Multiple sequence alignment - TraesCS4B01G198200

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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 TraesCS4B01G198200 chr4B 100.000 2234 0 0 1 2234 427068505 427070738 0.000000e+00 4126.0
1 TraesCS4B01G198200 chr4A 94.826 1836 71 14 76 1902 120143229 120141409 0.000000e+00 2843.0
2 TraesCS4B01G198200 chr4A 95.161 248 12 0 1987 2234 120141414 120141167 2.080000e-105 392.0
3 TraesCS4B01G198200 chr4D 94.552 1854 52 10 76 1902 345428813 345430644 0.000000e+00 2819.0
4 TraesCS4B01G198200 chr4D 95.219 251 9 1 1987 2234 345430639 345430889 5.780000e-106 394.0
5 TraesCS4B01G198200 chr4D 96.364 55 2 0 8 62 345415618 345415672 8.500000e-15 91.6
6 TraesCS4B01G198200 chr7B 91.667 636 43 8 654 1281 486675355 486675988 0.000000e+00 872.0
7 TraesCS4B01G198200 chr2B 91.707 627 42 8 654 1272 51990482 51991106 0.000000e+00 861.0
8 TraesCS4B01G198200 chr2B 90.909 88 8 0 1906 1993 682915851 682915938 3.900000e-23 119.0
9 TraesCS4B01G198200 chr2B 90.588 85 8 0 1898 1982 435504868 435504952 1.810000e-21 113.0
10 TraesCS4B01G198200 chr5B 91.680 625 45 6 654 1272 237113741 237114364 0.000000e+00 859.0
11 TraesCS4B01G198200 chr5B 92.771 83 6 0 1900 1982 449753557 449753639 1.080000e-23 121.0
12 TraesCS4B01G198200 chr1A 91.429 630 42 8 654 1275 453783256 453782631 0.000000e+00 854.0
13 TraesCS4B01G198200 chr1A 92.771 83 6 0 1900 1982 270001503 270001585 1.080000e-23 121.0
14 TraesCS4B01G198200 chr5A 91.228 627 45 8 654 1272 603009450 603010074 0.000000e+00 845.0
15 TraesCS4B01G198200 chr3B 90.881 636 39 9 657 1275 188240159 188239526 0.000000e+00 835.0
16 TraesCS4B01G198200 chr3B 86.735 98 13 0 1891 1988 433852537 433852634 2.350000e-20 110.0
17 TraesCS4B01G198200 chr1B 88.694 628 41 14 654 1272 216530918 216531524 0.000000e+00 739.0
18 TraesCS4B01G198200 chr7D 87.163 631 45 14 654 1275 70124957 70124354 0.000000e+00 684.0
19 TraesCS4B01G198200 chr6B 92.683 82 5 1 1901 1982 560797857 560797937 1.400000e-22 117.0
20 TraesCS4B01G198200 chr2A 90.805 87 7 1 1901 1987 127204673 127204758 5.040000e-22 115.0
21 TraesCS4B01G198200 chr2A 88.298 94 10 1 1889 1982 551450261 551450353 6.520000e-21 111.0
22 TraesCS4B01G198200 chr6A 90.588 85 8 0 1901 1985 198073687 198073603 1.810000e-21 113.0


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 TraesCS4B01G198200 chr4B 427068505 427070738 2233 False 4126.0 4126 100.0000 1 2234 1 chr4B.!!$F1 2233
1 TraesCS4B01G198200 chr4A 120141167 120143229 2062 True 1617.5 2843 94.9935 76 2234 2 chr4A.!!$R1 2158
2 TraesCS4B01G198200 chr4D 345428813 345430889 2076 False 1606.5 2819 94.8855 76 2234 2 chr4D.!!$F2 2158
3 TraesCS4B01G198200 chr7B 486675355 486675988 633 False 872.0 872 91.6670 654 1281 1 chr7B.!!$F1 627
4 TraesCS4B01G198200 chr2B 51990482 51991106 624 False 861.0 861 91.7070 654 1272 1 chr2B.!!$F1 618
5 TraesCS4B01G198200 chr5B 237113741 237114364 623 False 859.0 859 91.6800 654 1272 1 chr5B.!!$F1 618
6 TraesCS4B01G198200 chr1A 453782631 453783256 625 True 854.0 854 91.4290 654 1275 1 chr1A.!!$R1 621
7 TraesCS4B01G198200 chr5A 603009450 603010074 624 False 845.0 845 91.2280 654 1272 1 chr5A.!!$F1 618
8 TraesCS4B01G198200 chr3B 188239526 188240159 633 True 835.0 835 90.8810 657 1275 1 chr3B.!!$R1 618
9 TraesCS4B01G198200 chr1B 216530918 216531524 606 False 739.0 739 88.6940 654 1272 1 chr1B.!!$F1 618
10 TraesCS4B01G198200 chr7D 70124354 70124957 603 True 684.0 684 87.1630 654 1275 1 chr7D.!!$R1 621

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
225 226 2.485814 GACTTGTTCCAAGATGCTGGAC 59.514 50.0 10.73 0.0 45.37 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1815 1873 0.772124 TCTGCCCTTTCCCTGGAAGT 60.772 55.0 0.0 0.0 35.38 3.01 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
22 23 4.727507 CAGGAGACATAACTACTGCAGT 57.272 45.455 25.12 25.12 41.14 4.40
23 24 5.836821 CAGGAGACATAACTACTGCAGTA 57.163 43.478 24.63 24.63 41.14 2.74
24 25 6.208988 CAGGAGACATAACTACTGCAGTAA 57.791 41.667 25.95 13.18 41.14 2.24
25 26 6.810911 CAGGAGACATAACTACTGCAGTAAT 58.189 40.000 25.95 15.29 41.14 1.89
26 27 7.268586 CAGGAGACATAACTACTGCAGTAATT 58.731 38.462 25.95 24.25 41.14 1.40
27 28 8.414003 CAGGAGACATAACTACTGCAGTAATTA 58.586 37.037 25.14 25.14 41.14 1.40
28 29 8.634444 AGGAGACATAACTACTGCAGTAATTAG 58.366 37.037 26.32 19.75 36.04 1.73
29 30 7.382759 GGAGACATAACTACTGCAGTAATTAGC 59.617 40.741 26.32 19.25 36.04 3.09
30 31 7.782049 AGACATAACTACTGCAGTAATTAGCA 58.218 34.615 26.32 11.59 36.04 3.49
31 32 8.258007 AGACATAACTACTGCAGTAATTAGCAA 58.742 33.333 26.32 11.27 40.73 3.91
32 33 8.964476 ACATAACTACTGCAGTAATTAGCAAT 57.036 30.769 26.32 12.83 40.73 3.56
33 34 9.046296 ACATAACTACTGCAGTAATTAGCAATC 57.954 33.333 26.32 0.00 40.73 2.67
34 35 9.045223 CATAACTACTGCAGTAATTAGCAATCA 57.955 33.333 26.32 9.70 40.73 2.57
35 36 7.545362 AACTACTGCAGTAATTAGCAATCAG 57.455 36.000 25.95 14.47 40.73 2.90
36 37 6.644347 ACTACTGCAGTAATTAGCAATCAGT 58.356 36.000 25.95 15.09 40.73 3.41
37 38 7.106239 ACTACTGCAGTAATTAGCAATCAGTT 58.894 34.615 25.95 0.00 40.73 3.16
38 39 8.258007 ACTACTGCAGTAATTAGCAATCAGTTA 58.742 33.333 25.95 1.05 40.73 2.24
39 40 7.308782 ACTGCAGTAATTAGCAATCAGTTAC 57.691 36.000 20.16 0.00 40.73 2.50
40 41 7.106239 ACTGCAGTAATTAGCAATCAGTTACT 58.894 34.615 20.16 0.00 40.73 2.24
41 42 7.278868 ACTGCAGTAATTAGCAATCAGTTACTC 59.721 37.037 20.16 0.00 40.73 2.59
42 43 6.255670 TGCAGTAATTAGCAATCAGTTACTCG 59.744 38.462 0.00 0.00 37.90 4.18
43 44 6.255887 GCAGTAATTAGCAATCAGTTACTCGT 59.744 38.462 0.00 0.00 34.39 4.18
44 45 7.613146 CAGTAATTAGCAATCAGTTACTCGTG 58.387 38.462 0.00 0.00 34.39 4.35
45 46 7.275779 CAGTAATTAGCAATCAGTTACTCGTGT 59.724 37.037 0.00 0.00 34.39 4.49
46 47 7.817962 AGTAATTAGCAATCAGTTACTCGTGTT 59.182 33.333 0.00 0.00 31.87 3.32
47 48 9.079833 GTAATTAGCAATCAGTTACTCGTGTTA 57.920 33.333 0.00 0.00 0.00 2.41
48 49 6.939551 TTAGCAATCAGTTACTCGTGTTAC 57.060 37.500 0.00 0.00 0.00 2.50
49 50 5.135508 AGCAATCAGTTACTCGTGTTACT 57.864 39.130 3.62 3.62 36.62 2.24
50 51 5.539048 AGCAATCAGTTACTCGTGTTACTT 58.461 37.500 6.55 0.00 34.31 2.24
51 52 5.989777 AGCAATCAGTTACTCGTGTTACTTT 59.010 36.000 6.55 0.00 34.31 2.66
52 53 6.482308 AGCAATCAGTTACTCGTGTTACTTTT 59.518 34.615 6.55 2.26 34.31 2.27
53 54 7.012044 AGCAATCAGTTACTCGTGTTACTTTTT 59.988 33.333 6.55 1.95 34.31 1.94
103 104 6.614694 TTCCAGTGTTAATTGTAGGCTAGA 57.385 37.500 0.00 0.00 0.00 2.43
184 185 5.320277 AGAAGTCCAATTTTCAGAGGGAAG 58.680 41.667 0.00 0.00 36.72 3.46
225 226 2.485814 GACTTGTTCCAAGATGCTGGAC 59.514 50.000 10.73 0.00 45.37 4.02
351 353 2.486982 CACTCTGTTTTGATGCCTCCAG 59.513 50.000 0.00 0.00 0.00 3.86
579 585 6.656632 TCAAGCATTACCATTTACCAACAA 57.343 33.333 0.00 0.00 0.00 2.83
690 706 9.471702 AGAACTATGAAAAATTCACATCAGGAT 57.528 29.630 0.00 0.00 43.48 3.24
785 805 5.965033 AGAGGATCCAATTGATGTACAGT 57.035 39.130 15.82 0.00 33.66 3.55
869 901 8.839310 AGCAATACAGAACCATGATATACTTC 57.161 34.615 0.00 0.00 0.00 3.01
1206 1239 1.559682 GACCAAGCCTTATCCCAGTCA 59.440 52.381 0.00 0.00 0.00 3.41
1272 1306 4.669206 ACCTGCAAACATGTTTTCATCA 57.331 36.364 21.26 14.97 38.64 3.07
1313 1347 2.286365 ATGTGGATGTTTTCACCGGT 57.714 45.000 0.00 0.00 33.29 5.28
1378 1413 5.411669 CCACCTACAATTTCCAGTTACTCAC 59.588 44.000 0.00 0.00 0.00 3.51
1387 1422 5.482163 TTCCAGTTACTCACACATCATCA 57.518 39.130 0.00 0.00 0.00 3.07
1432 1467 6.387192 TCAGGAAAATCCTCCAATCAAGTA 57.613 37.500 0.00 0.00 45.66 2.24
1454 1489 9.444600 AAGTAGTTATATGGTGTTTGGTACTTG 57.555 33.333 0.00 0.00 0.00 3.16
1495 1530 4.461198 GAGGTTCCTTTTCTTCAAGTGGA 58.539 43.478 0.00 0.00 0.00 4.02
1496 1531 4.867086 AGGTTCCTTTTCTTCAAGTGGAA 58.133 39.130 0.00 0.00 30.71 3.53
1539 1574 9.764363 TTACGAAATATAACATGCTCTGAGATT 57.236 29.630 9.28 0.00 0.00 2.40
1627 1662 8.517062 AGGAATCACATATCCTTTTCTTTCAG 57.483 34.615 0.00 0.00 43.59 3.02
1726 1781 7.097192 TGTCAATCTAGTTGTACTGGATGTTC 58.903 38.462 6.47 2.29 44.23 3.18
1730 1785 3.764237 AGTTGTACTGGATGTTCCGTT 57.236 42.857 0.00 0.00 40.17 4.44
1737 1795 5.533154 TGTACTGGATGTTCCGTTGATTTTT 59.467 36.000 0.00 0.00 40.17 1.94
1794 1852 4.961438 AAAAAGCAATGATTGGTCCTGT 57.039 36.364 10.57 0.00 41.14 4.00
1799 1857 5.391312 AGCAATGATTGGTCCTGTAAAAC 57.609 39.130 3.70 0.00 36.50 2.43
1902 1960 9.233232 CTCTGGTGTTTGTTTCTTTGTATTTAC 57.767 33.333 0.00 0.00 0.00 2.01
1906 1964 9.454585 GGTGTTTGTTTCTTTGTATTTACTACC 57.545 33.333 0.00 0.00 0.00 3.18
1909 1967 9.888878 GTTTGTTTCTTTGTATTTACTACCTCC 57.111 33.333 0.00 0.00 0.00 4.30
1910 1968 7.894376 TGTTTCTTTGTATTTACTACCTCCG 57.106 36.000 0.00 0.00 0.00 4.63
1911 1969 7.444299 TGTTTCTTTGTATTTACTACCTCCGT 58.556 34.615 0.00 0.00 0.00 4.69
1912 1970 7.599998 TGTTTCTTTGTATTTACTACCTCCGTC 59.400 37.037 0.00 0.00 0.00 4.79
1913 1971 6.212888 TCTTTGTATTTACTACCTCCGTCC 57.787 41.667 0.00 0.00 0.00 4.79
1914 1972 5.127682 TCTTTGTATTTACTACCTCCGTCCC 59.872 44.000 0.00 0.00 0.00 4.46
1915 1973 3.979911 TGTATTTACTACCTCCGTCCCA 58.020 45.455 0.00 0.00 0.00 4.37
1916 1974 4.549668 TGTATTTACTACCTCCGTCCCAT 58.450 43.478 0.00 0.00 0.00 4.00
1917 1975 5.704354 TGTATTTACTACCTCCGTCCCATA 58.296 41.667 0.00 0.00 0.00 2.74
1918 1976 6.135454 TGTATTTACTACCTCCGTCCCATAA 58.865 40.000 0.00 0.00 0.00 1.90
1919 1977 6.783977 TGTATTTACTACCTCCGTCCCATAAT 59.216 38.462 0.00 0.00 0.00 1.28
1920 1978 7.949565 TGTATTTACTACCTCCGTCCCATAATA 59.050 37.037 0.00 0.00 0.00 0.98
1921 1979 8.975295 GTATTTACTACCTCCGTCCCATAATAT 58.025 37.037 0.00 0.00 0.00 1.28
1923 1981 8.954834 TTTACTACCTCCGTCCCATAATATAA 57.045 34.615 0.00 0.00 0.00 0.98
1924 1982 8.585471 TTACTACCTCCGTCCCATAATATAAG 57.415 38.462 0.00 0.00 0.00 1.73
1925 1983 6.797707 ACTACCTCCGTCCCATAATATAAGA 58.202 40.000 0.00 0.00 0.00 2.10
1926 1984 7.243824 ACTACCTCCGTCCCATAATATAAGAA 58.756 38.462 0.00 0.00 0.00 2.52
1927 1985 7.899709 ACTACCTCCGTCCCATAATATAAGAAT 59.100 37.037 0.00 0.00 0.00 2.40
1928 1986 6.947464 ACCTCCGTCCCATAATATAAGAATG 58.053 40.000 0.00 0.00 0.00 2.67
1929 1987 5.817816 CCTCCGTCCCATAATATAAGAATGC 59.182 44.000 0.00 0.00 0.00 3.56
1930 1988 6.352222 CCTCCGTCCCATAATATAAGAATGCT 60.352 42.308 0.00 0.00 0.00 3.79
1931 1989 7.016153 TCCGTCCCATAATATAAGAATGCTT 57.984 36.000 0.00 0.00 38.15 3.91
1932 1990 7.458397 TCCGTCCCATAATATAAGAATGCTTT 58.542 34.615 0.00 0.00 35.56 3.51
1933 1991 7.942341 TCCGTCCCATAATATAAGAATGCTTTT 59.058 33.333 0.00 0.00 35.56 2.27
1934 1992 8.576442 CCGTCCCATAATATAAGAATGCTTTTT 58.424 33.333 0.00 0.00 35.56 1.94
1961 2019 9.485206 ACATTAGTGTAGTATCAAAAACGTTCT 57.515 29.630 0.00 0.00 36.63 3.01
1975 2033 9.588774 TCAAAAACGTTCTTATATTTTGAGACG 57.411 29.630 14.74 0.00 42.07 4.18
1976 2034 8.837059 CAAAAACGTTCTTATATTTTGAGACGG 58.163 33.333 11.95 0.00 41.26 4.79
1977 2035 7.894376 AAACGTTCTTATATTTTGAGACGGA 57.106 32.000 0.00 0.00 0.00 4.69
1978 2036 7.521509 AACGTTCTTATATTTTGAGACGGAG 57.478 36.000 0.00 0.00 0.00 4.63
1979 2037 6.040878 ACGTTCTTATATTTTGAGACGGAGG 58.959 40.000 0.00 0.00 0.00 4.30
1980 2038 5.462398 CGTTCTTATATTTTGAGACGGAGGG 59.538 44.000 0.00 0.00 0.00 4.30
1981 2039 6.579865 GTTCTTATATTTTGAGACGGAGGGA 58.420 40.000 0.00 0.00 0.00 4.20
1982 2040 6.801718 TCTTATATTTTGAGACGGAGGGAA 57.198 37.500 0.00 0.00 0.00 3.97
1983 2041 7.374975 TCTTATATTTTGAGACGGAGGGAAT 57.625 36.000 0.00 0.00 0.00 3.01
1984 2042 8.486942 TCTTATATTTTGAGACGGAGGGAATA 57.513 34.615 0.00 0.00 0.00 1.75
1985 2043 8.365647 TCTTATATTTTGAGACGGAGGGAATAC 58.634 37.037 0.00 0.00 0.00 1.89
1986 2044 6.749036 ATATTTTGAGACGGAGGGAATACT 57.251 37.500 0.00 0.00 0.00 2.12
1987 2045 7.850935 ATATTTTGAGACGGAGGGAATACTA 57.149 36.000 0.00 0.00 0.00 1.82
1988 2046 6.749036 ATTTTGAGACGGAGGGAATACTAT 57.251 37.500 0.00 0.00 0.00 2.12
1989 2047 6.555463 TTTTGAGACGGAGGGAATACTATT 57.445 37.500 0.00 0.00 0.00 1.73
1990 2048 6.555463 TTTGAGACGGAGGGAATACTATTT 57.445 37.500 0.00 0.00 0.00 1.40
1991 2049 7.664552 TTTGAGACGGAGGGAATACTATTTA 57.335 36.000 0.00 0.00 0.00 1.40
1992 2050 6.896021 TGAGACGGAGGGAATACTATTTAG 57.104 41.667 0.00 0.00 0.00 1.85
1993 2051 6.371278 TGAGACGGAGGGAATACTATTTAGT 58.629 40.000 0.00 0.00 40.24 2.24
1994 2052 6.489361 TGAGACGGAGGGAATACTATTTAGTC 59.511 42.308 0.00 0.00 37.73 2.59
2017 2075 6.089150 GTCGTGAAACCTCTTACATACTGTTC 59.911 42.308 0.00 0.00 0.00 3.18
2079 2140 8.123639 TCTTATAACAGTAGGATGTCATAGGC 57.876 38.462 0.00 0.00 31.50 3.93
2194 2255 7.065683 CACAAGGTGCACATATTATCAGTAACA 59.934 37.037 20.43 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.118956 ACTGCAGTAGTTATGTCTCCTGC 60.119 47.826 20.16 0.00 44.10 4.85
1 2 4.727507 ACTGCAGTAGTTATGTCTCCTG 57.272 45.455 20.16 0.00 35.67 3.86
2 3 7.425224 AATTACTGCAGTAGTTATGTCTCCT 57.575 36.000 27.47 5.84 40.89 3.69
3 4 7.382759 GCTAATTACTGCAGTAGTTATGTCTCC 59.617 40.741 30.56 16.72 40.89 3.71
4 5 7.921214 TGCTAATTACTGCAGTAGTTATGTCTC 59.079 37.037 30.56 20.50 40.89 3.36
5 6 7.782049 TGCTAATTACTGCAGTAGTTATGTCT 58.218 34.615 30.56 15.24 40.89 3.41
6 7 8.420374 TTGCTAATTACTGCAGTAGTTATGTC 57.580 34.615 30.56 23.81 40.89 3.06
7 8 8.964476 ATTGCTAATTACTGCAGTAGTTATGT 57.036 30.769 30.56 18.78 40.89 2.29
8 9 9.045223 TGATTGCTAATTACTGCAGTAGTTATG 57.955 33.333 30.56 25.25 40.89 1.90
9 10 9.265901 CTGATTGCTAATTACTGCAGTAGTTAT 57.734 33.333 30.56 21.70 40.89 1.89
10 11 8.258007 ACTGATTGCTAATTACTGCAGTAGTTA 58.742 33.333 29.28 29.28 40.89 2.24
11 12 7.106239 ACTGATTGCTAATTACTGCAGTAGTT 58.894 34.615 30.03 30.03 40.89 2.24
12 13 6.644347 ACTGATTGCTAATTACTGCAGTAGT 58.356 36.000 24.79 20.28 43.56 2.73
13 14 7.545362 AACTGATTGCTAATTACTGCAGTAG 57.455 36.000 24.79 17.07 40.46 2.57
14 15 8.258007 AGTAACTGATTGCTAATTACTGCAGTA 58.742 33.333 22.67 22.67 40.46 2.74
15 16 7.106239 AGTAACTGATTGCTAATTACTGCAGT 58.894 34.615 25.12 25.12 40.46 4.40
16 17 7.515841 CGAGTAACTGATTGCTAATTACTGCAG 60.516 40.741 13.48 13.48 40.46 4.41
17 18 6.255670 CGAGTAACTGATTGCTAATTACTGCA 59.744 38.462 0.00 0.00 36.47 4.41
18 19 6.255887 ACGAGTAACTGATTGCTAATTACTGC 59.744 38.462 0.00 0.00 36.47 4.40
19 20 7.275779 ACACGAGTAACTGATTGCTAATTACTG 59.724 37.037 0.00 0.00 36.47 2.74
20 21 7.321153 ACACGAGTAACTGATTGCTAATTACT 58.679 34.615 0.00 0.00 38.48 2.24
21 22 7.521509 ACACGAGTAACTGATTGCTAATTAC 57.478 36.000 0.00 0.00 29.85 1.89
22 23 9.079833 GTAACACGAGTAACTGATTGCTAATTA 57.920 33.333 0.00 0.00 29.85 1.40
23 24 7.817962 AGTAACACGAGTAACTGATTGCTAATT 59.182 33.333 0.00 0.00 29.85 1.40
24 25 7.321153 AGTAACACGAGTAACTGATTGCTAAT 58.679 34.615 0.00 0.00 29.85 1.73
25 26 6.684686 AGTAACACGAGTAACTGATTGCTAA 58.315 36.000 0.00 0.00 29.85 3.09
26 27 6.263516 AGTAACACGAGTAACTGATTGCTA 57.736 37.500 0.00 0.00 29.85 3.49
27 28 5.135508 AGTAACACGAGTAACTGATTGCT 57.864 39.130 0.00 0.00 32.80 3.91
28 29 5.840940 AAGTAACACGAGTAACTGATTGC 57.159 39.130 0.00 0.00 0.00 3.56
62 63 8.917088 ACACTGGAAAATTAATATATGCTGCTT 58.083 29.630 0.00 0.00 0.00 3.91
63 64 8.469309 ACACTGGAAAATTAATATATGCTGCT 57.531 30.769 0.00 0.00 0.00 4.24
73 74 9.869757 GCCTACAATTAACACTGGAAAATTAAT 57.130 29.630 0.00 0.00 0.00 1.40
74 75 9.084533 AGCCTACAATTAACACTGGAAAATTAA 57.915 29.630 0.00 0.00 0.00 1.40
98 99 1.599542 GTGGATTGTGGCGATTCTAGC 59.400 52.381 0.00 0.00 0.00 3.42
103 104 0.327924 TCCTGTGGATTGTGGCGATT 59.672 50.000 0.00 0.00 0.00 3.34
184 185 3.091545 TCAGACAAAGGCATTTCCATCC 58.908 45.455 0.00 0.00 37.29 3.51
225 226 2.765135 AGACCTGGTCATCAGATCTGTG 59.235 50.000 27.48 18.03 44.56 3.66
248 249 4.874966 CAGGACCATCTCATCTTGTCTTTC 59.125 45.833 0.00 0.00 0.00 2.62
384 386 9.938280 AAAGCAATTTAACTTACCTTATTTCCC 57.062 29.630 0.00 0.00 0.00 3.97
563 569 7.768807 AGCTTGTATTGTTGGTAAATGGTAA 57.231 32.000 0.00 0.00 0.00 2.85
564 570 7.337436 GGTAGCTTGTATTGTTGGTAAATGGTA 59.663 37.037 0.00 0.00 0.00 3.25
565 571 6.152154 GGTAGCTTGTATTGTTGGTAAATGGT 59.848 38.462 0.00 0.00 0.00 3.55
566 572 6.405397 GGGTAGCTTGTATTGTTGGTAAATGG 60.405 42.308 0.00 0.00 0.00 3.16
567 573 6.151985 TGGGTAGCTTGTATTGTTGGTAAATG 59.848 38.462 0.00 0.00 0.00 2.32
568 574 6.249951 TGGGTAGCTTGTATTGTTGGTAAAT 58.750 36.000 0.00 0.00 0.00 1.40
569 575 5.632118 TGGGTAGCTTGTATTGTTGGTAAA 58.368 37.500 0.00 0.00 0.00 2.01
709 726 6.328934 TGGGTCACCTAGAATAATATGCTGAA 59.671 38.462 0.00 0.00 37.76 3.02
785 805 7.790027 TCCTTCATTTTGGTGATTTTCTTCAA 58.210 30.769 0.00 0.00 0.00 2.69
1206 1239 4.356405 TTCAGGTGACACATCATCAACT 57.644 40.909 8.08 0.00 45.18 3.16
1272 1306 9.033481 CACATTTGATTGCCGAATTTTGTATAT 57.967 29.630 0.00 0.00 0.00 0.86
1313 1347 9.764363 AAAGAGATATAATCATCGCACTGTTTA 57.236 29.630 0.00 0.00 0.00 2.01
1387 1422 9.445878 CCTGAGCTACATATGAATTTGATATGT 57.554 33.333 20.41 20.41 45.09 2.29
1432 1467 8.380099 TCTTCAAGTACCAAACACCATATAACT 58.620 33.333 0.00 0.00 0.00 2.24
1454 1489 4.006319 CCTCCTGAACATTCAACCTCTTC 58.994 47.826 0.00 0.00 36.64 2.87
1495 1530 4.161565 TCGTAACATAAGCAGACTCCCATT 59.838 41.667 0.00 0.00 0.00 3.16
1496 1531 3.704566 TCGTAACATAAGCAGACTCCCAT 59.295 43.478 0.00 0.00 0.00 4.00
1539 1574 8.996651 TGAAGTATGATCCTAGTATTCAGTCA 57.003 34.615 0.00 0.00 0.00 3.41
1572 1607 5.344128 GCATTGTGTCATAAAGAGCAACAAG 59.656 40.000 0.00 0.00 0.00 3.16
1627 1662 5.510520 CCAGTTCTATTATCCAGCAGAGGAC 60.511 48.000 0.00 0.00 41.30 3.85
1815 1873 0.772124 TCTGCCCTTTCCCTGGAAGT 60.772 55.000 0.00 0.00 35.38 3.01
1872 1930 7.404671 ACAAAGAAACAAACACCAGAGTTAT 57.595 32.000 0.00 0.00 0.00 1.89
1902 1960 7.713734 TTCTTATATTATGGGACGGAGGTAG 57.286 40.000 0.00 0.00 0.00 3.18
1904 1962 6.576442 GCATTCTTATATTATGGGACGGAGGT 60.576 42.308 0.00 0.00 0.00 3.85
1905 1963 5.817816 GCATTCTTATATTATGGGACGGAGG 59.182 44.000 0.00 0.00 0.00 4.30
1906 1964 6.644347 AGCATTCTTATATTATGGGACGGAG 58.356 40.000 0.00 0.00 0.00 4.63
1907 1965 6.620877 AGCATTCTTATATTATGGGACGGA 57.379 37.500 0.00 0.00 0.00 4.69
1908 1966 7.687941 AAAGCATTCTTATATTATGGGACGG 57.312 36.000 0.00 0.00 31.02 4.79
1935 1993 9.485206 AGAACGTTTTTGATACTACACTAATGT 57.515 29.630 0.46 0.00 43.30 2.71
1949 2007 9.588774 CGTCTCAAAATATAAGAACGTTTTTGA 57.411 29.630 13.87 15.56 41.45 2.69
1950 2008 8.837059 CCGTCTCAAAATATAAGAACGTTTTTG 58.163 33.333 13.87 12.46 38.17 2.44
1951 2009 8.776470 TCCGTCTCAAAATATAAGAACGTTTTT 58.224 29.630 9.22 9.22 0.00 1.94
1952 2010 8.314143 TCCGTCTCAAAATATAAGAACGTTTT 57.686 30.769 0.46 0.00 0.00 2.43
1953 2011 7.064253 CCTCCGTCTCAAAATATAAGAACGTTT 59.936 37.037 0.46 0.00 0.00 3.60
1954 2012 6.534079 CCTCCGTCTCAAAATATAAGAACGTT 59.466 38.462 0.00 0.00 0.00 3.99
1955 2013 6.040878 CCTCCGTCTCAAAATATAAGAACGT 58.959 40.000 0.00 0.00 0.00 3.99
1956 2014 5.462398 CCCTCCGTCTCAAAATATAAGAACG 59.538 44.000 0.00 0.00 0.00 3.95
1957 2015 6.579865 TCCCTCCGTCTCAAAATATAAGAAC 58.420 40.000 0.00 0.00 0.00 3.01
1958 2016 6.801718 TCCCTCCGTCTCAAAATATAAGAA 57.198 37.500 0.00 0.00 0.00 2.52
1959 2017 6.801718 TTCCCTCCGTCTCAAAATATAAGA 57.198 37.500 0.00 0.00 0.00 2.10
1960 2018 8.368668 AGTATTCCCTCCGTCTCAAAATATAAG 58.631 37.037 0.00 0.00 0.00 1.73
1961 2019 8.258850 AGTATTCCCTCCGTCTCAAAATATAA 57.741 34.615 0.00 0.00 0.00 0.98
1962 2020 7.850935 AGTATTCCCTCCGTCTCAAAATATA 57.149 36.000 0.00 0.00 0.00 0.86
1963 2021 6.749036 AGTATTCCCTCCGTCTCAAAATAT 57.251 37.500 0.00 0.00 0.00 1.28
1964 2022 7.850935 ATAGTATTCCCTCCGTCTCAAAATA 57.149 36.000 0.00 0.00 0.00 1.40
1965 2023 6.749036 ATAGTATTCCCTCCGTCTCAAAAT 57.251 37.500 0.00 0.00 0.00 1.82
1966 2024 6.555463 AATAGTATTCCCTCCGTCTCAAAA 57.445 37.500 0.00 0.00 0.00 2.44
1967 2025 6.555463 AAATAGTATTCCCTCCGTCTCAAA 57.445 37.500 0.00 0.00 0.00 2.69
1968 2026 6.837568 ACTAAATAGTATTCCCTCCGTCTCAA 59.162 38.462 0.00 0.00 34.13 3.02
1969 2027 6.371278 ACTAAATAGTATTCCCTCCGTCTCA 58.629 40.000 0.00 0.00 34.13 3.27
1970 2028 6.348376 CGACTAAATAGTATTCCCTCCGTCTC 60.348 46.154 0.00 0.00 36.50 3.36
1971 2029 5.472820 CGACTAAATAGTATTCCCTCCGTCT 59.527 44.000 0.00 0.00 36.50 4.18
1972 2030 5.240403 ACGACTAAATAGTATTCCCTCCGTC 59.760 44.000 0.00 0.00 36.50 4.79
1973 2031 5.009410 CACGACTAAATAGTATTCCCTCCGT 59.991 44.000 0.00 1.08 36.50 4.69
1974 2032 5.240183 TCACGACTAAATAGTATTCCCTCCG 59.760 44.000 0.00 0.52 36.50 4.63
1975 2033 6.645790 TCACGACTAAATAGTATTCCCTCC 57.354 41.667 0.00 0.00 36.50 4.30
1976 2034 7.437565 GGTTTCACGACTAAATAGTATTCCCTC 59.562 40.741 0.00 0.00 36.50 4.30
1977 2035 7.125356 AGGTTTCACGACTAAATAGTATTCCCT 59.875 37.037 0.00 0.00 36.50 4.20
1978 2036 7.270779 AGGTTTCACGACTAAATAGTATTCCC 58.729 38.462 0.00 0.00 36.50 3.97
1979 2037 8.196103 AGAGGTTTCACGACTAAATAGTATTCC 58.804 37.037 0.00 0.00 36.50 3.01
1980 2038 9.583765 AAGAGGTTTCACGACTAAATAGTATTC 57.416 33.333 0.00 0.00 36.50 1.75
1983 2041 9.013229 TGTAAGAGGTTTCACGACTAAATAGTA 57.987 33.333 0.00 0.00 36.50 1.82
1984 2042 7.889469 TGTAAGAGGTTTCACGACTAAATAGT 58.111 34.615 0.00 0.00 39.71 2.12
1985 2043 8.928270 ATGTAAGAGGTTTCACGACTAAATAG 57.072 34.615 0.00 0.00 0.00 1.73
1986 2044 9.793252 GTATGTAAGAGGTTTCACGACTAAATA 57.207 33.333 0.00 0.00 0.00 1.40
1987 2045 8.529476 AGTATGTAAGAGGTTTCACGACTAAAT 58.471 33.333 0.00 0.00 0.00 1.40
1988 2046 7.811236 CAGTATGTAAGAGGTTTCACGACTAAA 59.189 37.037 0.00 0.00 0.00 1.85
1989 2047 7.310664 CAGTATGTAAGAGGTTTCACGACTAA 58.689 38.462 0.00 0.00 0.00 2.24
1990 2048 6.849502 CAGTATGTAAGAGGTTTCACGACTA 58.150 40.000 0.00 0.00 0.00 2.59
1991 2049 5.710984 CAGTATGTAAGAGGTTTCACGACT 58.289 41.667 0.00 0.00 0.00 4.18
2079 2140 9.398170 CAACATTATTTTGAAGTGGAACAGTAG 57.602 33.333 0.00 0.00 43.84 2.57


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

AutoCloner maintained by Alex Coulton.