Multiple sequence alignment - TraesCS2D01G210900

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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 TraesCS2D01G210900 chr2D 100.000 2558 0 0 1 2558 167706774 167704217 0.000000e+00 4724.0
1 TraesCS2D01G210900 chr2D 85.981 107 15 0 2452 2558 446656600 446656706 5.780000e-22 115.0
2 TraesCS2D01G210900 chr2D 82.000 100 16 2 2452 2550 32459226 32459128 1.630000e-12 84.2
3 TraesCS2D01G210900 chr2D 94.118 51 3 0 348 398 167706396 167706346 7.590000e-11 78.7
4 TraesCS2D01G210900 chr2D 94.118 51 3 0 379 429 167706427 167706377 7.590000e-11 78.7
5 TraesCS2D01G210900 chr2B 92.270 2471 86 41 15 2448 230282615 230285017 0.000000e+00 3408.0
6 TraesCS2D01G210900 chr2B 83.929 112 16 2 2448 2558 664364392 664364502 3.480000e-19 106.0
7 TraesCS2D01G210900 chr2A 92.873 1824 77 32 271 2061 182889373 182891176 0.000000e+00 2599.0
8 TraesCS2D01G210900 chr2A 92.481 399 22 2 2058 2448 182891449 182891847 4.780000e-157 564.0
9 TraesCS2D01G210900 chr2A 95.263 190 7 2 41 228 182889175 182889364 1.490000e-77 300.0
10 TraesCS2D01G210900 chr2A 95.833 48 2 0 348 395 182889482 182889529 7.590000e-11 78.7
11 TraesCS2D01G210900 chr4B 91.589 107 9 0 2452 2558 484999951 485000057 5.700000e-32 148.0
12 TraesCS2D01G210900 chrUn 90.000 110 10 1 2449 2557 36175718 36175827 9.540000e-30 141.0
13 TraesCS2D01G210900 chr6D 88.679 106 9 3 2454 2558 435945807 435945704 2.670000e-25 126.0
14 TraesCS2D01G210900 chr6A 86.916 107 14 0 2452 2558 520652067 520651961 1.240000e-23 121.0
15 TraesCS2D01G210900 chr1D 82.000 100 16 2 2452 2550 152727311 152727213 1.630000e-12 84.2


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 TraesCS2D01G210900 chr2D 167704217 167706774 2557 True 1627.133333 4724 96.078667 1 2558 3 chr2D.!!$R2 2557
1 TraesCS2D01G210900 chr2B 230282615 230285017 2402 False 3408.000000 3408 92.270000 15 2448 1 chr2B.!!$F1 2433
2 TraesCS2D01G210900 chr2A 182889175 182891847 2672 False 885.425000 2599 94.112500 41 2448 4 chr2A.!!$F1 2407

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
414 427 0.537371 CTGGTCCGGTTGCCTTTTCT 60.537 55.0 0.0 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2398 2760 2.581354 GTCAGGACATGCGGCTCT 59.419 61.111 0.0 0.0 0.0 4.09 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 4.065281 GCCGGCCTGTAGACGTGT 62.065 66.667 18.11 0.00 0.00 4.49
122 123 4.603535 AAGCCAAGTTGCCCCGCT 62.604 61.111 0.00 0.00 0.00 5.52
191 199 0.608130 ATGCTTGTGACCTGCGACTA 59.392 50.000 0.00 0.00 0.00 2.59
232 240 2.493907 GATACGGGAGGATCTGGCGC 62.494 65.000 0.00 0.00 46.94 6.53
233 241 3.733507 TACGGGAGGATCTGGCGCT 62.734 63.158 7.64 0.00 33.73 5.92
234 242 4.598894 CGGGAGGATCTGGCGCTG 62.599 72.222 7.64 0.11 33.73 5.18
235 243 4.247380 GGGAGGATCTGGCGCTGG 62.247 72.222 7.64 0.00 33.73 4.85
236 244 4.925861 GGAGGATCTGGCGCTGGC 62.926 72.222 7.64 0.00 34.57 4.85
414 427 0.537371 CTGGTCCGGTTGCCTTTTCT 60.537 55.000 0.00 0.00 0.00 2.52
701 717 1.673767 AGACCCACATGTCATCCCTT 58.326 50.000 0.00 0.00 37.73 3.95
709 725 5.195940 CCACATGTCATCCCTTCATTAGTT 58.804 41.667 0.00 0.00 0.00 2.24
722 738 3.942829 TCATTAGTTGCTGAAGAGGGTG 58.057 45.455 0.00 0.00 0.00 4.61
778 804 1.971149 TGGACAGGAGGACAATGGAT 58.029 50.000 0.00 0.00 0.00 3.41
789 815 4.275810 AGGACAATGGATGAACAATCAGG 58.724 43.478 0.00 0.00 39.39 3.86
794 820 5.539574 ACAATGGATGAACAATCAGGTGAAA 59.460 36.000 0.00 0.00 39.39 2.69
874 907 2.489971 TCGGAGTTTTGATTTCGCTGT 58.510 42.857 0.00 0.00 0.00 4.40
963 1001 2.743928 CTTGGCGGTGAGTGGCTC 60.744 66.667 0.00 0.00 0.00 4.70
964 1002 3.241530 TTGGCGGTGAGTGGCTCT 61.242 61.111 0.00 0.00 0.00 4.09
965 1003 3.535629 TTGGCGGTGAGTGGCTCTG 62.536 63.158 0.00 0.00 0.00 3.35
967 1005 4.385405 GCGGTGAGTGGCTCTGCT 62.385 66.667 0.00 0.00 38.89 4.24
968 1006 2.125753 CGGTGAGTGGCTCTGCTC 60.126 66.667 0.00 0.00 0.00 4.26
1004 1046 0.179018 CTCCTCCCGCCTTAAATGGG 60.179 60.000 0.79 0.79 44.75 4.00
1132 1177 2.605601 TCCTGCAGCTGCTCCTCA 60.606 61.111 36.61 17.40 42.66 3.86
1217 1262 2.756283 CGCGACCCTTCCTCCTCT 60.756 66.667 0.00 0.00 0.00 3.69
1675 1738 9.095065 GAGTGCCGTTCTTTATTCTCTTTATTA 57.905 33.333 0.00 0.00 0.00 0.98
1676 1739 8.880750 AGTGCCGTTCTTTATTCTCTTTATTAC 58.119 33.333 0.00 0.00 0.00 1.89
1749 1817 0.741915 CTACCGAGTGAGGAAGGCTC 59.258 60.000 0.00 0.00 34.73 4.70
1805 1873 8.127954 CGAGTTTAGTTTGATCCTACTACTACC 58.872 40.741 4.11 1.87 0.00 3.18
1971 2041 6.335471 TGTTCTGACAAGATTGCAATCATT 57.665 33.333 34.59 23.82 37.89 2.57
2009 2079 4.376109 GCTGGCGTTTTACTATATTCGAGC 60.376 45.833 0.00 0.00 0.00 5.03
2034 2104 5.526115 CAGATTGTGCTTGAGTTTCATGTT 58.474 37.500 0.00 0.00 0.00 2.71
2035 2105 6.671190 CAGATTGTGCTTGAGTTTCATGTTA 58.329 36.000 0.00 0.00 0.00 2.41
2036 2106 6.800408 CAGATTGTGCTTGAGTTTCATGTTAG 59.200 38.462 0.00 0.00 0.00 2.34
2078 2428 4.517075 CACTGATACTACTAGCTAGCTGCA 59.483 45.833 27.68 7.31 45.94 4.41
2095 2445 3.383825 GCTGCATGGATCTGGAGAAAATT 59.616 43.478 7.54 0.00 36.78 1.82
2266 2620 0.037882 GGCTGCTTTGCTTCCCTTTC 60.038 55.000 0.00 0.00 0.00 2.62
2329 2691 6.751888 GGAAATCCATATGTACAACAAGTTGC 59.248 38.462 12.54 0.00 38.87 4.17
2398 2760 6.994421 TCTATGGCTGATAGTACCAAATCA 57.006 37.500 0.00 0.00 36.94 2.57
2434 2796 2.009755 GCGTAGGCTGTCGTATCGC 61.010 63.158 13.49 0.00 35.83 4.58
2437 2799 1.196127 CGTAGGCTGTCGTATCGCATA 59.804 52.381 0.00 0.00 0.00 3.14
2438 2800 2.350102 CGTAGGCTGTCGTATCGCATAA 60.350 50.000 0.00 0.00 0.00 1.90
2450 2812 4.954933 GCATAACCTCAGGGCGAA 57.045 55.556 0.00 0.00 35.63 4.70
2451 2813 3.403936 GCATAACCTCAGGGCGAAT 57.596 52.632 0.00 0.00 35.63 3.34
2452 2814 0.947244 GCATAACCTCAGGGCGAATG 59.053 55.000 0.00 0.00 35.63 2.67
2453 2815 1.475034 GCATAACCTCAGGGCGAATGA 60.475 52.381 0.00 0.00 35.63 2.57
2454 2816 2.917933 CATAACCTCAGGGCGAATGAA 58.082 47.619 0.00 0.00 35.63 2.57
2455 2817 2.691409 TAACCTCAGGGCGAATGAAG 57.309 50.000 0.00 0.00 35.63 3.02
2456 2818 0.693049 AACCTCAGGGCGAATGAAGT 59.307 50.000 0.00 0.00 35.63 3.01
2457 2819 0.250513 ACCTCAGGGCGAATGAAGTC 59.749 55.000 0.00 0.00 35.63 3.01
2458 2820 0.539051 CCTCAGGGCGAATGAAGTCT 59.461 55.000 0.00 0.00 0.00 3.24
2459 2821 1.649664 CTCAGGGCGAATGAAGTCTG 58.350 55.000 0.00 0.00 0.00 3.51
2460 2822 0.976641 TCAGGGCGAATGAAGTCTGT 59.023 50.000 0.00 0.00 0.00 3.41
2461 2823 1.347707 TCAGGGCGAATGAAGTCTGTT 59.652 47.619 0.00 0.00 0.00 3.16
2462 2824 2.154462 CAGGGCGAATGAAGTCTGTTT 58.846 47.619 0.00 0.00 0.00 2.83
2463 2825 2.554032 CAGGGCGAATGAAGTCTGTTTT 59.446 45.455 0.00 0.00 0.00 2.43
2464 2826 3.751175 CAGGGCGAATGAAGTCTGTTTTA 59.249 43.478 0.00 0.00 0.00 1.52
2465 2827 4.215399 CAGGGCGAATGAAGTCTGTTTTAA 59.785 41.667 0.00 0.00 0.00 1.52
2466 2828 4.825085 AGGGCGAATGAAGTCTGTTTTAAA 59.175 37.500 0.00 0.00 0.00 1.52
2467 2829 4.915667 GGGCGAATGAAGTCTGTTTTAAAC 59.084 41.667 0.20 0.20 0.00 2.01
2468 2830 4.915667 GGCGAATGAAGTCTGTTTTAAACC 59.084 41.667 5.32 0.00 0.00 3.27
2469 2831 5.278315 GGCGAATGAAGTCTGTTTTAAACCT 60.278 40.000 5.32 0.00 0.00 3.50
2470 2832 6.206498 GCGAATGAAGTCTGTTTTAAACCTT 58.794 36.000 5.32 1.82 0.00 3.50
2471 2833 7.357303 GCGAATGAAGTCTGTTTTAAACCTTA 58.643 34.615 5.32 0.00 0.00 2.69
2472 2834 7.858879 GCGAATGAAGTCTGTTTTAAACCTTAA 59.141 33.333 5.32 0.00 0.00 1.85
2473 2835 9.724839 CGAATGAAGTCTGTTTTAAACCTTAAA 57.275 29.630 5.32 0.00 0.00 1.52
2477 2839 9.233649 TGAAGTCTGTTTTAAACCTTAAACTCA 57.766 29.630 5.32 0.00 35.73 3.41
2483 2845 9.827411 CTGTTTTAAACCTTAAACTCATAGAGC 57.173 33.333 5.32 0.00 35.73 4.09
2484 2846 9.569122 TGTTTTAAACCTTAAACTCATAGAGCT 57.431 29.630 5.32 0.00 35.73 4.09
2487 2849 9.569122 TTTAAACCTTAAACTCATAGAGCTTGT 57.431 29.630 0.00 0.00 32.04 3.16
2488 2850 7.674471 AAACCTTAAACTCATAGAGCTTGTC 57.326 36.000 0.00 0.00 32.04 3.18
2489 2851 5.411781 ACCTTAAACTCATAGAGCTTGTCG 58.588 41.667 0.00 0.00 32.04 4.35
2490 2852 5.185249 ACCTTAAACTCATAGAGCTTGTCGA 59.815 40.000 0.00 0.00 32.04 4.20
2491 2853 6.100004 CCTTAAACTCATAGAGCTTGTCGAA 58.900 40.000 0.00 0.00 32.04 3.71
2492 2854 6.590292 CCTTAAACTCATAGAGCTTGTCGAAA 59.410 38.462 0.00 0.00 32.04 3.46
2493 2855 7.278868 CCTTAAACTCATAGAGCTTGTCGAAAT 59.721 37.037 0.00 0.00 32.04 2.17
2494 2856 8.547967 TTAAACTCATAGAGCTTGTCGAAATT 57.452 30.769 0.00 0.00 32.04 1.82
2495 2857 9.647797 TTAAACTCATAGAGCTTGTCGAAATTA 57.352 29.630 0.00 0.00 32.04 1.40
2496 2858 8.547967 AAACTCATAGAGCTTGTCGAAATTAA 57.452 30.769 0.00 0.00 32.04 1.40
2497 2859 8.547967 AACTCATAGAGCTTGTCGAAATTAAA 57.452 30.769 0.00 0.00 32.04 1.52
2498 2860 7.965045 ACTCATAGAGCTTGTCGAAATTAAAC 58.035 34.615 0.00 0.00 32.04 2.01
2499 2861 7.064728 ACTCATAGAGCTTGTCGAAATTAAACC 59.935 37.037 0.00 0.00 32.04 3.27
2500 2862 6.315393 TCATAGAGCTTGTCGAAATTAAACCC 59.685 38.462 0.00 0.00 0.00 4.11
2501 2863 4.652822 AGAGCTTGTCGAAATTAAACCCT 58.347 39.130 0.00 0.00 0.00 4.34
2502 2864 4.695928 AGAGCTTGTCGAAATTAAACCCTC 59.304 41.667 0.00 0.00 0.00 4.30
2503 2865 4.394729 AGCTTGTCGAAATTAAACCCTCA 58.605 39.130 0.00 0.00 0.00 3.86
2504 2866 4.215613 AGCTTGTCGAAATTAAACCCTCAC 59.784 41.667 0.00 0.00 0.00 3.51
2505 2867 4.215613 GCTTGTCGAAATTAAACCCTCACT 59.784 41.667 0.00 0.00 0.00 3.41
2506 2868 5.278315 GCTTGTCGAAATTAAACCCTCACTT 60.278 40.000 0.00 0.00 0.00 3.16
2507 2869 6.702716 TTGTCGAAATTAAACCCTCACTTT 57.297 33.333 0.00 0.00 0.00 2.66
2508 2870 6.702716 TGTCGAAATTAAACCCTCACTTTT 57.297 33.333 0.00 0.00 0.00 2.27
2509 2871 6.500041 TGTCGAAATTAAACCCTCACTTTTG 58.500 36.000 0.00 0.00 0.00 2.44
2510 2872 6.319152 TGTCGAAATTAAACCCTCACTTTTGA 59.681 34.615 0.00 0.00 0.00 2.69
2511 2873 7.148052 TGTCGAAATTAAACCCTCACTTTTGAA 60.148 33.333 0.00 0.00 0.00 2.69
2512 2874 7.865889 GTCGAAATTAAACCCTCACTTTTGAAT 59.134 33.333 0.00 0.00 0.00 2.57
2513 2875 8.079809 TCGAAATTAAACCCTCACTTTTGAATC 58.920 33.333 0.00 0.00 0.00 2.52
2514 2876 7.328493 CGAAATTAAACCCTCACTTTTGAATCC 59.672 37.037 0.00 0.00 0.00 3.01
2515 2877 6.605471 ATTAAACCCTCACTTTTGAATCCC 57.395 37.500 0.00 0.00 0.00 3.85
2516 2878 3.903530 AACCCTCACTTTTGAATCCCT 57.096 42.857 0.00 0.00 0.00 4.20
2517 2879 3.160679 ACCCTCACTTTTGAATCCCTG 57.839 47.619 0.00 0.00 0.00 4.45
2518 2880 2.716424 ACCCTCACTTTTGAATCCCTGA 59.284 45.455 0.00 0.00 0.00 3.86
2519 2881 3.140144 ACCCTCACTTTTGAATCCCTGAA 59.860 43.478 0.00 0.00 0.00 3.02
2520 2882 4.151883 CCCTCACTTTTGAATCCCTGAAA 58.848 43.478 0.00 0.00 0.00 2.69
2521 2883 4.774200 CCCTCACTTTTGAATCCCTGAAAT 59.226 41.667 0.00 0.00 0.00 2.17
2522 2884 5.246883 CCCTCACTTTTGAATCCCTGAAATT 59.753 40.000 0.00 0.00 0.00 1.82
2523 2885 6.161381 CCTCACTTTTGAATCCCTGAAATTG 58.839 40.000 0.00 0.00 0.00 2.32
2524 2886 6.100404 TCACTTTTGAATCCCTGAAATTGG 57.900 37.500 0.00 0.00 0.00 3.16
2525 2887 5.602145 TCACTTTTGAATCCCTGAAATTGGT 59.398 36.000 0.00 0.00 0.00 3.67
2526 2888 6.780031 TCACTTTTGAATCCCTGAAATTGGTA 59.220 34.615 0.00 0.00 0.00 3.25
2527 2889 6.868339 CACTTTTGAATCCCTGAAATTGGTAC 59.132 38.462 0.00 0.00 0.00 3.34
2528 2890 5.993748 TTTGAATCCCTGAAATTGGTACC 57.006 39.130 4.43 4.43 0.00 3.34
2529 2891 3.976015 TGAATCCCTGAAATTGGTACCC 58.024 45.455 10.07 0.00 0.00 3.69
2530 2892 3.596046 TGAATCCCTGAAATTGGTACCCT 59.404 43.478 10.07 0.00 0.00 4.34
2531 2893 4.791334 TGAATCCCTGAAATTGGTACCCTA 59.209 41.667 10.07 0.00 0.00 3.53
2532 2894 5.254267 TGAATCCCTGAAATTGGTACCCTAA 59.746 40.000 10.07 0.00 0.00 2.69
2533 2895 4.579647 TCCCTGAAATTGGTACCCTAAC 57.420 45.455 10.07 0.00 0.00 2.34
2534 2896 3.267551 TCCCTGAAATTGGTACCCTAACC 59.732 47.826 10.07 0.00 40.19 2.85
2535 2897 3.268595 CCCTGAAATTGGTACCCTAACCT 59.731 47.826 10.07 0.00 40.44 3.50
2536 2898 4.524053 CCTGAAATTGGTACCCTAACCTC 58.476 47.826 10.07 0.00 40.44 3.85
2537 2899 4.227527 CCTGAAATTGGTACCCTAACCTCT 59.772 45.833 10.07 0.00 40.44 3.69
2538 2900 5.281037 CCTGAAATTGGTACCCTAACCTCTT 60.281 44.000 10.07 0.00 40.44 2.85
2539 2901 6.208840 TGAAATTGGTACCCTAACCTCTTT 57.791 37.500 10.07 0.00 40.44 2.52
2540 2902 6.007703 TGAAATTGGTACCCTAACCTCTTTG 58.992 40.000 10.07 0.00 40.44 2.77
2541 2903 5.853572 AATTGGTACCCTAACCTCTTTGA 57.146 39.130 10.07 0.00 40.44 2.69
2542 2904 6.402981 AATTGGTACCCTAACCTCTTTGAT 57.597 37.500 10.07 0.00 40.44 2.57
2543 2905 5.431179 TTGGTACCCTAACCTCTTTGATC 57.569 43.478 10.07 0.00 40.44 2.92
2544 2906 3.778629 TGGTACCCTAACCTCTTTGATCC 59.221 47.826 10.07 0.00 40.44 3.36
2545 2907 4.038633 GGTACCCTAACCTCTTTGATCCT 58.961 47.826 0.00 0.00 36.53 3.24
2546 2908 4.141688 GGTACCCTAACCTCTTTGATCCTG 60.142 50.000 0.00 0.00 36.53 3.86
2547 2909 2.846827 ACCCTAACCTCTTTGATCCTGG 59.153 50.000 0.00 0.00 0.00 4.45
2548 2910 2.846827 CCCTAACCTCTTTGATCCTGGT 59.153 50.000 0.00 0.00 0.00 4.00
2549 2911 3.118223 CCCTAACCTCTTTGATCCTGGTC 60.118 52.174 0.00 0.00 0.00 4.02
2550 2912 3.519510 CCTAACCTCTTTGATCCTGGTCA 59.480 47.826 0.00 0.00 0.00 4.02
2551 2913 4.164988 CCTAACCTCTTTGATCCTGGTCAT 59.835 45.833 0.00 0.00 0.00 3.06
2552 2914 4.664688 AACCTCTTTGATCCTGGTCATT 57.335 40.909 0.00 0.00 0.00 2.57
2553 2915 5.779241 AACCTCTTTGATCCTGGTCATTA 57.221 39.130 0.00 0.00 0.00 1.90
2554 2916 5.983333 ACCTCTTTGATCCTGGTCATTAT 57.017 39.130 0.00 0.00 0.00 1.28
2555 2917 5.934781 ACCTCTTTGATCCTGGTCATTATC 58.065 41.667 0.00 0.00 0.00 1.75
2556 2918 5.429762 ACCTCTTTGATCCTGGTCATTATCA 59.570 40.000 0.00 0.00 0.00 2.15
2557 2919 6.069440 ACCTCTTTGATCCTGGTCATTATCAA 60.069 38.462 4.21 4.21 36.75 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.814294 GTCTACAGGCCGGCCACG 62.814 72.222 45.13 36.04 38.92 4.94
8 9 4.814294 CGTCTACAGGCCGGCCAC 62.814 72.222 45.13 32.08 38.92 5.01
10 11 4.814294 CACGTCTACAGGCCGGCC 62.814 72.222 39.29 39.29 0.00 6.13
11 12 2.609183 CTACACGTCTACAGGCCGGC 62.609 65.000 21.18 21.18 0.00 6.13
12 13 1.310933 ACTACACGTCTACAGGCCGG 61.311 60.000 0.00 0.00 0.00 6.13
13 14 0.524862 AACTACACGTCTACAGGCCG 59.475 55.000 0.00 0.00 0.00 6.13
145 152 0.952010 GCATGTTAACGTGTCGGGGT 60.952 55.000 24.88 0.00 35.38 4.95
234 242 2.472909 CCTTTTCGATGGAGCCGCC 61.473 63.158 0.00 0.00 37.10 6.13
235 243 2.472909 CCCTTTTCGATGGAGCCGC 61.473 63.158 0.00 0.00 0.00 6.53
236 244 2.472909 GCCCTTTTCGATGGAGCCG 61.473 63.158 0.00 0.00 0.00 5.52
237 245 1.378514 TGCCCTTTTCGATGGAGCC 60.379 57.895 0.00 0.00 0.00 4.70
414 427 1.153329 ACTGCACACGAAACGGGAA 60.153 52.632 0.00 0.00 32.98 3.97
637 653 5.373812 CTGGGGAAATTGACCAGTAGTAT 57.626 43.478 12.74 0.00 45.21 2.12
638 654 4.837093 CTGGGGAAATTGACCAGTAGTA 57.163 45.455 12.74 0.00 45.21 1.82
639 655 3.721087 CTGGGGAAATTGACCAGTAGT 57.279 47.619 12.74 0.00 45.21 2.73
660 676 3.723772 TCCACATGTTGGGACAGTG 57.276 52.632 12.53 0.00 46.92 3.66
682 698 1.561542 GAAGGGATGACATGTGGGTCT 59.438 52.381 1.15 0.00 38.61 3.85
701 717 3.327757 ACACCCTCTTCAGCAACTAATGA 59.672 43.478 0.00 0.00 0.00 2.57
709 725 0.250467 GCTCAACACCCTCTTCAGCA 60.250 55.000 0.00 0.00 0.00 4.41
722 738 7.698836 ATGTGTTTAACTTGAAATGCTCAAC 57.301 32.000 0.00 0.00 39.20 3.18
774 800 3.501828 CGTTTCACCTGATTGTTCATCCA 59.498 43.478 0.00 0.00 0.00 3.41
778 804 3.491639 CGTACGTTTCACCTGATTGTTCA 59.508 43.478 7.22 0.00 0.00 3.18
789 815 2.920579 TAAAACCGCGTACGTTTCAC 57.079 45.000 17.90 0.00 37.70 3.18
794 820 1.565305 TGTGTTAAAACCGCGTACGT 58.435 45.000 17.90 0.00 37.70 3.57
874 907 4.975631 TCCGGTTTTATTCTTGTTCCAGA 58.024 39.130 0.00 0.00 0.00 3.86
956 994 1.544825 TAAAGCCGAGCAGAGCCACT 61.545 55.000 0.00 0.00 0.00 4.00
963 1001 2.000447 GTAGTGGTTAAAGCCGAGCAG 59.000 52.381 0.00 0.00 0.00 4.24
964 1002 1.345089 TGTAGTGGTTAAAGCCGAGCA 59.655 47.619 0.00 0.00 0.00 4.26
965 1003 1.730612 GTGTAGTGGTTAAAGCCGAGC 59.269 52.381 0.00 0.00 0.00 5.03
966 1004 3.251571 GAGTGTAGTGGTTAAAGCCGAG 58.748 50.000 0.00 0.00 0.00 4.63
967 1005 2.028748 GGAGTGTAGTGGTTAAAGCCGA 60.029 50.000 0.00 0.00 0.00 5.54
968 1006 2.028385 AGGAGTGTAGTGGTTAAAGCCG 60.028 50.000 0.00 0.00 0.00 5.52
1210 1255 2.131067 GCGGAGGAGGAAGAGGAGG 61.131 68.421 0.00 0.00 0.00 4.30
1675 1738 5.977635 TGTACATTGCAGCATCTAAGTAGT 58.022 37.500 0.00 0.00 0.00 2.73
1676 1739 7.330454 CCTATGTACATTGCAGCATCTAAGTAG 59.670 40.741 14.77 0.00 0.00 2.57
1749 1817 6.182039 TCTCAGATGAACCAAAAATTAGCG 57.818 37.500 0.00 0.00 0.00 4.26
2034 2104 6.017357 CAGTGTATCACCAAGCTATCGTACTA 60.017 42.308 0.00 0.00 34.49 1.82
2035 2105 4.888239 AGTGTATCACCAAGCTATCGTACT 59.112 41.667 0.00 0.00 34.49 2.73
2036 2106 4.976731 CAGTGTATCACCAAGCTATCGTAC 59.023 45.833 0.00 0.00 34.49 3.67
2078 2428 9.732130 GCTACTAATAATTTTCTCCAGATCCAT 57.268 33.333 0.00 0.00 0.00 3.41
2095 2445 4.142026 ACATGTGTCGCCAAGCTACTAATA 60.142 41.667 0.00 0.00 0.00 0.98
2329 2691 7.377766 TCGAATTGAATAAGTTCCCTTCAAG 57.622 36.000 11.50 0.00 40.91 3.02
2372 2734 8.439971 TGATTTGGTACTATCAGCCATAGAAAT 58.560 33.333 7.19 3.47 37.27 2.17
2398 2760 2.581354 GTCAGGACATGCGGCTCT 59.419 61.111 0.00 0.00 0.00 4.09
2434 2796 2.620251 TCATTCGCCCTGAGGTTATG 57.380 50.000 0.00 0.00 34.57 1.90
2437 2799 0.693049 ACTTCATTCGCCCTGAGGTT 59.307 50.000 0.00 0.00 29.60 3.50
2438 2800 0.250513 GACTTCATTCGCCCTGAGGT 59.749 55.000 0.00 0.00 35.86 3.85
2451 2813 9.233649 TGAGTTTAAGGTTTAAAACAGACTTCA 57.766 29.630 5.94 0.00 37.92 3.02
2457 2819 9.827411 GCTCTATGAGTTTAAGGTTTAAAACAG 57.173 33.333 5.94 0.00 37.92 3.16
2458 2820 9.569122 AGCTCTATGAGTTTAAGGTTTAAAACA 57.431 29.630 5.94 1.85 37.92 2.83
2461 2823 9.569122 ACAAGCTCTATGAGTTTAAGGTTTAAA 57.431 29.630 0.00 0.00 31.66 1.52
2462 2824 9.216117 GACAAGCTCTATGAGTTTAAGGTTTAA 57.784 33.333 0.00 0.00 31.66 1.52
2463 2825 7.544566 CGACAAGCTCTATGAGTTTAAGGTTTA 59.455 37.037 0.00 0.00 31.66 2.01
2464 2826 6.369065 CGACAAGCTCTATGAGTTTAAGGTTT 59.631 38.462 0.00 0.00 31.66 3.27
2465 2827 5.869888 CGACAAGCTCTATGAGTTTAAGGTT 59.130 40.000 0.00 0.00 31.66 3.50
2466 2828 5.185249 TCGACAAGCTCTATGAGTTTAAGGT 59.815 40.000 0.00 0.00 31.66 3.50
2467 2829 5.651530 TCGACAAGCTCTATGAGTTTAAGG 58.348 41.667 0.00 0.00 31.66 2.69
2468 2830 7.582435 TTTCGACAAGCTCTATGAGTTTAAG 57.418 36.000 0.00 0.00 31.66 1.85
2469 2831 8.547967 AATTTCGACAAGCTCTATGAGTTTAA 57.452 30.769 0.00 0.00 31.66 1.52
2470 2832 9.647797 TTAATTTCGACAAGCTCTATGAGTTTA 57.352 29.630 0.00 0.00 31.66 2.01
2471 2833 8.547967 TTAATTTCGACAAGCTCTATGAGTTT 57.452 30.769 0.00 0.00 33.57 2.66
2472 2834 8.443937 GTTTAATTTCGACAAGCTCTATGAGTT 58.556 33.333 0.00 0.00 31.39 3.01
2473 2835 7.064728 GGTTTAATTTCGACAAGCTCTATGAGT 59.935 37.037 0.00 0.00 31.39 3.41
2474 2836 7.402640 GGTTTAATTTCGACAAGCTCTATGAG 58.597 38.462 0.00 0.00 0.00 2.90
2475 2837 6.315393 GGGTTTAATTTCGACAAGCTCTATGA 59.685 38.462 0.00 0.00 0.00 2.15
2476 2838 6.316390 AGGGTTTAATTTCGACAAGCTCTATG 59.684 38.462 0.00 0.00 0.00 2.23
2477 2839 6.415573 AGGGTTTAATTTCGACAAGCTCTAT 58.584 36.000 0.00 0.00 0.00 1.98
2478 2840 5.801380 AGGGTTTAATTTCGACAAGCTCTA 58.199 37.500 0.00 0.00 0.00 2.43
2479 2841 4.652822 AGGGTTTAATTTCGACAAGCTCT 58.347 39.130 0.00 0.00 0.00 4.09
2480 2842 4.454504 TGAGGGTTTAATTTCGACAAGCTC 59.545 41.667 0.00 0.00 0.00 4.09
2481 2843 4.215613 GTGAGGGTTTAATTTCGACAAGCT 59.784 41.667 0.00 0.00 0.00 3.74
2482 2844 4.215613 AGTGAGGGTTTAATTTCGACAAGC 59.784 41.667 0.00 0.00 0.00 4.01
2483 2845 5.941948 AGTGAGGGTTTAATTTCGACAAG 57.058 39.130 0.00 0.00 0.00 3.16
2484 2846 6.702716 AAAGTGAGGGTTTAATTTCGACAA 57.297 33.333 0.00 0.00 0.00 3.18
2485 2847 6.319152 TCAAAAGTGAGGGTTTAATTTCGACA 59.681 34.615 0.00 0.00 0.00 4.35
2486 2848 6.731164 TCAAAAGTGAGGGTTTAATTTCGAC 58.269 36.000 0.00 0.00 0.00 4.20
2487 2849 6.945938 TCAAAAGTGAGGGTTTAATTTCGA 57.054 33.333 0.00 0.00 0.00 3.71
2488 2850 7.328493 GGATTCAAAAGTGAGGGTTTAATTTCG 59.672 37.037 0.00 0.00 34.49 3.46
2489 2851 7.602644 GGGATTCAAAAGTGAGGGTTTAATTTC 59.397 37.037 0.00 0.00 34.49 2.17
2490 2852 7.292356 AGGGATTCAAAAGTGAGGGTTTAATTT 59.708 33.333 0.00 0.00 34.49 1.82
2491 2853 6.787458 AGGGATTCAAAAGTGAGGGTTTAATT 59.213 34.615 0.00 0.00 34.49 1.40
2492 2854 6.211384 CAGGGATTCAAAAGTGAGGGTTTAAT 59.789 38.462 0.00 0.00 34.49 1.40
2493 2855 5.538433 CAGGGATTCAAAAGTGAGGGTTTAA 59.462 40.000 0.00 0.00 34.49 1.52
2494 2856 5.076873 CAGGGATTCAAAAGTGAGGGTTTA 58.923 41.667 0.00 0.00 34.49 2.01
2495 2857 3.897505 CAGGGATTCAAAAGTGAGGGTTT 59.102 43.478 0.00 0.00 34.49 3.27
2496 2858 3.140144 TCAGGGATTCAAAAGTGAGGGTT 59.860 43.478 0.00 0.00 34.49 4.11
2497 2859 2.716424 TCAGGGATTCAAAAGTGAGGGT 59.284 45.455 0.00 0.00 34.49 4.34
2498 2860 3.439857 TCAGGGATTCAAAAGTGAGGG 57.560 47.619 0.00 0.00 34.49 4.30
2499 2861 5.990120 ATTTCAGGGATTCAAAAGTGAGG 57.010 39.130 0.00 0.00 34.49 3.86
2500 2862 6.161381 CCAATTTCAGGGATTCAAAAGTGAG 58.839 40.000 0.00 0.00 34.49 3.51
2501 2863 5.602145 ACCAATTTCAGGGATTCAAAAGTGA 59.398 36.000 0.00 0.00 30.57 3.41
2502 2864 5.857268 ACCAATTTCAGGGATTCAAAAGTG 58.143 37.500 0.00 0.00 0.00 3.16
2503 2865 6.014584 GGTACCAATTTCAGGGATTCAAAAGT 60.015 38.462 7.15 0.00 0.00 2.66
2504 2866 6.398095 GGTACCAATTTCAGGGATTCAAAAG 58.602 40.000 7.15 0.00 0.00 2.27
2505 2867 6.353404 GGTACCAATTTCAGGGATTCAAAA 57.647 37.500 7.15 0.00 0.00 2.44
2506 2868 5.993748 GGTACCAATTTCAGGGATTCAAA 57.006 39.130 7.15 0.00 0.00 2.69
2524 2886 4.141688 CCAGGATCAAAGAGGTTAGGGTAC 60.142 50.000 0.00 0.00 0.00 3.34
2525 2887 4.037927 CCAGGATCAAAGAGGTTAGGGTA 58.962 47.826 0.00 0.00 0.00 3.69
2526 2888 2.846827 CCAGGATCAAAGAGGTTAGGGT 59.153 50.000 0.00 0.00 0.00 4.34
2527 2889 2.846827 ACCAGGATCAAAGAGGTTAGGG 59.153 50.000 0.00 0.00 0.00 3.53
2528 2890 3.519510 TGACCAGGATCAAAGAGGTTAGG 59.480 47.826 0.00 0.00 31.57 2.69
2529 2891 4.826274 TGACCAGGATCAAAGAGGTTAG 57.174 45.455 0.00 0.00 31.57 2.34
2530 2892 5.779241 AATGACCAGGATCAAAGAGGTTA 57.221 39.130 0.00 0.00 31.57 2.85
2531 2893 4.664688 AATGACCAGGATCAAAGAGGTT 57.335 40.909 0.00 0.00 31.57 3.50
2532 2894 5.429762 TGATAATGACCAGGATCAAAGAGGT 59.570 40.000 0.00 0.00 34.76 3.85
2533 2895 5.933617 TGATAATGACCAGGATCAAAGAGG 58.066 41.667 0.00 0.00 30.82 3.69


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

AutoCloner maintained by Alex Coulton.