Multiple sequence alignment - TraesCS2A01G344400

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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 TraesCS2A01G344400 chr2A 100.000 2804 0 0 1 2804 581576258 581579061 0.000000e+00 5179
1 TraesCS2A01G344400 chr2A 96.564 815 13 4 1 810 507385379 507386183 0.000000e+00 1336
2 TraesCS2A01G344400 chr2A 96.154 312 11 1 493 804 581569367 581569057 2.490000e-140 508
3 TraesCS2A01G344400 chr2D 92.177 2007 104 25 808 2804 414401421 414403384 0.000000e+00 2787
4 TraesCS2A01G344400 chr2B 91.022 2005 121 32 808 2804 488008851 488010804 0.000000e+00 2651
5 TraesCS2A01G344400 chr3A 97.277 808 19 1 1 805 171626353 171625546 0.000000e+00 1367
6 TraesCS2A01G344400 chr3A 80.000 205 30 7 1630 1828 71235847 71235648 1.050000e-29 141
7 TraesCS2A01G344400 chr4A 96.910 809 21 2 1 805 621805104 621805912 0.000000e+00 1352
8 TraesCS2A01G344400 chr6B 94.963 814 33 6 1 806 245660571 245661384 0.000000e+00 1269
9 TraesCS2A01G344400 chr6B 93.350 812 38 7 1 804 225314920 225314117 0.000000e+00 1186
10 TraesCS2A01G344400 chr6B 85.484 186 23 2 1617 1802 39324848 39324667 1.030000e-44 191
11 TraesCS2A01G344400 chr7A 93.850 813 39 6 1 805 299416112 299415303 0.000000e+00 1214
12 TraesCS2A01G344400 chr7D 92.005 813 46 12 1 804 550879154 550878352 0.000000e+00 1123
13 TraesCS2A01G344400 chr3B 91.288 815 54 7 1 808 809218732 809219536 0.000000e+00 1096
14 TraesCS2A01G344400 chr4B 91.572 795 55 9 19 804 473579736 473580527 0.000000e+00 1086
15 TraesCS2A01G344400 chr5D 83.518 904 84 34 927 1803 513978096 513978961 0.000000e+00 784
16 TraesCS2A01G344400 chr5A 92.537 402 30 0 1402 1803 641733449 641733850 6.730000e-161 577
17 TraesCS2A01G344400 chr5A 82.469 405 44 17 924 1318 641733020 641733407 2.080000e-86 329
18 TraesCS2A01G344400 chr5B 92.289 402 31 0 1402 1803 644890066 644890467 3.130000e-159 571
19 TraesCS2A01G344400 chr5B 81.295 417 40 16 927 1318 644889621 644890024 1.260000e-78 303


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 TraesCS2A01G344400 chr2A 581576258 581579061 2803 False 5179 5179 100.000 1 2804 1 chr2A.!!$F2 2803
1 TraesCS2A01G344400 chr2A 507385379 507386183 804 False 1336 1336 96.564 1 810 1 chr2A.!!$F1 809
2 TraesCS2A01G344400 chr2D 414401421 414403384 1963 False 2787 2787 92.177 808 2804 1 chr2D.!!$F1 1996
3 TraesCS2A01G344400 chr2B 488008851 488010804 1953 False 2651 2651 91.022 808 2804 1 chr2B.!!$F1 1996
4 TraesCS2A01G344400 chr3A 171625546 171626353 807 True 1367 1367 97.277 1 805 1 chr3A.!!$R2 804
5 TraesCS2A01G344400 chr4A 621805104 621805912 808 False 1352 1352 96.910 1 805 1 chr4A.!!$F1 804
6 TraesCS2A01G344400 chr6B 245660571 245661384 813 False 1269 1269 94.963 1 806 1 chr6B.!!$F1 805
7 TraesCS2A01G344400 chr6B 225314117 225314920 803 True 1186 1186 93.350 1 804 1 chr6B.!!$R2 803
8 TraesCS2A01G344400 chr7A 299415303 299416112 809 True 1214 1214 93.850 1 805 1 chr7A.!!$R1 804
9 TraesCS2A01G344400 chr7D 550878352 550879154 802 True 1123 1123 92.005 1 804 1 chr7D.!!$R1 803
10 TraesCS2A01G344400 chr3B 809218732 809219536 804 False 1096 1096 91.288 1 808 1 chr3B.!!$F1 807
11 TraesCS2A01G344400 chr4B 473579736 473580527 791 False 1086 1086 91.572 19 804 1 chr4B.!!$F1 785
12 TraesCS2A01G344400 chr5D 513978096 513978961 865 False 784 784 83.518 927 1803 1 chr5D.!!$F1 876
13 TraesCS2A01G344400 chr5A 641733020 641733850 830 False 453 577 87.503 924 1803 2 chr5A.!!$F1 879
14 TraesCS2A01G344400 chr5B 644889621 644890467 846 False 437 571 86.792 927 1803 2 chr5B.!!$F1 876

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
982 1011 0.179073 AATCGTCTTCCATCTGCCGG 60.179 55.0 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1952 2022 0.038892 CCATTGACCTGCTTGTGTGC 60.039 55.0 0.0 0.0 0.0 4.57 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
544 562 4.479993 GGCTGGAGCTGGTGCGAT 62.480 66.667 0.00 0.00 45.42 4.58
593 611 1.595993 GGCTCGTCCTAGTCAGCACA 61.596 60.000 0.00 0.00 33.22 4.57
596 614 1.801913 CGTCCTAGTCAGCACACGC 60.802 63.158 0.00 0.00 38.99 5.34
752 770 6.920210 TGACACGCAAAAATTAACAATCATGA 59.080 30.769 0.00 0.00 0.00 3.07
817 835 5.123820 GCAATTAACTCCACTAAGCACATCA 59.876 40.000 0.00 0.00 0.00 3.07
822 840 1.089920 CCACTAAGCACATCAGCACC 58.910 55.000 0.00 0.00 36.85 5.01
833 851 3.191791 CACATCAGCACCATTTGACATGA 59.808 43.478 0.00 0.00 0.00 3.07
837 855 3.021695 CAGCACCATTTGACATGATCCT 58.978 45.455 0.00 0.00 0.00 3.24
864 882 1.394697 GCGTCCAACACAAATCAACG 58.605 50.000 0.00 0.00 0.00 4.10
885 903 8.704234 TCAACGAAAAACACAAAATATAATGCC 58.296 29.630 0.00 0.00 0.00 4.40
888 906 9.046296 ACGAAAAACACAAAATATAATGCCAAA 57.954 25.926 0.00 0.00 0.00 3.28
900 927 8.491331 AATATAATGCCAAACAATTTCACCAC 57.509 30.769 0.00 0.00 0.00 4.16
901 928 3.834489 ATGCCAAACAATTTCACCACA 57.166 38.095 0.00 0.00 0.00 4.17
902 929 3.176552 TGCCAAACAATTTCACCACAG 57.823 42.857 0.00 0.00 0.00 3.66
903 930 2.499289 TGCCAAACAATTTCACCACAGT 59.501 40.909 0.00 0.00 0.00 3.55
904 931 3.055530 TGCCAAACAATTTCACCACAGTT 60.056 39.130 0.00 0.00 0.00 3.16
905 932 3.938334 GCCAAACAATTTCACCACAGTTT 59.062 39.130 0.00 0.00 0.00 2.66
906 933 4.394610 GCCAAACAATTTCACCACAGTTTT 59.605 37.500 0.00 0.00 0.00 2.43
907 934 5.106357 GCCAAACAATTTCACCACAGTTTTT 60.106 36.000 0.00 0.00 0.00 1.94
948 977 4.815533 TTCAGAGGACTTTCTCATCCTG 57.184 45.455 0.00 0.00 45.74 3.86
949 978 3.102972 TCAGAGGACTTTCTCATCCTGG 58.897 50.000 0.00 0.00 45.74 4.45
982 1011 0.179073 AATCGTCTTCCATCTGCCGG 60.179 55.000 0.00 0.00 0.00 6.13
986 1015 4.473520 CTTCCATCTGCCGGCCGT 62.474 66.667 26.77 6.75 0.00 5.68
1001 1030 2.044806 GCCGTGCTATCCAGTCCCAT 62.045 60.000 0.00 0.00 0.00 4.00
1008 1037 1.631071 TATCCAGTCCCATGGCGCAA 61.631 55.000 10.83 0.00 40.41 4.85
1038 1070 2.503356 CACCTACCTCTCAAGCTTCCAT 59.497 50.000 0.00 0.00 0.00 3.41
1044 1076 0.694771 TCTCAAGCTTCCATGCCACT 59.305 50.000 0.00 0.00 0.00 4.00
1048 1080 3.818787 GCTTCCATGCCACTGCCG 61.819 66.667 0.00 0.00 36.33 5.69
1263 1313 2.203788 TGGCTCACCGAGTTCCCT 60.204 61.111 0.00 0.00 39.70 4.20
1299 1351 1.214589 CCGCAACAGTACTACCGCT 59.785 57.895 0.00 0.00 0.00 5.52
1302 1354 1.135603 CGCAACAGTACTACCGCTACA 60.136 52.381 0.00 0.00 0.00 2.74
1355 1421 6.149640 CCTCATGATGCATTTCATTCCTAGAG 59.850 42.308 0.00 4.38 34.09 2.43
1356 1422 6.834107 TCATGATGCATTTCATTCCTAGAGA 58.166 36.000 0.00 0.00 34.09 3.10
1357 1423 6.935208 TCATGATGCATTTCATTCCTAGAGAG 59.065 38.462 0.00 0.00 34.09 3.20
1359 1425 6.522946 TGATGCATTTCATTCCTAGAGAGAG 58.477 40.000 0.00 0.00 35.05 3.20
1360 1426 6.325804 TGATGCATTTCATTCCTAGAGAGAGA 59.674 38.462 0.00 0.00 35.05 3.10
1387 1457 2.945008 CTCAACTGCTGAACTGAAACCA 59.055 45.455 0.00 0.00 32.17 3.67
1392 1462 1.205064 CTGAACTGAAACCAGCGCG 59.795 57.895 0.00 0.00 35.09 6.86
1716 1786 2.359230 GAGAAGTTGCAGGCGGCT 60.359 61.111 5.25 5.25 45.15 5.52
1752 1822 1.683917 GACGCTGACATAGGATCCTGT 59.316 52.381 25.28 15.72 0.00 4.00
1803 1873 4.574674 AGTCATGACAAGAATGGCCTAA 57.425 40.909 27.02 0.00 31.48 2.69
1853 1923 5.645067 TCATGAACTGTAAATTCTGCCTCAG 59.355 40.000 0.00 0.00 0.00 3.35
1881 1951 0.176680 CAGGATAGCCTCAGTGCGTT 59.823 55.000 0.00 0.00 44.80 4.84
1914 1984 5.945191 TGCATTTGGTGATACTGAGAAATGA 59.055 36.000 0.00 0.00 34.25 2.57
1928 1998 5.332707 TGAGAAATGACACGATTCTAGTCG 58.667 41.667 1.49 1.49 46.56 4.18
1943 2013 6.968131 TTCTAGTCGTGAATGAAGAATTGG 57.032 37.500 0.00 0.00 0.00 3.16
1944 2014 6.037786 TCTAGTCGTGAATGAAGAATTGGT 57.962 37.500 0.00 0.00 0.00 3.67
1945 2015 5.869344 TCTAGTCGTGAATGAAGAATTGGTG 59.131 40.000 0.00 0.00 0.00 4.17
1949 2019 4.002982 CGTGAATGAAGAATTGGTGGAGA 58.997 43.478 0.00 0.00 0.00 3.71
1950 2020 4.637534 CGTGAATGAAGAATTGGTGGAGAT 59.362 41.667 0.00 0.00 0.00 2.75
1951 2021 5.817296 CGTGAATGAAGAATTGGTGGAGATA 59.183 40.000 0.00 0.00 0.00 1.98
1952 2022 6.018425 CGTGAATGAAGAATTGGTGGAGATAG 60.018 42.308 0.00 0.00 0.00 2.08
1953 2023 5.824624 TGAATGAAGAATTGGTGGAGATAGC 59.175 40.000 0.00 0.00 0.00 2.97
1954 2024 4.842531 TGAAGAATTGGTGGAGATAGCA 57.157 40.909 0.00 0.00 0.00 3.49
1955 2025 4.517285 TGAAGAATTGGTGGAGATAGCAC 58.483 43.478 0.00 0.00 0.00 4.40
1956 2026 4.019411 TGAAGAATTGGTGGAGATAGCACA 60.019 41.667 0.00 0.00 0.00 4.57
1957 2027 3.878778 AGAATTGGTGGAGATAGCACAC 58.121 45.455 0.00 0.00 0.00 3.82
1958 2028 3.264193 AGAATTGGTGGAGATAGCACACA 59.736 43.478 7.89 0.00 36.87 3.72
1959 2029 3.719268 ATTGGTGGAGATAGCACACAA 57.281 42.857 7.89 0.00 36.87 3.33
1960 2030 2.768253 TGGTGGAGATAGCACACAAG 57.232 50.000 7.89 0.00 36.87 3.16
1961 2031 1.339055 TGGTGGAGATAGCACACAAGC 60.339 52.381 7.89 0.00 36.87 4.01
1962 2032 1.339055 GGTGGAGATAGCACACAAGCA 60.339 52.381 7.89 0.00 36.87 3.91
1963 2033 2.005451 GTGGAGATAGCACACAAGCAG 58.995 52.381 1.59 0.00 36.85 4.24
1964 2034 1.065926 TGGAGATAGCACACAAGCAGG 60.066 52.381 0.00 0.00 36.85 4.85
1965 2035 1.065854 GGAGATAGCACACAAGCAGGT 60.066 52.381 0.00 0.00 36.85 4.00
1966 2036 2.275318 GAGATAGCACACAAGCAGGTC 58.725 52.381 0.00 0.00 36.85 3.85
1967 2037 1.625315 AGATAGCACACAAGCAGGTCA 59.375 47.619 0.00 0.00 36.85 4.02
1968 2038 2.038952 AGATAGCACACAAGCAGGTCAA 59.961 45.455 0.00 0.00 36.85 3.18
1969 2039 2.566833 TAGCACACAAGCAGGTCAAT 57.433 45.000 0.00 0.00 36.85 2.57
1970 2040 0.956633 AGCACACAAGCAGGTCAATG 59.043 50.000 0.00 0.00 36.85 2.82
1971 2041 0.038892 GCACACAAGCAGGTCAATGG 60.039 55.000 0.00 0.00 0.00 3.16
1972 2042 1.608055 CACACAAGCAGGTCAATGGA 58.392 50.000 0.00 0.00 0.00 3.41
1973 2043 1.955778 CACACAAGCAGGTCAATGGAA 59.044 47.619 0.00 0.00 0.00 3.53
1974 2044 2.559668 CACACAAGCAGGTCAATGGAAT 59.440 45.455 0.00 0.00 0.00 3.01
1975 2045 2.559668 ACACAAGCAGGTCAATGGAATG 59.440 45.455 0.00 0.00 0.00 2.67
1976 2046 1.547372 ACAAGCAGGTCAATGGAATGC 59.453 47.619 1.03 1.03 37.95 3.56
1977 2047 1.546923 CAAGCAGGTCAATGGAATGCA 59.453 47.619 10.39 0.00 39.35 3.96
1978 2048 2.154567 AGCAGGTCAATGGAATGCAT 57.845 45.000 10.39 0.00 39.35 3.96
1979 2049 2.029623 AGCAGGTCAATGGAATGCATC 58.970 47.619 0.00 0.00 39.35 3.91
1980 2050 2.029623 GCAGGTCAATGGAATGCATCT 58.970 47.619 0.00 0.00 37.73 2.90
1981 2051 2.429610 GCAGGTCAATGGAATGCATCTT 59.570 45.455 0.00 0.00 37.73 2.40
1982 2052 3.490419 GCAGGTCAATGGAATGCATCTTC 60.490 47.826 0.00 0.00 37.73 2.87
1983 2053 3.067742 CAGGTCAATGGAATGCATCTTCC 59.932 47.826 11.51 11.51 44.23 3.46
1984 2054 2.363359 GGTCAATGGAATGCATCTTCCC 59.637 50.000 15.02 8.17 43.47 3.97
1985 2055 3.025978 GTCAATGGAATGCATCTTCCCA 58.974 45.455 15.02 12.87 43.47 4.37
1986 2056 3.067742 GTCAATGGAATGCATCTTCCCAG 59.932 47.826 15.02 6.45 43.47 4.45
1987 2057 1.700955 ATGGAATGCATCTTCCCAGC 58.299 50.000 15.02 0.00 43.47 4.85
1988 2058 0.332293 TGGAATGCATCTTCCCAGCA 59.668 50.000 15.02 0.00 43.47 4.41
1989 2059 1.272592 TGGAATGCATCTTCCCAGCAA 60.273 47.619 15.02 0.00 43.47 3.91
1990 2060 2.037144 GGAATGCATCTTCCCAGCAAT 58.963 47.619 7.74 0.00 42.15 3.56
1991 2061 2.433239 GGAATGCATCTTCCCAGCAATT 59.567 45.455 7.74 0.00 42.15 2.32
1992 2062 3.638160 GGAATGCATCTTCCCAGCAATTA 59.362 43.478 7.74 0.00 42.15 1.40
1993 2063 4.261909 GGAATGCATCTTCCCAGCAATTAG 60.262 45.833 7.74 0.00 42.15 1.73
1994 2064 3.370840 TGCATCTTCCCAGCAATTAGT 57.629 42.857 0.00 0.00 34.97 2.24
1995 2065 3.700538 TGCATCTTCCCAGCAATTAGTT 58.299 40.909 0.00 0.00 34.97 2.24
1996 2066 4.854173 TGCATCTTCCCAGCAATTAGTTA 58.146 39.130 0.00 0.00 34.97 2.24
2013 2083 9.169468 CAATTAGTTATTAATACAAGCCAAGCG 57.831 33.333 0.00 0.00 31.68 4.68
2057 2170 4.944930 ACACCTACAGAGCTCAACTACTAG 59.055 45.833 17.77 4.70 0.00 2.57
2069 2182 6.768861 AGCTCAACTACTAGTAGTACCATCAG 59.231 42.308 30.89 20.53 44.96 2.90
2280 2393 1.852309 ACATTACTGATGGCCCATGGA 59.148 47.619 15.22 0.00 40.21 3.41
2295 2408 0.186873 ATGGATGGGATGGGACTTGC 59.813 55.000 0.00 0.00 0.00 4.01
2401 2514 1.227999 CCCGAGCAGCAAAACGAAGA 61.228 55.000 0.00 0.00 0.00 2.87
2461 2574 5.243426 ACAAGTTCACAAACATTAGCGTT 57.757 34.783 0.00 0.00 37.88 4.84
2489 2604 2.642254 CCACCCAAGCATGGCTGTG 61.642 63.158 1.35 6.42 46.09 3.66
2526 2641 5.009610 AGTTGTAGGTTGTAAAATGGCACTG 59.990 40.000 0.00 0.00 0.00 3.66
2563 2678 5.217978 TGTACACCCTAGTTTTGGTACTG 57.782 43.478 0.00 0.00 33.94 2.74
2657 2772 5.293079 GGAGAAGATAACATCACTCAAGCAC 59.707 44.000 0.00 0.00 37.00 4.40
2688 2803 8.759782 AGCTCTTGTTAATAGCCTAAAGAGTTA 58.240 33.333 10.35 0.00 41.61 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 4.141711 TGAACTCTGTTTGCTGGAGTACTT 60.142 41.667 0.00 0.00 39.09 2.24
544 562 2.283529 GCTCTCCAACCTGGTCCGA 61.284 63.158 0.00 0.00 39.03 4.55
817 835 3.053842 AGAGGATCATGTCAAATGGTGCT 60.054 43.478 0.00 0.00 37.82 4.40
822 840 3.564644 GCTGGAGAGGATCATGTCAAATG 59.435 47.826 6.85 0.00 37.82 2.32
833 851 3.532155 GGACGCGCTGGAGAGGAT 61.532 66.667 5.73 0.00 0.00 3.24
837 855 3.611674 TGTTGGACGCGCTGGAGA 61.612 61.111 5.73 0.00 0.00 3.71
934 961 3.927142 CGTTACACCAGGATGAGAAAGTC 59.073 47.826 0.00 0.00 39.69 3.01
935 962 3.864921 GCGTTACACCAGGATGAGAAAGT 60.865 47.826 0.00 0.00 39.69 2.66
964 993 1.443407 CCGGCAGATGGAAGACGAT 59.557 57.895 0.00 0.00 0.00 3.73
982 1011 2.044806 ATGGGACTGGATAGCACGGC 62.045 60.000 0.00 0.00 0.00 5.68
986 1015 1.839191 GCCATGGGACTGGATAGCA 59.161 57.895 15.13 0.00 38.69 3.49
1008 1037 3.015145 AGGTAGGTGCCCGCCATT 61.015 61.111 0.17 0.00 0.00 3.16
1014 1043 1.222113 GCTTGAGAGGTAGGTGCCC 59.778 63.158 0.00 0.00 0.00 5.36
1015 1044 0.615850 AAGCTTGAGAGGTAGGTGCC 59.384 55.000 0.00 0.00 32.23 5.01
1205 1255 4.838486 GCTCCTCGTCGGCGTCAG 62.838 72.222 10.18 4.92 39.49 3.51
1299 1351 9.251440 GGTGATATAGTATGTATGGGAAGTGTA 57.749 37.037 0.00 0.00 0.00 2.90
1302 1354 8.177456 TGAGGTGATATAGTATGTATGGGAAGT 58.823 37.037 0.00 0.00 0.00 3.01
1355 1421 0.175531 GCAGTTGAGGCCTCTCTCTC 59.824 60.000 32.28 18.49 40.58 3.20
1356 1422 0.252193 AGCAGTTGAGGCCTCTCTCT 60.252 55.000 32.28 22.78 40.58 3.10
1357 1423 0.108233 CAGCAGTTGAGGCCTCTCTC 60.108 60.000 32.28 21.09 40.58 3.20
1359 1425 0.322975 TTCAGCAGTTGAGGCCTCTC 59.677 55.000 32.28 23.74 37.07 3.20
1360 1426 0.036022 GTTCAGCAGTTGAGGCCTCT 59.964 55.000 32.28 10.99 37.07 3.69
1387 1457 2.108514 CACCACATTCATCCGCGCT 61.109 57.895 5.56 0.00 0.00 5.92
1392 1462 1.065199 TCCTCTGCACCACATTCATCC 60.065 52.381 0.00 0.00 0.00 3.51
1716 1786 0.034756 CGTCATCCTTGGTGGTGACA 59.965 55.000 16.18 0.00 42.06 3.58
1752 1822 5.352293 CAGTATGAGCTTTGTGTCAGCATAA 59.648 40.000 0.00 0.00 39.69 1.90
1839 1909 5.899547 TGGATAGAGTCTGAGGCAGAATTTA 59.100 40.000 1.86 0.00 42.46 1.40
1853 1923 4.016444 CTGAGGCTATCCTGGATAGAGTC 58.984 52.174 36.49 30.02 43.17 3.36
1881 1951 7.772757 TCAGTATCACCAAATGCACATTACATA 59.227 33.333 0.00 0.00 0.00 2.29
1928 1998 6.238593 GCTATCTCCACCAATTCTTCATTCAC 60.239 42.308 0.00 0.00 0.00 3.18
1937 2007 3.609853 TGTGTGCTATCTCCACCAATTC 58.390 45.455 0.00 0.00 32.30 2.17
1943 2013 2.005451 CTGCTTGTGTGCTATCTCCAC 58.995 52.381 0.00 0.00 0.00 4.02
1944 2014 1.065926 CCTGCTTGTGTGCTATCTCCA 60.066 52.381 0.00 0.00 0.00 3.86
1945 2015 1.065854 ACCTGCTTGTGTGCTATCTCC 60.066 52.381 0.00 0.00 0.00 3.71
1949 2019 2.566833 TTGACCTGCTTGTGTGCTAT 57.433 45.000 0.00 0.00 0.00 2.97
1950 2020 2.153645 CATTGACCTGCTTGTGTGCTA 58.846 47.619 0.00 0.00 0.00 3.49
1951 2021 0.956633 CATTGACCTGCTTGTGTGCT 59.043 50.000 0.00 0.00 0.00 4.40
1952 2022 0.038892 CCATTGACCTGCTTGTGTGC 60.039 55.000 0.00 0.00 0.00 4.57
1953 2023 1.608055 TCCATTGACCTGCTTGTGTG 58.392 50.000 0.00 0.00 0.00 3.82
1954 2024 2.363306 TTCCATTGACCTGCTTGTGT 57.637 45.000 0.00 0.00 0.00 3.72
1955 2025 2.673043 GCATTCCATTGACCTGCTTGTG 60.673 50.000 0.00 0.00 0.00 3.33
1956 2026 1.547372 GCATTCCATTGACCTGCTTGT 59.453 47.619 0.00 0.00 0.00 3.16
1957 2027 1.546923 TGCATTCCATTGACCTGCTTG 59.453 47.619 0.00 0.00 32.92 4.01
1958 2028 1.927487 TGCATTCCATTGACCTGCTT 58.073 45.000 0.00 0.00 32.92 3.91
1959 2029 2.029623 GATGCATTCCATTGACCTGCT 58.970 47.619 0.00 0.00 33.29 4.24
1960 2030 2.029623 AGATGCATTCCATTGACCTGC 58.970 47.619 0.00 0.00 33.29 4.85
1961 2031 3.067742 GGAAGATGCATTCCATTGACCTG 59.932 47.826 13.21 0.00 46.77 4.00
1962 2032 3.294214 GGAAGATGCATTCCATTGACCT 58.706 45.455 13.21 0.00 46.77 3.85
1963 2033 3.722728 GGAAGATGCATTCCATTGACC 57.277 47.619 13.21 0.81 46.77 4.02
1970 2040 1.477553 TTGCTGGGAAGATGCATTCC 58.522 50.000 10.17 10.17 46.82 3.01
1971 2041 3.814005 AATTGCTGGGAAGATGCATTC 57.186 42.857 0.00 0.00 36.55 2.67
1972 2042 4.284178 ACTAATTGCTGGGAAGATGCATT 58.716 39.130 0.00 0.00 36.55 3.56
1973 2043 3.907221 ACTAATTGCTGGGAAGATGCAT 58.093 40.909 0.00 0.00 36.55 3.96
1974 2044 3.370840 ACTAATTGCTGGGAAGATGCA 57.629 42.857 0.00 0.00 34.69 3.96
1975 2045 6.396829 AATAACTAATTGCTGGGAAGATGC 57.603 37.500 0.00 0.00 0.00 3.91
1981 2051 8.846211 GCTTGTATTAATAACTAATTGCTGGGA 58.154 33.333 0.00 0.00 32.28 4.37
1982 2052 8.082242 GGCTTGTATTAATAACTAATTGCTGGG 58.918 37.037 0.00 0.00 32.28 4.45
1983 2053 8.629158 TGGCTTGTATTAATAACTAATTGCTGG 58.371 33.333 0.00 0.00 32.28 4.85
1986 2056 8.968242 GCTTGGCTTGTATTAATAACTAATTGC 58.032 33.333 0.00 0.00 32.28 3.56
1987 2057 9.169468 CGCTTGGCTTGTATTAATAACTAATTG 57.831 33.333 0.00 0.00 32.28 2.32
1988 2058 9.116067 TCGCTTGGCTTGTATTAATAACTAATT 57.884 29.630 0.00 0.00 32.28 1.40
1989 2059 8.671384 TCGCTTGGCTTGTATTAATAACTAAT 57.329 30.769 0.00 0.00 34.47 1.73
1990 2060 8.671384 ATCGCTTGGCTTGTATTAATAACTAA 57.329 30.769 0.00 0.00 0.00 2.24
1991 2061 9.767228 TTATCGCTTGGCTTGTATTAATAACTA 57.233 29.630 0.00 0.00 0.00 2.24
1992 2062 8.671384 TTATCGCTTGGCTTGTATTAATAACT 57.329 30.769 0.00 0.00 0.00 2.24
1993 2063 9.724839 TTTTATCGCTTGGCTTGTATTAATAAC 57.275 29.630 0.00 0.00 0.00 1.89
1994 2064 9.944663 CTTTTATCGCTTGGCTTGTATTAATAA 57.055 29.630 0.00 0.00 0.00 1.40
1995 2065 8.564574 CCTTTTATCGCTTGGCTTGTATTAATA 58.435 33.333 0.00 0.00 0.00 0.98
1996 2066 7.425606 CCTTTTATCGCTTGGCTTGTATTAAT 58.574 34.615 0.00 0.00 0.00 1.40
2057 2170 5.295950 TCTAGCGTAGACTGATGGTACTAC 58.704 45.833 0.00 0.00 33.98 2.73
2069 2182 7.569957 GCTTTGATACTCTACTCTAGCGTAGAC 60.570 44.444 16.80 9.19 40.55 2.59
2280 2393 1.217057 ACTGGCAAGTCCCATCCCAT 61.217 55.000 0.00 0.00 33.64 4.00
2295 2408 4.511527 AGTCTATGCAGTCAATTCACTGG 58.488 43.478 11.72 0.00 43.61 4.00
2401 2514 3.601443 ACAAGCGAGTCTATTTGCTCT 57.399 42.857 0.00 0.00 36.80 4.09
2461 2574 2.334977 TGCTTGGGTGGAGACTCTAAA 58.665 47.619 1.74 0.00 0.00 1.85
2489 2604 6.094464 ACAACCTACAACTGTTTTCCTTGTAC 59.906 38.462 0.00 0.00 30.76 2.90
2526 2641 7.349412 AGGGTGTACAGTCTCACTATAATTC 57.651 40.000 0.00 0.00 35.26 2.17
2688 2803 9.120538 CCATAGCACTTGTATGGTATTAACTTT 57.879 33.333 1.62 0.00 40.45 2.66
2705 2820 7.065803 GTGTACATTTGTAACATCCATAGCACT 59.934 37.037 0.00 0.00 31.52 4.40
2713 2828 7.197071 TGTGAAGTGTACATTTGTAACATCC 57.803 36.000 8.51 0.00 31.52 3.51


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

AutoCloner maintained by Alex Coulton.