Multiple sequence alignment - TraesCS1B01G140500

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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 TraesCS1B01G140500 chr1B 100.000 2903 0 0 1 2903 186517365 186520267 0.000000e+00 5361.0
1 TraesCS1B01G140500 chr1D 94.129 1022 56 3 857 1874 122544909 122545930 0.000000e+00 1552.0
2 TraesCS1B01G140500 chr1D 90.789 760 60 2 2153 2903 469126532 469125774 0.000000e+00 1007.0
3 TraesCS1B01G140500 chr1D 81.592 804 146 2 1 803 112868638 112869440 0.000000e+00 664.0
4 TraesCS1B01G140500 chr1A 94.355 992 53 2 886 1874 134000501 134001492 0.000000e+00 1519.0
5 TraesCS1B01G140500 chr1A 94.737 38 2 0 2177 2214 455232132 455232169 3.120000e-05 60.2
6 TraesCS1B01G140500 chr4B 93.267 1010 58 2 1903 2903 376247695 376246687 0.000000e+00 1480.0
7 TraesCS1B01G140500 chr4B 90.668 793 74 0 1 793 660542897 660542105 0.000000e+00 1055.0
8 TraesCS1B01G140500 chr4A 87.017 1009 119 4 1903 2901 137385604 137386610 0.000000e+00 1127.0
9 TraesCS1B01G140500 chr7B 87.687 804 95 4 1 803 27271696 27272496 0.000000e+00 933.0
10 TraesCS1B01G140500 chr7B 72.609 230 58 4 2648 2875 322024171 322024397 1.440000e-08 71.3
11 TraesCS1B01G140500 chr5B 85.554 803 111 5 1 801 23344618 23343819 0.000000e+00 835.0
12 TraesCS1B01G140500 chr5B 78.634 805 162 9 3 802 353424925 353424126 2.560000e-145 525.0
13 TraesCS1B01G140500 chr2B 84.472 805 119 6 1 802 58234943 58235744 0.000000e+00 789.0
14 TraesCS1B01G140500 chr2B 78.121 809 166 10 1 804 476394024 476394826 1.200000e-138 503.0
15 TraesCS1B01G140500 chr2D 82.156 807 136 8 1 803 596038593 596039395 0.000000e+00 686.0
16 TraesCS1B01G140500 chr2D 87.947 531 54 2 2382 2903 207221459 207221988 4.110000e-173 617.0
17 TraesCS1B01G140500 chr3D 80.549 802 154 2 1 801 132233100 132233900 1.480000e-172 616.0
18 TraesCS1B01G140500 chr6B 89.598 423 29 7 2491 2903 581398923 581399340 9.220000e-145 523.0
19 TraesCS1B01G140500 chr4D 90.000 50 4 1 2655 2703 316225646 316225597 2.420000e-06 63.9
20 TraesCS1B01G140500 chr5A 100.000 28 0 0 2184 2211 334994067 334994094 5.000000e-03 52.8


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 TraesCS1B01G140500 chr1B 186517365 186520267 2902 False 5361 5361 100.000 1 2903 1 chr1B.!!$F1 2902
1 TraesCS1B01G140500 chr1D 122544909 122545930 1021 False 1552 1552 94.129 857 1874 1 chr1D.!!$F2 1017
2 TraesCS1B01G140500 chr1D 469125774 469126532 758 True 1007 1007 90.789 2153 2903 1 chr1D.!!$R1 750
3 TraesCS1B01G140500 chr1D 112868638 112869440 802 False 664 664 81.592 1 803 1 chr1D.!!$F1 802
4 TraesCS1B01G140500 chr1A 134000501 134001492 991 False 1519 1519 94.355 886 1874 1 chr1A.!!$F1 988
5 TraesCS1B01G140500 chr4B 376246687 376247695 1008 True 1480 1480 93.267 1903 2903 1 chr4B.!!$R1 1000
6 TraesCS1B01G140500 chr4B 660542105 660542897 792 True 1055 1055 90.668 1 793 1 chr4B.!!$R2 792
7 TraesCS1B01G140500 chr4A 137385604 137386610 1006 False 1127 1127 87.017 1903 2901 1 chr4A.!!$F1 998
8 TraesCS1B01G140500 chr7B 27271696 27272496 800 False 933 933 87.687 1 803 1 chr7B.!!$F1 802
9 TraesCS1B01G140500 chr5B 23343819 23344618 799 True 835 835 85.554 1 801 1 chr5B.!!$R1 800
10 TraesCS1B01G140500 chr5B 353424126 353424925 799 True 525 525 78.634 3 802 1 chr5B.!!$R2 799
11 TraesCS1B01G140500 chr2B 58234943 58235744 801 False 789 789 84.472 1 802 1 chr2B.!!$F1 801
12 TraesCS1B01G140500 chr2B 476394024 476394826 802 False 503 503 78.121 1 804 1 chr2B.!!$F2 803
13 TraesCS1B01G140500 chr2D 596038593 596039395 802 False 686 686 82.156 1 803 1 chr2D.!!$F2 802
14 TraesCS1B01G140500 chr2D 207221459 207221988 529 False 617 617 87.947 2382 2903 1 chr2D.!!$F1 521
15 TraesCS1B01G140500 chr3D 132233100 132233900 800 False 616 616 80.549 1 801 1 chr3D.!!$F1 800

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
841 844 0.106268 TCAGCCACCCACAACATGTT 60.106 50.0 4.92 4.92 0.0 2.71 F
844 847 0.249826 GCCACCCACAACATGTTTGG 60.250 55.0 22.63 22.63 0.0 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1843 1848 0.034574 ACAGGCTTCACACAACACCA 60.035 50.0 0.00 0.0 0.0 4.17 R
2019 2026 0.321653 GGCATTGGAACTGACGTCCT 60.322 55.0 14.12 0.0 0.0 3.85 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
39 40 4.436998 CCCACCGGAGTCAGTCGC 62.437 72.222 9.46 0.00 0.00 5.19
152 153 2.186532 TTGGCTGGCACGTAATAACA 57.813 45.000 2.29 0.00 0.00 2.41
164 165 3.836562 ACGTAATAACACAAGAGAGGGGT 59.163 43.478 0.00 0.00 0.00 4.95
232 233 1.656587 TGGGTGAGTGGCAGTCTATT 58.343 50.000 22.08 0.00 0.00 1.73
321 322 1.606668 GGTGAAAGCAAATGTGGACGA 59.393 47.619 0.00 0.00 0.00 4.20
322 323 2.034053 GGTGAAAGCAAATGTGGACGAA 59.966 45.455 0.00 0.00 0.00 3.85
325 326 1.609208 AAGCAAATGTGGACGAAGCT 58.391 45.000 0.00 0.00 0.00 3.74
429 430 1.131638 TTCCCTCAGTGCACAGAACT 58.868 50.000 21.04 0.00 0.00 3.01
431 432 0.107456 CCCTCAGTGCACAGAACTGT 59.893 55.000 21.04 1.32 44.42 3.55
621 622 1.177401 GCATCAAGGGAAAGGTGGAC 58.823 55.000 0.00 0.00 0.00 4.02
642 643 4.151883 ACAGTAACCTGGGTTAGACGTTA 58.848 43.478 11.95 0.00 43.36 3.18
692 693 1.670811 GGGAGTGTGTGGCGAATAATG 59.329 52.381 0.00 0.00 0.00 1.90
748 749 0.969149 TCTTGCAGACTGTGTCGGAT 59.031 50.000 3.99 0.00 37.67 4.18
754 755 2.359214 GCAGACTGTGTCGGATGAGATA 59.641 50.000 3.99 0.00 37.67 1.98
820 823 3.961480 AAAAGCTAGGGATTTGTTGGC 57.039 42.857 0.00 0.00 31.01 4.52
821 824 1.463674 AAGCTAGGGATTTGTTGGCG 58.536 50.000 0.00 0.00 0.00 5.69
822 825 0.328258 AGCTAGGGATTTGTTGGCGT 59.672 50.000 0.00 0.00 0.00 5.68
823 826 0.733150 GCTAGGGATTTGTTGGCGTC 59.267 55.000 0.00 0.00 0.00 5.19
824 827 1.948611 GCTAGGGATTTGTTGGCGTCA 60.949 52.381 0.00 0.00 0.00 4.35
825 828 2.009774 CTAGGGATTTGTTGGCGTCAG 58.990 52.381 0.00 0.00 0.00 3.51
826 829 1.212751 GGGATTTGTTGGCGTCAGC 59.787 57.895 0.00 0.00 44.18 4.26
836 839 3.660111 GCGTCAGCCACCCACAAC 61.660 66.667 0.00 0.00 37.42 3.32
837 840 2.203139 CGTCAGCCACCCACAACA 60.203 61.111 0.00 0.00 0.00 3.33
838 841 1.600636 CGTCAGCCACCCACAACAT 60.601 57.895 0.00 0.00 0.00 2.71
839 842 1.855213 CGTCAGCCACCCACAACATG 61.855 60.000 0.00 0.00 0.00 3.21
840 843 0.823356 GTCAGCCACCCACAACATGT 60.823 55.000 0.00 0.00 0.00 3.21
841 844 0.106268 TCAGCCACCCACAACATGTT 60.106 50.000 4.92 4.92 0.00 2.71
842 845 0.752054 CAGCCACCCACAACATGTTT 59.248 50.000 8.77 0.00 0.00 2.83
843 846 0.752054 AGCCACCCACAACATGTTTG 59.248 50.000 8.77 10.54 0.00 2.93
844 847 0.249826 GCCACCCACAACATGTTTGG 60.250 55.000 22.63 22.63 0.00 3.28
845 848 0.249826 CCACCCACAACATGTTTGGC 60.250 55.000 23.51 0.00 0.00 4.52
846 849 0.463204 CACCCACAACATGTTTGGCA 59.537 50.000 23.51 0.00 0.00 4.92
847 850 1.134580 CACCCACAACATGTTTGGCAA 60.135 47.619 23.51 0.00 0.00 4.52
848 851 1.767681 ACCCACAACATGTTTGGCAAT 59.232 42.857 23.51 13.98 0.00 3.56
849 852 2.968574 ACCCACAACATGTTTGGCAATA 59.031 40.909 23.51 0.00 0.00 1.90
850 853 3.582208 ACCCACAACATGTTTGGCAATAT 59.418 39.130 23.51 0.00 0.00 1.28
851 854 4.041444 ACCCACAACATGTTTGGCAATATT 59.959 37.500 23.51 8.82 0.00 1.28
852 855 4.392445 CCCACAACATGTTTGGCAATATTG 59.608 41.667 23.51 11.27 0.00 1.90
853 856 5.236282 CCACAACATGTTTGGCAATATTGA 58.764 37.500 19.73 0.00 0.00 2.57
854 857 5.120519 CCACAACATGTTTGGCAATATTGAC 59.879 40.000 19.73 17.33 36.50 3.18
855 858 4.922692 ACAACATGTTTGGCAATATTGACG 59.077 37.500 19.73 4.91 39.74 4.35
880 883 1.406539 CAAAGAATCCCATTCGGCCTG 59.593 52.381 0.00 0.00 43.92 4.85
895 899 0.321919 GCCTGCACTCTGGATGAACA 60.322 55.000 0.00 0.00 33.56 3.18
906 910 1.909302 TGGATGAACAAGGGAGAGACC 59.091 52.381 0.00 0.00 38.08 3.85
931 935 4.965814 ACTATCATCTCGCACCAATTCAT 58.034 39.130 0.00 0.00 0.00 2.57
972 976 0.396556 TCCCCAGATCCGATCGTTCA 60.397 55.000 15.09 0.00 0.00 3.18
1068 1072 4.821589 GCCCTCCGCTTCTCCACG 62.822 72.222 0.00 0.00 0.00 4.94
1070 1074 2.125912 CCTCCGCTTCTCCACGTG 60.126 66.667 9.08 9.08 0.00 4.49
1078 1082 3.741830 TTCTCCACGTGTGCCGCAA 62.742 57.895 15.65 0.00 41.42 4.85
1102 1106 2.690881 CCGTTCCATCCCCTCCCA 60.691 66.667 0.00 0.00 0.00 4.37
1143 1147 1.531840 CCCCTCCGACATCCGATCT 60.532 63.158 0.00 0.00 41.76 2.75
1179 1183 1.507140 TCGCATATTCTTCCAGGGGT 58.493 50.000 0.00 0.00 0.00 4.95
1188 1192 0.909610 CTTCCAGGGGTAGTGAGGCA 60.910 60.000 0.00 0.00 0.00 4.75
1241 1245 0.392461 GCCATGCTAAAGTCCGGTGA 60.392 55.000 0.00 0.00 0.00 4.02
1293 1297 1.522668 TCAGCGTACATTGCAAGCTT 58.477 45.000 4.94 0.00 35.82 3.74
1305 1309 1.079266 CAAGCTTGCTCTCCTCGCT 60.079 57.895 14.65 0.00 0.00 4.93
1308 1312 1.143620 GCTTGCTCTCCTCGCTGAT 59.856 57.895 0.00 0.00 0.00 2.90
1327 1331 3.710722 CCAGGGTCGCTCTGGCTT 61.711 66.667 11.97 0.00 44.29 4.35
1328 1332 2.348998 CAGGGTCGCTCTGGCTTT 59.651 61.111 0.00 0.00 36.09 3.51
1468 1472 1.400737 GGGTGCCTACTACGACAGAT 58.599 55.000 0.00 0.00 0.00 2.90
1485 1489 5.640357 CGACAGATACTCCTACACTATCCTC 59.360 48.000 0.00 0.00 0.00 3.71
1502 1506 1.845627 CTCATCCAGGGCCTGTGTGT 61.846 60.000 30.68 11.62 0.00 3.72
1507 1511 2.842462 AGGGCCTGTGTGTCGTGA 60.842 61.111 4.50 0.00 0.00 4.35
1621 1625 2.047274 GCAAGGCTAGGCGTGTCA 60.047 61.111 27.88 0.00 0.00 3.58
1626 1630 2.435693 GGCTAGGCGTGTCAGGGAT 61.436 63.158 0.00 0.00 0.00 3.85
1630 1634 4.408821 GGCGTGTCAGGGATGCCA 62.409 66.667 5.86 0.00 45.06 4.92
1686 1690 1.071041 GTGCCAAACGTCGTGACTTAC 60.071 52.381 0.00 0.00 0.00 2.34
1701 1705 4.218417 GTGACTTACAATGCCTTGATTGGT 59.782 41.667 8.84 2.20 37.60 3.67
1719 1723 1.056660 GTGGACTTTGTCAGGAGGGA 58.943 55.000 0.07 0.00 33.68 4.20
1740 1744 3.417069 AGGTTCGATGATGTGACCAAA 57.583 42.857 3.21 0.00 0.00 3.28
1843 1848 0.251922 AAAGTGGAGCATGGTGCCAT 60.252 50.000 14.15 0.00 46.52 4.40
1880 1887 4.747810 CCTGTGAAGGGCATTGATTTAAC 58.252 43.478 0.00 0.00 0.00 2.01
1881 1888 4.220382 CCTGTGAAGGGCATTGATTTAACA 59.780 41.667 0.00 0.00 0.00 2.41
1882 1889 5.389859 TGTGAAGGGCATTGATTTAACAG 57.610 39.130 0.00 0.00 0.00 3.16
1883 1890 4.832266 TGTGAAGGGCATTGATTTAACAGT 59.168 37.500 0.00 0.00 0.00 3.55
1884 1891 6.007076 TGTGAAGGGCATTGATTTAACAGTA 58.993 36.000 0.00 0.00 0.00 2.74
1885 1892 6.491745 TGTGAAGGGCATTGATTTAACAGTAA 59.508 34.615 0.00 0.00 0.00 2.24
1886 1893 7.014711 TGTGAAGGGCATTGATTTAACAGTAAA 59.985 33.333 0.00 0.00 33.76 2.01
1887 1894 8.034804 GTGAAGGGCATTGATTTAACAGTAAAT 58.965 33.333 0.00 0.00 41.64 1.40
1888 1895 8.034215 TGAAGGGCATTGATTTAACAGTAAATG 58.966 33.333 0.00 0.00 39.53 2.32
1889 1896 6.877236 AGGGCATTGATTTAACAGTAAATGG 58.123 36.000 0.00 0.00 39.53 3.16
1890 1897 5.523552 GGGCATTGATTTAACAGTAAATGGC 59.476 40.000 10.28 10.28 44.96 4.40
1891 1898 6.340522 GGCATTGATTTAACAGTAAATGGCT 58.659 36.000 11.19 0.00 43.37 4.75
1892 1899 6.818142 GGCATTGATTTAACAGTAAATGGCTT 59.182 34.615 11.19 0.00 43.37 4.35
1893 1900 7.010460 GGCATTGATTTAACAGTAAATGGCTTC 59.990 37.037 11.19 0.00 43.37 3.86
1894 1901 7.253750 GCATTGATTTAACAGTAAATGGCTTCG 60.254 37.037 0.00 0.00 39.53 3.79
1895 1902 6.189677 TGATTTAACAGTAAATGGCTTCGG 57.810 37.500 0.00 0.00 39.53 4.30
1896 1903 5.708230 TGATTTAACAGTAAATGGCTTCGGT 59.292 36.000 0.00 0.00 39.53 4.69
1897 1904 5.365403 TTTAACAGTAAATGGCTTCGGTG 57.635 39.130 0.00 0.00 0.00 4.94
1898 1905 1.821216 ACAGTAAATGGCTTCGGTGG 58.179 50.000 0.00 0.00 0.00 4.61
1899 1906 1.349688 ACAGTAAATGGCTTCGGTGGA 59.650 47.619 0.00 0.00 0.00 4.02
1900 1907 2.026262 ACAGTAAATGGCTTCGGTGGAT 60.026 45.455 0.00 0.00 0.00 3.41
1901 1908 2.355756 CAGTAAATGGCTTCGGTGGATG 59.644 50.000 0.00 0.00 0.00 3.51
1912 1919 1.000843 TCGGTGGATGACAACACTCAG 59.999 52.381 11.83 6.05 36.22 3.35
2040 2047 1.079503 GACGTCAGTTCCAATGCCTC 58.920 55.000 11.55 0.00 0.00 4.70
2087 2094 1.003866 GTCACCACTGCTTTTCGTGAC 60.004 52.381 3.19 3.19 44.46 3.67
2093 2100 1.498865 CTGCTTTTCGTGACCGCTGT 61.499 55.000 0.00 0.00 0.00 4.40
2100 2107 2.736144 TCGTGACCGCTGTAGATTTT 57.264 45.000 0.00 0.00 0.00 1.82
2158 2165 1.306997 CTGAGCCTACCCTTCCCCA 60.307 63.158 0.00 0.00 0.00 4.96
2181 2188 0.820226 GGAACACTACGGACTACCCC 59.180 60.000 0.00 0.00 0.00 4.95
2196 2203 0.250793 ACCCCGTCATTCAATACGCA 59.749 50.000 0.00 0.00 37.78 5.24
2219 2226 4.937620 AGACGACACAATCATTGTTATGCT 59.062 37.500 0.00 0.00 43.23 3.79
2220 2227 6.035975 CAGACGACACAATCATTGTTATGCTA 59.964 38.462 0.00 0.00 43.23 3.49
2276 2283 4.815533 TTCTCTCAGACTATGCTGCTTT 57.184 40.909 0.00 0.00 35.86 3.51
2291 2298 1.885887 TGCTTTGATTGGGCTACACAC 59.114 47.619 0.00 0.00 0.00 3.82
2308 2315 5.751243 ACACACTAACTTCCACAAATCAC 57.249 39.130 0.00 0.00 0.00 3.06
2342 2349 2.038329 CACCCCGGACACCCTCTA 59.962 66.667 0.73 0.00 0.00 2.43
2388 2395 0.895100 GCACTGTGGGAAAGATGCCA 60.895 55.000 10.21 0.00 45.98 4.92
2409 2416 1.668826 TCACCTATCTTGGGTTGCCT 58.331 50.000 0.00 0.00 34.44 4.75
2488 2495 1.872313 GAAGGATCACTGCTGCTATGC 59.128 52.381 0.00 0.00 0.00 3.14
2592 2608 3.936372 AAAGTCGTAGCACAGCTAGAA 57.064 42.857 0.00 0.00 42.11 2.10
2612 2628 4.878397 AGAAAAGATTAGGAGGCATTGTCG 59.122 41.667 0.00 0.00 0.00 4.35
2716 2732 6.189133 GGTGGTTTGGGTATCATTAACCTTA 58.811 40.000 0.00 0.00 37.23 2.69
2717 2733 6.664384 GGTGGTTTGGGTATCATTAACCTTAA 59.336 38.462 0.00 0.00 37.23 1.85
2773 2789 4.013728 TGCACAAATTCTATAACCGCCTT 58.986 39.130 0.00 0.00 0.00 4.35
2788 2804 1.279025 GCCTTGACATCCCCTGGGTA 61.279 60.000 12.71 0.00 36.47 3.69
2803 2819 2.774234 CTGGGTACAACTGATCTGGGAT 59.226 50.000 4.49 0.00 0.00 3.85
2806 2822 3.709653 GGGTACAACTGATCTGGGATACA 59.290 47.826 4.49 0.00 39.74 2.29
2854 2870 2.756760 CCAGGATCCTTGTGGTTCATTG 59.243 50.000 13.00 0.00 34.54 2.82
2862 2878 1.979855 TGTGGTTCATTGTGGTGGAG 58.020 50.000 0.00 0.00 0.00 3.86
2873 2889 5.189539 TCATTGTGGTGGAGAGATGTTATGA 59.810 40.000 0.00 0.00 0.00 2.15
2888 2904 6.652481 AGATGTTATGAAACTCAGTCCAACAG 59.348 38.462 0.00 0.00 36.51 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 2.957402 TGCTAATGCATTCTAGGGGG 57.043 50.000 16.86 0.39 45.31 5.40
58 59 1.366319 ACCAAGTCAGGAGCCATCTT 58.634 50.000 0.00 0.00 0.00 2.40
152 153 3.581332 TCAATTCGTTACCCCTCTCTTGT 59.419 43.478 0.00 0.00 0.00 3.16
164 165 2.459060 TCCGCACCTTCAATTCGTTA 57.541 45.000 0.00 0.00 0.00 3.18
232 233 0.254178 GCTTGCTCTTCCTCCCATGA 59.746 55.000 0.00 0.00 0.00 3.07
341 342 2.180276 CACACCTACTCCACCTAGCTT 58.820 52.381 0.00 0.00 0.00 3.74
429 430 1.833630 CATAGAGCTCCACCCTTGACA 59.166 52.381 10.93 0.00 0.00 3.58
431 432 0.833287 GCATAGAGCTCCACCCTTGA 59.167 55.000 10.93 0.00 41.15 3.02
544 545 3.838903 ACGGTGATAAGTCCTTCTCCTTT 59.161 43.478 0.00 0.00 0.00 3.11
621 622 3.672767 AACGTCTAACCCAGGTTACTG 57.327 47.619 5.15 0.00 44.51 2.74
642 643 4.081862 ACAAATGAGCTGCATTGTTAGCAT 60.082 37.500 14.52 1.77 46.25 3.79
692 693 3.067461 TCATGCAACCACACCTTACAAAC 59.933 43.478 0.00 0.00 0.00 2.93
748 749 4.946160 AATTTCCCAACCAGGTATCTCA 57.054 40.909 0.00 0.00 34.66 3.27
754 755 8.270137 ACTTTATTTAAATTTCCCAACCAGGT 57.730 30.769 5.91 0.00 34.66 4.00
804 807 0.733150 GACGCCAACAAATCCCTAGC 59.267 55.000 0.00 0.00 0.00 3.42
805 808 2.009774 CTGACGCCAACAAATCCCTAG 58.990 52.381 0.00 0.00 0.00 3.02
806 809 1.948611 GCTGACGCCAACAAATCCCTA 60.949 52.381 0.00 0.00 0.00 3.53
807 810 1.244019 GCTGACGCCAACAAATCCCT 61.244 55.000 0.00 0.00 0.00 4.20
808 811 1.212751 GCTGACGCCAACAAATCCC 59.787 57.895 0.00 0.00 0.00 3.85
809 812 4.868195 GCTGACGCCAACAAATCC 57.132 55.556 0.00 0.00 0.00 3.01
819 822 3.660111 GTTGTGGGTGGCTGACGC 61.660 66.667 0.00 0.00 38.02 5.19
820 823 1.600636 ATGTTGTGGGTGGCTGACG 60.601 57.895 0.00 0.00 0.00 4.35
821 824 0.823356 ACATGTTGTGGGTGGCTGAC 60.823 55.000 0.00 0.00 0.00 3.51
822 825 0.106268 AACATGTTGTGGGTGGCTGA 60.106 50.000 11.07 0.00 0.00 4.26
823 826 0.752054 AAACATGTTGTGGGTGGCTG 59.248 50.000 12.82 0.00 0.00 4.85
824 827 0.752054 CAAACATGTTGTGGGTGGCT 59.248 50.000 12.82 0.00 0.00 4.75
825 828 0.249826 CCAAACATGTTGTGGGTGGC 60.250 55.000 22.18 0.00 31.60 5.01
826 829 0.249826 GCCAAACATGTTGTGGGTGG 60.250 55.000 26.88 23.11 38.34 4.61
827 830 0.463204 TGCCAAACATGTTGTGGGTG 59.537 50.000 26.88 16.66 32.71 4.61
828 831 1.198713 TTGCCAAACATGTTGTGGGT 58.801 45.000 26.88 7.64 32.71 4.51
829 832 2.547299 ATTGCCAAACATGTTGTGGG 57.453 45.000 26.88 22.07 32.71 4.61
830 833 5.120519 GTCAATATTGCCAAACATGTTGTGG 59.879 40.000 24.10 24.10 35.39 4.17
831 834 5.164070 CGTCAATATTGCCAAACATGTTGTG 60.164 40.000 12.82 11.99 0.00 3.33
832 835 4.922692 CGTCAATATTGCCAAACATGTTGT 59.077 37.500 12.82 0.00 0.00 3.32
833 836 5.159925 TCGTCAATATTGCCAAACATGTTG 58.840 37.500 12.82 6.46 0.00 3.33
834 837 5.384063 TCGTCAATATTGCCAAACATGTT 57.616 34.783 10.76 4.92 0.00 2.71
835 838 5.048083 ACTTCGTCAATATTGCCAAACATGT 60.048 36.000 10.76 0.00 0.00 3.21
836 839 5.401550 ACTTCGTCAATATTGCCAAACATG 58.598 37.500 10.76 0.00 0.00 3.21
837 840 5.182950 TGACTTCGTCAATATTGCCAAACAT 59.817 36.000 10.76 0.00 39.78 2.71
838 841 4.517075 TGACTTCGTCAATATTGCCAAACA 59.483 37.500 10.76 2.80 39.78 2.83
839 842 5.041951 TGACTTCGTCAATATTGCCAAAC 57.958 39.130 10.76 2.99 39.78 2.93
840 843 5.697473 TTGACTTCGTCAATATTGCCAAA 57.303 34.783 10.76 3.79 45.88 3.28
849 852 9.215771 CGAATGGGATTCTTTGACTTCGTCAAT 62.216 40.741 9.91 0.00 40.72 2.57
850 853 7.993166 CGAATGGGATTCTTTGACTTCGTCAA 61.993 42.308 5.40 5.40 41.90 3.18
851 854 3.762407 TGGGATTCTTTGACTTCGTCA 57.238 42.857 0.00 0.00 41.09 4.35
852 855 4.201724 CGAATGGGATTCTTTGACTTCGTC 60.202 45.833 0.00 0.00 37.13 4.20
853 856 3.684788 CGAATGGGATTCTTTGACTTCGT 59.315 43.478 0.00 0.00 37.13 3.85
854 857 3.063997 CCGAATGGGATTCTTTGACTTCG 59.936 47.826 0.00 0.00 38.47 3.79
855 858 3.181496 GCCGAATGGGATTCTTTGACTTC 60.181 47.826 0.00 0.00 38.47 3.01
862 865 0.753111 GCAGGCCGAATGGGATTCTT 60.753 55.000 0.00 0.00 38.47 2.52
869 872 2.110967 CAGAGTGCAGGCCGAATGG 61.111 63.158 0.00 0.00 38.77 3.16
880 883 1.003580 TCCCTTGTTCATCCAGAGTGC 59.996 52.381 0.00 0.00 0.00 4.40
895 899 3.383698 TGATAGTTCGGTCTCTCCCTT 57.616 47.619 0.00 0.00 0.00 3.95
906 910 2.492019 TGGTGCGAGATGATAGTTCG 57.508 50.000 0.00 0.00 37.40 3.95
931 935 1.492176 GAATCAGGGGAAGATGCTGGA 59.508 52.381 0.00 0.00 0.00 3.86
972 976 3.009143 GTGGGAGTTTAGTGATGGGAAGT 59.991 47.826 0.00 0.00 0.00 3.01
1135 1139 0.882042 GCGGCATTGTGAGATCGGAT 60.882 55.000 0.00 0.00 0.00 4.18
1143 1147 1.451927 GATGAGGGCGGCATTGTGA 60.452 57.895 12.47 0.00 0.00 3.58
1217 1221 3.454960 GACTTTAGCATGGCGCCGC 62.455 63.158 23.90 20.42 44.04 6.53
1241 1245 1.522569 GTACAGCAATCGGGAGGCT 59.477 57.895 0.00 0.00 38.70 4.58
1252 1256 0.677288 AGCGTGTTGTAGGTACAGCA 59.323 50.000 2.84 2.84 43.56 4.41
1293 1297 2.498248 GCATCAGCGAGGAGAGCA 59.502 61.111 0.00 0.00 37.01 4.26
1305 1309 2.685017 AGAGCGACCCTGGCATCA 60.685 61.111 0.00 0.00 0.00 3.07
1316 1320 1.003476 TGCATCAAAGCCAGAGCGA 60.003 52.632 0.00 0.00 46.67 4.93
1468 1472 5.222151 CCTGGATGAGGATAGTGTAGGAGTA 60.222 48.000 0.00 0.00 46.33 2.59
1485 1489 1.377725 GACACACAGGCCCTGGATG 60.378 63.158 16.70 14.77 35.51 3.51
1593 1597 1.273986 TAGCCTTGCAGAGCCCATCA 61.274 55.000 6.43 0.00 0.00 3.07
1621 1625 0.178924 AACAAAGCCTTGGCATCCCT 60.179 50.000 14.54 0.00 36.82 4.20
1626 1630 1.382420 ACCCAACAAAGCCTTGGCA 60.382 52.632 14.54 0.00 37.45 4.92
1630 1634 2.242043 CATCTCACCCAACAAAGCCTT 58.758 47.619 0.00 0.00 0.00 4.35
1686 1690 2.173519 AGTCCACCAATCAAGGCATTG 58.826 47.619 4.34 4.34 37.80 2.82
1701 1705 1.699634 CTTCCCTCCTGACAAAGTCCA 59.300 52.381 0.00 0.00 0.00 4.02
1719 1723 3.417069 TTGGTCACATCATCGAACCTT 57.583 42.857 0.00 0.00 0.00 3.50
1740 1744 4.773674 TGCATCTCCATTTTCTCCAACAAT 59.226 37.500 0.00 0.00 0.00 2.71
1843 1848 0.034574 ACAGGCTTCACACAACACCA 60.035 50.000 0.00 0.00 0.00 4.17
1870 1877 7.093945 ACCGAAGCCATTTACTGTTAAATCAAT 60.094 33.333 0.00 0.00 36.00 2.57
1874 1881 5.105917 CCACCGAAGCCATTTACTGTTAAAT 60.106 40.000 0.00 0.00 38.26 1.40
1875 1882 4.216687 CCACCGAAGCCATTTACTGTTAAA 59.783 41.667 0.00 0.00 0.00 1.52
1876 1883 3.754323 CCACCGAAGCCATTTACTGTTAA 59.246 43.478 0.00 0.00 0.00 2.01
1877 1884 3.008157 TCCACCGAAGCCATTTACTGTTA 59.992 43.478 0.00 0.00 0.00 2.41
1878 1885 2.159382 CCACCGAAGCCATTTACTGTT 58.841 47.619 0.00 0.00 0.00 3.16
1879 1886 1.349688 TCCACCGAAGCCATTTACTGT 59.650 47.619 0.00 0.00 0.00 3.55
1880 1887 2.107950 TCCACCGAAGCCATTTACTG 57.892 50.000 0.00 0.00 0.00 2.74
1881 1888 2.238646 TCATCCACCGAAGCCATTTACT 59.761 45.455 0.00 0.00 0.00 2.24
1882 1889 2.354821 GTCATCCACCGAAGCCATTTAC 59.645 50.000 0.00 0.00 0.00 2.01
1883 1890 2.026729 TGTCATCCACCGAAGCCATTTA 60.027 45.455 0.00 0.00 0.00 1.40
1884 1891 1.271871 TGTCATCCACCGAAGCCATTT 60.272 47.619 0.00 0.00 0.00 2.32
1885 1892 0.327924 TGTCATCCACCGAAGCCATT 59.672 50.000 0.00 0.00 0.00 3.16
1886 1893 0.327924 TTGTCATCCACCGAAGCCAT 59.672 50.000 0.00 0.00 0.00 4.40
1887 1894 0.605319 GTTGTCATCCACCGAAGCCA 60.605 55.000 0.00 0.00 0.00 4.75
1888 1895 0.605319 TGTTGTCATCCACCGAAGCC 60.605 55.000 0.00 0.00 0.00 4.35
1889 1896 0.517316 GTGTTGTCATCCACCGAAGC 59.483 55.000 0.00 0.00 0.00 3.86
1890 1897 2.069273 GAGTGTTGTCATCCACCGAAG 58.931 52.381 0.00 0.00 31.88 3.79
1891 1898 1.414550 TGAGTGTTGTCATCCACCGAA 59.585 47.619 0.00 0.00 31.88 4.30
1892 1899 1.000843 CTGAGTGTTGTCATCCACCGA 59.999 52.381 0.00 0.00 31.88 4.69
1893 1900 1.432514 CTGAGTGTTGTCATCCACCG 58.567 55.000 0.78 0.00 31.88 4.94
1894 1901 1.160137 GCTGAGTGTTGTCATCCACC 58.840 55.000 0.78 0.00 31.88 4.61
1895 1902 1.160137 GGCTGAGTGTTGTCATCCAC 58.840 55.000 0.00 0.00 33.61 4.02
1896 1903 0.764271 TGGCTGAGTGTTGTCATCCA 59.236 50.000 0.00 0.00 39.81 3.41
1897 1904 1.741706 CATGGCTGAGTGTTGTCATCC 59.258 52.381 0.00 0.00 33.95 3.51
1898 1905 2.703416 TCATGGCTGAGTGTTGTCATC 58.297 47.619 0.00 0.00 0.00 2.92
1899 1906 2.865119 TCATGGCTGAGTGTTGTCAT 57.135 45.000 0.00 0.00 0.00 3.06
1900 1907 2.815503 CAATCATGGCTGAGTGTTGTCA 59.184 45.455 0.00 0.00 41.41 3.58
1901 1908 3.076621 TCAATCATGGCTGAGTGTTGTC 58.923 45.455 11.92 0.00 45.39 3.18
1935 1942 5.014202 AGCCATTTACTGTTAAATCCCGTT 58.986 37.500 0.00 0.00 36.00 4.44
1937 1944 5.576447 AAGCCATTTACTGTTAAATCCCG 57.424 39.130 0.00 0.00 36.00 5.14
2019 2026 0.321653 GGCATTGGAACTGACGTCCT 60.322 55.000 14.12 0.00 0.00 3.85
2022 2029 0.687354 AGAGGCATTGGAACTGACGT 59.313 50.000 0.00 0.00 0.00 4.34
2040 2047 1.227823 TCCTTGGCGAACACCACAG 60.228 57.895 0.00 0.00 40.19 3.66
2158 2165 3.615155 GGTAGTCCGTAGTGTTCCTAGT 58.385 50.000 0.00 0.00 0.00 2.57
2181 2188 2.035674 GTCGTCTGCGTATTGAATGACG 60.036 50.000 8.21 8.21 45.51 4.35
2196 2203 4.937620 AGCATAACAATGATTGTGTCGTCT 59.062 37.500 12.09 3.46 44.59 4.18
2219 2226 3.338250 CTTGGGTGGGGCAGGCTA 61.338 66.667 0.00 0.00 0.00 3.93
2276 2283 4.564821 GGAAGTTAGTGTGTAGCCCAATCA 60.565 45.833 0.00 0.00 0.00 2.57
2291 2298 3.758554 CAGGGGTGATTTGTGGAAGTTAG 59.241 47.826 0.00 0.00 0.00 2.34
2308 2315 1.686115 GGTGTTGATTGGGATCAGGGG 60.686 57.143 0.00 0.00 42.90 4.79
2342 2349 6.493458 ACCAAAGATTGTAGCTATGTTTTGGT 59.507 34.615 23.53 23.53 0.00 3.67
2388 2395 2.582636 AGGCAACCCAAGATAGGTGAAT 59.417 45.455 0.00 0.00 37.78 2.57
2488 2495 6.319658 AGTTTACCAGCATAAGACATCATTGG 59.680 38.462 0.00 0.00 0.00 3.16
2592 2608 4.487714 TCGACAATGCCTCCTAATCTTT 57.512 40.909 0.00 0.00 0.00 2.52
2626 2642 2.972348 ACTCTTGGTACCTTGGTCAGA 58.028 47.619 14.36 4.22 0.00 3.27
2637 2653 3.236047 TGCCAGTGAGTTACTCTTGGTA 58.764 45.455 25.44 21.67 37.60 3.25
2716 2732 7.218614 TCAACAAAGCATCATTCTGGATTTTT 58.781 30.769 0.00 0.00 0.00 1.94
2717 2733 6.761312 TCAACAAAGCATCATTCTGGATTTT 58.239 32.000 0.00 0.00 0.00 1.82
2773 2789 0.988832 GTTGTACCCAGGGGATGTCA 59.011 55.000 11.37 0.00 38.96 3.58
2788 2804 7.179338 GGATAGTATGTATCCCAGATCAGTTGT 59.821 40.741 0.00 0.00 37.98 3.32
2803 2819 5.771165 TGGTATTGCGTGAGGATAGTATGTA 59.229 40.000 0.00 0.00 0.00 2.29
2806 2822 4.587262 TGTGGTATTGCGTGAGGATAGTAT 59.413 41.667 0.00 0.00 0.00 2.12
2854 2870 5.491982 AGTTTCATAACATCTCTCCACCAC 58.508 41.667 0.00 0.00 36.70 4.16
2862 2878 6.650807 TGTTGGACTGAGTTTCATAACATCTC 59.349 38.462 0.00 0.00 36.70 2.75
2873 2889 3.947834 CCTTTGACTGTTGGACTGAGTTT 59.052 43.478 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.