Multiple sequence alignment - TraesCS4D01G087300

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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 TraesCS4D01G087300 chr4D 100.000 2456 0 0 1 2456 62548510 62550965 0.000000e+00 4536.0
1 TraesCS4D01G087300 chr4B 95.000 1520 74 1 937 2456 92463997 92465514 0.000000e+00 2385.0
2 TraesCS4D01G087300 chr4B 95.307 831 32 5 1 830 92463166 92463990 0.000000e+00 1312.0
3 TraesCS4D01G087300 chr4A 93.517 1527 83 13 940 2456 534258718 534257198 0.000000e+00 2257.0
4 TraesCS4D01G087300 chr4A 92.977 655 37 5 175 829 534259374 534258729 0.000000e+00 946.0
5 TraesCS4D01G087300 chr4A 96.032 126 3 2 1 125 534259496 534259372 1.150000e-48 204.0
6 TraesCS4D01G087300 chr2A 96.552 116 4 0 825 940 242021117 242021232 2.490000e-45 193.0
7 TraesCS4D01G087300 chr5A 97.000 100 2 1 825 924 566112081 566111983 1.510000e-37 167.0
8 TraesCS4D01G087300 chr1B 87.912 91 8 3 825 914 551651633 551651545 1.200000e-18 104.0
9 TraesCS4D01G087300 chr1B 89.362 47 4 1 105 150 355077066 355077020 9.490000e-05 58.4
10 TraesCS4D01G087300 chr5B 97.222 36 0 1 90 124 34488743 34488708 2.640000e-05 60.2


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G087300 chr4D 62548510 62550965 2455 False 4536.000000 4536 100.000000 1 2456 1 chr4D.!!$F1 2455
1 TraesCS4D01G087300 chr4B 92463166 92465514 2348 False 1848.500000 2385 95.153500 1 2456 2 chr4B.!!$F1 2455
2 TraesCS4D01G087300 chr4A 534257198 534259496 2298 True 1135.666667 2257 94.175333 1 2456 3 chr4A.!!$R1 2455

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
876 878 0.035056 GCCCTCAAAAGCCAGCTCTA 60.035 55.0 0.0 0.0 0.0 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2041 2050 0.387239 GCGGAAGGTTGTGCATGAAC 60.387 55.0 0.0 0.0 0.0 3.18 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
158 160 1.893137 ACGTGTTAGAGGCACATGAGA 59.107 47.619 0.00 0.00 36.71 3.27
168 170 4.398358 AGAGGCACATGAGAATGTTGATTG 59.602 41.667 0.00 0.00 31.37 2.67
232 234 4.154195 AGTGAAAGAACGGTGTTATGCATC 59.846 41.667 0.19 0.00 0.00 3.91
388 390 5.312895 TGTGTTTGTAGGTATGACAATGCT 58.687 37.500 0.00 0.00 36.71 3.79
391 393 8.261522 TGTGTTTGTAGGTATGACAATGCTATA 58.738 33.333 0.00 0.00 36.71 1.31
643 645 5.927115 AGTTGTTCTTCTACTTGATTCGGAC 59.073 40.000 0.00 0.00 0.00 4.79
645 647 5.470368 TGTTCTTCTACTTGATTCGGACAG 58.530 41.667 0.00 0.00 0.00 3.51
789 791 7.285172 TGCATTAACATTATACTCCACATTGCT 59.715 33.333 0.00 0.00 0.00 3.91
831 833 8.275758 CAGGTAGACCTATATATGAGGCTAGAA 58.724 40.741 0.00 0.00 46.65 2.10
832 834 9.020644 AGGTAGACCTATATATGAGGCTAGAAT 57.979 37.037 0.00 0.00 46.48 2.40
833 835 9.649316 GGTAGACCTATATATGAGGCTAGAATT 57.351 37.037 0.00 0.00 37.63 2.17
839 841 9.829507 CCTATATATGAGGCTAGAATTTTCTGG 57.170 37.037 3.07 1.35 38.19 3.86
845 847 2.420058 CTAGAATTTTCTGGCCCGGT 57.580 50.000 0.00 0.00 38.19 5.28
846 848 2.017049 CTAGAATTTTCTGGCCCGGTG 58.983 52.381 0.00 0.00 38.19 4.94
847 849 0.404040 AGAATTTTCTGGCCCGGTGA 59.596 50.000 0.00 0.00 35.89 4.02
848 850 0.811281 GAATTTTCTGGCCCGGTGAG 59.189 55.000 0.00 0.00 0.00 3.51
849 851 0.611896 AATTTTCTGGCCCGGTGAGG 60.612 55.000 0.00 0.00 40.63 3.86
857 859 2.584608 CCCGGTGAGGCTAGTTGG 59.415 66.667 0.00 0.00 39.21 3.77
858 860 2.125106 CCGGTGAGGCTAGTTGGC 60.125 66.667 0.00 0.00 42.15 4.52
866 868 3.356814 GGCTAGTTGGCCCTCAAAA 57.643 52.632 0.00 0.00 45.92 2.44
867 869 1.177401 GGCTAGTTGGCCCTCAAAAG 58.823 55.000 0.00 0.00 45.92 2.27
868 870 0.528017 GCTAGTTGGCCCTCAAAAGC 59.472 55.000 0.00 0.00 38.56 3.51
874 876 3.282271 GCCCTCAAAAGCCAGCTC 58.718 61.111 0.00 0.00 0.00 4.09
875 877 1.303970 GCCCTCAAAAGCCAGCTCT 60.304 57.895 0.00 0.00 0.00 4.09
876 878 0.035056 GCCCTCAAAAGCCAGCTCTA 60.035 55.000 0.00 0.00 0.00 2.43
877 879 1.743996 CCCTCAAAAGCCAGCTCTAC 58.256 55.000 0.00 0.00 0.00 2.59
878 880 1.680249 CCCTCAAAAGCCAGCTCTACC 60.680 57.143 0.00 0.00 0.00 3.18
879 881 1.003580 CCTCAAAAGCCAGCTCTACCA 59.996 52.381 0.00 0.00 0.00 3.25
880 882 2.553028 CCTCAAAAGCCAGCTCTACCAA 60.553 50.000 0.00 0.00 0.00 3.67
881 883 3.149196 CTCAAAAGCCAGCTCTACCAAA 58.851 45.455 0.00 0.00 0.00 3.28
882 884 2.884639 TCAAAAGCCAGCTCTACCAAAC 59.115 45.455 0.00 0.00 0.00 2.93
883 885 1.523758 AAAGCCAGCTCTACCAAACG 58.476 50.000 0.00 0.00 0.00 3.60
884 886 0.955919 AAGCCAGCTCTACCAAACGC 60.956 55.000 0.00 0.00 0.00 4.84
885 887 1.376037 GCCAGCTCTACCAAACGCT 60.376 57.895 0.00 0.00 0.00 5.07
886 888 0.955919 GCCAGCTCTACCAAACGCTT 60.956 55.000 0.00 0.00 0.00 4.68
887 889 1.674817 GCCAGCTCTACCAAACGCTTA 60.675 52.381 0.00 0.00 0.00 3.09
888 890 2.906354 CCAGCTCTACCAAACGCTTAT 58.094 47.619 0.00 0.00 0.00 1.73
889 891 2.866762 CCAGCTCTACCAAACGCTTATC 59.133 50.000 0.00 0.00 0.00 1.75
890 892 2.866762 CAGCTCTACCAAACGCTTATCC 59.133 50.000 0.00 0.00 0.00 2.59
891 893 2.766828 AGCTCTACCAAACGCTTATCCT 59.233 45.455 0.00 0.00 0.00 3.24
892 894 2.866762 GCTCTACCAAACGCTTATCCTG 59.133 50.000 0.00 0.00 0.00 3.86
893 895 3.458189 CTCTACCAAACGCTTATCCTGG 58.542 50.000 0.00 0.00 0.00 4.45
894 896 1.940613 CTACCAAACGCTTATCCTGGC 59.059 52.381 0.00 0.00 0.00 4.85
895 897 0.328258 ACCAAACGCTTATCCTGGCT 59.672 50.000 0.00 0.00 0.00 4.75
896 898 1.017387 CCAAACGCTTATCCTGGCTC 58.983 55.000 0.00 0.00 0.00 4.70
897 899 0.652592 CAAACGCTTATCCTGGCTCG 59.347 55.000 0.00 0.00 0.00 5.03
898 900 0.462047 AAACGCTTATCCTGGCTCGG 60.462 55.000 0.00 0.00 0.00 4.63
899 901 2.663188 CGCTTATCCTGGCTCGGC 60.663 66.667 0.00 0.00 0.00 5.54
900 902 2.505982 GCTTATCCTGGCTCGGCA 59.494 61.111 0.00 0.00 0.00 5.69
901 903 1.153168 GCTTATCCTGGCTCGGCAA 60.153 57.895 0.00 0.00 0.00 4.52
902 904 1.162800 GCTTATCCTGGCTCGGCAAG 61.163 60.000 0.00 0.00 0.00 4.01
906 908 3.785859 CCTGGCTCGGCAAGGCTA 61.786 66.667 12.19 0.00 43.38 3.93
907 909 3.112205 CCTGGCTCGGCAAGGCTAT 62.112 63.158 12.19 0.00 43.38 2.97
908 910 1.758440 CCTGGCTCGGCAAGGCTATA 61.758 60.000 12.19 0.00 43.38 1.31
909 911 3.255387 CCTGGCTCGGCAAGGCTATAA 62.255 57.143 12.19 0.00 43.38 0.98
910 912 2.618165 GGCTCGGCAAGGCTATAAC 58.382 57.895 4.84 0.00 46.82 1.89
911 913 0.885150 GGCTCGGCAAGGCTATAACC 60.885 60.000 4.84 0.00 46.82 2.85
912 914 1.222115 GCTCGGCAAGGCTATAACCG 61.222 60.000 10.17 10.17 45.15 4.44
913 915 0.104304 CTCGGCAAGGCTATAACCGT 59.896 55.000 14.44 0.00 44.17 4.83
914 916 0.538118 TCGGCAAGGCTATAACCGTT 59.462 50.000 14.44 0.00 44.17 4.44
915 917 1.065998 TCGGCAAGGCTATAACCGTTT 60.066 47.619 14.44 0.00 44.17 3.60
916 918 1.741145 CGGCAAGGCTATAACCGTTTT 59.259 47.619 8.69 0.00 39.05 2.43
917 919 2.162809 CGGCAAGGCTATAACCGTTTTT 59.837 45.455 8.69 0.00 39.05 1.94
918 920 3.507786 GGCAAGGCTATAACCGTTTTTG 58.492 45.455 0.00 0.00 33.69 2.44
919 921 2.921121 GCAAGGCTATAACCGTTTTTGC 59.079 45.455 2.26 2.26 32.24 3.68
920 922 3.507786 CAAGGCTATAACCGTTTTTGCC 58.492 45.455 15.75 15.75 39.19 4.52
921 923 2.097036 AGGCTATAACCGTTTTTGCCC 58.903 47.619 18.49 6.21 39.68 5.36
922 924 1.819903 GGCTATAACCGTTTTTGCCCA 59.180 47.619 13.54 0.00 33.45 5.36
923 925 2.159296 GGCTATAACCGTTTTTGCCCAG 60.159 50.000 13.54 0.00 33.45 4.45
924 926 2.159296 GCTATAACCGTTTTTGCCCAGG 60.159 50.000 0.00 0.00 0.00 4.45
925 927 2.296073 ATAACCGTTTTTGCCCAGGA 57.704 45.000 0.00 0.00 0.00 3.86
926 928 2.068834 TAACCGTTTTTGCCCAGGAA 57.931 45.000 0.00 0.00 0.00 3.36
927 929 1.419381 AACCGTTTTTGCCCAGGAAT 58.581 45.000 0.00 0.00 0.00 3.01
928 930 0.966179 ACCGTTTTTGCCCAGGAATC 59.034 50.000 0.00 0.00 0.00 2.52
929 931 0.965439 CCGTTTTTGCCCAGGAATCA 59.035 50.000 0.00 0.00 0.00 2.57
930 932 1.342819 CCGTTTTTGCCCAGGAATCAA 59.657 47.619 0.00 0.00 0.00 2.57
931 933 2.224161 CCGTTTTTGCCCAGGAATCAAA 60.224 45.455 0.00 0.00 0.00 2.69
932 934 2.799978 CGTTTTTGCCCAGGAATCAAAC 59.200 45.455 0.00 0.00 30.45 2.93
933 935 2.799978 GTTTTTGCCCAGGAATCAAACG 59.200 45.455 0.00 0.00 30.45 3.60
934 936 1.698506 TTTGCCCAGGAATCAAACGT 58.301 45.000 0.00 0.00 0.00 3.99
935 937 1.698506 TTGCCCAGGAATCAAACGTT 58.301 45.000 0.00 0.00 0.00 3.99
936 938 1.243902 TGCCCAGGAATCAAACGTTC 58.756 50.000 0.00 0.00 0.00 3.95
937 939 0.526211 GCCCAGGAATCAAACGTTCC 59.474 55.000 0.00 0.00 44.39 3.62
938 940 1.173913 CCCAGGAATCAAACGTTCCC 58.826 55.000 0.00 0.00 45.00 3.97
1101 1103 1.559682 TCCCCCTCTTCAACAGCATAC 59.440 52.381 0.00 0.00 0.00 2.39
1413 1415 5.421277 TCGTTTCCTGTTAACAACTTCTCA 58.579 37.500 10.03 0.00 0.00 3.27
1480 1482 8.374743 AGATTAATGGGTTAGCAACAAAAACAT 58.625 29.630 0.00 0.00 0.00 2.71
1684 1686 1.322538 GCAAATCATGTTCCGGCCCT 61.323 55.000 0.00 0.00 0.00 5.19
1685 1687 1.185315 CAAATCATGTTCCGGCCCTT 58.815 50.000 0.00 0.00 0.00 3.95
1821 1823 4.620567 CGTCTGTGGACATGATACAGGAAA 60.621 45.833 20.28 6.69 42.21 3.13
1850 1852 2.555227 CCAACCCTACACCTCAAATGCT 60.555 50.000 0.00 0.00 0.00 3.79
1858 1860 2.549754 ACACCTCAAATGCTCGTCTTTG 59.450 45.455 0.00 0.00 34.41 2.77
1908 1911 4.350245 TCTGCTAAACAACCTAGCCTAGA 58.650 43.478 0.00 0.00 40.95 2.43
1925 1928 4.120589 CCTAGACTTCCGCCAAATAGTTC 58.879 47.826 0.00 0.00 0.00 3.01
2164 2174 8.789881 AAATGAAACAACATGCATGAAAAATG 57.210 26.923 32.75 21.74 0.00 2.32
2213 2223 2.417651 CCGAATACCTGCAAACGTCCTA 60.418 50.000 0.00 0.00 0.00 2.94
2221 2231 2.616842 CTGCAAACGTCCTACAGGTTTT 59.383 45.455 0.00 0.00 40.38 2.43
2222 2232 3.806380 TGCAAACGTCCTACAGGTTTTA 58.194 40.909 0.00 0.00 40.38 1.52
2352 2362 2.893489 GAGCCCAAGACAAAAATGACCT 59.107 45.455 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 22 6.257411 CCTATTAACTCGACGTCTAGAGTCAA 59.743 42.308 22.54 15.97 45.91 3.18
142 144 4.937620 TCAACATTCTCATGTGCCTCTAAC 59.062 41.667 0.00 0.00 43.34 2.34
144 146 4.824479 TCAACATTCTCATGTGCCTCTA 57.176 40.909 0.00 0.00 43.34 2.43
158 160 7.093509 GGGTTGGAATACTTACCAATCAACATT 60.094 37.037 10.60 0.00 45.74 2.71
279 281 4.607293 AACCCTTGAAAGCTGATTTTCC 57.393 40.909 0.00 0.00 36.46 3.13
280 282 5.164233 GCTAACCCTTGAAAGCTGATTTTC 58.836 41.667 0.00 0.00 37.53 2.29
281 283 4.588528 TGCTAACCCTTGAAAGCTGATTTT 59.411 37.500 0.00 0.00 35.95 1.82
282 284 4.151883 TGCTAACCCTTGAAAGCTGATTT 58.848 39.130 0.00 0.00 35.95 2.17
643 645 8.190784 GGAATCCAAAATAATGTTGAGGTACTG 58.809 37.037 0.00 0.00 41.55 2.74
645 647 8.062065 TGGAATCCAAAATAATGTTGAGGTAC 57.938 34.615 0.00 0.00 0.00 3.34
709 711 5.999600 CCCATCATGCATAGTGTTTATCTCA 59.000 40.000 0.00 0.00 0.00 3.27
723 725 5.962641 ACATAGAGAGATATCCCATCATGCA 59.037 40.000 0.00 0.00 0.00 3.96
789 791 6.864151 TCTACCTGTAGAGTACTGTAGACA 57.136 41.667 12.21 5.27 38.06 3.41
831 833 1.000896 CCTCACCGGGCCAGAAAAT 60.001 57.895 6.32 0.00 0.00 1.82
832 834 2.434331 CCTCACCGGGCCAGAAAA 59.566 61.111 6.32 0.00 0.00 2.29
833 835 4.344865 GCCTCACCGGGCCAGAAA 62.345 66.667 6.32 0.00 45.92 2.52
840 842 2.584608 CCAACTAGCCTCACCGGG 59.415 66.667 6.32 0.00 0.00 5.73
841 843 2.125106 GCCAACTAGCCTCACCGG 60.125 66.667 0.00 0.00 0.00 5.28
849 851 0.528017 GCTTTTGAGGGCCAACTAGC 59.472 55.000 6.18 4.00 36.30 3.42
850 852 1.177401 GGCTTTTGAGGGCCAACTAG 58.823 55.000 6.18 0.00 46.84 2.57
851 853 3.356814 GGCTTTTGAGGGCCAACTA 57.643 52.632 6.18 0.00 46.84 2.24
852 854 4.198087 GGCTTTTGAGGGCCAACT 57.802 55.556 6.18 0.00 46.84 3.16
857 859 0.035056 TAGAGCTGGCTTTTGAGGGC 60.035 55.000 0.00 0.00 0.00 5.19
858 860 1.680249 GGTAGAGCTGGCTTTTGAGGG 60.680 57.143 0.00 0.00 0.00 4.30
859 861 1.003580 TGGTAGAGCTGGCTTTTGAGG 59.996 52.381 0.00 0.00 0.00 3.86
860 862 2.479566 TGGTAGAGCTGGCTTTTGAG 57.520 50.000 0.00 0.00 0.00 3.02
861 863 2.884639 GTTTGGTAGAGCTGGCTTTTGA 59.115 45.455 0.00 0.00 0.00 2.69
862 864 2.350772 CGTTTGGTAGAGCTGGCTTTTG 60.351 50.000 0.00 0.00 0.00 2.44
863 865 1.880027 CGTTTGGTAGAGCTGGCTTTT 59.120 47.619 0.00 0.00 0.00 2.27
864 866 1.523758 CGTTTGGTAGAGCTGGCTTT 58.476 50.000 0.00 0.00 0.00 3.51
865 867 0.955919 GCGTTTGGTAGAGCTGGCTT 60.956 55.000 0.00 0.00 0.00 4.35
866 868 1.376037 GCGTTTGGTAGAGCTGGCT 60.376 57.895 0.00 0.00 0.00 4.75
867 869 0.955919 AAGCGTTTGGTAGAGCTGGC 60.956 55.000 0.00 0.00 40.17 4.85
868 870 2.380084 TAAGCGTTTGGTAGAGCTGG 57.620 50.000 0.00 0.00 40.17 4.85
869 871 2.866762 GGATAAGCGTTTGGTAGAGCTG 59.133 50.000 0.00 0.00 40.17 4.24
870 872 2.766828 AGGATAAGCGTTTGGTAGAGCT 59.233 45.455 0.00 0.00 42.35 4.09
871 873 2.866762 CAGGATAAGCGTTTGGTAGAGC 59.133 50.000 0.00 0.00 0.00 4.09
872 874 3.458189 CCAGGATAAGCGTTTGGTAGAG 58.542 50.000 0.00 0.00 0.00 2.43
873 875 2.419574 GCCAGGATAAGCGTTTGGTAGA 60.420 50.000 0.00 0.00 0.00 2.59
874 876 1.940613 GCCAGGATAAGCGTTTGGTAG 59.059 52.381 0.00 0.00 0.00 3.18
875 877 1.557832 AGCCAGGATAAGCGTTTGGTA 59.442 47.619 0.00 0.00 0.00 3.25
876 878 0.328258 AGCCAGGATAAGCGTTTGGT 59.672 50.000 0.00 0.00 0.00 3.67
877 879 1.017387 GAGCCAGGATAAGCGTTTGG 58.983 55.000 0.00 0.00 0.00 3.28
878 880 0.652592 CGAGCCAGGATAAGCGTTTG 59.347 55.000 0.00 0.00 0.00 2.93
879 881 0.462047 CCGAGCCAGGATAAGCGTTT 60.462 55.000 0.00 0.00 0.00 3.60
880 882 1.144057 CCGAGCCAGGATAAGCGTT 59.856 57.895 0.00 0.00 0.00 4.84
881 883 2.815308 CCGAGCCAGGATAAGCGT 59.185 61.111 0.00 0.00 0.00 5.07
882 884 2.663188 GCCGAGCCAGGATAAGCG 60.663 66.667 0.00 0.00 0.00 4.68
883 885 1.153168 TTGCCGAGCCAGGATAAGC 60.153 57.895 0.00 0.00 0.00 3.09
884 886 0.533755 CCTTGCCGAGCCAGGATAAG 60.534 60.000 9.52 3.10 43.15 1.73
885 887 1.526887 CCTTGCCGAGCCAGGATAA 59.473 57.895 9.52 0.00 43.15 1.75
886 888 3.106986 GCCTTGCCGAGCCAGGATA 62.107 63.158 16.76 0.00 43.15 2.59
887 889 4.496336 GCCTTGCCGAGCCAGGAT 62.496 66.667 16.76 0.00 43.15 3.24
889 891 1.758440 TATAGCCTTGCCGAGCCAGG 61.758 60.000 10.46 10.46 43.32 4.45
890 892 0.106708 TTATAGCCTTGCCGAGCCAG 59.893 55.000 0.00 0.00 0.00 4.85
891 893 0.179056 GTTATAGCCTTGCCGAGCCA 60.179 55.000 0.00 0.00 0.00 4.75
892 894 0.885150 GGTTATAGCCTTGCCGAGCC 60.885 60.000 0.00 0.00 0.00 4.70
893 895 1.222115 CGGTTATAGCCTTGCCGAGC 61.222 60.000 3.94 0.00 44.57 5.03
894 896 0.104304 ACGGTTATAGCCTTGCCGAG 59.896 55.000 8.31 0.00 44.57 4.63
895 897 0.538118 AACGGTTATAGCCTTGCCGA 59.462 50.000 8.31 0.00 44.57 5.54
896 898 1.375551 AAACGGTTATAGCCTTGCCG 58.624 50.000 3.94 0.00 46.83 5.69
897 899 3.507786 CAAAAACGGTTATAGCCTTGCC 58.492 45.455 3.94 0.00 0.00 4.52
898 900 2.921121 GCAAAAACGGTTATAGCCTTGC 59.079 45.455 12.42 12.42 31.85 4.01
899 901 3.507786 GGCAAAAACGGTTATAGCCTTG 58.492 45.455 17.75 2.91 37.67 3.61
900 902 2.494471 GGGCAAAAACGGTTATAGCCTT 59.506 45.455 21.68 0.00 40.40 4.35
901 903 2.097036 GGGCAAAAACGGTTATAGCCT 58.903 47.619 21.68 0.00 40.40 4.58
902 904 1.819903 TGGGCAAAAACGGTTATAGCC 59.180 47.619 17.13 17.13 39.86 3.93
903 905 2.159296 CCTGGGCAAAAACGGTTATAGC 60.159 50.000 0.00 0.00 0.00 2.97
904 906 3.349022 TCCTGGGCAAAAACGGTTATAG 58.651 45.455 0.00 0.00 0.00 1.31
905 907 3.436577 TCCTGGGCAAAAACGGTTATA 57.563 42.857 0.00 0.00 0.00 0.98
906 908 2.296073 TCCTGGGCAAAAACGGTTAT 57.704 45.000 0.00 0.00 0.00 1.89
907 909 2.068834 TTCCTGGGCAAAAACGGTTA 57.931 45.000 0.00 0.00 0.00 2.85
908 910 1.343142 GATTCCTGGGCAAAAACGGTT 59.657 47.619 0.00 0.00 0.00 4.44
909 911 0.966179 GATTCCTGGGCAAAAACGGT 59.034 50.000 0.00 0.00 0.00 4.83
910 912 0.965439 TGATTCCTGGGCAAAAACGG 59.035 50.000 0.00 0.00 0.00 4.44
911 913 2.799978 GTTTGATTCCTGGGCAAAAACG 59.200 45.455 10.36 0.00 33.80 3.60
912 914 2.799978 CGTTTGATTCCTGGGCAAAAAC 59.200 45.455 10.36 8.18 33.80 2.43
913 915 2.432510 ACGTTTGATTCCTGGGCAAAAA 59.567 40.909 10.36 0.00 33.80 1.94
914 916 2.035632 ACGTTTGATTCCTGGGCAAAA 58.964 42.857 10.36 0.00 33.80 2.44
915 917 1.698506 ACGTTTGATTCCTGGGCAAA 58.301 45.000 0.00 0.16 0.00 3.68
916 918 1.611491 GAACGTTTGATTCCTGGGCAA 59.389 47.619 0.46 0.00 0.00 4.52
917 919 1.243902 GAACGTTTGATTCCTGGGCA 58.756 50.000 0.46 0.00 0.00 5.36
918 920 0.526211 GGAACGTTTGATTCCTGGGC 59.474 55.000 0.46 0.00 42.15 5.36
919 921 1.173913 GGGAACGTTTGATTCCTGGG 58.826 55.000 0.46 0.00 44.43 4.45
920 922 2.200373 AGGGAACGTTTGATTCCTGG 57.800 50.000 0.46 0.00 44.43 4.45
921 923 4.324267 ACTAAGGGAACGTTTGATTCCTG 58.676 43.478 0.46 0.00 44.43 3.86
922 924 4.041198 TGACTAAGGGAACGTTTGATTCCT 59.959 41.667 0.46 2.40 44.43 3.36
923 925 4.153655 GTGACTAAGGGAACGTTTGATTCC 59.846 45.833 0.46 0.00 44.31 3.01
924 926 4.753107 TGTGACTAAGGGAACGTTTGATTC 59.247 41.667 0.46 0.00 37.67 2.52
925 927 4.710324 TGTGACTAAGGGAACGTTTGATT 58.290 39.130 0.46 0.01 37.67 2.57
926 928 4.345859 TGTGACTAAGGGAACGTTTGAT 57.654 40.909 0.46 0.00 37.67 2.57
927 929 3.823281 TGTGACTAAGGGAACGTTTGA 57.177 42.857 0.46 0.00 37.67 2.69
928 930 4.513692 TGATTGTGACTAAGGGAACGTTTG 59.486 41.667 0.46 0.00 37.67 2.93
929 931 4.710324 TGATTGTGACTAAGGGAACGTTT 58.290 39.130 0.46 0.00 37.67 3.60
930 932 4.345859 TGATTGTGACTAAGGGAACGTT 57.654 40.909 0.00 0.00 40.54 3.99
931 933 4.223032 AGATGATTGTGACTAAGGGAACGT 59.777 41.667 0.00 0.00 0.00 3.99
932 934 4.759782 AGATGATTGTGACTAAGGGAACG 58.240 43.478 0.00 0.00 0.00 3.95
933 935 5.586643 GGAAGATGATTGTGACTAAGGGAAC 59.413 44.000 0.00 0.00 0.00 3.62
934 936 5.250543 TGGAAGATGATTGTGACTAAGGGAA 59.749 40.000 0.00 0.00 0.00 3.97
935 937 4.782691 TGGAAGATGATTGTGACTAAGGGA 59.217 41.667 0.00 0.00 0.00 4.20
936 938 4.878397 GTGGAAGATGATTGTGACTAAGGG 59.122 45.833 0.00 0.00 0.00 3.95
937 939 5.491070 TGTGGAAGATGATTGTGACTAAGG 58.509 41.667 0.00 0.00 0.00 2.69
938 940 7.984050 AGTATGTGGAAGATGATTGTGACTAAG 59.016 37.037 0.00 0.00 0.00 2.18
1101 1103 0.524392 CGTACTTCTCCAGCAGCTCG 60.524 60.000 0.00 0.00 0.00 5.03
1251 1253 1.138036 CTGGATGTTGCCATGCACG 59.862 57.895 0.00 0.00 43.51 5.34
1347 1349 1.283347 AGATGAGCTGGTCACCATGT 58.717 50.000 12.27 0.00 38.28 3.21
1480 1482 9.248291 GTTGATCTAACAAAATCAAGAAGCAAA 57.752 29.630 0.00 0.00 41.28 3.68
1684 1686 6.929625 TGGTTCAGTGATTTCTTTGTGAAAA 58.070 32.000 0.00 0.00 46.32 2.29
1821 1823 1.074889 GGTGTAGGGTTGGATGGTTGT 59.925 52.381 0.00 0.00 0.00 3.32
1908 1911 3.950397 TGATGAACTATTTGGCGGAAGT 58.050 40.909 0.00 0.00 0.00 3.01
1925 1928 3.507786 CAGATGGTTGTTGTGCATGATG 58.492 45.455 0.00 0.00 0.00 3.07
2031 2040 1.202817 TGTGCATGAACATCCATGTGC 59.797 47.619 1.03 0.00 44.25 4.57
2041 2050 0.387239 GCGGAAGGTTGTGCATGAAC 60.387 55.000 0.00 0.00 0.00 3.18
2042 2051 1.523154 GGCGGAAGGTTGTGCATGAA 61.523 55.000 0.00 0.00 0.00 2.57
2197 2207 1.274167 CCTGTAGGACGTTTGCAGGTA 59.726 52.381 21.78 0.00 41.15 3.08
2213 2223 3.005367 CCGCAAACCAGAATAAAACCTGT 59.995 43.478 0.00 0.00 0.00 4.00
2221 2231 4.524714 TCCAAAATTCCGCAAACCAGAATA 59.475 37.500 0.00 0.00 30.21 1.75
2222 2232 3.323403 TCCAAAATTCCGCAAACCAGAAT 59.677 39.130 0.00 0.00 0.00 2.40
2332 2342 2.629617 CAGGTCATTTTTGTCTTGGGCT 59.370 45.455 0.00 0.00 0.00 5.19
2352 2362 2.637382 AGTGATGTACATGTGGACACCA 59.363 45.455 14.43 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.