Multiple sequence alignment - TraesCS4A01G167900

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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 TraesCS4A01G167900 chr4A 100.000 2728 0 0 1 2728 418073416 418070689 0.000000e+00 5038
1 TraesCS4A01G167900 chr7A 93.018 1905 102 16 2 1888 140769419 140767528 0.000000e+00 2752
2 TraesCS4A01G167900 chr4B 92.677 1898 113 10 1 1888 551784277 551786158 0.000000e+00 2712
3 TraesCS4A01G167900 chr4B 92.571 1898 115 10 1 1888 551729669 551731550 0.000000e+00 2700
4 TraesCS4A01G167900 chr4B 90.915 1442 111 7 459 1888 633911517 633910084 0.000000e+00 1919
5 TraesCS4A01G167900 chr4B 90.869 1358 90 15 543 1888 14029209 14027874 0.000000e+00 1790
6 TraesCS4A01G167900 chr4B 91.482 857 59 10 1037 1888 584911661 584910814 0.000000e+00 1166
7 TraesCS4A01G167900 chr4B 91.365 857 60 10 1037 1888 584886320 584885473 0.000000e+00 1160
8 TraesCS4A01G167900 chr4B 89.805 461 37 7 1432 1888 584860610 584860156 1.410000e-162 582
9 TraesCS4A01G167900 chr2D 92.680 1899 96 12 7 1888 591013551 591015423 0.000000e+00 2697
10 TraesCS4A01G167900 chr2D 93.318 1721 99 9 1 1713 487337604 487335892 0.000000e+00 2527
11 TraesCS4A01G167900 chr4D 91.430 1902 125 24 1 1886 414225151 414227030 0.000000e+00 2575
12 TraesCS4A01G167900 chr7D 93.672 1675 93 8 1 1670 535833496 535831830 0.000000e+00 2494
13 TraesCS4A01G167900 chr7D 89.568 1898 159 26 3 1886 432740977 432739105 0.000000e+00 2372
14 TraesCS4A01G167900 chr3B 90.373 1901 146 21 1 1886 478551391 478549513 0.000000e+00 2462
15 TraesCS4A01G167900 chr7B 88.080 1896 195 18 1 1883 238000714 238002591 0.000000e+00 2220
16 TraesCS4A01G167900 chr2B 86.667 255 19 13 1638 1886 612692317 612692072 4.480000e-68 268
17 TraesCS4A01G167900 chr3A 73.053 809 158 38 1919 2694 571335244 571336025 5.870000e-57 231


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 TraesCS4A01G167900 chr4A 418070689 418073416 2727 True 5038 5038 100.000 1 2728 1 chr4A.!!$R1 2727
1 TraesCS4A01G167900 chr7A 140767528 140769419 1891 True 2752 2752 93.018 2 1888 1 chr7A.!!$R1 1886
2 TraesCS4A01G167900 chr4B 551784277 551786158 1881 False 2712 2712 92.677 1 1888 1 chr4B.!!$F2 1887
3 TraesCS4A01G167900 chr4B 551729669 551731550 1881 False 2700 2700 92.571 1 1888 1 chr4B.!!$F1 1887
4 TraesCS4A01G167900 chr4B 633910084 633911517 1433 True 1919 1919 90.915 459 1888 1 chr4B.!!$R5 1429
5 TraesCS4A01G167900 chr4B 14027874 14029209 1335 True 1790 1790 90.869 543 1888 1 chr4B.!!$R1 1345
6 TraesCS4A01G167900 chr4B 584910814 584911661 847 True 1166 1166 91.482 1037 1888 1 chr4B.!!$R4 851
7 TraesCS4A01G167900 chr4B 584885473 584886320 847 True 1160 1160 91.365 1037 1888 1 chr4B.!!$R3 851
8 TraesCS4A01G167900 chr2D 591013551 591015423 1872 False 2697 2697 92.680 7 1888 1 chr2D.!!$F1 1881
9 TraesCS4A01G167900 chr2D 487335892 487337604 1712 True 2527 2527 93.318 1 1713 1 chr2D.!!$R1 1712
10 TraesCS4A01G167900 chr4D 414225151 414227030 1879 False 2575 2575 91.430 1 1886 1 chr4D.!!$F1 1885
11 TraesCS4A01G167900 chr7D 535831830 535833496 1666 True 2494 2494 93.672 1 1670 1 chr7D.!!$R2 1669
12 TraesCS4A01G167900 chr7D 432739105 432740977 1872 True 2372 2372 89.568 3 1886 1 chr7D.!!$R1 1883
13 TraesCS4A01G167900 chr3B 478549513 478551391 1878 True 2462 2462 90.373 1 1886 1 chr3B.!!$R1 1885
14 TraesCS4A01G167900 chr7B 238000714 238002591 1877 False 2220 2220 88.080 1 1883 1 chr7B.!!$F1 1882
15 TraesCS4A01G167900 chr3A 571335244 571336025 781 False 231 231 73.053 1919 2694 1 chr3A.!!$F1 775

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
979 1036 0.250597 GAAGGGGTTGGCGTTGTAGT 60.251 55.0 0.0 0.0 0.0 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2187 2300 0.031994 AAAGCATCACAACAACCGGC 59.968 50.0 0.0 0.0 0.0 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
79 80 2.757077 CCCTCACCGCTCCCTTTT 59.243 61.111 0.00 0.00 0.00 2.27
150 151 2.027377 CAGAGCAAGAAGACCACCAGAT 60.027 50.000 0.00 0.00 0.00 2.90
235 238 4.002906 TCGACATGCAGTACTTTTTCCT 57.997 40.909 0.00 0.00 0.00 3.36
297 307 6.960542 GGAATGGGGAATAGAGGTAGATAAGA 59.039 42.308 0.00 0.00 0.00 2.10
346 383 9.653287 TTCATAGTACTTCAAACTAGTTCATGG 57.347 33.333 8.95 3.15 33.15 3.66
620 677 2.966732 GCTCCCCACCAATGACCGA 61.967 63.158 0.00 0.00 0.00 4.69
976 1033 2.203437 GGAAGGGGTTGGCGTTGT 60.203 61.111 0.00 0.00 0.00 3.32
979 1036 0.250597 GAAGGGGTTGGCGTTGTAGT 60.251 55.000 0.00 0.00 0.00 2.73
982 1039 0.820482 GGGGTTGGCGTTGTAGTTGT 60.820 55.000 0.00 0.00 0.00 3.32
1050 1115 0.912968 AGGGGGTGGGTAAGTAGTGC 60.913 60.000 0.00 0.00 0.00 4.40
1074 1139 3.908103 GGGCAGGGTGAGTAAATATAGGA 59.092 47.826 0.00 0.00 0.00 2.94
1144 1209 4.334552 TGCTCTTCAATAAGCCATGAACA 58.665 39.130 0.00 0.00 37.73 3.18
1430 1500 0.179032 TCCTTGCACCGAAGCTTGAA 60.179 50.000 2.10 0.00 34.99 2.69
1471 1541 0.103390 TTCACCAAGCACTTCGTCGA 59.897 50.000 0.00 0.00 0.00 4.20
1502 1572 5.063880 ACGGAGTTCAAGCTTAGAAACAAT 58.936 37.500 16.38 2.30 37.78 2.71
1582 1652 1.454539 GTTGGGCCACCTACACAGT 59.545 57.895 5.23 0.00 41.41 3.55
1592 1662 3.368427 CCACCTACACAGTCGTTCATCAT 60.368 47.826 0.00 0.00 0.00 2.45
1603 1673 6.145535 CAGTCGTTCATCATATCAAGATCGA 58.854 40.000 0.00 0.00 31.98 3.59
1622 1692 3.054166 CGACTACATGGTGACGTTCAAA 58.946 45.455 0.00 0.00 0.00 2.69
1770 1842 5.646577 AAGTACTACGAGTCTGCTTTGAT 57.353 39.130 0.00 0.00 0.00 2.57
1888 1985 2.031807 GCTCTGCTTATGATGTGTGCTG 59.968 50.000 0.00 0.00 0.00 4.41
1889 1986 3.528532 CTCTGCTTATGATGTGTGCTGA 58.471 45.455 0.00 0.00 0.00 4.26
1890 1987 3.528532 TCTGCTTATGATGTGTGCTGAG 58.471 45.455 0.00 0.00 0.00 3.35
1891 1988 2.612672 CTGCTTATGATGTGTGCTGAGG 59.387 50.000 0.00 0.00 0.00 3.86
1892 1989 1.945394 GCTTATGATGTGTGCTGAGGG 59.055 52.381 0.00 0.00 0.00 4.30
1893 1990 2.569059 CTTATGATGTGTGCTGAGGGG 58.431 52.381 0.00 0.00 0.00 4.79
1894 1991 0.839277 TATGATGTGTGCTGAGGGGG 59.161 55.000 0.00 0.00 0.00 5.40
1895 1992 1.210204 ATGATGTGTGCTGAGGGGGT 61.210 55.000 0.00 0.00 0.00 4.95
1896 1993 1.377725 GATGTGTGCTGAGGGGGTG 60.378 63.158 0.00 0.00 0.00 4.61
1897 1994 2.826777 GATGTGTGCTGAGGGGGTGG 62.827 65.000 0.00 0.00 0.00 4.61
1898 1995 3.249189 GTGTGCTGAGGGGGTGGA 61.249 66.667 0.00 0.00 0.00 4.02
1899 1996 2.204136 TGTGCTGAGGGGGTGGAT 60.204 61.111 0.00 0.00 0.00 3.41
1900 1997 1.852157 TGTGCTGAGGGGGTGGATT 60.852 57.895 0.00 0.00 0.00 3.01
1901 1998 1.384191 GTGCTGAGGGGGTGGATTT 59.616 57.895 0.00 0.00 0.00 2.17
1902 1999 0.251787 GTGCTGAGGGGGTGGATTTT 60.252 55.000 0.00 0.00 0.00 1.82
1903 2000 0.039618 TGCTGAGGGGGTGGATTTTC 59.960 55.000 0.00 0.00 0.00 2.29
1904 2001 1.032114 GCTGAGGGGGTGGATTTTCG 61.032 60.000 0.00 0.00 0.00 3.46
1905 2002 0.328258 CTGAGGGGGTGGATTTTCGT 59.672 55.000 0.00 0.00 0.00 3.85
1906 2003 0.037590 TGAGGGGGTGGATTTTCGTG 59.962 55.000 0.00 0.00 0.00 4.35
1907 2004 0.679960 GAGGGGGTGGATTTTCGTGG 60.680 60.000 0.00 0.00 0.00 4.94
1908 2005 1.137594 AGGGGGTGGATTTTCGTGGA 61.138 55.000 0.00 0.00 0.00 4.02
1909 2006 0.963856 GGGGGTGGATTTTCGTGGAC 60.964 60.000 0.00 0.00 0.00 4.02
1910 2007 0.963856 GGGGTGGATTTTCGTGGACC 60.964 60.000 0.00 0.00 0.00 4.46
1911 2008 0.037734 GGGTGGATTTTCGTGGACCT 59.962 55.000 0.00 0.00 0.00 3.85
1912 2009 1.165270 GGTGGATTTTCGTGGACCTG 58.835 55.000 0.00 0.00 0.00 4.00
1913 2010 1.271163 GGTGGATTTTCGTGGACCTGA 60.271 52.381 0.00 0.00 0.00 3.86
1914 2011 2.076863 GTGGATTTTCGTGGACCTGAG 58.923 52.381 0.00 0.00 0.00 3.35
1915 2012 1.697432 TGGATTTTCGTGGACCTGAGT 59.303 47.619 0.00 0.00 0.00 3.41
1916 2013 2.105821 TGGATTTTCGTGGACCTGAGTT 59.894 45.455 0.00 0.00 0.00 3.01
1917 2014 3.146847 GGATTTTCGTGGACCTGAGTTT 58.853 45.455 0.00 0.00 0.00 2.66
1918 2015 3.058224 GGATTTTCGTGGACCTGAGTTTG 60.058 47.826 0.00 0.00 0.00 2.93
1919 2016 2.992124 TTTCGTGGACCTGAGTTTGA 57.008 45.000 0.00 0.00 0.00 2.69
1920 2017 2.992124 TTCGTGGACCTGAGTTTGAA 57.008 45.000 0.00 0.00 0.00 2.69
1921 2018 2.992124 TCGTGGACCTGAGTTTGAAA 57.008 45.000 0.00 0.00 0.00 2.69
1922 2019 3.485463 TCGTGGACCTGAGTTTGAAAT 57.515 42.857 0.00 0.00 0.00 2.17
1923 2020 3.138304 TCGTGGACCTGAGTTTGAAATG 58.862 45.455 0.00 0.00 0.00 2.32
1924 2021 3.138304 CGTGGACCTGAGTTTGAAATGA 58.862 45.455 0.00 0.00 0.00 2.57
1930 2027 2.751806 CCTGAGTTTGAAATGAGCTCCC 59.248 50.000 12.15 0.00 0.00 4.30
1999 2104 4.219999 GCCTCCTCCGCTGCTCTC 62.220 72.222 0.00 0.00 0.00 3.20
2000 2105 3.898509 CCTCCTCCGCTGCTCTCG 61.899 72.222 0.00 0.00 0.00 4.04
2001 2106 4.567385 CTCCTCCGCTGCTCTCGC 62.567 72.222 0.00 0.00 0.00 5.03
2044 2149 4.416601 CCCCTCCCCCTCTCCGTT 62.417 72.222 0.00 0.00 0.00 4.44
2054 2161 3.114647 CTCTCCGTTCTCCTCGCCG 62.115 68.421 0.00 0.00 0.00 6.46
2057 2164 4.493747 CCGTTCTCCTCGCCGTCC 62.494 72.222 0.00 0.00 0.00 4.79
2089 2196 4.699522 GGCGGACTTGGCGGAGTT 62.700 66.667 0.00 0.00 0.00 3.01
2092 2199 3.056328 GGACTTGGCGGAGTTGGC 61.056 66.667 0.00 0.00 0.00 4.52
2200 2313 4.939368 CCGGGCCGGTTGTTGTGA 62.939 66.667 36.52 0.00 42.73 3.58
2201 2314 2.671619 CGGGCCGGTTGTTGTGAT 60.672 61.111 20.56 0.00 0.00 3.06
2202 2315 2.961768 GGGCCGGTTGTTGTGATG 59.038 61.111 1.90 0.00 0.00 3.07
2204 2317 2.268076 GGCCGGTTGTTGTGATGCT 61.268 57.895 1.90 0.00 0.00 3.79
2205 2318 1.659794 GCCGGTTGTTGTGATGCTT 59.340 52.632 1.90 0.00 0.00 3.91
2206 2319 0.031994 GCCGGTTGTTGTGATGCTTT 59.968 50.000 1.90 0.00 0.00 3.51
2207 2320 1.930371 GCCGGTTGTTGTGATGCTTTC 60.930 52.381 1.90 0.00 0.00 2.62
2208 2321 1.608590 CCGGTTGTTGTGATGCTTTCT 59.391 47.619 0.00 0.00 0.00 2.52
2210 2323 2.662791 CGGTTGTTGTGATGCTTTCTCG 60.663 50.000 0.00 0.00 0.00 4.04
2213 2326 0.790866 GTTGTGATGCTTTCTCGCGC 60.791 55.000 0.00 0.00 0.00 6.86
2214 2327 1.911293 TTGTGATGCTTTCTCGCGCC 61.911 55.000 0.00 0.00 0.00 6.53
2216 2329 2.512515 GATGCTTTCTCGCGCCCT 60.513 61.111 0.00 0.00 0.00 5.19
2217 2330 2.045926 ATGCTTTCTCGCGCCCTT 60.046 55.556 0.00 0.00 0.00 3.95
2219 2332 3.050275 GCTTTCTCGCGCCCTTGT 61.050 61.111 0.00 0.00 0.00 3.16
2222 2335 3.509137 TTTCTCGCGCCCTTGTCGT 62.509 57.895 0.00 0.00 0.00 4.34
2223 2336 2.981977 TTTCTCGCGCCCTTGTCGTT 62.982 55.000 0.00 0.00 0.00 3.85
2224 2337 3.479269 CTCGCGCCCTTGTCGTTC 61.479 66.667 0.00 0.00 0.00 3.95
2225 2338 3.916392 CTCGCGCCCTTGTCGTTCT 62.916 63.158 0.00 0.00 0.00 3.01
2226 2339 2.126228 CGCGCCCTTGTCGTTCTA 60.126 61.111 0.00 0.00 0.00 2.10
2228 2341 2.098831 GCGCCCTTGTCGTTCTACC 61.099 63.158 0.00 0.00 0.00 3.18
2231 2344 1.804326 CCCTTGTCGTTCTACCGCG 60.804 63.158 0.00 0.00 0.00 6.46
2232 2345 1.210931 CCTTGTCGTTCTACCGCGA 59.789 57.895 8.23 0.00 34.54 5.87
2237 2350 2.960129 CGTTCTACCGCGATGCCC 60.960 66.667 8.23 0.00 0.00 5.36
2252 2365 2.815308 CCCTCGCTATTGACGCCT 59.185 61.111 0.00 0.00 0.00 5.52
2253 2366 2.038690 CCCTCGCTATTGACGCCTA 58.961 57.895 0.00 0.00 0.00 3.93
2281 2394 4.410400 CGCCTTGGGACCCAGGAC 62.410 72.222 23.95 11.78 31.89 3.85
2282 2395 4.048470 GCCTTGGGACCCAGGACC 62.048 72.222 23.95 10.48 31.89 4.46
2363 2476 3.872603 TGCACGTCCTGGCACCTT 61.873 61.111 0.00 0.00 34.58 3.50
2435 2560 3.782443 GGTTCTCCGCCCATCCGT 61.782 66.667 0.00 0.00 0.00 4.69
2444 2569 4.907034 CCCATCCGTCGCGTCTCG 62.907 72.222 5.77 9.96 40.15 4.04
2465 2590 0.807667 CCTTCAGACCCTTCATCGCG 60.808 60.000 0.00 0.00 0.00 5.87
2466 2591 0.173481 CTTCAGACCCTTCATCGCGA 59.827 55.000 13.09 13.09 0.00 5.87
2468 2593 1.215382 CAGACCCTTCATCGCGACA 59.785 57.895 12.93 0.00 0.00 4.35
2500 2625 4.479993 GCTGCGCCTGTCTCCCAT 62.480 66.667 4.18 0.00 0.00 4.00
2501 2626 2.202987 CTGCGCCTGTCTCCCATC 60.203 66.667 4.18 0.00 0.00 3.51
2502 2627 3.746949 CTGCGCCTGTCTCCCATCC 62.747 68.421 4.18 0.00 0.00 3.51
2504 2629 4.899239 CGCCTGTCTCCCATCCGC 62.899 72.222 0.00 0.00 0.00 5.54
2506 2631 3.461773 CCTGTCTCCCATCCGCGT 61.462 66.667 4.92 0.00 0.00 6.01
2507 2632 2.579201 CTGTCTCCCATCCGCGTT 59.421 61.111 4.92 0.00 0.00 4.84
2511 2636 4.547367 CTCCCATCCGCGTTCCCC 62.547 72.222 4.92 0.00 0.00 4.81
2516 2641 3.072468 ATCCGCGTTCCCCGAAGA 61.072 61.111 4.92 0.00 39.56 2.87
2517 2642 2.432300 ATCCGCGTTCCCCGAAGAT 61.432 57.895 4.92 0.00 39.56 2.40
2519 2644 2.183300 CGCGTTCCCCGAAGATCA 59.817 61.111 0.00 0.00 39.56 2.92
2528 2653 2.109799 CGAAGATCATGGCCCGCT 59.890 61.111 0.00 0.00 0.00 5.52
2529 2654 1.958205 CGAAGATCATGGCCCGCTC 60.958 63.158 0.00 0.00 0.00 5.03
2607 2732 3.710722 CGTCCTCCCTGCCTTGCT 61.711 66.667 0.00 0.00 0.00 3.91
2620 2745 4.641645 TTGCTGGCTGGACCGTGG 62.642 66.667 0.00 0.00 43.94 4.94
2641 2766 4.776322 CCTGGGCCGAACGCATCA 62.776 66.667 0.00 0.00 40.94 3.07
2699 2824 4.888325 CCCCCTCCCGGATCAGCT 62.888 72.222 0.73 0.00 0.00 4.24
2700 2825 3.554342 CCCCTCCCGGATCAGCTG 61.554 72.222 7.63 7.63 0.00 4.24
2701 2826 4.247380 CCCTCCCGGATCAGCTGC 62.247 72.222 9.47 0.00 0.00 5.25
2702 2827 3.160047 CCTCCCGGATCAGCTGCT 61.160 66.667 9.47 0.00 0.00 4.24
2703 2828 2.108566 CTCCCGGATCAGCTGCTG 59.891 66.667 23.31 23.31 0.00 4.41
2704 2829 3.457625 CTCCCGGATCAGCTGCTGG 62.458 68.421 27.79 12.53 31.51 4.85
2705 2830 4.559063 CCCGGATCAGCTGCTGGG 62.559 72.222 27.79 20.17 43.90 4.45
2715 2840 4.415150 CTGCTGGGCCGGTGTCAT 62.415 66.667 15.16 0.00 0.00 3.06
2716 2841 4.720902 TGCTGGGCCGGTGTCATG 62.721 66.667 15.16 0.00 0.00 3.07
2718 2843 3.716195 CTGGGCCGGTGTCATGGA 61.716 66.667 3.48 0.00 0.00 3.41
2719 2844 3.253061 TGGGCCGGTGTCATGGAA 61.253 61.111 1.90 0.00 0.00 3.53
2720 2845 2.275418 GGGCCGGTGTCATGGAAT 59.725 61.111 1.90 0.00 0.00 3.01
2721 2846 1.379843 GGGCCGGTGTCATGGAATT 60.380 57.895 1.90 0.00 0.00 2.17
2722 2847 1.666209 GGGCCGGTGTCATGGAATTG 61.666 60.000 1.90 0.00 0.00 2.32
2723 2848 0.965363 GGCCGGTGTCATGGAATTGT 60.965 55.000 1.90 0.00 0.00 2.71
2724 2849 0.451783 GCCGGTGTCATGGAATTGTC 59.548 55.000 1.90 0.00 0.00 3.18
2725 2850 1.819928 CCGGTGTCATGGAATTGTCA 58.180 50.000 0.00 0.00 0.00 3.58
2726 2851 1.468520 CCGGTGTCATGGAATTGTCAC 59.531 52.381 0.00 0.00 35.70 3.67
2727 2852 1.128507 CGGTGTCATGGAATTGTCACG 59.871 52.381 0.00 0.00 36.79 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 0.840722 GAGTGGGGGAGAGTGGGAAA 60.841 60.000 0.00 0.00 0.00 3.13
79 80 2.169590 GAGAGTGGGGGAGAGTGGGA 62.170 65.000 0.00 0.00 0.00 4.37
150 151 4.812476 CGCTCGCCGGTGATGGAA 62.812 66.667 19.93 0.00 0.00 3.53
203 204 3.243873 ACTGCATGTCGAACAGAGAGAAA 60.244 43.478 11.59 0.00 35.38 2.52
235 238 1.244816 ATCTATCGCCGGATCGAACA 58.755 50.000 5.05 0.00 42.15 3.18
297 307 7.338703 TGAACTCGTATGAACTACCTCTACATT 59.661 37.037 0.00 0.00 0.00 2.71
346 383 5.646606 GCATCTACCTCTATTCCGATCTTC 58.353 45.833 0.00 0.00 0.00 2.87
457 505 5.392272 CGATGAACAAGAAGATGAATGCCAA 60.392 40.000 0.00 0.00 0.00 4.52
462 510 3.310774 CGGCGATGAACAAGAAGATGAAT 59.689 43.478 0.00 0.00 0.00 2.57
778 835 1.194781 ACGCTGATTCCTGACCCAGT 61.195 55.000 0.00 0.00 0.00 4.00
896 953 3.340789 GTGACCGCACCAAGTTCC 58.659 61.111 0.00 0.00 39.14 3.62
1050 1115 3.864789 ATATTTACTCACCCTGCCCAG 57.135 47.619 0.00 0.00 0.00 4.45
1074 1139 0.260230 TTCTCCTCCTCTCCATCGCT 59.740 55.000 0.00 0.00 0.00 4.93
1144 1209 0.179045 GGAGTCAGGCACAACACAGT 60.179 55.000 0.00 0.00 0.00 3.55
1471 1541 2.436087 CTTGAACTCCGTCGGCACCT 62.436 60.000 6.34 0.00 0.00 4.00
1493 1563 2.419574 GGAGCAGCCGGTATTGTTTCTA 60.420 50.000 1.90 0.00 0.00 2.10
1496 1566 0.328258 AGGAGCAGCCGGTATTGTTT 59.672 50.000 1.90 0.00 43.43 2.83
1502 1572 2.284331 TTCCAGGAGCAGCCGGTA 60.284 61.111 1.90 0.00 43.43 4.02
1582 1652 6.319141 AGTCGATCTTGATATGATGAACGA 57.681 37.500 6.39 6.39 32.88 3.85
1592 1662 5.277828 CGTCACCATGTAGTCGATCTTGATA 60.278 44.000 0.00 0.00 0.00 2.15
1603 1673 4.056050 GAGTTTGAACGTCACCATGTAGT 58.944 43.478 0.00 0.00 0.00 2.73
1622 1692 1.606889 GGTGTCGGGAGTGAGGAGT 60.607 63.158 0.00 0.00 0.00 3.85
1770 1842 9.853555 CAAGCATAAACCATAAACATAAACAGA 57.146 29.630 0.00 0.00 0.00 3.41
1888 1985 0.679960 CCACGAAAATCCACCCCCTC 60.680 60.000 0.00 0.00 0.00 4.30
1889 1986 1.137594 TCCACGAAAATCCACCCCCT 61.138 55.000 0.00 0.00 0.00 4.79
1890 1987 0.963856 GTCCACGAAAATCCACCCCC 60.964 60.000 0.00 0.00 0.00 5.40
1891 1988 0.963856 GGTCCACGAAAATCCACCCC 60.964 60.000 0.00 0.00 0.00 4.95
1892 1989 0.037734 AGGTCCACGAAAATCCACCC 59.962 55.000 0.00 0.00 0.00 4.61
1893 1990 1.165270 CAGGTCCACGAAAATCCACC 58.835 55.000 0.00 0.00 0.00 4.61
1894 1991 2.076863 CTCAGGTCCACGAAAATCCAC 58.923 52.381 0.00 0.00 0.00 4.02
1895 1992 1.697432 ACTCAGGTCCACGAAAATCCA 59.303 47.619 0.00 0.00 0.00 3.41
1896 1993 2.474410 ACTCAGGTCCACGAAAATCC 57.526 50.000 0.00 0.00 0.00 3.01
1897 1994 3.813166 TCAAACTCAGGTCCACGAAAATC 59.187 43.478 0.00 0.00 0.00 2.17
1898 1995 3.815809 TCAAACTCAGGTCCACGAAAAT 58.184 40.909 0.00 0.00 0.00 1.82
1899 1996 3.269538 TCAAACTCAGGTCCACGAAAA 57.730 42.857 0.00 0.00 0.00 2.29
1900 1997 2.992124 TCAAACTCAGGTCCACGAAA 57.008 45.000 0.00 0.00 0.00 3.46
1901 1998 2.992124 TTCAAACTCAGGTCCACGAA 57.008 45.000 0.00 0.00 0.00 3.85
1902 1999 2.992124 TTTCAAACTCAGGTCCACGA 57.008 45.000 0.00 0.00 0.00 4.35
1903 2000 3.138304 TCATTTCAAACTCAGGTCCACG 58.862 45.455 0.00 0.00 0.00 4.94
1904 2001 3.057946 GCTCATTTCAAACTCAGGTCCAC 60.058 47.826 0.00 0.00 0.00 4.02
1905 2002 3.149196 GCTCATTTCAAACTCAGGTCCA 58.851 45.455 0.00 0.00 0.00 4.02
1906 2003 3.416156 AGCTCATTTCAAACTCAGGTCC 58.584 45.455 0.00 0.00 0.00 4.46
1907 2004 3.438434 GGAGCTCATTTCAAACTCAGGTC 59.562 47.826 17.19 0.00 0.00 3.85
1908 2005 3.416156 GGAGCTCATTTCAAACTCAGGT 58.584 45.455 17.19 0.00 0.00 4.00
1909 2006 2.751806 GGGAGCTCATTTCAAACTCAGG 59.248 50.000 17.19 0.00 0.00 3.86
1910 2007 2.417933 CGGGAGCTCATTTCAAACTCAG 59.582 50.000 17.19 0.00 0.00 3.35
1911 2008 2.426522 CGGGAGCTCATTTCAAACTCA 58.573 47.619 17.19 0.00 0.00 3.41
1982 2087 4.219999 GAGAGCAGCGGAGGAGGC 62.220 72.222 0.00 0.00 0.00 4.70
2027 2132 4.416601 AACGGAGAGGGGGAGGGG 62.417 72.222 0.00 0.00 0.00 4.79
2031 2136 2.226149 GAGGAGAACGGAGAGGGGGA 62.226 65.000 0.00 0.00 0.00 4.81
2033 2138 2.122167 CGAGGAGAACGGAGAGGGG 61.122 68.421 0.00 0.00 0.00 4.79
2036 2141 2.802106 GGCGAGGAGAACGGAGAG 59.198 66.667 0.00 0.00 0.00 3.20
2037 2142 3.132139 CGGCGAGGAGAACGGAGA 61.132 66.667 0.00 0.00 0.00 3.71
2038 2143 3.398353 GACGGCGAGGAGAACGGAG 62.398 68.421 16.62 0.00 0.00 4.63
2039 2144 3.437795 GACGGCGAGGAGAACGGA 61.438 66.667 16.62 0.00 0.00 4.69
2041 2146 4.493747 GGGACGGCGAGGAGAACG 62.494 72.222 16.62 0.00 0.00 3.95
2042 2147 4.144703 GGGGACGGCGAGGAGAAC 62.145 72.222 16.62 0.00 0.00 3.01
2075 2182 3.056328 GCCAACTCCGCCAAGTCC 61.056 66.667 0.00 0.00 0.00 3.85
2187 2300 0.031994 AAAGCATCACAACAACCGGC 59.968 50.000 0.00 0.00 0.00 6.13
2189 2302 2.662791 CGAGAAAGCATCACAACAACCG 60.663 50.000 0.00 0.00 0.00 4.44
2193 2306 0.512518 CGCGAGAAAGCATCACAACA 59.487 50.000 0.00 0.00 36.85 3.33
2195 2308 1.497278 GCGCGAGAAAGCATCACAA 59.503 52.632 12.10 0.00 36.85 3.33
2197 2310 2.401195 GGCGCGAGAAAGCATCAC 59.599 61.111 12.10 0.00 36.85 3.06
2198 2311 2.803155 AAGGGCGCGAGAAAGCATCA 62.803 55.000 12.10 0.00 36.85 3.07
2200 2313 2.045926 AAGGGCGCGAGAAAGCAT 60.046 55.556 12.10 0.00 36.85 3.79
2201 2314 3.049674 CAAGGGCGCGAGAAAGCA 61.050 61.111 12.10 0.00 36.85 3.91
2202 2315 3.028366 GACAAGGGCGCGAGAAAGC 62.028 63.158 12.10 0.00 0.00 3.51
2204 2317 2.736995 CGACAAGGGCGCGAGAAA 60.737 61.111 12.10 0.00 0.00 2.52
2205 2318 3.509137 AACGACAAGGGCGCGAGAA 62.509 57.895 12.10 0.00 0.00 2.87
2206 2319 3.909258 GAACGACAAGGGCGCGAGA 62.909 63.158 12.10 0.00 0.00 4.04
2207 2320 2.537792 TAGAACGACAAGGGCGCGAG 62.538 60.000 12.10 0.00 0.00 5.03
2208 2321 2.628696 TAGAACGACAAGGGCGCGA 61.629 57.895 12.10 0.00 0.00 5.87
2210 2323 2.098831 GGTAGAACGACAAGGGCGC 61.099 63.158 0.00 0.00 0.00 6.53
2213 2326 1.804326 CGCGGTAGAACGACAAGGG 60.804 63.158 0.00 0.00 35.47 3.95
2214 2327 0.179145 ATCGCGGTAGAACGACAAGG 60.179 55.000 6.13 0.00 41.76 3.61
2216 2329 1.074319 GCATCGCGGTAGAACGACAA 61.074 55.000 6.13 0.00 41.76 3.18
2217 2330 1.515519 GCATCGCGGTAGAACGACA 60.516 57.895 6.13 0.00 41.76 4.35
2219 2332 2.103538 GGCATCGCGGTAGAACGA 59.896 61.111 6.13 0.00 43.33 3.85
2222 2335 2.812499 GAGGGCATCGCGGTAGAA 59.188 61.111 6.13 0.00 0.00 2.10
2223 2336 3.592814 CGAGGGCATCGCGGTAGA 61.593 66.667 9.16 0.00 45.98 2.59
2231 2344 1.560860 GCGTCAATAGCGAGGGCATC 61.561 60.000 0.00 0.00 43.41 3.91
2232 2345 1.595382 GCGTCAATAGCGAGGGCAT 60.595 57.895 0.00 0.00 43.41 4.40
2237 2350 0.952280 TCCTAGGCGTCAATAGCGAG 59.048 55.000 2.96 0.00 35.00 5.03
2242 2355 2.614829 GGCTTTCCTAGGCGTCAATA 57.385 50.000 2.96 0.00 39.90 1.90
2243 2356 3.478540 GGCTTTCCTAGGCGTCAAT 57.521 52.632 2.96 0.00 39.90 2.57
2252 2365 3.712907 AAGGCGGCGGCTTTCCTA 61.713 61.111 38.36 0.00 46.16 2.94
2346 2459 3.872603 AAGGTGCCAGGACGTGCA 61.873 61.111 10.52 1.21 34.54 4.57
2356 2469 2.027460 CAACCGTTGCAAGGTGCC 59.973 61.111 17.23 0.00 44.23 5.01
2420 2545 3.833645 CGACGGATGGGCGGAGAA 61.834 66.667 0.00 0.00 0.00 2.87
2427 2552 4.907034 CGAGACGCGACGGATGGG 62.907 72.222 15.93 0.00 44.57 4.00
2439 2564 1.545706 AAGGGTCTGAAGGGCGAGAC 61.546 60.000 0.00 0.00 38.32 3.36
2440 2565 1.229209 AAGGGTCTGAAGGGCGAGA 60.229 57.895 0.00 0.00 0.00 4.04
2441 2566 1.219393 GAAGGGTCTGAAGGGCGAG 59.781 63.158 0.00 0.00 0.00 5.03
2444 2569 0.462759 CGATGAAGGGTCTGAAGGGC 60.463 60.000 0.00 0.00 0.00 5.19
2447 2572 0.173481 TCGCGATGAAGGGTCTGAAG 59.827 55.000 3.71 0.00 0.00 3.02
2450 2575 0.179100 ATGTCGCGATGAAGGGTCTG 60.179 55.000 14.06 0.00 0.00 3.51
2451 2576 0.537188 AATGTCGCGATGAAGGGTCT 59.463 50.000 14.06 0.00 0.00 3.85
2453 2578 0.806102 CGAATGTCGCGATGAAGGGT 60.806 55.000 14.06 0.00 31.14 4.34
2504 2629 1.160329 GCCATGATCTTCGGGGAACG 61.160 60.000 0.00 0.00 46.11 3.95
2506 2631 1.531748 GGCCATGATCTTCGGGGAA 59.468 57.895 0.00 0.00 0.00 3.97
2507 2632 2.452064 GGGCCATGATCTTCGGGGA 61.452 63.158 4.39 0.00 0.00 4.81
2511 2636 1.958205 GAGCGGGCCATGATCTTCG 60.958 63.158 4.39 0.00 0.00 3.79
2513 2638 2.512896 GGAGCGGGCCATGATCTT 59.487 61.111 4.39 0.00 0.00 2.40
2592 2717 3.333219 CCAGCAAGGCAGGGAGGA 61.333 66.667 0.00 0.00 31.34 3.71
2631 2756 2.514592 AGGCCCATGATGCGTTCG 60.515 61.111 0.00 0.00 0.00 3.95
2633 2758 2.124151 GGAGGCCCATGATGCGTT 60.124 61.111 0.00 0.00 0.00 4.84
2634 2759 4.195334 GGGAGGCCCATGATGCGT 62.195 66.667 0.00 0.00 44.65 5.24
2698 2823 4.415150 ATGACACCGGCCCAGCAG 62.415 66.667 0.00 0.00 0.00 4.24
2699 2824 4.720902 CATGACACCGGCCCAGCA 62.721 66.667 0.00 0.00 0.00 4.41
2701 2826 2.556840 ATTCCATGACACCGGCCCAG 62.557 60.000 0.00 0.00 0.00 4.45
2702 2827 2.148723 AATTCCATGACACCGGCCCA 62.149 55.000 0.00 0.00 0.00 5.36
2703 2828 1.379843 AATTCCATGACACCGGCCC 60.380 57.895 0.00 0.00 0.00 5.80
2704 2829 0.965363 ACAATTCCATGACACCGGCC 60.965 55.000 0.00 0.00 0.00 6.13
2705 2830 0.451783 GACAATTCCATGACACCGGC 59.548 55.000 0.00 0.00 0.00 6.13
2706 2831 1.468520 GTGACAATTCCATGACACCGG 59.531 52.381 0.00 0.00 39.16 5.28
2707 2832 1.128507 CGTGACAATTCCATGACACCG 59.871 52.381 0.00 0.00 41.04 4.94
2708 2833 2.900122 CGTGACAATTCCATGACACC 57.100 50.000 0.00 0.00 41.04 4.16


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

AutoCloner maintained by Alex Coulton.