Multiple sequence alignment - TraesCS7D01G319900

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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 TraesCS7D01G319900 chr7D 100.000 2639 0 0 1 2639 409491035 409493673 0.000000e+00 4874.0
1 TraesCS7D01G319900 chr7A 87.918 1763 104 39 118 1857 470590740 470592416 0.000000e+00 1975.0
2 TraesCS7D01G319900 chr7A 88.430 121 9 2 1 118 470590593 470590711 9.850000e-30 141.0
3 TraesCS7D01G319900 chr7B 93.480 1319 49 21 560 1864 424054368 424055663 0.000000e+00 1925.0
4 TraesCS7D01G319900 chr7B 91.031 223 18 1 304 524 424054069 424054291 1.540000e-77 300.0
5 TraesCS7D01G319900 chr2D 96.949 295 8 1 2345 2639 36353785 36353492 6.560000e-136 494.0
6 TraesCS7D01G319900 chr2D 85.680 412 29 12 1899 2282 36354444 36354035 8.790000e-110 407.0
7 TraesCS7D01G319900 chr5A 85.242 454 31 14 1898 2325 123020968 123020525 4.030000e-118 435.0
8 TraesCS7D01G319900 chr5A 94.231 156 9 0 2484 2639 123020223 123020068 3.390000e-59 239.0
9 TraesCS7D01G319900 chr3D 76.152 499 76 33 1155 1624 488060324 488060808 3.420000e-54 222.0
10 TraesCS7D01G319900 chr3D 93.478 46 3 0 481 526 86338711 86338666 4.710000e-08 69.4
11 TraesCS7D01G319900 chr3B 75.600 500 77 36 1155 1624 650841907 650842391 3.440000e-49 206.0
12 TraesCS7D01G319900 chr6A 92.105 38 3 0 489 526 432764280 432764243 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 TraesCS7D01G319900 chr7D 409491035 409493673 2638 False 4874.0 4874 100.0000 1 2639 1 chr7D.!!$F1 2638
1 TraesCS7D01G319900 chr7A 470590593 470592416 1823 False 1058.0 1975 88.1740 1 1857 2 chr7A.!!$F1 1856
2 TraesCS7D01G319900 chr7B 424054069 424055663 1594 False 1112.5 1925 92.2555 304 1864 2 chr7B.!!$F1 1560
3 TraesCS7D01G319900 chr2D 36353492 36354444 952 True 450.5 494 91.3145 1899 2639 2 chr2D.!!$R1 740
4 TraesCS7D01G319900 chr5A 123020068 123020968 900 True 337.0 435 89.7365 1898 2639 2 chr5A.!!$R1 741

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
870 977 0.040067 GCAAACAGCACCTACAGCAC 60.04 55.0 0.0 0.0 44.79 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1864 1981 1.002134 ACAACCTTGGCGCTGCTAT 60.002 52.632 7.64 0.0 0.0 2.97 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
64 68 5.302357 CTGTTTATCTTCTCCAAACAGCC 57.698 43.478 12.01 0.00 46.96 4.85
89 93 0.613777 CTAGGGGTGGTGTTGACTCC 59.386 60.000 0.00 0.00 0.00 3.85
97 101 1.073199 GTGTTGACTCCACCCCTGG 59.927 63.158 0.00 0.00 39.23 4.45
98 102 1.385347 TGTTGACTCCACCCCTGGT 60.385 57.895 0.00 0.00 38.90 4.00
118 122 0.317519 GTCGGCCAAAACAAAGACGG 60.318 55.000 2.24 0.00 0.00 4.79
125 158 1.001378 CAAAACAAAGACGGGAGCCTG 60.001 52.381 0.00 0.00 0.00 4.85
162 195 1.544093 CCTTATCCTCGGCACATGCAT 60.544 52.381 6.15 0.00 44.36 3.96
187 221 3.490759 CATGCACGTGCCGAGGAC 61.491 66.667 35.72 9.11 41.18 3.85
189 223 3.529341 ATGCACGTGCCGAGGACAA 62.529 57.895 35.72 16.53 41.18 3.18
211 245 6.153851 ACAATGATCATCTTGGCATTGAAAGA 59.846 34.615 17.99 5.12 46.37 2.52
223 257 3.251729 GCATTGAAAGACTCAACTCTGCA 59.748 43.478 6.65 0.00 46.80 4.41
233 267 8.621532 AAGACTCAACTCTGCATTTGTTTATA 57.378 30.769 0.00 0.00 0.00 0.98
237 271 9.236006 ACTCAACTCTGCATTTGTTTATATTCT 57.764 29.630 0.00 0.00 0.00 2.40
263 297 9.064706 TCGTAATTAGGTGGTGTTTCAATTTTA 57.935 29.630 5.16 0.00 0.00 1.52
329 370 5.306394 GCCTAGGTCTATTAACAACATCCC 58.694 45.833 11.31 0.00 0.00 3.85
387 430 2.194271 AGTTTATCGCTCAAGCTACGC 58.806 47.619 0.00 0.00 39.32 4.42
431 474 4.056125 CTCCGCCACTGCTGACGA 62.056 66.667 0.00 0.00 34.43 4.20
501 544 2.954792 ACTACCTCCGTCCGGAATTAT 58.045 47.619 5.23 0.00 44.66 1.28
526 569 5.912892 TGACGCTGAAATGGATGTATCTAA 58.087 37.500 0.00 0.00 0.00 2.10
530 573 6.767902 ACGCTGAAATGGATGTATCTAAATGT 59.232 34.615 0.00 0.00 0.00 2.71
532 575 8.438513 CGCTGAAATGGATGTATCTAAATGTAG 58.561 37.037 0.00 0.00 0.00 2.74
533 576 8.725148 GCTGAAATGGATGTATCTAAATGTAGG 58.275 37.037 0.00 0.00 0.00 3.18
534 577 9.784531 CTGAAATGGATGTATCTAAATGTAGGT 57.215 33.333 0.00 0.00 0.00 3.08
535 578 9.778741 TGAAATGGATGTATCTAAATGTAGGTC 57.221 33.333 0.00 0.00 0.00 3.85
554 597 4.381411 GGTCTACATACCTCCATTTCAGC 58.619 47.826 0.00 0.00 36.53 4.26
555 598 4.051922 GTCTACATACCTCCATTTCAGCG 58.948 47.826 0.00 0.00 0.00 5.18
556 599 3.704566 TCTACATACCTCCATTTCAGCGT 59.295 43.478 0.00 0.00 0.00 5.07
557 600 4.891168 TCTACATACCTCCATTTCAGCGTA 59.109 41.667 0.00 0.00 0.00 4.42
561 646 1.207329 ACCTCCATTTCAGCGTAGGAC 59.793 52.381 0.00 0.00 0.00 3.85
564 649 0.810031 CCATTTCAGCGTAGGACGGG 60.810 60.000 0.70 0.00 42.82 5.28
571 656 1.201647 CAGCGTAGGACGGGGTATATG 59.798 57.143 0.70 0.00 42.82 1.78
586 671 4.396790 GGGTATATGTTTTCGACAAGCCAA 59.603 41.667 0.00 0.00 42.62 4.52
623 708 2.745492 GCAGCAGCACTCTGACCC 60.745 66.667 0.00 0.00 42.95 4.46
627 712 2.745698 CAGCACTCTGACCCAGCA 59.254 61.111 0.00 0.00 42.95 4.41
628 713 1.375652 CAGCACTCTGACCCAGCAG 60.376 63.158 0.00 0.00 42.95 4.24
629 714 2.046507 GCACTCTGACCCAGCAGG 60.047 66.667 0.00 0.00 43.78 4.85
640 725 3.230608 CCAGCAGGGTCATCTAGGA 57.769 57.895 0.00 0.00 0.00 2.94
641 726 1.500474 CCAGCAGGGTCATCTAGGAA 58.500 55.000 0.00 0.00 0.00 3.36
644 729 3.117738 CCAGCAGGGTCATCTAGGAAAAT 60.118 47.826 0.00 0.00 0.00 1.82
659 746 8.807948 TCTAGGAAAATAAAAATGGAGGTGAG 57.192 34.615 0.00 0.00 0.00 3.51
660 747 8.611257 TCTAGGAAAATAAAAATGGAGGTGAGA 58.389 33.333 0.00 0.00 0.00 3.27
662 749 8.491045 AGGAAAATAAAAATGGAGGTGAGAAA 57.509 30.769 0.00 0.00 0.00 2.52
663 750 8.588472 AGGAAAATAAAAATGGAGGTGAGAAAG 58.412 33.333 0.00 0.00 0.00 2.62
718 813 2.021723 GCTCCACTTGACCACCAACAA 61.022 52.381 0.00 0.00 0.00 2.83
719 814 2.374184 CTCCACTTGACCACCAACAAA 58.626 47.619 0.00 0.00 0.00 2.83
720 815 2.757868 CTCCACTTGACCACCAACAAAA 59.242 45.455 0.00 0.00 0.00 2.44
721 816 2.494073 TCCACTTGACCACCAACAAAAC 59.506 45.455 0.00 0.00 0.00 2.43
722 817 2.232452 CCACTTGACCACCAACAAAACA 59.768 45.455 0.00 0.00 0.00 2.83
737 832 7.818930 ACCAACAAAACATAATTAGGCTGATTG 59.181 33.333 14.19 2.36 0.00 2.67
738 833 7.278424 CCAACAAAACATAATTAGGCTGATTGG 59.722 37.037 14.19 8.88 0.00 3.16
754 861 5.287674 TGATTGGAAGTCAATTTTGGCAA 57.712 34.783 0.00 0.00 45.36 4.52
781 888 5.860941 AAGGATGGACATGTAGTAGACTG 57.139 43.478 0.00 0.00 0.00 3.51
822 929 4.603610 CCTCCTCCTATAAAACCCCATCAT 59.396 45.833 0.00 0.00 0.00 2.45
826 933 4.320398 TCCTATAAAACCCCATCATCCCA 58.680 43.478 0.00 0.00 0.00 4.37
827 934 4.353788 TCCTATAAAACCCCATCATCCCAG 59.646 45.833 0.00 0.00 0.00 4.45
850 957 1.142870 CCTTCTCTCCCACCAACACAA 59.857 52.381 0.00 0.00 0.00 3.33
851 958 2.498167 CTTCTCTCCCACCAACACAAG 58.502 52.381 0.00 0.00 0.00 3.16
852 959 0.108585 TCTCTCCCACCAACACAAGC 59.891 55.000 0.00 0.00 0.00 4.01
853 960 0.179020 CTCTCCCACCAACACAAGCA 60.179 55.000 0.00 0.00 0.00 3.91
854 961 0.257328 TCTCCCACCAACACAAGCAA 59.743 50.000 0.00 0.00 0.00 3.91
855 962 1.110442 CTCCCACCAACACAAGCAAA 58.890 50.000 0.00 0.00 0.00 3.68
856 963 0.820871 TCCCACCAACACAAGCAAAC 59.179 50.000 0.00 0.00 0.00 2.93
857 964 0.534412 CCCACCAACACAAGCAAACA 59.466 50.000 0.00 0.00 0.00 2.83
858 965 1.471327 CCCACCAACACAAGCAAACAG 60.471 52.381 0.00 0.00 0.00 3.16
859 966 1.280066 CACCAACACAAGCAAACAGC 58.720 50.000 0.00 0.00 46.19 4.40
869 976 2.330254 GCAAACAGCACCTACAGCA 58.670 52.632 0.00 0.00 44.79 4.41
870 977 0.040067 GCAAACAGCACCTACAGCAC 60.040 55.000 0.00 0.00 44.79 4.40
871 978 1.308047 CAAACAGCACCTACAGCACA 58.692 50.000 0.00 0.00 0.00 4.57
872 979 1.002468 CAAACAGCACCTACAGCACAC 60.002 52.381 0.00 0.00 0.00 3.82
873 980 0.180171 AACAGCACCTACAGCACACA 59.820 50.000 0.00 0.00 0.00 3.72
874 981 0.532862 ACAGCACCTACAGCACACAC 60.533 55.000 0.00 0.00 0.00 3.82
879 986 1.738099 CCTACAGCACACACGCTCC 60.738 63.158 0.00 0.00 41.38 4.70
882 989 1.460273 TACAGCACACACGCTCCTCA 61.460 55.000 0.00 0.00 41.38 3.86
893 1000 0.891373 CGCTCCTCACTCTCCAAAGA 59.109 55.000 0.00 0.00 0.00 2.52
900 1007 3.260380 CCTCACTCTCCAAAGACAGTCAT 59.740 47.826 2.66 0.00 0.00 3.06
950 1061 1.959899 GCCACGAACATCTCACAGCG 61.960 60.000 0.00 0.00 0.00 5.18
1035 1146 1.982395 CACCCTGGTGCTCCTCGTA 60.982 63.158 2.89 0.00 39.39 3.43
1039 1150 2.283604 TGGTGCTCCTCGTAGCCA 60.284 61.111 6.34 0.00 42.05 4.75
1596 1707 3.230115 GCTCAAACAGCTCTGCTCT 57.770 52.632 0.00 0.00 45.83 4.09
1629 1740 2.042537 ATCTCCCTCCTCAGCGCA 60.043 61.111 11.47 0.00 0.00 6.09
1871 1988 5.746307 TGATGAGACAATTTGATAGCAGC 57.254 39.130 2.79 0.00 0.00 5.25
1872 1989 4.271776 TGATGAGACAATTTGATAGCAGCG 59.728 41.667 2.79 0.00 0.00 5.18
1873 1990 2.352651 TGAGACAATTTGATAGCAGCGC 59.647 45.455 0.00 0.00 0.00 5.92
1874 1991 1.672881 AGACAATTTGATAGCAGCGCC 59.327 47.619 2.29 0.00 0.00 6.53
1875 1992 1.401552 GACAATTTGATAGCAGCGCCA 59.598 47.619 2.29 0.00 0.00 5.69
1876 1993 1.818060 ACAATTTGATAGCAGCGCCAA 59.182 42.857 2.29 0.00 0.00 4.52
1877 1994 2.159338 ACAATTTGATAGCAGCGCCAAG 60.159 45.455 2.29 0.00 0.00 3.61
1878 1995 1.027357 ATTTGATAGCAGCGCCAAGG 58.973 50.000 2.29 0.00 0.00 3.61
1879 1996 0.322456 TTTGATAGCAGCGCCAAGGT 60.322 50.000 2.29 2.40 0.00 3.50
1880 1997 0.322456 TTGATAGCAGCGCCAAGGTT 60.322 50.000 2.29 0.00 0.00 3.50
1881 1998 1.026182 TGATAGCAGCGCCAAGGTTG 61.026 55.000 2.29 0.00 0.00 3.77
1882 1999 1.002134 ATAGCAGCGCCAAGGTTGT 60.002 52.632 2.29 0.00 0.00 3.32
1883 2000 1.308069 ATAGCAGCGCCAAGGTTGTG 61.308 55.000 2.29 0.00 0.00 3.33
1884 2001 2.390306 TAGCAGCGCCAAGGTTGTGA 62.390 55.000 2.29 0.00 0.00 3.58
1885 2002 2.949106 CAGCGCCAAGGTTGTGAG 59.051 61.111 2.29 0.00 0.00 3.51
1886 2003 2.980233 AGCGCCAAGGTTGTGAGC 60.980 61.111 2.29 0.81 0.00 4.26
1887 2004 4.043200 GCGCCAAGGTTGTGAGCC 62.043 66.667 0.00 0.00 0.00 4.70
1888 2005 3.365265 CGCCAAGGTTGTGAGCCC 61.365 66.667 0.00 0.00 0.00 5.19
1889 2006 3.365265 GCCAAGGTTGTGAGCCCG 61.365 66.667 0.00 0.00 0.00 6.13
1890 2007 3.365265 CCAAGGTTGTGAGCCCGC 61.365 66.667 0.00 0.00 0.00 6.13
1891 2008 2.281761 CAAGGTTGTGAGCCCGCT 60.282 61.111 0.00 0.00 0.00 5.52
1892 2009 2.032681 AAGGTTGTGAGCCCGCTC 59.967 61.111 9.82 9.82 43.01 5.03
1893 2010 3.553095 AAGGTTGTGAGCCCGCTCC 62.553 63.158 13.93 6.28 42.09 4.70
1894 2011 4.021925 GGTTGTGAGCCCGCTCCT 62.022 66.667 13.93 0.00 42.09 3.69
1895 2012 2.032681 GTTGTGAGCCCGCTCCTT 59.967 61.111 13.93 0.00 42.09 3.36
1896 2013 2.035442 GTTGTGAGCCCGCTCCTTC 61.035 63.158 13.93 5.65 42.09 3.46
1912 2029 4.541648 TCCCTAGCCCGCTCCTCC 62.542 72.222 0.00 0.00 0.00 4.30
1915 2032 4.860881 CTAGCCCGCTCCTCCCCA 62.861 72.222 0.00 0.00 0.00 4.96
1998 2116 1.601477 TCGTCCACACACCTCGCTA 60.601 57.895 0.00 0.00 0.00 4.26
2033 2151 3.710631 ATGGCCTCCTCCCCTCCA 61.711 66.667 3.32 0.00 0.00 3.86
2130 2248 2.431683 GCCAGGTGCTCTGTTCCA 59.568 61.111 6.83 0.00 41.83 3.53
2338 2482 2.665185 GGAGTGTCCGCGCTGTTT 60.665 61.111 5.56 0.00 35.28 2.83
2339 2483 2.668280 GGAGTGTCCGCGCTGTTTC 61.668 63.158 5.56 0.00 35.28 2.78
2340 2484 1.954146 GAGTGTCCGCGCTGTTTCA 60.954 57.895 5.56 0.00 35.28 2.69
2341 2485 1.891060 GAGTGTCCGCGCTGTTTCAG 61.891 60.000 5.56 0.00 35.28 3.02
2429 2760 4.980903 CGCCGCAACTGCACCAAC 62.981 66.667 2.12 0.00 42.21 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 5.366829 AAAACTTAGATGGTTACCGCAAC 57.633 39.130 0.00 0.00 36.32 4.17
58 62 3.007581 CCCCTAGGTGTAGGCTGTT 57.992 57.895 8.29 0.00 44.39 3.16
79 83 1.073199 CCAGGGGTGGAGTCAACAC 59.927 63.158 0.00 0.00 38.10 3.32
80 84 1.385347 ACCAGGGGTGGAGTCAACA 60.385 57.895 0.00 0.00 32.98 3.33
97 101 1.835121 GTCTTTGTTTTGGCCGACAC 58.165 50.000 1.94 1.94 0.00 3.67
98 102 0.378962 CGTCTTTGTTTTGGCCGACA 59.621 50.000 0.00 0.00 0.00 4.35
104 108 0.313987 GGCTCCCGTCTTTGTTTTGG 59.686 55.000 0.00 0.00 0.00 3.28
118 122 0.737715 CTTACACGAGTGCAGGCTCC 60.738 60.000 2.76 0.00 32.11 4.70
125 158 2.656560 AGGATCACTTACACGAGTGC 57.343 50.000 2.76 0.00 45.20 4.40
141 174 0.106708 GCATGTGCCGAGGATAAGGA 59.893 55.000 0.00 0.00 34.31 3.36
142 175 0.179048 TGCATGTGCCGAGGATAAGG 60.179 55.000 2.07 0.00 41.18 2.69
143 176 1.534163 CATGCATGTGCCGAGGATAAG 59.466 52.381 18.91 0.00 41.18 1.73
146 179 1.225426 ACATGCATGTGCCGAGGAT 59.775 52.632 30.92 2.97 40.03 3.24
162 195 2.281414 CACGTGCATGGGTCCACA 60.281 61.111 11.36 0.00 32.37 4.17
187 221 6.475727 GTCTTTCAATGCCAAGATGATCATTG 59.524 38.462 10.14 5.86 44.12 2.82
189 223 5.892119 AGTCTTTCAATGCCAAGATGATCAT 59.108 36.000 8.25 8.25 31.71 2.45
211 245 9.236006 AGAATATAAACAAATGCAGAGTTGAGT 57.764 29.630 12.93 4.57 31.48 3.41
233 267 6.469410 TGAAACACCACCTAATTACGAGAAT 58.531 36.000 0.00 0.00 0.00 2.40
237 271 7.513371 AAATTGAAACACCACCTAATTACGA 57.487 32.000 0.00 0.00 0.00 3.43
247 281 9.744468 AGTCTTACAATAAAATTGAAACACCAC 57.256 29.630 6.64 0.00 0.00 4.16
297 331 7.506114 TGTTAATAGACCTAGGCCTAAATGTG 58.494 38.462 14.85 1.08 0.00 3.21
306 340 5.071923 AGGGATGTTGTTAATAGACCTAGGC 59.928 44.000 9.30 1.39 0.00 3.93
329 370 9.121517 CAGTACTTTGTAAGATGAAATTGCAAG 57.878 33.333 4.94 0.00 34.46 4.01
501 544 5.185454 AGATACATCCATTTCAGCGTCAAA 58.815 37.500 0.00 0.00 0.00 2.69
532 575 4.381411 GCTGAAATGGAGGTATGTAGACC 58.619 47.826 0.00 0.00 40.08 3.85
533 576 4.051922 CGCTGAAATGGAGGTATGTAGAC 58.948 47.826 0.00 0.00 0.00 2.59
534 577 3.704566 ACGCTGAAATGGAGGTATGTAGA 59.295 43.478 0.00 0.00 0.00 2.59
535 578 4.060038 ACGCTGAAATGGAGGTATGTAG 57.940 45.455 0.00 0.00 0.00 2.74
538 581 3.069586 TCCTACGCTGAAATGGAGGTATG 59.930 47.826 0.00 0.00 0.00 2.39
539 582 3.069729 GTCCTACGCTGAAATGGAGGTAT 59.930 47.826 0.00 0.00 0.00 2.73
540 583 2.429610 GTCCTACGCTGAAATGGAGGTA 59.570 50.000 0.00 0.00 0.00 3.08
541 584 1.207329 GTCCTACGCTGAAATGGAGGT 59.793 52.381 0.00 0.00 0.00 3.85
542 585 1.802880 CGTCCTACGCTGAAATGGAGG 60.803 57.143 0.00 0.00 33.65 4.30
543 586 1.560923 CGTCCTACGCTGAAATGGAG 58.439 55.000 0.00 0.00 33.65 3.86
544 587 0.174845 CCGTCCTACGCTGAAATGGA 59.825 55.000 0.00 0.00 40.91 3.41
545 588 0.810031 CCCGTCCTACGCTGAAATGG 60.810 60.000 0.00 0.00 40.91 3.16
546 589 0.810031 CCCCGTCCTACGCTGAAATG 60.810 60.000 0.00 0.00 40.91 2.32
547 590 1.262640 ACCCCGTCCTACGCTGAAAT 61.263 55.000 0.00 0.00 40.91 2.17
548 591 0.611618 TACCCCGTCCTACGCTGAAA 60.612 55.000 0.00 0.00 40.91 2.69
549 592 0.396139 ATACCCCGTCCTACGCTGAA 60.396 55.000 0.00 0.00 40.91 3.02
552 595 1.202976 ACATATACCCCGTCCTACGCT 60.203 52.381 0.00 0.00 40.91 5.07
554 597 4.301628 GAAAACATATACCCCGTCCTACG 58.698 47.826 0.00 0.00 42.11 3.51
555 598 4.037923 TCGAAAACATATACCCCGTCCTAC 59.962 45.833 0.00 0.00 0.00 3.18
556 599 4.037923 GTCGAAAACATATACCCCGTCCTA 59.962 45.833 0.00 0.00 0.00 2.94
557 600 3.033184 TCGAAAACATATACCCCGTCCT 58.967 45.455 0.00 0.00 0.00 3.85
561 646 3.001939 GCTTGTCGAAAACATATACCCCG 59.998 47.826 0.00 0.00 37.82 5.73
564 649 5.554822 TTGGCTTGTCGAAAACATATACC 57.445 39.130 0.00 0.00 37.82 2.73
571 656 4.860072 AGAAAGATTGGCTTGTCGAAAAC 58.140 39.130 0.00 0.00 36.80 2.43
623 708 3.634397 TTTTCCTAGATGACCCTGCTG 57.366 47.619 0.00 0.00 0.00 4.41
627 712 8.343787 TCCATTTTTATTTTCCTAGATGACCCT 58.656 33.333 0.00 0.00 0.00 4.34
628 713 8.533569 TCCATTTTTATTTTCCTAGATGACCC 57.466 34.615 0.00 0.00 0.00 4.46
629 714 8.633561 CCTCCATTTTTATTTTCCTAGATGACC 58.366 37.037 0.00 0.00 0.00 4.02
632 717 9.189156 TCACCTCCATTTTTATTTTCCTAGATG 57.811 33.333 0.00 0.00 0.00 2.90
633 718 9.413734 CTCACCTCCATTTTTATTTTCCTAGAT 57.586 33.333 0.00 0.00 0.00 1.98
634 719 8.611257 TCTCACCTCCATTTTTATTTTCCTAGA 58.389 33.333 0.00 0.00 0.00 2.43
635 720 8.807948 TCTCACCTCCATTTTTATTTTCCTAG 57.192 34.615 0.00 0.00 0.00 3.02
636 721 9.594936 TTTCTCACCTCCATTTTTATTTTCCTA 57.405 29.630 0.00 0.00 0.00 2.94
637 722 8.491045 TTTCTCACCTCCATTTTTATTTTCCT 57.509 30.769 0.00 0.00 0.00 3.36
638 723 8.585018 TCTTTCTCACCTCCATTTTTATTTTCC 58.415 33.333 0.00 0.00 0.00 3.13
639 724 9.631452 CTCTTTCTCACCTCCATTTTTATTTTC 57.369 33.333 0.00 0.00 0.00 2.29
640 725 9.367160 TCTCTTTCTCACCTCCATTTTTATTTT 57.633 29.630 0.00 0.00 0.00 1.82
641 726 8.940397 TCTCTTTCTCACCTCCATTTTTATTT 57.060 30.769 0.00 0.00 0.00 1.40
644 729 7.745717 TCTTCTCTTTCTCACCTCCATTTTTA 58.254 34.615 0.00 0.00 0.00 1.52
659 746 5.146010 TGCTTCCTCTCTTCTTCTCTTTC 57.854 43.478 0.00 0.00 0.00 2.62
660 747 5.760484 ATGCTTCCTCTCTTCTTCTCTTT 57.240 39.130 0.00 0.00 0.00 2.52
662 749 5.305128 CCATATGCTTCCTCTCTTCTTCTCT 59.695 44.000 0.00 0.00 0.00 3.10
663 750 5.540911 CCATATGCTTCCTCTCTTCTTCTC 58.459 45.833 0.00 0.00 0.00 2.87
709 796 5.868801 CAGCCTAATTATGTTTTGTTGGTGG 59.131 40.000 0.00 0.00 0.00 4.61
718 813 7.615365 TGACTTCCAATCAGCCTAATTATGTTT 59.385 33.333 0.00 0.00 0.00 2.83
719 814 7.118723 TGACTTCCAATCAGCCTAATTATGTT 58.881 34.615 0.00 0.00 0.00 2.71
720 815 6.662755 TGACTTCCAATCAGCCTAATTATGT 58.337 36.000 0.00 0.00 0.00 2.29
721 816 7.572523 TTGACTTCCAATCAGCCTAATTATG 57.427 36.000 0.00 0.00 0.00 1.90
722 817 8.773033 AATTGACTTCCAATCAGCCTAATTAT 57.227 30.769 0.00 0.00 44.28 1.28
737 832 3.467374 TGGTTGCCAAAATTGACTTCC 57.533 42.857 0.00 0.00 0.00 3.46
738 833 5.639082 CCTTATGGTTGCCAAAATTGACTTC 59.361 40.000 0.00 0.00 36.95 3.01
769 876 2.552093 ACCTGGCCAGTCTACTACAT 57.448 50.000 30.63 2.26 0.00 2.29
770 877 3.461378 TTACCTGGCCAGTCTACTACA 57.539 47.619 30.63 3.41 0.00 2.74
771 878 3.321396 GGATTACCTGGCCAGTCTACTAC 59.679 52.174 30.63 14.84 0.00 2.73
772 879 3.573695 GGATTACCTGGCCAGTCTACTA 58.426 50.000 30.63 10.45 0.00 1.82
773 880 2.399580 GGATTACCTGGCCAGTCTACT 58.600 52.381 30.63 13.69 0.00 2.57
774 881 1.416772 GGGATTACCTGGCCAGTCTAC 59.583 57.143 30.63 16.82 35.85 2.59
822 929 1.613630 GGGAGAGAAGGCACTGGGA 60.614 63.158 0.00 0.00 40.86 4.37
827 934 0.606673 GTTGGTGGGAGAGAAGGCAC 60.607 60.000 0.00 0.00 0.00 5.01
850 957 0.179020 TGCTGTAGGTGCTGTTTGCT 60.179 50.000 0.00 0.00 43.37 3.91
851 958 0.040067 GTGCTGTAGGTGCTGTTTGC 60.040 55.000 0.00 0.00 43.25 3.68
852 959 1.002468 GTGTGCTGTAGGTGCTGTTTG 60.002 52.381 0.00 0.00 0.00 2.93
853 960 1.308998 GTGTGCTGTAGGTGCTGTTT 58.691 50.000 0.00 0.00 0.00 2.83
854 961 0.180171 TGTGTGCTGTAGGTGCTGTT 59.820 50.000 0.00 0.00 0.00 3.16
855 962 0.532862 GTGTGTGCTGTAGGTGCTGT 60.533 55.000 0.00 0.00 0.00 4.40
856 963 1.560004 CGTGTGTGCTGTAGGTGCTG 61.560 60.000 0.00 0.00 0.00 4.41
857 964 1.300931 CGTGTGTGCTGTAGGTGCT 60.301 57.895 0.00 0.00 0.00 4.40
858 965 2.954753 GCGTGTGTGCTGTAGGTGC 61.955 63.158 0.00 0.00 0.00 5.01
859 966 1.300931 AGCGTGTGTGCTGTAGGTG 60.301 57.895 0.00 0.00 45.28 4.00
860 967 3.138625 AGCGTGTGTGCTGTAGGT 58.861 55.556 0.00 0.00 45.28 3.08
867 974 2.024319 GAGTGAGGAGCGTGTGTGC 61.024 63.158 0.00 0.00 0.00 4.57
868 975 0.387878 GAGAGTGAGGAGCGTGTGTG 60.388 60.000 0.00 0.00 0.00 3.82
869 976 1.528292 GGAGAGTGAGGAGCGTGTGT 61.528 60.000 0.00 0.00 0.00 3.72
870 977 1.214062 GGAGAGTGAGGAGCGTGTG 59.786 63.158 0.00 0.00 0.00 3.82
871 978 0.827925 TTGGAGAGTGAGGAGCGTGT 60.828 55.000 0.00 0.00 0.00 4.49
872 979 0.318441 TTTGGAGAGTGAGGAGCGTG 59.682 55.000 0.00 0.00 0.00 5.34
873 980 0.605589 CTTTGGAGAGTGAGGAGCGT 59.394 55.000 0.00 0.00 0.00 5.07
874 981 0.891373 TCTTTGGAGAGTGAGGAGCG 59.109 55.000 0.00 0.00 0.00 5.03
879 986 4.533919 ATGACTGTCTTTGGAGAGTGAG 57.466 45.455 9.51 0.00 44.53 3.51
882 989 5.808366 TGTTATGACTGTCTTTGGAGAGT 57.192 39.130 9.51 0.00 46.68 3.24
893 1000 4.013267 AGCTGCTTCTTGTTATGACTGT 57.987 40.909 0.00 0.00 0.00 3.55
921 1032 0.179234 TGTTCGTGGCTCTGTGGAAA 59.821 50.000 0.00 0.00 0.00 3.13
950 1061 2.549926 GAAGAAGGCAGCTAGCTTCTC 58.450 52.381 16.46 9.11 44.79 2.87
1629 1740 3.122369 AGCTTTGCTTCAGCTGGTT 57.878 47.368 15.13 0.00 46.25 3.67
1857 1974 2.456989 CTTGGCGCTGCTATCAAATTG 58.543 47.619 7.64 0.00 0.00 2.32
1859 1976 1.027357 CCTTGGCGCTGCTATCAAAT 58.973 50.000 7.64 0.00 0.00 2.32
1862 1979 1.026182 CAACCTTGGCGCTGCTATCA 61.026 55.000 7.64 0.00 0.00 2.15
1863 1980 1.026718 ACAACCTTGGCGCTGCTATC 61.027 55.000 7.64 0.00 0.00 2.08
1864 1981 1.002134 ACAACCTTGGCGCTGCTAT 60.002 52.632 7.64 0.00 0.00 2.97
1865 1982 1.965930 CACAACCTTGGCGCTGCTA 60.966 57.895 7.64 0.00 0.00 3.49
1866 1983 3.289834 CACAACCTTGGCGCTGCT 61.290 61.111 7.64 0.00 0.00 4.24
1867 1984 3.259425 CTCACAACCTTGGCGCTGC 62.259 63.158 7.64 0.00 0.00 5.25
1868 1985 2.949106 CTCACAACCTTGGCGCTG 59.051 61.111 7.64 0.00 0.00 5.18
1869 1986 2.980233 GCTCACAACCTTGGCGCT 60.980 61.111 7.64 0.00 0.00 5.92
1870 1987 4.043200 GGCTCACAACCTTGGCGC 62.043 66.667 0.00 0.00 0.00 6.53
1871 1988 3.365265 GGGCTCACAACCTTGGCG 61.365 66.667 0.00 0.00 0.00 5.69
1872 1989 3.365265 CGGGCTCACAACCTTGGC 61.365 66.667 0.00 0.00 0.00 4.52
1873 1990 3.365265 GCGGGCTCACAACCTTGG 61.365 66.667 0.00 0.00 0.00 3.61
1874 1991 2.281761 AGCGGGCTCACAACCTTG 60.282 61.111 0.00 0.00 0.00 3.61
1875 1992 2.032681 GAGCGGGCTCACAACCTT 59.967 61.111 15.45 0.00 42.31 3.50
1876 1993 4.021925 GGAGCGGGCTCACAACCT 62.022 66.667 21.10 0.00 44.40 3.50
1877 1994 3.553095 AAGGAGCGGGCTCACAACC 62.553 63.158 21.10 5.22 44.40 3.77
1878 1995 2.032681 AAGGAGCGGGCTCACAAC 59.967 61.111 21.10 4.95 44.40 3.32
1879 1996 2.347490 GAAGGAGCGGGCTCACAA 59.653 61.111 21.10 0.00 44.40 3.33
1880 1997 3.706373 GGAAGGAGCGGGCTCACA 61.706 66.667 21.10 0.00 44.40 3.58
1881 1998 4.475135 GGGAAGGAGCGGGCTCAC 62.475 72.222 21.10 11.12 44.40 3.51
1882 1999 3.311511 TAGGGAAGGAGCGGGCTCA 62.312 63.158 21.10 0.00 44.40 4.26
1883 2000 2.444140 TAGGGAAGGAGCGGGCTC 60.444 66.667 12.17 12.17 42.04 4.70
1884 2001 2.444895 CTAGGGAAGGAGCGGGCT 60.445 66.667 0.00 0.00 0.00 5.19
1885 2002 4.243008 GCTAGGGAAGGAGCGGGC 62.243 72.222 0.00 0.00 0.00 6.13
1886 2003 3.551407 GGCTAGGGAAGGAGCGGG 61.551 72.222 0.00 0.00 39.72 6.13
1887 2004 3.551407 GGGCTAGGGAAGGAGCGG 61.551 72.222 0.00 0.00 39.72 5.52
1888 2005 3.917760 CGGGCTAGGGAAGGAGCG 61.918 72.222 0.00 0.00 39.72 5.03
1889 2006 4.243008 GCGGGCTAGGGAAGGAGC 62.243 72.222 0.00 0.00 38.00 4.70
1890 2007 2.444895 AGCGGGCTAGGGAAGGAG 60.445 66.667 0.00 0.00 0.00 3.69
1891 2008 2.444140 GAGCGGGCTAGGGAAGGA 60.444 66.667 0.00 0.00 0.00 3.36
1892 2009 3.551407 GGAGCGGGCTAGGGAAGG 61.551 72.222 0.00 0.00 0.00 3.46
1893 2010 2.444895 AGGAGCGGGCTAGGGAAG 60.445 66.667 0.00 0.00 0.00 3.46
1894 2011 2.444140 GAGGAGCGGGCTAGGGAA 60.444 66.667 0.00 0.00 0.00 3.97
1895 2012 4.541648 GGAGGAGCGGGCTAGGGA 62.542 72.222 0.00 0.00 0.00 4.20
1991 2109 3.597728 GAGACGGGCCTAGCGAGG 61.598 72.222 8.78 8.78 46.93 4.63
2082 2200 4.082523 CGGGCCGGAAGAGCTTGA 62.083 66.667 20.56 0.00 0.00 3.02
2220 2364 2.606519 CGGACCACCTCCCAGGAA 60.607 66.667 0.00 0.00 37.67 3.36
2333 2477 1.571460 GTGCTCCGTGCTGAAACAG 59.429 57.895 0.00 0.00 43.37 3.16
2334 2478 1.891919 GGTGCTCCGTGCTGAAACA 60.892 57.895 0.00 0.00 43.37 2.83
2335 2479 2.617274 GGGTGCTCCGTGCTGAAAC 61.617 63.158 0.00 0.00 43.37 2.78
2336 2480 2.281484 GGGTGCTCCGTGCTGAAA 60.281 61.111 0.00 0.00 43.37 2.69
2473 2804 4.752594 CGGAGGGGGAGGGGGAAA 62.753 72.222 0.00 0.00 0.00 3.13


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

AutoCloner maintained by Alex Coulton.