Multiple sequence alignment - TraesCS4A01G340000

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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 TraesCS4A01G340000 chr4A 100.000 2654 0 0 1 2654 621428057 621430710 0.000000e+00 4902.0
1 TraesCS4A01G340000 chr5D 94.798 1807 77 5 1 1791 549805397 549807202 0.000000e+00 2800.0
2 TraesCS4A01G340000 chr5D 93.433 335 17 5 2187 2519 549807535 549807866 2.370000e-135 492.0
3 TraesCS4A01G340000 chr5D 90.254 236 12 5 1940 2168 101470416 101470647 5.550000e-77 298.0
4 TraesCS4A01G340000 chr5D 94.286 140 8 0 2515 2654 549807918 549808057 5.750000e-52 215.0
5 TraesCS4A01G340000 chr5D 97.500 80 2 0 1864 1943 549807459 549807538 1.280000e-28 137.0
6 TraesCS4A01G340000 chr5B 94.341 1449 70 6 500 1941 701392494 701393937 0.000000e+00 2211.0
7 TraesCS4A01G340000 chr5B 96.142 337 11 2 2185 2519 701393937 701394273 1.390000e-152 549.0
8 TraesCS4A01G340000 chr5B 88.444 450 45 5 1 447 701392031 701392476 1.080000e-148 536.0
9 TraesCS4A01G340000 chr5B 93.985 133 8 0 2515 2647 701394325 701394457 4.480000e-48 202.0
10 TraesCS4A01G340000 chr7D 88.811 286 16 6 1940 2209 63379824 63380109 1.180000e-88 337.0
11 TraesCS4A01G340000 chr3A 90.909 242 13 6 1934 2168 13523433 13523194 1.530000e-82 316.0
12 TraesCS4A01G340000 chr3D 90.833 240 14 5 1937 2168 182200275 182200514 5.510000e-82 315.0
13 TraesCS4A01G340000 chr3D 91.416 233 13 4 1940 2165 500140145 500140377 1.980000e-81 313.0
14 TraesCS4A01G340000 chr2D 91.064 235 15 2 1940 2168 537440069 537440303 1.980000e-81 313.0
15 TraesCS4A01G340000 chr1D 90.295 237 15 5 1939 2168 399231014 399230779 1.190000e-78 303.0
16 TraesCS4A01G340000 chr3B 90.000 230 19 2 1940 2165 655507291 655507520 7.180000e-76 294.0
17 TraesCS4A01G340000 chr3B 89.655 232 18 2 1940 2165 554920320 554920551 9.290000e-75 291.0
18 TraesCS4A01G340000 chr1B 96.970 33 1 0 560 592 689386694 689386726 3.690000e-04 56.5


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 TraesCS4A01G340000 chr4A 621428057 621430710 2653 False 4902.0 4902 100.00000 1 2654 1 chr4A.!!$F1 2653
1 TraesCS4A01G340000 chr5D 549805397 549808057 2660 False 911.0 2800 95.00425 1 2654 4 chr5D.!!$F2 2653
2 TraesCS4A01G340000 chr5B 701392031 701394457 2426 False 874.5 2211 93.22800 1 2647 4 chr5B.!!$F1 2646

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
125 129 1.000233 TTGCCAATCCCCGCATCTT 60.000 52.632 0.00 0.0 34.35 2.40 F
460 465 1.002990 CCAGTGACATGCTCTGCCA 60.003 57.895 11.37 0.0 36.91 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1446 1465 1.073923 AGGGCTTTCATTTCGTCCTGT 59.926 47.619 0.0 0.0 0.0 4.00 R
2170 2378 0.702902 AGTACTCCCTCCGTCCTTGA 59.297 55.000 0.0 0.0 0.0 3.02 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
33 34 4.866486 CACATTCATCTCATTCGTGACTGA 59.134 41.667 0.00 0.00 0.00 3.41
77 81 2.685380 CGGCTCCCTCTGACCCTT 60.685 66.667 0.00 0.00 0.00 3.95
113 117 5.278758 GCTTGGTATAAAACTCAGTTGCCAA 60.279 40.000 0.00 1.20 33.22 4.52
115 119 6.509418 TGGTATAAAACTCAGTTGCCAATC 57.491 37.500 0.00 0.00 0.00 2.67
125 129 1.000233 TTGCCAATCCCCGCATCTT 60.000 52.632 0.00 0.00 34.35 2.40
170 174 4.749099 CCCATTCTCTCTCATTAAAGCTCG 59.251 45.833 0.00 0.00 0.00 5.03
225 230 4.280425 GGTTTTGGAAATACCGGGTGTTTA 59.720 41.667 20.02 4.99 42.61 2.01
231 236 2.521105 ATACCGGGTGTTTAGATCGC 57.479 50.000 10.66 0.00 0.00 4.58
283 288 3.684788 CGCTGCCTACACATAACTTCTTT 59.315 43.478 0.00 0.00 0.00 2.52
298 303 5.438761 ACTTCTTTGCGCTCATAAACTTT 57.561 34.783 9.73 0.00 0.00 2.66
299 304 5.215160 ACTTCTTTGCGCTCATAAACTTTG 58.785 37.500 9.73 0.00 0.00 2.77
382 387 8.394971 TCTTTTGCATCTCAAAGTTATTCTCA 57.605 30.769 8.14 0.00 44.62 3.27
457 462 3.921257 TGTCCAGTGACATGCTCTG 57.079 52.632 10.39 10.39 46.40 3.35
460 465 1.002990 CCAGTGACATGCTCTGCCA 60.003 57.895 11.37 0.00 36.91 4.92
467 472 2.224597 TGACATGCTCTGCCAGAAAGAA 60.225 45.455 0.00 0.00 0.00 2.52
475 480 5.062528 GCTCTGCCAGAAAGAATATAAGCT 58.937 41.667 0.00 0.00 0.00 3.74
484 489 8.180267 CCAGAAAGAATATAAGCTTTGACACTG 58.820 37.037 3.20 3.86 34.69 3.66
517 534 1.923204 GTTGTAGATCAGCAGAGCGTG 59.077 52.381 0.00 0.00 34.73 5.34
609 627 4.494091 AACACTCCAGGATCGATCAATT 57.506 40.909 25.93 8.92 0.00 2.32
681 699 3.198635 ACAGGCTAGTAAGACATGCACAT 59.801 43.478 0.00 0.00 30.50 3.21
690 708 9.708222 CTAGTAAGACATGCACATAAAATCAAC 57.292 33.333 0.00 0.00 0.00 3.18
694 712 2.254918 TGCACATAAAATCAACCGCG 57.745 45.000 0.00 0.00 0.00 6.46
723 741 2.086610 AGATTGGTGGCCACTTTTGT 57.913 45.000 33.91 16.36 30.78 2.83
750 768 5.048504 GTGCTCTTGAAAGAATGATTGGTGA 60.049 40.000 0.00 0.00 34.03 4.02
777 795 1.841663 CGGGTGTGCTCCTCAAAACG 61.842 60.000 0.00 0.00 0.00 3.60
871 889 2.202987 GCTCTCATGGCCTCACGG 60.203 66.667 3.32 0.00 0.00 4.94
926 945 4.929479 TGGCCACCTTCATAAACTTACAT 58.071 39.130 0.00 0.00 0.00 2.29
965 984 3.313526 CGGAAGCAATACCATCTTCTTGG 59.686 47.826 0.00 0.00 42.82 3.61
990 1009 2.696775 TCCCTCAACCACTTGTTAGGA 58.303 47.619 0.00 0.00 34.69 2.94
1252 1271 2.609916 GCCGCTGGAGATAAGAAGAAAC 59.390 50.000 0.00 0.00 0.00 2.78
1280 1299 7.994911 TGATGAAATTGTCACTGCCTATAAGAT 59.005 33.333 0.00 0.00 39.72 2.40
1470 1489 1.439679 ACGAAATGAAAGCCCTCGTC 58.560 50.000 0.00 0.00 38.27 4.20
1499 1518 3.112075 CGTCGTCGCTGCCAACAT 61.112 61.111 0.00 0.00 0.00 2.71
1935 2143 7.658261 CATGTGATTTCTGATGGCATAAAGAT 58.342 34.615 11.85 0.63 0.00 2.40
1939 2147 8.844244 GTGATTTCTGATGGCATAAAGATTACT 58.156 33.333 11.85 0.52 0.00 2.24
1943 2151 9.547753 TTTCTGATGGCATAAAGATTACTACTC 57.452 33.333 11.85 0.00 0.00 2.59
1944 2152 7.671302 TCTGATGGCATAAAGATTACTACTCC 58.329 38.462 0.00 0.00 0.00 3.85
1945 2153 6.769512 TGATGGCATAAAGATTACTACTCCC 58.230 40.000 0.00 0.00 0.00 4.30
1946 2154 6.558775 TGATGGCATAAAGATTACTACTCCCT 59.441 38.462 0.00 0.00 0.00 4.20
1947 2155 6.420913 TGGCATAAAGATTACTACTCCCTC 57.579 41.667 0.00 0.00 0.00 4.30
1948 2156 6.143915 TGGCATAAAGATTACTACTCCCTCT 58.856 40.000 0.00 0.00 0.00 3.69
1949 2157 6.042093 TGGCATAAAGATTACTACTCCCTCTG 59.958 42.308 0.00 0.00 0.00 3.35
1950 2158 6.042208 GGCATAAAGATTACTACTCCCTCTGT 59.958 42.308 0.00 0.00 0.00 3.41
1951 2159 7.149307 GCATAAAGATTACTACTCCCTCTGTC 58.851 42.308 0.00 0.00 0.00 3.51
1952 2160 7.662897 CATAAAGATTACTACTCCCTCTGTCC 58.337 42.308 0.00 0.00 0.00 4.02
1953 2161 5.475398 AAGATTACTACTCCCTCTGTCCT 57.525 43.478 0.00 0.00 0.00 3.85
1954 2162 5.475398 AGATTACTACTCCCTCTGTCCTT 57.525 43.478 0.00 0.00 0.00 3.36
1955 2163 5.205056 AGATTACTACTCCCTCTGTCCTTG 58.795 45.833 0.00 0.00 0.00 3.61
1956 2164 4.669866 TTACTACTCCCTCTGTCCTTGA 57.330 45.455 0.00 0.00 0.00 3.02
1957 2165 3.544698 ACTACTCCCTCTGTCCTTGAA 57.455 47.619 0.00 0.00 0.00 2.69
1958 2166 3.858135 ACTACTCCCTCTGTCCTTGAAA 58.142 45.455 0.00 0.00 0.00 2.69
1959 2167 4.232091 ACTACTCCCTCTGTCCTTGAAAA 58.768 43.478 0.00 0.00 0.00 2.29
1960 2168 4.658901 ACTACTCCCTCTGTCCTTGAAAAA 59.341 41.667 0.00 0.00 0.00 1.94
1961 2169 4.092116 ACTCCCTCTGTCCTTGAAAAAG 57.908 45.455 0.00 0.00 0.00 2.27
1962 2170 3.459969 ACTCCCTCTGTCCTTGAAAAAGT 59.540 43.478 0.00 0.00 0.00 2.66
1963 2171 3.817647 CTCCCTCTGTCCTTGAAAAAGTG 59.182 47.826 0.00 0.00 0.00 3.16
1964 2172 3.202151 TCCCTCTGTCCTTGAAAAAGTGT 59.798 43.478 0.00 0.00 0.00 3.55
1965 2173 4.410883 TCCCTCTGTCCTTGAAAAAGTGTA 59.589 41.667 0.00 0.00 0.00 2.90
1966 2174 4.515567 CCCTCTGTCCTTGAAAAAGTGTAC 59.484 45.833 0.00 0.00 0.00 2.90
1967 2175 5.368989 CCTCTGTCCTTGAAAAAGTGTACT 58.631 41.667 0.00 0.00 0.00 2.73
1968 2176 5.823045 CCTCTGTCCTTGAAAAAGTGTACTT 59.177 40.000 0.00 0.00 37.91 2.24
1969 2177 6.238484 CCTCTGTCCTTGAAAAAGTGTACTTG 60.238 42.308 0.00 0.00 36.12 3.16
1970 2178 5.065988 TCTGTCCTTGAAAAAGTGTACTTGC 59.934 40.000 0.00 0.00 36.12 4.01
1971 2179 4.702612 TGTCCTTGAAAAAGTGTACTTGCA 59.297 37.500 0.00 0.00 36.12 4.08
1972 2180 5.359576 TGTCCTTGAAAAAGTGTACTTGCAT 59.640 36.000 0.00 0.00 36.12 3.96
1973 2181 6.127479 TGTCCTTGAAAAAGTGTACTTGCATT 60.127 34.615 0.00 0.00 36.12 3.56
1974 2182 6.198966 GTCCTTGAAAAAGTGTACTTGCATTG 59.801 38.462 0.00 0.00 36.12 2.82
1975 2183 5.463061 CCTTGAAAAAGTGTACTTGCATTGG 59.537 40.000 0.00 1.26 36.12 3.16
1976 2184 5.843673 TGAAAAAGTGTACTTGCATTGGA 57.156 34.783 0.00 0.00 36.12 3.53
1977 2185 6.214191 TGAAAAAGTGTACTTGCATTGGAA 57.786 33.333 0.00 0.00 36.12 3.53
1978 2186 6.634805 TGAAAAAGTGTACTTGCATTGGAAA 58.365 32.000 0.00 0.00 36.12 3.13
1979 2187 6.756074 TGAAAAAGTGTACTTGCATTGGAAAG 59.244 34.615 0.00 0.00 36.12 2.62
1980 2188 5.852282 AAAGTGTACTTGCATTGGAAAGT 57.148 34.783 0.00 0.00 45.20 2.66
1981 2189 5.438761 AAGTGTACTTGCATTGGAAAGTC 57.561 39.130 0.00 0.00 38.62 3.01
1982 2190 4.460263 AGTGTACTTGCATTGGAAAGTCA 58.540 39.130 0.00 0.00 38.62 3.41
1983 2191 4.887071 AGTGTACTTGCATTGGAAAGTCAA 59.113 37.500 0.00 0.00 38.62 3.18
1984 2192 5.359576 AGTGTACTTGCATTGGAAAGTCAAA 59.640 36.000 0.00 0.00 38.62 2.69
1985 2193 5.458779 GTGTACTTGCATTGGAAAGTCAAAC 59.541 40.000 0.00 0.00 38.62 2.93
1986 2194 5.359576 TGTACTTGCATTGGAAAGTCAAACT 59.640 36.000 0.00 0.00 38.62 2.66
1987 2195 5.343307 ACTTGCATTGGAAAGTCAAACTT 57.657 34.783 0.00 0.00 38.62 2.66
2022 2230 8.542497 TGACCGCATTTATACAATAATAGACC 57.458 34.615 0.00 0.00 0.00 3.85
2023 2231 8.151596 TGACCGCATTTATACAATAATAGACCA 58.848 33.333 0.00 0.00 0.00 4.02
2024 2232 8.911918 ACCGCATTTATACAATAATAGACCAA 57.088 30.769 0.00 0.00 0.00 3.67
2025 2233 9.515226 ACCGCATTTATACAATAATAGACCAAT 57.485 29.630 0.00 0.00 0.00 3.16
2057 2265 9.208022 TGCCATCAAATTAGTAGATTAGATTCG 57.792 33.333 0.00 0.00 0.00 3.34
2058 2266 9.209175 GCCATCAAATTAGTAGATTAGATTCGT 57.791 33.333 0.00 0.00 0.00 3.85
2124 2332 9.439500 AAGCATTGATATATTTTTGCACAAACT 57.561 25.926 0.00 0.00 32.66 2.66
2125 2333 9.090692 AGCATTGATATATTTTTGCACAAACTC 57.909 29.630 0.00 0.00 32.66 3.01
2126 2334 8.051909 GCATTGATATATTTTTGCACAAACTCG 58.948 33.333 0.00 0.00 0.00 4.18
2127 2335 8.533965 CATTGATATATTTTTGCACAAACTCGG 58.466 33.333 0.00 0.00 0.00 4.63
2128 2336 7.151999 TGATATATTTTTGCACAAACTCGGT 57.848 32.000 0.00 0.00 0.00 4.69
2129 2337 7.247728 TGATATATTTTTGCACAAACTCGGTC 58.752 34.615 0.00 0.00 0.00 4.79
2130 2338 3.791973 ATTTTTGCACAAACTCGGTCA 57.208 38.095 0.00 0.00 0.00 4.02
2131 2339 3.577649 TTTTTGCACAAACTCGGTCAA 57.422 38.095 0.00 0.00 0.00 3.18
2132 2340 3.577649 TTTTGCACAAACTCGGTCAAA 57.422 38.095 0.00 0.00 0.00 2.69
2133 2341 2.553079 TTGCACAAACTCGGTCAAAC 57.447 45.000 0.00 0.00 0.00 2.93
2134 2342 1.745232 TGCACAAACTCGGTCAAACT 58.255 45.000 0.00 0.00 0.00 2.66
2135 2343 2.088423 TGCACAAACTCGGTCAAACTT 58.912 42.857 0.00 0.00 0.00 2.66
2136 2344 2.490115 TGCACAAACTCGGTCAAACTTT 59.510 40.909 0.00 0.00 0.00 2.66
2137 2345 2.851824 GCACAAACTCGGTCAAACTTTG 59.148 45.455 0.00 0.00 0.00 2.77
2138 2346 3.426963 GCACAAACTCGGTCAAACTTTGA 60.427 43.478 0.00 0.00 37.33 2.69
2153 2361 6.635030 AAACTTTGACATAGTTTGACCCTC 57.365 37.500 19.30 0.00 42.54 4.30
2154 2362 4.652822 ACTTTGACATAGTTTGACCCTCC 58.347 43.478 0.00 0.00 0.00 4.30
2155 2363 4.104102 ACTTTGACATAGTTTGACCCTCCA 59.896 41.667 0.00 0.00 0.00 3.86
2156 2364 4.715534 TTGACATAGTTTGACCCTCCAA 57.284 40.909 0.00 0.00 0.00 3.53
2157 2365 4.015872 TGACATAGTTTGACCCTCCAAC 57.984 45.455 0.00 0.00 0.00 3.77
2158 2366 3.392947 TGACATAGTTTGACCCTCCAACA 59.607 43.478 0.00 0.00 0.00 3.33
2159 2367 4.141367 TGACATAGTTTGACCCTCCAACAA 60.141 41.667 0.00 0.00 0.00 2.83
2160 2368 4.798882 ACATAGTTTGACCCTCCAACAAA 58.201 39.130 0.00 0.00 0.00 2.83
2161 2369 4.827284 ACATAGTTTGACCCTCCAACAAAG 59.173 41.667 0.00 0.00 34.86 2.77
2162 2370 3.382083 AGTTTGACCCTCCAACAAAGT 57.618 42.857 0.00 0.00 34.86 2.66
2163 2371 3.708451 AGTTTGACCCTCCAACAAAGTT 58.292 40.909 0.00 0.00 34.79 2.66
2164 2372 3.447229 AGTTTGACCCTCCAACAAAGTTG 59.553 43.478 3.00 3.00 34.79 3.16
2165 2373 3.374042 TTGACCCTCCAACAAAGTTGA 57.626 42.857 11.19 0.00 0.00 3.18
2166 2374 3.374042 TGACCCTCCAACAAAGTTGAA 57.626 42.857 11.19 0.00 0.00 2.69
2167 2375 3.702792 TGACCCTCCAACAAAGTTGAAA 58.297 40.909 11.19 0.00 0.00 2.69
2168 2376 4.285863 TGACCCTCCAACAAAGTTGAAAT 58.714 39.130 11.19 0.00 0.00 2.17
2169 2377 4.714308 TGACCCTCCAACAAAGTTGAAATT 59.286 37.500 11.19 0.00 0.00 1.82
2170 2378 5.188751 TGACCCTCCAACAAAGTTGAAATTT 59.811 36.000 11.19 0.00 0.00 1.82
2171 2379 5.670485 ACCCTCCAACAAAGTTGAAATTTC 58.330 37.500 11.41 11.41 0.00 2.17
2172 2380 5.188751 ACCCTCCAACAAAGTTGAAATTTCA 59.811 36.000 16.91 16.91 34.92 2.69
2173 2381 6.112058 CCCTCCAACAAAGTTGAAATTTCAA 58.888 36.000 26.01 26.01 44.31 2.69
2174 2382 6.258507 CCCTCCAACAAAGTTGAAATTTCAAG 59.741 38.462 29.34 20.74 46.80 3.02
2175 2383 6.258507 CCTCCAACAAAGTTGAAATTTCAAGG 59.741 38.462 29.34 23.83 46.80 3.61
2176 2384 6.940739 TCCAACAAAGTTGAAATTTCAAGGA 58.059 32.000 29.34 25.33 46.80 3.36
2177 2385 6.816140 TCCAACAAAGTTGAAATTTCAAGGAC 59.184 34.615 29.34 20.23 46.80 3.85
2178 2386 6.237808 CCAACAAAGTTGAAATTTCAAGGACG 60.238 38.462 29.34 20.75 46.80 4.79
2179 2387 5.348164 ACAAAGTTGAAATTTCAAGGACGG 58.652 37.500 29.34 20.26 46.80 4.79
2180 2388 5.126384 ACAAAGTTGAAATTTCAAGGACGGA 59.874 36.000 29.34 8.00 46.80 4.69
2181 2389 5.438761 AAGTTGAAATTTCAAGGACGGAG 57.561 39.130 29.34 0.00 46.80 4.63
2182 2390 3.821033 AGTTGAAATTTCAAGGACGGAGG 59.179 43.478 29.34 0.00 46.80 4.30
2183 2391 2.790433 TGAAATTTCAAGGACGGAGGG 58.210 47.619 18.45 0.00 33.55 4.30
2184 2392 2.373836 TGAAATTTCAAGGACGGAGGGA 59.626 45.455 18.45 0.00 33.55 4.20
2185 2393 2.789409 AATTTCAAGGACGGAGGGAG 57.211 50.000 0.00 0.00 0.00 4.30
2254 2466 2.640346 TTTAGCGTGCTACGATGTCA 57.360 45.000 11.94 0.00 46.05 3.58
2405 2618 7.118101 GGTTACTATCGTACAATTTCAACCACA 59.882 37.037 7.95 0.00 0.00 4.17
2467 2680 3.157881 GCTTTAAAGCCTCCTTGAAGGT 58.842 45.455 26.60 0.00 46.20 3.50
2479 2692 2.516225 GAAGGTATGGGCCGCACC 60.516 66.667 16.53 16.53 37.93 5.01
2504 2718 9.988815 CCATTAGCATATTACTTCTCTACTGTT 57.011 33.333 0.00 0.00 0.00 3.16
2563 2833 5.414144 GTGAGAAATCTCTGCCTTTAAAGCT 59.586 40.000 9.86 0.00 43.25 3.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 1.750206 TGCTGCAACACATTGACAACT 59.250 42.857 0.00 0.00 38.15 3.16
77 81 7.174253 AGTTTTATACCAAGCTTTTCATGTCGA 59.826 33.333 0.00 0.00 0.00 4.20
113 117 3.520721 TGATGATGATAAGATGCGGGGAT 59.479 43.478 0.00 0.00 0.00 3.85
115 119 3.268330 CTGATGATGATAAGATGCGGGG 58.732 50.000 0.00 0.00 0.00 5.73
125 129 1.336240 CGAGGTGCGCTGATGATGATA 60.336 52.381 9.73 0.00 0.00 2.15
190 194 2.683968 TCCAAAACCGAGATTCTCACG 58.316 47.619 13.88 5.50 0.00 4.35
225 230 2.188994 GCTCAAGGCAGGCGATCT 59.811 61.111 0.00 0.00 41.35 2.75
283 288 3.674225 CGCAAAGTTTATGAGCGCA 57.326 47.368 11.47 0.00 41.95 6.09
299 304 1.725706 GACATAGATGAGCATCTGCGC 59.274 52.381 20.26 0.00 46.80 6.09
456 461 6.658816 TGTCAAAGCTTATATTCTTTCTGGCA 59.341 34.615 0.00 0.00 30.79 4.92
457 462 6.969473 GTGTCAAAGCTTATATTCTTTCTGGC 59.031 38.462 0.00 0.00 30.79 4.85
460 465 7.885399 ACCAGTGTCAAAGCTTATATTCTTTCT 59.115 33.333 0.00 0.00 30.79 2.52
467 472 6.109359 GTCTCACCAGTGTCAAAGCTTATAT 58.891 40.000 0.00 0.00 0.00 0.86
517 534 7.386851 TCCTAGTATAATAAGCATGGCTCAAC 58.613 38.462 0.00 0.00 38.25 3.18
609 627 2.761559 CATGTAGTGTTGGTCGGTTCA 58.238 47.619 0.00 0.00 0.00 3.18
649 667 2.977772 ACTAGCCTGTGATCTCTTGC 57.022 50.000 0.00 0.00 0.00 4.01
681 699 3.139850 TCTGGTTTCGCGGTTGATTTTA 58.860 40.909 6.13 0.00 0.00 1.52
690 708 1.135689 CCAATCTTTCTGGTTTCGCGG 60.136 52.381 6.13 0.00 0.00 6.46
694 712 2.029020 GGCCACCAATCTTTCTGGTTTC 60.029 50.000 0.00 0.00 45.13 2.78
723 741 5.182570 CCAATCATTCTTTCAAGAGCACAGA 59.817 40.000 0.00 0.00 36.22 3.41
750 768 0.893727 GGAGCACACCCGAAATTGGT 60.894 55.000 0.00 0.00 36.21 3.67
871 889 2.769095 AGGAGATGGTGTCTAAAGAGGC 59.231 50.000 0.00 0.00 37.29 4.70
926 945 2.324330 CGGTGAGATGTTTGCGCCA 61.324 57.895 4.18 0.00 32.58 5.69
965 984 3.356529 ACAAGTGGTTGAGGGATGATC 57.643 47.619 0.00 0.00 37.10 2.92
990 1009 2.825532 GACCATGGCCATTGTAAGTTGT 59.174 45.455 21.70 6.54 0.00 3.32
1087 1106 3.009723 TCTCTTCAATGGATTTGTCGCC 58.990 45.455 0.00 0.00 36.65 5.54
1252 1271 4.778534 AGGCAGTGACAATTTCATCAAG 57.221 40.909 0.00 0.00 36.32 3.02
1446 1465 1.073923 AGGGCTTTCATTTCGTCCTGT 59.926 47.619 0.00 0.00 0.00 4.00
1470 1489 1.444553 GACGACGGTCTGCTGGAAG 60.445 63.158 6.57 0.00 40.15 3.46
1499 1518 2.195411 TTGCAGACTGGGCAAGCA 59.805 55.556 4.26 0.00 45.57 3.91
1935 2143 4.669866 TCAAGGACAGAGGGAGTAGTAA 57.330 45.455 0.00 0.00 0.00 2.24
1939 2147 4.658901 ACTTTTTCAAGGACAGAGGGAGTA 59.341 41.667 0.00 0.00 33.82 2.59
1940 2148 3.459969 ACTTTTTCAAGGACAGAGGGAGT 59.540 43.478 0.00 0.00 33.82 3.85
1941 2149 3.817647 CACTTTTTCAAGGACAGAGGGAG 59.182 47.826 0.00 0.00 33.82 4.30
1942 2150 3.202151 ACACTTTTTCAAGGACAGAGGGA 59.798 43.478 0.00 0.00 33.82 4.20
1943 2151 3.555966 ACACTTTTTCAAGGACAGAGGG 58.444 45.455 0.00 0.00 33.82 4.30
1944 2152 5.368989 AGTACACTTTTTCAAGGACAGAGG 58.631 41.667 0.00 0.00 33.82 3.69
1945 2153 6.719365 CAAGTACACTTTTTCAAGGACAGAG 58.281 40.000 0.00 0.00 33.82 3.35
1946 2154 5.065988 GCAAGTACACTTTTTCAAGGACAGA 59.934 40.000 0.00 0.00 33.82 3.41
1947 2155 5.163663 TGCAAGTACACTTTTTCAAGGACAG 60.164 40.000 0.00 0.00 33.82 3.51
1948 2156 4.702612 TGCAAGTACACTTTTTCAAGGACA 59.297 37.500 0.00 0.00 33.82 4.02
1949 2157 5.243426 TGCAAGTACACTTTTTCAAGGAC 57.757 39.130 0.00 0.00 33.82 3.85
1950 2158 6.272318 CAATGCAAGTACACTTTTTCAAGGA 58.728 36.000 0.00 0.00 33.82 3.36
1951 2159 5.463061 CCAATGCAAGTACACTTTTTCAAGG 59.537 40.000 0.00 0.00 33.82 3.61
1952 2160 6.272318 TCCAATGCAAGTACACTTTTTCAAG 58.728 36.000 0.00 0.00 33.11 3.02
1953 2161 6.214191 TCCAATGCAAGTACACTTTTTCAA 57.786 33.333 0.00 0.00 33.11 2.69
1954 2162 5.843673 TCCAATGCAAGTACACTTTTTCA 57.156 34.783 0.00 0.00 33.11 2.69
1955 2163 6.756542 ACTTTCCAATGCAAGTACACTTTTTC 59.243 34.615 0.00 0.00 33.11 2.29
1956 2164 6.639563 ACTTTCCAATGCAAGTACACTTTTT 58.360 32.000 0.00 0.00 33.11 1.94
1957 2165 6.127479 TGACTTTCCAATGCAAGTACACTTTT 60.127 34.615 0.00 0.00 33.22 2.27
1958 2166 5.359576 TGACTTTCCAATGCAAGTACACTTT 59.640 36.000 0.00 0.00 33.22 2.66
1959 2167 4.887071 TGACTTTCCAATGCAAGTACACTT 59.113 37.500 0.00 0.00 33.22 3.16
1960 2168 4.460263 TGACTTTCCAATGCAAGTACACT 58.540 39.130 0.00 0.00 33.22 3.55
1961 2169 4.829064 TGACTTTCCAATGCAAGTACAC 57.171 40.909 0.00 0.00 33.22 2.90
1962 2170 5.359576 AGTTTGACTTTCCAATGCAAGTACA 59.640 36.000 0.00 0.00 33.22 2.90
1963 2171 5.831997 AGTTTGACTTTCCAATGCAAGTAC 58.168 37.500 0.00 0.00 33.22 2.73
1964 2172 6.463995 AAGTTTGACTTTCCAATGCAAGTA 57.536 33.333 0.00 0.00 34.11 2.24
1965 2173 5.343307 AAGTTTGACTTTCCAATGCAAGT 57.657 34.783 0.00 0.00 34.11 3.16
1966 2174 6.667007 AAAAGTTTGACTTTCCAATGCAAG 57.333 33.333 6.53 0.00 46.78 4.01
1996 2204 8.995220 GGTCTATTATTGTATAAATGCGGTCAA 58.005 33.333 0.00 0.00 0.00 3.18
1997 2205 8.151596 TGGTCTATTATTGTATAAATGCGGTCA 58.848 33.333 0.00 0.00 0.00 4.02
1998 2206 8.542497 TGGTCTATTATTGTATAAATGCGGTC 57.458 34.615 0.00 0.00 0.00 4.79
1999 2207 8.911918 TTGGTCTATTATTGTATAAATGCGGT 57.088 30.769 0.00 0.00 0.00 5.68
2031 2239 9.208022 CGAATCTAATCTACTAATTTGATGGCA 57.792 33.333 0.00 0.00 33.39 4.92
2032 2240 9.209175 ACGAATCTAATCTACTAATTTGATGGC 57.791 33.333 0.00 0.00 33.39 4.40
2083 2291 5.782047 TCAATGCTTGTGAAACCAAATAGG 58.218 37.500 0.00 0.00 45.67 2.57
2087 2295 9.941325 AAATATATCAATGCTTGTGAAACCAAA 57.059 25.926 0.00 0.00 34.36 3.28
2088 2296 9.941325 AAAATATATCAATGCTTGTGAAACCAA 57.059 25.926 0.00 0.00 34.36 3.67
2089 2297 9.941325 AAAAATATATCAATGCTTGTGAAACCA 57.059 25.926 0.00 0.00 34.36 3.67
2091 2299 9.693157 GCAAAAATATATCAATGCTTGTGAAAC 57.307 29.630 8.52 0.00 37.35 2.78
2092 2300 9.433153 TGCAAAAATATATCAATGCTTGTGAAA 57.567 25.926 14.10 0.00 34.97 2.69
2093 2301 8.871862 GTGCAAAAATATATCAATGCTTGTGAA 58.128 29.630 14.10 0.00 34.97 3.18
2094 2302 8.033626 TGTGCAAAAATATATCAATGCTTGTGA 58.966 29.630 14.10 0.00 34.97 3.58
2095 2303 8.187354 TGTGCAAAAATATATCAATGCTTGTG 57.813 30.769 14.10 0.24 34.97 3.33
2096 2304 8.774890 TTGTGCAAAAATATATCAATGCTTGT 57.225 26.923 14.10 0.00 34.97 3.16
2097 2305 9.480538 GTTTGTGCAAAAATATATCAATGCTTG 57.519 29.630 5.11 0.00 34.97 4.01
2098 2306 9.439500 AGTTTGTGCAAAAATATATCAATGCTT 57.561 25.926 5.11 0.00 34.97 3.91
2099 2307 9.090692 GAGTTTGTGCAAAAATATATCAATGCT 57.909 29.630 5.11 0.00 34.97 3.79
2100 2308 8.051909 CGAGTTTGTGCAAAAATATATCAATGC 58.948 33.333 5.11 8.75 31.33 3.56
2101 2309 8.533965 CCGAGTTTGTGCAAAAATATATCAATG 58.466 33.333 5.11 0.00 31.33 2.82
2102 2310 8.250332 ACCGAGTTTGTGCAAAAATATATCAAT 58.750 29.630 5.11 0.00 31.33 2.57
2103 2311 7.598278 ACCGAGTTTGTGCAAAAATATATCAA 58.402 30.769 5.11 0.00 31.33 2.57
2104 2312 7.094592 TGACCGAGTTTGTGCAAAAATATATCA 60.095 33.333 5.11 4.10 31.33 2.15
2105 2313 7.247728 TGACCGAGTTTGTGCAAAAATATATC 58.752 34.615 5.11 1.66 31.33 1.63
2106 2314 7.151999 TGACCGAGTTTGTGCAAAAATATAT 57.848 32.000 5.11 0.00 31.33 0.86
2107 2315 6.561737 TGACCGAGTTTGTGCAAAAATATA 57.438 33.333 5.11 0.00 31.33 0.86
2108 2316 5.446143 TGACCGAGTTTGTGCAAAAATAT 57.554 34.783 5.11 0.00 31.33 1.28
2109 2317 4.902443 TGACCGAGTTTGTGCAAAAATA 57.098 36.364 5.11 0.00 31.33 1.40
2110 2318 3.791973 TGACCGAGTTTGTGCAAAAAT 57.208 38.095 5.11 0.00 31.33 1.82
2111 2319 3.577649 TTGACCGAGTTTGTGCAAAAA 57.422 38.095 0.00 0.00 31.33 1.94
2112 2320 3.057174 AGTTTGACCGAGTTTGTGCAAAA 60.057 39.130 0.00 0.00 31.33 2.44
2113 2321 2.490115 AGTTTGACCGAGTTTGTGCAAA 59.510 40.909 0.00 0.00 0.00 3.68
2114 2322 2.088423 AGTTTGACCGAGTTTGTGCAA 58.912 42.857 0.00 0.00 0.00 4.08
2115 2323 1.745232 AGTTTGACCGAGTTTGTGCA 58.255 45.000 0.00 0.00 0.00 4.57
2116 2324 2.844122 AAGTTTGACCGAGTTTGTGC 57.156 45.000 0.00 0.00 0.00 4.57
2117 2325 4.349663 TCAAAGTTTGACCGAGTTTGTG 57.650 40.909 14.35 0.00 38.17 3.33
2130 2338 5.535030 GGAGGGTCAAACTATGTCAAAGTTT 59.465 40.000 0.00 0.00 45.64 2.66
2131 2339 5.070685 GGAGGGTCAAACTATGTCAAAGTT 58.929 41.667 0.00 0.00 38.82 2.66
2132 2340 4.104102 TGGAGGGTCAAACTATGTCAAAGT 59.896 41.667 0.00 0.00 0.00 2.66
2133 2341 4.651778 TGGAGGGTCAAACTATGTCAAAG 58.348 43.478 0.00 0.00 0.00 2.77
2134 2342 4.715534 TGGAGGGTCAAACTATGTCAAA 57.284 40.909 0.00 0.00 0.00 2.69
2135 2343 4.141367 TGTTGGAGGGTCAAACTATGTCAA 60.141 41.667 0.00 0.00 0.00 3.18
2136 2344 3.392947 TGTTGGAGGGTCAAACTATGTCA 59.607 43.478 0.00 0.00 0.00 3.58
2137 2345 4.015872 TGTTGGAGGGTCAAACTATGTC 57.984 45.455 0.00 0.00 0.00 3.06
2138 2346 4.447138 TTGTTGGAGGGTCAAACTATGT 57.553 40.909 0.00 0.00 0.00 2.29
2139 2347 4.827284 ACTTTGTTGGAGGGTCAAACTATG 59.173 41.667 0.00 0.00 0.00 2.23
2140 2348 5.061721 ACTTTGTTGGAGGGTCAAACTAT 57.938 39.130 0.00 0.00 0.00 2.12
2141 2349 4.513406 ACTTTGTTGGAGGGTCAAACTA 57.487 40.909 0.00 0.00 0.00 2.24
2142 2350 3.382083 ACTTTGTTGGAGGGTCAAACT 57.618 42.857 0.00 0.00 0.00 2.66
2143 2351 3.445805 TCAACTTTGTTGGAGGGTCAAAC 59.554 43.478 10.05 0.00 0.00 2.93
2144 2352 3.702792 TCAACTTTGTTGGAGGGTCAAA 58.297 40.909 10.05 0.00 0.00 2.69
2145 2353 3.374042 TCAACTTTGTTGGAGGGTCAA 57.626 42.857 10.05 0.00 0.00 3.18
2146 2354 3.374042 TTCAACTTTGTTGGAGGGTCA 57.626 42.857 10.05 0.00 0.00 4.02
2147 2355 4.937201 ATTTCAACTTTGTTGGAGGGTC 57.063 40.909 10.05 0.00 0.00 4.46
2148 2356 5.188751 TGAAATTTCAACTTTGTTGGAGGGT 59.811 36.000 18.45 0.00 33.55 4.34
2149 2357 5.669477 TGAAATTTCAACTTTGTTGGAGGG 58.331 37.500 18.45 0.00 33.55 4.30
2150 2358 6.258507 CCTTGAAATTTCAACTTTGTTGGAGG 59.741 38.462 26.01 18.24 41.88 4.30
2151 2359 7.010460 GTCCTTGAAATTTCAACTTTGTTGGAG 59.990 37.037 26.01 13.95 41.88 3.86
2152 2360 6.816140 GTCCTTGAAATTTCAACTTTGTTGGA 59.184 34.615 26.01 23.89 41.88 3.53
2153 2361 6.237808 CGTCCTTGAAATTTCAACTTTGTTGG 60.238 38.462 26.01 22.36 41.88 3.77
2154 2362 6.237808 CCGTCCTTGAAATTTCAACTTTGTTG 60.238 38.462 26.01 15.69 41.88 3.33
2155 2363 5.810074 CCGTCCTTGAAATTTCAACTTTGTT 59.190 36.000 26.01 0.00 41.88 2.83
2156 2364 5.126384 TCCGTCCTTGAAATTTCAACTTTGT 59.874 36.000 26.01 0.00 41.88 2.83
2157 2365 5.587289 TCCGTCCTTGAAATTTCAACTTTG 58.413 37.500 26.01 17.23 41.88 2.77
2158 2366 5.221244 CCTCCGTCCTTGAAATTTCAACTTT 60.221 40.000 26.01 0.00 41.88 2.66
2159 2367 4.278419 CCTCCGTCCTTGAAATTTCAACTT 59.722 41.667 26.01 0.00 41.88 2.66
2160 2368 3.821033 CCTCCGTCCTTGAAATTTCAACT 59.179 43.478 26.01 0.00 41.88 3.16
2161 2369 3.057526 CCCTCCGTCCTTGAAATTTCAAC 60.058 47.826 26.01 17.71 41.88 3.18
2162 2370 3.153919 CCCTCCGTCCTTGAAATTTCAA 58.846 45.455 27.39 27.39 44.31 2.69
2163 2371 2.373836 TCCCTCCGTCCTTGAAATTTCA 59.626 45.455 16.91 16.91 34.92 2.69
2164 2372 3.010420 CTCCCTCCGTCCTTGAAATTTC 58.990 50.000 11.41 11.41 0.00 2.17
2165 2373 2.375509 ACTCCCTCCGTCCTTGAAATTT 59.624 45.455 0.00 0.00 0.00 1.82
2166 2374 1.985895 ACTCCCTCCGTCCTTGAAATT 59.014 47.619 0.00 0.00 0.00 1.82
2167 2375 1.657804 ACTCCCTCCGTCCTTGAAAT 58.342 50.000 0.00 0.00 0.00 2.17
2168 2376 1.897802 GTACTCCCTCCGTCCTTGAAA 59.102 52.381 0.00 0.00 0.00 2.69
2169 2377 1.076677 AGTACTCCCTCCGTCCTTGAA 59.923 52.381 0.00 0.00 0.00 2.69
2170 2378 0.702902 AGTACTCCCTCCGTCCTTGA 59.297 55.000 0.00 0.00 0.00 3.02
2171 2379 1.204941 CAAGTACTCCCTCCGTCCTTG 59.795 57.143 0.00 0.00 0.00 3.61
2172 2380 1.076677 TCAAGTACTCCCTCCGTCCTT 59.923 52.381 0.00 0.00 0.00 3.36
2173 2381 0.702902 TCAAGTACTCCCTCCGTCCT 59.297 55.000 0.00 0.00 0.00 3.85
2174 2382 1.777941 ATCAAGTACTCCCTCCGTCC 58.222 55.000 0.00 0.00 0.00 4.79
2175 2383 6.645790 TTTATATCAAGTACTCCCTCCGTC 57.354 41.667 0.00 0.00 0.00 4.79
2176 2384 7.442656 CAATTTATATCAAGTACTCCCTCCGT 58.557 38.462 0.00 0.00 0.00 4.69
2177 2385 6.369065 GCAATTTATATCAAGTACTCCCTCCG 59.631 42.308 0.00 0.00 0.00 4.63
2178 2386 7.454225 AGCAATTTATATCAAGTACTCCCTCC 58.546 38.462 0.00 0.00 0.00 4.30
2179 2387 8.910351 AAGCAATTTATATCAAGTACTCCCTC 57.090 34.615 0.00 0.00 0.00 4.30
2181 2389 9.998106 TCTAAGCAATTTATATCAAGTACTCCC 57.002 33.333 0.00 0.00 0.00 4.30
2220 2432 3.552604 GCTAAATTGTGAGGCGAAACA 57.447 42.857 0.00 0.00 0.00 2.83
2254 2466 1.227380 GTGCCGGAAGATCAGCGAT 60.227 57.895 5.05 0.00 0.00 4.58
2405 2618 6.827586 ACCGTTGTTGTAATTCCATTGTAT 57.172 33.333 0.00 0.00 0.00 2.29
2463 2676 2.223464 AATGGTGCGGCCCATACCTT 62.223 55.000 19.05 9.06 44.55 3.50
2467 2680 1.228124 GCTAATGGTGCGGCCCATA 60.228 57.895 19.05 9.77 44.55 2.74
2504 2718 4.253685 CTGAGAGGGCGAGAATTTAAACA 58.746 43.478 0.00 0.00 0.00 2.83
2563 2833 1.586154 GCGCTAAAGCTTTGGAGGCA 61.586 55.000 25.01 1.79 39.32 4.75
2599 2869 0.832983 TTTTGGGCTTGGATGCAGCT 60.833 50.000 0.22 0.00 37.43 4.24


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

AutoCloner maintained by Alex Coulton.