Multiple sequence alignment - TraesCS7D01G018100

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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 TraesCS7D01G018100 chr7D 100.000 2309 0 0 1 2309 8080759 8083067 0.000000e+00 4265.0
1 TraesCS7D01G018100 chr7D 99.492 787 4 0 1 787 23563047 23563833 0.000000e+00 1432.0
2 TraesCS7D01G018100 chr7D 99.365 787 5 0 1 787 135763997 135763211 0.000000e+00 1426.0
3 TraesCS7D01G018100 chr7D 99.365 787 5 0 1 787 135769058 135769844 0.000000e+00 1426.0
4 TraesCS7D01G018100 chr7D 99.490 784 4 0 4 787 400291708 400290925 0.000000e+00 1426.0
5 TraesCS7D01G018100 chr7D 99.238 787 6 0 1 787 14171046 14170260 0.000000e+00 1421.0
6 TraesCS7D01G018100 chr7D 98.819 762 9 0 782 1543 23563863 23564624 0.000000e+00 1358.0
7 TraesCS7D01G018100 chr7D 98.819 762 9 0 782 1543 135769874 135770635 0.000000e+00 1358.0
8 TraesCS7D01G018100 chr7D 98.817 761 9 0 783 1543 14170229 14169469 0.000000e+00 1356.0
9 TraesCS7D01G018100 chr7D 98.425 762 12 0 782 1543 135763181 135762420 0.000000e+00 1341.0
10 TraesCS7D01G018100 chr7D 98.425 762 12 0 782 1543 400290895 400290134 0.000000e+00 1341.0
11 TraesCS7D01G018100 chr3A 99.238 787 6 0 1 787 176141283 176140497 0.000000e+00 1421.0
12 TraesCS7D01G018100 chr2D 99.238 787 6 0 1 787 70659403 70658617 0.000000e+00 1421.0
13 TraesCS7D01G018100 chr2D 98.427 763 12 0 782 1544 70658587 70657825 0.000000e+00 1343.0
14 TraesCS7D01G018100 chr3D 99.111 787 7 0 1 787 564344173 564344959 0.000000e+00 1415.0
15 TraesCS7D01G018100 chr3D 98.688 762 10 0 782 1543 564344989 564345750 0.000000e+00 1352.0
16 TraesCS7D01G018100 chr6D 98.983 787 8 0 1 787 402531242 402530456 0.000000e+00 1410.0
17 TraesCS7D01G018100 chr6D 98.949 761 8 0 782 1542 402530426 402529666 0.000000e+00 1362.0
18 TraesCS7D01G018100 chr5D 98.688 762 10 0 782 1543 460678772 460679533 0.000000e+00 1352.0
19 TraesCS7D01G018100 chr7A 86.400 375 27 16 1935 2297 8638367 8638729 2.780000e-104 388.0
20 TraesCS7D01G018100 chr7A 93.665 221 11 2 1541 1760 8638025 8638243 6.150000e-86 327.0
21 TraesCS7D01G018100 chr7A 91.398 93 1 2 1820 1906 8638275 8638366 1.120000e-23 121.0
22 TraesCS7D01G018100 chr7A 91.667 72 5 1 1879 1950 56213387 56213457 5.250000e-17 99.0
23 TraesCS7D01G018100 chr7A 97.368 38 0 1 1793 1829 8638236 8638273 1.920000e-06 63.9


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 TraesCS7D01G018100 chr7D 8080759 8083067 2308 False 4265.000 4265 100.00000 1 2309 1 chr7D.!!$F1 2308
1 TraesCS7D01G018100 chr7D 23563047 23564624 1577 False 1395.000 1432 99.15550 1 1543 2 chr7D.!!$F2 1542
2 TraesCS7D01G018100 chr7D 135769058 135770635 1577 False 1392.000 1426 99.09200 1 1543 2 chr7D.!!$F3 1542
3 TraesCS7D01G018100 chr7D 14169469 14171046 1577 True 1388.500 1421 99.02750 1 1543 2 chr7D.!!$R1 1542
4 TraesCS7D01G018100 chr7D 135762420 135763997 1577 True 1383.500 1426 98.89500 1 1543 2 chr7D.!!$R2 1542
5 TraesCS7D01G018100 chr7D 400290134 400291708 1574 True 1383.500 1426 98.95750 4 1543 2 chr7D.!!$R3 1539
6 TraesCS7D01G018100 chr3A 176140497 176141283 786 True 1421.000 1421 99.23800 1 787 1 chr3A.!!$R1 786
7 TraesCS7D01G018100 chr2D 70657825 70659403 1578 True 1382.000 1421 98.83250 1 1544 2 chr2D.!!$R1 1543
8 TraesCS7D01G018100 chr3D 564344173 564345750 1577 False 1383.500 1415 98.89950 1 1543 2 chr3D.!!$F1 1542
9 TraesCS7D01G018100 chr6D 402529666 402531242 1576 True 1386.000 1410 98.96600 1 1542 2 chr6D.!!$R1 1541
10 TraesCS7D01G018100 chr5D 460678772 460679533 761 False 1352.000 1352 98.68800 782 1543 1 chr5D.!!$F1 761
11 TraesCS7D01G018100 chr7A 8638025 8638729 704 False 224.975 388 92.20775 1541 2297 4 chr7A.!!$F2 756

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
601 602 3.446442 ACAGATTGAAGGTGCCATCTT 57.554 42.857 0.0 0.0 0.0 2.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1769 1806 0.108138 CACACGGGGGTTCAGATCTC 60.108 60.0 0.0 0.0 0.0 2.75 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
522 523 5.781210 TTGGCATGACATTTTGTTCACTA 57.219 34.783 0.00 0.00 0.00 2.74
601 602 3.446442 ACAGATTGAAGGTGCCATCTT 57.554 42.857 0.00 0.00 0.00 2.40
1243 1279 7.361031 GCATTGAGAAGAATATGCTGGATAGTG 60.361 40.741 0.00 0.00 40.08 2.74
1539 1575 1.040646 TCGAAATCATAGAGCCGGCT 58.959 50.000 33.48 33.48 0.00 5.52
1590 1626 4.154347 GTCCTCCTCAGCAGGGCG 62.154 72.222 0.00 0.00 40.80 6.13
1687 1724 2.203788 TGGGGCAGGACTTCGACT 60.204 61.111 0.00 0.00 0.00 4.18
1723 1760 4.115199 GGGGGCGAGATTGGCTGT 62.115 66.667 0.00 0.00 34.31 4.40
1735 1772 1.830587 TTGGCTGTGCTGACGGAGAT 61.831 55.000 0.00 0.00 0.00 2.75
1743 1780 1.065126 TGCTGACGGAGATGAGAGAGA 60.065 52.381 0.00 0.00 0.00 3.10
1744 1781 1.603802 GCTGACGGAGATGAGAGAGAG 59.396 57.143 0.00 0.00 0.00 3.20
1745 1782 2.221169 CTGACGGAGATGAGAGAGAGG 58.779 57.143 0.00 0.00 0.00 3.69
1746 1783 1.840635 TGACGGAGATGAGAGAGAGGA 59.159 52.381 0.00 0.00 0.00 3.71
1748 1785 2.878406 GACGGAGATGAGAGAGAGGAAG 59.122 54.545 0.00 0.00 0.00 3.46
1750 1787 3.053991 ACGGAGATGAGAGAGAGGAAGAA 60.054 47.826 0.00 0.00 0.00 2.52
1751 1788 4.144297 CGGAGATGAGAGAGAGGAAGAAT 58.856 47.826 0.00 0.00 0.00 2.40
1752 1789 4.216257 CGGAGATGAGAGAGAGGAAGAATC 59.784 50.000 0.00 0.00 0.00 2.52
1753 1790 5.139727 GGAGATGAGAGAGAGGAAGAATCA 58.860 45.833 0.00 0.00 0.00 2.57
1754 1791 5.242393 GGAGATGAGAGAGAGGAAGAATCAG 59.758 48.000 0.00 0.00 0.00 2.90
1755 1792 6.017211 AGATGAGAGAGAGGAAGAATCAGA 57.983 41.667 0.00 0.00 0.00 3.27
1756 1793 6.066690 AGATGAGAGAGAGGAAGAATCAGAG 58.933 44.000 0.00 0.00 0.00 3.35
1757 1794 4.535781 TGAGAGAGAGGAAGAATCAGAGG 58.464 47.826 0.00 0.00 0.00 3.69
1758 1795 4.229353 TGAGAGAGAGGAAGAATCAGAGGA 59.771 45.833 0.00 0.00 0.00 3.71
1759 1796 4.796606 AGAGAGAGGAAGAATCAGAGGAG 58.203 47.826 0.00 0.00 0.00 3.69
1760 1797 4.478317 AGAGAGAGGAAGAATCAGAGGAGA 59.522 45.833 0.00 0.00 0.00 3.71
1761 1798 5.135020 AGAGAGAGGAAGAATCAGAGGAGAT 59.865 44.000 0.00 0.00 0.00 2.75
1762 1799 5.142639 AGAGAGGAAGAATCAGAGGAGATG 58.857 45.833 0.00 0.00 0.00 2.90
1763 1800 4.225573 AGAGGAAGAATCAGAGGAGATGG 58.774 47.826 0.00 0.00 0.00 3.51
1764 1801 4.078688 AGAGGAAGAATCAGAGGAGATGGA 60.079 45.833 0.00 0.00 0.00 3.41
1765 1802 4.225573 AGGAAGAATCAGAGGAGATGGAG 58.774 47.826 0.00 0.00 0.00 3.86
1766 1803 4.078688 AGGAAGAATCAGAGGAGATGGAGA 60.079 45.833 0.00 0.00 0.00 3.71
1767 1804 4.840115 GGAAGAATCAGAGGAGATGGAGAT 59.160 45.833 0.00 0.00 0.00 2.75
1768 1805 5.279607 GGAAGAATCAGAGGAGATGGAGATG 60.280 48.000 0.00 0.00 0.00 2.90
1769 1806 4.161876 AGAATCAGAGGAGATGGAGATGG 58.838 47.826 0.00 0.00 0.00 3.51
1770 1807 3.919304 ATCAGAGGAGATGGAGATGGA 57.081 47.619 0.00 0.00 0.00 3.41
1771 1808 3.241834 TCAGAGGAGATGGAGATGGAG 57.758 52.381 0.00 0.00 0.00 3.86
1772 1809 2.788215 TCAGAGGAGATGGAGATGGAGA 59.212 50.000 0.00 0.00 0.00 3.71
1773 1810 3.402025 TCAGAGGAGATGGAGATGGAGAT 59.598 47.826 0.00 0.00 0.00 2.75
1774 1811 3.765511 CAGAGGAGATGGAGATGGAGATC 59.234 52.174 0.00 0.00 0.00 2.75
1775 1812 3.664127 AGAGGAGATGGAGATGGAGATCT 59.336 47.826 0.00 0.00 42.02 2.75
1776 1813 3.765511 GAGGAGATGGAGATGGAGATCTG 59.234 52.174 0.00 0.00 39.19 2.90
1777 1814 3.402025 AGGAGATGGAGATGGAGATCTGA 59.598 47.826 0.00 0.00 39.19 3.27
1778 1815 4.140734 AGGAGATGGAGATGGAGATCTGAA 60.141 45.833 0.00 0.00 39.19 3.02
1779 1816 4.021192 GGAGATGGAGATGGAGATCTGAAC 60.021 50.000 0.00 0.00 39.19 3.18
1780 1817 3.903090 AGATGGAGATGGAGATCTGAACC 59.097 47.826 0.00 0.00 39.19 3.62
1781 1818 2.402564 TGGAGATGGAGATCTGAACCC 58.597 52.381 0.00 0.00 39.19 4.11
1782 1819 1.696884 GGAGATGGAGATCTGAACCCC 59.303 57.143 0.00 0.00 39.19 4.95
1783 1820 1.696884 GAGATGGAGATCTGAACCCCC 59.303 57.143 0.00 0.00 39.19 5.40
1784 1821 0.394565 GATGGAGATCTGAACCCCCG 59.605 60.000 0.00 0.00 0.00 5.73
1785 1822 0.326618 ATGGAGATCTGAACCCCCGT 60.327 55.000 0.00 0.00 0.00 5.28
1786 1823 1.264749 TGGAGATCTGAACCCCCGTG 61.265 60.000 0.00 0.00 0.00 4.94
1787 1824 1.265454 GGAGATCTGAACCCCCGTGT 61.265 60.000 0.00 0.00 0.00 4.49
1788 1825 0.108138 GAGATCTGAACCCCCGTGTG 60.108 60.000 0.00 0.00 0.00 3.82
1789 1826 1.745489 GATCTGAACCCCCGTGTGC 60.745 63.158 0.00 0.00 0.00 4.57
1790 1827 2.463589 GATCTGAACCCCCGTGTGCA 62.464 60.000 0.00 0.00 0.00 4.57
1791 1828 2.469465 ATCTGAACCCCCGTGTGCAG 62.469 60.000 0.00 0.00 42.40 4.41
1849 1904 8.414003 TCTGGAAGTAGTATTGTCATACACATC 58.586 37.037 0.00 0.00 35.19 3.06
1871 1926 7.387948 ACATCTAAGTTCGTTGCTTTAATCTGT 59.612 33.333 0.00 0.00 0.00 3.41
1913 1968 4.883240 TGCACAGCAGAAGAAGCA 57.117 50.000 0.00 0.00 33.32 3.91
1914 1969 2.625375 TGCACAGCAGAAGAAGCAG 58.375 52.632 0.00 0.00 33.32 4.24
1915 1970 0.887836 TGCACAGCAGAAGAAGCAGG 60.888 55.000 0.00 0.00 33.32 4.85
1916 1971 0.888285 GCACAGCAGAAGAAGCAGGT 60.888 55.000 0.00 0.00 0.00 4.00
1917 1972 0.873054 CACAGCAGAAGAAGCAGGTG 59.127 55.000 0.00 0.00 34.75 4.00
1918 1973 0.471617 ACAGCAGAAGAAGCAGGTGT 59.528 50.000 0.00 0.00 37.82 4.16
1919 1974 1.155042 CAGCAGAAGAAGCAGGTGTC 58.845 55.000 0.00 0.00 0.00 3.67
1920 1975 0.036022 AGCAGAAGAAGCAGGTGTCC 59.964 55.000 0.00 0.00 0.00 4.02
1921 1976 0.957888 GCAGAAGAAGCAGGTGTCCC 60.958 60.000 0.00 0.00 0.00 4.46
1922 1977 0.689623 CAGAAGAAGCAGGTGTCCCT 59.310 55.000 0.00 0.00 44.02 4.20
1923 1978 0.980423 AGAAGAAGCAGGTGTCCCTC 59.020 55.000 0.00 0.00 39.89 4.30
1924 1979 0.980423 GAAGAAGCAGGTGTCCCTCT 59.020 55.000 0.00 0.00 39.89 3.69
1925 1980 2.180276 GAAGAAGCAGGTGTCCCTCTA 58.820 52.381 0.00 0.00 39.89 2.43
1926 1981 2.327325 AGAAGCAGGTGTCCCTCTAA 57.673 50.000 0.00 0.00 39.89 2.10
1927 1982 2.839228 AGAAGCAGGTGTCCCTCTAAT 58.161 47.619 0.00 0.00 39.89 1.73
1928 1983 3.995636 AGAAGCAGGTGTCCCTCTAATA 58.004 45.455 0.00 0.00 39.89 0.98
1929 1984 4.561752 AGAAGCAGGTGTCCCTCTAATAT 58.438 43.478 0.00 0.00 39.89 1.28
1930 1985 5.716979 AGAAGCAGGTGTCCCTCTAATATA 58.283 41.667 0.00 0.00 39.89 0.86
1931 1986 6.326970 AGAAGCAGGTGTCCCTCTAATATAT 58.673 40.000 0.00 0.00 39.89 0.86
1932 1987 6.789959 AGAAGCAGGTGTCCCTCTAATATATT 59.210 38.462 2.97 2.97 39.89 1.28
1933 1988 7.293535 AGAAGCAGGTGTCCCTCTAATATATTT 59.706 37.037 2.68 0.00 39.89 1.40
1958 2013 5.371115 ACCACATGTAAGTTATGTTGTGC 57.629 39.130 0.00 0.00 36.67 4.57
1961 2016 3.119990 ACATGTAAGTTATGTTGTGCGGC 60.120 43.478 0.00 0.00 35.32 6.53
1973 2028 0.036483 TGTGCGGCTTAGCTTGATGA 60.036 50.000 3.59 0.00 38.13 2.92
2012 2090 5.847111 AGTTATGTTCTACCGCATACTCA 57.153 39.130 0.00 0.00 0.00 3.41
2013 2091 6.216801 AGTTATGTTCTACCGCATACTCAA 57.783 37.500 0.00 0.00 0.00 3.02
2014 2092 6.817184 AGTTATGTTCTACCGCATACTCAAT 58.183 36.000 0.00 0.00 0.00 2.57
2015 2093 7.272978 AGTTATGTTCTACCGCATACTCAATT 58.727 34.615 0.00 0.00 0.00 2.32
2016 2094 7.769044 AGTTATGTTCTACCGCATACTCAATTT 59.231 33.333 0.00 0.00 0.00 1.82
2017 2095 6.604735 ATGTTCTACCGCATACTCAATTTC 57.395 37.500 0.00 0.00 0.00 2.17
2018 2096 4.873827 TGTTCTACCGCATACTCAATTTCC 59.126 41.667 0.00 0.00 0.00 3.13
2019 2097 4.067972 TCTACCGCATACTCAATTTCCC 57.932 45.455 0.00 0.00 0.00 3.97
2020 2098 3.709653 TCTACCGCATACTCAATTTCCCT 59.290 43.478 0.00 0.00 0.00 4.20
2021 2099 2.643551 ACCGCATACTCAATTTCCCTG 58.356 47.619 0.00 0.00 0.00 4.45
2036 2114 4.729552 TTCCCTGCCATTCTGCTAATAT 57.270 40.909 0.00 0.00 0.00 1.28
2101 2179 4.989797 TGCAAGCATTTCGAAACATTTCAT 59.010 33.333 13.81 0.00 37.01 2.57
2108 2186 6.944400 GCATTTCGAAACATTTCATTTCTTCG 59.056 34.615 13.81 0.00 37.01 3.79
2152 2230 1.046472 TGGACACAGACGGGTGAGTT 61.046 55.000 10.50 0.00 41.32 3.01
2181 2259 4.713792 TGAGGCTTCTTCCTTCTTCTTT 57.286 40.909 0.00 0.00 36.38 2.52
2209 2287 4.554330 GCGAGAAAGCATGAGGATTCATTC 60.554 45.833 0.00 0.00 42.12 2.67
2240 2318 7.346751 AGCTCTTTATTTTTGTGTTTCTCCA 57.653 32.000 0.00 0.00 0.00 3.86
2264 2342 1.802960 AGTTTCTTGTGAGCTGCATCG 59.197 47.619 1.02 0.00 0.00 3.84
2286 2364 3.589988 GACTGACTCCAACCTATGTGTG 58.410 50.000 0.00 0.00 0.00 3.82
2297 2375 4.235079 ACCTATGTGTGCACCATTGTAT 57.765 40.909 20.96 10.24 0.00 2.29
2298 2376 4.599041 ACCTATGTGTGCACCATTGTATT 58.401 39.130 20.96 4.70 0.00 1.89
2299 2377 5.016173 ACCTATGTGTGCACCATTGTATTT 58.984 37.500 20.96 4.12 0.00 1.40
2300 2378 5.480073 ACCTATGTGTGCACCATTGTATTTT 59.520 36.000 20.96 3.54 0.00 1.82
2301 2379 6.014669 ACCTATGTGTGCACCATTGTATTTTT 60.015 34.615 20.96 2.97 0.00 1.94
2302 2380 6.531240 CCTATGTGTGCACCATTGTATTTTTC 59.469 38.462 20.96 0.00 0.00 2.29
2303 2381 5.528043 TGTGTGCACCATTGTATTTTTCT 57.472 34.783 15.69 0.00 0.00 2.52
2304 2382 5.288015 TGTGTGCACCATTGTATTTTTCTG 58.712 37.500 15.69 0.00 0.00 3.02
2305 2383 5.163468 TGTGTGCACCATTGTATTTTTCTGT 60.163 36.000 15.69 0.00 0.00 3.41
2306 2384 5.175491 GTGTGCACCATTGTATTTTTCTGTG 59.825 40.000 15.69 0.00 0.00 3.66
2307 2385 5.163468 TGTGCACCATTGTATTTTTCTGTGT 60.163 36.000 15.69 0.00 0.00 3.72
2308 2386 6.039829 TGTGCACCATTGTATTTTTCTGTGTA 59.960 34.615 15.69 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
522 523 6.714810 TGCAACTTCTTACTCACCATGTTTAT 59.285 34.615 0.00 0.00 0.00 1.40
694 695 9.970395 TTTTTCTAGTAATACGTCTCTTGACAA 57.030 29.630 0.00 0.00 43.06 3.18
1089 1125 2.167075 AGGTACGGTCAAAAGGATACGG 59.833 50.000 0.00 0.00 46.39 4.02
1243 1279 6.592994 TCATCAATGAGAGTGTCAAGATCAAC 59.407 38.462 0.00 0.00 39.19 3.18
1305 1341 3.877559 CATGCTAACCTCCAGTGATCAA 58.122 45.455 0.00 0.00 0.00 2.57
1484 1520 1.301623 CGACCAGTGGGCCCAATAA 59.698 57.895 30.64 0.00 37.90 1.40
1571 1607 3.465403 CCCTGCTGAGGAGGACGG 61.465 72.222 22.54 0.45 42.93 4.79
1590 1626 1.631071 CCTTCCTCTTCCCCCTCTGC 61.631 65.000 0.00 0.00 0.00 4.26
1591 1627 0.252927 ACCTTCCTCTTCCCCCTCTG 60.253 60.000 0.00 0.00 0.00 3.35
1592 1628 0.498685 AACCTTCCTCTTCCCCCTCT 59.501 55.000 0.00 0.00 0.00 3.69
1687 1724 0.319555 CTTTCCTCAACGTCTCCGCA 60.320 55.000 0.00 0.00 37.70 5.69
1707 1744 2.825836 CACAGCCAATCTCGCCCC 60.826 66.667 0.00 0.00 0.00 5.80
1723 1760 1.065126 TCTCTCTCATCTCCGTCAGCA 60.065 52.381 0.00 0.00 0.00 4.41
1735 1772 4.229353 TCCTCTGATTCTTCCTCTCTCTCA 59.771 45.833 0.00 0.00 0.00 3.27
1743 1780 4.078688 TCTCCATCTCCTCTGATTCTTCCT 60.079 45.833 0.00 0.00 0.00 3.36
1744 1781 4.222336 TCTCCATCTCCTCTGATTCTTCC 58.778 47.826 0.00 0.00 0.00 3.46
1745 1782 5.279607 CCATCTCCATCTCCTCTGATTCTTC 60.280 48.000 0.00 0.00 0.00 2.87
1746 1783 4.594062 CCATCTCCATCTCCTCTGATTCTT 59.406 45.833 0.00 0.00 0.00 2.52
1748 1785 4.158786 TCCATCTCCATCTCCTCTGATTC 58.841 47.826 0.00 0.00 0.00 2.52
1750 1787 3.402025 TCTCCATCTCCATCTCCTCTGAT 59.598 47.826 0.00 0.00 0.00 2.90
1751 1788 2.788215 TCTCCATCTCCATCTCCTCTGA 59.212 50.000 0.00 0.00 0.00 3.27
1752 1789 3.241834 TCTCCATCTCCATCTCCTCTG 57.758 52.381 0.00 0.00 0.00 3.35
1753 1790 3.664127 AGATCTCCATCTCCATCTCCTCT 59.336 47.826 0.00 0.00 33.71 3.69
1754 1791 3.765511 CAGATCTCCATCTCCATCTCCTC 59.234 52.174 0.00 0.00 37.25 3.71
1755 1792 3.402025 TCAGATCTCCATCTCCATCTCCT 59.598 47.826 0.00 0.00 37.25 3.69
1756 1793 3.777087 TCAGATCTCCATCTCCATCTCC 58.223 50.000 0.00 0.00 37.25 3.71
1757 1794 4.021192 GGTTCAGATCTCCATCTCCATCTC 60.021 50.000 0.00 0.00 37.25 2.75
1758 1795 3.903090 GGTTCAGATCTCCATCTCCATCT 59.097 47.826 0.00 0.00 37.25 2.90
1759 1796 3.007831 GGGTTCAGATCTCCATCTCCATC 59.992 52.174 0.00 0.00 37.25 3.51
1760 1797 2.978278 GGGTTCAGATCTCCATCTCCAT 59.022 50.000 0.00 0.00 37.25 3.41
1761 1798 2.402564 GGGTTCAGATCTCCATCTCCA 58.597 52.381 0.00 0.00 37.25 3.86
1762 1799 1.696884 GGGGTTCAGATCTCCATCTCC 59.303 57.143 0.00 0.00 37.25 3.71
1763 1800 1.696884 GGGGGTTCAGATCTCCATCTC 59.303 57.143 0.00 0.00 37.25 2.75
1764 1801 1.813102 GGGGGTTCAGATCTCCATCT 58.187 55.000 0.00 0.00 40.32 2.90
1765 1802 0.394565 CGGGGGTTCAGATCTCCATC 59.605 60.000 0.00 0.00 0.00 3.51
1766 1803 0.326618 ACGGGGGTTCAGATCTCCAT 60.327 55.000 0.00 0.00 0.00 3.41
1767 1804 1.080354 ACGGGGGTTCAGATCTCCA 59.920 57.895 0.00 0.00 0.00 3.86
1768 1805 1.265454 ACACGGGGGTTCAGATCTCC 61.265 60.000 0.00 0.00 0.00 3.71
1769 1806 0.108138 CACACGGGGGTTCAGATCTC 60.108 60.000 0.00 0.00 0.00 2.75
1770 1807 1.983224 CACACGGGGGTTCAGATCT 59.017 57.895 0.00 0.00 0.00 2.75
1771 1808 1.745489 GCACACGGGGGTTCAGATC 60.745 63.158 0.00 0.00 0.00 2.75
1772 1809 2.351276 GCACACGGGGGTTCAGAT 59.649 61.111 0.00 0.00 0.00 2.90
1773 1810 3.164977 TGCACACGGGGGTTCAGA 61.165 61.111 0.00 0.00 0.00 3.27
1774 1811 2.669569 CTGCACACGGGGGTTCAG 60.670 66.667 0.00 0.00 0.00 3.02
1775 1812 4.947147 GCTGCACACGGGGGTTCA 62.947 66.667 0.00 0.00 0.00 3.18
1776 1813 4.947147 TGCTGCACACGGGGGTTC 62.947 66.667 0.00 0.00 0.00 3.62
1777 1814 4.954970 CTGCTGCACACGGGGGTT 62.955 66.667 0.00 0.00 0.00 4.11
1781 1818 3.947132 CTCCTCTGCTGCACACGGG 62.947 68.421 0.00 0.00 0.00 5.28
1782 1819 2.433838 CTCCTCTGCTGCACACGG 60.434 66.667 0.00 0.00 0.00 4.94
1783 1820 2.433838 CCTCCTCTGCTGCACACG 60.434 66.667 0.00 0.00 0.00 4.49
1784 1821 2.046507 CCCTCCTCTGCTGCACAC 60.047 66.667 0.00 0.00 0.00 3.82
1785 1822 2.527624 ACCCTCCTCTGCTGCACA 60.528 61.111 0.00 0.00 0.00 4.57
1786 1823 2.046507 CACCCTCCTCTGCTGCAC 60.047 66.667 0.00 0.00 0.00 4.57
1787 1824 3.324930 CCACCCTCCTCTGCTGCA 61.325 66.667 0.88 0.88 0.00 4.41
1788 1825 4.106925 CCCACCCTCCTCTGCTGC 62.107 72.222 0.00 0.00 0.00 5.25
1789 1826 2.190488 GAACCCACCCTCCTCTGCTG 62.190 65.000 0.00 0.00 0.00 4.41
1790 1827 1.920835 GAACCCACCCTCCTCTGCT 60.921 63.158 0.00 0.00 0.00 4.24
1791 1828 1.779061 TTGAACCCACCCTCCTCTGC 61.779 60.000 0.00 0.00 0.00 4.26
1849 1904 8.492748 TGTAACAGATTAAAGCAACGAACTTAG 58.507 33.333 0.00 0.00 0.00 2.18
1914 1969 8.312564 GTGGTAGAAATATATTAGAGGGACACC 58.687 40.741 0.00 0.04 0.00 4.16
1915 1970 8.867097 TGTGGTAGAAATATATTAGAGGGACAC 58.133 37.037 0.00 4.12 0.00 3.67
1916 1971 9.615660 ATGTGGTAGAAATATATTAGAGGGACA 57.384 33.333 0.00 0.00 0.00 4.02
1917 1972 9.877178 CATGTGGTAGAAATATATTAGAGGGAC 57.123 37.037 0.00 0.00 0.00 4.46
1918 1973 9.615660 ACATGTGGTAGAAATATATTAGAGGGA 57.384 33.333 0.00 0.00 0.00 4.20
1930 1985 9.515226 ACAACATAACTTACATGTGGTAGAAAT 57.485 29.630 9.11 0.71 38.51 2.17
1931 1986 8.779303 CACAACATAACTTACATGTGGTAGAAA 58.221 33.333 9.11 0.00 38.27 2.52
1932 1987 7.094975 GCACAACATAACTTACATGTGGTAGAA 60.095 37.037 9.11 0.00 38.27 2.10
1933 1988 6.370442 GCACAACATAACTTACATGTGGTAGA 59.630 38.462 9.11 0.34 38.27 2.59
1958 2013 4.391216 CAGGAATATCATCAAGCTAAGCCG 59.609 45.833 0.00 0.00 0.00 5.52
1961 2016 8.632906 ATTTCCAGGAATATCATCAAGCTAAG 57.367 34.615 1.58 0.00 0.00 2.18
1991 2046 7.478520 AATTGAGTATGCGGTAGAACATAAC 57.521 36.000 0.00 0.00 30.89 1.89
1993 2048 6.704493 GGAAATTGAGTATGCGGTAGAACATA 59.296 38.462 0.00 0.00 0.00 2.29
2010 2088 1.826720 GCAGAATGGCAGGGAAATTGA 59.173 47.619 0.00 0.00 35.86 2.57
2011 2089 1.829222 AGCAGAATGGCAGGGAAATTG 59.171 47.619 0.00 0.00 35.86 2.32
2012 2090 2.242882 AGCAGAATGGCAGGGAAATT 57.757 45.000 0.00 0.00 35.86 1.82
2013 2091 3.386932 TTAGCAGAATGGCAGGGAAAT 57.613 42.857 0.00 0.00 35.86 2.17
2014 2092 2.897271 TTAGCAGAATGGCAGGGAAA 57.103 45.000 0.00 0.00 35.86 3.13
2015 2093 4.104579 TGATATTAGCAGAATGGCAGGGAA 59.895 41.667 0.00 0.00 35.86 3.97
2016 2094 3.652387 TGATATTAGCAGAATGGCAGGGA 59.348 43.478 0.00 0.00 35.86 4.20
2017 2095 4.025040 TGATATTAGCAGAATGGCAGGG 57.975 45.455 0.00 0.00 35.86 4.45
2018 2096 5.621555 GCATTGATATTAGCAGAATGGCAGG 60.622 44.000 0.00 0.00 35.86 4.85
2019 2097 5.399858 GCATTGATATTAGCAGAATGGCAG 58.600 41.667 0.00 0.00 35.86 4.85
2020 2098 4.083164 CGCATTGATATTAGCAGAATGGCA 60.083 41.667 0.00 0.00 35.86 4.92
2021 2099 4.083110 ACGCATTGATATTAGCAGAATGGC 60.083 41.667 0.00 0.00 35.86 4.40
2036 2114 3.670359 GCTATGACTTGCAAACGCATTGA 60.670 43.478 15.86 1.96 41.85 2.57
2057 2135 2.856222 AGATGCCTAGCAATACAAGGC 58.144 47.619 5.64 5.64 43.62 4.35
2132 2210 1.290324 CTCACCCGTCTGTGTCCAG 59.710 63.158 0.00 0.00 40.25 3.86
2133 2211 1.046472 AACTCACCCGTCTGTGTCCA 61.046 55.000 0.00 0.00 37.51 4.02
2134 2212 0.963962 TAACTCACCCGTCTGTGTCC 59.036 55.000 0.00 0.00 37.51 4.02
2135 2213 1.338973 TGTAACTCACCCGTCTGTGTC 59.661 52.381 0.00 0.00 37.51 3.67
2136 2214 1.405872 TGTAACTCACCCGTCTGTGT 58.594 50.000 0.00 0.00 37.51 3.72
2137 2215 2.519377 TTGTAACTCACCCGTCTGTG 57.481 50.000 0.00 0.00 37.59 3.66
2138 2216 2.168936 TGTTTGTAACTCACCCGTCTGT 59.831 45.455 0.00 0.00 0.00 3.41
2145 2223 3.412386 AGCCTCATGTTTGTAACTCACC 58.588 45.455 0.00 0.00 0.00 4.02
2146 2224 4.757149 AGAAGCCTCATGTTTGTAACTCAC 59.243 41.667 0.00 0.00 0.00 3.51
2152 2230 4.640771 AGGAAGAAGCCTCATGTTTGTA 57.359 40.909 0.00 0.00 30.76 2.41
2181 2259 2.884012 TCCTCATGCTTTCTCGCAAAAA 59.116 40.909 0.00 0.00 44.06 1.94
2188 2266 5.435820 GGAATGAATCCTCATGCTTTCTC 57.564 43.478 0.00 0.00 45.56 2.87
2214 2292 8.908903 TGGAGAAACACAAAAATAAAGAGCTTA 58.091 29.630 0.00 0.00 0.00 3.09
2217 2295 6.142320 CGTGGAGAAACACAAAAATAAAGAGC 59.858 38.462 0.00 0.00 41.38 4.09
2218 2296 6.636850 CCGTGGAGAAACACAAAAATAAAGAG 59.363 38.462 0.00 0.00 41.38 2.85
2219 2297 6.319152 TCCGTGGAGAAACACAAAAATAAAGA 59.681 34.615 0.00 0.00 41.38 2.52
2220 2298 6.500041 TCCGTGGAGAAACACAAAAATAAAG 58.500 36.000 0.00 0.00 41.38 1.85
2240 2318 1.871080 CAGCTCACAAGAAACTCCGT 58.129 50.000 0.00 0.00 0.00 4.69


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

AutoCloner maintained by Alex Coulton.