Multiple sequence alignment - TraesCS3B01G129900

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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 TraesCS3B01G129900 chr3B 100.000 2669 0 0 1 2669 111941804 111944472 0.000000e+00 4929.0
1 TraesCS3B01G129900 chr3B 87.755 49 5 1 2465 2512 661991357 661991405 3.710000e-04 56.5
2 TraesCS3B01G129900 chr3A 85.691 2432 161 88 256 2578 78709498 78711851 0.000000e+00 2390.0
3 TraesCS3B01G129900 chr3A 91.286 241 9 3 1 237 78709280 78709512 4.290000e-83 318.0
4 TraesCS3B01G129900 chr3A 87.273 110 14 0 1446 1555 374446644 374446753 2.790000e-25 126.0
5 TraesCS3B01G129900 chr3A 85.039 127 15 4 2395 2518 640553435 640553560 2.790000e-25 126.0
6 TraesCS3B01G129900 chr3D 88.357 2027 109 52 1 1947 67350015 67351994 0.000000e+00 2318.0
7 TraesCS3B01G129900 chr3D 83.239 710 65 22 2006 2669 67352165 67352866 1.060000e-168 603.0
8 TraesCS3B01G129900 chr3D 87.273 110 14 0 1446 1555 286190171 286190280 2.790000e-25 126.0
9 TraesCS3B01G129900 chr3D 91.398 93 4 4 2432 2521 500842805 500842714 1.000000e-24 124.0
10 TraesCS3B01G129900 chr1A 86.667 225 30 0 1343 1567 135182902 135182678 1.590000e-62 250.0
11 TraesCS3B01G129900 chr5D 81.944 72 6 6 2547 2615 390420865 390420932 1.000000e-03 54.7


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 TraesCS3B01G129900 chr3B 111941804 111944472 2668 False 4929.0 4929 100.0000 1 2669 1 chr3B.!!$F1 2668
1 TraesCS3B01G129900 chr3A 78709280 78711851 2571 False 1354.0 2390 88.4885 1 2578 2 chr3A.!!$F3 2577
2 TraesCS3B01G129900 chr3D 67350015 67352866 2851 False 1460.5 2318 85.7980 1 2669 2 chr3D.!!$F2 2668

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
239 244 0.57539 CGCGTTGTCTCGTTGTCTTT 59.425 50.0 0.0 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1898 2026 0.105408 ATGATTGGCCCCGTACGTAC 59.895 55.0 15.9 15.9 0.0 3.67 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
44 45 1.212441 AGTAGGCTAGCTAGGTGTCGT 59.788 52.381 22.10 9.30 0.00 4.34
80 81 3.907260 CTGGTCAGGTGCACCGCAT 62.907 63.158 29.68 10.56 41.91 4.73
164 169 1.094785 CGCTCATTTGGACCCGAAAT 58.905 50.000 0.00 0.00 0.00 2.17
166 171 1.818674 GCTCATTTGGACCCGAAATGT 59.181 47.619 13.99 0.00 40.32 2.71
169 174 2.823154 TCATTTGGACCCGAAATGTTCC 59.177 45.455 13.99 0.00 40.32 3.62
190 195 2.749621 CTCAGCTGGATTTTGGGTGTAC 59.250 50.000 15.13 0.00 0.00 2.90
191 196 2.375174 TCAGCTGGATTTTGGGTGTACT 59.625 45.455 15.13 0.00 0.00 2.73
192 197 2.749621 CAGCTGGATTTTGGGTGTACTC 59.250 50.000 5.57 0.00 0.00 2.59
193 198 2.092323 GCTGGATTTTGGGTGTACTCC 58.908 52.381 5.35 5.35 0.00 3.85
194 199 2.290960 GCTGGATTTTGGGTGTACTCCT 60.291 50.000 13.44 0.00 0.00 3.69
195 200 3.814316 GCTGGATTTTGGGTGTACTCCTT 60.814 47.826 13.44 0.00 0.00 3.36
225 230 3.799755 GGATTTGAGCGCCGCGTT 61.800 61.111 15.34 8.56 0.00 4.84
226 231 2.574212 GATTTGAGCGCCGCGTTG 60.574 61.111 15.34 0.00 0.00 4.10
227 232 3.308878 GATTTGAGCGCCGCGTTGT 62.309 57.895 15.34 0.00 0.00 3.32
228 233 3.308878 ATTTGAGCGCCGCGTTGTC 62.309 57.895 15.34 9.52 0.00 3.18
229 234 4.961511 TTGAGCGCCGCGTTGTCT 62.962 61.111 15.34 2.13 0.00 3.41
234 239 4.409588 CGCCGCGTTGTCTCGTTG 62.410 66.667 4.92 0.00 0.00 4.10
235 240 3.335534 GCCGCGTTGTCTCGTTGT 61.336 61.111 4.92 0.00 0.00 3.32
236 241 2.844146 CCGCGTTGTCTCGTTGTC 59.156 61.111 4.92 0.00 0.00 3.18
237 242 1.660575 CCGCGTTGTCTCGTTGTCT 60.661 57.895 4.92 0.00 0.00 3.41
238 243 1.213094 CCGCGTTGTCTCGTTGTCTT 61.213 55.000 4.92 0.00 0.00 3.01
239 244 0.575390 CGCGTTGTCTCGTTGTCTTT 59.425 50.000 0.00 0.00 0.00 2.52
240 245 1.005347 CGCGTTGTCTCGTTGTCTTTT 60.005 47.619 0.00 0.00 0.00 2.27
241 246 2.625828 GCGTTGTCTCGTTGTCTTTTC 58.374 47.619 0.00 0.00 0.00 2.29
242 247 2.284417 GCGTTGTCTCGTTGTCTTTTCT 59.716 45.455 0.00 0.00 0.00 2.52
243 248 3.242316 GCGTTGTCTCGTTGTCTTTTCTT 60.242 43.478 0.00 0.00 0.00 2.52
244 249 4.726876 GCGTTGTCTCGTTGTCTTTTCTTT 60.727 41.667 0.00 0.00 0.00 2.52
245 250 5.321516 CGTTGTCTCGTTGTCTTTTCTTTT 58.678 37.500 0.00 0.00 0.00 2.27
246 251 5.793457 CGTTGTCTCGTTGTCTTTTCTTTTT 59.207 36.000 0.00 0.00 0.00 1.94
247 252 6.957077 CGTTGTCTCGTTGTCTTTTCTTTTTA 59.043 34.615 0.00 0.00 0.00 1.52
248 253 7.162062 CGTTGTCTCGTTGTCTTTTCTTTTTAG 59.838 37.037 0.00 0.00 0.00 1.85
249 254 7.011828 TGTCTCGTTGTCTTTTCTTTTTAGG 57.988 36.000 0.00 0.00 0.00 2.69
250 255 6.037830 TGTCTCGTTGTCTTTTCTTTTTAGGG 59.962 38.462 0.00 0.00 0.00 3.53
251 256 5.529800 TCTCGTTGTCTTTTCTTTTTAGGGG 59.470 40.000 0.00 0.00 0.00 4.79
252 257 5.438833 TCGTTGTCTTTTCTTTTTAGGGGA 58.561 37.500 0.00 0.00 0.00 4.81
253 258 5.529800 TCGTTGTCTTTTCTTTTTAGGGGAG 59.470 40.000 0.00 0.00 0.00 4.30
254 259 5.529800 CGTTGTCTTTTCTTTTTAGGGGAGA 59.470 40.000 0.00 0.00 0.00 3.71
255 260 6.512903 CGTTGTCTTTTCTTTTTAGGGGAGAC 60.513 42.308 0.00 0.00 34.41 3.36
256 261 5.061179 TGTCTTTTCTTTTTAGGGGAGACG 58.939 41.667 0.00 0.00 36.08 4.18
273 278 2.794910 AGACGTTGTCTCGTTGTCATTG 59.205 45.455 0.00 0.00 38.71 2.82
276 281 2.639751 GTTGTCTCGTTGTCATTGCAC 58.360 47.619 0.00 0.00 0.00 4.57
280 285 2.090658 GTCTCGTTGTCATTGCACGTAG 59.909 50.000 0.00 0.00 0.00 3.51
282 287 3.058085 TCTCGTTGTCATTGCACGTAGTA 60.058 43.478 0.00 0.00 41.61 1.82
283 288 2.981805 TCGTTGTCATTGCACGTAGTAC 59.018 45.455 0.00 0.00 41.61 2.73
319 336 2.579207 TTACTTTCGCGGATCTGAGG 57.421 50.000 6.13 0.00 0.00 3.86
427 468 0.974383 ACAGTGCAGTACTACACCCC 59.026 55.000 20.40 0.00 37.60 4.95
470 517 1.874345 ATGTACCGGCCGATCGATCC 61.874 60.000 30.73 15.85 0.00 3.36
474 521 3.661131 CGGCCGATCGATCCGACT 61.661 66.667 31.28 0.00 45.53 4.18
667 750 1.267574 CCTCTTGACTAGCCAGGCCA 61.268 60.000 8.22 0.00 0.00 5.36
886 975 2.030893 CGTGGGTAGTATAAATCGCGGA 60.031 50.000 6.13 0.00 0.00 5.54
1040 1134 3.197614 CAGCCATGAAGCCTGCTG 58.802 61.111 5.21 5.21 44.43 4.41
1042 1136 3.066190 GCCATGAAGCCTGCTGCA 61.066 61.111 1.50 1.50 44.83 4.41
1046 1140 3.557903 ATGAAGCCTGCTGCACGGT 62.558 57.895 0.92 8.39 44.83 4.83
1085 1179 2.489971 CTTGTACAACTTCCAAGCCGA 58.510 47.619 3.59 0.00 30.29 5.54
1089 1183 1.523758 ACAACTTCCAAGCCGATGAC 58.476 50.000 0.00 0.00 0.00 3.06
1104 1198 4.329545 GACCCCTTCGTGGCAGCA 62.330 66.667 0.00 0.00 0.00 4.41
1146 1240 2.602267 TTCCCGGAGCTCGTGGAA 60.602 61.111 24.17 24.17 42.01 3.53
1306 1400 2.840102 CTTCGGCGAGGGGGAGAT 60.840 66.667 11.60 0.00 0.00 2.75
1327 1421 0.832135 GGGAGGGATCGGTGCTATGA 60.832 60.000 0.00 0.00 0.00 2.15
1329 1423 0.318762 GAGGGATCGGTGCTATGACC 59.681 60.000 0.00 0.00 0.00 4.02
1492 1586 4.388499 GCGGGGTGAAGAAGCGGA 62.388 66.667 0.00 0.00 0.00 5.54
1671 1777 0.733729 CCTCGGAGTCCTACTGAACG 59.266 60.000 7.77 0.00 0.00 3.95
1694 1807 1.669779 GCTACTGATCGACCAGTACGT 59.330 52.381 15.97 0.00 44.82 3.57
1708 1821 2.756760 CAGTACGTAGCTGGTTCCCTTA 59.243 50.000 13.92 0.00 0.00 2.69
1716 1831 5.121298 CGTAGCTGGTTCCCTTAGTTTTTAC 59.879 44.000 0.00 0.00 0.00 2.01
1718 1833 3.189910 GCTGGTTCCCTTAGTTTTTACGG 59.810 47.826 0.00 0.00 0.00 4.02
1725 1840 5.550290 TCCCTTAGTTTTTACGGTCGATTT 58.450 37.500 0.00 0.00 0.00 2.17
1726 1841 5.997129 TCCCTTAGTTTTTACGGTCGATTTT 59.003 36.000 0.00 0.00 0.00 1.82
1727 1842 7.158021 TCCCTTAGTTTTTACGGTCGATTTTA 58.842 34.615 0.00 0.00 0.00 1.52
1728 1843 7.117667 TCCCTTAGTTTTTACGGTCGATTTTAC 59.882 37.037 0.00 0.00 0.00 2.01
1729 1844 6.949877 CCTTAGTTTTTACGGTCGATTTTACG 59.050 38.462 0.00 0.00 0.00 3.18
1730 1845 5.268107 AGTTTTTACGGTCGATTTTACGG 57.732 39.130 0.00 0.00 0.00 4.02
1731 1846 4.749598 AGTTTTTACGGTCGATTTTACGGT 59.250 37.500 0.00 0.00 35.04 4.83
1732 1847 5.236263 AGTTTTTACGGTCGATTTTACGGTT 59.764 36.000 0.00 0.00 33.18 4.44
1739 1863 3.181397 GTCGATTTTACGGTTCGGATGA 58.819 45.455 0.00 0.00 33.82 2.92
1752 1876 5.060569 CGGTTCGGATGAATGTATACGATTC 59.939 44.000 15.45 15.45 42.52 2.52
1758 1882 4.685824 TGAATGTATACGATTCGTTGCG 57.314 40.909 17.93 0.00 41.54 4.85
1759 1883 3.060807 TGAATGTATACGATTCGTTGCGC 60.061 43.478 17.93 0.00 41.54 6.09
1760 1884 1.202203 TGTATACGATTCGTTGCGCC 58.798 50.000 17.93 2.52 41.54 6.53
1762 1886 0.935831 TATACGATTCGTTGCGCCGG 60.936 55.000 17.93 0.00 41.54 6.13
1817 1945 2.127270 CACGTCCATTGTGCACGC 60.127 61.111 13.13 0.00 37.02 5.34
1844 1972 3.682315 CGATCGACGGCGTGCATC 61.682 66.667 21.19 17.04 38.98 3.91
1848 1976 3.976375 CGACGGCGTGCATCATCG 61.976 66.667 21.19 9.28 0.00 3.84
1856 1984 1.718178 GCGTGCATCATCGATCTGTAG 59.282 52.381 0.00 0.00 0.00 2.74
1883 2011 6.276847 AGAAAATAAATTGGTGCACGAACAA 58.723 32.000 16.96 12.61 0.00 2.83
1884 2012 6.758886 AGAAAATAAATTGGTGCACGAACAAA 59.241 30.769 16.96 5.33 0.00 2.83
1886 2014 8.594881 AAAATAAATTGGTGCACGAACAAATA 57.405 26.923 16.96 10.11 0.00 1.40
1892 2020 4.355437 TGGTGCACGAACAAATAAACAAG 58.645 39.130 11.45 0.00 0.00 3.16
1898 2026 2.086849 CGAACAAATAAACAAGCGCACG 59.913 45.455 11.47 1.39 0.00 5.34
1915 2043 1.589727 CGTACGTACGGGGCCAATC 60.590 63.158 34.54 1.44 45.30 2.67
1916 2044 1.516892 GTACGTACGGGGCCAATCA 59.483 57.895 21.06 0.00 0.00 2.57
1917 2045 0.105408 GTACGTACGGGGCCAATCAT 59.895 55.000 21.06 0.00 0.00 2.45
1918 2046 0.390124 TACGTACGGGGCCAATCATC 59.610 55.000 21.06 0.00 0.00 2.92
1919 2047 1.597027 CGTACGGGGCCAATCATCC 60.597 63.158 7.57 0.00 0.00 3.51
1949 2195 1.754803 TGGTAGGCTCCACAATACGAG 59.245 52.381 0.00 0.00 31.96 4.18
1953 2199 0.535335 GGCTCCACAATACGAGTCCA 59.465 55.000 0.00 0.00 0.00 4.02
1958 2204 2.835156 TCCACAATACGAGTCCATCCAA 59.165 45.455 0.00 0.00 0.00 3.53
1965 2211 5.878406 ATACGAGTCCATCCAATCTTTCT 57.122 39.130 0.00 0.00 0.00 2.52
1970 2216 5.453057 CGAGTCCATCCAATCTTTCTGATCT 60.453 44.000 0.00 0.00 33.57 2.75
1971 2217 5.927819 AGTCCATCCAATCTTTCTGATCTC 58.072 41.667 0.00 0.00 33.57 2.75
2008 2254 9.842775 TCAAAATAATCATGCTCTCTATGTTCT 57.157 29.630 0.00 0.00 0.00 3.01
2016 2262 3.771479 TGCTCTCTATGTTCTGTGGACAT 59.229 43.478 0.00 0.00 0.00 3.06
2017 2263 4.956075 TGCTCTCTATGTTCTGTGGACATA 59.044 41.667 0.00 0.00 0.00 2.29
2026 2272 4.036262 TGTTCTGTGGACATAACTGCAAAC 59.964 41.667 8.85 0.00 35.01 2.93
2027 2273 3.814625 TCTGTGGACATAACTGCAAACA 58.185 40.909 0.00 0.00 0.00 2.83
2029 2275 4.642437 TCTGTGGACATAACTGCAAACAAA 59.358 37.500 0.00 0.00 0.00 2.83
2030 2276 4.677584 TGTGGACATAACTGCAAACAAAC 58.322 39.130 0.00 0.00 0.00 2.93
2040 2286 3.438781 ACTGCAAACAAACTGAGTTCGAA 59.561 39.130 0.00 0.00 0.00 3.71
2049 2302 3.644884 ACTGAGTTCGAACGAGTTGAT 57.355 42.857 22.83 6.88 0.00 2.57
2061 2314 3.292460 ACGAGTTGATCTAGCTAGGCTT 58.708 45.455 20.58 6.22 40.44 4.35
2063 2316 3.316588 CGAGTTGATCTAGCTAGGCTTGA 59.683 47.826 20.58 1.27 43.40 3.02
2080 2333 3.725010 GCTTGACACTAAAATTCGAGCGG 60.725 47.826 0.00 0.00 37.11 5.52
2081 2334 3.306917 TGACACTAAAATTCGAGCGGA 57.693 42.857 0.00 0.00 0.00 5.54
2083 2336 5.001237 TGACACTAAAATTCGAGCGGATA 57.999 39.130 0.00 0.00 0.00 2.59
2092 2345 5.968387 AATTCGAGCGGATACAAACTAAG 57.032 39.130 0.00 0.00 0.00 2.18
2115 2368 4.894798 GAAGCTCAAGTTCGAGTTGTAG 57.105 45.455 8.86 6.93 35.33 2.74
2125 2378 4.280174 AGTTCGAGTTGTAGAAAGTGGCTA 59.720 41.667 0.00 0.00 0.00 3.93
2131 2384 5.316987 AGTTGTAGAAAGTGGCTAATGCTT 58.683 37.500 0.00 0.00 39.59 3.91
2133 2386 7.112779 AGTTGTAGAAAGTGGCTAATGCTTAT 58.887 34.615 0.00 0.00 39.59 1.73
2154 2407 7.568497 GCTTATCTTGTAATGATCTCAAGTCGC 60.568 40.741 14.72 11.19 39.36 5.19
2162 2415 8.946085 TGTAATGATCTCAAGTCGCTTTTAAAT 58.054 29.630 0.00 0.00 0.00 1.40
2171 2424 7.853524 TCAAGTCGCTTTTAAATTAGTTTCGA 58.146 30.769 0.00 0.00 0.00 3.71
2173 2426 6.828672 AGTCGCTTTTAAATTAGTTTCGAGG 58.171 36.000 0.00 0.00 0.00 4.63
2242 2496 2.831685 AGGACGCAACACAACATAGA 57.168 45.000 0.00 0.00 0.00 1.98
2244 2498 3.067106 AGGACGCAACACAACATAGAAG 58.933 45.455 0.00 0.00 0.00 2.85
2319 2587 9.784531 ATTTATTCTTTCTCAACTGAAGACTGA 57.215 29.630 0.00 0.00 0.00 3.41
2365 2635 5.179368 CGTGGATGAGCTAACAAGAGAAAAA 59.821 40.000 0.00 0.00 0.00 1.94
2366 2636 6.128172 CGTGGATGAGCTAACAAGAGAAAAAT 60.128 38.462 0.00 0.00 0.00 1.82
2428 2698 2.949177 AGTTAACACACTGGCCATGA 57.051 45.000 5.51 0.00 0.00 3.07
2429 2699 3.439857 AGTTAACACACTGGCCATGAT 57.560 42.857 5.51 0.00 0.00 2.45
2532 2812 3.596940 ATGATAGTACACCCTCCGTCT 57.403 47.619 0.00 0.00 0.00 4.18
2546 2829 4.523173 CCCTCCGTCTCATATTAGTTGCTA 59.477 45.833 0.00 0.00 0.00 3.49
2551 2838 8.365399 TCCGTCTCATATTAGTTGCTAAAATG 57.635 34.615 0.00 0.00 29.35 2.32
2552 2839 8.201464 TCCGTCTCATATTAGTTGCTAAAATGA 58.799 33.333 0.00 0.00 29.35 2.57
2578 2865 5.756833 TGTATCTAGATGCATTTCAGTGCTG 59.243 40.000 18.36 0.00 45.27 4.41
2579 2866 4.476628 TCTAGATGCATTTCAGTGCTGA 57.523 40.909 0.00 0.00 45.27 4.26
2580 2867 4.186926 TCTAGATGCATTTCAGTGCTGAC 58.813 43.478 0.00 0.00 45.27 3.51
2581 2868 1.736126 AGATGCATTTCAGTGCTGACG 59.264 47.619 0.00 0.00 45.27 4.35
2586 2888 2.908634 CATTTCAGTGCTGACGACAAC 58.091 47.619 0.79 0.00 39.66 3.32
2595 2897 3.555956 GTGCTGACGACAACTAATATGGG 59.444 47.826 0.00 0.00 0.00 4.00
2597 2899 3.802685 GCTGACGACAACTAATATGGGAC 59.197 47.826 0.00 0.00 0.00 4.46
2599 2901 3.695556 TGACGACAACTAATATGGGACGA 59.304 43.478 0.00 0.00 0.00 4.20
2619 2921 9.413048 GGGACGAAGAGAGTAATAAATTATCTG 57.587 37.037 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 8.212312 TCCCACTAACTCTTAATTTTGTGTACA 58.788 33.333 0.00 0.00 0.00 2.90
164 169 2.517959 CCAAAATCCAGCTGAGGAACA 58.482 47.619 17.39 0.00 41.92 3.18
166 171 1.428912 ACCCAAAATCCAGCTGAGGAA 59.571 47.619 17.39 0.00 41.92 3.36
169 174 1.915141 ACACCCAAAATCCAGCTGAG 58.085 50.000 17.39 5.49 0.00 3.35
190 195 0.671781 CCGCAACAGTGGAGAAGGAG 60.672 60.000 0.00 0.00 34.82 3.69
191 196 1.118965 TCCGCAACAGTGGAGAAGGA 61.119 55.000 0.00 0.00 37.03 3.36
192 197 0.036010 ATCCGCAACAGTGGAGAAGG 60.036 55.000 4.00 0.00 44.55 3.46
193 198 1.813513 AATCCGCAACAGTGGAGAAG 58.186 50.000 4.00 0.00 44.55 2.85
194 199 1.879380 CAAATCCGCAACAGTGGAGAA 59.121 47.619 4.00 0.00 44.55 2.87
195 200 1.071542 TCAAATCCGCAACAGTGGAGA 59.928 47.619 4.00 0.00 44.55 3.71
222 227 4.516092 AAGAAAAGACAACGAGACAACG 57.484 40.909 0.00 0.00 39.31 4.10
223 228 7.428472 CCTAAAAAGAAAAGACAACGAGACAAC 59.572 37.037 0.00 0.00 0.00 3.32
224 229 7.414762 CCCTAAAAAGAAAAGACAACGAGACAA 60.415 37.037 0.00 0.00 0.00 3.18
225 230 6.037830 CCCTAAAAAGAAAAGACAACGAGACA 59.962 38.462 0.00 0.00 0.00 3.41
226 231 6.427974 CCCTAAAAAGAAAAGACAACGAGAC 58.572 40.000 0.00 0.00 0.00 3.36
227 232 5.529800 CCCCTAAAAAGAAAAGACAACGAGA 59.470 40.000 0.00 0.00 0.00 4.04
228 233 5.529800 TCCCCTAAAAAGAAAAGACAACGAG 59.470 40.000 0.00 0.00 0.00 4.18
229 234 5.438833 TCCCCTAAAAAGAAAAGACAACGA 58.561 37.500 0.00 0.00 0.00 3.85
230 235 5.529800 TCTCCCCTAAAAAGAAAAGACAACG 59.470 40.000 0.00 0.00 0.00 4.10
231 236 6.512903 CGTCTCCCCTAAAAAGAAAAGACAAC 60.513 42.308 0.00 0.00 33.23 3.32
232 237 5.529800 CGTCTCCCCTAAAAAGAAAAGACAA 59.470 40.000 0.00 0.00 33.23 3.18
233 238 5.061179 CGTCTCCCCTAAAAAGAAAAGACA 58.939 41.667 0.00 0.00 33.23 3.41
234 239 5.061853 ACGTCTCCCCTAAAAAGAAAAGAC 58.938 41.667 0.00 0.00 0.00 3.01
235 240 5.300411 ACGTCTCCCCTAAAAAGAAAAGA 57.700 39.130 0.00 0.00 0.00 2.52
236 241 5.298527 ACAACGTCTCCCCTAAAAAGAAAAG 59.701 40.000 0.00 0.00 0.00 2.27
237 242 5.195185 ACAACGTCTCCCCTAAAAAGAAAA 58.805 37.500 0.00 0.00 0.00 2.29
238 243 4.784177 ACAACGTCTCCCCTAAAAAGAAA 58.216 39.130 0.00 0.00 0.00 2.52
239 244 4.102054 AGACAACGTCTCCCCTAAAAAGAA 59.898 41.667 0.00 0.00 38.71 2.52
240 245 3.644738 AGACAACGTCTCCCCTAAAAAGA 59.355 43.478 0.00 0.00 38.71 2.52
241 246 4.004196 AGACAACGTCTCCCCTAAAAAG 57.996 45.455 0.00 0.00 38.71 2.27
252 257 2.794910 CAATGACAACGAGACAACGTCT 59.205 45.455 0.00 0.00 46.42 4.18
253 258 2.659291 GCAATGACAACGAGACAACGTC 60.659 50.000 0.00 0.00 45.83 4.34
255 260 1.260297 TGCAATGACAACGAGACAACG 59.740 47.619 0.00 0.00 39.31 4.10
256 261 2.639751 GTGCAATGACAACGAGACAAC 58.360 47.619 0.00 0.00 0.00 3.32
301 318 0.102481 GCCTCAGATCCGCGAAAGTA 59.898 55.000 8.23 0.00 0.00 2.24
319 336 4.527564 ACTACGTACGTATAAACATCGGC 58.472 43.478 26.98 0.00 0.00 5.54
414 455 3.873910 CTGGATTTGGGGTGTAGTACTG 58.126 50.000 5.39 0.00 0.00 2.74
427 468 2.283617 CGATCTTCGTCAGCTGGATTTG 59.716 50.000 15.13 2.30 34.72 2.32
470 517 0.179171 ATGTACGTTCCTCGCAGTCG 60.179 55.000 0.00 0.00 44.19 4.18
474 521 2.034179 CCATCTATGTACGTTCCTCGCA 59.966 50.000 0.00 0.00 44.19 5.10
504 553 0.660595 GCCATCGACGATCGTACAGG 60.661 60.000 22.79 20.21 41.35 4.00
667 750 1.078143 GGCAGTCCGGAGAAGCAAT 60.078 57.895 20.37 0.00 0.00 3.56
886 975 0.394352 GGAATTCCTCGTGGCATGGT 60.394 55.000 17.73 0.00 0.00 3.55
897 986 2.568623 ACTGCTTTGACGGAATTCCT 57.431 45.000 22.05 9.35 0.00 3.36
940 1029 0.171007 TGCTACGTTACCGGTAGTGC 59.829 55.000 15.20 15.27 38.78 4.40
1053 1147 1.218316 GTACAAGGAGGAGCCGGTG 59.782 63.158 1.90 0.00 43.43 4.94
1054 1148 0.834687 TTGTACAAGGAGGAGCCGGT 60.835 55.000 3.59 0.00 43.43 5.28
1056 1150 0.608640 AGTTGTACAAGGAGGAGCCG 59.391 55.000 8.98 0.00 43.43 5.52
1058 1152 2.038557 TGGAAGTTGTACAAGGAGGAGC 59.961 50.000 8.98 0.00 0.00 4.70
1085 1179 2.671070 CTGCCACGAAGGGGTCAT 59.329 61.111 0.00 0.00 38.09 3.06
1301 1395 1.915769 CCGATCCCTCCCCATCTCC 60.916 68.421 0.00 0.00 0.00 3.71
1306 1400 2.326529 ATAGCACCGATCCCTCCCCA 62.327 60.000 0.00 0.00 0.00 4.96
1308 1402 0.832135 TCATAGCACCGATCCCTCCC 60.832 60.000 0.00 0.00 0.00 4.30
1517 1611 0.455005 GTAGGTGGTGAGGACGTAGC 59.545 60.000 0.00 0.00 0.00 3.58
1671 1777 1.394618 ACTGGTCGATCAGTAGCTCC 58.605 55.000 29.49 2.43 45.18 4.70
1708 1821 4.749598 ACCGTAAAATCGACCGTAAAAACT 59.250 37.500 0.00 0.00 0.00 2.66
1716 1831 0.641783 CCGAACCGTAAAATCGACCG 59.358 55.000 0.00 0.00 38.82 4.79
1718 1833 3.181397 TCATCCGAACCGTAAAATCGAC 58.819 45.455 0.00 0.00 38.82 4.20
1725 1840 5.008514 TCGTATACATTCATCCGAACCGTAA 59.991 40.000 3.32 0.00 32.81 3.18
1726 1841 4.514816 TCGTATACATTCATCCGAACCGTA 59.485 41.667 3.32 0.00 32.81 4.02
1727 1842 3.316029 TCGTATACATTCATCCGAACCGT 59.684 43.478 3.32 0.00 32.81 4.83
1728 1843 3.892522 TCGTATACATTCATCCGAACCG 58.107 45.455 3.32 0.00 32.81 4.44
1729 1844 5.060569 CGAATCGTATACATTCATCCGAACC 59.939 44.000 19.23 1.97 32.81 3.62
1730 1845 5.628193 ACGAATCGTATACATTCATCCGAAC 59.372 40.000 6.47 3.83 38.73 3.95
1731 1846 5.765176 ACGAATCGTATACATTCATCCGAA 58.235 37.500 6.47 0.00 38.73 4.30
1732 1847 5.366829 ACGAATCGTATACATTCATCCGA 57.633 39.130 6.47 5.09 38.73 4.55
1739 1863 2.220133 GGCGCAACGAATCGTATACATT 59.780 45.455 9.30 2.33 39.99 2.71
1762 1886 3.276846 GTGACGGCACACCACCAC 61.277 66.667 18.77 0.00 44.51 4.16
1793 1921 0.950836 CACAATGGACGTGGAAAGCA 59.049 50.000 0.00 0.00 0.00 3.91
1797 1925 2.326222 GTGCACAATGGACGTGGAA 58.674 52.632 13.17 0.00 36.41 3.53
1817 1945 2.505498 CGTCGATCGGCGTTTCCAG 61.505 63.158 32.27 3.89 41.80 3.86
1838 1966 5.284864 TCTTTCTACAGATCGATGATGCAC 58.715 41.667 0.54 0.00 0.00 4.57
1856 1984 7.043059 TGTTCGTGCACCAATTTATTTTCTTTC 60.043 33.333 12.15 0.00 0.00 2.62
1883 2011 1.794116 ACGTACGTGCGCTTGTTTATT 59.206 42.857 26.01 0.00 34.88 1.40
1884 2012 1.421382 ACGTACGTGCGCTTGTTTAT 58.579 45.000 26.01 0.34 34.88 1.40
1886 2014 0.503961 GTACGTACGTGCGCTTGTTT 59.496 50.000 30.25 7.89 34.88 2.83
1898 2026 0.105408 ATGATTGGCCCCGTACGTAC 59.895 55.000 15.90 15.90 0.00 3.67
1911 2039 2.564062 ACCAACTTGCCAAGGATGATTG 59.436 45.455 9.64 3.77 0.00 2.67
1912 2040 2.893424 ACCAACTTGCCAAGGATGATT 58.107 42.857 9.64 0.00 0.00 2.57
1915 2043 2.094675 CCTACCAACTTGCCAAGGATG 58.905 52.381 9.64 7.40 0.00 3.51
1916 2044 1.616994 GCCTACCAACTTGCCAAGGAT 60.617 52.381 9.64 0.00 0.00 3.24
1917 2045 0.251165 GCCTACCAACTTGCCAAGGA 60.251 55.000 9.64 0.00 0.00 3.36
1918 2046 0.251341 AGCCTACCAACTTGCCAAGG 60.251 55.000 9.64 0.00 0.00 3.61
1919 2047 1.168714 GAGCCTACCAACTTGCCAAG 58.831 55.000 2.11 2.11 0.00 3.61
1949 2195 5.062528 GGAGATCAGAAAGATTGGATGGAC 58.937 45.833 0.00 0.00 37.00 4.02
1953 2199 9.933240 ATTTTAAGGAGATCAGAAAGATTGGAT 57.067 29.630 0.00 0.00 37.00 3.41
1983 2229 9.880064 CAGAACATAGAGAGCATGATTATTTTG 57.120 33.333 0.00 0.00 0.00 2.44
1984 2230 9.624373 ACAGAACATAGAGAGCATGATTATTTT 57.376 29.630 0.00 0.00 0.00 1.82
1986 2232 7.660617 CCACAGAACATAGAGAGCATGATTATT 59.339 37.037 0.00 0.00 0.00 1.40
1987 2233 7.015974 TCCACAGAACATAGAGAGCATGATTAT 59.984 37.037 0.00 0.00 0.00 1.28
1989 2235 5.129980 TCCACAGAACATAGAGAGCATGATT 59.870 40.000 0.00 0.00 0.00 2.57
1991 2237 4.026052 TCCACAGAACATAGAGAGCATGA 58.974 43.478 0.00 0.00 0.00 3.07
1993 2239 3.771479 TGTCCACAGAACATAGAGAGCAT 59.229 43.478 0.00 0.00 0.00 3.79
1994 2240 3.165071 TGTCCACAGAACATAGAGAGCA 58.835 45.455 0.00 0.00 0.00 4.26
1998 2244 5.521735 GCAGTTATGTCCACAGAACATAGAG 59.478 44.000 17.17 5.17 46.98 2.43
2001 2247 5.159273 TGCAGTTATGTCCACAGAACATA 57.841 39.130 17.17 2.98 46.98 2.29
2002 2248 4.019792 TGCAGTTATGTCCACAGAACAT 57.980 40.909 17.17 2.72 46.98 2.71
2003 2249 3.483808 TGCAGTTATGTCCACAGAACA 57.516 42.857 17.17 0.00 46.98 3.18
2004 2250 4.036262 TGTTTGCAGTTATGTCCACAGAAC 59.964 41.667 8.82 8.82 45.48 3.01
2005 2251 4.203226 TGTTTGCAGTTATGTCCACAGAA 58.797 39.130 0.00 0.00 0.00 3.02
2006 2252 3.814625 TGTTTGCAGTTATGTCCACAGA 58.185 40.909 0.00 0.00 0.00 3.41
2007 2253 4.566545 TTGTTTGCAGTTATGTCCACAG 57.433 40.909 0.00 0.00 0.00 3.66
2008 2254 4.400884 AGTTTGTTTGCAGTTATGTCCACA 59.599 37.500 0.00 0.00 0.00 4.17
2016 2262 4.632251 TCGAACTCAGTTTGTTTGCAGTTA 59.368 37.500 4.61 0.00 0.00 2.24
2017 2263 3.438781 TCGAACTCAGTTTGTTTGCAGTT 59.561 39.130 4.61 0.00 0.00 3.16
2026 2272 3.550275 TCAACTCGTTCGAACTCAGTTTG 59.450 43.478 27.27 22.92 31.30 2.93
2027 2273 3.777478 TCAACTCGTTCGAACTCAGTTT 58.223 40.909 27.27 16.48 31.30 2.66
2029 2275 3.253677 AGATCAACTCGTTCGAACTCAGT 59.746 43.478 24.80 21.55 0.00 3.41
2030 2276 3.827625 AGATCAACTCGTTCGAACTCAG 58.172 45.455 24.80 20.96 0.00 3.35
2040 2286 2.938838 AGCCTAGCTAGATCAACTCGT 58.061 47.619 22.70 0.00 36.99 4.18
2049 2302 5.995565 TTTTAGTGTCAAGCCTAGCTAGA 57.004 39.130 22.70 0.00 38.25 2.43
2061 2314 3.306917 TCCGCTCGAATTTTAGTGTCA 57.693 42.857 0.00 0.00 0.00 3.58
2063 2316 4.751060 TGTATCCGCTCGAATTTTAGTGT 58.249 39.130 0.00 0.00 0.00 3.55
2080 2333 5.348997 ACTTGAGCTTCGCTTAGTTTGTATC 59.651 40.000 0.00 0.00 39.88 2.24
2081 2334 5.238583 ACTTGAGCTTCGCTTAGTTTGTAT 58.761 37.500 0.00 0.00 39.88 2.29
2083 2336 3.467803 ACTTGAGCTTCGCTTAGTTTGT 58.532 40.909 0.00 0.00 39.88 2.83
2092 2345 1.136502 CAACTCGAACTTGAGCTTCGC 60.137 52.381 0.00 0.00 40.29 4.70
2104 2357 3.746045 AGCCACTTTCTACAACTCGAA 57.254 42.857 0.00 0.00 0.00 3.71
2107 2360 4.938226 AGCATTAGCCACTTTCTACAACTC 59.062 41.667 0.00 0.00 43.56 3.01
2110 2363 7.338710 AGATAAGCATTAGCCACTTTCTACAA 58.661 34.615 0.00 0.00 37.78 2.41
2112 2365 7.281100 ACAAGATAAGCATTAGCCACTTTCTAC 59.719 37.037 0.00 0.00 37.78 2.59
2115 2368 6.442513 ACAAGATAAGCATTAGCCACTTTC 57.557 37.500 0.00 0.00 37.78 2.62
2125 2378 9.624373 ACTTGAGATCATTACAAGATAAGCATT 57.376 29.630 20.29 2.52 42.12 3.56
2131 2384 7.043961 AGCGACTTGAGATCATTACAAGATA 57.956 36.000 20.29 0.00 42.12 1.98
2133 2386 5.330455 AGCGACTTGAGATCATTACAAGA 57.670 39.130 20.29 0.00 42.12 3.02
2212 2465 6.216801 TGTGTTGCGTCCTATCTAGTTAAT 57.783 37.500 0.00 0.00 0.00 1.40
2228 2482 4.829064 TTGGTCTTCTATGTTGTGTTGC 57.171 40.909 0.00 0.00 0.00 4.17
2302 2570 8.410673 AAGTAGTATCAGTCTTCAGTTGAGAA 57.589 34.615 0.00 0.00 0.00 2.87
2319 2587 9.095065 CCACGAACTTTTGCTATTAAGTAGTAT 57.905 33.333 0.00 0.00 33.66 2.12
2339 2607 3.509967 TCTCTTGTTAGCTCATCCACGAA 59.490 43.478 0.00 0.00 0.00 3.85
2403 2673 4.098155 TGGCCAGTGTGTTAACTATCCTA 58.902 43.478 0.00 0.00 0.00 2.94
2419 2689 2.716814 GCCTCAAGATCATGGCCAG 58.283 57.895 13.05 3.43 39.49 4.85
2428 2698 5.831103 TGGAGAAAATTTAGGCCTCAAGAT 58.169 37.500 9.68 0.00 0.00 2.40
2429 2699 5.255397 TGGAGAAAATTTAGGCCTCAAGA 57.745 39.130 9.68 0.00 0.00 3.02
2513 2790 2.240414 TGAGACGGAGGGTGTACTATCA 59.760 50.000 0.00 0.00 0.00 2.15
2514 2791 2.928334 TGAGACGGAGGGTGTACTATC 58.072 52.381 0.00 0.00 0.00 2.08
2515 2792 3.596940 ATGAGACGGAGGGTGTACTAT 57.403 47.619 0.00 0.00 0.00 2.12
2516 2793 4.719026 ATATGAGACGGAGGGTGTACTA 57.281 45.455 0.00 0.00 0.00 1.82
2517 2794 3.596940 ATATGAGACGGAGGGTGTACT 57.403 47.619 0.00 0.00 0.00 2.73
2518 2795 4.826183 ACTAATATGAGACGGAGGGTGTAC 59.174 45.833 0.00 0.00 0.00 2.90
2551 2838 7.296660 GCACTGAAATGCATCTAGATACATTC 58.703 38.462 24.92 19.16 45.39 2.67
2552 2839 7.199541 GCACTGAAATGCATCTAGATACATT 57.800 36.000 20.94 20.94 45.39 2.71
2578 2865 4.297299 TCGTCCCATATTAGTTGTCGTC 57.703 45.455 0.00 0.00 0.00 4.20
2579 2866 4.400251 TCTTCGTCCCATATTAGTTGTCGT 59.600 41.667 0.00 0.00 0.00 4.34
2580 2867 4.928601 TCTTCGTCCCATATTAGTTGTCG 58.071 43.478 0.00 0.00 0.00 4.35
2581 2868 6.145338 TCTCTTCGTCCCATATTAGTTGTC 57.855 41.667 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.