Multiple sequence alignment - TraesCS4B01G263700

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 TraesCS4B01G263700 chr4B 100.000 2435 0 0 1 2435 534720884 534723318 0.000000 4497.0
1 TraesCS4B01G263700 chr4D 90.324 2501 114 63 1 2435 434821532 434823970 0.000000 3160.0
2 TraesCS4B01G263700 chr4A 86.805 2554 168 87 1 2435 36313056 36315559 0.000000 2693.0
3 TraesCS4B01G263700 chr5B 100.000 32 0 0 2068 2099 479886832 479886863 0.000026 60.2
4 TraesCS4B01G263700 chr6A 96.875 32 0 1 360 391 467933634 467933604 0.004000 52.8


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 TraesCS4B01G263700 chr4B 534720884 534723318 2434 False 4497 4497 100.000 1 2435 1 chr4B.!!$F1 2434
1 TraesCS4B01G263700 chr4D 434821532 434823970 2438 False 3160 3160 90.324 1 2435 1 chr4D.!!$F1 2434
2 TraesCS4B01G263700 chr4A 36313056 36315559 2503 False 2693 2693 86.805 1 2435 1 chr4A.!!$F1 2434

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
385 401 0.10339 CAAACCCAACCGAACCCAAC 59.897 55.0 0.0 0.0 0.0 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1938 2072 0.249398 ACAGGAGATGTGTAACCCGC 59.751 55.0 0.0 0.0 41.91 6.13 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
49 51 2.698855 AACCTTGGTGATCGATGAGG 57.301 50.000 0.54 4.81 0.00 3.86
186 200 3.581265 ACCAACCCTTCCGAGTTTAAA 57.419 42.857 0.00 0.00 0.00 1.52
233 249 4.316645 GTCAAGGGTTAGAGGACAAAGAC 58.683 47.826 0.00 0.00 0.00 3.01
377 393 0.179097 CACCAAACCAAACCCAACCG 60.179 55.000 0.00 0.00 0.00 4.44
381 397 0.825410 AAACCAAACCCAACCGAACC 59.175 50.000 0.00 0.00 0.00 3.62
382 398 1.044231 AACCAAACCCAACCGAACCC 61.044 55.000 0.00 0.00 0.00 4.11
383 399 1.455959 CCAAACCCAACCGAACCCA 60.456 57.895 0.00 0.00 0.00 4.51
384 400 1.043673 CCAAACCCAACCGAACCCAA 61.044 55.000 0.00 0.00 0.00 4.12
385 401 0.103390 CAAACCCAACCGAACCCAAC 59.897 55.000 0.00 0.00 0.00 3.77
386 402 1.044231 AAACCCAACCGAACCCAACC 61.044 55.000 0.00 0.00 0.00 3.77
387 403 2.599281 CCCAACCGAACCCAACCC 60.599 66.667 0.00 0.00 0.00 4.11
388 404 2.599281 CCAACCGAACCCAACCCC 60.599 66.667 0.00 0.00 0.00 4.95
389 405 2.599281 CAACCGAACCCAACCCCC 60.599 66.667 0.00 0.00 0.00 5.40
390 406 2.779598 AACCGAACCCAACCCCCT 60.780 61.111 0.00 0.00 0.00 4.79
391 407 1.463804 AACCGAACCCAACCCCCTA 60.464 57.895 0.00 0.00 0.00 3.53
392 408 1.782201 AACCGAACCCAACCCCCTAC 61.782 60.000 0.00 0.00 0.00 3.18
393 409 2.672908 CGAACCCAACCCCCTACC 59.327 66.667 0.00 0.00 0.00 3.18
394 410 2.225596 CGAACCCAACCCCCTACCA 61.226 63.158 0.00 0.00 0.00 3.25
395 411 1.381463 GAACCCAACCCCCTACCAC 59.619 63.158 0.00 0.00 0.00 4.16
396 412 1.072459 AACCCAACCCCCTACCACT 60.072 57.895 0.00 0.00 0.00 4.00
397 413 0.196631 AACCCAACCCCCTACCACTA 59.803 55.000 0.00 0.00 0.00 2.74
454 488 2.342650 GCGCCACACCATCCATGTT 61.343 57.895 0.00 0.00 0.00 2.71
615 649 2.442236 TGGATCCCTTGGATTTGAGC 57.558 50.000 9.90 0.00 43.27 4.26
758 803 2.040043 CCTGATGCCTCCTCCCCT 60.040 66.667 0.00 0.00 0.00 4.79
819 864 1.450312 CCCTCAACCAGTGATCGGC 60.450 63.158 0.00 0.00 35.07 5.54
908 961 1.542030 CATACCCACCTAGCTAGCTCG 59.458 57.143 23.26 15.60 0.00 5.03
909 962 0.822532 TACCCACCTAGCTAGCTCGC 60.823 60.000 23.26 1.10 0.00 5.03
910 963 1.830408 CCCACCTAGCTAGCTCGCT 60.830 63.158 23.26 17.70 43.83 4.93
911 964 1.657556 CCACCTAGCTAGCTCGCTC 59.342 63.158 23.26 0.00 41.30 5.03
1105 1161 1.198713 GCAGAGGGTCAAGGAGATGA 58.801 55.000 0.00 0.00 0.00 2.92
1113 1169 1.018840 TCAAGGAGATGAGGGAGGGA 58.981 55.000 0.00 0.00 0.00 4.20
1442 1510 5.335269 CCTCGCTTCATCTGTAATATCGTCT 60.335 44.000 0.00 0.00 0.00 4.18
1443 1511 6.128254 CCTCGCTTCATCTGTAATATCGTCTA 60.128 42.308 0.00 0.00 0.00 2.59
1444 1512 6.600350 TCGCTTCATCTGTAATATCGTCTAC 58.400 40.000 0.00 0.00 0.00 2.59
1445 1513 5.505100 CGCTTCATCTGTAATATCGTCTACG 59.495 44.000 0.00 0.00 41.45 3.51
1574 1652 6.156519 CCTGTTGGGTTACTTTAATTTGAGC 58.843 40.000 0.00 0.00 0.00 4.26
1576 1654 7.354751 TGTTGGGTTACTTTAATTTGAGCTT 57.645 32.000 0.00 0.00 0.00 3.74
1601 1686 4.381718 CCCAGCTAGTCACACTACTTTACC 60.382 50.000 0.00 0.00 0.00 2.85
1703 1795 3.242349 GCATCTCTCAGAATGCGACTTTG 60.242 47.826 6.19 0.00 34.76 2.77
1707 1799 5.965922 TCTCTCAGAATGCGACTTTGAATA 58.034 37.500 0.00 0.00 34.76 1.75
1708 1800 5.807520 TCTCTCAGAATGCGACTTTGAATAC 59.192 40.000 0.00 0.00 34.76 1.89
1709 1801 4.562789 TCTCAGAATGCGACTTTGAATACG 59.437 41.667 0.00 0.00 34.76 3.06
1714 1809 5.744345 AGAATGCGACTTTGAATACGACTAG 59.256 40.000 0.00 0.00 0.00 2.57
1728 1823 8.886719 TGAATACGACTAGTTTCTCTTTATCGA 58.113 33.333 0.00 0.00 32.12 3.59
1744 1839 8.692110 TCTTTATCGAAATACACACGTATGTT 57.308 30.769 4.08 0.00 38.37 2.71
1745 1840 8.800972 TCTTTATCGAAATACACACGTATGTTC 58.199 33.333 4.08 0.00 38.37 3.18
1752 1847 8.588789 CGAAATACACACGTATGTTCATAAAGA 58.411 33.333 4.08 0.00 38.37 2.52
1760 1855 7.439955 ACACGTATGTTCATAAAGACAGACAAA 59.560 33.333 0.00 0.00 34.46 2.83
1763 1858 9.265938 CGTATGTTCATAAAGACAGACAAAATG 57.734 33.333 0.00 0.00 0.00 2.32
1766 1861 7.648142 TGTTCATAAAGACAGACAAAATGACC 58.352 34.615 0.00 0.00 0.00 4.02
1767 1862 7.502226 TGTTCATAAAGACAGACAAAATGACCT 59.498 33.333 0.00 0.00 0.00 3.85
1768 1863 8.352942 GTTCATAAAGACAGACAAAATGACCTT 58.647 33.333 0.00 0.00 0.00 3.50
1769 1864 7.874940 TCATAAAGACAGACAAAATGACCTTG 58.125 34.615 0.00 0.00 0.00 3.61
1770 1865 7.719193 TCATAAAGACAGACAAAATGACCTTGA 59.281 33.333 0.00 0.00 0.00 3.02
1771 1866 5.757850 AAGACAGACAAAATGACCTTGAC 57.242 39.130 0.00 0.00 0.00 3.18
1772 1867 5.041191 AGACAGACAAAATGACCTTGACT 57.959 39.130 0.00 0.00 30.53 3.41
1773 1868 5.440610 AGACAGACAAAATGACCTTGACTT 58.559 37.500 0.00 0.00 28.41 3.01
1775 1870 5.894807 ACAGACAAAATGACCTTGACTTTG 58.105 37.500 0.00 0.00 34.04 2.77
1779 1875 7.168637 CAGACAAAATGACCTTGACTTTGATTG 59.831 37.037 0.00 0.00 32.57 2.67
1787 1883 8.287439 TGACCTTGACTTTGATTGTAAAAAGA 57.713 30.769 2.38 0.00 36.96 2.52
1799 1895 8.351495 TGATTGTAAAAAGAACATTTGTGAGC 57.649 30.769 0.00 0.00 0.00 4.26
1801 1897 7.754069 TTGTAAAAAGAACATTTGTGAGCTG 57.246 32.000 0.00 0.00 0.00 4.24
1802 1898 6.862209 TGTAAAAAGAACATTTGTGAGCTGT 58.138 32.000 0.00 0.00 0.00 4.40
1803 1899 7.319646 TGTAAAAAGAACATTTGTGAGCTGTT 58.680 30.769 0.00 0.00 35.89 3.16
1804 1900 6.651755 AAAAAGAACATTTGTGAGCTGTTG 57.348 33.333 0.00 0.00 33.46 3.33
1805 1901 4.989279 AAGAACATTTGTGAGCTGTTGT 57.011 36.364 0.00 0.00 33.46 3.32
1806 1902 4.989279 AGAACATTTGTGAGCTGTTGTT 57.011 36.364 0.00 0.00 33.46 2.83
1807 1903 4.925068 AGAACATTTGTGAGCTGTTGTTC 58.075 39.130 0.00 1.52 41.88 3.18
1808 1904 4.398988 AGAACATTTGTGAGCTGTTGTTCA 59.601 37.500 13.98 0.00 43.23 3.18
1809 1905 4.297299 ACATTTGTGAGCTGTTGTTCAG 57.703 40.909 0.00 0.00 46.12 3.02
1810 1906 3.696051 ACATTTGTGAGCTGTTGTTCAGT 59.304 39.130 0.00 0.00 45.23 3.41
1811 1907 4.881273 ACATTTGTGAGCTGTTGTTCAGTA 59.119 37.500 0.00 0.00 45.23 2.74
1815 1911 6.449635 TTGTGAGCTGTTGTTCAGTAAAAT 57.550 33.333 0.00 0.00 45.23 1.82
1819 1915 7.275341 TGTGAGCTGTTGTTCAGTAAAATTTTG 59.725 33.333 13.76 0.00 45.23 2.44
1830 1926 6.397272 TCAGTAAAATTTTGCACATGGGATC 58.603 36.000 19.29 0.00 0.00 3.36
1837 1933 2.123018 TGCACATGGGATCCTCCTAT 57.877 50.000 12.58 0.00 38.36 2.57
1842 1938 3.692257 CATGGGATCCTCCTATGTGTC 57.308 52.381 12.58 0.00 46.62 3.67
1843 1939 2.866923 TGGGATCCTCCTATGTGTCA 57.133 50.000 12.58 0.00 36.57 3.58
1844 1940 3.129262 TGGGATCCTCCTATGTGTCAA 57.871 47.619 12.58 0.00 36.57 3.18
1845 1941 3.668821 TGGGATCCTCCTATGTGTCAAT 58.331 45.455 12.58 0.00 36.57 2.57
1846 1942 3.392285 TGGGATCCTCCTATGTGTCAATG 59.608 47.826 12.58 0.00 36.57 2.82
1855 1956 7.888021 TCCTCCTATGTGTCAATGTAACAAAAT 59.112 33.333 0.00 0.00 0.00 1.82
1873 1974 5.303971 CAAAATATTGTTGGCCCAAGTTCA 58.696 37.500 0.00 0.00 0.00 3.18
1874 1975 5.760484 AAATATTGTTGGCCCAAGTTCAT 57.240 34.783 0.00 0.00 0.00 2.57
1876 1977 6.469782 AATATTGTTGGCCCAAGTTCATAG 57.530 37.500 0.00 0.00 0.00 2.23
1877 1978 3.517296 TTGTTGGCCCAAGTTCATAGA 57.483 42.857 0.00 0.00 0.00 1.98
1895 1996 3.662247 AGAGAACCAGAGTAACAACCG 57.338 47.619 0.00 0.00 0.00 4.44
1896 1997 3.228453 AGAGAACCAGAGTAACAACCGA 58.772 45.455 0.00 0.00 0.00 4.69
1897 1998 3.833070 AGAGAACCAGAGTAACAACCGAT 59.167 43.478 0.00 0.00 0.00 4.18
1898 1999 4.283722 AGAGAACCAGAGTAACAACCGATT 59.716 41.667 0.00 0.00 0.00 3.34
1900 2001 6.014840 AGAGAACCAGAGTAACAACCGATTAA 60.015 38.462 0.00 0.00 0.00 1.40
1901 2002 5.930569 AGAACCAGAGTAACAACCGATTAAC 59.069 40.000 0.00 0.00 0.00 2.01
1902 2003 4.240096 ACCAGAGTAACAACCGATTAACG 58.760 43.478 0.00 0.00 42.18 3.18
1925 2059 2.828520 CAGAGACACTACACATGGGAGT 59.171 50.000 0.00 0.00 0.00 3.85
1935 2069 4.521130 ACACATGGGAGTATACGCATAG 57.479 45.455 0.00 0.00 40.50 2.23
1937 2071 4.587262 ACACATGGGAGTATACGCATAGAA 59.413 41.667 0.00 0.00 40.50 2.10
1938 2072 5.164233 CACATGGGAGTATACGCATAGAAG 58.836 45.833 8.93 0.00 40.50 2.85
1949 2083 2.018542 GCATAGAAGCGGGTTACACA 57.981 50.000 0.00 0.00 0.00 3.72
1950 2084 2.561569 GCATAGAAGCGGGTTACACAT 58.438 47.619 0.00 0.00 0.00 3.21
1957 2091 0.249398 GCGGGTTACACATCTCCTGT 59.751 55.000 0.00 0.00 39.20 4.00
1961 2095 3.132289 CGGGTTACACATCTCCTGTATGT 59.868 47.826 0.00 0.00 38.08 2.29
2023 2157 7.709269 AAATATAAAGATACGTGCATGTCGT 57.291 32.000 16.44 10.67 43.86 4.34
2024 2158 6.929587 ATATAAAGATACGTGCATGTCGTC 57.070 37.500 16.44 14.73 41.72 4.20
2025 2159 1.545759 AAGATACGTGCATGTCGTCG 58.454 50.000 16.44 2.14 41.72 5.12
2038 2172 0.299895 GTCGTCGCATCAGCAGATTG 59.700 55.000 0.00 0.00 42.27 2.67
2040 2174 0.723414 CGTCGCATCAGCAGATTGTT 59.277 50.000 0.00 0.00 42.27 2.83
2042 2176 2.348362 CGTCGCATCAGCAGATTGTTTA 59.652 45.455 0.00 0.00 42.27 2.01
2043 2177 3.542875 CGTCGCATCAGCAGATTGTTTAG 60.543 47.826 0.00 0.00 42.27 1.85
2044 2178 2.938451 TCGCATCAGCAGATTGTTTAGG 59.062 45.455 0.00 0.00 42.27 2.69
2045 2179 2.938451 CGCATCAGCAGATTGTTTAGGA 59.062 45.455 0.00 0.00 42.27 2.94
2046 2180 3.562973 CGCATCAGCAGATTGTTTAGGAT 59.437 43.478 0.00 0.00 42.27 3.24
2047 2181 4.036027 CGCATCAGCAGATTGTTTAGGATT 59.964 41.667 0.00 0.00 42.27 3.01
2048 2182 5.237127 CGCATCAGCAGATTGTTTAGGATTA 59.763 40.000 0.00 0.00 42.27 1.75
2091 2225 1.787155 CACGCACACACTACTCAACTC 59.213 52.381 0.00 0.00 0.00 3.01
2139 2277 2.817834 GCATCACGCACGGGCTAA 60.818 61.111 8.62 0.00 41.79 3.09
2140 2278 3.089784 CATCACGCACGGGCTAAC 58.910 61.111 8.62 0.00 38.10 2.34
2141 2279 1.447838 CATCACGCACGGGCTAACT 60.448 57.895 8.62 0.00 38.10 2.24
2142 2280 0.179121 CATCACGCACGGGCTAACTA 60.179 55.000 8.62 0.00 38.10 2.24
2143 2281 0.102481 ATCACGCACGGGCTAACTAG 59.898 55.000 8.62 0.00 38.10 2.57
2167 2321 7.326454 AGTAGTCTACTGACACGAAGTATACA 58.674 38.462 11.88 0.00 45.20 2.29
2176 2330 2.034812 CACGAAGTATACAGGCTCCTCC 59.965 54.545 5.50 0.00 41.61 4.30
2191 2345 2.973899 TCCGTCAGGAGCTGAAGC 59.026 61.111 0.00 0.00 42.46 3.86
2258 2412 2.783135 CCAGGCTATTCAATATGGCGT 58.217 47.619 0.00 0.00 0.00 5.68
2299 2453 0.605319 ATTTTGAGCCGAGCCGACAA 60.605 50.000 0.00 0.00 0.00 3.18
2302 2456 4.415332 GAGCCGAGCCGACAACGA 62.415 66.667 0.00 0.00 42.66 3.85
2379 2542 2.703798 CGGAAACATGCCTGCTGGG 61.704 63.158 12.06 1.66 38.36 4.45
2395 2558 1.153309 GGGCATGCAAAAGCATCCC 60.153 57.895 21.36 16.51 33.70 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 51 0.461693 GGACAGGAGCTGCTCATCAC 60.462 60.000 28.95 17.68 34.37 3.06
186 200 6.266323 GCCTCTCTTCTTTTTCGTTTTTCTT 58.734 36.000 0.00 0.00 0.00 2.52
233 249 3.378339 GTCGTATAGGATTTCGTGGTGG 58.622 50.000 0.00 0.00 0.00 4.61
301 317 0.835276 GCCGGGGAGGTAGTACAAAT 59.165 55.000 2.18 0.00 43.70 2.32
377 393 1.138228 AGTGGTAGGGGGTTGGGTTC 61.138 60.000 0.00 0.00 0.00 3.62
381 397 0.548197 TGGTAGTGGTAGGGGGTTGG 60.548 60.000 0.00 0.00 0.00 3.77
382 398 0.616891 GTGGTAGTGGTAGGGGGTTG 59.383 60.000 0.00 0.00 0.00 3.77
383 399 0.906282 CGTGGTAGTGGTAGGGGGTT 60.906 60.000 0.00 0.00 0.00 4.11
384 400 1.305549 CGTGGTAGTGGTAGGGGGT 60.306 63.158 0.00 0.00 0.00 4.95
385 401 1.000739 TCGTGGTAGTGGTAGGGGG 59.999 63.158 0.00 0.00 0.00 5.40
386 402 1.325476 GGTCGTGGTAGTGGTAGGGG 61.325 65.000 0.00 0.00 0.00 4.79
387 403 0.612732 TGGTCGTGGTAGTGGTAGGG 60.613 60.000 0.00 0.00 0.00 3.53
388 404 0.529378 GTGGTCGTGGTAGTGGTAGG 59.471 60.000 0.00 0.00 0.00 3.18
389 405 1.542492 AGTGGTCGTGGTAGTGGTAG 58.458 55.000 0.00 0.00 0.00 3.18
390 406 2.224744 TGTAGTGGTCGTGGTAGTGGTA 60.225 50.000 0.00 0.00 0.00 3.25
391 407 1.251251 GTAGTGGTCGTGGTAGTGGT 58.749 55.000 0.00 0.00 0.00 4.16
392 408 1.068055 GTGTAGTGGTCGTGGTAGTGG 60.068 57.143 0.00 0.00 0.00 4.00
393 409 1.884579 AGTGTAGTGGTCGTGGTAGTG 59.115 52.381 0.00 0.00 0.00 2.74
394 410 2.283145 AGTGTAGTGGTCGTGGTAGT 57.717 50.000 0.00 0.00 0.00 2.73
395 411 2.097142 GCTAGTGTAGTGGTCGTGGTAG 59.903 54.545 0.00 0.00 0.00 3.18
396 412 2.086869 GCTAGTGTAGTGGTCGTGGTA 58.913 52.381 0.00 0.00 0.00 3.25
397 413 0.886563 GCTAGTGTAGTGGTCGTGGT 59.113 55.000 0.00 0.00 0.00 4.16
454 488 2.740506 ATGCATGGACATGGACATGA 57.259 45.000 26.41 15.97 45.55 3.07
615 649 2.176546 CATGTGTTTCCGCGCCAG 59.823 61.111 0.00 0.00 0.00 4.85
758 803 5.708697 CCGGGGTATATATATGTATGCGAGA 59.291 44.000 5.44 0.00 0.00 4.04
819 864 1.434696 CTAGCAAGCCGCAAATGGG 59.565 57.895 0.00 0.00 46.13 4.00
908 961 3.512033 CTCACTTGTAGTGGGTAGAGC 57.488 52.381 6.96 0.00 45.94 4.09
966 1019 1.254975 TGCTTACGAGTAGCTGGCCA 61.255 55.000 4.71 4.71 0.00 5.36
1105 1161 2.041928 CAGCTCCCTTCCCTCCCT 59.958 66.667 0.00 0.00 0.00 4.20
1574 1652 3.511934 AGTAGTGTGACTAGCTGGGAAAG 59.488 47.826 0.85 0.00 30.12 2.62
1576 1654 3.170991 AGTAGTGTGACTAGCTGGGAA 57.829 47.619 0.85 0.00 30.12 3.97
1703 1795 9.713740 TTCGATAAAGAGAAACTAGTCGTATTC 57.286 33.333 0.00 0.00 32.66 1.75
1707 1799 9.500864 GTATTTCGATAAAGAGAAACTAGTCGT 57.499 33.333 0.00 0.00 38.90 4.34
1708 1800 9.499585 TGTATTTCGATAAAGAGAAACTAGTCG 57.500 33.333 0.00 0.00 38.90 4.18
1714 1809 7.727017 ACGTGTGTATTTCGATAAAGAGAAAC 58.273 34.615 0.00 0.00 38.90 2.78
1728 1823 9.210329 TGTCTTTATGAACATACGTGTGTATTT 57.790 29.630 18.74 2.86 39.28 1.40
1736 1831 7.956420 TTTGTCTGTCTTTATGAACATACGT 57.044 32.000 0.00 0.00 0.00 3.57
1737 1832 9.265938 CATTTTGTCTGTCTTTATGAACATACG 57.734 33.333 0.00 0.00 0.00 3.06
1744 1839 7.719193 TCAAGGTCATTTTGTCTGTCTTTATGA 59.281 33.333 0.00 0.00 0.00 2.15
1745 1840 7.805071 GTCAAGGTCATTTTGTCTGTCTTTATG 59.195 37.037 0.00 0.00 0.00 1.90
1752 1847 5.652014 TCAAAGTCAAGGTCATTTTGTCTGT 59.348 36.000 0.00 0.00 32.22 3.41
1760 1855 9.533253 CTTTTTACAATCAAAGTCAAGGTCATT 57.467 29.630 0.00 0.00 0.00 2.57
1763 1858 9.020813 GTTCTTTTTACAATCAAAGTCAAGGTC 57.979 33.333 0.00 0.00 32.67 3.85
1765 1860 8.925161 TGTTCTTTTTACAATCAAAGTCAAGG 57.075 30.769 0.00 0.00 32.67 3.61
1773 1868 8.816144 GCTCACAAATGTTCTTTTTACAATCAA 58.184 29.630 0.00 0.00 0.00 2.57
1775 1870 8.482429 CAGCTCACAAATGTTCTTTTTACAATC 58.518 33.333 0.00 0.00 0.00 2.67
1779 1875 7.275560 ACAACAGCTCACAAATGTTCTTTTTAC 59.724 33.333 0.00 0.00 35.04 2.01
1787 1883 4.675510 CTGAACAACAGCTCACAAATGTT 58.324 39.130 0.00 0.00 39.86 2.71
1801 1897 7.125113 CCATGTGCAAAATTTTACTGAACAAC 58.875 34.615 2.44 0.00 0.00 3.32
1802 1898 6.259608 CCCATGTGCAAAATTTTACTGAACAA 59.740 34.615 2.44 0.00 0.00 2.83
1803 1899 5.757320 CCCATGTGCAAAATTTTACTGAACA 59.243 36.000 2.44 3.89 0.00 3.18
1804 1900 5.988561 TCCCATGTGCAAAATTTTACTGAAC 59.011 36.000 2.44 0.00 0.00 3.18
1805 1901 6.166984 TCCCATGTGCAAAATTTTACTGAA 57.833 33.333 2.44 0.00 0.00 3.02
1806 1902 5.798125 TCCCATGTGCAAAATTTTACTGA 57.202 34.783 2.44 0.00 0.00 3.41
1807 1903 5.581874 GGATCCCATGTGCAAAATTTTACTG 59.418 40.000 2.44 0.00 0.00 2.74
1808 1904 5.484998 AGGATCCCATGTGCAAAATTTTACT 59.515 36.000 8.55 0.00 0.00 2.24
1809 1905 5.733676 AGGATCCCATGTGCAAAATTTTAC 58.266 37.500 8.55 0.00 0.00 2.01
1810 1906 5.976458 GAGGATCCCATGTGCAAAATTTTA 58.024 37.500 8.55 0.00 0.00 1.52
1811 1907 4.835678 GAGGATCCCATGTGCAAAATTTT 58.164 39.130 8.55 0.00 0.00 1.82
1830 1926 7.447374 TTTTGTTACATTGACACATAGGAGG 57.553 36.000 0.00 0.00 0.00 4.30
1855 1956 5.045213 TCTCTATGAACTTGGGCCAACAATA 60.045 40.000 16.66 9.60 0.00 1.90
1873 1974 5.014858 TCGGTTGTTACTCTGGTTCTCTAT 58.985 41.667 0.00 0.00 0.00 1.98
1874 1975 4.401022 TCGGTTGTTACTCTGGTTCTCTA 58.599 43.478 0.00 0.00 0.00 2.43
1876 1977 3.655276 TCGGTTGTTACTCTGGTTCTC 57.345 47.619 0.00 0.00 0.00 2.87
1877 1978 4.618920 AATCGGTTGTTACTCTGGTTCT 57.381 40.909 0.00 0.00 0.00 3.01
1891 1992 3.255149 AGTGTCTCTGTCGTTAATCGGTT 59.745 43.478 0.00 0.00 40.32 4.44
1893 1994 3.489180 AGTGTCTCTGTCGTTAATCGG 57.511 47.619 0.00 0.00 40.32 4.18
1895 1996 5.696822 TGTGTAGTGTCTCTGTCGTTAATC 58.303 41.667 0.00 0.00 0.00 1.75
1896 1997 5.700722 TGTGTAGTGTCTCTGTCGTTAAT 57.299 39.130 0.00 0.00 0.00 1.40
1897 1998 5.458015 CATGTGTAGTGTCTCTGTCGTTAA 58.542 41.667 0.00 0.00 0.00 2.01
1898 1999 4.082949 CCATGTGTAGTGTCTCTGTCGTTA 60.083 45.833 0.00 0.00 0.00 3.18
1900 2001 2.229062 CCATGTGTAGTGTCTCTGTCGT 59.771 50.000 0.00 0.00 0.00 4.34
1901 2002 2.416027 CCCATGTGTAGTGTCTCTGTCG 60.416 54.545 0.00 0.00 0.00 4.35
1902 2003 2.826128 TCCCATGTGTAGTGTCTCTGTC 59.174 50.000 0.00 0.00 0.00 3.51
1925 2059 6.947562 TGTGTAACCCGCTTCTATGCGTATA 61.948 44.000 8.06 0.00 44.75 1.47
1935 2069 1.207329 AGGAGATGTGTAACCCGCTTC 59.793 52.381 0.00 0.00 34.36 3.86
1937 2071 0.537188 CAGGAGATGTGTAACCCGCT 59.463 55.000 0.00 0.00 34.36 5.52
1938 2072 0.249398 ACAGGAGATGTGTAACCCGC 59.751 55.000 0.00 0.00 41.91 6.13
1940 2074 4.442706 CACATACAGGAGATGTGTAACCC 58.557 47.826 7.45 0.00 45.99 4.11
1997 2131 8.061857 ACGACATGCACGTATCTTTATATTTTG 58.938 33.333 15.09 0.00 42.17 2.44
1998 2132 8.138365 ACGACATGCACGTATCTTTATATTTT 57.862 30.769 15.09 0.00 42.17 1.82
1999 2133 7.358105 CGACGACATGCACGTATCTTTATATTT 60.358 37.037 16.30 0.00 43.97 1.40
2002 2136 4.907582 CGACGACATGCACGTATCTTTATA 59.092 41.667 16.30 0.00 43.97 0.98
2003 2137 3.729217 CGACGACATGCACGTATCTTTAT 59.271 43.478 16.30 0.00 43.97 1.40
2012 2146 2.317689 GATGCGACGACATGCACG 59.682 61.111 0.00 10.57 45.07 5.34
2023 2157 2.938451 CCTAAACAATCTGCTGATGCGA 59.062 45.455 6.88 0.00 43.34 5.10
2024 2158 2.938451 TCCTAAACAATCTGCTGATGCG 59.062 45.455 6.88 4.49 43.34 4.73
2025 2159 5.511234 AATCCTAAACAATCTGCTGATGC 57.489 39.130 6.88 0.00 40.20 3.91
2067 2201 1.129326 GAGTAGTGTGTGCGTGTGAC 58.871 55.000 0.00 0.00 0.00 3.67
2068 2202 0.741915 TGAGTAGTGTGTGCGTGTGA 59.258 50.000 0.00 0.00 0.00 3.58
2091 2225 3.526931 TCTTCTCCTTGCCATACTTCG 57.473 47.619 0.00 0.00 0.00 3.79
2139 2277 5.792741 ACTTCGTGTCAGTAGACTACTAGT 58.207 41.667 14.79 9.94 45.20 2.57
2140 2278 8.967218 GTATACTTCGTGTCAGTAGACTACTAG 58.033 40.741 14.79 9.34 45.20 2.57
2141 2279 8.470002 TGTATACTTCGTGTCAGTAGACTACTA 58.530 37.037 14.79 0.00 45.20 1.82
2142 2280 7.326454 TGTATACTTCGTGTCAGTAGACTACT 58.674 38.462 9.45 9.45 45.20 2.57
2143 2281 7.254387 CCTGTATACTTCGTGTCAGTAGACTAC 60.254 44.444 4.32 4.32 45.20 2.73
2176 2330 2.290122 ATCCGCTTCAGCTCCTGACG 62.290 60.000 0.00 0.00 40.46 4.35
2243 2397 2.503331 TGGGCACGCCATATTGAATAG 58.497 47.619 10.83 0.00 37.98 1.73
2258 2412 0.327924 ATGAGATCACGGTTTGGGCA 59.672 50.000 0.00 0.00 0.00 5.36
2322 2476 3.256631 GGTCTTTCTTCACCCTGTACGTA 59.743 47.826 0.00 0.00 0.00 3.57
2324 2478 2.036733 TGGTCTTTCTTCACCCTGTACG 59.963 50.000 0.00 0.00 0.00 3.67
2325 2479 3.323979 TCTGGTCTTTCTTCACCCTGTAC 59.676 47.826 0.00 0.00 0.00 2.90
2395 2558 2.610694 CCAGTCACCAGCACGCTTG 61.611 63.158 0.00 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.