Multiple sequence alignment - TraesCS7A01G553300

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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 TraesCS7A01G553300 chr7A 100.000 2411 0 0 1 2411 726207033 726209443 0.000000e+00 4453
1 TraesCS7A01G553300 chr7A 93.835 957 50 6 495 1443 6649703 6650658 0.000000e+00 1432
2 TraesCS7A01G553300 chr7A 96.758 401 12 1 2011 2411 726362558 726362957 0.000000e+00 667
3 TraesCS7A01G553300 chr7A 96.758 401 12 1 2011 2411 726365687 726366086 0.000000e+00 667
4 TraesCS7A01G553300 chr7A 96.509 401 12 2 2011 2411 726120546 726120944 0.000000e+00 662
5 TraesCS7A01G553300 chr7A 96.509 401 12 2 2011 2411 726343063 726343461 0.000000e+00 662
6 TraesCS7A01G553300 chr7A 96.259 401 14 1 2011 2411 726272357 726272756 0.000000e+00 656
7 TraesCS7A01G553300 chr7A 95.388 412 16 3 1441 1851 726116643 726117052 0.000000e+00 652
8 TraesCS7A01G553300 chr7A 95.146 412 16 4 1441 1851 726268476 726268884 0.000000e+00 647
9 TraesCS7A01G553300 chr7A 95.146 412 16 4 1441 1851 726339194 726339602 0.000000e+00 647
10 TraesCS7A01G553300 chr7A 94.903 412 15 5 1441 1851 726358679 726359085 7.270000e-180 640
11 TraesCS7A01G553300 chr7A 94.264 401 23 0 2011 2411 726265643 726266043 4.410000e-172 614
12 TraesCS7A01G553300 chr7A 94.264 401 23 0 2011 2411 726336362 726336762 4.410000e-172 614
13 TraesCS7A01G553300 chr7A 94.015 401 23 1 2011 2411 726136731 726137130 7.370000e-170 606
14 TraesCS7A01G553300 chr7A 94.737 342 17 1 1 342 6648895 6649235 4.560000e-147 531
15 TraesCS7A01G553300 chr7A 88.643 361 20 11 1443 1803 726274446 726274785 1.030000e-113 420
16 TraesCS7A01G553300 chr7A 95.673 208 9 0 339 546 6649508 6649715 3.840000e-88 335
17 TraesCS7A01G553300 chr1A 96.741 1442 44 3 1 1441 345460851 345462290 0.000000e+00 2399
18 TraesCS7A01G553300 chr1A 97.098 448 13 0 958 1405 30258961 30259408 0.000000e+00 756
19 TraesCS7A01G553300 chr2A 95.985 1345 53 1 103 1447 35822217 35820874 0.000000e+00 2183
20 TraesCS7A01G553300 chr2A 96.296 108 4 0 1 108 35823913 35823806 6.850000e-41 178
21 TraesCS7A01G553300 chr5A 95.936 689 27 1 375 1063 4766008 4766695 0.000000e+00 1116
22 TraesCS7A01G553300 chrUn 96.509 401 12 2 2011 2411 356490604 356490206 0.000000e+00 662
23 TraesCS7A01G553300 chrUn 94.834 271 11 3 1582 1851 467983040 467983308 1.030000e-113 420
24 TraesCS7A01G553300 chrUn 89.614 337 21 10 1467 1803 337346666 337346344 1.330000e-112 416
25 TraesCS7A01G553300 chrUn 95.714 140 3 2 1441 1580 439109228 439109364 3.120000e-54 222
26 TraesCS7A01G553300 chr7D 92.379 433 27 6 1453 1884 629871256 629871683 1.580000e-171 612
27 TraesCS7A01G553300 chr7B 91.480 446 28 9 1443 1884 732750544 732750983 2.650000e-169 604
28 TraesCS7A01G553300 chr5B 78.549 317 58 9 1130 1442 670079398 670079708 1.460000e-47 200
29 TraesCS7A01G553300 chr5D 83.420 193 24 4 1699 1884 455852809 455852618 3.190000e-39 172
30 TraesCS7A01G553300 chr2B 82.990 194 23 6 1699 1884 780601837 780601646 1.480000e-37 167


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 TraesCS7A01G553300 chr7A 726207033 726209443 2410 False 4453.00 4453 100.000000 1 2411 1 chr7A.!!$F2 2410
1 TraesCS7A01G553300 chr7A 6648895 6650658 1763 False 766.00 1432 94.748333 1 1443 3 chr7A.!!$F3 1442
2 TraesCS7A01G553300 chr7A 726358679 726366086 7407 False 658.00 667 96.139667 1441 2411 3 chr7A.!!$F7 970
3 TraesCS7A01G553300 chr7A 726116643 726120944 4301 False 657.00 662 95.948500 1441 2411 2 chr7A.!!$F4 970
4 TraesCS7A01G553300 chr7A 726336362 726343461 7099 False 641.00 662 95.306333 1441 2411 3 chr7A.!!$F6 970
5 TraesCS7A01G553300 chr7A 726265643 726274785 9142 False 584.25 656 93.578000 1441 2411 4 chr7A.!!$F5 970
6 TraesCS7A01G553300 chr1A 345460851 345462290 1439 False 2399.00 2399 96.741000 1 1441 1 chr1A.!!$F2 1440
7 TraesCS7A01G553300 chr2A 35820874 35823913 3039 True 1180.50 2183 96.140500 1 1447 2 chr2A.!!$R1 1446
8 TraesCS7A01G553300 chr5A 4766008 4766695 687 False 1116.00 1116 95.936000 375 1063 1 chr5A.!!$F1 688

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
516 2428 0.178903 AGGAGGTTCAGGCCTGTACA 60.179 55.0 34.8 18.69 39.34 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1858 3777 0.035317 AAGAAGCATCGCACACTGGA 59.965 50.0 0.0 0.0 0.0 3.86 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
403 2274 0.990374 AGCCTGGGATCTCATATGGC 59.010 55.000 15.00 15.00 39.19 4.40
486 2358 3.567164 CCACTGAAGCAACAATGAAGTCT 59.433 43.478 0.00 0.00 0.00 3.24
516 2428 0.178903 AGGAGGTTCAGGCCTGTACA 60.179 55.000 34.80 18.69 39.34 2.90
568 2480 0.815213 TGCGCTAATTAGCTGCCCAG 60.815 55.000 32.02 20.43 46.85 4.45
794 2706 3.558418 GTCTCACGTAGGTTTCTTGCAAA 59.442 43.478 0.00 0.00 0.00 3.68
976 2890 1.823899 GATGGGTCGTTCATGGCCC 60.824 63.158 0.00 1.22 41.42 5.80
1063 2977 4.623932 ATTAGAGGACTTGTGAACTGCA 57.376 40.909 0.00 0.00 0.00 4.41
1187 3101 5.655532 AGGCTGTGCATTTGATTTCTTCTAT 59.344 36.000 0.00 0.00 0.00 1.98
1250 3164 5.353678 AGATTAGATTGTTGCTGTCTCAAGC 59.646 40.000 0.00 0.00 43.82 4.01
1257 3171 3.621953 GCTGTCTCAAGCAAGGAGT 57.378 52.632 0.00 0.00 43.01 3.85
1580 3498 5.351233 TCGTACCATTAAAAACAGTGCAG 57.649 39.130 0.00 0.00 0.00 4.41
1737 3656 0.393077 CTTCCACGGGAGACTTGTGT 59.607 55.000 0.00 0.00 35.72 3.72
1758 3677 6.441284 TGTGTCCTAGTAGTATTTAGGCCAAA 59.559 38.462 5.01 3.96 37.05 3.28
1817 3736 2.279741 ACTATGCACGCATCAACGATT 58.720 42.857 7.99 0.00 37.82 3.34
1834 3753 5.947228 ACGATTGCATCATTTATCGGAAT 57.053 34.783 17.68 0.00 42.95 3.01
1841 3760 4.023792 GCATCATTTATCGGAATGAGCACA 60.024 41.667 12.76 0.00 46.02 4.57
1844 3763 1.934589 TTATCGGAATGAGCACACGG 58.065 50.000 0.00 0.00 0.00 4.94
1847 3766 1.215382 CGGAATGAGCACACGGAGA 59.785 57.895 0.00 0.00 0.00 3.71
1851 3770 2.749621 GGAATGAGCACACGGAGAAAAT 59.250 45.455 0.00 0.00 0.00 1.82
1852 3771 3.191371 GGAATGAGCACACGGAGAAAATT 59.809 43.478 0.00 0.00 0.00 1.82
1853 3772 4.394920 GGAATGAGCACACGGAGAAAATTA 59.605 41.667 0.00 0.00 0.00 1.40
1854 3773 5.447818 GGAATGAGCACACGGAGAAAATTAG 60.448 44.000 0.00 0.00 0.00 1.73
1855 3774 4.002906 TGAGCACACGGAGAAAATTAGT 57.997 40.909 0.00 0.00 0.00 2.24
1857 3776 4.213270 TGAGCACACGGAGAAAATTAGTTG 59.787 41.667 0.00 0.00 0.00 3.16
1858 3777 4.134563 AGCACACGGAGAAAATTAGTTGT 58.865 39.130 0.00 0.00 0.00 3.32
1859 3778 4.213482 AGCACACGGAGAAAATTAGTTGTC 59.787 41.667 0.00 0.00 0.00 3.18
1860 3779 4.612939 GCACACGGAGAAAATTAGTTGTCC 60.613 45.833 0.00 0.00 37.54 4.02
1863 3782 4.755123 CACGGAGAAAATTAGTTGTCCAGT 59.245 41.667 6.81 3.54 40.22 4.00
1864 3783 4.755123 ACGGAGAAAATTAGTTGTCCAGTG 59.245 41.667 6.81 0.00 40.22 3.66
1866 3785 5.334105 CGGAGAAAATTAGTTGTCCAGTGTG 60.334 44.000 6.81 0.00 40.22 3.82
1867 3786 5.438761 AGAAAATTAGTTGTCCAGTGTGC 57.561 39.130 0.00 0.00 0.00 4.57
1868 3787 3.896648 AAATTAGTTGTCCAGTGTGCG 57.103 42.857 0.00 0.00 0.00 5.34
1869 3788 2.831685 ATTAGTTGTCCAGTGTGCGA 57.168 45.000 0.00 0.00 0.00 5.10
1870 3789 2.831685 TTAGTTGTCCAGTGTGCGAT 57.168 45.000 0.00 0.00 0.00 4.58
1871 3790 2.078849 TAGTTGTCCAGTGTGCGATG 57.921 50.000 0.00 0.00 0.00 3.84
1872 3791 1.207593 GTTGTCCAGTGTGCGATGC 59.792 57.895 0.00 0.00 0.00 3.91
1873 3792 1.071299 TTGTCCAGTGTGCGATGCT 59.929 52.632 0.00 0.00 0.00 3.79
1874 3793 0.534877 TTGTCCAGTGTGCGATGCTT 60.535 50.000 0.00 0.00 0.00 3.91
1875 3794 0.950555 TGTCCAGTGTGCGATGCTTC 60.951 55.000 0.00 0.00 0.00 3.86
1876 3795 0.671781 GTCCAGTGTGCGATGCTTCT 60.672 55.000 0.00 0.00 0.00 2.85
1877 3796 0.035317 TCCAGTGTGCGATGCTTCTT 59.965 50.000 0.00 0.00 0.00 2.52
1878 3797 0.167470 CCAGTGTGCGATGCTTCTTG 59.833 55.000 0.00 0.00 0.00 3.02
1879 3798 1.150827 CAGTGTGCGATGCTTCTTGA 58.849 50.000 0.00 0.00 0.00 3.02
1880 3799 1.736126 CAGTGTGCGATGCTTCTTGAT 59.264 47.619 0.00 0.00 0.00 2.57
1881 3800 2.931969 CAGTGTGCGATGCTTCTTGATA 59.068 45.455 0.00 0.00 0.00 2.15
1882 3801 2.932614 AGTGTGCGATGCTTCTTGATAC 59.067 45.455 0.00 0.00 0.00 2.24
1884 3803 2.672874 TGTGCGATGCTTCTTGATACAC 59.327 45.455 0.00 0.00 0.00 2.90
1885 3804 2.030946 GTGCGATGCTTCTTGATACACC 59.969 50.000 0.00 0.00 0.00 4.16
1892 6567 5.452078 TGCTTCTTGATACACCAAAAAGG 57.548 39.130 0.00 0.00 45.67 3.11
1894 6569 5.241506 TGCTTCTTGATACACCAAAAAGGAG 59.758 40.000 0.00 0.00 41.22 3.69
1895 6570 5.703876 CTTCTTGATACACCAAAAAGGAGC 58.296 41.667 0.00 0.00 41.22 4.70
1896 6571 4.079253 TCTTGATACACCAAAAAGGAGCC 58.921 43.478 0.00 0.00 41.22 4.70
1899 6574 2.738587 TACACCAAAAAGGAGCCACA 57.261 45.000 0.00 0.00 41.22 4.17
1901 6576 1.963515 ACACCAAAAAGGAGCCACATC 59.036 47.619 0.00 0.00 41.22 3.06
1906 6581 5.047092 CACCAAAAAGGAGCCACATCTATTT 60.047 40.000 0.00 0.00 41.22 1.40
1908 6583 6.043127 ACCAAAAAGGAGCCACATCTATTTTT 59.957 34.615 0.00 0.00 41.22 1.94
1909 6584 6.591448 CCAAAAAGGAGCCACATCTATTTTTC 59.409 38.462 0.00 0.00 41.22 2.29
1910 6585 7.381323 CAAAAAGGAGCCACATCTATTTTTCT 58.619 34.615 0.00 0.00 31.63 2.52
1912 6587 8.829373 AAAAGGAGCCACATCTATTTTTCTAT 57.171 30.769 0.00 0.00 0.00 1.98
1978 7350 7.589958 TTAAAGTATTTTGAAAGGAGCCACA 57.410 32.000 0.00 0.00 40.09 4.17
1979 7351 6.670695 AAAGTATTTTGAAAGGAGCCACAT 57.329 33.333 0.00 0.00 31.62 3.21
1980 7352 5.904362 AGTATTTTGAAAGGAGCCACATC 57.096 39.130 0.00 0.00 0.00 3.06
1981 7353 5.574188 AGTATTTTGAAAGGAGCCACATCT 58.426 37.500 0.00 0.00 0.00 2.90
1982 7354 6.721318 AGTATTTTGAAAGGAGCCACATCTA 58.279 36.000 0.00 0.00 0.00 1.98
1983 7355 7.349598 AGTATTTTGAAAGGAGCCACATCTAT 58.650 34.615 0.00 0.00 0.00 1.98
1984 7356 7.836183 AGTATTTTGAAAGGAGCCACATCTATT 59.164 33.333 0.00 0.00 0.00 1.73
1985 7357 9.120538 GTATTTTGAAAGGAGCCACATCTATTA 57.879 33.333 0.00 0.00 0.00 0.98
1986 7358 8.773033 ATTTTGAAAGGAGCCACATCTATTAT 57.227 30.769 0.00 0.00 0.00 1.28
1987 7359 9.866655 ATTTTGAAAGGAGCCACATCTATTATA 57.133 29.630 0.00 0.00 0.00 0.98
1988 7360 9.866655 TTTTGAAAGGAGCCACATCTATTATAT 57.133 29.630 0.00 0.00 0.00 0.86
1990 7362 9.944376 TTGAAAGGAGCCACATCTATTATATAC 57.056 33.333 0.00 0.00 0.00 1.47
1991 7363 9.100197 TGAAAGGAGCCACATCTATTATATACA 57.900 33.333 0.00 0.00 0.00 2.29
1992 7364 9.372369 GAAAGGAGCCACATCTATTATATACAC 57.628 37.037 0.00 0.00 0.00 2.90
1993 7365 7.425224 AGGAGCCACATCTATTATATACACC 57.575 40.000 0.00 0.00 0.00 4.16
1994 7366 6.959954 AGGAGCCACATCTATTATATACACCA 59.040 38.462 0.00 0.00 0.00 4.17
1995 7367 7.457852 AGGAGCCACATCTATTATATACACCAA 59.542 37.037 0.00 0.00 0.00 3.67
1996 7368 8.100791 GGAGCCACATCTATTATATACACCAAA 58.899 37.037 0.00 0.00 0.00 3.28
1997 7369 9.502091 GAGCCACATCTATTATATACACCAAAA 57.498 33.333 0.00 0.00 0.00 2.44
1998 7370 9.860650 AGCCACATCTATTATATACACCAAAAA 57.139 29.630 0.00 0.00 0.00 1.94
2015 7387 5.806089 CAAAAATTAGTTGGAACGAGCAC 57.194 39.130 0.00 0.00 0.00 4.40
2016 7388 5.277825 CAAAAATTAGTTGGAACGAGCACA 58.722 37.500 0.00 0.00 0.00 4.57
2017 7389 5.705609 AAAATTAGTTGGAACGAGCACAT 57.294 34.783 0.00 0.00 0.00 3.21
2018 7390 5.705609 AAATTAGTTGGAACGAGCACATT 57.294 34.783 0.00 0.00 0.00 2.71
2019 7391 4.685169 ATTAGTTGGAACGAGCACATTG 57.315 40.909 0.00 0.00 0.00 2.82
2020 7392 2.254546 AGTTGGAACGAGCACATTGA 57.745 45.000 0.00 0.00 0.00 2.57
2021 7393 2.783135 AGTTGGAACGAGCACATTGAT 58.217 42.857 0.00 0.00 0.00 2.57
2022 7394 3.149196 AGTTGGAACGAGCACATTGATT 58.851 40.909 0.00 0.00 0.00 2.57
2023 7395 3.569701 AGTTGGAACGAGCACATTGATTT 59.430 39.130 0.00 0.00 0.00 2.17
2024 7396 4.037923 AGTTGGAACGAGCACATTGATTTT 59.962 37.500 0.00 0.00 0.00 1.82
2025 7397 4.159377 TGGAACGAGCACATTGATTTTC 57.841 40.909 0.00 0.00 0.00 2.29
2026 7398 3.567585 TGGAACGAGCACATTGATTTTCA 59.432 39.130 0.00 0.00 0.00 2.69
2027 7399 3.914364 GGAACGAGCACATTGATTTTCAC 59.086 43.478 0.00 0.00 0.00 3.18
2028 7400 4.536065 GAACGAGCACATTGATTTTCACA 58.464 39.130 0.00 0.00 0.00 3.58
2029 7401 4.151258 ACGAGCACATTGATTTTCACAG 57.849 40.909 0.00 0.00 0.00 3.66
2030 7402 3.058016 ACGAGCACATTGATTTTCACAGG 60.058 43.478 0.00 0.00 0.00 4.00
2031 7403 3.189080 CGAGCACATTGATTTTCACAGGA 59.811 43.478 0.00 0.00 0.00 3.86
2032 7404 4.670992 CGAGCACATTGATTTTCACAGGAG 60.671 45.833 0.00 0.00 0.00 3.69
2033 7405 3.057033 AGCACATTGATTTTCACAGGAGC 60.057 43.478 0.00 0.00 0.00 4.70
2034 7406 3.841643 CACATTGATTTTCACAGGAGCC 58.158 45.455 0.00 0.00 0.00 4.70
2035 7407 3.256383 CACATTGATTTTCACAGGAGCCA 59.744 43.478 0.00 0.00 0.00 4.75
2036 7408 3.256631 ACATTGATTTTCACAGGAGCCAC 59.743 43.478 0.00 0.00 0.00 5.01
2037 7409 2.655090 TGATTTTCACAGGAGCCACA 57.345 45.000 0.00 0.00 0.00 4.17
2038 7410 3.159213 TGATTTTCACAGGAGCCACAT 57.841 42.857 0.00 0.00 0.00 3.21
2039 7411 3.084039 TGATTTTCACAGGAGCCACATC 58.916 45.455 0.00 0.00 0.00 3.06
2040 7412 2.957402 TTTTCACAGGAGCCACATCT 57.043 45.000 0.00 0.00 0.00 2.90
2041 7413 4.019411 TGATTTTCACAGGAGCCACATCTA 60.019 41.667 0.00 0.00 0.00 1.98
2042 7414 4.574674 TTTTCACAGGAGCCACATCTAT 57.425 40.909 0.00 0.00 0.00 1.98
2043 7415 3.827008 TTCACAGGAGCCACATCTATC 57.173 47.619 0.00 0.00 0.00 2.08
2044 7416 3.037851 TCACAGGAGCCACATCTATCT 57.962 47.619 0.00 0.00 0.00 1.98
2045 7417 3.378512 TCACAGGAGCCACATCTATCTT 58.621 45.455 0.00 0.00 0.00 2.40
2046 7418 3.386078 TCACAGGAGCCACATCTATCTTC 59.614 47.826 0.00 0.00 0.00 2.87
2047 7419 3.387374 CACAGGAGCCACATCTATCTTCT 59.613 47.826 0.00 0.00 0.00 2.85
2048 7420 4.586421 CACAGGAGCCACATCTATCTTCTA 59.414 45.833 0.00 0.00 0.00 2.10
2049 7421 5.245751 CACAGGAGCCACATCTATCTTCTAT 59.754 44.000 0.00 0.00 0.00 1.98
2050 7422 5.843421 ACAGGAGCCACATCTATCTTCTATT 59.157 40.000 0.00 0.00 0.00 1.73
2051 7423 7.013220 ACAGGAGCCACATCTATCTTCTATTA 58.987 38.462 0.00 0.00 0.00 0.98
2052 7424 7.677745 ACAGGAGCCACATCTATCTTCTATTAT 59.322 37.037 0.00 0.00 0.00 1.28
2053 7425 9.194972 CAGGAGCCACATCTATCTTCTATTATA 57.805 37.037 0.00 0.00 0.00 0.98
2054 7426 9.950306 AGGAGCCACATCTATCTTCTATTATAT 57.050 33.333 0.00 0.00 0.00 0.86
2240 7612 2.380064 TTTGGTTTGAGCCTGACCAT 57.620 45.000 0.00 0.00 42.59 3.55
2320 7692 3.282021 CATGTGGTTGGATGGTTAGGAG 58.718 50.000 0.00 0.00 0.00 3.69
2333 7705 7.016268 TGGATGGTTAGGAGAATAGTGGTATTC 59.984 40.741 0.00 0.00 43.51 1.75
2402 7774 0.960364 TCACTTTCCTTGGATGCGGC 60.960 55.000 0.00 0.00 0.00 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
197 1792 7.650903 TCAATATCTCATCAATGTCGACTTGAG 59.349 37.037 24.46 21.38 36.16 3.02
403 2274 2.674380 GGGTGGCACTTGGCTCTG 60.674 66.667 18.45 0.00 44.01 3.35
486 2358 0.253044 GAACCTCCTGCATGTGCCTA 59.747 55.000 2.07 0.00 41.18 3.93
516 2428 3.137176 CCTCCACATCACTCCCACATATT 59.863 47.826 0.00 0.00 0.00 1.28
794 2706 4.811557 GCATCAGAAGCGAGGTTAAATAGT 59.188 41.667 0.00 0.00 0.00 2.12
939 2853 0.680618 CCACATTGAGCTTTGCCCAA 59.319 50.000 0.00 0.00 0.00 4.12
976 2890 2.579201 CCCTGCTGTACCGTCAGG 59.421 66.667 15.78 15.78 45.24 3.86
1063 2977 1.744368 CTGCTTCCAGCGCATCAGT 60.744 57.895 11.47 0.00 46.26 3.41
1187 3101 2.259618 GCGCTGAACGATCTTGTTCTA 58.740 47.619 0.00 2.16 46.59 2.10
1362 3280 0.457443 TGATGCTCGCAATCTCGTCT 59.543 50.000 0.00 0.00 0.00 4.18
1580 3498 7.586747 TGTGAACGATATTTTTAAGTGGAACC 58.413 34.615 0.00 0.00 37.80 3.62
1614 3532 8.322906 TGTAGACATAAGTTCTGGACATTTTG 57.677 34.615 0.00 0.00 0.00 2.44
1615 3533 8.375506 TCTGTAGACATAAGTTCTGGACATTTT 58.624 33.333 0.00 0.00 0.00 1.82
1702 3621 6.395629 CCGTGGAAGAACTTTCTGTAGATAA 58.604 40.000 0.00 0.00 37.65 1.75
1717 3636 0.679505 CACAAGTCTCCCGTGGAAGA 59.320 55.000 0.00 0.00 0.00 2.87
1737 3656 7.983166 TTCTTTGGCCTAAATACTACTAGGA 57.017 36.000 3.32 0.00 37.47 2.94
1758 3677 2.955660 TCAAAAGGGCACACGATTTTCT 59.044 40.909 0.00 0.00 0.00 2.52
1817 3736 4.023792 GTGCTCATTCCGATAAATGATGCA 60.024 41.667 17.39 17.39 42.97 3.96
1834 3753 4.002906 ACTAATTTTCTCCGTGTGCTCA 57.997 40.909 0.00 0.00 0.00 4.26
1841 3760 4.755123 CACTGGACAACTAATTTTCTCCGT 59.245 41.667 0.00 0.00 0.00 4.69
1844 3763 5.452777 GCACACTGGACAACTAATTTTCTC 58.547 41.667 0.00 0.00 0.00 2.87
1847 3766 3.880490 TCGCACACTGGACAACTAATTTT 59.120 39.130 0.00 0.00 0.00 1.82
1851 3770 2.412870 CATCGCACACTGGACAACTAA 58.587 47.619 0.00 0.00 0.00 2.24
1852 3771 1.939381 GCATCGCACACTGGACAACTA 60.939 52.381 0.00 0.00 0.00 2.24
1853 3772 1.230635 GCATCGCACACTGGACAACT 61.231 55.000 0.00 0.00 0.00 3.16
1854 3773 1.207593 GCATCGCACACTGGACAAC 59.792 57.895 0.00 0.00 0.00 3.32
1855 3774 0.534877 AAGCATCGCACACTGGACAA 60.535 50.000 0.00 0.00 0.00 3.18
1857 3776 0.671781 AGAAGCATCGCACACTGGAC 60.672 55.000 0.00 0.00 0.00 4.02
1858 3777 0.035317 AAGAAGCATCGCACACTGGA 59.965 50.000 0.00 0.00 0.00 3.86
1859 3778 0.167470 CAAGAAGCATCGCACACTGG 59.833 55.000 0.00 0.00 0.00 4.00
1860 3779 1.150827 TCAAGAAGCATCGCACACTG 58.849 50.000 0.00 0.00 0.00 3.66
1863 3782 2.672874 GTGTATCAAGAAGCATCGCACA 59.327 45.455 0.00 0.00 0.00 4.57
1864 3783 2.030946 GGTGTATCAAGAAGCATCGCAC 59.969 50.000 0.00 0.00 0.00 5.34
1866 3785 2.279741 TGGTGTATCAAGAAGCATCGC 58.720 47.619 0.00 0.00 0.00 4.58
1867 3786 4.944962 TTTGGTGTATCAAGAAGCATCG 57.055 40.909 0.00 0.00 0.00 3.84
1868 3787 6.071952 TCCTTTTTGGTGTATCAAGAAGCATC 60.072 38.462 3.36 0.00 37.46 3.91
1869 3788 5.774690 TCCTTTTTGGTGTATCAAGAAGCAT 59.225 36.000 3.36 0.00 37.46 3.79
1870 3789 5.136828 TCCTTTTTGGTGTATCAAGAAGCA 58.863 37.500 3.36 0.00 37.46 3.91
1871 3790 5.703876 CTCCTTTTTGGTGTATCAAGAAGC 58.296 41.667 3.36 0.00 37.46 3.86
1872 3791 5.335976 GGCTCCTTTTTGGTGTATCAAGAAG 60.336 44.000 2.17 2.17 38.09 2.85
1873 3792 4.522789 GGCTCCTTTTTGGTGTATCAAGAA 59.477 41.667 0.00 0.00 37.07 2.52
1874 3793 4.079253 GGCTCCTTTTTGGTGTATCAAGA 58.921 43.478 0.00 0.00 37.07 3.02
1875 3794 3.826157 TGGCTCCTTTTTGGTGTATCAAG 59.174 43.478 0.00 0.00 37.07 3.02
1876 3795 3.572255 GTGGCTCCTTTTTGGTGTATCAA 59.428 43.478 0.00 0.00 37.07 2.57
1877 3796 3.153919 GTGGCTCCTTTTTGGTGTATCA 58.846 45.455 0.00 0.00 37.07 2.15
1878 3797 3.153919 TGTGGCTCCTTTTTGGTGTATC 58.846 45.455 0.00 0.00 37.07 2.24
1879 3798 3.237268 TGTGGCTCCTTTTTGGTGTAT 57.763 42.857 0.00 0.00 37.07 2.29
1880 3799 2.738587 TGTGGCTCCTTTTTGGTGTA 57.261 45.000 0.00 0.00 37.07 2.90
1881 3800 1.963515 GATGTGGCTCCTTTTTGGTGT 59.036 47.619 0.00 0.00 37.07 4.16
1882 3801 2.242043 AGATGTGGCTCCTTTTTGGTG 58.758 47.619 0.00 0.00 37.07 4.17
1884 3803 5.665916 AAATAGATGTGGCTCCTTTTTGG 57.334 39.130 0.00 0.00 37.10 3.28
1885 3804 7.381323 AGAAAAATAGATGTGGCTCCTTTTTG 58.619 34.615 0.00 0.00 29.99 2.44
1955 7327 7.669722 AGATGTGGCTCCTTTCAAAATACTTTA 59.330 33.333 0.00 0.00 0.00 1.85
1965 7337 9.100197 TGTATATAATAGATGTGGCTCCTTTCA 57.900 33.333 0.00 0.00 0.00 2.69
1966 7338 9.372369 GTGTATATAATAGATGTGGCTCCTTTC 57.628 37.037 0.00 0.00 0.00 2.62
1967 7339 8.322091 GGTGTATATAATAGATGTGGCTCCTTT 58.678 37.037 0.00 0.00 0.00 3.11
1968 7340 7.457852 TGGTGTATATAATAGATGTGGCTCCTT 59.542 37.037 0.00 0.00 0.00 3.36
1969 7341 6.959954 TGGTGTATATAATAGATGTGGCTCCT 59.040 38.462 0.00 0.00 0.00 3.69
1970 7342 7.182817 TGGTGTATATAATAGATGTGGCTCC 57.817 40.000 0.00 0.00 0.00 4.70
1971 7343 9.502091 TTTTGGTGTATATAATAGATGTGGCTC 57.498 33.333 0.00 0.00 0.00 4.70
1972 7344 9.860650 TTTTTGGTGTATATAATAGATGTGGCT 57.139 29.630 0.00 0.00 0.00 4.75
1985 7357 9.233649 TCGTTCCAACTAATTTTTGGTGTATAT 57.766 29.630 14.92 0.00 43.60 0.86
1986 7358 8.618702 TCGTTCCAACTAATTTTTGGTGTATA 57.381 30.769 14.92 0.00 43.60 1.47
1987 7359 7.513371 TCGTTCCAACTAATTTTTGGTGTAT 57.487 32.000 14.92 0.00 43.60 2.29
1988 7360 6.513720 GCTCGTTCCAACTAATTTTTGGTGTA 60.514 38.462 14.92 3.85 43.60 2.90
1989 7361 5.735070 GCTCGTTCCAACTAATTTTTGGTGT 60.735 40.000 14.92 0.00 43.60 4.16
1990 7362 4.679654 GCTCGTTCCAACTAATTTTTGGTG 59.320 41.667 14.92 8.87 43.60 4.17
1991 7363 4.339814 TGCTCGTTCCAACTAATTTTTGGT 59.660 37.500 14.92 0.00 43.60 3.67
1992 7364 4.679654 GTGCTCGTTCCAACTAATTTTTGG 59.320 41.667 10.86 10.86 44.39 3.28
1993 7365 5.277825 TGTGCTCGTTCCAACTAATTTTTG 58.722 37.500 0.00 0.00 0.00 2.44
1994 7366 5.508200 TGTGCTCGTTCCAACTAATTTTT 57.492 34.783 0.00 0.00 0.00 1.94
1995 7367 5.705609 ATGTGCTCGTTCCAACTAATTTT 57.294 34.783 0.00 0.00 0.00 1.82
1996 7368 5.240623 TCAATGTGCTCGTTCCAACTAATTT 59.759 36.000 0.00 0.00 0.00 1.82
1997 7369 4.759693 TCAATGTGCTCGTTCCAACTAATT 59.240 37.500 0.00 0.00 0.00 1.40
1998 7370 4.323417 TCAATGTGCTCGTTCCAACTAAT 58.677 39.130 0.00 0.00 0.00 1.73
1999 7371 3.734463 TCAATGTGCTCGTTCCAACTAA 58.266 40.909 0.00 0.00 0.00 2.24
2000 7372 3.394674 TCAATGTGCTCGTTCCAACTA 57.605 42.857 0.00 0.00 0.00 2.24
2001 7373 2.254546 TCAATGTGCTCGTTCCAACT 57.745 45.000 0.00 0.00 0.00 3.16
2002 7374 3.559238 AATCAATGTGCTCGTTCCAAC 57.441 42.857 0.00 0.00 0.00 3.77
2003 7375 4.037327 TGAAAATCAATGTGCTCGTTCCAA 59.963 37.500 0.00 0.00 0.00 3.53
2004 7376 3.567585 TGAAAATCAATGTGCTCGTTCCA 59.432 39.130 0.00 0.00 0.00 3.53
2005 7377 3.914364 GTGAAAATCAATGTGCTCGTTCC 59.086 43.478 0.00 0.00 0.00 3.62
2006 7378 4.536065 TGTGAAAATCAATGTGCTCGTTC 58.464 39.130 0.00 0.00 0.00 3.95
2007 7379 4.539870 CTGTGAAAATCAATGTGCTCGTT 58.460 39.130 0.00 0.00 0.00 3.85
2008 7380 3.058016 CCTGTGAAAATCAATGTGCTCGT 60.058 43.478 0.00 0.00 0.00 4.18
2009 7381 3.189080 TCCTGTGAAAATCAATGTGCTCG 59.811 43.478 0.00 0.00 0.00 5.03
2010 7382 4.730657 CTCCTGTGAAAATCAATGTGCTC 58.269 43.478 0.00 0.00 0.00 4.26
2011 7383 3.057033 GCTCCTGTGAAAATCAATGTGCT 60.057 43.478 0.00 0.00 0.00 4.40
2012 7384 3.248266 GCTCCTGTGAAAATCAATGTGC 58.752 45.455 0.00 0.00 0.00 4.57
2013 7385 3.256383 TGGCTCCTGTGAAAATCAATGTG 59.744 43.478 0.00 0.00 0.00 3.21
2014 7386 3.256631 GTGGCTCCTGTGAAAATCAATGT 59.743 43.478 0.00 0.00 0.00 2.71
2015 7387 3.256383 TGTGGCTCCTGTGAAAATCAATG 59.744 43.478 0.00 0.00 0.00 2.82
2016 7388 3.499338 TGTGGCTCCTGTGAAAATCAAT 58.501 40.909 0.00 0.00 0.00 2.57
2017 7389 2.942804 TGTGGCTCCTGTGAAAATCAA 58.057 42.857 0.00 0.00 0.00 2.57
2018 7390 2.655090 TGTGGCTCCTGTGAAAATCA 57.345 45.000 0.00 0.00 0.00 2.57
2019 7391 3.350833 AGATGTGGCTCCTGTGAAAATC 58.649 45.455 0.00 0.00 0.00 2.17
2020 7392 3.446442 AGATGTGGCTCCTGTGAAAAT 57.554 42.857 0.00 0.00 0.00 1.82
2021 7393 2.957402 AGATGTGGCTCCTGTGAAAA 57.043 45.000 0.00 0.00 0.00 2.29
2022 7394 3.776969 AGATAGATGTGGCTCCTGTGAAA 59.223 43.478 0.00 0.00 0.00 2.69
2023 7395 3.378512 AGATAGATGTGGCTCCTGTGAA 58.621 45.455 0.00 0.00 0.00 3.18
2024 7396 3.037851 AGATAGATGTGGCTCCTGTGA 57.962 47.619 0.00 0.00 0.00 3.58
2025 7397 3.387374 AGAAGATAGATGTGGCTCCTGTG 59.613 47.826 0.00 0.00 0.00 3.66
2026 7398 3.652055 AGAAGATAGATGTGGCTCCTGT 58.348 45.455 0.00 0.00 0.00 4.00
2027 7399 5.999205 ATAGAAGATAGATGTGGCTCCTG 57.001 43.478 0.00 0.00 0.00 3.86
2028 7400 9.950306 ATATAATAGAAGATAGATGTGGCTCCT 57.050 33.333 0.00 0.00 0.00 3.69
2211 7583 4.407296 AGGCTCAAACCAAAATGTTAACCA 59.593 37.500 2.48 0.00 0.00 3.67
2213 7585 5.462068 GTCAGGCTCAAACCAAAATGTTAAC 59.538 40.000 0.00 0.00 0.00 2.01
2240 7612 6.877236 TGTTGATTGATCACTAGACTATGCA 58.123 36.000 0.00 0.00 36.36 3.96
2320 7692 2.224793 GGGCTGGGGAATACCACTATTC 60.225 54.545 0.00 0.00 42.91 1.75
2333 7705 3.105248 TCATGGGATGGGCTGGGG 61.105 66.667 0.00 0.00 0.00 4.96


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

AutoCloner maintained by Alex Coulton.