Multiple sequence alignment - TraesCS3B01G190000

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 TraesCS3B01G190000 chr3B 100.000 2086 0 0 515 2600 202385616 202387701 0.000000e+00 3853.0
1 TraesCS3B01G190000 chr3B 100.000 196 0 0 1 196 202385102 202385297 1.900000e-96 363.0
2 TraesCS3B01G190000 chr3B 95.833 120 5 0 1912 2031 828461668 828461787 7.340000e-46 195.0
3 TraesCS3B01G190000 chr3B 93.077 130 8 1 1906 2035 475816882 475817010 3.420000e-44 189.0
4 TraesCS3B01G190000 chr3D 95.238 1407 51 11 515 1915 140417357 140418753 0.000000e+00 2213.0
5 TraesCS3B01G190000 chr3D 94.609 575 26 4 2027 2600 140419969 140420539 0.000000e+00 885.0
6 TraesCS3B01G190000 chr3D 91.549 142 11 1 50 191 140417089 140417229 7.340000e-46 195.0
7 TraesCS3B01G190000 chr3A 97.917 1104 20 3 813 1915 158170437 158171538 0.000000e+00 1908.0
8 TraesCS3B01G190000 chr3A 89.294 411 21 13 2191 2600 158171658 158172046 6.460000e-136 494.0
9 TraesCS3B01G190000 chr3A 93.651 126 8 0 2027 2152 158171535 158171660 3.420000e-44 189.0
10 TraesCS3B01G190000 chr3A 100.000 28 0 0 737 764 724073075 724073102 5.000000e-03 52.8
11 TraesCS3B01G190000 chr5B 97.436 117 3 0 1914 2030 402870180 402870296 1.580000e-47 200.0
12 TraesCS3B01G190000 chr2D 95.968 124 4 1 1911 2034 158283411 158283289 1.580000e-47 200.0
13 TraesCS3B01G190000 chrUn 96.639 119 4 0 1913 2031 100620762 100620880 5.680000e-47 198.0
14 TraesCS3B01G190000 chrUn 88.235 51 0 5 712 762 92940415 92940459 3.610000e-04 56.5
15 TraesCS3B01G190000 chr7B 95.902 122 5 0 1911 2032 252178053 252178174 5.680000e-47 198.0
16 TraesCS3B01G190000 chr7B 95.902 122 5 0 1910 2031 462842113 462842234 5.680000e-47 198.0
17 TraesCS3B01G190000 chr4B 93.893 131 6 2 1914 2044 141455924 141456052 2.040000e-46 196.0
18 TraesCS3B01G190000 chr1D 91.912 136 10 1 1909 2043 284915951 284915816 3.420000e-44 189.0
19 TraesCS3B01G190000 chr2A 96.875 32 1 0 164 195 652431428 652431459 1.000000e-03 54.7


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 TraesCS3B01G190000 chr3B 202385102 202387701 2599 False 2108.000000 3853 100.000000 1 2600 2 chr3B.!!$F3 2599
1 TraesCS3B01G190000 chr3D 140417089 140420539 3450 False 1097.666667 2213 93.798667 50 2600 3 chr3D.!!$F1 2550
2 TraesCS3B01G190000 chr3A 158170437 158172046 1609 False 863.666667 1908 93.620667 813 2600 3 chr3A.!!$F2 1787

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
805 809 0.029567 GACGTCCGATGCCTAGACAG 59.97 60.0 3.51 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1913 1921 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.0 13.64 0.0 46.06 2.59 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
17 18 4.361253 TCAGAGTTCAAGTGCGGC 57.639 55.556 0.00 0.00 0.00 6.53
18 19 1.748403 TCAGAGTTCAAGTGCGGCT 59.252 52.632 0.00 0.00 0.00 5.52
19 20 0.319900 TCAGAGTTCAAGTGCGGCTC 60.320 55.000 0.00 0.00 0.00 4.70
20 21 0.320247 CAGAGTTCAAGTGCGGCTCT 60.320 55.000 0.00 0.00 37.04 4.09
21 22 1.067565 CAGAGTTCAAGTGCGGCTCTA 60.068 52.381 4.83 0.00 35.09 2.43
22 23 1.618837 AGAGTTCAAGTGCGGCTCTAA 59.381 47.619 4.83 0.00 35.09 2.10
23 24 1.727335 GAGTTCAAGTGCGGCTCTAAC 59.273 52.381 4.83 7.21 0.00 2.34
24 25 1.344763 AGTTCAAGTGCGGCTCTAACT 59.655 47.619 12.18 12.18 31.32 2.24
25 26 2.143925 GTTCAAGTGCGGCTCTAACTT 58.856 47.619 4.83 1.25 34.52 2.66
27 28 1.070134 TCAAGTGCGGCTCTAACTTGT 59.930 47.619 22.42 0.00 46.94 3.16
28 29 1.461127 CAAGTGCGGCTCTAACTTGTC 59.539 52.381 17.84 0.00 43.67 3.18
29 30 0.037232 AGTGCGGCTCTAACTTGTCC 60.037 55.000 2.18 0.00 0.00 4.02
30 31 0.037232 GTGCGGCTCTAACTTGTCCT 60.037 55.000 0.00 0.00 0.00 3.85
31 32 0.685097 TGCGGCTCTAACTTGTCCTT 59.315 50.000 0.00 0.00 0.00 3.36
32 33 1.079503 GCGGCTCTAACTTGTCCTTG 58.920 55.000 0.00 0.00 0.00 3.61
33 34 1.337823 GCGGCTCTAACTTGTCCTTGA 60.338 52.381 0.00 0.00 0.00 3.02
34 35 2.611518 CGGCTCTAACTTGTCCTTGAG 58.388 52.381 0.00 0.00 0.00 3.02
35 36 2.675317 CGGCTCTAACTTGTCCTTGAGG 60.675 54.545 0.00 0.00 0.00 3.86
36 37 2.567615 GGCTCTAACTTGTCCTTGAGGA 59.432 50.000 0.00 0.00 43.08 3.71
47 48 3.272574 TCCTTGAGGATGTTGATGAGC 57.727 47.619 0.00 0.00 39.78 4.26
48 49 2.842496 TCCTTGAGGATGTTGATGAGCT 59.158 45.455 0.00 0.00 39.78 4.09
62 63 1.466856 TGAGCTTGTTGATGCCCATC 58.533 50.000 1.35 1.35 38.29 3.51
65 66 1.005097 AGCTTGTTGATGCCCATCTGA 59.995 47.619 9.44 0.00 38.60 3.27
74 75 3.949754 TGATGCCCATCTGAATGAAGTTC 59.050 43.478 9.44 0.00 38.60 3.01
81 82 2.143122 TCTGAATGAAGTTCCACACGC 58.857 47.619 0.00 0.00 35.91 5.34
143 144 4.873129 CGCCATCGCTGCCGTAGT 62.873 66.667 0.00 0.00 35.54 2.73
154 155 2.101770 CCGTAGTCGCCGGTTCTC 59.898 66.667 1.90 0.00 40.59 2.87
157 158 0.522915 CGTAGTCGCCGGTTCTCTTC 60.523 60.000 1.90 0.00 0.00 2.87
158 159 0.810016 GTAGTCGCCGGTTCTCTTCT 59.190 55.000 1.90 0.00 0.00 2.85
159 160 1.201880 GTAGTCGCCGGTTCTCTTCTT 59.798 52.381 1.90 0.00 0.00 2.52
160 161 0.038159 AGTCGCCGGTTCTCTTCTTG 60.038 55.000 1.90 0.00 0.00 3.02
170 171 2.668212 TCTTCTTGTTGGCGGCCG 60.668 61.111 24.05 24.05 0.00 6.13
191 192 0.992695 AAACCCTAGAGGAGGTTGGC 59.007 55.000 0.00 0.00 45.68 4.52
194 195 0.833949 CCCTAGAGGAGGTTGGCTTC 59.166 60.000 0.00 0.00 45.03 3.86
544 545 9.628500 ATTATGATTAGGGGTTTTGTCTCTAAC 57.372 33.333 0.00 0.00 0.00 2.34
578 580 3.695816 GAAAAGTTCGCTTTGCTTCTGT 58.304 40.909 0.00 0.00 45.86 3.41
635 637 2.424302 CGGACACGGGGTTCACTT 59.576 61.111 0.00 0.00 36.18 3.16
651 653 3.407698 TCACTTTTGCCGCAGATCTTAA 58.592 40.909 0.00 0.00 0.00 1.85
653 655 3.058293 CACTTTTGCCGCAGATCTTAACA 60.058 43.478 0.00 0.00 0.00 2.41
660 662 4.273235 TGCCGCAGATCTTAACAACATATG 59.727 41.667 0.00 0.00 0.00 1.78
661 663 4.511454 GCCGCAGATCTTAACAACATATGA 59.489 41.667 10.38 0.00 0.00 2.15
673 677 9.986833 CTTAACAACATATGATCAATCAAACGA 57.013 29.630 10.38 0.00 40.69 3.85
674 678 9.767684 TTAACAACATATGATCAATCAAACGAC 57.232 29.630 10.38 0.00 40.69 4.34
676 680 7.466805 ACAACATATGATCAATCAAACGACAG 58.533 34.615 10.38 0.00 40.69 3.51
681 685 9.558648 CATATGATCAATCAAACGACAGAAAAA 57.441 29.630 0.00 0.00 40.69 1.94
721 725 2.417933 CACGAAAGGGCAGAGAAATCAG 59.582 50.000 0.00 0.00 0.00 2.90
724 728 3.311871 CGAAAGGGCAGAGAAATCAGATG 59.688 47.826 0.00 0.00 0.00 2.90
729 733 4.165565 AGGGCAGAGAAATCAGATGATGAA 59.834 41.667 0.00 0.00 42.53 2.57
730 734 4.515944 GGGCAGAGAAATCAGATGATGAAG 59.484 45.833 0.00 0.00 42.53 3.02
733 737 6.072948 GGCAGAGAAATCAGATGATGAAGATG 60.073 42.308 0.00 0.00 42.53 2.90
736 740 8.769891 CAGAGAAATCAGATGATGAAGATGAAG 58.230 37.037 0.00 0.00 42.53 3.02
737 741 8.706521 AGAGAAATCAGATGATGAAGATGAAGA 58.293 33.333 0.00 0.00 42.53 2.87
738 742 9.496873 GAGAAATCAGATGATGAAGATGAAGAT 57.503 33.333 0.00 0.00 42.53 2.40
739 743 9.278978 AGAAATCAGATGATGAAGATGAAGATG 57.721 33.333 0.00 0.00 42.53 2.90
740 744 9.274206 GAAATCAGATGATGAAGATGAAGATGA 57.726 33.333 0.00 0.00 42.53 2.92
741 745 9.628500 AAATCAGATGATGAAGATGAAGATGAA 57.372 29.630 0.00 0.00 42.53 2.57
742 746 8.610248 ATCAGATGATGAAGATGAAGATGAAC 57.390 34.615 0.00 0.00 42.53 3.18
775 779 3.866703 ATAGATGAGACCCGAGAGACA 57.133 47.619 0.00 0.00 0.00 3.41
779 783 2.516227 TGAGACCCGAGAGACAAGAT 57.484 50.000 0.00 0.00 0.00 2.40
785 789 1.550524 CCCGAGAGACAAGATGGTGAA 59.449 52.381 0.00 0.00 0.00 3.18
796 800 1.135139 AGATGGTGAAGACGTCCGATG 59.865 52.381 13.01 0.00 0.00 3.84
798 802 1.810030 GGTGAAGACGTCCGATGCC 60.810 63.158 13.01 5.00 0.00 4.40
805 809 0.029567 GACGTCCGATGCCTAGACAG 59.970 60.000 3.51 0.00 0.00 3.51
817 821 4.922206 TGCCTAGACAGATCCAAAAACAT 58.078 39.130 0.00 0.00 0.00 2.71
1533 1541 1.088340 TCGTCCTCGTGGATCTCGTC 61.088 60.000 9.83 0.00 45.29 4.20
1742 1750 5.244755 ACAAATAATGGTTGTGAATTGGGC 58.755 37.500 0.00 0.00 37.80 5.36
1790 1798 5.129650 GGCCTGAATCTCTTCTACTAAAGGT 59.870 44.000 0.00 0.00 32.29 3.50
1887 1895 0.329596 GGAGGATCTGGGCACAGTTT 59.670 55.000 17.28 4.70 45.14 2.66
1907 1915 6.318144 CAGTTTCAGATATTGTGAGATGGCTT 59.682 38.462 0.00 0.00 0.00 4.35
1908 1916 6.318144 AGTTTCAGATATTGTGAGATGGCTTG 59.682 38.462 0.00 0.00 0.00 4.01
1909 1917 4.132336 TCAGATATTGTGAGATGGCTTGC 58.868 43.478 0.00 0.00 0.00 4.01
1911 1919 4.337274 CAGATATTGTGAGATGGCTTGCAA 59.663 41.667 0.00 0.00 0.00 4.08
1912 1920 4.579340 AGATATTGTGAGATGGCTTGCAAG 59.421 41.667 22.44 22.44 0.00 4.01
1913 1921 1.985473 TTGTGAGATGGCTTGCAAGT 58.015 45.000 26.55 8.09 0.00 3.16
1914 1922 2.857186 TGTGAGATGGCTTGCAAGTA 57.143 45.000 26.55 16.74 0.00 2.24
1915 1923 2.426522 TGTGAGATGGCTTGCAAGTAC 58.573 47.619 26.55 19.72 0.00 2.73
1916 1924 2.038952 TGTGAGATGGCTTGCAAGTACT 59.961 45.455 26.55 18.99 0.00 2.73
1917 1925 2.675348 GTGAGATGGCTTGCAAGTACTC 59.325 50.000 26.55 24.64 0.00 2.59
1919 1927 1.065126 AGATGGCTTGCAAGTACTCCC 60.065 52.381 26.55 18.69 0.00 4.30
1921 1929 0.324943 TGGCTTGCAAGTACTCCCTC 59.675 55.000 26.55 8.00 0.00 4.30
1922 1930 0.393132 GGCTTGCAAGTACTCCCTCC 60.393 60.000 26.55 13.24 0.00 4.30
1923 1931 0.741221 GCTTGCAAGTACTCCCTCCG 60.741 60.000 26.55 0.00 0.00 4.63
1925 1933 0.606604 TTGCAAGTACTCCCTCCGTC 59.393 55.000 0.00 0.00 0.00 4.79
1926 1934 1.255667 TGCAAGTACTCCCTCCGTCC 61.256 60.000 0.00 0.00 0.00 4.79
1927 1935 1.807886 CAAGTACTCCCTCCGTCCG 59.192 63.158 0.00 0.00 0.00 4.79
1928 1936 1.379576 AAGTACTCCCTCCGTCCGG 60.380 63.158 0.00 0.00 0.00 5.14
1930 1938 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
1932 1940 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
1934 1942 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
1935 1943 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
1936 1944 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
1937 1945 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
1938 1946 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
1939 1947 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
1940 1948 1.135315 TCCGTCCGGAAATACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
1941 1949 1.274596 CGTCCGGAAATACTTGTCGG 58.725 55.000 5.23 0.00 41.80 4.79
1942 1950 1.135315 CGTCCGGAAATACTTGTCGGA 60.135 52.381 5.23 0.00 46.06 4.55
1943 1951 2.953466 TCCGGAAATACTTGTCGGAG 57.047 50.000 0.00 0.00 43.84 4.63
1944 1952 2.449464 TCCGGAAATACTTGTCGGAGA 58.551 47.619 0.00 0.00 43.84 3.71
1945 1953 2.827322 TCCGGAAATACTTGTCGGAGAA 59.173 45.455 0.00 0.00 43.84 2.87
1946 1954 3.258872 TCCGGAAATACTTGTCGGAGAAA 59.741 43.478 0.00 0.00 43.84 2.52
1947 1955 4.081309 TCCGGAAATACTTGTCGGAGAAAT 60.081 41.667 0.00 0.00 43.84 2.17
1948 1956 4.034048 CCGGAAATACTTGTCGGAGAAATG 59.966 45.833 0.00 0.00 42.94 2.32
1949 1957 4.494199 CGGAAATACTTGTCGGAGAAATGC 60.494 45.833 0.00 0.00 39.69 3.56
1950 1958 4.394920 GGAAATACTTGTCGGAGAAATGCA 59.605 41.667 0.00 0.00 39.69 3.96
1951 1959 5.066505 GGAAATACTTGTCGGAGAAATGCAT 59.933 40.000 0.00 0.00 39.69 3.96
1952 1960 6.260050 GGAAATACTTGTCGGAGAAATGCATA 59.740 38.462 0.00 0.00 39.69 3.14
1953 1961 7.201696 GGAAATACTTGTCGGAGAAATGCATAA 60.202 37.037 0.00 0.00 39.69 1.90
1954 1962 7.624360 AATACTTGTCGGAGAAATGCATAAA 57.376 32.000 0.00 0.00 39.69 1.40
1955 1963 5.957842 ACTTGTCGGAGAAATGCATAAAA 57.042 34.783 0.00 0.00 39.69 1.52
1956 1964 6.325919 ACTTGTCGGAGAAATGCATAAAAA 57.674 33.333 0.00 0.00 39.69 1.94
1957 1965 6.924111 ACTTGTCGGAGAAATGCATAAAAAT 58.076 32.000 0.00 0.00 39.69 1.82
1958 1966 6.808212 ACTTGTCGGAGAAATGCATAAAAATG 59.192 34.615 0.00 0.00 39.69 2.32
1959 1967 5.649557 TGTCGGAGAAATGCATAAAAATGG 58.350 37.500 0.00 0.00 39.69 3.16
1960 1968 5.417266 TGTCGGAGAAATGCATAAAAATGGA 59.583 36.000 0.00 0.00 39.69 3.41
1962 1970 6.980397 GTCGGAGAAATGCATAAAAATGGATT 59.020 34.615 0.00 0.00 43.01 3.01
2003 2011 9.698309 ATACGTCTAGATACATTCATTCCTTTG 57.302 33.333 0.00 0.00 0.00 2.77
2004 2012 7.782049 ACGTCTAGATACATTCATTCCTTTGA 58.218 34.615 0.00 0.00 0.00 2.69
2005 2013 7.707035 ACGTCTAGATACATTCATTCCTTTGAC 59.293 37.037 0.00 0.00 0.00 3.18
2006 2014 7.706607 CGTCTAGATACATTCATTCCTTTGACA 59.293 37.037 0.00 0.00 0.00 3.58
2008 2016 9.605275 TCTAGATACATTCATTCCTTTGACAAG 57.395 33.333 0.00 0.00 0.00 3.16
2009 2017 9.388506 CTAGATACATTCATTCCTTTGACAAGT 57.611 33.333 0.00 0.00 0.00 3.16
2011 2019 9.911788 AGATACATTCATTCCTTTGACAAGTAT 57.088 29.630 0.00 0.00 0.00 2.12
2015 2023 8.306761 ACATTCATTCCTTTGACAAGTATTTCC 58.693 33.333 0.00 0.00 0.00 3.13
2016 2024 6.494893 TCATTCCTTTGACAAGTATTTCCG 57.505 37.500 0.00 0.00 0.00 4.30
2017 2025 5.414454 TCATTCCTTTGACAAGTATTTCCGG 59.586 40.000 0.00 0.00 0.00 5.14
2018 2026 4.627284 TCCTTTGACAAGTATTTCCGGA 57.373 40.909 0.00 0.00 0.00 5.14
2019 2027 4.320870 TCCTTTGACAAGTATTTCCGGAC 58.679 43.478 1.83 0.00 0.00 4.79
2020 2028 3.124636 CCTTTGACAAGTATTTCCGGACG 59.875 47.826 1.83 0.00 0.00 4.79
2021 2029 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
2024 2032 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
2025 2033 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
2061 3172 0.237498 GCTAAGACGGGCAACACAAC 59.763 55.000 0.00 0.00 39.74 3.32
2080 3191 1.659794 GTGTGCAAGTTGGCGGATT 59.340 52.632 4.75 0.00 36.28 3.01
2215 3326 1.376553 GTTGAGGAGGCTGTGCTCC 60.377 63.158 0.00 0.00 42.96 4.70
2247 3358 5.189934 CAGGGTTAGGTTTCTAGATTGGACT 59.810 44.000 0.00 0.00 0.00 3.85
2409 3520 9.817365 CTTGTGTAGTTCAATTTCAGTATCAAG 57.183 33.333 0.00 0.00 0.00 3.02
2448 3559 8.343168 TGTTACCCATATCGAAAACATTTTCT 57.657 30.769 13.66 1.03 43.27 2.52
2450 3561 9.634163 GTTACCCATATCGAAAACATTTTCTTT 57.366 29.630 13.66 5.18 43.27 2.52
2523 3634 5.864474 AGAGCTAACAACGTTATCAGTTCAG 59.136 40.000 0.00 1.82 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.319900 GAGCCGCACTTGAACTCTGA 60.320 55.000 0.00 0.00 0.00 3.27
1 2 0.320247 AGAGCCGCACTTGAACTCTG 60.320 55.000 0.00 0.00 36.39 3.35
2 3 1.257743 TAGAGCCGCACTTGAACTCT 58.742 50.000 0.00 0.00 40.65 3.24
3 4 1.727335 GTTAGAGCCGCACTTGAACTC 59.273 52.381 0.00 0.00 0.00 3.01
4 5 1.344763 AGTTAGAGCCGCACTTGAACT 59.655 47.619 0.00 0.00 31.91 3.01
5 6 1.797025 AGTTAGAGCCGCACTTGAAC 58.203 50.000 0.00 0.00 0.00 3.18
6 7 2.543777 AAGTTAGAGCCGCACTTGAA 57.456 45.000 0.00 0.00 29.36 2.69
9 10 1.608283 GGACAAGTTAGAGCCGCACTT 60.608 52.381 0.00 0.00 0.00 3.16
10 11 0.037232 GGACAAGTTAGAGCCGCACT 60.037 55.000 0.00 0.00 0.00 4.40
11 12 0.037232 AGGACAAGTTAGAGCCGCAC 60.037 55.000 0.00 0.00 0.00 5.34
12 13 0.685097 AAGGACAAGTTAGAGCCGCA 59.315 50.000 0.00 0.00 0.00 5.69
13 14 1.079503 CAAGGACAAGTTAGAGCCGC 58.920 55.000 0.00 0.00 0.00 6.53
14 15 2.611518 CTCAAGGACAAGTTAGAGCCG 58.388 52.381 0.00 0.00 0.00 5.52
15 16 2.567615 TCCTCAAGGACAAGTTAGAGCC 59.432 50.000 0.00 0.00 39.78 4.70
16 17 3.963428 TCCTCAAGGACAAGTTAGAGC 57.037 47.619 0.00 0.00 39.78 4.09
28 29 3.278668 AGCTCATCAACATCCTCAAGG 57.721 47.619 0.00 0.00 0.00 3.61
29 30 4.008330 ACAAGCTCATCAACATCCTCAAG 58.992 43.478 0.00 0.00 0.00 3.02
30 31 4.025040 ACAAGCTCATCAACATCCTCAA 57.975 40.909 0.00 0.00 0.00 3.02
31 32 3.708403 ACAAGCTCATCAACATCCTCA 57.292 42.857 0.00 0.00 0.00 3.86
32 33 4.005650 TCAACAAGCTCATCAACATCCTC 58.994 43.478 0.00 0.00 0.00 3.71
33 34 4.025040 TCAACAAGCTCATCAACATCCT 57.975 40.909 0.00 0.00 0.00 3.24
34 35 4.669318 CATCAACAAGCTCATCAACATCC 58.331 43.478 0.00 0.00 0.00 3.51
35 36 4.103357 GCATCAACAAGCTCATCAACATC 58.897 43.478 0.00 0.00 0.00 3.06
36 37 3.119245 GGCATCAACAAGCTCATCAACAT 60.119 43.478 0.00 0.00 0.00 2.71
37 38 2.229543 GGCATCAACAAGCTCATCAACA 59.770 45.455 0.00 0.00 0.00 3.33
38 39 2.416431 GGGCATCAACAAGCTCATCAAC 60.416 50.000 0.00 0.00 0.00 3.18
39 40 1.820519 GGGCATCAACAAGCTCATCAA 59.179 47.619 0.00 0.00 0.00 2.57
40 41 1.272037 TGGGCATCAACAAGCTCATCA 60.272 47.619 0.00 0.00 36.06 3.07
41 42 1.466856 TGGGCATCAACAAGCTCATC 58.533 50.000 0.00 0.00 36.06 2.92
42 43 2.154567 ATGGGCATCAACAAGCTCAT 57.845 45.000 0.00 0.00 46.26 2.90
43 44 1.005097 AGATGGGCATCAACAAGCTCA 59.995 47.619 0.00 0.00 46.66 4.26
44 45 1.404391 CAGATGGGCATCAACAAGCTC 59.596 52.381 0.00 0.00 40.22 4.09
45 46 1.005097 TCAGATGGGCATCAACAAGCT 59.995 47.619 0.00 0.00 40.22 3.74
46 47 1.466856 TCAGATGGGCATCAACAAGC 58.533 50.000 0.00 0.00 40.22 4.01
47 48 3.697542 TCATTCAGATGGGCATCAACAAG 59.302 43.478 0.00 0.00 40.22 3.16
48 49 3.699413 TCATTCAGATGGGCATCAACAA 58.301 40.909 0.00 0.00 40.22 2.83
62 63 1.197721 GGCGTGTGGAACTTCATTCAG 59.802 52.381 0.00 0.00 39.30 3.02
65 66 0.110486 AGGGCGTGTGGAACTTCATT 59.890 50.000 0.00 0.00 38.04 2.57
74 75 2.184020 TTGATCTGGAGGGCGTGTGG 62.184 60.000 0.00 0.00 0.00 4.17
81 82 2.928334 CAAGACCATTGATCTGGAGGG 58.072 52.381 7.95 1.28 39.73 4.30
143 144 0.391597 AACAAGAAGAGAACCGGCGA 59.608 50.000 9.30 0.00 0.00 5.54
154 155 4.404654 GCGGCCGCCAACAAGAAG 62.405 66.667 39.89 0.00 34.56 2.85
157 158 4.277593 TTTGCGGCCGCCAACAAG 62.278 61.111 44.42 6.66 41.09 3.16
158 159 4.577246 GTTTGCGGCCGCCAACAA 62.577 61.111 44.35 32.31 43.47 2.83
170 171 1.340114 CCAACCTCCTCTAGGGTTTGC 60.340 57.143 0.00 0.00 46.28 3.68
524 525 5.494390 ACGTTAGAGACAAAACCCCTAAT 57.506 39.130 0.00 0.00 0.00 1.73
534 535 5.013568 TCCAACTGAAACGTTAGAGACAA 57.986 39.130 0.00 0.00 0.00 3.18
544 545 4.271687 CGAACTTTTCTCCAACTGAAACG 58.728 43.478 0.00 0.00 33.77 3.60
570 571 2.528818 CCTGGACCCCACAGAAGCA 61.529 63.158 0.00 0.00 38.20 3.91
578 580 2.124996 CCTCCTTCCTGGACCCCA 59.875 66.667 0.00 0.00 40.56 4.96
628 630 1.537202 AGATCTGCGGCAAAAGTGAAC 59.463 47.619 3.44 0.00 0.00 3.18
635 637 2.881513 TGTTGTTAAGATCTGCGGCAAA 59.118 40.909 3.44 0.00 0.00 3.68
651 653 7.334171 TCTGTCGTTTGATTGATCATATGTTGT 59.666 33.333 1.90 0.00 36.56 3.32
653 655 7.848223 TCTGTCGTTTGATTGATCATATGTT 57.152 32.000 1.90 0.00 36.56 2.71
681 685 2.744202 GTGCTTTCACGTCATCCTGATT 59.256 45.455 0.00 0.00 32.98 2.57
682 686 2.350522 GTGCTTTCACGTCATCCTGAT 58.649 47.619 0.00 0.00 32.98 2.90
683 687 1.795768 GTGCTTTCACGTCATCCTGA 58.204 50.000 0.00 0.00 32.98 3.86
705 709 4.165565 TCATCATCTGATTTCTCTGCCCTT 59.834 41.667 0.00 0.00 31.21 3.95
708 712 5.366460 TCTTCATCATCTGATTTCTCTGCC 58.634 41.667 0.00 0.00 32.72 4.85
775 779 1.254026 TCGGACGTCTTCACCATCTT 58.746 50.000 16.46 0.00 0.00 2.40
779 783 1.080093 GCATCGGACGTCTTCACCA 60.080 57.895 16.46 0.00 0.00 4.17
785 789 0.393944 TGTCTAGGCATCGGACGTCT 60.394 55.000 16.46 0.00 33.21 4.18
796 800 4.943705 TGATGTTTTTGGATCTGTCTAGGC 59.056 41.667 0.00 0.00 0.00 3.93
817 821 7.805163 TGCTTCTTCCTGGATATCTAAAATGA 58.195 34.615 0.00 0.00 0.00 2.57
1156 1164 1.532078 TGGAGTGGGTGACGTAGCA 60.532 57.895 0.00 0.00 0.00 3.49
1742 1750 6.459298 CCATAGTTTTGCTCAGCCTTTATGAG 60.459 42.308 0.00 0.00 45.71 2.90
1790 1798 1.765904 TGAACACACACTTGGCCTCTA 59.234 47.619 3.32 0.00 0.00 2.43
1887 1895 4.132336 GCAAGCCATCTCACAATATCTGA 58.868 43.478 0.00 0.00 0.00 3.27
1907 1915 1.255667 GGACGGAGGGAGTACTTGCA 61.256 60.000 0.00 0.00 0.00 4.08
1908 1916 1.516423 GGACGGAGGGAGTACTTGC 59.484 63.158 0.00 0.00 0.00 4.01
1909 1917 1.664321 CCGGACGGAGGGAGTACTTG 61.664 65.000 4.40 0.00 37.50 3.16
1911 1919 1.856539 TTCCGGACGGAGGGAGTACT 61.857 60.000 13.64 0.00 46.06 2.73
1912 1920 0.967380 TTTCCGGACGGAGGGAGTAC 60.967 60.000 13.64 0.00 46.06 2.73
1913 1921 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
1914 1922 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
1915 1923 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
1916 1924 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
1917 1925 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
1919 1927 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
1921 1929 1.274596 CGACAAGTATTTCCGGACGG 58.725 55.000 1.83 3.96 0.00 4.79
1922 1930 1.135315 TCCGACAAGTATTTCCGGACG 60.135 52.381 1.83 0.00 43.47 4.79
1923 1931 2.165030 TCTCCGACAAGTATTTCCGGAC 59.835 50.000 1.83 0.00 43.47 4.79
1925 1933 2.953466 TCTCCGACAAGTATTTCCGG 57.047 50.000 0.00 0.00 41.36 5.14
1926 1934 4.494199 GCATTTCTCCGACAAGTATTTCCG 60.494 45.833 0.00 0.00 0.00 4.30
1927 1935 4.394920 TGCATTTCTCCGACAAGTATTTCC 59.605 41.667 0.00 0.00 0.00 3.13
1928 1936 5.545658 TGCATTTCTCCGACAAGTATTTC 57.454 39.130 0.00 0.00 0.00 2.17
1930 1938 7.624360 TTTATGCATTTCTCCGACAAGTATT 57.376 32.000 3.54 0.00 0.00 1.89
1932 1940 7.441890 TTTTTATGCATTTCTCCGACAAGTA 57.558 32.000 3.54 0.00 0.00 2.24
1934 1942 6.254157 CCATTTTTATGCATTTCTCCGACAAG 59.746 38.462 3.54 0.00 0.00 3.16
1935 1943 6.071672 TCCATTTTTATGCATTTCTCCGACAA 60.072 34.615 3.54 0.00 0.00 3.18
1936 1944 5.417266 TCCATTTTTATGCATTTCTCCGACA 59.583 36.000 3.54 0.00 0.00 4.35
1937 1945 5.890334 TCCATTTTTATGCATTTCTCCGAC 58.110 37.500 3.54 0.00 0.00 4.79
1938 1946 6.713762 ATCCATTTTTATGCATTTCTCCGA 57.286 33.333 3.54 0.00 0.00 4.55
1939 1947 7.775397 AAATCCATTTTTATGCATTTCTCCG 57.225 32.000 3.54 0.00 0.00 4.63
1977 1985 9.698309 CAAAGGAATGAATGTATCTAGACGTAT 57.302 33.333 0.00 0.00 0.00 3.06
1978 1986 8.909923 TCAAAGGAATGAATGTATCTAGACGTA 58.090 33.333 0.00 0.00 0.00 3.57
1980 1988 7.706607 TGTCAAAGGAATGAATGTATCTAGACG 59.293 37.037 0.00 0.00 0.00 4.18
1981 1989 8.948631 TGTCAAAGGAATGAATGTATCTAGAC 57.051 34.615 0.00 0.00 0.00 2.59
1983 1991 9.388506 ACTTGTCAAAGGAATGAATGTATCTAG 57.611 33.333 0.00 0.00 37.76 2.43
1985 1993 9.911788 ATACTTGTCAAAGGAATGAATGTATCT 57.088 29.630 0.00 0.00 37.76 1.98
1989 1997 8.306761 GGAAATACTTGTCAAAGGAATGAATGT 58.693 33.333 0.00 0.00 37.76 2.71
1990 1998 7.485913 CGGAAATACTTGTCAAAGGAATGAATG 59.514 37.037 0.00 0.00 37.76 2.67
1994 2002 5.414454 TCCGGAAATACTTGTCAAAGGAATG 59.586 40.000 0.00 0.00 37.76 2.67
1996 2004 4.758165 GTCCGGAAATACTTGTCAAAGGAA 59.242 41.667 5.23 0.00 37.76 3.36
1997 2005 4.320870 GTCCGGAAATACTTGTCAAAGGA 58.679 43.478 5.23 0.00 37.76 3.36
1999 2007 3.124636 CCGTCCGGAAATACTTGTCAAAG 59.875 47.826 5.23 0.00 37.11 2.77
2000 2008 3.068560 CCGTCCGGAAATACTTGTCAAA 58.931 45.455 5.23 0.00 37.50 2.69
2001 2009 2.299582 TCCGTCCGGAAATACTTGTCAA 59.700 45.455 5.23 0.00 42.05 3.18
2002 2010 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
2003 2011 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
2004 2012 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
2005 2013 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
2006 2014 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
2008 2016 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
2009 2017 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
2011 2019 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
2012 2020 0.754217 CATACTCCCTCCGTCCGGAA 60.754 60.000 5.23 0.00 44.66 4.30
2015 2023 0.882474 GATCATACTCCCTCCGTCCG 59.118 60.000 0.00 0.00 0.00 4.79
2016 2024 1.996798 TGATCATACTCCCTCCGTCC 58.003 55.000 0.00 0.00 0.00 4.79
2017 2025 3.157881 TCATGATCATACTCCCTCCGTC 58.842 50.000 8.15 0.00 0.00 4.79
2018 2026 3.244887 TCATGATCATACTCCCTCCGT 57.755 47.619 8.15 0.00 0.00 4.69
2019 2027 4.607293 TTTCATGATCATACTCCCTCCG 57.393 45.455 8.15 0.00 0.00 4.63
2020 2028 4.699257 GCATTTCATGATCATACTCCCTCC 59.301 45.833 8.15 0.00 0.00 4.30
2021 2029 5.558818 AGCATTTCATGATCATACTCCCTC 58.441 41.667 8.15 0.00 0.00 4.30
2024 2032 7.148672 CGTCTTAGCATTTCATGATCATACTCC 60.149 40.741 8.15 0.00 0.00 3.85
2025 2033 7.148672 CCGTCTTAGCATTTCATGATCATACTC 60.149 40.741 8.15 0.00 0.00 2.59
2061 3172 2.128853 AATCCGCCAACTTGCACACG 62.129 55.000 0.00 0.00 0.00 4.49
2080 3191 5.057819 TGTGTAACACAAGATAAAAGCCGA 58.942 37.500 0.00 0.00 45.67 5.54
2215 3326 1.995376 AACCTAACCCTGGCAACTTG 58.005 50.000 0.00 0.00 37.61 3.16
2448 3559 9.647797 ATGTTCTCGTCACATGTTATAAGTAAA 57.352 29.630 0.00 0.00 33.42 2.01
2494 3605 8.853469 ACTGATAACGTTGTTAGCTCTATAAC 57.147 34.615 15.27 0.00 36.40 1.89


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

AutoCloner maintained by Alex Coulton.