Multiple sequence alignment - TraesCS5B01G396100

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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 TraesCS5B01G396100 chr5B 100.000 2811 0 0 1 2811 573141492 573144302 0.000000e+00 5192.0
1 TraesCS5B01G396100 chr5D 90.794 2683 129 47 1 2649 465905086 465907684 0.000000e+00 3478.0
2 TraesCS5B01G396100 chr5A 88.009 2627 147 71 75 2632 586306807 586309334 0.000000e+00 2952.0
3 TraesCS5B01G396100 chr5A 88.976 127 9 3 2688 2811 586309335 586309459 4.850000e-33 152.0
4 TraesCS5B01G396100 chr5A 100.000 39 0 0 1 39 586306759 586306797 3.880000e-09 73.1


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 TraesCS5B01G396100 chr5B 573141492 573144302 2810 False 5192.000000 5192 100.000000 1 2811 1 chr5B.!!$F1 2810
1 TraesCS5B01G396100 chr5D 465905086 465907684 2598 False 3478.000000 3478 90.794000 1 2649 1 chr5D.!!$F1 2648
2 TraesCS5B01G396100 chr5A 586306759 586309459 2700 False 1059.033333 2952 92.328333 1 2811 3 chr5A.!!$F1 2810

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
39 40 0.111639 GACCACCCAGGGTTAAGCAA 59.888 55.0 9.12 0.0 42.53 3.91 F
1084 1142 0.102120 GCTCGACAGGATCAGAGGTG 59.898 60.0 0.00 0.0 32.14 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1108 1166 1.110442 ACAGCTTCTGATCGGAGGAG 58.890 55.0 17.37 8.25 35.18 3.69 R
2664 2765 0.108615 GCTAGCTGAACGAAGAGCCA 60.109 55.0 7.70 0.00 35.69 4.75 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
39 40 0.111639 GACCACCCAGGGTTAAGCAA 59.888 55.000 9.12 0.00 42.53 3.91
42 43 1.618343 CCACCCAGGGTTAAGCAAAAG 59.382 52.381 9.12 0.00 31.02 2.27
43 44 1.000843 CACCCAGGGTTAAGCAAAAGC 59.999 52.381 9.12 0.00 31.02 3.51
44 45 1.133167 ACCCAGGGTTAAGCAAAAGCT 60.133 47.619 4.76 0.00 27.29 3.74
45 46 1.546029 CCCAGGGTTAAGCAAAAGCTC 59.454 52.381 7.03 0.00 0.00 4.09
67 72 2.603473 CCCTCCCACAGTCACCGA 60.603 66.667 0.00 0.00 0.00 4.69
69 74 1.004918 CCTCCCACAGTCACCGAAC 60.005 63.158 0.00 0.00 0.00 3.95
164 169 3.987868 GCGAGAACACTACAAACTGATCA 59.012 43.478 0.00 0.00 0.00 2.92
190 195 1.085091 GTCACATCCAGCTTGCTCTG 58.915 55.000 0.00 0.00 0.00 3.35
193 198 2.124819 ATCCAGCTTGCTCTGCCG 60.125 61.111 0.00 0.00 32.87 5.69
374 387 4.043200 GTGTGCCGCTGCCTTTCC 62.043 66.667 0.00 0.00 36.33 3.13
375 388 4.577677 TGTGCCGCTGCCTTTCCA 62.578 61.111 0.00 0.00 36.33 3.53
376 389 4.043200 GTGCCGCTGCCTTTCCAC 62.043 66.667 0.00 0.00 36.33 4.02
382 395 4.351054 CTGCCTTTCCACGCCCCT 62.351 66.667 0.00 0.00 0.00 4.79
383 396 3.868200 CTGCCTTTCCACGCCCCTT 62.868 63.158 0.00 0.00 0.00 3.95
384 397 2.600470 GCCTTTCCACGCCCCTTT 60.600 61.111 0.00 0.00 0.00 3.11
385 398 2.207229 GCCTTTCCACGCCCCTTTT 61.207 57.895 0.00 0.00 0.00 2.27
423 445 1.078143 CCCGGCTTCTTCTTCCCAG 60.078 63.158 0.00 0.00 0.00 4.45
474 496 2.753452 AGGTGACGGACGCATATATAGG 59.247 50.000 0.00 0.00 0.00 2.57
475 497 2.490903 GGTGACGGACGCATATATAGGT 59.509 50.000 0.00 0.00 0.00 3.08
528 554 1.227102 CCCGCATCCAATTCCCTCA 59.773 57.895 0.00 0.00 0.00 3.86
610 651 3.326836 TCAAGGTGATGCACATCGTTA 57.673 42.857 6.17 0.00 40.63 3.18
619 660 4.582240 TGATGCACATCGTTATCTCTCTCT 59.418 41.667 6.17 0.00 40.63 3.10
637 684 3.627123 TCTCTCTCTCTCGCAATCAGAAG 59.373 47.826 0.00 0.00 0.00 2.85
702 749 1.804396 TTGTGCCATGCCGAACCTTG 61.804 55.000 0.00 0.00 0.00 3.61
861 915 0.796312 CAGTTGGTTTGGTCGATCGG 59.204 55.000 16.41 0.00 0.00 4.18
864 918 0.320946 TTGGTTTGGTCGATCGGTCC 60.321 55.000 16.41 17.70 0.00 4.46
915 969 3.407698 TGCGCCTCTGTTTCATTTTCTA 58.592 40.909 4.18 0.00 0.00 2.10
916 970 3.188460 TGCGCCTCTGTTTCATTTTCTAC 59.812 43.478 4.18 0.00 0.00 2.59
940 994 1.273606 TCTGTTCTGCGAAGGAAGAGG 59.726 52.381 0.00 0.00 35.61 3.69
941 995 1.001406 CTGTTCTGCGAAGGAAGAGGT 59.999 52.381 0.00 0.00 32.64 3.85
942 996 1.270305 TGTTCTGCGAAGGAAGAGGTG 60.270 52.381 0.00 0.00 0.00 4.00
943 997 0.321671 TTCTGCGAAGGAAGAGGTGG 59.678 55.000 0.00 0.00 0.00 4.61
944 998 0.541998 TCTGCGAAGGAAGAGGTGGA 60.542 55.000 0.00 0.00 0.00 4.02
945 999 0.539051 CTGCGAAGGAAGAGGTGGAT 59.461 55.000 0.00 0.00 0.00 3.41
957 1013 5.012046 GGAAGAGGTGGATGTGGAAAATTTT 59.988 40.000 2.28 2.28 0.00 1.82
962 1018 3.747529 GTGGATGTGGAAAATTTTGGCTG 59.252 43.478 8.47 0.00 0.00 4.85
972 1028 5.640783 GGAAAATTTTGGCTGGAATTCTGAG 59.359 40.000 8.47 3.22 0.00 3.35
973 1029 6.423776 AAAATTTTGGCTGGAATTCTGAGA 57.576 33.333 1.75 0.00 0.00 3.27
974 1030 5.656213 AATTTTGGCTGGAATTCTGAGAG 57.344 39.130 5.23 0.00 0.00 3.20
976 1032 1.661463 TGGCTGGAATTCTGAGAGGT 58.339 50.000 5.23 0.00 0.00 3.85
978 1034 1.280421 GGCTGGAATTCTGAGAGGTGT 59.720 52.381 5.23 0.00 0.00 4.16
980 1036 2.354259 CTGGAATTCTGAGAGGTGTGC 58.646 52.381 5.23 0.00 0.00 4.57
981 1037 1.338105 TGGAATTCTGAGAGGTGTGCG 60.338 52.381 5.23 0.00 0.00 5.34
982 1038 1.338200 GGAATTCTGAGAGGTGTGCGT 60.338 52.381 5.23 0.00 0.00 5.24
1084 1142 0.102120 GCTCGACAGGATCAGAGGTG 59.898 60.000 0.00 0.00 32.14 4.00
1189 1253 0.456995 CAGAGAAGGGCGAGTTCGTC 60.457 60.000 3.27 0.00 44.28 4.20
1279 1343 1.181741 TCTCCGACAAGCTCTGCTGT 61.182 55.000 0.00 0.00 39.62 4.40
1315 1379 3.500299 TCATCAAGGAGATCGAGATCGTC 59.500 47.826 7.37 5.93 42.48 4.20
1553 1617 3.691342 CGCCCAAGGTCGTGGAGA 61.691 66.667 4.53 0.00 41.65 3.71
1555 1619 1.672854 CGCCCAAGGTCGTGGAGATA 61.673 60.000 4.53 0.00 41.65 1.98
1613 1677 3.200593 CATCGGACTGCTGCTGCC 61.201 66.667 13.47 7.95 38.71 4.85
1614 1678 3.709633 ATCGGACTGCTGCTGCCA 61.710 61.111 13.47 0.56 38.71 4.92
1660 1730 2.034687 TCCTGCAAGCAAGAGCCC 59.965 61.111 0.00 0.00 43.56 5.19
1817 1896 1.787012 CGCCATCATGTGATCGATCA 58.213 50.000 23.99 23.99 31.21 2.92
1822 1901 4.142881 GCCATCATGTGATCGATCAATCAG 60.143 45.833 28.83 18.21 38.75 2.90
1824 1903 6.161381 CCATCATGTGATCGATCAATCAGTA 58.839 40.000 28.83 15.29 38.75 2.74
1825 1904 6.090493 CCATCATGTGATCGATCAATCAGTAC 59.910 42.308 28.83 15.20 38.75 2.73
1826 1905 6.396829 TCATGTGATCGATCAATCAGTACT 57.603 37.500 28.83 6.82 38.75 2.73
1834 1913 6.283161 TCGATCAATCAGTACTAGTACGTG 57.717 41.667 23.87 20.92 40.80 4.49
1896 1975 1.064952 GCTACGTTGCCGCCATTAATT 59.935 47.619 11.09 0.00 37.70 1.40
1900 1979 0.454196 GTTGCCGCCATTAATTCGGT 59.546 50.000 20.64 0.00 44.58 4.69
1976 2064 3.057456 CGCCACATATACACCTACTCTCC 60.057 52.174 0.00 0.00 0.00 3.71
1979 2067 4.893524 CCACATATACACCTACTCTCCACA 59.106 45.833 0.00 0.00 0.00 4.17
2104 2199 3.013219 GAGGATCCGAGATCGATCATCA 58.987 50.000 26.47 8.33 43.02 3.07
2109 2204 2.550180 TCCGAGATCGATCATCAGTGTC 59.450 50.000 26.47 12.49 43.02 3.67
2110 2205 2.351253 CCGAGATCGATCATCAGTGTCC 60.351 54.545 26.47 0.00 43.02 4.02
2128 2225 0.388520 CCGTCGTCTCATTGTCAGCA 60.389 55.000 0.00 0.00 0.00 4.41
2266 2363 3.020274 TCACCAGCTTTACTTTGTTGCA 58.980 40.909 0.00 0.00 0.00 4.08
2273 2370 3.184986 GCTTTACTTTGTTGCAATGCCTG 59.815 43.478 0.59 0.00 0.00 4.85
2338 2435 9.982291 TGCTTTCTCGTGTATTATTTATTGTTC 57.018 29.630 0.00 0.00 0.00 3.18
2343 2440 9.647797 TCTCGTGTATTATTTATTGTTCTGTGT 57.352 29.630 0.00 0.00 0.00 3.72
2416 2513 1.743321 GAGGAGCGTCATCAGGAGGG 61.743 65.000 0.00 0.00 32.04 4.30
2482 2579 0.611714 GGGAGGAGGTGTTAAAGCGA 59.388 55.000 0.00 0.00 0.00 4.93
2486 2583 1.359459 GGAGGTGTTAAAGCGAGCGG 61.359 60.000 0.00 0.00 0.00 5.52
2535 2632 0.543410 AGACGGTGGTGGGTGACATA 60.543 55.000 0.00 0.00 0.00 2.29
2536 2633 0.108329 GACGGTGGTGGGTGACATAG 60.108 60.000 0.00 0.00 0.00 2.23
2540 2637 1.568504 GTGGTGGGTGACATAGAGGA 58.431 55.000 0.00 0.00 0.00 3.71
2570 2667 1.937546 GATGGAGGCCAAGCAAACCG 61.938 60.000 5.01 0.00 36.95 4.44
2598 2695 2.740055 GTGGCTGGCTGTGTCGAG 60.740 66.667 2.00 0.00 0.00 4.04
2628 2729 0.963962 AACAGAGGCCATGCAAACAG 59.036 50.000 5.01 0.00 0.00 3.16
2632 2733 0.529378 GAGGCCATGCAAACAGAAGG 59.471 55.000 5.01 0.00 0.00 3.46
2633 2734 1.079612 GGCCATGCAAACAGAAGGC 60.080 57.895 0.00 0.00 39.91 4.35
2634 2735 1.667151 GCCATGCAAACAGAAGGCA 59.333 52.632 0.00 0.00 40.19 4.75
2635 2736 0.389426 GCCATGCAAACAGAAGGCAG 60.389 55.000 0.00 0.00 41.40 4.85
2636 2737 0.245539 CCATGCAAACAGAAGGCAGG 59.754 55.000 0.00 0.00 41.40 4.85
2637 2738 0.245539 CATGCAAACAGAAGGCAGGG 59.754 55.000 0.00 0.00 41.40 4.45
2638 2739 0.901580 ATGCAAACAGAAGGCAGGGG 60.902 55.000 0.00 0.00 41.40 4.79
2639 2740 1.228552 GCAAACAGAAGGCAGGGGA 60.229 57.895 0.00 0.00 0.00 4.81
2640 2741 0.613012 GCAAACAGAAGGCAGGGGAT 60.613 55.000 0.00 0.00 0.00 3.85
2641 2742 1.180029 CAAACAGAAGGCAGGGGATG 58.820 55.000 0.00 0.00 0.00 3.51
2642 2743 0.779997 AAACAGAAGGCAGGGGATGT 59.220 50.000 0.00 0.00 0.00 3.06
2643 2744 0.038744 AACAGAAGGCAGGGGATGTG 59.961 55.000 0.00 0.00 0.00 3.21
2644 2745 1.136329 ACAGAAGGCAGGGGATGTGT 61.136 55.000 0.00 0.00 0.00 3.72
2645 2746 0.679002 CAGAAGGCAGGGGATGTGTG 60.679 60.000 0.00 0.00 0.00 3.82
2646 2747 1.136329 AGAAGGCAGGGGATGTGTGT 61.136 55.000 0.00 0.00 0.00 3.72
2647 2748 0.618458 GAAGGCAGGGGATGTGTGTA 59.382 55.000 0.00 0.00 0.00 2.90
2648 2749 1.212935 GAAGGCAGGGGATGTGTGTAT 59.787 52.381 0.00 0.00 0.00 2.29
2649 2750 0.548031 AGGCAGGGGATGTGTGTATG 59.452 55.000 0.00 0.00 0.00 2.39
2650 2751 0.255890 GGCAGGGGATGTGTGTATGT 59.744 55.000 0.00 0.00 0.00 2.29
2651 2752 1.382522 GCAGGGGATGTGTGTATGTG 58.617 55.000 0.00 0.00 0.00 3.21
2652 2753 1.340017 GCAGGGGATGTGTGTATGTGT 60.340 52.381 0.00 0.00 0.00 3.72
2653 2754 2.358957 CAGGGGATGTGTGTATGTGTG 58.641 52.381 0.00 0.00 0.00 3.82
2654 2755 1.985159 AGGGGATGTGTGTATGTGTGT 59.015 47.619 0.00 0.00 0.00 3.72
2655 2756 2.083774 GGGGATGTGTGTATGTGTGTG 58.916 52.381 0.00 0.00 0.00 3.82
2656 2757 2.552155 GGGGATGTGTGTATGTGTGTGT 60.552 50.000 0.00 0.00 0.00 3.72
2657 2758 2.483877 GGGATGTGTGTATGTGTGTGTG 59.516 50.000 0.00 0.00 0.00 3.82
2658 2759 3.138304 GGATGTGTGTATGTGTGTGTGT 58.862 45.455 0.00 0.00 0.00 3.72
2659 2760 3.186409 GGATGTGTGTATGTGTGTGTGTC 59.814 47.826 0.00 0.00 0.00 3.67
2660 2761 3.535280 TGTGTGTATGTGTGTGTGTCT 57.465 42.857 0.00 0.00 0.00 3.41
2661 2762 3.453424 TGTGTGTATGTGTGTGTGTCTC 58.547 45.455 0.00 0.00 0.00 3.36
2662 2763 3.132111 TGTGTGTATGTGTGTGTGTCTCT 59.868 43.478 0.00 0.00 0.00 3.10
2663 2764 4.119862 GTGTGTATGTGTGTGTGTCTCTT 58.880 43.478 0.00 0.00 0.00 2.85
2664 2765 4.570772 GTGTGTATGTGTGTGTGTCTCTTT 59.429 41.667 0.00 0.00 0.00 2.52
2665 2766 4.570369 TGTGTATGTGTGTGTGTCTCTTTG 59.430 41.667 0.00 0.00 0.00 2.77
2666 2767 4.024893 GTGTATGTGTGTGTGTCTCTTTGG 60.025 45.833 0.00 0.00 0.00 3.28
2667 2768 1.378531 TGTGTGTGTGTCTCTTTGGC 58.621 50.000 0.00 0.00 0.00 4.52
2668 2769 1.065491 TGTGTGTGTGTCTCTTTGGCT 60.065 47.619 0.00 0.00 0.00 4.75
2669 2770 1.599542 GTGTGTGTGTCTCTTTGGCTC 59.400 52.381 0.00 0.00 0.00 4.70
2670 2771 1.486310 TGTGTGTGTCTCTTTGGCTCT 59.514 47.619 0.00 0.00 0.00 4.09
2671 2772 2.092968 TGTGTGTGTCTCTTTGGCTCTT 60.093 45.455 0.00 0.00 0.00 2.85
2672 2773 2.545946 GTGTGTGTCTCTTTGGCTCTTC 59.454 50.000 0.00 0.00 0.00 2.87
2673 2774 1.795286 GTGTGTCTCTTTGGCTCTTCG 59.205 52.381 0.00 0.00 0.00 3.79
2674 2775 1.412710 TGTGTCTCTTTGGCTCTTCGT 59.587 47.619 0.00 0.00 0.00 3.85
2675 2776 2.158957 TGTGTCTCTTTGGCTCTTCGTT 60.159 45.455 0.00 0.00 0.00 3.85
2676 2777 2.476997 GTGTCTCTTTGGCTCTTCGTTC 59.523 50.000 0.00 0.00 0.00 3.95
2677 2778 2.102420 TGTCTCTTTGGCTCTTCGTTCA 59.898 45.455 0.00 0.00 0.00 3.18
2678 2779 2.734079 GTCTCTTTGGCTCTTCGTTCAG 59.266 50.000 0.00 0.00 0.00 3.02
2679 2780 1.462670 CTCTTTGGCTCTTCGTTCAGC 59.537 52.381 0.00 0.00 34.65 4.26
2680 2781 1.070758 TCTTTGGCTCTTCGTTCAGCT 59.929 47.619 0.00 0.00 35.82 4.24
2681 2782 2.299013 TCTTTGGCTCTTCGTTCAGCTA 59.701 45.455 0.00 0.00 35.82 3.32
2682 2783 2.370281 TTGGCTCTTCGTTCAGCTAG 57.630 50.000 0.00 0.00 35.82 3.42
2683 2784 0.108615 TGGCTCTTCGTTCAGCTAGC 60.109 55.000 6.62 6.62 35.82 3.42
2684 2785 0.174617 GGCTCTTCGTTCAGCTAGCT 59.825 55.000 12.68 12.68 35.82 3.32
2685 2786 1.405821 GGCTCTTCGTTCAGCTAGCTA 59.594 52.381 18.86 0.00 35.82 3.32
2686 2787 2.456010 GCTCTTCGTTCAGCTAGCTAC 58.544 52.381 18.86 12.37 32.48 3.58
2710 2811 1.339055 GCTGGGGGCAATTTTTCTTCC 60.339 52.381 0.00 0.00 41.35 3.46
2711 2812 1.977129 CTGGGGGCAATTTTTCTTCCA 59.023 47.619 0.00 0.00 0.00 3.53
2712 2813 1.977129 TGGGGGCAATTTTTCTTCCAG 59.023 47.619 0.00 0.00 0.00 3.86
2713 2814 2.256306 GGGGGCAATTTTTCTTCCAGA 58.744 47.619 0.00 0.00 0.00 3.86
2719 2820 4.560128 GCAATTTTTCTTCCAGAGGGTTC 58.440 43.478 0.00 0.00 34.93 3.62
2727 2828 4.655963 TCTTCCAGAGGGTTCAAATTCAG 58.344 43.478 0.00 0.00 34.93 3.02
2729 2830 1.470098 CCAGAGGGTTCAAATTCAGCG 59.530 52.381 0.00 0.00 0.00 5.18
2776 2877 1.462791 CGTTGTTTGTTTCGTGAGGC 58.537 50.000 0.00 0.00 0.00 4.70
2792 2896 1.478510 GAGGCGGAGAATCAGAAGTCA 59.521 52.381 0.00 0.00 36.25 3.41
2802 2906 3.902881 ATCAGAAGTCACATCCACCTC 57.097 47.619 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 3.009714 GGGAGGGGTCGGAGCTTT 61.010 66.667 7.19 0.00 0.00 3.51
43 44 3.077556 CTGTGGGAGGGGTCGGAG 61.078 72.222 0.00 0.00 0.00 4.63
44 45 3.899545 GACTGTGGGAGGGGTCGGA 62.900 68.421 0.00 0.00 0.00 4.55
45 46 3.391382 GACTGTGGGAGGGGTCGG 61.391 72.222 0.00 0.00 0.00 4.79
67 72 3.944945 GGAACCACCCGACCGGTT 61.945 66.667 9.42 2.49 45.36 4.44
69 74 3.712907 ATGGAACCACCCGACCGG 61.713 66.667 0.00 0.00 38.00 5.28
126 131 2.031516 CGCACTGTGAGGAAGGCAG 61.032 63.158 12.86 0.00 36.41 4.85
164 169 1.346062 AGCTGGATGTGACACTGAGT 58.654 50.000 7.20 0.00 0.00 3.41
190 195 1.134491 AGTAAATCTACTGGTGGCGGC 60.134 52.381 0.00 0.00 36.98 6.53
217 222 1.999648 AGCTCCCTGCATTTTTCACA 58.000 45.000 0.00 0.00 45.94 3.58
354 367 4.873810 AAGGCAGCGGCACACACA 62.874 61.111 11.88 0.00 43.71 3.72
374 387 0.890996 AGAAGCTGAAAAGGGGCGTG 60.891 55.000 0.00 0.00 0.00 5.34
375 388 0.690762 TAGAAGCTGAAAAGGGGCGT 59.309 50.000 0.00 0.00 0.00 5.68
376 389 1.373570 CTAGAAGCTGAAAAGGGGCG 58.626 55.000 0.00 0.00 0.00 6.13
377 390 1.098869 GCTAGAAGCTGAAAAGGGGC 58.901 55.000 0.00 0.00 38.45 5.80
423 445 4.475135 GGGGAGGAGACTTGCCGC 62.475 72.222 0.00 0.00 44.43 6.53
474 496 1.529010 GCGGTGTGAATGAATACGCAC 60.529 52.381 0.00 0.00 44.32 5.34
475 497 0.724549 GCGGTGTGAATGAATACGCA 59.275 50.000 0.00 0.00 44.32 5.24
512 538 1.303309 GAGTGAGGGAATTGGATGCG 58.697 55.000 0.00 0.00 0.00 4.73
513 539 1.064463 TGGAGTGAGGGAATTGGATGC 60.064 52.381 0.00 0.00 0.00 3.91
563 589 2.586245 CTCCCTGCAATGCGAGGA 59.414 61.111 20.13 17.32 31.74 3.71
610 651 3.558931 TTGCGAGAGAGAGAGAGAGAT 57.441 47.619 0.00 0.00 0.00 2.75
619 660 1.821136 TGCTTCTGATTGCGAGAGAGA 59.179 47.619 0.00 0.00 0.00 3.10
637 684 3.800506 GCAGTCCTAAATCAAATGCATGC 59.199 43.478 11.82 11.82 32.58 4.06
702 749 2.325082 ACACGCTTCCGCCATCAAC 61.325 57.895 0.00 0.00 38.22 3.18
861 915 1.220477 GCAGAGCAAGAGAGGGGAC 59.780 63.158 0.00 0.00 0.00 4.46
864 918 1.141449 CGAGCAGAGCAAGAGAGGG 59.859 63.158 0.00 0.00 0.00 4.30
915 969 1.412710 TCCTTCGCAGAACAGAGTTGT 59.587 47.619 0.00 0.00 45.90 3.32
916 970 2.154854 TCCTTCGCAGAACAGAGTTG 57.845 50.000 0.00 0.00 45.90 3.16
940 994 3.747529 CAGCCAAAATTTTCCACATCCAC 59.252 43.478 0.00 0.00 0.00 4.02
941 995 3.244491 CCAGCCAAAATTTTCCACATCCA 60.244 43.478 0.00 0.00 0.00 3.41
942 996 3.007831 TCCAGCCAAAATTTTCCACATCC 59.992 43.478 0.00 0.00 0.00 3.51
943 997 4.270245 TCCAGCCAAAATTTTCCACATC 57.730 40.909 0.00 0.00 0.00 3.06
944 998 4.703379 TTCCAGCCAAAATTTTCCACAT 57.297 36.364 0.00 0.00 0.00 3.21
945 999 4.703379 ATTCCAGCCAAAATTTTCCACA 57.297 36.364 0.00 0.00 0.00 4.17
957 1013 1.280133 CACCTCTCAGAATTCCAGCCA 59.720 52.381 0.65 0.00 0.00 4.75
962 1018 1.338200 ACGCACACCTCTCAGAATTCC 60.338 52.381 0.65 0.00 0.00 3.01
972 1028 1.813753 ACACACACACGCACACCTC 60.814 57.895 0.00 0.00 0.00 3.85
973 1029 2.106074 CACACACACACGCACACCT 61.106 57.895 0.00 0.00 0.00 4.00
974 1030 2.403186 CACACACACACGCACACC 59.597 61.111 0.00 0.00 0.00 4.16
976 1032 1.813337 CTCCACACACACACGCACA 60.813 57.895 0.00 0.00 0.00 4.57
978 1034 1.813337 CACTCCACACACACACGCA 60.813 57.895 0.00 0.00 0.00 5.24
980 1036 1.765161 CTGCACTCCACACACACACG 61.765 60.000 0.00 0.00 0.00 4.49
981 1037 0.461870 TCTGCACTCCACACACACAC 60.462 55.000 0.00 0.00 0.00 3.82
982 1038 0.469494 ATCTGCACTCCACACACACA 59.531 50.000 0.00 0.00 0.00 3.72
1108 1166 1.110442 ACAGCTTCTGATCGGAGGAG 58.890 55.000 17.37 8.25 35.18 3.69
1252 1316 1.347817 GCTTGTCGGAGAGCTTGTCG 61.348 60.000 6.15 0.00 36.95 4.35
1279 1343 3.548770 CTTGATGATCTTGCAGGCCTTA 58.451 45.455 0.00 0.00 0.00 2.69
1502 1566 4.115199 CTCCTTCTTGGGCGGGGG 62.115 72.222 0.00 0.00 36.20 5.40
1503 1567 4.115199 CCTCCTTCTTGGGCGGGG 62.115 72.222 0.00 0.00 36.20 5.73
1504 1568 3.009115 TCCTCCTTCTTGGGCGGG 61.009 66.667 0.00 0.00 36.20 6.13
1553 1617 2.902423 TACGGCCACGGGTACGGTAT 62.902 60.000 2.24 0.00 46.48 2.73
1597 1661 3.709633 TGGCAGCAGCAGTCCGAT 61.710 61.111 2.65 0.00 44.61 4.18
1641 1711 2.876219 GCTCTTGCTTGCAGGAGC 59.124 61.111 32.58 32.58 44.77 4.70
1642 1712 2.045131 GGGCTCTTGCTTGCAGGAG 61.045 63.158 24.28 24.28 39.59 3.69
1680 1750 3.210012 ATGTTGAACTGGGGCGGCT 62.210 57.895 9.56 0.00 0.00 5.52
1817 1896 6.176183 AGTGTACCACGTACTAGTACTGATT 58.824 40.000 26.36 16.23 39.49 2.57
1822 1901 3.307242 CGGAGTGTACCACGTACTAGTAC 59.693 52.174 21.06 21.06 39.49 2.73
1824 1903 2.289694 ACGGAGTGTACCACGTACTAGT 60.290 50.000 0.00 0.00 42.51 2.57
1825 1904 2.350522 ACGGAGTGTACCACGTACTAG 58.649 52.381 3.79 0.00 42.51 2.57
1826 1905 2.472695 ACGGAGTGTACCACGTACTA 57.527 50.000 3.79 0.00 42.51 1.82
1844 1923 4.340246 GGTGGTGGGAACGGGGAC 62.340 72.222 0.00 0.00 0.00 4.46
1845 1924 4.902258 TGGTGGTGGGAACGGGGA 62.902 66.667 0.00 0.00 0.00 4.81
1846 1925 4.344865 CTGGTGGTGGGAACGGGG 62.345 72.222 0.00 0.00 0.00 5.73
1976 2064 3.506067 GGGAAATAAACAGTGAGGGTGTG 59.494 47.826 0.00 0.00 0.00 3.82
1979 2067 2.993863 AGGGGAAATAAACAGTGAGGGT 59.006 45.455 0.00 0.00 0.00 4.34
2104 2199 0.959553 ACAATGAGACGACGGACACT 59.040 50.000 0.00 0.00 0.00 3.55
2109 2204 0.388520 TGCTGACAATGAGACGACGG 60.389 55.000 0.00 0.00 0.00 4.79
2110 2205 0.710567 GTGCTGACAATGAGACGACG 59.289 55.000 0.00 0.00 0.00 5.12
2193 2290 4.588106 AGATCAGAGTGCAGCATACATAGT 59.412 41.667 0.00 0.00 0.00 2.12
2194 2291 4.924462 CAGATCAGAGTGCAGCATACATAG 59.076 45.833 0.00 0.00 0.00 2.23
2195 2292 4.586001 TCAGATCAGAGTGCAGCATACATA 59.414 41.667 0.00 0.00 0.00 2.29
2203 2300 2.431419 ACTCCATCAGATCAGAGTGCAG 59.569 50.000 10.63 0.00 38.15 4.41
2266 2363 1.672356 GGACACAGACGCAGGCATT 60.672 57.895 0.00 0.00 0.00 3.56
2273 2370 3.302347 CTCCTGGGGACACAGACGC 62.302 68.421 2.51 0.00 40.97 5.19
2338 2435 2.872245 CGCCCCATCTTTACATACACAG 59.128 50.000 0.00 0.00 0.00 3.66
2343 2440 4.879545 GTCTTTTCGCCCCATCTTTACATA 59.120 41.667 0.00 0.00 0.00 2.29
2451 2548 2.442272 CCTCCCGTCCCGATCAGT 60.442 66.667 0.00 0.00 0.00 3.41
2482 2579 2.257409 GACACATCATCCACCCCGCT 62.257 60.000 0.00 0.00 0.00 5.52
2486 2583 1.819632 GGCGACACATCATCCACCC 60.820 63.158 0.00 0.00 0.00 4.61
2535 2632 2.775960 TCCATCTGTTCATGCATCCTCT 59.224 45.455 0.00 0.00 0.00 3.69
2536 2633 3.139850 CTCCATCTGTTCATGCATCCTC 58.860 50.000 0.00 0.00 0.00 3.71
2540 2637 1.688772 GCCTCCATCTGTTCATGCAT 58.311 50.000 0.00 0.00 0.00 3.96
2585 2682 0.249447 TGTGAACTCGACACAGCCAG 60.249 55.000 3.42 0.00 42.20 4.85
2598 2695 1.002792 GGCCTCTGTTTTCGTGTGAAC 60.003 52.381 0.00 0.00 32.71 3.18
2628 2729 0.618458 TACACACATCCCCTGCCTTC 59.382 55.000 0.00 0.00 0.00 3.46
2632 2733 1.340017 ACACATACACACATCCCCTGC 60.340 52.381 0.00 0.00 0.00 4.85
2633 2734 2.290260 ACACACATACACACATCCCCTG 60.290 50.000 0.00 0.00 0.00 4.45
2634 2735 1.985159 ACACACATACACACATCCCCT 59.015 47.619 0.00 0.00 0.00 4.79
2635 2736 2.083774 CACACACATACACACATCCCC 58.916 52.381 0.00 0.00 0.00 4.81
2636 2737 2.483877 CACACACACATACACACATCCC 59.516 50.000 0.00 0.00 0.00 3.85
2637 2738 3.138304 ACACACACACATACACACATCC 58.862 45.455 0.00 0.00 0.00 3.51
2638 2739 4.058124 AGACACACACACATACACACATC 58.942 43.478 0.00 0.00 0.00 3.06
2639 2740 4.058124 GAGACACACACACATACACACAT 58.942 43.478 0.00 0.00 0.00 3.21
2640 2741 3.132111 AGAGACACACACACATACACACA 59.868 43.478 0.00 0.00 0.00 3.72
2641 2742 3.717707 AGAGACACACACACATACACAC 58.282 45.455 0.00 0.00 0.00 3.82
2642 2743 4.400529 AAGAGACACACACACATACACA 57.599 40.909 0.00 0.00 0.00 3.72
2643 2744 4.024893 CCAAAGAGACACACACACATACAC 60.025 45.833 0.00 0.00 0.00 2.90
2644 2745 4.126437 CCAAAGAGACACACACACATACA 58.874 43.478 0.00 0.00 0.00 2.29
2645 2746 3.058914 GCCAAAGAGACACACACACATAC 60.059 47.826 0.00 0.00 0.00 2.39
2646 2747 3.138304 GCCAAAGAGACACACACACATA 58.862 45.455 0.00 0.00 0.00 2.29
2647 2748 1.949525 GCCAAAGAGACACACACACAT 59.050 47.619 0.00 0.00 0.00 3.21
2648 2749 1.065491 AGCCAAAGAGACACACACACA 60.065 47.619 0.00 0.00 0.00 3.72
2649 2750 1.599542 GAGCCAAAGAGACACACACAC 59.400 52.381 0.00 0.00 0.00 3.82
2650 2751 1.486310 AGAGCCAAAGAGACACACACA 59.514 47.619 0.00 0.00 0.00 3.72
2651 2752 2.246719 AGAGCCAAAGAGACACACAC 57.753 50.000 0.00 0.00 0.00 3.82
2652 2753 2.803133 CGAAGAGCCAAAGAGACACACA 60.803 50.000 0.00 0.00 0.00 3.72
2653 2754 1.795286 CGAAGAGCCAAAGAGACACAC 59.205 52.381 0.00 0.00 0.00 3.82
2654 2755 1.412710 ACGAAGAGCCAAAGAGACACA 59.587 47.619 0.00 0.00 0.00 3.72
2655 2756 2.156343 ACGAAGAGCCAAAGAGACAC 57.844 50.000 0.00 0.00 0.00 3.67
2656 2757 2.102420 TGAACGAAGAGCCAAAGAGACA 59.898 45.455 0.00 0.00 0.00 3.41
2657 2758 2.734079 CTGAACGAAGAGCCAAAGAGAC 59.266 50.000 0.00 0.00 0.00 3.36
2658 2759 2.868044 GCTGAACGAAGAGCCAAAGAGA 60.868 50.000 0.00 0.00 0.00 3.10
2659 2760 1.462670 GCTGAACGAAGAGCCAAAGAG 59.537 52.381 0.00 0.00 0.00 2.85
2660 2761 1.070758 AGCTGAACGAAGAGCCAAAGA 59.929 47.619 0.00 0.00 35.69 2.52
2661 2762 1.517242 AGCTGAACGAAGAGCCAAAG 58.483 50.000 0.00 0.00 35.69 2.77
2662 2763 2.688507 CTAGCTGAACGAAGAGCCAAA 58.311 47.619 0.00 0.00 35.69 3.28
2663 2764 1.673033 GCTAGCTGAACGAAGAGCCAA 60.673 52.381 7.70 0.00 35.69 4.52
2664 2765 0.108615 GCTAGCTGAACGAAGAGCCA 60.109 55.000 7.70 0.00 35.69 4.75
2665 2766 0.174617 AGCTAGCTGAACGAAGAGCC 59.825 55.000 18.57 0.00 35.69 4.70
2666 2767 2.456010 GTAGCTAGCTGAACGAAGAGC 58.544 52.381 27.68 0.00 35.28 4.09
2667 2768 2.685897 AGGTAGCTAGCTGAACGAAGAG 59.314 50.000 27.68 0.00 31.96 2.85
2668 2769 2.724454 AGGTAGCTAGCTGAACGAAGA 58.276 47.619 27.68 0.85 31.96 2.87
2669 2770 3.549221 GCTAGGTAGCTAGCTGAACGAAG 60.549 52.174 35.59 20.88 46.32 3.79
2670 2771 2.358267 GCTAGGTAGCTAGCTGAACGAA 59.642 50.000 35.59 12.35 46.32 3.85
2671 2772 1.948145 GCTAGGTAGCTAGCTGAACGA 59.052 52.381 35.59 13.03 46.32 3.85
2672 2773 2.409152 GCTAGGTAGCTAGCTGAACG 57.591 55.000 35.59 18.31 46.32 3.95
2683 2784 0.846693 AATTGCCCCCAGCTAGGTAG 59.153 55.000 0.00 0.00 44.23 3.18
2684 2785 1.304891 AAATTGCCCCCAGCTAGGTA 58.695 50.000 0.00 0.00 44.23 3.08
2685 2786 0.413434 AAAATTGCCCCCAGCTAGGT 59.587 50.000 0.00 0.00 44.23 3.08
2686 2787 1.482182 GAAAAATTGCCCCCAGCTAGG 59.518 52.381 0.00 0.00 44.23 3.02
2691 2792 1.977129 TGGAAGAAAAATTGCCCCCAG 59.023 47.619 0.00 0.00 0.00 4.45
2710 2811 1.470098 CCGCTGAATTTGAACCCTCTG 59.530 52.381 0.00 0.00 0.00 3.35
2711 2812 1.351017 TCCGCTGAATTTGAACCCTCT 59.649 47.619 0.00 0.00 0.00 3.69
2712 2813 1.821216 TCCGCTGAATTTGAACCCTC 58.179 50.000 0.00 0.00 0.00 4.30
2713 2814 2.286365 TTCCGCTGAATTTGAACCCT 57.714 45.000 0.00 0.00 0.00 4.34
2719 2820 2.227388 AGCTCACTTTCCGCTGAATTTG 59.773 45.455 0.00 0.00 31.82 2.32
2727 2828 1.004440 AGGTGAGCTCACTTTCCGC 60.004 57.895 38.17 24.12 45.73 5.54
2729 2830 1.403514 CGAGAGGTGAGCTCACTTTCC 60.404 57.143 38.17 25.81 45.73 3.13
2776 2877 3.118992 TGGATGTGACTTCTGATTCTCCG 60.119 47.826 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.