Multiple sequence alignment - TraesCS1B01G390200

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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 TraesCS1B01G390200 chr1B 100.000 2468 0 0 1 2468 623831937 623834404 0.000000e+00 4558.0
1 TraesCS1B01G390200 chr1B 90.091 1645 98 25 1 1623 623913997 623915598 0.000000e+00 2074.0
2 TraesCS1B01G390200 chr1B 92.396 434 31 1 2034 2465 623886154 623886587 3.490000e-173 617.0
3 TraesCS1B01G390200 chr1B 91.275 447 36 3 2020 2465 623824729 623825173 7.550000e-170 606.0
4 TraesCS1B01G390200 chr1B 92.011 363 29 0 995 1357 623822637 623822999 6.090000e-141 510.0
5 TraesCS1B01G390200 chr1B 88.235 374 44 0 984 1357 623885304 623885677 4.840000e-122 448.0
6 TraesCS1B01G390200 chr1B 89.147 258 27 1 392 648 496360312 496360055 1.100000e-83 320.0
7 TraesCS1B01G390200 chr1A 89.645 1941 105 47 2 1861 548404099 548406024 0.000000e+00 2383.0
8 TraesCS1B01G390200 chr1D 93.078 1647 75 19 1 1623 453404344 453405975 0.000000e+00 2374.0
9 TraesCS1B01G390200 chr1D 90.798 1793 97 32 1 1758 453475626 453477385 0.000000e+00 2335.0
10 TraesCS1B01G390200 chr1D 91.778 450 34 3 2020 2468 453350145 453350592 7.490000e-175 623.0
11 TraesCS1B01G390200 chr1D 90.000 370 30 3 995 1357 453347712 453348081 2.870000e-129 472.0
12 TraesCS1B01G390200 chr1D 88.346 266 30 1 382 646 178458764 178459029 3.960000e-83 318.0
13 TraesCS1B01G390200 chr1D 94.340 53 3 0 2413 2465 453464864 453464916 5.660000e-12 82.4
14 TraesCS1B01G390200 chr2D 89.844 256 25 1 392 646 491379763 491380018 6.580000e-86 327.0
15 TraesCS1B01G390200 chr7B 89.453 256 26 1 392 646 732473874 732474129 3.060000e-84 322.0
16 TraesCS1B01G390200 chr3B 89.147 258 27 1 392 648 26935825 26936082 1.100000e-83 320.0
17 TraesCS1B01G390200 chr3A 74.502 251 46 15 13 257 121314657 121314895 2.610000e-15 93.5
18 TraesCS1B01G390200 chr2A 97.143 35 1 0 2237 2271 652378976 652379010 2.650000e-05 60.2


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 TraesCS1B01G390200 chr1B 623831937 623834404 2467 False 4558.0 4558 100.0000 1 2468 1 chr1B.!!$F1 2467
1 TraesCS1B01G390200 chr1B 623913997 623915598 1601 False 2074.0 2074 90.0910 1 1623 1 chr1B.!!$F2 1622
2 TraesCS1B01G390200 chr1B 623822637 623825173 2536 False 558.0 606 91.6430 995 2465 2 chr1B.!!$F3 1470
3 TraesCS1B01G390200 chr1B 623885304 623886587 1283 False 532.5 617 90.3155 984 2465 2 chr1B.!!$F4 1481
4 TraesCS1B01G390200 chr1A 548404099 548406024 1925 False 2383.0 2383 89.6450 2 1861 1 chr1A.!!$F1 1859
5 TraesCS1B01G390200 chr1D 453404344 453405975 1631 False 2374.0 2374 93.0780 1 1623 1 chr1D.!!$F2 1622
6 TraesCS1B01G390200 chr1D 453475626 453477385 1759 False 2335.0 2335 90.7980 1 1758 1 chr1D.!!$F4 1757
7 TraesCS1B01G390200 chr1D 453347712 453350592 2880 False 547.5 623 90.8890 995 2468 2 chr1D.!!$F5 1473

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
125 126 0.31179 ACGTCGAAGTTTGGCGAGTA 59.688 50.0 23.44 0.0 37.18 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1633 3230 0.098025 CAAACACACACACCGGACAC 59.902 55.0 9.46 0.0 0.0 3.67 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
29 30 1.730064 GCACTGGCGAGTTTATTTCGA 59.270 47.619 0.00 0.00 40.36 3.71
59 60 1.678728 GGCTAATGTGCTACACTGCCA 60.679 52.381 16.30 0.00 37.26 4.92
77 78 2.223711 GCCAAGTTTCTTTCTTTCGCCA 60.224 45.455 0.00 0.00 0.00 5.69
90 91 2.358322 TTCGCCAAGTCCCTTTTTCT 57.642 45.000 0.00 0.00 0.00 2.52
125 126 0.311790 ACGTCGAAGTTTGGCGAGTA 59.688 50.000 23.44 0.00 37.18 2.59
188 189 1.025812 CATTACTCCGTCGAGCTCCT 58.974 55.000 8.47 0.00 40.03 3.69
618 645 9.106070 ACTTTGACTTAGAACAAAACGTAGAAT 57.894 29.630 0.00 0.00 35.95 2.40
732 767 5.185454 TGTCAACTTGGTGCATAGGATTAG 58.815 41.667 0.00 0.00 0.00 1.73
817 875 3.537874 GCTCGGGGCGTGTAGGAT 61.538 66.667 0.00 0.00 0.00 3.24
818 876 2.198287 GCTCGGGGCGTGTAGGATA 61.198 63.158 0.00 0.00 0.00 2.59
819 877 1.957562 CTCGGGGCGTGTAGGATAG 59.042 63.158 0.00 0.00 0.00 2.08
820 878 1.524863 CTCGGGGCGTGTAGGATAGG 61.525 65.000 0.00 0.00 0.00 2.57
821 879 1.529948 CGGGGCGTGTAGGATAGGA 60.530 63.158 0.00 0.00 0.00 2.94
868 928 5.045578 TCCCTGGCCAAGAGCTATATAAATC 60.046 44.000 7.01 0.00 43.05 2.17
922 999 2.890311 CCGGAGAGCAACTCATCTATCT 59.110 50.000 0.00 0.00 46.54 1.98
923 1000 4.075682 CCGGAGAGCAACTCATCTATCTA 58.924 47.826 0.00 0.00 46.54 1.98
924 1001 4.704540 CCGGAGAGCAACTCATCTATCTAT 59.295 45.833 0.00 0.00 46.54 1.98
925 1002 5.163663 CCGGAGAGCAACTCATCTATCTATC 60.164 48.000 0.00 0.00 46.54 2.08
926 1003 5.163663 CGGAGAGCAACTCATCTATCTATCC 60.164 48.000 11.83 0.00 46.54 2.59
927 1004 5.714333 GGAGAGCAACTCATCTATCTATCCA 59.286 44.000 11.83 0.00 46.54 3.41
928 1005 6.380846 GGAGAGCAACTCATCTATCTATCCAT 59.619 42.308 11.83 0.00 46.54 3.41
929 1006 7.408756 AGAGCAACTCATCTATCTATCCATC 57.591 40.000 0.00 0.00 32.06 3.51
930 1007 6.095300 AGAGCAACTCATCTATCTATCCATCG 59.905 42.308 0.00 0.00 32.06 3.84
1107 1190 4.142337 TGTGACTACGAGTTTGTTGTCTCA 60.142 41.667 12.92 12.39 42.55 3.27
1149 1232 0.528017 GCACGGACTCAGATCTCACA 59.472 55.000 0.00 0.00 0.00 3.58
1357 1447 1.952133 TGCCGTTCCGTCGACTTTG 60.952 57.895 14.70 2.05 0.00 2.77
1475 3066 2.336809 GATCCTCTAGCACGGCGG 59.663 66.667 13.24 0.66 0.00 6.13
1603 3200 3.008517 TTCCGGCAGCTCCCATGA 61.009 61.111 0.00 0.00 0.00 3.07
1609 3206 1.613836 GGCAGCTCCCATGAATAAGG 58.386 55.000 0.00 0.00 0.00 2.69
1613 3210 2.947652 CAGCTCCCATGAATAAGGTGTG 59.052 50.000 0.00 0.00 33.67 3.82
1626 3223 0.183492 AGGTGTGCCTTGTCATGTGT 59.817 50.000 0.00 0.00 44.18 3.72
1628 3225 1.535462 GGTGTGCCTTGTCATGTGTAC 59.465 52.381 0.00 0.00 0.00 2.90
1629 3226 1.194547 GTGTGCCTTGTCATGTGTACG 59.805 52.381 0.00 0.00 0.00 3.67
1631 3228 2.036089 TGTGCCTTGTCATGTGTACGTA 59.964 45.455 0.00 0.00 0.00 3.57
1633 3230 1.652124 GCCTTGTCATGTGTACGTACG 59.348 52.381 20.18 15.01 0.00 3.67
1634 3231 2.923605 GCCTTGTCATGTGTACGTACGT 60.924 50.000 25.98 25.98 0.00 3.57
1644 3267 0.725784 GTACGTACGTGTCCGGTGTG 60.726 60.000 30.25 0.00 38.78 3.82
1647 3270 1.066257 GTACGTGTCCGGTGTGTGT 59.934 57.895 0.00 0.00 38.78 3.72
1649 3272 1.665264 TACGTGTCCGGTGTGTGTGT 61.665 55.000 0.00 0.00 38.78 3.72
1650 3273 1.812093 CGTGTCCGGTGTGTGTGTT 60.812 57.895 0.00 0.00 0.00 3.32
1651 3274 1.363145 CGTGTCCGGTGTGTGTGTTT 61.363 55.000 0.00 0.00 0.00 2.83
1656 3279 0.816018 CCGGTGTGTGTGTTTGGCTA 60.816 55.000 0.00 0.00 0.00 3.93
1661 3284 3.435671 GGTGTGTGTGTTTGGCTATCTAC 59.564 47.826 0.00 0.00 0.00 2.59
1688 3311 3.145551 GCCGGGCTCCTCGTCTTA 61.146 66.667 12.87 0.00 0.00 2.10
1689 3312 2.499827 GCCGGGCTCCTCGTCTTAT 61.500 63.158 12.87 0.00 0.00 1.73
1699 3322 5.059833 GCTCCTCGTCTTATTTTCCATCAT 58.940 41.667 0.00 0.00 0.00 2.45
1706 3329 7.881142 TCGTCTTATTTTCCATCATTGTTGTT 58.119 30.769 0.00 0.00 0.00 2.83
1715 3342 5.841810 TCCATCATTGTTGTTCTTGTTTCC 58.158 37.500 0.00 0.00 0.00 3.13
1716 3343 5.598005 TCCATCATTGTTGTTCTTGTTTCCT 59.402 36.000 0.00 0.00 0.00 3.36
1717 3344 6.098124 TCCATCATTGTTGTTCTTGTTTCCTT 59.902 34.615 0.00 0.00 0.00 3.36
1718 3345 6.762661 CCATCATTGTTGTTCTTGTTTCCTTT 59.237 34.615 0.00 0.00 0.00 3.11
1719 3346 7.042523 CCATCATTGTTGTTCTTGTTTCCTTTC 60.043 37.037 0.00 0.00 0.00 2.62
1764 3391 6.461110 AATAAGATCCTGCCTTCATTGTTG 57.539 37.500 0.00 0.00 0.00 3.33
1765 3392 3.446442 AGATCCTGCCTTCATTGTTGT 57.554 42.857 0.00 0.00 0.00 3.32
1767 3394 3.760684 AGATCCTGCCTTCATTGTTGTTC 59.239 43.478 0.00 0.00 0.00 3.18
1769 3396 3.565307 TCCTGCCTTCATTGTTGTTCTT 58.435 40.909 0.00 0.00 0.00 2.52
1770 3397 4.724399 TCCTGCCTTCATTGTTGTTCTTA 58.276 39.130 0.00 0.00 0.00 2.10
1773 3400 6.267471 TCCTGCCTTCATTGTTGTTCTTATTT 59.733 34.615 0.00 0.00 0.00 1.40
1775 3402 7.116805 CCTGCCTTCATTGTTGTTCTTATTTTC 59.883 37.037 0.00 0.00 0.00 2.29
1776 3403 6.928492 TGCCTTCATTGTTGTTCTTATTTTCC 59.072 34.615 0.00 0.00 0.00 3.13
1777 3404 6.928492 GCCTTCATTGTTGTTCTTATTTTCCA 59.072 34.615 0.00 0.00 0.00 3.53
1797 3522 3.769300 CCATGATCCATCCATGCATGATT 59.231 43.478 28.31 11.70 39.89 2.57
1802 3527 4.710313 TCCATCCATGCATGATTACTCA 57.290 40.909 28.31 2.62 35.41 3.41
1804 3529 5.250982 TCCATCCATGCATGATTACTCATC 58.749 41.667 28.31 0.00 40.20 2.92
1814 3539 6.166279 GCATGATTACTCATCTATTTCCCGA 58.834 40.000 0.00 0.00 40.20 5.14
1825 3550 0.462047 ATTTCCCGACGTGCATCCTC 60.462 55.000 0.00 0.00 0.00 3.71
1826 3551 1.541310 TTTCCCGACGTGCATCCTCT 61.541 55.000 0.00 0.00 0.00 3.69
1852 3577 6.872020 GCCGTGTATGTATATATCCAGTTTGT 59.128 38.462 0.00 0.00 0.00 2.83
1861 3586 9.303116 TGTATATATCCAGTTTGTTGTTTGGTT 57.697 29.630 0.00 0.00 32.51 3.67
1866 3591 6.347859 TCCAGTTTGTTGTTTGGTTTAAGT 57.652 33.333 0.00 0.00 32.51 2.24
1867 3592 7.463961 TCCAGTTTGTTGTTTGGTTTAAGTA 57.536 32.000 0.00 0.00 32.51 2.24
1869 3594 6.251801 CCAGTTTGTTGTTTGGTTTAAGTACG 59.748 38.462 0.00 0.00 0.00 3.67
1870 3595 5.801444 AGTTTGTTGTTTGGTTTAAGTACGC 59.199 36.000 0.00 0.00 0.00 4.42
1872 3597 3.620374 TGTTGTTTGGTTTAAGTACGCGA 59.380 39.130 15.93 0.00 0.00 5.87
1873 3598 4.206088 GTTGTTTGGTTTAAGTACGCGAG 58.794 43.478 15.93 0.00 0.00 5.03
1874 3599 2.221517 TGTTTGGTTTAAGTACGCGAGC 59.778 45.455 15.93 4.57 0.00 5.03
1875 3600 2.151881 TTGGTTTAAGTACGCGAGCA 57.848 45.000 15.93 0.09 0.00 4.26
1876 3601 2.373540 TGGTTTAAGTACGCGAGCAT 57.626 45.000 15.93 0.00 0.00 3.79
1877 3602 3.507103 TGGTTTAAGTACGCGAGCATA 57.493 42.857 15.93 0.00 0.00 3.14
1878 3603 3.181397 TGGTTTAAGTACGCGAGCATAC 58.819 45.455 15.93 4.51 0.00 2.39
1879 3604 3.119388 TGGTTTAAGTACGCGAGCATACT 60.119 43.478 15.93 7.29 32.93 2.12
1880 3605 3.242248 GGTTTAAGTACGCGAGCATACTG 59.758 47.826 15.93 0.00 31.93 2.74
1881 3606 3.770263 TTAAGTACGCGAGCATACTGT 57.230 42.857 15.93 4.11 31.93 3.55
1882 3607 1.909376 AAGTACGCGAGCATACTGTG 58.091 50.000 15.93 0.00 31.93 3.66
1884 3609 1.201647 AGTACGCGAGCATACTGTGTT 59.798 47.619 15.93 0.00 30.34 3.32
1885 3610 1.582502 GTACGCGAGCATACTGTGTTC 59.417 52.381 15.93 0.00 34.98 3.18
1893 3618 4.641954 GAGCATACTGTGTTCGTTGATTG 58.358 43.478 0.00 0.00 0.00 2.67
1894 3619 4.314961 AGCATACTGTGTTCGTTGATTGA 58.685 39.130 0.00 0.00 0.00 2.57
1898 3644 6.620518 GCATACTGTGTTCGTTGATTGAATGA 60.621 38.462 0.00 0.00 0.00 2.57
1901 3647 7.433708 ACTGTGTTCGTTGATTGAATGAATA 57.566 32.000 0.00 0.00 40.83 1.75
1903 3649 7.173218 ACTGTGTTCGTTGATTGAATGAATACT 59.827 33.333 15.02 0.00 45.32 2.12
1908 3654 9.000018 GTTCGTTGATTGAATGAATACTAAAGC 58.000 33.333 0.00 0.00 40.83 3.51
1910 3656 9.594478 TCGTTGATTGAATGAATACTAAAGCTA 57.406 29.630 0.00 0.00 0.00 3.32
1932 3679 4.207165 ACCAGCACATCAAAACTTACACT 58.793 39.130 0.00 0.00 0.00 3.55
1933 3680 4.275936 ACCAGCACATCAAAACTTACACTC 59.724 41.667 0.00 0.00 0.00 3.51
1934 3681 4.320494 CCAGCACATCAAAACTTACACTCC 60.320 45.833 0.00 0.00 0.00 3.85
1940 3687 5.299279 ACATCAAAACTTACACTCCCAACAG 59.701 40.000 0.00 0.00 0.00 3.16
1999 4732 3.767711 ACAAAAATGGAGACCCTCTTCC 58.232 45.455 0.00 0.00 0.00 3.46
2004 4737 4.682021 AATGGAGACCCTCTTCCAAAAT 57.318 40.909 0.00 0.00 35.71 1.82
2016 4749 3.966665 TCTTCCAAAATTCCTGCACCTTT 59.033 39.130 0.00 0.00 0.00 3.11
2018 4751 2.368221 TCCAAAATTCCTGCACCTTTGG 59.632 45.455 11.39 11.39 44.84 3.28
2023 4838 2.905415 TTCCTGCACCTTTGGATCAT 57.095 45.000 0.00 0.00 0.00 2.45
2028 4843 5.271598 TCCTGCACCTTTGGATCATATTTT 58.728 37.500 0.00 0.00 0.00 1.82
2049 4864 7.775053 TTTTGCCAACTAATCTCATAGGTTT 57.225 32.000 0.00 0.00 0.00 3.27
2081 4899 1.704641 ATCTGCCCGTAGATGTAGCA 58.295 50.000 0.00 0.00 36.12 3.49
2156 4974 4.034410 GGATCCTTTCTTCTACCTCCTGT 58.966 47.826 3.84 0.00 0.00 4.00
2157 4975 4.141824 GGATCCTTTCTTCTACCTCCTGTG 60.142 50.000 3.84 0.00 0.00 3.66
2161 4979 0.888619 TCTTCTACCTCCTGTGTGCG 59.111 55.000 0.00 0.00 0.00 5.34
2174 4992 3.394800 TGTGCGTCTCGTACACATC 57.605 52.632 8.73 0.00 46.10 3.06
2199 5017 2.224354 GGACTCGTTTGTGGTTTCCCTA 60.224 50.000 0.00 0.00 0.00 3.53
2204 5022 4.658063 TCGTTTGTGGTTTCCCTATTGAT 58.342 39.130 0.00 0.00 0.00 2.57
2208 5026 4.649267 TGTGGTTTCCCTATTGATCACA 57.351 40.909 0.00 0.00 0.00 3.58
2215 5033 5.880164 TTCCCTATTGATCACATAACCGA 57.120 39.130 0.00 0.00 0.00 4.69
2235 5053 5.422970 ACCGATAACACTATCACAACCCTTA 59.577 40.000 0.00 0.00 34.62 2.69
2264 5082 9.809096 TTTGTATGACTTTGTTGCTTAATCAAA 57.191 25.926 0.00 0.00 0.00 2.69
2311 5129 1.107945 TGTTCGTGCGGATGGATCTA 58.892 50.000 0.00 0.00 0.00 1.98
2312 5130 1.202371 TGTTCGTGCGGATGGATCTAC 60.202 52.381 0.00 0.00 0.00 2.59
2352 5170 7.812191 TGAATAGCGCAACTTTATTTCATTGTT 59.188 29.630 11.47 0.00 0.00 2.83
2357 5175 6.281056 CGCAACTTTATTTCATTGTTCAACG 58.719 36.000 0.00 0.00 0.00 4.10
2378 5196 5.805728 ACGAAAAGAGGGATACAAAGATGT 58.194 37.500 0.00 0.00 43.74 3.06
2379 5197 5.875359 ACGAAAAGAGGGATACAAAGATGTC 59.125 40.000 0.00 0.00 41.05 3.06
2416 5235 2.350458 AAACATGATGCCCCACCGC 61.350 57.895 0.00 0.00 0.00 5.68
2446 5265 4.218852 GGTCGCCATTCTAGCTAGTCTATT 59.781 45.833 20.10 0.00 0.00 1.73
2447 5266 5.279056 GGTCGCCATTCTAGCTAGTCTATTT 60.279 44.000 20.10 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 0.460284 CACATTAGCCGAGTTCCGCT 60.460 55.000 0.95 0.95 36.84 5.52
59 60 4.202020 GGACTTGGCGAAAGAAAGAAACTT 60.202 41.667 4.90 0.00 39.38 2.66
90 91 0.464735 ACGTTTGCCTAGTGTGCCAA 60.465 50.000 0.00 0.00 0.00 4.52
94 95 1.455786 CTTCGACGTTTGCCTAGTGTG 59.544 52.381 0.00 0.00 0.00 3.82
95 96 1.068127 ACTTCGACGTTTGCCTAGTGT 59.932 47.619 0.00 0.00 0.00 3.55
125 126 1.005630 GACTTGACAGTGGCGAGCT 60.006 57.895 13.67 0.47 31.22 4.09
128 129 0.396435 ATTGGACTTGACAGTGGCGA 59.604 50.000 0.00 0.00 31.22 5.54
131 132 5.939883 TCTTGATAATTGGACTTGACAGTGG 59.060 40.000 0.00 0.00 31.22 4.00
188 189 3.125829 GCTTCGCTGAGTTCAATTCATCA 59.874 43.478 0.00 0.00 0.00 3.07
388 391 0.459063 ACTTATTCGCGGACGGAACC 60.459 55.000 6.13 0.00 40.63 3.62
596 603 7.011576 TGCAATTCTACGTTTTGTTCTAAGTCA 59.988 33.333 0.00 0.00 0.00 3.41
618 645 1.001068 TCCGTCCGTGAATAAGTGCAA 59.999 47.619 0.00 0.00 0.00 4.08
817 875 2.288213 CCGTGCGATTATGCTTCTCCTA 60.288 50.000 0.00 0.00 35.36 2.94
818 876 1.539065 CCGTGCGATTATGCTTCTCCT 60.539 52.381 0.00 0.00 35.36 3.69
819 877 0.861837 CCGTGCGATTATGCTTCTCC 59.138 55.000 0.00 0.00 35.36 3.71
820 878 1.258982 CACCGTGCGATTATGCTTCTC 59.741 52.381 0.00 0.00 35.36 2.87
821 879 1.134818 TCACCGTGCGATTATGCTTCT 60.135 47.619 0.00 0.00 35.36 2.85
922 999 7.667635 GTCTATAGATGGATGGATCGATGGATA 59.332 40.741 0.54 0.00 31.13 2.59
923 1000 6.493115 GTCTATAGATGGATGGATCGATGGAT 59.507 42.308 0.54 0.00 31.13 3.41
924 1001 5.830457 GTCTATAGATGGATGGATCGATGGA 59.170 44.000 0.54 0.00 0.00 3.41
925 1002 5.832595 AGTCTATAGATGGATGGATCGATGG 59.167 44.000 0.54 0.00 0.00 3.51
926 1003 6.957920 AGTCTATAGATGGATGGATCGATG 57.042 41.667 0.54 0.00 0.00 3.84
927 1004 7.500892 GTGTAGTCTATAGATGGATGGATCGAT 59.499 40.741 5.57 0.00 0.00 3.59
928 1005 6.824196 GTGTAGTCTATAGATGGATGGATCGA 59.176 42.308 5.57 0.00 0.00 3.59
929 1006 6.038825 GGTGTAGTCTATAGATGGATGGATCG 59.961 46.154 5.57 0.00 0.00 3.69
930 1007 6.038825 CGGTGTAGTCTATAGATGGATGGATC 59.961 46.154 5.57 0.00 0.00 3.36
1066 1149 1.069765 ACAGTTGCACCGGACTCTG 59.930 57.895 9.46 14.34 0.00 3.35
1067 1150 1.069765 CACAGTTGCACCGGACTCT 59.930 57.895 9.46 0.14 0.00 3.24
1068 1151 1.227556 ACACAGTTGCACCGGACTC 60.228 57.895 9.46 0.00 0.00 3.36
1069 1152 1.523711 CACACAGTTGCACCGGACT 60.524 57.895 9.46 0.00 0.00 3.85
1070 1153 1.522806 TCACACAGTTGCACCGGAC 60.523 57.895 9.46 0.00 0.00 4.79
1071 1154 1.522806 GTCACACAGTTGCACCGGA 60.523 57.895 9.46 0.00 0.00 5.14
1107 1190 3.056304 CGCCCAATTTTCATTGAACGTT 58.944 40.909 0.00 0.00 42.35 3.99
1357 1447 2.036571 CCCCGTTCCGCTTTACCAC 61.037 63.158 0.00 0.00 0.00 4.16
1475 3066 1.895231 TCCTGATCATGCATGGCGC 60.895 57.895 25.97 15.48 42.89 6.53
1558 3155 5.875930 AGGAAACTAAACAAAACAGTCACG 58.124 37.500 0.00 0.00 40.61 4.35
1609 3206 1.194547 CGTACACATGACAAGGCACAC 59.805 52.381 0.00 0.00 0.00 3.82
1613 3210 1.652124 CGTACGTACACATGACAAGGC 59.348 52.381 24.50 0.00 0.00 4.35
1623 3220 0.725784 CACCGGACACGTACGTACAC 60.726 60.000 22.34 14.41 38.78 2.90
1624 3221 1.163420 ACACCGGACACGTACGTACA 61.163 55.000 22.34 0.00 38.78 2.90
1626 3223 1.163420 ACACACCGGACACGTACGTA 61.163 55.000 22.34 0.00 38.78 3.57
1628 3225 2.012414 CACACACCGGACACGTACG 61.012 63.158 15.01 15.01 38.78 3.67
1629 3226 1.066257 ACACACACCGGACACGTAC 59.934 57.895 9.46 0.00 38.78 3.67
1631 3228 2.202824 CACACACACCGGACACGT 60.203 61.111 9.46 0.00 38.78 4.49
1633 3230 0.098025 CAAACACACACACCGGACAC 59.902 55.000 9.46 0.00 0.00 3.67
1634 3231 1.027255 CCAAACACACACACCGGACA 61.027 55.000 9.46 0.00 0.00 4.02
1644 3267 6.456501 CCTATAGGTAGATAGCCAAACACAC 58.543 44.000 10.96 0.00 0.00 3.82
1647 3270 5.152193 TGCCTATAGGTAGATAGCCAAACA 58.848 41.667 20.10 1.99 37.57 2.83
1661 3284 2.925170 AGCCCGGCTGCCTATAGG 60.925 66.667 12.38 15.01 37.57 2.57
1680 3303 7.530010 ACAACAATGATGGAAAATAAGACGAG 58.470 34.615 0.00 0.00 0.00 4.18
1685 3308 9.480053 ACAAGAACAACAATGATGGAAAATAAG 57.520 29.630 0.00 0.00 0.00 1.73
1687 3310 9.829507 AAACAAGAACAACAATGATGGAAAATA 57.170 25.926 0.00 0.00 0.00 1.40
1688 3311 8.735692 AAACAAGAACAACAATGATGGAAAAT 57.264 26.923 0.00 0.00 0.00 1.82
1689 3312 7.279758 GGAAACAAGAACAACAATGATGGAAAA 59.720 33.333 0.00 0.00 0.00 2.29
1699 3322 5.993748 AGGAAAGGAAACAAGAACAACAA 57.006 34.783 0.00 0.00 0.00 2.83
1706 3329 4.887655 GTGAGGAAAGGAAAGGAAACAAGA 59.112 41.667 0.00 0.00 0.00 3.02
1748 3375 3.228188 AGAACAACAATGAAGGCAGGA 57.772 42.857 0.00 0.00 0.00 3.86
1758 3385 8.814931 TGGATCATGGAAAATAAGAACAACAAT 58.185 29.630 0.00 0.00 0.00 2.71
1760 3387 7.773489 TGGATCATGGAAAATAAGAACAACA 57.227 32.000 0.00 0.00 0.00 3.33
1761 3388 7.922811 GGATGGATCATGGAAAATAAGAACAAC 59.077 37.037 0.00 0.00 0.00 3.32
1764 3391 7.587037 TGGATGGATCATGGAAAATAAGAAC 57.413 36.000 0.00 0.00 0.00 3.01
1765 3392 7.256048 GCATGGATGGATCATGGAAAATAAGAA 60.256 37.037 0.00 0.00 41.49 2.52
1767 3394 6.014925 TGCATGGATGGATCATGGAAAATAAG 60.015 38.462 0.00 0.00 39.40 1.73
1769 3396 5.395611 TGCATGGATGGATCATGGAAAATA 58.604 37.500 0.00 0.00 39.40 1.40
1770 3397 4.228010 TGCATGGATGGATCATGGAAAAT 58.772 39.130 0.00 0.00 39.40 1.82
1773 3400 3.161866 CATGCATGGATGGATCATGGAA 58.838 45.455 19.40 0.00 43.96 3.53
1775 3402 2.802719 TCATGCATGGATGGATCATGG 58.197 47.619 25.97 0.00 41.49 3.66
1776 3403 5.652452 AGTAATCATGCATGGATGGATCATG 59.348 40.000 25.97 12.93 43.39 3.07
1777 3404 5.827756 AGTAATCATGCATGGATGGATCAT 58.172 37.500 25.97 9.92 36.67 2.45
1797 3522 3.243301 GCACGTCGGGAAATAGATGAGTA 60.243 47.826 0.00 0.00 0.00 2.59
1802 3527 2.548067 GGATGCACGTCGGGAAATAGAT 60.548 50.000 0.00 0.00 0.00 1.98
1804 3529 1.202533 AGGATGCACGTCGGGAAATAG 60.203 52.381 0.00 0.00 0.00 1.73
1825 3550 6.208988 ACTGGATATATACATACACGGCAG 57.791 41.667 0.00 0.00 0.00 4.85
1826 3551 6.599356 AACTGGATATATACATACACGGCA 57.401 37.500 0.00 0.00 0.00 5.69
1852 3577 3.303263 GCTCGCGTACTTAAACCAAACAA 60.303 43.478 5.77 0.00 0.00 2.83
1861 3586 3.119743 ACACAGTATGCTCGCGTACTTAA 60.120 43.478 18.42 0.00 43.81 1.85
1862 3587 2.421073 ACACAGTATGCTCGCGTACTTA 59.579 45.455 18.42 0.00 43.81 2.24
1863 3588 1.201647 ACACAGTATGCTCGCGTACTT 59.798 47.619 18.42 9.52 43.81 2.24
1864 3589 0.809385 ACACAGTATGCTCGCGTACT 59.191 50.000 15.97 15.97 46.25 2.73
1865 3590 1.582502 GAACACAGTATGCTCGCGTAC 59.417 52.381 5.77 12.20 42.53 3.67
1866 3591 1.792632 CGAACACAGTATGCTCGCGTA 60.793 52.381 5.77 0.00 42.53 4.42
1867 3592 1.071019 CGAACACAGTATGCTCGCGT 61.071 55.000 5.77 0.00 42.53 6.01
1869 3594 1.068474 AACGAACACAGTATGCTCGC 58.932 50.000 0.00 0.00 42.53 5.03
1870 3595 2.324860 TCAACGAACACAGTATGCTCG 58.675 47.619 0.00 0.00 42.53 5.03
1872 3597 4.314961 TCAATCAACGAACACAGTATGCT 58.685 39.130 0.00 0.00 42.53 3.79
1873 3598 4.661993 TCAATCAACGAACACAGTATGC 57.338 40.909 0.00 0.00 42.53 3.14
1874 3599 6.830736 TCATTCAATCAACGAACACAGTATG 58.169 36.000 0.00 0.00 46.00 2.39
1875 3600 7.433708 TTCATTCAATCAACGAACACAGTAT 57.566 32.000 0.00 0.00 0.00 2.12
1876 3601 6.852858 TTCATTCAATCAACGAACACAGTA 57.147 33.333 0.00 0.00 0.00 2.74
1877 3602 5.749596 TTCATTCAATCAACGAACACAGT 57.250 34.783 0.00 0.00 0.00 3.55
1878 3603 7.521529 AGTATTCATTCAATCAACGAACACAG 58.478 34.615 0.00 0.00 0.00 3.66
1879 3604 7.433708 AGTATTCATTCAATCAACGAACACA 57.566 32.000 0.00 0.00 0.00 3.72
1880 3605 9.820229 TTTAGTATTCATTCAATCAACGAACAC 57.180 29.630 0.00 0.00 0.00 3.32
1882 3607 9.000018 GCTTTAGTATTCATTCAATCAACGAAC 58.000 33.333 0.00 0.00 0.00 3.95
1884 3609 8.492673 AGCTTTAGTATTCATTCAATCAACGA 57.507 30.769 0.00 0.00 0.00 3.85
1885 3610 9.638300 GTAGCTTTAGTATTCATTCAATCAACG 57.362 33.333 0.00 0.00 0.00 4.10
1887 3612 9.679661 TGGTAGCTTTAGTATTCATTCAATCAA 57.320 29.630 0.00 0.00 0.00 2.57
1888 3613 9.330063 CTGGTAGCTTTAGTATTCATTCAATCA 57.670 33.333 0.00 0.00 0.00 2.57
1889 3614 8.286097 GCTGGTAGCTTTAGTATTCATTCAATC 58.714 37.037 0.00 0.00 38.45 2.67
1890 3615 7.775093 TGCTGGTAGCTTTAGTATTCATTCAAT 59.225 33.333 0.00 0.00 42.97 2.57
1891 3616 7.065803 GTGCTGGTAGCTTTAGTATTCATTCAA 59.934 37.037 0.00 0.00 42.97 2.69
1893 3618 6.538742 TGTGCTGGTAGCTTTAGTATTCATTC 59.461 38.462 0.00 0.00 42.97 2.67
1894 3619 6.414732 TGTGCTGGTAGCTTTAGTATTCATT 58.585 36.000 0.00 0.00 42.97 2.57
1898 3644 5.989477 TGATGTGCTGGTAGCTTTAGTATT 58.011 37.500 0.00 0.00 42.97 1.89
1901 3647 3.981071 TGATGTGCTGGTAGCTTTAGT 57.019 42.857 0.00 0.00 42.97 2.24
1903 3649 5.070001 AGTTTTGATGTGCTGGTAGCTTTA 58.930 37.500 0.00 0.00 42.97 1.85
1908 3654 5.470098 AGTGTAAGTTTTGATGTGCTGGTAG 59.530 40.000 0.00 0.00 0.00 3.18
1910 3656 4.207165 AGTGTAAGTTTTGATGTGCTGGT 58.793 39.130 0.00 0.00 0.00 4.00
1932 3679 3.636300 CACAAGTTTTCCATCTGTTGGGA 59.364 43.478 4.99 0.00 46.45 4.37
1933 3680 3.799917 GCACAAGTTTTCCATCTGTTGGG 60.800 47.826 4.99 0.00 46.45 4.12
1940 3687 1.266718 TGCTCGCACAAGTTTTCCATC 59.733 47.619 0.00 0.00 0.00 3.51
1987 4718 4.013050 CAGGAATTTTGGAAGAGGGTCTC 58.987 47.826 0.00 0.00 0.00 3.36
1988 4719 3.815757 GCAGGAATTTTGGAAGAGGGTCT 60.816 47.826 0.00 0.00 0.00 3.85
1999 4732 3.749665 TCCAAAGGTGCAGGAATTTTG 57.250 42.857 0.00 0.00 0.00 2.44
2004 4737 2.905415 ATGATCCAAAGGTGCAGGAA 57.095 45.000 0.00 0.00 34.62 3.36
2016 4749 7.779326 TGAGATTAGTTGGCAAAATATGATCCA 59.221 33.333 0.00 0.00 0.00 3.41
2023 4838 9.474313 AAACCTATGAGATTAGTTGGCAAAATA 57.526 29.630 0.00 0.00 0.00 1.40
2028 4843 9.474313 AAAATAAACCTATGAGATTAGTTGGCA 57.526 29.630 0.00 0.00 0.00 4.92
2049 4864 8.241497 TCTACGGGCAGATAGTTAAGAAAATA 57.759 34.615 0.00 0.00 0.00 1.40
2056 4871 5.048224 GCTACATCTACGGGCAGATAGTTAA 60.048 44.000 0.00 0.00 33.41 2.01
2192 5010 6.241882 TCGGTTATGTGATCAATAGGGAAA 57.758 37.500 0.00 0.00 0.00 3.13
2199 5017 9.424319 GATAGTGTTATCGGTTATGTGATCAAT 57.576 33.333 0.00 0.00 0.00 2.57
2204 5022 7.102847 TGTGATAGTGTTATCGGTTATGTGA 57.897 36.000 0.00 0.00 38.83 3.58
2208 5026 6.099269 AGGGTTGTGATAGTGTTATCGGTTAT 59.901 38.462 0.00 0.00 38.83 1.89
2215 5033 9.010029 CAAAGTTAAGGGTTGTGATAGTGTTAT 57.990 33.333 0.00 0.00 0.00 1.89
2235 5053 9.463443 GATTAAGCAACAAAGTCATACAAAGTT 57.537 29.630 0.00 0.00 0.00 2.66
2264 5082 8.040727 GGTTATCTTTAGAACATGGGCAATTTT 58.959 33.333 0.00 0.00 0.00 1.82
2311 5129 8.607441 TGCGCTATTCATCTAAAAATATCTGT 57.393 30.769 9.73 0.00 0.00 3.41
2312 5130 9.322776 GTTGCGCTATTCATCTAAAAATATCTG 57.677 33.333 9.73 0.00 0.00 2.90
2352 5170 5.860611 TCTTTGTATCCCTCTTTTCGTTGA 58.139 37.500 0.00 0.00 0.00 3.18
2357 5175 6.180472 TGGACATCTTTGTATCCCTCTTTTC 58.820 40.000 0.00 0.00 35.79 2.29
2416 5235 2.002586 CTAGAATGGCGACCACACTTG 58.997 52.381 0.50 2.29 35.80 3.16
2446 5265 2.230992 CGTGAAAGCAATGGGGAATCAA 59.769 45.455 0.00 0.00 0.00 2.57
2447 5266 1.818060 CGTGAAAGCAATGGGGAATCA 59.182 47.619 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.