Multiple sequence alignment - TraesCS5D01G413000

Loading Multiple Alignment...

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 TraesCS5D01G413000 chr5D 100.000 2228 0 0 1 2228 476011758 476013985 0.000000e+00 4115.0
1 TraesCS5D01G413000 chr5B 91.653 1773 79 36 35 1786 583473307 583475031 0.000000e+00 2390.0
2 TraesCS5D01G413000 chr5B 90.537 391 25 4 1836 2223 583475027 583475408 7.100000e-140 507.0
3 TraesCS5D01G413000 chr5A 88.162 1436 58 46 198 1569 595408663 595410050 0.000000e+00 1607.0
4 TraesCS5D01G413000 chr5A 91.094 393 31 4 1839 2228 595413425 595413816 1.520000e-146 529.0
5 TraesCS5D01G413000 chr5A 90.991 222 20 0 1565 1786 595413204 595413425 1.290000e-77 300.0
6 TraesCS5D01G413000 chr6A 90.164 61 3 3 1788 1846 573849285 573849226 2.370000e-10 76.8
7 TraesCS5D01G413000 chr4B 93.878 49 1 2 1801 1848 132052073 132052026 3.070000e-09 73.1
8 TraesCS5D01G413000 chr4A 93.878 49 1 2 1801 1848 488253513 488253560 3.070000e-09 73.1
9 TraesCS5D01G413000 chr3D 93.617 47 3 0 1801 1847 443421471 443421517 1.100000e-08 71.3
10 TraesCS5D01G413000 chr7B 91.837 49 4 0 1801 1849 225738738 225738786 3.970000e-08 69.4
11 TraesCS5D01G413000 chr7B 91.667 48 3 1 1802 1848 435114663 435114710 5.140000e-07 65.8
12 TraesCS5D01G413000 chr3B 95.349 43 2 0 1802 1844 572266754 572266796 3.970000e-08 69.4
13 TraesCS5D01G413000 chr3B 91.667 48 4 0 1801 1848 326583481 326583434 1.430000e-07 67.6
14 TraesCS5D01G413000 chr1A 88.462 52 4 2 1802 1852 507911744 507911794 6.640000e-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 TraesCS5D01G413000 chr5D 476011758 476013985 2227 False 4115.0 4115 100.000000 1 2228 1 chr5D.!!$F1 2227
1 TraesCS5D01G413000 chr5B 583473307 583475408 2101 False 1448.5 2390 91.095000 35 2223 2 chr5B.!!$F1 2188
2 TraesCS5D01G413000 chr5A 595408663 595413816 5153 False 812.0 1607 90.082333 198 2228 3 chr5A.!!$F1 2030

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
164 165 0.034756 ATCGTGTGTTAGCCAGTGCA 59.965 50.0 0.0 0.0 41.13 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1673 4905 0.394762 GGTTGGATCATGCCAGCTGA 60.395 55.0 17.39 0.0 39.52 4.26 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
31 32 8.354011 CTTCTTATACATTACCAAGAAGTCGG 57.646 38.462 12.56 0.00 44.50 4.79
32 33 7.649533 TCTTATACATTACCAAGAAGTCGGA 57.350 36.000 0.00 0.00 0.00 4.55
33 34 7.713750 TCTTATACATTACCAAGAAGTCGGAG 58.286 38.462 0.00 0.00 0.00 4.63
50 51 1.585297 GAGGTTTTTGGAACGGACGA 58.415 50.000 0.00 0.00 0.00 4.20
60 61 2.159071 TGGAACGGACGAGAAACTCAAA 60.159 45.455 0.00 0.00 0.00 2.69
122 123 8.458573 TTTGCTTCAATTCTTACCAGAAACTA 57.541 30.769 0.00 0.00 42.53 2.24
141 142 8.643324 AGAAACTAAGACATGAAGTACAGAAGT 58.357 33.333 0.00 0.00 0.00 3.01
164 165 0.034756 ATCGTGTGTTAGCCAGTGCA 59.965 50.000 0.00 0.00 41.13 4.57
177 178 2.854805 GCCAGTGCAAACGTTTTCTCTC 60.855 50.000 11.66 4.93 37.47 3.20
179 180 3.003689 CCAGTGCAAACGTTTTCTCTCAT 59.996 43.478 11.66 0.00 0.00 2.90
310 311 1.318576 GGATCGGGCATAAACCTTGG 58.681 55.000 0.00 0.00 0.00 3.61
325 326 4.130286 ACCTTGGTCAGATTCTTCGATC 57.870 45.455 0.00 0.00 0.00 3.69
349 350 2.049228 CGGATCAAATACTACGTCCGC 58.951 52.381 0.00 0.00 41.55 5.54
661 669 2.881827 CATGGCAAATGCACGGCG 60.882 61.111 4.80 4.80 44.36 6.46
752 760 2.007113 AAACAAAACACCGGCCCGAC 62.007 55.000 3.71 0.00 0.00 4.79
754 762 4.550697 AAAACACCGGCCCGACGT 62.551 61.111 3.71 0.00 0.00 4.34
816 839 4.760840 GCAGCTCGCGAGTCGTGA 62.761 66.667 34.46 25.83 44.12 4.35
825 848 1.959899 GCGAGTCGTGAGTGCCAATG 61.960 60.000 15.08 0.00 0.00 2.82
889 915 3.421844 GCACCCAGAGTAAAAGGAACAT 58.578 45.455 0.00 0.00 0.00 2.71
894 920 4.010349 CCAGAGTAAAAGGAACATCCACC 58.990 47.826 0.00 0.00 39.61 4.61
897 923 4.105697 AGAGTAAAAGGAACATCCACCCAA 59.894 41.667 0.00 0.00 39.61 4.12
898 924 4.149598 AGTAAAAGGAACATCCACCCAAC 58.850 43.478 0.00 0.00 39.61 3.77
899 925 2.765689 AAAGGAACATCCACCCAACA 57.234 45.000 0.00 0.00 39.61 3.33
900 926 1.995376 AAGGAACATCCACCCAACAC 58.005 50.000 0.00 0.00 39.61 3.32
901 927 0.112412 AGGAACATCCACCCAACACC 59.888 55.000 0.00 0.00 39.61 4.16
902 928 0.178975 GGAACATCCACCCAACACCA 60.179 55.000 0.00 0.00 36.28 4.17
903 929 1.698506 GAACATCCACCCAACACCAA 58.301 50.000 0.00 0.00 0.00 3.67
904 930 1.339929 GAACATCCACCCAACACCAAC 59.660 52.381 0.00 0.00 0.00 3.77
905 931 0.260230 ACATCCACCCAACACCAACA 59.740 50.000 0.00 0.00 0.00 3.33
906 932 0.673437 CATCCACCCAACACCAACAC 59.327 55.000 0.00 0.00 0.00 3.32
924 950 2.149578 CACCCAAGCAGTGAAAGAGAG 58.850 52.381 0.00 0.00 37.42 3.20
930 956 1.003003 AGCAGTGAAAGAGAGGAAGCC 59.997 52.381 0.00 0.00 0.00 4.35
931 957 1.719600 CAGTGAAAGAGAGGAAGCCG 58.280 55.000 0.00 0.00 0.00 5.52
932 958 0.610687 AGTGAAAGAGAGGAAGCCGG 59.389 55.000 0.00 0.00 0.00 6.13
933 959 0.608640 GTGAAAGAGAGGAAGCCGGA 59.391 55.000 5.05 0.00 0.00 5.14
934 960 0.898320 TGAAAGAGAGGAAGCCGGAG 59.102 55.000 5.05 0.00 0.00 4.63
935 961 0.461163 GAAAGAGAGGAAGCCGGAGC 60.461 60.000 5.05 0.00 40.32 4.70
999 1049 1.135257 GCAGAGCGAAGAGTTAGAGCA 60.135 52.381 0.00 0.00 0.00 4.26
1313 1373 1.139853 GGCACAAGGGAGGAGTCTATG 59.860 57.143 0.00 0.00 0.00 2.23
1326 1386 1.089920 GTCTATGCCTTGTGCTGTGG 58.910 55.000 0.00 0.00 42.00 4.17
1327 1387 0.692476 TCTATGCCTTGTGCTGTGGT 59.308 50.000 0.00 0.00 42.00 4.16
1328 1388 1.073763 TCTATGCCTTGTGCTGTGGTT 59.926 47.619 0.00 0.00 42.00 3.67
1329 1389 1.200716 CTATGCCTTGTGCTGTGGTTG 59.799 52.381 0.00 0.00 42.00 3.77
1330 1390 0.756442 ATGCCTTGTGCTGTGGTTGT 60.756 50.000 0.00 0.00 42.00 3.32
1331 1391 1.066257 GCCTTGTGCTGTGGTTGTG 59.934 57.895 0.00 0.00 36.87 3.33
1332 1392 1.666209 GCCTTGTGCTGTGGTTGTGT 61.666 55.000 0.00 0.00 36.87 3.72
1402 1470 4.440250 CGTAGTAGTAGTGCTCATGCCTTT 60.440 45.833 0.00 0.00 38.71 3.11
1587 4819 6.210385 TGGTGATACATTTGCTATTGTGGTTT 59.790 34.615 6.04 0.00 0.00 3.27
1590 4822 7.598493 GTGATACATTTGCTATTGTGGTTTTGT 59.402 33.333 6.04 0.00 0.00 2.83
1599 4831 7.271511 TGCTATTGTGGTTTTGTTCAATCTTT 58.728 30.769 0.00 0.00 33.48 2.52
1637 4869 4.806640 TTAAGAACGACGGGGAGTTTAT 57.193 40.909 0.00 0.00 0.00 1.40
1639 4871 3.790152 AGAACGACGGGGAGTTTATAC 57.210 47.619 0.00 0.00 0.00 1.47
1673 4905 6.421801 GCATTTTGTCAAGAGCTGTTTATTGT 59.578 34.615 0.00 0.00 0.00 2.71
1785 5020 0.388520 CACGAGATGCTCCAACGACA 60.389 55.000 0.00 0.00 0.00 4.35
1786 5021 0.109086 ACGAGATGCTCCAACGACAG 60.109 55.000 0.00 0.00 0.00 3.51
1787 5022 0.171231 CGAGATGCTCCAACGACAGA 59.829 55.000 0.00 0.00 0.00 3.41
1788 5023 1.634702 GAGATGCTCCAACGACAGAC 58.365 55.000 0.00 0.00 0.00 3.51
1789 5024 1.203523 GAGATGCTCCAACGACAGACT 59.796 52.381 0.00 0.00 0.00 3.24
1790 5025 1.203523 AGATGCTCCAACGACAGACTC 59.796 52.381 0.00 0.00 0.00 3.36
1791 5026 0.247736 ATGCTCCAACGACAGACTCC 59.752 55.000 0.00 0.00 0.00 3.85
1792 5027 1.079750 GCTCCAACGACAGACTCCC 60.080 63.158 0.00 0.00 0.00 4.30
1793 5028 1.536943 GCTCCAACGACAGACTCCCT 61.537 60.000 0.00 0.00 0.00 4.20
1794 5029 0.528470 CTCCAACGACAGACTCCCTC 59.472 60.000 0.00 0.00 0.00 4.30
1795 5030 0.898789 TCCAACGACAGACTCCCTCC 60.899 60.000 0.00 0.00 0.00 4.30
1796 5031 1.213013 CAACGACAGACTCCCTCCG 59.787 63.158 0.00 0.00 0.00 4.63
1797 5032 1.228490 AACGACAGACTCCCTCCGT 60.228 57.895 0.00 0.00 34.17 4.69
1798 5033 1.242665 AACGACAGACTCCCTCCGTC 61.243 60.000 0.00 0.00 32.39 4.79
1799 5034 2.408241 CGACAGACTCCCTCCGTCC 61.408 68.421 0.00 0.00 31.83 4.79
1800 5035 2.037527 ACAGACTCCCTCCGTCCC 59.962 66.667 0.00 0.00 31.83 4.46
1801 5036 2.360980 CAGACTCCCTCCGTCCCT 59.639 66.667 0.00 0.00 31.83 4.20
1802 5037 1.212934 ACAGACTCCCTCCGTCCCTA 61.213 60.000 0.00 0.00 31.83 3.53
1803 5038 0.466555 CAGACTCCCTCCGTCCCTAG 60.467 65.000 0.00 0.00 31.83 3.02
1804 5039 0.920271 AGACTCCCTCCGTCCCTAGT 60.920 60.000 0.00 0.00 31.83 2.57
1805 5040 0.752376 GACTCCCTCCGTCCCTAGTG 60.752 65.000 0.00 0.00 0.00 2.74
1806 5041 1.306970 CTCCCTCCGTCCCTAGTGT 59.693 63.158 0.00 0.00 0.00 3.55
1807 5042 0.752376 CTCCCTCCGTCCCTAGTGTC 60.752 65.000 0.00 0.00 0.00 3.67
1808 5043 1.000019 CCCTCCGTCCCTAGTGTCA 60.000 63.158 0.00 0.00 0.00 3.58
1809 5044 0.613853 CCCTCCGTCCCTAGTGTCAA 60.614 60.000 0.00 0.00 0.00 3.18
1810 5045 1.263356 CCTCCGTCCCTAGTGTCAAA 58.737 55.000 0.00 0.00 0.00 2.69
1811 5046 1.621814 CCTCCGTCCCTAGTGTCAAAA 59.378 52.381 0.00 0.00 0.00 2.44
1812 5047 2.038033 CCTCCGTCCCTAGTGTCAAAAA 59.962 50.000 0.00 0.00 0.00 1.94
1813 5048 3.064931 CTCCGTCCCTAGTGTCAAAAAC 58.935 50.000 0.00 0.00 0.00 2.43
1814 5049 1.796459 CCGTCCCTAGTGTCAAAAACG 59.204 52.381 0.00 0.00 0.00 3.60
1815 5050 2.476821 CGTCCCTAGTGTCAAAAACGT 58.523 47.619 0.00 0.00 0.00 3.99
1816 5051 2.473984 CGTCCCTAGTGTCAAAAACGTC 59.526 50.000 0.00 0.00 0.00 4.34
1817 5052 3.725490 GTCCCTAGTGTCAAAAACGTCT 58.275 45.455 0.00 0.00 0.00 4.18
1818 5053 4.124970 GTCCCTAGTGTCAAAAACGTCTT 58.875 43.478 0.00 0.00 0.00 3.01
1819 5054 5.291971 GTCCCTAGTGTCAAAAACGTCTTA 58.708 41.667 0.00 0.00 0.00 2.10
1820 5055 5.176406 GTCCCTAGTGTCAAAAACGTCTTAC 59.824 44.000 0.00 0.00 0.00 2.34
1821 5056 5.051816 CCCTAGTGTCAAAAACGTCTTACA 58.948 41.667 0.00 0.00 0.00 2.41
1822 5057 5.699458 CCCTAGTGTCAAAAACGTCTTACAT 59.301 40.000 0.00 0.00 0.00 2.29
1823 5058 6.204108 CCCTAGTGTCAAAAACGTCTTACATT 59.796 38.462 0.00 0.00 0.00 2.71
1824 5059 7.385752 CCCTAGTGTCAAAAACGTCTTACATTA 59.614 37.037 0.00 0.00 0.00 1.90
1825 5060 8.932791 CCTAGTGTCAAAAACGTCTTACATTAT 58.067 33.333 0.00 0.00 0.00 1.28
1826 5061 9.741168 CTAGTGTCAAAAACGTCTTACATTATG 57.259 33.333 0.00 0.00 0.00 1.90
1827 5062 7.581476 AGTGTCAAAAACGTCTTACATTATGG 58.419 34.615 0.00 0.00 0.00 2.74
1828 5063 6.799925 GTGTCAAAAACGTCTTACATTATGGG 59.200 38.462 0.00 0.00 0.00 4.00
1829 5064 6.711194 TGTCAAAAACGTCTTACATTATGGGA 59.289 34.615 0.00 0.00 0.00 4.37
1830 5065 7.019418 GTCAAAAACGTCTTACATTATGGGAC 58.981 38.462 0.00 1.75 0.00 4.46
1833 5068 3.720949 CGTCTTACATTATGGGACGGA 57.279 47.619 20.50 2.30 43.69 4.69
1834 5069 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
1887 5122 3.492353 CGGCATCATCCCCACCCT 61.492 66.667 0.00 0.00 0.00 4.34
1897 5132 2.663196 CCCACCCTCACCTTCGAC 59.337 66.667 0.00 0.00 0.00 4.20
1902 5137 1.321074 ACCCTCACCTTCGACGATCC 61.321 60.000 0.00 0.00 0.00 3.36
1920 5157 3.806949 TCCATAGGATTGTATTGCCCC 57.193 47.619 0.00 0.00 0.00 5.80
1948 5185 7.216973 AGTCGAACACTCTACTTGAACTTAT 57.783 36.000 0.00 0.00 0.00 1.73
1977 5214 7.286316 CCTACTGGAAATGGCTATTCTTTGAAT 59.714 37.037 0.00 0.00 34.57 2.57
2009 5246 2.108700 CACGAAACGCCAAGACTTTTG 58.891 47.619 0.00 0.00 0.00 2.44
2033 5270 0.319040 CGAGGACATCCATACTGCGG 60.319 60.000 0.00 0.00 38.89 5.69
2124 5361 1.217882 ACCTTTCTTCGTGCGTGAAG 58.782 50.000 10.60 10.60 45.37 3.02
2177 5414 2.806244 GAGTGGCGATGTGTTAACTTGT 59.194 45.455 7.22 0.00 0.00 3.16
2223 5461 5.574188 AGTGCCACTCTTAAAGAAATCCAT 58.426 37.500 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 8.070034 TCCGACTTCTTGGTAATGTATAAGAA 57.930 34.615 0.00 0.00 36.96 2.52
8 9 7.201884 CCTCCGACTTCTTGGTAATGTATAAGA 60.202 40.741 0.00 0.00 0.00 2.10
9 10 6.924060 CCTCCGACTTCTTGGTAATGTATAAG 59.076 42.308 0.00 0.00 0.00 1.73
10 11 6.381994 ACCTCCGACTTCTTGGTAATGTATAA 59.618 38.462 0.00 0.00 0.00 0.98
11 12 5.895534 ACCTCCGACTTCTTGGTAATGTATA 59.104 40.000 0.00 0.00 0.00 1.47
12 13 4.715297 ACCTCCGACTTCTTGGTAATGTAT 59.285 41.667 0.00 0.00 0.00 2.29
13 14 4.091549 ACCTCCGACTTCTTGGTAATGTA 58.908 43.478 0.00 0.00 0.00 2.29
14 15 2.904434 ACCTCCGACTTCTTGGTAATGT 59.096 45.455 0.00 0.00 0.00 2.71
15 16 3.611766 ACCTCCGACTTCTTGGTAATG 57.388 47.619 0.00 0.00 0.00 1.90
16 17 4.635699 AAACCTCCGACTTCTTGGTAAT 57.364 40.909 0.00 0.00 0.00 1.89
17 18 4.426736 AAAACCTCCGACTTCTTGGTAA 57.573 40.909 0.00 0.00 0.00 2.85
18 19 4.131596 CAAAAACCTCCGACTTCTTGGTA 58.868 43.478 0.00 0.00 0.00 3.25
19 20 2.949644 CAAAAACCTCCGACTTCTTGGT 59.050 45.455 0.00 0.00 0.00 3.67
20 21 2.293399 CCAAAAACCTCCGACTTCTTGG 59.707 50.000 0.00 0.00 0.00 3.61
21 22 3.211045 TCCAAAAACCTCCGACTTCTTG 58.789 45.455 0.00 0.00 0.00 3.02
22 23 3.570912 TCCAAAAACCTCCGACTTCTT 57.429 42.857 0.00 0.00 0.00 2.52
23 24 3.211865 GTTCCAAAAACCTCCGACTTCT 58.788 45.455 0.00 0.00 0.00 2.85
24 25 2.032290 CGTTCCAAAAACCTCCGACTTC 60.032 50.000 0.00 0.00 0.00 3.01
25 26 1.944709 CGTTCCAAAAACCTCCGACTT 59.055 47.619 0.00 0.00 0.00 3.01
26 27 1.589803 CGTTCCAAAAACCTCCGACT 58.410 50.000 0.00 0.00 0.00 4.18
27 28 0.589708 CCGTTCCAAAAACCTCCGAC 59.410 55.000 0.00 0.00 0.00 4.79
28 29 0.469070 TCCGTTCCAAAAACCTCCGA 59.531 50.000 0.00 0.00 0.00 4.55
29 30 0.589708 GTCCGTTCCAAAAACCTCCG 59.410 55.000 0.00 0.00 0.00 4.63
30 31 0.589708 CGTCCGTTCCAAAAACCTCC 59.410 55.000 0.00 0.00 0.00 4.30
31 32 1.529865 CTCGTCCGTTCCAAAAACCTC 59.470 52.381 0.00 0.00 0.00 3.85
32 33 1.139455 TCTCGTCCGTTCCAAAAACCT 59.861 47.619 0.00 0.00 0.00 3.50
33 34 1.585297 TCTCGTCCGTTCCAAAAACC 58.415 50.000 0.00 0.00 0.00 3.27
82 83 8.976986 ATTGAAGCAAAATATCTCAGTGAAAC 57.023 30.769 0.00 0.00 0.00 2.78
83 84 9.630098 GAATTGAAGCAAAATATCTCAGTGAAA 57.370 29.630 0.00 0.00 0.00 2.69
122 123 5.368145 TGCAACTTCTGTACTTCATGTCTT 58.632 37.500 0.00 0.00 0.00 3.01
141 142 1.155889 CTGGCTAACACACGATGCAA 58.844 50.000 0.00 0.00 0.00 4.08
164 165 5.817816 AGTTCAGACATGAGAGAAAACGTTT 59.182 36.000 7.96 7.96 36.61 3.60
177 178 1.808945 GGCAGGTGAAGTTCAGACATG 59.191 52.381 5.62 4.83 0.00 3.21
179 180 0.108585 GGGCAGGTGAAGTTCAGACA 59.891 55.000 5.62 0.00 0.00 3.41
291 292 1.318576 CCAAGGTTTATGCCCGATCC 58.681 55.000 0.00 0.00 0.00 3.36
292 293 1.947456 GACCAAGGTTTATGCCCGATC 59.053 52.381 0.00 0.00 0.00 3.69
293 294 1.283613 TGACCAAGGTTTATGCCCGAT 59.716 47.619 0.00 0.00 0.00 4.18
294 295 0.693622 TGACCAAGGTTTATGCCCGA 59.306 50.000 0.00 0.00 0.00 5.14
295 296 1.094785 CTGACCAAGGTTTATGCCCG 58.905 55.000 0.00 0.00 0.00 6.13
296 297 2.507407 TCTGACCAAGGTTTATGCCC 57.493 50.000 0.00 0.00 0.00 5.36
310 311 1.269831 CGGGGGATCGAAGAATCTGAC 60.270 57.143 0.00 0.00 43.58 3.51
325 326 1.690352 ACGTAGTATTTGATCCGGGGG 59.310 52.381 0.00 0.00 41.94 5.40
360 361 3.414700 GTCCAGGTTCGCTGCACG 61.415 66.667 0.00 2.79 45.62 5.34
361 362 3.414700 CGTCCAGGTTCGCTGCAC 61.415 66.667 0.00 0.00 0.00 4.57
362 363 4.680237 CCGTCCAGGTTCGCTGCA 62.680 66.667 0.00 0.00 34.51 4.41
364 365 4.680237 TGCCGTCCAGGTTCGCTG 62.680 66.667 2.15 0.00 43.70 5.18
365 366 4.681978 GTGCCGTCCAGGTTCGCT 62.682 66.667 2.15 0.00 43.70 4.93
366 367 4.980805 TGTGCCGTCCAGGTTCGC 62.981 66.667 2.15 0.00 43.70 4.70
469 470 2.815647 GCGGTGACTACTGGCTGC 60.816 66.667 0.00 0.00 33.62 5.25
812 835 2.981560 GCACCCATTGGCACTCACG 61.982 63.158 0.00 0.00 33.59 4.35
813 836 2.964978 GCACCCATTGGCACTCAC 59.035 61.111 0.00 0.00 33.59 3.51
825 848 1.603739 GGTGTGAAGGAAGGCACCC 60.604 63.158 0.00 0.00 43.96 4.61
879 905 2.698274 GTGTTGGGTGGATGTTCCTTTT 59.302 45.455 0.00 0.00 37.46 2.27
889 915 1.076632 GGTGTTGGTGTTGGGTGGA 60.077 57.895 0.00 0.00 0.00 4.02
894 920 1.326213 TGCTTGGGTGTTGGTGTTGG 61.326 55.000 0.00 0.00 0.00 3.77
897 923 1.037030 CACTGCTTGGGTGTTGGTGT 61.037 55.000 0.00 0.00 0.00 4.16
898 924 0.751277 TCACTGCTTGGGTGTTGGTG 60.751 55.000 0.00 0.00 36.25 4.17
899 925 0.033601 TTCACTGCTTGGGTGTTGGT 60.034 50.000 0.00 0.00 36.25 3.67
900 926 1.067516 CTTTCACTGCTTGGGTGTTGG 59.932 52.381 0.00 0.00 36.25 3.77
901 927 2.023673 TCTTTCACTGCTTGGGTGTTG 58.976 47.619 0.00 0.00 36.25 3.33
902 928 2.092429 TCTCTTTCACTGCTTGGGTGTT 60.092 45.455 0.00 0.00 36.25 3.32
903 929 1.490490 TCTCTTTCACTGCTTGGGTGT 59.510 47.619 0.00 0.00 36.25 4.16
904 930 2.149578 CTCTCTTTCACTGCTTGGGTG 58.850 52.381 0.00 0.00 36.17 4.61
905 931 1.072965 CCTCTCTTTCACTGCTTGGGT 59.927 52.381 0.00 0.00 0.00 4.51
906 932 1.349026 TCCTCTCTTTCACTGCTTGGG 59.651 52.381 0.00 0.00 0.00 4.12
930 956 1.040339 AGGCTCTTGAGGTAGCTCCG 61.040 60.000 18.90 10.25 41.99 4.63
931 957 1.138069 GAAGGCTCTTGAGGTAGCTCC 59.862 57.143 18.90 3.27 38.80 4.70
932 958 2.107366 AGAAGGCTCTTGAGGTAGCTC 58.893 52.381 15.12 15.12 38.80 4.09
933 959 2.246091 AGAAGGCTCTTGAGGTAGCT 57.754 50.000 0.00 0.00 38.80 3.32
934 960 3.342377 AAAGAAGGCTCTTGAGGTAGC 57.658 47.619 0.00 0.00 41.23 3.58
935 961 4.257731 GGAAAAGAAGGCTCTTGAGGTAG 58.742 47.826 0.00 0.00 41.23 3.18
936 962 3.650942 TGGAAAAGAAGGCTCTTGAGGTA 59.349 43.478 0.00 0.00 41.23 3.08
937 963 2.443255 TGGAAAAGAAGGCTCTTGAGGT 59.557 45.455 0.00 0.00 41.23 3.85
938 964 3.080319 CTGGAAAAGAAGGCTCTTGAGG 58.920 50.000 0.00 0.00 41.23 3.86
944 970 1.082690 CTCGCTGGAAAAGAAGGCTC 58.917 55.000 0.00 0.00 0.00 4.70
999 1049 4.047125 CCGACCACCCCAGCCATT 62.047 66.667 0.00 0.00 0.00 3.16
1254 1310 2.273557 CCCTGGAATTTACACGTACGG 58.726 52.381 21.06 11.05 0.00 4.02
1313 1373 1.066257 CACAACCACAGCACAAGGC 59.934 57.895 0.00 0.00 45.30 4.35
1326 1386 2.052782 ACAAGAGGAACCCACACAAC 57.947 50.000 0.00 0.00 0.00 3.32
1327 1387 2.506231 TGTACAAGAGGAACCCACACAA 59.494 45.455 0.00 0.00 0.00 3.33
1328 1388 2.120312 TGTACAAGAGGAACCCACACA 58.880 47.619 0.00 0.00 0.00 3.72
1329 1389 2.922740 TGTACAAGAGGAACCCACAC 57.077 50.000 0.00 0.00 0.00 3.82
1330 1390 4.564821 GCTTATGTACAAGAGGAACCCACA 60.565 45.833 0.00 0.00 0.00 4.17
1331 1391 3.939592 GCTTATGTACAAGAGGAACCCAC 59.060 47.826 0.00 0.00 0.00 4.61
1332 1392 3.844211 AGCTTATGTACAAGAGGAACCCA 59.156 43.478 0.00 0.00 0.00 4.51
1414 1482 8.466798 ACTGGCCGCATAATTTATTTATTATCC 58.533 33.333 0.00 0.00 30.24 2.59
1416 1484 9.638239 CAACTGGCCGCATAATTTATTTATTAT 57.362 29.630 0.00 0.00 32.30 1.28
1417 1485 8.851145 TCAACTGGCCGCATAATTTATTTATTA 58.149 29.630 0.00 0.00 0.00 0.98
1418 1486 7.721402 TCAACTGGCCGCATAATTTATTTATT 58.279 30.769 0.00 0.00 0.00 1.40
1469 1537 9.559732 CCATTCAAAGGATACAGTCATACATAA 57.440 33.333 0.00 0.00 41.41 1.90
1587 4819 9.889128 AGAAAGAAATGGAAAAAGATTGAACAA 57.111 25.926 0.00 0.00 0.00 2.83
1612 4844 3.396560 ACTCCCCGTCGTTCTTAAAAAG 58.603 45.455 0.00 0.00 0.00 2.27
1618 4850 3.766051 AGTATAAACTCCCCGTCGTTCTT 59.234 43.478 0.00 0.00 0.00 2.52
1623 4855 4.110482 CAAGAAGTATAAACTCCCCGTCG 58.890 47.826 0.00 0.00 33.75 5.12
1624 4856 3.869832 GCAAGAAGTATAAACTCCCCGTC 59.130 47.826 0.00 0.00 33.75 4.79
1637 4869 5.299028 TCTTGACAAAATGCTGCAAGAAGTA 59.701 36.000 6.36 0.00 41.17 2.24
1639 4871 4.613944 TCTTGACAAAATGCTGCAAGAAG 58.386 39.130 6.36 0.00 41.17 2.85
1673 4905 0.394762 GGTTGGATCATGCCAGCTGA 60.395 55.000 17.39 0.00 39.52 4.26
1785 5020 0.920271 ACTAGGGACGGAGGGAGTCT 60.920 60.000 0.00 0.00 38.58 3.24
1786 5021 0.752376 CACTAGGGACGGAGGGAGTC 60.752 65.000 0.00 0.00 37.86 3.36
1787 5022 1.306970 CACTAGGGACGGAGGGAGT 59.693 63.158 0.00 0.00 0.00 3.85
1788 5023 0.752376 GACACTAGGGACGGAGGGAG 60.752 65.000 0.00 0.00 0.00 4.30
1789 5024 1.305623 GACACTAGGGACGGAGGGA 59.694 63.158 0.00 0.00 0.00 4.20
1790 5025 0.613853 TTGACACTAGGGACGGAGGG 60.614 60.000 0.00 0.00 0.00 4.30
1791 5026 1.263356 TTTGACACTAGGGACGGAGG 58.737 55.000 0.00 0.00 0.00 4.30
1792 5027 3.064931 GTTTTTGACACTAGGGACGGAG 58.935 50.000 0.00 0.00 0.00 4.63
1793 5028 2.546373 CGTTTTTGACACTAGGGACGGA 60.546 50.000 0.00 0.00 0.00 4.69
1794 5029 1.796459 CGTTTTTGACACTAGGGACGG 59.204 52.381 0.00 0.00 0.00 4.79
1795 5030 2.473984 GACGTTTTTGACACTAGGGACG 59.526 50.000 0.00 0.00 35.59 4.79
1796 5031 3.725490 AGACGTTTTTGACACTAGGGAC 58.275 45.455 0.00 0.00 0.00 4.46
1797 5032 4.411256 AAGACGTTTTTGACACTAGGGA 57.589 40.909 0.00 0.00 0.00 4.20
1798 5033 5.051816 TGTAAGACGTTTTTGACACTAGGG 58.948 41.667 0.00 0.00 0.00 3.53
1799 5034 6.780706 ATGTAAGACGTTTTTGACACTAGG 57.219 37.500 0.00 0.00 0.00 3.02
1800 5035 9.741168 CATAATGTAAGACGTTTTTGACACTAG 57.259 33.333 0.00 0.00 0.00 2.57
1801 5036 8.714179 CCATAATGTAAGACGTTTTTGACACTA 58.286 33.333 0.00 0.00 0.00 2.74
1802 5037 7.308348 CCCATAATGTAAGACGTTTTTGACACT 60.308 37.037 0.00 0.00 0.00 3.55
1803 5038 6.799925 CCCATAATGTAAGACGTTTTTGACAC 59.200 38.462 0.00 0.00 0.00 3.67
1804 5039 6.711194 TCCCATAATGTAAGACGTTTTTGACA 59.289 34.615 0.00 0.00 0.00 3.58
1805 5040 7.019418 GTCCCATAATGTAAGACGTTTTTGAC 58.981 38.462 0.00 0.00 0.00 3.18
1806 5041 6.128499 CGTCCCATAATGTAAGACGTTTTTGA 60.128 38.462 0.00 0.00 43.89 2.69
1807 5042 6.019152 CGTCCCATAATGTAAGACGTTTTTG 58.981 40.000 0.00 0.00 43.89 2.44
1808 5043 5.122711 CCGTCCCATAATGTAAGACGTTTTT 59.877 40.000 9.63 0.00 46.62 1.94
1809 5044 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
1810 5045 4.081531 TCCGTCCCATAATGTAAGACGTTT 60.082 41.667 9.63 0.00 46.62 3.60
1811 5046 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
1812 5047 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
1814 5049 4.098960 TCACTCCGTCCCATAATGTAAGAC 59.901 45.833 0.00 0.00 0.00 3.01
1815 5050 4.283337 TCACTCCGTCCCATAATGTAAGA 58.717 43.478 0.00 0.00 0.00 2.10
1816 5051 4.665833 TCACTCCGTCCCATAATGTAAG 57.334 45.455 0.00 0.00 0.00 2.34
1817 5052 5.623956 ATTCACTCCGTCCCATAATGTAA 57.376 39.130 0.00 0.00 0.00 2.41
1818 5053 6.072649 TCTATTCACTCCGTCCCATAATGTA 58.927 40.000 0.00 0.00 0.00 2.29
1819 5054 4.899457 TCTATTCACTCCGTCCCATAATGT 59.101 41.667 0.00 0.00 0.00 2.71
1820 5055 5.468540 TCTATTCACTCCGTCCCATAATG 57.531 43.478 0.00 0.00 0.00 1.90
1821 5056 5.839063 TCTTCTATTCACTCCGTCCCATAAT 59.161 40.000 0.00 0.00 0.00 1.28
1822 5057 5.205821 TCTTCTATTCACTCCGTCCCATAA 58.794 41.667 0.00 0.00 0.00 1.90
1823 5058 4.800023 TCTTCTATTCACTCCGTCCCATA 58.200 43.478 0.00 0.00 0.00 2.74
1824 5059 3.643237 TCTTCTATTCACTCCGTCCCAT 58.357 45.455 0.00 0.00 0.00 4.00
1825 5060 3.095912 TCTTCTATTCACTCCGTCCCA 57.904 47.619 0.00 0.00 0.00 4.37
1826 5061 4.022155 GGTATCTTCTATTCACTCCGTCCC 60.022 50.000 0.00 0.00 0.00 4.46
1827 5062 4.583489 TGGTATCTTCTATTCACTCCGTCC 59.417 45.833 0.00 0.00 0.00 4.79
1828 5063 5.521544 GTGGTATCTTCTATTCACTCCGTC 58.478 45.833 0.00 0.00 0.00 4.79
1829 5064 4.036498 CGTGGTATCTTCTATTCACTCCGT 59.964 45.833 0.00 0.00 0.00 4.69
1830 5065 4.275196 TCGTGGTATCTTCTATTCACTCCG 59.725 45.833 0.00 0.00 0.00 4.63
1831 5066 5.278561 CCTCGTGGTATCTTCTATTCACTCC 60.279 48.000 0.00 0.00 0.00 3.85
1832 5067 5.531659 TCCTCGTGGTATCTTCTATTCACTC 59.468 44.000 2.99 0.00 34.23 3.51
1833 5068 5.446860 TCCTCGTGGTATCTTCTATTCACT 58.553 41.667 2.99 0.00 34.23 3.41
1834 5069 5.769484 TCCTCGTGGTATCTTCTATTCAC 57.231 43.478 2.99 0.00 34.23 3.18
1835 5070 6.978674 AATCCTCGTGGTATCTTCTATTCA 57.021 37.500 2.99 0.00 34.23 2.57
1836 5071 6.647067 CCAAATCCTCGTGGTATCTTCTATTC 59.353 42.308 2.99 0.00 34.23 1.75
1837 5072 6.525629 CCAAATCCTCGTGGTATCTTCTATT 58.474 40.000 2.99 0.00 34.23 1.73
1887 5122 1.954382 CCTATGGATCGTCGAAGGTGA 59.046 52.381 0.00 0.00 0.00 4.02
1897 5132 3.941483 GGGCAATACAATCCTATGGATCG 59.059 47.826 0.00 0.00 42.27 3.69
1902 5137 3.074390 TCCAGGGGCAATACAATCCTATG 59.926 47.826 0.00 0.00 0.00 2.23
1942 5179 7.394144 AGCCATTTCCAGTAGGATATAAGTT 57.606 36.000 0.00 0.00 45.26 2.66
1948 5185 7.633018 AAGAATAGCCATTTCCAGTAGGATA 57.367 36.000 0.00 0.00 45.26 2.59
1977 5214 1.737838 GTTTCGTGCATCCCAGATCA 58.262 50.000 0.00 0.00 0.00 2.92
2009 5246 1.841556 TATGGATGTCCTCGCCCCC 60.842 63.158 0.09 0.00 36.82 5.40
2033 5270 3.309954 GTGATACCAAAGATGAAGGTCGC 59.690 47.826 0.00 0.00 36.87 5.19
2124 5361 3.429410 GCAAGGTGAATTACAAGGGCATC 60.429 47.826 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.