Multiple sequence alignment - TraesCS3B01G101100

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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 TraesCS3B01G101100 chr3B 100.000 2719 0 0 1 2719 68252474 68255192 0.000000e+00 5022.0
1 TraesCS3B01G101100 chr3B 87.829 304 26 10 1458 1753 68346269 68346569 2.000000e-91 346.0
2 TraesCS3B01G101100 chr3B 79.458 443 70 13 766 1196 67689481 67689914 7.360000e-76 294.0
3 TraesCS3B01G101100 chr3A 97.962 1472 23 6 293 1759 55483213 55484682 0.000000e+00 2545.0
4 TraesCS3B01G101100 chr3A 97.218 719 16 3 2003 2719 55484682 55485398 0.000000e+00 1214.0
5 TraesCS3B01G101100 chr3A 88.158 304 25 8 1458 1753 55500690 55500990 4.310000e-93 351.0
6 TraesCS3B01G101100 chr3A 81.321 439 61 15 769 1196 80790060 80790488 1.210000e-88 337.0
7 TraesCS3B01G101100 chr3D 96.154 1222 41 5 8 1225 43508350 43509569 0.000000e+00 1991.0
8 TraesCS3B01G101100 chr3D 92.809 1029 57 5 738 1759 43512966 43513984 0.000000e+00 1474.0
9 TraesCS3B01G101100 chr3D 90.669 718 49 12 2003 2709 43510092 43510802 0.000000e+00 939.0
10 TraesCS3B01G101100 chr3D 90.621 725 42 11 2003 2706 43568257 43568976 0.000000e+00 939.0
11 TraesCS3B01G101100 chr3D 95.756 377 16 0 37 413 43512241 43512617 2.320000e-170 608.0
12 TraesCS3B01G101100 chr3D 88.841 466 34 11 1304 1756 43509629 43510089 8.500000e-155 556.0
13 TraesCS3B01G101100 chr3D 91.690 361 18 4 2003 2351 43513984 43514344 8.750000e-135 490.0
14 TraesCS3B01G101100 chr3D 89.362 376 29 10 2338 2709 43533694 43534062 1.910000e-126 462.0
15 TraesCS3B01G101100 chr3D 87.399 373 35 9 1393 1759 43567891 43568257 4.190000e-113 418.0
16 TraesCS3B01G101100 chr3D 95.219 251 11 1 1756 2005 279935152 279935402 1.960000e-106 396.0
17 TraesCS3B01G101100 chr3D 90.878 296 23 2 446 741 43512612 43512903 7.060000e-106 394.0
18 TraesCS3B01G101100 chr3D 88.079 302 27 5 1459 1753 43726848 43727147 1.550000e-92 350.0
19 TraesCS3B01G101100 chr3D 87.043 301 28 6 233 527 43510278 43510573 2.020000e-86 329.0
20 TraesCS3B01G101100 chr3D 86.424 302 31 5 233 527 43568449 43568747 3.380000e-84 322.0
21 TraesCS3B01G101100 chr3D 86.705 173 17 2 233 399 43514172 43514344 1.290000e-43 187.0
22 TraesCS3B01G101100 chr3D 100.000 33 0 0 5 37 43511337 43511369 8.130000e-06 62.1
23 TraesCS3B01G101100 chr7B 97.674 258 5 1 1748 2005 158390715 158390971 2.480000e-120 442.0
24 TraesCS3B01G101100 chr7B 94.800 250 13 0 1756 2005 690292165 690292414 9.130000e-105 390.0
25 TraesCS3B01G101100 chr5D 95.528 246 11 0 1759 2004 350228910 350229155 7.060000e-106 394.0
26 TraesCS3B01G101100 chr4D 95.181 249 12 0 1759 2007 8196527 8196279 7.060000e-106 394.0
27 TraesCS3B01G101100 chr4D 94.118 255 14 1 1752 2005 503567025 503566771 1.180000e-103 387.0
28 TraesCS3B01G101100 chr1D 95.528 246 10 1 1761 2005 40914832 40915077 2.540000e-105 392.0
29 TraesCS3B01G101100 chr1A 95.181 249 11 1 1756 2004 84798284 84798531 2.540000e-105 392.0
30 TraesCS3B01G101100 chr1A 94.800 250 13 0 1757 2006 552263072 552262823 9.130000e-105 390.0
31 TraesCS3B01G101100 chr6B 87.879 132 8 2 1213 1336 342987147 342987016 6.070000e-32 148.0
32 TraesCS3B01G101100 chr6A 87.879 132 8 3 1213 1336 297712114 297712245 6.070000e-32 148.0
33 TraesCS3B01G101100 chr6D 87.121 132 9 2 1213 1336 218448880 218449011 2.820000e-30 143.0


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 TraesCS3B01G101100 chr3B 68252474 68255192 2718 False 5022.000000 5022 100.0000 1 2719 1 chr3B.!!$F2 2718
1 TraesCS3B01G101100 chr3A 55483213 55485398 2185 False 1879.500000 2545 97.5900 293 2719 2 chr3A.!!$F3 2426
2 TraesCS3B01G101100 chr3D 43508350 43514344 5994 False 703.010000 1991 92.0545 5 2709 10 chr3D.!!$F4 2704
3 TraesCS3B01G101100 chr3D 43567891 43568976 1085 False 559.666667 939 88.1480 233 2706 3 chr3D.!!$F5 2473

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
178 182 0.535335 GTGAACGGCCCTAGTCATGA 59.465 55.0 0.0 0.0 0.0 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1962 2006 0.040204 CCAAAGGGGCAGATCCAACT 59.96 55.0 0.0 0.0 36.21 3.16 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
24 25 5.045869 TCTGGGGTTGTATCTTAGACTTTGG 60.046 44.000 0.00 0.00 0.00 3.28
70 71 8.614469 ATGTACTTCTCTCTTCCTTTTCTTTG 57.386 34.615 0.00 0.00 0.00 2.77
71 72 6.483640 TGTACTTCTCTCTTCCTTTTCTTTGC 59.516 38.462 0.00 0.00 0.00 3.68
118 122 2.765689 ACCCAATTTGAGTCCCACAA 57.234 45.000 0.00 0.00 0.00 3.33
128 132 1.630878 GAGTCCCACAACCTCTTGGAT 59.369 52.381 0.00 0.00 34.46 3.41
140 144 2.568956 CCTCTTGGATTCTGTGACCTCA 59.431 50.000 0.00 0.00 34.57 3.86
146 150 3.452264 TGGATTCTGTGACCTCACCATAG 59.548 47.826 2.98 0.00 45.88 2.23
158 162 4.160329 CCTCACCATAGCCTAGGATTGTA 58.840 47.826 14.75 0.00 0.00 2.41
168 172 2.483188 CCTAGGATTGTAGTGAACGGCC 60.483 54.545 1.05 0.00 0.00 6.13
178 182 0.535335 GTGAACGGCCCTAGTCATGA 59.465 55.000 0.00 0.00 0.00 3.07
185 189 2.768527 CGGCCCTAGTCATGATATGGAT 59.231 50.000 0.00 0.00 0.00 3.41
303 307 4.529377 ACTACATCCCGTCCTGTTTTTCTA 59.471 41.667 0.00 0.00 0.00 2.10
359 363 7.819900 ACCTGATATACTATCTTTTGCCGATTC 59.180 37.037 0.00 0.00 0.00 2.52
376 380 5.412594 GCCGATTCAAGGATGAGCAATATTA 59.587 40.000 0.00 0.00 36.78 0.98
380 384 8.013947 CGATTCAAGGATGAGCAATATTAACAG 58.986 37.037 0.00 0.00 36.78 3.16
608 613 1.228124 CGTCCAGCTGTTTTCCCCA 60.228 57.895 13.81 0.00 0.00 4.96
651 656 6.052360 GGGAACAAAAGCAATTGGAAAGTTA 58.948 36.000 7.72 0.00 34.56 2.24
1050 1055 2.434428 CTCATGTGCCTTCTGCTTCTT 58.566 47.619 0.00 0.00 42.00 2.52
1200 1205 7.973388 TCAATCAGTTTAGGTGTTTTTGACTTG 59.027 33.333 0.00 0.00 0.00 3.16
1291 1321 6.318900 CCCTCACCCTTGTACATATTTCTTTC 59.681 42.308 0.00 0.00 0.00 2.62
1653 1696 1.825090 AACTTGCAATGATCCAGCGA 58.175 45.000 0.00 0.00 0.00 4.93
1758 1802 7.076983 AGTTTTCGTCGTGTGTTTTTCTTTAA 58.923 30.769 0.00 0.00 0.00 1.52
1759 1803 6.835719 TTTCGTCGTGTGTTTTTCTTTAAC 57.164 33.333 0.00 0.00 0.00 2.01
1760 1804 5.783100 TCGTCGTGTGTTTTTCTTTAACT 57.217 34.783 0.00 0.00 0.00 2.24
1761 1805 6.884096 TCGTCGTGTGTTTTTCTTTAACTA 57.116 33.333 0.00 0.00 0.00 2.24
1762 1806 6.925600 TCGTCGTGTGTTTTTCTTTAACTAG 58.074 36.000 0.00 0.00 0.00 2.57
1763 1807 6.531240 TCGTCGTGTGTTTTTCTTTAACTAGT 59.469 34.615 0.00 0.00 0.00 2.57
1764 1808 7.700234 TCGTCGTGTGTTTTTCTTTAACTAGTA 59.300 33.333 0.00 0.00 0.00 1.82
1765 1809 8.320295 CGTCGTGTGTTTTTCTTTAACTAGTAA 58.680 33.333 0.00 0.00 0.00 2.24
1766 1810 9.971744 GTCGTGTGTTTTTCTTTAACTAGTAAA 57.028 29.630 0.00 0.00 0.00 2.01
1770 1814 9.440784 TGTGTTTTTCTTTAACTAGTAAATGCG 57.559 29.630 0.00 0.00 31.22 4.73
1771 1815 8.414923 GTGTTTTTCTTTAACTAGTAAATGCGC 58.585 33.333 0.00 0.00 31.22 6.09
1772 1816 8.129840 TGTTTTTCTTTAACTAGTAAATGCGCA 58.870 29.630 14.96 14.96 31.22 6.09
1773 1817 8.414923 GTTTTTCTTTAACTAGTAAATGCGCAC 58.585 33.333 14.90 0.00 31.22 5.34
1774 1818 5.444586 TCTTTAACTAGTAAATGCGCACG 57.555 39.130 14.90 0.00 31.22 5.34
1775 1819 4.925054 TCTTTAACTAGTAAATGCGCACGT 59.075 37.500 14.90 5.96 31.22 4.49
1776 1820 4.571375 TTAACTAGTAAATGCGCACGTG 57.429 40.909 14.90 12.28 0.00 4.49
1777 1821 0.719465 ACTAGTAAATGCGCACGTGC 59.281 50.000 30.42 30.42 37.78 5.34
1797 1841 4.899516 TGCAACGCACGTTAATATTTAGG 58.100 39.130 8.26 0.00 36.46 2.69
1798 1842 4.392445 TGCAACGCACGTTAATATTTAGGT 59.608 37.500 8.26 0.00 36.46 3.08
1799 1843 5.579904 TGCAACGCACGTTAATATTTAGGTA 59.420 36.000 8.26 0.00 36.46 3.08
1800 1844 6.091849 TGCAACGCACGTTAATATTTAGGTAA 59.908 34.615 8.26 0.00 36.46 2.85
1801 1845 7.127686 GCAACGCACGTTAATATTTAGGTAAT 58.872 34.615 8.26 0.00 36.46 1.89
1802 1846 8.274939 GCAACGCACGTTAATATTTAGGTAATA 58.725 33.333 8.26 0.00 36.46 0.98
1830 1874 9.624697 ATTAATTGCACGCAAATATTAGGTATG 57.375 29.630 8.76 0.00 39.55 2.39
1831 1875 6.633500 ATTGCACGCAAATATTAGGTATGT 57.367 33.333 8.76 0.00 39.55 2.29
1832 1876 6.443934 TTGCACGCAAATATTAGGTATGTT 57.556 33.333 1.07 0.00 32.44 2.71
1833 1877 7.555306 TTGCACGCAAATATTAGGTATGTTA 57.445 32.000 1.07 0.00 32.44 2.41
1834 1878 7.737972 TGCACGCAAATATTAGGTATGTTAT 57.262 32.000 0.00 0.00 0.00 1.89
1835 1879 8.160521 TGCACGCAAATATTAGGTATGTTATT 57.839 30.769 0.00 0.00 0.00 1.40
1836 1880 9.274206 TGCACGCAAATATTAGGTATGTTATTA 57.726 29.630 0.00 0.00 0.00 0.98
1863 1907 9.685828 TTTGTTTGTTAATCCTGTAATTAGTGC 57.314 29.630 0.00 0.00 0.00 4.40
1864 1908 8.397575 TGTTTGTTAATCCTGTAATTAGTGCA 57.602 30.769 0.00 0.00 0.00 4.57
1865 1909 8.851145 TGTTTGTTAATCCTGTAATTAGTGCAA 58.149 29.630 0.00 0.00 0.00 4.08
1866 1910 9.855021 GTTTGTTAATCCTGTAATTAGTGCAAT 57.145 29.630 0.00 0.00 0.00 3.56
1873 1917 8.766994 ATCCTGTAATTAGTGCAATATTTGGT 57.233 30.769 10.62 0.00 0.00 3.67
1874 1918 9.860650 ATCCTGTAATTAGTGCAATATTTGGTA 57.139 29.630 10.62 0.00 0.00 3.25
1875 1919 9.860650 TCCTGTAATTAGTGCAATATTTGGTAT 57.139 29.630 10.62 0.00 0.00 2.73
1876 1920 9.897744 CCTGTAATTAGTGCAATATTTGGTATG 57.102 33.333 10.62 0.00 0.00 2.39
1901 1945 9.847706 TGATATTAATTGCATGTTAAACACGTT 57.152 25.926 8.36 0.00 0.00 3.99
1916 1960 2.911198 CGTTTAACGCTCGCCATTG 58.089 52.632 4.11 0.00 33.65 2.82
1917 1961 0.520412 CGTTTAACGCTCGCCATTGG 60.520 55.000 4.11 0.00 33.65 3.16
1918 1962 0.800012 GTTTAACGCTCGCCATTGGA 59.200 50.000 6.95 0.00 0.00 3.53
1919 1963 1.083489 TTTAACGCTCGCCATTGGAG 58.917 50.000 6.95 2.84 34.62 3.86
1924 1968 3.805267 CTCGCCATTGGAGCAGTC 58.195 61.111 6.95 0.00 0.00 3.51
1925 1969 1.220206 CTCGCCATTGGAGCAGTCT 59.780 57.895 6.95 0.00 0.00 3.24
1926 1970 0.461548 CTCGCCATTGGAGCAGTCTA 59.538 55.000 6.95 0.00 0.00 2.59
1927 1971 0.461548 TCGCCATTGGAGCAGTCTAG 59.538 55.000 6.95 0.00 0.00 2.43
1928 1972 0.531532 CGCCATTGGAGCAGTCTAGG 60.532 60.000 6.95 0.00 0.00 3.02
1929 1973 0.543749 GCCATTGGAGCAGTCTAGGT 59.456 55.000 6.95 0.00 0.00 3.08
1930 1974 1.474143 GCCATTGGAGCAGTCTAGGTC 60.474 57.143 6.95 0.00 35.36 3.85
1931 1975 1.202463 CCATTGGAGCAGTCTAGGTCG 60.202 57.143 0.00 0.00 36.90 4.79
1932 1976 1.478510 CATTGGAGCAGTCTAGGTCGT 59.521 52.381 0.00 0.00 36.90 4.34
1933 1977 1.629043 TTGGAGCAGTCTAGGTCGTT 58.371 50.000 0.00 0.00 36.90 3.85
1934 1978 0.888619 TGGAGCAGTCTAGGTCGTTG 59.111 55.000 0.00 0.00 36.90 4.10
1935 1979 0.173708 GGAGCAGTCTAGGTCGTTGG 59.826 60.000 0.00 0.00 36.90 3.77
1936 1980 1.174783 GAGCAGTCTAGGTCGTTGGA 58.825 55.000 0.00 0.00 0.00 3.53
1937 1981 1.751924 GAGCAGTCTAGGTCGTTGGAT 59.248 52.381 0.00 0.00 0.00 3.41
1938 1982 2.166664 GAGCAGTCTAGGTCGTTGGATT 59.833 50.000 0.00 0.00 0.00 3.01
1939 1983 2.093973 AGCAGTCTAGGTCGTTGGATTG 60.094 50.000 0.00 0.00 0.00 2.67
1940 1984 2.094182 GCAGTCTAGGTCGTTGGATTGA 60.094 50.000 0.00 0.00 0.00 2.57
1941 1985 3.512680 CAGTCTAGGTCGTTGGATTGAC 58.487 50.000 0.00 0.00 0.00 3.18
1942 1986 3.193691 CAGTCTAGGTCGTTGGATTGACT 59.806 47.826 0.00 0.00 35.45 3.41
1943 1987 3.833070 AGTCTAGGTCGTTGGATTGACTT 59.167 43.478 0.00 0.00 35.45 3.01
1944 1988 5.014858 AGTCTAGGTCGTTGGATTGACTTA 58.985 41.667 0.00 0.00 35.45 2.24
1945 1989 5.125739 AGTCTAGGTCGTTGGATTGACTTAG 59.874 44.000 5.46 5.46 42.75 2.18
1946 1990 5.014858 TCTAGGTCGTTGGATTGACTTAGT 58.985 41.667 10.13 0.00 42.29 2.24
1947 1991 4.618920 AGGTCGTTGGATTGACTTAGTT 57.381 40.909 0.00 0.00 35.45 2.24
1948 1992 4.969484 AGGTCGTTGGATTGACTTAGTTT 58.031 39.130 0.00 0.00 35.45 2.66
1949 1993 4.755123 AGGTCGTTGGATTGACTTAGTTTG 59.245 41.667 0.00 0.00 35.45 2.93
1950 1994 4.753107 GGTCGTTGGATTGACTTAGTTTGA 59.247 41.667 0.00 0.00 35.45 2.69
1951 1995 5.411669 GGTCGTTGGATTGACTTAGTTTGAT 59.588 40.000 0.00 0.00 35.45 2.57
1952 1996 6.307155 GTCGTTGGATTGACTTAGTTTGATG 58.693 40.000 0.00 0.00 32.37 3.07
1953 1997 5.411361 TCGTTGGATTGACTTAGTTTGATGG 59.589 40.000 0.00 0.00 0.00 3.51
1954 1998 5.402398 GTTGGATTGACTTAGTTTGATGGC 58.598 41.667 0.00 0.00 0.00 4.40
1955 1999 4.016444 TGGATTGACTTAGTTTGATGGCC 58.984 43.478 0.00 0.00 0.00 5.36
1956 2000 3.065371 GGATTGACTTAGTTTGATGGCCG 59.935 47.826 0.00 0.00 0.00 6.13
1957 2001 3.410631 TTGACTTAGTTTGATGGCCGA 57.589 42.857 0.00 0.00 0.00 5.54
1958 2002 2.972625 TGACTTAGTTTGATGGCCGAG 58.027 47.619 0.00 0.00 0.00 4.63
1959 2003 2.565391 TGACTTAGTTTGATGGCCGAGA 59.435 45.455 0.00 0.00 0.00 4.04
1960 2004 3.197766 TGACTTAGTTTGATGGCCGAGAT 59.802 43.478 0.00 0.00 0.00 2.75
1961 2005 3.798202 ACTTAGTTTGATGGCCGAGATC 58.202 45.455 0.00 0.00 0.00 2.75
1962 2006 3.197766 ACTTAGTTTGATGGCCGAGATCA 59.802 43.478 0.00 0.00 0.00 2.92
1963 2007 2.322355 AGTTTGATGGCCGAGATCAG 57.678 50.000 0.00 0.00 31.52 2.90
1964 2008 1.556911 AGTTTGATGGCCGAGATCAGT 59.443 47.619 0.00 0.00 31.52 3.41
1965 2009 2.026822 AGTTTGATGGCCGAGATCAGTT 60.027 45.455 0.00 0.00 31.52 3.16
1966 2010 2.028420 TTGATGGCCGAGATCAGTTG 57.972 50.000 0.00 0.00 31.52 3.16
1967 2011 0.178767 TGATGGCCGAGATCAGTTGG 59.821 55.000 0.00 0.00 0.00 3.77
1968 2012 0.465705 GATGGCCGAGATCAGTTGGA 59.534 55.000 0.00 0.00 0.00 3.53
1969 2013 1.071385 GATGGCCGAGATCAGTTGGAT 59.929 52.381 0.00 0.00 39.53 3.41
1977 2021 3.033746 ATCAGTTGGATCTGCCCCT 57.966 52.632 0.00 0.00 35.63 4.79
1978 2022 1.302907 ATCAGTTGGATCTGCCCCTT 58.697 50.000 0.00 0.00 35.63 3.95
1979 2023 1.075601 TCAGTTGGATCTGCCCCTTT 58.924 50.000 0.00 0.00 35.63 3.11
1980 2024 1.180029 CAGTTGGATCTGCCCCTTTG 58.820 55.000 0.00 0.00 34.97 2.77
1981 2025 0.040204 AGTTGGATCTGCCCCTTTGG 59.960 55.000 0.00 0.00 34.97 3.28
1997 2041 6.867519 CCCTTTGGGTCTTTTTATATTGGT 57.132 37.500 0.00 0.00 38.25 3.67
1998 2042 7.964666 CCCTTTGGGTCTTTTTATATTGGTA 57.035 36.000 0.00 0.00 38.25 3.25
1999 2043 8.547481 CCCTTTGGGTCTTTTTATATTGGTAT 57.453 34.615 0.00 0.00 38.25 2.73
2000 2044 9.649316 CCCTTTGGGTCTTTTTATATTGGTATA 57.351 33.333 0.00 0.00 38.25 1.47
2017 2061 4.917040 TGGTATAGATAAAGGGGCCATTGA 59.083 41.667 3.25 0.00 0.00 2.57
2463 2528 7.830697 AGACTGAATTGGATGAACACAATATCA 59.169 33.333 0.00 0.00 36.36 2.15
2549 2614 7.840931 ACTGAATTTTTGGGATATGAAACCTC 58.159 34.615 0.00 0.00 0.00 3.85
2597 2662 2.270850 GCGTGGAATGGGTGCCTA 59.729 61.111 0.00 0.00 0.00 3.93
2605 2670 2.615493 GGAATGGGTGCCTATGGTATCG 60.615 54.545 0.00 0.00 0.00 2.92
2712 2777 3.350163 CAGCCCTTCCCCACCCAT 61.350 66.667 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.395231 GCCACCAAAGTCTAAGATACAACC 59.605 45.833 0.00 0.00 0.00 3.77
8 9 4.901197 TGCCACCAAAGTCTAAGATACA 57.099 40.909 0.00 0.00 0.00 2.29
10 11 5.584649 CGAATTGCCACCAAAGTCTAAGATA 59.415 40.000 0.00 0.00 34.05 1.98
11 12 4.396166 CGAATTGCCACCAAAGTCTAAGAT 59.604 41.667 0.00 0.00 34.05 2.40
24 25 1.249407 TTACAACCCCGAATTGCCAC 58.751 50.000 0.00 0.00 0.00 5.01
89 93 4.265073 ACTCAAATTGGGTAGCACTCATC 58.735 43.478 0.00 0.00 0.00 2.92
118 122 2.569404 GAGGTCACAGAATCCAAGAGGT 59.431 50.000 0.00 0.00 35.89 3.85
140 144 4.816126 TCACTACAATCCTAGGCTATGGT 58.184 43.478 2.96 0.00 0.00 3.55
146 150 2.822764 CCGTTCACTACAATCCTAGGC 58.177 52.381 2.96 0.00 0.00 3.93
158 162 0.537188 CATGACTAGGGCCGTTCACT 59.463 55.000 1.81 0.00 0.00 3.41
168 172 3.520721 TGGGCATCCATATCATGACTAGG 59.479 47.826 0.00 0.00 38.32 3.02
178 182 2.891026 GCATCCCATTGGGCATCCATAT 60.891 50.000 17.60 0.17 43.94 1.78
185 189 4.811709 AATGCATCCCATTGGGCA 57.188 50.000 17.60 11.99 43.94 5.36
283 287 2.951229 AGAAAAACAGGACGGGATGT 57.049 45.000 0.00 0.00 0.00 3.06
303 307 8.313292 ACATTAACACCATTTAATCAAGCACAT 58.687 29.630 0.00 0.00 30.65 3.21
471 475 3.700038 CCGTCCTCCTGTTCTATACTTGT 59.300 47.826 0.00 0.00 0.00 3.16
566 571 7.176690 ACGATGGACAATTCATTTAGGAAAACT 59.823 33.333 0.00 0.00 0.00 2.66
608 613 2.037511 CCCACTGCATGTTGAACCATTT 59.962 45.455 0.00 0.00 0.00 2.32
651 656 6.057533 TGCCTTCTATTTGTTGATGATCGAT 58.942 36.000 0.00 0.00 0.00 3.59
862 867 2.027460 GCCAGTGGTTGTTTGCGG 59.973 61.111 11.74 0.00 0.00 5.69
873 878 2.882876 GCAAGATGGCAGCCAGTG 59.117 61.111 21.51 17.87 36.75 3.66
1050 1055 0.955428 GGACTTGATCGCTGGTGCAA 60.955 55.000 0.00 0.00 39.64 4.08
1156 1161 1.134521 TGATCAATACGACAGCACCCC 60.135 52.381 0.00 0.00 0.00 4.95
1291 1321 6.347240 GGAGAGCTGCGTATCATTTCAATAAG 60.347 42.308 0.00 0.00 0.00 1.73
1758 1802 0.719465 GCACGTGCGCATTTACTAGT 59.281 50.000 26.77 0.00 0.00 2.57
1759 1803 0.718904 TGCACGTGCGCATTTACTAG 59.281 50.000 33.22 0.66 45.83 2.57
1760 1804 1.136197 GTTGCACGTGCGCATTTACTA 60.136 47.619 33.22 11.66 45.83 1.82
1761 1805 0.385473 GTTGCACGTGCGCATTTACT 60.385 50.000 33.22 0.00 45.83 2.24
1762 1806 1.652148 CGTTGCACGTGCGCATTTAC 61.652 55.000 33.22 21.25 45.83 2.01
1763 1807 1.439529 CGTTGCACGTGCGCATTTA 60.440 52.632 33.22 14.00 45.83 1.40
1764 1808 2.725450 CGTTGCACGTGCGCATTT 60.725 55.556 33.22 0.00 45.83 2.32
1775 1819 4.392445 ACCTAAATATTAACGTGCGTTGCA 59.608 37.500 18.63 6.89 38.92 4.08
1776 1820 4.900664 ACCTAAATATTAACGTGCGTTGC 58.099 39.130 18.63 0.00 38.92 4.17
1804 1848 9.624697 CATACCTAATATTTGCGTGCAATTAAT 57.375 29.630 8.26 5.37 35.70 1.40
1805 1849 8.625651 ACATACCTAATATTTGCGTGCAATTAA 58.374 29.630 8.26 0.00 35.70 1.40
1806 1850 8.160521 ACATACCTAATATTTGCGTGCAATTA 57.839 30.769 8.26 9.59 35.70 1.40
1807 1851 7.038154 ACATACCTAATATTTGCGTGCAATT 57.962 32.000 8.26 7.60 35.70 2.32
1808 1852 6.633500 ACATACCTAATATTTGCGTGCAAT 57.367 33.333 8.26 1.93 35.70 3.56
1809 1853 6.443934 AACATACCTAATATTTGCGTGCAA 57.556 33.333 2.58 2.58 0.00 4.08
1810 1854 7.737972 ATAACATACCTAATATTTGCGTGCA 57.262 32.000 0.00 0.00 0.00 4.57
1837 1881 9.685828 GCACTAATTACAGGATTAACAAACAAA 57.314 29.630 0.00 0.00 0.00 2.83
1838 1882 8.851145 TGCACTAATTACAGGATTAACAAACAA 58.149 29.630 0.00 0.00 0.00 2.83
1839 1883 8.397575 TGCACTAATTACAGGATTAACAAACA 57.602 30.769 0.00 0.00 0.00 2.83
1840 1884 9.855021 ATTGCACTAATTACAGGATTAACAAAC 57.145 29.630 0.00 0.00 0.00 2.93
1847 1891 9.200817 ACCAAATATTGCACTAATTACAGGATT 57.799 29.630 0.00 0.00 0.00 3.01
1848 1892 8.766994 ACCAAATATTGCACTAATTACAGGAT 57.233 30.769 0.00 0.00 0.00 3.24
1849 1893 9.860650 ATACCAAATATTGCACTAATTACAGGA 57.139 29.630 0.00 0.00 0.00 3.86
1850 1894 9.897744 CATACCAAATATTGCACTAATTACAGG 57.102 33.333 0.00 0.00 0.00 4.00
1875 1919 9.847706 AACGTGTTTAACATGCAATTAATATCA 57.152 25.926 16.24 5.58 38.65 2.15
1891 1935 2.348404 GGCGAGCGTTAAACGTGTTTAA 60.348 45.455 12.58 12.58 44.73 1.52
1892 1936 1.192090 GGCGAGCGTTAAACGTGTTTA 59.808 47.619 1.18 1.18 44.73 2.01
1893 1937 0.041926 GGCGAGCGTTAAACGTGTTT 60.042 50.000 3.21 3.21 44.73 2.83
1894 1938 1.152989 TGGCGAGCGTTAAACGTGTT 61.153 50.000 0.00 0.00 44.73 3.32
1895 1939 0.947180 ATGGCGAGCGTTAAACGTGT 60.947 50.000 0.00 0.00 44.73 4.49
1896 1940 0.165079 AATGGCGAGCGTTAAACGTG 59.835 50.000 0.00 0.00 44.73 4.49
1897 1941 0.165079 CAATGGCGAGCGTTAAACGT 59.835 50.000 0.00 0.00 44.73 3.99
1898 1942 0.520412 CCAATGGCGAGCGTTAAACG 60.520 55.000 0.00 0.00 45.88 3.60
1899 1943 0.800012 TCCAATGGCGAGCGTTAAAC 59.200 50.000 0.00 0.00 0.00 2.01
1900 1944 1.083489 CTCCAATGGCGAGCGTTAAA 58.917 50.000 0.00 0.00 0.00 1.52
1901 1945 1.366111 GCTCCAATGGCGAGCGTTAA 61.366 55.000 0.00 0.00 43.04 2.01
1902 1946 1.813753 GCTCCAATGGCGAGCGTTA 60.814 57.895 0.00 0.00 43.04 3.18
1903 1947 3.127533 GCTCCAATGGCGAGCGTT 61.128 61.111 0.00 0.00 43.04 4.84
1907 1951 0.461548 TAGACTGCTCCAATGGCGAG 59.538 55.000 0.00 0.00 0.00 5.03
1908 1952 0.461548 CTAGACTGCTCCAATGGCGA 59.538 55.000 0.00 0.00 0.00 5.54
1909 1953 0.531532 CCTAGACTGCTCCAATGGCG 60.532 60.000 0.00 0.00 0.00 5.69
1910 1954 0.543749 ACCTAGACTGCTCCAATGGC 59.456 55.000 0.00 0.00 0.00 4.40
1911 1955 1.202463 CGACCTAGACTGCTCCAATGG 60.202 57.143 0.00 0.00 0.00 3.16
1912 1956 1.478510 ACGACCTAGACTGCTCCAATG 59.521 52.381 0.00 0.00 0.00 2.82
1913 1957 1.853963 ACGACCTAGACTGCTCCAAT 58.146 50.000 0.00 0.00 0.00 3.16
1914 1958 1.272490 CAACGACCTAGACTGCTCCAA 59.728 52.381 0.00 0.00 0.00 3.53
1915 1959 0.888619 CAACGACCTAGACTGCTCCA 59.111 55.000 0.00 0.00 0.00 3.86
1916 1960 0.173708 CCAACGACCTAGACTGCTCC 59.826 60.000 0.00 0.00 0.00 4.70
1917 1961 1.174783 TCCAACGACCTAGACTGCTC 58.825 55.000 0.00 0.00 0.00 4.26
1918 1962 1.853963 ATCCAACGACCTAGACTGCT 58.146 50.000 0.00 0.00 0.00 4.24
1919 1963 2.094182 TCAATCCAACGACCTAGACTGC 60.094 50.000 0.00 0.00 0.00 4.40
1920 1964 3.193691 AGTCAATCCAACGACCTAGACTG 59.806 47.826 0.00 0.00 34.17 3.51
1921 1965 3.432378 AGTCAATCCAACGACCTAGACT 58.568 45.455 0.00 0.00 32.33 3.24
1922 1966 3.870633 AGTCAATCCAACGACCTAGAC 57.129 47.619 0.00 0.00 32.33 2.59
1923 1967 5.014858 ACTAAGTCAATCCAACGACCTAGA 58.985 41.667 0.00 0.00 32.71 2.43
1924 1968 5.326200 ACTAAGTCAATCCAACGACCTAG 57.674 43.478 0.00 0.00 33.98 3.02
1925 1969 5.733620 AACTAAGTCAATCCAACGACCTA 57.266 39.130 0.00 0.00 32.33 3.08
1926 1970 4.618920 AACTAAGTCAATCCAACGACCT 57.381 40.909 0.00 0.00 32.33 3.85
1927 1971 4.753107 TCAAACTAAGTCAATCCAACGACC 59.247 41.667 0.00 0.00 32.33 4.79
1928 1972 5.917541 TCAAACTAAGTCAATCCAACGAC 57.082 39.130 0.00 0.00 0.00 4.34
1929 1973 5.411361 CCATCAAACTAAGTCAATCCAACGA 59.589 40.000 0.00 0.00 0.00 3.85
1930 1974 5.631026 CCATCAAACTAAGTCAATCCAACG 58.369 41.667 0.00 0.00 0.00 4.10
1931 1975 5.402398 GCCATCAAACTAAGTCAATCCAAC 58.598 41.667 0.00 0.00 0.00 3.77
1932 1976 4.462483 GGCCATCAAACTAAGTCAATCCAA 59.538 41.667 0.00 0.00 0.00 3.53
1933 1977 4.016444 GGCCATCAAACTAAGTCAATCCA 58.984 43.478 0.00 0.00 0.00 3.41
1934 1978 3.065371 CGGCCATCAAACTAAGTCAATCC 59.935 47.826 2.24 0.00 0.00 3.01
1935 1979 3.938963 TCGGCCATCAAACTAAGTCAATC 59.061 43.478 2.24 0.00 0.00 2.67
1936 1980 3.941483 CTCGGCCATCAAACTAAGTCAAT 59.059 43.478 2.24 0.00 0.00 2.57
1937 1981 3.007506 TCTCGGCCATCAAACTAAGTCAA 59.992 43.478 2.24 0.00 0.00 3.18
1938 1982 2.565391 TCTCGGCCATCAAACTAAGTCA 59.435 45.455 2.24 0.00 0.00 3.41
1939 1983 3.247006 TCTCGGCCATCAAACTAAGTC 57.753 47.619 2.24 0.00 0.00 3.01
1940 1984 3.197766 TGATCTCGGCCATCAAACTAAGT 59.802 43.478 2.24 0.00 0.00 2.24
1941 1985 3.797039 TGATCTCGGCCATCAAACTAAG 58.203 45.455 2.24 0.00 0.00 2.18
1942 1986 3.197766 ACTGATCTCGGCCATCAAACTAA 59.802 43.478 2.24 0.00 29.74 2.24
1943 1987 2.766263 ACTGATCTCGGCCATCAAACTA 59.234 45.455 2.24 0.00 29.74 2.24
1944 1988 1.556911 ACTGATCTCGGCCATCAAACT 59.443 47.619 2.24 0.00 29.74 2.66
1945 1989 2.029838 ACTGATCTCGGCCATCAAAC 57.970 50.000 2.24 0.00 29.74 2.93
1946 1990 2.358957 CAACTGATCTCGGCCATCAAA 58.641 47.619 2.24 0.00 29.74 2.69
1947 1991 1.407299 CCAACTGATCTCGGCCATCAA 60.407 52.381 2.24 0.00 29.74 2.57
1948 1992 0.178767 CCAACTGATCTCGGCCATCA 59.821 55.000 2.24 3.52 0.00 3.07
1949 1993 0.465705 TCCAACTGATCTCGGCCATC 59.534 55.000 2.24 0.00 0.00 3.51
1950 1994 1.071385 GATCCAACTGATCTCGGCCAT 59.929 52.381 2.24 0.00 45.46 4.40
1951 1995 0.465705 GATCCAACTGATCTCGGCCA 59.534 55.000 2.24 0.00 45.46 5.36
1952 1996 3.297391 GATCCAACTGATCTCGGCC 57.703 57.895 0.00 0.00 45.46 6.13
1959 2003 1.302907 AAGGGGCAGATCCAACTGAT 58.697 50.000 0.00 0.00 39.94 2.90
1960 2004 1.075601 AAAGGGGCAGATCCAACTGA 58.924 50.000 0.00 0.00 39.94 3.41
1961 2005 1.180029 CAAAGGGGCAGATCCAACTG 58.820 55.000 0.00 0.00 40.43 3.16
1962 2006 0.040204 CCAAAGGGGCAGATCCAACT 59.960 55.000 0.00 0.00 36.21 3.16
1963 2007 2.583472 CCAAAGGGGCAGATCCAAC 58.417 57.895 0.00 0.00 36.21 3.77
1986 2030 9.984590 GGCCCCTTTATCTATACCAATATAAAA 57.015 33.333 0.00 0.00 0.00 1.52
1987 2031 9.129870 TGGCCCCTTTATCTATACCAATATAAA 57.870 33.333 0.00 0.00 0.00 1.40
1988 2032 8.703142 TGGCCCCTTTATCTATACCAATATAA 57.297 34.615 0.00 0.00 0.00 0.98
1989 2033 8.885900 ATGGCCCCTTTATCTATACCAATATA 57.114 34.615 0.00 0.00 0.00 0.86
1990 2034 7.787517 ATGGCCCCTTTATCTATACCAATAT 57.212 36.000 0.00 0.00 0.00 1.28
1991 2035 7.240828 TCAATGGCCCCTTTATCTATACCAATA 59.759 37.037 0.00 0.00 0.00 1.90
1992 2036 6.046643 TCAATGGCCCCTTTATCTATACCAAT 59.953 38.462 0.00 0.00 0.00 3.16
1993 2037 5.374154 TCAATGGCCCCTTTATCTATACCAA 59.626 40.000 0.00 0.00 0.00 3.67
1994 2038 4.917040 TCAATGGCCCCTTTATCTATACCA 59.083 41.667 0.00 0.00 0.00 3.25
1995 2039 5.514500 TCAATGGCCCCTTTATCTATACC 57.486 43.478 0.00 0.00 0.00 2.73
1996 2040 5.358160 GCATCAATGGCCCCTTTATCTATAC 59.642 44.000 0.00 0.00 0.00 1.47
1997 2041 5.509498 GCATCAATGGCCCCTTTATCTATA 58.491 41.667 0.00 0.00 0.00 1.31
1998 2042 4.347607 GCATCAATGGCCCCTTTATCTAT 58.652 43.478 0.00 0.00 0.00 1.98
1999 2043 3.500289 GGCATCAATGGCCCCTTTATCTA 60.500 47.826 0.00 0.00 45.87 1.98
2000 2044 2.601905 GCATCAATGGCCCCTTTATCT 58.398 47.619 0.00 0.00 0.00 1.98
2001 2045 1.620323 GGCATCAATGGCCCCTTTATC 59.380 52.381 0.00 0.00 45.87 1.75
2017 2061 2.629137 TGAGTCAAGCATGTTTTGGCAT 59.371 40.909 15.70 4.71 32.71 4.40
2433 2497 5.248248 TGTGTTCATCCAATTCAGTCTCCTA 59.752 40.000 0.00 0.00 0.00 2.94
2463 2528 4.348020 TGTATTTCCCCACTAGACCTCT 57.652 45.455 0.00 0.00 0.00 3.69
2597 2662 2.452064 CCAGGGCCACCGATACCAT 61.452 63.158 6.18 0.00 43.47 3.55
2605 2670 0.261696 ACCATAATTCCAGGGCCACC 59.738 55.000 6.18 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.