Multiple sequence alignment - TraesCS5B01G124000

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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 TraesCS5B01G124000 chr5B 100.000 2822 0 0 1 2822 223648993 223646172 0.000000e+00 5212
1 TraesCS5B01G124000 chr5A 95.884 2551 96 8 1 2546 271497328 271494782 0.000000e+00 4120
2 TraesCS5B01G124000 chr5A 86.471 170 19 4 2517 2683 271494757 271494589 1.730000e-42 183
3 TraesCS5B01G124000 chr5D 96.667 1980 52 4 718 2683 210057882 210055903 0.000000e+00 3278
4 TraesCS5B01G124000 chr5D 95.720 701 24 3 1 700 210058672 210057977 0.000000e+00 1123
5 TraesCS5B01G124000 chr5D 90.972 144 12 1 2680 2822 554400751 554400608 2.870000e-45 193
6 TraesCS5B01G124000 chr1B 79.195 894 170 14 733 1614 679749273 679748384 8.650000e-170 606
7 TraesCS5B01G124000 chr1A 78.499 893 178 12 733 1614 586954097 586953208 8.770000e-160 573
8 TraesCS5B01G124000 chr1A 89.933 149 14 1 2675 2822 8599876 8600024 1.030000e-44 191
9 TraesCS5B01G124000 chr1D 82.031 640 110 5 978 1614 487953021 487952384 8.890000e-150 540
10 TraesCS5B01G124000 chr7B 91.837 147 10 2 2678 2822 701324334 701324480 1.330000e-48 204
11 TraesCS5B01G124000 chr3D 91.837 147 11 1 2677 2822 279675001 279674855 1.330000e-48 204
12 TraesCS5B01G124000 chr3B 91.892 148 9 2 2677 2822 259369661 259369515 1.330000e-48 204
13 TraesCS5B01G124000 chr2D 90.541 148 12 2 2677 2822 313718400 313718547 7.980000e-46 195
14 TraesCS5B01G124000 chr7D 90.541 148 11 3 2677 2822 440589315 440589461 2.870000e-45 193
15 TraesCS5B01G124000 chr7D 90.476 147 12 2 2677 2822 500978954 500979099 2.870000e-45 193
16 TraesCS5B01G124000 chr6B 89.865 148 14 1 2676 2822 647952932 647952785 3.710000e-44 189


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 TraesCS5B01G124000 chr5B 223646172 223648993 2821 True 5212.0 5212 100.0000 1 2822 1 chr5B.!!$R1 2821
1 TraesCS5B01G124000 chr5A 271494589 271497328 2739 True 2151.5 4120 91.1775 1 2683 2 chr5A.!!$R1 2682
2 TraesCS5B01G124000 chr5D 210055903 210058672 2769 True 2200.5 3278 96.1935 1 2683 2 chr5D.!!$R2 2682
3 TraesCS5B01G124000 chr1B 679748384 679749273 889 True 606.0 606 79.1950 733 1614 1 chr1B.!!$R1 881
4 TraesCS5B01G124000 chr1A 586953208 586954097 889 True 573.0 573 78.4990 733 1614 1 chr1A.!!$R1 881
5 TraesCS5B01G124000 chr1D 487952384 487953021 637 True 540.0 540 82.0310 978 1614 1 chr1D.!!$R1 636

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
175 176 0.032017 ATAGGAGAGCACCCTTCGGT 60.032 55.0 0.0 0.0 46.31 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1884 1977 0.039708 GTTGTTCTGCAAGCTCCAGC 60.04 55.0 8.97 4.44 37.83 4.85 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
157 158 1.285962 CCCTGACCCCATTCAGTTGAT 59.714 52.381 0.00 0.00 41.40 2.57
175 176 0.032017 ATAGGAGAGCACCCTTCGGT 60.032 55.000 0.00 0.00 46.31 4.69
176 177 0.627451 TAGGAGAGCACCCTTCGGTA 59.373 55.000 0.00 0.00 42.04 4.02
212 213 9.173939 GAATTTGTTCAGATAGTGACTTGTTTG 57.826 33.333 0.00 0.00 33.71 2.93
219 220 6.318648 TCAGATAGTGACTTGTTTGTTTTGCT 59.681 34.615 0.00 0.00 0.00 3.91
247 248 4.324874 CCTTCTCTGAAACCTGAATCCCAT 60.325 45.833 0.00 0.00 0.00 4.00
317 318 9.646427 TCTACTTCAAATTCTTCTTTAGCTCTC 57.354 33.333 0.00 0.00 0.00 3.20
331 332 9.654663 TTCTTTAGCTCTCCTATTTGTTAGTTC 57.345 33.333 0.00 0.00 0.00 3.01
338 339 5.092554 TCCTATTTGTTAGTTCGATGCCA 57.907 39.130 0.00 0.00 0.00 4.92
351 353 5.647658 AGTTCGATGCCATTCACTGATTAAA 59.352 36.000 0.00 0.00 0.00 1.52
375 377 4.650734 TCTTTACATCATGTTGCTGGTCA 58.349 39.130 0.00 0.00 0.00 4.02
399 401 9.515226 TCATTTAGGCAGTTTCACTTAAGTATT 57.485 29.630 8.04 0.00 0.00 1.89
407 409 8.770828 GCAGTTTCACTTAAGTATTGAGTTGTA 58.229 33.333 8.04 0.00 42.85 2.41
409 411 8.975439 AGTTTCACTTAAGTATTGAGTTGTACG 58.025 33.333 8.04 0.00 42.85 3.67
412 414 7.819644 TCACTTAAGTATTGAGTTGTACGCTA 58.180 34.615 8.04 0.00 42.85 4.26
416 418 8.991243 TTAAGTATTGAGTTGTACGCTAATGT 57.009 30.769 0.00 0.00 0.00 2.71
522 524 4.527038 TCAAATCTAGGACGGTCTCAGTTT 59.473 41.667 8.23 4.50 0.00 2.66
572 574 0.250124 TCTGTGTGTTTACGGGCAGG 60.250 55.000 0.00 0.00 0.00 4.85
909 994 4.269183 CATGCCTATGAACCAGGTTACAA 58.731 43.478 4.25 0.00 36.36 2.41
1075 1168 1.823250 GCAAGGGAAAGAAGGGCTCAA 60.823 52.381 0.00 0.00 0.00 3.02
1098 1191 2.109126 GCAGCGGATGAAGTGGACC 61.109 63.158 0.00 0.00 0.00 4.46
1120 1213 6.852664 ACCGATTCAATGGTTAAGCTTTTAG 58.147 36.000 3.20 0.00 33.81 1.85
1334 1427 2.563179 CAGATATCCTTGGTCGGGGTAG 59.437 54.545 0.00 0.00 0.00 3.18
1418 1511 3.067106 TGAAAGATGACGCAAGGAAGAC 58.933 45.455 0.00 0.00 46.39 3.01
1555 1648 6.420008 GTGCAAAGAGGAAAATGATATGATGC 59.580 38.462 0.00 0.00 0.00 3.91
1708 1801 1.339291 CAGCAGATCACGAGGATGCTA 59.661 52.381 3.35 0.00 34.12 3.49
1750 1843 0.968901 ACACGAATGTAGCCGGAGGA 60.969 55.000 5.05 0.00 45.94 3.71
1783 1876 4.546570 TGGAATCGCACTAGATATCAACG 58.453 43.478 5.32 1.39 0.00 4.10
1819 1912 1.537202 GAACGAGCTTGGCTTTGACAT 59.463 47.619 5.79 0.00 39.88 3.06
1860 1953 4.924305 ATCTGCAGAGCTTGAAAAACAA 57.076 36.364 22.96 0.00 36.97 2.83
1873 1966 7.281549 AGCTTGAAAAACAATGCTTGAAAATCT 59.718 29.630 3.37 0.00 38.66 2.40
1884 1977 5.401550 TGCTTGAAAATCTAAAATGAGGCG 58.598 37.500 0.00 0.00 0.00 5.52
2157 2250 3.476552 CCTTCTAGTTCACTGGTGCAAA 58.523 45.455 0.00 0.00 0.00 3.68
2370 2463 5.119931 TGCATCATTAGTTTTTCGCAAGT 57.880 34.783 0.00 0.00 39.48 3.16
2556 2707 1.930914 TCCTCTGTCTAACCCTAGCCT 59.069 52.381 0.00 0.00 0.00 4.58
2567 2718 2.409570 ACCCTAGCCTAACATCCCTTC 58.590 52.381 0.00 0.00 0.00 3.46
2568 2719 2.293586 ACCCTAGCCTAACATCCCTTCA 60.294 50.000 0.00 0.00 0.00 3.02
2599 2750 1.680651 CCCCAAATTGGTGCCGCTA 60.681 57.895 11.52 0.00 35.17 4.26
2604 2755 2.356135 CAAATTGGTGCCGCTACTACT 58.644 47.619 0.00 0.00 0.00 2.57
2617 2768 2.099263 GCTACTACTTGCATGTCCTCGA 59.901 50.000 8.74 0.00 0.00 4.04
2626 2777 1.454111 ATGTCCTCGACTAGCCGCT 60.454 57.895 0.00 0.00 33.15 5.52
2644 2795 2.996621 CGCTGCTTAGTTTCTGCTTAGT 59.003 45.455 0.00 0.00 0.00 2.24
2655 2806 3.508840 GCTTAGTTGGCGCCGCAT 61.509 61.111 23.90 12.33 0.00 4.73
2672 2823 0.460284 CATCCCTGAGTGTACGCCAC 60.460 60.000 1.98 0.00 44.89 5.01
2683 2834 3.072486 TACGCCACGCTCTTAGGCC 62.072 63.158 0.00 0.00 45.56 5.19
2685 2836 4.858680 GCCACGCTCTTAGGCCCC 62.859 72.222 0.00 0.00 42.58 5.80
2686 2837 3.083997 CCACGCTCTTAGGCCCCT 61.084 66.667 0.00 0.00 0.00 4.79
2687 2838 2.501610 CACGCTCTTAGGCCCCTC 59.498 66.667 0.00 0.00 0.00 4.30
2688 2839 2.764547 ACGCTCTTAGGCCCCTCC 60.765 66.667 0.00 0.00 0.00 4.30
2689 2840 3.551407 CGCTCTTAGGCCCCTCCC 61.551 72.222 0.00 0.00 34.51 4.30
2690 2841 2.366972 GCTCTTAGGCCCCTCCCA 60.367 66.667 0.00 0.00 34.51 4.37
2691 2842 2.447714 GCTCTTAGGCCCCTCCCAG 61.448 68.421 0.00 0.00 34.51 4.45
2692 2843 1.003573 CTCTTAGGCCCCTCCCAGT 59.996 63.158 0.00 0.00 34.51 4.00
2693 2844 1.306997 TCTTAGGCCCCTCCCAGTG 60.307 63.158 0.00 0.00 34.51 3.66
2694 2845 3.015145 TTAGGCCCCTCCCAGTGC 61.015 66.667 0.00 0.00 34.51 4.40
2695 2846 3.579451 TTAGGCCCCTCCCAGTGCT 62.579 63.158 0.00 0.00 34.51 4.40
2699 2850 3.721706 CCCCTCCCAGTGCTCCAC 61.722 72.222 0.00 0.00 34.10 4.02
2700 2851 2.930019 CCCTCCCAGTGCTCCACA 60.930 66.667 0.00 0.00 36.74 4.17
2701 2852 2.304056 CCCTCCCAGTGCTCCACAT 61.304 63.158 0.00 0.00 36.74 3.21
2702 2853 1.687612 CCTCCCAGTGCTCCACATT 59.312 57.895 0.00 0.00 36.74 2.71
2703 2854 0.679002 CCTCCCAGTGCTCCACATTG 60.679 60.000 0.00 0.00 36.74 2.82
2704 2855 0.037303 CTCCCAGTGCTCCACATTGT 59.963 55.000 0.00 0.00 36.74 2.71
2705 2856 1.278985 CTCCCAGTGCTCCACATTGTA 59.721 52.381 0.00 0.00 36.74 2.41
2706 2857 1.003118 TCCCAGTGCTCCACATTGTAC 59.997 52.381 0.00 0.00 36.74 2.90
2707 2858 1.271325 CCCAGTGCTCCACATTGTACA 60.271 52.381 0.00 0.00 36.74 2.90
2708 2859 2.079158 CCAGTGCTCCACATTGTACAG 58.921 52.381 0.00 0.00 36.74 2.74
2709 2860 2.079158 CAGTGCTCCACATTGTACAGG 58.921 52.381 0.00 0.00 36.74 4.00
2710 2861 1.699634 AGTGCTCCACATTGTACAGGT 59.300 47.619 0.00 0.00 36.74 4.00
2711 2862 1.806542 GTGCTCCACATTGTACAGGTG 59.193 52.381 17.99 17.99 34.08 4.00
2712 2863 1.419762 TGCTCCACATTGTACAGGTGT 59.580 47.619 21.23 15.92 0.00 4.16
2713 2864 2.158682 TGCTCCACATTGTACAGGTGTT 60.159 45.455 21.23 5.01 0.00 3.32
2714 2865 3.071747 TGCTCCACATTGTACAGGTGTTA 59.928 43.478 21.23 12.27 0.00 2.41
2715 2866 4.069304 GCTCCACATTGTACAGGTGTTAA 58.931 43.478 21.23 9.92 0.00 2.01
2716 2867 4.154195 GCTCCACATTGTACAGGTGTTAAG 59.846 45.833 21.23 16.63 0.00 1.85
2717 2868 4.069304 TCCACATTGTACAGGTGTTAAGC 58.931 43.478 21.23 0.00 0.00 3.09
2718 2869 3.190535 CCACATTGTACAGGTGTTAAGCC 59.809 47.826 21.23 0.00 0.00 4.35
2719 2870 4.072131 CACATTGTACAGGTGTTAAGCCT 58.928 43.478 17.12 0.00 36.66 4.58
2720 2871 4.518970 CACATTGTACAGGTGTTAAGCCTT 59.481 41.667 17.12 0.00 33.31 4.35
2721 2872 5.009610 CACATTGTACAGGTGTTAAGCCTTT 59.990 40.000 17.12 0.00 33.31 3.11
2722 2873 5.240844 ACATTGTACAGGTGTTAAGCCTTTC 59.759 40.000 9.44 0.00 33.31 2.62
2723 2874 4.425180 TGTACAGGTGTTAAGCCTTTCA 57.575 40.909 0.00 0.00 33.31 2.69
2724 2875 4.131596 TGTACAGGTGTTAAGCCTTTCAC 58.868 43.478 0.00 4.58 33.31 3.18
2725 2876 2.218603 ACAGGTGTTAAGCCTTTCACG 58.781 47.619 6.45 0.00 33.31 4.35
2726 2877 2.218603 CAGGTGTTAAGCCTTTCACGT 58.781 47.619 6.45 4.83 33.31 4.49
2727 2878 3.181463 ACAGGTGTTAAGCCTTTCACGTA 60.181 43.478 0.00 0.00 33.31 3.57
2728 2879 3.432252 CAGGTGTTAAGCCTTTCACGTAG 59.568 47.826 0.00 0.00 33.31 3.51
2729 2880 2.740447 GGTGTTAAGCCTTTCACGTAGG 59.260 50.000 0.00 0.00 35.80 3.18
2758 2909 9.995003 AAAAATCTGATGTGGCAAGTTATTTAA 57.005 25.926 0.00 0.00 0.00 1.52
2759 2910 9.995003 AAAATCTGATGTGGCAAGTTATTTAAA 57.005 25.926 0.00 0.00 0.00 1.52
2760 2911 9.995003 AAATCTGATGTGGCAAGTTATTTAAAA 57.005 25.926 0.00 0.00 0.00 1.52
2761 2912 9.643693 AATCTGATGTGGCAAGTTATTTAAAAG 57.356 29.630 0.00 0.00 0.00 2.27
2762 2913 7.601856 TCTGATGTGGCAAGTTATTTAAAAGG 58.398 34.615 0.00 0.00 0.00 3.11
2763 2914 7.450014 TCTGATGTGGCAAGTTATTTAAAAGGA 59.550 33.333 0.00 0.00 0.00 3.36
2764 2915 7.601856 TGATGTGGCAAGTTATTTAAAAGGAG 58.398 34.615 0.00 0.00 0.00 3.69
2765 2916 7.450014 TGATGTGGCAAGTTATTTAAAAGGAGA 59.550 33.333 0.00 0.00 0.00 3.71
2766 2917 7.214467 TGTGGCAAGTTATTTAAAAGGAGAG 57.786 36.000 0.00 0.00 0.00 3.20
2767 2918 7.001674 TGTGGCAAGTTATTTAAAAGGAGAGA 58.998 34.615 0.00 0.00 0.00 3.10
2768 2919 7.504238 TGTGGCAAGTTATTTAAAAGGAGAGAA 59.496 33.333 0.00 0.00 0.00 2.87
2769 2920 8.357402 GTGGCAAGTTATTTAAAAGGAGAGAAA 58.643 33.333 0.00 0.00 0.00 2.52
2770 2921 9.088987 TGGCAAGTTATTTAAAAGGAGAGAAAT 57.911 29.630 0.00 0.00 0.00 2.17
2771 2922 9.358872 GGCAAGTTATTTAAAAGGAGAGAAATG 57.641 33.333 0.00 0.00 0.00 2.32
2778 2929 7.510549 TTTAAAAGGAGAGAAATGAGTGTGG 57.489 36.000 0.00 0.00 0.00 4.17
2779 2930 4.713792 AAAGGAGAGAAATGAGTGTGGT 57.286 40.909 0.00 0.00 0.00 4.16
2780 2931 3.692257 AGGAGAGAAATGAGTGTGGTG 57.308 47.619 0.00 0.00 0.00 4.17
2781 2932 3.242867 AGGAGAGAAATGAGTGTGGTGA 58.757 45.455 0.00 0.00 0.00 4.02
2782 2933 3.843027 AGGAGAGAAATGAGTGTGGTGAT 59.157 43.478 0.00 0.00 0.00 3.06
2783 2934 4.081198 AGGAGAGAAATGAGTGTGGTGATC 60.081 45.833 0.00 0.00 0.00 2.92
2784 2935 4.187694 GAGAGAAATGAGTGTGGTGATCC 58.812 47.826 0.00 0.00 0.00 3.36
2785 2936 3.054802 AGAGAAATGAGTGTGGTGATCCC 60.055 47.826 0.00 0.00 0.00 3.85
2786 2937 2.644299 AGAAATGAGTGTGGTGATCCCA 59.356 45.455 0.00 0.00 42.51 4.37
2813 2964 2.919666 AAATGCTATGCGTGTGAACC 57.080 45.000 0.00 0.00 0.00 3.62
2814 2965 2.113860 AATGCTATGCGTGTGAACCT 57.886 45.000 0.00 0.00 0.00 3.50
2815 2966 2.979814 ATGCTATGCGTGTGAACCTA 57.020 45.000 0.00 0.00 0.00 3.08
2816 2967 2.293677 TGCTATGCGTGTGAACCTAG 57.706 50.000 0.00 0.00 0.00 3.02
2817 2968 1.134818 TGCTATGCGTGTGAACCTAGG 60.135 52.381 7.41 7.41 0.00 3.02
2818 2969 1.571919 CTATGCGTGTGAACCTAGGC 58.428 55.000 9.30 0.00 0.00 3.93
2819 2970 0.899019 TATGCGTGTGAACCTAGGCA 59.101 50.000 9.30 0.00 41.22 4.75
2820 2971 0.036164 ATGCGTGTGAACCTAGGCAA 59.964 50.000 9.30 0.00 40.49 4.52
2821 2972 0.179043 TGCGTGTGAACCTAGGCAAA 60.179 50.000 9.30 0.00 35.10 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.308690 GGGTAGGTCTTCACTCGCTAT 58.691 52.381 0.00 0.00 0.00 2.97
212 213 2.880890 TCAGAGAAGGAGCAAGCAAAAC 59.119 45.455 0.00 0.00 0.00 2.43
219 220 2.705658 TCAGGTTTCAGAGAAGGAGCAA 59.294 45.455 0.00 0.00 0.00 3.91
247 248 5.588240 CATCAGACCTAAGTTACGTATGCA 58.412 41.667 0.00 0.00 0.00 3.96
317 318 6.038161 TGAATGGCATCGAACTAACAAATAGG 59.962 38.462 0.00 0.00 35.81 2.57
331 332 6.732154 AGATTTTAATCAGTGAATGGCATCG 58.268 36.000 0.00 0.00 37.89 3.84
351 353 5.711506 TGACCAGCAACATGATGTAAAGATT 59.288 36.000 0.00 0.00 30.62 2.40
399 401 8.127327 GTCTCTTATACATTAGCGTACAACTCA 58.873 37.037 0.00 0.00 0.00 3.41
407 409 5.515797 TGCAGTCTCTTATACATTAGCGT 57.484 39.130 0.00 0.00 0.00 5.07
409 411 8.600449 AAGATTGCAGTCTCTTATACATTAGC 57.400 34.615 12.63 0.00 30.08 3.09
437 439 4.260990 CGGCACAGTTCAACAGTAAATTCA 60.261 41.667 0.00 0.00 0.00 2.57
629 631 5.705441 TCCAACGCAAGAAAGTAATTCAGAT 59.295 36.000 0.00 0.00 40.72 2.90
712 797 6.889722 CCCAAAGGATCATTCCACTACTAAAA 59.110 38.462 0.00 0.00 45.30 1.52
713 798 6.216662 TCCCAAAGGATCATTCCACTACTAAA 59.783 38.462 0.00 0.00 45.30 1.85
909 994 4.021102 ATTCCGACAAGTGGTCAGAATT 57.979 40.909 3.59 0.00 46.54 2.17
1075 1168 1.028330 CACTTCATCCGCTGCCATGT 61.028 55.000 0.00 0.00 0.00 3.21
1098 1191 9.274065 GTAACTAAAAGCTTAACCATTGAATCG 57.726 33.333 0.00 0.00 0.00 3.34
1120 1213 4.171754 CCAGTGTAGGACGCTAAAGTAAC 58.828 47.826 0.00 0.00 36.71 2.50
1126 1219 1.816835 CTCACCAGTGTAGGACGCTAA 59.183 52.381 0.00 0.00 36.71 3.09
1127 1220 1.460504 CTCACCAGTGTAGGACGCTA 58.539 55.000 0.00 0.00 36.71 4.26
1334 1427 2.297701 TCTCCACAACCTTGCAAGTTC 58.702 47.619 24.35 0.00 0.00 3.01
1418 1511 2.462456 TAAGTGCCTTGAGCTCAGTG 57.538 50.000 17.43 12.92 44.23 3.66
1555 1648 0.809241 GCATCTCCACTTGCTCCTCG 60.809 60.000 0.00 0.00 35.95 4.63
1641 1734 3.688049 AAGCCCCCTTTATTGCTATGT 57.312 42.857 0.00 0.00 32.82 2.29
1692 1785 4.437239 CAAAACTAGCATCCTCGTGATCT 58.563 43.478 0.00 0.00 0.00 2.75
1708 1801 3.381590 GCACTCAAAGAGTTCCCAAAACT 59.618 43.478 0.00 0.00 41.37 2.66
1750 1843 1.774254 TGCGATTCCATGGGGATTAGT 59.226 47.619 13.02 0.00 44.48 2.24
1764 1857 5.833082 ACTTCGTTGATATCTAGTGCGATT 58.167 37.500 3.98 0.00 0.00 3.34
1803 1896 3.376546 CCTTCTATGTCAAAGCCAAGCTC 59.623 47.826 0.00 0.00 38.25 4.09
1819 1912 6.986817 GCAGATTGCAATACTAAGTCCTTCTA 59.013 38.462 12.97 0.00 44.26 2.10
1860 1953 6.038356 CGCCTCATTTTAGATTTTCAAGCAT 58.962 36.000 0.00 0.00 0.00 3.79
1873 1966 2.780595 GCTCCAGCGCCTCATTTTA 58.219 52.632 2.29 0.00 0.00 1.52
1884 1977 0.039708 GTTGTTCTGCAAGCTCCAGC 60.040 55.000 8.97 4.44 37.83 4.85
2157 2250 2.919228 AGACTTGCTGAACGGAAAAGT 58.081 42.857 0.00 0.00 33.91 2.66
2271 2364 5.772521 AGAACGAAAATTGCAAGCTGTTAT 58.227 33.333 4.94 0.03 0.00 1.89
2556 2707 5.560724 CAAAAGAGAGGTGAAGGGATGTTA 58.439 41.667 0.00 0.00 0.00 2.41
2567 2718 0.178964 TTGGGGGCAAAAGAGAGGTG 60.179 55.000 0.00 0.00 0.00 4.00
2568 2719 0.560688 TTTGGGGGCAAAAGAGAGGT 59.439 50.000 0.00 0.00 0.00 3.85
2599 2750 2.171840 AGTCGAGGACATGCAAGTAGT 58.828 47.619 0.00 0.00 34.60 2.73
2604 2755 0.175760 GGCTAGTCGAGGACATGCAA 59.824 55.000 0.00 0.00 35.79 4.08
2626 2777 3.502211 GCCAACTAAGCAGAAACTAAGCA 59.498 43.478 0.00 0.00 0.00 3.91
2637 2788 4.998400 TGCGGCGCCAACTAAGCA 62.998 61.111 30.82 23.31 0.00 3.91
2655 2806 3.373226 GTGGCGTACACTCAGGGA 58.627 61.111 5.33 0.00 46.72 4.20
2672 2823 3.551407 GGGAGGGGCCTAAGAGCG 61.551 72.222 0.84 0.00 36.66 5.03
2675 2826 1.306997 CACTGGGAGGGGCCTAAGA 60.307 63.158 0.84 0.00 36.66 2.10
2683 2834 1.856539 AATGTGGAGCACTGGGAGGG 61.857 60.000 0.00 0.00 35.11 4.30
2684 2835 0.679002 CAATGTGGAGCACTGGGAGG 60.679 60.000 0.00 0.00 35.11 4.30
2685 2836 0.037303 ACAATGTGGAGCACTGGGAG 59.963 55.000 0.00 0.00 35.11 4.30
2686 2837 1.003118 GTACAATGTGGAGCACTGGGA 59.997 52.381 0.00 0.00 35.11 4.37
2687 2838 1.271325 TGTACAATGTGGAGCACTGGG 60.271 52.381 0.00 0.00 35.11 4.45
2688 2839 2.079158 CTGTACAATGTGGAGCACTGG 58.921 52.381 0.00 0.00 35.11 4.00
2689 2840 2.079158 CCTGTACAATGTGGAGCACTG 58.921 52.381 0.00 0.00 35.11 3.66
2690 2841 1.699634 ACCTGTACAATGTGGAGCACT 59.300 47.619 5.91 0.00 35.11 4.40
2691 2842 1.806542 CACCTGTACAATGTGGAGCAC 59.193 52.381 14.49 0.00 34.56 4.40
2692 2843 1.419762 ACACCTGTACAATGTGGAGCA 59.580 47.619 22.30 0.00 34.33 4.26
2693 2844 2.185004 ACACCTGTACAATGTGGAGC 57.815 50.000 22.30 0.00 34.33 4.70
2694 2845 4.154195 GCTTAACACCTGTACAATGTGGAG 59.846 45.833 22.30 17.45 34.33 3.86
2695 2846 4.069304 GCTTAACACCTGTACAATGTGGA 58.931 43.478 22.30 11.67 34.33 4.02
2696 2847 3.190535 GGCTTAACACCTGTACAATGTGG 59.809 47.826 22.30 12.27 34.33 4.17
2697 2848 4.072131 AGGCTTAACACCTGTACAATGTG 58.928 43.478 18.73 18.73 35.72 3.21
2698 2849 4.367039 AGGCTTAACACCTGTACAATGT 57.633 40.909 6.61 6.61 35.72 2.71
2699 2850 5.240623 TGAAAGGCTTAACACCTGTACAATG 59.759 40.000 0.00 0.84 37.67 2.82
2700 2851 5.240844 GTGAAAGGCTTAACACCTGTACAAT 59.759 40.000 19.75 0.00 37.67 2.71
2701 2852 4.577283 GTGAAAGGCTTAACACCTGTACAA 59.423 41.667 19.75 0.00 37.67 2.41
2702 2853 4.131596 GTGAAAGGCTTAACACCTGTACA 58.868 43.478 19.75 0.00 37.67 2.90
2703 2854 3.185797 CGTGAAAGGCTTAACACCTGTAC 59.814 47.826 22.49 0.00 37.67 2.90
2704 2855 3.181463 ACGTGAAAGGCTTAACACCTGTA 60.181 43.478 22.49 0.00 37.67 2.74
2705 2856 2.218603 CGTGAAAGGCTTAACACCTGT 58.781 47.619 22.49 0.00 37.67 4.00
2706 2857 2.218603 ACGTGAAAGGCTTAACACCTG 58.781 47.619 22.49 15.69 37.67 4.00
2707 2858 2.632987 ACGTGAAAGGCTTAACACCT 57.367 45.000 22.49 13.73 40.02 4.00
2708 2859 2.740447 CCTACGTGAAAGGCTTAACACC 59.260 50.000 22.49 11.42 0.00 4.16
2732 2883 9.995003 TTAAATAACTTGCCACATCAGATTTTT 57.005 25.926 0.00 0.00 0.00 1.94
2733 2884 9.995003 TTTAAATAACTTGCCACATCAGATTTT 57.005 25.926 0.00 0.00 0.00 1.82
2734 2885 9.995003 TTTTAAATAACTTGCCACATCAGATTT 57.005 25.926 0.00 0.00 0.00 2.17
2735 2886 9.643693 CTTTTAAATAACTTGCCACATCAGATT 57.356 29.630 0.00 0.00 0.00 2.40
2736 2887 8.253113 CCTTTTAAATAACTTGCCACATCAGAT 58.747 33.333 0.00 0.00 0.00 2.90
2737 2888 7.450014 TCCTTTTAAATAACTTGCCACATCAGA 59.550 33.333 0.00 0.00 0.00 3.27
2738 2889 7.601856 TCCTTTTAAATAACTTGCCACATCAG 58.398 34.615 0.00 0.00 0.00 2.90
2739 2890 7.450014 TCTCCTTTTAAATAACTTGCCACATCA 59.550 33.333 0.00 0.00 0.00 3.07
2740 2891 7.826690 TCTCCTTTTAAATAACTTGCCACATC 58.173 34.615 0.00 0.00 0.00 3.06
2741 2892 7.669722 TCTCTCCTTTTAAATAACTTGCCACAT 59.330 33.333 0.00 0.00 0.00 3.21
2742 2893 7.001674 TCTCTCCTTTTAAATAACTTGCCACA 58.998 34.615 0.00 0.00 0.00 4.17
2743 2894 7.448748 TCTCTCCTTTTAAATAACTTGCCAC 57.551 36.000 0.00 0.00 0.00 5.01
2744 2895 8.472007 TTTCTCTCCTTTTAAATAACTTGCCA 57.528 30.769 0.00 0.00 0.00 4.92
2745 2896 9.358872 CATTTCTCTCCTTTTAAATAACTTGCC 57.641 33.333 0.00 0.00 0.00 4.52
2752 2903 9.231297 CCACACTCATTTCTCTCCTTTTAAATA 57.769 33.333 0.00 0.00 0.00 1.40
2753 2904 7.725844 ACCACACTCATTTCTCTCCTTTTAAAT 59.274 33.333 0.00 0.00 0.00 1.40
2754 2905 7.013274 CACCACACTCATTTCTCTCCTTTTAAA 59.987 37.037 0.00 0.00 0.00 1.52
2755 2906 6.486657 CACCACACTCATTTCTCTCCTTTTAA 59.513 38.462 0.00 0.00 0.00 1.52
2756 2907 5.997746 CACCACACTCATTTCTCTCCTTTTA 59.002 40.000 0.00 0.00 0.00 1.52
2757 2908 4.823989 CACCACACTCATTTCTCTCCTTTT 59.176 41.667 0.00 0.00 0.00 2.27
2758 2909 4.103153 TCACCACACTCATTTCTCTCCTTT 59.897 41.667 0.00 0.00 0.00 3.11
2759 2910 3.648067 TCACCACACTCATTTCTCTCCTT 59.352 43.478 0.00 0.00 0.00 3.36
2760 2911 3.242867 TCACCACACTCATTTCTCTCCT 58.757 45.455 0.00 0.00 0.00 3.69
2761 2912 3.685139 TCACCACACTCATTTCTCTCC 57.315 47.619 0.00 0.00 0.00 3.71
2762 2913 4.187694 GGATCACCACACTCATTTCTCTC 58.812 47.826 0.00 0.00 35.97 3.20
2763 2914 3.054802 GGGATCACCACACTCATTTCTCT 60.055 47.826 0.00 0.00 39.85 3.10
2764 2915 3.274288 GGGATCACCACACTCATTTCTC 58.726 50.000 0.00 0.00 39.85 2.87
2765 2916 2.644299 TGGGATCACCACACTCATTTCT 59.356 45.455 0.00 0.00 46.80 2.52
2766 2917 3.071874 TGGGATCACCACACTCATTTC 57.928 47.619 0.00 0.00 46.80 2.17
2792 2943 3.255642 AGGTTCACACGCATAGCATTTTT 59.744 39.130 0.00 0.00 0.00 1.94
2793 2944 2.819608 AGGTTCACACGCATAGCATTTT 59.180 40.909 0.00 0.00 0.00 1.82
2794 2945 2.436417 AGGTTCACACGCATAGCATTT 58.564 42.857 0.00 0.00 0.00 2.32
2795 2946 2.113860 AGGTTCACACGCATAGCATT 57.886 45.000 0.00 0.00 0.00 3.56
2796 2947 2.483714 CCTAGGTTCACACGCATAGCAT 60.484 50.000 0.00 0.00 0.00 3.79
2797 2948 1.134818 CCTAGGTTCACACGCATAGCA 60.135 52.381 0.00 0.00 0.00 3.49
2798 2949 1.571919 CCTAGGTTCACACGCATAGC 58.428 55.000 0.00 0.00 0.00 2.97
2799 2950 1.134818 TGCCTAGGTTCACACGCATAG 60.135 52.381 11.31 0.00 0.00 2.23
2800 2951 0.899019 TGCCTAGGTTCACACGCATA 59.101 50.000 11.31 0.00 0.00 3.14
2801 2952 0.036164 TTGCCTAGGTTCACACGCAT 59.964 50.000 11.31 0.00 0.00 4.73
2802 2953 0.179043 TTTGCCTAGGTTCACACGCA 60.179 50.000 11.31 0.00 0.00 5.24
2803 2954 2.624169 TTTGCCTAGGTTCACACGC 58.376 52.632 11.31 0.00 0.00 5.34


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

AutoCloner maintained by Alex Coulton.