Multiple sequence alignment - TraesCS6B01G138100

Loading Multiple Alignment...

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 TraesCS6B01G138100 chr6B 100.000 2341 0 0 1 2341 135503149 135505489 0.000000e+00 4324.0
1 TraesCS6B01G138100 chr6B 82.741 591 70 19 1315 1888 135578493 135579068 4.490000e-137 497.0
2 TraesCS6B01G138100 chr6B 87.500 136 12 4 1890 2022 135504903 135505036 4.030000e-33 152.0
3 TraesCS6B01G138100 chr6B 87.500 136 12 4 1755 1888 135505038 135505170 4.030000e-33 152.0
4 TraesCS6B01G138100 chr6B 86.614 127 16 1 1188 1313 135519272 135519398 3.140000e-29 139.0
5 TraesCS6B01G138100 chr6B 77.404 208 38 9 336 540 374333211 374333010 5.290000e-22 115.0
6 TraesCS6B01G138100 chr6D 96.343 793 27 2 799 1590 61754708 61755499 0.000000e+00 1303.0
7 TraesCS6B01G138100 chr6D 95.658 806 32 3 1 804 61753786 61754590 0.000000e+00 1291.0
8 TraesCS6B01G138100 chr6D 95.254 295 11 3 1594 1888 61756605 61756896 4.560000e-127 464.0
9 TraesCS6B01G138100 chr6D 96.255 267 8 2 2077 2341 61761122 61761388 9.930000e-119 436.0
10 TraesCS6B01G138100 chr6D 93.158 190 11 1 1890 2079 61756766 61756953 6.370000e-71 278.0
11 TraesCS6B01G138100 chr6A 95.209 814 35 2 749 1558 79023001 79023814 0.000000e+00 1284.0
12 TraesCS6B01G138100 chr6A 93.168 805 38 10 1550 2341 79024607 79025407 0.000000e+00 1166.0
13 TraesCS6B01G138100 chr6A 93.110 537 33 3 1 535 79007089 79007623 0.000000e+00 784.0
14 TraesCS6B01G138100 chr6A 94.656 131 7 0 594 724 79022700 79022830 1.100000e-48 204.0
15 TraesCS6B01G138100 chr6A 100.000 38 0 0 722 759 79022953 79022990 1.160000e-08 71.3


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 TraesCS6B01G138100 chr6B 135503149 135505489 2340 False 1542.666667 4324 91.666667 1 2341 3 chr6B.!!$F3 2340
1 TraesCS6B01G138100 chr6B 135578493 135579068 575 False 497.000000 497 82.741000 1315 1888 1 chr6B.!!$F2 573
2 TraesCS6B01G138100 chr6D 61753786 61756953 3167 False 834.000000 1303 95.103250 1 2079 4 chr6D.!!$F2 2078
3 TraesCS6B01G138100 chr6A 79007089 79007623 534 False 784.000000 784 93.110000 1 535 1 chr6A.!!$F1 534
4 TraesCS6B01G138100 chr6A 79022700 79025407 2707 False 681.325000 1284 95.758250 594 2341 4 chr6A.!!$F2 1747

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
388 391 0.037605 CCGCGTGAGGTAAGTTCCTT 60.038 55.0 4.92 0.0 38.02 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1986 4184 0.033504 GAACGTGCTCTCCCTGTTGA 59.966 55.0 0.0 0.0 0.0 3.18 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 3.057876 GTGTGCATGTTATGAAAACCGGA 60.058 43.478 9.46 0.00 0.00 5.14
263 264 4.892934 TGGGCATTAGTCAACTGAAAAACT 59.107 37.500 0.00 0.00 0.00 2.66
278 279 7.458397 ACTGAAAAACTATTCATACCCAGTCA 58.542 34.615 0.00 0.00 38.55 3.41
316 319 1.343069 GAGGATTCGAGGGCTACCAT 58.657 55.000 0.00 0.00 40.13 3.55
388 391 0.037605 CCGCGTGAGGTAAGTTCCTT 60.038 55.000 4.92 0.00 38.02 3.36
400 403 6.401394 AGGTAAGTTCCTTACGTGGATAAAC 58.599 40.000 0.00 0.00 44.95 2.01
415 418 7.851508 CGTGGATAAACGTGAGATTAATGATT 58.148 34.615 0.00 0.00 38.74 2.57
544 547 1.334059 CCAAACTACTTGCACAGCGTG 60.334 52.381 4.61 4.61 36.51 5.34
549 552 0.660488 TACTTGCACAGCGTGGTTTG 59.340 50.000 10.02 0.00 33.64 2.93
556 559 2.450160 CACAGCGTGGTTTGTCTTTTC 58.550 47.619 1.40 0.00 0.00 2.29
568 571 3.207265 TGTCTTTTCAGGCTACTTGCA 57.793 42.857 0.00 0.00 45.15 4.08
698 702 5.455392 AGATGTTTTTGTCTTCAAGCATCG 58.545 37.500 0.00 0.00 40.05 3.84
759 888 4.335416 CTGGTCCAAACATCAATACAGGT 58.665 43.478 0.00 0.00 0.00 4.00
797 947 8.543774 CAATACAGGATCTACGAAAATCAACTC 58.456 37.037 0.00 0.00 0.00 3.01
818 1092 2.202987 CTCAGGCTGTGGGCGATC 60.203 66.667 15.27 0.00 42.94 3.69
987 1266 6.407074 CGACACAGGAAGGAAAGGAATATAGT 60.407 42.308 0.00 0.00 0.00 2.12
1021 1300 0.902531 GGCTCCTACCAGTAGCAACA 59.097 55.000 0.00 0.00 38.01 3.33
1169 1448 1.425412 GTCGACGGTTGTGTGCTAAT 58.575 50.000 0.00 0.00 0.00 1.73
1182 1461 4.142403 TGTGTGCTAATCTGCTTAATTGCC 60.142 41.667 0.00 0.00 0.00 4.52
1227 1506 1.295423 GTACCCGAGAAAGCCTGCA 59.705 57.895 0.00 0.00 0.00 4.41
1369 1648 6.044046 AGCCGTCGATATGTTTTGTTATGTA 58.956 36.000 0.00 0.00 0.00 2.29
1389 1668 2.073816 ACTGGAACGATTTTGCGTAGG 58.926 47.619 0.00 0.00 44.86 3.18
1401 1681 0.252103 TGCGTAGGGAGGGAGACTTT 60.252 55.000 0.00 0.00 0.00 2.66
1494 1774 5.475719 ACAAATTCTGCAATGGTTGATCTG 58.524 37.500 6.80 0.00 0.00 2.90
1559 1840 5.798132 AGCCCTCCAATCAAAAGAAAAATC 58.202 37.500 0.00 0.00 0.00 2.17
1732 3918 2.200373 AGGGGACGTTTCATTTGAGG 57.800 50.000 0.00 0.00 0.00 3.86
1741 3927 2.420628 TTCATTTGAGGCAAGCAACG 57.579 45.000 0.00 0.00 0.00 4.10
1822 4020 4.905866 CACATGCAAAAGTACTTTCTCACG 59.094 41.667 20.78 15.42 31.45 4.35
1823 4021 4.574828 ACATGCAAAAGTACTTTCTCACGT 59.425 37.500 20.78 15.98 31.45 4.49
1824 4022 4.530094 TGCAAAAGTACTTTCTCACGTG 57.470 40.909 20.78 9.94 31.45 4.49
1825 4023 3.311322 TGCAAAAGTACTTTCTCACGTGG 59.689 43.478 20.78 6.71 31.45 4.94
1826 4024 3.311596 GCAAAAGTACTTTCTCACGTGGT 59.688 43.478 20.78 7.69 31.45 4.16
1827 4025 4.785341 GCAAAAGTACTTTCTCACGTGGTG 60.785 45.833 20.78 12.72 31.46 4.17
1828 4026 2.814280 AGTACTTTCTCACGTGGTGG 57.186 50.000 17.00 6.73 33.87 4.61
1829 4027 1.145803 GTACTTTCTCACGTGGTGGC 58.854 55.000 17.00 0.00 33.87 5.01
1830 4028 0.753867 TACTTTCTCACGTGGTGGCA 59.246 50.000 17.00 0.00 33.87 4.92
1831 4029 0.108585 ACTTTCTCACGTGGTGGCAT 59.891 50.000 17.00 0.00 33.87 4.40
1832 4030 0.798776 CTTTCTCACGTGGTGGCATC 59.201 55.000 17.00 0.00 33.87 3.91
1833 4031 0.605319 TTTCTCACGTGGTGGCATCC 60.605 55.000 17.00 0.00 33.87 3.51
1834 4032 2.436646 CTCACGTGGTGGCATCCC 60.437 66.667 17.00 0.00 33.87 3.85
1835 4033 3.245346 TCACGTGGTGGCATCCCA 61.245 61.111 17.00 0.00 39.32 4.37
1845 4043 2.307496 TGGCATCCCACTGACATTTT 57.693 45.000 0.00 0.00 35.79 1.82
1846 4044 2.607499 TGGCATCCCACTGACATTTTT 58.393 42.857 0.00 0.00 35.79 1.94
1847 4045 2.562298 TGGCATCCCACTGACATTTTTC 59.438 45.455 0.00 0.00 35.79 2.29
1848 4046 2.827921 GGCATCCCACTGACATTTTTCT 59.172 45.455 0.00 0.00 0.00 2.52
1849 4047 3.259123 GGCATCCCACTGACATTTTTCTT 59.741 43.478 0.00 0.00 0.00 2.52
1850 4048 4.462483 GGCATCCCACTGACATTTTTCTTA 59.538 41.667 0.00 0.00 0.00 2.10
1851 4049 5.402398 GCATCCCACTGACATTTTTCTTAC 58.598 41.667 0.00 0.00 0.00 2.34
1852 4050 5.048083 GCATCCCACTGACATTTTTCTTACA 60.048 40.000 0.00 0.00 0.00 2.41
1853 4051 6.516527 GCATCCCACTGACATTTTTCTTACAA 60.517 38.462 0.00 0.00 0.00 2.41
1854 4052 6.385649 TCCCACTGACATTTTTCTTACAAC 57.614 37.500 0.00 0.00 0.00 3.32
1855 4053 5.888724 TCCCACTGACATTTTTCTTACAACA 59.111 36.000 0.00 0.00 0.00 3.33
1856 4054 5.977129 CCCACTGACATTTTTCTTACAACAC 59.023 40.000 0.00 0.00 0.00 3.32
1857 4055 6.405286 CCCACTGACATTTTTCTTACAACACA 60.405 38.462 0.00 0.00 0.00 3.72
1858 4056 6.692681 CCACTGACATTTTTCTTACAACACAG 59.307 38.462 0.00 0.00 0.00 3.66
1859 4057 7.415095 CCACTGACATTTTTCTTACAACACAGA 60.415 37.037 0.00 0.00 0.00 3.41
1860 4058 7.641411 CACTGACATTTTTCTTACAACACAGAG 59.359 37.037 0.00 0.00 0.00 3.35
1861 4059 7.552687 ACTGACATTTTTCTTACAACACAGAGA 59.447 33.333 0.00 0.00 0.00 3.10
1862 4060 7.919690 TGACATTTTTCTTACAACACAGAGAG 58.080 34.615 0.00 0.00 0.00 3.20
1863 4061 7.768582 TGACATTTTTCTTACAACACAGAGAGA 59.231 33.333 0.00 0.00 0.00 3.10
1864 4062 8.147642 ACATTTTTCTTACAACACAGAGAGAG 57.852 34.615 0.00 0.00 0.00 3.20
1865 4063 6.604735 TTTTTCTTACAACACAGAGAGAGC 57.395 37.500 0.00 0.00 0.00 4.09
1866 4064 4.937201 TTCTTACAACACAGAGAGAGCA 57.063 40.909 0.00 0.00 0.00 4.26
1867 4065 4.244425 TCTTACAACACAGAGAGAGCAC 57.756 45.455 0.00 0.00 0.00 4.40
1868 4066 2.706555 TACAACACAGAGAGAGCACG 57.293 50.000 0.00 0.00 0.00 5.34
1869 4067 0.747255 ACAACACAGAGAGAGCACGT 59.253 50.000 0.00 0.00 0.00 4.49
1870 4068 1.137086 ACAACACAGAGAGAGCACGTT 59.863 47.619 0.00 0.00 0.00 3.99
1871 4069 1.789464 CAACACAGAGAGAGCACGTTC 59.211 52.381 0.00 0.00 0.00 3.95
1872 4070 1.032794 ACACAGAGAGAGCACGTTCA 58.967 50.000 0.00 0.00 0.00 3.18
1873 4071 1.615883 ACACAGAGAGAGCACGTTCAT 59.384 47.619 0.00 0.00 0.00 2.57
1874 4072 1.991264 CACAGAGAGAGCACGTTCATG 59.009 52.381 0.00 0.00 0.00 3.07
1875 4073 0.997932 CAGAGAGAGCACGTTCATGC 59.002 55.000 0.00 0.00 46.50 4.06
1881 4079 4.556052 GCACGTTCATGCATGCAA 57.444 50.000 26.68 13.69 45.39 4.08
1882 4080 2.811792 GCACGTTCATGCATGCAAA 58.188 47.368 26.68 13.01 45.39 3.68
1883 4081 1.352114 GCACGTTCATGCATGCAAAT 58.648 45.000 26.68 6.15 45.39 2.32
1884 4082 1.727880 GCACGTTCATGCATGCAAATT 59.272 42.857 26.68 5.25 45.39 1.82
1885 4083 2.222640 GCACGTTCATGCATGCAAATTC 60.223 45.455 26.68 14.39 45.39 2.17
1886 4084 3.247442 CACGTTCATGCATGCAAATTCT 58.753 40.909 26.68 4.34 0.00 2.40
1887 4085 3.676172 CACGTTCATGCATGCAAATTCTT 59.324 39.130 26.68 3.45 0.00 2.52
1888 4086 3.676172 ACGTTCATGCATGCAAATTCTTG 59.324 39.130 26.68 17.21 35.49 3.02
1889 4087 3.676172 CGTTCATGCATGCAAATTCTTGT 59.324 39.130 26.68 1.67 34.79 3.16
1890 4088 4.858140 CGTTCATGCATGCAAATTCTTGTA 59.142 37.500 26.68 8.22 34.79 2.41
1891 4089 5.345472 CGTTCATGCATGCAAATTCTTGTAA 59.655 36.000 26.68 10.28 34.79 2.41
1892 4090 6.128876 CGTTCATGCATGCAAATTCTTGTAAA 60.129 34.615 26.68 5.66 34.79 2.01
1893 4091 6.709145 TCATGCATGCAAATTCTTGTAAAC 57.291 33.333 26.68 0.00 34.79 2.01
1894 4092 6.221659 TCATGCATGCAAATTCTTGTAAACA 58.778 32.000 26.68 0.00 34.79 2.83
1895 4093 5.903764 TGCATGCAAATTCTTGTAAACAC 57.096 34.783 20.30 0.00 34.79 3.32
1896 4094 5.354767 TGCATGCAAATTCTTGTAAACACA 58.645 33.333 20.30 0.00 34.79 3.72
1897 4095 5.990386 TGCATGCAAATTCTTGTAAACACAT 59.010 32.000 20.30 0.00 34.79 3.21
1898 4096 6.073711 TGCATGCAAATTCTTGTAAACACATG 60.074 34.615 20.30 0.00 34.79 3.21
1899 4097 6.073657 GCATGCAAATTCTTGTAAACACATGT 60.074 34.615 14.21 0.00 32.53 3.21
1900 4098 7.518689 GCATGCAAATTCTTGTAAACACATGTT 60.519 33.333 14.21 0.00 35.90 2.71
1901 4099 7.840342 TGCAAATTCTTGTAAACACATGTTT 57.160 28.000 14.08 14.08 40.72 2.83
1902 4100 8.261492 TGCAAATTCTTGTAAACACATGTTTT 57.739 26.923 14.78 3.54 38.65 2.43
1903 4101 9.371136 TGCAAATTCTTGTAAACACATGTTTTA 57.629 25.926 14.78 2.55 38.65 1.52
1934 4132 8.996024 AATAAAGGCCAACAAATATACACAAC 57.004 30.769 5.01 0.00 0.00 3.32
1935 4133 4.695217 AGGCCAACAAATATACACAACG 57.305 40.909 5.01 0.00 0.00 4.10
1936 4134 4.076394 AGGCCAACAAATATACACAACGT 58.924 39.130 5.01 0.00 0.00 3.99
1937 4135 5.247084 AGGCCAACAAATATACACAACGTA 58.753 37.500 5.01 0.00 0.00 3.57
1938 4136 5.122711 AGGCCAACAAATATACACAACGTAC 59.877 40.000 5.01 0.00 31.27 3.67
1939 4137 5.122711 GGCCAACAAATATACACAACGTACT 59.877 40.000 0.00 0.00 31.27 2.73
1940 4138 6.348704 GGCCAACAAATATACACAACGTACTT 60.349 38.462 0.00 0.00 31.27 2.24
1941 4139 6.521821 GCCAACAAATATACACAACGTACTTG 59.478 38.462 0.00 0.00 35.77 3.16
1942 4140 6.521821 CCAACAAATATACACAACGTACTTGC 59.478 38.462 0.00 0.00 32.41 4.01
1943 4141 6.788684 ACAAATATACACAACGTACTTGCA 57.211 33.333 0.00 0.00 32.41 4.08
1944 4142 7.192148 ACAAATATACACAACGTACTTGCAA 57.808 32.000 0.00 0.00 32.41 4.08
1945 4143 7.640852 ACAAATATACACAACGTACTTGCAAA 58.359 30.769 0.00 0.00 32.41 3.68
1946 4144 8.129840 ACAAATATACACAACGTACTTGCAAAA 58.870 29.630 0.00 0.00 32.41 2.44
1947 4145 8.626576 CAAATATACACAACGTACTTGCAAAAG 58.373 33.333 0.00 0.00 32.41 2.27
1948 4146 5.744666 ATACACAACGTACTTGCAAAAGT 57.255 34.783 0.00 0.00 36.82 2.66
1949 4147 3.753842 ACACAACGTACTTGCAAAAGTG 58.246 40.909 0.00 4.55 34.37 3.16
1950 4148 6.010387 ATACACAACGTACTTGCAAAAGTGC 61.010 40.000 0.00 0.00 41.41 4.40
1951 4149 8.110142 ATACACAACGTACTTGCAAAAGTGCT 62.110 38.462 0.00 0.00 41.52 4.40
1952 4150 9.482627 ATACACAACGTACTTGCAAAAGTGCTT 62.483 37.037 0.00 0.00 41.52 3.91
1986 4184 3.198417 GGCATCCCAATGACATTTTTCCT 59.802 43.478 0.00 0.00 40.97 3.36
2093 4433 8.253113 ACAAATGGTTAATTCAATCAGTGATCC 58.747 33.333 5.98 1.20 35.70 3.36
2099 4439 8.348507 GGTTAATTCAATCAGTGATCCATCTTC 58.651 37.037 5.98 0.00 35.70 2.87
2116 4456 6.538742 TCCATCTTCGATGGTGAGTTTATTTC 59.461 38.462 19.26 0.00 40.06 2.17
2133 4473 7.591426 AGTTTATTTCGATGACTGCTTCAAAAC 59.409 33.333 0.00 0.00 37.92 2.43
2147 4487 6.173339 TGCTTCAAAACGAGATCCTATCTTT 58.827 36.000 0.00 0.00 40.38 2.52
2189 4529 6.657836 AGCAATTAAGTTATGTCACCGTAC 57.342 37.500 0.00 0.00 0.00 3.67
2190 4530 5.290158 AGCAATTAAGTTATGTCACCGTACG 59.710 40.000 8.69 8.69 0.00 3.67
2191 4531 5.486706 CAATTAAGTTATGTCACCGTACGC 58.513 41.667 10.49 0.00 0.00 4.42
2217 4557 9.477484 CTGTCATGTTAGTAGTAAATATCCACC 57.523 37.037 0.00 0.00 0.00 4.61
2229 4569 7.548097 AGTAAATATCCACCATGATAGCTACG 58.452 38.462 0.00 0.00 31.09 3.51
2230 4570 5.344743 AATATCCACCATGATAGCTACGG 57.655 43.478 0.00 0.00 31.09 4.02
2263 4603 9.520515 ACCAGATAATAATGGGTATGCTTTTAG 57.479 33.333 0.00 0.00 41.13 1.85
2270 4610 8.766994 ATAATGGGTATGCTTTTAGACATTGT 57.233 30.769 0.00 0.00 0.00 2.71
2292 4632 5.764686 TGTAATGTAATGCAATGCTAGAGGG 59.235 40.000 6.82 0.00 0.00 4.30
2296 4636 2.338577 ATGCAATGCTAGAGGGTCAC 57.661 50.000 6.82 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 6.218746 GTGTGAAGATTCTGCCAAAATTCTT 58.781 36.000 0.00 0.00 0.00 2.52
177 178 1.002684 CCCGTCTCCGATAGTCGAAAG 60.003 57.143 0.22 0.00 43.74 2.62
263 264 4.338400 CACGAGACTGACTGGGTATGAATA 59.662 45.833 0.00 0.00 0.00 1.75
270 271 1.179814 GGTCACGAGACTGACTGGGT 61.180 60.000 12.77 0.00 44.36 4.51
278 279 0.243907 CATCCAACGGTCACGAGACT 59.756 55.000 12.77 0.00 44.36 3.24
316 319 4.624604 GCCGGATGAAGGTAGAAAAAGGTA 60.625 45.833 5.05 0.00 0.00 3.08
400 403 5.395325 ACGCTCAAATCATTAATCTCACG 57.605 39.130 0.00 0.00 0.00 4.35
415 418 1.529438 CTTTTGCTTCCGTACGCTCAA 59.471 47.619 10.49 7.59 0.00 3.02
479 482 2.607635 GCTGAGAAGAAACACACACGAA 59.392 45.455 0.00 0.00 0.00 3.85
544 547 4.793028 GCAAGTAGCCTGAAAAGACAAACC 60.793 45.833 0.00 0.00 37.23 3.27
549 552 2.878406 TGTGCAAGTAGCCTGAAAAGAC 59.122 45.455 0.00 0.00 44.83 3.01
556 559 6.683974 AAACTATATTGTGCAAGTAGCCTG 57.316 37.500 0.00 0.00 44.83 4.85
698 702 0.103208 CCCCAGCGTGAGTGATAGTC 59.897 60.000 0.00 0.00 0.00 2.59
759 888 9.745880 GTAGATCCTGTATTGATTTTCGTAGAA 57.254 33.333 0.00 0.00 45.90 2.10
797 947 2.046507 GCCCACAGCCTGAGTGAG 60.047 66.667 0.00 0.00 39.30 3.51
818 1092 1.767289 GTAGATACGGGCATGACACG 58.233 55.000 0.00 5.48 0.00 4.49
889 1164 8.935844 GGAAAACAAAATCACAGAATTATTCCC 58.064 33.333 0.78 0.00 0.00 3.97
949 1225 2.289444 CCTGTGTCGATGGTAGTTGGTT 60.289 50.000 0.00 0.00 0.00 3.67
987 1266 4.640771 AGGAGCCATGAGAAACAGTTAA 57.359 40.909 0.00 0.00 0.00 2.01
1021 1300 0.759436 ACCAGACACAAGACCCGAGT 60.759 55.000 0.00 0.00 0.00 4.18
1156 1435 5.567138 ATTAAGCAGATTAGCACACAACC 57.433 39.130 0.00 0.00 36.85 3.77
1169 1448 4.202461 CCACCTATAGGGCAATTAAGCAGA 60.202 45.833 22.91 0.00 40.27 4.26
1182 1461 1.687123 CTTCGTCCACCCACCTATAGG 59.313 57.143 17.73 17.73 42.17 2.57
1227 1506 0.768221 TGAAGTCCTGCTGGGGTCTT 60.768 55.000 10.07 11.54 34.45 3.01
1369 1648 2.073816 CCTACGCAAAATCGTTCCAGT 58.926 47.619 0.00 0.00 43.15 4.00
1401 1681 5.626142 TGAACCTAGGTGTGCATAGAAAAA 58.374 37.500 17.14 0.00 31.18 1.94
1423 1703 9.599322 GTTTACTGATTGTTTCTGTATGAACTG 57.401 33.333 0.00 0.00 38.22 3.16
1455 1735 7.017645 CAGAATTTGTCTCAAGAATACAACCG 58.982 38.462 0.00 0.00 32.70 4.44
1494 1774 8.154649 TCTTTCACAAAAGAAGGAAGACATAC 57.845 34.615 0.00 0.00 46.09 2.39
1559 1840 4.155826 TCATAGCCATCAAAGGTTTGTTCG 59.844 41.667 2.49 0.00 39.18 3.95
1591 2673 9.613428 TGTCCCAACTGATAGTTAAGATTTATG 57.387 33.333 0.00 0.00 36.03 1.90
1732 3918 1.838913 TTTTCTGCTTCGTTGCTTGC 58.161 45.000 4.36 0.00 0.00 4.01
1741 3927 6.806120 ACACGTGTTTAAATTTTCTGCTTC 57.194 33.333 17.22 0.00 0.00 3.86
1823 4021 1.499913 ATGTCAGTGGGATGCCACCA 61.500 55.000 30.59 22.00 41.19 4.17
1824 4022 0.323725 AATGTCAGTGGGATGCCACC 60.324 55.000 30.59 17.20 41.19 4.61
1825 4023 1.549203 AAATGTCAGTGGGATGCCAC 58.451 50.000 27.69 27.69 40.64 5.01
1826 4024 2.307496 AAAATGTCAGTGGGATGCCA 57.693 45.000 0.00 0.00 0.00 4.92
1827 4025 2.827921 AGAAAAATGTCAGTGGGATGCC 59.172 45.455 0.00 0.00 0.00 4.40
1828 4026 4.525912 AAGAAAAATGTCAGTGGGATGC 57.474 40.909 0.00 0.00 0.00 3.91
1829 4027 6.573664 TGTAAGAAAAATGTCAGTGGGATG 57.426 37.500 0.00 0.00 0.00 3.51
1830 4028 6.549364 TGTTGTAAGAAAAATGTCAGTGGGAT 59.451 34.615 0.00 0.00 0.00 3.85
1831 4029 5.888724 TGTTGTAAGAAAAATGTCAGTGGGA 59.111 36.000 0.00 0.00 0.00 4.37
1832 4030 5.977129 GTGTTGTAAGAAAAATGTCAGTGGG 59.023 40.000 0.00 0.00 0.00 4.61
1833 4031 6.559810 TGTGTTGTAAGAAAAATGTCAGTGG 58.440 36.000 0.00 0.00 0.00 4.00
1834 4032 7.471721 TCTGTGTTGTAAGAAAAATGTCAGTG 58.528 34.615 0.00 0.00 0.00 3.66
1835 4033 7.552687 TCTCTGTGTTGTAAGAAAAATGTCAGT 59.447 33.333 0.00 0.00 0.00 3.41
1836 4034 7.919690 TCTCTGTGTTGTAAGAAAAATGTCAG 58.080 34.615 0.00 0.00 0.00 3.51
1837 4035 7.768582 TCTCTCTGTGTTGTAAGAAAAATGTCA 59.231 33.333 0.00 0.00 0.00 3.58
1838 4036 8.142994 TCTCTCTGTGTTGTAAGAAAAATGTC 57.857 34.615 0.00 0.00 0.00 3.06
1839 4037 7.254932 GCTCTCTCTGTGTTGTAAGAAAAATGT 60.255 37.037 0.00 0.00 0.00 2.71
1840 4038 7.074502 GCTCTCTCTGTGTTGTAAGAAAAATG 58.925 38.462 0.00 0.00 0.00 2.32
1841 4039 6.767902 TGCTCTCTCTGTGTTGTAAGAAAAAT 59.232 34.615 0.00 0.00 0.00 1.82
1842 4040 6.037172 GTGCTCTCTCTGTGTTGTAAGAAAAA 59.963 38.462 0.00 0.00 0.00 1.94
1843 4041 5.523916 GTGCTCTCTCTGTGTTGTAAGAAAA 59.476 40.000 0.00 0.00 0.00 2.29
1844 4042 5.050490 GTGCTCTCTCTGTGTTGTAAGAAA 58.950 41.667 0.00 0.00 0.00 2.52
1845 4043 4.621991 GTGCTCTCTCTGTGTTGTAAGAA 58.378 43.478 0.00 0.00 0.00 2.52
1846 4044 3.304726 CGTGCTCTCTCTGTGTTGTAAGA 60.305 47.826 0.00 0.00 0.00 2.10
1847 4045 2.983136 CGTGCTCTCTCTGTGTTGTAAG 59.017 50.000 0.00 0.00 0.00 2.34
1848 4046 2.361119 ACGTGCTCTCTCTGTGTTGTAA 59.639 45.455 0.00 0.00 0.00 2.41
1849 4047 1.954382 ACGTGCTCTCTCTGTGTTGTA 59.046 47.619 0.00 0.00 0.00 2.41
1850 4048 0.747255 ACGTGCTCTCTCTGTGTTGT 59.253 50.000 0.00 0.00 0.00 3.32
1851 4049 1.789464 GAACGTGCTCTCTCTGTGTTG 59.211 52.381 0.00 0.00 0.00 3.33
1852 4050 1.409064 TGAACGTGCTCTCTCTGTGTT 59.591 47.619 0.00 0.00 0.00 3.32
1853 4051 1.032794 TGAACGTGCTCTCTCTGTGT 58.967 50.000 0.00 0.00 0.00 3.72
1854 4052 1.991264 CATGAACGTGCTCTCTCTGTG 59.009 52.381 0.00 0.00 0.00 3.66
1855 4053 1.671261 GCATGAACGTGCTCTCTCTGT 60.671 52.381 11.15 0.00 41.82 3.41
1856 4054 0.997932 GCATGAACGTGCTCTCTCTG 59.002 55.000 11.15 0.00 41.82 3.35
1857 4055 0.605083 TGCATGAACGTGCTCTCTCT 59.395 50.000 17.77 0.00 45.27 3.10
1858 4056 1.326852 CATGCATGAACGTGCTCTCTC 59.673 52.381 22.59 0.00 45.27 3.20
1859 4057 1.366679 CATGCATGAACGTGCTCTCT 58.633 50.000 22.59 0.87 45.27 3.10
1860 4058 0.247974 GCATGCATGAACGTGCTCTC 60.248 55.000 30.64 4.36 46.77 3.20
1861 4059 1.798735 GCATGCATGAACGTGCTCT 59.201 52.632 30.64 5.08 46.77 4.09
1862 4060 4.372235 GCATGCATGAACGTGCTC 57.628 55.556 30.64 5.89 46.77 4.26
1865 4063 3.247442 AGAATTTGCATGCATGAACGTG 58.753 40.909 30.64 4.39 0.00 4.49
1866 4064 3.581024 AGAATTTGCATGCATGAACGT 57.419 38.095 30.64 8.05 0.00 3.99
1867 4065 3.676172 ACAAGAATTTGCATGCATGAACG 59.324 39.130 30.64 9.62 37.85 3.95
1868 4066 6.709145 TTACAAGAATTTGCATGCATGAAC 57.291 33.333 30.64 13.87 37.85 3.18
1869 4067 6.704937 TGTTTACAAGAATTTGCATGCATGAA 59.295 30.769 30.64 18.49 37.85 2.57
1870 4068 6.145858 GTGTTTACAAGAATTTGCATGCATGA 59.854 34.615 30.64 14.01 37.85 3.07
1871 4069 6.073711 TGTGTTTACAAGAATTTGCATGCATG 60.074 34.615 23.37 22.70 37.85 4.06
1872 4070 5.990386 TGTGTTTACAAGAATTTGCATGCAT 59.010 32.000 23.37 6.60 37.85 3.96
1873 4071 5.354767 TGTGTTTACAAGAATTTGCATGCA 58.645 33.333 18.46 18.46 37.85 3.96
1874 4072 5.903764 TGTGTTTACAAGAATTTGCATGC 57.096 34.783 11.82 11.82 37.85 4.06
1875 4073 7.410800 ACATGTGTTTACAAGAATTTGCATG 57.589 32.000 0.00 0.00 40.84 4.06
1876 4074 8.436046 AAACATGTGTTTACAAGAATTTGCAT 57.564 26.923 9.24 0.00 45.47 3.96
1877 4075 7.840342 AAACATGTGTTTACAAGAATTTGCA 57.160 28.000 9.24 0.00 45.47 4.08
1908 4106 9.430623 GTTGTGTATATTTGTTGGCCTTTATTT 57.569 29.630 3.32 0.00 0.00 1.40
1909 4107 7.757624 CGTTGTGTATATTTGTTGGCCTTTATT 59.242 33.333 3.32 0.00 0.00 1.40
1910 4108 7.094118 ACGTTGTGTATATTTGTTGGCCTTTAT 60.094 33.333 3.32 0.00 0.00 1.40
1911 4109 6.207025 ACGTTGTGTATATTTGTTGGCCTTTA 59.793 34.615 3.32 0.00 0.00 1.85
1912 4110 5.010213 ACGTTGTGTATATTTGTTGGCCTTT 59.990 36.000 3.32 0.00 0.00 3.11
1913 4111 4.521256 ACGTTGTGTATATTTGTTGGCCTT 59.479 37.500 3.32 0.00 0.00 4.35
1914 4112 4.076394 ACGTTGTGTATATTTGTTGGCCT 58.924 39.130 3.32 0.00 0.00 5.19
1915 4113 4.428615 ACGTTGTGTATATTTGTTGGCC 57.571 40.909 0.00 0.00 0.00 5.36
1916 4114 6.173191 AGTACGTTGTGTATATTTGTTGGC 57.827 37.500 0.00 0.00 35.02 4.52
1917 4115 6.521821 GCAAGTACGTTGTGTATATTTGTTGG 59.478 38.462 0.00 0.00 38.55 3.77
1918 4116 7.072647 TGCAAGTACGTTGTGTATATTTGTTG 58.927 34.615 0.00 0.00 38.55 3.33
1919 4117 7.192148 TGCAAGTACGTTGTGTATATTTGTT 57.808 32.000 0.00 0.00 38.55 2.83
1920 4118 6.788684 TGCAAGTACGTTGTGTATATTTGT 57.211 33.333 0.00 0.00 38.55 2.83
1921 4119 8.495554 TTTTGCAAGTACGTTGTGTATATTTG 57.504 30.769 0.00 0.00 38.55 2.32
1922 4120 8.347035 ACTTTTGCAAGTACGTTGTGTATATTT 58.653 29.630 0.00 0.00 41.81 1.40
1923 4121 7.801315 CACTTTTGCAAGTACGTTGTGTATATT 59.199 33.333 0.00 0.00 41.69 1.28
1924 4122 7.295201 CACTTTTGCAAGTACGTTGTGTATAT 58.705 34.615 0.00 0.00 41.69 0.86
1925 4123 6.651308 CACTTTTGCAAGTACGTTGTGTATA 58.349 36.000 0.00 0.00 41.69 1.47
1926 4124 5.507077 CACTTTTGCAAGTACGTTGTGTAT 58.493 37.500 0.00 0.00 41.69 2.29
1927 4125 4.899516 CACTTTTGCAAGTACGTTGTGTA 58.100 39.130 0.00 0.00 41.69 2.90
1928 4126 3.753842 CACTTTTGCAAGTACGTTGTGT 58.246 40.909 0.00 0.00 41.69 3.72
1942 4140 2.097466 ACCACGTGAGAAAGCACTTTTG 59.903 45.455 19.30 0.00 36.65 2.44
1943 4141 2.097466 CACCACGTGAGAAAGCACTTTT 59.903 45.455 19.30 0.00 35.23 2.27
1944 4142 1.670811 CACCACGTGAGAAAGCACTTT 59.329 47.619 19.30 0.00 35.23 2.66
1945 4143 1.299541 CACCACGTGAGAAAGCACTT 58.700 50.000 19.30 0.00 35.23 3.16
1946 4144 0.532862 CCACCACGTGAGAAAGCACT 60.533 55.000 19.30 0.00 35.23 4.40
1947 4145 1.941812 CCACCACGTGAGAAAGCAC 59.058 57.895 19.30 0.00 35.23 4.40
1948 4146 1.891919 GCCACCACGTGAGAAAGCA 60.892 57.895 19.30 0.00 35.23 3.91
1949 4147 1.237285 ATGCCACCACGTGAGAAAGC 61.237 55.000 19.30 12.59 35.23 3.51
1950 4148 0.798776 GATGCCACCACGTGAGAAAG 59.201 55.000 19.30 1.55 35.23 2.62
1951 4149 0.605319 GGATGCCACCACGTGAGAAA 60.605 55.000 19.30 0.00 35.23 2.52
1952 4150 1.003839 GGATGCCACCACGTGAGAA 60.004 57.895 19.30 0.00 35.23 2.87
1953 4151 2.662596 GGATGCCACCACGTGAGA 59.337 61.111 19.30 0.00 35.23 3.27
1954 4152 2.436646 GGGATGCCACCACGTGAG 60.437 66.667 19.30 9.89 35.23 3.51
1955 4153 2.135903 ATTGGGATGCCACCACGTGA 62.136 55.000 19.30 0.00 37.82 4.35
1956 4154 1.678635 ATTGGGATGCCACCACGTG 60.679 57.895 4.96 9.08 37.82 4.49
1957 4155 1.678635 CATTGGGATGCCACCACGT 60.679 57.895 4.96 0.00 37.82 4.49
1958 4156 1.378382 TCATTGGGATGCCACCACG 60.378 57.895 4.96 0.00 37.82 4.94
1986 4184 0.033504 GAACGTGCTCTCCCTGTTGA 59.966 55.000 0.00 0.00 0.00 3.18
2088 4428 3.033909 ACTCACCATCGAAGATGGATCA 58.966 45.455 29.37 14.51 45.12 2.92
2093 4433 6.255670 TCGAAATAAACTCACCATCGAAGATG 59.744 38.462 3.21 3.21 45.12 2.90
2099 4439 5.520288 AGTCATCGAAATAAACTCACCATCG 59.480 40.000 0.00 0.00 0.00 3.84
2116 4456 2.731451 TCTCGTTTTGAAGCAGTCATCG 59.269 45.455 0.00 0.00 35.70 3.84
2160 4500 9.221775 CGGTGACATAACTTAATTGCTAAATTC 57.778 33.333 0.00 0.00 37.23 2.17
2189 4529 7.865889 TGGATATTTACTACTAACATGACAGCG 59.134 37.037 0.00 0.00 0.00 5.18
2190 4530 8.979574 GTGGATATTTACTACTAACATGACAGC 58.020 37.037 0.00 0.00 0.00 4.40
2191 4531 9.477484 GGTGGATATTTACTACTAACATGACAG 57.523 37.037 0.00 0.00 0.00 3.51
2217 4557 4.521639 TGGTAACTACCCGTAGCTATCATG 59.478 45.833 0.00 0.00 45.87 3.07
2229 4569 7.325725 ACCCATTATTATCTGGTAACTACCC 57.674 40.000 3.45 0.00 45.87 3.69
2230 4570 9.886132 CATACCCATTATTATCTGGTAACTACC 57.114 37.037 0.00 0.00 46.62 3.18
2263 4603 8.344831 TCTAGCATTGCATTACATTACAATGTC 58.655 33.333 11.91 8.07 46.10 3.06
2270 4610 5.940617 ACCCTCTAGCATTGCATTACATTA 58.059 37.500 11.91 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.