Multiple sequence alignment - TraesCS2D01G529900

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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 TraesCS2D01G529900 chr2D 100.000 2953 0 0 1 2953 616929377 616926425 0.000000e+00 5454.0
1 TraesCS2D01G529900 chr2D 96.354 2770 40 17 1 2746 316145792 316143060 0.000000e+00 4499.0
2 TraesCS2D01G529900 chr2D 89.812 1384 109 12 1294 2657 59648730 59650101 0.000000e+00 1746.0
3 TraesCS2D01G529900 chr2D 91.874 886 68 4 274 1158 59647848 59648730 0.000000e+00 1234.0
4 TraesCS2D01G529900 chr2D 82.317 328 47 7 2407 2724 520551589 520551263 1.040000e-69 274.0
5 TraesCS2D01G529900 chr6D 97.707 2748 53 7 1 2746 436494333 436497072 0.000000e+00 4717.0
6 TraesCS2D01G529900 chr6B 92.935 2746 155 13 1 2726 55204668 55207394 0.000000e+00 3960.0
7 TraesCS2D01G529900 chr6B 83.224 304 39 8 2345 2637 472715273 472714971 4.850000e-68 268.0
8 TraesCS2D01G529900 chr6B 84.848 99 15 0 2628 2726 472714587 472714489 1.870000e-17 100.0
9 TraesCS2D01G529900 chr6B 86.441 59 8 0 2668 2726 663128176 663128118 6.830000e-07 65.8
10 TraesCS2D01G529900 chr3B 93.065 2062 118 9 1 2049 674481243 674479194 0.000000e+00 2992.0
11 TraesCS2D01G529900 chr3B 92.420 686 46 4 2045 2726 674478216 674477533 0.000000e+00 974.0
12 TraesCS2D01G529900 chr3B 84.596 396 45 8 2341 2726 534251102 534251491 2.150000e-101 379.0
13 TraesCS2D01G529900 chr5D 88.664 1385 124 12 1294 2657 376572735 376574107 0.000000e+00 1657.0
14 TraesCS2D01G529900 chr5D 91.422 886 72 4 274 1158 376571853 376572735 0.000000e+00 1212.0
15 TraesCS2D01G529900 chr5D 91.775 231 18 1 1 230 376571624 376571854 1.320000e-83 320.0
16 TraesCS2D01G529900 chr7D 84.733 393 58 2 434 824 402554964 402554572 2.760000e-105 392.0
17 TraesCS2D01G529900 chr7D 88.136 59 3 1 2668 2726 556287863 556287917 1.900000e-07 67.6
18 TraesCS2D01G529900 chr2B 90.769 65 4 2 2739 2801 752401672 752401608 5.240000e-13 86.1
19 TraesCS2D01G529900 chr6A 82.692 104 9 8 727 827 286424740 286424837 1.890000e-12 84.2
20 TraesCS2D01G529900 chr4B 82.609 92 14 2 734 824 497107023 497106933 2.440000e-11 80.5


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 TraesCS2D01G529900 chr2D 616926425 616929377 2952 True 5454 5454 100.000000 1 2953 1 chr2D.!!$R3 2952
1 TraesCS2D01G529900 chr2D 316143060 316145792 2732 True 4499 4499 96.354000 1 2746 1 chr2D.!!$R1 2745
2 TraesCS2D01G529900 chr2D 59647848 59650101 2253 False 1490 1746 90.843000 274 2657 2 chr2D.!!$F1 2383
3 TraesCS2D01G529900 chr6D 436494333 436497072 2739 False 4717 4717 97.707000 1 2746 1 chr6D.!!$F1 2745
4 TraesCS2D01G529900 chr6B 55204668 55207394 2726 False 3960 3960 92.935000 1 2726 1 chr6B.!!$F1 2725
5 TraesCS2D01G529900 chr3B 674477533 674481243 3710 True 1983 2992 92.742500 1 2726 2 chr3B.!!$R1 2725
6 TraesCS2D01G529900 chr5D 376571624 376574107 2483 False 1063 1657 90.620333 1 2657 3 chr5D.!!$F1 2656

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
452 454 0.108138 CGTGGATGGGTCCTGTCTTC 60.108 60.000 0.0 0.0 45.32 2.87 F
1023 1026 1.918293 ATCAGGCACACGGAGGGAA 60.918 57.895 0.0 0.0 0.00 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1727 1738 2.300437 GCAGGTCTTGTACTTCACCTCT 59.700 50.0 7.11 0.0 0.0 3.69 R
2777 3820 0.037447 GGCTATCCTCATCCCCAAGC 59.963 60.0 0.00 0.0 0.0 4.01 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
154 156 8.217188 TCCCCTTGGTTATTTACTTACTGTAA 57.783 34.615 0.00 0.00 39.17 2.41
369 371 8.314751 AGTGACACTTTCTATTTGCAGTAGTAT 58.685 33.333 1.07 0.00 0.00 2.12
452 454 0.108138 CGTGGATGGGTCCTGTCTTC 60.108 60.000 0.00 0.00 45.32 2.87
473 475 5.241403 TCTATTCTGCTTGTTTCTTCCCA 57.759 39.130 0.00 0.00 0.00 4.37
641 643 3.244526 TGTGTTGTACATGTGCTCATCCT 60.245 43.478 15.25 0.00 33.42 3.24
695 698 2.655090 TGCTGGTTGATTTGTCCTGA 57.345 45.000 0.00 0.00 0.00 3.86
1023 1026 1.918293 ATCAGGCACACGGAGGGAA 60.918 57.895 0.00 0.00 0.00 3.97
1118 1121 3.128349 TCGTTTGCTTGGTCAACTCTAC 58.872 45.455 0.00 0.00 0.00 2.59
1727 1738 4.518970 GTTCTTGCTGAAGATGGTTTACCA 59.481 41.667 3.71 3.71 42.19 3.25
1759 1770 0.613260 AAGACCTGCGCATCTTACCA 59.387 50.000 21.58 0.00 33.35 3.25
1933 1972 1.927487 TTGACTGCCCTCAAATGCAT 58.073 45.000 0.00 0.00 36.79 3.96
2216 3248 2.916934 TCTTGTGTTAGGTAAGGGGCAT 59.083 45.455 0.00 0.00 0.00 4.40
2218 3250 3.818295 TGTGTTAGGTAAGGGGCATTT 57.182 42.857 0.00 0.00 0.00 2.32
2219 3251 4.120946 TGTGTTAGGTAAGGGGCATTTT 57.879 40.909 0.00 0.00 0.00 1.82
2495 3527 2.325484 GGATGGGTGTTTGGAGGTTTT 58.675 47.619 0.00 0.00 0.00 2.43
2639 3674 8.086522 GTGATAATATCATGCTTTCATTGCCTT 58.913 33.333 6.21 0.00 42.04 4.35
2661 3696 4.913335 TTCTTATCGTCGGAATAGCAGT 57.087 40.909 0.00 0.00 0.00 4.40
2665 3700 1.746470 TCGTCGGAATAGCAGTCTGA 58.254 50.000 3.32 0.00 0.00 3.27
2674 3709 5.066117 CGGAATAGCAGTCTGAGTTACTACA 59.934 44.000 3.32 0.00 0.00 2.74
2740 3783 1.242076 GCGCCTTACCCGATCTAGTA 58.758 55.000 0.00 0.00 0.00 1.82
2741 3784 1.817447 GCGCCTTACCCGATCTAGTAT 59.183 52.381 0.00 0.00 0.00 2.12
2742 3785 2.415625 GCGCCTTACCCGATCTAGTATG 60.416 54.545 0.00 0.00 0.00 2.39
2743 3786 2.818432 CGCCTTACCCGATCTAGTATGT 59.182 50.000 0.00 0.00 0.00 2.29
2744 3787 4.005650 CGCCTTACCCGATCTAGTATGTA 58.994 47.826 0.00 0.00 0.00 2.29
2745 3788 4.639310 CGCCTTACCCGATCTAGTATGTAT 59.361 45.833 0.00 0.00 0.00 2.29
2746 3789 5.819379 CGCCTTACCCGATCTAGTATGTATA 59.181 44.000 0.00 0.00 0.00 1.47
2747 3790 6.018098 CGCCTTACCCGATCTAGTATGTATAG 60.018 46.154 0.00 0.00 0.00 1.31
2748 3791 6.827762 GCCTTACCCGATCTAGTATGTATAGT 59.172 42.308 0.00 0.00 0.00 2.12
2749 3792 7.012232 GCCTTACCCGATCTAGTATGTATAGTC 59.988 44.444 0.00 0.00 0.00 2.59
2750 3793 8.266473 CCTTACCCGATCTAGTATGTATAGTCT 58.734 40.741 0.00 0.00 0.00 3.24
2751 3794 9.100554 CTTACCCGATCTAGTATGTATAGTCTG 57.899 40.741 0.00 0.00 0.00 3.51
2752 3795 6.416415 ACCCGATCTAGTATGTATAGTCTGG 58.584 44.000 0.00 0.00 0.00 3.86
2753 3796 5.823570 CCCGATCTAGTATGTATAGTCTGGG 59.176 48.000 0.00 0.00 0.00 4.45
2754 3797 5.823570 CCGATCTAGTATGTATAGTCTGGGG 59.176 48.000 0.00 0.00 0.00 4.96
2755 3798 6.352823 CCGATCTAGTATGTATAGTCTGGGGA 60.353 46.154 0.00 0.00 0.00 4.81
2756 3799 6.539464 CGATCTAGTATGTATAGTCTGGGGAC 59.461 46.154 0.00 0.00 42.41 4.46
2773 3816 3.080641 CCCATGGGTGAGAGCACA 58.919 61.111 23.93 0.00 46.96 4.57
2774 3817 1.077930 CCCATGGGTGAGAGCACAG 60.078 63.158 23.93 0.00 46.96 3.66
2775 3818 1.556373 CCCATGGGTGAGAGCACAGA 61.556 60.000 23.93 0.00 46.96 3.41
2776 3819 0.545171 CCATGGGTGAGAGCACAGAT 59.455 55.000 2.85 0.00 46.96 2.90
2777 3820 1.664873 CATGGGTGAGAGCACAGATG 58.335 55.000 0.00 0.00 46.96 2.90
2788 3831 3.888424 CACAGATGCTTGGGGATGA 57.112 52.632 0.00 0.00 0.00 2.92
2789 3832 1.676746 CACAGATGCTTGGGGATGAG 58.323 55.000 0.00 0.00 0.00 2.90
2790 3833 0.549950 ACAGATGCTTGGGGATGAGG 59.450 55.000 0.00 0.00 0.00 3.86
2791 3834 0.841961 CAGATGCTTGGGGATGAGGA 59.158 55.000 0.00 0.00 0.00 3.71
2792 3835 1.424302 CAGATGCTTGGGGATGAGGAT 59.576 52.381 0.00 0.00 0.00 3.24
2793 3836 2.641321 CAGATGCTTGGGGATGAGGATA 59.359 50.000 0.00 0.00 0.00 2.59
2794 3837 2.911636 AGATGCTTGGGGATGAGGATAG 59.088 50.000 0.00 0.00 0.00 2.08
2795 3838 0.767375 TGCTTGGGGATGAGGATAGC 59.233 55.000 0.00 0.00 0.00 2.97
2796 3839 0.037447 GCTTGGGGATGAGGATAGCC 59.963 60.000 0.00 0.00 0.00 3.93
2806 3849 2.826337 AGGATAGCCTCGATGCACA 58.174 52.632 15.26 2.60 42.19 4.57
2807 3850 0.390860 AGGATAGCCTCGATGCACAC 59.609 55.000 15.26 5.19 42.19 3.82
2808 3851 0.104855 GGATAGCCTCGATGCACACA 59.895 55.000 15.26 0.00 0.00 3.72
2809 3852 1.270518 GGATAGCCTCGATGCACACAT 60.271 52.381 15.26 2.60 39.98 3.21
2810 3853 2.029020 GGATAGCCTCGATGCACACATA 60.029 50.000 15.26 0.00 36.35 2.29
2811 3854 2.800881 TAGCCTCGATGCACACATAG 57.199 50.000 15.26 0.00 36.35 2.23
2812 3855 0.826715 AGCCTCGATGCACACATAGT 59.173 50.000 15.26 0.00 36.35 2.12
2813 3856 1.208052 AGCCTCGATGCACACATAGTT 59.792 47.619 15.26 0.00 36.35 2.24
2814 3857 1.594862 GCCTCGATGCACACATAGTTC 59.405 52.381 7.89 0.00 36.35 3.01
2815 3858 1.854743 CCTCGATGCACACATAGTTCG 59.145 52.381 0.00 0.00 36.35 3.95
2816 3859 2.530177 CTCGATGCACACATAGTTCGT 58.470 47.619 0.00 0.00 36.35 3.85
2817 3860 3.488553 CCTCGATGCACACATAGTTCGTA 60.489 47.826 0.00 0.00 36.35 3.43
2818 3861 4.290969 CTCGATGCACACATAGTTCGTAT 58.709 43.478 0.00 0.00 36.35 3.06
2819 3862 4.041723 TCGATGCACACATAGTTCGTATG 58.958 43.478 0.00 0.00 43.89 2.39
2860 3903 6.683974 AAACAACTCCATAATTGATCCTCG 57.316 37.500 0.00 0.00 0.00 4.63
2861 3904 5.359194 ACAACTCCATAATTGATCCTCGT 57.641 39.130 0.00 0.00 0.00 4.18
2862 3905 5.118990 ACAACTCCATAATTGATCCTCGTG 58.881 41.667 0.00 0.00 0.00 4.35
2863 3906 3.733337 ACTCCATAATTGATCCTCGTGC 58.267 45.455 0.00 0.00 0.00 5.34
2864 3907 3.070018 CTCCATAATTGATCCTCGTGCC 58.930 50.000 0.00 0.00 0.00 5.01
2865 3908 2.705658 TCCATAATTGATCCTCGTGCCT 59.294 45.455 0.00 0.00 0.00 4.75
2866 3909 3.901222 TCCATAATTGATCCTCGTGCCTA 59.099 43.478 0.00 0.00 0.00 3.93
2867 3910 4.532126 TCCATAATTGATCCTCGTGCCTAT 59.468 41.667 0.00 0.00 0.00 2.57
2868 3911 5.719563 TCCATAATTGATCCTCGTGCCTATA 59.280 40.000 0.00 0.00 0.00 1.31
2869 3912 6.045318 CCATAATTGATCCTCGTGCCTATAG 58.955 44.000 0.00 0.00 0.00 1.31
2870 3913 4.543590 AATTGATCCTCGTGCCTATAGG 57.456 45.455 15.01 15.01 38.53 2.57
2894 3937 9.841295 AGGCAGGAAATTTATTTACTAATACGA 57.159 29.630 0.00 0.00 38.86 3.43
2895 3938 9.874215 GGCAGGAAATTTATTTACTAATACGAC 57.126 33.333 0.00 0.00 38.86 4.34
2905 3948 6.446781 TTTACTAATACGACTGTCTCCTGG 57.553 41.667 6.21 0.00 0.00 4.45
2906 3949 3.965694 ACTAATACGACTGTCTCCTGGT 58.034 45.455 6.21 0.00 0.00 4.00
2907 3950 4.342359 ACTAATACGACTGTCTCCTGGTT 58.658 43.478 6.21 0.00 0.00 3.67
2908 3951 3.870633 AATACGACTGTCTCCTGGTTC 57.129 47.619 6.21 0.00 0.00 3.62
2909 3952 2.281539 TACGACTGTCTCCTGGTTCA 57.718 50.000 6.21 0.00 0.00 3.18
2910 3953 1.633774 ACGACTGTCTCCTGGTTCAT 58.366 50.000 6.21 0.00 0.00 2.57
2911 3954 1.273606 ACGACTGTCTCCTGGTTCATG 59.726 52.381 6.21 0.00 0.00 3.07
2912 3955 1.273606 CGACTGTCTCCTGGTTCATGT 59.726 52.381 6.21 0.00 0.00 3.21
2913 3956 2.289072 CGACTGTCTCCTGGTTCATGTT 60.289 50.000 6.21 0.00 0.00 2.71
2914 3957 3.330267 GACTGTCTCCTGGTTCATGTTC 58.670 50.000 0.00 0.00 0.00 3.18
2915 3958 2.975489 ACTGTCTCCTGGTTCATGTTCT 59.025 45.455 0.00 0.00 0.00 3.01
2916 3959 3.007398 ACTGTCTCCTGGTTCATGTTCTC 59.993 47.826 0.00 0.00 0.00 2.87
2917 3960 3.242867 TGTCTCCTGGTTCATGTTCTCT 58.757 45.455 0.00 0.00 0.00 3.10
2918 3961 3.007290 TGTCTCCTGGTTCATGTTCTCTG 59.993 47.826 0.00 0.00 0.00 3.35
2919 3962 2.568956 TCTCCTGGTTCATGTTCTCTGG 59.431 50.000 0.00 0.00 0.00 3.86
2920 3963 1.003580 TCCTGGTTCATGTTCTCTGGC 59.996 52.381 0.00 0.00 0.00 4.85
2921 3964 1.271543 CCTGGTTCATGTTCTCTGGCA 60.272 52.381 0.00 0.00 0.00 4.92
2922 3965 1.808945 CTGGTTCATGTTCTCTGGCAC 59.191 52.381 0.00 0.00 0.00 5.01
2923 3966 1.168714 GGTTCATGTTCTCTGGCACC 58.831 55.000 0.00 0.00 0.00 5.01
2924 3967 1.271597 GGTTCATGTTCTCTGGCACCT 60.272 52.381 0.00 0.00 0.00 4.00
2925 3968 2.508526 GTTCATGTTCTCTGGCACCTT 58.491 47.619 0.00 0.00 0.00 3.50
2926 3969 3.559171 GGTTCATGTTCTCTGGCACCTTA 60.559 47.826 0.00 0.00 0.00 2.69
2927 3970 3.616956 TCATGTTCTCTGGCACCTTAG 57.383 47.619 0.00 0.00 0.00 2.18
2928 3971 2.237143 TCATGTTCTCTGGCACCTTAGG 59.763 50.000 0.00 0.00 0.00 2.69
2929 3972 0.984230 TGTTCTCTGGCACCTTAGGG 59.016 55.000 2.32 0.00 38.88 3.53
2930 3973 0.253327 GTTCTCTGGCACCTTAGGGG 59.747 60.000 2.32 0.00 41.89 4.79
2931 3974 0.118346 TTCTCTGGCACCTTAGGGGA 59.882 55.000 3.89 0.00 38.76 4.81
2932 3975 0.617820 TCTCTGGCACCTTAGGGGAC 60.618 60.000 3.89 0.00 38.76 4.46
2933 3976 1.961180 CTCTGGCACCTTAGGGGACG 61.961 65.000 3.89 0.00 38.76 4.79
2934 3977 2.203877 TGGCACCTTAGGGGACGT 60.204 61.111 3.89 0.00 38.76 4.34
2935 3978 2.240162 CTGGCACCTTAGGGGACGTC 62.240 65.000 3.89 7.13 38.76 4.34
2936 3979 2.582978 GCACCTTAGGGGACGTCC 59.417 66.667 27.04 27.04 38.76 4.79
2937 3980 2.890371 CACCTTAGGGGACGTCCG 59.110 66.667 27.68 15.31 38.76 4.79
2938 3981 1.679977 CACCTTAGGGGACGTCCGA 60.680 63.158 27.68 13.18 38.76 4.55
2939 3982 1.041447 CACCTTAGGGGACGTCCGAT 61.041 60.000 27.68 20.29 38.76 4.18
2940 3983 0.552848 ACCTTAGGGGACGTCCGATA 59.447 55.000 27.68 19.26 38.76 2.92
2941 3984 0.957362 CCTTAGGGGACGTCCGATAC 59.043 60.000 27.68 17.22 37.23 2.24
2942 3985 1.478288 CCTTAGGGGACGTCCGATACT 60.478 57.143 27.68 22.65 37.23 2.12
2943 3986 2.224621 CCTTAGGGGACGTCCGATACTA 60.225 54.545 27.68 21.71 37.23 1.82
2944 3987 2.550830 TAGGGGACGTCCGATACTAC 57.449 55.000 27.68 12.09 36.71 2.73
2945 3988 0.842635 AGGGGACGTCCGATACTACT 59.157 55.000 27.68 13.40 36.71 2.57
2946 3989 1.202746 AGGGGACGTCCGATACTACTC 60.203 57.143 27.68 10.62 36.71 2.59
2947 3990 1.233919 GGGACGTCCGATACTACTCC 58.766 60.000 27.68 6.46 36.71 3.85
2948 3991 1.202746 GGGACGTCCGATACTACTCCT 60.203 57.143 27.68 0.00 36.71 3.69
2949 3992 2.037772 GGGACGTCCGATACTACTCCTA 59.962 54.545 27.68 0.00 36.71 2.94
2950 3993 3.307339 GGGACGTCCGATACTACTCCTAT 60.307 52.174 27.68 0.00 36.71 2.57
2951 3994 3.683822 GGACGTCCGATACTACTCCTATG 59.316 52.174 20.85 0.00 0.00 2.23
2952 3995 4.562347 GGACGTCCGATACTACTCCTATGA 60.562 50.000 20.85 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 2.909965 GGGCACAAAAGCGGGTGA 60.910 61.111 0.00 0.00 37.18 4.02
88 89 5.881923 TTGTACTTAGTCCAGACCAAACT 57.118 39.130 0.00 0.00 0.00 2.66
154 156 5.104360 ACCTACTTATTGCCATCTGACACAT 60.104 40.000 0.00 0.00 0.00 3.21
286 288 9.277565 CAACAAATCAGAAAATATGGTAGTTCG 57.722 33.333 0.00 0.00 0.00 3.95
369 371 5.647658 CACCTAGTATCAATTGGCTCAACAA 59.352 40.000 5.42 0.00 34.41 2.83
452 454 5.416952 ACATGGGAAGAAACAAGCAGAATAG 59.583 40.000 0.00 0.00 0.00 1.73
473 475 5.191426 CACATCCAGAAAGATGAGGAACAT 58.809 41.667 8.44 0.00 45.43 2.71
641 643 6.014669 CAGATCCCTAAAAACAACAAATCCCA 60.015 38.462 0.00 0.00 0.00 4.37
695 698 0.398318 GAGAACAAGCAGACCCCAGT 59.602 55.000 0.00 0.00 0.00 4.00
824 827 5.118664 CGCCACCGTATATATGAACTTGAAG 59.881 44.000 3.36 0.00 0.00 3.02
1023 1026 0.888619 TCGCACCGATGAAGAAGAGT 59.111 50.000 0.00 0.00 0.00 3.24
1097 1100 2.325583 AGAGTTGACCAAGCAAACGA 57.674 45.000 0.00 0.00 0.00 3.85
1118 1121 3.189910 ACAAGTCTAGCACATGCATGTTG 59.810 43.478 29.48 22.76 45.16 3.33
1703 1714 4.518970 GGTAAACCATCTTCAGCAAGAACA 59.481 41.667 0.00 0.00 42.14 3.18
1727 1738 2.300437 GCAGGTCTTGTACTTCACCTCT 59.700 50.000 7.11 0.00 0.00 3.69
1809 1832 3.079578 CGCCATTGATCCTCATATGCTT 58.920 45.455 0.00 0.00 0.00 3.91
1933 1972 8.755977 AGGTACTTCATCTCGGTCTTAATTTTA 58.244 33.333 0.00 0.00 27.25 1.52
2218 3250 7.369607 TCAGAATCAAAATGATCGAAGCAAAA 58.630 30.769 0.00 0.00 35.76 2.44
2219 3251 6.912082 TCAGAATCAAAATGATCGAAGCAAA 58.088 32.000 0.00 0.00 35.76 3.68
2355 3387 3.594603 AATAGTGACGTCAGGAGTTGG 57.405 47.619 20.73 0.00 0.00 3.77
2495 3527 4.823442 CACCTATTCATAATGCAGCCTCAA 59.177 41.667 0.00 0.00 0.00 3.02
2639 3674 5.067413 AGACTGCTATTCCGACGATAAGAAA 59.933 40.000 0.00 0.00 0.00 2.52
2665 3700 8.490355 GCGTGTAATGTTAAGTTTGTAGTAACT 58.510 33.333 0.00 0.00 39.97 2.24
2674 3709 5.297278 TGGTCAAGCGTGTAATGTTAAGTTT 59.703 36.000 0.00 0.00 0.00 2.66
2726 3769 8.045507 CCAGACTATACATACTAGATCGGGTAA 58.954 40.741 0.00 0.00 0.00 2.85
2756 3799 1.077930 CTGTGCTCTCACCCATGGG 60.078 63.158 30.23 30.23 42.46 4.00
2757 3800 0.545171 ATCTGTGCTCTCACCCATGG 59.455 55.000 4.14 4.14 42.46 3.66
2758 3801 1.664873 CATCTGTGCTCTCACCCATG 58.335 55.000 0.00 0.00 42.46 3.66
2770 3813 1.676746 CTCATCCCCAAGCATCTGTG 58.323 55.000 0.00 0.00 0.00 3.66
2771 3814 0.549950 CCTCATCCCCAAGCATCTGT 59.450 55.000 0.00 0.00 0.00 3.41
2772 3815 0.841961 TCCTCATCCCCAAGCATCTG 59.158 55.000 0.00 0.00 0.00 2.90
2773 3816 1.830486 ATCCTCATCCCCAAGCATCT 58.170 50.000 0.00 0.00 0.00 2.90
2774 3817 2.617532 GCTATCCTCATCCCCAAGCATC 60.618 54.545 0.00 0.00 0.00 3.91
2775 3818 1.353694 GCTATCCTCATCCCCAAGCAT 59.646 52.381 0.00 0.00 0.00 3.79
2776 3819 0.767375 GCTATCCTCATCCCCAAGCA 59.233 55.000 0.00 0.00 0.00 3.91
2777 3820 0.037447 GGCTATCCTCATCCCCAAGC 59.963 60.000 0.00 0.00 0.00 4.01
2778 3821 1.739750 AGGCTATCCTCATCCCCAAG 58.260 55.000 0.00 0.00 38.72 3.61
2779 3822 3.999493 AGGCTATCCTCATCCCCAA 57.001 52.632 0.00 0.00 38.72 4.12
2787 3830 6.116539 TATGTGTGCATCGAGGCTATCCTC 62.117 50.000 23.78 2.27 43.96 3.71
2788 3831 4.319101 TATGTGTGCATCGAGGCTATCCT 61.319 47.826 23.78 7.82 39.90 3.24
2789 3832 0.104855 TGTGTGCATCGAGGCTATCC 59.895 55.000 23.78 8.90 34.04 2.59
2790 3833 2.160822 ATGTGTGCATCGAGGCTATC 57.839 50.000 23.78 13.54 34.04 2.08
2791 3834 2.630098 ACTATGTGTGCATCGAGGCTAT 59.370 45.455 23.78 13.83 36.58 2.97
2792 3835 2.031870 ACTATGTGTGCATCGAGGCTA 58.968 47.619 23.78 9.54 36.58 3.93
2793 3836 0.826715 ACTATGTGTGCATCGAGGCT 59.173 50.000 23.78 4.69 36.58 4.58
2794 3837 1.594862 GAACTATGTGTGCATCGAGGC 59.405 52.381 16.46 16.46 36.58 4.70
2795 3838 1.854743 CGAACTATGTGTGCATCGAGG 59.145 52.381 0.00 0.00 36.58 4.63
2796 3839 2.530177 ACGAACTATGTGTGCATCGAG 58.470 47.619 8.89 1.72 36.58 4.04
2797 3840 2.647529 ACGAACTATGTGTGCATCGA 57.352 45.000 8.89 0.00 36.58 3.59
2798 3841 3.796717 ACATACGAACTATGTGTGCATCG 59.203 43.478 0.00 0.00 43.39 3.84
2799 3842 4.209288 GGACATACGAACTATGTGTGCATC 59.791 45.833 2.21 0.00 44.78 3.91
2800 3843 4.119862 GGACATACGAACTATGTGTGCAT 58.880 43.478 2.21 0.00 44.78 3.96
2801 3844 3.194755 AGGACATACGAACTATGTGTGCA 59.805 43.478 2.21 0.00 44.78 4.57
2802 3845 3.782046 AGGACATACGAACTATGTGTGC 58.218 45.455 2.21 0.00 44.78 4.57
2803 3846 7.821595 TTTAAGGACATACGAACTATGTGTG 57.178 36.000 2.21 0.00 44.78 3.82
2834 3877 8.840321 CGAGGATCAATTATGGAGTTGTTTAAT 58.160 33.333 0.00 0.00 33.17 1.40
2835 3878 7.827236 ACGAGGATCAATTATGGAGTTGTTTAA 59.173 33.333 0.00 0.00 33.17 1.52
2836 3879 7.279981 CACGAGGATCAATTATGGAGTTGTTTA 59.720 37.037 0.00 0.00 33.17 2.01
2837 3880 6.094048 CACGAGGATCAATTATGGAGTTGTTT 59.906 38.462 0.00 0.00 33.17 2.83
2838 3881 5.586243 CACGAGGATCAATTATGGAGTTGTT 59.414 40.000 0.00 0.00 33.17 2.83
2839 3882 5.118990 CACGAGGATCAATTATGGAGTTGT 58.881 41.667 0.00 0.00 33.17 3.32
2840 3883 4.024556 GCACGAGGATCAATTATGGAGTTG 60.025 45.833 0.00 0.00 33.17 3.16
2841 3884 4.130118 GCACGAGGATCAATTATGGAGTT 58.870 43.478 0.00 0.00 33.17 3.01
2842 3885 3.495100 GGCACGAGGATCAATTATGGAGT 60.495 47.826 0.00 0.00 33.17 3.85
2843 3886 3.070018 GGCACGAGGATCAATTATGGAG 58.930 50.000 0.00 0.00 33.17 3.86
2844 3887 2.705658 AGGCACGAGGATCAATTATGGA 59.294 45.455 0.00 0.00 33.17 3.41
2845 3888 3.131709 AGGCACGAGGATCAATTATGG 57.868 47.619 0.00 0.00 33.17 2.74
2846 3889 6.045318 CCTATAGGCACGAGGATCAATTATG 58.955 44.000 5.67 0.00 33.17 1.90
2847 3890 6.227298 CCTATAGGCACGAGGATCAATTAT 57.773 41.667 5.67 0.00 33.17 1.28
2848 3891 5.661056 CCTATAGGCACGAGGATCAATTA 57.339 43.478 5.67 0.00 33.17 1.40
2849 3892 4.543590 CCTATAGGCACGAGGATCAATT 57.456 45.455 5.67 0.00 33.17 2.32
2868 3911 9.841295 TCGTATTAGTAAATAAATTTCCTGCCT 57.159 29.630 0.00 0.00 29.41 4.75
2869 3912 9.874215 GTCGTATTAGTAAATAAATTTCCTGCC 57.126 33.333 0.00 0.00 29.41 4.85
2879 3922 8.627403 CCAGGAGACAGTCGTATTAGTAAATAA 58.373 37.037 0.00 0.00 29.41 1.40
2880 3923 7.776969 ACCAGGAGACAGTCGTATTAGTAAATA 59.223 37.037 0.00 0.00 0.00 1.40
2881 3924 6.606395 ACCAGGAGACAGTCGTATTAGTAAAT 59.394 38.462 0.00 0.00 0.00 1.40
2882 3925 5.948162 ACCAGGAGACAGTCGTATTAGTAAA 59.052 40.000 0.00 0.00 0.00 2.01
2883 3926 5.503927 ACCAGGAGACAGTCGTATTAGTAA 58.496 41.667 0.00 0.00 0.00 2.24
2884 3927 5.108187 ACCAGGAGACAGTCGTATTAGTA 57.892 43.478 0.00 0.00 0.00 1.82
2885 3928 3.965694 ACCAGGAGACAGTCGTATTAGT 58.034 45.455 0.00 0.00 0.00 2.24
2886 3929 4.398358 TGAACCAGGAGACAGTCGTATTAG 59.602 45.833 0.00 0.00 0.00 1.73
2887 3930 4.338012 TGAACCAGGAGACAGTCGTATTA 58.662 43.478 0.00 0.00 0.00 0.98
2888 3931 3.162666 TGAACCAGGAGACAGTCGTATT 58.837 45.455 0.00 0.00 0.00 1.89
2889 3932 2.803956 TGAACCAGGAGACAGTCGTAT 58.196 47.619 0.00 0.00 0.00 3.06
2890 3933 2.281539 TGAACCAGGAGACAGTCGTA 57.718 50.000 0.00 0.00 0.00 3.43
2891 3934 1.273606 CATGAACCAGGAGACAGTCGT 59.726 52.381 0.00 0.00 0.00 4.34
2892 3935 1.273606 ACATGAACCAGGAGACAGTCG 59.726 52.381 0.00 0.00 0.00 4.18
2893 3936 3.007398 AGAACATGAACCAGGAGACAGTC 59.993 47.826 0.00 0.00 0.00 3.51
2894 3937 2.975489 AGAACATGAACCAGGAGACAGT 59.025 45.455 0.00 0.00 0.00 3.55
2895 3938 3.260380 AGAGAACATGAACCAGGAGACAG 59.740 47.826 0.00 0.00 0.00 3.51
2896 3939 3.007290 CAGAGAACATGAACCAGGAGACA 59.993 47.826 0.00 0.00 0.00 3.41
2897 3940 3.594134 CAGAGAACATGAACCAGGAGAC 58.406 50.000 0.00 0.00 0.00 3.36
2898 3941 2.568956 CCAGAGAACATGAACCAGGAGA 59.431 50.000 0.00 0.00 0.00 3.71
2899 3942 2.938756 GCCAGAGAACATGAACCAGGAG 60.939 54.545 0.00 0.00 0.00 3.69
2900 3943 1.003580 GCCAGAGAACATGAACCAGGA 59.996 52.381 0.00 0.00 0.00 3.86
2901 3944 1.271543 TGCCAGAGAACATGAACCAGG 60.272 52.381 0.00 0.00 0.00 4.45
2902 3945 1.808945 GTGCCAGAGAACATGAACCAG 59.191 52.381 0.00 0.00 0.00 4.00
2903 3946 1.545428 GGTGCCAGAGAACATGAACCA 60.545 52.381 0.00 0.00 0.00 3.67
2904 3947 1.168714 GGTGCCAGAGAACATGAACC 58.831 55.000 0.00 0.00 0.00 3.62
2905 3948 2.191128 AGGTGCCAGAGAACATGAAC 57.809 50.000 0.00 0.00 0.00 3.18
2906 3949 2.957402 AAGGTGCCAGAGAACATGAA 57.043 45.000 0.00 0.00 0.00 2.57
2907 3950 2.237143 CCTAAGGTGCCAGAGAACATGA 59.763 50.000 0.00 0.00 0.00 3.07
2908 3951 2.636830 CCTAAGGTGCCAGAGAACATG 58.363 52.381 0.00 0.00 0.00 3.21
2909 3952 1.561542 CCCTAAGGTGCCAGAGAACAT 59.438 52.381 0.00 0.00 0.00 2.71
2910 3953 0.984230 CCCTAAGGTGCCAGAGAACA 59.016 55.000 0.00 0.00 0.00 3.18
2911 3954 0.253327 CCCCTAAGGTGCCAGAGAAC 59.747 60.000 0.00 0.00 0.00 3.01
2912 3955 0.118346 TCCCCTAAGGTGCCAGAGAA 59.882 55.000 0.00 0.00 36.75 2.87
2913 3956 0.617820 GTCCCCTAAGGTGCCAGAGA 60.618 60.000 0.00 0.00 36.75 3.10
2914 3957 1.908483 GTCCCCTAAGGTGCCAGAG 59.092 63.158 0.00 0.00 36.75 3.35
2915 3958 1.987855 CGTCCCCTAAGGTGCCAGA 60.988 63.158 0.00 0.00 36.75 3.86
2916 3959 2.240162 GACGTCCCCTAAGGTGCCAG 62.240 65.000 3.51 0.00 36.75 4.85
2917 3960 2.203877 ACGTCCCCTAAGGTGCCA 60.204 61.111 0.00 0.00 36.75 4.92
2918 3961 2.582978 GACGTCCCCTAAGGTGCC 59.417 66.667 3.51 0.00 36.75 5.01
2919 3962 2.582978 GGACGTCCCCTAAGGTGC 59.417 66.667 24.75 0.00 36.75 5.01
2920 3963 1.041447 ATCGGACGTCCCCTAAGGTG 61.041 60.000 28.52 12.03 36.75 4.00
2921 3964 0.552848 TATCGGACGTCCCCTAAGGT 59.447 55.000 28.52 12.98 36.75 3.50
2922 3965 0.957362 GTATCGGACGTCCCCTAAGG 59.043 60.000 28.52 13.54 0.00 2.69
2923 3966 1.978454 AGTATCGGACGTCCCCTAAG 58.022 55.000 28.52 14.29 0.00 2.18
2924 3967 2.439507 AGTAGTATCGGACGTCCCCTAA 59.560 50.000 28.52 12.19 0.00 2.69
2925 3968 2.037772 GAGTAGTATCGGACGTCCCCTA 59.962 54.545 28.52 18.75 0.00 3.53
2926 3969 0.842635 AGTAGTATCGGACGTCCCCT 59.157 55.000 28.52 19.71 0.00 4.79
2927 3970 1.233919 GAGTAGTATCGGACGTCCCC 58.766 60.000 28.52 13.79 0.00 4.81
2928 3971 1.202746 AGGAGTAGTATCGGACGTCCC 60.203 57.143 28.52 14.51 31.10 4.46
2929 3972 2.252976 AGGAGTAGTATCGGACGTCC 57.747 55.000 25.28 25.28 0.00 4.79
2930 3973 4.564041 TCATAGGAGTAGTATCGGACGTC 58.436 47.826 7.13 7.13 0.00 4.34
2931 3974 4.613925 TCATAGGAGTAGTATCGGACGT 57.386 45.455 0.00 0.00 0.00 4.34


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

AutoCloner maintained by Alex Coulton.