Multiple sequence alignment - TraesCS1A01G286300

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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 TraesCS1A01G286300 chr1A 100.000 2597 0 0 1 2597 483035064 483032468 0.000000e+00 4796
1 TraesCS1A01G286300 chr1D 89.505 1877 119 30 40 1872 383321416 383319574 0.000000e+00 2303
2 TraesCS1A01G286300 chr1D 88.384 594 39 14 2017 2597 383319569 383318993 0.000000e+00 688
3 TraesCS1A01G286300 chr1B 85.647 1268 102 39 714 1927 513546071 513544830 0.000000e+00 1260
4 TraesCS1A01G286300 chr1B 85.020 741 78 22 40 776 513546799 513546088 0.000000e+00 723
5 TraesCS1A01G286300 chr1B 85.851 629 44 21 1977 2597 513544822 513544231 6.100000e-176 627
6 TraesCS1A01G286300 chr3A 83.590 390 53 10 993 1375 603803417 603803802 3.180000e-94 355
7 TraesCS1A01G286300 chr3A 90.385 104 10 0 1494 1597 603803919 603804022 1.250000e-28 137
8 TraesCS1A01G286300 chr3B 83.548 389 53 8 993 1375 611727461 611727844 1.140000e-93 353
9 TraesCS1A01G286300 chr3D 83.077 390 53 9 993 1375 461212843 461213226 2.470000e-90 342
10 TraesCS1A01G286300 chr3D 89.423 104 11 0 1494 1597 461213345 461213448 5.830000e-27 132


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 TraesCS1A01G286300 chr1A 483032468 483035064 2596 True 4796.0 4796 100.0000 1 2597 1 chr1A.!!$R1 2596
1 TraesCS1A01G286300 chr1D 383318993 383321416 2423 True 1495.5 2303 88.9445 40 2597 2 chr1D.!!$R1 2557
2 TraesCS1A01G286300 chr1B 513544231 513546799 2568 True 870.0 1260 85.5060 40 2597 3 chr1B.!!$R1 2557
3 TraesCS1A01G286300 chr3A 603803417 603804022 605 False 246.0 355 86.9875 993 1597 2 chr3A.!!$F1 604
4 TraesCS1A01G286300 chr3D 461212843 461213448 605 False 237.0 342 86.2500 993 1597 2 chr3D.!!$F1 604

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
126 131 1.228245 TGTTTGCTCCCTCTGTGCC 60.228 57.895 0.0 0.0 32.45 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2122 2308 0.107654 AAGTGGCCGCCTTCATAGAC 60.108 55.0 14.07 0.0 0.0 2.59 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
59 60 2.123640 CCTCTCCGTCCCCTCCTC 60.124 72.222 0.00 0.00 0.00 3.71
90 95 1.660917 CGTAGAGATCCTTCGGGCC 59.339 63.158 0.00 0.00 32.90 5.80
126 131 1.228245 TGTTTGCTCCCTCTGTGCC 60.228 57.895 0.00 0.00 32.45 5.01
129 134 2.731691 TTTGCTCCCTCTGTGCCGTC 62.732 60.000 0.00 0.00 32.45 4.79
143 148 1.515954 CCGTCGTGCCCACTCTTAT 59.484 57.895 0.00 0.00 0.00 1.73
175 180 7.728532 AGATCCTTGGTTTTGGTAGTTGTTTAT 59.271 33.333 0.00 0.00 0.00 1.40
176 181 7.045126 TCCTTGGTTTTGGTAGTTGTTTATG 57.955 36.000 0.00 0.00 0.00 1.90
213 242 3.252215 TGTTTTGTCTATCCGGTGCAAAG 59.748 43.478 0.00 0.00 31.87 2.77
320 350 2.030457 CGTAGTTTCATCCGTGAATGGC 59.970 50.000 0.00 0.00 43.49 4.40
366 396 7.487189 GTGTTTTTGCCATCATAGAGATTGAAG 59.513 37.037 0.00 0.00 33.72 3.02
368 398 7.563888 TTTTGCCATCATAGAGATTGAAGAG 57.436 36.000 0.00 0.00 33.72 2.85
398 428 4.512484 TGTTCTATTGCGGATCAATGACA 58.488 39.130 0.00 1.44 44.62 3.58
399 429 4.571984 TGTTCTATTGCGGATCAATGACAG 59.428 41.667 0.00 0.00 44.62 3.51
426 456 4.717233 ACTGATCTGTGACATCTGTCTC 57.283 45.455 11.35 8.39 44.99 3.36
482 513 7.015682 TGCCATAGAGGGAAACAAAATGTTTAA 59.984 33.333 8.34 0.00 43.46 1.52
551 582 3.119531 TGTGGCATATTTAGCTGTTGTGC 60.120 43.478 0.00 0.84 0.00 4.57
626 669 7.016153 AGGAAACCATTTACATGACAGTCTA 57.984 36.000 0.00 0.00 31.07 2.59
647 690 8.867097 AGTCTATCCTACTGTTTAAGTTTGTGA 58.133 33.333 0.00 0.00 40.56 3.58
662 705 6.811253 AGTTTGTGACTTGTTTCTGTGTTA 57.189 33.333 0.00 0.00 33.92 2.41
705 749 2.438021 TCTGAAGTAGTGGTGCCAAACT 59.562 45.455 0.00 0.00 0.00 2.66
708 752 4.980573 TGAAGTAGTGGTGCCAAACTAAT 58.019 39.130 7.61 0.00 30.94 1.73
741 863 9.396022 TGTTTACCTTTGCCAATTTTTCATTTA 57.604 25.926 0.00 0.00 0.00 1.40
749 871 8.600449 TTGCCAATTTTTCATTTACTTACCAG 57.400 30.769 0.00 0.00 0.00 4.00
767 889 5.505181 ACCAGTCTTCTAAACCATGATGT 57.495 39.130 0.00 0.00 0.00 3.06
814 936 6.020440 CACCTTGATTTATTTTATGTGCTGCG 60.020 38.462 0.00 0.00 0.00 5.18
827 949 2.032377 TGTGCTGCGCTTACTTTTGTAC 60.032 45.455 14.92 0.00 34.15 2.90
871 1011 1.543208 CCCAGTGTCAGTTTAGCTGCA 60.543 52.381 1.02 0.00 44.66 4.41
915 1055 6.018098 CCACTCATTACTCTTTGCATCTGATC 60.018 42.308 0.00 0.00 0.00 2.92
918 1058 8.427276 ACTCATTACTCTTTGCATCTGATCATA 58.573 33.333 0.00 0.00 0.00 2.15
948 1088 2.494059 ACTTAGCTGAAACGTGTGCAT 58.506 42.857 0.00 0.00 0.00 3.96
950 1090 3.315191 ACTTAGCTGAAACGTGTGCATTT 59.685 39.130 0.00 0.00 0.00 2.32
1147 1290 3.418684 AGCACGGTTAGTTCCATTTCT 57.581 42.857 0.00 0.00 0.00 2.52
1198 1344 3.683847 GCATGGATTACTCACTGCCTCTT 60.684 47.826 0.00 0.00 0.00 2.85
1276 1422 1.384525 TTGTTGTGGAGTTGAACGGG 58.615 50.000 0.00 0.00 0.00 5.28
1309 1455 1.078528 TGGAGTCATCAGTCCCCGT 59.921 57.895 0.00 0.00 41.15 5.28
1432 1596 3.800506 GCATTGCCATATTTTGAGCTCAC 59.199 43.478 18.03 2.51 0.00 3.51
1433 1597 4.678574 GCATTGCCATATTTTGAGCTCACA 60.679 41.667 18.03 7.33 0.00 3.58
1435 1599 5.664294 TTGCCATATTTTGAGCTCACAAT 57.336 34.783 26.55 26.55 31.87 2.71
1440 1604 6.038603 GCCATATTTTGAGCTCACAATCTGTA 59.961 38.462 27.01 13.37 29.99 2.74
1457 1626 5.272283 TCTGTAACGACTCTTCCAAGTTT 57.728 39.130 0.00 0.00 0.00 2.66
1717 1893 6.472163 GCCTTTGTTATGTTATGTTGGATTCG 59.528 38.462 0.00 0.00 0.00 3.34
1739 1915 7.246674 TCGGTTAATTATGAGATGCACTTTC 57.753 36.000 0.00 0.00 0.00 2.62
1754 1930 3.735746 GCACTTTCGAATTTTGGGTCTTG 59.264 43.478 0.00 0.00 0.00 3.02
1788 1964 8.533657 TGAATTATGACTTTGAAGATGCCATTT 58.466 29.630 0.00 0.00 0.00 2.32
1792 1968 3.656559 ACTTTGAAGATGCCATTTGTGC 58.343 40.909 0.00 0.00 0.00 4.57
1796 1972 2.291475 TGAAGATGCCATTTGTGCCCTA 60.291 45.455 0.00 0.00 0.00 3.53
1890 2075 3.681594 GCCCGTTTGGATCTTGAGTATGA 60.682 47.826 0.00 0.00 37.49 2.15
1892 2077 5.741964 GCCCGTTTGGATCTTGAGTATGATA 60.742 44.000 0.00 0.00 37.49 2.15
1894 2079 6.463049 CCCGTTTGGATCTTGAGTATGATACT 60.463 42.308 4.50 4.50 38.73 2.12
1895 2080 7.255836 CCCGTTTGGATCTTGAGTATGATACTA 60.256 40.741 4.88 0.00 36.84 1.82
1896 2081 8.307483 CCGTTTGGATCTTGAGTATGATACTAT 58.693 37.037 4.88 0.00 36.84 2.12
1922 2107 7.715265 TGTTATCTGTCTTTTGTCTCTGTTC 57.285 36.000 0.00 0.00 0.00 3.18
1927 2112 3.118261 TGTCTTTTGTCTCTGTTCTGGCT 60.118 43.478 0.00 0.00 0.00 4.75
1928 2113 3.249559 GTCTTTTGTCTCTGTTCTGGCTG 59.750 47.826 0.00 0.00 0.00 4.85
1930 2115 1.423584 TTGTCTCTGTTCTGGCTGGA 58.576 50.000 0.00 0.00 0.00 3.86
1931 2116 0.972134 TGTCTCTGTTCTGGCTGGAG 59.028 55.000 0.00 0.00 0.00 3.86
1932 2117 1.261480 GTCTCTGTTCTGGCTGGAGA 58.739 55.000 0.00 0.00 0.00 3.71
1933 2118 1.204467 GTCTCTGTTCTGGCTGGAGAG 59.796 57.143 0.00 0.00 34.34 3.20
1934 2119 1.076187 TCTCTGTTCTGGCTGGAGAGA 59.924 52.381 11.72 11.72 37.44 3.10
1935 2120 2.109774 CTCTGTTCTGGCTGGAGAGAT 58.890 52.381 0.00 0.00 33.37 2.75
1936 2121 2.500910 CTCTGTTCTGGCTGGAGAGATT 59.499 50.000 0.00 0.00 33.37 2.40
1937 2122 2.909006 TCTGTTCTGGCTGGAGAGATTT 59.091 45.455 0.00 0.00 0.00 2.17
1938 2123 3.328931 TCTGTTCTGGCTGGAGAGATTTT 59.671 43.478 0.00 0.00 0.00 1.82
1939 2124 4.077822 CTGTTCTGGCTGGAGAGATTTTT 58.922 43.478 0.00 0.00 0.00 1.94
1940 2125 3.822735 TGTTCTGGCTGGAGAGATTTTTG 59.177 43.478 0.00 0.00 0.00 2.44
1941 2126 3.795688 TCTGGCTGGAGAGATTTTTGT 57.204 42.857 0.00 0.00 0.00 2.83
1942 2127 4.104383 TCTGGCTGGAGAGATTTTTGTT 57.896 40.909 0.00 0.00 0.00 2.83
1943 2128 3.822735 TCTGGCTGGAGAGATTTTTGTTG 59.177 43.478 0.00 0.00 0.00 3.33
1944 2129 3.822735 CTGGCTGGAGAGATTTTTGTTGA 59.177 43.478 0.00 0.00 0.00 3.18
1945 2130 4.410099 TGGCTGGAGAGATTTTTGTTGAT 58.590 39.130 0.00 0.00 0.00 2.57
1946 2131 4.834496 TGGCTGGAGAGATTTTTGTTGATT 59.166 37.500 0.00 0.00 0.00 2.57
1947 2132 5.166398 GGCTGGAGAGATTTTTGTTGATTG 58.834 41.667 0.00 0.00 0.00 2.67
1948 2133 4.624452 GCTGGAGAGATTTTTGTTGATTGC 59.376 41.667 0.00 0.00 0.00 3.56
1949 2134 5.566230 GCTGGAGAGATTTTTGTTGATTGCT 60.566 40.000 0.00 0.00 0.00 3.91
1950 2135 6.409524 TGGAGAGATTTTTGTTGATTGCTT 57.590 33.333 0.00 0.00 0.00 3.91
1951 2136 6.819284 TGGAGAGATTTTTGTTGATTGCTTT 58.181 32.000 0.00 0.00 0.00 3.51
1952 2137 7.274447 TGGAGAGATTTTTGTTGATTGCTTTT 58.726 30.769 0.00 0.00 0.00 2.27
1953 2138 7.769970 TGGAGAGATTTTTGTTGATTGCTTTTT 59.230 29.630 0.00 0.00 0.00 1.94
1971 2156 1.323412 TTTTGTGTGGGGGATGTTCG 58.677 50.000 0.00 0.00 0.00 3.95
1972 2157 0.538516 TTTGTGTGGGGGATGTTCGG 60.539 55.000 0.00 0.00 0.00 4.30
1975 2160 2.150719 TGTGGGGGATGTTCGGTGT 61.151 57.895 0.00 0.00 0.00 4.16
1986 2171 1.305201 GTTCGGTGTTTGCTTCTCCA 58.695 50.000 0.00 0.00 0.00 3.86
1990 2175 3.270027 TCGGTGTTTGCTTCTCCATATG 58.730 45.455 0.00 0.00 0.00 1.78
1993 2178 4.816385 CGGTGTTTGCTTCTCCATATGTAT 59.184 41.667 1.24 0.00 0.00 2.29
1994 2179 5.050091 CGGTGTTTGCTTCTCCATATGTATC 60.050 44.000 1.24 0.00 0.00 2.24
1995 2180 6.058183 GGTGTTTGCTTCTCCATATGTATCT 58.942 40.000 1.24 0.00 0.00 1.98
1996 2181 6.017605 GGTGTTTGCTTCTCCATATGTATCTG 60.018 42.308 1.24 0.00 0.00 2.90
2005 2190 9.334947 CTTCTCCATATGTATCTGTCATTTTGT 57.665 33.333 1.24 0.00 0.00 2.83
2013 2198 6.653020 TGTATCTGTCATTTTGTATGCCTCT 58.347 36.000 0.00 0.00 0.00 3.69
2015 2200 7.928167 TGTATCTGTCATTTTGTATGCCTCTAG 59.072 37.037 0.00 0.00 0.00 2.43
2041 2226 4.949856 GCTGGAAGAATCTTATTTGGTGGA 59.050 41.667 0.00 0.00 34.07 4.02
2044 2229 6.310941 TGGAAGAATCTTATTTGGTGGACAA 58.689 36.000 0.00 0.00 37.28 3.18
2047 2232 7.761249 GGAAGAATCTTATTTGGTGGACAATTG 59.239 37.037 3.24 3.24 39.21 2.32
2048 2233 7.781324 AGAATCTTATTTGGTGGACAATTGT 57.219 32.000 11.78 11.78 39.21 2.71
2076 2261 9.736023 GTGCTTCTCAACCCTAAAATTTATATG 57.264 33.333 0.00 0.00 0.00 1.78
2077 2262 8.413229 TGCTTCTCAACCCTAAAATTTATATGC 58.587 33.333 0.00 0.00 0.00 3.14
2078 2263 8.633561 GCTTCTCAACCCTAAAATTTATATGCT 58.366 33.333 0.00 0.00 0.00 3.79
2083 2268 9.920946 TCAACCCTAAAATTTATATGCTTCTCT 57.079 29.630 0.00 0.00 0.00 3.10
2085 2270 9.920946 AACCCTAAAATTTATATGCTTCTCTCA 57.079 29.630 0.00 0.00 0.00 3.27
2086 2271 9.920946 ACCCTAAAATTTATATGCTTCTCTCAA 57.079 29.630 0.00 0.00 0.00 3.02
2120 2306 6.996509 AGCACATTGTTATTGGATCTTTGTT 58.003 32.000 0.00 0.00 0.00 2.83
2121 2307 7.444299 AGCACATTGTTATTGGATCTTTGTTT 58.556 30.769 0.00 0.00 0.00 2.83
2122 2308 7.385752 AGCACATTGTTATTGGATCTTTGTTTG 59.614 33.333 0.00 0.00 0.00 2.93
2123 2309 7.171337 GCACATTGTTATTGGATCTTTGTTTGT 59.829 33.333 0.00 0.00 0.00 2.83
2124 2310 8.702438 CACATTGTTATTGGATCTTTGTTTGTC 58.298 33.333 0.00 0.00 0.00 3.18
2125 2311 8.641541 ACATTGTTATTGGATCTTTGTTTGTCT 58.358 29.630 0.00 0.00 0.00 3.41
2129 2315 9.513906 TGTTATTGGATCTTTGTTTGTCTATGA 57.486 29.630 0.00 0.00 0.00 2.15
2132 2318 7.452880 TTGGATCTTTGTTTGTCTATGAAGG 57.547 36.000 0.00 0.00 0.00 3.46
2139 2325 0.392461 TTGTCTATGAAGGCGGCCAC 60.392 55.000 23.09 15.04 0.00 5.01
2154 2340 0.447801 GCCACTTCCACACGCTTATG 59.552 55.000 0.00 0.00 0.00 1.90
2166 2352 5.273170 CACACGCTTATGTAAATCATTGGG 58.727 41.667 0.00 0.00 37.91 4.12
2188 2378 6.824704 TGGGATTTATTTACGATTTCTCCGTT 59.175 34.615 0.00 0.00 40.95 4.44
2200 2390 5.163982 CGATTTCTCCGTTAACCAGTCTTTC 60.164 44.000 0.00 0.00 0.00 2.62
2304 2499 2.340328 GGGCCATTGACACGGAACC 61.340 63.158 4.39 0.00 0.00 3.62
2425 2620 4.752879 GTTAGCCGCCGGTGCTCA 62.753 66.667 21.56 10.40 40.23 4.26
2465 2667 1.142474 GTTTCGATTTGACCGTCCGT 58.858 50.000 0.00 0.00 0.00 4.69
2521 2723 1.541588 AGCAAAAGAATCCGGCAACTC 59.458 47.619 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 1.823041 GAGGGGGAGACGTACCTCG 60.823 68.421 10.40 0.00 40.01 4.63
28 29 4.256462 GAGGGGGAGACGTACCTC 57.744 66.667 10.40 6.87 42.31 3.85
29 30 1.614160 GAGAGGGGGAGACGTACCT 59.386 63.158 10.40 3.56 35.67 3.08
30 31 1.455402 GGAGAGGGGGAGACGTACC 60.455 68.421 0.00 0.00 0.00 3.34
31 32 1.823041 CGGAGAGGGGGAGACGTAC 60.823 68.421 0.00 0.00 0.00 3.67
32 33 2.262774 GACGGAGAGGGGGAGACGTA 62.263 65.000 0.00 0.00 34.43 3.57
33 34 3.641925 GACGGAGAGGGGGAGACGT 62.642 68.421 0.00 0.00 37.26 4.34
34 35 2.829458 GACGGAGAGGGGGAGACG 60.829 72.222 0.00 0.00 0.00 4.18
35 36 2.442458 GGACGGAGAGGGGGAGAC 60.442 72.222 0.00 0.00 0.00 3.36
36 37 3.752167 GGGACGGAGAGGGGGAGA 61.752 72.222 0.00 0.00 0.00 3.71
37 38 4.862823 GGGGACGGAGAGGGGGAG 62.863 77.778 0.00 0.00 0.00 4.30
66 67 0.384974 GAAGGATCTCTACGCGCGAG 60.385 60.000 39.36 27.33 0.00 5.03
90 95 3.058160 CCTTCAACGCCTGCCCTG 61.058 66.667 0.00 0.00 0.00 4.45
99 104 0.310854 GGGAGCAAACACCTTCAACG 59.689 55.000 0.00 0.00 0.00 4.10
126 131 0.999406 CAATAAGAGTGGGCACGACG 59.001 55.000 0.00 0.00 43.51 5.12
129 134 2.868583 CTGATCAATAAGAGTGGGCACG 59.131 50.000 0.00 0.00 36.20 5.34
133 138 5.822132 AGGATCTGATCAATAAGAGTGGG 57.178 43.478 18.64 0.00 0.00 4.61
136 141 6.821616 ACCAAGGATCTGATCAATAAGAGT 57.178 37.500 18.64 4.48 0.00 3.24
139 144 7.123247 ACCAAAACCAAGGATCTGATCAATAAG 59.877 37.037 18.64 6.26 0.00 1.73
143 148 4.739793 ACCAAAACCAAGGATCTGATCAA 58.260 39.130 18.64 0.00 0.00 2.57
213 242 2.980233 ACCCGAAGCTGCACTTGC 60.980 61.111 1.02 0.00 39.29 4.01
227 256 6.949352 ACATCTTAATTCATCATCACACCC 57.051 37.500 0.00 0.00 0.00 4.61
258 287 2.857744 GCGGACCCGTGATCCTAGG 61.858 68.421 0.82 0.82 42.09 3.02
320 350 2.491693 ACGCCCAATAATTTGACTGGTG 59.508 45.455 0.00 0.00 34.60 4.17
366 396 6.844696 TCCGCAATAGAACATATTTCACTC 57.155 37.500 0.00 0.00 0.00 3.51
368 398 7.189693 TGATCCGCAATAGAACATATTTCAC 57.810 36.000 0.00 0.00 0.00 3.18
398 428 1.078823 TGTCACAGATCAGTACCCCCT 59.921 52.381 0.00 0.00 0.00 4.79
399 429 1.568504 TGTCACAGATCAGTACCCCC 58.431 55.000 0.00 0.00 0.00 5.40
426 456 0.387622 CAACTCGGCAGCAATTGTGG 60.388 55.000 7.40 0.68 0.00 4.17
482 513 2.354805 GCCCAAACCGACTACTTGAGAT 60.355 50.000 0.00 0.00 0.00 2.75
486 517 0.250553 TGGCCCAAACCGACTACTTG 60.251 55.000 0.00 0.00 0.00 3.16
488 519 1.373812 GTGGCCCAAACCGACTACT 59.626 57.895 0.00 0.00 0.00 2.57
494 525 3.381136 CCATGGTGGCCCAAACCG 61.381 66.667 2.57 0.00 46.04 4.44
551 582 4.035675 GCAGTAAACCCTAGCAAAGCATAG 59.964 45.833 0.00 0.00 0.00 2.23
626 669 7.773690 ACAAGTCACAAACTTAAACAGTAGGAT 59.226 33.333 0.00 0.00 46.69 3.24
647 690 5.163652 GGACTTGCTTAACACAGAAACAAGT 60.164 40.000 5.26 5.26 46.38 3.16
652 695 4.947388 ACTTGGACTTGCTTAACACAGAAA 59.053 37.500 0.00 0.00 0.00 2.52
662 705 2.172717 ACACACCTACTTGGACTTGCTT 59.827 45.455 0.00 0.00 39.71 3.91
705 749 7.531857 TGGCAAAGGTAAACATCAAAGATTA 57.468 32.000 0.00 0.00 0.00 1.75
708 752 5.860941 TTGGCAAAGGTAAACATCAAAGA 57.139 34.783 0.00 0.00 0.00 2.52
741 863 6.681729 TCATGGTTTAGAAGACTGGTAAGT 57.318 37.500 0.00 0.00 40.21 2.24
785 907 8.034804 AGCACATAAAATAAATCAAGGTGGAAC 58.965 33.333 0.00 0.00 0.00 3.62
814 936 7.913297 TCAAATTGTGACAGTACAAAAGTAAGC 59.087 33.333 0.00 0.00 43.13 3.09
871 1011 4.590222 AGTGGCAAGATTGGTTTCTGAATT 59.410 37.500 0.00 0.00 0.00 2.17
918 1058 7.971722 ACACGTTTCAGCTAAGTTTAAAACAAT 59.028 29.630 0.00 0.00 0.00 2.71
932 1072 2.869233 AAAATGCACACGTTTCAGCT 57.131 40.000 0.00 0.00 33.82 4.24
935 1075 4.346970 CACACTAAAATGCACACGTTTCA 58.653 39.130 0.00 0.00 33.82 2.69
937 1077 3.129638 ACCACACTAAAATGCACACGTTT 59.870 39.130 0.00 0.00 36.55 3.60
941 1081 4.568152 AAGACCACACTAAAATGCACAC 57.432 40.909 0.00 0.00 0.00 3.82
942 1082 5.126779 TGTAAGACCACACTAAAATGCACA 58.873 37.500 0.00 0.00 0.00 4.57
1147 1290 5.939883 GGATAGTTGCATATAGAACATGGCA 59.060 40.000 0.00 0.00 0.00 4.92
1198 1344 4.646945 TCACCAATGTAACCTGCAGAAAAA 59.353 37.500 17.39 0.00 0.00 1.94
1276 1422 3.181475 TGACTCCACACTTGTTCAGTCTC 60.181 47.826 14.47 0.00 36.12 3.36
1309 1455 4.531854 TCTCCTTGACACCAACATCAAAA 58.468 39.130 0.00 0.00 34.52 2.44
1432 1596 5.230942 ACTTGGAAGAGTCGTTACAGATTG 58.769 41.667 0.00 0.00 0.00 2.67
1433 1597 5.470047 ACTTGGAAGAGTCGTTACAGATT 57.530 39.130 0.00 0.00 0.00 2.40
1435 1599 4.931661 AACTTGGAAGAGTCGTTACAGA 57.068 40.909 0.00 0.00 0.00 3.41
1440 1604 5.187687 TGGTAAAAACTTGGAAGAGTCGTT 58.812 37.500 0.00 0.00 0.00 3.85
1717 1893 7.246674 TCGAAAGTGCATCTCATAATTAACC 57.753 36.000 0.00 0.00 0.00 2.85
1739 1915 1.669795 GCAGGCAAGACCCAAAATTCG 60.670 52.381 0.00 0.00 40.58 3.34
1746 1922 2.046023 CATCGCAGGCAAGACCCA 60.046 61.111 0.00 0.00 40.58 4.51
1754 1930 4.035558 TCAAAGTCATAATTCATCGCAGGC 59.964 41.667 0.00 0.00 0.00 4.85
1788 1964 1.350684 ACACACATGACATAGGGCACA 59.649 47.619 0.00 0.00 0.00 4.57
1792 1968 3.084039 AGCAAACACACATGACATAGGG 58.916 45.455 0.00 0.00 0.00 3.53
1796 1972 2.489329 GGCTAGCAAACACACATGACAT 59.511 45.455 18.24 0.00 0.00 3.06
1894 2079 9.778741 ACAGAGACAAAAGACAGATAACAAATA 57.221 29.630 0.00 0.00 0.00 1.40
1895 2080 8.682936 ACAGAGACAAAAGACAGATAACAAAT 57.317 30.769 0.00 0.00 0.00 2.32
1896 2081 8.506168 AACAGAGACAAAAGACAGATAACAAA 57.494 30.769 0.00 0.00 0.00 2.83
1899 2084 7.095439 CCAGAACAGAGACAAAAGACAGATAAC 60.095 40.741 0.00 0.00 0.00 1.89
1901 2086 6.459066 CCAGAACAGAGACAAAAGACAGATA 58.541 40.000 0.00 0.00 0.00 1.98
1902 2087 5.303971 CCAGAACAGAGACAAAAGACAGAT 58.696 41.667 0.00 0.00 0.00 2.90
1903 2088 4.697514 CCAGAACAGAGACAAAAGACAGA 58.302 43.478 0.00 0.00 0.00 3.41
1904 2089 3.249559 GCCAGAACAGAGACAAAAGACAG 59.750 47.826 0.00 0.00 0.00 3.51
1906 2091 3.249559 CAGCCAGAACAGAGACAAAAGAC 59.750 47.826 0.00 0.00 0.00 3.01
1909 2094 2.172505 TCCAGCCAGAACAGAGACAAAA 59.827 45.455 0.00 0.00 0.00 2.44
1916 2101 2.244486 ATCTCTCCAGCCAGAACAGA 57.756 50.000 0.00 0.00 0.00 3.41
1919 2104 3.823304 ACAAAAATCTCTCCAGCCAGAAC 59.177 43.478 0.00 0.00 0.00 3.01
1922 2107 3.822735 TCAACAAAAATCTCTCCAGCCAG 59.177 43.478 0.00 0.00 0.00 4.85
1927 2112 6.409524 AAGCAATCAACAAAAATCTCTCCA 57.590 33.333 0.00 0.00 0.00 3.86
1928 2113 7.719778 AAAAGCAATCAACAAAAATCTCTCC 57.280 32.000 0.00 0.00 0.00 3.71
1951 2136 1.683917 CGAACATCCCCCACACAAAAA 59.316 47.619 0.00 0.00 0.00 1.94
1952 2137 1.323412 CGAACATCCCCCACACAAAA 58.677 50.000 0.00 0.00 0.00 2.44
1953 2138 0.538516 CCGAACATCCCCCACACAAA 60.539 55.000 0.00 0.00 0.00 2.83
1954 2139 1.074072 CCGAACATCCCCCACACAA 59.926 57.895 0.00 0.00 0.00 3.33
1955 2140 2.150719 ACCGAACATCCCCCACACA 61.151 57.895 0.00 0.00 0.00 3.72
1956 2141 1.674322 CACCGAACATCCCCCACAC 60.674 63.158 0.00 0.00 0.00 3.82
1957 2142 1.710996 AACACCGAACATCCCCCACA 61.711 55.000 0.00 0.00 0.00 4.17
1958 2143 0.538746 AAACACCGAACATCCCCCAC 60.539 55.000 0.00 0.00 0.00 4.61
1959 2144 0.538516 CAAACACCGAACATCCCCCA 60.539 55.000 0.00 0.00 0.00 4.96
1960 2145 1.873270 GCAAACACCGAACATCCCCC 61.873 60.000 0.00 0.00 0.00 5.40
1961 2146 0.893727 AGCAAACACCGAACATCCCC 60.894 55.000 0.00 0.00 0.00 4.81
1962 2147 0.958822 AAGCAAACACCGAACATCCC 59.041 50.000 0.00 0.00 0.00 3.85
1963 2148 1.880027 AGAAGCAAACACCGAACATCC 59.120 47.619 0.00 0.00 0.00 3.51
1964 2149 2.095718 GGAGAAGCAAACACCGAACATC 60.096 50.000 0.00 0.00 0.00 3.06
1965 2150 1.880027 GGAGAAGCAAACACCGAACAT 59.120 47.619 0.00 0.00 0.00 2.71
1966 2151 1.305201 GGAGAAGCAAACACCGAACA 58.695 50.000 0.00 0.00 0.00 3.18
1967 2152 1.305201 TGGAGAAGCAAACACCGAAC 58.695 50.000 0.00 0.00 0.00 3.95
1968 2153 2.270352 ATGGAGAAGCAAACACCGAA 57.730 45.000 0.00 0.00 0.00 4.30
1969 2154 3.270027 CATATGGAGAAGCAAACACCGA 58.730 45.455 0.00 0.00 0.00 4.69
1970 2155 3.009723 ACATATGGAGAAGCAAACACCG 58.990 45.455 7.80 0.00 0.00 4.94
1971 2156 6.017605 CAGATACATATGGAGAAGCAAACACC 60.018 42.308 7.80 0.00 0.00 4.16
1972 2157 6.540189 ACAGATACATATGGAGAAGCAAACAC 59.460 38.462 7.80 0.00 0.00 3.32
1975 2160 6.888105 TGACAGATACATATGGAGAAGCAAA 58.112 36.000 7.80 0.00 0.00 3.68
1986 2171 9.224267 GAGGCATACAAAATGACAGATACATAT 57.776 33.333 0.00 0.00 0.00 1.78
1990 2175 7.928706 ACTAGAGGCATACAAAATGACAGATAC 59.071 37.037 0.00 0.00 0.00 2.24
1993 2178 6.299805 ACTAGAGGCATACAAAATGACAGA 57.700 37.500 0.00 0.00 0.00 3.41
1994 2179 6.201806 GCTACTAGAGGCATACAAAATGACAG 59.798 42.308 0.00 0.00 0.00 3.51
1995 2180 6.049149 GCTACTAGAGGCATACAAAATGACA 58.951 40.000 0.00 0.00 0.00 3.58
1996 2181 6.201806 CAGCTACTAGAGGCATACAAAATGAC 59.798 42.308 0.00 0.00 0.00 3.06
2005 2190 4.455070 TCTTCCAGCTACTAGAGGCATA 57.545 45.455 0.00 0.00 0.00 3.14
2013 2198 7.987458 CACCAAATAAGATTCTTCCAGCTACTA 59.013 37.037 1.27 0.00 0.00 1.82
2015 2200 6.038714 CCACCAAATAAGATTCTTCCAGCTAC 59.961 42.308 1.27 0.00 0.00 3.58
2041 2226 3.821033 GGGTTGAGAAGCACTACAATTGT 59.179 43.478 16.68 16.68 0.00 2.71
2044 2229 5.499004 TTAGGGTTGAGAAGCACTACAAT 57.501 39.130 0.00 0.00 0.00 2.71
2047 2232 6.819397 AATTTTAGGGTTGAGAAGCACTAC 57.181 37.500 0.00 0.00 0.00 2.73
2076 2261 4.813161 TGCTTATGCTATGTTGAGAGAAGC 59.187 41.667 1.96 0.00 40.48 3.86
2077 2262 5.814188 TGTGCTTATGCTATGTTGAGAGAAG 59.186 40.000 1.96 0.00 40.48 2.85
2078 2263 5.733676 TGTGCTTATGCTATGTTGAGAGAA 58.266 37.500 1.96 0.00 40.48 2.87
2080 2265 6.037940 ACAATGTGCTTATGCTATGTTGAGAG 59.962 38.462 1.96 0.00 40.48 3.20
2082 2267 6.127810 ACAATGTGCTTATGCTATGTTGAG 57.872 37.500 1.96 0.00 40.48 3.02
2083 2268 6.513806 AACAATGTGCTTATGCTATGTTGA 57.486 33.333 1.96 0.00 40.48 3.18
2084 2269 8.748582 CAATAACAATGTGCTTATGCTATGTTG 58.251 33.333 16.38 11.88 40.48 3.33
2085 2270 7.922278 CCAATAACAATGTGCTTATGCTATGTT 59.078 33.333 1.96 9.57 40.48 2.71
2086 2271 7.285172 TCCAATAACAATGTGCTTATGCTATGT 59.715 33.333 1.96 0.00 40.48 2.29
2087 2272 7.650890 TCCAATAACAATGTGCTTATGCTATG 58.349 34.615 1.96 0.00 40.48 2.23
2088 2273 7.822161 TCCAATAACAATGTGCTTATGCTAT 57.178 32.000 1.96 0.00 40.48 2.97
2120 2306 0.392461 GTGGCCGCCTTCATAGACAA 60.392 55.000 11.61 0.00 0.00 3.18
2121 2307 1.220749 GTGGCCGCCTTCATAGACA 59.779 57.895 11.61 0.00 0.00 3.41
2122 2308 0.107654 AAGTGGCCGCCTTCATAGAC 60.108 55.000 14.07 0.00 0.00 2.59
2123 2309 0.178068 GAAGTGGCCGCCTTCATAGA 59.822 55.000 23.25 0.00 38.53 1.98
2124 2310 0.815615 GGAAGTGGCCGCCTTCATAG 60.816 60.000 27.01 0.00 40.06 2.23
2125 2311 1.223487 GGAAGTGGCCGCCTTCATA 59.777 57.895 27.01 0.00 40.06 2.15
2126 2312 2.044946 GGAAGTGGCCGCCTTCAT 60.045 61.111 27.01 3.48 40.06 2.57
2127 2313 3.565214 TGGAAGTGGCCGCCTTCA 61.565 61.111 27.01 13.68 40.06 3.02
2128 2314 3.056328 GTGGAAGTGGCCGCCTTC 61.056 66.667 21.13 21.13 38.05 3.46
2129 2315 3.884774 TGTGGAAGTGGCCGCCTT 61.885 61.111 14.07 10.21 37.65 4.35
2130 2316 4.643387 GTGTGGAAGTGGCCGCCT 62.643 66.667 14.07 0.00 37.65 5.52
2139 2325 5.794687 TGATTTACATAAGCGTGTGGAAG 57.205 39.130 1.05 0.00 33.62 3.46
2166 2352 9.642312 GGTTAACGGAGAAATCGTAAATAAATC 57.358 33.333 0.00 0.00 40.18 2.17
2173 2359 5.047802 AGACTGGTTAACGGAGAAATCGTAA 60.048 40.000 9.59 0.00 40.18 3.18
2174 2360 4.460382 AGACTGGTTAACGGAGAAATCGTA 59.540 41.667 9.59 0.00 40.18 3.43
2176 2362 3.846360 AGACTGGTTAACGGAGAAATCG 58.154 45.455 9.59 0.00 0.00 3.34
2188 2378 9.959721 AATAATAGAAGCTTGAAAGACTGGTTA 57.040 29.630 2.10 0.00 0.00 2.85
2304 2499 2.352814 CCAGTTCTGGACAACTAGACCG 60.353 54.545 13.02 0.00 34.70 4.79
2419 2614 1.448013 GAGGTTACCGGCTGAGCAC 60.448 63.158 6.82 0.00 0.00 4.40
2421 2616 1.448013 GTGAGGTTACCGGCTGAGC 60.448 63.158 0.00 0.00 0.00 4.26
2422 2617 1.218316 GGTGAGGTTACCGGCTGAG 59.782 63.158 0.00 0.00 0.00 3.35
2423 2618 3.384348 GGTGAGGTTACCGGCTGA 58.616 61.111 0.00 0.00 0.00 4.26
2521 2723 1.801771 CACCATGGCTTGCAAATGTTG 59.198 47.619 13.04 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.