 270 3.917988 AGCTCGATCGCATTGATAATCA 58.082 40.909 11.09 0.00 37.47 2.57
222 272 3.677121 GCTCGATCGCATTGATAATCACT 59.323 43.478 11.09 0.00 37.47 3.41
223 273 4.151335 GCTCGATCGCATTGATAATCACTT 59.849 41.667 11.09 0.00 37.47 3.16
224 274 5.580911 TCGATCGCATTGATAATCACTTG 57.419 39.130 11.09 0.00 37.47 3.16
225 275 5.049828 TCGATCGCATTGATAATCACTTGT 58.950 37.500 11.09 0.00 37.47 3.16
226 276 5.175673 TCGATCGCATTGATAATCACTTGTC 59.824 40.000 11.09 0.00 37.47 3.18
227 277 5.613360 CGATCGCATTGATAATCACTTGTCC 60.613 44.000 0.26 0.00 37.47 4.02
228 278 4.769688 TCGCATTGATAATCACTTGTCCT 58.230 39.130 0.00 0.00 0.00 3.85
229 279 5.185454 TCGCATTGATAATCACTTGTCCTT 58.815 37.500 0.00 0.00 0.00 3.36
256 306 4.541973 AAAGAATGCCCATTCCAGTTTC 57.458 40.909 15.36 0.00 46.28 2.78
258 308 3.359950 AGAATGCCCATTCCAGTTTCTC 58.640 45.455 15.36 0.00 46.28 2.87
259 309 2.905415 ATGCCCATTCCAGTTTCTCA 57.095 45.000 0.00 0.00 0.00 3.27
260 310 2.673775 TGCCCATTCCAGTTTCTCAA 57.326 45.000 0.00 0.00 0.00 3.02
261 311 2.956132 TGCCCATTCCAGTTTCTCAAA 58.044 42.857 0.00 0.00 0.00 2.69
262 312 3.303938 TGCCCATTCCAGTTTCTCAAAA 58.696 40.909 0.00 0.00 0.00 2.44
263 313 3.708631 TGCCCATTCCAGTTTCTCAAAAA 59.291 39.130 0.00 0.00 0.00 1.94
306 356 4.582701 TGGCATTCAAGACAATTTCGTT 57.417 36.364 0.00 0.00 0.00 3.85
308 358 4.037327 TGGCATTCAAGACAATTTCGTTCA 59.963 37.500 0.00 0.00 0.00 3.18
330 380 5.934625 TCAGTGTTGATCTTTAGCTTCTTCC 59.065 40.000 0.00 0.00 0.00 3.46
332 382 5.936956 AGTGTTGATCTTTAGCTTCTTCCTG 59.063 40.000 0.00 0.00 0.00 3.86
333 383 5.123027 GTGTTGATCTTTAGCTTCTTCCTGG 59.877 44.000 0.00 0.00 0.00 4.45
343 397 3.575687 AGCTTCTTCCTGGGAAAATGTTG 59.424 43.478 3.55 0.00 33.34 3.33
344 398 3.573967 GCTTCTTCCTGGGAAAATGTTGA 59.426 43.478 3.55 0.00 33.34 3.18
359 413 7.798052 GGAAAATGTTGAACAAATGGATTTTCG 59.202 33.333 18.46 0.00 33.68 3.46
375 429 5.745769 GGATTTTCGCAAGGAAGATCAAATC 59.254 40.000 8.59 0.00 44.20 2.17
381 435 6.115446 TCGCAAGGAAGATCAAATCTAACAT 58.885 36.000 0.00 0.00 36.81 2.71
382 436 6.599244 TCGCAAGGAAGATCAAATCTAACATT 59.401 34.615 0.00 0.00 36.81 2.71
383 437 7.121168 TCGCAAGGAAGATCAAATCTAACATTT 59.879 33.333 0.00 0.00 36.81 2.32
384 438 7.430502 CGCAAGGAAGATCAAATCTAACATTTC 59.569 37.037 0.00 0.00 39.08 2.17
385 439 8.465201 GCAAGGAAGATCAAATCTAACATTTCT 58.535 33.333 0.00 0.00 39.08 2.52
414 468 0.393077 ATTTAGAGATGCCCCCGTCG 59.607 55.000 0.00 0.00 32.12 5.12
492 554 5.814705 ACCTTGACGAATCTCATGAGAATTC 59.185 40.000 28.40 25.51 41.36 2.17
590 664 8.635877 TGTGCACGTTTAGAAAATAAACATTT 57.364 26.923 13.13 0.00 37.28 2.32
611 685 2.292267 AGTTTCTTGACTGTGGCACTG 58.708 47.619 21.14 21.14 0.00 3.66
681 758 3.374745 GTGCACTTCATGGTTGTTTCTG 58.625 45.455 10.32 0.00 0.00 3.02
736 813 6.149474 CCGTCCATTTGTTCTAATCTCTGTTT 59.851 38.462 0.00 0.00 0.00 2.83
739 816 8.447053 GTCCATTTGTTCTAATCTCTGTTTCTC 58.553 37.037 0.00 0.00 0.00 2.87
787 865 1.033574 GACTCCACGTAGCTGGCTAT 58.966 55.000 5.58 0.00 0.00 2.97
923 1012 2.105649 TCAAATCAAGCCAAAAACCCCC 59.894 45.455 0.00 0.00 0.00 5.40
941 1030 3.369576 CCCCCAAGCAAGAAGAGTAGTAC 60.370 52.174 0.00 0.00 0.00 2.73
981 1092 1.550976 CCAGGAGTCTTAGACCACCAC 59.449 57.143 21.45 5.49 34.02 4.16
998 1116 1.750778 CCACAGTCAGGTTTGCAGTTT 59.249 47.619 0.00 0.00 0.00 2.66
1090 1214 3.842923 CATGCGAGGCGAGGAGGT 61.843 66.667 0.00 0.00 0.00 3.85
1092 1216 2.660064 ATGCGAGGCGAGGAGGTTT 61.660 57.895 0.00 0.00 0.00 3.27
1150 1277 1.033746 CAAATCATCAGGGTGCCGCT 61.034 55.000 0.00 0.00 0.00 5.52
1275 1405 2.125512 GCTGCAGGGAACGATCGT 60.126 61.111 16.60 16.60 0.00 3.73
1298 1437 3.181377 CGTTGAAAAAGCGCAAAATGCTA 59.819 39.130 11.47 0.00 43.14 3.49
1487 1702 0.179059 TGTGCGTTGCCTTCTCTTCA 60.179 50.000 0.00 0.00 0.00 3.02
1599 1814 5.345702 CCTCGTCCTTCGTATCATTGTTTA 58.654 41.667 0.00 0.00 40.80 2.01
1667 1883 4.655027 GGCTAATTAGAAAAACCGAACGG 58.345 43.478 16.85 11.83 42.03 4.44
1678 1894 1.804601 ACCGAACGGAAACCAGATTC 58.195 50.000 20.14 0.00 38.96 2.52
1756 1975 2.270434 AGATACCCCACTCACACCAT 57.730 50.000 0.00 0.00 0.00 3.55
1759 1978 2.871096 TACCCCACTCACACCATTTC 57.129 50.000 0.00 0.00 0.00 2.17
1771 1990 1.821136 CACCATTTCAAAGAGGGCCTC 59.179 52.381 26.42 26.42 0.00 4.70
1812 2048 2.034124 TCATCGCCATCACTCTCATCA 58.966 47.619 0.00 0.00 0.00 3.07
1813 2049 2.133553 CATCGCCATCACTCTCATCAC 58.866 52.381 0.00 0.00 0.00 3.06
1819 2055 2.436911 CCATCACTCTCATCACCATCCA 59.563 50.000 0.00 0.00 0.00 3.41
1840 2076 2.922740 AAACCCTGAGCAAACGACTA 57.077 45.000 0.00 0.00 0.00 2.59
1845 2081 1.337821 CTGAGCAAACGACTACGACC 58.662 55.000 0.00 0.00 42.66 4.79
1847 2083 2.153645 TGAGCAAACGACTACGACCTA 58.846 47.619 0.00 0.00 42.66 3.08
1848 2084 2.161012 TGAGCAAACGACTACGACCTAG 59.839 50.000 0.00 0.00 42.66 3.02
1849 2085 1.135460 AGCAAACGACTACGACCTAGC 60.135 52.381 0.00 0.00 42.66 3.42
1850 2086 1.135460 GCAAACGACTACGACCTAGCT 60.135 52.381 0.00 0.00 42.66 3.32
1853 2089 2.680312 ACGACTACGACCTAGCTGTA 57.320 50.000 0.00 0.00 42.66 2.74
1886 2145 8.399425 CGACCGTATGAAGCTATATAAAGATCT 58.601 37.037 0.00 0.00 0.00 2.75
1889 2148 9.653067 CCGTATGAAGCTATATAAAGATCTACG 57.347 37.037 0.00 0.00 0.00 3.51
1893 2152 8.543862 TGAAGCTATATAAAGATCTACGTCGA 57.456 34.615 0.00 0.00 0.00 4.20
1894 2153 9.163899 TGAAGCTATATAAAGATCTACGTCGAT 57.836 33.333 1.63 1.63 0.00 3.59
1895 2154 9.991388 GAAGCTATATAAAGATCTACGTCGATT 57.009 33.333 3.86 0.00 0.00 3.34
1896 2155 9.991388 AAGCTATATAAAGATCTACGTCGATTC 57.009 33.333 3.86 0.00 0.00 2.52
1897 2156 8.329583 AGCTATATAAAGATCTACGTCGATTCG 58.670 37.037 3.86 0.00 0.00 3.34
1898 2157 7.110490 GCTATATAAAGATCTACGTCGATTCGC 59.890 40.741 3.86 0.00 0.00 4.70
1899 2158 3.416119 AAAGATCTACGTCGATTCGCA 57.584 42.857 3.86 0.00 0.00 5.10
1900 2159 3.416119 AAGATCTACGTCGATTCGCAA 57.584 42.857 3.86 0.00 0.00 4.85
1901 2160 3.416119 AGATCTACGTCGATTCGCAAA 57.584 42.857 3.86 0.00 0.00 3.68
1902 2161 3.766151 AGATCTACGTCGATTCGCAAAA 58.234 40.909 3.86 0.00 0.00 2.44
1903 2162 4.171005 AGATCTACGTCGATTCGCAAAAA 58.829 39.130 3.86 0.00 0.00 1.94
1938 2197 7.588143 AAAATGTGAAGATCTACGTCAAGAG 57.412 36.000 0.00 0.00 38.55 2.85
1945 2204 0.803117 TCTACGTCAAGAGTCAGCCG 59.197 55.000 0.00 0.00 0.00 5.52
1963 2222 1.006805 GCCTGCGATCAGATAGCGT 60.007 57.895 10.56 0.00 42.95 5.07
1964 2223 0.241213 GCCTGCGATCAGATAGCGTA 59.759 55.000 10.56 0.00 42.95 4.42
1989 2248 2.169769 TCCGACTCCAACAAAGAACTGT 59.830 45.455 0.00 0.00 0.00 3.55
1993 2252 5.238650 CCGACTCCAACAAAGAACTGTAAAT 59.761 40.000 0.00 0.00 0.00 1.40
2006 2265 8.854614 AAGAACTGTAAATGAGAACTAAGCAT 57.145 30.769 0.00 0.00 0.00 3.79
2047 2340 4.287067 AGAAGTTCATCTAGCCAGGAAACA 59.713 41.667 5.50 0.00 0.00 2.83
2049 2342 2.680339 GTTCATCTAGCCAGGAAACAGC 59.320 50.000 0.00 0.00 0.00 4.40
2051 2344 0.462759 ATCTAGCCAGGAAACAGCGC 60.463 55.000 0.00 0.00 37.01 5.92
2111 2405 2.762969 TAAAGCTGGGCATGCGTGGT 62.763 55.000 12.44 6.84 35.28 4.16
2122 2416 0.672889 ATGCGTGGTTGTCAATGCAA 59.327 45.000 0.00 0.00 40.70 4.08
2141 2435 6.154203 TGCAAATGAAGGTCATACAAAACA 57.846 33.333 0.00 0.00 35.76 2.83
2142 2436 5.982516 TGCAAATGAAGGTCATACAAAACAC 59.017 36.000 0.00 0.00 35.76 3.32
2166 2462 9.199184 CACAAACAAATCTAAGAAACGATATCG 57.801 33.333 23.18 23.18 46.33 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.357314 GGGAATTTTTGCTTAGTACTCCCTC 59.643 44.000 0.00 0.00 37.57 4.30
2 3 5.014202 TGGGAATTTTTGCTTAGTACTCCC 58.986 41.667 0.00 0.00 40.43 4.30
3 4 5.710567 ACTGGGAATTTTTGCTTAGTACTCC 59.289 40.000 0.00 0.00 0.00 3.85
4 5 6.819397 ACTGGGAATTTTTGCTTAGTACTC 57.181 37.500 0.00 0.00 0.00 2.59
6 7 9.923143 AATTTACTGGGAATTTTTGCTTAGTAC 57.077 29.630 0.00 0.00 0.00 2.73
72 73 9.713713 ACGGCCAATAATTTTTAAGTTATTGTT 57.286 25.926 19.93 7.13 42.52 2.83
73 74 9.713713 AACGGCCAATAATTTTTAAGTTATTGT 57.286 25.926 19.93 7.22 42.52 2.71
77 78 9.628746 GAAGAACGGCCAATAATTTTTAAGTTA 57.371 29.630 2.24 0.00 0.00 2.24
78 79 8.364894 AGAAGAACGGCCAATAATTTTTAAGTT 58.635 29.630 2.24 0.00 0.00 2.66
79 80 7.892609 AGAAGAACGGCCAATAATTTTTAAGT 58.107 30.769 2.24 0.00 0.00 2.24
80 81 8.757164 AAGAAGAACGGCCAATAATTTTTAAG 57.243 30.769 2.24 0.00 0.00 1.85
86 87 9.574516 AGATATAAAGAAGAACGGCCAATAATT 57.425 29.630 2.24 0.00 0.00 1.40
87 88 9.220767 GAGATATAAAGAAGAACGGCCAATAAT 57.779 33.333 2.24 0.00 0.00 1.28
88 89 8.208224 TGAGATATAAAGAAGAACGGCCAATAA 58.792 33.333 2.24 0.00 0.00 1.40
89 90 7.732025 TGAGATATAAAGAAGAACGGCCAATA 58.268 34.615 2.24 0.00 0.00 1.90
90 91 6.591935 TGAGATATAAAGAAGAACGGCCAAT 58.408 36.000 2.24 0.00 0.00 3.16
91 92 5.984725 TGAGATATAAAGAAGAACGGCCAA 58.015 37.500 2.24 0.00 0.00 4.52
92 93 5.607939 TGAGATATAAAGAAGAACGGCCA 57.392 39.130 2.24 0.00 0.00 5.36
93 94 5.409826 CCATGAGATATAAAGAAGAACGGCC 59.590 44.000 0.00 0.00 0.00 6.13
94 95 5.992217 ACCATGAGATATAAAGAAGAACGGC 59.008 40.000 0.00 0.00 0.00 5.68
95 96 6.425114 CCACCATGAGATATAAAGAAGAACGG 59.575 42.308 0.00 0.00 0.00 4.44
96 97 6.073548 GCCACCATGAGATATAAAGAAGAACG 60.074 42.308 0.00 0.00 0.00 3.95
97 98 6.073548 CGCCACCATGAGATATAAAGAAGAAC 60.074 42.308 0.00 0.00 0.00 3.01
98 99 5.991606 CGCCACCATGAGATATAAAGAAGAA 59.008 40.000 0.00 0.00 0.00 2.52
99 100 5.511373 CCGCCACCATGAGATATAAAGAAGA 60.511 44.000 0.00 0.00 0.00 2.87
100 101 4.692625 CCGCCACCATGAGATATAAAGAAG 59.307 45.833 0.00 0.00 0.00 2.85
101 102 4.102524 ACCGCCACCATGAGATATAAAGAA 59.897 41.667 0.00 0.00 0.00 2.52
102 103 3.646162 ACCGCCACCATGAGATATAAAGA 59.354 43.478 0.00 0.00 0.00 2.52
103 104 4.008074 ACCGCCACCATGAGATATAAAG 57.992 45.455 0.00 0.00 0.00 1.85
104 105 5.554437 TTACCGCCACCATGAGATATAAA 57.446 39.130 0.00 0.00 0.00 1.40
105 106 5.755409 ATTACCGCCACCATGAGATATAA 57.245 39.130 0.00 0.00 0.00 0.98
106 107 5.755409 AATTACCGCCACCATGAGATATA 57.245 39.130 0.00 0.00 0.00 0.86
107 108 4.640771 AATTACCGCCACCATGAGATAT 57.359 40.909 0.00 0.00 0.00 1.63
108 109 4.262721 GGTAATTACCGCCACCATGAGATA 60.263 45.833 18.70 0.00 36.50 1.98
109 110 3.496160 GGTAATTACCGCCACCATGAGAT 60.496 47.826 18.70 0.00 36.50 2.75
110 111 2.158871 GGTAATTACCGCCACCATGAGA 60.159 50.000 18.70 0.00 36.50 3.27
134 135 4.887748 AGAAGTGATCGAAGCAAAGAAGA 58.112 39.130 0.00 0.00 0.00 2.87
141 142 7.103641 AGGTAAATAAAGAAGTGATCGAAGCA 58.896 34.615 0.00 0.00 0.00 3.91
182 186 4.035017 CGAGCTAACGGCCAATAATTTTG 58.965 43.478 2.24 0.00 43.05 2.44
191 195 2.411701 CGATCGAGCTAACGGCCA 59.588 61.111 10.26 0.00 43.05 5.36
192 196 3.030882 GCGATCGAGCTAACGGCC 61.031 66.667 21.57 0.00 43.05 6.13
193 197 1.215655 AATGCGATCGAGCTAACGGC 61.216 55.000 21.57 0.00 42.19 5.68
194 198 0.504384 CAATGCGATCGAGCTAACGG 59.496 55.000 21.57 0.00 38.13 4.44
196 200 5.346011 TGATTATCAATGCGATCGAGCTAAC 59.654 40.000 21.57 0.00 38.13 2.34
217 267 7.653311 GCATTCTTTTAAACAAGGACAAGTGAT 59.347 33.333 0.00 0.00 0.00 3.06
218 268 6.978080 GCATTCTTTTAAACAAGGACAAGTGA 59.022 34.615 0.00 0.00 0.00 3.41
219 269 6.200854 GGCATTCTTTTAAACAAGGACAAGTG 59.799 38.462 0.00 0.00 0.00 3.16
220 270 6.280643 GGCATTCTTTTAAACAAGGACAAGT 58.719 36.000 0.00 0.00 0.00 3.16
222 272 5.129485 TGGGCATTCTTTTAAACAAGGACAA 59.871 36.000 0.00 0.00 0.00 3.18
223 273 4.651503 TGGGCATTCTTTTAAACAAGGACA 59.348 37.500 0.00 0.00 0.00 4.02
224 274 5.208463 TGGGCATTCTTTTAAACAAGGAC 57.792 39.130 0.00 0.00 0.00 3.85
225 275 6.432403 AATGGGCATTCTTTTAAACAAGGA 57.568 33.333 0.00 0.00 0.00 3.36
226 276 5.643348 GGAATGGGCATTCTTTTAAACAAGG 59.357 40.000 0.00 0.00 44.90 3.61
227 277 6.229733 TGGAATGGGCATTCTTTTAAACAAG 58.770 36.000 0.00 0.00 44.90 3.16
228 278 6.179906 TGGAATGGGCATTCTTTTAAACAA 57.820 33.333 0.00 0.00 44.90 2.83
229 279 5.306678 ACTGGAATGGGCATTCTTTTAAACA 59.693 36.000 0.00 0.00 44.90 2.83
306 356 5.934625 GGAAGAAGCTAAAGATCAACACTGA 59.065 40.000 0.00 0.00 35.56 3.41
308 358 5.936956 CAGGAAGAAGCTAAAGATCAACACT 59.063 40.000 0.00 0.00 0.00 3.55
330 380 5.609423 TCCATTTGTTCAACATTTTCCCAG 58.391 37.500 0.00 0.00 0.00 4.45
332 382 7.509141 AAATCCATTTGTTCAACATTTTCCC 57.491 32.000 0.00 0.00 0.00 3.97
333 383 7.798052 CGAAAATCCATTTGTTCAACATTTTCC 59.202 33.333 14.72 3.47 31.28 3.13
343 397 4.555262 TCCTTGCGAAAATCCATTTGTTC 58.445 39.130 0.00 0.00 0.00 3.18
344 398 4.599047 TCCTTGCGAAAATCCATTTGTT 57.401 36.364 0.00 0.00 0.00 2.83
359 413 8.465201 AGAAATGTTAGATTTGATCTTCCTTGC 58.535 33.333 0.00 0.00 40.76 4.01
382 436 8.686334 GGGCATCTCTAAATGTTTATGAAAGAA 58.314 33.333 0.00 0.00 0.00 2.52
383 437 7.285401 GGGGCATCTCTAAATGTTTATGAAAGA 59.715 37.037 0.00 0.00 0.00 2.52
384 438 7.428826 GGGGCATCTCTAAATGTTTATGAAAG 58.571 38.462 0.00 0.00 0.00 2.62
385 439 6.323739 GGGGGCATCTCTAAATGTTTATGAAA 59.676 38.462 0.00 0.00 0.00 2.69
386 440 5.833131 GGGGGCATCTCTAAATGTTTATGAA 59.167 40.000 0.00 0.00 0.00 2.57
387 441 5.385198 GGGGGCATCTCTAAATGTTTATGA 58.615 41.667 0.00 0.00 0.00 2.15
388 442 4.216257 CGGGGGCATCTCTAAATGTTTATG 59.784 45.833 0.00 0.00 0.00 1.90
492 554 6.346678 GCAGTCTCTTACACTAAACCTTTTCG 60.347 42.308 0.00 0.00 0.00 3.46
590 664 3.466836 CAGTGCCACAGTCAAGAAACTA 58.533 45.455 0.00 0.00 0.00 2.24
681 758 5.834239 TTACTTACTGTAAAAGTGCTCGC 57.166 39.130 6.28 0.00 40.26 5.03
736 813 5.248477 GCATCCAAAGGGTACTATATGGAGA 59.752 44.000 13.59 0.00 37.45 3.71
739 816 4.253685 CGCATCCAAAGGGTACTATATGG 58.746 47.826 0.00 0.00 34.93 2.74
787 865 6.718454 CGAGGGGTATGTATAAACTAGGAAGA 59.282 42.308 0.00 0.00 0.00 2.87
885 968 1.067295 TGAGAGGTTTGCCCAGTGAT 58.933 50.000 0.00 0.00 34.66 3.06
923 1012 6.043411 GGTATGGTACTACTCTTCTTGCTTG 58.957 44.000 0.00 0.00 0.00 4.01
981 1092 3.551454 CCATGAAACTGCAAACCTGACTG 60.551 47.826 0.00 0.00 0.00 3.51
998 1116 0.040058 ATGCTTGGAACCTGCCATGA 59.960 50.000 0.00 0.00 37.86 3.07
1074 1198 1.327690 TAAACCTCCTCGCCTCGCAT 61.328 55.000 0.00 0.00 0.00 4.73
1090 1214 4.761845 TGCCGACGCCGCCATAAA 62.762 61.111 0.00 0.00 0.00 1.40
1092 1216 4.761845 TTTGCCGACGCCGCCATA 62.762 61.111 0.00 0.00 0.00 2.74
1275 1405 2.034170 GCATTTTGCGCTTTTTCAACGA 60.034 40.909 9.73 0.00 31.71 3.85
1298 1437 0.252479 CAAGAGCTCTGTGCCCATCT 59.748 55.000 19.06 0.00 44.23 2.90
1487 1702 3.767711 TGAGATATACTGGCACCTCGAT 58.232 45.455 0.00 0.00 0.00 3.59
1558 1773 2.598565 AGGGTTTCAGCCTCCTTTTTC 58.401 47.619 0.00 0.00 43.92 2.29
1569 1784 0.317479 ACGAAGGACGAGGGTTTCAG 59.683 55.000 0.00 0.00 45.77 3.02
1599 1814 3.134804 ACGAAGGAATCCTCCATTTCGAT 59.865 43.478 22.50 7.99 45.53 3.59
1667 1883 8.519799 TCATAATTAACTGGGAATCTGGTTTC 57.480 34.615 0.00 0.00 0.00 2.78
1715 1932 0.867746 TGTGTGCTGCTCAACGATTC 59.132 50.000 5.91 0.00 0.00 2.52
1756 1975 0.606401 CAGCGAGGCCCTCTTTGAAA 60.606 55.000 9.52 0.00 0.00 2.69
1759 1978 1.449246 CTCAGCGAGGCCCTCTTTG 60.449 63.158 9.52 7.08 0.00 2.77
1785 2004 0.108186 GTGATGGCGATGACACCTGA 60.108 55.000 0.00 0.00 0.00 3.86
1812 2048 1.922447 TGCTCAGGGTTTATGGATGGT 59.078 47.619 0.00 0.00 0.00 3.55
1813 2049 2.734755 TGCTCAGGGTTTATGGATGG 57.265 50.000 0.00 0.00 0.00 3.51
1819 2055 3.418684 AGTCGTTTGCTCAGGGTTTAT 57.581 42.857 0.00 0.00 0.00 1.40
1845 2081 1.264557 CGGTCGATCACCTACAGCTAG 59.735 57.143 11.12 0.00 44.21 3.42
1847 2083 0.680280 ACGGTCGATCACCTACAGCT 60.680 55.000 11.12 0.00 44.21 4.24
1848 2084 1.019673 TACGGTCGATCACCTACAGC 58.980 55.000 11.12 0.00 44.21 4.40
1849 2085 2.876550 TCATACGGTCGATCACCTACAG 59.123 50.000 11.12 0.00 44.21 2.74
1850 2086 2.921821 TCATACGGTCGATCACCTACA 58.078 47.619 11.12 0.00 44.21 2.74
1853 2089 1.067212 GCTTCATACGGTCGATCACCT 59.933 52.381 11.12 3.54 44.21 4.00
1856 2092 7.619964 TTATATAGCTTCATACGGTCGATCA 57.380 36.000 0.00 0.00 0.00 2.92
1860 2096 8.399425 AGATCTTTATATAGCTTCATACGGTCG 58.601 37.037 0.00 0.00 0.00 4.79
1867 2126 9.163899 TCGACGTAGATCTTTATATAGCTTCAT 57.836 33.333 0.00 0.00 0.00 2.57
1913 2172 7.657761 ACTCTTGACGTAGATCTTCACATTTTT 59.342 33.333 0.00 0.00 0.00 1.94
1914 2173 7.155328 ACTCTTGACGTAGATCTTCACATTTT 58.845 34.615 0.00 0.00 0.00 1.82
1915 2174 6.692486 ACTCTTGACGTAGATCTTCACATTT 58.308 36.000 0.00 0.00 0.00 2.32
1916 2175 6.071896 TGACTCTTGACGTAGATCTTCACATT 60.072 38.462 0.00 0.00 0.00 2.71
1917 2176 5.416013 TGACTCTTGACGTAGATCTTCACAT 59.584 40.000 0.00 0.00 0.00 3.21
1918 2177 4.760204 TGACTCTTGACGTAGATCTTCACA 59.240 41.667 0.00 0.00 0.00 3.58
1919 2178 5.298197 TGACTCTTGACGTAGATCTTCAC 57.702 43.478 0.00 0.00 0.00 3.18
1920 2179 4.142578 GCTGACTCTTGACGTAGATCTTCA 60.143 45.833 0.00 0.00 0.00 3.02
1921 2180 4.347813 GCTGACTCTTGACGTAGATCTTC 58.652 47.826 0.00 0.00 0.00 2.87
1922 2181 3.129638 GGCTGACTCTTGACGTAGATCTT 59.870 47.826 0.00 0.00 0.00 2.40
1923 2182 2.685897 GGCTGACTCTTGACGTAGATCT 59.314 50.000 0.00 0.00 0.00 2.75
1924 2183 2.539953 CGGCTGACTCTTGACGTAGATC 60.540 54.545 0.00 0.00 0.00 2.75
1925 2184 1.402259 CGGCTGACTCTTGACGTAGAT 59.598 52.381 0.00 0.00 0.00 1.98
1928 2187 1.211969 GCGGCTGACTCTTGACGTA 59.788 57.895 0.00 0.00 0.00 3.57
1938 2197 4.819761 TGATCGCAGGCGGCTGAC 62.820 66.667 39.78 28.14 41.67 3.51
1945 2204 0.241213 TACGCTATCTGATCGCAGGC 59.759 55.000 13.63 3.16 42.53 4.85
1963 2222 2.631062 TCTTTGTTGGAGTCGGAGCTTA 59.369 45.455 0.00 0.00 0.00 3.09
1964 2223 1.416401 TCTTTGTTGGAGTCGGAGCTT 59.584 47.619 0.00 0.00 0.00 3.74
1989 2248 4.883585 CCAGCCATGCTTAGTTCTCATTTA 59.116 41.667 0.00 0.00 36.40 1.40
1993 2252 1.679944 GCCAGCCATGCTTAGTTCTCA 60.680 52.381 0.00 0.00 36.40 3.27
2019 2278 2.284190 GGCTAGATGAACTTCTGTGGC 58.716 52.381 0.00 0.00 0.00 5.01
2023 2315 4.478206 TTCCTGGCTAGATGAACTTCTG 57.522 45.455 0.00 0.00 0.00 3.02
2047 2340 0.029834 CTTTGTGCTGAAAGTGCGCT 59.970 50.000 9.73 0.00 41.05 5.92
2049 2342 3.924238 ACTTTGTGCTGAAAGTGCG 57.076 47.368 11.45 0.00 43.14 5.34
2111 2405 4.933505 TGACCTTCATTTGCATTGACAA 57.066 36.364 0.00 0.00 0.00 3.18
2122 2416 7.551585 TGTTTGTGTTTTGTATGACCTTCATT 58.448 30.769 0.00 0.00 38.26 2.57
2141 2435 8.388103 CCGATATCGTTTCTTAGATTTGTTTGT 58.612 33.333 22.81 0.00 37.74 2.83
2142 2436 7.850982 CCCGATATCGTTTCTTAGATTTGTTTG 59.149 37.037 22.81 1.89 37.74 2.93
2166 2462 1.300481 GAGCGACTTTATGCCTTCCC 58.700 55.000 0.00 0.00 0.00 3.97
2250 2546 5.894298 ACCATGTGCCTGAGAGAATATAA 57.106 39.130 0.00 0.00 0.00 0.98
2251 2547 5.048013 CGTACCATGTGCCTGAGAGAATATA 60.048 44.000 0.00 0.00 0.00 0.86


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

AutoCloner maintained by Alex Coulton.