Multiple sequence alignment - TraesCS1B01G390400

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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 TraesCS1B01G390400 chr1B 100.000 2537 0 0 1 2537 623938987 623936451 0.000000e+00 4686.0
1 TraesCS1B01G390400 chr7A 92.014 1991 120 15 1 1970 141058667 141056695 0.000000e+00 2760.0
2 TraesCS1B01G390400 chr7A 91.834 1996 120 13 1 1970 141653201 141651223 0.000000e+00 2743.0
3 TraesCS1B01G390400 chr7A 91.817 1992 124 13 1 1970 141903941 141901967 0.000000e+00 2739.0
4 TraesCS1B01G390400 chr7A 91.713 1991 121 14 1 1970 140769225 140767258 0.000000e+00 2723.0
5 TraesCS1B01G390400 chr7A 91.562 1991 130 12 1 1970 141312839 141310866 0.000000e+00 2712.0
6 TraesCS1B01G390400 chr7A 90.955 1990 130 12 1 1963 221704689 221706655 0.000000e+00 2632.0
7 TraesCS1B01G390400 chr4A 91.562 1991 130 12 1 1970 588660368 588658395 0.000000e+00 2712.0
8 TraesCS1B01G390400 chr4A 91.587 1676 114 14 1 1663 418073221 418071560 0.000000e+00 2289.0
9 TraesCS1B01G390400 chr3D 91.008 2013 120 21 1 1973 41618799 41616808 0.000000e+00 2658.0
10 TraesCS1B01G390400 chr3D 90.505 2001 136 22 1 1962 449746364 449748349 0.000000e+00 2593.0
11 TraesCS1B01G390400 chr3D 89.824 1985 168 19 1 1963 593766604 593764632 0.000000e+00 2516.0
12 TraesCS1B01G390400 chr3D 87.727 1980 176 38 1 1967 113913575 113911650 0.000000e+00 2248.0
13 TraesCS1B01G390400 chr3D 94.749 1257 54 3 718 1963 6288084 6289339 0.000000e+00 1945.0
14 TraesCS1B01G390400 chr5A 90.250 2000 157 18 1 1967 78332480 78334474 0.000000e+00 2579.0
15 TraesCS1B01G390400 chr4D 87.085 1990 195 28 1 1966 116524789 116522838 0.000000e+00 2194.0
16 TraesCS1B01G390400 chr2D 90.302 1124 76 9 1 1118 645998659 645999755 0.000000e+00 1441.0
17 TraesCS1B01G390400 chr5B 91.333 900 53 13 1080 1963 103528854 103527964 0.000000e+00 1206.0
18 TraesCS1B01G390400 chr1D 86.667 525 51 10 2029 2535 453419951 453419428 4.740000e-157 564.0
19 TraesCS1B01G390400 chr1D 80.663 181 18 12 1964 2132 453474711 453474536 9.530000e-25 124.0
20 TraesCS1B01G390400 chr1D 96.774 31 1 0 2069 2099 454657625 454657655 5.000000e-03 52.8
21 TraesCS1B01G390400 chr1A 79.310 174 30 5 1964 2132 548402080 548401908 1.590000e-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 TraesCS1B01G390400 chr1B 623936451 623938987 2536 True 4686 4686 100.000 1 2537 1 chr1B.!!$R1 2536
1 TraesCS1B01G390400 chr7A 141056695 141058667 1972 True 2760 2760 92.014 1 1970 1 chr7A.!!$R2 1969
2 TraesCS1B01G390400 chr7A 141651223 141653201 1978 True 2743 2743 91.834 1 1970 1 chr7A.!!$R4 1969
3 TraesCS1B01G390400 chr7A 141901967 141903941 1974 True 2739 2739 91.817 1 1970 1 chr7A.!!$R5 1969
4 TraesCS1B01G390400 chr7A 140767258 140769225 1967 True 2723 2723 91.713 1 1970 1 chr7A.!!$R1 1969
5 TraesCS1B01G390400 chr7A 141310866 141312839 1973 True 2712 2712 91.562 1 1970 1 chr7A.!!$R3 1969
6 TraesCS1B01G390400 chr7A 221704689 221706655 1966 False 2632 2632 90.955 1 1963 1 chr7A.!!$F1 1962
7 TraesCS1B01G390400 chr4A 588658395 588660368 1973 True 2712 2712 91.562 1 1970 1 chr4A.!!$R2 1969
8 TraesCS1B01G390400 chr4A 418071560 418073221 1661 True 2289 2289 91.587 1 1663 1 chr4A.!!$R1 1662
9 TraesCS1B01G390400 chr3D 41616808 41618799 1991 True 2658 2658 91.008 1 1973 1 chr3D.!!$R1 1972
10 TraesCS1B01G390400 chr3D 449746364 449748349 1985 False 2593 2593 90.505 1 1962 1 chr3D.!!$F2 1961
11 TraesCS1B01G390400 chr3D 593764632 593766604 1972 True 2516 2516 89.824 1 1963 1 chr3D.!!$R3 1962
12 TraesCS1B01G390400 chr3D 113911650 113913575 1925 True 2248 2248 87.727 1 1967 1 chr3D.!!$R2 1966
13 TraesCS1B01G390400 chr3D 6288084 6289339 1255 False 1945 1945 94.749 718 1963 1 chr3D.!!$F1 1245
14 TraesCS1B01G390400 chr5A 78332480 78334474 1994 False 2579 2579 90.250 1 1967 1 chr5A.!!$F1 1966
15 TraesCS1B01G390400 chr4D 116522838 116524789 1951 True 2194 2194 87.085 1 1966 1 chr4D.!!$R1 1965
16 TraesCS1B01G390400 chr2D 645998659 645999755 1096 False 1441 1441 90.302 1 1118 1 chr2D.!!$F1 1117
17 TraesCS1B01G390400 chr5B 103527964 103528854 890 True 1206 1206 91.333 1080 1963 1 chr5B.!!$R1 883
18 TraesCS1B01G390400 chr1D 453419428 453419951 523 True 564 564 86.667 2029 2535 1 chr1D.!!$R1 506

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
600 656 0.250234 TCGCTGGGTCAAGAATCAGG 59.75 55.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1989 2110 0.110486 TTGACCTCTTGACCTTGGGC 59.89 55.0 0.0 0.0 0.0 5.36 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
41 42 2.293122 CGACATGCAGAACTTTTTCCCA 59.707 45.455 0.00 0.00 31.28 4.37
82 87 2.683916 TCCACAGCGGAGGAGAATT 58.316 52.632 0.00 0.00 39.64 2.17
90 95 1.408822 GCGGAGGAGAATTGGGAACAT 60.409 52.381 0.00 0.00 42.32 2.71
101 106 8.437575 GGAGAATTGGGAACATAGGTAGATAAA 58.562 37.037 0.00 0.00 42.32 1.40
157 194 5.478407 TCAAACTAGTTCATGCAAGATCGA 58.522 37.500 8.95 0.00 0.00 3.59
289 334 3.277715 CTGGCCTTCATCTTCTTCTTCC 58.722 50.000 3.32 0.00 0.00 3.46
327 375 2.748647 TCATCGTCGTCCTCGGCA 60.749 61.111 0.00 0.00 42.21 5.69
353 401 1.271102 GAGGTCGATCTGCCAGGTATC 59.729 57.143 0.91 0.00 0.00 2.24
399 450 1.300971 GCATCTGCACCGCTTCTTCA 61.301 55.000 0.00 0.00 41.59 3.02
418 469 0.575333 ATCCTCCTTAGGCTCCCCAT 59.425 55.000 0.00 0.00 43.31 4.00
526 578 6.206634 CACCACTTCTTCCTTTGTTTAGCATA 59.793 38.462 0.00 0.00 0.00 3.14
537 589 4.794278 TGTTTAGCATAGTTGGAGACGA 57.206 40.909 0.00 0.00 0.00 4.20
541 593 3.014304 AGCATAGTTGGAGACGACCTA 57.986 47.619 0.00 0.00 46.68 3.08
600 656 0.250234 TCGCTGGGTCAAGAATCAGG 59.750 55.000 0.00 0.00 0.00 3.86
637 693 1.065926 CAGTGGCCTTCATGAGCACTA 60.066 52.381 3.32 0.00 30.49 2.74
737 795 4.779733 AGCCGACCACCCGAGGAT 62.780 66.667 0.00 0.00 0.00 3.24
908 967 2.380249 TGGAGAGGAGGAGAAGAGTGAA 59.620 50.000 0.00 0.00 0.00 3.18
928 987 6.261381 AGTGAAAGTCATGCCGTTTTAACTAA 59.739 34.615 0.00 0.00 0.00 2.24
1013 1072 0.917533 AGAGCAATGAGATGGGCACT 59.082 50.000 0.00 0.00 0.00 4.40
1174 1243 3.691049 GCAACAAGCACTTCAACTACA 57.309 42.857 0.00 0.00 44.79 2.74
1290 1360 4.893601 TTCGTTGCGGTGCCGACA 62.894 61.111 15.45 9.03 42.83 4.35
1489 1559 1.548719 ACGACGATGGAATTGAGGTCA 59.451 47.619 0.00 0.00 0.00 4.02
1490 1560 1.927174 CGACGATGGAATTGAGGTCAC 59.073 52.381 0.00 0.00 0.00 3.67
1602 1684 9.776158 CTGTTTATGTTTATGGTTTATGCGTAA 57.224 29.630 0.00 0.00 0.00 3.18
1680 1800 4.202192 CCTCTGCTCTGCTTATGATGTGTA 60.202 45.833 0.00 0.00 0.00 2.90
1739 1860 4.394729 CAACTAGCCAAAGAGGTTACCAA 58.605 43.478 3.51 0.00 40.61 3.67
1856 1977 1.001248 AAGAGGGCATGCAGGCAAT 59.999 52.632 26.25 12.77 46.44 3.56
1966 2087 1.858372 GCAACCAAACACGCCCGTAT 61.858 55.000 0.00 0.00 0.00 3.06
1970 2091 1.283736 CCAAACACGCCCGTATAGAC 58.716 55.000 0.00 0.00 0.00 2.59
1971 2092 1.134907 CCAAACACGCCCGTATAGACT 60.135 52.381 0.00 0.00 0.00 3.24
1972 2093 2.613691 CAAACACGCCCGTATAGACTT 58.386 47.619 0.00 0.00 0.00 3.01
1973 2094 2.997986 CAAACACGCCCGTATAGACTTT 59.002 45.455 0.00 0.00 0.00 2.66
1974 2095 2.288961 ACACGCCCGTATAGACTTTG 57.711 50.000 0.00 0.00 0.00 2.77
1975 2096 0.928229 CACGCCCGTATAGACTTTGC 59.072 55.000 0.00 0.00 0.00 3.68
1976 2097 0.179092 ACGCCCGTATAGACTTTGCC 60.179 55.000 0.00 0.00 0.00 4.52
1977 2098 0.179094 CGCCCGTATAGACTTTGCCA 60.179 55.000 0.00 0.00 0.00 4.92
1978 2099 1.296727 GCCCGTATAGACTTTGCCAC 58.703 55.000 0.00 0.00 0.00 5.01
1979 2100 1.406341 GCCCGTATAGACTTTGCCACA 60.406 52.381 0.00 0.00 0.00 4.17
1980 2101 2.277084 CCCGTATAGACTTTGCCACAC 58.723 52.381 0.00 0.00 0.00 3.82
1981 2102 2.093658 CCCGTATAGACTTTGCCACACT 60.094 50.000 0.00 0.00 0.00 3.55
1982 2103 2.930040 CCGTATAGACTTTGCCACACTG 59.070 50.000 0.00 0.00 0.00 3.66
1983 2104 2.348666 CGTATAGACTTTGCCACACTGC 59.651 50.000 0.00 0.00 0.00 4.40
1984 2105 1.826385 ATAGACTTTGCCACACTGCC 58.174 50.000 0.00 0.00 0.00 4.85
1985 2106 0.472044 TAGACTTTGCCACACTGCCA 59.528 50.000 0.00 0.00 0.00 4.92
1986 2107 0.395586 AGACTTTGCCACACTGCCAA 60.396 50.000 0.00 0.00 0.00 4.52
1987 2108 0.031178 GACTTTGCCACACTGCCAAG 59.969 55.000 0.00 0.00 39.27 3.61
1988 2109 0.684153 ACTTTGCCACACTGCCAAGT 60.684 50.000 0.00 0.00 41.01 3.16
1995 2116 3.045142 CACTGCCAAGTGCCCAAG 58.955 61.111 0.00 0.00 46.98 3.61
1996 2117 2.203538 ACTGCCAAGTGCCCAAGG 60.204 61.111 0.00 0.00 40.16 3.61
1997 2118 2.203538 CTGCCAAGTGCCCAAGGT 60.204 61.111 0.00 0.00 40.16 3.50
1998 2119 2.203480 TGCCAAGTGCCCAAGGTC 60.203 61.111 0.00 0.00 40.16 3.85
1999 2120 2.203480 GCCAAGTGCCCAAGGTCA 60.203 61.111 0.00 0.00 0.00 4.02
2000 2121 1.832167 GCCAAGTGCCCAAGGTCAA 60.832 57.895 0.00 0.00 0.00 3.18
2001 2122 1.809567 GCCAAGTGCCCAAGGTCAAG 61.810 60.000 0.00 0.00 0.00 3.02
2002 2123 0.178992 CCAAGTGCCCAAGGTCAAGA 60.179 55.000 0.00 0.00 0.00 3.02
2003 2124 1.242076 CAAGTGCCCAAGGTCAAGAG 58.758 55.000 0.00 0.00 0.00 2.85
2004 2125 0.111253 AAGTGCCCAAGGTCAAGAGG 59.889 55.000 0.00 0.00 0.00 3.69
2005 2126 1.062488 AGTGCCCAAGGTCAAGAGGT 61.062 55.000 0.00 0.00 0.00 3.85
2006 2127 0.606673 GTGCCCAAGGTCAAGAGGTC 60.607 60.000 0.00 0.00 0.00 3.85
2007 2128 1.059584 TGCCCAAGGTCAAGAGGTCA 61.060 55.000 0.00 0.00 0.00 4.02
2008 2129 0.110486 GCCCAAGGTCAAGAGGTCAA 59.890 55.000 0.00 0.00 0.00 3.18
2009 2130 1.897560 CCCAAGGTCAAGAGGTCAAC 58.102 55.000 0.00 0.00 0.00 3.18
2010 2131 1.545651 CCCAAGGTCAAGAGGTCAACC 60.546 57.143 0.00 0.00 0.00 3.77
2011 2132 1.142870 CCAAGGTCAAGAGGTCAACCA 59.857 52.381 1.33 0.00 38.89 3.67
2012 2133 2.222027 CAAGGTCAAGAGGTCAACCAC 58.778 52.381 1.33 0.00 38.89 4.16
2013 2134 1.507140 AGGTCAAGAGGTCAACCACA 58.493 50.000 1.33 0.00 38.89 4.17
2014 2135 1.843851 AGGTCAAGAGGTCAACCACAA 59.156 47.619 1.33 0.00 38.89 3.33
2015 2136 2.158755 AGGTCAAGAGGTCAACCACAAG 60.159 50.000 1.33 0.00 38.89 3.16
2016 2137 2.222027 GTCAAGAGGTCAACCACAAGG 58.778 52.381 1.33 0.00 38.89 3.61
2043 2164 3.955650 CCGGGGTGGTAGATACTATTG 57.044 52.381 0.00 0.00 0.00 1.90
2052 2173 7.839705 GGGTGGTAGATACTATTGGATCTATCA 59.160 40.741 15.85 15.85 41.40 2.15
2065 2186 4.192317 GGATCTATCAACTTTTCACCGCT 58.808 43.478 0.00 0.00 0.00 5.52
2073 2194 0.868406 CTTTTCACCGCTCTCCACAC 59.132 55.000 0.00 0.00 0.00 3.82
2078 2199 2.740055 CCGCTCTCCACACAGTGC 60.740 66.667 0.00 0.00 31.34 4.40
2107 2228 4.332268 GTCAAGAGATCAACTGGAATCAGC 59.668 45.833 0.00 0.00 44.59 4.26
2137 2258 7.393515 GGAAAATAGGAGTACAAGTGGTTGAAT 59.606 37.037 0.00 0.00 37.10 2.57
2141 2262 9.975218 AATAGGAGTACAAGTGGTTGAATTAAT 57.025 29.630 0.00 0.00 37.10 1.40
2166 2287 3.699025 TTTGGAAAAGGGGAAAGACCT 57.301 42.857 0.00 0.00 40.96 3.85
2171 2292 1.134438 AAAGGGGAAAGACCTCGGCT 61.134 55.000 0.00 0.00 45.50 5.52
2179 2300 0.326264 AAGACCTCGGCTTCTGCATT 59.674 50.000 0.00 0.00 41.91 3.56
2196 2321 4.530710 GCATTATCATGATGCACCCATT 57.469 40.909 18.72 0.00 46.96 3.16
2200 2325 6.740401 GCATTATCATGATGCACCCATTTTCT 60.740 38.462 18.72 0.00 46.96 2.52
2201 2326 6.795144 TTATCATGATGCACCCATTTTCTT 57.205 33.333 18.72 0.00 0.00 2.52
2203 2328 6.795144 ATCATGATGCACCCATTTTCTTTA 57.205 33.333 7.59 0.00 0.00 1.85
2206 2331 8.303780 TCATGATGCACCCATTTTCTTTATTA 57.696 30.769 0.00 0.00 0.00 0.98
2209 2334 9.956640 ATGATGCACCCATTTTCTTTATTAAAA 57.043 25.926 0.00 0.00 0.00 1.52
2253 2389 6.425417 TCATATCAACTAACACGACAAAAGCA 59.575 34.615 0.00 0.00 0.00 3.91
2258 2394 6.306837 TCAACTAACACGACAAAAGCAAAAAG 59.693 34.615 0.00 0.00 0.00 2.27
2259 2395 5.945155 ACTAACACGACAAAAGCAAAAAGA 58.055 33.333 0.00 0.00 0.00 2.52
2260 2396 6.383415 ACTAACACGACAAAAGCAAAAAGAA 58.617 32.000 0.00 0.00 0.00 2.52
2263 2399 5.911421 ACACGACAAAAGCAAAAAGAAAAC 58.089 33.333 0.00 0.00 0.00 2.43
2264 2400 5.463724 ACACGACAAAAGCAAAAAGAAAACA 59.536 32.000 0.00 0.00 0.00 2.83
2265 2401 6.147000 ACACGACAAAAGCAAAAAGAAAACAT 59.853 30.769 0.00 0.00 0.00 2.71
2267 2403 6.367422 ACGACAAAAGCAAAAAGAAAACATCA 59.633 30.769 0.00 0.00 0.00 3.07
2268 2404 6.678245 CGACAAAAGCAAAAAGAAAACATCAC 59.322 34.615 0.00 0.00 0.00 3.06
2269 2405 7.432350 ACAAAAGCAAAAAGAAAACATCACA 57.568 28.000 0.00 0.00 0.00 3.58
2271 2407 7.802720 ACAAAAGCAAAAAGAAAACATCACAAC 59.197 29.630 0.00 0.00 0.00 3.32
2273 2409 6.651755 AGCAAAAAGAAAACATCACAACTG 57.348 33.333 0.00 0.00 0.00 3.16
2274 2410 6.165577 AGCAAAAAGAAAACATCACAACTGT 58.834 32.000 0.00 0.00 0.00 3.55
2275 2411 6.091169 AGCAAAAAGAAAACATCACAACTGTG 59.909 34.615 3.33 3.33 46.91 3.66
2276 2412 6.672836 GCAAAAAGAAAACATCACAACTGTGG 60.673 38.462 9.87 0.00 45.65 4.17
2277 2413 5.913137 AAAGAAAACATCACAACTGTGGA 57.087 34.783 9.87 0.00 45.65 4.02
2333 2471 6.849085 AATTTATTACTGACATGCCAACCA 57.151 33.333 0.00 0.00 0.00 3.67
2336 2474 4.789012 ATTACTGACATGCCAACCAAAG 57.211 40.909 0.00 0.00 0.00 2.77
2352 2490 2.352323 CCAAAGCGGTTGAATAACACCC 60.352 50.000 0.00 0.00 39.87 4.61
2360 2498 1.240256 TGAATAACACCCGTGCAACC 58.760 50.000 0.00 0.00 0.00 3.77
2365 2503 0.889186 AACACCCGTGCAACCATCTC 60.889 55.000 0.00 0.00 0.00 2.75
2368 2506 1.746615 CCCGTGCAACCATCTCCAG 60.747 63.158 0.00 0.00 0.00 3.86
2371 2509 1.354337 CGTGCAACCATCTCCAGACG 61.354 60.000 0.00 0.00 0.00 4.18
2397 2535 6.978080 GTCAAATTAAACTTGTGAAGAGCCAA 59.022 34.615 0.00 0.00 0.00 4.52
2404 2542 4.523083 ACTTGTGAAGAGCCAAAACTACA 58.477 39.130 0.00 0.00 0.00 2.74
2418 2556 5.179555 CCAAAACTACAGTGGCTAAGAGAAC 59.820 44.000 0.00 0.00 0.00 3.01
2428 2566 1.475930 GCTAAGAGAACCATGGCTCCC 60.476 57.143 13.04 0.00 0.00 4.30
2440 2578 1.380302 GGCTCCCATGTTGGTCTGT 59.620 57.895 0.00 0.00 35.17 3.41
2442 2580 1.168714 GCTCCCATGTTGGTCTGTTC 58.831 55.000 0.00 0.00 35.17 3.18
2462 2600 4.436242 TCTATCTGTCAAACTGTCGTCC 57.564 45.455 0.00 0.00 0.00 4.79
2464 2602 2.971660 TCTGTCAAACTGTCGTCCAA 57.028 45.000 0.00 0.00 0.00 3.53
2472 2610 0.036952 ACTGTCGTCCAATGCTCCAG 60.037 55.000 0.00 0.00 0.00 3.86
2476 2614 2.440980 GTCCAATGCTCCAGGGCC 60.441 66.667 0.00 0.00 0.00 5.80
2477 2615 2.614969 TCCAATGCTCCAGGGCCT 60.615 61.111 0.00 0.00 0.00 5.19
2490 2628 3.222121 GGCCTGCTATGCTTGGGC 61.222 66.667 0.00 11.05 39.69 5.36
2503 2641 0.321564 CTTGGGCACTCATGGACGAA 60.322 55.000 0.00 0.00 0.00 3.85
2510 2648 3.557595 GGCACTCATGGACGAAAATCTAG 59.442 47.826 0.00 0.00 0.00 2.43
2535 2673 6.254589 GCTGAGCATATAGTTATGAACGGATC 59.745 42.308 0.00 0.00 37.94 3.36
2536 2674 6.322491 TGAGCATATAGTTATGAACGGATCG 58.678 40.000 0.00 0.00 37.94 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.612717 GCATGTCGAACAGAGAGAAGTGA 60.613 47.826 0.00 0.00 0.00 3.41
41 42 2.492088 TGAATCTATCGCCGGATCGAAT 59.508 45.455 5.05 0.00 42.15 3.34
77 82 8.778059 TGTTTATCTACCTATGTTCCCAATTCT 58.222 33.333 0.00 0.00 0.00 2.40
82 87 7.236847 CCCTATGTTTATCTACCTATGTTCCCA 59.763 40.741 0.00 0.00 0.00 4.37
90 95 8.513658 TGAACTACCCCTATGTTTATCTACCTA 58.486 37.037 0.00 0.00 0.00 3.08
101 106 7.359849 TGAACTAGTATGAACTACCCCTATGT 58.640 38.462 0.00 0.00 37.15 2.29
373 421 1.450848 CGGTGCAGATGCCAGTGAT 60.451 57.895 1.72 0.00 41.18 3.06
418 469 2.434185 GCTGTCGGCGGTCATTGA 60.434 61.111 7.21 0.00 0.00 2.57
526 578 4.383118 CCATGAATTAGGTCGTCTCCAACT 60.383 45.833 0.00 0.00 0.00 3.16
537 589 5.715439 TCATTCTGGACCATGAATTAGGT 57.285 39.130 13.41 0.00 41.83 3.08
541 593 5.512298 TGACATCATTCTGGACCATGAATT 58.488 37.500 13.41 3.65 33.13 2.17
592 648 2.831565 AGAGCTGAAGACCCTGATTCT 58.168 47.619 0.00 0.00 0.00 2.40
758 817 2.852281 GCCAACCCCTTCCCTTGGA 61.852 63.158 0.00 0.00 37.25 3.53
800 859 3.332393 TTCCTCCTCCCCATCGCCT 62.332 63.158 0.00 0.00 0.00 5.52
908 967 5.861787 GCATTTAGTTAAAACGGCATGACTT 59.138 36.000 0.00 0.00 33.22 3.01
928 987 5.655532 AGTTCATGGCTTATTGAAGAGCATT 59.344 36.000 5.83 0.00 40.63 3.56
1025 1084 2.193536 GCCCTTGTTGTCAACGGCT 61.194 57.895 19.95 0.00 45.50 5.52
1166 1235 4.020573 CCTGATGGTAGTGGTTGTAGTTGA 60.021 45.833 0.00 0.00 0.00 3.18
1174 1243 2.642171 TCCTCCTGATGGTAGTGGTT 57.358 50.000 0.00 0.00 34.23 3.67
1290 1360 3.118261 TGTTGTTCCTGAGCTTGAACTCT 60.118 43.478 19.17 0.00 41.10 3.24
1489 1559 2.030562 CTTCCCGCACTTGTCGGT 59.969 61.111 10.01 0.00 45.09 4.69
1490 1560 3.423154 GCTTCCCGCACTTGTCGG 61.423 66.667 5.44 5.44 46.05 4.79
1602 1684 7.732996 AGTAGTACCACACTTCATAACAGTTT 58.267 34.615 0.00 0.00 38.80 2.66
1680 1800 1.071699 ACTTCGGCACAACCATGTAGT 59.928 47.619 0.00 0.00 37.82 2.73
1739 1860 0.536233 TGTATGCAACGCCTGGTGTT 60.536 50.000 19.45 19.45 36.66 3.32
1835 1956 2.361992 CCTGCATGCCCTCTTGCA 60.362 61.111 16.68 5.87 46.78 4.08
1856 1977 2.288334 GCACCATCTGCATGTTGTTTGA 60.288 45.455 0.00 0.00 46.29 2.69
1904 2025 2.833943 TGCATAGCCTTCTCAACTCAGA 59.166 45.455 0.00 0.00 0.00 3.27
1966 2087 3.322514 GGCAGTGTGGCAAAGTCTA 57.677 52.632 0.00 0.00 43.14 2.59
1982 2103 1.809567 CTTGACCTTGGGCACTTGGC 61.810 60.000 0.00 0.00 43.74 4.52
1983 2104 0.178992 TCTTGACCTTGGGCACTTGG 60.179 55.000 0.00 0.00 0.00 3.61
1984 2105 1.242076 CTCTTGACCTTGGGCACTTG 58.758 55.000 0.00 0.00 0.00 3.16
1985 2106 0.111253 CCTCTTGACCTTGGGCACTT 59.889 55.000 0.00 0.00 0.00 3.16
1986 2107 1.062488 ACCTCTTGACCTTGGGCACT 61.062 55.000 0.00 0.00 0.00 4.40
1987 2108 0.606673 GACCTCTTGACCTTGGGCAC 60.607 60.000 0.00 0.00 0.00 5.01
1988 2109 1.059584 TGACCTCTTGACCTTGGGCA 61.060 55.000 0.00 0.00 34.84 5.36
1989 2110 0.110486 TTGACCTCTTGACCTTGGGC 59.890 55.000 0.00 0.00 0.00 5.36
1990 2111 1.545651 GGTTGACCTCTTGACCTTGGG 60.546 57.143 0.00 0.00 0.00 4.12
1991 2112 1.142870 TGGTTGACCTCTTGACCTTGG 59.857 52.381 1.34 0.00 36.82 3.61
1992 2113 2.222027 GTGGTTGACCTCTTGACCTTG 58.778 52.381 1.34 0.00 36.82 3.61
1993 2114 1.843851 TGTGGTTGACCTCTTGACCTT 59.156 47.619 1.34 0.00 36.82 3.50
1994 2115 1.507140 TGTGGTTGACCTCTTGACCT 58.493 50.000 1.34 0.00 36.82 3.85
1995 2116 2.222027 CTTGTGGTTGACCTCTTGACC 58.778 52.381 1.34 0.00 36.82 4.02
1996 2117 2.222027 CCTTGTGGTTGACCTCTTGAC 58.778 52.381 1.34 0.00 36.82 3.18
1997 2118 1.843851 ACCTTGTGGTTGACCTCTTGA 59.156 47.619 1.34 0.00 46.05 3.02
1998 2119 2.348411 ACCTTGTGGTTGACCTCTTG 57.652 50.000 1.34 0.00 46.05 3.02
1999 2120 3.181443 CCTTACCTTGTGGTTGACCTCTT 60.181 47.826 1.34 0.00 46.05 2.85
2000 2121 2.372172 CCTTACCTTGTGGTTGACCTCT 59.628 50.000 1.34 0.00 46.05 3.69
2001 2122 2.370849 TCCTTACCTTGTGGTTGACCTC 59.629 50.000 1.34 0.00 46.05 3.85
2002 2123 2.105993 GTCCTTACCTTGTGGTTGACCT 59.894 50.000 1.34 0.00 46.05 3.85
2003 2124 2.501261 GTCCTTACCTTGTGGTTGACC 58.499 52.381 0.00 0.00 46.05 4.02
2004 2125 2.501261 GGTCCTTACCTTGTGGTTGAC 58.499 52.381 0.00 0.00 46.05 3.18
2005 2126 1.071071 CGGTCCTTACCTTGTGGTTGA 59.929 52.381 0.00 0.00 46.05 3.18
2006 2127 1.519408 CGGTCCTTACCTTGTGGTTG 58.481 55.000 0.00 0.00 46.05 3.77
2007 2128 0.399075 CCGGTCCTTACCTTGTGGTT 59.601 55.000 0.00 0.00 46.05 3.67
2009 2130 1.298667 CCCGGTCCTTACCTTGTGG 59.701 63.158 0.00 0.00 44.35 4.17
2010 2131 1.298667 CCCCGGTCCTTACCTTGTG 59.701 63.158 0.00 0.00 44.35 3.33
2011 2132 1.151965 ACCCCGGTCCTTACCTTGT 60.152 57.895 0.00 0.00 44.35 3.16
2012 2133 1.298667 CACCCCGGTCCTTACCTTG 59.701 63.158 0.00 0.00 44.35 3.61
2013 2134 1.921857 CCACCCCGGTCCTTACCTT 60.922 63.158 0.00 0.00 44.35 3.50
2014 2135 2.285144 CCACCCCGGTCCTTACCT 60.285 66.667 0.00 0.00 44.35 3.08
2023 2144 2.565834 CCAATAGTATCTACCACCCCGG 59.434 54.545 0.00 0.00 42.50 5.73
2024 2145 3.503365 TCCAATAGTATCTACCACCCCG 58.497 50.000 0.00 0.00 0.00 5.73
2025 2146 5.342866 AGATCCAATAGTATCTACCACCCC 58.657 45.833 0.00 0.00 30.65 4.95
2026 2147 7.839705 TGATAGATCCAATAGTATCTACCACCC 59.160 40.741 0.00 0.00 37.49 4.61
2027 2148 8.824756 TGATAGATCCAATAGTATCTACCACC 57.175 38.462 0.00 0.00 37.49 4.61
2043 2164 4.192317 AGCGGTGAAAAGTTGATAGATCC 58.808 43.478 0.00 0.00 0.00 3.36
2052 2173 1.134220 TGTGGAGAGCGGTGAAAAGTT 60.134 47.619 0.00 0.00 0.00 2.66
2057 2178 1.367471 CTGTGTGGAGAGCGGTGAA 59.633 57.895 0.00 0.00 0.00 3.18
2065 2186 1.451504 CTTGGGCACTGTGTGGAGA 59.548 57.895 9.86 0.00 33.64 3.71
2073 2194 0.397941 TCTCTTGACCTTGGGCACTG 59.602 55.000 0.00 0.00 0.00 3.66
2078 2199 3.341823 CAGTTGATCTCTTGACCTTGGG 58.658 50.000 0.00 0.00 0.00 4.12
2107 2228 4.330074 CACTTGTACTCCTATTTTCCGCTG 59.670 45.833 0.00 0.00 0.00 5.18
2156 2277 0.391793 CAGAAGCCGAGGTCTTTCCC 60.392 60.000 0.00 0.00 36.75 3.97
2159 2280 0.326264 ATGCAGAAGCCGAGGTCTTT 59.674 50.000 0.00 0.00 41.13 2.52
2166 2287 3.473923 TCATGATAATGCAGAAGCCGA 57.526 42.857 0.00 0.00 41.13 5.54
2179 2300 6.795144 AAAGAAAATGGGTGCATCATGATA 57.205 33.333 8.15 0.00 0.00 2.15
2209 2334 8.328758 TGATATGATGTACTTCTTGGACCTTTT 58.671 33.333 9.87 0.00 0.00 2.27
2213 2338 7.275920 AGTTGATATGATGTACTTCTTGGACC 58.724 38.462 9.87 0.00 0.00 4.46
2214 2339 9.817809 TTAGTTGATATGATGTACTTCTTGGAC 57.182 33.333 9.87 2.72 0.00 4.02
2215 2340 9.817809 GTTAGTTGATATGATGTACTTCTTGGA 57.182 33.333 9.87 0.00 0.00 3.53
2216 2341 9.599866 TGTTAGTTGATATGATGTACTTCTTGG 57.400 33.333 9.87 0.00 0.00 3.61
2219 2344 8.683615 TCGTGTTAGTTGATATGATGTACTTCT 58.316 33.333 9.87 0.00 0.00 2.85
2220 2345 8.744011 GTCGTGTTAGTTGATATGATGTACTTC 58.256 37.037 1.85 1.85 0.00 3.01
2224 2360 8.989653 TTTGTCGTGTTAGTTGATATGATGTA 57.010 30.769 0.00 0.00 0.00 2.29
2230 2366 6.795098 TGCTTTTGTCGTGTTAGTTGATAT 57.205 33.333 0.00 0.00 0.00 1.63
2233 2369 4.948608 TTGCTTTTGTCGTGTTAGTTGA 57.051 36.364 0.00 0.00 0.00 3.18
2267 2403 9.912634 CAATTTTTCTATTGTATCCACAGTTGT 57.087 29.630 0.00 0.00 35.67 3.32
2268 2404 8.863049 GCAATTTTTCTATTGTATCCACAGTTG 58.137 33.333 0.00 0.00 37.72 3.16
2269 2405 8.584157 TGCAATTTTTCTATTGTATCCACAGTT 58.416 29.630 0.00 0.00 37.72 3.16
2271 2407 9.027129 CATGCAATTTTTCTATTGTATCCACAG 57.973 33.333 0.00 0.00 38.32 3.66
2273 2409 9.023967 GTCATGCAATTTTTCTATTGTATCCAC 57.976 33.333 0.00 0.00 38.32 4.02
2274 2410 8.970020 AGTCATGCAATTTTTCTATTGTATCCA 58.030 29.630 0.00 0.00 38.32 3.41
2275 2411 9.807649 AAGTCATGCAATTTTTCTATTGTATCC 57.192 29.630 0.00 0.00 38.32 2.59
2304 2442 7.939782 TGGCATGTCAGTAATAAATTATGTGG 58.060 34.615 0.00 0.00 0.00 4.17
2319 2457 0.387622 CGCTTTGGTTGGCATGTCAG 60.388 55.000 0.00 0.00 0.00 3.51
2352 2490 1.354337 CGTCTGGAGATGGTTGCACG 61.354 60.000 0.00 0.00 0.00 5.34
2360 2498 5.643777 AGTTTAATTTGACCGTCTGGAGATG 59.356 40.000 0.00 0.00 39.21 2.90
2365 2503 5.008217 TCACAAGTTTAATTTGACCGTCTGG 59.992 40.000 7.19 0.00 42.84 3.86
2368 2506 6.721321 TCTTCACAAGTTTAATTTGACCGTC 58.279 36.000 7.19 0.00 0.00 4.79
2371 2509 5.920840 GGCTCTTCACAAGTTTAATTTGACC 59.079 40.000 7.19 0.00 0.00 4.02
2397 2535 4.347000 TGGTTCTCTTAGCCACTGTAGTTT 59.653 41.667 0.00 0.00 32.74 2.66
2404 2542 1.065126 GCCATGGTTCTCTTAGCCACT 60.065 52.381 14.67 0.00 41.87 4.00
2428 2566 5.482006 TGACAGATAGAACAGACCAACATG 58.518 41.667 0.00 0.00 0.00 3.21
2440 2578 4.279922 TGGACGACAGTTTGACAGATAGAA 59.720 41.667 0.00 0.00 0.00 2.10
2442 2580 4.174411 TGGACGACAGTTTGACAGATAG 57.826 45.455 0.00 0.00 0.00 2.08
2462 2600 2.274948 TAGCAGGCCCTGGAGCATTG 62.275 60.000 13.78 1.39 31.21 2.82
2464 2602 1.773391 ATAGCAGGCCCTGGAGCAT 60.773 57.895 13.78 0.00 31.21 3.79
2472 2610 2.520260 CCCAAGCATAGCAGGCCC 60.520 66.667 0.00 0.00 0.00 5.80
2490 2628 4.269603 CAGCTAGATTTTCGTCCATGAGTG 59.730 45.833 0.00 0.00 0.00 3.51
2510 2648 5.470368 TCCGTTCATAACTATATGCTCAGC 58.530 41.667 0.00 0.00 39.04 4.26


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

AutoCloner maintained by Alex Coulton.