Multiple sequence alignment - TraesCS1B01G144700

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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 TraesCS1B01G144700 chr1B 100.000 2849 0 0 1 2849 197427373 197430221 0.000000e+00 5262
1 TraesCS1B01G144700 chr1B 83.871 124 17 3 2726 2849 677028285 677028405 6.450000e-22 115
2 TraesCS1B01G144700 chr1D 96.761 1914 53 6 761 2671 140785683 140783776 0.000000e+00 3182
3 TraesCS1B01G144700 chr1D 94.695 754 34 4 19 767 140786501 140785749 0.000000e+00 1166
4 TraesCS1B01G144700 chr1D 87.255 102 12 1 2748 2849 56232647 56232547 6.450000e-22 115
5 TraesCS1B01G144700 chr1D 83.761 117 18 1 2733 2849 5546670 5546555 3.000000e-20 110
6 TraesCS1B01G144700 chr1A 94.186 1892 65 18 758 2644 150006571 150008422 0.000000e+00 2843
7 TraesCS1B01G144700 chr1A 86.949 590 23 13 175 763 150005966 150006502 5.220000e-172 614
8 TraesCS1B01G144700 chr2D 86.842 114 14 1 2736 2849 324863273 324863385 2.980000e-25 126
9 TraesCS1B01G144700 chr2D 83.929 112 15 3 2736 2847 498492719 498492827 1.400000e-18 104
10 TraesCS1B01G144700 chr2D 82.456 114 19 1 2736 2849 543457812 543457924 6.500000e-17 99
11 TraesCS1B01G144700 chr7D 86.726 113 14 1 2737 2849 195543512 195543623 1.070000e-24 124
12 TraesCS1B01G144700 chr5D 85.965 114 15 1 2736 2849 438192522 438192634 1.390000e-23 121
13 TraesCS1B01G144700 chr7A 83.486 109 17 1 2735 2843 542626611 542626504 1.810000e-17 100


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 TraesCS1B01G144700 chr1B 197427373 197430221 2848 False 5262.0 5262 100.0000 1 2849 1 chr1B.!!$F1 2848
1 TraesCS1B01G144700 chr1D 140783776 140786501 2725 True 2174.0 3182 95.7280 19 2671 2 chr1D.!!$R3 2652
2 TraesCS1B01G144700 chr1A 150005966 150008422 2456 False 1728.5 2843 90.5675 175 2644 2 chr1A.!!$F1 2469

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
624 630 0.52847 GTGCACTAGAAGAGGTCGCT 59.472 55.0 10.32 0.0 0.0 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2460 2547 0.108424 CTCCAGTAGCACCAGCACTC 60.108 60.0 0.0 0.0 45.49 3.51 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
45 46 7.757941 TTTCATGATTTATGGTGAGACAACA 57.242 32.000 0.00 0.00 37.39 3.33
76 77 2.584791 CGCTGATTTTCTTTCGGGTTG 58.415 47.619 0.00 0.00 0.00 3.77
80 81 3.976169 TGATTTTCTTTCGGGTTGCAAG 58.024 40.909 0.00 0.00 0.00 4.01
97 98 6.947258 GTTGCAAGACAAGCATTATTTTGTT 58.053 32.000 0.00 0.00 42.33 2.83
102 103 9.405587 GCAAGACAAGCATTATTTTGTTTACTA 57.594 29.630 0.00 0.00 37.63 1.82
160 162 5.662674 TTCTTCCTTGCTACTACTTCCTC 57.337 43.478 0.00 0.00 0.00 3.71
334 340 4.230502 ACATGGATGGTTACTGGAAGGATT 59.769 41.667 0.00 0.00 39.30 3.01
434 440 3.502595 TCCTCCACGACGATTATCTCATC 59.497 47.826 0.00 0.00 0.00 2.92
619 625 6.166279 TCTGTTTTATGTGCACTAGAAGAGG 58.834 40.000 19.41 3.44 0.00 3.69
624 630 0.528470 GTGCACTAGAAGAGGTCGCT 59.472 55.000 10.32 0.00 0.00 4.93
630 636 3.100671 ACTAGAAGAGGTCGCTTCCAAT 58.899 45.455 10.11 0.00 44.14 3.16
631 637 3.515901 ACTAGAAGAGGTCGCTTCCAATT 59.484 43.478 10.11 0.00 44.14 2.32
633 639 4.762289 AGAAGAGGTCGCTTCCAATTAT 57.238 40.909 10.11 0.00 44.14 1.28
634 640 5.104259 AGAAGAGGTCGCTTCCAATTATT 57.896 39.130 10.11 0.00 44.14 1.40
635 641 5.501156 AGAAGAGGTCGCTTCCAATTATTT 58.499 37.500 10.11 0.00 44.14 1.40
636 642 5.946377 AGAAGAGGTCGCTTCCAATTATTTT 59.054 36.000 10.11 0.00 44.14 1.82
647 653 6.960992 GCTTCCAATTATTTTTCCGCATTTTC 59.039 34.615 0.00 0.00 0.00 2.29
668 674 1.964223 CTACCGAGCCATCCTACATGT 59.036 52.381 2.69 2.69 0.00 3.21
907 988 1.228894 AACTCGAGCTCCCTGACCA 60.229 57.895 13.61 0.00 0.00 4.02
950 1031 3.716006 CAGCACCACCGCGTCAAG 61.716 66.667 4.92 0.00 36.85 3.02
984 1065 1.453379 CTCCTCCTCCGCGTCCTTA 60.453 63.158 4.92 0.00 0.00 2.69
1191 1272 1.602888 CTTCTGCTGGGCACTGCTT 60.603 57.895 19.24 0.00 41.57 3.91
1257 1338 1.455959 CTACCTGCTCTACCGCCCT 60.456 63.158 0.00 0.00 0.00 5.19
1365 1446 4.363990 CAGCTCACCGTCACCGCT 62.364 66.667 0.00 0.00 0.00 5.52
1374 1455 1.290955 CGTCACCGCTAAGAACCCA 59.709 57.895 0.00 0.00 0.00 4.51
1416 1497 1.166989 ACGACGACTTCTCCTTCTCC 58.833 55.000 0.00 0.00 0.00 3.71
1473 1554 4.514585 ACCGTGCCTGGGTTTGCA 62.515 61.111 0.00 0.00 32.70 4.08
1515 1596 1.956477 GTTTTCACTGCCACCATCACT 59.044 47.619 0.00 0.00 0.00 3.41
1518 1599 1.303074 CACTGCCACCATCACTGCT 60.303 57.895 0.00 0.00 0.00 4.24
1522 1603 1.078214 GCCACCATCACTGCTGCTA 60.078 57.895 0.00 0.00 0.00 3.49
1541 1622 1.183676 AGTGTCACCGTAGACCCCAC 61.184 60.000 0.00 0.00 37.73 4.61
1940 2022 6.642950 GGAAAGTAGAGACCATGAATATCGTG 59.357 42.308 0.00 0.00 33.30 4.35
2224 2310 9.654663 GAAAATTGAGTATTGTGTAGTAGGAGT 57.345 33.333 0.00 0.00 0.00 3.85
2257 2343 4.188247 TGTGTCGGTAAGGAGAATCTTG 57.812 45.455 0.00 0.00 33.73 3.02
2314 2400 8.012957 ACAACAAAAACTGTATGGTGGAAATA 57.987 30.769 9.89 0.00 37.23 1.40
2425 2512 2.730672 GCTCACAGCTGTAACGCCG 61.731 63.158 21.20 6.12 38.45 6.46
2636 2723 1.120530 GGTGGAGTCACGGGATACAT 58.879 55.000 0.00 0.00 44.50 2.29
2648 2735 4.390603 CACGGGATACATGTTTCTTCGAAA 59.609 41.667 25.22 1.69 39.74 3.46
2652 2739 5.313623 GGATACATGTTTCTTCGAAACACG 58.686 41.667 20.46 16.34 42.18 4.49
2663 2750 0.172803 CGAAACACGGGGGAGACTAG 59.827 60.000 0.00 0.00 38.46 2.57
2667 2754 1.306970 CACGGGGGAGACTAGGACT 59.693 63.158 0.00 0.00 0.00 3.85
2668 2755 0.752376 CACGGGGGAGACTAGGACTC 60.752 65.000 9.70 9.70 0.00 3.36
2669 2756 0.920271 ACGGGGGAGACTAGGACTCT 60.920 60.000 15.33 0.85 35.10 3.24
2671 2758 1.493871 CGGGGGAGACTAGGACTCTTA 59.506 57.143 15.33 0.00 35.10 2.10
2672 2759 2.487625 CGGGGGAGACTAGGACTCTTAG 60.488 59.091 15.33 0.00 35.10 2.18
2673 2760 2.158430 GGGGGAGACTAGGACTCTTAGG 60.158 59.091 15.33 0.00 35.10 2.69
2674 2761 2.589720 GGGAGACTAGGACTCTTAGGC 58.410 57.143 15.33 0.00 35.10 3.93
2675 2762 2.589720 GGAGACTAGGACTCTTAGGCC 58.410 57.143 15.33 0.00 46.64 5.19
2682 2769 1.941325 GGACTCTTAGGCCATGTTCG 58.059 55.000 5.01 0.00 45.15 3.95
2683 2770 1.480954 GGACTCTTAGGCCATGTTCGA 59.519 52.381 5.01 0.00 45.15 3.71
2684 2771 2.482142 GGACTCTTAGGCCATGTTCGAG 60.482 54.545 5.01 4.24 45.15 4.04
2685 2772 1.482593 ACTCTTAGGCCATGTTCGAGG 59.517 52.381 5.01 0.00 0.00 4.63
2686 2773 0.830648 TCTTAGGCCATGTTCGAGGG 59.169 55.000 5.01 0.00 0.00 4.30
2691 2778 4.643795 CCATGTTCGAGGGCATGT 57.356 55.556 18.61 0.00 40.42 3.21
2692 2779 2.872408 CCATGTTCGAGGGCATGTT 58.128 52.632 18.61 0.00 40.42 2.71
2693 2780 1.176527 CCATGTTCGAGGGCATGTTT 58.823 50.000 18.61 0.00 40.42 2.83
2694 2781 1.135315 CCATGTTCGAGGGCATGTTTG 60.135 52.381 18.61 6.54 40.42 2.93
2695 2782 1.135315 CATGTTCGAGGGCATGTTTGG 60.135 52.381 14.53 0.00 38.06 3.28
2696 2783 0.179004 TGTTCGAGGGCATGTTTGGT 60.179 50.000 0.00 0.00 0.00 3.67
2697 2784 0.958822 GTTCGAGGGCATGTTTGGTT 59.041 50.000 0.00 0.00 0.00 3.67
2698 2785 1.068541 GTTCGAGGGCATGTTTGGTTC 60.069 52.381 0.00 0.00 0.00 3.62
2699 2786 0.109532 TCGAGGGCATGTTTGGTTCA 59.890 50.000 0.00 0.00 0.00 3.18
2700 2787 1.176527 CGAGGGCATGTTTGGTTCAT 58.823 50.000 0.00 0.00 0.00 2.57
2701 2788 2.026729 TCGAGGGCATGTTTGGTTCATA 60.027 45.455 0.00 0.00 0.00 2.15
2702 2789 2.752354 CGAGGGCATGTTTGGTTCATAA 59.248 45.455 0.00 0.00 0.00 1.90
2703 2790 3.181497 CGAGGGCATGTTTGGTTCATAAG 60.181 47.826 0.00 0.00 0.00 1.73
2704 2791 3.763897 GAGGGCATGTTTGGTTCATAAGT 59.236 43.478 0.00 0.00 0.00 2.24
2705 2792 4.159557 AGGGCATGTTTGGTTCATAAGTT 58.840 39.130 0.00 0.00 0.00 2.66
2706 2793 4.021192 AGGGCATGTTTGGTTCATAAGTTG 60.021 41.667 0.00 0.00 0.00 3.16
2707 2794 4.262420 GGGCATGTTTGGTTCATAAGTTGT 60.262 41.667 0.00 0.00 0.00 3.32
2708 2795 5.047660 GGGCATGTTTGGTTCATAAGTTGTA 60.048 40.000 0.00 0.00 0.00 2.41
2709 2796 6.092748 GGCATGTTTGGTTCATAAGTTGTAG 58.907 40.000 0.00 0.00 0.00 2.74
2710 2797 6.072175 GGCATGTTTGGTTCATAAGTTGTAGA 60.072 38.462 0.00 0.00 0.00 2.59
2711 2798 7.367285 GCATGTTTGGTTCATAAGTTGTAGAA 58.633 34.615 0.00 0.00 0.00 2.10
2712 2799 8.028938 GCATGTTTGGTTCATAAGTTGTAGAAT 58.971 33.333 0.00 0.00 0.00 2.40
2713 2800 9.345517 CATGTTTGGTTCATAAGTTGTAGAATG 57.654 33.333 0.00 0.00 0.00 2.67
2714 2801 8.458573 TGTTTGGTTCATAAGTTGTAGAATGT 57.541 30.769 0.00 0.00 0.00 2.71
2715 2802 8.908903 TGTTTGGTTCATAAGTTGTAGAATGTT 58.091 29.630 0.00 0.00 0.00 2.71
2716 2803 9.744468 GTTTGGTTCATAAGTTGTAGAATGTTT 57.256 29.630 0.00 0.00 0.00 2.83
2743 2830 9.686683 ATAAGTCCTAAAAATGCTGATAACTGT 57.313 29.630 0.00 0.00 0.00 3.55
2744 2831 8.409358 AAGTCCTAAAAATGCTGATAACTGTT 57.591 30.769 0.00 0.00 0.00 3.16
2745 2832 7.820648 AGTCCTAAAAATGCTGATAACTGTTG 58.179 34.615 2.69 0.00 0.00 3.33
2746 2833 6.528072 GTCCTAAAAATGCTGATAACTGTTGC 59.472 38.462 2.69 0.00 0.00 4.17
2747 2834 6.208402 TCCTAAAAATGCTGATAACTGTTGCA 59.792 34.615 2.69 4.51 38.05 4.08
2748 2835 6.308766 CCTAAAAATGCTGATAACTGTTGCAC 59.691 38.462 2.69 0.00 36.44 4.57
2749 2836 3.476295 AATGCTGATAACTGTTGCACG 57.524 42.857 2.69 0.00 36.44 5.34
2750 2837 1.877637 TGCTGATAACTGTTGCACGT 58.122 45.000 2.69 0.00 0.00 4.49
2751 2838 1.530720 TGCTGATAACTGTTGCACGTG 59.469 47.619 12.28 12.28 0.00 4.49
2752 2839 1.531149 GCTGATAACTGTTGCACGTGT 59.469 47.619 18.38 0.00 0.00 4.49
2753 2840 2.662791 GCTGATAACTGTTGCACGTGTG 60.663 50.000 18.38 5.37 0.00 3.82
2754 2841 2.799978 CTGATAACTGTTGCACGTGTGA 59.200 45.455 18.38 2.92 0.00 3.58
2755 2842 2.542178 TGATAACTGTTGCACGTGTGAC 59.458 45.455 18.38 15.83 0.00 3.67
2756 2843 2.011540 TAACTGTTGCACGTGTGACA 57.988 45.000 18.38 19.30 0.00 3.58
2757 2844 1.378531 AACTGTTGCACGTGTGACAT 58.621 45.000 18.38 5.68 0.00 3.06
2758 2845 0.937304 ACTGTTGCACGTGTGACATC 59.063 50.000 18.38 6.59 0.00 3.06
2759 2846 1.220529 CTGTTGCACGTGTGACATCT 58.779 50.000 18.38 0.00 0.00 2.90
2760 2847 2.223947 ACTGTTGCACGTGTGACATCTA 60.224 45.455 18.38 0.00 0.00 1.98
2761 2848 2.403259 TGTTGCACGTGTGACATCTAG 58.597 47.619 18.38 0.00 0.00 2.43
2762 2849 2.223947 TGTTGCACGTGTGACATCTAGT 60.224 45.455 18.38 0.00 0.00 2.57
2763 2850 2.064573 TGCACGTGTGACATCTAGTG 57.935 50.000 18.38 8.37 0.00 2.74
2764 2851 1.336795 TGCACGTGTGACATCTAGTGG 60.337 52.381 18.38 0.00 0.00 4.00
2765 2852 1.996292 CACGTGTGACATCTAGTGGG 58.004 55.000 7.58 0.00 0.00 4.61
2766 2853 1.544246 CACGTGTGACATCTAGTGGGA 59.456 52.381 7.58 0.00 0.00 4.37
2767 2854 2.166459 CACGTGTGACATCTAGTGGGAT 59.834 50.000 7.58 0.00 0.00 3.85
2768 2855 2.832129 ACGTGTGACATCTAGTGGGATT 59.168 45.455 0.00 0.00 0.00 3.01
2769 2856 3.190079 CGTGTGACATCTAGTGGGATTG 58.810 50.000 0.00 0.00 0.00 2.67
2770 2857 3.368427 CGTGTGACATCTAGTGGGATTGT 60.368 47.826 0.00 0.00 0.00 2.71
2771 2858 3.935203 GTGTGACATCTAGTGGGATTGTG 59.065 47.826 0.00 0.00 0.00 3.33
2772 2859 2.939103 GTGACATCTAGTGGGATTGTGC 59.061 50.000 0.00 0.00 0.00 4.57
2773 2860 2.092968 TGACATCTAGTGGGATTGTGCC 60.093 50.000 0.00 0.00 0.00 5.01
2774 2861 1.134401 ACATCTAGTGGGATTGTGCCG 60.134 52.381 0.00 0.00 0.00 5.69
2775 2862 0.179045 ATCTAGTGGGATTGTGCCGC 60.179 55.000 0.00 0.00 38.78 6.53
2776 2863 1.078497 CTAGTGGGATTGTGCCGCA 60.078 57.895 3.92 0.00 41.16 5.69
2777 2864 1.369091 CTAGTGGGATTGTGCCGCAC 61.369 60.000 16.93 16.93 41.16 5.34
2778 2865 4.101790 GTGGGATTGTGCCGCACG 62.102 66.667 18.41 0.00 38.33 5.34
2796 2883 3.625897 CCCTGTGTGGCACGGAGA 61.626 66.667 13.77 0.00 42.79 3.71
2797 2884 2.357517 CCTGTGTGGCACGGAGAC 60.358 66.667 13.77 6.00 42.79 3.36
2798 2885 2.421314 CTGTGTGGCACGGAGACA 59.579 61.111 13.77 10.55 42.79 3.41
2799 2886 1.227527 CTGTGTGGCACGGAGACAA 60.228 57.895 13.77 0.00 42.79 3.18
2800 2887 1.498865 CTGTGTGGCACGGAGACAAC 61.499 60.000 13.77 4.08 42.79 3.32
2801 2888 2.110213 TGTGGCACGGAGACAACC 59.890 61.111 13.77 0.00 0.00 3.77
2802 2889 2.668550 GTGGCACGGAGACAACCC 60.669 66.667 0.00 0.00 0.00 4.11
2803 2890 3.948719 TGGCACGGAGACAACCCC 61.949 66.667 0.00 0.00 0.00 4.95
2810 2897 3.384532 GAGACAACCCCGCCCGTA 61.385 66.667 0.00 0.00 0.00 4.02
2811 2898 3.654173 GAGACAACCCCGCCCGTAC 62.654 68.421 0.00 0.00 0.00 3.67
2818 2905 4.918129 CCCGCCCGTACGACGATG 62.918 72.222 25.50 15.27 46.05 3.84
2819 2906 4.183686 CCGCCCGTACGACGATGT 62.184 66.667 25.50 0.00 46.05 3.06
2820 2907 2.202518 CGCCCGTACGACGATGTT 60.203 61.111 18.76 0.00 46.05 2.71
2821 2908 2.219562 CGCCCGTACGACGATGTTC 61.220 63.158 18.76 0.00 46.05 3.18
2822 2909 2.219562 GCCCGTACGACGATGTTCG 61.220 63.158 18.76 0.00 46.05 3.95
2823 2910 1.425031 CCCGTACGACGATGTTCGA 59.575 57.895 18.76 0.00 46.05 3.71
2824 2911 0.179192 CCCGTACGACGATGTTCGAA 60.179 55.000 18.76 0.00 46.05 3.71
2825 2912 0.903187 CCGTACGACGATGTTCGAAC 59.097 55.000 21.42 21.42 46.05 3.95
2826 2913 0.553994 CGTACGACGATGTTCGAACG 59.446 55.000 22.48 13.81 46.05 3.95
2827 2914 0.289981 GTACGACGATGTTCGAACGC 59.710 55.000 22.48 15.82 43.74 4.84
2828 2915 0.110283 TACGACGATGTTCGAACGCA 60.110 50.000 22.48 7.37 43.74 5.24
2829 2916 1.334992 ACGACGATGTTCGAACGCAG 61.335 55.000 22.48 17.16 43.74 5.18
2830 2917 1.702299 GACGATGTTCGAACGCAGG 59.298 57.895 22.48 13.89 43.74 4.85
2831 2918 2.279937 GACGATGTTCGAACGCAGGC 62.280 60.000 22.48 14.23 43.74 4.85
2832 2919 2.395690 GATGTTCGAACGCAGGCG 59.604 61.111 22.48 12.71 46.03 5.52
2833 2920 2.048597 ATGTTCGAACGCAGGCGA 60.049 55.556 22.48 4.27 42.83 5.54
2834 2921 2.279937 GATGTTCGAACGCAGGCGAC 62.280 60.000 22.48 12.32 42.83 5.19
2835 2922 3.774702 GTTCGAACGCAGGCGACC 61.775 66.667 21.62 9.98 42.83 4.79
2836 2923 4.287781 TTCGAACGCAGGCGACCA 62.288 61.111 21.62 0.00 42.83 4.02
2839 2926 2.970324 GAACGCAGGCGACCACAA 60.970 61.111 21.62 0.00 42.83 3.33
2840 2927 3.236618 GAACGCAGGCGACCACAAC 62.237 63.158 21.62 0.04 42.83 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 9.076781 TGTCTCACCATAAATCATGAAAAGAAA 57.923 29.630 0.00 0.00 36.69 2.52
17 18 8.634335 TGTCTCACCATAAATCATGAAAAGAA 57.366 30.769 0.00 0.00 36.69 2.52
25 26 7.231317 ACAGTTTGTTGTCTCACCATAAATCAT 59.769 33.333 0.00 0.00 0.00 2.45
45 46 2.568623 AAATCAGCGGGAGACAGTTT 57.431 45.000 0.00 0.00 0.00 2.66
56 57 2.584791 CAACCCGAAAGAAAATCAGCG 58.415 47.619 0.00 0.00 0.00 5.18
76 77 8.298030 AGTAAACAAAATAATGCTTGTCTTGC 57.702 30.769 0.00 0.00 34.71 4.01
140 142 4.707448 TGAGAGGAAGTAGTAGCAAGGAAG 59.293 45.833 0.00 0.00 0.00 3.46
150 152 4.338795 TCCCAAGATGAGAGGAAGTAGT 57.661 45.455 0.00 0.00 0.00 2.73
160 162 4.776837 AGTGGCTATAGATCCCAAGATGAG 59.223 45.833 3.21 0.00 30.90 2.90
334 340 1.542472 CATGCAGCTGGTTTGATGTGA 59.458 47.619 17.12 0.00 0.00 3.58
434 440 6.658831 ACAACACGAAAGAACATCAATGTAG 58.341 36.000 0.00 0.00 40.80 2.74
619 625 3.546271 GCGGAAAAATAATTGGAAGCGAC 59.454 43.478 0.00 0.00 0.00 5.19
624 630 7.164803 AGGAAAATGCGGAAAAATAATTGGAA 58.835 30.769 0.00 0.00 0.00 3.53
630 636 5.415077 TCGGTAGGAAAATGCGGAAAAATAA 59.585 36.000 0.00 0.00 0.00 1.40
631 637 4.942483 TCGGTAGGAAAATGCGGAAAAATA 59.058 37.500 0.00 0.00 0.00 1.40
633 639 3.147629 TCGGTAGGAAAATGCGGAAAAA 58.852 40.909 0.00 0.00 0.00 1.94
634 640 2.745281 CTCGGTAGGAAAATGCGGAAAA 59.255 45.455 0.00 0.00 0.00 2.29
635 641 2.352388 CTCGGTAGGAAAATGCGGAAA 58.648 47.619 0.00 0.00 0.00 3.13
636 642 2.010043 GCTCGGTAGGAAAATGCGGAA 61.010 52.381 0.00 0.00 0.00 4.30
647 653 1.273606 CATGTAGGATGGCTCGGTAGG 59.726 57.143 0.00 0.00 0.00 3.18
907 988 0.106719 CTGGGTGGTTGAGTGGTTGT 60.107 55.000 0.00 0.00 0.00 3.32
970 1051 1.735376 GCAGATAAGGACGCGGAGGA 61.735 60.000 12.47 0.00 0.00 3.71
1191 1272 2.710902 CGCGAGGAGGATGACCACA 61.711 63.158 0.00 0.00 38.94 4.17
1257 1338 2.281484 GTGAAGCTGGGGCGTTGA 60.281 61.111 0.00 0.00 44.37 3.18
1365 1446 3.813166 CGAGCTTCTTGTTTGGGTTCTTA 59.187 43.478 0.00 0.00 0.00 2.10
1374 1455 6.308282 CGTAGAAATAGACGAGCTTCTTGTTT 59.692 38.462 0.00 0.00 30.90 2.83
1473 1554 2.342650 GGTGTTGCCGGCATCATGT 61.343 57.895 35.69 0.00 0.00 3.21
1515 1596 0.526211 CTACGGTGACACTAGCAGCA 59.474 55.000 5.39 0.00 33.59 4.41
1518 1599 1.171308 GGTCTACGGTGACACTAGCA 58.829 55.000 5.39 0.00 38.61 3.49
1522 1603 1.154454 TGGGGTCTACGGTGACACT 59.846 57.895 5.39 0.00 40.06 3.55
1716 1797 1.032114 CGGTGCCATTCTTCCCCTTC 61.032 60.000 0.00 0.00 0.00 3.46
1940 2022 5.801531 AACTTTTGAGGGAATTTACACCC 57.198 39.130 0.00 0.00 45.88 4.61
1997 2080 9.585099 AAGTTATACATGCACCAAAAATATGTG 57.415 29.630 0.00 0.00 34.22 3.21
2224 2310 6.097129 TCCTTACCGACACAATCACATGTATA 59.903 38.462 0.00 0.00 30.84 1.47
2225 2311 5.105106 TCCTTACCGACACAATCACATGTAT 60.105 40.000 0.00 0.00 30.84 2.29
2314 2400 6.005823 TCACATGACAAACATCTCCATTTCT 58.994 36.000 0.00 0.00 37.07 2.52
2425 2512 1.508632 TCTTTGGCGCTCAAGTACAC 58.491 50.000 7.64 0.00 36.62 2.90
2460 2547 0.108424 CTCCAGTAGCACCAGCACTC 60.108 60.000 0.00 0.00 45.49 3.51
2636 2723 1.301423 CCCCGTGTTTCGAAGAAACA 58.699 50.000 20.31 20.31 45.90 2.83
2648 2735 1.000107 GTCCTAGTCTCCCCCGTGT 60.000 63.158 0.00 0.00 0.00 4.49
2652 2739 2.158430 CCTAAGAGTCCTAGTCTCCCCC 60.158 59.091 8.08 0.00 32.93 5.40
2663 2750 1.480954 TCGAACATGGCCTAAGAGTCC 59.519 52.381 3.32 0.00 0.00 3.85
2667 2754 0.830648 CCCTCGAACATGGCCTAAGA 59.169 55.000 3.32 0.00 0.00 2.10
2668 2755 0.815615 GCCCTCGAACATGGCCTAAG 60.816 60.000 3.32 0.00 39.30 2.18
2669 2756 1.223487 GCCCTCGAACATGGCCTAA 59.777 57.895 3.32 0.00 39.30 2.69
2671 2758 2.683465 ATGCCCTCGAACATGGCCT 61.683 57.895 3.32 0.96 44.72 5.19
2672 2759 2.124151 ATGCCCTCGAACATGGCC 60.124 61.111 0.00 0.00 44.72 5.36
2673 2760 1.315257 AACATGCCCTCGAACATGGC 61.315 55.000 20.50 14.77 46.35 4.40
2674 2761 1.135315 CAAACATGCCCTCGAACATGG 60.135 52.381 20.50 4.85 46.35 3.66
2676 2763 1.176527 CCAAACATGCCCTCGAACAT 58.823 50.000 0.00 0.00 0.00 2.71
2677 2764 0.179004 ACCAAACATGCCCTCGAACA 60.179 50.000 0.00 0.00 0.00 3.18
2678 2765 0.958822 AACCAAACATGCCCTCGAAC 59.041 50.000 0.00 0.00 0.00 3.95
2679 2766 1.243902 GAACCAAACATGCCCTCGAA 58.756 50.000 0.00 0.00 0.00 3.71
2680 2767 0.109532 TGAACCAAACATGCCCTCGA 59.890 50.000 0.00 0.00 0.00 4.04
2681 2768 1.176527 ATGAACCAAACATGCCCTCG 58.823 50.000 0.00 0.00 0.00 4.63
2682 2769 3.763897 ACTTATGAACCAAACATGCCCTC 59.236 43.478 0.00 0.00 0.00 4.30
2683 2770 3.778265 ACTTATGAACCAAACATGCCCT 58.222 40.909 0.00 0.00 0.00 5.19
2684 2771 4.244862 CAACTTATGAACCAAACATGCCC 58.755 43.478 0.00 0.00 0.00 5.36
2685 2772 4.881920 ACAACTTATGAACCAAACATGCC 58.118 39.130 0.00 0.00 0.00 4.40
2686 2773 6.908825 TCTACAACTTATGAACCAAACATGC 58.091 36.000 0.00 0.00 0.00 4.06
2687 2774 9.345517 CATTCTACAACTTATGAACCAAACATG 57.654 33.333 0.00 0.00 0.00 3.21
2688 2775 9.077885 ACATTCTACAACTTATGAACCAAACAT 57.922 29.630 0.00 0.00 0.00 2.71
2689 2776 8.458573 ACATTCTACAACTTATGAACCAAACA 57.541 30.769 0.00 0.00 0.00 2.83
2690 2777 9.744468 AAACATTCTACAACTTATGAACCAAAC 57.256 29.630 0.00 0.00 0.00 2.93
2717 2804 9.686683 ACAGTTATCAGCATTTTTAGGACTTAT 57.313 29.630 0.00 0.00 0.00 1.73
2718 2805 9.515226 AACAGTTATCAGCATTTTTAGGACTTA 57.485 29.630 0.00 0.00 0.00 2.24
2719 2806 8.299570 CAACAGTTATCAGCATTTTTAGGACTT 58.700 33.333 0.00 0.00 0.00 3.01
2720 2807 7.575720 GCAACAGTTATCAGCATTTTTAGGACT 60.576 37.037 0.00 0.00 0.00 3.85
2721 2808 6.528072 GCAACAGTTATCAGCATTTTTAGGAC 59.472 38.462 0.00 0.00 0.00 3.85
2722 2809 6.208402 TGCAACAGTTATCAGCATTTTTAGGA 59.792 34.615 0.00 0.00 0.00 2.94
2723 2810 6.308766 GTGCAACAGTTATCAGCATTTTTAGG 59.691 38.462 0.00 0.00 37.56 2.69
2724 2811 6.032775 CGTGCAACAGTTATCAGCATTTTTAG 59.967 38.462 0.00 0.00 37.56 1.85
2725 2812 5.855925 CGTGCAACAGTTATCAGCATTTTTA 59.144 36.000 0.00 0.00 37.56 1.52
2726 2813 4.681025 CGTGCAACAGTTATCAGCATTTTT 59.319 37.500 0.00 0.00 37.56 1.94
2727 2814 4.229096 CGTGCAACAGTTATCAGCATTTT 58.771 39.130 0.00 0.00 37.56 1.82
2728 2815 3.253188 ACGTGCAACAGTTATCAGCATTT 59.747 39.130 0.00 0.00 37.56 2.32
2729 2816 2.813754 ACGTGCAACAGTTATCAGCATT 59.186 40.909 0.00 0.00 37.56 3.56
2730 2817 2.160219 CACGTGCAACAGTTATCAGCAT 59.840 45.455 0.82 0.00 37.56 3.79
2731 2818 1.530720 CACGTGCAACAGTTATCAGCA 59.469 47.619 0.82 0.00 35.74 4.41
2732 2819 1.531149 ACACGTGCAACAGTTATCAGC 59.469 47.619 17.22 0.00 35.74 4.26
2733 2820 2.799978 TCACACGTGCAACAGTTATCAG 59.200 45.455 17.22 0.00 35.74 2.90
2734 2821 2.542178 GTCACACGTGCAACAGTTATCA 59.458 45.455 17.22 0.00 35.74 2.15
2735 2822 2.542178 TGTCACACGTGCAACAGTTATC 59.458 45.455 17.22 0.00 35.74 1.75
2736 2823 2.556257 TGTCACACGTGCAACAGTTAT 58.444 42.857 17.22 0.00 35.74 1.89
2737 2824 2.011540 TGTCACACGTGCAACAGTTA 57.988 45.000 17.22 0.00 35.74 2.24
2738 2825 1.330521 GATGTCACACGTGCAACAGTT 59.669 47.619 22.87 11.61 35.74 3.16
2739 2826 0.937304 GATGTCACACGTGCAACAGT 59.063 50.000 22.87 14.04 35.74 3.55
2740 2827 1.220529 AGATGTCACACGTGCAACAG 58.779 50.000 22.87 7.70 35.74 3.16
2741 2828 2.223947 ACTAGATGTCACACGTGCAACA 60.224 45.455 21.44 21.44 35.74 3.33
2742 2829 2.155732 CACTAGATGTCACACGTGCAAC 59.844 50.000 17.22 14.48 0.00 4.17
2743 2830 2.403259 CACTAGATGTCACACGTGCAA 58.597 47.619 17.22 0.00 0.00 4.08
2744 2831 1.336795 CCACTAGATGTCACACGTGCA 60.337 52.381 17.22 6.09 0.00 4.57
2745 2832 1.350193 CCACTAGATGTCACACGTGC 58.650 55.000 17.22 0.00 0.00 5.34
2746 2833 1.544246 TCCCACTAGATGTCACACGTG 59.456 52.381 15.48 15.48 0.00 4.49
2747 2834 1.919240 TCCCACTAGATGTCACACGT 58.081 50.000 0.00 0.00 0.00 4.49
2748 2835 3.190079 CAATCCCACTAGATGTCACACG 58.810 50.000 0.00 0.00 0.00 4.49
2749 2836 3.935203 CACAATCCCACTAGATGTCACAC 59.065 47.826 0.00 0.00 0.00 3.82
2750 2837 3.619733 GCACAATCCCACTAGATGTCACA 60.620 47.826 0.00 0.00 0.00 3.58
2751 2838 2.939103 GCACAATCCCACTAGATGTCAC 59.061 50.000 0.00 0.00 0.00 3.67
2752 2839 2.092968 GGCACAATCCCACTAGATGTCA 60.093 50.000 0.00 0.00 0.00 3.58
2753 2840 2.565841 GGCACAATCCCACTAGATGTC 58.434 52.381 0.00 0.00 0.00 3.06
2754 2841 1.134401 CGGCACAATCCCACTAGATGT 60.134 52.381 0.00 0.00 0.00 3.06
2755 2842 1.586422 CGGCACAATCCCACTAGATG 58.414 55.000 0.00 0.00 0.00 2.90
2756 2843 0.179045 GCGGCACAATCCCACTAGAT 60.179 55.000 0.00 0.00 0.00 1.98
2757 2844 1.220749 GCGGCACAATCCCACTAGA 59.779 57.895 0.00 0.00 0.00 2.43
2758 2845 1.078497 TGCGGCACAATCCCACTAG 60.078 57.895 0.00 0.00 0.00 2.57
2759 2846 1.376683 GTGCGGCACAATCCCACTA 60.377 57.895 27.10 0.00 34.08 2.74
2760 2847 2.672996 GTGCGGCACAATCCCACT 60.673 61.111 27.10 0.00 34.08 4.00
2761 2848 4.101790 CGTGCGGCACAATCCCAC 62.102 66.667 30.23 3.46 33.40 4.61
2780 2867 2.357517 GTCTCCGTGCCACACAGG 60.358 66.667 0.00 1.06 41.84 4.00
2781 2868 1.227527 TTGTCTCCGTGCCACACAG 60.228 57.895 0.00 0.00 33.40 3.66
2782 2869 1.522806 GTTGTCTCCGTGCCACACA 60.523 57.895 0.00 0.00 33.40 3.72
2783 2870 2.251642 GGTTGTCTCCGTGCCACAC 61.252 63.158 0.00 0.00 0.00 3.82
2784 2871 2.110213 GGTTGTCTCCGTGCCACA 59.890 61.111 0.00 0.00 0.00 4.17
2785 2872 2.668550 GGGTTGTCTCCGTGCCAC 60.669 66.667 0.00 0.00 0.00 5.01
2786 2873 3.948719 GGGGTTGTCTCCGTGCCA 61.949 66.667 0.00 0.00 0.00 4.92
2793 2880 3.384532 TACGGGCGGGGTTGTCTC 61.385 66.667 0.00 0.00 0.00 3.36
2794 2881 3.698820 GTACGGGCGGGGTTGTCT 61.699 66.667 0.00 0.00 0.00 3.41
2801 2888 4.918129 CATCGTCGTACGGGCGGG 62.918 72.222 24.44 16.67 42.81 6.13
2802 2889 3.688475 AACATCGTCGTACGGGCGG 62.688 63.158 24.44 15.81 42.81 6.13
2803 2890 2.202518 AACATCGTCGTACGGGCG 60.203 61.111 16.52 19.27 42.81 6.13
2804 2891 2.219562 CGAACATCGTCGTACGGGC 61.220 63.158 16.52 8.01 42.81 6.13
2805 2892 0.179192 TTCGAACATCGTCGTACGGG 60.179 55.000 16.52 8.17 42.81 5.28
2806 2893 0.903187 GTTCGAACATCGTCGTACGG 59.097 55.000 23.12 0.00 42.81 4.02
2808 2895 0.289981 GCGTTCGAACATCGTCGTAC 59.710 55.000 26.71 0.00 41.35 3.67
2809 2896 0.110283 TGCGTTCGAACATCGTCGTA 60.110 50.000 26.71 9.48 41.35 3.43
2810 2897 1.334992 CTGCGTTCGAACATCGTCGT 61.335 55.000 26.71 0.00 41.35 4.34
2811 2898 1.337150 CTGCGTTCGAACATCGTCG 59.663 57.895 26.71 13.48 41.35 5.12
2812 2899 1.702299 CCTGCGTTCGAACATCGTC 59.298 57.895 26.71 10.89 41.35 4.20
2813 2900 2.380410 GCCTGCGTTCGAACATCGT 61.380 57.895 26.71 0.00 41.35 3.73
2814 2901 2.395690 GCCTGCGTTCGAACATCG 59.604 61.111 26.71 14.91 42.10 3.84
2815 2902 2.092291 TCGCCTGCGTTCGAACATC 61.092 57.895 26.71 17.74 40.74 3.06
2816 2903 2.048597 TCGCCTGCGTTCGAACAT 60.049 55.556 26.71 0.00 40.74 2.71
2817 2904 3.033764 GTCGCCTGCGTTCGAACA 61.034 61.111 26.71 8.62 40.74 3.18
2818 2905 3.774702 GGTCGCCTGCGTTCGAAC 61.775 66.667 18.47 18.47 40.74 3.95
2819 2906 4.287781 TGGTCGCCTGCGTTCGAA 62.288 61.111 11.68 0.00 40.74 3.71
2822 2909 2.970324 TTGTGGTCGCCTGCGTTC 60.970 61.111 11.68 6.23 40.74 3.95
2823 2910 3.276846 GTTGTGGTCGCCTGCGTT 61.277 61.111 11.68 0.00 40.74 4.84


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

AutoCloner maintained by Alex Coulton.