Multiple sequence alignment - TraesCS4B01G089600

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 TraesCS4B01G089600 chr4B 100.000 2411 0 0 1 2411 90758865 90761275 0.000000e+00 4453
1 TraesCS4B01G089600 chr4B 95.828 1438 59 1 3 1440 171120453 171121889 0.000000e+00 2322
2 TraesCS4B01G089600 chr4B 93.194 191 13 0 1957 2147 649583386 649583196 5.070000e-72 281
3 TraesCS4B01G089600 chr4B 92.188 192 15 0 1956 2147 252010601 252010792 3.050000e-69 272
4 TraesCS4B01G089600 chr4A 98.819 1440 17 0 1 1440 674778438 674779877 0.000000e+00 2566
5 TraesCS4B01G089600 chr4A 87.305 512 26 20 1445 1938 535237738 535237248 1.260000e-152 549
6 TraesCS4B01G089600 chr1B 96.263 1445 53 1 2 1445 22438503 22437059 0.000000e+00 2368
7 TraesCS4B01G089600 chr1B 96.125 1445 56 0 2 1446 22565146 22563702 0.000000e+00 2359
8 TraesCS4B01G089600 chr1B 95.712 1446 61 1 2 1446 22498478 22497033 0.000000e+00 2326
9 TraesCS4B01G089600 chr1B 95.367 1446 66 1 2 1446 22378752 22377307 0.000000e+00 2298
10 TraesCS4B01G089600 chr1B 84.300 414 49 6 1015 1428 447244085 447243688 8.080000e-105 390
11 TraesCS4B01G089600 chr1B 92.079 202 14 2 1959 2158 301635896 301635695 1.410000e-72 283
12 TraesCS4B01G089600 chr1B 91.837 196 16 0 1957 2152 554230554 554230749 8.490000e-70 274
13 TraesCS4B01G089600 chr7D 95.288 1443 66 2 1 1442 89059987 89061428 0.000000e+00 2287
14 TraesCS4B01G089600 chr7D 94.868 1442 57 1 1 1442 514921713 514920289 0.000000e+00 2237
15 TraesCS4B01G089600 chr4D 95.372 1426 66 0 1 1426 208377432 208378857 0.000000e+00 2268
16 TraesCS4B01G089600 chr4D 87.523 545 28 14 1445 1962 61951276 61950745 5.740000e-166 593
17 TraesCS4B01G089600 chr4D 89.892 277 10 5 2153 2411 61950740 61950464 8.250000e-90 340
18 TraesCS4B01G089600 chr3B 94.271 192 11 0 1959 2150 783202599 783202408 6.520000e-76 294
19 TraesCS4B01G089600 chr2B 94.180 189 11 0 1959 2147 526879634 526879822 3.030000e-74 289
20 TraesCS4B01G089600 chr2B 90.955 199 17 1 1953 2150 504195155 504194957 1.420000e-67 267
21 TraesCS4B01G089600 chr5B 93.264 193 13 0 1959 2151 584167045 584166853 3.920000e-73 285
22 TraesCS4B01G089600 chr3A 92.708 192 14 0 1959 2150 55256173 55255982 6.560000e-71 278


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 TraesCS4B01G089600 chr4B 90758865 90761275 2410 False 4453.0 4453 100.0000 1 2411 1 chr4B.!!$F1 2410
1 TraesCS4B01G089600 chr4B 171120453 171121889 1436 False 2322.0 2322 95.8280 3 1440 1 chr4B.!!$F2 1437
2 TraesCS4B01G089600 chr4A 674778438 674779877 1439 False 2566.0 2566 98.8190 1 1440 1 chr4A.!!$F1 1439
3 TraesCS4B01G089600 chr1B 22437059 22438503 1444 True 2368.0 2368 96.2630 2 1445 1 chr1B.!!$R2 1443
4 TraesCS4B01G089600 chr1B 22563702 22565146 1444 True 2359.0 2359 96.1250 2 1446 1 chr1B.!!$R4 1444
5 TraesCS4B01G089600 chr1B 22497033 22498478 1445 True 2326.0 2326 95.7120 2 1446 1 chr1B.!!$R3 1444
6 TraesCS4B01G089600 chr1B 22377307 22378752 1445 True 2298.0 2298 95.3670 2 1446 1 chr1B.!!$R1 1444
7 TraesCS4B01G089600 chr7D 89059987 89061428 1441 False 2287.0 2287 95.2880 1 1442 1 chr7D.!!$F1 1441
8 TraesCS4B01G089600 chr7D 514920289 514921713 1424 True 2237.0 2237 94.8680 1 1442 1 chr7D.!!$R1 1441
9 TraesCS4B01G089600 chr4D 208377432 208378857 1425 False 2268.0 2268 95.3720 1 1426 1 chr4D.!!$F1 1425
10 TraesCS4B01G089600 chr4D 61950464 61951276 812 True 466.5 593 88.7075 1445 2411 2 chr4D.!!$R1 966

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
586 588 2.057137 TGGCTGTTTCTTCTGCAACT 57.943 45.0 0.0 0.0 34.71 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1677 1692 0.881796 CGAAAAGCTCTGAAACCCCC 59.118 55.0 0.0 0.0 0.0 5.4 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
408 410 3.173965 CTCCTCTACAAGTGGAAAGGGA 58.826 50.000 0.00 0.00 37.43 4.20
586 588 2.057137 TGGCTGTTTCTTCTGCAACT 57.943 45.000 0.00 0.00 34.71 3.16
1460 1463 2.859273 AAGAAGCCGGGCGTCTGATG 62.859 60.000 32.93 0.00 45.60 3.07
1515 1528 1.306226 CCCGTCCCTTCTTCCTCCT 60.306 63.158 0.00 0.00 0.00 3.69
1516 1529 1.331399 CCCGTCCCTTCTTCCTCCTC 61.331 65.000 0.00 0.00 0.00 3.71
1517 1530 1.331399 CCGTCCCTTCTTCCTCCTCC 61.331 65.000 0.00 0.00 0.00 4.30
1520 1533 1.990060 CCCTTCTTCCTCCTCCGCA 60.990 63.158 0.00 0.00 0.00 5.69
1561 1576 1.214062 CGGCCGATGCTCTATCTCC 59.786 63.158 24.07 0.00 37.74 3.71
1599 1614 0.852136 GCGAAAACTTTGCAACGCAT 59.148 45.000 20.68 1.07 44.29 4.73
1600 1615 1.395820 GCGAAAACTTTGCAACGCATG 60.396 47.619 20.68 3.66 44.29 4.06
1642 1657 2.110835 TGCATGCGTGGTCAGTGT 59.889 55.556 14.09 0.00 0.00 3.55
1658 1673 3.576982 TCAGTGTCTCATTAAACCCTCGT 59.423 43.478 0.00 0.00 0.00 4.18
1751 1767 1.538047 TGTTTGATGCAGAGGCCTTC 58.462 50.000 6.77 0.00 40.13 3.46
1774 1790 2.668550 GTCCGAAAGTTGGGCGCT 60.669 61.111 7.64 0.00 0.00 5.92
1778 1794 3.373565 GAAAGTTGGGCGCTGGGG 61.374 66.667 7.64 0.00 0.00 4.96
1789 1805 2.118294 GCTGGGGTTGCCTTTCCT 59.882 61.111 0.00 0.00 0.00 3.36
1798 1814 4.198087 GCCTTTCCTGGCCTTTGT 57.802 55.556 3.32 0.00 46.82 2.83
1804 1824 3.895041 CCTTTCCTGGCCTTTGTTTTCTA 59.105 43.478 3.32 0.00 0.00 2.10
1826 1846 1.299850 CTCACCTCGTCACGTTGCA 60.300 57.895 0.00 0.00 0.00 4.08
1842 1862 3.060272 CGTTGCAGTAATAATGGAGCTCG 60.060 47.826 7.83 0.00 0.00 5.03
1892 1919 1.134848 TGCCCGCAAAAATAATCAGGC 60.135 47.619 0.00 0.00 39.64 4.85
1907 1934 1.068748 TCAGGCTCAGTACGAAACGAC 60.069 52.381 0.00 0.00 0.00 4.34
1962 1992 3.711348 AGCTCGCGCTGATTTAGC 58.289 55.556 5.56 2.81 46.86 3.09
1972 2002 3.813529 GCTGATTTAGCGAGTGTTTGT 57.186 42.857 0.00 0.00 43.63 2.83
1973 2003 4.147219 GCTGATTTAGCGAGTGTTTGTT 57.853 40.909 0.00 0.00 43.63 2.83
1974 2004 4.537015 GCTGATTTAGCGAGTGTTTGTTT 58.463 39.130 0.00 0.00 43.63 2.83
1975 2005 4.613031 GCTGATTTAGCGAGTGTTTGTTTC 59.387 41.667 0.00 0.00 43.63 2.78
1976 2006 5.103290 TGATTTAGCGAGTGTTTGTTTCC 57.897 39.130 0.00 0.00 0.00 3.13
1977 2007 4.576873 TGATTTAGCGAGTGTTTGTTTCCA 59.423 37.500 0.00 0.00 0.00 3.53
1978 2008 4.545823 TTTAGCGAGTGTTTGTTTCCAG 57.454 40.909 0.00 0.00 0.00 3.86
1979 2009 2.325583 AGCGAGTGTTTGTTTCCAGA 57.674 45.000 0.00 0.00 0.00 3.86
1980 2010 2.639065 AGCGAGTGTTTGTTTCCAGAA 58.361 42.857 0.00 0.00 0.00 3.02
1981 2011 3.013921 AGCGAGTGTTTGTTTCCAGAAA 58.986 40.909 0.00 0.00 0.00 2.52
1982 2012 3.632145 AGCGAGTGTTTGTTTCCAGAAAT 59.368 39.130 0.00 0.00 32.36 2.17
1983 2013 4.097892 AGCGAGTGTTTGTTTCCAGAAATT 59.902 37.500 0.00 0.00 32.36 1.82
1984 2014 4.803613 GCGAGTGTTTGTTTCCAGAAATTT 59.196 37.500 0.00 0.00 32.36 1.82
1985 2015 5.290885 GCGAGTGTTTGTTTCCAGAAATTTT 59.709 36.000 0.00 0.00 32.36 1.82
1986 2016 6.183360 GCGAGTGTTTGTTTCCAGAAATTTTT 60.183 34.615 0.00 0.00 32.36 1.94
2007 2037 7.576861 TTTTTGGTGTAGGGACTAGAAAAAG 57.423 36.000 0.00 0.00 44.14 2.27
2008 2038 5.899631 TTGGTGTAGGGACTAGAAAAAGT 57.100 39.130 0.00 0.00 44.14 2.66
2009 2039 5.479124 TGGTGTAGGGACTAGAAAAAGTC 57.521 43.478 0.00 0.00 44.14 3.01
2019 2049 6.483385 GACTAGAAAAAGTCCCTAGCAAAC 57.517 41.667 0.00 0.00 40.06 2.93
2020 2050 5.314529 ACTAGAAAAAGTCCCTAGCAAACC 58.685 41.667 0.00 0.00 34.70 3.27
2021 2051 4.178956 AGAAAAAGTCCCTAGCAAACCA 57.821 40.909 0.00 0.00 0.00 3.67
2022 2052 4.542697 AGAAAAAGTCCCTAGCAAACCAA 58.457 39.130 0.00 0.00 0.00 3.67
2023 2053 4.959839 AGAAAAAGTCCCTAGCAAACCAAA 59.040 37.500 0.00 0.00 0.00 3.28
2024 2054 4.665833 AAAAGTCCCTAGCAAACCAAAC 57.334 40.909 0.00 0.00 0.00 2.93
2025 2055 3.306472 AAGTCCCTAGCAAACCAAACA 57.694 42.857 0.00 0.00 0.00 2.83
2026 2056 3.525800 AGTCCCTAGCAAACCAAACAT 57.474 42.857 0.00 0.00 0.00 2.71
2027 2057 3.157087 AGTCCCTAGCAAACCAAACATG 58.843 45.455 0.00 0.00 0.00 3.21
2028 2058 2.231235 GTCCCTAGCAAACCAAACATGG 59.769 50.000 0.00 0.00 0.00 3.66
2029 2059 2.158385 TCCCTAGCAAACCAAACATGGT 60.158 45.455 0.00 0.00 45.55 3.55
2069 2099 7.859613 CTTTTTGCTAAAAGTCCTTAGAAGC 57.140 36.000 20.79 0.00 43.34 3.86
2070 2100 6.952773 TTTTGCTAAAAGTCCTTAGAAGCA 57.047 33.333 6.73 6.73 31.59 3.91
2071 2101 5.941948 TTGCTAAAAGTCCTTAGAAGCAC 57.058 39.130 9.21 0.00 31.59 4.40
2072 2102 4.324267 TGCTAAAAGTCCTTAGAAGCACC 58.676 43.478 6.73 0.00 31.59 5.01
2073 2103 4.041691 TGCTAAAAGTCCTTAGAAGCACCT 59.958 41.667 6.73 0.00 31.59 4.00
2074 2104 5.004448 GCTAAAAGTCCTTAGAAGCACCTT 58.996 41.667 0.00 0.00 31.59 3.50
2075 2105 5.122554 GCTAAAAGTCCTTAGAAGCACCTTC 59.877 44.000 0.00 0.00 40.45 3.46
2092 2122 3.740115 CCTTCTTGAGGGTCTTTTTCGA 58.260 45.455 0.00 0.00 42.26 3.71
2093 2123 4.134563 CCTTCTTGAGGGTCTTTTTCGAA 58.865 43.478 0.00 0.00 42.26 3.71
2094 2124 4.578928 CCTTCTTGAGGGTCTTTTTCGAAA 59.421 41.667 6.47 6.47 42.26 3.46
2095 2125 5.067283 CCTTCTTGAGGGTCTTTTTCGAAAA 59.933 40.000 19.08 19.08 42.26 2.29
2096 2126 5.751243 TCTTGAGGGTCTTTTTCGAAAAG 57.249 39.130 21.53 15.88 0.00 2.27
2097 2127 5.190677 TCTTGAGGGTCTTTTTCGAAAAGT 58.809 37.500 21.53 5.62 0.00 2.66
2098 2128 5.296035 TCTTGAGGGTCTTTTTCGAAAAGTC 59.704 40.000 21.53 15.40 0.00 3.01
2099 2129 3.881089 TGAGGGTCTTTTTCGAAAAGTCC 59.119 43.478 21.53 21.56 35.60 3.85
2100 2130 3.637998 GGGTCTTTTTCGAAAAGTCCC 57.362 47.619 27.49 27.49 44.22 4.46
2102 2132 4.224715 GGTCTTTTTCGAAAAGTCCCAG 57.775 45.455 21.53 16.04 31.97 4.45
2103 2133 3.004419 GGTCTTTTTCGAAAAGTCCCAGG 59.996 47.826 21.53 2.41 31.97 4.45
2104 2134 3.004419 GTCTTTTTCGAAAAGTCCCAGGG 59.996 47.826 21.53 0.00 0.00 4.45
2105 2135 3.117813 TCTTTTTCGAAAAGTCCCAGGGA 60.118 43.478 21.53 3.01 0.00 4.20
2118 2148 4.635699 TCCCAGGGACTAGAAAAAGTTC 57.364 45.455 3.01 0.00 36.02 3.01
2119 2149 4.240323 TCCCAGGGACTAGAAAAAGTTCT 58.760 43.478 3.01 0.00 46.18 3.01
2120 2150 5.408824 TCCCAGGGACTAGAAAAAGTTCTA 58.591 41.667 3.01 0.00 43.97 2.10
2121 2151 5.247792 TCCCAGGGACTAGAAAAAGTTCTAC 59.752 44.000 3.01 0.00 43.97 2.59
2122 2152 5.169295 CCAGGGACTAGAAAAAGTTCTACG 58.831 45.833 0.00 0.00 43.97 3.51
2123 2153 5.047519 CCAGGGACTAGAAAAAGTTCTACGA 60.048 44.000 0.00 0.00 43.97 3.43
2124 2154 5.862860 CAGGGACTAGAAAAAGTTCTACGAC 59.137 44.000 0.00 0.00 43.97 4.34
2125 2155 5.774184 AGGGACTAGAAAAAGTTCTACGACT 59.226 40.000 0.00 0.00 42.53 4.18
2126 2156 6.944862 AGGGACTAGAAAAAGTTCTACGACTA 59.055 38.462 0.00 0.00 42.53 2.59
2127 2157 7.121020 AGGGACTAGAAAAAGTTCTACGACTAG 59.879 40.741 0.00 0.00 42.53 2.57
2128 2158 7.120432 GGGACTAGAAAAAGTTCTACGACTAGA 59.880 40.741 0.00 0.00 42.53 2.43
2129 2159 8.177013 GGACTAGAAAAAGTTCTACGACTAGAG 58.823 40.741 0.00 0.00 42.53 2.43
2130 2160 8.845413 ACTAGAAAAAGTTCTACGACTAGAGA 57.155 34.615 0.00 0.00 42.53 3.10
2131 2161 9.282569 ACTAGAAAAAGTTCTACGACTAGAGAA 57.717 33.333 0.00 0.00 42.53 2.87
2133 2163 8.800231 AGAAAAAGTTCTACGACTAGAGAAAC 57.200 34.615 0.00 0.00 42.53 2.78
2134 2164 8.411683 AGAAAAAGTTCTACGACTAGAGAAACA 58.588 33.333 0.00 0.00 42.53 2.83
2135 2165 8.937634 AAAAAGTTCTACGACTAGAGAAACAA 57.062 30.769 0.00 0.00 33.59 2.83
2136 2166 8.937634 AAAAGTTCTACGACTAGAGAAACAAA 57.062 30.769 0.00 0.00 33.59 2.83
2137 2167 7.927305 AAGTTCTACGACTAGAGAAACAAAC 57.073 36.000 0.00 0.00 33.59 2.93
2138 2168 7.035840 AGTTCTACGACTAGAGAAACAAACA 57.964 36.000 0.00 0.00 33.59 2.83
2139 2169 6.916932 AGTTCTACGACTAGAGAAACAAACAC 59.083 38.462 0.00 0.00 33.59 3.32
2140 2170 5.766222 TCTACGACTAGAGAAACAAACACC 58.234 41.667 0.00 0.00 0.00 4.16
2141 2171 4.395959 ACGACTAGAGAAACAAACACCA 57.604 40.909 0.00 0.00 0.00 4.17
2142 2172 4.117685 ACGACTAGAGAAACAAACACCAC 58.882 43.478 0.00 0.00 0.00 4.16
2143 2173 3.493503 CGACTAGAGAAACAAACACCACC 59.506 47.826 0.00 0.00 0.00 4.61
2144 2174 4.704965 GACTAGAGAAACAAACACCACCT 58.295 43.478 0.00 0.00 0.00 4.00
2145 2175 5.112129 ACTAGAGAAACAAACACCACCTT 57.888 39.130 0.00 0.00 0.00 3.50
2146 2176 6.243216 ACTAGAGAAACAAACACCACCTTA 57.757 37.500 0.00 0.00 0.00 2.69
2147 2177 6.053650 ACTAGAGAAACAAACACCACCTTAC 58.946 40.000 0.00 0.00 0.00 2.34
2148 2178 5.112129 AGAGAAACAAACACCACCTTACT 57.888 39.130 0.00 0.00 0.00 2.24
2149 2179 6.243216 AGAGAAACAAACACCACCTTACTA 57.757 37.500 0.00 0.00 0.00 1.82
2150 2180 6.655930 AGAGAAACAAACACCACCTTACTAA 58.344 36.000 0.00 0.00 0.00 2.24
2151 2181 7.114095 AGAGAAACAAACACCACCTTACTAAA 58.886 34.615 0.00 0.00 0.00 1.85
2213 2246 7.762241 GTTTCTTTTAAACGAGATGCAGTAC 57.238 36.000 0.00 0.00 0.00 2.73
2214 2247 5.756950 TCTTTTAAACGAGATGCAGTACG 57.243 39.130 0.00 0.00 0.00 3.67
2217 2250 4.430137 TTAAACGAGATGCAGTACGACT 57.570 40.909 14.21 5.18 0.00 4.18
2244 2280 7.517614 TTTACTGCACAGACCATTCAATTTA 57.482 32.000 4.31 0.00 0.00 1.40
2265 2301 1.279496 TGAGGTTGACAGCTATGCCT 58.721 50.000 0.00 0.00 0.00 4.75
2296 2332 3.242549 CAGTGCTTGCAGATCAGAGTA 57.757 47.619 0.00 0.00 0.00 2.59
2298 2334 1.923204 GTGCTTGCAGATCAGAGTACG 59.077 52.381 0.00 0.00 0.00 3.67
2299 2335 0.926846 GCTTGCAGATCAGAGTACGC 59.073 55.000 0.00 0.00 0.00 4.42
2300 2336 1.470632 GCTTGCAGATCAGAGTACGCT 60.471 52.381 0.00 0.00 0.00 5.07
2301 2337 2.458951 CTTGCAGATCAGAGTACGCTC 58.541 52.381 0.00 0.00 41.94 5.03
2302 2338 1.463674 TGCAGATCAGAGTACGCTCA 58.536 50.000 0.00 0.00 44.00 4.26
2303 2339 1.818674 TGCAGATCAGAGTACGCTCAA 59.181 47.619 0.00 0.00 44.00 3.02
2359 2401 9.699410 CTCAGTTCTCTCCTATCTATCCATATT 57.301 37.037 0.00 0.00 0.00 1.28
2399 2447 1.737838 TTCAATGCACATCCCTCGTC 58.262 50.000 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
408 410 4.264352 TGAATATTGGAAGCCAGACCCTTT 60.264 41.667 0.00 0.00 33.81 3.11
586 588 3.051210 CTCCACACGCTCAGTCCA 58.949 61.111 0.00 0.00 0.00 4.02
1460 1463 1.531058 GCGGCCGTGTTATCAAATCAC 60.531 52.381 28.70 0.00 0.00 3.06
1500 1513 1.962321 GCGGAGGAGGAAGAAGGGAC 61.962 65.000 0.00 0.00 0.00 4.46
1550 1563 2.214347 CGAGAGAACGGAGATAGAGCA 58.786 52.381 0.00 0.00 0.00 4.26
1578 1593 1.142778 GCGTTGCAAAGTTTTCGCCA 61.143 50.000 16.36 0.00 38.16 5.69
1642 1657 2.935238 GCAGCACGAGGGTTTAATGAGA 60.935 50.000 0.00 0.00 0.00 3.27
1673 1688 1.719063 AAGCTCTGAAACCCCCAGCA 61.719 55.000 0.00 0.00 32.17 4.41
1677 1692 0.881796 CGAAAAGCTCTGAAACCCCC 59.118 55.000 0.00 0.00 0.00 5.40
1705 1720 3.174682 ATCACACACGCGCGCAAAA 62.175 52.632 32.58 11.39 0.00 2.44
1751 1767 2.403259 GCCCAACTTTCGGACAAATTG 58.597 47.619 0.00 0.00 0.00 2.32
1774 1790 2.525592 CCAGGAAAGGCAACCCCA 59.474 61.111 0.00 0.00 35.39 4.96
1789 1805 2.884639 GAGCAGTAGAAAACAAAGGCCA 59.115 45.455 5.01 0.00 0.00 5.36
1795 1811 3.181469 ACGAGGTGAGCAGTAGAAAACAA 60.181 43.478 0.00 0.00 0.00 2.83
1797 1813 2.987821 GACGAGGTGAGCAGTAGAAAAC 59.012 50.000 0.00 0.00 0.00 2.43
1798 1814 2.626266 TGACGAGGTGAGCAGTAGAAAA 59.374 45.455 0.00 0.00 0.00 2.29
1804 1824 1.735376 AACGTGACGAGGTGAGCAGT 61.735 55.000 13.70 0.00 0.00 4.40
1826 1846 3.305199 GCGTACCGAGCTCCATTATTACT 60.305 47.826 8.47 0.00 0.00 2.24
1842 1862 1.004918 AGCCTGAACACTGCGTACC 60.005 57.895 0.00 0.00 0.00 3.34
1874 1901 2.426738 TGAGCCTGATTATTTTTGCGGG 59.573 45.455 0.00 0.00 0.00 6.13
1892 1919 1.069703 TCACCGTCGTTTCGTACTGAG 60.070 52.381 0.00 0.00 0.00 3.35
1962 1992 6.885735 AAAATTTCTGGAAACAAACACTCG 57.114 33.333 0.00 0.00 42.06 4.18
1983 2013 7.120716 ACTTTTTCTAGTCCCTACACCAAAAA 58.879 34.615 0.00 0.00 0.00 1.94
1984 2014 6.665695 ACTTTTTCTAGTCCCTACACCAAAA 58.334 36.000 0.00 0.00 0.00 2.44
1985 2015 6.256643 ACTTTTTCTAGTCCCTACACCAAA 57.743 37.500 0.00 0.00 0.00 3.28
1986 2016 5.861727 GACTTTTTCTAGTCCCTACACCAA 58.138 41.667 0.00 0.00 38.88 3.67
1987 2017 5.479124 GACTTTTTCTAGTCCCTACACCA 57.521 43.478 0.00 0.00 38.88 4.17
1996 2026 5.411977 GGTTTGCTAGGGACTTTTTCTAGTC 59.588 44.000 0.00 0.00 43.05 2.59
1997 2027 5.163131 TGGTTTGCTAGGGACTTTTTCTAGT 60.163 40.000 0.00 0.00 41.75 2.57
1998 2028 5.313712 TGGTTTGCTAGGGACTTTTTCTAG 58.686 41.667 0.00 0.00 41.75 2.43
1999 2029 5.313280 TGGTTTGCTAGGGACTTTTTCTA 57.687 39.130 0.00 0.00 41.75 2.10
2000 2030 4.178956 TGGTTTGCTAGGGACTTTTTCT 57.821 40.909 0.00 0.00 41.75 2.52
2001 2031 4.929819 TTGGTTTGCTAGGGACTTTTTC 57.070 40.909 0.00 0.00 41.75 2.29
2002 2032 4.468153 TGTTTGGTTTGCTAGGGACTTTTT 59.532 37.500 0.00 0.00 41.75 1.94
2003 2033 4.027437 TGTTTGGTTTGCTAGGGACTTTT 58.973 39.130 0.00 0.00 41.75 2.27
2004 2034 3.637769 TGTTTGGTTTGCTAGGGACTTT 58.362 40.909 0.00 0.00 41.75 2.66
2005 2035 3.306472 TGTTTGGTTTGCTAGGGACTT 57.694 42.857 0.00 0.00 41.75 3.01
2006 2036 3.157087 CATGTTTGGTTTGCTAGGGACT 58.843 45.455 0.00 0.00 46.37 3.85
2007 2037 2.231235 CCATGTTTGGTTTGCTAGGGAC 59.769 50.000 0.00 0.00 38.30 4.46
2008 2038 2.524306 CCATGTTTGGTTTGCTAGGGA 58.476 47.619 0.00 0.00 38.30 4.20
2046 2076 7.200455 GTGCTTCTAAGGACTTTTAGCAAAAA 58.800 34.615 7.07 0.00 43.15 1.94
2047 2077 6.238925 GGTGCTTCTAAGGACTTTTAGCAAAA 60.239 38.462 13.12 0.00 45.42 2.44
2048 2078 5.240844 GGTGCTTCTAAGGACTTTTAGCAAA 59.759 40.000 13.12 0.00 45.42 3.68
2049 2079 4.760204 GGTGCTTCTAAGGACTTTTAGCAA 59.240 41.667 13.12 1.75 45.42 3.91
2050 2080 4.041691 AGGTGCTTCTAAGGACTTTTAGCA 59.958 41.667 13.12 9.74 45.42 3.49
2051 2081 4.580868 AGGTGCTTCTAAGGACTTTTAGC 58.419 43.478 13.12 0.00 45.42 3.09
2052 2082 6.729391 GAAGGTGCTTCTAAGGACTTTTAG 57.271 41.667 11.87 0.00 44.37 1.85
2065 2095 1.349357 AGACCCTCAAGAAGGTGCTTC 59.651 52.381 0.00 0.00 44.56 3.86
2066 2096 1.439543 AGACCCTCAAGAAGGTGCTT 58.560 50.000 0.00 0.00 44.56 3.91
2067 2097 1.439543 AAGACCCTCAAGAAGGTGCT 58.560 50.000 0.00 0.00 44.56 4.40
2068 2098 2.278332 AAAGACCCTCAAGAAGGTGC 57.722 50.000 0.00 0.00 44.56 5.01
2069 2099 3.251004 CGAAAAAGACCCTCAAGAAGGTG 59.749 47.826 0.00 0.00 44.56 4.00
2070 2100 3.135895 TCGAAAAAGACCCTCAAGAAGGT 59.864 43.478 0.00 0.00 44.56 3.50
2071 2101 3.740115 TCGAAAAAGACCCTCAAGAAGG 58.260 45.455 0.00 0.00 45.77 3.46
2072 2102 5.751243 TTTCGAAAAAGACCCTCAAGAAG 57.249 39.130 8.44 0.00 0.00 2.85
2073 2103 5.650703 ACTTTTCGAAAAAGACCCTCAAGAA 59.349 36.000 22.67 0.00 0.00 2.52
2074 2104 5.190677 ACTTTTCGAAAAAGACCCTCAAGA 58.809 37.500 22.67 0.00 0.00 3.02
2075 2105 5.500645 ACTTTTCGAAAAAGACCCTCAAG 57.499 39.130 22.67 10.42 0.00 3.02
2076 2106 4.337274 GGACTTTTCGAAAAAGACCCTCAA 59.663 41.667 22.67 0.00 36.53 3.02
2077 2107 3.881089 GGACTTTTCGAAAAAGACCCTCA 59.119 43.478 22.67 0.00 36.53 3.86
2078 2108 4.485024 GGACTTTTCGAAAAAGACCCTC 57.515 45.455 22.67 10.72 36.53 4.30
2081 2111 3.004419 CCTGGGACTTTTCGAAAAAGACC 59.996 47.826 22.67 21.80 39.97 3.85
2082 2112 3.004419 CCCTGGGACTTTTCGAAAAAGAC 59.996 47.826 22.67 15.84 0.00 3.01
2083 2113 3.117813 TCCCTGGGACTTTTCGAAAAAGA 60.118 43.478 22.67 2.75 0.00 2.52
2084 2114 3.219281 TCCCTGGGACTTTTCGAAAAAG 58.781 45.455 22.67 16.26 0.00 2.27
2085 2115 3.300239 TCCCTGGGACTTTTCGAAAAA 57.700 42.857 22.67 8.11 0.00 1.94
2096 2126 4.041815 AGAACTTTTTCTAGTCCCTGGGAC 59.958 45.833 34.02 34.02 42.50 4.46
2097 2127 4.240323 AGAACTTTTTCTAGTCCCTGGGA 58.760 43.478 12.53 12.53 40.54 4.37
2098 2128 4.642466 AGAACTTTTTCTAGTCCCTGGG 57.358 45.455 6.33 6.33 40.54 4.45
2099 2129 5.047519 TCGTAGAACTTTTTCTAGTCCCTGG 60.048 44.000 0.00 0.00 43.63 4.45
2100 2130 5.862860 GTCGTAGAACTTTTTCTAGTCCCTG 59.137 44.000 0.00 0.00 43.63 4.45
2101 2131 5.774184 AGTCGTAGAACTTTTTCTAGTCCCT 59.226 40.000 0.00 0.00 43.63 4.20
2102 2132 6.023357 AGTCGTAGAACTTTTTCTAGTCCC 57.977 41.667 0.00 0.00 43.63 4.46
2103 2133 8.038492 TCTAGTCGTAGAACTTTTTCTAGTCC 57.962 38.462 0.00 0.00 43.63 3.85
2104 2134 8.934825 TCTCTAGTCGTAGAACTTTTTCTAGTC 58.065 37.037 0.00 0.00 43.63 2.59
2105 2135 8.845413 TCTCTAGTCGTAGAACTTTTTCTAGT 57.155 34.615 0.00 0.00 43.63 2.57
2107 2137 9.890352 GTTTCTCTAGTCGTAGAACTTTTTCTA 57.110 33.333 0.00 0.00 42.44 2.10
2108 2138 8.411683 TGTTTCTCTAGTCGTAGAACTTTTTCT 58.588 33.333 0.00 0.00 44.70 2.52
2109 2139 8.571461 TGTTTCTCTAGTCGTAGAACTTTTTC 57.429 34.615 0.00 0.00 39.69 2.29
2110 2140 8.937634 TTGTTTCTCTAGTCGTAGAACTTTTT 57.062 30.769 0.00 0.00 39.69 1.94
2111 2141 8.815189 GTTTGTTTCTCTAGTCGTAGAACTTTT 58.185 33.333 0.00 0.00 39.69 2.27
2112 2142 7.977853 TGTTTGTTTCTCTAGTCGTAGAACTTT 59.022 33.333 0.00 0.00 39.69 2.66
2113 2143 7.434602 GTGTTTGTTTCTCTAGTCGTAGAACTT 59.565 37.037 0.00 0.00 39.69 2.66
2114 2144 6.916932 GTGTTTGTTTCTCTAGTCGTAGAACT 59.083 38.462 0.00 0.00 39.69 3.01
2115 2145 6.143598 GGTGTTTGTTTCTCTAGTCGTAGAAC 59.856 42.308 0.00 0.00 39.69 3.01
2116 2146 6.183360 TGGTGTTTGTTTCTCTAGTCGTAGAA 60.183 38.462 0.00 0.00 39.69 2.10
2117 2147 5.300034 TGGTGTTTGTTTCTCTAGTCGTAGA 59.700 40.000 0.00 0.00 33.96 2.59
2118 2148 5.401674 GTGGTGTTTGTTTCTCTAGTCGTAG 59.598 44.000 0.00 0.00 0.00 3.51
2119 2149 5.284079 GTGGTGTTTGTTTCTCTAGTCGTA 58.716 41.667 0.00 0.00 0.00 3.43
2120 2150 4.117685 GTGGTGTTTGTTTCTCTAGTCGT 58.882 43.478 0.00 0.00 0.00 4.34
2121 2151 3.493503 GGTGGTGTTTGTTTCTCTAGTCG 59.506 47.826 0.00 0.00 0.00 4.18
2122 2152 4.704965 AGGTGGTGTTTGTTTCTCTAGTC 58.295 43.478 0.00 0.00 0.00 2.59
2123 2153 4.772886 AGGTGGTGTTTGTTTCTCTAGT 57.227 40.909 0.00 0.00 0.00 2.57
2124 2154 6.289064 AGTAAGGTGGTGTTTGTTTCTCTAG 58.711 40.000 0.00 0.00 0.00 2.43
2125 2155 6.243216 AGTAAGGTGGTGTTTGTTTCTCTA 57.757 37.500 0.00 0.00 0.00 2.43
2126 2156 5.112129 AGTAAGGTGGTGTTTGTTTCTCT 57.888 39.130 0.00 0.00 0.00 3.10
2127 2157 6.930667 TTAGTAAGGTGGTGTTTGTTTCTC 57.069 37.500 0.00 0.00 0.00 2.87
2128 2158 7.340999 ACATTTAGTAAGGTGGTGTTTGTTTCT 59.659 33.333 3.38 0.00 0.00 2.52
2129 2159 7.485810 ACATTTAGTAAGGTGGTGTTTGTTTC 58.514 34.615 3.38 0.00 0.00 2.78
2130 2160 7.122948 TGACATTTAGTAAGGTGGTGTTTGTTT 59.877 33.333 3.38 0.00 0.00 2.83
2131 2161 6.603997 TGACATTTAGTAAGGTGGTGTTTGTT 59.396 34.615 3.38 0.00 0.00 2.83
2132 2162 6.123651 TGACATTTAGTAAGGTGGTGTTTGT 58.876 36.000 3.38 0.00 0.00 2.83
2133 2163 6.627395 TGACATTTAGTAAGGTGGTGTTTG 57.373 37.500 3.38 0.00 0.00 2.93
2134 2164 8.927675 TTATGACATTTAGTAAGGTGGTGTTT 57.072 30.769 0.00 0.00 0.00 2.83
2135 2165 9.528489 AATTATGACATTTAGTAAGGTGGTGTT 57.472 29.630 0.00 0.00 0.00 3.32
2136 2166 9.528489 AAATTATGACATTTAGTAAGGTGGTGT 57.472 29.630 0.00 0.00 0.00 4.16
2139 2169 9.801873 CCAAAATTATGACATTTAGTAAGGTGG 57.198 33.333 0.00 0.00 0.00 4.61
2140 2170 9.801873 CCCAAAATTATGACATTTAGTAAGGTG 57.198 33.333 0.00 0.00 0.00 4.00
2141 2171 8.977412 CCCCAAAATTATGACATTTAGTAAGGT 58.023 33.333 0.00 0.00 0.00 3.50
2142 2172 8.977412 ACCCCAAAATTATGACATTTAGTAAGG 58.023 33.333 0.00 0.00 0.00 2.69
2146 2176 9.719355 GAAAACCCCAAAATTATGACATTTAGT 57.281 29.630 0.00 0.00 0.00 2.24
2147 2177 9.942850 AGAAAACCCCAAAATTATGACATTTAG 57.057 29.630 0.00 0.00 0.00 1.85
2148 2178 9.717942 CAGAAAACCCCAAAATTATGACATTTA 57.282 29.630 0.00 0.00 0.00 1.40
2149 2179 7.174772 GCAGAAAACCCCAAAATTATGACATTT 59.825 33.333 0.00 0.00 0.00 2.32
2150 2180 6.654582 GCAGAAAACCCCAAAATTATGACATT 59.345 34.615 0.00 0.00 0.00 2.71
2151 2181 6.172630 GCAGAAAACCCCAAAATTATGACAT 58.827 36.000 0.00 0.00 0.00 3.06
2213 2246 2.221055 GGTCTGTGCAGTAAAACAGTCG 59.779 50.000 0.00 0.00 43.49 4.18
2214 2247 3.202906 TGGTCTGTGCAGTAAAACAGTC 58.797 45.455 0.00 0.00 43.49 3.51
2217 2250 4.203226 TGAATGGTCTGTGCAGTAAAACA 58.797 39.130 0.00 0.00 0.00 2.83
2228 2264 7.451255 TCAACCTCAATAAATTGAATGGTCTGT 59.549 33.333 13.87 1.20 45.26 3.41
2244 2280 2.240667 AGGCATAGCTGTCAACCTCAAT 59.759 45.455 0.00 0.00 0.00 2.57
2290 2326 1.204704 TCCATGGTTGAGCGTACTCTG 59.795 52.381 12.58 0.00 43.85 3.35
2296 2332 2.858622 CATGTCCATGGTTGAGCGT 58.141 52.632 12.58 0.00 35.24 5.07
2359 2401 9.905713 ATTGAATTTCATCTAGGTAGCAAGTAA 57.094 29.630 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.