Multiple sequence alignment - TraesCS4B01G184400

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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 TraesCS4B01G184400 chr4B 100.000 2393 0 0 1 2393 403625811 403623419 0.000000e+00 4420.0
1 TraesCS4B01G184400 chr4B 95.455 88 4 0 1917 2004 46952579 46952666 8.920000e-30 141.0
2 TraesCS4B01G184400 chr4D 91.882 1971 84 36 1 1918 323355974 323354027 0.000000e+00 2684.0
3 TraesCS4B01G184400 chr4D 92.746 386 20 3 2008 2393 323354043 323353666 3.480000e-153 551.0
4 TraesCS4B01G184400 chr4A 94.656 917 42 3 843 1753 148757562 148758477 0.000000e+00 1415.0
5 TraesCS4B01G184400 chr4A 90.162 864 57 19 1 841 148756505 148757363 0.000000e+00 1099.0
6 TraesCS4B01G184400 chr4A 91.969 386 23 4 2008 2393 148758671 148759048 3.500000e-148 534.0
7 TraesCS4B01G184400 chr4A 89.444 180 6 8 1749 1918 148758511 148758687 5.180000e-52 215.0
8 TraesCS4B01G184400 chr4A 92.593 81 5 1 1924 2004 691818343 691818264 5.410000e-22 115.0
9 TraesCS4B01G184400 chr4A 87.500 64 6 2 575 636 632220139 632220076 3.300000e-09 73.1
10 TraesCS4B01G184400 chr4A 95.238 42 2 0 575 616 312709284 312709243 1.540000e-07 67.6
11 TraesCS4B01G184400 chr2A 81.526 249 36 9 1150 1394 15270128 15270370 1.880000e-46 196.0
12 TraesCS4B01G184400 chr2A 91.667 48 4 0 575 622 513832714 513832667 1.540000e-07 67.6
13 TraesCS4B01G184400 chr2A 85.484 62 7 2 577 636 555817008 555816947 1.990000e-06 63.9
14 TraesCS4B01G184400 chr2D 81.124 249 37 10 1150 1394 13228795 13229037 8.730000e-45 191.0
15 TraesCS4B01G184400 chr2B 80.723 249 38 9 1150 1394 23878245 23878487 4.060000e-43 185.0
16 TraesCS4B01G184400 chr2B 95.455 88 3 1 1917 2004 758599429 758599343 3.210000e-29 139.0
17 TraesCS4B01G184400 chr2B 97.260 73 2 0 1936 2008 797928120 797928192 8.980000e-25 124.0
18 TraesCS4B01G184400 chr6B 97.727 88 0 2 1657 1742 32295643 32295730 1.480000e-32 150.0
19 TraesCS4B01G184400 chr6B 92.453 106 3 5 1660 1763 32019327 32019429 1.920000e-31 147.0
20 TraesCS4B01G184400 chr6B 95.062 81 3 1 1924 2004 545274838 545274759 2.500000e-25 126.0
21 TraesCS4B01G184400 chr6A 96.629 89 3 0 1664 1752 18580792 18580880 5.330000e-32 148.0
22 TraesCS4B01G184400 chr6A 87.500 136 7 9 1648 1776 520853860 520853728 5.330000e-32 148.0
23 TraesCS4B01G184400 chr3A 91.071 112 6 3 1645 1756 25368100 25367993 5.330000e-32 148.0
24 TraesCS4B01G184400 chr3A 93.939 99 0 5 1647 1743 8598683 8598777 6.890000e-31 145.0
25 TraesCS4B01G184400 chr3B 92.079 101 7 1 1665 1764 5587343 5587443 8.920000e-30 141.0
26 TraesCS4B01G184400 chr3B 83.784 148 19 5 284 427 633132660 633132514 4.150000e-28 135.0
27 TraesCS4B01G184400 chr3B 90.625 96 8 1 1918 2013 790580573 790580667 2.500000e-25 126.0
28 TraesCS4B01G184400 chr5B 92.784 97 6 1 1917 2013 369259338 369259243 3.210000e-29 139.0
29 TraesCS4B01G184400 chr5B 90.588 85 6 2 1923 2007 609107513 609107431 6.990000e-21 111.0
30 TraesCS4B01G184400 chr1B 95.000 80 3 1 1924 2003 578353079 578353157 8.980000e-25 124.0
31 TraesCS4B01G184400 chr7B 86.905 84 9 2 635 717 635941889 635941807 2.530000e-15 93.5


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 TraesCS4B01G184400 chr4B 403623419 403625811 2392 True 4420.00 4420 100.00000 1 2393 1 chr4B.!!$R1 2392
1 TraesCS4B01G184400 chr4D 323353666 323355974 2308 True 1617.50 2684 92.31400 1 2393 2 chr4D.!!$R1 2392
2 TraesCS4B01G184400 chr4A 148756505 148759048 2543 False 815.75 1415 91.55775 1 2393 4 chr4A.!!$F1 2392

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
148 160 0.605589 AGTCATGCGGGATAGCTAGC 59.394 55.0 6.62 6.62 38.13 3.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1914 2197 0.106708 AGGACAGACAGCGCAAAAGA 59.893 50.0 11.47 0.0 0.0 2.52 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
71 83 1.070134 GTGGTGTGAACTAGTGAGGCA 59.930 52.381 0.00 0.00 0.00 4.75
82 94 1.669115 GTGAGGCAAGAGAGCGCAA 60.669 57.895 11.47 0.00 34.64 4.85
111 123 1.215647 GAAGCGTCCCATCGTGTCT 59.784 57.895 0.00 0.00 0.00 3.41
118 130 1.067776 GTCCCATCGTGTCTCGTCTTT 60.068 52.381 0.00 0.00 40.80 2.52
131 143 3.896317 GTCTTTCTCAGGCGACAGT 57.104 52.632 0.00 0.00 0.00 3.55
134 146 1.895798 TCTTTCTCAGGCGACAGTCAT 59.104 47.619 0.41 0.00 0.00 3.06
142 154 1.067416 GCGACAGTCATGCGGGATA 59.933 57.895 0.41 0.00 0.00 2.59
148 160 0.605589 AGTCATGCGGGATAGCTAGC 59.394 55.000 6.62 6.62 38.13 3.42
150 162 1.179174 TCATGCGGGATAGCTAGCGT 61.179 55.000 9.55 1.66 38.13 5.07
154 166 1.516365 GCGGGATAGCTAGCGTCTGA 61.516 60.000 18.47 1.88 0.00 3.27
159 171 2.482721 GGATAGCTAGCGTCTGACTCTC 59.517 54.545 18.47 0.00 0.00 3.20
160 172 2.992124 TAGCTAGCGTCTGACTCTCT 57.008 50.000 9.55 0.00 0.00 3.10
170 183 4.804108 CGTCTGACTCTCTGAAAATGACT 58.196 43.478 6.21 0.00 0.00 3.41
220 233 6.605471 TCTAGAAGTGCTTTGAGGTTCATA 57.395 37.500 0.00 0.00 0.00 2.15
312 327 5.793026 TTTTGGTGAACTTTGACAAATGC 57.207 34.783 0.05 0.00 31.92 3.56
540 562 8.187913 TCAATTTTTATTGTTCATCAGGGTGA 57.812 30.769 0.00 0.00 33.49 4.02
542 564 9.439500 CAATTTTTATTGTTCATCAGGGTGAAT 57.561 29.630 0.00 0.00 39.99 2.57
565 587 7.722949 ATTTTTGAGCTTGGGATCAGAATAA 57.277 32.000 0.00 0.00 39.13 1.40
892 1116 2.060050 TTTGTCACAACGGGATTGGT 57.940 45.000 0.00 0.00 43.20 3.67
911 1135 1.401905 GTCCCCAAAAGATAAGCAGCG 59.598 52.381 0.00 0.00 0.00 5.18
952 1178 4.278513 CCCCAAACGGCCAGACCA 62.279 66.667 2.24 0.00 39.03 4.02
978 1204 3.149981 CAAAACCTTCTCTTCCACCCTC 58.850 50.000 0.00 0.00 0.00 4.30
1194 1420 2.031012 CTGGCGCAGAAGGTGACA 59.969 61.111 10.83 0.00 44.57 3.58
1398 1624 1.374343 CCTACGACAGCTAGCCGTGA 61.374 60.000 22.52 9.59 37.69 4.35
1410 1636 3.006756 GCCGTGAGTAGCTGCTCCA 62.007 63.158 26.42 13.37 34.74 3.86
1529 1756 3.831911 TGCTTTATTTGGCTTGGCTTACT 59.168 39.130 0.00 0.00 0.00 2.24
1555 1782 2.225019 AGCGAGCAGAGATTTGTTTGTG 59.775 45.455 0.00 0.00 0.00 3.33
1625 1860 1.078848 AAGGCAAGCTGCGAGGTAG 60.079 57.895 0.00 0.00 46.21 3.18
1626 1861 1.544825 AAGGCAAGCTGCGAGGTAGA 61.545 55.000 0.00 0.00 46.21 2.59
1627 1862 1.520342 GGCAAGCTGCGAGGTAGAG 60.520 63.158 0.00 0.00 46.21 2.43
1640 1875 4.202131 GCGAGGTAGAGTGCTAATTAAGGT 60.202 45.833 0.00 0.00 0.00 3.50
1641 1876 5.282510 CGAGGTAGAGTGCTAATTAAGGTG 58.717 45.833 0.00 0.00 0.00 4.00
1652 1887 7.320443 TGCTAATTAAGGTGCACTTCAATAG 57.680 36.000 17.98 12.90 40.64 1.73
1656 1891 7.880160 AATTAAGGTGCACTTCAATAGCATA 57.120 32.000 17.98 0.00 40.78 3.14
1657 1892 8.469309 AATTAAGGTGCACTTCAATAGCATAT 57.531 30.769 17.98 0.00 40.78 1.78
1778 2052 5.912892 TCTGTTTTTCCCCTTTGCTTTTAG 58.087 37.500 0.00 0.00 0.00 1.85
1788 2065 3.730715 CCTTTGCTTTTAGTTCGTTGCAG 59.269 43.478 0.00 0.00 0.00 4.41
1789 2066 2.399396 TGCTTTTAGTTCGTTGCAGC 57.601 45.000 0.00 0.00 0.00 5.25
1790 2067 1.673400 TGCTTTTAGTTCGTTGCAGCA 59.327 42.857 0.24 0.00 33.46 4.41
1814 2091 5.123502 AGCATGCTCTTTCAGAAACTATGTG 59.876 40.000 16.30 0.00 0.00 3.21
1817 2094 4.202461 TGCTCTTTCAGAAACTATGTGGGT 60.202 41.667 0.00 0.00 0.00 4.51
1818 2095 4.393371 GCTCTTTCAGAAACTATGTGGGTC 59.607 45.833 0.00 0.00 0.00 4.46
1819 2096 5.551233 CTCTTTCAGAAACTATGTGGGTCA 58.449 41.667 0.00 0.00 0.00 4.02
1820 2097 6.126863 TCTTTCAGAAACTATGTGGGTCAT 57.873 37.500 0.00 0.00 40.25 3.06
1821 2098 7.252612 TCTTTCAGAAACTATGTGGGTCATA 57.747 36.000 0.00 0.00 37.91 2.15
1822 2099 7.861629 TCTTTCAGAAACTATGTGGGTCATAT 58.138 34.615 0.00 0.00 38.21 1.78
1893 2176 6.608610 ACATTATTTCAGTTCGCTACAAACC 58.391 36.000 0.00 0.00 0.00 3.27
1922 2205 9.941991 CAATTATACATCAAAAGTTCTTTTGCG 57.058 29.630 24.47 20.58 40.65 4.85
1923 2206 7.561237 TTATACATCAAAAGTTCTTTTGCGC 57.439 32.000 24.47 0.00 40.65 6.09
1924 2207 4.045636 ACATCAAAAGTTCTTTTGCGCT 57.954 36.364 24.47 13.63 40.65 5.92
1925 2208 3.798337 ACATCAAAAGTTCTTTTGCGCTG 59.202 39.130 24.47 21.93 40.65 5.18
1926 2209 3.502191 TCAAAAGTTCTTTTGCGCTGT 57.498 38.095 24.47 0.00 40.65 4.40
1927 2210 3.434637 TCAAAAGTTCTTTTGCGCTGTC 58.565 40.909 24.47 0.00 40.65 3.51
1928 2211 3.128589 TCAAAAGTTCTTTTGCGCTGTCT 59.871 39.130 24.47 0.00 40.65 3.41
1929 2212 2.763249 AAGTTCTTTTGCGCTGTCTG 57.237 45.000 9.73 0.00 0.00 3.51
1930 2213 1.668419 AGTTCTTTTGCGCTGTCTGT 58.332 45.000 9.73 0.00 0.00 3.41
1931 2214 1.599542 AGTTCTTTTGCGCTGTCTGTC 59.400 47.619 9.73 0.00 0.00 3.51
1932 2215 0.944386 TTCTTTTGCGCTGTCTGTCC 59.056 50.000 9.73 0.00 0.00 4.02
1933 2216 0.106708 TCTTTTGCGCTGTCTGTCCT 59.893 50.000 9.73 0.00 0.00 3.85
1934 2217 1.343142 TCTTTTGCGCTGTCTGTCCTA 59.657 47.619 9.73 0.00 0.00 2.94
1935 2218 2.028112 TCTTTTGCGCTGTCTGTCCTAT 60.028 45.455 9.73 0.00 0.00 2.57
1936 2219 1.725641 TTTGCGCTGTCTGTCCTATG 58.274 50.000 9.73 0.00 0.00 2.23
1937 2220 0.894835 TTGCGCTGTCTGTCCTATGA 59.105 50.000 9.73 0.00 0.00 2.15
1938 2221 0.894835 TGCGCTGTCTGTCCTATGAA 59.105 50.000 9.73 0.00 0.00 2.57
1939 2222 1.482182 TGCGCTGTCTGTCCTATGAAT 59.518 47.619 9.73 0.00 0.00 2.57
1940 2223 2.093500 TGCGCTGTCTGTCCTATGAATT 60.093 45.455 9.73 0.00 0.00 2.17
1941 2224 3.132111 TGCGCTGTCTGTCCTATGAATTA 59.868 43.478 9.73 0.00 0.00 1.40
1942 2225 4.202253 TGCGCTGTCTGTCCTATGAATTAT 60.202 41.667 9.73 0.00 0.00 1.28
1943 2226 4.151335 GCGCTGTCTGTCCTATGAATTATG 59.849 45.833 0.00 0.00 0.00 1.90
1944 2227 5.292765 CGCTGTCTGTCCTATGAATTATGT 58.707 41.667 0.00 0.00 0.00 2.29
1945 2228 6.447162 CGCTGTCTGTCCTATGAATTATGTA 58.553 40.000 0.00 0.00 0.00 2.29
1946 2229 6.923508 CGCTGTCTGTCCTATGAATTATGTAA 59.076 38.462 0.00 0.00 0.00 2.41
1947 2230 7.115520 CGCTGTCTGTCCTATGAATTATGTAAG 59.884 40.741 0.00 0.00 0.00 2.34
1948 2231 7.386299 GCTGTCTGTCCTATGAATTATGTAAGG 59.614 40.741 0.00 0.00 0.00 2.69
1949 2232 8.319057 TGTCTGTCCTATGAATTATGTAAGGT 57.681 34.615 0.00 0.00 0.00 3.50
1950 2233 8.768397 TGTCTGTCCTATGAATTATGTAAGGTT 58.232 33.333 0.00 0.00 0.00 3.50
1951 2234 9.046296 GTCTGTCCTATGAATTATGTAAGGTTG 57.954 37.037 0.00 0.00 0.00 3.77
1952 2235 8.210946 TCTGTCCTATGAATTATGTAAGGTTGG 58.789 37.037 0.00 0.00 0.00 3.77
1953 2236 7.867921 TGTCCTATGAATTATGTAAGGTTGGT 58.132 34.615 0.00 0.00 0.00 3.67
1954 2237 8.333235 TGTCCTATGAATTATGTAAGGTTGGTT 58.667 33.333 0.00 0.00 0.00 3.67
1955 2238 9.185680 GTCCTATGAATTATGTAAGGTTGGTTT 57.814 33.333 0.00 0.00 0.00 3.27
1956 2239 9.762381 TCCTATGAATTATGTAAGGTTGGTTTT 57.238 29.630 0.00 0.00 0.00 2.43
1960 2243 8.472007 TGAATTATGTAAGGTTGGTTTTCAGT 57.528 30.769 0.00 0.00 0.00 3.41
1961 2244 9.575868 TGAATTATGTAAGGTTGGTTTTCAGTA 57.424 29.630 0.00 0.00 0.00 2.74
1965 2248 9.575868 TTATGTAAGGTTGGTTTTCAGTAATGA 57.424 29.630 0.00 0.00 0.00 2.57
1966 2249 7.883391 TGTAAGGTTGGTTTTCAGTAATGAA 57.117 32.000 0.56 0.56 0.00 2.57
1967 2250 8.294954 TGTAAGGTTGGTTTTCAGTAATGAAA 57.705 30.769 13.98 13.98 36.17 2.69
1968 2251 8.750298 TGTAAGGTTGGTTTTCAGTAATGAAAA 58.250 29.630 23.18 23.18 43.10 2.29
1969 2252 9.758651 GTAAGGTTGGTTTTCAGTAATGAAAAT 57.241 29.630 27.81 15.79 45.67 1.82
1970 2253 8.887036 AAGGTTGGTTTTCAGTAATGAAAATC 57.113 30.769 27.81 27.28 45.67 2.17
1971 2254 7.145323 AGGTTGGTTTTCAGTAATGAAAATCG 58.855 34.615 27.81 0.00 46.34 3.34
1972 2255 6.364976 GGTTGGTTTTCAGTAATGAAAATCGG 59.635 38.462 27.81 0.00 46.34 4.18
1973 2256 6.885952 TGGTTTTCAGTAATGAAAATCGGA 57.114 33.333 27.81 13.94 46.34 4.55
1974 2257 7.278461 TGGTTTTCAGTAATGAAAATCGGAA 57.722 32.000 27.81 13.33 46.34 4.30
1975 2258 7.367285 TGGTTTTCAGTAATGAAAATCGGAAG 58.633 34.615 27.81 0.00 46.34 3.46
1976 2259 6.806739 GGTTTTCAGTAATGAAAATCGGAAGG 59.193 38.462 27.81 0.00 45.67 3.46
1977 2260 6.509418 TTTCAGTAATGAAAATCGGAAGGG 57.491 37.500 15.48 0.00 35.17 3.95
1978 2261 4.523083 TCAGTAATGAAAATCGGAAGGGG 58.477 43.478 0.00 0.00 0.00 4.79
1979 2262 3.066760 CAGTAATGAAAATCGGAAGGGGC 59.933 47.826 0.00 0.00 0.00 5.80
1980 2263 1.102978 AATGAAAATCGGAAGGGGCG 58.897 50.000 0.00 0.00 0.00 6.13
1981 2264 0.254747 ATGAAAATCGGAAGGGGCGA 59.745 50.000 0.00 0.00 0.00 5.54
1982 2265 0.392461 TGAAAATCGGAAGGGGCGAG 60.392 55.000 0.00 0.00 0.00 5.03
1983 2266 1.715862 GAAAATCGGAAGGGGCGAGC 61.716 60.000 0.00 0.00 0.00 5.03
1984 2267 3.699134 AAATCGGAAGGGGCGAGCC 62.699 63.158 5.37 5.37 0.00 4.70
1994 2277 4.645809 GGCGAGCCCTTCTTTGAT 57.354 55.556 1.97 0.00 0.00 2.57
1995 2278 2.398803 GGCGAGCCCTTCTTTGATC 58.601 57.895 1.97 0.00 0.00 2.92
1996 2279 0.392998 GGCGAGCCCTTCTTTGATCA 60.393 55.000 1.97 0.00 0.00 2.92
1997 2280 1.453155 GCGAGCCCTTCTTTGATCAA 58.547 50.000 3.38 3.38 0.00 2.57
1998 2281 1.812571 GCGAGCCCTTCTTTGATCAAA 59.187 47.619 19.45 19.45 0.00 2.69
1999 2282 2.228822 GCGAGCCCTTCTTTGATCAAAA 59.771 45.455 20.82 7.31 0.00 2.44
2000 2283 3.305335 GCGAGCCCTTCTTTGATCAAAAA 60.305 43.478 20.82 15.77 0.00 1.94
2061 2344 6.003950 AGCCAGCATAAAAATACATACCGAT 58.996 36.000 0.00 0.00 0.00 4.18
2082 2365 6.128902 CCGATAAAAACATCTATACCGACAGC 60.129 42.308 0.00 0.00 0.00 4.40
2122 2405 4.816925 GCCTGAAAGACTGAACACTAAACT 59.183 41.667 0.00 0.00 34.07 2.66
2141 2424 9.787435 ACTAAACTGACAAAAACATCTATACCA 57.213 29.630 0.00 0.00 0.00 3.25
2179 2462 3.430236 GGTGTTCACCAAAGAAACCAAGG 60.430 47.826 16.01 0.00 33.13 3.61
2231 2514 1.740585 CGGTCTGAACCAACACAACAA 59.259 47.619 0.00 0.00 46.86 2.83
2263 2546 2.292016 CAGGTTATTGCACGGTGTTCAA 59.708 45.455 10.24 6.81 0.00 2.69
2272 2555 2.096819 GCACGGTGTTCAACAGAGAAAA 59.903 45.455 10.24 0.00 0.00 2.29
2300 2583 7.466804 AGATACAGGGGAAATGACAGTAAAAA 58.533 34.615 0.00 0.00 0.00 1.94
2318 2601 2.697147 AATGCTGAACCCACTGCGGT 62.697 55.000 0.00 0.00 37.93 5.68
2341 2624 6.929606 GGTATCTATTTCGTCCAAGTAATGCT 59.070 38.462 0.00 0.00 0.00 3.79
2347 2630 1.671850 CGTCCAAGTAATGCTCGGTGT 60.672 52.381 0.00 0.00 0.00 4.16
2348 2631 2.423577 GTCCAAGTAATGCTCGGTGTT 58.576 47.619 0.00 0.00 0.00 3.32
2349 2632 2.159627 GTCCAAGTAATGCTCGGTGTTG 59.840 50.000 0.00 0.00 0.00 3.33
2350 2633 1.468520 CCAAGTAATGCTCGGTGTTGG 59.531 52.381 0.00 0.00 0.00 3.77
2351 2634 1.135689 CAAGTAATGCTCGGTGTTGGC 60.136 52.381 0.00 0.00 0.00 4.52
2352 2635 0.036164 AGTAATGCTCGGTGTTGGCA 59.964 50.000 0.00 0.00 40.32 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 83 0.398318 AACTTCCCTTGCGCTCTCTT 59.602 50.000 9.73 0.00 0.00 2.85
82 94 1.209747 GGGACGCTTCATAACTTCCCT 59.790 52.381 0.00 0.00 39.81 4.20
111 123 0.241213 CTGTCGCCTGAGAAAGACGA 59.759 55.000 0.00 0.00 36.49 4.20
118 130 1.216444 GCATGACTGTCGCCTGAGA 59.784 57.895 0.00 0.00 0.00 3.27
131 143 1.179174 ACGCTAGCTATCCCGCATGA 61.179 55.000 13.93 0.00 0.00 3.07
134 146 1.528542 AGACGCTAGCTATCCCGCA 60.529 57.895 13.93 0.00 0.00 5.69
142 154 1.065782 TCAGAGAGTCAGACGCTAGCT 60.066 52.381 13.93 0.00 0.00 3.32
148 160 4.620609 CAGTCATTTTCAGAGAGTCAGACG 59.379 45.833 0.00 0.00 0.00 4.18
150 162 6.602410 ATCAGTCATTTTCAGAGAGTCAGA 57.398 37.500 0.00 0.00 0.00 3.27
154 166 5.788450 ACGAATCAGTCATTTTCAGAGAGT 58.212 37.500 0.00 0.00 0.00 3.24
159 171 5.808042 ATGGACGAATCAGTCATTTTCAG 57.192 39.130 0.00 0.00 42.62 3.02
160 172 5.123820 GGAATGGACGAATCAGTCATTTTCA 59.876 40.000 0.00 0.00 42.62 2.69
170 183 3.517901 ACTAAGTGGGAATGGACGAATCA 59.482 43.478 0.00 0.00 0.00 2.57
220 233 1.698506 TTGTCAAATTCTTGGCCCGT 58.301 45.000 0.00 0.00 36.24 5.28
312 327 8.296799 TGCTGAAATTTTGCAAGTATACAAAG 57.703 30.769 14.60 0.00 37.11 2.77
444 466 7.897575 TTTTGTGTGCTTGTAAAATTTCAGT 57.102 28.000 0.00 0.00 0.00 3.41
540 562 6.616237 ATTCTGATCCCAAGCTCAAAAATT 57.384 33.333 0.00 0.00 0.00 1.82
542 564 7.537596 TTTATTCTGATCCCAAGCTCAAAAA 57.462 32.000 0.00 0.00 0.00 1.94
622 644 7.681939 TCTCTTATTTAAGCACAATCCGTTT 57.318 32.000 0.00 0.00 33.40 3.60
623 645 7.606456 TCTTCTCTTATTTAAGCACAATCCGTT 59.394 33.333 0.00 0.00 33.40 4.44
625 647 7.064609 TGTCTTCTCTTATTTAAGCACAATCCG 59.935 37.037 0.00 0.00 33.40 4.18
663 688 7.122799 TGTTAAGATGGAGAAGAGAGAAATCGA 59.877 37.037 0.00 0.00 0.00 3.59
874 1098 1.600023 GACCAATCCCGTTGTGACAA 58.400 50.000 0.00 0.00 36.01 3.18
892 1116 1.681780 CCGCTGCTTATCTTTTGGGGA 60.682 52.381 0.00 0.00 0.00 4.81
907 1131 1.737838 TTTTATGTGGCTCTCCGCTG 58.262 50.000 0.00 0.00 43.26 5.18
952 1178 3.699538 GTGGAAGAGAAGGTTTTGGTTGT 59.300 43.478 0.00 0.00 0.00 3.32
978 1204 2.175184 CTTCGCACTTGGTTCGCAGG 62.175 60.000 0.00 0.00 0.00 4.85
1194 1420 1.153409 CGCCTGCTTGATGCTCTCT 60.153 57.895 0.00 0.00 43.37 3.10
1410 1636 2.042831 GCAATGGCAGAAGACGGCT 61.043 57.895 0.00 0.00 40.72 5.52
1483 1709 1.026584 ACCAAACTTACACGCCCAAC 58.973 50.000 0.00 0.00 0.00 3.77
1529 1756 6.371548 ACAAACAAATCTCTGCTCGCTTTATA 59.628 34.615 0.00 0.00 0.00 0.98
1640 1875 5.184711 TGTGTGATATGCTATTGAAGTGCA 58.815 37.500 0.00 0.00 41.13 4.57
1641 1876 5.739752 TGTGTGATATGCTATTGAAGTGC 57.260 39.130 0.00 0.00 0.00 4.40
1652 1887 4.497006 GCCACTCTGATTTGTGTGATATGC 60.497 45.833 0.00 0.00 34.51 3.14
1656 1891 2.079158 CGCCACTCTGATTTGTGTGAT 58.921 47.619 0.00 0.00 34.51 3.06
1657 1892 1.511850 CGCCACTCTGATTTGTGTGA 58.488 50.000 0.00 0.00 34.51 3.58
1809 2086 6.474140 AAGTACGTCAATATGACCCACATA 57.526 37.500 0.00 0.00 44.20 2.29
1814 2091 4.940463 TGCTAAGTACGTCAATATGACCC 58.060 43.478 0.00 0.00 44.20 4.46
1817 2094 6.040247 CCAGTTGCTAAGTACGTCAATATGA 58.960 40.000 0.00 0.00 0.00 2.15
1818 2095 5.810587 ACCAGTTGCTAAGTACGTCAATATG 59.189 40.000 0.00 0.00 0.00 1.78
1819 2096 5.974108 ACCAGTTGCTAAGTACGTCAATAT 58.026 37.500 0.00 0.00 0.00 1.28
1820 2097 5.395682 ACCAGTTGCTAAGTACGTCAATA 57.604 39.130 0.00 0.00 0.00 1.90
1821 2098 4.267349 ACCAGTTGCTAAGTACGTCAAT 57.733 40.909 0.00 0.00 0.00 2.57
1822 2099 3.738830 ACCAGTTGCTAAGTACGTCAA 57.261 42.857 0.00 0.00 0.00 3.18
1912 2195 1.334149 GGACAGACAGCGCAAAAGAAC 60.334 52.381 11.47 0.00 0.00 3.01
1913 2196 0.944386 GGACAGACAGCGCAAAAGAA 59.056 50.000 11.47 0.00 0.00 2.52
1914 2197 0.106708 AGGACAGACAGCGCAAAAGA 59.893 50.000 11.47 0.00 0.00 2.52
1915 2198 1.795768 TAGGACAGACAGCGCAAAAG 58.204 50.000 11.47 0.00 0.00 2.27
1916 2199 2.076100 CATAGGACAGACAGCGCAAAA 58.924 47.619 11.47 0.00 0.00 2.44
1917 2200 1.275010 TCATAGGACAGACAGCGCAAA 59.725 47.619 11.47 0.00 0.00 3.68
1918 2201 0.894835 TCATAGGACAGACAGCGCAA 59.105 50.000 11.47 0.00 0.00 4.85
1919 2202 0.894835 TTCATAGGACAGACAGCGCA 59.105 50.000 11.47 0.00 0.00 6.09
1920 2203 2.231215 ATTCATAGGACAGACAGCGC 57.769 50.000 0.00 0.00 0.00 5.92
1921 2204 5.292765 ACATAATTCATAGGACAGACAGCG 58.707 41.667 0.00 0.00 0.00 5.18
1922 2205 7.386299 CCTTACATAATTCATAGGACAGACAGC 59.614 40.741 0.00 0.00 0.00 4.40
1923 2206 8.424918 ACCTTACATAATTCATAGGACAGACAG 58.575 37.037 0.00 0.00 0.00 3.51
1924 2207 8.319057 ACCTTACATAATTCATAGGACAGACA 57.681 34.615 0.00 0.00 0.00 3.41
1925 2208 9.046296 CAACCTTACATAATTCATAGGACAGAC 57.954 37.037 0.00 0.00 0.00 3.51
1926 2209 8.210946 CCAACCTTACATAATTCATAGGACAGA 58.789 37.037 0.00 0.00 0.00 3.41
1927 2210 7.993183 ACCAACCTTACATAATTCATAGGACAG 59.007 37.037 0.00 0.00 0.00 3.51
1928 2211 7.867921 ACCAACCTTACATAATTCATAGGACA 58.132 34.615 0.00 0.00 0.00 4.02
1929 2212 8.747538 AACCAACCTTACATAATTCATAGGAC 57.252 34.615 0.00 0.00 0.00 3.85
1930 2213 9.762381 AAAACCAACCTTACATAATTCATAGGA 57.238 29.630 0.00 0.00 0.00 2.94
1934 2217 9.088987 ACTGAAAACCAACCTTACATAATTCAT 57.911 29.630 0.00 0.00 0.00 2.57
1935 2218 8.472007 ACTGAAAACCAACCTTACATAATTCA 57.528 30.769 0.00 0.00 0.00 2.57
1939 2222 9.575868 TCATTACTGAAAACCAACCTTACATAA 57.424 29.630 0.00 0.00 0.00 1.90
1940 2223 9.575868 TTCATTACTGAAAACCAACCTTACATA 57.424 29.630 0.00 0.00 38.43 2.29
1941 2224 8.472007 TTCATTACTGAAAACCAACCTTACAT 57.528 30.769 0.00 0.00 38.43 2.29
1942 2225 7.883391 TTCATTACTGAAAACCAACCTTACA 57.117 32.000 0.00 0.00 38.43 2.41
1954 2237 5.417580 CCCCTTCCGATTTTCATTACTGAAA 59.582 40.000 4.26 4.26 46.92 2.69
1955 2238 4.947388 CCCCTTCCGATTTTCATTACTGAA 59.053 41.667 0.00 0.00 39.62 3.02
1956 2239 4.523083 CCCCTTCCGATTTTCATTACTGA 58.477 43.478 0.00 0.00 0.00 3.41
1957 2240 3.066760 GCCCCTTCCGATTTTCATTACTG 59.933 47.826 0.00 0.00 0.00 2.74
1958 2241 3.288092 GCCCCTTCCGATTTTCATTACT 58.712 45.455 0.00 0.00 0.00 2.24
1959 2242 2.032924 CGCCCCTTCCGATTTTCATTAC 59.967 50.000 0.00 0.00 0.00 1.89
1960 2243 2.092861 TCGCCCCTTCCGATTTTCATTA 60.093 45.455 0.00 0.00 0.00 1.90
1961 2244 1.102978 CGCCCCTTCCGATTTTCATT 58.897 50.000 0.00 0.00 0.00 2.57
1962 2245 0.254747 TCGCCCCTTCCGATTTTCAT 59.745 50.000 0.00 0.00 0.00 2.57
1963 2246 0.392461 CTCGCCCCTTCCGATTTTCA 60.392 55.000 0.00 0.00 33.83 2.69
1964 2247 1.715862 GCTCGCCCCTTCCGATTTTC 61.716 60.000 0.00 0.00 33.83 2.29
1965 2248 1.749258 GCTCGCCCCTTCCGATTTT 60.749 57.895 0.00 0.00 33.83 1.82
1966 2249 2.124695 GCTCGCCCCTTCCGATTT 60.125 61.111 0.00 0.00 33.83 2.17
1967 2250 4.176752 GGCTCGCCCCTTCCGATT 62.177 66.667 0.00 0.00 33.83 3.34
1977 2260 0.392998 TGATCAAAGAAGGGCTCGCC 60.393 55.000 0.00 0.00 0.00 5.54
1978 2261 1.453155 TTGATCAAAGAAGGGCTCGC 58.547 50.000 5.45 0.00 0.00 5.03
1979 2262 4.503741 TTTTTGATCAAAGAAGGGCTCG 57.496 40.909 19.64 0.00 0.00 5.03
2004 2287 9.710900 GATTCCCAAGAACTTTTGATGTATTTT 57.289 29.630 0.00 0.00 33.97 1.82
2005 2288 8.314021 GGATTCCCAAGAACTTTTGATGTATTT 58.686 33.333 0.00 0.00 33.97 1.40
2006 2289 7.454380 TGGATTCCCAAGAACTTTTGATGTATT 59.546 33.333 0.00 0.00 40.09 1.89
2007 2290 6.953520 TGGATTCCCAAGAACTTTTGATGTAT 59.046 34.615 0.00 0.00 40.09 2.29
2008 2291 6.310941 TGGATTCCCAAGAACTTTTGATGTA 58.689 36.000 0.00 0.00 40.09 2.29
2009 2292 5.147032 TGGATTCCCAAGAACTTTTGATGT 58.853 37.500 0.00 0.00 40.09 3.06
2010 2293 5.726980 TGGATTCCCAAGAACTTTTGATG 57.273 39.130 0.00 0.00 40.09 3.07
2061 2344 4.505191 GCGCTGTCGGTATAGATGTTTTTA 59.495 41.667 0.00 0.00 35.95 1.52
2082 2365 3.121030 CTGGAAACCTCGGCTGCG 61.121 66.667 0.00 0.00 0.00 5.18
2122 2405 7.888021 ACTTGGATGGTATAGATGTTTTTGTCA 59.112 33.333 0.00 0.00 0.00 3.58
2141 2424 3.713826 ACACCGTGGAATTACTTGGAT 57.286 42.857 3.03 0.00 0.00 3.41
2179 2462 6.032042 CGATTGCACTTTATTTTTCCACGTAC 59.968 38.462 0.00 0.00 0.00 3.67
2186 2469 7.637709 AAACCTCGATTGCACTTTATTTTTC 57.362 32.000 0.00 0.00 0.00 2.29
2231 2514 6.239008 CCGTGCAATAACCTGGATGAAATAAT 60.239 38.462 0.00 0.00 0.00 1.28
2263 2546 4.597507 TCCCCTGTATCTTGTTTTCTCTGT 59.402 41.667 0.00 0.00 0.00 3.41
2272 2555 4.289672 ACTGTCATTTCCCCTGTATCTTGT 59.710 41.667 0.00 0.00 0.00 3.16
2300 2583 1.836999 TACCGCAGTGGGTTCAGCAT 61.837 55.000 4.64 0.00 44.64 3.79
2318 2601 6.861572 CGAGCATTACTTGGACGAAATAGATA 59.138 38.462 0.00 0.00 0.00 1.98
2341 2624 2.904866 GCCAACTGCCAACACCGA 60.905 61.111 0.00 0.00 0.00 4.69
2347 2630 0.250510 TACATCGTGCCAACTGCCAA 60.251 50.000 0.00 0.00 40.16 4.52
2348 2631 0.673333 CTACATCGTGCCAACTGCCA 60.673 55.000 0.00 0.00 40.16 4.92
2349 2632 0.673644 ACTACATCGTGCCAACTGCC 60.674 55.000 0.00 0.00 40.16 4.85
2350 2633 0.721718 GACTACATCGTGCCAACTGC 59.278 55.000 0.00 0.00 41.77 4.40
2351 2634 0.992072 CGACTACATCGTGCCAACTG 59.008 55.000 0.00 0.00 46.25 3.16
2352 2635 3.418675 CGACTACATCGTGCCAACT 57.581 52.632 0.00 0.00 46.25 3.16


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

AutoCloner maintained by Alex Coulton.