Multiple sequence alignment - TraesCS3D01G405800

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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 TraesCS3D01G405800 chr3D 100.000 5044 0 0 1 5044 520167834 520172877 0.000000e+00 9315
1 TraesCS3D01G405800 chr3D 96.443 4161 103 18 887 5044 40534303 40538421 0.000000e+00 6822
2 TraesCS3D01G405800 chr3D 97.124 3164 86 4 1883 5043 584735477 584738638 0.000000e+00 5334
3 TraesCS3D01G405800 chr3D 97.723 966 21 1 887 1852 584734510 584735474 0.000000e+00 1661
4 TraesCS3D01G405800 chr3D 95.970 794 26 2 1 793 40533504 40534292 0.000000e+00 1284
5 TraesCS3D01G405800 chr3D 95.970 794 26 2 1 793 584733711 584734499 0.000000e+00 1284
6 TraesCS3D01G405800 chr1D 97.934 4163 77 6 887 5044 404222879 404218721 0.000000e+00 7203
7 TraesCS3D01G405800 chr1D 97.140 4161 108 7 887 5044 33552494 33556646 0.000000e+00 7014
8 TraesCS3D01G405800 chr1D 98.487 793 12 0 1 793 404223682 404222890 0.000000e+00 1399
9 TraesCS3D01G405800 chr1D 96.096 794 25 2 1 793 33551695 33552483 0.000000e+00 1290
10 TraesCS3D01G405800 chr5D 97.573 4162 75 7 887 5044 520969817 520973956 0.000000e+00 7103
11 TraesCS3D01G405800 chr5D 97.481 794 19 1 1 793 520969013 520969806 0.000000e+00 1354
12 TraesCS3D01G405800 chr5D 81.204 681 120 8 1104 1780 504972467 504973143 4.440000e-150 542
13 TraesCS3D01G405800 chr5D 74.423 563 132 9 2964 3519 288116951 288117508 1.090000e-56 231
14 TraesCS3D01G405800 chr5D 78.788 231 45 3 2964 3192 504974424 504974652 8.750000e-33 152
15 TraesCS3D01G405800 chr3A 80.415 1399 224 38 1008 2388 608109951 608108585 0.000000e+00 1020
16 TraesCS3D01G405800 chr3A 75.085 2063 423 75 2458 4469 608108479 608106457 0.000000e+00 878
17 TraesCS3D01G405800 chr5A 85.513 780 107 5 1008 1784 234457883 234457107 0.000000e+00 809
18 TraesCS3D01G405800 chr2A 83.780 783 123 4 1007 1787 57921985 57921205 0.000000e+00 739
19 TraesCS3D01G405800 chrUn 97.674 387 8 1 1730 2115 480435609 480435995 0.000000e+00 664
20 TraesCS3D01G405800 chr4D 78.448 232 50 0 2964 3195 245840976 245840745 8.750000e-33 152


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 TraesCS3D01G405800 chr3D 520167834 520172877 5043 False 9315.000000 9315 100.0000 1 5044 1 chr3D.!!$F1 5043
1 TraesCS3D01G405800 chr3D 40533504 40538421 4917 False 4053.000000 6822 96.2065 1 5044 2 chr3D.!!$F2 5043
2 TraesCS3D01G405800 chr3D 584733711 584738638 4927 False 2759.666667 5334 96.9390 1 5043 3 chr3D.!!$F3 5042
3 TraesCS3D01G405800 chr1D 404218721 404223682 4961 True 4301.000000 7203 98.2105 1 5044 2 chr1D.!!$R1 5043
4 TraesCS3D01G405800 chr1D 33551695 33556646 4951 False 4152.000000 7014 96.6180 1 5044 2 chr1D.!!$F1 5043
5 TraesCS3D01G405800 chr5D 520969013 520973956 4943 False 4228.500000 7103 97.5270 1 5044 2 chr5D.!!$F3 5043
6 TraesCS3D01G405800 chr5D 504972467 504974652 2185 False 347.000000 542 79.9960 1104 3192 2 chr5D.!!$F2 2088
7 TraesCS3D01G405800 chr5D 288116951 288117508 557 False 231.000000 231 74.4230 2964 3519 1 chr5D.!!$F1 555
8 TraesCS3D01G405800 chr3A 608106457 608109951 3494 True 949.000000 1020 77.7500 1008 4469 2 chr3A.!!$R1 3461
9 TraesCS3D01G405800 chr5A 234457107 234457883 776 True 809.000000 809 85.5130 1008 1784 1 chr5A.!!$R1 776
10 TraesCS3D01G405800 chr2A 57921205 57921985 780 True 739.000000 739 83.7800 1007 1787 1 chr2A.!!$R1 780

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
807 809 0.107848 AAGCCCGCGTTAGCTGTAAT 60.108 50.000 15.08 0.0 39.87 1.89 F
809 811 0.730840 GCCCGCGTTAGCTGTAATTT 59.269 50.000 4.92 0.0 42.32 1.82 F
1121 1123 1.220477 GAAGAGCAGGCACCTCCTC 59.780 63.158 0.00 0.0 45.52 3.71 F
1479 1481 1.475280 GACGGGTGTGCATAGTCTACA 59.525 52.381 0.00 0.0 0.00 2.74 F
2075 2079 1.942657 GCAGCACGGATGACAACATAT 59.057 47.619 0.00 0.0 36.82 1.78 F
3283 3496 1.136305 GTCACTTAGGCCGCTCACATA 59.864 52.381 0.00 0.0 0.00 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2228 2256 0.742505 ATTGCCAGCATGTTGATCCG 59.257 50.000 11.60 0.0 0.00 4.18 R
2437 2484 1.066143 ACGCAGGAACGATTCAGGAAT 60.066 47.619 0.00 0.0 36.70 3.01 R
3049 3262 1.269831 GCAGACCGTCAGACTTCTGTT 60.270 52.381 21.65 0.0 44.12 3.16 R
3283 3496 7.362920 GGAAATTCCTGTAAATACACACATGCT 60.363 37.037 4.46 0.0 32.53 3.79 R
3635 3879 0.317269 CTGCCGCCGATAATGCTTTG 60.317 55.000 0.00 0.0 0.00 2.77 R
4532 4826 3.080300 TGCCCTCGGTTCACATATTTT 57.920 42.857 0.00 0.0 0.00 1.82 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
270 271 0.896940 CAGCAGCACTTCCCCAATGT 60.897 55.000 0.00 0.00 0.00 2.71
408 410 4.796110 ACCAGCCTCCATACATAATTGT 57.204 40.909 0.00 0.00 39.98 2.71
415 417 5.230942 CCTCCATACATAATTGTCGTCCTC 58.769 45.833 0.00 0.00 37.28 3.71
600 602 1.215382 CACTCTCGCATTCCGACCA 59.785 57.895 0.00 0.00 41.89 4.02
645 647 7.255569 CAGTCAATATACTAGGAACACGACAA 58.744 38.462 0.00 0.00 0.00 3.18
656 658 5.074115 AGGAACACGACAAATCCCAAAATA 58.926 37.500 0.00 0.00 32.15 1.40
786 788 4.967084 TTTACTCAACCTAGTGAAGCCA 57.033 40.909 0.00 0.00 0.00 4.75
793 795 1.490910 ACCTAGTGAAGCCATAAGCCC 59.509 52.381 0.00 0.00 45.47 5.19
794 796 1.541233 CCTAGTGAAGCCATAAGCCCG 60.541 57.143 0.00 0.00 45.47 6.13
795 797 0.179056 TAGTGAAGCCATAAGCCCGC 60.179 55.000 0.00 0.00 45.47 6.13
796 798 2.513666 TGAAGCCATAAGCCCGCG 60.514 61.111 0.00 0.00 45.47 6.46
797 799 2.513897 GAAGCCATAAGCCCGCGT 60.514 61.111 4.92 0.00 45.47 6.01
798 800 2.045340 AAGCCATAAGCCCGCGTT 60.045 55.556 4.92 0.00 45.47 4.84
799 801 0.812412 GAAGCCATAAGCCCGCGTTA 60.812 55.000 4.92 0.00 45.47 3.18
800 802 0.814010 AAGCCATAAGCCCGCGTTAG 60.814 55.000 4.92 0.00 45.47 2.34
801 803 2.893449 GCCATAAGCCCGCGTTAGC 61.893 63.158 4.92 4.96 36.11 3.09
804 806 0.810031 CATAAGCCCGCGTTAGCTGT 60.810 55.000 15.08 8.83 39.87 4.40
806 808 0.531657 TAAGCCCGCGTTAGCTGTAA 59.468 50.000 15.08 3.34 39.87 2.41
807 809 0.107848 AAGCCCGCGTTAGCTGTAAT 60.108 50.000 15.08 0.00 39.87 1.89
808 810 0.107848 AGCCCGCGTTAGCTGTAATT 60.108 50.000 13.83 0.00 42.32 1.40
809 811 0.730840 GCCCGCGTTAGCTGTAATTT 59.269 50.000 4.92 0.00 42.32 1.82
810 812 1.935199 GCCCGCGTTAGCTGTAATTTA 59.065 47.619 4.92 0.00 42.32 1.40
811 813 2.033151 GCCCGCGTTAGCTGTAATTTAG 60.033 50.000 4.92 0.00 42.32 1.85
812 814 2.033151 CCCGCGTTAGCTGTAATTTAGC 60.033 50.000 4.92 6.34 42.32 3.09
813 815 2.033151 CCGCGTTAGCTGTAATTTAGCC 60.033 50.000 4.92 0.00 42.07 3.93
814 816 2.033151 CGCGTTAGCTGTAATTTAGCCC 60.033 50.000 0.00 0.67 42.07 5.19
815 817 2.940410 GCGTTAGCTGTAATTTAGCCCA 59.060 45.455 0.00 0.00 42.07 5.36
816 818 3.564225 GCGTTAGCTGTAATTTAGCCCAT 59.436 43.478 0.00 0.00 42.07 4.00
817 819 4.036380 GCGTTAGCTGTAATTTAGCCCATT 59.964 41.667 0.00 0.00 42.07 3.16
818 820 5.237779 GCGTTAGCTGTAATTTAGCCCATTA 59.762 40.000 0.00 0.00 42.07 1.90
819 821 6.656003 CGTTAGCTGTAATTTAGCCCATTAC 58.344 40.000 0.00 4.15 42.07 1.89
820 822 6.482308 CGTTAGCTGTAATTTAGCCCATTACT 59.518 38.462 0.00 0.00 42.07 2.24
821 823 7.012044 CGTTAGCTGTAATTTAGCCCATTACTT 59.988 37.037 0.00 2.26 42.07 2.24
822 824 6.944234 AGCTGTAATTTAGCCCATTACTTC 57.056 37.500 9.89 4.32 42.07 3.01
823 825 6.423182 AGCTGTAATTTAGCCCATTACTTCA 58.577 36.000 9.89 0.00 42.07 3.02
824 826 7.062957 AGCTGTAATTTAGCCCATTACTTCAT 58.937 34.615 9.89 0.00 42.07 2.57
825 827 8.217799 AGCTGTAATTTAGCCCATTACTTCATA 58.782 33.333 9.89 0.00 42.07 2.15
826 828 8.290325 GCTGTAATTTAGCCCATTACTTCATAC 58.710 37.037 10.17 0.00 37.79 2.39
827 829 9.337396 CTGTAATTTAGCCCATTACTTCATACA 57.663 33.333 10.17 0.00 37.79 2.29
828 830 9.337396 TGTAATTTAGCCCATTACTTCATACAG 57.663 33.333 10.17 0.00 37.79 2.74
829 831 9.555727 GTAATTTAGCCCATTACTTCATACAGA 57.444 33.333 3.95 0.00 35.18 3.41
830 832 8.451908 AATTTAGCCCATTACTTCATACAGAC 57.548 34.615 0.00 0.00 0.00 3.51
831 833 6.553953 TTAGCCCATTACTTCATACAGACA 57.446 37.500 0.00 0.00 0.00 3.41
832 834 4.770795 AGCCCATTACTTCATACAGACAC 58.229 43.478 0.00 0.00 0.00 3.67
833 835 4.471386 AGCCCATTACTTCATACAGACACT 59.529 41.667 0.00 0.00 0.00 3.55
834 836 5.045578 AGCCCATTACTTCATACAGACACTT 60.046 40.000 0.00 0.00 0.00 3.16
835 837 5.648092 GCCCATTACTTCATACAGACACTTT 59.352 40.000 0.00 0.00 0.00 2.66
836 838 6.151144 GCCCATTACTTCATACAGACACTTTT 59.849 38.462 0.00 0.00 0.00 2.27
837 839 7.335924 GCCCATTACTTCATACAGACACTTTTA 59.664 37.037 0.00 0.00 0.00 1.52
838 840 8.883731 CCCATTACTTCATACAGACACTTTTAG 58.116 37.037 0.00 0.00 0.00 1.85
839 841 9.653287 CCATTACTTCATACAGACACTTTTAGA 57.347 33.333 0.00 0.00 0.00 2.10
844 846 9.694137 ACTTCATACAGACACTTTTAGAAGTAC 57.306 33.333 0.00 0.00 44.14 2.73
845 847 9.915629 CTTCATACAGACACTTTTAGAAGTACT 57.084 33.333 0.00 0.00 44.14 2.73
846 848 9.909644 TTCATACAGACACTTTTAGAAGTACTC 57.090 33.333 0.00 0.00 44.14 2.59
847 849 9.074576 TCATACAGACACTTTTAGAAGTACTCA 57.925 33.333 0.00 0.00 44.14 3.41
848 850 9.692749 CATACAGACACTTTTAGAAGTACTCAA 57.307 33.333 0.00 0.00 44.14 3.02
851 853 9.614792 ACAGACACTTTTAGAAGTACTCAAATT 57.385 29.630 0.00 0.00 44.14 1.82
853 855 9.832445 AGACACTTTTAGAAGTACTCAAATTCA 57.168 29.630 0.00 0.00 44.14 2.57
869 871 7.490962 TCAAATTCATTGAACTACAGAACGT 57.509 32.000 0.15 0.00 44.94 3.99
870 872 7.572759 TCAAATTCATTGAACTACAGAACGTC 58.427 34.615 0.15 0.00 44.94 4.34
871 873 7.225734 TCAAATTCATTGAACTACAGAACGTCA 59.774 33.333 0.15 0.00 44.94 4.35
872 874 6.712241 ATTCATTGAACTACAGAACGTCAG 57.288 37.500 0.15 0.00 0.00 3.51
873 875 3.987868 TCATTGAACTACAGAACGTCAGC 59.012 43.478 0.00 0.00 0.00 4.26
874 876 2.046283 TGAACTACAGAACGTCAGCG 57.954 50.000 0.00 0.00 44.93 5.18
884 886 4.778415 CGTCAGCGTCGTCCAGGG 62.778 72.222 0.00 0.00 0.00 4.45
885 887 3.371063 GTCAGCGTCGTCCAGGGA 61.371 66.667 0.00 0.00 0.00 4.20
886 888 3.062466 TCAGCGTCGTCCAGGGAG 61.062 66.667 0.00 0.00 0.00 4.30
887 889 3.062466 CAGCGTCGTCCAGGGAGA 61.062 66.667 0.00 0.00 0.00 3.71
888 890 2.282958 AGCGTCGTCCAGGGAGAA 60.283 61.111 0.00 0.00 0.00 2.87
889 891 1.682684 AGCGTCGTCCAGGGAGAAT 60.683 57.895 0.00 0.00 0.00 2.40
1121 1123 1.220477 GAAGAGCAGGCACCTCCTC 59.780 63.158 0.00 0.00 45.52 3.71
1479 1481 1.475280 GACGGGTGTGCATAGTCTACA 59.525 52.381 0.00 0.00 0.00 2.74
1837 1839 2.508867 CACCGAAATCTGTCATTTGCG 58.491 47.619 0.00 0.00 0.00 4.85
1973 1977 3.309682 CACGCATTAGTGATTTCGACCAT 59.690 43.478 0.00 0.00 44.43 3.55
2002 2006 4.512944 CCTGAAGAACATGATAACGATGGG 59.487 45.833 0.00 0.00 0.00 4.00
2062 2066 2.252747 CATGGTAAACATTGCAGCACG 58.747 47.619 0.00 0.00 37.84 5.34
2075 2079 1.942657 GCAGCACGGATGACAACATAT 59.057 47.619 0.00 0.00 36.82 1.78
2193 2221 3.611530 GCAACATACCTGATTGCAACGTT 60.612 43.478 0.00 0.00 46.37 3.99
2333 2379 2.901249 ACAGACACCAATACGTATGCC 58.099 47.619 9.24 0.00 0.00 4.40
3254 3467 2.922335 GCCGTTTGTCATCTTTTCCTGC 60.922 50.000 0.00 0.00 0.00 4.85
3283 3496 1.136305 GTCACTTAGGCCGCTCACATA 59.864 52.381 0.00 0.00 0.00 2.29
3635 3879 3.005897 ACATCCATACGCTGTCTATCCAC 59.994 47.826 0.00 0.00 0.00 4.02
3647 3891 5.333645 GCTGTCTATCCACAAAGCATTATCG 60.334 44.000 0.00 0.00 0.00 2.92
3653 3897 1.029408 ACAAAGCATTATCGGCGGCA 61.029 50.000 10.53 0.00 36.08 5.69
3906 4160 5.119279 CACAACACAGAGACGAGATTTTAGG 59.881 44.000 0.00 0.00 0.00 2.69
3924 4178 2.551270 AGGTTGGAAGCTACATGGAGA 58.449 47.619 9.87 0.00 34.49 3.71
4044 4298 4.248058 CGGTATAGTTTTCAACCTCCGTT 58.752 43.478 0.00 0.00 0.00 4.44
4532 4826 6.667848 TGACCTTCATCTTAATCACCAGTAGA 59.332 38.462 0.00 0.00 0.00 2.59
4565 4859 2.579873 CGAGGGCATCATTTTCATCCT 58.420 47.619 0.00 0.00 0.00 3.24
4714 5008 3.423539 TTTTAGCTGCATCTGAGGTGT 57.576 42.857 1.02 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
270 271 1.118356 AATGGCAGCGTGGGGAAAAA 61.118 50.000 0.00 0.00 0.00 1.94
408 410 1.000359 TGGCCTGAGATGAGGACGA 60.000 57.895 3.32 0.00 45.44 4.20
584 586 0.389817 TTGTGGTCGGAATGCGAGAG 60.390 55.000 0.00 0.00 0.00 3.20
600 602 2.225242 TGGCTAATGGGTGGATTGTTGT 60.225 45.455 0.00 0.00 0.00 3.32
645 647 5.155035 TGTGGGATCCATATTTTGGGATT 57.845 39.130 15.23 0.00 46.45 3.01
656 658 6.324770 GGAATAGAACAAATTGTGGGATCCAT 59.675 38.462 15.23 0.00 35.28 3.41
786 788 0.748450 TACAGCTAACGCGGGCTTAT 59.252 50.000 18.00 12.81 42.32 1.73
793 795 2.033151 GGGCTAAATTACAGCTAACGCG 60.033 50.000 3.53 3.53 42.32 6.01
794 796 2.940410 TGGGCTAAATTACAGCTAACGC 59.060 45.455 10.76 0.00 39.09 4.84
795 797 5.751243 AATGGGCTAAATTACAGCTAACG 57.249 39.130 10.76 0.00 39.09 3.18
796 798 7.803279 AGTAATGGGCTAAATTACAGCTAAC 57.197 36.000 15.51 4.36 41.13 2.34
797 799 8.050325 TGAAGTAATGGGCTAAATTACAGCTAA 58.950 33.333 15.51 2.21 41.13 3.09
798 800 7.570132 TGAAGTAATGGGCTAAATTACAGCTA 58.430 34.615 15.51 3.13 41.13 3.32
799 801 6.423182 TGAAGTAATGGGCTAAATTACAGCT 58.577 36.000 15.51 0.00 41.13 4.24
800 802 6.693315 TGAAGTAATGGGCTAAATTACAGC 57.307 37.500 15.51 3.84 41.13 4.40
801 803 9.337396 TGTATGAAGTAATGGGCTAAATTACAG 57.663 33.333 15.51 0.00 41.13 2.74
804 806 9.555727 GTCTGTATGAAGTAATGGGCTAAATTA 57.444 33.333 0.00 0.00 0.00 1.40
806 808 7.499232 GTGTCTGTATGAAGTAATGGGCTAAAT 59.501 37.037 0.00 0.00 0.00 1.40
807 809 6.821665 GTGTCTGTATGAAGTAATGGGCTAAA 59.178 38.462 0.00 0.00 0.00 1.85
808 810 6.156256 AGTGTCTGTATGAAGTAATGGGCTAA 59.844 38.462 0.00 0.00 0.00 3.09
809 811 5.661312 AGTGTCTGTATGAAGTAATGGGCTA 59.339 40.000 0.00 0.00 0.00 3.93
810 812 4.471386 AGTGTCTGTATGAAGTAATGGGCT 59.529 41.667 0.00 0.00 0.00 5.19
811 813 4.770795 AGTGTCTGTATGAAGTAATGGGC 58.229 43.478 0.00 0.00 0.00 5.36
812 814 7.687941 AAAAGTGTCTGTATGAAGTAATGGG 57.312 36.000 0.00 0.00 0.00 4.00
813 815 9.653287 TCTAAAAGTGTCTGTATGAAGTAATGG 57.347 33.333 0.00 0.00 0.00 3.16
818 820 9.694137 GTACTTCTAAAAGTGTCTGTATGAAGT 57.306 33.333 0.00 0.00 45.37 3.01
819 821 9.915629 AGTACTTCTAAAAGTGTCTGTATGAAG 57.084 33.333 1.17 0.00 45.37 3.02
820 822 9.909644 GAGTACTTCTAAAAGTGTCTGTATGAA 57.090 33.333 0.00 0.00 45.37 2.57
821 823 9.074576 TGAGTACTTCTAAAAGTGTCTGTATGA 57.925 33.333 0.00 0.00 45.37 2.15
822 824 9.692749 TTGAGTACTTCTAAAAGTGTCTGTATG 57.307 33.333 0.00 0.00 45.37 2.39
825 827 9.614792 AATTTGAGTACTTCTAAAAGTGTCTGT 57.385 29.630 0.00 0.00 45.37 3.41
827 829 9.832445 TGAATTTGAGTACTTCTAAAAGTGTCT 57.168 29.630 0.00 0.54 45.37 3.41
837 839 9.778741 TGTAGTTCAATGAATTTGAGTACTTCT 57.221 29.630 0.00 0.00 44.90 2.85
839 841 9.778741 TCTGTAGTTCAATGAATTTGAGTACTT 57.221 29.630 0.00 0.00 44.90 2.24
840 842 9.778741 TTCTGTAGTTCAATGAATTTGAGTACT 57.221 29.630 0.00 0.00 44.90 2.73
841 843 9.813080 GTTCTGTAGTTCAATGAATTTGAGTAC 57.187 33.333 0.00 0.00 44.90 2.73
842 844 8.708742 CGTTCTGTAGTTCAATGAATTTGAGTA 58.291 33.333 0.00 0.00 44.90 2.59
843 845 7.226720 ACGTTCTGTAGTTCAATGAATTTGAGT 59.773 33.333 0.00 0.00 44.90 3.41
844 846 7.576236 ACGTTCTGTAGTTCAATGAATTTGAG 58.424 34.615 0.00 0.00 44.90 3.02
845 847 7.225734 TGACGTTCTGTAGTTCAATGAATTTGA 59.774 33.333 0.00 0.00 42.62 2.69
846 848 7.351981 TGACGTTCTGTAGTTCAATGAATTTG 58.648 34.615 0.00 0.00 36.61 2.32
847 849 7.490962 TGACGTTCTGTAGTTCAATGAATTT 57.509 32.000 0.00 0.00 0.00 1.82
848 850 6.347725 GCTGACGTTCTGTAGTTCAATGAATT 60.348 38.462 0.00 0.00 0.00 2.17
849 851 5.120830 GCTGACGTTCTGTAGTTCAATGAAT 59.879 40.000 0.00 0.00 0.00 2.57
850 852 4.447724 GCTGACGTTCTGTAGTTCAATGAA 59.552 41.667 0.00 0.00 0.00 2.57
851 853 3.987868 GCTGACGTTCTGTAGTTCAATGA 59.012 43.478 0.00 0.00 0.00 2.57
852 854 3.181540 CGCTGACGTTCTGTAGTTCAATG 60.182 47.826 0.00 0.00 33.53 2.82
853 855 2.987149 CGCTGACGTTCTGTAGTTCAAT 59.013 45.455 0.00 0.00 33.53 2.57
854 856 2.390938 CGCTGACGTTCTGTAGTTCAA 58.609 47.619 0.00 0.00 33.53 2.69
855 857 2.046283 CGCTGACGTTCTGTAGTTCA 57.954 50.000 0.00 0.00 33.53 3.18
868 870 3.343788 CTCCCTGGACGACGCTGAC 62.344 68.421 0.00 0.00 0.00 3.51
869 871 3.062466 CTCCCTGGACGACGCTGA 61.062 66.667 0.00 0.00 0.00 4.26
870 872 1.949847 ATTCTCCCTGGACGACGCTG 61.950 60.000 0.00 0.00 0.00 5.18
871 873 1.682684 ATTCTCCCTGGACGACGCT 60.683 57.895 0.00 0.00 0.00 5.07
872 874 1.519455 CATTCTCCCTGGACGACGC 60.519 63.158 0.00 0.00 0.00 5.19
873 875 0.179134 GACATTCTCCCTGGACGACG 60.179 60.000 0.00 0.00 0.00 5.12
874 876 0.895530 TGACATTCTCCCTGGACGAC 59.104 55.000 0.00 0.00 0.00 4.34
875 877 1.866015 ATGACATTCTCCCTGGACGA 58.134 50.000 0.00 0.00 0.00 4.20
876 878 2.698855 AATGACATTCTCCCTGGACG 57.301 50.000 0.00 0.00 0.00 4.79
877 879 3.871594 CGTAAATGACATTCTCCCTGGAC 59.128 47.826 0.05 0.00 0.00 4.02
878 880 3.118408 CCGTAAATGACATTCTCCCTGGA 60.118 47.826 0.05 0.00 0.00 3.86
879 881 3.206150 CCGTAAATGACATTCTCCCTGG 58.794 50.000 0.05 0.00 0.00 4.45
880 882 3.871594 GACCGTAAATGACATTCTCCCTG 59.128 47.826 0.05 0.00 0.00 4.45
881 883 3.430374 CGACCGTAAATGACATTCTCCCT 60.430 47.826 0.05 0.00 0.00 4.20
882 884 2.864343 CGACCGTAAATGACATTCTCCC 59.136 50.000 0.05 0.00 0.00 4.30
883 885 3.777478 TCGACCGTAAATGACATTCTCC 58.223 45.455 0.05 0.00 0.00 3.71
884 886 5.968387 AATCGACCGTAAATGACATTCTC 57.032 39.130 0.05 0.00 0.00 2.87
885 887 5.005394 CGAAATCGACCGTAAATGACATTCT 59.995 40.000 0.05 0.00 43.02 2.40
886 888 5.188194 CGAAATCGACCGTAAATGACATTC 58.812 41.667 0.05 0.00 43.02 2.67
887 889 4.628333 ACGAAATCGACCGTAAATGACATT 59.372 37.500 10.16 0.00 43.02 2.71
888 890 4.178540 ACGAAATCGACCGTAAATGACAT 58.821 39.130 10.16 0.00 43.02 3.06
889 891 3.577667 ACGAAATCGACCGTAAATGACA 58.422 40.909 10.16 0.00 43.02 3.58
940 942 3.064931 GTTTGCGGATATAGTGCCTACC 58.935 50.000 0.00 0.00 0.00 3.18
1097 1099 0.543749 GGTGCCTGCTCTTCCATAGT 59.456 55.000 0.00 0.00 0.00 2.12
1121 1123 4.256920 ACTGAAATTCGAGATGTTGGAGG 58.743 43.478 0.00 0.00 0.00 4.30
1422 1424 4.759782 CGTCCTCTTTATGAAGGTCACAT 58.240 43.478 0.00 0.00 33.56 3.21
1479 1481 2.125106 GGAATTCCTCAGCCGCGT 60.125 61.111 17.73 0.00 0.00 6.01
1837 1839 4.887071 TGGGAATGAGCATGTACCATAAAC 59.113 41.667 0.00 0.00 0.00 2.01
1973 1977 7.722363 TCGTTATCATGTTCTTCAGGCTATTA 58.278 34.615 0.00 0.00 0.00 0.98
2002 2006 1.598701 GCCCTTCCCAATGTCAGTGC 61.599 60.000 0.00 0.00 0.00 4.40
2193 2221 1.423541 ACTGGCTGGTTGGATGTTGTA 59.576 47.619 0.00 0.00 0.00 2.41
2228 2256 0.742505 ATTGCCAGCATGTTGATCCG 59.257 50.000 11.60 0.00 0.00 4.18
2333 2379 5.163513 GCTGTACAAAATCAATTGGTCCAG 58.836 41.667 5.42 3.12 34.56 3.86
2427 2474 2.816087 CGATTCAGGAATAAGGGGCATG 59.184 50.000 0.00 0.00 0.00 4.06
2429 2476 1.843851 ACGATTCAGGAATAAGGGGCA 59.156 47.619 0.00 0.00 0.00 5.36
2431 2478 3.136626 AGGAACGATTCAGGAATAAGGGG 59.863 47.826 0.00 0.00 0.00 4.79
2432 2479 4.130118 CAGGAACGATTCAGGAATAAGGG 58.870 47.826 0.00 0.00 0.00 3.95
2437 2484 1.066143 ACGCAGGAACGATTCAGGAAT 60.066 47.619 0.00 0.00 36.70 3.01
3049 3262 1.269831 GCAGACCGTCAGACTTCTGTT 60.270 52.381 21.65 0.00 44.12 3.16
3283 3496 7.362920 GGAAATTCCTGTAAATACACACATGCT 60.363 37.037 4.46 0.00 32.53 3.79
3635 3879 0.317269 CTGCCGCCGATAATGCTTTG 60.317 55.000 0.00 0.00 0.00 2.77
3647 3891 2.491022 ATACTCGAGTCCTGCCGCC 61.491 63.158 23.89 0.00 0.00 6.13
3653 3897 3.621558 TGTGATGTCATACTCGAGTCCT 58.378 45.455 23.89 8.14 0.00 3.85
3906 4160 3.686726 CAGTTCTCCATGTAGCTTCCAAC 59.313 47.826 0.00 0.00 0.00 3.77
4044 4298 2.387757 GCATAGGGGCATCCAGAAAAA 58.612 47.619 0.00 0.00 38.24 1.94
4487 4781 3.197766 TCACATACTTTCAGGTGGCTAGG 59.802 47.826 0.00 0.00 32.29 3.02
4532 4826 3.080300 TGCCCTCGGTTCACATATTTT 57.920 42.857 0.00 0.00 0.00 1.82
4714 5008 4.022416 GTGTGAAGTTGGGCATGTCATTTA 60.022 41.667 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.