Multiple sequence alignment - TraesCS2A01G263800

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 TraesCS2A01G263800 chr2A 100.000 2423 0 0 1 2423 418820788 418823210 0.000000e+00 4475.0
1 TraesCS2A01G263800 chr2D 90.547 1957 79 40 1 1897 316288732 316286822 0.000000e+00 2492.0
2 TraesCS2A01G263800 chr2D 91.496 341 25 1 2087 2423 316286649 316286309 1.310000e-127 466.0
3 TraesCS2A01G263800 chr2B 90.321 1808 70 33 1 1749 384343450 384341689 0.000000e+00 2272.0
4 TraesCS2A01G263800 chr2B 85.625 160 17 1 2132 2285 384340037 384339878 1.930000e-36 163.0
5 TraesCS2A01G263800 chr2B 79.452 146 12 5 2276 2421 384338702 384338575 1.190000e-13 87.9
6 TraesCS2A01G263800 chr2B 90.196 51 5 0 1847 1897 384341473 384341423 1.550000e-07 67.6
7 TraesCS2A01G263800 chr7B 97.436 39 1 0 222 260 732496771 732496809 1.550000e-07 67.6
8 TraesCS2A01G263800 chr7A 97.436 39 1 0 222 260 169021787 169021825 1.550000e-07 67.6
9 TraesCS2A01G263800 chr7A 97.297 37 1 0 222 258 704610922 704610886 2.010000e-06 63.9
10 TraesCS2A01G263800 chr5D 95.000 40 2 0 221 260 133866408 133866369 2.010000e-06 63.9
11 TraesCS2A01G263800 chr3B 95.000 40 2 0 221 260 252583646 252583685 2.010000e-06 63.9
12 TraesCS2A01G263800 chr1B 89.796 49 4 1 199 246 149526269 149526221 7.230000e-06 62.1
13 TraesCS2A01G263800 chr4B 92.308 39 3 0 221 259 525301003 525300965 3.370000e-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 TraesCS2A01G263800 chr2A 418820788 418823210 2422 False 4475.000 4475 100.0000 1 2423 1 chr2A.!!$F1 2422
1 TraesCS2A01G263800 chr2D 316286309 316288732 2423 True 1479.000 2492 91.0215 1 2423 2 chr2D.!!$R1 2422
2 TraesCS2A01G263800 chr2B 384338575 384343450 4875 True 647.625 2272 86.3985 1 2421 4 chr2B.!!$R1 2420

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
769 813 0.037734 AAAGAAATCGGTCGGCCCTT 59.962 50.0 0.0 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2266 3691 0.034059 CCTAGCTAGTTGCATCCCGG 59.966 60.0 19.31 0.0 45.94 5.73 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
92 93 1.736645 CCTCCACACTAACACGGCG 60.737 63.158 4.80 4.80 0.00 6.46
154 155 0.378257 CATATCACGGCTGGCAACAC 59.622 55.000 1.08 0.00 46.17 3.32
171 172 5.227152 GCAACACTCCGGAAAATATTTGTT 58.773 37.500 5.23 3.81 0.00 2.83
175 176 7.284919 ACACTCCGGAAAATATTTGTTTCTT 57.715 32.000 5.23 0.00 35.68 2.52
176 177 7.722363 ACACTCCGGAAAATATTTGTTTCTTT 58.278 30.769 5.23 0.00 35.68 2.52
262 270 4.032960 TCTTTACCGTGGGAGTACTACA 57.967 45.455 7.57 1.22 0.00 2.74
362 396 8.493547 TCATATGTACTTATGAAGAGTCGTACG 58.506 37.037 22.55 9.53 36.03 3.67
368 402 1.153881 GAAGAGTCGTACGGTGGCC 60.154 63.158 16.52 0.00 0.00 5.36
460 495 2.119457 GCGTTTTCCTGCAACTGAAAG 58.881 47.619 6.02 0.00 42.29 2.62
518 553 7.698506 TCGAAGAGAGTAGAAATTACTGGAA 57.301 36.000 0.00 0.00 0.00 3.53
519 554 7.763356 TCGAAGAGAGTAGAAATTACTGGAAG 58.237 38.462 0.00 0.00 42.29 3.46
520 555 7.610692 TCGAAGAGAGTAGAAATTACTGGAAGA 59.389 37.037 0.00 0.00 37.43 2.87
521 556 7.913297 CGAAGAGAGTAGAAATTACTGGAAGAG 59.087 40.741 0.00 0.00 37.43 2.85
522 557 8.658840 AAGAGAGTAGAAATTACTGGAAGAGT 57.341 34.615 0.00 0.00 37.43 3.24
523 558 9.756571 AAGAGAGTAGAAATTACTGGAAGAGTA 57.243 33.333 0.00 0.00 37.43 2.59
524 559 9.403583 AGAGAGTAGAAATTACTGGAAGAGTAG 57.596 37.037 0.00 0.00 38.45 2.57
525 560 9.181061 GAGAGTAGAAATTACTGGAAGAGTAGT 57.819 37.037 0.00 0.00 38.45 2.73
631 675 3.554692 GTCGCCGACTGCCATTCG 61.555 66.667 10.56 0.00 36.24 3.34
700 744 1.021390 CGGTCAGGTCAGTGGCAATC 61.021 60.000 0.00 0.00 0.00 2.67
732 776 3.686726 CGTCCGGTAAGACAGTAACTACT 59.313 47.826 0.00 0.00 36.52 2.57
765 809 2.851534 CAAAGAAAGAAATCGGTCGGC 58.148 47.619 0.00 0.00 0.00 5.54
769 813 0.037734 AAAGAAATCGGTCGGCCCTT 59.962 50.000 0.00 0.00 0.00 3.95
771 815 0.676782 AGAAATCGGTCGGCCCTTTG 60.677 55.000 0.00 0.00 0.00 2.77
775 819 4.394712 CGGTCGGCCCTTTGCTCT 62.395 66.667 0.00 0.00 40.92 4.09
888 943 4.354587 CTTGCTTGATTAATTCTTCGGCC 58.645 43.478 0.00 0.00 0.00 6.13
889 944 2.354510 TGCTTGATTAATTCTTCGGCCG 59.645 45.455 22.12 22.12 0.00 6.13
890 945 2.854805 GCTTGATTAATTCTTCGGCCGC 60.855 50.000 23.51 2.12 0.00 6.53
891 946 1.305201 TGATTAATTCTTCGGCCGCC 58.695 50.000 23.51 0.00 0.00 6.13
892 947 0.591659 GATTAATTCTTCGGCCGCCC 59.408 55.000 23.51 0.00 0.00 6.13
908 963 1.920325 CCCCTCCAAGAGCAGACCA 60.920 63.158 0.00 0.00 0.00 4.02
956 1011 1.003118 TCGGCCAGCACTACAATCTTT 59.997 47.619 2.24 0.00 0.00 2.52
1097 1152 1.139095 GTCGATCCACCGGTGAGTC 59.861 63.158 36.07 27.76 0.00 3.36
1111 1166 3.037549 GGTGAGTCTCATCCTCATCCTT 58.962 50.000 5.68 0.00 40.79 3.36
1130 1185 3.551846 CTTCTCCTACCTCTCCTGTCTC 58.448 54.545 0.00 0.00 0.00 3.36
1156 1211 1.517257 CGTGGACGATGGAGCTGAC 60.517 63.158 0.00 0.00 43.02 3.51
1165 1220 2.433318 GGAGCTGACGAGTGGTGC 60.433 66.667 0.00 0.00 0.00 5.01
1230 1285 0.519999 GAACGTGCGAGTACGACGAT 60.520 55.000 19.51 6.10 46.46 3.73
1404 1459 3.077556 TGGAGCCGCCTCTTCTCC 61.078 66.667 0.00 0.00 45.02 3.71
1435 1511 1.066908 CCTTCTGATCTCTCGCCTGAC 59.933 57.143 0.00 0.00 0.00 3.51
1522 1599 4.023450 GCAGCTATGATATGAAGCAGCAAA 60.023 41.667 10.98 0.00 45.06 3.68
1527 1604 3.073678 TGATATGAAGCAGCAAACGTGT 58.926 40.909 0.00 0.00 0.00 4.49
1528 1605 2.967459 TATGAAGCAGCAAACGTGTG 57.033 45.000 0.00 0.00 0.00 3.82
1557 1634 1.484240 GAGGGAGAAGTGATGACCCAG 59.516 57.143 0.00 0.00 42.62 4.45
1571 1648 2.158959 CCCAGTGTCGATTCGCGTC 61.159 63.158 5.77 0.00 41.80 5.19
1575 1652 0.247576 AGTGTCGATTCGCGTCTACG 60.248 55.000 5.77 8.62 41.80 3.51
1576 1653 0.519999 GTGTCGATTCGCGTCTACGT 60.520 55.000 5.77 0.00 42.22 3.57
1577 1654 0.998669 TGTCGATTCGCGTCTACGTA 59.001 50.000 5.77 0.00 42.22 3.57
1578 1655 1.005662 TGTCGATTCGCGTCTACGTAG 60.006 52.381 16.73 16.73 42.22 3.51
1579 1656 1.005557 GTCGATTCGCGTCTACGTAGT 60.006 52.381 21.53 0.69 43.13 2.73
1580 1657 2.216488 GTCGATTCGCGTCTACGTAGTA 59.784 50.000 21.53 6.56 41.36 1.82
1581 1658 2.216488 TCGATTCGCGTCTACGTAGTAC 59.784 50.000 21.53 16.26 41.36 2.73
1582 1659 2.958120 CGATTCGCGTCTACGTAGTACG 60.958 54.545 27.97 27.97 40.65 3.67
1583 1660 5.960321 CGATTCGCGTCTACGTAGTACGG 62.960 56.522 30.44 24.13 39.73 4.02
1700 1778 1.602377 CCAGGGACAGTTTTGTTCGTC 59.398 52.381 0.00 0.00 37.76 4.20
1707 1785 2.544267 ACAGTTTTGTTCGTCTGCTAGC 59.456 45.455 8.10 8.10 32.28 3.42
1711 1789 2.232756 TTGTTCGTCTGCTAGCACAA 57.767 45.000 14.93 12.57 0.00 3.33
1712 1790 2.455674 TGTTCGTCTGCTAGCACAAT 57.544 45.000 14.93 0.00 0.00 2.71
1713 1791 3.586100 TGTTCGTCTGCTAGCACAATA 57.414 42.857 14.93 0.00 0.00 1.90
1714 1792 3.920446 TGTTCGTCTGCTAGCACAATAA 58.080 40.909 14.93 3.52 0.00 1.40
1718 1796 4.669318 TCGTCTGCTAGCACAATAAGTAC 58.331 43.478 14.93 3.15 0.00 2.73
1733 1811 9.438291 CACAATAAGTACATGCTAGTAATTTGC 57.562 33.333 7.03 0.00 34.53 3.68
1752 1990 3.963665 TGCTTGTCCATTTGAAAGTTCG 58.036 40.909 0.00 0.00 0.00 3.95
1763 2001 7.040062 TCCATTTGAAAGTTCGATTGGTATTGT 60.040 33.333 16.49 0.00 40.52 2.71
1838 2083 2.185867 GCGGGTGCCATCGTAAGA 59.814 61.111 0.00 0.00 44.04 2.10
1887 2132 9.753674 ACCATCCGATAATGTATTTTGGATATT 57.246 29.630 0.00 0.00 33.18 1.28
1897 2142 7.581213 TGTATTTTGGATATTTAGCCAGGTG 57.419 36.000 0.00 0.00 43.44 4.00
1898 2143 7.122715 TGTATTTTGGATATTTAGCCAGGTGT 58.877 34.615 0.00 0.00 43.44 4.16
1899 2144 5.913137 TTTTGGATATTTAGCCAGGTGTG 57.087 39.130 0.00 0.00 43.44 3.82
1902 2147 5.186256 TGGATATTTAGCCAGGTGTGAAA 57.814 39.130 0.00 0.00 36.73 2.69
1903 2148 5.575157 TGGATATTTAGCCAGGTGTGAAAA 58.425 37.500 0.00 0.00 36.73 2.29
1904 2149 6.194235 TGGATATTTAGCCAGGTGTGAAAAT 58.806 36.000 0.00 0.00 36.73 1.82
1905 2150 6.321181 TGGATATTTAGCCAGGTGTGAAAATC 59.679 38.462 0.00 0.00 36.73 2.17
1906 2151 4.701956 ATTTAGCCAGGTGTGAAAATCG 57.298 40.909 0.00 0.00 0.00 3.34
1907 2152 3.410631 TTAGCCAGGTGTGAAAATCGA 57.589 42.857 0.00 0.00 0.00 3.59
1908 2153 2.496899 AGCCAGGTGTGAAAATCGAT 57.503 45.000 0.00 0.00 0.00 3.59
1909 2154 2.086869 AGCCAGGTGTGAAAATCGATG 58.913 47.619 0.00 0.00 0.00 3.84
1911 2156 2.487762 GCCAGGTGTGAAAATCGATGAA 59.512 45.455 0.00 0.00 0.00 2.57
1912 2157 3.057596 GCCAGGTGTGAAAATCGATGAAA 60.058 43.478 0.00 0.00 0.00 2.69
1914 2159 4.151070 CAGGTGTGAAAATCGATGAAACG 58.849 43.478 0.00 0.00 0.00 3.60
1916 2161 3.187637 GGTGTGAAAATCGATGAAACGGA 59.812 43.478 0.00 0.00 0.00 4.69
1917 2162 4.148891 GTGTGAAAATCGATGAAACGGAC 58.851 43.478 0.00 0.00 0.00 4.79
1918 2163 3.187637 TGTGAAAATCGATGAAACGGACC 59.812 43.478 0.00 0.00 0.00 4.46
1919 2164 2.745281 TGAAAATCGATGAAACGGACCC 59.255 45.455 0.00 0.00 0.00 4.46
1920 2165 2.781681 AAATCGATGAAACGGACCCT 57.218 45.000 0.00 0.00 0.00 4.34
1921 2166 2.781681 AATCGATGAAACGGACCCTT 57.218 45.000 0.00 0.00 0.00 3.95
1922 2167 2.781681 ATCGATGAAACGGACCCTTT 57.218 45.000 0.00 0.00 0.00 3.11
1923 2168 2.554370 TCGATGAAACGGACCCTTTT 57.446 45.000 0.00 0.00 0.00 2.27
1925 2170 2.038033 TCGATGAAACGGACCCTTTTCT 59.962 45.455 15.86 5.20 35.88 2.52
1926 2171 3.258872 TCGATGAAACGGACCCTTTTCTA 59.741 43.478 15.86 6.25 35.88 2.10
1927 2172 3.998341 CGATGAAACGGACCCTTTTCTAA 59.002 43.478 15.86 1.54 35.88 2.10
1929 2174 4.153673 TGAAACGGACCCTTTTCTAACA 57.846 40.909 15.86 0.00 35.88 2.41
1932 2177 3.851458 ACGGACCCTTTTCTAACACTT 57.149 42.857 0.00 0.00 0.00 3.16
1933 2178 3.736720 ACGGACCCTTTTCTAACACTTC 58.263 45.455 0.00 0.00 0.00 3.01
1934 2179 3.135167 ACGGACCCTTTTCTAACACTTCA 59.865 43.478 0.00 0.00 0.00 3.02
1937 2182 4.885325 GGACCCTTTTCTAACACTTCAACA 59.115 41.667 0.00 0.00 0.00 3.33
1938 2183 5.220989 GGACCCTTTTCTAACACTTCAACAC 60.221 44.000 0.00 0.00 0.00 3.32
1939 2184 5.258051 ACCCTTTTCTAACACTTCAACACA 58.742 37.500 0.00 0.00 0.00 3.72
1940 2185 5.712917 ACCCTTTTCTAACACTTCAACACAA 59.287 36.000 0.00 0.00 0.00 3.33
1941 2186 6.209788 ACCCTTTTCTAACACTTCAACACAAA 59.790 34.615 0.00 0.00 0.00 2.83
1943 2188 7.763985 CCCTTTTCTAACACTTCAACACAAAAT 59.236 33.333 0.00 0.00 0.00 1.82
1944 2189 8.594687 CCTTTTCTAACACTTCAACACAAAATG 58.405 33.333 0.00 0.00 0.00 2.32
1945 2190 9.352784 CTTTTCTAACACTTCAACACAAAATGA 57.647 29.630 0.00 0.00 0.00 2.57
1946 2191 9.868277 TTTTCTAACACTTCAACACAAAATGAT 57.132 25.926 0.00 0.00 0.00 2.45
1947 2192 9.515020 TTTCTAACACTTCAACACAAAATGATC 57.485 29.630 0.00 0.00 0.00 2.92
1948 2193 7.648142 TCTAACACTTCAACACAAAATGATCC 58.352 34.615 0.00 0.00 0.00 3.36
1949 2194 4.858935 ACACTTCAACACAAAATGATCCG 58.141 39.130 0.00 0.00 0.00 4.18
1950 2195 4.229096 CACTTCAACACAAAATGATCCGG 58.771 43.478 0.00 0.00 0.00 5.14
1951 2196 4.023279 CACTTCAACACAAAATGATCCGGA 60.023 41.667 6.61 6.61 0.00 5.14
1952 2197 4.766891 ACTTCAACACAAAATGATCCGGAT 59.233 37.500 19.21 19.21 0.00 4.18
1954 2199 4.588899 TCAACACAAAATGATCCGGATCT 58.411 39.130 37.39 23.62 38.60 2.75
1955 2200 4.395854 TCAACACAAAATGATCCGGATCTG 59.604 41.667 37.39 29.88 38.60 2.90
1956 2201 4.220693 ACACAAAATGATCCGGATCTGA 57.779 40.909 37.39 23.53 38.60 3.27
1957 2202 4.588899 ACACAAAATGATCCGGATCTGAA 58.411 39.130 37.39 22.84 38.60 3.02
1959 2204 5.476599 ACACAAAATGATCCGGATCTGAAAA 59.523 36.000 37.39 22.15 38.60 2.29
1960 2205 6.153340 ACACAAAATGATCCGGATCTGAAAAT 59.847 34.615 37.39 23.26 38.60 1.82
1961 2206 7.339212 ACACAAAATGATCCGGATCTGAAAATA 59.661 33.333 37.39 20.80 38.60 1.40
1962 2207 8.355169 CACAAAATGATCCGGATCTGAAAATAT 58.645 33.333 37.39 21.97 38.60 1.28
1965 2210 9.971922 AAAATGATCCGGATCTGAAAATATTTC 57.028 29.630 37.39 14.86 38.60 2.17
1966 2211 8.696043 AATGATCCGGATCTGAAAATATTTCA 57.304 30.769 37.39 19.70 38.60 2.69
1967 2212 7.496529 TGATCCGGATCTGAAAATATTTCAC 57.503 36.000 37.39 12.85 38.60 3.18
1968 2213 7.053498 TGATCCGGATCTGAAAATATTTCACA 58.947 34.615 37.39 15.16 38.60 3.58
1969 2214 7.555914 TGATCCGGATCTGAAAATATTTCACAA 59.444 33.333 37.39 14.24 38.60 3.33
1970 2215 7.695480 TCCGGATCTGAAAATATTTCACAAA 57.305 32.000 0.00 0.00 0.00 2.83
1973 2218 7.485913 CCGGATCTGAAAATATTTCACAAACTG 59.514 37.037 2.08 5.16 0.00 3.16
1974 2219 8.236586 CGGATCTGAAAATATTTCACAAACTGA 58.763 33.333 0.10 0.67 0.00 3.41
1978 2223 9.300681 TCTGAAAATATTTCACAAACTGATCCT 57.699 29.630 0.10 0.00 0.00 3.24
1979 2224 9.918630 CTGAAAATATTTCACAAACTGATCCTT 57.081 29.630 0.10 0.00 0.00 3.36
1986 2231 6.522625 TTCACAAACTGATCCTTTTTCACA 57.477 33.333 0.00 0.00 0.00 3.58
1987 2232 6.713762 TCACAAACTGATCCTTTTTCACAT 57.286 33.333 0.00 0.00 0.00 3.21
1989 2234 6.320926 TCACAAACTGATCCTTTTTCACATGA 59.679 34.615 0.00 0.00 0.00 3.07
1990 2235 6.418819 CACAAACTGATCCTTTTTCACATGAC 59.581 38.462 0.00 0.00 0.00 3.06
1991 2236 5.362556 AACTGATCCTTTTTCACATGACG 57.637 39.130 0.00 0.00 0.00 4.35
1992 2237 4.389374 ACTGATCCTTTTTCACATGACGT 58.611 39.130 0.00 0.00 0.00 4.34
1995 2240 2.139917 TCCTTTTTCACATGACGTCCG 58.860 47.619 14.12 6.83 0.00 4.79
1996 2241 1.196808 CCTTTTTCACATGACGTCCGG 59.803 52.381 14.12 7.58 0.00 5.14
1997 2242 1.196808 CTTTTTCACATGACGTCCGGG 59.803 52.381 14.12 5.47 0.00 5.73
1999 2244 2.107041 TTTCACATGACGTCCGGGCT 62.107 55.000 14.12 0.00 0.00 5.19
2000 2245 2.779951 TTCACATGACGTCCGGGCTG 62.780 60.000 14.12 0.00 0.00 4.85
2001 2246 4.082523 ACATGACGTCCGGGCTGG 62.083 66.667 14.12 5.83 40.09 4.85
2002 2247 4.838152 CATGACGTCCGGGCTGGG 62.838 72.222 14.12 0.00 38.76 4.45
2046 3402 6.978343 TCTCCATATAGTGTTTTTGGTTCG 57.022 37.500 0.00 0.00 0.00 3.95
2060 3416 0.250513 GGTTCGCTGGTCCTCAAGAT 59.749 55.000 0.00 0.00 0.00 2.40
2101 3477 9.723601 TGTTAGTACGATAAAATGGGTTAGTTT 57.276 29.630 0.00 0.00 0.00 2.66
2176 3601 5.958955 AGCTTTTGTTGCCTCATCTTATTC 58.041 37.500 0.00 0.00 0.00 1.75
2265 3690 3.245586 TGTCTGGGTTTTTGGATAGGCAT 60.246 43.478 0.00 0.00 0.00 4.40
2266 3691 3.381590 GTCTGGGTTTTTGGATAGGCATC 59.618 47.826 0.00 0.00 0.00 3.91
2286 4896 1.040646 CGGGATGCAACTAGCTAGGA 58.959 55.000 24.35 6.14 45.94 2.94
2392 5006 7.815840 TCAATAATTCTCAACACCACAAAGA 57.184 32.000 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 93 2.153645 TCGATTCCATACATGCATGGC 58.846 47.619 29.41 5.66 44.47 4.40
154 155 7.328493 GGACAAAGAAACAAATATTTTCCGGAG 59.672 37.037 3.34 0.00 34.07 4.63
171 172 3.498481 CCACCCTGAAGATGGACAAAGAA 60.498 47.826 0.00 0.00 35.33 2.52
175 176 0.038166 GCCACCCTGAAGATGGACAA 59.962 55.000 5.12 0.00 35.33 3.18
176 177 1.685224 GCCACCCTGAAGATGGACA 59.315 57.895 5.12 0.00 35.33 4.02
248 252 4.825546 ACGATTATGTAGTACTCCCACG 57.174 45.455 0.00 0.52 0.00 4.94
286 294 4.105486 GTCTTCCCGCTTTGATAATTTGC 58.895 43.478 0.00 0.00 0.00 3.68
368 402 3.521529 CTCCCGCTAGGATTGGCCG 62.522 68.421 0.00 0.00 46.33 6.13
460 495 0.037975 TTTCTCCCTACGTGTTCCGC 60.038 55.000 0.00 0.00 41.42 5.54
498 533 9.403583 CTACTCTTCCAGTAATTTCTACTCTCT 57.596 37.037 0.00 0.00 37.13 3.10
499 534 9.181061 ACTACTCTTCCAGTAATTTCTACTCTC 57.819 37.037 0.00 0.00 37.13 3.20
518 553 6.522625 TCACTGTACGTACTCTACTACTCT 57.477 41.667 25.12 0.00 0.00 3.24
519 554 6.756074 ACATCACTGTACGTACTCTACTACTC 59.244 42.308 25.12 0.00 32.49 2.59
520 555 6.638610 ACATCACTGTACGTACTCTACTACT 58.361 40.000 25.12 0.85 32.49 2.57
521 556 6.900568 ACATCACTGTACGTACTCTACTAC 57.099 41.667 25.12 0.31 32.49 2.73
522 557 7.099120 TGAACATCACTGTACGTACTCTACTA 58.901 38.462 25.12 4.24 33.36 1.82
523 558 5.936372 TGAACATCACTGTACGTACTCTACT 59.064 40.000 25.12 6.13 33.36 2.57
524 559 6.174451 TGAACATCACTGTACGTACTCTAC 57.826 41.667 25.12 2.67 33.36 2.59
525 560 5.163784 GCTGAACATCACTGTACGTACTCTA 60.164 44.000 25.12 9.67 33.36 2.43
598 641 3.066814 ACGCTGGGTACGTCTCCC 61.067 66.667 18.37 18.37 40.28 4.30
631 675 1.741770 GACCACGTGGATGGAGCAC 60.742 63.158 40.21 15.64 43.02 4.40
647 691 2.582498 CGGAGTCCGGCGATTGAC 60.582 66.667 24.39 7.67 44.15 3.18
732 776 1.304254 TTCTTTGCTGTTGCGCTGTA 58.696 45.000 9.73 0.00 43.34 2.74
765 809 2.168313 GAGAGAGAGGAAGAGCAAAGGG 59.832 54.545 0.00 0.00 0.00 3.95
769 813 2.175202 GGTGAGAGAGAGGAAGAGCAA 58.825 52.381 0.00 0.00 0.00 3.91
771 815 1.111277 GGGTGAGAGAGAGGAAGAGC 58.889 60.000 0.00 0.00 0.00 4.09
775 819 0.411452 AGCTGGGTGAGAGAGAGGAA 59.589 55.000 0.00 0.00 0.00 3.36
888 943 3.393970 TCTGCTCTTGGAGGGGCG 61.394 66.667 0.00 0.00 32.15 6.13
889 944 2.270527 GTCTGCTCTTGGAGGGGC 59.729 66.667 0.00 0.00 32.15 5.80
890 945 1.908340 CTGGTCTGCTCTTGGAGGGG 61.908 65.000 0.00 0.00 32.15 4.79
891 946 1.601171 CTGGTCTGCTCTTGGAGGG 59.399 63.158 0.00 0.00 32.15 4.30
892 947 1.078567 GCTGGTCTGCTCTTGGAGG 60.079 63.158 0.00 0.00 32.15 4.30
900 955 2.898738 CCGATCAGCTGGTCTGCT 59.101 61.111 24.11 0.00 45.18 4.24
908 963 3.079478 TGCCTCTGCCGATCAGCT 61.079 61.111 2.00 0.00 42.56 4.24
926 981 0.176680 TGCTGGCCGAGAGAAATCTC 59.823 55.000 0.00 2.10 43.17 2.75
993 1048 1.078426 GGGGTACGACATGCTGCTT 60.078 57.895 0.00 0.00 0.00 3.91
1097 1152 3.831911 GGTAGGAGAAGGATGAGGATGAG 59.168 52.174 0.00 0.00 0.00 2.90
1111 1166 2.853430 AGAGACAGGAGAGGTAGGAGA 58.147 52.381 0.00 0.00 0.00 3.71
1156 1211 1.012086 CATGGATGAAGCACCACTCG 58.988 55.000 0.00 0.00 39.06 4.18
1165 1220 2.681848 GACCTGCAACTCATGGATGAAG 59.318 50.000 0.00 0.00 36.18 3.02
1197 1252 3.379445 GTTCGGACCTCCCTGCGA 61.379 66.667 0.00 0.00 31.48 5.10
1230 1285 1.301637 CTCCCACATGACGTGCACA 60.302 57.895 18.64 0.00 44.91 4.57
1435 1511 3.428282 CCTTTCGAAACCCGGCCG 61.428 66.667 21.04 21.04 39.14 6.13
1472 1548 2.490115 GTCAAGAGCGAAGAGAGAGGAA 59.510 50.000 0.00 0.00 0.00 3.36
1522 1599 4.039357 CTCCGTCTCCGCACACGT 62.039 66.667 0.00 0.00 37.70 4.49
1527 1604 3.578968 TTCTCCCTCCGTCTCCGCA 62.579 63.158 0.00 0.00 0.00 5.69
1528 1605 2.754658 TTCTCCCTCCGTCTCCGC 60.755 66.667 0.00 0.00 0.00 5.54
1557 1634 0.519999 ACGTAGACGCGAATCGACAC 60.520 55.000 15.93 1.20 44.43 3.67
1571 1648 4.976731 ACGTACATACTCCGTACTACGTAG 59.023 45.833 20.97 20.97 38.39 3.51
1575 1652 6.074005 GCAATACGTACATACTCCGTACTAC 58.926 44.000 0.00 0.00 39.56 2.73
1576 1653 5.107491 CGCAATACGTACATACTCCGTACTA 60.107 44.000 0.00 0.00 39.56 1.82
1577 1654 4.319046 CGCAATACGTACATACTCCGTACT 60.319 45.833 0.00 0.00 39.56 2.73
1578 1655 3.902465 CGCAATACGTACATACTCCGTAC 59.098 47.826 0.00 0.00 39.56 3.67
1579 1656 3.807071 TCGCAATACGTACATACTCCGTA 59.193 43.478 0.00 0.00 44.19 4.02
1580 1657 2.613595 TCGCAATACGTACATACTCCGT 59.386 45.455 0.00 0.00 44.19 4.69
1581 1658 3.223953 CTCGCAATACGTACATACTCCG 58.776 50.000 0.00 0.00 44.19 4.63
1582 1659 2.978489 GCTCGCAATACGTACATACTCC 59.022 50.000 0.00 0.00 44.19 3.85
1583 1660 3.664486 CAGCTCGCAATACGTACATACTC 59.336 47.826 0.00 0.00 44.19 2.59
1584 1661 3.066342 ACAGCTCGCAATACGTACATACT 59.934 43.478 0.00 0.00 44.19 2.12
1700 1778 4.813161 AGCATGTACTTATTGTGCTAGCAG 59.187 41.667 20.03 7.83 43.69 4.24
1707 1785 9.438291 GCAAATTACTAGCATGTACTTATTGTG 57.562 33.333 0.00 0.00 0.00 3.33
1711 1789 9.396022 ACAAGCAAATTACTAGCATGTACTTAT 57.604 29.630 0.00 0.00 38.27 1.73
1712 1790 8.786826 ACAAGCAAATTACTAGCATGTACTTA 57.213 30.769 0.00 0.00 38.27 2.24
1713 1791 7.148239 GGACAAGCAAATTACTAGCATGTACTT 60.148 37.037 0.00 0.00 39.87 2.24
1714 1792 6.316390 GGACAAGCAAATTACTAGCATGTACT 59.684 38.462 0.00 0.00 39.87 2.73
1718 1796 5.565592 TGGACAAGCAAATTACTAGCATG 57.434 39.130 0.00 0.00 33.61 4.06
1733 1811 5.630680 CCAATCGAACTTTCAAATGGACAAG 59.369 40.000 0.00 0.00 0.00 3.16
1850 2095 5.977171 TTATCGGATGGTATTTGTCAACG 57.023 39.130 0.00 0.00 0.00 4.10
1887 2132 3.410631 TCGATTTTCACACCTGGCTAA 57.589 42.857 0.00 0.00 0.00 3.09
1892 2137 4.151070 CGTTTCATCGATTTTCACACCTG 58.849 43.478 0.00 0.00 0.00 4.00
1897 2142 3.425758 GGGTCCGTTTCATCGATTTTCAC 60.426 47.826 0.00 0.00 0.00 3.18
1898 2143 2.745281 GGGTCCGTTTCATCGATTTTCA 59.255 45.455 0.00 0.00 0.00 2.69
1899 2144 3.007635 AGGGTCCGTTTCATCGATTTTC 58.992 45.455 0.00 0.00 0.00 2.29
1902 2147 2.781681 AAGGGTCCGTTTCATCGATT 57.218 45.000 0.00 0.00 0.00 3.34
1903 2148 2.781681 AAAGGGTCCGTTTCATCGAT 57.218 45.000 3.64 0.00 0.00 3.59
1904 2149 2.038033 AGAAAAGGGTCCGTTTCATCGA 59.962 45.455 23.20 0.00 43.41 3.59
1905 2150 2.423577 AGAAAAGGGTCCGTTTCATCG 58.576 47.619 23.20 0.00 43.41 3.84
1906 2151 4.758165 TGTTAGAAAAGGGTCCGTTTCATC 59.242 41.667 23.20 13.25 43.41 2.92
1907 2152 4.517832 GTGTTAGAAAAGGGTCCGTTTCAT 59.482 41.667 23.20 14.11 43.41 2.57
1908 2153 3.878699 GTGTTAGAAAAGGGTCCGTTTCA 59.121 43.478 23.20 11.44 43.41 2.69
1909 2154 4.132336 AGTGTTAGAAAAGGGTCCGTTTC 58.868 43.478 16.82 16.82 42.06 2.78
1911 2156 3.851458 AGTGTTAGAAAAGGGTCCGTT 57.149 42.857 0.00 0.00 0.00 4.44
1912 2157 3.135167 TGAAGTGTTAGAAAAGGGTCCGT 59.865 43.478 0.00 0.00 0.00 4.69
1914 2159 4.885325 TGTTGAAGTGTTAGAAAAGGGTCC 59.115 41.667 0.00 0.00 0.00 4.46
1916 2161 5.258051 TGTGTTGAAGTGTTAGAAAAGGGT 58.742 37.500 0.00 0.00 0.00 4.34
1917 2162 5.828299 TGTGTTGAAGTGTTAGAAAAGGG 57.172 39.130 0.00 0.00 0.00 3.95
1918 2163 8.594687 CATTTTGTGTTGAAGTGTTAGAAAAGG 58.405 33.333 0.00 0.00 0.00 3.11
1919 2164 9.352784 TCATTTTGTGTTGAAGTGTTAGAAAAG 57.647 29.630 0.00 0.00 0.00 2.27
1920 2165 9.868277 ATCATTTTGTGTTGAAGTGTTAGAAAA 57.132 25.926 0.00 0.00 0.00 2.29
1921 2166 9.515020 GATCATTTTGTGTTGAAGTGTTAGAAA 57.485 29.630 0.00 0.00 0.00 2.52
1922 2167 8.134895 GGATCATTTTGTGTTGAAGTGTTAGAA 58.865 33.333 0.00 0.00 0.00 2.10
1923 2168 7.519809 CGGATCATTTTGTGTTGAAGTGTTAGA 60.520 37.037 0.00 0.00 0.00 2.10
1925 2170 6.434596 CGGATCATTTTGTGTTGAAGTGTTA 58.565 36.000 0.00 0.00 0.00 2.41
1926 2171 5.280945 CGGATCATTTTGTGTTGAAGTGTT 58.719 37.500 0.00 0.00 0.00 3.32
1927 2172 4.261572 CCGGATCATTTTGTGTTGAAGTGT 60.262 41.667 0.00 0.00 0.00 3.55
1929 2174 4.141287 TCCGGATCATTTTGTGTTGAAGT 58.859 39.130 0.00 0.00 0.00 3.01
1932 2177 4.395854 CAGATCCGGATCATTTTGTGTTGA 59.604 41.667 38.83 0.00 40.22 3.18
1933 2178 4.395854 TCAGATCCGGATCATTTTGTGTTG 59.604 41.667 38.83 26.34 40.22 3.33
1934 2179 4.588899 TCAGATCCGGATCATTTTGTGTT 58.411 39.130 38.83 17.59 40.22 3.32
1937 2182 6.780457 ATTTTCAGATCCGGATCATTTTGT 57.220 33.333 38.83 19.68 40.22 2.83
1938 2183 9.754382 AAATATTTTCAGATCCGGATCATTTTG 57.246 29.630 38.83 29.15 40.22 2.44
1939 2184 9.971922 GAAATATTTTCAGATCCGGATCATTTT 57.028 29.630 38.83 24.99 40.22 1.82
1940 2185 9.135189 TGAAATATTTTCAGATCCGGATCATTT 57.865 29.630 38.83 31.17 40.22 2.32
1941 2186 8.571336 GTGAAATATTTTCAGATCCGGATCATT 58.429 33.333 38.83 26.21 40.22 2.57
1943 2188 7.053498 TGTGAAATATTTTCAGATCCGGATCA 58.947 34.615 38.83 22.80 40.22 2.92
1944 2189 7.496529 TGTGAAATATTTTCAGATCCGGATC 57.503 36.000 33.14 33.14 38.09 3.36
1945 2190 7.880160 TTGTGAAATATTTTCAGATCCGGAT 57.120 32.000 19.21 19.21 0.00 4.18
1946 2191 7.393234 AGTTTGTGAAATATTTTCAGATCCGGA 59.607 33.333 6.61 6.61 0.00 5.14
1947 2192 7.485913 CAGTTTGTGAAATATTTTCAGATCCGG 59.514 37.037 1.43 0.00 0.00 5.14
1948 2193 8.236586 TCAGTTTGTGAAATATTTTCAGATCCG 58.763 33.333 1.43 0.00 29.64 4.18
1952 2197 9.300681 AGGATCAGTTTGTGAAATATTTTCAGA 57.699 29.630 1.43 0.00 39.19 3.27
1959 2204 9.696917 GTGAAAAAGGATCAGTTTGTGAAATAT 57.303 29.630 0.00 0.00 39.19 1.28
1960 2205 8.690884 TGTGAAAAAGGATCAGTTTGTGAAATA 58.309 29.630 0.00 0.00 39.19 1.40
1961 2206 7.555087 TGTGAAAAAGGATCAGTTTGTGAAAT 58.445 30.769 0.00 0.00 39.19 2.17
1962 2207 6.929625 TGTGAAAAAGGATCAGTTTGTGAAA 58.070 32.000 0.00 0.00 39.19 2.69
1965 2210 6.418819 GTCATGTGAAAAAGGATCAGTTTGTG 59.581 38.462 0.00 0.00 0.00 3.33
1966 2211 6.507023 GTCATGTGAAAAAGGATCAGTTTGT 58.493 36.000 0.00 0.00 0.00 2.83
1967 2212 5.626543 CGTCATGTGAAAAAGGATCAGTTTG 59.373 40.000 0.00 0.00 0.00 2.93
1968 2213 5.299279 ACGTCATGTGAAAAAGGATCAGTTT 59.701 36.000 0.00 0.00 0.00 2.66
1969 2214 4.821805 ACGTCATGTGAAAAAGGATCAGTT 59.178 37.500 0.00 0.00 0.00 3.16
1970 2215 4.389374 ACGTCATGTGAAAAAGGATCAGT 58.611 39.130 0.00 0.00 0.00 3.41
1973 2218 3.181520 CGGACGTCATGTGAAAAAGGATC 60.182 47.826 18.91 0.00 0.00 3.36
1974 2219 2.742053 CGGACGTCATGTGAAAAAGGAT 59.258 45.455 18.91 0.00 0.00 3.24
1976 2221 1.196808 CCGGACGTCATGTGAAAAAGG 59.803 52.381 18.91 0.78 0.00 3.11
1977 2222 1.196808 CCCGGACGTCATGTGAAAAAG 59.803 52.381 18.91 0.00 0.00 2.27
1978 2223 1.231221 CCCGGACGTCATGTGAAAAA 58.769 50.000 18.91 0.00 0.00 1.94
1979 2224 1.231958 GCCCGGACGTCATGTGAAAA 61.232 55.000 18.91 0.00 0.00 2.29
1980 2225 1.669760 GCCCGGACGTCATGTGAAA 60.670 57.895 18.91 0.00 0.00 2.69
1981 2226 2.047655 GCCCGGACGTCATGTGAA 60.048 61.111 18.91 0.00 0.00 3.18
1982 2227 2.994995 AGCCCGGACGTCATGTGA 60.995 61.111 18.91 0.00 0.00 3.58
1983 2228 2.815211 CAGCCCGGACGTCATGTG 60.815 66.667 18.91 1.27 0.00 3.21
1984 2229 4.082523 CCAGCCCGGACGTCATGT 62.083 66.667 18.91 0.00 36.56 3.21
1986 2231 3.968837 TACCCAGCCCGGACGTCAT 62.969 63.158 18.91 0.00 36.56 3.06
1987 2232 3.968837 ATACCCAGCCCGGACGTCA 62.969 63.158 18.91 0.00 36.56 4.35
1989 2234 3.467226 CATACCCAGCCCGGACGT 61.467 66.667 0.73 0.00 36.56 4.34
1990 2235 3.441011 GACATACCCAGCCCGGACG 62.441 68.421 0.73 0.00 36.56 4.79
1991 2236 2.064581 AGACATACCCAGCCCGGAC 61.065 63.158 0.73 0.00 36.56 4.79
1992 2237 2.063979 CAGACATACCCAGCCCGGA 61.064 63.158 0.73 0.00 36.56 5.14
1995 2240 1.153086 CTGCAGACATACCCAGCCC 60.153 63.158 8.42 0.00 0.00 5.19
1996 2241 0.253044 TTCTGCAGACATACCCAGCC 59.747 55.000 18.03 0.00 0.00 4.85
1997 2242 2.113860 TTTCTGCAGACATACCCAGC 57.886 50.000 18.03 0.00 0.00 4.85
1999 2244 8.439971 AGATTATATTTTCTGCAGACATACCCA 58.560 33.333 18.03 0.00 0.00 4.51
2000 2245 8.854614 AGATTATATTTTCTGCAGACATACCC 57.145 34.615 18.03 6.39 0.00 3.69
2001 2246 8.940952 GGAGATTATATTTTCTGCAGACATACC 58.059 37.037 18.03 8.34 31.34 2.73
2002 2247 9.494271 TGGAGATTATATTTTCTGCAGACATAC 57.506 33.333 18.03 4.43 35.69 2.39
2134 3553 7.859325 AAAGCTACAAAGAGTTGAAGTACAA 57.141 32.000 0.00 0.00 38.20 2.41
2139 3558 6.020360 GCAACAAAAGCTACAAAGAGTTGAAG 60.020 38.462 0.00 0.00 37.80 3.02
2228 3653 5.630121 ACCCAGACAATTTCAGTTCATGTA 58.370 37.500 0.00 0.00 0.00 2.29
2265 3690 1.040646 CTAGCTAGTTGCATCCCGGA 58.959 55.000 12.92 0.00 45.94 5.14
2266 3691 0.034059 CCTAGCTAGTTGCATCCCGG 59.966 60.000 19.31 0.00 45.94 5.73
2322 4932 1.276138 CCATATGTGCCGAGCTATCCA 59.724 52.381 1.24 0.00 0.00 3.41
2389 5003 2.679342 TTGCCCGCCTAGCCATCTT 61.679 57.895 0.00 0.00 0.00 2.40
2392 5006 2.572333 AATGTTGCCCGCCTAGCCAT 62.572 55.000 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.