Multiple sequence alignment - TraesCS6A01G155200

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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 TraesCS6A01G155200 chr6A 100.000 4082 0 0 1 4082 143961499 143965580 0.000000e+00 7539.0
1 TraesCS6A01G155200 chr6D 96.769 1950 56 7 1 1949 115541929 115543872 0.000000e+00 3245.0
2 TraesCS6A01G155200 chr6D 95.193 1581 43 7 2031 3611 115543870 115545417 0.000000e+00 2468.0
3 TraesCS6A01G155200 chr6D 95.634 481 14 2 3608 4082 115545451 115545930 0.000000e+00 765.0
4 TraesCS6A01G155200 chr6D 92.553 94 5 2 1942 2034 26359307 26359215 2.560000e-27 134.0
5 TraesCS6A01G155200 chr6D 89.216 102 7 4 1948 2048 216847278 216847376 1.540000e-24 124.0
6 TraesCS6A01G155200 chr6B 95.599 1954 75 7 2 1949 204919745 204921693 0.000000e+00 3121.0
7 TraesCS6A01G155200 chr6B 95.800 1381 54 3 2233 3611 204921861 204923239 0.000000e+00 2226.0
8 TraesCS6A01G155200 chr6B 96.000 475 15 4 3608 4082 204923273 204923743 0.000000e+00 769.0
9 TraesCS6A01G155200 chr6B 94.220 173 10 0 2031 2203 204921691 204921863 8.700000e-67 265.0
10 TraesCS6A01G155200 chr6B 90.625 96 6 3 1939 2033 35362645 35362738 1.540000e-24 124.0
11 TraesCS6A01G155200 chr6B 83.168 101 12 5 1944 2043 58815426 58815522 2.020000e-13 87.9
12 TraesCS6A01G155200 chr7A 82.580 907 142 12 1036 1930 678580701 678581603 0.000000e+00 785.0
13 TraesCS6A01G155200 chr7A 83.149 362 61 0 2726 3087 678581655 678582016 8.460000e-87 331.0
14 TraesCS6A01G155200 chr7D 82.470 907 143 13 1036 1930 587070265 587071167 0.000000e+00 780.0
15 TraesCS6A01G155200 chr7D 83.621 348 57 0 2740 3087 587071234 587071581 1.090000e-85 327.0
16 TraesCS6A01G155200 chr7B 81.698 907 150 12 1036 1930 657932969 657933871 0.000000e+00 741.0
17 TraesCS6A01G155200 chr7B 82.873 362 62 0 2726 3087 657933923 657934284 3.930000e-85 326.0
18 TraesCS6A01G155200 chr7B 91.837 98 5 3 1945 2041 715301933 715302028 2.560000e-27 134.0
19 TraesCS6A01G155200 chr7B 89.247 93 8 2 1948 2039 6997735 6997826 9.270000e-22 115.0
20 TraesCS6A01G155200 chr7B 85.567 97 11 3 1948 2043 730232690 730232784 9.340000e-17 99.0
21 TraesCS6A01G155200 chr4B 92.473 93 5 2 1948 2039 40170069 40169978 9.210000e-27 132.0
22 TraesCS6A01G155200 chr3B 93.333 90 4 2 1945 2033 816514524 816514612 9.210000e-27 132.0
23 TraesCS6A01G155200 chr3B 89.474 95 7 3 1948 2041 460106296 460106388 2.580000e-22 117.0
24 TraesCS6A01G155200 chr3B 90.805 87 6 2 1948 2033 808971531 808971616 9.270000e-22 115.0
25 TraesCS6A01G155200 chrUn 92.222 90 5 2 1948 2036 97273184 97273096 4.280000e-25 126.0
26 TraesCS6A01G155200 chr2B 91.489 94 5 3 1948 2040 685280514 685280605 4.280000e-25 126.0
27 TraesCS6A01G155200 chr2A 90.722 97 6 3 1945 2040 193876554 193876460 4.280000e-25 126.0
28 TraesCS6A01G155200 chr3A 91.304 92 5 3 1948 2038 72473529 72473618 5.540000e-24 122.0
29 TraesCS6A01G155200 chr4A 90.217 92 6 3 1952 2042 586386324 586386235 2.580000e-22 117.0


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 TraesCS6A01G155200 chr6A 143961499 143965580 4081 False 7539.000000 7539 100.000000 1 4082 1 chr6A.!!$F1 4081
1 TraesCS6A01G155200 chr6D 115541929 115545930 4001 False 2159.333333 3245 95.865333 1 4082 3 chr6D.!!$F2 4081
2 TraesCS6A01G155200 chr6B 204919745 204923743 3998 False 1595.250000 3121 95.404750 2 4082 4 chr6B.!!$F3 4080
3 TraesCS6A01G155200 chr7A 678580701 678582016 1315 False 558.000000 785 82.864500 1036 3087 2 chr7A.!!$F1 2051
4 TraesCS6A01G155200 chr7D 587070265 587071581 1316 False 553.500000 780 83.045500 1036 3087 2 chr7D.!!$F1 2051
5 TraesCS6A01G155200 chr7B 657932969 657934284 1315 False 533.500000 741 82.285500 1036 3087 2 chr7B.!!$F4 2051

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
931 938 0.250858 TCGTGGGTGTACGGAAGAGA 60.251 55.0 0.0 0.0 43.85 3.10 F
1176 1192 0.249398 GTGGCTCCGTTACCATGTCT 59.751 55.0 0.0 0.0 38.46 3.41 F
1962 1978 0.339162 TATGTACCCCCTCCGTTCCA 59.661 55.0 0.0 0.0 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2231 2247 0.255890 AGAGCCCGGTGCATACAATT 59.744 50.0 15.92 0.0 44.83 2.32 R
2660 2677 0.320771 TTGGCGAGAGAGGAGCAAAC 60.321 55.0 0.00 0.0 0.00 2.93 R
3825 3885 0.599728 TTTGTTTCATTGCGCAGGCC 60.600 50.0 11.31 0.0 38.85 5.19 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
21 22 1.140852 TCAACATGGACCATCCGATCC 59.859 52.381 3.21 0.00 40.17 3.36
43 44 0.509499 GACGAACGCACCAAATTCGA 59.491 50.000 12.10 0.00 46.28 3.71
63 64 1.289066 CGGGAGAGCAGTCGAACAA 59.711 57.895 0.00 0.00 0.00 2.83
84 85 6.087522 ACAACTTTGATCGTTTTGTCGAAAA 58.912 32.000 0.00 0.00 42.99 2.29
106 107 2.353803 CCGCCTGGCTAACACCTATATC 60.354 54.545 17.92 0.00 0.00 1.63
212 213 1.550072 TCCTATTTTTGCAGCCAAGGC 59.450 47.619 2.02 2.02 42.33 4.35
242 244 1.850345 AGGACTGAACCAAGAAACCCA 59.150 47.619 0.00 0.00 0.00 4.51
313 315 2.364317 CGCCCCCTCTCTCTCCAA 60.364 66.667 0.00 0.00 0.00 3.53
434 436 0.399233 AATCCTTCTCCTCCCCTCCG 60.399 60.000 0.00 0.00 0.00 4.63
497 499 1.221021 CCTGCCGGGGTAAGAAGTC 59.779 63.158 2.18 0.00 0.00 3.01
542 545 3.192230 CCAATCGCGCGGCTGTTA 61.192 61.111 31.69 9.99 0.00 2.41
566 569 0.461870 TTCGGGTGATCGATTGCTGG 60.462 55.000 0.00 0.00 39.03 4.85
599 602 3.782443 GGAGGCGGATGGGTCGTT 61.782 66.667 0.00 0.00 0.00 3.85
605 608 3.810896 GGATGGGTCGTTTGCGCC 61.811 66.667 4.18 0.00 38.14 6.53
613 616 4.368808 CGTTTGCGCCTCACCGTG 62.369 66.667 4.18 0.00 0.00 4.94
682 685 2.674220 GCTGGGAAGGGTCTGGAGG 61.674 68.421 0.00 0.00 0.00 4.30
694 701 4.140924 AGGGTCTGGAGGAATTTTTCTTGT 60.141 41.667 0.00 0.00 0.00 3.16
732 739 4.053295 GGCTTAAAGTTCGTGTGTAGACA 58.947 43.478 0.00 0.00 0.00 3.41
837 844 7.148373 TGGTTGTAAGATAAGCGATTTTGGTAC 60.148 37.037 0.00 0.00 0.00 3.34
846 853 4.533222 AGCGATTTTGGTACTTTCAAACG 58.467 39.130 0.00 0.00 34.34 3.60
858 865 6.741358 GGTACTTTCAAACGAGAATTACATGC 59.259 38.462 0.00 0.00 0.00 4.06
913 920 4.024218 CAGCTTGCTATAATTGCAGGTCTC 60.024 45.833 0.00 0.00 41.71 3.36
931 938 0.250858 TCGTGGGTGTACGGAAGAGA 60.251 55.000 0.00 0.00 43.85 3.10
1176 1192 0.249398 GTGGCTCCGTTACCATGTCT 59.751 55.000 0.00 0.00 38.46 3.41
1254 1270 2.671070 CTCCGTGATGCCCCAACT 59.329 61.111 0.00 0.00 0.00 3.16
1461 1477 3.007323 GGGAAGCTGTACCGGGGT 61.007 66.667 6.32 0.00 0.00 4.95
1551 1567 1.668751 TCGTTGGAACAGCAGTTTGTC 59.331 47.619 0.00 0.00 40.47 3.18
1942 1958 7.433719 CGTAAGTTCAATTGATGTTTGGTTTCA 59.566 33.333 9.40 0.00 0.00 2.69
1949 1965 9.853555 TCAATTGATGTTTGGTTTCATATGTAC 57.146 29.630 3.38 2.67 0.00 2.90
1950 1966 9.086336 CAATTGATGTTTGGTTTCATATGTACC 57.914 33.333 17.49 17.49 0.00 3.34
1951 1967 6.767524 TGATGTTTGGTTTCATATGTACCC 57.232 37.500 19.94 7.85 0.00 3.69
1952 1968 5.654650 TGATGTTTGGTTTCATATGTACCCC 59.345 40.000 19.94 10.30 0.00 4.95
1953 1969 4.345854 TGTTTGGTTTCATATGTACCCCC 58.654 43.478 19.94 11.93 0.00 5.40
1954 1970 4.044825 TGTTTGGTTTCATATGTACCCCCT 59.955 41.667 19.94 0.00 0.00 4.79
1955 1971 4.513406 TTGGTTTCATATGTACCCCCTC 57.487 45.455 19.94 3.60 0.00 4.30
1956 1972 2.781174 TGGTTTCATATGTACCCCCTCC 59.219 50.000 19.94 7.78 0.00 4.30
1957 1973 2.224450 GGTTTCATATGTACCCCCTCCG 60.224 54.545 14.89 0.00 0.00 4.63
1958 1974 2.436911 GTTTCATATGTACCCCCTCCGT 59.563 50.000 1.90 0.00 0.00 4.69
1959 1975 2.482414 TCATATGTACCCCCTCCGTT 57.518 50.000 1.90 0.00 0.00 4.44
1960 1976 2.322658 TCATATGTACCCCCTCCGTTC 58.677 52.381 1.90 0.00 0.00 3.95
1961 1977 1.346722 CATATGTACCCCCTCCGTTCC 59.653 57.143 0.00 0.00 0.00 3.62
1962 1978 0.339162 TATGTACCCCCTCCGTTCCA 59.661 55.000 0.00 0.00 0.00 3.53
1963 1979 0.548197 ATGTACCCCCTCCGTTCCAA 60.548 55.000 0.00 0.00 0.00 3.53
1964 1980 0.767446 TGTACCCCCTCCGTTCCAAA 60.767 55.000 0.00 0.00 0.00 3.28
1965 1981 0.401356 GTACCCCCTCCGTTCCAAAA 59.599 55.000 0.00 0.00 0.00 2.44
1966 1982 1.005097 GTACCCCCTCCGTTCCAAAAT 59.995 52.381 0.00 0.00 0.00 1.82
1967 1983 1.374572 ACCCCCTCCGTTCCAAAATA 58.625 50.000 0.00 0.00 0.00 1.40
1968 1984 1.283905 ACCCCCTCCGTTCCAAAATAG 59.716 52.381 0.00 0.00 0.00 1.73
1969 1985 1.562475 CCCCCTCCGTTCCAAAATAGA 59.438 52.381 0.00 0.00 0.00 1.98
1970 1986 2.174854 CCCCCTCCGTTCCAAAATAGAT 59.825 50.000 0.00 0.00 0.00 1.98
1971 1987 3.214328 CCCCTCCGTTCCAAAATAGATG 58.786 50.000 0.00 0.00 0.00 2.90
1972 1988 3.118038 CCCCTCCGTTCCAAAATAGATGA 60.118 47.826 0.00 0.00 0.00 2.92
1973 1989 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
1974 1990 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
1975 1991 4.384208 CCTCCGTTCCAAAATAGATGACCT 60.384 45.833 0.00 0.00 0.00 3.85
1976 1992 4.513442 TCCGTTCCAAAATAGATGACCTG 58.487 43.478 0.00 0.00 0.00 4.00
1977 1993 4.224147 TCCGTTCCAAAATAGATGACCTGA 59.776 41.667 0.00 0.00 0.00 3.86
1978 1994 4.332819 CCGTTCCAAAATAGATGACCTGAC 59.667 45.833 0.00 0.00 0.00 3.51
1979 1995 5.178797 CGTTCCAAAATAGATGACCTGACT 58.821 41.667 0.00 0.00 0.00 3.41
1980 1996 5.643777 CGTTCCAAAATAGATGACCTGACTT 59.356 40.000 0.00 0.00 0.00 3.01
1981 1997 6.149474 CGTTCCAAAATAGATGACCTGACTTT 59.851 38.462 0.00 0.00 0.00 2.66
1982 1998 7.333423 CGTTCCAAAATAGATGACCTGACTTTA 59.667 37.037 0.00 0.00 0.00 1.85
1983 1999 8.669243 GTTCCAAAATAGATGACCTGACTTTAG 58.331 37.037 0.00 0.00 0.00 1.85
1984 2000 7.918076 TCCAAAATAGATGACCTGACTTTAGT 58.082 34.615 0.00 0.00 0.00 2.24
1985 2001 9.042450 TCCAAAATAGATGACCTGACTTTAGTA 57.958 33.333 0.00 0.00 0.00 1.82
1986 2002 9.099454 CCAAAATAGATGACCTGACTTTAGTAC 57.901 37.037 0.00 0.00 0.00 2.73
1987 2003 9.653287 CAAAATAGATGACCTGACTTTAGTACA 57.347 33.333 0.00 0.00 0.00 2.90
1990 2006 9.877178 AATAGATGACCTGACTTTAGTACAAAG 57.123 33.333 13.08 13.08 0.00 2.77
1991 2007 7.304497 AGATGACCTGACTTTAGTACAAAGT 57.696 36.000 17.67 17.67 42.62 2.66
1992 2008 7.736893 AGATGACCTGACTTTAGTACAAAGTT 58.263 34.615 18.29 8.00 40.27 2.66
1993 2009 8.867097 AGATGACCTGACTTTAGTACAAAGTTA 58.133 33.333 18.29 14.96 40.27 2.24
1994 2010 9.141400 GATGACCTGACTTTAGTACAAAGTTAG 57.859 37.037 21.98 21.98 40.27 2.34
1995 2011 8.015185 TGACCTGACTTTAGTACAAAGTTAGT 57.985 34.615 24.24 19.23 40.28 2.24
1996 2012 9.135189 TGACCTGACTTTAGTACAAAGTTAGTA 57.865 33.333 24.24 15.64 40.28 1.82
2023 2039 8.970691 AAAATTGAGTCATCTATTTTGGAACG 57.029 30.769 11.47 0.00 44.08 3.95
2024 2040 6.683974 ATTGAGTCATCTATTTTGGAACGG 57.316 37.500 0.00 0.00 0.00 4.44
2025 2041 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
2026 2042 5.989477 TGAGTCATCTATTTTGGAACGGAT 58.011 37.500 0.00 0.00 0.00 4.18
2027 2043 5.817296 TGAGTCATCTATTTTGGAACGGATG 59.183 40.000 0.00 0.00 32.78 3.51
2028 2044 5.126067 AGTCATCTATTTTGGAACGGATGG 58.874 41.667 0.00 0.00 32.58 3.51
2029 2045 5.104527 AGTCATCTATTTTGGAACGGATGGA 60.105 40.000 0.00 0.00 32.58 3.41
2030 2046 5.237344 GTCATCTATTTTGGAACGGATGGAG 59.763 44.000 0.00 0.00 32.58 3.86
2031 2047 4.837093 TCTATTTTGGAACGGATGGAGT 57.163 40.909 0.00 0.00 0.00 3.85
2032 2048 5.943349 TCTATTTTGGAACGGATGGAGTA 57.057 39.130 0.00 0.00 0.00 2.59
2110 2126 1.064758 TGCCAAATCCTGTATCCGCTT 60.065 47.619 0.00 0.00 0.00 4.68
2153 2169 3.482786 CGTAGAACATTCAACTGCTTGC 58.517 45.455 0.00 0.00 0.00 4.01
2199 2215 9.599866 TGTGATATTTACAAACTGTCCATAGAG 57.400 33.333 0.00 0.00 0.00 2.43
2230 2246 2.292267 CACAATGTACCTGGATGCTCC 58.708 52.381 0.00 0.00 36.96 4.70
2231 2247 1.915489 ACAATGTACCTGGATGCTCCA 59.085 47.619 0.00 5.03 45.98 3.86
2271 2287 7.222999 GGCTCTCATATAACTCAAACTGTACAC 59.777 40.741 0.00 0.00 0.00 2.90
2289 2305 2.488545 ACACGTTGTTGCCTTGTGTTAA 59.511 40.909 0.00 0.00 40.63 2.01
2304 2320 7.119846 GCCTTGTGTTAAACAGAAGTATCATCT 59.880 37.037 0.00 0.00 44.97 2.90
2461 2477 3.558931 AAGCATGGTCCATCGTAATCA 57.441 42.857 0.00 0.00 0.00 2.57
2634 2651 5.694910 TGGTAGAGAATTGTTTCACTTCGAC 59.305 40.000 0.00 0.00 34.97 4.20
2660 2677 5.290643 GTCTCATAGTAACAAGCTGCTTCTG 59.709 44.000 12.82 5.81 0.00 3.02
2665 2682 2.214387 AACAAGCTGCTTCTGTTTGC 57.786 45.000 12.82 0.00 29.76 3.68
2956 2974 1.442520 CGCTGTTGGGATGCAAACG 60.443 57.895 0.00 0.00 0.00 3.60
3179 3197 2.209273 TGTGTTCATCGTTGTCAGTGG 58.791 47.619 0.00 0.00 0.00 4.00
3286 3304 3.756434 GCCTTGTATGCTAACAAAGACCA 59.244 43.478 6.03 0.00 38.81 4.02
3412 3430 0.249120 TCGGTTGCCTGGACACTATG 59.751 55.000 0.00 0.00 0.00 2.23
3416 3434 2.504367 GTTGCCTGGACACTATGTTGT 58.496 47.619 0.00 0.00 0.00 3.32
3435 3453 7.897575 TGTTGTGGTTCATAATATTTTTGCC 57.102 32.000 0.00 0.00 0.00 4.52
3489 3507 6.322201 GGTAACCTGTCAATTGGATCAATCAT 59.678 38.462 5.42 0.00 32.43 2.45
3513 3531 5.875224 TGTCACTTGATCCAAAGGTTATGA 58.125 37.500 0.00 0.00 0.00 2.15
3601 3619 8.848474 ACTTGTTGAGCTGTATATTTTAGTGT 57.152 30.769 0.00 0.00 0.00 3.55
3613 3667 9.098355 TGTATATTTTAGTGTCTGTTCTGCATC 57.902 33.333 0.00 0.00 0.00 3.91
3683 3737 2.536365 CTAACGCGAGCTGTTTGGATA 58.464 47.619 15.93 0.00 0.00 2.59
3713 3767 1.478510 GAGGAGACAGGATCGCTTTCA 59.521 52.381 0.00 0.00 0.00 2.69
3903 3963 1.550976 CTATGATACCCCTCTTCCGGC 59.449 57.143 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 4.485834 TGCGTTCGTCCGGGATCG 62.486 66.667 0.00 6.35 33.47 3.69
21 22 1.847890 AATTTGGTGCGTTCGTCCGG 61.848 55.000 0.00 0.00 0.00 5.14
28 29 1.206578 CGCTCGAATTTGGTGCGTT 59.793 52.632 16.37 0.00 41.45 4.84
43 44 2.676822 TTCGACTGCTCTCCCGCT 60.677 61.111 0.00 0.00 0.00 5.52
84 85 0.981277 ATAGGTGTTAGCCAGGCGGT 60.981 55.000 5.55 0.00 33.28 5.68
190 191 3.853475 CCTTGGCTGCAAAAATAGGAAG 58.147 45.455 0.50 0.00 0.00 3.46
193 194 1.736696 CGCCTTGGCTGCAAAAATAGG 60.737 52.381 10.12 0.00 0.00 2.57
207 208 2.045926 CCTTCCCTCACCGCCTTG 60.046 66.667 0.00 0.00 0.00 3.61
212 213 0.037232 GTTCAGTCCTTCCCTCACCG 60.037 60.000 0.00 0.00 0.00 4.94
242 244 0.323957 GGTTTACACCCCGAGCTTCT 59.676 55.000 0.00 0.00 37.03 2.85
465 467 2.586245 CAGGAAGCAGGCCGATCA 59.414 61.111 0.00 0.00 0.00 2.92
537 540 3.991773 TCGATCACCCGAAAAACTAACAG 59.008 43.478 0.00 0.00 35.42 3.16
542 545 2.161609 GCAATCGATCACCCGAAAAACT 59.838 45.455 0.00 0.00 42.22 2.66
566 569 0.974836 CTCCAAATCGCGCGAAAAAC 59.025 50.000 38.07 0.00 0.00 2.43
605 608 2.111043 AACCCAGCACACGGTGAG 59.889 61.111 16.29 8.32 43.56 3.51
613 616 4.645921 GGCGCAACAACCCAGCAC 62.646 66.667 10.83 0.00 0.00 4.40
694 701 6.837048 ACTTTAAGCCCTTCAACCTAGAAAAA 59.163 34.615 0.00 0.00 0.00 1.94
837 844 6.843676 CAGCATGTAATTCTCGTTTGAAAG 57.156 37.500 0.00 0.00 0.00 2.62
858 865 8.206325 AGAAATGAGTTATCAAGCATACACAG 57.794 34.615 0.00 0.00 39.39 3.66
913 920 0.170561 CTCTCTTCCGTACACCCACG 59.829 60.000 0.00 0.00 41.59 4.94
931 938 6.711277 TGTACATCCTCAACTAAGAAATGCT 58.289 36.000 0.00 0.00 0.00 3.79
1176 1192 0.747644 CCACACTGCTGTTGTCCACA 60.748 55.000 0.00 0.00 0.00 4.17
1191 1207 2.649034 GACTCGTTCGAGCCCACA 59.351 61.111 19.90 0.00 35.81 4.17
1254 1270 0.607762 TGCCAACCGAATAGCTTGCA 60.608 50.000 0.00 0.00 0.00 4.08
1461 1477 5.428253 GCAACATCTTCTCCAATGTAGGTA 58.572 41.667 0.00 0.00 35.10 3.08
1464 1480 4.264253 TGGCAACATCTTCTCCAATGTAG 58.736 43.478 0.00 0.00 46.17 2.74
1509 1525 5.632764 CGATTGTGCTCTCTCGATATCATTT 59.367 40.000 3.12 0.00 33.07 2.32
1551 1567 8.432805 AGGGTAGATAACATCATAACTTCTTGG 58.567 37.037 0.00 0.00 0.00 3.61
1942 1958 1.061967 TGGAACGGAGGGGGTACATAT 60.062 52.381 0.00 0.00 0.00 1.78
1949 1965 1.562475 TCTATTTTGGAACGGAGGGGG 59.438 52.381 0.00 0.00 0.00 5.40
1950 1966 3.118038 TCATCTATTTTGGAACGGAGGGG 60.118 47.826 0.00 0.00 0.00 4.79
1951 1967 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
1952 1968 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
1953 1969 4.572389 CAGGTCATCTATTTTGGAACGGAG 59.428 45.833 0.00 0.00 0.00 4.63
1954 1970 4.224147 TCAGGTCATCTATTTTGGAACGGA 59.776 41.667 0.00 0.00 0.00 4.69
1955 1971 4.332819 GTCAGGTCATCTATTTTGGAACGG 59.667 45.833 0.00 0.00 0.00 4.44
1956 1972 5.178797 AGTCAGGTCATCTATTTTGGAACG 58.821 41.667 0.00 0.00 0.00 3.95
1957 1973 7.454260 AAAGTCAGGTCATCTATTTTGGAAC 57.546 36.000 0.00 0.00 0.00 3.62
1958 1974 8.383175 ACTAAAGTCAGGTCATCTATTTTGGAA 58.617 33.333 0.00 0.00 0.00 3.53
1959 1975 7.918076 ACTAAAGTCAGGTCATCTATTTTGGA 58.082 34.615 0.00 0.00 0.00 3.53
1960 1976 9.099454 GTACTAAAGTCAGGTCATCTATTTTGG 57.901 37.037 0.00 0.00 0.00 3.28
1961 1977 9.653287 TGTACTAAAGTCAGGTCATCTATTTTG 57.347 33.333 0.00 0.00 0.00 2.44
1964 1980 9.877178 CTTTGTACTAAAGTCAGGTCATCTATT 57.123 33.333 0.00 0.00 0.00 1.73
1965 1981 9.036980 ACTTTGTACTAAAGTCAGGTCATCTAT 57.963 33.333 14.04 0.00 35.76 1.98
1966 1982 8.418597 ACTTTGTACTAAAGTCAGGTCATCTA 57.581 34.615 14.04 0.00 35.76 1.98
1967 1983 7.304497 ACTTTGTACTAAAGTCAGGTCATCT 57.696 36.000 14.04 0.00 35.76 2.90
1968 1984 7.964604 AACTTTGTACTAAAGTCAGGTCATC 57.035 36.000 17.83 0.00 39.36 2.92
1969 1985 8.648693 ACTAACTTTGTACTAAAGTCAGGTCAT 58.351 33.333 17.83 8.16 39.36 3.06
1970 1986 8.015185 ACTAACTTTGTACTAAAGTCAGGTCA 57.985 34.615 17.83 5.38 39.36 4.02
1998 2014 8.028938 CCGTTCCAAAATAGATGACTCAATTTT 58.971 33.333 0.00 0.00 33.07 1.82
1999 2015 7.393234 TCCGTTCCAAAATAGATGACTCAATTT 59.607 33.333 0.00 0.00 0.00 1.82
2000 2016 6.884295 TCCGTTCCAAAATAGATGACTCAATT 59.116 34.615 0.00 0.00 0.00 2.32
2001 2017 6.414732 TCCGTTCCAAAATAGATGACTCAAT 58.585 36.000 0.00 0.00 0.00 2.57
2002 2018 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
2003 2019 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
2004 2020 5.237344 CCATCCGTTCCAAAATAGATGACTC 59.763 44.000 0.00 0.00 32.55 3.36
2005 2021 5.104527 TCCATCCGTTCCAAAATAGATGACT 60.105 40.000 0.00 0.00 32.55 3.41
2006 2022 5.123227 TCCATCCGTTCCAAAATAGATGAC 58.877 41.667 0.00 0.00 32.55 3.06
2007 2023 5.104527 ACTCCATCCGTTCCAAAATAGATGA 60.105 40.000 0.00 0.00 32.55 2.92
2008 2024 5.126067 ACTCCATCCGTTCCAAAATAGATG 58.874 41.667 0.00 0.00 31.49 2.90
2009 2025 5.373812 ACTCCATCCGTTCCAAAATAGAT 57.626 39.130 0.00 0.00 0.00 1.98
2010 2026 4.837093 ACTCCATCCGTTCCAAAATAGA 57.163 40.909 0.00 0.00 0.00 1.98
2011 2027 9.587772 CTATATACTCCATCCGTTCCAAAATAG 57.412 37.037 0.00 0.00 0.00 1.73
2012 2028 9.096823 ACTATATACTCCATCCGTTCCAAAATA 57.903 33.333 0.00 0.00 0.00 1.40
2013 2029 7.974504 ACTATATACTCCATCCGTTCCAAAAT 58.025 34.615 0.00 0.00 0.00 1.82
2014 2030 7.369551 ACTATATACTCCATCCGTTCCAAAA 57.630 36.000 0.00 0.00 0.00 2.44
2015 2031 6.989155 ACTATATACTCCATCCGTTCCAAA 57.011 37.500 0.00 0.00 0.00 3.28
2016 2032 6.989155 AACTATATACTCCATCCGTTCCAA 57.011 37.500 0.00 0.00 0.00 3.53
2017 2033 8.114102 AGATAACTATATACTCCATCCGTTCCA 58.886 37.037 0.00 0.00 0.00 3.53
2018 2034 8.522542 AGATAACTATATACTCCATCCGTTCC 57.477 38.462 0.00 0.00 0.00 3.62
2020 2036 9.529823 TGAAGATAACTATATACTCCATCCGTT 57.470 33.333 0.00 0.00 0.00 4.44
2021 2037 9.529823 TTGAAGATAACTATATACTCCATCCGT 57.470 33.333 0.00 0.00 0.00 4.69
2022 2038 9.790389 GTTGAAGATAACTATATACTCCATCCG 57.210 37.037 0.00 0.00 0.00 4.18
2110 2126 4.992319 CGGTGAAGGTTTGACAACTGTATA 59.008 41.667 0.00 0.00 32.90 1.47
2120 2136 3.823281 TGTTCTACGGTGAAGGTTTGA 57.177 42.857 0.00 0.00 0.00 2.69
2230 2246 0.381801 GAGCCCGGTGCATACAATTG 59.618 55.000 15.92 3.24 44.83 2.32
2231 2247 0.255890 AGAGCCCGGTGCATACAATT 59.744 50.000 15.92 0.00 44.83 2.32
2271 2287 3.502920 TGTTTAACACAAGGCAACAACG 58.497 40.909 0.00 0.00 41.41 4.10
2289 2305 6.041069 GGCACTAGGTAGATGATACTTCTGTT 59.959 42.308 0.00 0.00 0.00 3.16
2304 2320 6.184068 TGCAAAATTAAGATGGCACTAGGTA 58.816 36.000 0.00 0.00 0.00 3.08
2397 2413 8.947115 GGAACTGTTGTATAATAGACTTGCTTT 58.053 33.333 0.00 0.00 0.00 3.51
2415 2431 5.675684 ATGGACAAAAAGTTGGAACTGTT 57.324 34.783 0.00 0.00 38.08 3.16
2461 2477 6.935771 TGCCAACTCTGCAATATTTCAATTTT 59.064 30.769 0.00 0.00 35.40 1.82
2490 2506 6.396450 CCTACTACCCTACTGTTGAGAAAAC 58.604 44.000 0.00 0.00 0.00 2.43
2551 2567 7.728847 AAACAGAAAAGGGAAAATTGTATGC 57.271 32.000 0.00 0.00 0.00 3.14
2634 2651 4.753233 AGCAGCTTGTTACTATGAGACAG 58.247 43.478 0.00 0.00 0.00 3.51
2660 2677 0.320771 TTGGCGAGAGAGGAGCAAAC 60.321 55.000 0.00 0.00 0.00 2.93
2665 2682 2.284190 GGAATTTTGGCGAGAGAGGAG 58.716 52.381 0.00 0.00 0.00 3.69
2956 2974 1.244019 AATGGTGGGCGAACTTCAGC 61.244 55.000 0.00 0.00 0.00 4.26
3179 3197 2.640581 AAAGGCACACAGACCCCACC 62.641 60.000 0.00 0.00 0.00 4.61
3286 3304 5.722021 ATTAACACGGAAAAGCTCCATTT 57.278 34.783 0.00 0.00 45.74 2.32
3362 3380 7.864379 ACAGAAATCAACATGATGAAGAACAAC 59.136 33.333 9.94 0.00 37.15 3.32
3412 3430 8.546597 AAGGCAAAAATATTATGAACCACAAC 57.453 30.769 5.57 0.00 0.00 3.32
3489 3507 6.303054 TCATAACCTTTGGATCAAGTGACAA 58.697 36.000 0.00 0.00 0.00 3.18
3513 3531 8.843262 CATATGTTGAAGTGTCACCATGATTAT 58.157 33.333 0.00 0.00 37.45 1.28
3601 3619 7.785033 TGTCTTCAATATAGATGCAGAACAGA 58.215 34.615 0.00 0.00 0.00 3.41
3613 3667 6.530913 CCATCACGGTTGTCTTCAATATAG 57.469 41.667 0.00 0.00 35.92 1.31
3683 3737 2.439507 TCCTGTCTCCTCAAAGCAAACT 59.560 45.455 0.00 0.00 0.00 2.66
3825 3885 0.599728 TTTGTTTCATTGCGCAGGCC 60.600 50.000 11.31 0.00 38.85 5.19


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

AutoCloner maintained by Alex Coulton.