Multiple sequence alignment - TraesCS6B01G114400

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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 TraesCS6B01G114400 chr6B 100.000 2888 0 0 1 2888 96656272 96653385 0.000000e+00 5334.0
1 TraesCS6B01G114400 chr6D 93.884 1357 41 18 731 2076 41206782 41208107 0.000000e+00 2008.0
2 TraesCS6B01G114400 chr6D 91.951 733 33 11 2158 2888 41208886 41209594 0.000000e+00 1003.0
3 TraesCS6B01G114400 chr6D 94.314 299 17 0 398 696 41205309 41205607 2.620000e-125 459.0
4 TraesCS6B01G114400 chr6D 91.406 256 15 5 1 251 41204126 41204379 7.660000e-91 344.0
5 TraesCS6B01G114400 chr6A 88.815 1654 96 41 398 2005 51760083 51761693 0.000000e+00 1947.0
6 TraesCS6B01G114400 chr6A 87.726 277 18 8 2312 2582 51761947 51762213 2.790000e-80 309.0
7 TraesCS6B01G114400 chr6A 84.270 178 17 4 2103 2271 51761771 51761946 2.300000e-36 163.0
8 TraesCS6B01G114400 chr6A 88.764 89 4 2 1 83 51758797 51758885 1.420000e-18 104.0
9 TraesCS6B01G114400 chr4D 87.776 859 97 7 983 1837 504597385 504598239 0.000000e+00 998.0
10 TraesCS6B01G114400 chr4B 89.770 782 77 2 1063 1844 651514489 651515267 0.000000e+00 998.0
11 TraesCS6B01G114400 chr5A 88.645 775 88 0 1063 1837 689251931 689252705 0.000000e+00 944.0
12 TraesCS6B01G114400 chr7B 85.921 831 100 14 1007 1825 1437023 1437848 0.000000e+00 870.0
13 TraesCS6B01G114400 chr7B 86.352 762 102 2 1065 1825 1482355 1483115 0.000000e+00 830.0
14 TraesCS6B01G114400 chr7B 95.238 42 2 0 487 528 618506031 618505990 1.860000e-07 67.6
15 TraesCS6B01G114400 chr7B 95.238 42 2 0 487 528 627876321 627876280 1.860000e-07 67.6
16 TraesCS6B01G114400 chr4A 85.181 830 108 10 1007 1825 603666144 603666969 0.000000e+00 837.0
17 TraesCS6B01G114400 chr5D 86.107 763 104 2 1063 1824 556273504 556272743 0.000000e+00 821.0
18 TraesCS6B01G114400 chr1B 81.752 137 16 5 2283 2412 312183808 312183942 3.940000e-19 106.0
19 TraesCS6B01G114400 chr1D 88.235 51 6 0 487 537 405052119 405052069 8.640000e-06 62.1


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 TraesCS6B01G114400 chr6B 96653385 96656272 2887 True 5334.00 5334 100.00000 1 2888 1 chr6B.!!$R1 2887
1 TraesCS6B01G114400 chr6D 41204126 41209594 5468 False 953.50 2008 92.88875 1 2888 4 chr6D.!!$F1 2887
2 TraesCS6B01G114400 chr6A 51758797 51762213 3416 False 630.75 1947 87.39375 1 2582 4 chr6A.!!$F1 2581
3 TraesCS6B01G114400 chr4D 504597385 504598239 854 False 998.00 998 87.77600 983 1837 1 chr4D.!!$F1 854
4 TraesCS6B01G114400 chr4B 651514489 651515267 778 False 998.00 998 89.77000 1063 1844 1 chr4B.!!$F1 781
5 TraesCS6B01G114400 chr5A 689251931 689252705 774 False 944.00 944 88.64500 1063 1837 1 chr5A.!!$F1 774
6 TraesCS6B01G114400 chr7B 1437023 1437848 825 False 870.00 870 85.92100 1007 1825 1 chr7B.!!$F1 818
7 TraesCS6B01G114400 chr7B 1482355 1483115 760 False 830.00 830 86.35200 1065 1825 1 chr7B.!!$F2 760
8 TraesCS6B01G114400 chr4A 603666144 603666969 825 False 837.00 837 85.18100 1007 1825 1 chr4A.!!$F1 818
9 TraesCS6B01G114400 chr5D 556272743 556273504 761 True 821.00 821 86.10700 1063 1824 1 chr5D.!!$R1 761

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
166 626 1.135915 AGCTAGGCACACAATCGAGAG 59.864 52.381 0.0 0.0 0.0 3.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1934 4444 0.241749 TGGCGTCGTTCTTACATCGT 59.758 50.0 0.0 0.0 0.0 3.73 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
45 52 4.605640 ACTACAAACTTGCAATGCCATT 57.394 36.364 1.53 0.00 0.00 3.16
88 95 9.747898 AGATGAGAATATATACGAGGTCTTTCT 57.252 33.333 0.00 0.00 0.00 2.52
102 109 5.281314 AGGTCTTTCTAGATGCCTTAGGAA 58.719 41.667 0.69 0.00 31.86 3.36
116 123 4.339530 GCCTTAGGAAAATGTCTCCCATTC 59.660 45.833 0.69 0.00 43.04 2.67
121 128 3.195610 GGAAAATGTCTCCCATTCCCAAC 59.804 47.826 0.00 0.00 43.04 3.77
131 138 1.537135 CCATTCCCAACGCGTTTTTGT 60.537 47.619 24.21 4.74 0.00 2.83
166 626 1.135915 AGCTAGGCACACAATCGAGAG 59.864 52.381 0.00 0.00 0.00 3.20
202 662 8.975663 TTGATACTATCCTAGTTCTCGAAGAA 57.024 34.615 0.00 0.00 40.14 2.52
248 711 6.704493 ACTCAATTTGTAACGAAGCTAGACAA 59.296 34.615 0.00 0.00 0.00 3.18
249 712 7.387948 ACTCAATTTGTAACGAAGCTAGACAAT 59.612 33.333 0.00 0.00 30.61 2.71
250 713 8.766000 TCAATTTGTAACGAAGCTAGACAATA 57.234 30.769 0.00 0.00 30.61 1.90
251 714 9.378551 TCAATTTGTAACGAAGCTAGACAATAT 57.621 29.630 0.00 0.00 30.61 1.28
252 715 9.638300 CAATTTGTAACGAAGCTAGACAATATC 57.362 33.333 0.00 0.00 30.61 1.63
253 716 7.445900 TTTGTAACGAAGCTAGACAATATCG 57.554 36.000 0.00 0.00 36.45 2.92
255 718 6.788243 TGTAACGAAGCTAGACAATATCGAA 58.212 36.000 7.14 0.00 34.62 3.71
257 720 6.994868 AACGAAGCTAGACAATATCGAATC 57.005 37.500 7.14 0.00 34.62 2.52
258 721 5.462405 ACGAAGCTAGACAATATCGAATCC 58.538 41.667 7.14 0.00 34.62 3.01
260 723 6.096036 CGAAGCTAGACAATATCGAATCCAT 58.904 40.000 0.00 0.00 32.38 3.41
261 724 6.587990 CGAAGCTAGACAATATCGAATCCATT 59.412 38.462 0.00 0.00 32.38 3.16
262 725 7.755373 CGAAGCTAGACAATATCGAATCCATTA 59.245 37.037 0.00 0.00 32.38 1.90
263 726 9.424319 GAAGCTAGACAATATCGAATCCATTAA 57.576 33.333 0.00 0.00 0.00 1.40
264 727 9.950496 AAGCTAGACAATATCGAATCCATTAAT 57.050 29.630 0.00 0.00 0.00 1.40
347 1659 5.649831 GCAACCTCCTTCTCAAATCATAGTT 59.350 40.000 0.00 0.00 0.00 2.24
368 1680 7.665561 AGTTGTAAAAATTTTGTGCTGTGTT 57.334 28.000 3.73 0.00 0.00 3.32
369 1681 8.764524 AGTTGTAAAAATTTTGTGCTGTGTTA 57.235 26.923 3.73 0.00 0.00 2.41
370 1682 9.209175 AGTTGTAAAAATTTTGTGCTGTGTTAA 57.791 25.926 3.73 0.00 0.00 2.01
371 1683 9.813080 GTTGTAAAAATTTTGTGCTGTGTTAAA 57.187 25.926 3.73 0.00 0.00 1.52
376 1688 9.986833 AAAAATTTTGTGCTGTGTTAAATTCTC 57.013 25.926 3.73 0.00 30.48 2.87
377 1689 8.947055 AAATTTTGTGCTGTGTTAAATTCTCT 57.053 26.923 0.00 0.00 30.48 3.10
381 1693 9.515020 TTTTGTGCTGTGTTAAATTCTCTAAAG 57.485 29.630 0.00 0.00 0.00 1.85
382 1694 8.445275 TTGTGCTGTGTTAAATTCTCTAAAGA 57.555 30.769 0.00 0.00 0.00 2.52
383 1695 8.621532 TGTGCTGTGTTAAATTCTCTAAAGAT 57.378 30.769 0.00 0.00 0.00 2.40
384 1696 9.066892 TGTGCTGTGTTAAATTCTCTAAAGATT 57.933 29.630 0.00 0.00 0.00 2.40
385 1697 9.334693 GTGCTGTGTTAAATTCTCTAAAGATTG 57.665 33.333 0.00 0.00 0.00 2.67
386 1698 9.283768 TGCTGTGTTAAATTCTCTAAAGATTGA 57.716 29.630 0.00 0.00 0.00 2.57
387 1699 9.548208 GCTGTGTTAAATTCTCTAAAGATTGAC 57.452 33.333 0.00 0.00 0.00 3.18
389 1701 9.010029 TGTGTTAAATTCTCTAAAGATTGACCC 57.990 33.333 0.00 0.00 0.00 4.46
390 1702 8.175716 GTGTTAAATTCTCTAAAGATTGACCCG 58.824 37.037 0.00 0.00 0.00 5.28
391 1703 5.819825 AAATTCTCTAAAGATTGACCCGC 57.180 39.130 0.00 0.00 0.00 6.13
392 1704 3.973206 TTCTCTAAAGATTGACCCGCA 57.027 42.857 0.00 0.00 0.00 5.69
393 1705 3.973206 TCTCTAAAGATTGACCCGCAA 57.027 42.857 0.00 0.00 41.53 4.85
394 1706 4.280436 TCTCTAAAGATTGACCCGCAAA 57.720 40.909 0.00 0.00 40.48 3.68
395 1707 4.647611 TCTCTAAAGATTGACCCGCAAAA 58.352 39.130 0.00 0.00 40.48 2.44
396 1708 5.067273 TCTCTAAAGATTGACCCGCAAAAA 58.933 37.500 0.00 0.00 40.48 1.94
568 1883 7.996098 TGAGGTATTTTTGGAAAGTAAGGAG 57.004 36.000 0.00 0.00 0.00 3.69
581 1897 6.462628 GGAAAGTAAGGAGTATAGCCGTCAAT 60.463 42.308 0.00 0.00 0.00 2.57
601 1917 7.860373 CGTCAATGGTTAAGAAATTTTGAGTGA 59.140 33.333 0.00 0.00 0.00 3.41
855 3358 6.553100 CCTTGTGGTTCCTCTCTTCTCTATAT 59.447 42.308 0.00 0.00 0.00 0.86
856 3359 7.726291 CCTTGTGGTTCCTCTCTTCTCTATATA 59.274 40.741 0.00 0.00 0.00 0.86
857 3360 9.308000 CTTGTGGTTCCTCTCTTCTCTATATAT 57.692 37.037 0.00 0.00 0.00 0.86
859 3362 9.967451 TGTGGTTCCTCTCTTCTCTATATATAG 57.033 37.037 12.84 12.84 0.00 1.31
909 3412 4.510340 GCTATGGACACAATACTTAACCGG 59.490 45.833 0.00 0.00 0.00 5.28
932 3435 7.230510 CCGGTTCTTAATTATTTCCATCCATCA 59.769 37.037 0.00 0.00 0.00 3.07
941 3444 9.650714 AATTATTTCCATCCATCAATCTCTTCA 57.349 29.630 0.00 0.00 0.00 3.02
942 3445 8.687292 TTATTTCCATCCATCAATCTCTTCAG 57.313 34.615 0.00 0.00 0.00 3.02
944 3447 5.032327 TCCATCCATCAATCTCTTCAGTG 57.968 43.478 0.00 0.00 0.00 3.66
945 3448 4.472470 TCCATCCATCAATCTCTTCAGTGT 59.528 41.667 0.00 0.00 0.00 3.55
946 3449 4.815308 CCATCCATCAATCTCTTCAGTGTC 59.185 45.833 0.00 0.00 0.00 3.67
947 3450 5.396548 CCATCCATCAATCTCTTCAGTGTCT 60.397 44.000 0.00 0.00 0.00 3.41
948 3451 5.336150 TCCATCAATCTCTTCAGTGTCTC 57.664 43.478 0.00 0.00 0.00 3.36
949 3452 5.022122 TCCATCAATCTCTTCAGTGTCTCT 58.978 41.667 0.00 0.00 0.00 3.10
950 3453 5.483231 TCCATCAATCTCTTCAGTGTCTCTT 59.517 40.000 0.00 0.00 0.00 2.85
951 3454 5.811613 CCATCAATCTCTTCAGTGTCTCTTC 59.188 44.000 0.00 0.00 0.00 2.87
952 3455 6.351202 CCATCAATCTCTTCAGTGTCTCTTCT 60.351 42.308 0.00 0.00 0.00 2.85
953 3456 6.662865 TCAATCTCTTCAGTGTCTCTTCTT 57.337 37.500 0.00 0.00 0.00 2.52
954 3457 7.060383 TCAATCTCTTCAGTGTCTCTTCTTT 57.940 36.000 0.00 0.00 0.00 2.52
955 3458 7.504403 TCAATCTCTTCAGTGTCTCTTCTTTT 58.496 34.615 0.00 0.00 0.00 2.27
956 3459 7.440556 TCAATCTCTTCAGTGTCTCTTCTTTTG 59.559 37.037 0.00 0.00 0.00 2.44
957 3460 5.053145 TCTCTTCAGTGTCTCTTCTTTTGC 58.947 41.667 0.00 0.00 0.00 3.68
1365 3874 2.124819 CTGCTGCTGGCGAGGAAT 60.125 61.111 0.00 0.00 45.43 3.01
1647 4156 2.582498 CTCATCGGGTTCGCGGTC 60.582 66.667 6.13 0.00 36.13 4.79
1897 4406 3.181367 GCTGTTGATGGAGCCACG 58.819 61.111 0.00 0.00 0.00 4.94
1899 4408 2.359850 TGTTGATGGAGCCACGCC 60.360 61.111 0.00 0.00 0.00 5.68
1900 4409 2.359850 GTTGATGGAGCCACGCCA 60.360 61.111 0.00 0.00 37.78 5.69
1902 4411 1.675310 TTGATGGAGCCACGCCAAG 60.675 57.895 0.00 0.00 36.81 3.61
1903 4412 2.123248 TTGATGGAGCCACGCCAAGA 62.123 55.000 0.00 0.00 36.81 3.02
1904 4413 1.817099 GATGGAGCCACGCCAAGAG 60.817 63.158 0.00 0.00 36.81 2.85
1906 4415 1.630126 ATGGAGCCACGCCAAGAGAT 61.630 55.000 0.00 0.00 36.81 2.75
1907 4416 1.817099 GGAGCCACGCCAAGAGATG 60.817 63.158 0.00 0.00 0.00 2.90
1908 4417 1.219124 GAGCCACGCCAAGAGATGA 59.781 57.895 0.00 0.00 0.00 2.92
1921 4431 4.216472 CCAAGAGATGATGATGGCAATCAG 59.784 45.833 10.16 0.00 45.88 2.90
1934 4444 2.692557 GGCAATCAGTCTGAGAGAGCTA 59.307 50.000 8.82 0.00 0.00 3.32
1935 4445 3.490761 GGCAATCAGTCTGAGAGAGCTAC 60.491 52.174 8.82 0.00 0.00 3.58
1938 4448 3.552132 TCAGTCTGAGAGAGCTACGAT 57.448 47.619 0.00 0.00 0.00 3.73
1940 4450 2.942376 CAGTCTGAGAGAGCTACGATGT 59.058 50.000 0.00 0.00 0.00 3.06
1941 4451 4.123506 CAGTCTGAGAGAGCTACGATGTA 58.876 47.826 0.00 0.00 0.00 2.29
1942 4452 4.572795 CAGTCTGAGAGAGCTACGATGTAA 59.427 45.833 0.00 0.00 0.00 2.41
1943 4453 4.814234 AGTCTGAGAGAGCTACGATGTAAG 59.186 45.833 0.00 0.00 0.00 2.34
1950 4464 3.027710 GAGCTACGATGTAAGAACGACG 58.972 50.000 0.00 0.00 34.52 5.12
1965 4479 0.865769 CGACGCCAGTACTGCTTTTT 59.134 50.000 17.86 0.00 0.00 1.94
2071 4586 3.002791 CGCTCTATGAACAAGGAAAGCA 58.997 45.455 0.00 0.00 0.00 3.91
2076 4591 6.529477 GCTCTATGAACAAGGAAAGCAAAATC 59.471 38.462 0.00 0.00 0.00 2.17
2078 4593 8.125978 TCTATGAACAAGGAAAGCAAAATCAT 57.874 30.769 0.00 0.00 0.00 2.45
2079 4594 8.246180 TCTATGAACAAGGAAAGCAAAATCATC 58.754 33.333 0.00 0.00 0.00 2.92
2081 4596 5.305128 TGAACAAGGAAAGCAAAATCATCCT 59.695 36.000 0.00 0.00 42.22 3.24
2087 4602 5.956563 AGGAAAGCAAAATCATCCTTGAGAT 59.043 36.000 0.00 0.00 37.20 2.75
2088 4603 6.439692 AGGAAAGCAAAATCATCCTTGAGATT 59.560 34.615 0.00 0.00 37.20 2.40
2089 4604 7.038516 AGGAAAGCAAAATCATCCTTGAGATTT 60.039 33.333 0.00 0.00 44.03 2.17
2091 4606 8.913487 AAAGCAAAATCATCCTTGAGATTTTT 57.087 26.923 9.63 0.00 46.58 1.94
2092 4607 8.543862 AAGCAAAATCATCCTTGAGATTTTTC 57.456 30.769 9.63 6.35 46.58 2.29
2093 4608 7.904205 AGCAAAATCATCCTTGAGATTTTTCT 58.096 30.769 9.63 8.18 46.58 2.52
2094 4609 8.033626 AGCAAAATCATCCTTGAGATTTTTCTC 58.966 33.333 9.63 0.00 46.58 2.87
2095 4610 7.816031 GCAAAATCATCCTTGAGATTTTTCTCA 59.184 33.333 9.63 1.65 46.58 3.27
2096 4611 9.701098 CAAAATCATCCTTGAGATTTTTCTCAA 57.299 29.630 15.46 15.46 46.58 3.02
2097 4612 9.702494 AAAATCATCCTTGAGATTTTTCTCAAC 57.298 29.630 13.01 0.00 46.58 3.18
2125 4640 4.078336 AGAGATTAGGGATCCTGTCCTTGA 60.078 45.833 12.58 0.00 46.91 3.02
2224 5486 1.386533 AGGATGCTTCTGATTTGCCG 58.613 50.000 0.00 0.00 0.00 5.69
2233 5495 1.130373 TCTGATTTGCCGAATTGTCGC 59.870 47.619 0.00 0.00 46.28 5.19
2251 5513 7.716768 TTGTCGCAAATATTATCGGTAATGA 57.283 32.000 11.27 0.00 32.84 2.57
2253 5515 8.317891 TGTCGCAAATATTATCGGTAATGATT 57.682 30.769 11.27 3.31 32.84 2.57
2303 5565 4.275443 TGCATGGCAAAATGAAGGTTTTTC 59.725 37.500 0.00 0.00 34.76 2.29
2308 5570 1.778334 AAATGAAGGTTTTTCGCGGC 58.222 45.000 6.13 0.00 0.00 6.53
2488 5756 1.247567 TGTTTGCTGCTTAAGAGGGC 58.752 50.000 6.67 7.19 0.00 5.19
2529 5797 5.491070 CTGAAAACCAGGACAGTGATATGA 58.509 41.667 0.00 0.00 39.23 2.15
2530 5798 5.491070 TGAAAACCAGGACAGTGATATGAG 58.509 41.667 0.00 0.00 0.00 2.90
2531 5799 3.550437 AACCAGGACAGTGATATGAGC 57.450 47.619 0.00 0.00 0.00 4.26
2532 5800 2.470990 ACCAGGACAGTGATATGAGCA 58.529 47.619 0.00 0.00 0.00 4.26
2533 5801 3.044156 ACCAGGACAGTGATATGAGCAT 58.956 45.455 0.00 0.00 0.00 3.79
2534 5802 3.181457 ACCAGGACAGTGATATGAGCATG 60.181 47.826 0.00 0.00 0.00 4.06
2557 5825 2.437850 GCAAATGCGAGCAAACTGG 58.562 52.632 0.57 0.00 0.00 4.00
2575 5843 3.571401 ACTGGCAAGTGAAGAAAAGATGG 59.429 43.478 0.00 0.00 34.48 3.51
2601 5869 0.699399 TTCTCGAGGACCCTCTCTGT 59.301 55.000 13.56 0.00 40.69 3.41
2616 5884 0.391228 TCTGTACACACACGGCACAT 59.609 50.000 0.00 0.00 0.00 3.21
2617 5885 0.512518 CTGTACACACACGGCACATG 59.487 55.000 0.00 0.00 0.00 3.21
2618 5886 1.206578 GTACACACACGGCACATGC 59.793 57.895 0.00 0.00 41.14 4.06
2619 5887 1.070615 TACACACACGGCACATGCT 59.929 52.632 3.48 0.00 41.70 3.79
2637 5905 0.028902 CTGACATGCATGTGATGGCG 59.971 55.000 35.92 12.75 41.95 5.69
2673 5941 0.960364 GATGCTTTCTCCGGGCACAA 60.960 55.000 0.00 0.00 38.83 3.33
2682 5950 2.705658 TCTCCGGGCACAAGATTATCAT 59.294 45.455 0.00 0.00 0.00 2.45
2742 6010 5.123344 ACAATAAGTTTGTATGCTTCGGGTC 59.877 40.000 0.00 0.00 0.00 4.46
2776 6044 3.539604 AGAGAGGCAATGAAAAGATCCG 58.460 45.455 0.00 0.00 0.00 4.18
2792 6060 1.743252 CCGCAAACTCAGCTCCCTC 60.743 63.158 0.00 0.00 0.00 4.30
2794 6062 1.018226 CGCAAACTCAGCTCCCTCAG 61.018 60.000 0.00 0.00 0.00 3.35
2808 6076 1.981495 CCCTCAGAGAACTCAAAGGGT 59.019 52.381 22.41 0.00 43.30 4.34
2884 6153 6.968904 CCTCAAAGGATTGATGTATTTTGACG 59.031 38.462 0.00 0.00 44.29 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 9.563748 TGCAAGTTTGTAGTAGGTAATTAACTT 57.436 29.630 8.65 0.00 35.61 2.66
88 95 5.163195 GGGAGACATTTTCCTAAGGCATCTA 60.163 44.000 0.00 0.00 35.01 1.98
116 123 2.223294 TGTTCTACAAAAACGCGTTGGG 60.223 45.455 27.34 19.43 0.00 4.12
121 128 7.843482 TGGTATATATGTTCTACAAAAACGCG 58.157 34.615 3.53 3.53 0.00 6.01
131 138 6.951778 TGTGCCTAGCTGGTATATATGTTCTA 59.048 38.462 0.00 0.00 38.35 2.10
166 626 5.482908 AGGATAGTATCAATCATTCGGTGC 58.517 41.667 12.19 0.00 0.00 5.01
202 662 2.430465 TCTAGCTTAGTCGTCGGTTGT 58.570 47.619 0.00 0.00 0.00 3.32
320 1631 3.760151 TGATTTGAGAAGGAGGTTGCATG 59.240 43.478 0.00 0.00 0.00 4.06
368 1680 6.411376 TGCGGGTCAATCTTTAGAGAATTTA 58.589 36.000 0.00 0.00 35.07 1.40
369 1681 5.253330 TGCGGGTCAATCTTTAGAGAATTT 58.747 37.500 0.00 0.00 35.07 1.82
370 1682 4.843728 TGCGGGTCAATCTTTAGAGAATT 58.156 39.130 0.00 0.00 35.07 2.17
371 1683 4.487714 TGCGGGTCAATCTTTAGAGAAT 57.512 40.909 0.00 0.00 35.07 2.40
372 1684 3.973206 TGCGGGTCAATCTTTAGAGAA 57.027 42.857 0.00 0.00 35.07 2.87
373 1685 3.973206 TTGCGGGTCAATCTTTAGAGA 57.027 42.857 0.00 0.00 36.09 3.10
374 1686 5.371115 TTTTTGCGGGTCAATCTTTAGAG 57.629 39.130 0.00 0.00 34.12 2.43
541 1856 9.457436 TCCTTACTTTCCAAAAATACCTCATAC 57.543 33.333 0.00 0.00 0.00 2.39
568 1883 6.913873 TTTCTTAACCATTGACGGCTATAC 57.086 37.500 0.00 0.00 0.00 1.47
601 1917 7.995488 CCTCCTCTGGTTCACAAATAATATCTT 59.005 37.037 0.00 0.00 0.00 2.40
614 1930 2.000803 TCCTCTACCTCCTCTGGTTCA 58.999 52.381 0.00 0.00 41.22 3.18
615 1931 2.024751 ACTCCTCTACCTCCTCTGGTTC 60.025 54.545 0.00 0.00 41.22 3.62
696 2020 2.954318 CCAAAAGGGCATCCTATGTCAG 59.046 50.000 0.00 0.00 44.07 3.51
697 2021 2.358090 CCCAAAAGGGCATCCTATGTCA 60.358 50.000 0.00 0.00 44.07 3.58
698 2022 2.310538 CCCAAAAGGGCATCCTATGTC 58.689 52.381 0.00 0.00 44.07 3.06
699 2023 1.645919 ACCCAAAAGGGCATCCTATGT 59.354 47.619 0.00 0.00 44.07 2.29
700 2024 2.034124 CACCCAAAAGGGCATCCTATG 58.966 52.381 0.00 0.00 44.07 2.23
701 2025 1.645919 ACACCCAAAAGGGCATCCTAT 59.354 47.619 0.00 0.00 44.07 2.57
702 2026 1.005450 GACACCCAAAAGGGCATCCTA 59.995 52.381 0.00 0.00 44.07 2.94
704 2028 0.251787 AGACACCCAAAAGGGCATCC 60.252 55.000 0.00 0.00 41.63 3.51
705 2029 1.632589 AAGACACCCAAAAGGGCATC 58.367 50.000 0.00 0.00 41.63 3.91
706 2030 2.101640 AAAGACACCCAAAAGGGCAT 57.898 45.000 0.00 0.00 41.63 4.40
707 2031 1.760029 GAAAAGACACCCAAAAGGGCA 59.240 47.619 0.00 0.00 41.63 5.36
708 2032 1.760029 TGAAAAGACACCCAAAAGGGC 59.240 47.619 0.00 0.00 41.63 5.19
709 2033 4.687901 ATTGAAAAGACACCCAAAAGGG 57.312 40.909 0.00 0.00 41.63 3.95
745 3218 3.126343 GCACCATTTACTAACCACGGAAG 59.874 47.826 0.00 0.00 0.00 3.46
881 3384 2.505407 AGTATTGTGTCCATAGCCTGCA 59.495 45.455 0.00 0.00 0.00 4.41
887 3390 5.667466 ACCGGTTAAGTATTGTGTCCATAG 58.333 41.667 0.00 0.00 0.00 2.23
932 3435 6.204495 GCAAAAGAAGAGACACTGAAGAGATT 59.796 38.462 0.00 0.00 0.00 2.40
941 3444 2.548920 CGGGAGCAAAAGAAGAGACACT 60.549 50.000 0.00 0.00 0.00 3.55
942 3445 1.801178 CGGGAGCAAAAGAAGAGACAC 59.199 52.381 0.00 0.00 0.00 3.67
944 3447 2.457366 TCGGGAGCAAAAGAAGAGAC 57.543 50.000 0.00 0.00 0.00 3.36
945 3448 3.007940 TGATTCGGGAGCAAAAGAAGAGA 59.992 43.478 0.00 0.00 0.00 3.10
946 3449 3.338249 TGATTCGGGAGCAAAAGAAGAG 58.662 45.455 0.00 0.00 0.00 2.85
947 3450 3.417069 TGATTCGGGAGCAAAAGAAGA 57.583 42.857 0.00 0.00 0.00 2.87
948 3451 4.156556 TGATTGATTCGGGAGCAAAAGAAG 59.843 41.667 0.00 0.00 0.00 2.85
949 3452 4.078537 TGATTGATTCGGGAGCAAAAGAA 58.921 39.130 0.00 0.00 0.00 2.52
950 3453 3.684908 TGATTGATTCGGGAGCAAAAGA 58.315 40.909 0.00 0.00 0.00 2.52
951 3454 3.733077 GCTGATTGATTCGGGAGCAAAAG 60.733 47.826 0.00 0.00 0.00 2.27
952 3455 2.164219 GCTGATTGATTCGGGAGCAAAA 59.836 45.455 0.00 0.00 0.00 2.44
953 3456 1.745087 GCTGATTGATTCGGGAGCAAA 59.255 47.619 0.00 0.00 0.00 3.68
954 3457 1.065199 AGCTGATTGATTCGGGAGCAA 60.065 47.619 0.00 0.00 0.00 3.91
955 3458 0.543277 AGCTGATTGATTCGGGAGCA 59.457 50.000 0.00 0.00 0.00 4.26
956 3459 0.942962 CAGCTGATTGATTCGGGAGC 59.057 55.000 8.42 0.00 0.00 4.70
957 3460 2.481854 CTCAGCTGATTGATTCGGGAG 58.518 52.381 18.63 0.00 0.00 4.30
1626 4135 2.184322 GCGAACCCGATGAGCAGA 59.816 61.111 0.00 0.00 38.22 4.26
1899 4408 4.822350 ACTGATTGCCATCATCATCTCTTG 59.178 41.667 0.20 0.00 38.81 3.02
1900 4409 5.050126 ACTGATTGCCATCATCATCTCTT 57.950 39.130 0.20 0.00 38.81 2.85
1902 4411 4.452795 CAGACTGATTGCCATCATCATCTC 59.547 45.833 0.20 0.00 38.81 2.75
1903 4412 4.102681 TCAGACTGATTGCCATCATCATCT 59.897 41.667 0.00 2.80 38.81 2.90
1904 4413 4.386711 TCAGACTGATTGCCATCATCATC 58.613 43.478 0.00 0.61 38.81 2.92
1906 4415 3.453353 TCTCAGACTGATTGCCATCATCA 59.547 43.478 5.42 0.00 38.81 3.07
1907 4416 4.059511 CTCTCAGACTGATTGCCATCATC 58.940 47.826 5.42 2.26 38.81 2.92
1908 4417 3.710165 TCTCTCAGACTGATTGCCATCAT 59.290 43.478 5.42 0.00 38.81 2.45
1915 4425 3.625313 TCGTAGCTCTCTCAGACTGATTG 59.375 47.826 5.42 2.20 0.00 2.67
1921 4431 4.812091 TCTTACATCGTAGCTCTCTCAGAC 59.188 45.833 0.00 0.00 0.00 3.51
1934 4444 0.241749 TGGCGTCGTTCTTACATCGT 59.758 50.000 0.00 0.00 0.00 3.73
1935 4445 0.914551 CTGGCGTCGTTCTTACATCG 59.085 55.000 0.00 0.00 0.00 3.84
1938 4448 1.881973 AGTACTGGCGTCGTTCTTACA 59.118 47.619 0.00 0.00 0.00 2.41
1940 4450 1.401931 GCAGTACTGGCGTCGTTCTTA 60.402 52.381 23.95 0.00 0.00 2.10
1941 4451 0.666577 GCAGTACTGGCGTCGTTCTT 60.667 55.000 23.95 0.00 0.00 2.52
1942 4452 1.080705 GCAGTACTGGCGTCGTTCT 60.081 57.895 23.95 0.00 0.00 3.01
1943 4453 0.666577 AAGCAGTACTGGCGTCGTTC 60.667 55.000 23.95 4.97 36.08 3.95
2023 4537 8.798859 AGCAGAAGTTACTGATTGTTCATATT 57.201 30.769 0.00 0.00 39.94 1.28
2087 4602 9.502035 TCCCTAATCTCTATAGGTTGAGAAAAA 57.498 33.333 0.00 0.00 41.82 1.94
2088 4603 9.676129 ATCCCTAATCTCTATAGGTTGAGAAAA 57.324 33.333 0.00 0.00 41.82 2.29
2089 4604 9.315363 GATCCCTAATCTCTATAGGTTGAGAAA 57.685 37.037 0.00 0.00 41.82 2.52
2090 4605 7.896496 GGATCCCTAATCTCTATAGGTTGAGAA 59.104 40.741 0.00 0.00 41.82 2.87
2091 4606 7.242953 AGGATCCCTAATCTCTATAGGTTGAGA 59.757 40.741 8.55 0.00 38.62 3.27
2092 4607 7.341769 CAGGATCCCTAATCTCTATAGGTTGAG 59.658 44.444 8.55 0.00 38.62 3.02
2093 4608 7.185565 CAGGATCCCTAATCTCTATAGGTTGA 58.814 42.308 8.55 0.00 38.62 3.18
2094 4609 6.957020 ACAGGATCCCTAATCTCTATAGGTTG 59.043 42.308 8.55 0.00 38.62 3.77
2095 4610 7.122311 ACAGGATCCCTAATCTCTATAGGTT 57.878 40.000 8.55 0.00 38.62 3.50
2096 4611 6.297948 GGACAGGATCCCTAATCTCTATAGGT 60.298 46.154 8.55 0.00 42.46 3.08
2097 4612 6.133356 GGACAGGATCCCTAATCTCTATAGG 58.867 48.000 8.55 0.00 42.46 2.57
2154 4669 3.960755 TGATCCTCGTGACATGGAGTATT 59.039 43.478 0.00 0.00 32.95 1.89
2155 4670 3.566351 TGATCCTCGTGACATGGAGTAT 58.434 45.455 0.00 0.00 32.95 2.12
2193 5455 4.018484 GAAGCATCCTTCATCTATGCCT 57.982 45.455 0.00 0.00 45.66 4.75
2203 5465 2.223433 CGGCAAATCAGAAGCATCCTTC 60.223 50.000 0.00 0.00 46.29 3.46
2205 5467 1.065199 TCGGCAAATCAGAAGCATCCT 60.065 47.619 0.00 0.00 0.00 3.24
2206 5468 1.382522 TCGGCAAATCAGAAGCATCC 58.617 50.000 0.00 0.00 0.00 3.51
2208 5470 3.194116 ACAATTCGGCAAATCAGAAGCAT 59.806 39.130 0.00 0.00 32.60 3.79
2224 5486 9.051027 CATTACCGATAATATTTGCGACAATTC 57.949 33.333 10.17 0.00 29.44 2.17
2282 5544 4.611130 GCGAAAAACCTTCATTTTGCCATG 60.611 41.667 0.00 0.00 39.13 3.66
2283 5545 3.498018 GCGAAAAACCTTCATTTTGCCAT 59.502 39.130 0.00 0.00 39.13 4.40
2284 5546 2.869192 GCGAAAAACCTTCATTTTGCCA 59.131 40.909 0.00 0.00 39.13 4.92
2285 5547 2.096958 CGCGAAAAACCTTCATTTTGCC 60.097 45.455 0.00 0.00 41.02 4.52
2286 5548 2.096958 CCGCGAAAAACCTTCATTTTGC 60.097 45.455 8.23 0.00 40.80 3.68
2287 5549 2.096958 GCCGCGAAAAACCTTCATTTTG 60.097 45.455 8.23 0.00 32.12 2.44
2288 5550 2.131972 GCCGCGAAAAACCTTCATTTT 58.868 42.857 8.23 0.00 33.13 1.82
2303 5565 2.159585 TCTTGACACATAAATTGCCGCG 60.160 45.455 0.00 0.00 0.00 6.46
2308 5570 8.929827 TTGCCATATTCTTGACACATAAATTG 57.070 30.769 0.00 0.00 0.00 2.32
2473 5741 1.285280 TTAGGCCCTCTTAAGCAGCA 58.715 50.000 0.00 0.00 0.00 4.41
2513 5781 3.070590 TCATGCTCATATCACTGTCCTGG 59.929 47.826 0.00 0.00 0.00 4.45
2529 5797 0.961857 TCGCATTTGCTGGTCATGCT 60.962 50.000 0.51 0.00 41.06 3.79
2530 5798 0.524816 CTCGCATTTGCTGGTCATGC 60.525 55.000 0.51 0.00 40.03 4.06
2531 5799 0.524816 GCTCGCATTTGCTGGTCATG 60.525 55.000 0.51 0.00 39.32 3.07
2532 5800 0.961857 TGCTCGCATTTGCTGGTCAT 60.962 50.000 0.51 0.00 39.32 3.06
2533 5801 1.171549 TTGCTCGCATTTGCTGGTCA 61.172 50.000 0.51 0.00 39.32 4.02
2534 5802 0.039256 TTTGCTCGCATTTGCTGGTC 60.039 50.000 0.51 0.00 39.32 4.02
2557 5825 3.814945 CGACCATCTTTTCTTCACTTGC 58.185 45.455 0.00 0.00 0.00 4.01
2575 5843 1.153997 GGTCCTCGAGAACAGCGAC 60.154 63.158 15.71 11.20 33.71 5.19
2601 5869 1.070615 AGCATGTGCCGTGTGTGTA 59.929 52.632 0.57 0.00 43.38 2.90
2617 5885 0.248907 GCCATCACATGCATGTCAGC 60.249 55.000 29.23 22.88 39.39 4.26
2618 5886 0.028902 CGCCATCACATGCATGTCAG 59.971 55.000 29.23 18.99 39.39 3.51
2619 5887 1.378124 CCGCCATCACATGCATGTCA 61.378 55.000 29.23 18.88 39.39 3.58
2620 5888 1.357690 CCGCCATCACATGCATGTC 59.642 57.895 29.23 16.41 39.39 3.06
2621 5889 0.966875 AACCGCCATCACATGCATGT 60.967 50.000 26.61 26.61 42.84 3.21
2622 5890 1.002142 CTAACCGCCATCACATGCATG 60.002 52.381 25.09 25.09 0.00 4.06
2623 5891 1.134128 TCTAACCGCCATCACATGCAT 60.134 47.619 0.00 0.00 0.00 3.96
2637 5905 4.327680 AGCATCAGGTGTTCTTTCTAACC 58.672 43.478 0.00 0.00 0.00 2.85
2673 5941 4.242811 TCCCAACCTGGCTATGATAATCT 58.757 43.478 0.00 0.00 35.79 2.40
2682 5950 2.238646 CACTACAATCCCAACCTGGCTA 59.761 50.000 0.00 0.00 35.79 3.93
2742 6010 4.727507 TGCCTCTCTCTAGCTTTTGTAG 57.272 45.455 0.00 0.00 0.00 2.74
2776 6044 0.322975 TCTGAGGGAGCTGAGTTTGC 59.677 55.000 0.00 0.00 0.00 3.68
2808 6076 5.755409 TCTCACTTAAGCAAATCAGGGTA 57.245 39.130 1.29 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.