Multiple sequence alignment - TraesCS3D01G273100

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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 TraesCS3D01G273100 chr3D 100.000 3182 0 0 1 3182 378575469 378578650 0.000000e+00 5877.0
1 TraesCS3D01G273100 chr3B 94.314 2515 96 15 1 2471 493652246 493654757 0.000000e+00 3808.0
2 TraesCS3D01G273100 chr3B 93.096 449 26 4 2736 3182 493654998 493655443 0.000000e+00 652.0
3 TraesCS3D01G273100 chr3B 92.208 77 4 2 2584 2659 493654910 493654985 1.210000e-19 108.0
4 TraesCS3D01G273100 chr3B 89.796 49 5 0 2247 2295 772331022 772330974 2.650000e-06 63.9
5 TraesCS3D01G273100 chr3A 91.926 2118 99 26 243 2330 502508325 502510400 0.000000e+00 2898.0
6 TraesCS3D01G273100 chr3A 90.832 469 23 6 2715 3182 502510732 502511181 7.550000e-171 610.0
7 TraesCS3D01G273100 chr3A 96.000 250 10 0 1 250 502508263 502508512 1.060000e-109 407.0
8 TraesCS3D01G273100 chr3A 89.474 190 10 2 2334 2513 502510442 502510631 6.860000e-57 231.0
9 TraesCS3D01G273100 chr4B 94.286 35 0 2 2330 2364 663935594 663935626 6.000000e-03 52.8


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 TraesCS3D01G273100 chr3D 378575469 378578650 3181 False 5877.000000 5877 100.000 1 3182 1 chr3D.!!$F1 3181
1 TraesCS3D01G273100 chr3B 493652246 493655443 3197 False 1522.666667 3808 93.206 1 3182 3 chr3B.!!$F1 3181
2 TraesCS3D01G273100 chr3A 502508263 502511181 2918 False 1036.500000 2898 92.058 1 3182 4 chr3A.!!$F1 3181

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
851 853 0.108585 TCCTTTCTGCAAGCCGACTT 59.891 50.0 0.0 0.0 36.19 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2702 2863 0.037697 ACGTAGAGCACCATCGCAAA 60.038 50.0 0.0 0.0 0.0 3.68 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
25 26 4.925054 CACACACCAAATGGACAATTCATC 59.075 41.667 6.42 0.00 38.94 2.92
148 149 6.582636 CATCAGCCTATTAGAACACAACCTA 58.417 40.000 0.00 0.00 0.00 3.08
269 271 9.990868 AGTAAACACATCTAATTTTCCCCTAAT 57.009 29.630 0.00 0.00 0.00 1.73
288 290 7.563556 CCCCTAATTTTTCATGTAACATACCCT 59.436 37.037 0.00 0.00 0.00 4.34
370 372 8.754080 TCTTAAATTGTGGAAAGAAACCTCAAA 58.246 29.630 0.00 0.00 41.77 2.69
400 402 3.074412 AGGCAGTTAATCAAACACCTCG 58.926 45.455 0.00 0.00 40.88 4.63
431 433 3.164358 CGACTATCCGCATTATCGTCAG 58.836 50.000 0.00 0.00 0.00 3.51
446 448 2.035193 TCGTCAGCCATCTAATCTCAGC 59.965 50.000 0.00 0.00 0.00 4.26
695 697 6.893958 AGTATTAGACAAACAGCTCAATCG 57.106 37.500 0.00 0.00 0.00 3.34
699 701 2.037772 AGACAAACAGCTCAATCGGAGT 59.962 45.455 0.00 0.00 45.88 3.85
757 759 2.383527 CGAAGAAGCGGAGTGGTGC 61.384 63.158 0.00 0.00 0.00 5.01
794 796 1.377856 GCAAGGGAAGTGGAGGAGC 60.378 63.158 0.00 0.00 0.00 4.70
851 853 0.108585 TCCTTTCTGCAAGCCGACTT 59.891 50.000 0.00 0.00 36.19 3.01
968 980 3.058224 GTGGCATTTTGTGGACTGTACTC 60.058 47.826 0.00 0.00 0.00 2.59
973 985 2.787601 TTGTGGACTGTACTCGTGTC 57.212 50.000 0.00 0.00 0.00 3.67
1383 1398 0.340208 TCTTCTTCTCCCTCCTCCCC 59.660 60.000 0.00 0.00 0.00 4.81
1386 1401 1.456705 CTTCTCCCTCCTCCCCTCG 60.457 68.421 0.00 0.00 0.00 4.63
1389 1404 4.144727 TCCCTCCTCCCCTCGCTC 62.145 72.222 0.00 0.00 0.00 5.03
1602 1617 0.892755 TGTACATGGACACCGTCTCC 59.107 55.000 6.68 0.00 32.47 3.71
1774 1789 0.179134 CCTCACGTACAGCTACCTGC 60.179 60.000 0.00 0.00 43.02 4.85
1827 1842 4.821589 GCCCGGGAGCTGTTCGAG 62.822 72.222 29.31 0.00 0.00 4.04
2140 2158 2.581354 GCCTGGATGCTGACGAGT 59.419 61.111 0.00 0.00 0.00 4.18
2160 2178 2.180674 CACGAGAGGTGGTGATCGA 58.819 57.895 0.00 0.00 43.16 3.59
2178 2196 0.973423 GACGACGACGACAAAGTAGC 59.027 55.000 15.32 0.00 42.66 3.58
2184 2202 1.912110 CGACGACAAAGTAGCTAGCAC 59.088 52.381 18.83 12.89 0.00 4.40
2200 2218 1.884579 AGCACAGAATTCAGCAGGTTG 59.115 47.619 8.44 0.00 0.00 3.77
2216 2244 3.683340 CAGGTTGATATCTGCATCGGATG 59.317 47.826 13.63 13.63 31.33 3.51
2217 2245 3.580022 AGGTTGATATCTGCATCGGATGA 59.420 43.478 21.69 6.13 31.33 2.92
2218 2246 3.931468 GGTTGATATCTGCATCGGATGAG 59.069 47.826 21.69 14.66 31.33 2.90
2323 2351 5.283294 TGAAATGAATGAACAAGCACACTG 58.717 37.500 0.00 0.00 0.00 3.66
2324 2352 3.928727 ATGAATGAACAAGCACACTGG 57.071 42.857 0.00 0.00 0.00 4.00
2332 2360 4.335315 TGAACAAGCACACTGGAACTAAAG 59.665 41.667 0.00 0.00 0.00 1.85
2356 2422 9.890629 AAGCTGTAGAACATCTTATATTTGTGA 57.109 29.630 0.00 0.00 33.33 3.58
2390 2456 1.538512 GAGTCATGTGTGCAATGTGCT 59.461 47.619 1.43 0.00 45.31 4.40
2483 2589 1.261989 TTATCACTACGCGCGAACAC 58.738 50.000 39.36 0.00 0.00 3.32
2501 2607 4.067972 ACACCACGTCTTCTAAACACAT 57.932 40.909 0.00 0.00 0.00 3.21
2524 2685 3.222603 GTGGAATGAACCAAGGAACTGT 58.777 45.455 0.00 0.00 40.86 3.55
2528 2689 4.938226 GGAATGAACCAAGGAACTGTCTAG 59.062 45.833 0.00 0.00 40.86 2.43
2542 2703 6.153680 GGAACTGTCTAGATTCCTTCTTCTCA 59.846 42.308 14.05 0.00 39.11 3.27
2543 2704 6.524101 ACTGTCTAGATTCCTTCTTCTCAC 57.476 41.667 0.00 0.00 35.79 3.51
2544 2705 6.013379 ACTGTCTAGATTCCTTCTTCTCACA 58.987 40.000 0.00 0.00 35.79 3.58
2545 2706 6.667414 ACTGTCTAGATTCCTTCTTCTCACAT 59.333 38.462 0.00 0.00 35.79 3.21
2546 2707 7.180051 ACTGTCTAGATTCCTTCTTCTCACATT 59.820 37.037 0.00 0.00 35.79 2.71
2547 2708 7.911651 TGTCTAGATTCCTTCTTCTCACATTT 58.088 34.615 0.00 0.00 35.79 2.32
2548 2709 7.821359 TGTCTAGATTCCTTCTTCTCACATTTG 59.179 37.037 0.00 0.00 35.79 2.32
2549 2710 7.821846 GTCTAGATTCCTTCTTCTCACATTTGT 59.178 37.037 0.00 0.00 35.79 2.83
2550 2711 8.378565 TCTAGATTCCTTCTTCTCACATTTGTT 58.621 33.333 0.00 0.00 35.79 2.83
2551 2712 7.830099 AGATTCCTTCTTCTCACATTTGTTT 57.170 32.000 0.00 0.00 0.00 2.83
2552 2713 8.242729 AGATTCCTTCTTCTCACATTTGTTTT 57.757 30.769 0.00 0.00 0.00 2.43
2553 2714 8.699130 AGATTCCTTCTTCTCACATTTGTTTTT 58.301 29.630 0.00 0.00 0.00 1.94
2554 2715 9.965824 GATTCCTTCTTCTCACATTTGTTTTTA 57.034 29.630 0.00 0.00 0.00 1.52
2556 2717 9.581099 TTCCTTCTTCTCACATTTGTTTTTAAC 57.419 29.630 0.00 0.00 0.00 2.01
2557 2718 8.744652 TCCTTCTTCTCACATTTGTTTTTAACA 58.255 29.630 0.00 0.00 40.21 2.41
2558 2719 8.807581 CCTTCTTCTCACATTTGTTTTTAACAC 58.192 33.333 0.00 0.00 41.97 3.32
2559 2720 9.352784 CTTCTTCTCACATTTGTTTTTAACACA 57.647 29.630 0.00 0.00 41.97 3.72
2560 2721 9.698309 TTCTTCTCACATTTGTTTTTAACACAA 57.302 25.926 0.00 0.00 41.97 3.33
2561 2722 9.868277 TCTTCTCACATTTGTTTTTAACACAAT 57.132 25.926 0.00 0.00 41.97 2.71
2568 2729 9.862371 ACATTTGTTTTTAACACAATACAGACA 57.138 25.926 0.00 0.00 41.97 3.41
2570 2731 9.862371 ATTTGTTTTTAACACAATACAGACACA 57.138 25.926 0.00 0.00 41.97 3.72
2571 2732 9.692749 TTTGTTTTTAACACAATACAGACACAA 57.307 25.926 0.00 0.00 41.97 3.33
2572 2733 8.903570 TGTTTTTAACACAATACAGACACAAG 57.096 30.769 0.00 0.00 36.25 3.16
2573 2734 8.516234 TGTTTTTAACACAATACAGACACAAGT 58.484 29.630 0.00 0.00 36.25 3.16
2574 2735 8.794406 GTTTTTAACACAATACAGACACAAGTG 58.206 33.333 0.00 0.00 0.00 3.16
2575 2736 6.612247 TTAACACAATACAGACACAAGTGG 57.388 37.500 5.08 0.00 34.19 4.00
2576 2737 3.476552 ACACAATACAGACACAAGTGGG 58.523 45.455 5.08 0.00 34.19 4.61
2577 2738 3.135712 ACACAATACAGACACAAGTGGGA 59.864 43.478 5.08 0.00 34.19 4.37
2578 2739 4.133820 CACAATACAGACACAAGTGGGAA 58.866 43.478 5.08 0.00 34.19 3.97
2579 2740 4.024048 CACAATACAGACACAAGTGGGAAC 60.024 45.833 5.08 0.00 34.19 3.62
2580 2741 2.519377 TACAGACACAAGTGGGAACG 57.481 50.000 5.08 0.00 34.19 3.95
2581 2742 0.539986 ACAGACACAAGTGGGAACGT 59.460 50.000 5.08 0.00 34.19 3.99
2582 2743 1.217882 CAGACACAAGTGGGAACGTC 58.782 55.000 5.08 0.00 34.19 4.34
2583 2744 1.120530 AGACACAAGTGGGAACGTCT 58.879 50.000 5.08 0.00 34.19 4.18
2584 2745 1.068741 AGACACAAGTGGGAACGTCTC 59.931 52.381 5.08 0.00 34.19 3.36
2585 2746 0.106149 ACACAAGTGGGAACGTCTCC 59.894 55.000 5.08 7.90 44.54 3.71
2586 2747 0.393077 CACAAGTGGGAACGTCTCCT 59.607 55.000 13.94 0.00 44.68 3.69
2587 2748 1.129058 ACAAGTGGGAACGTCTCCTT 58.871 50.000 13.94 1.98 44.68 3.36
2588 2749 1.070289 ACAAGTGGGAACGTCTCCTTC 59.930 52.381 13.94 8.94 44.68 3.46
2589 2750 1.344763 CAAGTGGGAACGTCTCCTTCT 59.655 52.381 13.94 10.45 44.68 2.85
2590 2751 1.718280 AGTGGGAACGTCTCCTTCTT 58.282 50.000 13.94 0.00 44.68 2.52
2591 2752 1.619332 AGTGGGAACGTCTCCTTCTTC 59.381 52.381 13.94 0.00 44.68 2.87
2592 2753 1.619332 GTGGGAACGTCTCCTTCTTCT 59.381 52.381 13.94 0.00 44.68 2.85
2593 2754 1.893801 TGGGAACGTCTCCTTCTTCTC 59.106 52.381 13.94 0.00 44.68 2.87
2603 2764 4.158025 GTCTCCTTCTTCTCGTATTGGTGA 59.842 45.833 0.00 0.00 0.00 4.02
2654 2815 0.750850 TGGTAGAGCTATTGCCGACC 59.249 55.000 10.81 10.81 40.80 4.79
2665 2826 1.466025 TTGCCGACCCAACTCTACGT 61.466 55.000 0.00 0.00 0.00 3.57
2670 2831 0.807496 GACCCAACTCTACGTACGCT 59.193 55.000 16.72 5.36 0.00 5.07
2672 2833 1.200948 ACCCAACTCTACGTACGCTTC 59.799 52.381 16.72 0.00 0.00 3.86
2673 2834 1.471684 CCCAACTCTACGTACGCTTCT 59.528 52.381 16.72 0.00 0.00 2.85
2674 2835 2.094854 CCCAACTCTACGTACGCTTCTT 60.095 50.000 16.72 0.00 0.00 2.52
2675 2836 3.572584 CCAACTCTACGTACGCTTCTTT 58.427 45.455 16.72 0.37 0.00 2.52
2676 2837 3.364023 CCAACTCTACGTACGCTTCTTTG 59.636 47.826 16.72 13.02 0.00 2.77
2677 2838 3.911661 ACTCTACGTACGCTTCTTTGT 57.088 42.857 16.72 2.70 0.00 2.83
2678 2839 4.234530 ACTCTACGTACGCTTCTTTGTT 57.765 40.909 16.72 0.00 0.00 2.83
2679 2840 4.225208 ACTCTACGTACGCTTCTTTGTTC 58.775 43.478 16.72 0.00 0.00 3.18
2680 2841 4.023365 ACTCTACGTACGCTTCTTTGTTCT 60.023 41.667 16.72 0.00 0.00 3.01
2681 2842 4.863491 TCTACGTACGCTTCTTTGTTCTT 58.137 39.130 16.72 0.00 0.00 2.52
2682 2843 5.284079 TCTACGTACGCTTCTTTGTTCTTT 58.716 37.500 16.72 0.00 0.00 2.52
2683 2844 4.870221 ACGTACGCTTCTTTGTTCTTTT 57.130 36.364 16.72 0.00 0.00 2.27
2684 2845 5.225899 ACGTACGCTTCTTTGTTCTTTTT 57.774 34.783 16.72 0.00 0.00 1.94
2715 2876 3.451141 TTTTCTTTTTGCGATGGTGCT 57.549 38.095 0.00 0.00 35.36 4.40
2716 2877 2.704725 TTCTTTTTGCGATGGTGCTC 57.295 45.000 0.00 0.00 35.36 4.26
2717 2878 1.896220 TCTTTTTGCGATGGTGCTCT 58.104 45.000 0.00 0.00 35.36 4.09
2718 2879 3.052455 TCTTTTTGCGATGGTGCTCTA 57.948 42.857 0.00 0.00 35.36 2.43
2719 2880 2.742053 TCTTTTTGCGATGGTGCTCTAC 59.258 45.455 0.00 0.00 35.36 2.59
2720 2881 1.075542 TTTTGCGATGGTGCTCTACG 58.924 50.000 0.00 0.00 35.36 3.51
2721 2882 0.037697 TTTGCGATGGTGCTCTACGT 60.038 50.000 0.00 0.00 35.36 3.57
2722 2883 0.812549 TTGCGATGGTGCTCTACGTA 59.187 50.000 0.00 0.00 35.36 3.57
2723 2884 0.099968 TGCGATGGTGCTCTACGTAC 59.900 55.000 0.00 0.00 35.36 3.67
2724 2885 0.928908 GCGATGGTGCTCTACGTACG 60.929 60.000 15.01 15.01 0.00 3.67
2725 2886 0.316772 CGATGGTGCTCTACGTACGG 60.317 60.000 21.06 2.32 0.00 4.02
2726 2887 0.594284 GATGGTGCTCTACGTACGGC 60.594 60.000 21.06 13.52 0.00 5.68
2778 2939 1.787847 CCGTGCCAATCGACTCAAC 59.212 57.895 0.00 0.00 0.00 3.18
2890 3053 6.741992 TGCAGATAACTCAACAATAACCTG 57.258 37.500 0.00 0.00 0.00 4.00
2933 3096 2.032808 ACTTTTTCGCTCTTGCTTCGAC 60.033 45.455 0.00 0.00 36.97 4.20
2934 3097 0.865769 TTTTCGCTCTTGCTTCGACC 59.134 50.000 0.00 0.00 36.97 4.79
2961 3124 6.972901 AGTTGCTCTTACAAAGTTGCTTTTAC 59.027 34.615 0.00 0.00 30.60 2.01
2999 3162 6.041182 GGGTAAGTTTAAGACCAAAACCATGT 59.959 38.462 0.00 0.00 37.51 3.21
3000 3163 7.418139 GGGTAAGTTTAAGACCAAAACCATGTT 60.418 37.037 0.00 0.00 37.51 2.71
3073 3236 1.162505 TTTCTCCCCCAAATGGACCA 58.837 50.000 0.00 0.00 37.39 4.02
3087 3250 5.841957 AATGGACCATCTGTAATTTGCTC 57.158 39.130 7.63 0.00 0.00 4.26
3156 3319 2.438021 GACATAGGCACAATCACCCCTA 59.562 50.000 0.00 0.00 34.68 3.53
3158 3321 3.117888 ACATAGGCACAATCACCCCTAAG 60.118 47.826 0.00 0.00 33.94 2.18
3166 3329 0.685458 ATCACCCCTAAGCCGTACGT 60.685 55.000 15.21 0.00 0.00 3.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 7.716738 CTATTGAAGCATGAAGAAAAAGTCG 57.283 36.000 0.00 0.00 0.00 4.18
51 52 3.287222 TGTGCTTCCTGTTAGCTGTTTT 58.713 40.909 0.00 0.00 39.38 2.43
107 108 4.099266 GCTGATGCTTCCTCTCTAAGAGAA 59.901 45.833 7.53 0.67 39.29 2.87
148 149 5.441718 TCTTCCCACTATTCATGAGCTTT 57.558 39.130 0.00 0.00 0.00 3.51
269 271 9.667107 CTCTAAGAGGGTATGTTACATGAAAAA 57.333 33.333 8.26 0.00 0.00 1.94
288 290 5.133660 AGGCTCATAGACTTCCTCTCTAAGA 59.866 44.000 0.00 0.00 17.74 2.10
305 307 2.290323 GGTTGTGTTCCAGTAGGCTCAT 60.290 50.000 0.00 0.00 33.74 2.90
354 356 6.326064 TCAATGGAATTTGAGGTTTCTTTCCA 59.674 34.615 4.81 4.81 44.70 3.53
370 372 6.211184 TGTTTGATTAACTGCCTCAATGGAAT 59.789 34.615 0.00 0.00 37.64 3.01
380 382 2.812011 ACGAGGTGTTTGATTAACTGCC 59.188 45.455 0.00 0.00 37.64 4.85
400 402 0.527817 CGGATAGTCGGCTTGTGGAC 60.528 60.000 0.00 0.00 0.00 4.02
431 433 1.530293 CGCTTGCTGAGATTAGATGGC 59.470 52.381 0.00 0.00 0.00 4.40
446 448 6.417635 ACAGTTATGTTTGAATGTTTCGCTTG 59.582 34.615 0.00 0.00 35.63 4.01
675 677 4.832248 TCCGATTGAGCTGTTTGTCTAAT 58.168 39.130 0.00 0.00 0.00 1.73
695 697 2.728817 CGGTCGGCCTGATACTCC 59.271 66.667 3.66 0.00 0.00 3.85
951 954 4.056050 GACACGAGTACAGTCCACAAAAT 58.944 43.478 0.00 0.00 0.00 1.82
968 980 2.278596 CGGGGATACTGCGACACG 60.279 66.667 0.00 0.00 0.00 4.49
1339 1354 2.804090 GGTGCGGTCGAACTCGTC 60.804 66.667 0.00 0.00 40.80 4.20
1827 1842 2.578664 CCTTTGCCCCGCATTTCC 59.421 61.111 0.00 0.00 38.76 3.13
1917 1932 1.407656 TATCCCACATCACCCGCTCC 61.408 60.000 0.00 0.00 0.00 4.70
2035 2050 0.839853 CCCATCTCCTCCATCTCCCC 60.840 65.000 0.00 0.00 0.00 4.81
2088 2103 1.140407 CGTCGTCTTGGATCGAAGCC 61.140 60.000 12.27 0.35 37.81 4.35
2094 2109 0.248134 CGTCCTCGTCGTCTTGGATC 60.248 60.000 0.00 0.00 0.00 3.36
2140 2158 1.591703 GATCACCACCTCTCGTGCA 59.408 57.895 0.00 0.00 41.53 4.57
2160 2178 0.590195 AGCTACTTTGTCGTCGTCGT 59.410 50.000 1.33 0.00 38.33 4.34
2178 2196 2.983229 ACCTGCTGAATTCTGTGCTAG 58.017 47.619 13.17 10.61 0.00 3.42
2184 2202 6.301687 CAGATATCAACCTGCTGAATTCTG 57.698 41.667 7.05 7.51 34.65 3.02
2200 2218 6.551385 AAAAACTCATCCGATGCAGATATC 57.449 37.500 3.25 0.00 0.00 1.63
2332 2360 8.768955 CCTCACAAATATAAGATGTTCTACAGC 58.231 37.037 0.00 0.00 34.13 4.40
2356 2422 0.787084 TGACTCTGTTCCTCCCTCCT 59.213 55.000 0.00 0.00 0.00 3.69
2390 2456 2.647529 ACTCGCATGTATCGTTGTGA 57.352 45.000 0.00 0.00 0.00 3.58
2451 2520 7.516155 GCGCGTAGTGATAATTCAAGACATTTA 60.516 37.037 8.43 0.00 43.07 1.40
2501 2607 2.176798 AGTTCCTTGGTTCATTCCACCA 59.823 45.455 0.00 0.00 42.90 4.17
2524 2685 7.911651 ACAAATGTGAGAAGAAGGAATCTAGA 58.088 34.615 0.00 0.00 37.42 2.43
2528 2689 8.877808 AAAAACAAATGTGAGAAGAAGGAATC 57.122 30.769 0.00 0.00 0.00 2.52
2542 2703 9.862371 TGTCTGTATTGTGTTAAAAACAAATGT 57.138 25.926 8.57 0.00 44.16 2.71
2544 2705 9.862371 TGTGTCTGTATTGTGTTAAAAACAAAT 57.138 25.926 8.57 4.11 44.16 2.32
2545 2706 9.692749 TTGTGTCTGTATTGTGTTAAAAACAAA 57.307 25.926 8.57 0.00 44.16 2.83
2546 2707 9.347934 CTTGTGTCTGTATTGTGTTAAAAACAA 57.652 29.630 7.28 7.28 44.16 2.83
2547 2708 8.516234 ACTTGTGTCTGTATTGTGTTAAAAACA 58.484 29.630 0.00 0.00 39.52 2.83
2548 2709 8.794406 CACTTGTGTCTGTATTGTGTTAAAAAC 58.206 33.333 0.00 0.00 0.00 2.43
2549 2710 7.971168 CCACTTGTGTCTGTATTGTGTTAAAAA 59.029 33.333 0.00 0.00 0.00 1.94
2550 2711 7.415765 CCCACTTGTGTCTGTATTGTGTTAAAA 60.416 37.037 0.00 0.00 0.00 1.52
2551 2712 6.038825 CCCACTTGTGTCTGTATTGTGTTAAA 59.961 38.462 0.00 0.00 0.00 1.52
2552 2713 5.529430 CCCACTTGTGTCTGTATTGTGTTAA 59.471 40.000 0.00 0.00 0.00 2.01
2553 2714 5.060506 CCCACTTGTGTCTGTATTGTGTTA 58.939 41.667 0.00 0.00 0.00 2.41
2554 2715 3.882888 CCCACTTGTGTCTGTATTGTGTT 59.117 43.478 0.00 0.00 0.00 3.32
2555 2716 3.135712 TCCCACTTGTGTCTGTATTGTGT 59.864 43.478 0.00 0.00 0.00 3.72
2556 2717 3.738982 TCCCACTTGTGTCTGTATTGTG 58.261 45.455 0.00 0.00 0.00 3.33
2557 2718 4.134563 GTTCCCACTTGTGTCTGTATTGT 58.865 43.478 0.00 0.00 0.00 2.71
2558 2719 3.186409 CGTTCCCACTTGTGTCTGTATTG 59.814 47.826 0.00 0.00 0.00 1.90
2559 2720 3.181458 ACGTTCCCACTTGTGTCTGTATT 60.181 43.478 0.00 0.00 0.00 1.89
2560 2721 2.367567 ACGTTCCCACTTGTGTCTGTAT 59.632 45.455 0.00 0.00 0.00 2.29
2561 2722 1.758280 ACGTTCCCACTTGTGTCTGTA 59.242 47.619 0.00 0.00 0.00 2.74
2562 2723 0.539986 ACGTTCCCACTTGTGTCTGT 59.460 50.000 0.00 0.00 0.00 3.41
2563 2724 1.202533 AGACGTTCCCACTTGTGTCTG 60.203 52.381 0.00 0.00 35.52 3.51
2564 2725 1.068741 GAGACGTTCCCACTTGTGTCT 59.931 52.381 0.00 0.00 39.24 3.41
2565 2726 1.499049 GAGACGTTCCCACTTGTGTC 58.501 55.000 0.00 0.00 0.00 3.67
2566 2727 0.106149 GGAGACGTTCCCACTTGTGT 59.894 55.000 0.00 0.00 40.37 3.72
2567 2728 2.914379 GGAGACGTTCCCACTTGTG 58.086 57.895 0.00 0.00 40.37 3.33
2576 2737 2.993449 ACGAGAAGAAGGAGACGTTC 57.007 50.000 0.00 0.00 0.00 3.95
2577 2738 4.380655 CCAATACGAGAAGAAGGAGACGTT 60.381 45.833 0.00 0.00 35.66 3.99
2578 2739 3.128938 CCAATACGAGAAGAAGGAGACGT 59.871 47.826 0.00 0.00 37.68 4.34
2579 2740 3.128938 ACCAATACGAGAAGAAGGAGACG 59.871 47.826 0.00 0.00 0.00 4.18
2580 2741 4.158025 TCACCAATACGAGAAGAAGGAGAC 59.842 45.833 0.00 0.00 0.00 3.36
2581 2742 4.341487 TCACCAATACGAGAAGAAGGAGA 58.659 43.478 0.00 0.00 0.00 3.71
2582 2743 4.158764 ACTCACCAATACGAGAAGAAGGAG 59.841 45.833 0.00 0.00 33.33 3.69
2583 2744 4.082190 CACTCACCAATACGAGAAGAAGGA 60.082 45.833 0.00 0.00 33.33 3.36
2584 2745 4.177026 CACTCACCAATACGAGAAGAAGG 58.823 47.826 0.00 0.00 33.33 3.46
2585 2746 4.810790 ACACTCACCAATACGAGAAGAAG 58.189 43.478 0.00 0.00 33.33 2.85
2586 2747 4.866508 ACACTCACCAATACGAGAAGAA 57.133 40.909 0.00 0.00 33.33 2.52
2587 2748 5.970317 TTACACTCACCAATACGAGAAGA 57.030 39.130 0.00 0.00 33.33 2.87
2588 2749 8.135529 TCATATTACACTCACCAATACGAGAAG 58.864 37.037 0.00 0.00 33.33 2.85
2589 2750 8.002984 TCATATTACACTCACCAATACGAGAA 57.997 34.615 0.00 0.00 33.33 2.87
2590 2751 7.576861 TCATATTACACTCACCAATACGAGA 57.423 36.000 0.00 0.00 33.33 4.04
2591 2752 6.363626 GCTCATATTACACTCACCAATACGAG 59.636 42.308 0.00 0.00 31.13 4.18
2592 2753 6.183360 TGCTCATATTACACTCACCAATACGA 60.183 38.462 0.00 0.00 0.00 3.43
2593 2754 5.983118 TGCTCATATTACACTCACCAATACG 59.017 40.000 0.00 0.00 0.00 3.06
2603 2764 6.658816 TCAAATGTTGGTGCTCATATTACACT 59.341 34.615 0.00 0.00 34.70 3.55
2638 2799 1.138266 GTTGGGTCGGCAATAGCTCTA 59.862 52.381 0.00 0.00 41.70 2.43
2639 2800 0.107654 GTTGGGTCGGCAATAGCTCT 60.108 55.000 0.00 0.00 41.70 4.09
2640 2801 0.107654 AGTTGGGTCGGCAATAGCTC 60.108 55.000 0.00 0.00 41.70 4.09
2641 2802 0.107654 GAGTTGGGTCGGCAATAGCT 60.108 55.000 0.00 0.00 41.70 3.32
2642 2803 0.107654 AGAGTTGGGTCGGCAATAGC 60.108 55.000 0.00 0.00 41.10 2.97
2643 2804 2.798499 CGTAGAGTTGGGTCGGCAATAG 60.798 54.545 0.00 0.00 0.00 1.73
2644 2805 1.135527 CGTAGAGTTGGGTCGGCAATA 59.864 52.381 0.00 0.00 0.00 1.90
2645 2806 0.108329 CGTAGAGTTGGGTCGGCAAT 60.108 55.000 0.00 0.00 0.00 3.56
2646 2807 1.290955 CGTAGAGTTGGGTCGGCAA 59.709 57.895 0.00 0.00 0.00 4.52
2654 2815 2.915738 AGAAGCGTACGTAGAGTTGG 57.084 50.000 17.90 0.00 0.00 3.77
2694 2855 3.791245 AGCACCATCGCAAAAAGAAAAA 58.209 36.364 0.00 0.00 0.00 1.94
2695 2856 3.068024 AGAGCACCATCGCAAAAAGAAAA 59.932 39.130 0.00 0.00 0.00 2.29
2696 2857 2.622942 AGAGCACCATCGCAAAAAGAAA 59.377 40.909 0.00 0.00 0.00 2.52
2697 2858 2.229792 AGAGCACCATCGCAAAAAGAA 58.770 42.857 0.00 0.00 0.00 2.52
2698 2859 1.896220 AGAGCACCATCGCAAAAAGA 58.104 45.000 0.00 0.00 0.00 2.52
2699 2860 2.474526 CGTAGAGCACCATCGCAAAAAG 60.475 50.000 0.00 0.00 0.00 2.27
2700 2861 1.463056 CGTAGAGCACCATCGCAAAAA 59.537 47.619 0.00 0.00 0.00 1.94
2701 2862 1.075542 CGTAGAGCACCATCGCAAAA 58.924 50.000 0.00 0.00 0.00 2.44
2702 2863 0.037697 ACGTAGAGCACCATCGCAAA 60.038 50.000 0.00 0.00 0.00 3.68
2703 2864 0.812549 TACGTAGAGCACCATCGCAA 59.187 50.000 0.00 0.00 0.00 4.85
2704 2865 0.099968 GTACGTAGAGCACCATCGCA 59.900 55.000 0.00 0.00 0.00 5.10
2705 2866 0.928908 CGTACGTAGAGCACCATCGC 60.929 60.000 7.22 0.00 0.00 4.58
2706 2867 0.316772 CCGTACGTAGAGCACCATCG 60.317 60.000 15.21 0.00 0.00 3.84
2707 2868 0.594284 GCCGTACGTAGAGCACCATC 60.594 60.000 15.21 0.00 0.00 3.51
2708 2869 1.035932 AGCCGTACGTAGAGCACCAT 61.036 55.000 15.21 0.00 0.00 3.55
2709 2870 1.246056 AAGCCGTACGTAGAGCACCA 61.246 55.000 15.21 0.00 0.00 4.17
2710 2871 0.801067 CAAGCCGTACGTAGAGCACC 60.801 60.000 15.21 0.00 0.00 5.01
2711 2872 0.169672 TCAAGCCGTACGTAGAGCAC 59.830 55.000 15.21 0.00 0.00 4.40
2712 2873 0.169672 GTCAAGCCGTACGTAGAGCA 59.830 55.000 15.21 0.00 0.00 4.26
2713 2874 0.860618 CGTCAAGCCGTACGTAGAGC 60.861 60.000 15.21 10.30 34.48 4.09
2714 2875 0.860618 GCGTCAAGCCGTACGTAGAG 60.861 60.000 15.21 0.00 41.10 2.43
2715 2876 1.135315 GCGTCAAGCCGTACGTAGA 59.865 57.895 15.21 3.40 41.10 2.59
2716 2877 3.671723 GCGTCAAGCCGTACGTAG 58.328 61.111 15.21 0.29 41.10 3.51
2778 2939 1.667724 CTATTTGCCTGCGAGTCTTGG 59.332 52.381 0.00 0.00 0.00 3.61
2907 3070 3.609103 GCAAGAGCGAAAAAGTCTTCA 57.391 42.857 0.00 0.00 0.00 3.02
2933 3096 4.044426 GCAACTTTGTAAGAGCAACTTGG 58.956 43.478 6.46 0.00 39.38 3.61
2934 3097 4.925068 AGCAACTTTGTAAGAGCAACTTG 58.075 39.130 6.46 0.00 39.38 3.16
2999 3162 5.620206 TCTGTAGAATGAGCCTGACAAAAA 58.380 37.500 0.00 0.00 0.00 1.94
3000 3163 5.227569 TCTGTAGAATGAGCCTGACAAAA 57.772 39.130 0.00 0.00 0.00 2.44
3073 3236 6.183360 GCCTGAAGAATGAGCAAATTACAGAT 60.183 38.462 0.00 0.00 0.00 2.90
3087 3250 2.208431 GTCCGATCAGCCTGAAGAATG 58.792 52.381 0.00 0.00 0.00 2.67
3128 3291 1.485294 TTGTGCCTATGTCCACCGGT 61.485 55.000 0.00 0.00 0.00 5.28
3156 3319 3.184541 CTGCAACTTATACGTACGGCTT 58.815 45.455 21.06 6.17 0.00 4.35
3158 3321 1.856597 CCTGCAACTTATACGTACGGC 59.143 52.381 21.06 10.89 0.00 5.68


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

AutoCloner maintained by Alex Coulton.