Multiple sequence alignment - TraesCS4D01G053200

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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 TraesCS4D01G053200 chr4D 100.000 2339 0 0 797 3135 29179642 29177304 0.000000e+00 4320
1 TraesCS4D01G053200 chr4D 100.000 103 0 0 1 103 29180438 29180336 1.150000e-44 191
2 TraesCS4D01G053200 chr4D 97.087 103 3 0 1 103 379686621 379686723 1.160000e-39 174
3 TraesCS4D01G053200 chr4A 96.198 1762 53 7 797 2548 574382391 574384148 0.000000e+00 2870
4 TraesCS4D01G053200 chr4A 82.482 548 39 34 2596 3135 574384154 574384652 8.040000e-116 427
5 TraesCS4D01G053200 chr4B 96.232 1433 38 4 847 2273 41746452 41745030 0.000000e+00 2333
6 TraesCS4D01G053200 chr4B 88.722 399 29 10 2739 3127 41744676 41744284 1.020000e-129 473
7 TraesCS4D01G053200 chr4B 96.104 77 3 0 2336 2412 41745030 41744954 3.280000e-25 126
8 TraesCS4D01G053200 chr5D 99.029 103 1 0 1 103 506077707 506077605 5.340000e-43 185
9 TraesCS4D01G053200 chr5D 98.058 103 2 0 1 103 543350071 543349969 2.480000e-41 180
10 TraesCS4D01G053200 chr3A 97.087 103 3 0 1 103 669770901 669770799 1.160000e-39 174
11 TraesCS4D01G053200 chr7D 96.117 103 4 0 1 103 628710535 628710433 5.380000e-38 169
12 TraesCS4D01G053200 chr1A 96.117 103 4 0 1 103 372548148 372548046 5.380000e-38 169
13 TraesCS4D01G053200 chr6D 95.146 103 5 0 1 103 237825252 237825150 2.500000e-36 163
14 TraesCS4D01G053200 chr3D 95.146 103 5 0 1 103 161705999 161706101 2.500000e-36 163
15 TraesCS4D01G053200 chr2A 95.146 103 5 0 1 103 133468324 133468426 2.500000e-36 163


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 TraesCS4D01G053200 chr4D 29177304 29180438 3134 True 2255.500000 4320 100.000 1 3135 2 chr4D.!!$R1 3134
1 TraesCS4D01G053200 chr4A 574382391 574384652 2261 False 1648.500000 2870 89.340 797 3135 2 chr4A.!!$F1 2338
2 TraesCS4D01G053200 chr4B 41744284 41746452 2168 True 977.333333 2333 93.686 847 3127 3 chr4B.!!$R1 2280

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
60 61 0.179936 GATCCTTGGAGACCCAGCTG 59.820 60.000 6.78 6.78 44.60 4.24 F
61 62 1.919600 ATCCTTGGAGACCCAGCTGC 61.920 60.000 8.66 0.00 44.60 5.25 F
62 63 2.045536 CTTGGAGACCCAGCTGCC 60.046 66.667 8.66 4.06 44.60 4.85 F
1917 1924 0.691078 TACCTGAGGGCCATGGAGAC 60.691 60.000 18.40 4.25 35.63 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1025 1026 2.562635 CAATGCAGACAGGAGGATGAG 58.437 52.381 0.00 0.00 0.00 2.90 R
1070 1077 2.894387 GCTCTGGATCGCCTGTGC 60.894 66.667 0.00 0.00 42.57 4.57 R
2113 2124 6.170506 TGAATTACACACCCTGATCAGTAAC 58.829 40.000 21.11 3.66 0.00 2.50 R
2955 3076 0.526096 ATGCGAAAATGATGGTGCGC 60.526 50.000 0.00 0.00 44.15 6.09 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
17 18 4.724516 AGGGAGCTGGATCTGGAG 57.275 61.111 0.00 0.00 0.00 3.86
18 19 1.765657 AGGGAGCTGGATCTGGAGC 60.766 63.158 0.00 0.00 35.28 4.70
21 22 3.968773 AGCTGGATCTGGAGCTCC 58.031 61.111 26.78 26.78 41.94 4.70
22 23 1.765657 AGCTGGATCTGGAGCTCCC 60.766 63.158 29.95 14.11 41.94 4.30
23 24 2.817056 GCTGGATCTGGAGCTCCCC 61.817 68.421 29.95 22.68 34.29 4.81
24 25 1.074623 CTGGATCTGGAGCTCCCCT 60.075 63.158 29.95 14.22 34.29 4.79
25 26 1.383664 TGGATCTGGAGCTCCCCTG 60.384 63.158 29.95 19.04 34.29 4.45
26 27 2.146061 GGATCTGGAGCTCCCCTGG 61.146 68.421 29.95 16.52 34.29 4.45
27 28 2.040043 ATCTGGAGCTCCCCTGGG 60.040 66.667 29.95 14.14 34.29 4.45
32 33 3.478274 GAGCTCCCCTGGGCAGAG 61.478 72.222 8.19 11.17 34.68 3.35
45 46 4.933064 CAGAGCGGCGTCGGATCC 62.933 72.222 13.05 0.00 36.79 3.36
47 48 4.208686 GAGCGGCGTCGGATCCTT 62.209 66.667 13.05 0.00 36.79 3.36
48 49 4.514577 AGCGGCGTCGGATCCTTG 62.515 66.667 13.05 0.00 36.79 3.61
50 51 3.833645 CGGCGTCGGATCCTTGGA 61.834 66.667 10.75 0.00 0.00 3.53
51 52 2.107141 GGCGTCGGATCCTTGGAG 59.893 66.667 10.75 0.00 0.00 3.86
52 53 2.423898 GGCGTCGGATCCTTGGAGA 61.424 63.158 10.75 0.00 0.00 3.71
53 54 1.227002 GCGTCGGATCCTTGGAGAC 60.227 63.158 10.75 8.35 0.00 3.36
54 55 1.437986 CGTCGGATCCTTGGAGACC 59.562 63.158 10.75 1.14 0.00 3.85
55 56 1.823976 GTCGGATCCTTGGAGACCC 59.176 63.158 10.75 3.79 0.00 4.46
56 57 0.976073 GTCGGATCCTTGGAGACCCA 60.976 60.000 10.75 0.00 41.64 4.51
57 58 0.687757 TCGGATCCTTGGAGACCCAG 60.688 60.000 10.75 0.00 44.60 4.45
58 59 1.529309 GGATCCTTGGAGACCCAGC 59.471 63.158 3.84 0.00 44.60 4.85
59 60 0.985490 GGATCCTTGGAGACCCAGCT 60.985 60.000 3.84 0.00 44.60 4.24
60 61 0.179936 GATCCTTGGAGACCCAGCTG 59.820 60.000 6.78 6.78 44.60 4.24
61 62 1.919600 ATCCTTGGAGACCCAGCTGC 61.920 60.000 8.66 0.00 44.60 5.25
62 63 2.045536 CTTGGAGACCCAGCTGCC 60.046 66.667 8.66 4.06 44.60 4.85
63 64 3.635268 CTTGGAGACCCAGCTGCCC 62.635 68.421 8.66 4.39 44.60 5.36
64 65 4.980592 TGGAGACCCAGCTGCCCA 62.981 66.667 8.66 7.03 37.58 5.36
65 66 4.416738 GGAGACCCAGCTGCCCAC 62.417 72.222 8.66 0.00 0.00 4.61
66 67 4.767255 GAGACCCAGCTGCCCACG 62.767 72.222 8.66 0.00 0.00 4.94
1025 1026 4.168291 CGCCAGCCTCTTCCTCCC 62.168 72.222 0.00 0.00 0.00 4.30
1917 1924 0.691078 TACCTGAGGGCCATGGAGAC 60.691 60.000 18.40 4.25 35.63 3.36
2113 2124 1.334054 GCAGCAAGCAAGTTGATTCG 58.666 50.000 7.16 3.18 44.79 3.34
2148 2159 3.191162 GTGTGTAATTCAGGCATTGCAGA 59.809 43.478 11.39 4.96 30.40 4.26
2232 2246 8.162878 TCATTTTGCTATGATGAGAAGAATCC 57.837 34.615 0.00 0.00 29.82 3.01
2276 2293 1.835483 GCACAGAAGTCACTGGCACG 61.835 60.000 0.00 0.00 41.59 5.34
2289 2306 1.372872 GGCACGTGTGGATTTTGGC 60.373 57.895 18.38 0.00 0.00 4.52
2319 2336 3.531538 TGCAGACTAATGTTTCCGGATC 58.468 45.455 4.15 2.09 0.00 3.36
2452 2469 1.651138 GATCTCTTCGACAACACGCAG 59.349 52.381 0.00 0.00 0.00 5.18
2548 2565 6.176896 TCGGATGATCAAACCAAACTGAATA 58.823 36.000 18.14 0.00 0.00 1.75
2549 2566 6.316140 TCGGATGATCAAACCAAACTGAATAG 59.684 38.462 18.14 3.11 0.00 1.73
2550 2567 6.268566 GGATGATCAAACCAAACTGAATAGC 58.731 40.000 14.74 0.00 0.00 2.97
2551 2568 6.127647 GGATGATCAAACCAAACTGAATAGCA 60.128 38.462 14.74 0.00 0.00 3.49
2553 2570 6.446318 TGATCAAACCAAACTGAATAGCAAC 58.554 36.000 0.00 0.00 0.00 4.17
2555 2572 4.646945 TCAAACCAAACTGAATAGCAACCA 59.353 37.500 0.00 0.00 0.00 3.67
2556 2573 4.584327 AACCAAACTGAATAGCAACCAC 57.416 40.909 0.00 0.00 0.00 4.16
2557 2574 3.561143 ACCAAACTGAATAGCAACCACA 58.439 40.909 0.00 0.00 0.00 4.17
2558 2575 3.569701 ACCAAACTGAATAGCAACCACAG 59.430 43.478 0.00 0.00 35.14 3.66
2559 2576 3.568538 CAAACTGAATAGCAACCACAGC 58.431 45.455 0.00 0.00 32.67 4.40
2560 2577 2.867109 ACTGAATAGCAACCACAGCT 57.133 45.000 0.00 0.00 45.77 4.24
2574 2591 8.981659 AGCAACCACAGCTATATATATACATGA 58.018 33.333 0.00 0.00 41.32 3.07
2575 2592 9.599866 GCAACCACAGCTATATATATACATGAA 57.400 33.333 0.00 0.00 0.00 2.57
2589 2606 9.996554 ATATATACATGAATTCAGACGTTCCAA 57.003 29.630 14.54 0.00 0.00 3.53
2590 2607 8.731275 ATATACATGAATTCAGACGTTCCAAA 57.269 30.769 14.54 0.00 0.00 3.28
2591 2608 5.362556 ACATGAATTCAGACGTTCCAAAG 57.637 39.130 14.54 0.00 0.00 2.77
2592 2609 3.896648 TGAATTCAGACGTTCCAAAGC 57.103 42.857 3.38 0.00 0.00 3.51
2593 2610 3.476552 TGAATTCAGACGTTCCAAAGCT 58.523 40.909 3.38 0.00 0.00 3.74
2594 2611 3.250762 TGAATTCAGACGTTCCAAAGCTG 59.749 43.478 3.38 0.00 0.00 4.24
2595 2612 2.613026 TTCAGACGTTCCAAAGCTGA 57.387 45.000 0.00 0.00 34.11 4.26
2596 2613 2.839486 TCAGACGTTCCAAAGCTGAT 57.161 45.000 0.00 0.00 31.24 2.90
2597 2614 3.126001 TCAGACGTTCCAAAGCTGATT 57.874 42.857 0.00 0.00 31.24 2.57
2621 2638 0.249322 AGCAACAAGCAAGCAAGCTG 60.249 50.000 3.54 1.87 45.89 4.24
2622 2639 0.249155 GCAACAAGCAAGCAAGCTGA 60.249 50.000 3.54 0.00 45.89 4.26
2623 2640 1.604693 GCAACAAGCAAGCAAGCTGAT 60.605 47.619 3.54 0.00 45.89 2.90
2624 2641 2.750948 CAACAAGCAAGCAAGCTGATT 58.249 42.857 3.54 0.00 45.89 2.57
2626 2643 4.300803 CAACAAGCAAGCAAGCTGATTAA 58.699 39.130 3.54 0.00 45.89 1.40
2635 2652 5.629079 AGCAAGCTGATTAAACAGTAACC 57.371 39.130 13.56 0.00 39.73 2.85
2649 2676 5.505181 ACAGTAACCAGGAATTCAGACAT 57.495 39.130 7.93 0.00 0.00 3.06
2706 2741 4.977741 AGCATTTTTGTCTGCATTTTCG 57.022 36.364 0.00 0.00 40.88 3.46
2755 2847 3.403038 TCACCTTCTGCAACTTAAGAGC 58.597 45.455 10.09 13.01 0.00 4.09
2810 2931 5.689514 CGTTTGATGCTGTTTTATTTCCACA 59.310 36.000 0.00 0.00 0.00 4.17
2811 2932 6.129115 CGTTTGATGCTGTTTTATTTCCACAG 60.129 38.462 0.00 0.00 40.86 3.66
2812 2933 5.389859 TGATGCTGTTTTATTTCCACAGG 57.610 39.130 0.00 0.00 38.72 4.00
2813 2934 4.220382 TGATGCTGTTTTATTTCCACAGGG 59.780 41.667 0.00 0.00 38.72 4.45
2814 2935 2.298729 TGCTGTTTTATTTCCACAGGGC 59.701 45.455 0.00 0.00 38.72 5.19
2815 2936 2.562738 GCTGTTTTATTTCCACAGGGCT 59.437 45.455 0.00 0.00 38.72 5.19
2816 2937 3.761752 GCTGTTTTATTTCCACAGGGCTA 59.238 43.478 0.00 0.00 38.72 3.93
2817 2938 4.219725 GCTGTTTTATTTCCACAGGGCTAA 59.780 41.667 0.00 0.00 38.72 3.09
2818 2939 5.622233 GCTGTTTTATTTCCACAGGGCTAAG 60.622 44.000 0.00 0.00 38.72 2.18
2819 2940 5.636123 TGTTTTATTTCCACAGGGCTAAGA 58.364 37.500 0.00 0.00 0.00 2.10
2820 2941 5.710099 TGTTTTATTTCCACAGGGCTAAGAG 59.290 40.000 0.00 0.00 0.00 2.85
2821 2942 4.503714 TTATTTCCACAGGGCTAAGAGG 57.496 45.455 0.00 0.00 0.00 3.69
2822 2943 2.038863 TTTCCACAGGGCTAAGAGGA 57.961 50.000 0.00 0.00 0.00 3.71
2823 2944 1.573108 TTCCACAGGGCTAAGAGGAG 58.427 55.000 0.00 0.00 0.00 3.69
2824 2945 0.978146 TCCACAGGGCTAAGAGGAGC 60.978 60.000 0.00 0.00 42.05 4.70
2825 2946 0.980231 CCACAGGGCTAAGAGGAGCT 60.980 60.000 0.00 0.00 42.43 4.09
2826 2947 0.177604 CACAGGGCTAAGAGGAGCTG 59.822 60.000 0.00 0.00 42.43 4.24
2827 2948 0.252467 ACAGGGCTAAGAGGAGCTGT 60.252 55.000 0.00 0.00 42.43 4.40
2828 2949 0.908198 CAGGGCTAAGAGGAGCTGTT 59.092 55.000 0.00 0.00 42.43 3.16
2829 2950 1.280421 CAGGGCTAAGAGGAGCTGTTT 59.720 52.381 0.00 0.00 42.43 2.83
2830 2951 1.988846 AGGGCTAAGAGGAGCTGTTTT 59.011 47.619 0.00 0.00 42.43 2.43
2831 2952 3.055094 CAGGGCTAAGAGGAGCTGTTTTA 60.055 47.826 0.00 0.00 42.43 1.52
2832 2953 3.783082 AGGGCTAAGAGGAGCTGTTTTAT 59.217 43.478 0.00 0.00 42.43 1.40
2833 2954 4.228438 AGGGCTAAGAGGAGCTGTTTTATT 59.772 41.667 0.00 0.00 42.43 1.40
2834 2955 4.950475 GGGCTAAGAGGAGCTGTTTTATTT 59.050 41.667 0.00 0.00 42.43 1.40
2835 2956 5.066634 GGGCTAAGAGGAGCTGTTTTATTTC 59.933 44.000 0.00 0.00 42.43 2.17
2836 2957 5.066634 GGCTAAGAGGAGCTGTTTTATTTCC 59.933 44.000 0.00 0.00 42.43 3.13
2837 2958 5.648092 GCTAAGAGGAGCTGTTTTATTTCCA 59.352 40.000 0.00 0.00 39.50 3.53
2838 2959 5.966742 AAGAGGAGCTGTTTTATTTCCAC 57.033 39.130 0.00 0.00 0.00 4.02
2839 2960 4.985538 AGAGGAGCTGTTTTATTTCCACA 58.014 39.130 0.00 0.00 0.00 4.17
2864 2985 5.277250 GCGAGATGATCATTTCTTTCAGACC 60.277 44.000 20.48 0.48 0.00 3.85
2881 3002 4.707448 TCAGACCAAGACTAGTCAGATTCC 59.293 45.833 24.44 8.95 35.38 3.01
2934 3055 4.927978 ATCATTCAAACAACCGAACCAA 57.072 36.364 0.00 0.00 0.00 3.67
2941 3062 6.392625 TCAAACAACCGAACCAAATCAATA 57.607 33.333 0.00 0.00 0.00 1.90
2948 3069 9.418045 ACAACCGAACCAAATCAATATTAAAAG 57.582 29.630 0.00 0.00 0.00 2.27
2950 3071 9.634163 AACCGAACCAAATCAATATTAAAAGAC 57.366 29.630 0.00 0.00 0.00 3.01
2952 3073 9.289303 CCGAACCAAATCAATATTAAAAGACAG 57.711 33.333 0.00 0.00 0.00 3.51
2953 3074 8.798153 CGAACCAAATCAATATTAAAAGACAGC 58.202 33.333 0.00 0.00 0.00 4.40
2954 3075 9.860898 GAACCAAATCAATATTAAAAGACAGCT 57.139 29.630 0.00 0.00 0.00 4.24
2955 3076 9.643693 AACCAAATCAATATTAAAAGACAGCTG 57.356 29.630 13.48 13.48 0.00 4.24
2958 3079 4.908736 TCAATATTAAAAGACAGCTGCGC 58.091 39.130 15.27 0.00 0.00 6.09
2959 3080 4.394610 TCAATATTAAAAGACAGCTGCGCA 59.605 37.500 15.27 10.98 0.00 6.09
2961 3082 0.591170 TTAAAAGACAGCTGCGCACC 59.409 50.000 15.27 0.00 0.00 5.01
2963 3084 1.174712 AAAAGACAGCTGCGCACCAT 61.175 50.000 15.27 0.00 0.00 3.55
2964 3085 1.580845 AAAGACAGCTGCGCACCATC 61.581 55.000 15.27 2.03 0.00 3.51
2967 3093 1.651240 GACAGCTGCGCACCATCATT 61.651 55.000 15.27 0.00 0.00 2.57
2978 3104 4.151070 CGCACCATCATTTTCGCATATAC 58.849 43.478 0.00 0.00 0.00 1.47
2996 3127 9.940166 CGCATATACGAAACCACATAGTATATA 57.060 33.333 0.00 0.00 38.29 0.86
3027 3159 4.508492 TCTTCTACTGATCGATCGACTCAC 59.492 45.833 22.06 12.53 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.765657 GCTCCAGATCCAGCTCCCT 60.766 63.158 2.36 0.00 32.48 4.20
1 2 1.765657 AGCTCCAGATCCAGCTCCC 60.766 63.158 5.75 0.00 42.60 4.30
2 3 3.968773 AGCTCCAGATCCAGCTCC 58.031 61.111 5.75 0.00 42.60 4.70
9 10 2.146061 CCCAGGGGAGCTCCAGATC 61.146 68.421 33.29 18.73 37.91 2.75
10 11 2.040043 CCCAGGGGAGCTCCAGAT 60.040 66.667 33.29 15.97 37.91 2.90
15 16 3.478274 CTCTGCCCAGGGGAGCTC 61.478 72.222 22.59 4.71 41.08 4.09
28 29 4.933064 GGATCCGACGCCGCTCTG 62.933 72.222 0.00 0.00 0.00 3.35
30 31 4.208686 AAGGATCCGACGCCGCTC 62.209 66.667 5.98 0.00 0.00 5.03
31 32 4.514577 CAAGGATCCGACGCCGCT 62.515 66.667 5.98 0.00 0.00 5.52
33 34 3.774959 CTCCAAGGATCCGACGCCG 62.775 68.421 5.98 0.00 0.00 6.46
34 35 2.107141 CTCCAAGGATCCGACGCC 59.893 66.667 5.98 0.00 0.00 5.68
35 36 1.227002 GTCTCCAAGGATCCGACGC 60.227 63.158 5.98 0.00 0.00 5.19
36 37 1.437986 GGTCTCCAAGGATCCGACG 59.562 63.158 5.98 0.00 0.00 5.12
37 38 0.976073 TGGGTCTCCAAGGATCCGAC 60.976 60.000 5.98 7.14 40.73 4.79
38 39 0.687757 CTGGGTCTCCAAGGATCCGA 60.688 60.000 5.98 0.00 43.51 4.55
39 40 1.826024 CTGGGTCTCCAAGGATCCG 59.174 63.158 5.98 0.00 43.51 4.18
40 41 0.985490 AGCTGGGTCTCCAAGGATCC 60.985 60.000 2.48 2.48 43.51 3.36
41 42 0.179936 CAGCTGGGTCTCCAAGGATC 59.820 60.000 5.57 0.00 43.51 3.36
42 43 1.919600 GCAGCTGGGTCTCCAAGGAT 61.920 60.000 17.12 0.00 43.51 3.24
43 44 2.596851 GCAGCTGGGTCTCCAAGGA 61.597 63.158 17.12 0.00 43.51 3.36
44 45 2.045536 GCAGCTGGGTCTCCAAGG 60.046 66.667 17.12 0.00 43.51 3.61
45 46 2.045536 GGCAGCTGGGTCTCCAAG 60.046 66.667 17.12 0.00 43.51 3.61
46 47 3.650950 GGGCAGCTGGGTCTCCAA 61.651 66.667 17.12 0.00 43.51 3.53
47 48 4.980592 TGGGCAGCTGGGTCTCCA 62.981 66.667 17.12 5.96 41.58 3.86
48 49 4.416738 GTGGGCAGCTGGGTCTCC 62.417 72.222 17.12 7.34 0.00 3.71
49 50 4.767255 CGTGGGCAGCTGGGTCTC 62.767 72.222 17.12 0.00 0.00 3.36
1025 1026 2.562635 CAATGCAGACAGGAGGATGAG 58.437 52.381 0.00 0.00 0.00 2.90
1070 1077 2.894387 GCTCTGGATCGCCTGTGC 60.894 66.667 0.00 0.00 42.57 4.57
2113 2124 6.170506 TGAATTACACACCCTGATCAGTAAC 58.829 40.000 21.11 3.66 0.00 2.50
2148 2159 4.220693 TGCTATACATCAACAGCCTTGT 57.779 40.909 0.00 0.00 39.87 3.16
2214 2228 6.002704 ACCATTGGATTCTTCTCATCATAGC 58.997 40.000 10.37 0.00 0.00 2.97
2232 2246 2.034939 TGCTCAGCAAGTTTCACCATTG 59.965 45.455 0.00 0.00 34.76 2.82
2276 2293 0.961019 TGCAGAGCCAAAATCCACAC 59.039 50.000 0.00 0.00 0.00 3.82
2304 2321 3.388024 TCCCAGAGATCCGGAAACATTAG 59.612 47.826 9.01 0.00 0.00 1.73
2313 2330 1.532794 CCCTCTCCCAGAGATCCGG 60.533 68.421 0.00 0.00 45.07 5.14
2319 2336 3.205815 CTCTGTCCCTCTCCCAGAG 57.794 63.158 0.00 0.00 44.30 3.35
2452 2469 5.148568 GTCTCTACTCTTGTCTGAAACGAC 58.851 45.833 0.00 0.00 34.52 4.34
2455 2472 6.016610 ACTCTGTCTCTACTCTTGTCTGAAAC 60.017 42.308 0.00 0.00 0.00 2.78
2548 2565 8.981659 TCATGTATATATATAGCTGTGGTTGCT 58.018 33.333 2.53 0.00 43.79 3.91
2549 2566 9.599866 TTCATGTATATATATAGCTGTGGTTGC 57.400 33.333 2.53 0.00 0.00 4.17
2563 2580 9.996554 TTGGAACGTCTGAATTCATGTATATAT 57.003 29.630 8.96 0.00 0.00 0.86
2564 2581 9.825109 TTTGGAACGTCTGAATTCATGTATATA 57.175 29.630 8.96 0.00 0.00 0.86
2565 2582 8.731275 TTTGGAACGTCTGAATTCATGTATAT 57.269 30.769 8.96 0.00 0.00 0.86
2566 2583 7.201609 GCTTTGGAACGTCTGAATTCATGTATA 60.202 37.037 8.96 0.00 0.00 1.47
2567 2584 6.403636 GCTTTGGAACGTCTGAATTCATGTAT 60.404 38.462 8.96 0.00 0.00 2.29
2568 2585 5.106712 GCTTTGGAACGTCTGAATTCATGTA 60.107 40.000 8.96 0.00 0.00 2.29
2569 2586 4.320494 GCTTTGGAACGTCTGAATTCATGT 60.320 41.667 8.96 5.50 0.00 3.21
2570 2587 4.083110 AGCTTTGGAACGTCTGAATTCATG 60.083 41.667 8.96 4.85 0.00 3.07
2571 2588 4.074970 AGCTTTGGAACGTCTGAATTCAT 58.925 39.130 8.96 0.00 0.00 2.57
2572 2589 3.250762 CAGCTTTGGAACGTCTGAATTCA 59.749 43.478 8.12 8.12 0.00 2.57
2573 2590 3.498397 TCAGCTTTGGAACGTCTGAATTC 59.502 43.478 0.00 0.00 31.62 2.17
2574 2591 3.476552 TCAGCTTTGGAACGTCTGAATT 58.523 40.909 0.00 0.00 31.62 2.17
2575 2592 3.126001 TCAGCTTTGGAACGTCTGAAT 57.874 42.857 0.00 0.00 31.62 2.57
2576 2593 2.613026 TCAGCTTTGGAACGTCTGAA 57.387 45.000 0.00 0.00 31.62 3.02
2577 2594 2.839486 ATCAGCTTTGGAACGTCTGA 57.161 45.000 3.68 3.68 38.05 3.27
2578 2595 5.356882 TTTAATCAGCTTTGGAACGTCTG 57.643 39.130 0.00 0.00 0.00 3.51
2579 2596 6.385649 TTTTTAATCAGCTTTGGAACGTCT 57.614 33.333 0.00 0.00 0.00 4.18
2580 2597 5.117135 GCTTTTTAATCAGCTTTGGAACGTC 59.883 40.000 0.00 0.00 32.87 4.34
2581 2598 4.982295 GCTTTTTAATCAGCTTTGGAACGT 59.018 37.500 0.00 0.00 32.87 3.99
2582 2599 4.981674 TGCTTTTTAATCAGCTTTGGAACG 59.018 37.500 7.67 0.00 36.92 3.95
2583 2600 6.257630 TGTTGCTTTTTAATCAGCTTTGGAAC 59.742 34.615 7.67 0.00 36.92 3.62
2584 2601 6.344500 TGTTGCTTTTTAATCAGCTTTGGAA 58.656 32.000 7.67 0.00 36.92 3.53
2585 2602 5.911752 TGTTGCTTTTTAATCAGCTTTGGA 58.088 33.333 7.67 0.00 36.92 3.53
2586 2603 6.601741 TTGTTGCTTTTTAATCAGCTTTGG 57.398 33.333 7.67 0.00 36.92 3.28
2587 2604 6.131389 GCTTGTTGCTTTTTAATCAGCTTTG 58.869 36.000 7.67 0.00 36.92 2.77
2588 2605 5.816777 TGCTTGTTGCTTTTTAATCAGCTTT 59.183 32.000 7.67 0.00 43.37 3.51
2589 2606 5.358922 TGCTTGTTGCTTTTTAATCAGCTT 58.641 33.333 7.67 0.00 43.37 3.74
2590 2607 4.947645 TGCTTGTTGCTTTTTAATCAGCT 58.052 34.783 7.67 0.00 43.37 4.24
2591 2608 5.655893 TTGCTTGTTGCTTTTTAATCAGC 57.344 34.783 0.36 0.36 43.37 4.26
2592 2609 5.234757 TGCTTGCTTGTTGCTTTTTAATCAG 59.765 36.000 0.00 0.00 43.37 2.90
2593 2610 5.114780 TGCTTGCTTGTTGCTTTTTAATCA 58.885 33.333 0.00 0.00 43.37 2.57
2594 2611 5.655893 TGCTTGCTTGTTGCTTTTTAATC 57.344 34.783 0.00 0.00 43.37 1.75
2595 2612 5.504501 GCTTGCTTGCTTGTTGCTTTTTAAT 60.505 36.000 0.00 0.00 43.37 1.40
2596 2613 4.201802 GCTTGCTTGCTTGTTGCTTTTTAA 60.202 37.500 0.00 0.00 43.37 1.52
2597 2614 3.309410 GCTTGCTTGCTTGTTGCTTTTTA 59.691 39.130 0.00 0.00 43.37 1.52
2621 2638 8.451748 GTCTGAATTCCTGGTTACTGTTTAATC 58.548 37.037 2.27 0.00 0.00 1.75
2622 2639 7.942341 TGTCTGAATTCCTGGTTACTGTTTAAT 59.058 33.333 2.27 0.00 0.00 1.40
2623 2640 7.284074 TGTCTGAATTCCTGGTTACTGTTTAA 58.716 34.615 2.27 0.00 0.00 1.52
2624 2641 6.833041 TGTCTGAATTCCTGGTTACTGTTTA 58.167 36.000 2.27 0.00 0.00 2.01
2626 2643 5.304686 TGTCTGAATTCCTGGTTACTGTT 57.695 39.130 2.27 0.00 0.00 3.16
2635 2652 4.482386 CAACTGCAATGTCTGAATTCCTG 58.518 43.478 2.27 0.00 0.00 3.86
2693 2728 6.499172 TGATTAACAAACGAAAATGCAGACA 58.501 32.000 0.00 0.00 0.00 3.41
2755 2847 6.183360 CCTCTTTCAGAAATCAGCCAACATAG 60.183 42.308 0.00 0.00 0.00 2.23
2810 2931 1.662686 AAACAGCTCCTCTTAGCCCT 58.337 50.000 0.00 0.00 43.86 5.19
2811 2932 2.498644 AAAACAGCTCCTCTTAGCCC 57.501 50.000 0.00 0.00 43.86 5.19
2812 2933 5.066634 GGAAATAAAACAGCTCCTCTTAGCC 59.933 44.000 0.00 0.00 43.86 3.93
2813 2934 5.648092 TGGAAATAAAACAGCTCCTCTTAGC 59.352 40.000 0.00 0.00 43.11 3.09
2814 2935 6.655003 TGTGGAAATAAAACAGCTCCTCTTAG 59.345 38.462 0.00 0.00 0.00 2.18
2815 2936 6.539173 TGTGGAAATAAAACAGCTCCTCTTA 58.461 36.000 0.00 0.00 0.00 2.10
2816 2937 5.385198 TGTGGAAATAAAACAGCTCCTCTT 58.615 37.500 0.00 0.00 0.00 2.85
2817 2938 4.985538 TGTGGAAATAAAACAGCTCCTCT 58.014 39.130 0.00 0.00 0.00 3.69
2818 2939 5.302357 CTGTGGAAATAAAACAGCTCCTC 57.698 43.478 0.00 0.00 35.34 3.71
2824 2945 5.122239 TCATCTCGCTGTGGAAATAAAACAG 59.878 40.000 0.00 0.00 43.37 3.16
2825 2946 5.000591 TCATCTCGCTGTGGAAATAAAACA 58.999 37.500 0.00 0.00 0.00 2.83
2826 2947 5.545658 TCATCTCGCTGTGGAAATAAAAC 57.454 39.130 0.00 0.00 0.00 2.43
2827 2948 5.879777 TGATCATCTCGCTGTGGAAATAAAA 59.120 36.000 0.00 0.00 0.00 1.52
2828 2949 5.427378 TGATCATCTCGCTGTGGAAATAAA 58.573 37.500 0.00 0.00 0.00 1.40
2829 2950 5.022282 TGATCATCTCGCTGTGGAAATAA 57.978 39.130 0.00 0.00 0.00 1.40
2830 2951 4.670896 TGATCATCTCGCTGTGGAAATA 57.329 40.909 0.00 0.00 0.00 1.40
2831 2952 3.548745 TGATCATCTCGCTGTGGAAAT 57.451 42.857 0.00 0.00 0.00 2.17
2832 2953 3.548745 ATGATCATCTCGCTGTGGAAA 57.451 42.857 1.18 0.00 0.00 3.13
2833 2954 3.548745 AATGATCATCTCGCTGTGGAA 57.451 42.857 9.06 0.00 0.00 3.53
2834 2955 3.133542 AGAAATGATCATCTCGCTGTGGA 59.866 43.478 9.06 0.00 0.00 4.02
2835 2956 3.464907 AGAAATGATCATCTCGCTGTGG 58.535 45.455 9.06 0.00 0.00 4.17
2836 2957 5.064325 TGAAAGAAATGATCATCTCGCTGTG 59.936 40.000 9.06 0.00 0.00 3.66
2837 2958 5.181009 TGAAAGAAATGATCATCTCGCTGT 58.819 37.500 9.06 0.00 0.00 4.40
2838 2959 5.522824 TCTGAAAGAAATGATCATCTCGCTG 59.477 40.000 9.06 4.75 42.31 5.18
2839 2960 5.668471 TCTGAAAGAAATGATCATCTCGCT 58.332 37.500 9.06 1.45 42.31 4.93
2864 2985 7.164230 AGTTACAGGAATCTGACTAGTCTTG 57.836 40.000 23.01 15.46 43.49 3.02
2881 3002 9.626045 GAATTCCCTGTGAAATTTTAGTTACAG 57.374 33.333 0.00 0.00 36.33 2.74
2953 3074 1.135699 GCGAAAATGATGGTGCGCAG 61.136 55.000 12.22 0.00 43.45 5.18
2954 3075 1.154054 GCGAAAATGATGGTGCGCA 60.154 52.632 5.66 5.66 43.45 6.09
2955 3076 0.526096 ATGCGAAAATGATGGTGCGC 60.526 50.000 0.00 0.00 44.15 6.09
2958 3079 5.590104 TCGTATATGCGAAAATGATGGTG 57.410 39.130 13.77 0.00 37.99 4.17
2996 3127 6.915300 CGATCGATCAGTAGAAGAGTGAAAAT 59.085 38.462 24.40 0.00 40.96 1.82
2997 3129 6.093633 TCGATCGATCAGTAGAAGAGTGAAAA 59.906 38.462 24.40 0.00 40.96 2.29
2998 3130 5.585047 TCGATCGATCAGTAGAAGAGTGAAA 59.415 40.000 24.40 0.00 40.96 2.69
3000 3132 4.508492 GTCGATCGATCAGTAGAAGAGTGA 59.492 45.833 22.50 6.67 41.84 3.41
3002 3134 4.699637 AGTCGATCGATCAGTAGAAGAGT 58.300 43.478 22.50 11.56 0.00 3.24
3027 3159 1.728971 GCTCTGTCGTGGTTGAATGAG 59.271 52.381 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.