Multiple sequence alignment - TraesCS2A01G426800

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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 TraesCS2A01G426800 chr2A 100.000 1455 0 0 1 1455 679988196 679986742 0.000000e+00 2687
1 TraesCS2A01G426800 chr2A 96.426 1455 52 0 1 1455 447899692 447898238 0.000000e+00 2399
2 TraesCS2A01G426800 chr2A 100.000 632 0 0 1762 2393 679986435 679985804 0.000000e+00 1168
3 TraesCS2A01G426800 chr3A 97.938 1455 30 0 1 1455 110312759 110311305 0.000000e+00 2521
4 TraesCS2A01G426800 chr7A 97.119 1458 39 1 1 1455 7844591 7843134 0.000000e+00 2457
5 TraesCS2A01G426800 chr7A 89.416 1455 153 1 1 1455 20254408 20252955 0.000000e+00 1832
6 TraesCS2A01G426800 chr7A 88.668 1456 163 2 1 1455 270771073 270772527 0.000000e+00 1773
7 TraesCS2A01G426800 chr4A 96.888 1446 45 0 1 1446 546006792 546005347 0.000000e+00 2422
8 TraesCS2A01G426800 chr5A 92.234 1455 113 0 1 1455 707721226 707722680 0.000000e+00 2061
9 TraesCS2A01G426800 chr5A 89.828 1455 147 1 1 1455 622529042 622527589 0.000000e+00 1866
10 TraesCS2A01G426800 chr6B 86.607 1456 193 2 1 1455 68900866 68902320 0.000000e+00 1607
11 TraesCS2A01G426800 chr2B 80.273 659 63 41 1774 2393 640102475 640101845 3.650000e-118 435
12 TraesCS2A01G426800 chr2D 80.687 466 39 21 1774 2215 537457512 537457074 4.970000e-82 315


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 TraesCS2A01G426800 chr2A 679985804 679988196 2392 True 1927.5 2687 100.000 1 2393 2 chr2A.!!$R2 2392
1 TraesCS2A01G426800 chr2A 447898238 447899692 1454 True 2399.0 2399 96.426 1 1455 1 chr2A.!!$R1 1454
2 TraesCS2A01G426800 chr3A 110311305 110312759 1454 True 2521.0 2521 97.938 1 1455 1 chr3A.!!$R1 1454
3 TraesCS2A01G426800 chr7A 7843134 7844591 1457 True 2457.0 2457 97.119 1 1455 1 chr7A.!!$R1 1454
4 TraesCS2A01G426800 chr7A 20252955 20254408 1453 True 1832.0 1832 89.416 1 1455 1 chr7A.!!$R2 1454
5 TraesCS2A01G426800 chr7A 270771073 270772527 1454 False 1773.0 1773 88.668 1 1455 1 chr7A.!!$F1 1454
6 TraesCS2A01G426800 chr4A 546005347 546006792 1445 True 2422.0 2422 96.888 1 1446 1 chr4A.!!$R1 1445
7 TraesCS2A01G426800 chr5A 707721226 707722680 1454 False 2061.0 2061 92.234 1 1455 1 chr5A.!!$F1 1454
8 TraesCS2A01G426800 chr5A 622527589 622529042 1453 True 1866.0 1866 89.828 1 1455 1 chr5A.!!$R1 1454
9 TraesCS2A01G426800 chr6B 68900866 68902320 1454 False 1607.0 1607 86.607 1 1455 1 chr6B.!!$F1 1454
10 TraesCS2A01G426800 chr2B 640101845 640102475 630 True 435.0 435 80.273 1774 2393 1 chr2B.!!$R1 619

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
759 760 1.653151 GGAACCGTCTGTCTAATGCC 58.347 55.0 0.0 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2258 2307 0.038166 GAGGGAATGGCTTGGACACA 59.962 55.0 0.0 0.0 0.0 3.72 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
414 415 5.592104 AAAATCTGGAAGTTCAAAACCGT 57.408 34.783 5.01 0.00 33.76 4.83
714 715 4.788679 AGGTTTTAGTGGCTACTGTTTGT 58.211 39.130 13.76 0.00 37.78 2.83
759 760 1.653151 GGAACCGTCTGTCTAATGCC 58.347 55.000 0.00 0.00 0.00 4.40
762 763 2.230940 CCGTCTGTCTAATGCCGCG 61.231 63.158 0.00 0.00 0.00 6.46
901 905 7.446319 CCTCCATTATTGCTGAAGATGATACAA 59.554 37.037 0.00 0.00 0.00 2.41
963 967 4.568956 TCAAAGTCAAGATCTTCGCATGA 58.431 39.130 4.57 4.40 0.00 3.07
1192 1196 2.108952 GGCCTCAATCCCAATATCTGGT 59.891 50.000 0.00 0.00 44.76 4.00
1322 1326 6.601217 GCTGATTTCTCTCTATGGGTTTTTCT 59.399 38.462 0.00 0.00 0.00 2.52
1845 1854 1.594293 CAAACGTGAGGCCGAGTGT 60.594 57.895 0.00 0.00 0.00 3.55
1849 1858 2.280797 GTGAGGCCGAGTGTGCAA 60.281 61.111 0.00 0.00 0.00 4.08
1858 1867 1.571460 GAGTGTGCAAAGGCGTGAG 59.429 57.895 0.00 0.00 45.35 3.51
1894 1903 4.759693 TCACAGTTACGAAAATGCATTCCT 59.240 37.500 13.38 2.77 34.03 3.36
1896 1905 5.343058 CACAGTTACGAAAATGCATTCCTTG 59.657 40.000 13.38 9.50 34.03 3.61
1897 1906 5.240623 ACAGTTACGAAAATGCATTCCTTGA 59.759 36.000 13.38 0.00 34.03 3.02
1898 1907 6.071952 ACAGTTACGAAAATGCATTCCTTGAT 60.072 34.615 13.38 0.00 34.03 2.57
1899 1908 6.252015 CAGTTACGAAAATGCATTCCTTGATG 59.748 38.462 13.38 2.15 0.00 3.07
1912 1926 6.493116 CATTCCTTGATGCAGAGTTTACATC 58.507 40.000 0.00 0.00 40.48 3.06
1919 1933 7.509141 TGATGCAGAGTTTACATCAAAAAGA 57.491 32.000 2.60 0.00 45.27 2.52
1920 1934 7.587629 TGATGCAGAGTTTACATCAAAAAGAG 58.412 34.615 2.60 0.00 45.27 2.85
1921 1935 7.445096 TGATGCAGAGTTTACATCAAAAAGAGA 59.555 33.333 2.60 0.00 45.27 3.10
1922 1936 7.566760 TGCAGAGTTTACATCAAAAAGAGAA 57.433 32.000 0.00 0.00 0.00 2.87
1924 1938 7.080724 GCAGAGTTTACATCAAAAAGAGAAGG 58.919 38.462 0.00 0.00 0.00 3.46
1925 1939 7.080724 CAGAGTTTACATCAAAAAGAGAAGGC 58.919 38.462 0.00 0.00 0.00 4.35
1926 1940 6.772716 AGAGTTTACATCAAAAAGAGAAGGCA 59.227 34.615 0.00 0.00 0.00 4.75
1927 1941 7.449704 AGAGTTTACATCAAAAAGAGAAGGCAT 59.550 33.333 0.00 0.00 0.00 4.40
1928 1942 7.373493 AGTTTACATCAAAAAGAGAAGGCATG 58.627 34.615 0.00 0.00 0.00 4.06
1930 1944 3.575256 ACATCAAAAAGAGAAGGCATGCA 59.425 39.130 21.36 0.00 0.00 3.96
1931 1945 3.648339 TCAAAAAGAGAAGGCATGCAC 57.352 42.857 21.36 9.10 0.00 4.57
1932 1946 2.957680 TCAAAAAGAGAAGGCATGCACA 59.042 40.909 21.36 0.00 0.00 4.57
1933 1947 3.054878 CAAAAAGAGAAGGCATGCACAC 58.945 45.455 21.36 9.48 0.00 3.82
1934 1948 1.251251 AAAGAGAAGGCATGCACACC 58.749 50.000 21.36 1.15 0.00 4.16
1935 1949 0.610232 AAGAGAAGGCATGCACACCC 60.610 55.000 21.36 5.28 0.00 4.61
1936 1950 2.036256 AGAAGGCATGCACACCCC 59.964 61.111 21.36 0.00 0.00 4.95
1937 1951 2.283101 GAAGGCATGCACACCCCA 60.283 61.111 21.36 0.00 0.00 4.96
1938 1952 2.283388 AAGGCATGCACACCCCAG 60.283 61.111 21.36 0.00 0.00 4.45
1973 1987 7.410800 TGCATAAAGCTTGTGATTTTTCTTG 57.589 32.000 14.41 0.00 45.94 3.02
1975 1989 7.169645 TGCATAAAGCTTGTGATTTTTCTTGTC 59.830 33.333 14.41 0.00 45.94 3.18
1976 1990 7.169645 GCATAAAGCTTGTGATTTTTCTTGTCA 59.830 33.333 14.41 0.00 41.15 3.58
1977 1991 9.199982 CATAAAGCTTGTGATTTTTCTTGTCAT 57.800 29.630 0.00 0.00 33.52 3.06
1980 1994 9.768662 AAAGCTTGTGATTTTTCTTGTCATATT 57.231 25.926 0.00 0.00 0.00 1.28
2014 2030 1.802636 CCATACCGGCACAGCTTTG 59.197 57.895 0.00 0.00 0.00 2.77
2028 2044 4.338118 CACAGCTTTGTTGGGAAGTTAAGA 59.662 41.667 0.00 0.00 0.00 2.10
2030 2046 5.010012 ACAGCTTTGTTGGGAAGTTAAGATG 59.990 40.000 0.00 0.00 35.72 2.90
2089 2112 6.183360 ACAAGTAGCAACATATCCGAGTACAT 60.183 38.462 0.00 0.00 0.00 2.29
2099 2122 7.749808 ACATATCCGAGTACATATTAGTCACG 58.250 38.462 0.00 0.00 0.00 4.35
2101 2124 8.613482 CATATCCGAGTACATATTAGTCACGAT 58.387 37.037 0.00 0.00 0.00 3.73
2126 2149 4.272504 ACCAACTTTGTACATGAACGACAG 59.727 41.667 0.00 0.00 0.00 3.51
2187 2210 1.503542 GCAGCACATGTGTACCAGC 59.496 57.895 26.01 17.96 0.00 4.85
2206 2229 3.431233 CAGCACAGTCACACTCACATTAG 59.569 47.826 0.00 0.00 0.00 1.73
2209 2232 4.240888 CACAGTCACACTCACATTAGAGG 58.759 47.826 0.00 0.00 39.97 3.69
2234 2283 2.618559 CCATCCACACCATCACATGACA 60.619 50.000 0.00 0.00 0.00 3.58
2235 2284 2.183478 TCCACACCATCACATGACAC 57.817 50.000 0.00 0.00 0.00 3.67
2236 2285 0.798159 CCACACCATCACATGACACG 59.202 55.000 0.00 0.00 0.00 4.49
2237 2286 0.166597 CACACCATCACATGACACGC 59.833 55.000 0.00 0.00 0.00 5.34
2238 2287 0.250252 ACACCATCACATGACACGCA 60.250 50.000 0.00 0.00 0.00 5.24
2244 2293 1.082821 CACATGACACGCACCAACG 60.083 57.895 0.00 0.00 39.50 4.10
2250 2299 4.920112 CACGCACCAACGTCCCCA 62.920 66.667 0.00 0.00 46.34 4.96
2258 2307 1.184970 CCAACGTCCCCAATTGCCTT 61.185 55.000 0.00 0.00 0.00 4.35
2259 2308 0.038343 CAACGTCCCCAATTGCCTTG 60.038 55.000 0.00 0.00 34.42 3.61
2260 2309 0.469144 AACGTCCCCAATTGCCTTGT 60.469 50.000 0.00 0.00 32.61 3.16
2261 2310 1.178534 ACGTCCCCAATTGCCTTGTG 61.179 55.000 0.00 0.00 32.61 3.33
2262 2311 1.178534 CGTCCCCAATTGCCTTGTGT 61.179 55.000 0.00 0.00 32.61 3.72
2263 2312 0.603065 GTCCCCAATTGCCTTGTGTC 59.397 55.000 0.00 0.00 32.61 3.67
2264 2313 0.541764 TCCCCAATTGCCTTGTGTCC 60.542 55.000 0.00 0.00 32.61 4.02
2265 2314 0.831288 CCCCAATTGCCTTGTGTCCA 60.831 55.000 0.00 0.00 32.61 4.02
2268 2317 1.606224 CCAATTGCCTTGTGTCCAAGC 60.606 52.381 0.00 0.00 45.57 4.01
2276 2325 0.482446 TTGTGTCCAAGCCATTCCCT 59.518 50.000 0.00 0.00 0.00 4.20
2278 2327 0.329596 GTGTCCAAGCCATTCCCTCT 59.670 55.000 0.00 0.00 0.00 3.69
2281 2330 0.253347 TCCAAGCCATTCCCTCTCCT 60.253 55.000 0.00 0.00 0.00 3.69
2283 2332 2.061061 CCAAGCCATTCCCTCTCCTAT 58.939 52.381 0.00 0.00 0.00 2.57
2285 2334 3.848975 CCAAGCCATTCCCTCTCCTATAT 59.151 47.826 0.00 0.00 0.00 0.86
2286 2335 5.032846 CCAAGCCATTCCCTCTCCTATATA 58.967 45.833 0.00 0.00 0.00 0.86
2288 2337 5.291100 AGCCATTCCCTCTCCTATATACA 57.709 43.478 0.00 0.00 0.00 2.29
2289 2338 5.026790 AGCCATTCCCTCTCCTATATACAC 58.973 45.833 0.00 0.00 0.00 2.90
2291 2340 4.717280 CCATTCCCTCTCCTATATACACCC 59.283 50.000 0.00 0.00 0.00 4.61
2292 2341 5.342017 CATTCCCTCTCCTATATACACCCA 58.658 45.833 0.00 0.00 0.00 4.51
2293 2342 4.399483 TCCCTCTCCTATATACACCCAC 57.601 50.000 0.00 0.00 0.00 4.61
2294 2343 3.730594 TCCCTCTCCTATATACACCCACA 59.269 47.826 0.00 0.00 0.00 4.17
2295 2344 4.090090 CCCTCTCCTATATACACCCACAG 58.910 52.174 0.00 0.00 0.00 3.66
2296 2345 4.449376 CCCTCTCCTATATACACCCACAGT 60.449 50.000 0.00 0.00 0.00 3.55
2307 2361 2.460853 CCCACAGTGACACCCCCTT 61.461 63.158 0.62 0.00 0.00 3.95
2326 2380 1.597461 GTGGCCTCACACTCCTACC 59.403 63.158 3.32 0.00 43.13 3.18
2327 2381 1.157513 TGGCCTCACACTCCTACCA 59.842 57.895 3.32 0.00 0.00 3.25
2328 2382 1.192146 TGGCCTCACACTCCTACCAC 61.192 60.000 3.32 0.00 0.00 4.16
2329 2383 0.905337 GGCCTCACACTCCTACCACT 60.905 60.000 0.00 0.00 0.00 4.00
2347 2401 1.824224 CTGCCACTCTCCACTGCTCA 61.824 60.000 0.00 0.00 0.00 4.26
2354 2408 2.946329 ACTCTCCACTGCTCATACGTAG 59.054 50.000 0.08 0.00 0.00 3.51
2370 2424 1.202463 CGTAGGATCCCAGAGCAAGTG 60.202 57.143 8.55 0.00 0.00 3.16
2372 2426 0.617413 AGGATCCCAGAGCAAGTGTG 59.383 55.000 8.55 0.00 0.00 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
414 415 5.126061 GGAGGAGAATTTCATAAGCAAGCAA 59.874 40.000 0.00 0.00 0.00 3.91
714 715 0.749818 TCGCCAACAAGCTGGTTTGA 60.750 50.000 9.22 3.04 38.86 2.69
762 763 1.741770 ACAATCCAACTCGCGAGCC 60.742 57.895 34.83 0.00 0.00 4.70
901 905 2.443255 AGACAAAGTCATGGTGAGGGTT 59.557 45.455 0.00 0.00 34.60 4.11
963 967 2.361357 CGGTCACGGAGGAGGAGT 60.361 66.667 0.00 0.00 36.18 3.85
1140 1144 2.357881 TGTTGGAGCAGAGCAGCG 60.358 61.111 0.00 0.00 40.15 5.18
1192 1196 1.957177 GATAGTCAGAGCCACCGATGA 59.043 52.381 0.00 0.00 0.00 2.92
1322 1326 9.354673 AGATATTGTCTTCTTCCTTTTTGAACA 57.645 29.630 0.00 0.00 31.47 3.18
1767 1774 9.832445 TCTACAAGATCAGTTTTCTTAACAGTT 57.168 29.630 0.00 0.00 32.27 3.16
1768 1775 9.262358 GTCTACAAGATCAGTTTTCTTAACAGT 57.738 33.333 0.00 0.00 32.27 3.55
1769 1776 9.482627 AGTCTACAAGATCAGTTTTCTTAACAG 57.517 33.333 0.00 0.00 32.27 3.16
1812 1821 2.030893 ACGTTTGGACATGCATGTTGAG 60.031 45.455 31.82 20.81 41.95 3.02
1814 1823 2.052891 CACGTTTGGACATGCATGTTG 58.947 47.619 31.82 20.23 41.95 3.33
1845 1854 2.515757 TGCACTCACGCCTTTGCA 60.516 55.556 0.00 0.00 42.60 4.08
1849 1858 0.391661 CCATACTGCACTCACGCCTT 60.392 55.000 0.00 0.00 0.00 4.35
1858 1867 2.185004 ACTGTGAACCCATACTGCAC 57.815 50.000 0.00 0.00 0.00 4.57
1896 1905 7.810658 TCTCTTTTTGATGTAAACTCTGCATC 58.189 34.615 0.00 0.00 44.88 3.91
1897 1906 7.750229 TCTCTTTTTGATGTAAACTCTGCAT 57.250 32.000 0.00 0.00 32.29 3.96
1898 1907 7.255242 CCTTCTCTTTTTGATGTAAACTCTGCA 60.255 37.037 0.00 0.00 0.00 4.41
1899 1908 7.080724 CCTTCTCTTTTTGATGTAAACTCTGC 58.919 38.462 0.00 0.00 0.00 4.26
1900 1909 7.080724 GCCTTCTCTTTTTGATGTAAACTCTG 58.919 38.462 0.00 0.00 0.00 3.35
1901 1910 6.772716 TGCCTTCTCTTTTTGATGTAAACTCT 59.227 34.615 0.00 0.00 0.00 3.24
1902 1911 6.970484 TGCCTTCTCTTTTTGATGTAAACTC 58.030 36.000 0.00 0.00 0.00 3.01
1903 1912 6.959639 TGCCTTCTCTTTTTGATGTAAACT 57.040 33.333 0.00 0.00 0.00 2.66
1904 1913 6.089954 GCATGCCTTCTCTTTTTGATGTAAAC 59.910 38.462 6.36 0.00 0.00 2.01
1912 1926 3.054878 GTGTGCATGCCTTCTCTTTTTG 58.945 45.455 16.68 0.00 0.00 2.44
1916 1930 0.610232 GGGTGTGCATGCCTTCTCTT 60.610 55.000 16.68 0.00 0.00 2.85
1917 1931 1.001641 GGGTGTGCATGCCTTCTCT 60.002 57.895 16.68 0.00 0.00 3.10
1918 1932 2.048603 GGGGTGTGCATGCCTTCTC 61.049 63.158 16.68 4.82 0.00 2.87
1919 1933 2.036256 GGGGTGTGCATGCCTTCT 59.964 61.111 16.68 0.00 0.00 2.85
1920 1934 2.283101 TGGGGTGTGCATGCCTTC 60.283 61.111 16.68 6.46 0.00 3.46
1921 1935 2.283388 CTGGGGTGTGCATGCCTT 60.283 61.111 16.68 0.00 0.00 4.35
1924 1938 3.072468 ATGCTGGGGTGTGCATGC 61.072 61.111 11.82 11.82 46.58 4.06
1930 1944 2.601367 GTTGCCATGCTGGGGTGT 60.601 61.111 4.65 0.00 38.19 4.16
1931 1945 1.985662 ATGTTGCCATGCTGGGGTG 60.986 57.895 4.65 0.00 38.19 4.61
1932 1946 1.985662 CATGTTGCCATGCTGGGGT 60.986 57.895 4.65 0.00 41.88 4.95
1933 1947 2.897207 CATGTTGCCATGCTGGGG 59.103 61.111 4.65 0.00 41.88 4.96
1940 1954 3.527533 CAAGCTTTATGCATGTTGCCAT 58.472 40.909 10.16 0.20 44.23 4.40
1941 1955 2.962125 CAAGCTTTATGCATGTTGCCA 58.038 42.857 10.16 0.00 44.23 4.92
1970 1984 8.768955 GCCTTTGATGTACTCTAATATGACAAG 58.231 37.037 0.00 0.00 0.00 3.16
1973 1987 7.217200 TGGCCTTTGATGTACTCTAATATGAC 58.783 38.462 3.32 0.00 0.00 3.06
1975 1989 9.155975 GTATGGCCTTTGATGTACTCTAATATG 57.844 37.037 3.32 0.00 0.00 1.78
1976 1990 8.322091 GGTATGGCCTTTGATGTACTCTAATAT 58.678 37.037 3.32 0.00 0.00 1.28
1977 1991 7.524863 CGGTATGGCCTTTGATGTACTCTAATA 60.525 40.741 3.32 0.00 34.25 0.98
1978 1992 6.534634 GGTATGGCCTTTGATGTACTCTAAT 58.465 40.000 3.32 0.00 0.00 1.73
1979 1993 5.452776 CGGTATGGCCTTTGATGTACTCTAA 60.453 44.000 3.32 0.00 34.25 2.10
1980 1994 4.038763 CGGTATGGCCTTTGATGTACTCTA 59.961 45.833 3.32 0.00 34.25 2.43
1983 1997 2.158813 CCGGTATGGCCTTTGATGTACT 60.159 50.000 3.32 0.00 34.25 2.73
1985 1999 2.631160 CCGGTATGGCCTTTGATGTA 57.369 50.000 3.32 0.00 34.25 2.29
1986 2000 3.494850 CCGGTATGGCCTTTGATGT 57.505 52.632 3.32 0.00 34.25 3.06
2007 2023 5.241506 TCATCTTAACTTCCCAACAAAGCTG 59.758 40.000 0.00 0.00 0.00 4.24
2014 2030 8.847196 AGTAGTTTTTCATCTTAACTTCCCAAC 58.153 33.333 0.00 0.00 34.26 3.77
2028 2044 8.877864 TGGATGGTCAATTAGTAGTTTTTCAT 57.122 30.769 0.00 0.00 0.00 2.57
2030 2046 9.573133 CAATGGATGGTCAATTAGTAGTTTTTC 57.427 33.333 0.00 0.00 0.00 2.29
2041 2064 2.093869 GTGCAGCAATGGATGGTCAATT 60.094 45.455 0.00 0.00 37.77 2.32
2042 2065 1.479323 GTGCAGCAATGGATGGTCAAT 59.521 47.619 0.00 0.00 37.77 2.57
2043 2066 0.889994 GTGCAGCAATGGATGGTCAA 59.110 50.000 0.00 0.00 37.77 3.18
2044 2067 0.251253 TGTGCAGCAATGGATGGTCA 60.251 50.000 0.00 0.00 37.77 4.02
2045 2068 0.889994 TTGTGCAGCAATGGATGGTC 59.110 50.000 0.00 0.00 37.77 4.02
2046 2069 0.604578 GTTGTGCAGCAATGGATGGT 59.395 50.000 0.00 0.00 39.55 3.55
2047 2070 0.604073 TGTTGTGCAGCAATGGATGG 59.396 50.000 0.00 0.00 39.55 3.51
2048 2071 2.288579 ACTTGTTGTGCAGCAATGGATG 60.289 45.455 0.00 0.00 39.55 3.51
2073 2096 8.235226 CGTGACTAATATGTACTCGGATATGTT 58.765 37.037 0.00 0.00 0.00 2.71
2089 2112 6.460781 ACAAAGTTGGTGATCGTGACTAATA 58.539 36.000 0.00 0.00 0.00 0.98
2099 2122 5.178623 TCGTTCATGTACAAAGTTGGTGATC 59.821 40.000 0.00 0.00 0.00 2.92
2101 2124 4.271533 GTCGTTCATGTACAAAGTTGGTGA 59.728 41.667 0.00 0.00 0.00 4.02
2126 2149 5.628134 CGATTTGTTCCAAGTTTAGCTACC 58.372 41.667 0.00 0.00 0.00 3.18
2187 2210 4.021981 TCCTCTAATGTGAGTGTGACTGTG 60.022 45.833 0.00 0.00 32.50 3.66
2190 2213 5.511545 GGTTTCCTCTAATGTGAGTGTGACT 60.512 44.000 0.00 0.00 32.50 3.41
2206 2229 2.290896 TGATGGTGTGGATGGTTTCCTC 60.291 50.000 0.00 0.00 45.68 3.71
2209 2232 2.513753 TGTGATGGTGTGGATGGTTTC 58.486 47.619 0.00 0.00 0.00 2.78
2218 2267 0.166597 GCGTGTCATGTGATGGTGTG 59.833 55.000 0.00 0.00 0.00 3.82
2225 2274 1.494766 CGTTGGTGCGTGTCATGTGA 61.495 55.000 0.00 0.00 0.00 3.58
2235 2284 2.265182 AATTGGGGACGTTGGTGCG 61.265 57.895 0.00 0.00 34.95 5.34
2236 2285 1.288752 CAATTGGGGACGTTGGTGC 59.711 57.895 0.00 0.00 0.00 5.01
2237 2286 1.288752 GCAATTGGGGACGTTGGTG 59.711 57.895 7.72 0.00 0.00 4.17
2238 2287 1.906333 GGCAATTGGGGACGTTGGT 60.906 57.895 7.72 0.00 0.00 3.67
2258 2307 0.038166 GAGGGAATGGCTTGGACACA 59.962 55.000 0.00 0.00 0.00 3.72
2259 2308 0.329596 AGAGGGAATGGCTTGGACAC 59.670 55.000 0.00 0.00 0.00 3.67
2260 2309 0.620556 GAGAGGGAATGGCTTGGACA 59.379 55.000 0.00 0.00 0.00 4.02
2261 2310 0.106967 GGAGAGGGAATGGCTTGGAC 60.107 60.000 0.00 0.00 0.00 4.02
2262 2311 0.253347 AGGAGAGGGAATGGCTTGGA 60.253 55.000 0.00 0.00 0.00 3.53
2263 2312 1.511613 TAGGAGAGGGAATGGCTTGG 58.488 55.000 0.00 0.00 0.00 3.61
2264 2313 5.485353 TGTATATAGGAGAGGGAATGGCTTG 59.515 44.000 0.00 0.00 0.00 4.01
2265 2314 5.485708 GTGTATATAGGAGAGGGAATGGCTT 59.514 44.000 0.00 0.00 0.00 4.35
2268 2317 4.717280 GGGTGTATATAGGAGAGGGAATGG 59.283 50.000 0.00 0.00 0.00 3.16
2276 2325 5.138276 GTCACTGTGGGTGTATATAGGAGA 58.862 45.833 8.11 0.00 45.50 3.71
2278 2327 4.647853 GTGTCACTGTGGGTGTATATAGGA 59.352 45.833 8.11 0.00 45.50 2.94
2281 2330 3.707611 GGGTGTCACTGTGGGTGTATATA 59.292 47.826 8.11 0.00 45.50 0.86
2283 2332 1.903860 GGGTGTCACTGTGGGTGTATA 59.096 52.381 8.11 0.00 45.50 1.47
2285 2334 1.412453 GGGGTGTCACTGTGGGTGTA 61.412 60.000 8.11 0.00 45.50 2.90
2286 2335 2.752807 GGGGTGTCACTGTGGGTGT 61.753 63.158 8.11 0.00 45.50 4.16
2288 2337 3.175710 GGGGGTGTCACTGTGGGT 61.176 66.667 8.11 0.00 0.00 4.51
2289 2338 2.460853 AAGGGGGTGTCACTGTGGG 61.461 63.158 8.11 0.00 0.00 4.61
2291 2340 0.819259 CACAAGGGGGTGTCACTGTG 60.819 60.000 0.17 0.17 34.09 3.66
2292 2341 1.531748 CACAAGGGGGTGTCACTGT 59.468 57.895 2.35 0.00 34.09 3.55
2293 2342 1.228245 CCACAAGGGGGTGTCACTG 60.228 63.158 2.35 0.00 37.06 3.66
2294 2343 3.133365 GCCACAAGGGGGTGTCACT 62.133 63.158 2.35 0.00 37.06 3.41
2295 2344 2.597510 GCCACAAGGGGGTGTCAC 60.598 66.667 0.00 0.00 37.06 3.67
2296 2345 3.897122 GGCCACAAGGGGGTGTCA 61.897 66.667 0.00 0.00 37.06 3.58
2297 2346 3.569200 GAGGCCACAAGGGGGTGTC 62.569 68.421 5.01 0.00 37.06 3.67
2324 2378 1.460305 AGTGGAGAGTGGCAGTGGT 60.460 57.895 0.00 0.00 0.00 4.16
2325 2379 1.004080 CAGTGGAGAGTGGCAGTGG 60.004 63.158 0.00 0.00 0.00 4.00
2326 2380 1.670406 GCAGTGGAGAGTGGCAGTG 60.670 63.158 0.00 0.00 0.00 3.66
2327 2381 1.825281 GAGCAGTGGAGAGTGGCAGT 61.825 60.000 0.00 0.00 0.00 4.40
2328 2382 1.079266 GAGCAGTGGAGAGTGGCAG 60.079 63.158 0.00 0.00 0.00 4.85
2329 2383 1.196766 ATGAGCAGTGGAGAGTGGCA 61.197 55.000 0.00 0.00 0.00 4.92
2347 2401 2.677542 TGCTCTGGGATCCTACGTAT 57.322 50.000 12.58 0.00 0.00 3.06
2354 2408 1.028868 GCACACTTGCTCTGGGATCC 61.029 60.000 1.92 1.92 46.17 3.36
2374 2428 2.835431 ATGTCTCCTCTCCGGCCG 60.835 66.667 21.04 21.04 0.00 6.13
2375 2429 2.818132 CATGTCTCCTCTCCGGCC 59.182 66.667 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.