Multiple sequence alignment - TraesCS1A01G132900

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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 TraesCS1A01G132900 chr1A 100.000 2909 0 0 1 2909 184936439 184933531 0.000000e+00 5373
1 TraesCS1A01G132900 chr6B 98.721 2737 27 7 1 2734 610805865 610808596 0.000000e+00 4854
2 TraesCS1A01G132900 chr6B 83.133 1334 184 29 822 2130 103963362 103964679 0.000000e+00 1179
3 TraesCS1A01G132900 chr7B 97.580 2727 58 6 1 2724 574510876 574513597 0.000000e+00 4663
4 TraesCS1A01G132900 chr7A 94.697 2376 100 9 360 2724 32589644 32587284 0.000000e+00 3666
5 TraesCS1A01G132900 chr7A 96.545 1968 60 4 1 1963 255889372 255887408 0.000000e+00 3251
6 TraesCS1A01G132900 chr7A 86.094 1956 243 19 3 1938 88959661 88957715 0.000000e+00 2078
7 TraesCS1A01G132900 chr7A 85.985 1955 247 17 3 1938 722320039 722318093 0.000000e+00 2067
8 TraesCS1A01G132900 chr7A 85.892 964 114 6 1097 2041 171878764 171877804 0.000000e+00 1007
9 TraesCS1A01G132900 chr5A 87.694 2064 222 20 1 2041 663074075 663076129 0.000000e+00 2375
10 TraesCS1A01G132900 chr5A 92.424 132 8 2 2594 2724 36865968 36866098 1.380000e-43 187
11 TraesCS1A01G132900 chrUn 99.116 1245 11 0 1480 2724 259654538 259653294 0.000000e+00 2239
12 TraesCS1A01G132900 chrUn 99.281 973 7 0 1 973 445250997 445251969 0.000000e+00 1759
13 TraesCS1A01G132900 chrUn 86.109 1123 131 19 822 1926 98277487 98276372 0.000000e+00 1186
14 TraesCS1A01G132900 chrUn 85.788 964 115 6 1097 2041 386814551 386813591 0.000000e+00 1002
15 TraesCS1A01G132900 chrUn 100.000 411 0 0 2049 2459 477615150 477614740 0.000000e+00 760
16 TraesCS1A01G132900 chrUn 83.030 165 24 4 2561 2723 62698328 62698166 2.340000e-31 147
17 TraesCS1A01G132900 chr3A 84.022 1427 181 22 7 1419 47783913 47785306 0.000000e+00 1328
18 TraesCS1A01G132900 chr6A 83.271 1333 180 28 822 2130 53257554 53256241 0.000000e+00 1186
19 TraesCS1A01G132900 chr5D 87.215 219 24 4 2508 2724 475169669 475169885 2.240000e-61 246
20 TraesCS1A01G132900 chr2D 82.258 186 32 1 2725 2909 436073623 436073808 3.000000e-35 159
21 TraesCS1A01G132900 chr3D 85.507 138 18 2 2589 2724 548522458 548522321 3.020000e-30 143
22 TraesCS1A01G132900 chr7D 84.722 144 19 3 2589 2730 12389766 12389908 1.090000e-29 141


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 TraesCS1A01G132900 chr1A 184933531 184936439 2908 True 5373 5373 100.000 1 2909 1 chr1A.!!$R1 2908
1 TraesCS1A01G132900 chr6B 610805865 610808596 2731 False 4854 4854 98.721 1 2734 1 chr6B.!!$F2 2733
2 TraesCS1A01G132900 chr6B 103963362 103964679 1317 False 1179 1179 83.133 822 2130 1 chr6B.!!$F1 1308
3 TraesCS1A01G132900 chr7B 574510876 574513597 2721 False 4663 4663 97.580 1 2724 1 chr7B.!!$F1 2723
4 TraesCS1A01G132900 chr7A 32587284 32589644 2360 True 3666 3666 94.697 360 2724 1 chr7A.!!$R1 2364
5 TraesCS1A01G132900 chr7A 255887408 255889372 1964 True 3251 3251 96.545 1 1963 1 chr7A.!!$R4 1962
6 TraesCS1A01G132900 chr7A 88957715 88959661 1946 True 2078 2078 86.094 3 1938 1 chr7A.!!$R2 1935
7 TraesCS1A01G132900 chr7A 722318093 722320039 1946 True 2067 2067 85.985 3 1938 1 chr7A.!!$R5 1935
8 TraesCS1A01G132900 chr7A 171877804 171878764 960 True 1007 1007 85.892 1097 2041 1 chr7A.!!$R3 944
9 TraesCS1A01G132900 chr5A 663074075 663076129 2054 False 2375 2375 87.694 1 2041 1 chr5A.!!$F2 2040
10 TraesCS1A01G132900 chrUn 259653294 259654538 1244 True 2239 2239 99.116 1480 2724 1 chrUn.!!$R3 1244
11 TraesCS1A01G132900 chrUn 445250997 445251969 972 False 1759 1759 99.281 1 973 1 chrUn.!!$F1 972
12 TraesCS1A01G132900 chrUn 98276372 98277487 1115 True 1186 1186 86.109 822 1926 1 chrUn.!!$R2 1104
13 TraesCS1A01G132900 chrUn 386813591 386814551 960 True 1002 1002 85.788 1097 2041 1 chrUn.!!$R4 944
14 TraesCS1A01G132900 chr3A 47783913 47785306 1393 False 1328 1328 84.022 7 1419 1 chr3A.!!$F1 1412
15 TraesCS1A01G132900 chr6A 53256241 53257554 1313 True 1186 1186 83.271 822 2130 1 chr6A.!!$R1 1308

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
44 45 0.340558 TCCGGGTTGGGAAGGATCTA 59.659 55.000 0.0 0.0 38.76 1.98 F
579 582 3.417069 TCTGTCCACCGAAACATCATT 57.583 42.857 0.0 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1818 1847 2.693069 AGTTCTGTCTTTCCAGCATCG 58.307 47.619 0.0 0.0 32.32 3.84 R
2132 2168 4.458989 ACATGACACAACAATACCCACATC 59.541 41.667 0.0 0.0 0.00 3.06 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
44 45 0.340558 TCCGGGTTGGGAAGGATCTA 59.659 55.000 0.00 0.00 38.76 1.98
484 487 3.580731 TCTGATACGACAACAAATGCGA 58.419 40.909 0.00 0.00 34.24 5.10
579 582 3.417069 TCTGTCCACCGAAACATCATT 57.583 42.857 0.00 0.00 0.00 2.57
1818 1847 1.299541 CTATCCGTGTCATTGGTGGC 58.700 55.000 0.00 0.00 0.00 5.01
1883 1912 2.159626 ACAAAGTGGTGTTTGTTCGTCG 60.160 45.455 0.00 0.00 46.26 5.12
2132 2168 8.072567 GGATATTTTCATCTCTTTCATCAACCG 58.927 37.037 0.00 0.00 0.00 4.44
2468 2513 8.462811 TGTTTGTATCTGTTTTTGCTCACTTTA 58.537 29.630 0.00 0.00 0.00 1.85
2724 2769 1.332375 TCAAACTACCAAACACGCTGC 59.668 47.619 0.00 0.00 0.00 5.25
2725 2770 0.306533 AAACTACCAAACACGCTGCG 59.693 50.000 21.91 21.91 0.00 5.18
2727 2772 0.531090 ACTACCAAACACGCTGCGAA 60.531 50.000 30.47 2.40 0.00 4.70
2728 2773 0.163788 CTACCAAACACGCTGCGAAG 59.836 55.000 30.47 21.65 0.00 3.79
2730 2775 0.884704 ACCAAACACGCTGCGAAGAT 60.885 50.000 30.47 12.33 0.00 2.40
2733 2778 2.474526 CCAAACACGCTGCGAAGATAAG 60.475 50.000 30.47 11.28 0.00 1.73
2735 2780 0.460284 ACACGCTGCGAAGATAAGGG 60.460 55.000 30.47 8.21 0.00 3.95
2736 2781 1.144057 ACGCTGCGAAGATAAGGGG 59.856 57.895 30.47 0.00 0.00 4.79
2737 2782 1.327690 ACGCTGCGAAGATAAGGGGA 61.328 55.000 30.47 0.00 0.00 4.81
2738 2783 0.179084 CGCTGCGAAGATAAGGGGAA 60.179 55.000 18.66 0.00 0.00 3.97
2739 2784 1.742411 CGCTGCGAAGATAAGGGGAAA 60.742 52.381 18.66 0.00 0.00 3.13
2740 2785 1.943340 GCTGCGAAGATAAGGGGAAAG 59.057 52.381 0.00 0.00 0.00 2.62
2741 2786 2.565841 CTGCGAAGATAAGGGGAAAGG 58.434 52.381 0.00 0.00 0.00 3.11
2742 2787 2.170607 CTGCGAAGATAAGGGGAAAGGA 59.829 50.000 0.00 0.00 0.00 3.36
2743 2788 2.093128 TGCGAAGATAAGGGGAAAGGAC 60.093 50.000 0.00 0.00 0.00 3.85
2744 2789 2.745482 GCGAAGATAAGGGGAAAGGACC 60.745 54.545 0.00 0.00 0.00 4.46
2745 2790 2.504175 CGAAGATAAGGGGAAAGGACCA 59.496 50.000 0.00 0.00 0.00 4.02
2746 2791 3.681874 CGAAGATAAGGGGAAAGGACCAC 60.682 52.174 0.00 0.00 0.00 4.16
2747 2792 2.206223 AGATAAGGGGAAAGGACCACC 58.794 52.381 0.00 0.00 33.07 4.61
2748 2793 1.920351 GATAAGGGGAAAGGACCACCA 59.080 52.381 0.00 0.00 38.94 4.17
2749 2794 1.835895 TAAGGGGAAAGGACCACCAA 58.164 50.000 0.00 0.00 38.94 3.67
2750 2795 0.482887 AAGGGGAAAGGACCACCAAG 59.517 55.000 0.00 0.00 38.94 3.61
2751 2796 0.402861 AGGGGAAAGGACCACCAAGA 60.403 55.000 0.00 0.00 38.94 3.02
2752 2797 0.481128 GGGGAAAGGACCACCAAGAA 59.519 55.000 0.00 0.00 38.94 2.52
2753 2798 1.133294 GGGGAAAGGACCACCAAGAAA 60.133 52.381 0.00 0.00 38.94 2.52
2754 2799 2.239400 GGGAAAGGACCACCAAGAAAG 58.761 52.381 0.00 0.00 38.94 2.62
2755 2800 2.239400 GGAAAGGACCACCAAGAAAGG 58.761 52.381 0.00 0.00 38.94 3.11
2756 2801 2.158519 GGAAAGGACCACCAAGAAAGGA 60.159 50.000 0.00 0.00 38.94 3.36
2757 2802 2.658807 AAGGACCACCAAGAAAGGAC 57.341 50.000 0.00 0.00 38.94 3.85
2758 2803 1.518367 AGGACCACCAAGAAAGGACA 58.482 50.000 0.00 0.00 38.94 4.02
2759 2804 1.850345 AGGACCACCAAGAAAGGACAA 59.150 47.619 0.00 0.00 38.94 3.18
2760 2805 2.447047 AGGACCACCAAGAAAGGACAAT 59.553 45.455 0.00 0.00 38.94 2.71
2761 2806 2.558359 GGACCACCAAGAAAGGACAATG 59.442 50.000 0.00 0.00 35.97 2.82
2762 2807 3.486383 GACCACCAAGAAAGGACAATGA 58.514 45.455 0.00 0.00 0.00 2.57
2763 2808 3.888930 GACCACCAAGAAAGGACAATGAA 59.111 43.478 0.00 0.00 0.00 2.57
2764 2809 3.891366 ACCACCAAGAAAGGACAATGAAG 59.109 43.478 0.00 0.00 0.00 3.02
2765 2810 4.144297 CCACCAAGAAAGGACAATGAAGA 58.856 43.478 0.00 0.00 0.00 2.87
2766 2811 4.217118 CCACCAAGAAAGGACAATGAAGAG 59.783 45.833 0.00 0.00 0.00 2.85
2767 2812 3.823304 ACCAAGAAAGGACAATGAAGAGC 59.177 43.478 0.00 0.00 0.00 4.09
2768 2813 3.192212 CCAAGAAAGGACAATGAAGAGCC 59.808 47.826 0.00 0.00 0.00 4.70
2769 2814 3.078891 AGAAAGGACAATGAAGAGCCC 57.921 47.619 0.00 0.00 0.00 5.19
2770 2815 2.095461 GAAAGGACAATGAAGAGCCCC 58.905 52.381 0.00 0.00 0.00 5.80
2771 2816 0.035056 AAGGACAATGAAGAGCCCCG 60.035 55.000 0.00 0.00 0.00 5.73
2772 2817 2.115291 GGACAATGAAGAGCCCCGC 61.115 63.158 0.00 0.00 0.00 6.13
2773 2818 2.044946 ACAATGAAGAGCCCCGCC 60.045 61.111 0.00 0.00 0.00 6.13
2774 2819 2.830370 CAATGAAGAGCCCCGCCC 60.830 66.667 0.00 0.00 0.00 6.13
2775 2820 3.338250 AATGAAGAGCCCCGCCCA 61.338 61.111 0.00 0.00 0.00 5.36
2776 2821 3.645268 AATGAAGAGCCCCGCCCAC 62.645 63.158 0.00 0.00 0.00 4.61
2778 2823 4.785453 GAAGAGCCCCGCCCACTG 62.785 72.222 0.00 0.00 0.00 3.66
2782 2827 4.715130 AGCCCCGCCCACTGAGTA 62.715 66.667 0.00 0.00 0.00 2.59
2783 2828 4.468689 GCCCCGCCCACTGAGTAC 62.469 72.222 0.00 0.00 0.00 2.73
2784 2829 3.000819 CCCCGCCCACTGAGTACA 61.001 66.667 0.00 0.00 0.00 2.90
2796 2841 3.721087 CTGAGTACAGGGGGACAAAAT 57.279 47.619 0.00 0.00 40.14 1.82
2797 2842 4.837093 CTGAGTACAGGGGGACAAAATA 57.163 45.455 0.00 0.00 40.14 1.40
2798 2843 5.174037 CTGAGTACAGGGGGACAAAATAA 57.826 43.478 0.00 0.00 40.14 1.40
2799 2844 5.566469 CTGAGTACAGGGGGACAAAATAAA 58.434 41.667 0.00 0.00 40.14 1.40
2800 2845 6.147437 TGAGTACAGGGGGACAAAATAAAT 57.853 37.500 0.00 0.00 0.00 1.40
2801 2846 6.557568 TGAGTACAGGGGGACAAAATAAATT 58.442 36.000 0.00 0.00 0.00 1.82
2802 2847 6.661805 TGAGTACAGGGGGACAAAATAAATTC 59.338 38.462 0.00 0.00 0.00 2.17
2803 2848 5.955959 AGTACAGGGGGACAAAATAAATTCC 59.044 40.000 0.00 0.00 0.00 3.01
2804 2849 4.757692 ACAGGGGGACAAAATAAATTCCA 58.242 39.130 0.00 0.00 0.00 3.53
2805 2850 4.530553 ACAGGGGGACAAAATAAATTCCAC 59.469 41.667 0.00 0.00 0.00 4.02
2806 2851 4.481368 GGGGGACAAAATAAATTCCACC 57.519 45.455 0.00 0.00 44.58 4.61
2807 2852 4.101114 GGGGGACAAAATAAATTCCACCT 58.899 43.478 0.14 0.00 46.92 4.00
2808 2853 4.081142 GGGGGACAAAATAAATTCCACCTG 60.081 45.833 0.14 0.00 46.92 4.00
2809 2854 4.775253 GGGGACAAAATAAATTCCACCTGA 59.225 41.667 0.00 0.00 0.00 3.86
2810 2855 5.105351 GGGGACAAAATAAATTCCACCTGAG 60.105 44.000 0.00 0.00 0.00 3.35
2811 2856 5.105351 GGGACAAAATAAATTCCACCTGAGG 60.105 44.000 0.00 0.00 0.00 3.86
2812 2857 5.480422 GGACAAAATAAATTCCACCTGAGGT 59.520 40.000 0.00 0.00 35.62 3.85
2827 2872 6.783708 ACCTGAGGTGAAAACATTAAACAA 57.216 33.333 1.77 0.00 32.98 2.83
2828 2873 6.805713 ACCTGAGGTGAAAACATTAAACAAG 58.194 36.000 1.77 0.00 32.98 3.16
2829 2874 6.605594 ACCTGAGGTGAAAACATTAAACAAGA 59.394 34.615 1.77 0.00 32.98 3.02
2830 2875 7.287696 ACCTGAGGTGAAAACATTAAACAAGAT 59.712 33.333 1.77 0.00 32.98 2.40
2831 2876 8.792633 CCTGAGGTGAAAACATTAAACAAGATA 58.207 33.333 0.00 0.00 0.00 1.98
2842 2887 8.766000 ACATTAAACAAGATATACGTCACACA 57.234 30.769 0.00 0.00 0.00 3.72
2843 2888 9.378551 ACATTAAACAAGATATACGTCACACAT 57.621 29.630 0.00 0.00 0.00 3.21
2847 2892 8.589335 AAACAAGATATACGTCACACATATCC 57.411 34.615 10.33 0.00 33.83 2.59
2848 2893 6.688578 ACAAGATATACGTCACACATATCCC 58.311 40.000 10.33 0.00 33.83 3.85
2849 2894 6.266786 ACAAGATATACGTCACACATATCCCA 59.733 38.462 10.33 0.00 33.83 4.37
2850 2895 6.911250 AGATATACGTCACACATATCCCAA 57.089 37.500 10.33 0.00 33.83 4.12
2851 2896 7.297936 AGATATACGTCACACATATCCCAAA 57.702 36.000 10.33 0.00 33.83 3.28
2852 2897 7.378966 AGATATACGTCACACATATCCCAAAG 58.621 38.462 10.33 0.00 33.83 2.77
2853 2898 3.973206 ACGTCACACATATCCCAAAGA 57.027 42.857 0.00 0.00 0.00 2.52
2854 2899 3.861840 ACGTCACACATATCCCAAAGAG 58.138 45.455 0.00 0.00 0.00 2.85
2855 2900 3.198068 CGTCACACATATCCCAAAGAGG 58.802 50.000 0.00 0.00 37.03 3.69
2867 2912 1.338020 CCAAAGAGGGAACACAAGTGC 59.662 52.381 0.00 0.00 0.00 4.40
2868 2913 1.002468 CAAAGAGGGAACACAAGTGCG 60.002 52.381 0.00 0.00 0.00 5.34
2869 2914 1.166531 AAGAGGGAACACAAGTGCGC 61.167 55.000 0.00 0.00 36.51 6.09
2870 2915 1.891919 GAGGGAACACAAGTGCGCA 60.892 57.895 5.66 5.66 38.67 6.09
2871 2916 2.117941 GAGGGAACACAAGTGCGCAC 62.118 60.000 32.79 32.79 38.67 5.34
2872 2917 2.186826 GGGAACACAAGTGCGCACT 61.187 57.895 36.44 36.44 44.94 4.40
2873 2918 0.882927 GGGAACACAAGTGCGCACTA 60.883 55.000 40.76 1.53 41.58 2.74
2874 2919 0.941542 GGAACACAAGTGCGCACTAA 59.058 50.000 40.76 1.06 41.58 2.24
2875 2920 1.069906 GGAACACAAGTGCGCACTAAG 60.070 52.381 40.76 34.65 41.58 2.18
2876 2921 0.944386 AACACAAGTGCGCACTAAGG 59.056 50.000 40.76 32.15 41.58 2.69
2877 2922 0.884704 ACACAAGTGCGCACTAAGGG 60.885 55.000 40.76 35.55 41.58 3.95
2878 2923 0.602638 CACAAGTGCGCACTAAGGGA 60.603 55.000 40.76 0.00 41.58 4.20
2879 2924 0.602905 ACAAGTGCGCACTAAGGGAC 60.603 55.000 40.76 13.12 41.58 4.46
2880 2925 0.602638 CAAGTGCGCACTAAGGGACA 60.603 55.000 40.76 0.00 41.58 4.02
2881 2926 0.324943 AAGTGCGCACTAAGGGACAT 59.675 50.000 40.76 21.62 41.58 3.06
2882 2927 0.108138 AGTGCGCACTAAGGGACATC 60.108 55.000 40.15 9.87 40.43 3.06
2883 2928 0.108138 GTGCGCACTAAGGGACATCT 60.108 55.000 32.55 0.00 0.00 2.90
2884 2929 1.136305 GTGCGCACTAAGGGACATCTA 59.864 52.381 32.55 0.00 0.00 1.98
2885 2930 2.039418 TGCGCACTAAGGGACATCTAT 58.961 47.619 5.66 0.00 0.00 1.98
2886 2931 2.224042 TGCGCACTAAGGGACATCTATG 60.224 50.000 5.66 0.00 0.00 2.23
2887 2932 2.224066 GCGCACTAAGGGACATCTATGT 60.224 50.000 0.30 0.00 45.16 2.29
2899 2944 3.501349 ACATCTATGTCATAGAGCCGGT 58.499 45.455 23.50 16.56 44.44 5.28
2900 2945 3.508012 ACATCTATGTCATAGAGCCGGTC 59.492 47.826 23.50 0.00 44.44 4.79
2901 2946 2.152016 TCTATGTCATAGAGCCGGTCG 58.848 52.381 17.07 0.00 36.98 4.79
2902 2947 2.152016 CTATGTCATAGAGCCGGTCGA 58.848 52.381 13.79 0.00 34.77 4.20
2903 2948 0.669077 ATGTCATAGAGCCGGTCGAC 59.331 55.000 7.13 7.13 0.00 4.20
2904 2949 1.359475 GTCATAGAGCCGGTCGACC 59.641 63.158 25.28 25.28 0.00 4.79
2905 2950 1.826921 TCATAGAGCCGGTCGACCC 60.827 63.158 28.52 15.65 0.00 4.46
2906 2951 1.828660 CATAGAGCCGGTCGACCCT 60.829 63.158 28.52 20.32 0.00 4.34
2907 2952 0.536687 CATAGAGCCGGTCGACCCTA 60.537 60.000 28.52 22.17 0.00 3.53
2908 2953 0.184451 ATAGAGCCGGTCGACCCTAA 59.816 55.000 28.52 12.41 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 3.402681 CACCCTCCCATCAGCCGT 61.403 66.667 0.00 0.00 0.00 5.68
484 487 8.228206 TCTAGATATTGTTCACAGGGATCTACT 58.772 37.037 0.00 0.00 0.00 2.57
579 582 3.253677 GTCTCTTTTCTCAGTCCACTCGA 59.746 47.826 0.00 0.00 0.00 4.04
1818 1847 2.693069 AGTTCTGTCTTTCCAGCATCG 58.307 47.619 0.00 0.00 32.32 3.84
2132 2168 4.458989 ACATGACACAACAATACCCACATC 59.541 41.667 0.00 0.00 0.00 3.06
2468 2513 7.255942 GCCAAGTAAAAATGATGGGCAGTATAT 60.256 37.037 0.00 0.00 39.88 0.86
2724 2769 2.504175 TGGTCCTTTCCCCTTATCTTCG 59.496 50.000 0.00 0.00 0.00 3.79
2725 2770 3.371702 GGTGGTCCTTTCCCCTTATCTTC 60.372 52.174 0.00 0.00 0.00 2.87
2727 2772 2.206223 GGTGGTCCTTTCCCCTTATCT 58.794 52.381 0.00 0.00 0.00 1.98
2728 2773 1.920351 TGGTGGTCCTTTCCCCTTATC 59.080 52.381 0.00 0.00 34.23 1.75
2730 2775 1.708551 CTTGGTGGTCCTTTCCCCTTA 59.291 52.381 0.00 0.00 34.23 2.69
2733 2778 0.481128 TTCTTGGTGGTCCTTTCCCC 59.519 55.000 0.00 0.00 34.23 4.81
2735 2780 2.158519 TCCTTTCTTGGTGGTCCTTTCC 60.159 50.000 0.00 0.00 34.23 3.13
2736 2781 2.885266 GTCCTTTCTTGGTGGTCCTTTC 59.115 50.000 0.00 0.00 34.23 2.62
2737 2782 2.243736 TGTCCTTTCTTGGTGGTCCTTT 59.756 45.455 0.00 0.00 34.23 3.11
2738 2783 1.850345 TGTCCTTTCTTGGTGGTCCTT 59.150 47.619 0.00 0.00 34.23 3.36
2739 2784 1.518367 TGTCCTTTCTTGGTGGTCCT 58.482 50.000 0.00 0.00 34.23 3.85
2740 2785 2.358322 TTGTCCTTTCTTGGTGGTCC 57.642 50.000 0.00 0.00 0.00 4.46
2741 2786 3.486383 TCATTGTCCTTTCTTGGTGGTC 58.514 45.455 0.00 0.00 0.00 4.02
2742 2787 3.593442 TCATTGTCCTTTCTTGGTGGT 57.407 42.857 0.00 0.00 0.00 4.16
2743 2788 4.144297 TCTTCATTGTCCTTTCTTGGTGG 58.856 43.478 0.00 0.00 0.00 4.61
2744 2789 4.320788 GCTCTTCATTGTCCTTTCTTGGTG 60.321 45.833 0.00 0.00 0.00 4.17
2745 2790 3.823304 GCTCTTCATTGTCCTTTCTTGGT 59.177 43.478 0.00 0.00 0.00 3.67
2746 2791 3.192212 GGCTCTTCATTGTCCTTTCTTGG 59.808 47.826 0.00 0.00 0.00 3.61
2747 2792 3.192212 GGGCTCTTCATTGTCCTTTCTTG 59.808 47.826 0.00 0.00 0.00 3.02
2748 2793 3.425659 GGGCTCTTCATTGTCCTTTCTT 58.574 45.455 0.00 0.00 0.00 2.52
2749 2794 2.291217 GGGGCTCTTCATTGTCCTTTCT 60.291 50.000 0.00 0.00 0.00 2.52
2750 2795 2.095461 GGGGCTCTTCATTGTCCTTTC 58.905 52.381 0.00 0.00 0.00 2.62
2751 2796 1.614317 CGGGGCTCTTCATTGTCCTTT 60.614 52.381 0.00 0.00 0.00 3.11
2752 2797 0.035056 CGGGGCTCTTCATTGTCCTT 60.035 55.000 0.00 0.00 0.00 3.36
2753 2798 1.604378 CGGGGCTCTTCATTGTCCT 59.396 57.895 0.00 0.00 0.00 3.85
2754 2799 2.115291 GCGGGGCTCTTCATTGTCC 61.115 63.158 0.00 0.00 0.00 4.02
2755 2800 2.115291 GGCGGGGCTCTTCATTGTC 61.115 63.158 0.00 0.00 0.00 3.18
2756 2801 2.044946 GGCGGGGCTCTTCATTGT 60.045 61.111 0.00 0.00 0.00 2.71
2757 2802 2.830370 GGGCGGGGCTCTTCATTG 60.830 66.667 0.00 0.00 0.00 2.82
2758 2803 3.338250 TGGGCGGGGCTCTTCATT 61.338 61.111 0.00 0.00 0.00 2.57
2759 2804 4.115199 GTGGGCGGGGCTCTTCAT 62.115 66.667 0.00 0.00 0.00 2.57
2761 2806 4.785453 CAGTGGGCGGGGCTCTTC 62.785 72.222 0.00 0.00 0.00 2.87
2765 2810 4.715130 TACTCAGTGGGCGGGGCT 62.715 66.667 0.00 0.00 0.00 5.19
2766 2811 4.468689 GTACTCAGTGGGCGGGGC 62.469 72.222 0.00 0.00 0.00 5.80
2767 2812 3.000819 TGTACTCAGTGGGCGGGG 61.001 66.667 0.00 0.00 0.00 5.73
2768 2813 2.579201 CTGTACTCAGTGGGCGGG 59.421 66.667 0.00 0.00 36.97 6.13
2769 2814 2.579201 CCTGTACTCAGTGGGCGG 59.421 66.667 0.00 0.00 39.82 6.13
2770 2815 2.579201 CCCTGTACTCAGTGGGCG 59.421 66.667 0.00 0.00 39.82 6.13
2771 2816 2.990479 CCCCTGTACTCAGTGGGC 59.010 66.667 0.00 0.00 41.57 5.36
2773 2818 0.544357 TGTCCCCCTGTACTCAGTGG 60.544 60.000 0.00 0.00 38.62 4.00
2774 2819 1.348064 TTGTCCCCCTGTACTCAGTG 58.652 55.000 0.00 0.00 39.82 3.66
2775 2820 2.112279 TTTGTCCCCCTGTACTCAGT 57.888 50.000 0.00 0.00 39.82 3.41
2776 2821 3.721087 ATTTTGTCCCCCTGTACTCAG 57.279 47.619 0.00 0.00 41.01 3.35
2777 2822 5.586155 TTTATTTTGTCCCCCTGTACTCA 57.414 39.130 0.00 0.00 0.00 3.41
2778 2823 6.096423 GGAATTTATTTTGTCCCCCTGTACTC 59.904 42.308 0.00 0.00 0.00 2.59
2779 2824 5.955959 GGAATTTATTTTGTCCCCCTGTACT 59.044 40.000 0.00 0.00 0.00 2.73
2780 2825 5.717654 TGGAATTTATTTTGTCCCCCTGTAC 59.282 40.000 0.00 0.00 0.00 2.90
2781 2826 5.717654 GTGGAATTTATTTTGTCCCCCTGTA 59.282 40.000 0.00 0.00 0.00 2.74
2782 2827 4.530553 GTGGAATTTATTTTGTCCCCCTGT 59.469 41.667 0.00 0.00 0.00 4.00
2783 2828 4.081142 GGTGGAATTTATTTTGTCCCCCTG 60.081 45.833 0.00 0.00 0.00 4.45
2784 2829 4.101114 GGTGGAATTTATTTTGTCCCCCT 58.899 43.478 0.00 0.00 0.00 4.79
2785 2830 4.081142 CAGGTGGAATTTATTTTGTCCCCC 60.081 45.833 0.00 0.00 0.00 5.40
2786 2831 4.775253 TCAGGTGGAATTTATTTTGTCCCC 59.225 41.667 0.00 0.00 0.00 4.81
2787 2832 5.105351 CCTCAGGTGGAATTTATTTTGTCCC 60.105 44.000 0.00 0.00 0.00 4.46
2788 2833 5.480422 ACCTCAGGTGGAATTTATTTTGTCC 59.520 40.000 0.00 0.00 32.98 4.02
2789 2834 6.590234 ACCTCAGGTGGAATTTATTTTGTC 57.410 37.500 0.00 0.00 32.98 3.18
2804 2849 6.605594 TCTTGTTTAATGTTTTCACCTCAGGT 59.394 34.615 0.00 0.00 35.62 4.00
2805 2850 7.038154 TCTTGTTTAATGTTTTCACCTCAGG 57.962 36.000 0.00 0.00 0.00 3.86
2816 2861 9.210329 TGTGTGACGTATATCTTGTTTAATGTT 57.790 29.630 0.00 0.00 0.00 2.71
2817 2862 8.766000 TGTGTGACGTATATCTTGTTTAATGT 57.234 30.769 0.00 0.00 0.00 2.71
2821 2866 9.687210 GGATATGTGTGACGTATATCTTGTTTA 57.313 33.333 12.65 0.00 35.28 2.01
2822 2867 7.656137 GGGATATGTGTGACGTATATCTTGTTT 59.344 37.037 12.65 0.00 35.28 2.83
2823 2868 7.152645 GGGATATGTGTGACGTATATCTTGTT 58.847 38.462 12.65 0.00 35.28 2.83
2824 2869 6.266786 TGGGATATGTGTGACGTATATCTTGT 59.733 38.462 12.65 0.00 35.28 3.16
2825 2870 6.687604 TGGGATATGTGTGACGTATATCTTG 58.312 40.000 12.65 0.00 35.28 3.02
2826 2871 6.911250 TGGGATATGTGTGACGTATATCTT 57.089 37.500 12.65 0.00 35.28 2.40
2827 2872 6.911250 TTGGGATATGTGTGACGTATATCT 57.089 37.500 12.65 0.00 35.28 1.98
2828 2873 7.375834 TCTTTGGGATATGTGTGACGTATATC 58.624 38.462 6.70 6.70 30.89 1.63
2829 2874 7.297936 TCTTTGGGATATGTGTGACGTATAT 57.702 36.000 0.00 0.00 30.89 0.86
2830 2875 6.239204 CCTCTTTGGGATATGTGTGACGTATA 60.239 42.308 0.00 0.00 30.89 1.47
2831 2876 5.453339 CCTCTTTGGGATATGTGTGACGTAT 60.453 44.000 0.00 0.00 33.27 3.06
2832 2877 4.142026 CCTCTTTGGGATATGTGTGACGTA 60.142 45.833 0.00 0.00 0.00 3.57
2833 2878 3.369471 CCTCTTTGGGATATGTGTGACGT 60.369 47.826 0.00 0.00 0.00 4.34
2834 2879 3.198068 CCTCTTTGGGATATGTGTGACG 58.802 50.000 0.00 0.00 0.00 4.35
2847 2892 1.338020 GCACTTGTGTTCCCTCTTTGG 59.662 52.381 2.61 0.00 0.00 3.28
2848 2893 1.002468 CGCACTTGTGTTCCCTCTTTG 60.002 52.381 2.61 0.00 0.00 2.77
2849 2894 1.308998 CGCACTTGTGTTCCCTCTTT 58.691 50.000 2.61 0.00 0.00 2.52
2850 2895 1.166531 GCGCACTTGTGTTCCCTCTT 61.167 55.000 0.30 0.00 0.00 2.85
2851 2896 1.598130 GCGCACTTGTGTTCCCTCT 60.598 57.895 0.30 0.00 0.00 3.69
2852 2897 1.891919 TGCGCACTTGTGTTCCCTC 60.892 57.895 5.66 0.00 0.00 4.30
2853 2898 2.186826 GTGCGCACTTGTGTTCCCT 61.187 57.895 32.55 0.00 0.00 4.20
2854 2899 0.882927 TAGTGCGCACTTGTGTTCCC 60.883 55.000 44.31 13.92 42.54 3.97
2855 2900 0.941542 TTAGTGCGCACTTGTGTTCC 59.058 50.000 44.31 14.73 42.54 3.62
2856 2901 1.069906 CCTTAGTGCGCACTTGTGTTC 60.070 52.381 44.31 15.53 42.54 3.18
2857 2902 0.944386 CCTTAGTGCGCACTTGTGTT 59.056 50.000 44.31 24.23 42.54 3.32
2858 2903 0.884704 CCCTTAGTGCGCACTTGTGT 60.885 55.000 44.31 24.97 42.54 3.72
2859 2904 0.602638 TCCCTTAGTGCGCACTTGTG 60.603 55.000 44.31 31.33 42.54 3.33
2860 2905 0.602905 GTCCCTTAGTGCGCACTTGT 60.603 55.000 44.31 25.74 42.54 3.16
2861 2906 0.602638 TGTCCCTTAGTGCGCACTTG 60.603 55.000 44.31 33.87 42.54 3.16
2862 2907 0.324943 ATGTCCCTTAGTGCGCACTT 59.675 50.000 44.31 28.53 42.54 3.16
2863 2908 0.108138 GATGTCCCTTAGTGCGCACT 60.108 55.000 41.46 41.46 45.02 4.40
2864 2909 0.108138 AGATGTCCCTTAGTGCGCAC 60.108 55.000 32.79 32.79 0.00 5.34
2865 2910 1.480789 TAGATGTCCCTTAGTGCGCA 58.519 50.000 5.66 5.66 0.00 6.09
2866 2911 2.224066 ACATAGATGTCCCTTAGTGCGC 60.224 50.000 0.00 0.00 35.87 6.09
2867 2912 3.735237 ACATAGATGTCCCTTAGTGCG 57.265 47.619 0.00 0.00 35.87 5.34
2878 2923 3.501349 ACCGGCTCTATGACATAGATGT 58.499 45.455 22.48 15.07 45.16 3.06
2879 2924 3.426829 CGACCGGCTCTATGACATAGATG 60.427 52.174 22.48 17.26 40.82 2.90
2880 2925 2.750166 CGACCGGCTCTATGACATAGAT 59.250 50.000 22.48 9.88 40.82 1.98
2881 2926 2.152016 CGACCGGCTCTATGACATAGA 58.848 52.381 21.26 21.26 39.46 1.98
2882 2927 2.095668 GTCGACCGGCTCTATGACATAG 60.096 54.545 15.25 15.25 0.00 2.23
2883 2928 1.878088 GTCGACCGGCTCTATGACATA 59.122 52.381 3.51 0.00 0.00 2.29
2884 2929 0.669077 GTCGACCGGCTCTATGACAT 59.331 55.000 3.51 0.00 0.00 3.06
2885 2930 1.381928 GGTCGACCGGCTCTATGACA 61.382 60.000 20.85 0.00 0.00 3.58
2886 2931 1.359475 GGTCGACCGGCTCTATGAC 59.641 63.158 20.85 0.16 0.00 3.06
2887 2932 1.826921 GGGTCGACCGGCTCTATGA 60.827 63.158 27.68 0.00 36.71 2.15
2888 2933 0.536687 TAGGGTCGACCGGCTCTATG 60.537 60.000 27.68 0.00 46.96 2.23
2889 2934 0.184451 TTAGGGTCGACCGGCTCTAT 59.816 55.000 27.68 9.95 46.96 1.98
2890 2935 1.609239 TTAGGGTCGACCGGCTCTA 59.391 57.895 27.68 19.42 46.96 2.43
2891 2936 2.357836 TTAGGGTCGACCGGCTCT 59.642 61.111 27.68 20.44 46.96 4.09


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

AutoCloner maintained by Alex Coulton.