Multiple sequence alignment - TraesCS4B01G208800

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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 TraesCS4B01G208800 chr4B 100.000 3371 0 0 1 3371 446328857 446332227 0.000 6226.0
1 TraesCS4B01G208800 chr4D 95.980 2438 80 3 938 3357 360957883 360955446 0.000 3943.0
2 TraesCS4B01G208800 chr4A 95.989 1446 51 3 957 2395 103721720 103723165 0.000 2342.0
3 TraesCS4B01G208800 chr4A 94.112 1002 35 9 2392 3371 103723628 103724627 0.000 1502.0
4 TraesCS4B01G208800 chr7B 95.609 797 32 2 1 795 377875082 377875877 0.000 1275.0
5 TraesCS4B01G208800 chr7B 100.000 28 0 0 1269 1296 134503807 134503834 0.006 52.8
6 TraesCS4B01G208800 chr1D 95.597 795 34 1 1 795 2902653 2903446 0.000 1273.0
7 TraesCS4B01G208800 chr5B 95.346 795 31 3 1 795 530961586 530962374 0.000 1258.0
8 TraesCS4B01G208800 chr2B 95.220 795 37 1 1 795 666925329 666926122 0.000 1256.0
9 TraesCS4B01G208800 chr2B 95.094 795 38 1 1 795 511148795 511149588 0.000 1251.0
10 TraesCS4B01G208800 chr3B 95.094 795 38 1 1 795 147897939 147897146 0.000 1251.0
11 TraesCS4B01G208800 chr7D 94.969 795 38 2 1 795 550638009 550638801 0.000 1245.0
12 TraesCS4B01G208800 chr7D 95.141 782 37 1 1 782 604461717 604462497 0.000 1232.0
13 TraesCS4B01G208800 chr6B 94.591 795 42 1 1 795 197816303 197815510 0.000 1229.0


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 TraesCS4B01G208800 chr4B 446328857 446332227 3370 False 6226 6226 100.0000 1 3371 1 chr4B.!!$F1 3370
1 TraesCS4B01G208800 chr4D 360955446 360957883 2437 True 3943 3943 95.9800 938 3357 1 chr4D.!!$R1 2419
2 TraesCS4B01G208800 chr4A 103721720 103724627 2907 False 1922 2342 95.0505 957 3371 2 chr4A.!!$F1 2414
3 TraesCS4B01G208800 chr7B 377875082 377875877 795 False 1275 1275 95.6090 1 795 1 chr7B.!!$F2 794
4 TraesCS4B01G208800 chr1D 2902653 2903446 793 False 1273 1273 95.5970 1 795 1 chr1D.!!$F1 794
5 TraesCS4B01G208800 chr5B 530961586 530962374 788 False 1258 1258 95.3460 1 795 1 chr5B.!!$F1 794
6 TraesCS4B01G208800 chr2B 666925329 666926122 793 False 1256 1256 95.2200 1 795 1 chr2B.!!$F2 794
7 TraesCS4B01G208800 chr2B 511148795 511149588 793 False 1251 1251 95.0940 1 795 1 chr2B.!!$F1 794
8 TraesCS4B01G208800 chr3B 147897146 147897939 793 True 1251 1251 95.0940 1 795 1 chr3B.!!$R1 794
9 TraesCS4B01G208800 chr7D 550638009 550638801 792 False 1245 1245 94.9690 1 795 1 chr7D.!!$F1 794
10 TraesCS4B01G208800 chr7D 604461717 604462497 780 False 1232 1232 95.1410 1 782 1 chr7D.!!$F2 781
11 TraesCS4B01G208800 chr6B 197815510 197816303 793 True 1229 1229 94.5910 1 795 1 chr6B.!!$R1 794

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
869 876 0.043637 TTGGAGGGGAGGTAATCGGT 59.956 55.0 0.0 0.0 0.00 4.69 F
870 877 0.043637 TGGAGGGGAGGTAATCGGTT 59.956 55.0 0.0 0.0 0.00 4.44 F
919 926 0.179100 CACCCAGGATGCGACTACTG 60.179 60.0 0.0 0.0 31.97 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2012 2026 2.185350 CGATGCCGTGCTCCTCTT 59.815 61.111 0.0 0.0 0.00 2.85 R
2032 2046 2.202810 GTAGTGCTCCAGCCTCGC 60.203 66.667 0.0 0.0 41.18 5.03 R
2648 3141 3.315191 AGTGGTATGTTGTTGTTGAGTGC 59.685 43.478 0.0 0.0 0.00 4.40 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
76 79 1.537814 TTGCGGTGGTAGGACGACAT 61.538 55.000 0.00 0.00 0.00 3.06
211 214 2.689983 ACTTTGCTTGCTACTTGTGCTT 59.310 40.909 0.00 0.00 0.00 3.91
292 295 1.444933 TCATTGGTGAGGTTCCAGGT 58.555 50.000 0.00 0.00 36.28 4.00
358 361 6.294010 CGTATAGCAACTGCAACTATAGAGGA 60.294 42.308 6.78 0.00 45.16 3.71
370 373 7.780271 TGCAACTATAGAGGATTCAAGACTAGA 59.220 37.037 6.78 0.00 0.00 2.43
561 564 0.970640 TGGCGTTGGTGTTCTAGCTA 59.029 50.000 0.00 0.00 0.00 3.32
599 602 2.565834 GCTCACCAACTAGGGTACAAGA 59.434 50.000 0.00 0.00 43.89 3.02
692 695 4.279671 CCAAACAAAGTGCACTTGGGTATA 59.720 41.667 32.33 0.00 36.12 1.47
704 707 6.001460 GCACTTGGGTATATACCTAATGCAA 58.999 40.000 32.00 25.07 44.32 4.08
736 743 1.405391 GCAGGCAACCAAACAACTTGT 60.405 47.619 0.00 0.00 32.65 3.16
777 784 0.850100 TTTTCCTCAACCAGGCTGGA 59.150 50.000 38.99 16.89 43.08 3.86
782 789 1.272092 CCTCAACCAGGCTGGATTGAA 60.272 52.381 38.99 22.83 40.96 2.69
785 792 3.303938 TCAACCAGGCTGGATTGAAAAA 58.696 40.909 38.99 18.65 40.96 1.94
804 811 5.989551 AAAAACTATGCAAGCCTTTTGTG 57.010 34.783 0.00 0.00 0.00 3.33
805 812 4.935352 AAACTATGCAAGCCTTTTGTGA 57.065 36.364 0.00 0.00 0.00 3.58
806 813 4.510038 AACTATGCAAGCCTTTTGTGAG 57.490 40.909 0.00 0.00 0.00 3.51
807 814 3.754965 ACTATGCAAGCCTTTTGTGAGA 58.245 40.909 0.00 0.00 0.00 3.27
808 815 4.144297 ACTATGCAAGCCTTTTGTGAGAA 58.856 39.130 0.00 0.00 0.00 2.87
809 816 4.584325 ACTATGCAAGCCTTTTGTGAGAAA 59.416 37.500 0.00 0.00 0.00 2.52
810 817 3.163630 TGCAAGCCTTTTGTGAGAAAC 57.836 42.857 0.00 0.00 0.00 2.78
811 818 2.760092 TGCAAGCCTTTTGTGAGAAACT 59.240 40.909 0.00 0.00 0.00 2.66
812 819 3.195396 TGCAAGCCTTTTGTGAGAAACTT 59.805 39.130 0.00 0.00 0.00 2.66
813 820 3.553105 GCAAGCCTTTTGTGAGAAACTTG 59.447 43.478 0.00 0.00 37.05 3.16
814 821 4.114794 CAAGCCTTTTGTGAGAAACTTGG 58.885 43.478 0.00 0.00 31.81 3.61
815 822 3.365472 AGCCTTTTGTGAGAAACTTGGT 58.635 40.909 0.00 0.00 0.00 3.67
816 823 3.769300 AGCCTTTTGTGAGAAACTTGGTT 59.231 39.130 0.00 0.00 0.00 3.67
817 824 4.222810 AGCCTTTTGTGAGAAACTTGGTTT 59.777 37.500 0.00 0.00 38.54 3.27
827 834 4.380841 GAAACTTGGTTTCGGGAACTTT 57.619 40.909 7.28 0.00 41.59 2.66
828 835 5.503662 GAAACTTGGTTTCGGGAACTTTA 57.496 39.130 7.28 0.00 41.59 1.85
829 836 6.080648 GAAACTTGGTTTCGGGAACTTTAT 57.919 37.500 7.28 0.00 41.59 1.40
830 837 5.447624 AACTTGGTTTCGGGAACTTTATG 57.552 39.130 0.00 0.00 38.35 1.90
831 838 3.824443 ACTTGGTTTCGGGAACTTTATGG 59.176 43.478 0.00 0.00 38.35 2.74
832 839 2.797786 TGGTTTCGGGAACTTTATGGG 58.202 47.619 0.00 0.00 38.35 4.00
833 840 2.097036 GGTTTCGGGAACTTTATGGGG 58.903 52.381 0.00 0.00 38.35 4.96
834 841 2.555892 GGTTTCGGGAACTTTATGGGGT 60.556 50.000 0.00 0.00 38.35 4.95
835 842 2.751259 GTTTCGGGAACTTTATGGGGTC 59.249 50.000 0.00 0.00 35.31 4.46
836 843 0.913924 TCGGGAACTTTATGGGGTCC 59.086 55.000 0.00 0.00 0.00 4.46
837 844 0.916809 CGGGAACTTTATGGGGTCCT 59.083 55.000 0.00 0.00 0.00 3.85
838 845 1.283905 CGGGAACTTTATGGGGTCCTT 59.716 52.381 0.00 0.00 0.00 3.36
839 846 2.735151 GGGAACTTTATGGGGTCCTTG 58.265 52.381 0.00 0.00 0.00 3.61
840 847 2.623239 GGGAACTTTATGGGGTCCTTGG 60.623 54.545 0.00 0.00 0.00 3.61
841 848 2.042569 GGAACTTTATGGGGTCCTTGGT 59.957 50.000 0.00 0.00 0.00 3.67
842 849 3.267551 GGAACTTTATGGGGTCCTTGGTA 59.732 47.826 0.00 0.00 0.00 3.25
843 850 4.524053 GAACTTTATGGGGTCCTTGGTAG 58.476 47.826 0.00 0.00 0.00 3.18
844 851 3.810623 ACTTTATGGGGTCCTTGGTAGA 58.189 45.455 0.00 0.00 0.00 2.59
845 852 3.780850 ACTTTATGGGGTCCTTGGTAGAG 59.219 47.826 0.00 0.00 0.00 2.43
846 853 1.802553 TATGGGGTCCTTGGTAGAGC 58.197 55.000 0.00 0.00 0.00 4.09
857 864 0.918983 TGGTAGAGCCATTTGGAGGG 59.081 55.000 0.00 0.00 43.61 4.30
858 865 0.183731 GGTAGAGCCATTTGGAGGGG 59.816 60.000 0.00 0.00 37.39 4.79
859 866 1.213296 GTAGAGCCATTTGGAGGGGA 58.787 55.000 0.00 0.00 37.39 4.81
860 867 1.141858 GTAGAGCCATTTGGAGGGGAG 59.858 57.143 0.00 0.00 37.39 4.30
861 868 1.228510 GAGCCATTTGGAGGGGAGG 59.771 63.158 0.00 0.00 37.39 4.30
862 869 1.544917 AGCCATTTGGAGGGGAGGT 60.545 57.895 0.00 0.00 37.39 3.85
863 870 0.253630 AGCCATTTGGAGGGGAGGTA 60.254 55.000 0.00 0.00 37.39 3.08
864 871 0.629058 GCCATTTGGAGGGGAGGTAA 59.371 55.000 0.00 0.00 37.39 2.85
865 872 1.217942 GCCATTTGGAGGGGAGGTAAT 59.782 52.381 0.00 0.00 37.39 1.89
866 873 2.753168 GCCATTTGGAGGGGAGGTAATC 60.753 54.545 0.00 0.00 37.39 1.75
867 874 2.487265 CCATTTGGAGGGGAGGTAATCG 60.487 54.545 0.00 0.00 37.39 3.34
868 875 1.209621 TTTGGAGGGGAGGTAATCGG 58.790 55.000 0.00 0.00 0.00 4.18
869 876 0.043637 TTGGAGGGGAGGTAATCGGT 59.956 55.000 0.00 0.00 0.00 4.69
870 877 0.043637 TGGAGGGGAGGTAATCGGTT 59.956 55.000 0.00 0.00 0.00 4.44
871 878 1.210538 GGAGGGGAGGTAATCGGTTT 58.789 55.000 0.00 0.00 0.00 3.27
872 879 2.293051 TGGAGGGGAGGTAATCGGTTTA 60.293 50.000 0.00 0.00 0.00 2.01
873 880 2.977580 GGAGGGGAGGTAATCGGTTTAT 59.022 50.000 0.00 0.00 0.00 1.40
874 881 3.244457 GGAGGGGAGGTAATCGGTTTATG 60.244 52.174 0.00 0.00 0.00 1.90
875 882 3.644738 GAGGGGAGGTAATCGGTTTATGA 59.355 47.826 0.00 0.00 0.00 2.15
876 883 4.240323 AGGGGAGGTAATCGGTTTATGAT 58.760 43.478 0.00 0.00 0.00 2.45
877 884 5.408824 AGGGGAGGTAATCGGTTTATGATA 58.591 41.667 0.00 0.00 0.00 2.15
878 885 5.847817 AGGGGAGGTAATCGGTTTATGATAA 59.152 40.000 0.00 0.00 0.00 1.75
879 886 6.330778 AGGGGAGGTAATCGGTTTATGATAAA 59.669 38.462 0.00 0.00 0.00 1.40
880 887 6.653740 GGGGAGGTAATCGGTTTATGATAAAG 59.346 42.308 0.00 0.00 0.00 1.85
881 888 7.447594 GGGAGGTAATCGGTTTATGATAAAGA 58.552 38.462 0.00 0.00 0.00 2.52
882 889 7.387122 GGGAGGTAATCGGTTTATGATAAAGAC 59.613 40.741 0.00 0.00 0.00 3.01
883 890 7.387122 GGAGGTAATCGGTTTATGATAAAGACC 59.613 40.741 0.00 0.00 0.00 3.85
887 894 4.191662 CGGTTTATGATAAAGACCGTGC 57.808 45.455 16.43 0.00 45.94 5.34
888 895 3.869246 CGGTTTATGATAAAGACCGTGCT 59.131 43.478 16.43 0.00 45.94 4.40
889 896 4.331717 CGGTTTATGATAAAGACCGTGCTT 59.668 41.667 16.43 0.00 45.94 3.91
890 897 5.163794 CGGTTTATGATAAAGACCGTGCTTT 60.164 40.000 16.43 5.30 45.94 3.51
891 898 6.255950 GGTTTATGATAAAGACCGTGCTTTC 58.744 40.000 0.00 0.00 38.85 2.62
892 899 6.128117 GGTTTATGATAAAGACCGTGCTTTCA 60.128 38.462 0.00 0.00 38.85 2.69
893 900 7.302524 GTTTATGATAAAGACCGTGCTTTCAA 58.697 34.615 0.00 0.00 38.85 2.69
894 901 5.957842 ATGATAAAGACCGTGCTTTCAAA 57.042 34.783 3.39 0.00 38.85 2.69
895 902 5.103290 TGATAAAGACCGTGCTTTCAAAC 57.897 39.130 3.39 0.00 38.85 2.93
896 903 4.576873 TGATAAAGACCGTGCTTTCAAACA 59.423 37.500 3.39 0.00 38.85 2.83
897 904 2.844122 AAGACCGTGCTTTCAAACAC 57.156 45.000 0.00 0.00 0.00 3.32
903 910 1.822581 GTGCTTTCAAACACGACACC 58.177 50.000 0.00 0.00 0.00 4.16
904 911 0.736053 TGCTTTCAAACACGACACCC 59.264 50.000 0.00 0.00 0.00 4.61
905 912 0.736053 GCTTTCAAACACGACACCCA 59.264 50.000 0.00 0.00 0.00 4.51
906 913 1.268539 GCTTTCAAACACGACACCCAG 60.269 52.381 0.00 0.00 0.00 4.45
907 914 1.333619 CTTTCAAACACGACACCCAGG 59.666 52.381 0.00 0.00 0.00 4.45
908 915 0.542333 TTCAAACACGACACCCAGGA 59.458 50.000 0.00 0.00 0.00 3.86
909 916 0.762418 TCAAACACGACACCCAGGAT 59.238 50.000 0.00 0.00 0.00 3.24
910 917 0.874390 CAAACACGACACCCAGGATG 59.126 55.000 0.00 0.00 0.00 3.51
911 918 0.889186 AAACACGACACCCAGGATGC 60.889 55.000 0.00 0.00 31.97 3.91
912 919 2.815211 CACGACACCCAGGATGCG 60.815 66.667 0.00 0.00 31.97 4.73
913 920 2.994995 ACGACACCCAGGATGCGA 60.995 61.111 4.80 0.00 31.97 5.10
914 921 2.509336 CGACACCCAGGATGCGAC 60.509 66.667 0.00 0.00 31.97 5.19
915 922 2.982130 GACACCCAGGATGCGACT 59.018 61.111 0.00 0.00 31.97 4.18
916 923 1.663379 CGACACCCAGGATGCGACTA 61.663 60.000 0.00 0.00 31.97 2.59
917 924 0.179108 GACACCCAGGATGCGACTAC 60.179 60.000 0.00 0.00 31.97 2.73
918 925 0.614979 ACACCCAGGATGCGACTACT 60.615 55.000 0.00 0.00 31.97 2.57
919 926 0.179100 CACCCAGGATGCGACTACTG 60.179 60.000 0.00 0.00 31.97 2.74
920 927 0.614979 ACCCAGGATGCGACTACTGT 60.615 55.000 0.00 0.00 31.97 3.55
921 928 0.537188 CCCAGGATGCGACTACTGTT 59.463 55.000 0.00 0.00 31.97 3.16
922 929 1.471676 CCCAGGATGCGACTACTGTTC 60.472 57.143 0.00 0.00 31.97 3.18
923 930 1.471676 CCAGGATGCGACTACTGTTCC 60.472 57.143 0.00 0.00 31.97 3.62
924 931 1.204704 CAGGATGCGACTACTGTTCCA 59.795 52.381 0.00 0.00 0.00 3.53
925 932 1.899814 AGGATGCGACTACTGTTCCAA 59.100 47.619 0.00 0.00 0.00 3.53
926 933 2.301870 AGGATGCGACTACTGTTCCAAA 59.698 45.455 0.00 0.00 0.00 3.28
927 934 2.415512 GGATGCGACTACTGTTCCAAAC 59.584 50.000 0.00 0.00 0.00 2.93
928 935 2.902705 TGCGACTACTGTTCCAAACT 57.097 45.000 0.00 0.00 0.00 2.66
929 936 2.479837 TGCGACTACTGTTCCAAACTG 58.520 47.619 0.00 0.00 36.53 3.16
930 937 1.798813 GCGACTACTGTTCCAAACTGG 59.201 52.381 0.00 0.00 39.43 4.00
931 938 2.547218 GCGACTACTGTTCCAAACTGGA 60.547 50.000 0.00 0.00 46.61 3.86
940 947 1.228124 CCAAACTGGAACGCCCTGA 60.228 57.895 8.05 0.00 40.96 3.86
948 955 0.320160 GGAACGCCCTGAAAGTACGT 60.320 55.000 0.00 0.00 44.00 3.57
1219 1233 1.289066 CTCGCCTCGGACAAAGTCA 59.711 57.895 0.00 0.00 33.68 3.41
1292 1306 0.382636 CGCAAGGTGTTCGACGAAAC 60.383 55.000 12.67 12.16 0.00 2.78
1477 1491 3.518003 GCAGAATGGCCAGCGATT 58.482 55.556 13.05 0.00 35.86 3.34
1566 1580 1.899814 TCGGTGCTGAACTTCCAGTAT 59.100 47.619 0.00 0.00 36.57 2.12
1763 1777 3.172575 CGCGCTCGTCGACATGTT 61.173 61.111 17.16 0.00 41.67 2.71
1910 1924 1.667154 CTCTTCGACCGGATGCTGGA 61.667 60.000 9.46 0.00 33.36 3.86
1944 1958 1.663702 GGACCACCTGACGTTCACG 60.664 63.158 0.00 0.00 46.33 4.35
1962 1976 1.598130 GGCCGTTCTGACAGCTTGT 60.598 57.895 0.00 0.00 29.86 3.16
1995 2009 4.144703 GTCGAGACCGGGAAGGCC 62.145 72.222 6.32 0.00 46.52 5.19
2012 2026 2.436469 CCTGTACCAGCGCATGCA 60.436 61.111 19.57 3.32 46.23 3.96
2617 3110 1.341531 ACACATACTCGAGCATAGGGC 59.658 52.381 13.61 0.00 45.30 5.19
2705 3198 8.328864 GGATTATTGACTCGAATTACACACTTC 58.671 37.037 0.00 0.00 0.00 3.01
3017 3519 1.021390 GGTGAAGTGTGGATGGCTCG 61.021 60.000 0.00 0.00 0.00 5.03
3044 3546 5.801350 AACATGTAATCCACAATGAGTCG 57.199 39.130 0.00 0.00 41.55 4.18
3209 3711 4.079827 AGCAGGCCTCCTAATGCT 57.920 55.556 0.00 5.48 43.92 3.79
3257 3759 4.133820 TGGATACCAAACGCATCATAAGG 58.866 43.478 0.00 0.00 0.00 2.69
3281 3783 1.570813 GAAACCCAAGCTGTGCAAAC 58.429 50.000 0.00 0.00 0.00 2.93
3305 3807 0.734889 AGCAATCGGAATGGCTTTCG 59.265 50.000 6.99 0.00 39.24 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 79 1.780309 ACCACCACATCCAAAAGAGGA 59.220 47.619 0.00 0.00 43.01 3.71
211 214 4.521639 AGAGTTGAAGCAGCAAATCAATGA 59.478 37.500 17.24 0.00 43.21 2.57
292 295 5.885912 GGCTTCTTCCCATGAACTATAAACA 59.114 40.000 0.00 0.00 0.00 2.83
358 361 2.568956 TGCTGCCTGTCTAGTCTTGAAT 59.431 45.455 0.00 0.00 0.00 2.57
370 373 0.466922 AAGCTTGTTCTGCTGCCTGT 60.467 50.000 0.00 0.00 41.03 4.00
409 412 3.521529 GACACTGCTGCCTCCGTGT 62.522 63.158 11.88 11.88 42.72 4.49
561 564 4.202441 GTGAGCTTACCCACAATGATCAT 58.798 43.478 1.18 1.18 33.72 2.45
599 602 1.663643 CGGCGTACATGTTGTGCTTAT 59.336 47.619 2.30 0.00 30.49 1.73
657 660 2.706339 TTGTTTGGTTGGCTGCATTT 57.294 40.000 0.50 0.00 0.00 2.32
692 695 4.827789 TCCCTAGTCCTTGCATTAGGTAT 58.172 43.478 4.36 0.00 36.63 2.73
704 707 0.621571 TTGCCTGCATCCCTAGTCCT 60.622 55.000 0.00 0.00 0.00 3.85
782 789 5.669477 TCACAAAAGGCTTGCATAGTTTTT 58.331 33.333 0.00 0.00 0.00 1.94
785 792 4.144297 TCTCACAAAAGGCTTGCATAGTT 58.856 39.130 0.00 0.00 0.00 2.24
786 793 3.754965 TCTCACAAAAGGCTTGCATAGT 58.245 40.909 0.00 0.00 0.00 2.12
795 802 3.801114 ACCAAGTTTCTCACAAAAGGC 57.199 42.857 0.00 0.00 0.00 4.35
796 803 4.798387 CGAAACCAAGTTTCTCACAAAAGG 59.202 41.667 15.90 0.00 46.55 3.11
797 804 4.798387 CCGAAACCAAGTTTCTCACAAAAG 59.202 41.667 15.90 1.16 46.55 2.27
798 805 4.381079 CCCGAAACCAAGTTTCTCACAAAA 60.381 41.667 15.90 0.00 46.55 2.44
799 806 3.129638 CCCGAAACCAAGTTTCTCACAAA 59.870 43.478 15.90 0.00 46.55 2.83
800 807 2.685897 CCCGAAACCAAGTTTCTCACAA 59.314 45.455 15.90 0.00 46.55 3.33
801 808 2.092861 TCCCGAAACCAAGTTTCTCACA 60.093 45.455 15.90 0.00 46.55 3.58
802 809 2.567985 TCCCGAAACCAAGTTTCTCAC 58.432 47.619 15.90 0.00 46.55 3.51
803 810 2.946990 GTTCCCGAAACCAAGTTTCTCA 59.053 45.455 15.90 0.26 46.55 3.27
804 811 3.211865 AGTTCCCGAAACCAAGTTTCTC 58.788 45.455 15.90 4.36 46.55 2.87
805 812 3.292492 AGTTCCCGAAACCAAGTTTCT 57.708 42.857 15.90 0.00 46.55 2.52
806 813 4.380841 AAAGTTCCCGAAACCAAGTTTC 57.619 40.909 9.63 9.63 45.65 2.78
807 814 5.221362 CCATAAAGTTCCCGAAACCAAGTTT 60.221 40.000 0.00 0.00 38.76 2.66
808 815 4.279922 CCATAAAGTTCCCGAAACCAAGTT 59.720 41.667 0.00 0.00 38.76 2.66
809 816 3.824443 CCATAAAGTTCCCGAAACCAAGT 59.176 43.478 0.00 0.00 38.76 3.16
810 817 3.192633 CCCATAAAGTTCCCGAAACCAAG 59.807 47.826 0.00 0.00 38.76 3.61
811 818 3.158676 CCCATAAAGTTCCCGAAACCAA 58.841 45.455 0.00 0.00 38.76 3.67
812 819 2.555670 CCCCATAAAGTTCCCGAAACCA 60.556 50.000 0.00 0.00 38.76 3.67
813 820 2.097036 CCCCATAAAGTTCCCGAAACC 58.903 52.381 0.00 0.00 38.76 3.27
814 821 2.751259 GACCCCATAAAGTTCCCGAAAC 59.249 50.000 0.00 0.00 38.21 2.78
815 822 2.291089 GGACCCCATAAAGTTCCCGAAA 60.291 50.000 0.00 0.00 0.00 3.46
816 823 1.282738 GGACCCCATAAAGTTCCCGAA 59.717 52.381 0.00 0.00 0.00 4.30
817 824 0.913924 GGACCCCATAAAGTTCCCGA 59.086 55.000 0.00 0.00 0.00 5.14
818 825 0.916809 AGGACCCCATAAAGTTCCCG 59.083 55.000 0.00 0.00 0.00 5.14
819 826 2.623239 CCAAGGACCCCATAAAGTTCCC 60.623 54.545 0.00 0.00 0.00 3.97
820 827 2.042569 ACCAAGGACCCCATAAAGTTCC 59.957 50.000 0.00 0.00 0.00 3.62
821 828 3.451402 ACCAAGGACCCCATAAAGTTC 57.549 47.619 0.00 0.00 0.00 3.01
822 829 4.180723 TCTACCAAGGACCCCATAAAGTT 58.819 43.478 0.00 0.00 0.00 2.66
823 830 3.780850 CTCTACCAAGGACCCCATAAAGT 59.219 47.826 0.00 0.00 0.00 2.66
824 831 3.433740 GCTCTACCAAGGACCCCATAAAG 60.434 52.174 0.00 0.00 0.00 1.85
825 832 2.508300 GCTCTACCAAGGACCCCATAAA 59.492 50.000 0.00 0.00 0.00 1.40
826 833 2.124411 GCTCTACCAAGGACCCCATAA 58.876 52.381 0.00 0.00 0.00 1.90
827 834 1.694693 GGCTCTACCAAGGACCCCATA 60.695 57.143 0.00 0.00 38.86 2.74
828 835 0.988678 GGCTCTACCAAGGACCCCAT 60.989 60.000 0.00 0.00 38.86 4.00
829 836 1.615424 GGCTCTACCAAGGACCCCA 60.615 63.158 0.00 0.00 38.86 4.96
830 837 3.321445 GGCTCTACCAAGGACCCC 58.679 66.667 0.00 0.00 38.86 4.95
839 846 0.183731 CCCCTCCAAATGGCTCTACC 59.816 60.000 0.00 0.00 39.84 3.18
840 847 1.141858 CTCCCCTCCAAATGGCTCTAC 59.858 57.143 0.00 0.00 34.44 2.59
841 848 1.511613 CTCCCCTCCAAATGGCTCTA 58.488 55.000 0.00 0.00 34.44 2.43
842 849 1.284841 CCTCCCCTCCAAATGGCTCT 61.285 60.000 0.00 0.00 34.44 4.09
843 850 1.228510 CCTCCCCTCCAAATGGCTC 59.771 63.158 0.00 0.00 34.44 4.70
844 851 0.253630 TACCTCCCCTCCAAATGGCT 60.254 55.000 0.00 0.00 34.44 4.75
845 852 0.629058 TTACCTCCCCTCCAAATGGC 59.371 55.000 0.00 0.00 34.44 4.40
846 853 2.487265 CGATTACCTCCCCTCCAAATGG 60.487 54.545 0.00 0.00 0.00 3.16
847 854 2.487265 CCGATTACCTCCCCTCCAAATG 60.487 54.545 0.00 0.00 0.00 2.32
848 855 1.774856 CCGATTACCTCCCCTCCAAAT 59.225 52.381 0.00 0.00 0.00 2.32
849 856 1.209621 CCGATTACCTCCCCTCCAAA 58.790 55.000 0.00 0.00 0.00 3.28
850 857 0.043637 ACCGATTACCTCCCCTCCAA 59.956 55.000 0.00 0.00 0.00 3.53
851 858 0.043637 AACCGATTACCTCCCCTCCA 59.956 55.000 0.00 0.00 0.00 3.86
852 859 1.210538 AAACCGATTACCTCCCCTCC 58.789 55.000 0.00 0.00 0.00 4.30
853 860 3.644738 TCATAAACCGATTACCTCCCCTC 59.355 47.826 0.00 0.00 0.00 4.30
854 861 3.660959 TCATAAACCGATTACCTCCCCT 58.339 45.455 0.00 0.00 0.00 4.79
855 862 4.635699 ATCATAAACCGATTACCTCCCC 57.364 45.455 0.00 0.00 0.00 4.81
856 863 7.387122 GTCTTTATCATAAACCGATTACCTCCC 59.613 40.741 0.00 0.00 0.00 4.30
857 864 7.387122 GGTCTTTATCATAAACCGATTACCTCC 59.613 40.741 0.00 0.00 0.00 4.30
858 865 8.307921 GGTCTTTATCATAAACCGATTACCTC 57.692 38.462 0.00 0.00 0.00 3.85
867 874 5.813080 AAGCACGGTCTTTATCATAAACC 57.187 39.130 0.00 0.00 0.00 3.27
868 875 6.837992 TGAAAGCACGGTCTTTATCATAAAC 58.162 36.000 4.49 0.00 36.50 2.01
869 876 7.441890 TTGAAAGCACGGTCTTTATCATAAA 57.558 32.000 4.49 0.00 36.50 1.40
870 877 7.041030 TGTTTGAAAGCACGGTCTTTATCATAA 60.041 33.333 4.49 0.00 36.50 1.90
871 878 6.428465 TGTTTGAAAGCACGGTCTTTATCATA 59.572 34.615 4.49 0.00 36.50 2.15
872 879 5.240623 TGTTTGAAAGCACGGTCTTTATCAT 59.759 36.000 4.49 0.00 36.50 2.45
873 880 4.576873 TGTTTGAAAGCACGGTCTTTATCA 59.423 37.500 4.49 0.00 36.50 2.15
874 881 4.909880 GTGTTTGAAAGCACGGTCTTTATC 59.090 41.667 4.49 0.00 36.50 1.75
875 882 4.855531 GTGTTTGAAAGCACGGTCTTTAT 58.144 39.130 4.49 0.00 36.50 1.40
876 883 4.281525 GTGTTTGAAAGCACGGTCTTTA 57.718 40.909 4.49 0.00 36.50 1.85
877 884 3.145212 GTGTTTGAAAGCACGGTCTTT 57.855 42.857 4.20 4.20 38.85 2.52
878 885 2.844122 GTGTTTGAAAGCACGGTCTT 57.156 45.000 0.00 0.00 30.66 3.01
884 891 1.533129 GGGTGTCGTGTTTGAAAGCAC 60.533 52.381 0.38 0.38 36.87 4.40
885 892 0.736053 GGGTGTCGTGTTTGAAAGCA 59.264 50.000 0.00 0.00 0.00 3.91
886 893 0.736053 TGGGTGTCGTGTTTGAAAGC 59.264 50.000 0.00 0.00 0.00 3.51
887 894 1.333619 CCTGGGTGTCGTGTTTGAAAG 59.666 52.381 0.00 0.00 0.00 2.62
888 895 1.065345 TCCTGGGTGTCGTGTTTGAAA 60.065 47.619 0.00 0.00 0.00 2.69
889 896 0.542333 TCCTGGGTGTCGTGTTTGAA 59.458 50.000 0.00 0.00 0.00 2.69
890 897 0.762418 ATCCTGGGTGTCGTGTTTGA 59.238 50.000 0.00 0.00 0.00 2.69
891 898 0.874390 CATCCTGGGTGTCGTGTTTG 59.126 55.000 0.00 0.00 0.00 2.93
892 899 0.889186 GCATCCTGGGTGTCGTGTTT 60.889 55.000 9.05 0.00 0.00 2.83
893 900 1.302511 GCATCCTGGGTGTCGTGTT 60.303 57.895 9.05 0.00 0.00 3.32
894 901 2.347490 GCATCCTGGGTGTCGTGT 59.653 61.111 9.05 0.00 0.00 4.49
895 902 2.815211 CGCATCCTGGGTGTCGTG 60.815 66.667 9.05 0.00 0.00 4.35
896 903 2.994995 TCGCATCCTGGGTGTCGT 60.995 61.111 18.50 0.00 0.00 4.34
897 904 1.663379 TAGTCGCATCCTGGGTGTCG 61.663 60.000 9.05 12.46 0.00 4.35
898 905 0.179108 GTAGTCGCATCCTGGGTGTC 60.179 60.000 9.05 0.07 0.00 3.67
899 906 0.614979 AGTAGTCGCATCCTGGGTGT 60.615 55.000 9.05 0.00 0.00 4.16
900 907 0.179100 CAGTAGTCGCATCCTGGGTG 60.179 60.000 1.54 1.54 0.00 4.61
901 908 0.614979 ACAGTAGTCGCATCCTGGGT 60.615 55.000 0.00 0.00 0.00 4.51
902 909 0.537188 AACAGTAGTCGCATCCTGGG 59.463 55.000 0.00 0.00 0.00 4.45
903 910 1.471676 GGAACAGTAGTCGCATCCTGG 60.472 57.143 0.00 0.00 0.00 4.45
904 911 1.204704 TGGAACAGTAGTCGCATCCTG 59.795 52.381 0.00 0.00 0.00 3.86
905 912 1.557099 TGGAACAGTAGTCGCATCCT 58.443 50.000 0.00 0.00 0.00 3.24
906 913 2.380084 TTGGAACAGTAGTCGCATCC 57.620 50.000 0.00 0.00 42.39 3.51
907 914 3.123621 CAGTTTGGAACAGTAGTCGCATC 59.876 47.826 0.00 0.00 42.39 3.91
908 915 3.067106 CAGTTTGGAACAGTAGTCGCAT 58.933 45.455 0.00 0.00 42.39 4.73
909 916 2.479837 CAGTTTGGAACAGTAGTCGCA 58.520 47.619 0.00 0.00 42.39 5.10
910 917 1.798813 CCAGTTTGGAACAGTAGTCGC 59.201 52.381 0.00 0.00 40.96 5.19
911 918 3.380479 TCCAGTTTGGAACAGTAGTCG 57.620 47.619 0.00 0.00 45.00 4.18
921 928 1.228124 CAGGGCGTTCCAGTTTGGA 60.228 57.895 0.00 0.00 46.61 3.53
922 929 0.821711 TTCAGGGCGTTCCAGTTTGG 60.822 55.000 0.14 0.00 39.43 3.28
923 930 1.001378 CTTTCAGGGCGTTCCAGTTTG 60.001 52.381 0.14 0.00 38.24 2.93
924 931 1.318576 CTTTCAGGGCGTTCCAGTTT 58.681 50.000 0.14 0.00 38.24 2.66
925 932 0.182775 ACTTTCAGGGCGTTCCAGTT 59.817 50.000 0.14 0.00 38.24 3.16
926 933 1.053424 TACTTTCAGGGCGTTCCAGT 58.947 50.000 0.14 0.00 38.24 4.00
927 934 1.439679 GTACTTTCAGGGCGTTCCAG 58.560 55.000 0.14 0.00 38.24 3.86
928 935 0.320073 CGTACTTTCAGGGCGTTCCA 60.320 55.000 0.00 0.00 38.24 3.53
929 936 0.320160 ACGTACTTTCAGGGCGTTCC 60.320 55.000 0.00 0.00 31.37 3.62
930 937 0.788391 CACGTACTTTCAGGGCGTTC 59.212 55.000 0.00 0.00 33.28 3.95
931 938 0.105408 ACACGTACTTTCAGGGCGTT 59.895 50.000 0.00 0.00 33.28 4.84
932 939 0.599204 CACACGTACTTTCAGGGCGT 60.599 55.000 0.00 0.00 36.13 5.68
933 940 0.599204 ACACACGTACTTTCAGGGCG 60.599 55.000 0.00 0.00 0.00 6.13
934 941 0.865769 CACACACGTACTTTCAGGGC 59.134 55.000 0.00 0.00 0.00 5.19
935 942 2.234300 ACACACACGTACTTTCAGGG 57.766 50.000 0.00 0.00 0.00 4.45
948 955 0.039798 GCCGACTCGAAGTACACACA 60.040 55.000 0.00 0.00 0.00 3.72
1047 1055 1.882352 CGGGTGAAAAAGAGGTGGAGG 60.882 57.143 0.00 0.00 0.00 4.30
1101 1109 1.048724 CGGAAGCAGGGTAGGGATCA 61.049 60.000 0.00 0.00 0.00 2.92
1104 1112 1.987855 CACGGAAGCAGGGTAGGGA 60.988 63.158 0.00 0.00 0.00 4.20
1500 1514 1.379044 CACATCTGGCTGGAACCCC 60.379 63.158 0.00 0.00 0.00 4.95
1569 1583 2.048127 AACAGGGTTCGCGCTCTC 60.048 61.111 5.56 0.00 38.41 3.20
1962 1976 3.323758 GACCATGCCACCGTAGCCA 62.324 63.158 0.00 0.00 0.00 4.75
2012 2026 2.185350 CGATGCCGTGCTCCTCTT 59.815 61.111 0.00 0.00 0.00 2.85
2032 2046 2.202810 GTAGTGCTCCAGCCTCGC 60.203 66.667 0.00 0.00 41.18 5.03
2648 3141 3.315191 AGTGGTATGTTGTTGTTGAGTGC 59.685 43.478 0.00 0.00 0.00 4.40
2705 3198 7.978975 GCTAGAAATATCAGGGCTAGTTCTATG 59.021 40.741 0.00 0.91 36.05 2.23
3028 3530 3.442625 ACTCGTCGACTCATTGTGGATTA 59.557 43.478 14.70 0.00 35.89 1.75
3128 3630 2.055042 AGAGCAGGACAGGCTACGG 61.055 63.158 0.00 0.00 42.78 4.02
3209 3711 1.000163 GACTCTGGTGTTCGAGAAGCA 60.000 52.381 0.00 1.99 0.00 3.91
3257 3759 1.600916 ACAGCTTGGGTTTCCTCGC 60.601 57.895 0.00 0.00 0.00 5.03
3305 3807 4.280677 AGCCTGACTCATTATCTACTCAGC 59.719 45.833 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.