Multiple sequence alignment - TraesCS3D01G153700

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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 TraesCS3D01G153700 chr3D 100.000 2922 0 0 1 2922 120630526 120633447 0.000000e+00 5397.0
1 TraesCS3D01G153700 chr3B 92.195 2729 112 40 1 2648 172702242 172704950 0.000000e+00 3766.0
2 TraesCS3D01G153700 chr3B 90.476 63 4 1 2802 2864 172724521 172724581 6.710000e-12 82.4
3 TraesCS3D01G153700 chr3A 92.602 2663 117 40 31 2643 127355816 127353184 0.000000e+00 3753.0
4 TraesCS3D01G153700 chr3A 92.174 115 6 3 2675 2789 127353108 127352997 3.010000e-35 159.0
5 TraesCS3D01G153700 chr3A 100.000 29 0 0 1 29 127356093 127356065 1.000000e-03 54.7
6 TraesCS3D01G153700 chr7D 100.000 30 0 0 2876 2905 433744965 433744994 4.070000e-04 56.5


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 TraesCS3D01G153700 chr3D 120630526 120633447 2921 False 5397.000000 5397 100.000000 1 2922 1 chr3D.!!$F1 2921
1 TraesCS3D01G153700 chr3B 172702242 172704950 2708 False 3766.000000 3766 92.195000 1 2648 1 chr3B.!!$F1 2647
2 TraesCS3D01G153700 chr3A 127352997 127356093 3096 True 1322.233333 3753 94.925333 1 2789 3 chr3A.!!$R1 2788

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
408 684 1.672854 TACAATCCGGCCAGTCTCCG 61.673 60.000 2.24 0.0 46.05 4.63 F
460 736 1.726865 CAGCGCAGAGATCTCGAGT 59.273 57.895 16.97 0.0 34.09 4.18 F
943 1240 2.186644 CGGCCGGTGACATGATCA 59.813 61.111 20.10 0.0 33.79 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1236 1552 0.585838 CCGCGCACATATATTGCACA 59.414 50.000 8.75 0.0 40.2 4.57 R
1580 1908 1.679898 CACCACCCTCACCTCCTTC 59.320 63.158 0.00 0.0 0.0 3.46 R
2883 3285 0.109532 TTGTGGGTCGGCATTGAAGA 59.890 50.000 0.00 0.0 0.0 2.87 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
35 283 7.120285 AGCTTAGCATGCATGGTATAAATGTAG 59.880 37.037 32.65 25.55 40.08 2.74
408 684 1.672854 TACAATCCGGCCAGTCTCCG 61.673 60.000 2.24 0.00 46.05 4.63
460 736 1.726865 CAGCGCAGAGATCTCGAGT 59.273 57.895 16.97 0.00 34.09 4.18
542 818 4.101448 AGGCCTGCGTCACCATCC 62.101 66.667 3.11 0.00 0.00 3.51
555 831 2.780040 CATCCCATGCCCCCTCCT 60.780 66.667 0.00 0.00 0.00 3.69
560 836 2.311854 CCATGCCCCCTCCTGTCTT 61.312 63.158 0.00 0.00 0.00 3.01
601 877 8.383175 ACATTCTATTGGATATTACCCACGAAT 58.617 33.333 0.00 0.00 32.58 3.34
607 883 6.673839 TGGATATTACCCACGAATCATACA 57.326 37.500 0.00 0.00 0.00 2.29
608 884 7.068686 TGGATATTACCCACGAATCATACAA 57.931 36.000 0.00 0.00 0.00 2.41
896 1181 6.274672 ACTCTAGATCTAGGCTAATCTGGACT 59.725 42.308 26.02 12.66 35.39 3.85
943 1240 2.186644 CGGCCGGTGACATGATCA 59.813 61.111 20.10 0.00 33.79 2.92
1063 1374 4.062991 CCGCACTGAAAACCTTAGTACTT 58.937 43.478 0.00 0.00 0.00 2.24
1077 1391 5.535783 CCTTAGTACTTCTACCTAGCTTCCC 59.464 48.000 0.00 0.00 0.00 3.97
1109 1423 3.436243 AGGAAGAGAGAATCCAACGAGT 58.564 45.455 0.00 0.00 38.23 4.18
1212 1527 2.563620 TCGGTCTGTATACCTTGCACAA 59.436 45.455 0.00 0.00 37.39 3.33
1235 1551 7.436080 ACAAAAATATAATGGCTTGCATCTTCG 59.564 33.333 0.00 0.00 0.00 3.79
1236 1552 6.639632 AAATATAATGGCTTGCATCTTCGT 57.360 33.333 0.00 0.00 0.00 3.85
1237 1553 3.976793 ATAATGGCTTGCATCTTCGTG 57.023 42.857 0.00 0.00 0.00 4.35
1653 1983 4.139786 ACATCCAGGCAGTTATAAGCATG 58.860 43.478 4.80 4.80 41.74 4.06
1657 1987 4.349048 TCCAGGCAGTTATAAGCATGATCT 59.651 41.667 11.59 0.24 44.53 2.75
1686 2016 1.607628 CTTTGAGCATCTGCCATAGCC 59.392 52.381 0.00 0.00 43.38 3.93
1718 2048 7.872881 GCTTGGTTTATTATAAGCTAAGTCCC 58.127 38.462 19.64 6.22 41.60 4.46
1881 2217 7.646922 GTGCGTACTGTACTACTTAATTAGCAT 59.353 37.037 15.35 0.00 0.00 3.79
1995 2339 6.716628 ACCCTGCAATGTAATGGTGATTATAG 59.283 38.462 0.00 0.00 0.00 1.31
2120 2468 4.640201 TCTGACTTTTGGGTCTTGTTTCTG 59.360 41.667 0.00 0.00 37.16 3.02
2134 2482 7.362056 GGTCTTGTTTCTGTATGCAATATGTGT 60.362 37.037 0.00 0.00 0.00 3.72
2372 2729 2.084681 CGTGAGCGTACGTGGTTCC 61.085 63.158 17.90 0.00 39.13 3.62
2501 2858 4.575885 ACTGTACGTGTGCCTATCATTTT 58.424 39.130 0.00 0.00 0.00 1.82
2538 2895 2.270986 CCTGACAAAGCTGCCACCC 61.271 63.158 0.00 0.00 0.00 4.61
2582 2940 6.130723 CGCGCGAATAGGAAAACATATAAAA 58.869 36.000 28.94 0.00 0.00 1.52
2584 2942 7.201149 CGCGCGAATAGGAAAACATATAAAATG 60.201 37.037 28.94 0.00 0.00 2.32
2606 2964 8.900983 AATGAAAAAGGATGTATCTAGAGCTC 57.099 34.615 5.27 5.27 0.00 4.09
2612 2970 8.948401 AAAGGATGTATCTAGAGCTCATCTAA 57.052 34.615 17.77 0.00 40.06 2.10
2614 2972 8.348285 AGGATGTATCTAGAGCTCATCTAAAC 57.652 38.462 17.77 7.28 40.06 2.01
2615 2973 7.947332 AGGATGTATCTAGAGCTCATCTAAACA 59.053 37.037 17.77 12.66 40.06 2.83
2688 3090 3.198236 TTTCTGGTTGCTGCAGCGC 62.198 57.895 32.11 25.85 45.83 5.92
2702 3104 4.084888 GCGCCGGTCGTTTTCCTG 62.085 66.667 17.38 0.00 41.07 3.86
2708 3110 0.319405 CGGTCGTTTTCCTGTACCCT 59.681 55.000 0.00 0.00 0.00 4.34
2715 3117 3.586892 GTTTTCCTGTACCCTCTTCTCG 58.413 50.000 0.00 0.00 0.00 4.04
2716 3118 2.893215 TTCCTGTACCCTCTTCTCGA 57.107 50.000 0.00 0.00 0.00 4.04
2717 3119 2.125773 TCCTGTACCCTCTTCTCGAC 57.874 55.000 0.00 0.00 0.00 4.20
2718 3120 1.104630 CCTGTACCCTCTTCTCGACC 58.895 60.000 0.00 0.00 0.00 4.79
2765 3167 8.302438 ACAATCCCGTAGCATAGTATTACTAAC 58.698 37.037 7.61 3.90 33.89 2.34
2789 3191 8.575649 ACTACAGAACCAGAAAAAGAAAAAGA 57.424 30.769 0.00 0.00 0.00 2.52
2790 3192 9.020731 ACTACAGAACCAGAAAAAGAAAAAGAA 57.979 29.630 0.00 0.00 0.00 2.52
2791 3193 9.290483 CTACAGAACCAGAAAAAGAAAAAGAAC 57.710 33.333 0.00 0.00 0.00 3.01
2792 3194 7.666623 ACAGAACCAGAAAAAGAAAAAGAACA 58.333 30.769 0.00 0.00 0.00 3.18
2793 3195 7.814587 ACAGAACCAGAAAAAGAAAAAGAACAG 59.185 33.333 0.00 0.00 0.00 3.16
2794 3196 7.276438 CAGAACCAGAAAAAGAAAAAGAACAGG 59.724 37.037 0.00 0.00 0.00 4.00
2795 3197 6.605471 ACCAGAAAAAGAAAAAGAACAGGT 57.395 33.333 0.00 0.00 0.00 4.00
2796 3198 7.004555 ACCAGAAAAAGAAAAAGAACAGGTT 57.995 32.000 0.00 0.00 0.00 3.50
2797 3199 7.450074 ACCAGAAAAAGAAAAAGAACAGGTTT 58.550 30.769 0.00 0.00 0.00 3.27
2798 3200 7.936847 ACCAGAAAAAGAAAAAGAACAGGTTTT 59.063 29.630 0.00 0.00 0.00 2.43
2799 3201 8.783093 CCAGAAAAAGAAAAAGAACAGGTTTTT 58.217 29.630 0.00 0.00 39.30 1.94
2800 3202 9.597999 CAGAAAAAGAAAAAGAACAGGTTTTTG 57.402 29.630 0.00 0.00 37.25 2.44
2801 3203 8.783093 AGAAAAAGAAAAAGAACAGGTTTTTGG 58.217 29.630 0.00 0.00 37.25 3.28
2802 3204 8.458573 AAAAAGAAAAAGAACAGGTTTTTGGT 57.541 26.923 0.00 0.00 37.25 3.67
2803 3205 7.667043 AAAGAAAAAGAACAGGTTTTTGGTC 57.333 32.000 0.00 0.00 37.25 4.02
2804 3206 6.605471 AGAAAAAGAACAGGTTTTTGGTCT 57.395 33.333 0.00 0.00 46.80 3.85
2805 3207 6.631016 AGAAAAAGAACAGGTTTTTGGTCTC 58.369 36.000 0.00 0.00 44.14 3.36
2806 3208 5.993748 AAAAGAACAGGTTTTTGGTCTCA 57.006 34.783 0.00 0.00 44.14 3.27
2807 3209 5.582689 AAAGAACAGGTTTTTGGTCTCAG 57.417 39.130 0.00 0.00 44.14 3.35
2808 3210 3.555966 AGAACAGGTTTTTGGTCTCAGG 58.444 45.455 0.00 0.00 41.14 3.86
2809 3211 3.202151 AGAACAGGTTTTTGGTCTCAGGA 59.798 43.478 0.00 0.00 41.14 3.86
2810 3212 3.884037 ACAGGTTTTTGGTCTCAGGAT 57.116 42.857 0.00 0.00 0.00 3.24
2811 3213 3.490348 ACAGGTTTTTGGTCTCAGGATG 58.510 45.455 0.00 0.00 37.54 3.51
2812 3214 3.117512 ACAGGTTTTTGGTCTCAGGATGT 60.118 43.478 0.00 0.00 37.40 3.06
2813 3215 4.104102 ACAGGTTTTTGGTCTCAGGATGTA 59.896 41.667 0.00 0.00 37.40 2.29
2814 3216 5.222130 ACAGGTTTTTGGTCTCAGGATGTAT 60.222 40.000 0.00 0.00 37.40 2.29
2815 3217 5.355350 CAGGTTTTTGGTCTCAGGATGTATC 59.645 44.000 0.00 0.00 37.40 2.24
2816 3218 4.332819 GGTTTTTGGTCTCAGGATGTATCG 59.667 45.833 0.00 0.00 37.40 2.92
2817 3219 5.175859 GTTTTTGGTCTCAGGATGTATCGA 58.824 41.667 0.00 0.00 37.40 3.59
2818 3220 4.655762 TTTGGTCTCAGGATGTATCGAG 57.344 45.455 0.00 0.00 37.40 4.04
2819 3221 3.298686 TGGTCTCAGGATGTATCGAGT 57.701 47.619 0.00 0.00 37.40 4.18
2820 3222 4.432980 TGGTCTCAGGATGTATCGAGTA 57.567 45.455 0.00 0.00 37.40 2.59
2821 3223 4.135306 TGGTCTCAGGATGTATCGAGTAC 58.865 47.826 0.00 0.00 37.40 2.73
2822 3224 4.141459 TGGTCTCAGGATGTATCGAGTACT 60.141 45.833 0.00 0.00 37.40 2.73
2823 3225 4.214545 GGTCTCAGGATGTATCGAGTACTG 59.785 50.000 0.00 0.00 37.40 2.74
2824 3226 5.057819 GTCTCAGGATGTATCGAGTACTGA 58.942 45.833 0.00 0.00 37.40 3.41
2825 3227 5.527951 GTCTCAGGATGTATCGAGTACTGAA 59.472 44.000 0.00 0.00 37.40 3.02
2826 3228 5.527951 TCTCAGGATGTATCGAGTACTGAAC 59.472 44.000 0.00 0.00 37.40 3.18
2827 3229 5.190677 TCAGGATGTATCGAGTACTGAACA 58.809 41.667 0.00 0.00 37.40 3.18
2828 3230 5.066117 TCAGGATGTATCGAGTACTGAACAC 59.934 44.000 0.00 2.45 37.40 3.32
2829 3231 4.338682 AGGATGTATCGAGTACTGAACACC 59.661 45.833 0.00 4.13 34.27 4.16
2830 3232 4.499357 GGATGTATCGAGTACTGAACACCC 60.499 50.000 0.00 0.00 34.27 4.61
2831 3233 3.423749 TGTATCGAGTACTGAACACCCA 58.576 45.455 0.00 0.00 34.27 4.51
2832 3234 4.021229 TGTATCGAGTACTGAACACCCAT 58.979 43.478 0.00 0.00 34.27 4.00
2833 3235 5.195185 TGTATCGAGTACTGAACACCCATA 58.805 41.667 0.00 0.00 34.27 2.74
2834 3236 5.831525 TGTATCGAGTACTGAACACCCATAT 59.168 40.000 0.00 0.00 34.27 1.78
2835 3237 5.871396 ATCGAGTACTGAACACCCATATT 57.129 39.130 0.00 0.00 0.00 1.28
2836 3238 5.670792 TCGAGTACTGAACACCCATATTT 57.329 39.130 0.00 0.00 0.00 1.40
2837 3239 6.045072 TCGAGTACTGAACACCCATATTTT 57.955 37.500 0.00 0.00 0.00 1.82
2838 3240 6.103997 TCGAGTACTGAACACCCATATTTTC 58.896 40.000 0.00 0.00 0.00 2.29
2839 3241 5.293569 CGAGTACTGAACACCCATATTTTCC 59.706 44.000 0.00 0.00 0.00 3.13
2840 3242 5.183228 AGTACTGAACACCCATATTTTCCG 58.817 41.667 0.00 0.00 0.00 4.30
2841 3243 2.752903 ACTGAACACCCATATTTTCCGC 59.247 45.455 0.00 0.00 0.00 5.54
2842 3244 2.752354 CTGAACACCCATATTTTCCGCA 59.248 45.455 0.00 0.00 0.00 5.69
2843 3245 3.157881 TGAACACCCATATTTTCCGCAA 58.842 40.909 0.00 0.00 0.00 4.85
2844 3246 3.766591 TGAACACCCATATTTTCCGCAAT 59.233 39.130 0.00 0.00 0.00 3.56
2845 3247 4.221703 TGAACACCCATATTTTCCGCAATT 59.778 37.500 0.00 0.00 0.00 2.32
2846 3248 4.817318 ACACCCATATTTTCCGCAATTT 57.183 36.364 0.00 0.00 0.00 1.82
2847 3249 4.502962 ACACCCATATTTTCCGCAATTTG 58.497 39.130 0.00 0.00 0.00 2.32
2848 3250 4.221703 ACACCCATATTTTCCGCAATTTGA 59.778 37.500 0.00 0.00 0.00 2.69
2849 3251 4.805192 CACCCATATTTTCCGCAATTTGAG 59.195 41.667 0.00 0.00 0.00 3.02
2850 3252 3.803778 CCCATATTTTCCGCAATTTGAGC 59.196 43.478 0.00 0.00 0.00 4.26
2851 3253 4.441913 CCCATATTTTCCGCAATTTGAGCT 60.442 41.667 0.00 0.00 0.00 4.09
2852 3254 4.741676 CCATATTTTCCGCAATTTGAGCTC 59.258 41.667 6.82 6.82 0.00 4.09
2853 3255 3.940209 ATTTTCCGCAATTTGAGCTCA 57.060 38.095 13.74 13.74 0.00 4.26
2854 3256 3.724508 TTTTCCGCAATTTGAGCTCAA 57.275 38.095 25.16 25.16 0.00 3.02
2870 3272 8.547967 TTGAGCTCAAAGTATTTACTAGTTGG 57.452 34.615 26.61 0.00 35.03 3.77
2871 3273 7.103641 TGAGCTCAAAGTATTTACTAGTTGGG 58.896 38.462 15.67 0.00 35.03 4.12
2872 3274 5.880887 AGCTCAAAGTATTTACTAGTTGGGC 59.119 40.000 14.85 14.85 44.76 5.36
2873 3275 5.880887 GCTCAAAGTATTTACTAGTTGGGCT 59.119 40.000 15.19 0.00 42.77 5.19
2874 3276 7.046033 GCTCAAAGTATTTACTAGTTGGGCTA 58.954 38.462 15.19 0.00 42.77 3.93
2875 3277 7.715686 GCTCAAAGTATTTACTAGTTGGGCTAT 59.284 37.037 15.19 0.00 42.77 2.97
2880 3282 8.203681 AGTATTTACTAGTTGGGCTATAAGGG 57.796 38.462 0.00 0.00 34.13 3.95
2881 3283 4.968971 TTACTAGTTGGGCTATAAGGGC 57.031 45.455 0.00 0.00 0.00 5.19
2882 3284 2.771688 ACTAGTTGGGCTATAAGGGCA 58.228 47.619 0.00 0.00 0.00 5.36
2883 3285 3.327439 ACTAGTTGGGCTATAAGGGCAT 58.673 45.455 0.00 0.00 0.00 4.40
2884 3286 2.959465 AGTTGGGCTATAAGGGCATC 57.041 50.000 0.00 0.00 0.00 3.91
2885 3287 2.422746 AGTTGGGCTATAAGGGCATCT 58.577 47.619 0.00 0.00 0.00 2.90
2886 3288 2.785857 AGTTGGGCTATAAGGGCATCTT 59.214 45.455 0.00 0.00 39.40 2.40
2887 3289 3.149981 GTTGGGCTATAAGGGCATCTTC 58.850 50.000 0.00 0.00 36.93 2.87
2888 3290 2.417652 TGGGCTATAAGGGCATCTTCA 58.582 47.619 0.00 0.00 36.93 3.02
2889 3291 2.782925 TGGGCTATAAGGGCATCTTCAA 59.217 45.455 0.00 0.00 36.93 2.69
2890 3292 3.398967 TGGGCTATAAGGGCATCTTCAAT 59.601 43.478 0.00 0.00 36.93 2.57
2891 3293 3.760684 GGGCTATAAGGGCATCTTCAATG 59.239 47.826 0.00 0.00 36.93 2.82
2892 3294 3.192212 GGCTATAAGGGCATCTTCAATGC 59.808 47.826 1.40 1.40 43.85 3.56
2898 3300 1.729881 GCATCTTCAATGCCGACCC 59.270 57.895 0.00 0.00 39.01 4.46
2899 3301 1.031571 GCATCTTCAATGCCGACCCA 61.032 55.000 0.00 0.00 39.01 4.51
2900 3302 0.734889 CATCTTCAATGCCGACCCAC 59.265 55.000 0.00 0.00 0.00 4.61
2901 3303 0.327924 ATCTTCAATGCCGACCCACA 59.672 50.000 0.00 0.00 0.00 4.17
2902 3304 0.109532 TCTTCAATGCCGACCCACAA 59.890 50.000 0.00 0.00 0.00 3.33
2903 3305 0.958091 CTTCAATGCCGACCCACAAA 59.042 50.000 0.00 0.00 0.00 2.83
2904 3306 0.671251 TTCAATGCCGACCCACAAAC 59.329 50.000 0.00 0.00 0.00 2.93
2905 3307 1.175983 TCAATGCCGACCCACAAACC 61.176 55.000 0.00 0.00 0.00 3.27
2906 3308 1.152830 AATGCCGACCCACAAACCT 59.847 52.632 0.00 0.00 0.00 3.50
2907 3309 0.402504 AATGCCGACCCACAAACCTA 59.597 50.000 0.00 0.00 0.00 3.08
2908 3310 0.322187 ATGCCGACCCACAAACCTAC 60.322 55.000 0.00 0.00 0.00 3.18
2909 3311 1.673337 GCCGACCCACAAACCTACC 60.673 63.158 0.00 0.00 0.00 3.18
2910 3312 1.375013 CCGACCCACAAACCTACCG 60.375 63.158 0.00 0.00 0.00 4.02
2911 3313 2.030958 CGACCCACAAACCTACCGC 61.031 63.158 0.00 0.00 0.00 5.68
2912 3314 1.373812 GACCCACAAACCTACCGCT 59.626 57.895 0.00 0.00 0.00 5.52
2913 3315 0.609662 GACCCACAAACCTACCGCTA 59.390 55.000 0.00 0.00 0.00 4.26
2914 3316 0.322648 ACCCACAAACCTACCGCTAC 59.677 55.000 0.00 0.00 0.00 3.58
2915 3317 0.611714 CCCACAAACCTACCGCTACT 59.388 55.000 0.00 0.00 0.00 2.57
2916 3318 1.674817 CCCACAAACCTACCGCTACTG 60.675 57.143 0.00 0.00 0.00 2.74
2917 3319 1.001633 CCACAAACCTACCGCTACTGT 59.998 52.381 0.00 0.00 0.00 3.55
2918 3320 2.549349 CCACAAACCTACCGCTACTGTT 60.549 50.000 0.00 0.00 0.00 3.16
2919 3321 2.735134 CACAAACCTACCGCTACTGTTC 59.265 50.000 0.00 0.00 0.00 3.18
2920 3322 1.990563 CAAACCTACCGCTACTGTTCG 59.009 52.381 0.00 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 334 5.627499 ATGCTGTACACTTGTATGTTTGG 57.373 39.130 0.00 0.00 33.85 3.28
292 549 2.277756 GCTCGCAGTACGTACGGG 60.278 66.667 24.09 21.97 44.19 5.28
313 582 2.048784 TGAGTGTGAGCAGAGCGC 60.049 61.111 0.00 0.00 42.91 5.92
321 590 0.036010 GGATGGGGTGTGAGTGTGAG 60.036 60.000 0.00 0.00 0.00 3.51
322 591 1.488705 GGGATGGGGTGTGAGTGTGA 61.489 60.000 0.00 0.00 0.00 3.58
323 592 1.002134 GGGATGGGGTGTGAGTGTG 60.002 63.158 0.00 0.00 0.00 3.82
324 593 0.846427 ATGGGATGGGGTGTGAGTGT 60.846 55.000 0.00 0.00 0.00 3.55
325 594 0.107017 GATGGGATGGGGTGTGAGTG 60.107 60.000 0.00 0.00 0.00 3.51
326 595 1.281925 GGATGGGATGGGGTGTGAGT 61.282 60.000 0.00 0.00 0.00 3.41
460 736 1.270907 GAGCTGGAAGAGGTCAAGGA 58.729 55.000 0.00 0.00 46.77 3.36
542 818 2.276309 GAAGACAGGAGGGGGCATGG 62.276 65.000 0.00 0.00 0.00 3.66
555 831 2.303022 GTCTCTGATGGTTGGGAAGACA 59.697 50.000 0.00 0.00 0.00 3.41
560 836 3.184628 AGAATGTCTCTGATGGTTGGGA 58.815 45.455 0.00 0.00 31.12 4.37
869 1154 5.652014 CCAGATTAGCCTAGATCTAGAGTGG 59.348 48.000 28.04 18.05 35.21 4.00
896 1181 4.161189 AGCTAGCTGCATCTTTCTTACTGA 59.839 41.667 18.57 0.00 45.94 3.41
943 1240 0.546267 AGAGGAGGTGGTCACATGCT 60.546 55.000 9.35 9.35 46.04 3.79
1063 1374 2.928334 CTACACGGGAAGCTAGGTAGA 58.072 52.381 0.00 0.00 32.09 2.59
1077 1391 1.329292 CTCTCTTCCTCGAGCTACACG 59.671 57.143 6.99 0.00 0.00 4.49
1109 1423 2.751436 GCTTCGCCATTGCTCCCA 60.751 61.111 0.00 0.00 34.43 4.37
1212 1527 6.919662 CACGAAGATGCAAGCCATTATATTTT 59.080 34.615 0.00 0.00 33.29 1.82
1235 1551 1.660052 CCGCGCACATATATTGCACAC 60.660 52.381 8.75 7.21 40.20 3.82
1236 1552 0.585838 CCGCGCACATATATTGCACA 59.414 50.000 8.75 0.00 40.20 4.57
1237 1553 0.586319 ACCGCGCACATATATTGCAC 59.414 50.000 8.75 8.36 40.20 4.57
1393 1709 2.278596 AATCCGTCGACGATGGCG 60.279 61.111 37.65 20.96 43.02 5.69
1447 1763 3.716353 TCCATGCATGTGAGGTTATAGGT 59.284 43.478 24.58 0.00 0.00 3.08
1580 1908 1.679898 CACCACCCTCACCTCCTTC 59.320 63.158 0.00 0.00 0.00 3.46
1715 2045 1.830279 ACTGATCAACGTACTCGGGA 58.170 50.000 0.00 0.00 41.85 5.14
1718 2048 2.596452 AGCAACTGATCAACGTACTCG 58.404 47.619 0.00 0.00 43.34 4.18
1857 2189 8.571461 AATGCTAATTAAGTAGTACAGTACGC 57.429 34.615 11.30 3.03 0.00 4.42
1918 2258 7.151694 TCAGTAGACCCTAGCTAGTAAGATT 57.848 40.000 19.31 3.02 0.00 2.40
1954 2297 3.664107 CAGGGTTCGATCTTCAAAGTCA 58.336 45.455 0.00 0.00 0.00 3.41
1967 2311 2.091541 ACCATTACATTGCAGGGTTCG 58.908 47.619 0.00 0.00 0.00 3.95
2048 2396 4.440663 CCGAAAGAGAGTACATGCATGAGA 60.441 45.833 32.75 16.96 0.00 3.27
2362 2719 2.354891 CACGCACGGAACCACGTA 60.355 61.111 0.00 0.00 46.75 3.57
2501 2858 1.719709 CAGAGCGATACGTGTCGGA 59.280 57.895 31.29 0.00 41.72 4.55
2549 2906 3.834447 TATTCGCGCGGATCCCACG 62.834 63.158 29.89 15.70 0.00 4.94
2552 2909 2.430382 TTCCTATTCGCGCGGATCCC 62.430 60.000 29.89 0.00 0.00 3.85
2559 2916 7.801315 TCATTTTATATGTTTTCCTATTCGCGC 59.199 33.333 0.00 0.00 0.00 6.86
2582 2940 8.027524 TGAGCTCTAGATACATCCTTTTTCAT 57.972 34.615 16.19 0.00 0.00 2.57
2584 2942 8.367156 AGATGAGCTCTAGATACATCCTTTTTC 58.633 37.037 16.19 5.82 38.32 2.29
2649 3007 9.498307 CAGAAACACAAGAACGTATAAAAAGTT 57.502 29.630 0.00 0.00 32.03 2.66
2650 3008 8.126700 CCAGAAACACAAGAACGTATAAAAAGT 58.873 33.333 0.00 0.00 0.00 2.66
2651 3009 8.126700 ACCAGAAACACAAGAACGTATAAAAAG 58.873 33.333 0.00 0.00 0.00 2.27
2655 3025 6.512091 GCAACCAGAAACACAAGAACGTATAA 60.512 38.462 0.00 0.00 0.00 0.98
2664 3034 1.134753 TGCAGCAACCAGAAACACAAG 59.865 47.619 0.00 0.00 0.00 3.16
2688 3090 0.671472 GGGTACAGGAAAACGACCGG 60.671 60.000 0.00 0.00 0.00 5.28
2690 3092 1.622312 AGAGGGTACAGGAAAACGACC 59.378 52.381 0.00 0.00 0.00 4.79
2691 3093 3.006644 AGAAGAGGGTACAGGAAAACGAC 59.993 47.826 0.00 0.00 0.00 4.34
2702 3104 1.939255 CTACGGTCGAGAAGAGGGTAC 59.061 57.143 0.00 0.00 0.00 3.34
2708 3110 1.002888 ACTCCACTACGGTCGAGAAGA 59.997 52.381 0.00 0.00 34.93 2.87
2715 3117 0.323178 TCCTCCACTCCACTACGGTC 60.323 60.000 0.00 0.00 35.57 4.79
2716 3118 0.323542 CTCCTCCACTCCACTACGGT 60.324 60.000 0.00 0.00 35.57 4.83
2717 3119 1.668101 GCTCCTCCACTCCACTACGG 61.668 65.000 0.00 0.00 0.00 4.02
2718 3120 0.965866 TGCTCCTCCACTCCACTACG 60.966 60.000 0.00 0.00 0.00 3.51
2765 3167 9.290483 GTTCTTTTTCTTTTTCTGGTTCTGTAG 57.710 33.333 0.00 0.00 0.00 2.74
2782 3184 6.394809 TGAGACCAAAAACCTGTTCTTTTTC 58.605 36.000 0.00 0.00 30.09 2.29
2787 3189 3.202151 TCCTGAGACCAAAAACCTGTTCT 59.798 43.478 0.00 0.00 0.00 3.01
2788 3190 3.551846 TCCTGAGACCAAAAACCTGTTC 58.448 45.455 0.00 0.00 0.00 3.18
2789 3191 3.662759 TCCTGAGACCAAAAACCTGTT 57.337 42.857 0.00 0.00 0.00 3.16
2790 3192 3.117512 ACATCCTGAGACCAAAAACCTGT 60.118 43.478 0.00 0.00 0.00 4.00
2791 3193 3.490348 ACATCCTGAGACCAAAAACCTG 58.510 45.455 0.00 0.00 0.00 4.00
2792 3194 3.884037 ACATCCTGAGACCAAAAACCT 57.116 42.857 0.00 0.00 0.00 3.50
2793 3195 4.332819 CGATACATCCTGAGACCAAAAACC 59.667 45.833 0.00 0.00 0.00 3.27
2794 3196 5.175859 TCGATACATCCTGAGACCAAAAAC 58.824 41.667 0.00 0.00 0.00 2.43
2795 3197 5.046591 ACTCGATACATCCTGAGACCAAAAA 60.047 40.000 0.00 0.00 32.81 1.94
2796 3198 4.466370 ACTCGATACATCCTGAGACCAAAA 59.534 41.667 0.00 0.00 32.81 2.44
2797 3199 4.023980 ACTCGATACATCCTGAGACCAAA 58.976 43.478 0.00 0.00 32.81 3.28
2798 3200 3.632333 ACTCGATACATCCTGAGACCAA 58.368 45.455 0.00 0.00 32.81 3.67
2799 3201 3.298686 ACTCGATACATCCTGAGACCA 57.701 47.619 0.00 0.00 32.81 4.02
2800 3202 4.214545 CAGTACTCGATACATCCTGAGACC 59.785 50.000 0.00 0.00 36.09 3.85
2801 3203 5.057819 TCAGTACTCGATACATCCTGAGAC 58.942 45.833 0.00 0.00 36.09 3.36
2802 3204 5.291905 TCAGTACTCGATACATCCTGAGA 57.708 43.478 0.00 0.00 36.09 3.27
2803 3205 5.297029 TGTTCAGTACTCGATACATCCTGAG 59.703 44.000 0.00 0.00 36.09 3.35
2804 3206 5.066117 GTGTTCAGTACTCGATACATCCTGA 59.934 44.000 0.00 0.00 36.09 3.86
2805 3207 5.274718 GTGTTCAGTACTCGATACATCCTG 58.725 45.833 0.00 0.00 36.09 3.86
2806 3208 4.338682 GGTGTTCAGTACTCGATACATCCT 59.661 45.833 0.00 0.00 36.09 3.24
2807 3209 4.499357 GGGTGTTCAGTACTCGATACATCC 60.499 50.000 15.35 15.35 36.09 3.51
2808 3210 4.097437 TGGGTGTTCAGTACTCGATACATC 59.903 45.833 0.00 3.26 36.09 3.06
2809 3211 4.021229 TGGGTGTTCAGTACTCGATACAT 58.979 43.478 0.00 0.00 36.09 2.29
2810 3212 3.423749 TGGGTGTTCAGTACTCGATACA 58.576 45.455 0.00 0.51 36.09 2.29
2811 3213 4.650754 ATGGGTGTTCAGTACTCGATAC 57.349 45.455 0.00 0.00 0.00 2.24
2812 3214 6.971726 AATATGGGTGTTCAGTACTCGATA 57.028 37.500 0.00 0.00 0.00 2.92
2813 3215 5.871396 AATATGGGTGTTCAGTACTCGAT 57.129 39.130 0.00 0.00 0.00 3.59
2814 3216 5.670792 AAATATGGGTGTTCAGTACTCGA 57.329 39.130 0.00 0.00 0.00 4.04
2815 3217 5.293569 GGAAAATATGGGTGTTCAGTACTCG 59.706 44.000 0.00 0.00 0.00 4.18
2816 3218 5.293569 CGGAAAATATGGGTGTTCAGTACTC 59.706 44.000 0.00 0.00 0.00 2.59
2817 3219 5.183228 CGGAAAATATGGGTGTTCAGTACT 58.817 41.667 0.00 0.00 0.00 2.73
2818 3220 4.201881 GCGGAAAATATGGGTGTTCAGTAC 60.202 45.833 0.00 0.00 0.00 2.73
2819 3221 3.942748 GCGGAAAATATGGGTGTTCAGTA 59.057 43.478 0.00 0.00 0.00 2.74
2820 3222 2.752903 GCGGAAAATATGGGTGTTCAGT 59.247 45.455 0.00 0.00 0.00 3.41
2821 3223 2.752354 TGCGGAAAATATGGGTGTTCAG 59.248 45.455 0.00 0.00 0.00 3.02
2822 3224 2.796557 TGCGGAAAATATGGGTGTTCA 58.203 42.857 0.00 0.00 0.00 3.18
2823 3225 3.859411 TTGCGGAAAATATGGGTGTTC 57.141 42.857 0.00 0.00 0.00 3.18
2824 3226 4.817318 AATTGCGGAAAATATGGGTGTT 57.183 36.364 0.00 0.00 0.00 3.32
2825 3227 4.221703 TCAAATTGCGGAAAATATGGGTGT 59.778 37.500 0.00 0.00 0.00 4.16
2826 3228 4.753233 TCAAATTGCGGAAAATATGGGTG 58.247 39.130 0.00 0.00 0.00 4.61
2827 3229 4.680440 GCTCAAATTGCGGAAAATATGGGT 60.680 41.667 0.00 0.00 0.00 4.51
2828 3230 3.803778 GCTCAAATTGCGGAAAATATGGG 59.196 43.478 0.00 0.00 0.00 4.00
2829 3231 4.685924 AGCTCAAATTGCGGAAAATATGG 58.314 39.130 0.00 0.00 35.28 2.74
2830 3232 5.342433 TGAGCTCAAATTGCGGAAAATATG 58.658 37.500 15.67 0.00 35.28 1.78
2831 3233 5.581126 TGAGCTCAAATTGCGGAAAATAT 57.419 34.783 15.67 0.00 35.28 1.28
2832 3234 5.384063 TTGAGCTCAAATTGCGGAAAATA 57.616 34.783 26.61 0.00 32.11 1.40
2833 3235 3.940209 TGAGCTCAAATTGCGGAAAAT 57.060 38.095 15.67 0.00 35.28 1.82
2834 3236 3.724508 TTGAGCTCAAATTGCGGAAAA 57.275 38.095 26.61 0.00 32.11 2.29
2835 3237 3.068024 ACTTTGAGCTCAAATTGCGGAAA 59.932 39.130 35.40 15.41 43.92 3.13
2836 3238 2.622942 ACTTTGAGCTCAAATTGCGGAA 59.377 40.909 35.40 16.08 43.92 4.30
2837 3239 2.229792 ACTTTGAGCTCAAATTGCGGA 58.770 42.857 35.40 16.76 43.92 5.54
2838 3240 2.712057 ACTTTGAGCTCAAATTGCGG 57.288 45.000 35.40 26.45 43.92 5.69
2839 3241 7.023575 AGTAAATACTTTGAGCTCAAATTGCG 58.976 34.615 35.40 26.76 43.92 4.85
2840 3242 9.495754 CTAGTAAATACTTTGAGCTCAAATTGC 57.504 33.333 35.40 28.37 43.92 3.56
2844 3246 8.999431 CCAACTAGTAAATACTTTGAGCTCAAA 58.001 33.333 33.65 33.65 42.90 2.69
2845 3247 7.606456 CCCAACTAGTAAATACTTTGAGCTCAA 59.394 37.037 25.16 25.16 37.73 3.02
2846 3248 7.103641 CCCAACTAGTAAATACTTTGAGCTCA 58.896 38.462 13.74 13.74 37.73 4.26
2847 3249 6.037281 GCCCAACTAGTAAATACTTTGAGCTC 59.963 42.308 6.82 6.82 37.73 4.09
2848 3250 5.880887 GCCCAACTAGTAAATACTTTGAGCT 59.119 40.000 0.00 0.00 37.73 4.09
2849 3251 5.880887 AGCCCAACTAGTAAATACTTTGAGC 59.119 40.000 0.00 1.63 37.73 4.26
2854 3256 8.657712 CCCTTATAGCCCAACTAGTAAATACTT 58.342 37.037 0.00 0.00 37.73 2.24
2855 3257 7.256583 GCCCTTATAGCCCAACTAGTAAATACT 60.257 40.741 0.00 0.00 40.24 2.12
2856 3258 6.877855 GCCCTTATAGCCCAACTAGTAAATAC 59.122 42.308 0.00 0.00 33.29 1.89
2857 3259 6.559539 TGCCCTTATAGCCCAACTAGTAAATA 59.440 38.462 0.00 0.00 33.29 1.40
2858 3260 5.371472 TGCCCTTATAGCCCAACTAGTAAAT 59.629 40.000 0.00 0.00 33.29 1.40
2859 3261 4.722781 TGCCCTTATAGCCCAACTAGTAAA 59.277 41.667 0.00 0.00 33.29 2.01
2860 3262 4.300345 TGCCCTTATAGCCCAACTAGTAA 58.700 43.478 0.00 0.00 33.29 2.24
2861 3263 3.931317 TGCCCTTATAGCCCAACTAGTA 58.069 45.455 0.00 0.00 33.29 1.82
2862 3264 2.771688 TGCCCTTATAGCCCAACTAGT 58.228 47.619 0.00 0.00 33.29 2.57
2863 3265 3.584848 AGATGCCCTTATAGCCCAACTAG 59.415 47.826 0.00 0.00 33.29 2.57
2864 3266 3.598264 AGATGCCCTTATAGCCCAACTA 58.402 45.455 0.00 0.00 34.64 2.24
2865 3267 2.422746 AGATGCCCTTATAGCCCAACT 58.577 47.619 0.00 0.00 0.00 3.16
2866 3268 2.959465 AGATGCCCTTATAGCCCAAC 57.041 50.000 0.00 0.00 0.00 3.77
2867 3269 2.782925 TGAAGATGCCCTTATAGCCCAA 59.217 45.455 0.00 0.00 34.68 4.12
2868 3270 2.417652 TGAAGATGCCCTTATAGCCCA 58.582 47.619 0.00 0.00 34.68 5.36
2869 3271 3.508845 TTGAAGATGCCCTTATAGCCC 57.491 47.619 0.00 0.00 34.68 5.19
2870 3272 3.192212 GCATTGAAGATGCCCTTATAGCC 59.808 47.826 0.00 0.00 39.01 3.93
2871 3273 4.431661 GCATTGAAGATGCCCTTATAGC 57.568 45.455 0.00 0.00 39.01 2.97
2880 3282 1.031571 TGGGTCGGCATTGAAGATGC 61.032 55.000 2.50 2.50 43.85 3.91
2881 3283 0.734889 GTGGGTCGGCATTGAAGATG 59.265 55.000 0.00 0.00 0.00 2.90
2882 3284 0.327924 TGTGGGTCGGCATTGAAGAT 59.672 50.000 0.00 0.00 0.00 2.40
2883 3285 0.109532 TTGTGGGTCGGCATTGAAGA 59.890 50.000 0.00 0.00 0.00 2.87
2884 3286 0.958091 TTTGTGGGTCGGCATTGAAG 59.042 50.000 0.00 0.00 0.00 3.02
2885 3287 0.671251 GTTTGTGGGTCGGCATTGAA 59.329 50.000 0.00 0.00 0.00 2.69
2886 3288 1.175983 GGTTTGTGGGTCGGCATTGA 61.176 55.000 0.00 0.00 0.00 2.57
2887 3289 1.178534 AGGTTTGTGGGTCGGCATTG 61.179 55.000 0.00 0.00 0.00 2.82
2888 3290 0.402504 TAGGTTTGTGGGTCGGCATT 59.597 50.000 0.00 0.00 0.00 3.56
2889 3291 0.322187 GTAGGTTTGTGGGTCGGCAT 60.322 55.000 0.00 0.00 0.00 4.40
2890 3292 1.071814 GTAGGTTTGTGGGTCGGCA 59.928 57.895 0.00 0.00 0.00 5.69
2891 3293 1.673337 GGTAGGTTTGTGGGTCGGC 60.673 63.158 0.00 0.00 0.00 5.54
2892 3294 1.375013 CGGTAGGTTTGTGGGTCGG 60.375 63.158 0.00 0.00 0.00 4.79
2893 3295 2.030958 GCGGTAGGTTTGTGGGTCG 61.031 63.158 0.00 0.00 0.00 4.79
2894 3296 0.609662 TAGCGGTAGGTTTGTGGGTC 59.390 55.000 0.00 0.00 0.00 4.46
2895 3297 0.322648 GTAGCGGTAGGTTTGTGGGT 59.677 55.000 0.00 0.00 0.00 4.51
2896 3298 0.611714 AGTAGCGGTAGGTTTGTGGG 59.388 55.000 0.00 0.00 0.00 4.61
2897 3299 1.001633 ACAGTAGCGGTAGGTTTGTGG 59.998 52.381 0.00 0.00 0.00 4.17
2898 3300 2.450609 ACAGTAGCGGTAGGTTTGTG 57.549 50.000 0.00 0.00 0.00 3.33
2899 3301 2.608752 CGAACAGTAGCGGTAGGTTTGT 60.609 50.000 11.52 4.69 0.00 2.83
2900 3302 1.990563 CGAACAGTAGCGGTAGGTTTG 59.009 52.381 11.52 10.89 0.00 2.93
2901 3303 1.067354 CCGAACAGTAGCGGTAGGTTT 60.067 52.381 11.52 0.00 42.49 3.27
2902 3304 0.529378 CCGAACAGTAGCGGTAGGTT 59.471 55.000 10.39 10.39 42.49 3.50
2903 3305 2.187073 CCGAACAGTAGCGGTAGGT 58.813 57.895 0.00 0.00 42.49 3.08


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

AutoCloner maintained by Alex Coulton.