Multiple sequence alignment - TraesCS6B01G277600

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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 TraesCS6B01G277600 chr6B 100.000 3243 0 0 1 3243 502485438 502482196 0.000000e+00 5989.0
1 TraesCS6B01G277600 chr6D 94.926 1813 61 16 1 1807 320227139 320228926 0.000000e+00 2809.0
2 TraesCS6B01G277600 chr6D 96.796 905 25 3 1903 2807 320228988 320229888 0.000000e+00 1507.0
3 TraesCS6B01G277600 chr6D 89.394 132 12 1 2806 2935 320230137 320230268 7.200000e-37 165.0
4 TraesCS6B01G277600 chr6D 95.714 70 3 0 3172 3241 320232600 320232669 2.640000e-21 113.0
5 TraesCS6B01G277600 chr6A 94.090 846 38 10 1970 2807 457686835 457687676 0.000000e+00 1275.0
6 TraesCS6B01G277600 chr6A 94.756 820 35 5 1 816 457684566 457685381 0.000000e+00 1269.0
7 TraesCS6B01G277600 chr6A 90.619 970 72 11 860 1816 457685763 457686726 0.000000e+00 1269.0
8 TraesCS6B01G277600 chr6A 91.116 439 29 6 2806 3241 457687914 457688345 1.300000e-163 586.0
9 TraesCS6B01G277600 chr6A 97.826 46 1 0 1911 1956 457686794 457686839 2.680000e-11 80.5
10 TraesCS6B01G277600 chr2D 83.333 276 44 2 1016 1290 523028490 523028764 1.490000e-63 254.0
11 TraesCS6B01G277600 chr2D 76.033 242 54 4 1051 1290 220670866 220671105 4.390000e-24 122.0
12 TraesCS6B01G277600 chr2B 83.273 275 46 0 1016 1290 616934591 616934865 1.490000e-63 254.0
13 TraesCS6B01G277600 chr2B 87.261 157 18 2 2089 2244 616934971 616935126 9.250000e-41 178.0
14 TraesCS6B01G277600 chr2B 76.033 242 52 6 1052 1290 290519758 290519996 1.580000e-23 121.0
15 TraesCS6B01G277600 chr2A 83.333 276 44 2 1016 1290 668242743 668243017 1.490000e-63 254.0
16 TraesCS6B01G277600 chr2A 87.179 156 20 0 2089 2244 668243106 668243261 9.250000e-41 178.0
17 TraesCS6B01G277600 chr4D 84.211 95 15 0 1197 1291 387441858 387441952 3.450000e-15 93.5
18 TraesCS6B01G277600 chr4B 84.211 95 15 0 1197 1291 475811323 475811417 3.450000e-15 93.5
19 TraesCS6B01G277600 chr4A 84.211 95 15 0 1197 1291 68689450 68689544 3.450000e-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 TraesCS6B01G277600 chr6B 502482196 502485438 3242 True 5989.0 5989 100.0000 1 3243 1 chr6B.!!$R1 3242
1 TraesCS6B01G277600 chr6D 320227139 320232669 5530 False 1148.5 2809 94.2075 1 3241 4 chr6D.!!$F1 3240
2 TraesCS6B01G277600 chr6A 457684566 457688345 3779 False 895.9 1275 93.6814 1 3241 5 chr6A.!!$F1 3240
3 TraesCS6B01G277600 chr2B 616934591 616935126 535 False 216.0 254 85.2670 1016 2244 2 chr2B.!!$F2 1228
4 TraesCS6B01G277600 chr2A 668242743 668243261 518 False 216.0 254 85.2560 1016 2244 2 chr2A.!!$F1 1228

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
63 64 0.471191 CCATGCAGGCTGGATAGACA 59.529 55.0 21.56 6.95 35.70 3.41 F
1849 2206 0.108041 AATGAATCGGCGGTTACGGT 60.108 50.0 4.89 0.00 41.36 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1871 2228 0.039256 TGTGTACAGACCGTAACCGC 60.039 55.0 0.0 0.0 0.0 5.68 R
2822 3509 0.105760 AGGAGATGCTGTCCGAGGAT 60.106 55.0 0.0 0.0 39.3 3.24 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
63 64 0.471191 CCATGCAGGCTGGATAGACA 59.529 55.000 21.56 6.95 35.70 3.41
93 94 2.031314 CAGCTATTTGAGGACATGCGTG 59.969 50.000 3.82 3.82 0.00 5.34
180 181 1.413808 GGAGGATCAAGGAGGCCTACT 60.414 57.143 13.46 13.46 36.25 2.57
182 183 1.008938 AGGATCAAGGAGGCCTACTGT 59.991 52.381 21.39 8.03 31.13 3.55
215 216 1.141019 GCCATTCGAGCCGAGTACA 59.859 57.895 0.00 0.00 37.14 2.90
512 514 5.979517 TGCACTCGTGTCAGATATATCAAAG 59.020 40.000 15.08 4.75 0.00 2.77
551 553 4.885325 ACGACACCATAAAAAGGAAGTGTT 59.115 37.500 0.00 0.00 38.49 3.32
580 584 5.930135 AGAGTAAATACACACCATCCCATC 58.070 41.667 0.00 0.00 0.00 3.51
609 613 4.118410 TGTTTTGATGCTGCAACGATTTT 58.882 34.783 6.36 0.00 0.00 1.82
808 813 1.617018 GGCCTTCAAATCTTGCCCCC 61.617 60.000 0.00 0.00 36.07 5.40
858 1201 3.003173 CCTCTTCCCCTCGCCACA 61.003 66.667 0.00 0.00 0.00 4.17
928 1271 2.092753 AGCATCAACCATGGTGAGTAGG 60.093 50.000 20.60 7.22 41.89 3.18
935 1278 0.552848 CATGGTGAGTAGGGCCCAAT 59.447 55.000 27.56 9.21 0.00 3.16
1308 1651 1.901591 AACACCTGCTTGGATCACAG 58.098 50.000 0.00 0.00 39.71 3.66
1397 1750 1.708341 ATGAAAGGCAGTTGCTGGTT 58.292 45.000 3.88 0.00 41.70 3.67
1467 1820 5.066246 TGCATGTTAGATCAATGCATTTCGA 59.934 36.000 9.83 5.50 42.46 3.71
1601 1957 8.514594 CAGATTTGTTTCATATTACACAGGTGT 58.485 33.333 10.26 10.26 46.87 4.16
1673 2029 7.985752 GGACACTTACTAGCTTATTTACCACAT 59.014 37.037 0.00 0.00 0.00 3.21
1796 2153 0.736325 CAGACCGTAACGCCAAGGAG 60.736 60.000 0.00 0.00 0.00 3.69
1816 2173 3.790152 GGACATGCCTTGATCTTTTCC 57.210 47.619 0.00 0.00 0.00 3.13
1817 2174 2.428530 GGACATGCCTTGATCTTTTCCC 59.571 50.000 0.00 0.00 0.00 3.97
1819 2176 1.406539 CATGCCTTGATCTTTTCCCCG 59.593 52.381 0.00 0.00 0.00 5.73
1823 2180 3.288092 GCCTTGATCTTTTCCCCGTATT 58.712 45.455 0.00 0.00 0.00 1.89
1824 2181 4.080243 TGCCTTGATCTTTTCCCCGTATTA 60.080 41.667 0.00 0.00 0.00 0.98
1827 2184 6.148976 GCCTTGATCTTTTCCCCGTATTATAC 59.851 42.308 0.00 0.00 0.00 1.47
1829 2186 7.883311 CCTTGATCTTTTCCCCGTATTATACAT 59.117 37.037 3.16 0.00 0.00 2.29
1830 2187 9.938280 CTTGATCTTTTCCCCGTATTATACATA 57.062 33.333 3.16 0.00 0.00 2.29
1838 2195 8.936070 TTCCCCGTATTATACATAATGAATCG 57.064 34.615 3.16 4.97 34.91 3.34
1839 2196 7.494211 TCCCCGTATTATACATAATGAATCGG 58.506 38.462 3.16 11.20 35.93 4.18
1840 2197 6.202188 CCCCGTATTATACATAATGAATCGGC 59.798 42.308 3.16 0.00 35.49 5.54
1841 2198 6.074516 CCCGTATTATACATAATGAATCGGCG 60.075 42.308 0.00 0.00 35.49 6.46
1842 2199 6.074516 CCGTATTATACATAATGAATCGGCGG 60.075 42.308 7.21 0.00 34.91 6.13
1843 2200 6.474427 CGTATTATACATAATGAATCGGCGGT 59.526 38.462 7.21 0.00 34.91 5.68
1845 2202 9.304731 GTATTATACATAATGAATCGGCGGTTA 57.695 33.333 4.89 0.00 34.91 2.85
1846 2203 7.585286 TTATACATAATGAATCGGCGGTTAC 57.415 36.000 4.89 0.00 0.00 2.50
1848 2205 1.855513 TAATGAATCGGCGGTTACGG 58.144 50.000 4.89 0.00 41.36 4.02
1849 2206 0.108041 AATGAATCGGCGGTTACGGT 60.108 50.000 4.89 0.00 41.36 4.83
1850 2207 0.529119 ATGAATCGGCGGTTACGGTC 60.529 55.000 4.89 0.00 41.36 4.79
1852 2209 1.143969 GAATCGGCGGTTACGGTCTG 61.144 60.000 4.89 0.00 41.36 3.51
1853 2210 1.880819 AATCGGCGGTTACGGTCTGT 61.881 55.000 2.20 0.00 41.36 3.41
1855 2212 1.226491 CGGCGGTTACGGTCTGTAG 60.226 63.158 0.00 0.00 41.36 2.74
1857 2214 0.179153 GGCGGTTACGGTCTGTAGAC 60.179 60.000 3.43 3.43 44.04 2.59
1867 2224 4.233123 CGGTCTGTAGACTGTACACAAA 57.767 45.455 11.79 0.00 44.33 2.83
1868 2225 4.806330 CGGTCTGTAGACTGTACACAAAT 58.194 43.478 11.79 0.00 44.33 2.32
1869 2226 4.857588 CGGTCTGTAGACTGTACACAAATC 59.142 45.833 11.79 0.00 44.33 2.17
1871 2228 5.864474 GGTCTGTAGACTGTACACAAATCAG 59.136 44.000 11.45 0.00 44.20 2.90
1872 2229 5.346281 GTCTGTAGACTGTACACAAATCAGC 59.654 44.000 4.81 0.00 41.65 4.26
1875 2232 2.037251 AGACTGTACACAAATCAGCGGT 59.963 45.455 0.00 0.00 33.12 5.68
1876 2233 2.806244 GACTGTACACAAATCAGCGGTT 59.194 45.455 0.00 0.00 33.12 4.44
1877 2234 3.991773 GACTGTACACAAATCAGCGGTTA 59.008 43.478 0.00 0.00 33.12 2.85
1878 2235 3.744426 ACTGTACACAAATCAGCGGTTAC 59.256 43.478 0.00 0.00 33.12 2.50
1879 2236 2.732500 TGTACACAAATCAGCGGTTACG 59.267 45.455 0.00 0.00 44.63 3.18
1880 2237 1.153353 ACACAAATCAGCGGTTACGG 58.847 50.000 0.00 0.00 41.36 4.02
1889 2246 2.729378 GCGGTTACGGTCTGTACAC 58.271 57.895 0.00 0.00 41.36 2.90
1890 2247 0.039256 GCGGTTACGGTCTGTACACA 60.039 55.000 0.00 0.00 41.36 3.72
1891 2248 1.602668 GCGGTTACGGTCTGTACACAA 60.603 52.381 0.00 0.00 41.36 3.33
1892 2249 2.741612 CGGTTACGGTCTGTACACAAA 58.258 47.619 0.00 0.00 36.18 2.83
1893 2250 3.319755 CGGTTACGGTCTGTACACAAAT 58.680 45.455 0.00 0.00 36.18 2.32
1894 2251 3.742369 CGGTTACGGTCTGTACACAAATT 59.258 43.478 0.00 0.00 36.18 1.82
1895 2252 4.922692 CGGTTACGGTCTGTACACAAATTA 59.077 41.667 0.00 0.00 36.18 1.40
1896 2253 5.164061 CGGTTACGGTCTGTACACAAATTAC 60.164 44.000 0.00 0.00 36.18 1.89
1897 2254 5.695816 GGTTACGGTCTGTACACAAATTACA 59.304 40.000 0.00 0.00 31.20 2.41
1898 2255 6.369615 GGTTACGGTCTGTACACAAATTACAT 59.630 38.462 0.00 0.00 31.20 2.29
1899 2256 5.856126 ACGGTCTGTACACAAATTACATG 57.144 39.130 0.00 0.00 0.00 3.21
1900 2257 5.543714 ACGGTCTGTACACAAATTACATGA 58.456 37.500 0.00 0.00 0.00 3.07
1901 2258 5.992829 ACGGTCTGTACACAAATTACATGAA 59.007 36.000 0.00 0.00 0.00 2.57
1909 2266 8.941977 TGTACACAAATTACATGAACATAGACC 58.058 33.333 0.00 0.00 0.00 3.85
1947 2304 1.528129 CTTCCTGGTTTCAGTGCTCC 58.472 55.000 0.00 0.00 39.31 4.70
1951 2308 0.671781 CTGGTTTCAGTGCTCCGGAG 60.672 60.000 27.83 27.83 36.30 4.63
1952 2309 1.371558 GGTTTCAGTGCTCCGGAGT 59.628 57.895 31.43 10.49 0.00 3.85
1953 2310 0.670854 GGTTTCAGTGCTCCGGAGTC 60.671 60.000 31.43 23.14 0.00 3.36
1954 2311 0.318762 GTTTCAGTGCTCCGGAGTCT 59.681 55.000 31.43 25.10 0.00 3.24
1955 2312 0.318441 TTTCAGTGCTCCGGAGTCTG 59.682 55.000 32.99 32.99 35.54 3.51
1956 2313 0.827925 TTCAGTGCTCCGGAGTCTGT 60.828 55.000 34.77 19.37 35.63 3.41
1957 2314 0.037734 TCAGTGCTCCGGAGTCTGTA 59.962 55.000 34.77 25.95 35.63 2.74
1958 2315 0.171455 CAGTGCTCCGGAGTCTGTAC 59.829 60.000 31.67 23.21 32.44 2.90
1959 2316 0.251209 AGTGCTCCGGAGTCTGTACA 60.251 55.000 31.43 17.34 0.00 2.90
1960 2317 0.818296 GTGCTCCGGAGTCTGTACAT 59.182 55.000 31.43 0.00 0.00 2.29
1961 2318 2.022195 GTGCTCCGGAGTCTGTACATA 58.978 52.381 31.43 4.75 0.00 2.29
1962 2319 2.426024 GTGCTCCGGAGTCTGTACATAA 59.574 50.000 31.43 4.07 0.00 1.90
1963 2320 2.426024 TGCTCCGGAGTCTGTACATAAC 59.574 50.000 31.43 11.44 0.00 1.89
1964 2321 2.541178 GCTCCGGAGTCTGTACATAACG 60.541 54.545 31.43 3.15 0.00 3.18
1965 2322 2.941064 CTCCGGAGTCTGTACATAACGA 59.059 50.000 24.04 0.00 0.00 3.85
1966 2323 3.346315 TCCGGAGTCTGTACATAACGAA 58.654 45.455 0.00 0.00 0.00 3.85
1967 2324 3.949754 TCCGGAGTCTGTACATAACGAAT 59.050 43.478 0.00 0.00 0.00 3.34
1968 2325 4.400251 TCCGGAGTCTGTACATAACGAATT 59.600 41.667 0.00 0.00 0.00 2.17
2191 2619 2.293318 CCAGGTGGAGCTACAGGCA 61.293 63.158 0.00 0.00 44.79 4.75
2255 2685 2.489073 GCCCTCTGAAGAAGAAAACCCA 60.489 50.000 0.00 0.00 33.37 4.51
2619 3052 9.943163 CCGATACTGTGATCTGTCTATATATTG 57.057 37.037 0.00 0.00 0.00 1.90
2666 3099 6.405538 ACAAATCATATTTTCGGGTGCAAAT 58.594 32.000 0.00 0.00 0.00 2.32
2710 3143 5.796935 CAGATGCGTAATTTGTTCCTTCAAG 59.203 40.000 0.00 0.00 0.00 3.02
2714 3147 6.432107 TGCGTAATTTGTTCCTTCAAGTAAC 58.568 36.000 0.00 0.00 0.00 2.50
2739 3172 2.558359 ACTACATTGTTTCTGGGCAAGC 59.442 45.455 0.00 0.00 0.00 4.01
2740 3173 1.412079 ACATTGTTTCTGGGCAAGCA 58.588 45.000 0.00 0.00 0.00 3.91
2750 3183 4.342862 TCTGGGCAAGCATAGATTAGAC 57.657 45.455 0.00 0.00 0.00 2.59
2816 3503 2.162608 ACAGAGACGATTCAAGACCTCG 59.837 50.000 0.00 0.00 38.34 4.63
2817 3504 2.420372 CAGAGACGATTCAAGACCTCGA 59.580 50.000 7.87 0.00 36.32 4.04
2822 3509 2.496070 ACGATTCAAGACCTCGAATCCA 59.504 45.455 5.42 0.00 42.94 3.41
2826 3513 2.752030 TCAAGACCTCGAATCCATCCT 58.248 47.619 0.00 0.00 0.00 3.24
2920 3609 4.154347 GAGCGGCAGGGAGGTGAG 62.154 72.222 1.45 0.00 0.00 3.51
2945 5762 2.657296 CACGTTGCGTCGTCTGGT 60.657 61.111 3.11 0.00 42.27 4.00
2954 5771 1.283793 GTCGTCTGGTCGTTCCGAA 59.716 57.895 0.00 0.00 37.72 4.30
3043 5883 3.120105 CTGACGAGCTCCGCCATA 58.880 61.111 8.47 0.00 43.32 2.74
3175 6017 2.346597 GGTTTTCCGACATGGCCAA 58.653 52.632 10.96 0.00 37.80 4.52
3214 6056 2.754375 GACTTCCCCGCCTTCCAA 59.246 61.111 0.00 0.00 0.00 3.53
3224 6066 1.671742 GCCTTCCAAGACGAGGACA 59.328 57.895 0.00 0.00 34.19 4.02
3241 6083 1.140161 CATTGCCGGGCTTGATGTG 59.860 57.895 21.46 6.09 0.00 3.21
3242 6084 2.713967 ATTGCCGGGCTTGATGTGC 61.714 57.895 21.46 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 3.010584 TCCTCAAATAGCTGAAGGCCTTT 59.989 43.478 21.54 5.98 43.05 3.11
93 94 2.491152 CACCACGCCATGAATGCC 59.509 61.111 0.00 0.00 0.00 4.40
180 181 5.467735 CGAATGGCATATCTTTGATGAGACA 59.532 40.000 0.00 0.00 0.00 3.41
182 183 5.857268 TCGAATGGCATATCTTTGATGAGA 58.143 37.500 0.00 0.00 0.00 3.27
215 216 1.374947 CAGAACACCCCACACCGAT 59.625 57.895 0.00 0.00 0.00 4.18
529 531 5.432885 AACACTTCCTTTTTATGGTGTCG 57.567 39.130 0.00 0.00 36.99 4.35
551 553 9.016438 GGGATGGTGTGTATTTACTCTTAAAAA 57.984 33.333 0.00 0.00 30.86 1.94
580 584 2.557924 TGCAGCATCAAAACAAGGGTAG 59.442 45.455 0.00 0.00 0.00 3.18
609 613 0.787084 AGACAGACCCTCCCTCAGAA 59.213 55.000 0.00 0.00 0.00 3.02
858 1201 1.692411 GTTGAGAAGCAAACAGGGGT 58.308 50.000 0.00 0.00 38.44 4.95
928 1271 3.091545 TGTGAAAGAATGAGATTGGGCC 58.908 45.455 0.00 0.00 0.00 5.80
1056 1399 2.575532 TCCTGGAACTTGAGTTTGCAG 58.424 47.619 0.00 3.60 38.56 4.41
1491 1847 9.809096 TGTGTTCAATTATTGCTTGTAGAAAAA 57.191 25.926 0.00 0.00 0.00 1.94
1492 1848 9.243637 GTGTGTTCAATTATTGCTTGTAGAAAA 57.756 29.630 0.00 0.00 0.00 2.29
1601 1957 7.450014 TGATCTAACAAAATTACAGGCTTTGGA 59.550 33.333 0.00 0.00 34.94 3.53
1673 2029 6.514870 CGTTGGATTTCTGTTTCCATTTCTCA 60.515 38.462 0.00 0.00 41.52 3.27
1758 2114 7.083858 CGGTCTGTACACAAATTTGAATTCAT 58.916 34.615 24.64 0.00 0.00 2.57
1796 2153 2.428530 GGGAAAAGATCAAGGCATGTCC 59.571 50.000 0.00 0.00 0.00 4.02
1816 2173 6.074516 CGCCGATTCATTATGTATAATACGGG 60.075 42.308 19.84 10.84 36.34 5.28
1817 2174 6.074516 CCGCCGATTCATTATGTATAATACGG 60.075 42.308 17.17 17.17 37.39 4.02
1819 2176 7.766219 ACCGCCGATTCATTATGTATAATAC 57.234 36.000 0.00 0.00 32.05 1.89
1823 2180 5.801444 CGTAACCGCCGATTCATTATGTATA 59.199 40.000 0.00 0.00 0.00 1.47
1824 2181 4.624024 CGTAACCGCCGATTCATTATGTAT 59.376 41.667 0.00 0.00 0.00 2.29
1827 2184 2.156891 CCGTAACCGCCGATTCATTATG 59.843 50.000 0.00 0.00 0.00 1.90
1829 2186 1.136695 ACCGTAACCGCCGATTCATTA 59.863 47.619 0.00 0.00 0.00 1.90
1830 2187 0.108041 ACCGTAACCGCCGATTCATT 60.108 50.000 0.00 0.00 0.00 2.57
1831 2188 0.529119 GACCGTAACCGCCGATTCAT 60.529 55.000 0.00 0.00 0.00 2.57
1832 2189 1.153784 GACCGTAACCGCCGATTCA 60.154 57.895 0.00 0.00 0.00 2.57
1834 2191 1.153706 CAGACCGTAACCGCCGATT 60.154 57.895 0.00 0.00 0.00 3.34
1836 2193 1.647545 CTACAGACCGTAACCGCCGA 61.648 60.000 0.00 0.00 0.00 5.54
1837 2194 1.226491 CTACAGACCGTAACCGCCG 60.226 63.158 0.00 0.00 0.00 6.46
1838 2195 0.179153 GTCTACAGACCGTAACCGCC 60.179 60.000 0.00 0.00 39.07 6.13
1839 2196 0.807496 AGTCTACAGACCGTAACCGC 59.193 55.000 5.76 0.00 45.85 5.68
1840 2197 1.808945 ACAGTCTACAGACCGTAACCG 59.191 52.381 5.76 0.00 45.85 4.44
1841 2198 3.753272 TGTACAGTCTACAGACCGTAACC 59.247 47.826 6.96 0.00 45.85 2.85
1842 2199 4.214119 TGTGTACAGTCTACAGACCGTAAC 59.786 45.833 6.96 8.25 45.85 2.50
1843 2200 4.388485 TGTGTACAGTCTACAGACCGTAA 58.612 43.478 6.96 0.00 45.85 3.18
1845 2202 2.854963 TGTGTACAGTCTACAGACCGT 58.145 47.619 5.76 4.75 45.85 4.83
1846 2203 3.909776 TTGTGTACAGTCTACAGACCG 57.090 47.619 5.76 0.00 45.85 4.79
1848 2205 5.346281 GCTGATTTGTGTACAGTCTACAGAC 59.654 44.000 17.53 0.91 45.08 3.51
1849 2206 5.470368 GCTGATTTGTGTACAGTCTACAGA 58.530 41.667 17.53 1.14 34.60 3.41
1850 2207 4.324669 CGCTGATTTGTGTACAGTCTACAG 59.675 45.833 0.00 5.45 34.60 2.74
1852 2209 3.612860 CCGCTGATTTGTGTACAGTCTAC 59.387 47.826 0.00 0.00 34.60 2.59
1853 2210 3.257375 ACCGCTGATTTGTGTACAGTCTA 59.743 43.478 0.00 0.00 34.60 2.59
1855 2212 2.413837 ACCGCTGATTTGTGTACAGTC 58.586 47.619 0.00 0.00 34.60 3.51
1857 2214 3.181534 CGTAACCGCTGATTTGTGTACAG 60.182 47.826 0.00 0.00 35.14 2.74
1859 2216 2.093152 CCGTAACCGCTGATTTGTGTAC 59.907 50.000 0.00 0.00 0.00 2.90
1860 2217 2.288948 ACCGTAACCGCTGATTTGTGTA 60.289 45.455 0.00 0.00 0.00 2.90
1865 2222 1.001633 ACAGACCGTAACCGCTGATTT 59.998 47.619 0.00 0.00 31.29 2.17
1867 2224 1.133790 GTACAGACCGTAACCGCTGAT 59.866 52.381 0.00 0.00 31.29 2.90
1868 2225 0.523072 GTACAGACCGTAACCGCTGA 59.477 55.000 0.00 0.00 31.29 4.26
1869 2226 0.241749 TGTACAGACCGTAACCGCTG 59.758 55.000 0.00 0.00 32.52 5.18
1871 2228 0.039256 TGTGTACAGACCGTAACCGC 60.039 55.000 0.00 0.00 0.00 5.68
1872 2229 2.420628 TTGTGTACAGACCGTAACCG 57.579 50.000 0.00 0.00 0.00 4.44
1875 2232 7.153315 TCATGTAATTTGTGTACAGACCGTAA 58.847 34.615 0.00 0.00 35.04 3.18
1876 2233 6.689554 TCATGTAATTTGTGTACAGACCGTA 58.310 36.000 0.00 0.00 35.04 4.02
1877 2234 5.543714 TCATGTAATTTGTGTACAGACCGT 58.456 37.500 0.00 0.00 35.04 4.83
1878 2235 6.073494 TGTTCATGTAATTTGTGTACAGACCG 60.073 38.462 0.00 0.00 35.04 4.79
1879 2236 7.197071 TGTTCATGTAATTTGTGTACAGACC 57.803 36.000 0.00 0.00 35.04 3.85
1880 2237 9.973246 CTATGTTCATGTAATTTGTGTACAGAC 57.027 33.333 0.00 0.00 35.04 3.51
1881 2238 9.936759 TCTATGTTCATGTAATTTGTGTACAGA 57.063 29.630 0.00 0.00 35.04 3.41
1882 2239 9.973246 GTCTATGTTCATGTAATTTGTGTACAG 57.027 33.333 0.00 0.00 35.04 2.74
1883 2240 8.941977 GGTCTATGTTCATGTAATTTGTGTACA 58.058 33.333 0.00 0.00 35.98 2.90
1884 2241 8.114290 CGGTCTATGTTCATGTAATTTGTGTAC 58.886 37.037 0.00 0.00 0.00 2.90
1885 2242 7.820386 ACGGTCTATGTTCATGTAATTTGTGTA 59.180 33.333 0.00 0.00 0.00 2.90
1886 2243 6.653320 ACGGTCTATGTTCATGTAATTTGTGT 59.347 34.615 0.00 0.00 0.00 3.72
1887 2244 7.072177 ACGGTCTATGTTCATGTAATTTGTG 57.928 36.000 0.00 0.00 0.00 3.33
1888 2245 7.681939 AACGGTCTATGTTCATGTAATTTGT 57.318 32.000 0.00 0.00 0.00 2.83
1889 2246 8.450964 AGAAACGGTCTATGTTCATGTAATTTG 58.549 33.333 0.00 0.00 33.56 2.32
1890 2247 8.561738 AGAAACGGTCTATGTTCATGTAATTT 57.438 30.769 0.00 0.00 33.56 1.82
1891 2248 8.561738 AAGAAACGGTCTATGTTCATGTAATT 57.438 30.769 0.00 0.00 34.56 1.40
1892 2249 8.041323 AGAAGAAACGGTCTATGTTCATGTAAT 58.959 33.333 0.00 0.00 34.56 1.89
1893 2250 7.383687 AGAAGAAACGGTCTATGTTCATGTAA 58.616 34.615 0.00 0.00 34.56 2.41
1894 2251 6.931838 AGAAGAAACGGTCTATGTTCATGTA 58.068 36.000 0.00 0.00 34.56 2.29
1895 2252 5.794894 AGAAGAAACGGTCTATGTTCATGT 58.205 37.500 0.00 0.00 34.56 3.21
1896 2253 7.330946 TGTTAGAAGAAACGGTCTATGTTCATG 59.669 37.037 0.00 0.00 34.56 3.07
1897 2254 7.383687 TGTTAGAAGAAACGGTCTATGTTCAT 58.616 34.615 0.00 0.00 34.56 2.57
1898 2255 6.751157 TGTTAGAAGAAACGGTCTATGTTCA 58.249 36.000 0.00 0.00 34.56 3.18
1899 2256 7.621633 GCTTGTTAGAAGAAACGGTCTATGTTC 60.622 40.741 0.00 0.00 34.56 3.18
1900 2257 6.147328 GCTTGTTAGAAGAAACGGTCTATGTT 59.853 38.462 0.00 0.00 34.56 2.71
1901 2258 5.638234 GCTTGTTAGAAGAAACGGTCTATGT 59.362 40.000 0.00 0.00 34.56 2.29
1909 2266 4.458708 GAAGCAGCTTGTTAGAAGAAACG 58.541 43.478 13.91 0.00 31.76 3.60
1947 2304 5.100259 ACAATTCGTTATGTACAGACTCCG 58.900 41.667 0.33 0.00 0.00 4.63
1951 2308 5.347635 TGCAGACAATTCGTTATGTACAGAC 59.652 40.000 0.33 1.84 0.00 3.51
1952 2309 5.474825 TGCAGACAATTCGTTATGTACAGA 58.525 37.500 0.33 0.00 0.00 3.41
1953 2310 5.778161 TGCAGACAATTCGTTATGTACAG 57.222 39.130 0.33 0.00 0.00 2.74
1954 2311 6.735678 ATTGCAGACAATTCGTTATGTACA 57.264 33.333 0.00 0.00 44.21 2.90
1955 2312 7.736017 CGATATTGCAGACAATTCGTTATGTAC 59.264 37.037 0.00 0.00 44.21 2.90
1956 2313 7.436970 ACGATATTGCAGACAATTCGTTATGTA 59.563 33.333 16.10 0.00 46.08 2.29
1957 2314 6.257849 ACGATATTGCAGACAATTCGTTATGT 59.742 34.615 16.10 0.00 46.08 2.29
1958 2315 6.649436 ACGATATTGCAGACAATTCGTTATG 58.351 36.000 16.10 0.00 46.08 1.90
1959 2316 6.844696 ACGATATTGCAGACAATTCGTTAT 57.155 33.333 16.10 0.00 46.08 1.89
1960 2317 7.758613 TTACGATATTGCAGACAATTCGTTA 57.241 32.000 21.77 15.54 46.08 3.18
1961 2318 6.656314 TTACGATATTGCAGACAATTCGTT 57.344 33.333 21.77 13.04 46.08 3.85
1963 2320 6.792250 GGATTTACGATATTGCAGACAATTCG 59.208 38.462 15.28 15.28 44.21 3.34
1964 2321 7.865707 AGGATTTACGATATTGCAGACAATTC 58.134 34.615 0.00 0.00 44.21 2.17
1965 2322 7.807977 AGGATTTACGATATTGCAGACAATT 57.192 32.000 0.00 0.00 44.21 2.32
1967 2324 8.725405 TTAAGGATTTACGATATTGCAGACAA 57.275 30.769 0.00 0.00 40.87 3.18
1968 2325 7.042051 GCTTAAGGATTTACGATATTGCAGACA 60.042 37.037 4.29 0.00 0.00 3.41
2191 2619 2.754658 ATCTCGCTCGGGTCGGTT 60.755 61.111 0.00 0.00 0.00 4.44
2255 2685 2.454538 ACGTAGTAAGTAGCTGGGCTT 58.545 47.619 0.00 0.60 41.94 4.35
2619 3052 1.087501 GACGGCAAAGGTTCCTGATC 58.912 55.000 0.00 0.00 0.00 2.92
2666 3099 2.290832 TGTTGCAATCTGGGCATGTCTA 60.291 45.455 0.59 0.00 41.58 2.59
2694 3127 9.841295 AGTACAGTTACTTGAAGGAACAAATTA 57.159 29.630 21.39 4.89 34.66 1.40
2697 3130 8.259411 TGTAGTACAGTTACTTGAAGGAACAAA 58.741 33.333 21.39 4.34 39.43 2.83
2710 3143 6.128363 GCCCAGAAACAATGTAGTACAGTTAC 60.128 42.308 9.25 0.00 0.00 2.50
2714 3147 4.323417 TGCCCAGAAACAATGTAGTACAG 58.677 43.478 9.25 0.00 0.00 2.74
2809 3496 1.323412 CGAGGATGGATTCGAGGTCT 58.677 55.000 0.00 0.00 39.06 3.85
2816 3503 0.465705 TGCTGTCCGAGGATGGATTC 59.534 55.000 0.00 0.00 40.91 2.52
2817 3504 1.071385 GATGCTGTCCGAGGATGGATT 59.929 52.381 0.00 0.00 40.91 3.01
2822 3509 0.105760 AGGAGATGCTGTCCGAGGAT 60.106 55.000 0.00 0.00 39.30 3.24
2826 3513 3.941081 GGAGGAGATGCTGTCCGA 58.059 61.111 0.00 0.00 39.30 4.55
2954 5771 1.006758 TCTGGACTATCTTCGGGGTGT 59.993 52.381 0.00 0.00 0.00 4.16
3086 5927 1.759881 GGAGATGCTCATGGGAGGG 59.240 63.158 0.00 0.00 41.67 4.30
3088 5929 1.370437 CCGGAGATGCTCATGGGAG 59.630 63.158 0.00 0.00 44.33 4.30
3152 5994 0.953471 CCATGTCGGAAAACCGAGCA 60.953 55.000 11.61 12.41 43.02 4.26
3154 5996 1.644786 GGCCATGTCGGAAAACCGAG 61.645 60.000 11.61 1.89 43.02 4.63
3155 5997 1.673009 GGCCATGTCGGAAAACCGA 60.673 57.895 7.27 7.27 40.03 4.69
3156 5998 1.519751 TTGGCCATGTCGGAAAACCG 61.520 55.000 6.09 0.00 36.56 4.44
3157 5999 0.894835 ATTGGCCATGTCGGAAAACC 59.105 50.000 6.09 0.00 36.56 3.27
3158 6000 1.135112 GGATTGGCCATGTCGGAAAAC 60.135 52.381 6.09 0.00 36.56 2.43
3159 6001 1.181786 GGATTGGCCATGTCGGAAAA 58.818 50.000 6.09 0.00 36.56 2.29
3175 6017 1.751351 TGAAGATCTGCGACTTCGGAT 59.249 47.619 0.00 0.00 43.46 4.18
3214 6056 2.579201 CCGGCAATGTCCTCGTCT 59.421 61.111 0.00 0.00 0.00 4.18
3224 6066 2.713967 GCACATCAAGCCCGGCAAT 61.714 57.895 13.15 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.