Multiple sequence alignment - TraesCS2B01G273500

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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 TraesCS2B01G273500 chr2B 100.000 3632 0 0 1 3632 374804088 374800457 0.000000e+00 6708.0
1 TraesCS2B01G273500 chr2B 98.678 605 7 1 1 605 51995075 51994472 0.000000e+00 1072.0
2 TraesCS2B01G273500 chr2B 94.218 467 20 3 1 467 96107587 96108046 0.000000e+00 706.0
3 TraesCS2B01G273500 chr2B 97.633 169 4 0 2721 2889 374801297 374801129 1.280000e-74 291.0
4 TraesCS2B01G273500 chr2B 97.633 169 4 0 2792 2960 374801368 374801200 1.280000e-74 291.0
5 TraesCS2B01G273500 chr2B 96.939 98 3 0 2721 2818 374801226 374801129 8.070000e-37 165.0
6 TraesCS2B01G273500 chr2B 96.939 98 3 0 2863 2960 374801368 374801271 8.070000e-37 165.0
7 TraesCS2B01G273500 chr2A 94.842 2249 73 15 588 2818 386297420 386295197 0.000000e+00 3470.0
8 TraesCS2B01G273500 chr2A 97.399 769 20 0 2863 3631 386295294 386294526 0.000000e+00 1310.0
9 TraesCS2B01G273500 chr2A 96.939 98 3 0 2792 2889 386295294 386295197 8.070000e-37 165.0
10 TraesCS2B01G273500 chr2D 95.488 2017 64 14 785 2782 306533063 306531055 0.000000e+00 3195.0
11 TraesCS2B01G273500 chr2D 95.974 770 19 7 2863 3631 306531117 306530359 0.000000e+00 1240.0
12 TraesCS2B01G273500 chr2D 93.651 63 3 1 2792 2853 306531117 306531055 3.860000e-15 93.5
13 TraesCS2B01G273500 chr7B 98.056 463 8 1 1 463 639080955 639080494 0.000000e+00 804.0
14 TraesCS2B01G273500 chr1B 94.409 465 18 3 1 465 630603633 630604089 0.000000e+00 708.0
15 TraesCS2B01G273500 chr1B 94.218 467 18 5 1 465 610897481 610897940 0.000000e+00 704.0
16 TraesCS2B01G273500 chr1B 94.714 454 18 3 1 453 571977566 571977118 0.000000e+00 701.0
17 TraesCS2B01G273500 chr4A 94.218 467 19 4 1 466 675951925 675951466 0.000000e+00 706.0
18 TraesCS2B01G273500 chr3B 93.576 467 25 2 1 467 434637255 434636794 0.000000e+00 691.0
19 TraesCS2B01G273500 chr6D 93.590 468 21 4 1 466 450350279 450349819 0.000000e+00 689.0
20 TraesCS2B01G273500 chr3D 93.617 47 3 0 3555 3601 254109869 254109915 1.810000e-08 71.3
21 TraesCS2B01G273500 chr3A 86.364 66 7 2 3555 3620 335471216 335471153 1.810000e-08 71.3
22 TraesCS2B01G273500 chr3A 91.111 45 4 0 3557 3601 468533887 468533843 1.090000e-05 62.1


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 TraesCS2B01G273500 chr2B 374800457 374804088 3631 True 1524.000000 6708 97.828800 1 3632 5 chr2B.!!$R2 3631
1 TraesCS2B01G273500 chr2B 51994472 51995075 603 True 1072.000000 1072 98.678000 1 605 1 chr2B.!!$R1 604
2 TraesCS2B01G273500 chr2A 386294526 386297420 2894 True 1648.333333 3470 96.393333 588 3631 3 chr2A.!!$R1 3043
3 TraesCS2B01G273500 chr2D 306530359 306533063 2704 True 1509.500000 3195 95.037667 785 3631 3 chr2D.!!$R1 2846

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
822 826 1.006832 CAACGATGTCAACGGATCCC 58.993 55.0 6.06 0.0 34.93 3.85 F
1543 1569 0.690762 CTTCCTTTTCCCCTCGACCA 59.309 55.0 0.00 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2622 2663 0.257039 CTGCCTGGCCTTATGTTCCT 59.743 55.0 17.53 0.00 0.0 3.36 R
2633 2674 0.319297 CTTGCTTGAAACTGCCTGGC 60.319 55.0 12.87 12.87 0.0 4.85 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
421 422 6.713762 ACTTTCCTGAAAAATGTCATGACA 57.286 33.333 29.67 29.67 46.44 3.58
506 507 5.761165 TTTGGATGTGTGCATGATAGATG 57.239 39.130 0.00 0.00 35.07 2.90
530 531 4.877823 TGCAGATGTCTGGTGTTATTCATC 59.122 41.667 11.66 0.00 43.94 2.92
636 637 3.909430 TGGAATACCACGCGAGATAATC 58.091 45.455 15.93 0.00 41.77 1.75
736 738 8.822652 ATTTTTGATTTTCATGTTCAGTCTCC 57.177 30.769 0.00 0.00 0.00 3.71
737 739 5.611796 TTGATTTTCATGTTCAGTCTCCG 57.388 39.130 0.00 0.00 0.00 4.63
758 762 2.683362 GCCCTTGGAGCAAATACAGTAC 59.317 50.000 0.00 0.00 0.00 2.73
759 763 3.622455 GCCCTTGGAGCAAATACAGTACT 60.622 47.826 0.00 0.00 0.00 2.73
760 764 4.383770 GCCCTTGGAGCAAATACAGTACTA 60.384 45.833 0.00 0.00 0.00 1.82
782 786 3.866379 TTCTTGGTGGCTGCCGCAT 62.866 57.895 31.09 0.00 38.10 4.73
800 804 2.621338 CATATTCACAGTCACACGGCT 58.379 47.619 0.00 0.00 0.00 5.52
822 826 1.006832 CAACGATGTCAACGGATCCC 58.993 55.000 6.06 0.00 34.93 3.85
890 895 8.860088 CCTTTTATTATTCCCGAGAAAATCCAT 58.140 33.333 0.00 0.00 35.09 3.41
892 897 9.640952 TTTTATTATTCCCGAGAAAATCCATCT 57.359 29.630 0.00 0.00 35.09 2.90
940 961 3.737850 CTCTTCTCCAGAACACAGCTTT 58.262 45.455 0.00 0.00 0.00 3.51
1093 1116 7.338957 TGCCCAATTGATTTGTTTCTTTTCTTT 59.661 29.630 7.12 0.00 33.15 2.52
1539 1565 2.615747 GGTTCTCTTCCTTTTCCCCTCG 60.616 54.545 0.00 0.00 0.00 4.63
1543 1569 0.690762 CTTCCTTTTCCCCTCGACCA 59.309 55.000 0.00 0.00 0.00 4.02
1587 1614 8.576442 ACATTGCTAAGCACTTATTAAGTTTGT 58.424 29.630 6.34 0.00 40.46 2.83
1588 1615 8.853345 CATTGCTAAGCACTTATTAAGTTTGTG 58.147 33.333 6.34 0.00 40.46 3.33
1589 1616 7.504924 TGCTAAGCACTTATTAAGTTTGTGT 57.495 32.000 6.34 0.00 40.46 3.72
1590 1617 8.610248 TGCTAAGCACTTATTAAGTTTGTGTA 57.390 30.769 6.34 0.00 40.46 2.90
1635 1662 4.631813 GTGACGGAGGGAATATTATGATGC 59.368 45.833 0.00 0.00 0.00 3.91
1774 1802 1.494721 ACTCACCCATTCCAGTGTTGT 59.505 47.619 0.00 0.00 35.45 3.32
1775 1803 2.154462 CTCACCCATTCCAGTGTTGTC 58.846 52.381 0.00 0.00 35.45 3.18
1858 1886 5.060569 CGAAAAGATGAAAGCATTGCAAGAG 59.939 40.000 11.91 0.80 34.11 2.85
1908 1936 7.316640 TCAGAGAAGTTTCTGCATTAGTACTC 58.683 38.462 0.00 0.00 43.39 2.59
1915 1943 4.776795 TCTGCATTAGTACTCGTGTTCA 57.223 40.909 0.00 0.00 0.00 3.18
1919 1947 5.102313 TGCATTAGTACTCGTGTTCATGAG 58.898 41.667 17.25 17.25 38.21 2.90
1935 1963 6.258947 TGTTCATGAGTCATTGTTACGTTTGA 59.741 34.615 1.86 0.00 0.00 2.69
2078 2106 7.452880 TCAAAATCACACCCTGAATTTCTAG 57.547 36.000 0.00 0.00 30.73 2.43
2394 2435 1.341209 CCAAGAAACCCTTTCCTGCAC 59.659 52.381 0.00 0.00 40.54 4.57
2430 2471 2.182827 ACAGCAGCATCTCAGGTTAGA 58.817 47.619 0.00 0.00 0.00 2.10
2568 2609 2.868583 CCAGAATCATCAGTTACTGCCG 59.131 50.000 7.61 1.04 0.00 5.69
2622 2663 1.879380 CCATCTTTTGCTGACGGAACA 59.121 47.619 0.00 0.00 0.00 3.18
2633 2674 3.262420 CTGACGGAACAGGAACATAAGG 58.738 50.000 0.00 0.00 34.64 2.69
2771 2812 9.781425 ATATCAGTAGATGAATCTCCCAGTAAT 57.219 33.333 0.00 0.00 42.53 1.89
2773 2814 8.410673 TCAGTAGATGAATCTCCCAGTAATAC 57.589 38.462 0.00 0.00 38.32 1.89
2774 2815 7.175119 TCAGTAGATGAATCTCCCAGTAATACG 59.825 40.741 0.00 0.00 38.32 3.06
2775 2816 7.175119 CAGTAGATGAATCTCCCAGTAATACGA 59.825 40.741 0.00 0.00 38.32 3.43
2776 2817 6.978674 AGATGAATCTCCCAGTAATACGAA 57.021 37.500 0.00 0.00 29.30 3.85
2777 2818 6.987386 AGATGAATCTCCCAGTAATACGAAG 58.013 40.000 0.00 0.00 29.30 3.79
2778 2819 6.551601 AGATGAATCTCCCAGTAATACGAAGT 59.448 38.462 0.00 0.00 37.19 3.01
2779 2820 6.540438 TGAATCTCCCAGTAATACGAAGTT 57.460 37.500 0.00 0.00 37.78 2.66
2780 2821 6.942976 TGAATCTCCCAGTAATACGAAGTTT 58.057 36.000 0.00 0.00 37.78 2.66
2781 2822 6.816640 TGAATCTCCCAGTAATACGAAGTTTG 59.183 38.462 0.00 0.00 37.78 2.93
2782 2823 4.501071 TCTCCCAGTAATACGAAGTTTGC 58.499 43.478 0.00 0.00 37.78 3.68
2783 2824 4.222145 TCTCCCAGTAATACGAAGTTTGCT 59.778 41.667 0.00 0.00 37.78 3.91
2784 2825 5.419788 TCTCCCAGTAATACGAAGTTTGCTA 59.580 40.000 0.00 0.00 37.78 3.49
2785 2826 6.097839 TCTCCCAGTAATACGAAGTTTGCTAT 59.902 38.462 0.00 0.00 37.78 2.97
2786 2827 6.278363 TCCCAGTAATACGAAGTTTGCTATC 58.722 40.000 0.00 0.00 37.78 2.08
2787 2828 5.175126 CCCAGTAATACGAAGTTTGCTATCG 59.825 44.000 0.00 0.00 37.78 2.92
2788 2829 5.175126 CCAGTAATACGAAGTTTGCTATCGG 59.825 44.000 0.00 0.00 37.78 4.18
2789 2830 5.747197 CAGTAATACGAAGTTTGCTATCGGT 59.253 40.000 0.00 0.00 37.78 4.69
2790 2831 6.914215 CAGTAATACGAAGTTTGCTATCGGTA 59.086 38.462 0.00 0.00 37.78 4.02
2791 2832 7.433131 CAGTAATACGAAGTTTGCTATCGGTAA 59.567 37.037 0.00 0.00 37.78 2.85
2792 2833 7.975616 AGTAATACGAAGTTTGCTATCGGTAAA 59.024 33.333 0.00 0.00 37.78 2.01
2793 2834 4.916099 ACGAAGTTTGCTATCGGTAAAC 57.084 40.909 0.00 0.00 46.16 2.01
2800 2841 6.237313 GTTTGCTATCGGTAAACTGAAACT 57.763 37.500 0.00 0.00 43.74 2.66
2801 2842 6.304882 GTTTGCTATCGGTAAACTGAAACTC 58.695 40.000 0.00 0.00 43.74 3.01
2802 2843 4.501071 TGCTATCGGTAAACTGAAACTCC 58.499 43.478 0.00 0.00 34.49 3.85
2803 2844 4.020928 TGCTATCGGTAAACTGAAACTCCA 60.021 41.667 0.00 0.00 34.49 3.86
2804 2845 4.933400 GCTATCGGTAAACTGAAACTCCAA 59.067 41.667 0.00 0.00 34.49 3.53
2805 2846 5.585047 GCTATCGGTAAACTGAAACTCCAAT 59.415 40.000 0.00 0.00 34.49 3.16
2806 2847 6.759827 GCTATCGGTAAACTGAAACTCCAATA 59.240 38.462 0.00 0.00 34.49 1.90
2807 2848 7.042658 GCTATCGGTAAACTGAAACTCCAATAG 60.043 40.741 0.00 0.00 34.49 1.73
2808 2849 5.484715 TCGGTAAACTGAAACTCCAATAGG 58.515 41.667 0.00 0.00 0.00 2.57
2809 2850 4.094442 CGGTAAACTGAAACTCCAATAGGC 59.906 45.833 0.00 0.00 33.74 3.93
2810 2851 5.007682 GGTAAACTGAAACTCCAATAGGCA 58.992 41.667 0.00 0.00 33.74 4.75
2811 2852 5.652452 GGTAAACTGAAACTCCAATAGGCAT 59.348 40.000 0.00 0.00 33.74 4.40
2812 2853 5.649782 AAACTGAAACTCCAATAGGCATG 57.350 39.130 0.00 0.00 33.74 4.06
2813 2854 4.307032 ACTGAAACTCCAATAGGCATGT 57.693 40.909 0.00 0.00 33.74 3.21
2814 2855 5.435686 ACTGAAACTCCAATAGGCATGTA 57.564 39.130 0.00 0.00 33.74 2.29
2815 2856 6.006275 ACTGAAACTCCAATAGGCATGTAT 57.994 37.500 0.00 0.00 33.74 2.29
2856 2897 7.630082 TCTCCCAGTAATACAAAGTTTGCTAT 58.370 34.615 15.59 9.54 0.00 2.97
2857 2898 7.769044 TCTCCCAGTAATACAAAGTTTGCTATC 59.231 37.037 15.59 3.40 0.00 2.08
2858 2899 6.537301 TCCCAGTAATACAAAGTTTGCTATCG 59.463 38.462 15.59 0.00 0.00 2.92
2859 2900 6.238374 CCCAGTAATACAAAGTTTGCTATCGG 60.238 42.308 15.59 7.61 0.00 4.18
2860 2901 6.315393 CCAGTAATACAAAGTTTGCTATCGGT 59.685 38.462 15.59 0.00 0.00 4.69
2861 2902 7.493320 CCAGTAATACAAAGTTTGCTATCGGTA 59.507 37.037 15.59 0.00 0.00 4.02
2862 2903 8.875803 CAGTAATACAAAGTTTGCTATCGGTAA 58.124 33.333 15.59 0.00 0.00 2.85
2863 2904 9.439500 AGTAATACAAAGTTTGCTATCGGTAAA 57.561 29.630 15.59 0.00 0.00 2.01
2864 2905 9.481800 GTAATACAAAGTTTGCTATCGGTAAAC 57.518 33.333 15.59 0.00 46.16 2.01
2871 2912 6.237313 GTTTGCTATCGGTAAACTGAAACT 57.763 37.500 0.00 0.00 43.74 2.66
2872 2913 6.665465 GTTTGCTATCGGTAAACTGAAACTT 58.335 36.000 0.00 0.00 43.74 2.66
2873 2914 6.476243 TTGCTATCGGTAAACTGAAACTTC 57.524 37.500 0.00 0.00 34.49 3.01
2874 2915 5.543714 TGCTATCGGTAAACTGAAACTTCA 58.456 37.500 0.00 0.00 34.49 3.02
2875 2916 5.992829 TGCTATCGGTAAACTGAAACTTCAA 59.007 36.000 0.00 0.00 36.64 2.69
2876 2917 6.653320 TGCTATCGGTAAACTGAAACTTCAAT 59.347 34.615 0.00 0.00 36.64 2.57
2877 2918 7.820386 TGCTATCGGTAAACTGAAACTTCAATA 59.180 33.333 0.00 0.00 36.64 1.90
2878 2919 8.328864 GCTATCGGTAAACTGAAACTTCAATAG 58.671 37.037 0.00 0.00 36.64 1.73
2879 2920 7.611213 ATCGGTAAACTGAAACTTCAATAGG 57.389 36.000 0.00 0.00 36.64 2.57
2880 2921 5.410439 TCGGTAAACTGAAACTTCAATAGGC 59.590 40.000 0.00 0.00 36.64 3.93
2881 2922 5.180492 CGGTAAACTGAAACTTCAATAGGCA 59.820 40.000 0.00 0.00 36.64 4.75
2882 2923 6.128007 CGGTAAACTGAAACTTCAATAGGCAT 60.128 38.462 0.00 0.00 36.64 4.40
2883 2924 7.029563 GGTAAACTGAAACTTCAATAGGCATG 58.970 38.462 0.00 0.00 36.64 4.06
2884 2925 6.655078 AAACTGAAACTTCAATAGGCATGT 57.345 33.333 0.00 0.00 36.64 3.21
2885 2926 7.759489 AAACTGAAACTTCAATAGGCATGTA 57.241 32.000 0.00 0.00 36.64 2.29
2886 2927 7.944729 AACTGAAACTTCAATAGGCATGTAT 57.055 32.000 0.00 0.00 36.64 2.29
2887 2928 9.461312 AAACTGAAACTTCAATAGGCATGTATA 57.539 29.630 0.00 0.00 36.64 1.47
2888 2929 9.632638 AACTGAAACTTCAATAGGCATGTATAT 57.367 29.630 0.00 0.00 36.64 0.86
2913 2954 9.781425 ATATCAGTAGATGAATCTCCCAGTAAT 57.219 33.333 0.00 0.00 42.53 1.89
2915 2956 8.410673 TCAGTAGATGAATCTCCCAGTAATAC 57.589 38.462 0.00 0.00 38.32 1.89
2916 2957 8.004801 TCAGTAGATGAATCTCCCAGTAATACA 58.995 37.037 0.00 0.00 38.32 2.29
2917 2958 8.642432 CAGTAGATGAATCTCCCAGTAATACAA 58.358 37.037 0.00 0.00 38.32 2.41
2918 2959 9.213777 AGTAGATGAATCTCCCAGTAATACAAA 57.786 33.333 0.00 0.00 38.32 2.83
2919 2960 9.482627 GTAGATGAATCTCCCAGTAATACAAAG 57.517 37.037 0.00 0.00 38.32 2.77
2920 2961 8.095452 AGATGAATCTCCCAGTAATACAAAGT 57.905 34.615 0.00 0.00 29.30 2.66
2921 2962 8.552296 AGATGAATCTCCCAGTAATACAAAGTT 58.448 33.333 0.00 0.00 29.30 2.66
2922 2963 9.178758 GATGAATCTCCCAGTAATACAAAGTTT 57.821 33.333 0.00 0.00 0.00 2.66
2923 2964 8.335532 TGAATCTCCCAGTAATACAAAGTTTG 57.664 34.615 14.13 14.13 0.00 2.93
2924 2965 6.759497 ATCTCCCAGTAATACAAAGTTTGC 57.241 37.500 15.59 0.00 0.00 3.68
2925 2966 5.876357 TCTCCCAGTAATACAAAGTTTGCT 58.124 37.500 15.59 5.82 0.00 3.91
2926 2967 7.011499 TCTCCCAGTAATACAAAGTTTGCTA 57.989 36.000 15.59 7.75 0.00 3.49
2960 3001 6.662755 TGAAACTCCAATAGGCATGTAGATT 58.337 36.000 0.00 0.00 33.74 2.40
2988 3029 6.671614 AATAATGTGCAGGCATGATTTTTG 57.328 33.333 0.62 0.00 28.09 2.44
2998 3039 7.035004 GCAGGCATGATTTTTGTTGAGTTATA 58.965 34.615 0.62 0.00 0.00 0.98
3156 3197 8.059461 TCCTGTCCAATCAGTAGATTAACTCTA 58.941 37.037 0.00 0.00 42.46 2.43
3207 3248 5.419542 TCTTTCGCTGCTACATTCAATAGT 58.580 37.500 0.00 0.00 0.00 2.12
3264 3305 4.119136 GTTCACAAACAATTGGGTTGAGG 58.881 43.478 23.37 16.61 40.95 3.86
3419 3460 8.065407 GTGTTATTGCCGAAAATTATCGTCATA 58.935 33.333 0.00 0.00 41.16 2.15
3603 3644 8.365647 TGAAGTTCTAGGTTTGTCCTAAGTAAG 58.634 37.037 4.17 0.00 46.81 2.34
3631 3672 8.126700 ACGTCTTTAAGTTTTACCAAGTTCATG 58.873 33.333 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
403 404 4.452114 TCGTCTGTCATGACATTTTTCAGG 59.548 41.667 28.00 14.14 41.01 3.86
421 422 5.757850 AGCAAATTGAGTTTCTTTCGTCT 57.242 34.783 0.00 0.00 0.00 4.18
506 507 4.002982 TGAATAACACCAGACATCTGCAC 58.997 43.478 3.18 0.00 42.47 4.57
530 531 5.900339 AATGTAGCACGGATACAATAACG 57.100 39.130 6.18 0.00 37.94 3.18
632 633 1.471327 CGGCGAAAACCTACCCGATTA 60.471 52.381 0.00 0.00 41.34 1.75
636 637 2.816520 CCGGCGAAAACCTACCCG 60.817 66.667 9.30 0.00 38.71 5.28
642 643 1.575922 GTAACCACCGGCGAAAACC 59.424 57.895 9.30 0.00 0.00 3.27
736 738 0.734889 CTGTATTTGCTCCAAGGGCG 59.265 55.000 0.00 0.00 0.00 6.13
737 739 1.839424 ACTGTATTTGCTCCAAGGGC 58.161 50.000 0.00 0.00 0.00 5.19
758 762 2.415893 CGGCAGCCACCAAGAAAAATAG 60.416 50.000 13.30 0.00 0.00 1.73
759 763 1.543802 CGGCAGCCACCAAGAAAAATA 59.456 47.619 13.30 0.00 0.00 1.40
760 764 0.318120 CGGCAGCCACCAAGAAAAAT 59.682 50.000 13.30 0.00 0.00 1.82
782 786 1.616374 TCAGCCGTGTGACTGTGAATA 59.384 47.619 0.00 0.00 35.37 1.75
822 826 1.696063 CTGCATTTGTATGGAGGGGG 58.304 55.000 0.00 0.00 44.04 5.40
1059 1080 4.834496 ACAAATCAATTGGGCAGAGAGAAA 59.166 37.500 5.42 0.00 43.66 2.52
1062 1083 4.796038 AACAAATCAATTGGGCAGAGAG 57.204 40.909 5.42 0.00 43.66 3.20
1063 1084 4.834496 AGAAACAAATCAATTGGGCAGAGA 59.166 37.500 5.42 0.00 43.66 3.10
1093 1116 2.822561 TCACAAGGAACAACAAGCACAA 59.177 40.909 0.00 0.00 0.00 3.33
1539 1565 4.773117 GTCTCCGCCGACGTGGTC 62.773 72.222 0.00 0.00 40.82 4.02
1587 1614 4.277672 GGTTCAGCCGAGACTATACATACA 59.722 45.833 0.00 0.00 0.00 2.29
1588 1615 4.796369 GGTTCAGCCGAGACTATACATAC 58.204 47.826 0.00 0.00 0.00 2.39
1774 1802 2.023673 CAAGACTGGTTTGCAACAGGA 58.976 47.619 18.25 0.00 39.00 3.86
1775 1803 1.750778 ACAAGACTGGTTTGCAACAGG 59.249 47.619 18.25 5.96 39.00 4.00
1858 1886 0.958382 TGTTGCAATGGGGTACGAGC 60.958 55.000 0.59 0.00 0.00 5.03
1908 1936 4.149922 ACGTAACAATGACTCATGAACACG 59.850 41.667 0.00 11.82 0.00 4.49
1915 1943 6.861065 ACTTCAAACGTAACAATGACTCAT 57.139 33.333 0.00 0.00 0.00 2.90
1919 1947 6.020995 CACCAAACTTCAAACGTAACAATGAC 60.021 38.462 0.00 0.00 0.00 3.06
1935 1963 3.025322 TCAACCATCCACACCAAACTT 57.975 42.857 0.00 0.00 0.00 2.66
2078 2106 2.160417 CCGTGCTTGATTGAGGAGAAAC 59.840 50.000 0.00 0.00 0.00 2.78
2341 2382 3.134442 ACACCATTGTTTTGCATCTGGTT 59.866 39.130 0.00 0.00 39.81 3.67
2342 2383 2.699846 ACACCATTGTTTTGCATCTGGT 59.300 40.909 0.00 0.00 41.40 4.00
2343 2384 3.006110 AGACACCATTGTTTTGCATCTGG 59.994 43.478 0.00 0.00 35.47 3.86
2344 2385 3.985279 CAGACACCATTGTTTTGCATCTG 59.015 43.478 0.00 0.00 35.47 2.90
2345 2386 3.638160 ACAGACACCATTGTTTTGCATCT 59.362 39.130 0.00 0.00 35.47 2.90
2346 2387 3.737266 CACAGACACCATTGTTTTGCATC 59.263 43.478 0.00 0.00 35.47 3.91
2347 2388 3.493002 CCACAGACACCATTGTTTTGCAT 60.493 43.478 0.00 0.00 35.47 3.96
2348 2389 2.159128 CCACAGACACCATTGTTTTGCA 60.159 45.455 0.00 0.00 35.47 4.08
2349 2390 2.159114 ACCACAGACACCATTGTTTTGC 60.159 45.455 0.00 0.00 35.47 3.68
2350 2391 3.130164 TCACCACAGACACCATTGTTTTG 59.870 43.478 0.00 0.00 35.47 2.44
2351 2392 3.360867 TCACCACAGACACCATTGTTTT 58.639 40.909 0.00 0.00 35.47 2.43
2352 2393 2.951642 CTCACCACAGACACCATTGTTT 59.048 45.455 0.00 0.00 35.47 2.83
2394 2435 1.935300 GCTGTTAGTGTGTCGTCTGGG 60.935 57.143 0.00 0.00 0.00 4.45
2430 2471 3.967987 AGGAGGAGACTAACTGTGTTGTT 59.032 43.478 0.00 0.00 44.43 2.83
2568 2609 1.198637 GAAGCTGGCATGTCAGTGTTC 59.801 52.381 27.17 23.77 37.12 3.18
2622 2663 0.257039 CTGCCTGGCCTTATGTTCCT 59.743 55.000 17.53 0.00 0.00 3.36
2633 2674 0.319297 CTTGCTTGAAACTGCCTGGC 60.319 55.000 12.87 12.87 0.00 4.85
2708 2749 9.918630 ATTGGAGTTTCAGTTCATTGATAAAAG 57.081 29.630 0.00 0.00 0.00 2.27
2714 2755 5.415701 GCCTATTGGAGTTTCAGTTCATTGA 59.584 40.000 0.00 0.00 34.57 2.57
2719 2760 4.702131 ACATGCCTATTGGAGTTTCAGTTC 59.298 41.667 0.00 0.00 34.57 3.01
2765 2806 5.747197 ACCGATAGCAAACTTCGTATTACTG 59.253 40.000 0.00 0.00 0.00 2.74
2768 2809 7.975616 AGTTTACCGATAGCAAACTTCGTATTA 59.024 33.333 0.00 0.00 43.08 0.98
2770 2811 6.255020 CAGTTTACCGATAGCAAACTTCGTAT 59.745 38.462 0.00 0.00 43.08 3.06
2771 2812 5.574055 CAGTTTACCGATAGCAAACTTCGTA 59.426 40.000 0.00 0.00 43.08 3.43
2772 2813 4.387862 CAGTTTACCGATAGCAAACTTCGT 59.612 41.667 0.00 0.00 43.08 3.85
2773 2814 4.624024 TCAGTTTACCGATAGCAAACTTCG 59.376 41.667 0.00 0.00 43.08 3.79
2774 2815 6.476243 TTCAGTTTACCGATAGCAAACTTC 57.524 37.500 0.00 0.00 43.08 3.01
2775 2816 6.485648 AGTTTCAGTTTACCGATAGCAAACTT 59.514 34.615 0.00 0.00 43.08 2.66
2776 2817 5.995897 AGTTTCAGTTTACCGATAGCAAACT 59.004 36.000 0.00 0.00 45.05 2.66
2777 2818 6.237313 AGTTTCAGTTTACCGATAGCAAAC 57.763 37.500 0.00 0.00 38.80 2.93
2778 2819 5.410439 GGAGTTTCAGTTTACCGATAGCAAA 59.590 40.000 0.00 0.00 0.00 3.68
2779 2820 4.933400 GGAGTTTCAGTTTACCGATAGCAA 59.067 41.667 0.00 0.00 0.00 3.91
2780 2821 4.020928 TGGAGTTTCAGTTTACCGATAGCA 60.021 41.667 0.00 0.00 0.00 3.49
2781 2822 4.501071 TGGAGTTTCAGTTTACCGATAGC 58.499 43.478 0.00 0.00 0.00 2.97
2782 2823 7.438459 CCTATTGGAGTTTCAGTTTACCGATAG 59.562 40.741 0.00 0.00 39.59 2.08
2783 2824 7.270047 CCTATTGGAGTTTCAGTTTACCGATA 58.730 38.462 0.00 0.00 34.57 2.92
2784 2825 6.113411 CCTATTGGAGTTTCAGTTTACCGAT 58.887 40.000 0.00 0.00 34.57 4.18
2785 2826 5.484715 CCTATTGGAGTTTCAGTTTACCGA 58.515 41.667 0.00 0.00 34.57 4.69
2786 2827 4.094442 GCCTATTGGAGTTTCAGTTTACCG 59.906 45.833 0.00 0.00 34.57 4.02
2787 2828 5.007682 TGCCTATTGGAGTTTCAGTTTACC 58.992 41.667 0.00 0.00 34.57 2.85
2788 2829 6.151144 ACATGCCTATTGGAGTTTCAGTTTAC 59.849 38.462 0.00 0.00 34.57 2.01
2789 2830 6.245408 ACATGCCTATTGGAGTTTCAGTTTA 58.755 36.000 0.00 0.00 34.57 2.01
2790 2831 5.079643 ACATGCCTATTGGAGTTTCAGTTT 58.920 37.500 0.00 0.00 34.57 2.66
2791 2832 4.666512 ACATGCCTATTGGAGTTTCAGTT 58.333 39.130 0.00 0.00 34.57 3.16
2792 2833 4.307032 ACATGCCTATTGGAGTTTCAGT 57.693 40.909 0.00 0.00 34.57 3.41
2793 2834 9.896645 ATATATACATGCCTATTGGAGTTTCAG 57.103 33.333 0.00 0.00 34.57 3.02
2794 2835 9.890629 GATATATACATGCCTATTGGAGTTTCA 57.109 33.333 0.00 0.00 34.57 2.69
2795 2836 9.890629 TGATATATACATGCCTATTGGAGTTTC 57.109 33.333 0.00 0.00 34.57 2.78
2796 2837 9.896645 CTGATATATACATGCCTATTGGAGTTT 57.103 33.333 0.00 0.00 34.57 2.66
2797 2838 9.051259 ACTGATATATACATGCCTATTGGAGTT 57.949 33.333 0.00 0.00 34.57 3.01
2798 2839 8.615360 ACTGATATATACATGCCTATTGGAGT 57.385 34.615 0.00 0.00 34.57 3.85
2800 2841 9.936329 TCTACTGATATATACATGCCTATTGGA 57.064 33.333 0.00 0.00 34.57 3.53
2856 2897 5.410439 GCCTATTGAAGTTTCAGTTTACCGA 59.590 40.000 0.00 0.00 38.61 4.69
2857 2898 5.180492 TGCCTATTGAAGTTTCAGTTTACCG 59.820 40.000 0.00 0.00 38.61 4.02
2858 2899 6.569179 TGCCTATTGAAGTTTCAGTTTACC 57.431 37.500 0.00 0.00 38.61 2.85
2859 2900 7.593825 ACATGCCTATTGAAGTTTCAGTTTAC 58.406 34.615 0.00 0.00 38.61 2.01
2860 2901 7.759489 ACATGCCTATTGAAGTTTCAGTTTA 57.241 32.000 0.00 0.00 38.61 2.01
2861 2902 6.655078 ACATGCCTATTGAAGTTTCAGTTT 57.345 33.333 0.00 0.00 38.61 2.66
2862 2903 7.944729 ATACATGCCTATTGAAGTTTCAGTT 57.055 32.000 0.00 0.00 38.61 3.16
2887 2928 9.781425 ATTACTGGGAGATTCATCTACTGATAT 57.219 33.333 0.00 0.00 37.89 1.63
2889 2930 9.030452 GTATTACTGGGAGATTCATCTACTGAT 57.970 37.037 0.00 0.00 37.89 2.90
2890 2931 8.004801 TGTATTACTGGGAGATTCATCTACTGA 58.995 37.037 0.00 0.00 37.89 3.41
2891 2932 8.183104 TGTATTACTGGGAGATTCATCTACTG 57.817 38.462 0.00 0.00 37.89 2.74
2892 2933 8.783660 TTGTATTACTGGGAGATTCATCTACT 57.216 34.615 0.00 0.00 37.89 2.57
2893 2934 9.482627 CTTTGTATTACTGGGAGATTCATCTAC 57.517 37.037 0.00 0.00 37.25 2.59
2894 2935 9.213777 ACTTTGTATTACTGGGAGATTCATCTA 57.786 33.333 0.00 0.00 37.25 1.98
2895 2936 8.095452 ACTTTGTATTACTGGGAGATTCATCT 57.905 34.615 0.00 0.00 40.50 2.90
2896 2937 8.738645 AACTTTGTATTACTGGGAGATTCATC 57.261 34.615 0.00 0.00 0.00 2.92
2897 2938 8.960591 CAAACTTTGTATTACTGGGAGATTCAT 58.039 33.333 0.00 0.00 0.00 2.57
2898 2939 7.094377 GCAAACTTTGTATTACTGGGAGATTCA 60.094 37.037 3.48 0.00 0.00 2.57
2899 2940 7.121315 AGCAAACTTTGTATTACTGGGAGATTC 59.879 37.037 3.48 0.00 0.00 2.52
2900 2941 6.948309 AGCAAACTTTGTATTACTGGGAGATT 59.052 34.615 3.48 0.00 0.00 2.40
2901 2942 6.485171 AGCAAACTTTGTATTACTGGGAGAT 58.515 36.000 3.48 0.00 0.00 2.75
2902 2943 5.876357 AGCAAACTTTGTATTACTGGGAGA 58.124 37.500 3.48 0.00 0.00 3.71
2903 2944 7.254455 CGATAGCAAACTTTGTATTACTGGGAG 60.254 40.741 3.48 0.00 0.00 4.30
2904 2945 6.537301 CGATAGCAAACTTTGTATTACTGGGA 59.463 38.462 3.48 0.00 0.00 4.37
2905 2946 6.238374 CCGATAGCAAACTTTGTATTACTGGG 60.238 42.308 3.48 0.00 0.00 4.45
2906 2947 6.315393 ACCGATAGCAAACTTTGTATTACTGG 59.685 38.462 3.48 1.06 0.00 4.00
2907 2948 7.303634 ACCGATAGCAAACTTTGTATTACTG 57.696 36.000 3.48 0.00 0.00 2.74
2908 2949 9.439500 TTTACCGATAGCAAACTTTGTATTACT 57.561 29.630 3.48 0.00 0.00 2.24
2909 2950 9.481800 GTTTACCGATAGCAAACTTTGTATTAC 57.518 33.333 3.48 0.00 36.88 1.89
2910 2951 9.439500 AGTTTACCGATAGCAAACTTTGTATTA 57.561 29.630 3.48 0.00 43.08 0.98
2911 2952 8.234546 CAGTTTACCGATAGCAAACTTTGTATT 58.765 33.333 3.48 0.00 43.08 1.89
2912 2953 7.604927 TCAGTTTACCGATAGCAAACTTTGTAT 59.395 33.333 3.48 1.11 43.08 2.29
2913 2954 6.930164 TCAGTTTACCGATAGCAAACTTTGTA 59.070 34.615 3.48 0.00 43.08 2.41
2914 2955 5.761234 TCAGTTTACCGATAGCAAACTTTGT 59.239 36.000 3.48 0.00 43.08 2.83
2915 2956 6.236017 TCAGTTTACCGATAGCAAACTTTG 57.764 37.500 0.00 0.00 43.08 2.77
2916 2957 6.870971 TTCAGTTTACCGATAGCAAACTTT 57.129 33.333 0.00 0.00 43.08 2.66
2917 2958 6.485648 AGTTTCAGTTTACCGATAGCAAACTT 59.514 34.615 0.00 0.00 43.08 2.66
2918 2959 5.995897 AGTTTCAGTTTACCGATAGCAAACT 59.004 36.000 0.00 0.00 45.05 2.66
2919 2960 6.237313 AGTTTCAGTTTACCGATAGCAAAC 57.763 37.500 0.00 0.00 38.80 2.93
2920 2961 5.410439 GGAGTTTCAGTTTACCGATAGCAAA 59.590 40.000 0.00 0.00 0.00 3.68
2921 2962 4.933400 GGAGTTTCAGTTTACCGATAGCAA 59.067 41.667 0.00 0.00 0.00 3.91
2922 2963 4.020928 TGGAGTTTCAGTTTACCGATAGCA 60.021 41.667 0.00 0.00 0.00 3.49
2923 2964 4.501071 TGGAGTTTCAGTTTACCGATAGC 58.499 43.478 0.00 0.00 0.00 2.97
2924 2965 7.438459 CCTATTGGAGTTTCAGTTTACCGATAG 59.562 40.741 0.00 0.00 39.59 2.08
2925 2966 7.270047 CCTATTGGAGTTTCAGTTTACCGATA 58.730 38.462 0.00 0.00 34.57 2.92
2926 2967 6.113411 CCTATTGGAGTTTCAGTTTACCGAT 58.887 40.000 0.00 0.00 34.57 4.18
2960 3001 4.276642 TCATGCCTGCACATTATTTACCA 58.723 39.130 0.00 0.00 0.00 3.25
3057 3098 1.092348 GGCAATTCGGTAGGTTCCAC 58.908 55.000 0.00 0.00 0.00 4.02
3156 3197 1.426041 GATGTACAACCGCCGCGATT 61.426 55.000 15.93 0.00 0.00 3.34
3264 3305 2.126467 GTCTGCATCAAGAGAGCGATC 58.874 52.381 0.00 0.00 0.00 3.69
3419 3460 4.103153 ACATCGGTCCAATGATCCTGTATT 59.897 41.667 0.00 0.00 0.00 1.89
3603 3644 6.609237 ACTTGGTAAAACTTAAAGACGTCC 57.391 37.500 13.01 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.