Multiple sequence alignment - TraesCS2D01G195600

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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 TraesCS2D01G195600 chr2D 100.000 2934 0 0 1 2934 142065614 142062681 0.000000e+00 5419.0
1 TraesCS2D01G195600 chr2D 94.545 55 3 0 2699 2753 142062864 142062810 5.210000e-13 86.1
2 TraesCS2D01G195600 chr2D 94.545 55 3 0 2751 2805 142062916 142062862 5.210000e-13 86.1
3 TraesCS2D01G195600 chr2A 93.905 2789 97 26 1 2750 159066115 159068869 0.000000e+00 4141.0
4 TraesCS2D01G195600 chr2B 93.157 2718 99 30 94 2753 200083277 200080589 0.000000e+00 3908.0
5 TraesCS2D01G195600 chr2B 92.174 115 3 3 6 114 200083409 200083295 1.090000e-34 158.0
6 TraesCS2D01G195600 chr2B 88.372 129 9 4 1800 1928 200081621 200081499 1.820000e-32 150.0
7 TraesCS2D01G195600 chr6B 84.559 136 20 1 2784 2919 583189749 583189883 1.830000e-27 134.0
8 TraesCS2D01G195600 chr7D 86.207 116 14 2 2765 2879 562416522 562416408 1.100000e-24 124.0
9 TraesCS2D01G195600 chr4D 82.069 145 24 2 2765 2907 15550404 15550548 3.970000e-24 122.0
10 TraesCS2D01G195600 chr1A 79.470 151 29 2 2784 2934 586426093 586425945 4.000000e-19 106.0
11 TraesCS2D01G195600 chr3A 86.170 94 13 0 2791 2884 477318635 477318728 5.170000e-18 102.0
12 TraesCS2D01G195600 chr3A 87.805 82 10 0 2791 2872 477313078 477313159 2.410000e-16 97.1
13 TraesCS2D01G195600 chr5D 87.059 85 10 1 2599 2682 485911062 485911146 8.660000e-16 95.3
14 TraesCS2D01G195600 chr3D 83.168 101 14 2 2784 2884 297469374 297469277 4.030000e-14 89.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G195600 chr2D 142062681 142065614 2933 True 1863.733333 5419 96.363333 1 2934 3 chr2D.!!$R1 2933
1 TraesCS2D01G195600 chr2A 159066115 159068869 2754 False 4141.000000 4141 93.905000 1 2750 1 chr2A.!!$F1 2749
2 TraesCS2D01G195600 chr2B 200080589 200083409 2820 True 1405.333333 3908 91.234333 6 2753 3 chr2B.!!$R1 2747

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
76 78 0.564767 GCGAATCACTGCGTACGTAC 59.435 55.0 17.9 15.9 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1973 2076 0.039618 TTGATCTTTCTGGCCACCCC 59.96 55.0 0.0 0.0 0.0 4.95 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
68 70 4.565704 GCGCTCGCGAATCACTGC 62.566 66.667 16.26 8.10 42.83 4.40
76 78 0.564767 GCGAATCACTGCGTACGTAC 59.435 55.000 17.90 15.90 0.00 3.67
77 79 1.186030 CGAATCACTGCGTACGTACC 58.814 55.000 19.67 12.75 0.00 3.34
141 187 1.299976 GCAGGGAAATCACGAGGGT 59.700 57.895 0.00 0.00 0.00 4.34
202 256 2.048597 CAACCCGTACGCTGCTCA 60.049 61.111 10.49 0.00 0.00 4.26
226 280 2.363680 AGGTCATGATCGAGCTAGTTGG 59.636 50.000 0.90 0.00 41.80 3.77
300 369 6.985117 TGATAAACCAACTGTACGAGTAGTT 58.015 36.000 0.00 0.00 37.61 2.24
320 395 0.800683 TTTATGTGCGAGCTCGACGG 60.801 55.000 38.74 11.33 43.02 4.79
398 475 2.632377 CTCGTGGATTACTTGGTGCAT 58.368 47.619 0.00 0.00 0.00 3.96
411 488 6.320494 ACTTGGTGCATATTCGTACAAAAA 57.680 33.333 0.00 0.00 0.00 1.94
412 489 6.146898 ACTTGGTGCATATTCGTACAAAAAC 58.853 36.000 0.00 0.00 0.00 2.43
413 490 5.950758 TGGTGCATATTCGTACAAAAACT 57.049 34.783 0.00 0.00 0.00 2.66
414 491 7.173562 ACTTGGTGCATATTCGTACAAAAACTA 59.826 33.333 0.00 0.00 0.00 2.24
415 492 7.618502 TGGTGCATATTCGTACAAAAACTAT 57.381 32.000 0.00 0.00 0.00 2.12
418 495 6.910433 GTGCATATTCGTACAAAAACTATGGG 59.090 38.462 0.00 0.00 0.00 4.00
420 497 7.121463 TGCATATTCGTACAAAAACTATGGGTT 59.879 33.333 0.00 0.00 40.28 4.11
422 499 9.284594 CATATTCGTACAAAAACTATGGGTTTG 57.715 33.333 0.00 0.00 46.18 2.93
423 500 6.939132 TTCGTACAAAAACTATGGGTTTGA 57.061 33.333 12.44 0.00 46.18 2.69
426 503 6.711194 TCGTACAAAAACTATGGGTTTGATGA 59.289 34.615 12.44 2.21 46.18 2.92
519 598 2.613026 ATCGTGATTATCCGGTTGCA 57.387 45.000 0.00 0.00 0.00 4.08
642 732 0.787183 GTGTCGCTTTGCTCTCTGTC 59.213 55.000 0.00 0.00 0.00 3.51
669 759 6.546972 AGATTCTCACCGTTTTCTTTCTTC 57.453 37.500 0.00 0.00 0.00 2.87
675 765 5.636837 TCACCGTTTTCTTTCTTCTTGTTG 58.363 37.500 0.00 0.00 0.00 3.33
676 766 5.182380 TCACCGTTTTCTTTCTTCTTGTTGT 59.818 36.000 0.00 0.00 0.00 3.32
677 767 5.861787 CACCGTTTTCTTTCTTCTTGTTGTT 59.138 36.000 0.00 0.00 0.00 2.83
729 819 6.441222 AGTAGTATTTCCCATCTCTACACCA 58.559 40.000 0.00 0.00 32.82 4.17
855 952 4.689549 TCGCCCCCGACTTCCAGA 62.690 66.667 0.00 0.00 38.82 3.86
856 953 3.470888 CGCCCCCGACTTCCAGAT 61.471 66.667 0.00 0.00 36.29 2.90
857 954 2.998949 GCCCCCGACTTCCAGATT 59.001 61.111 0.00 0.00 0.00 2.40
898 995 7.255451 CCACAGAGGAACAGCTAAACAAATTAA 60.255 37.037 0.00 0.00 41.22 1.40
1043 1141 2.833794 CTTCAAGGACGTTGACAAGGA 58.166 47.619 14.50 0.00 45.23 3.36
1044 1142 2.992124 TCAAGGACGTTGACAAGGAA 57.008 45.000 14.50 0.00 40.45 3.36
1056 1154 1.205893 GACAAGGAAGAGCCGATGAGT 59.794 52.381 0.00 0.00 43.43 3.41
1768 1868 2.354343 GGCAAGAAGGGCAGCTCT 59.646 61.111 0.00 0.00 0.00 4.09
1852 1955 3.551259 GGTGATTTCGCCCAGAAGA 57.449 52.632 0.00 0.00 40.40 2.87
1973 2076 5.061789 CGTGTTGTAAATAGTCGTCAAACG 58.938 41.667 0.00 0.00 44.19 3.60
1975 2078 4.448395 TGTTGTAAATAGTCGTCAAACGGG 59.552 41.667 0.00 0.00 42.81 5.28
2160 2267 0.316841 AAAATTCGGGCAACATGCGT 59.683 45.000 0.00 0.00 46.21 5.24
2356 2463 5.039333 GGAGATAAACATGTGAATTGCTGC 58.961 41.667 0.00 0.00 0.00 5.25
2358 2465 6.038603 GGAGATAAACATGTGAATTGCTGCTA 59.961 38.462 0.00 0.00 0.00 3.49
2374 2486 4.095334 TGCTGCTATGATGTTTGATGTCAC 59.905 41.667 0.00 0.00 0.00 3.67
2407 2519 4.877378 TGGTCTACTTTGTTACCGTCAT 57.123 40.909 0.00 0.00 34.60 3.06
2509 2640 0.037232 CTCTTTGTCAGTCGGTCCCC 60.037 60.000 0.00 0.00 0.00 4.81
2577 2711 7.407393 TTTTCCAGCACATCATATTTGATCA 57.593 32.000 0.00 0.00 40.70 2.92
2592 2726 0.036732 GATCACACCTTCCCAGTGCA 59.963 55.000 0.00 0.00 38.87 4.57
2693 2827 2.554893 GGTAAATCACCGCACTTTTCCA 59.445 45.455 0.00 0.00 37.63 3.53
2709 2843 1.083806 TCCAGTGCGCTGCTTAATCG 61.084 55.000 22.03 6.43 41.26 3.34
2710 2844 1.361668 CCAGTGCGCTGCTTAATCGT 61.362 55.000 22.03 0.00 41.26 3.73
2711 2845 1.277326 CAGTGCGCTGCTTAATCGTA 58.723 50.000 15.44 0.00 35.77 3.43
2712 2846 1.860950 CAGTGCGCTGCTTAATCGTAT 59.139 47.619 15.44 0.00 35.77 3.06
2713 2847 2.285220 CAGTGCGCTGCTTAATCGTATT 59.715 45.455 15.44 0.00 35.77 1.89
2714 2848 3.489416 CAGTGCGCTGCTTAATCGTATTA 59.511 43.478 15.44 0.00 35.77 0.98
2715 2849 4.026062 CAGTGCGCTGCTTAATCGTATTAA 60.026 41.667 15.44 0.00 35.77 1.40
2716 2850 4.750098 AGTGCGCTGCTTAATCGTATTAAT 59.250 37.500 9.73 0.00 0.00 1.40
2717 2851 5.236478 AGTGCGCTGCTTAATCGTATTAATT 59.764 36.000 9.73 0.00 0.00 1.40
2718 2852 6.422701 AGTGCGCTGCTTAATCGTATTAATTA 59.577 34.615 9.73 0.00 0.00 1.40
2719 2853 6.515340 GTGCGCTGCTTAATCGTATTAATTAC 59.485 38.462 9.73 0.00 0.00 1.89
2720 2854 6.422701 TGCGCTGCTTAATCGTATTAATTACT 59.577 34.615 9.73 0.00 0.00 2.24
2721 2855 7.042321 TGCGCTGCTTAATCGTATTAATTACTT 60.042 33.333 9.73 0.00 0.00 2.24
2722 2856 8.430063 GCGCTGCTTAATCGTATTAATTACTTA 58.570 33.333 0.00 0.00 0.00 2.24
2723 2857 9.723299 CGCTGCTTAATCGTATTAATTACTTAC 57.277 33.333 0.00 0.00 0.00 2.34
2742 2876 6.896883 ACTTACCCTCTATACCAATTTCACC 58.103 40.000 0.00 0.00 0.00 4.02
2743 2877 6.677076 ACTTACCCTCTATACCAATTTCACCT 59.323 38.462 0.00 0.00 0.00 4.00
2744 2878 7.184022 ACTTACCCTCTATACCAATTTCACCTT 59.816 37.037 0.00 0.00 0.00 3.50
2745 2879 8.626917 TTACCCTCTATACCAATTTCACCTTA 57.373 34.615 0.00 0.00 0.00 2.69
2746 2880 7.519347 ACCCTCTATACCAATTTCACCTTAA 57.481 36.000 0.00 0.00 0.00 1.85
2747 2881 8.114301 ACCCTCTATACCAATTTCACCTTAAT 57.886 34.615 0.00 0.00 0.00 1.40
2748 2882 8.566109 ACCCTCTATACCAATTTCACCTTAATT 58.434 33.333 0.00 0.00 0.00 1.40
2749 2883 9.421399 CCCTCTATACCAATTTCACCTTAATTT 57.579 33.333 0.00 0.00 0.00 1.82
2751 2885 9.736023 CTCTATACCAATTTCACCTTAATTTGC 57.264 33.333 0.00 0.00 0.00 3.68
2752 2886 9.474313 TCTATACCAATTTCACCTTAATTTGCT 57.526 29.630 0.00 0.00 0.00 3.91
2753 2887 9.520204 CTATACCAATTTCACCTTAATTTGCTG 57.480 33.333 0.00 0.00 0.00 4.41
2754 2888 4.996758 ACCAATTTCACCTTAATTTGCTGC 59.003 37.500 0.00 0.00 0.00 5.25
2755 2889 5.221702 ACCAATTTCACCTTAATTTGCTGCT 60.222 36.000 0.00 0.00 0.00 4.24
2756 2890 5.702209 CCAATTTCACCTTAATTTGCTGCTT 59.298 36.000 0.00 0.00 0.00 3.91
2757 2891 6.873076 CCAATTTCACCTTAATTTGCTGCTTA 59.127 34.615 0.00 0.00 0.00 3.09
2758 2892 7.387397 CCAATTTCACCTTAATTTGCTGCTTAA 59.613 33.333 0.00 0.00 0.00 1.85
2759 2893 8.938906 CAATTTCACCTTAATTTGCTGCTTAAT 58.061 29.630 0.00 0.00 0.00 1.40
2760 2894 9.506018 AATTTCACCTTAATTTGCTGCTTAATT 57.494 25.926 14.44 14.44 0.00 1.40
2761 2895 7.887996 TTCACCTTAATTTGCTGCTTAATTG 57.112 32.000 17.52 8.40 0.00 2.32
2841 2975 9.438291 CTTATCAAACTATAAAGCAAATCACGG 57.562 33.333 0.00 0.00 0.00 4.94
2842 2976 6.189677 TCAAACTATAAAGCAAATCACGGG 57.810 37.500 0.00 0.00 0.00 5.28
2843 2977 4.632538 AACTATAAAGCAAATCACGGGC 57.367 40.909 0.00 0.00 0.00 6.13
2844 2978 3.616219 ACTATAAAGCAAATCACGGGCA 58.384 40.909 0.00 0.00 0.00 5.36
2845 2979 3.627577 ACTATAAAGCAAATCACGGGCAG 59.372 43.478 0.00 0.00 0.00 4.85
2846 2980 1.173043 TAAAGCAAATCACGGGCAGG 58.827 50.000 0.00 0.00 0.00 4.85
2847 2981 0.539438 AAAGCAAATCACGGGCAGGA 60.539 50.000 0.00 0.00 0.00 3.86
2848 2982 0.323725 AAGCAAATCACGGGCAGGAT 60.324 50.000 0.00 0.00 0.00 3.24
2849 2983 0.323725 AGCAAATCACGGGCAGGATT 60.324 50.000 0.00 0.00 35.34 3.01
2850 2984 0.532115 GCAAATCACGGGCAGGATTT 59.468 50.000 7.76 7.76 42.72 2.17
2851 2985 1.748493 GCAAATCACGGGCAGGATTTA 59.252 47.619 11.43 0.00 40.68 1.40
2852 2986 2.223572 GCAAATCACGGGCAGGATTTAG 60.224 50.000 11.43 8.72 40.68 1.85
2853 2987 3.016736 CAAATCACGGGCAGGATTTAGT 58.983 45.455 11.43 0.00 40.68 2.24
2854 2988 4.196193 CAAATCACGGGCAGGATTTAGTA 58.804 43.478 11.43 0.00 40.68 1.82
2855 2989 4.497291 AATCACGGGCAGGATTTAGTAA 57.503 40.909 0.00 0.00 29.77 2.24
2856 2990 3.985019 TCACGGGCAGGATTTAGTAAA 57.015 42.857 0.00 0.00 0.00 2.01
2857 2991 3.602483 TCACGGGCAGGATTTAGTAAAC 58.398 45.455 0.00 0.00 0.00 2.01
2858 2992 3.008157 TCACGGGCAGGATTTAGTAAACA 59.992 43.478 0.00 0.00 0.00 2.83
2859 2993 3.945285 CACGGGCAGGATTTAGTAAACAT 59.055 43.478 0.00 0.00 0.00 2.71
2860 2994 4.398044 CACGGGCAGGATTTAGTAAACATT 59.602 41.667 0.00 0.00 0.00 2.71
2861 2995 5.014202 ACGGGCAGGATTTAGTAAACATTT 58.986 37.500 0.00 0.00 0.00 2.32
2862 2996 6.094325 CACGGGCAGGATTTAGTAAACATTTA 59.906 38.462 0.00 0.00 0.00 1.40
2863 2997 6.831868 ACGGGCAGGATTTAGTAAACATTTAT 59.168 34.615 0.00 0.00 0.00 1.40
2864 2998 7.340999 ACGGGCAGGATTTAGTAAACATTTATT 59.659 33.333 0.00 0.00 0.00 1.40
2865 2999 8.194769 CGGGCAGGATTTAGTAAACATTTATTT 58.805 33.333 0.00 0.00 0.00 1.40
2866 3000 9.313118 GGGCAGGATTTAGTAAACATTTATTTG 57.687 33.333 0.00 0.00 0.00 2.32
2867 3001 8.817100 GGCAGGATTTAGTAAACATTTATTTGC 58.183 33.333 0.00 1.02 0.00 3.68
2868 3002 9.364989 GCAGGATTTAGTAAACATTTATTTGCA 57.635 29.630 0.00 0.00 0.00 4.08
2874 3008 9.817809 TTTAGTAAACATTTATTTGCACAACCA 57.182 25.926 0.00 0.00 0.00 3.67
2875 3009 7.707774 AGTAAACATTTATTTGCACAACCAC 57.292 32.000 0.00 0.00 0.00 4.16
2876 3010 7.268586 AGTAAACATTTATTTGCACAACCACA 58.731 30.769 0.00 0.00 0.00 4.17
2877 3011 7.930865 AGTAAACATTTATTTGCACAACCACAT 59.069 29.630 0.00 0.00 0.00 3.21
2878 3012 7.565323 AAACATTTATTTGCACAACCACATT 57.435 28.000 0.00 0.00 0.00 2.71
2879 3013 8.668510 AAACATTTATTTGCACAACCACATTA 57.331 26.923 0.00 0.00 0.00 1.90
2880 3014 8.668510 AACATTTATTTGCACAACCACATTAA 57.331 26.923 0.00 0.00 0.00 1.40
2881 3015 8.845413 ACATTTATTTGCACAACCACATTAAT 57.155 26.923 0.00 0.00 0.00 1.40
2882 3016 9.935241 ACATTTATTTGCACAACCACATTAATA 57.065 25.926 0.00 0.00 0.00 0.98
2885 3019 8.939201 TTATTTGCACAACCACATTAATATGG 57.061 30.769 11.34 11.34 42.13 2.74
2886 3020 6.596309 TTTGCACAACCACATTAATATGGA 57.404 33.333 19.68 0.00 39.46 3.41
2887 3021 6.788598 TTGCACAACCACATTAATATGGAT 57.211 33.333 19.68 4.59 39.46 3.41
2888 3022 7.888250 TTGCACAACCACATTAATATGGATA 57.112 32.000 19.68 0.00 39.46 2.59
2889 3023 7.509141 TGCACAACCACATTAATATGGATAG 57.491 36.000 19.68 10.32 39.46 2.08
2890 3024 6.016360 TGCACAACCACATTAATATGGATAGC 60.016 38.462 19.68 14.36 39.46 2.97
2891 3025 6.207417 GCACAACCACATTAATATGGATAGCT 59.793 38.462 19.68 0.00 39.46 3.32
2892 3026 7.390440 GCACAACCACATTAATATGGATAGCTA 59.610 37.037 19.68 0.00 39.46 3.32
2893 3027 9.283768 CACAACCACATTAATATGGATAGCTAA 57.716 33.333 19.68 0.00 39.46 3.09
2902 3036 8.703604 TTAATATGGATAGCTAATTCACGAGC 57.296 34.615 0.00 0.00 39.08 5.03
2915 3049 9.622004 GCTAATTCACGAGCTAACATACTATAA 57.378 33.333 0.00 0.00 35.73 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 70 2.159421 AGCAGAATGTCAGGTACGTACG 60.159 50.000 18.98 15.01 39.31 3.67
76 78 6.988580 TCATGATTTAGTAGCAGAATGTCAGG 59.011 38.462 0.00 0.00 39.31 3.86
77 79 7.307278 GCTCATGATTTAGTAGCAGAATGTCAG 60.307 40.741 0.00 0.00 39.31 3.51
141 187 2.592574 AGGTCACGACGTCGGTCA 60.593 61.111 37.89 20.52 43.61 4.02
226 280 2.104530 GCTAGTTCCGCCCGTCTC 59.895 66.667 0.00 0.00 0.00 3.36
300 369 0.989164 CGTCGAGCTCGCACATAAAA 59.011 50.000 30.97 8.61 39.60 1.52
320 395 1.635663 CGTCGATCCTGTTGGTTGCC 61.636 60.000 0.00 0.00 34.23 4.52
398 475 8.618702 TCAAACCCATAGTTTTTGTACGAATA 57.381 30.769 0.00 0.00 46.79 1.75
411 488 8.768397 TCTAAGTAACATCATCAAACCCATAGT 58.232 33.333 0.00 0.00 0.00 2.12
412 489 9.613428 TTCTAAGTAACATCATCAAACCCATAG 57.387 33.333 0.00 0.00 0.00 2.23
413 490 9.967451 TTTCTAAGTAACATCATCAAACCCATA 57.033 29.630 0.00 0.00 0.00 2.74
414 491 8.877864 TTTCTAAGTAACATCATCAAACCCAT 57.122 30.769 0.00 0.00 0.00 4.00
415 492 8.877864 ATTTCTAAGTAACATCATCAAACCCA 57.122 30.769 0.00 0.00 0.00 4.51
563 644 6.817641 TGAATTGTATGCATGGGAAATTGTTC 59.182 34.615 10.16 2.55 0.00 3.18
642 732 5.931441 AAGAAAACGGTGAGAATCTTCAG 57.069 39.130 0.00 0.00 34.92 3.02
669 759 2.968655 GCGTTAAGCCGTTAACAACAAG 59.031 45.455 6.39 0.00 45.82 3.16
675 765 0.093535 GTCCGCGTTAAGCCGTTAAC 59.906 55.000 4.92 0.00 43.20 2.01
676 766 0.319383 TGTCCGCGTTAAGCCGTTAA 60.319 50.000 4.92 0.00 44.76 2.01
677 767 1.008361 GTGTCCGCGTTAAGCCGTTA 61.008 55.000 4.92 0.00 44.76 3.18
729 819 0.537143 TTGCTTGCCACGATTGACCT 60.537 50.000 0.00 0.00 0.00 3.85
851 948 0.393537 GCTGGGTGACTGGAATCTGG 60.394 60.000 0.00 0.00 0.00 3.86
852 949 0.393537 GGCTGGGTGACTGGAATCTG 60.394 60.000 0.00 0.00 0.00 2.90
853 950 1.566298 GGGCTGGGTGACTGGAATCT 61.566 60.000 0.00 0.00 0.00 2.40
854 951 1.077429 GGGCTGGGTGACTGGAATC 60.077 63.158 0.00 0.00 0.00 2.52
855 952 2.616458 GGGGCTGGGTGACTGGAAT 61.616 63.158 0.00 0.00 0.00 3.01
856 953 3.256960 GGGGCTGGGTGACTGGAA 61.257 66.667 0.00 0.00 0.00 3.53
857 954 4.590553 TGGGGCTGGGTGACTGGA 62.591 66.667 0.00 0.00 0.00 3.86
898 995 3.288308 CTTGCTCCGGTGTCGCTCT 62.288 63.158 0.00 0.00 34.56 4.09
1311 1409 4.400567 AGCTTGAACTTGCACTTCTTCTTT 59.599 37.500 5.19 0.00 0.00 2.52
1458 1556 1.444553 CTTCTTCTTCGTCGGCGCT 60.445 57.895 3.52 0.00 38.14 5.92
1768 1868 0.327924 AAATCACCTCATGGTCGCCA 59.672 50.000 1.01 1.01 46.60 5.69
1796 1896 1.612726 GCTCTTCTTGCCATGTGACCT 60.613 52.381 0.00 0.00 0.00 3.85
1798 1898 1.467734 CTGCTCTTCTTGCCATGTGAC 59.532 52.381 0.00 0.00 0.00 3.67
1850 1953 5.564550 ACTACTTTTCTTGCCATGTGATCT 58.435 37.500 0.00 0.00 0.00 2.75
1851 1954 5.886960 ACTACTTTTCTTGCCATGTGATC 57.113 39.130 0.00 0.00 0.00 2.92
1852 1955 5.355350 GCTACTACTTTTCTTGCCATGTGAT 59.645 40.000 0.00 0.00 0.00 3.06
1973 2076 0.039618 TTGATCTTTCTGGCCACCCC 59.960 55.000 0.00 0.00 0.00 4.95
1975 2078 4.021192 TGAAATTTGATCTTTCTGGCCACC 60.021 41.667 0.00 0.00 34.43 4.61
2374 2486 5.241506 ACAAAGTAGACCAATGACCAATGTG 59.758 40.000 0.00 0.00 0.00 3.21
2407 2519 4.119442 AGCGAGACGAAAGCCTATTTTA 57.881 40.909 0.00 0.00 0.00 1.52
2509 2640 1.798626 TGGGGAGATGTGATGAGAGG 58.201 55.000 0.00 0.00 0.00 3.69
2560 2694 5.762825 AGGTGTGATCAAATATGATGTGC 57.237 39.130 0.00 0.00 46.30 4.57
2577 2711 2.515901 GGTGCACTGGGAAGGTGT 59.484 61.111 17.98 0.00 37.07 4.16
2687 2821 1.313772 TTAAGCAGCGCACTGGAAAA 58.686 45.000 11.47 0.00 44.63 2.29
2693 2827 2.225068 ATACGATTAAGCAGCGCACT 57.775 45.000 11.47 2.96 0.00 4.40
2716 2850 8.488668 GGTGAAATTGGTATAGAGGGTAAGTAA 58.511 37.037 0.00 0.00 0.00 2.24
2717 2851 7.847848 AGGTGAAATTGGTATAGAGGGTAAGTA 59.152 37.037 0.00 0.00 0.00 2.24
2718 2852 6.677076 AGGTGAAATTGGTATAGAGGGTAAGT 59.323 38.462 0.00 0.00 0.00 2.24
2719 2853 7.138054 AGGTGAAATTGGTATAGAGGGTAAG 57.862 40.000 0.00 0.00 0.00 2.34
2720 2854 7.519347 AAGGTGAAATTGGTATAGAGGGTAA 57.481 36.000 0.00 0.00 0.00 2.85
2721 2855 8.626917 TTAAGGTGAAATTGGTATAGAGGGTA 57.373 34.615 0.00 0.00 0.00 3.69
2722 2856 7.519347 TTAAGGTGAAATTGGTATAGAGGGT 57.481 36.000 0.00 0.00 0.00 4.34
2723 2857 8.996651 AATTAAGGTGAAATTGGTATAGAGGG 57.003 34.615 0.00 0.00 0.00 4.30
2725 2859 9.736023 GCAAATTAAGGTGAAATTGGTATAGAG 57.264 33.333 0.00 0.00 0.00 2.43
2726 2860 9.474313 AGCAAATTAAGGTGAAATTGGTATAGA 57.526 29.630 0.00 0.00 0.00 1.98
2727 2861 9.520204 CAGCAAATTAAGGTGAAATTGGTATAG 57.480 33.333 4.50 0.00 36.64 1.31
2728 2862 7.978975 GCAGCAAATTAAGGTGAAATTGGTATA 59.021 33.333 12.56 0.00 36.64 1.47
2729 2863 6.818142 GCAGCAAATTAAGGTGAAATTGGTAT 59.182 34.615 12.56 0.00 36.64 2.73
2730 2864 6.014669 AGCAGCAAATTAAGGTGAAATTGGTA 60.015 34.615 12.56 0.00 36.64 3.25
2731 2865 4.996758 GCAGCAAATTAAGGTGAAATTGGT 59.003 37.500 12.56 0.00 36.64 3.67
2732 2866 5.240121 AGCAGCAAATTAAGGTGAAATTGG 58.760 37.500 12.56 0.00 36.64 3.16
2733 2867 6.790285 AAGCAGCAAATTAAGGTGAAATTG 57.210 33.333 12.56 0.00 36.64 2.32
2734 2868 9.506018 AATTAAGCAGCAAATTAAGGTGAAATT 57.494 25.926 12.56 10.88 36.64 1.82
2735 2869 8.938906 CAATTAAGCAGCAAATTAAGGTGAAAT 58.061 29.630 12.56 6.89 36.64 2.17
2736 2870 7.930865 ACAATTAAGCAGCAAATTAAGGTGAAA 59.069 29.630 12.56 5.32 36.64 2.69
2737 2871 7.441017 ACAATTAAGCAGCAAATTAAGGTGAA 58.559 30.769 12.56 1.31 36.64 3.18
2738 2872 6.991938 ACAATTAAGCAGCAAATTAAGGTGA 58.008 32.000 12.56 0.00 36.64 4.02
2739 2873 8.931385 ATACAATTAAGCAGCAAATTAAGGTG 57.069 30.769 0.00 5.83 37.53 4.00
2815 2949 9.438291 CCGTGATTTGCTTTATAGTTTGATAAG 57.562 33.333 0.00 0.00 0.00 1.73
2816 2950 8.402472 CCCGTGATTTGCTTTATAGTTTGATAA 58.598 33.333 0.00 0.00 0.00 1.75
2817 2951 7.468084 GCCCGTGATTTGCTTTATAGTTTGATA 60.468 37.037 0.00 0.00 0.00 2.15
2818 2952 6.680378 GCCCGTGATTTGCTTTATAGTTTGAT 60.680 38.462 0.00 0.00 0.00 2.57
2819 2953 5.392595 GCCCGTGATTTGCTTTATAGTTTGA 60.393 40.000 0.00 0.00 0.00 2.69
2820 2954 4.798387 GCCCGTGATTTGCTTTATAGTTTG 59.202 41.667 0.00 0.00 0.00 2.93
2821 2955 4.461081 TGCCCGTGATTTGCTTTATAGTTT 59.539 37.500 0.00 0.00 0.00 2.66
2822 2956 4.013728 TGCCCGTGATTTGCTTTATAGTT 58.986 39.130 0.00 0.00 0.00 2.24
2823 2957 3.616219 TGCCCGTGATTTGCTTTATAGT 58.384 40.909 0.00 0.00 0.00 2.12
2824 2958 3.003689 CCTGCCCGTGATTTGCTTTATAG 59.996 47.826 0.00 0.00 0.00 1.31
2825 2959 2.948979 CCTGCCCGTGATTTGCTTTATA 59.051 45.455 0.00 0.00 0.00 0.98
2826 2960 1.750778 CCTGCCCGTGATTTGCTTTAT 59.249 47.619 0.00 0.00 0.00 1.40
2827 2961 1.173043 CCTGCCCGTGATTTGCTTTA 58.827 50.000 0.00 0.00 0.00 1.85
2828 2962 0.539438 TCCTGCCCGTGATTTGCTTT 60.539 50.000 0.00 0.00 0.00 3.51
2829 2963 0.323725 ATCCTGCCCGTGATTTGCTT 60.324 50.000 0.00 0.00 0.00 3.91
2830 2964 0.323725 AATCCTGCCCGTGATTTGCT 60.324 50.000 0.00 0.00 0.00 3.91
2831 2965 0.532115 AAATCCTGCCCGTGATTTGC 59.468 50.000 0.00 0.00 39.17 3.68
2832 2966 3.016736 ACTAAATCCTGCCCGTGATTTG 58.983 45.455 7.52 2.04 40.43 2.32
2833 2967 3.366052 ACTAAATCCTGCCCGTGATTT 57.634 42.857 0.00 0.00 42.28 2.17
2834 2968 4.497291 TTACTAAATCCTGCCCGTGATT 57.503 40.909 0.00 0.00 32.72 2.57
2835 2969 4.196971 GTTTACTAAATCCTGCCCGTGAT 58.803 43.478 0.00 0.00 0.00 3.06
2836 2970 3.008157 TGTTTACTAAATCCTGCCCGTGA 59.992 43.478 0.00 0.00 0.00 4.35
2837 2971 3.340034 TGTTTACTAAATCCTGCCCGTG 58.660 45.455 0.00 0.00 0.00 4.94
2838 2972 3.706600 TGTTTACTAAATCCTGCCCGT 57.293 42.857 0.00 0.00 0.00 5.28
2839 2973 5.576447 AAATGTTTACTAAATCCTGCCCG 57.424 39.130 0.00 0.00 0.00 6.13
2840 2974 9.313118 CAAATAAATGTTTACTAAATCCTGCCC 57.687 33.333 0.00 0.00 0.00 5.36
2841 2975 8.817100 GCAAATAAATGTTTACTAAATCCTGCC 58.183 33.333 0.00 0.00 0.00 4.85
2842 2976 9.364989 TGCAAATAAATGTTTACTAAATCCTGC 57.635 29.630 0.00 0.00 0.00 4.85
2848 2982 9.817809 TGGTTGTGCAAATAAATGTTTACTAAA 57.182 25.926 0.00 0.00 0.00 1.85
2849 2983 9.250624 GTGGTTGTGCAAATAAATGTTTACTAA 57.749 29.630 0.00 0.00 0.00 2.24
2850 2984 8.414003 TGTGGTTGTGCAAATAAATGTTTACTA 58.586 29.630 0.00 0.00 0.00 1.82
2851 2985 7.268586 TGTGGTTGTGCAAATAAATGTTTACT 58.731 30.769 0.00 0.00 0.00 2.24
2852 2986 7.470289 TGTGGTTGTGCAAATAAATGTTTAC 57.530 32.000 0.00 0.00 0.00 2.01
2853 2987 8.668510 AATGTGGTTGTGCAAATAAATGTTTA 57.331 26.923 0.00 0.00 0.00 2.01
2854 2988 7.565323 AATGTGGTTGTGCAAATAAATGTTT 57.435 28.000 0.00 0.00 0.00 2.83
2855 2989 8.668510 TTAATGTGGTTGTGCAAATAAATGTT 57.331 26.923 0.00 0.00 0.00 2.71
2856 2990 8.845413 ATTAATGTGGTTGTGCAAATAAATGT 57.155 26.923 0.00 0.00 0.00 2.71
2859 2993 9.376075 CCATATTAATGTGGTTGTGCAAATAAA 57.624 29.630 20.14 0.00 34.70 1.40
2860 2994 8.753133 TCCATATTAATGTGGTTGTGCAAATAA 58.247 29.630 25.34 4.40 39.73 1.40
2861 2995 8.298729 TCCATATTAATGTGGTTGTGCAAATA 57.701 30.769 25.34 4.85 39.73 1.40
2862 2996 7.180322 TCCATATTAATGTGGTTGTGCAAAT 57.820 32.000 25.34 0.00 39.73 2.32
2863 2997 6.596309 TCCATATTAATGTGGTTGTGCAAA 57.404 33.333 25.34 6.11 39.73 3.68
2864 2998 6.788598 ATCCATATTAATGTGGTTGTGCAA 57.211 33.333 25.34 9.41 39.73 4.08
2865 2999 6.016360 GCTATCCATATTAATGTGGTTGTGCA 60.016 38.462 25.34 10.03 39.73 4.57
2866 3000 6.207417 AGCTATCCATATTAATGTGGTTGTGC 59.793 38.462 25.34 22.77 39.73 4.57
2867 3001 7.750229 AGCTATCCATATTAATGTGGTTGTG 57.250 36.000 25.34 16.72 39.73 3.33
2876 3010 9.319143 GCTCGTGAATTAGCTATCCATATTAAT 57.681 33.333 0.00 0.00 35.80 1.40
2877 3011 8.703604 GCTCGTGAATTAGCTATCCATATTAA 57.296 34.615 0.00 0.00 35.80 1.40
2889 3023 9.622004 TTATAGTATGTTAGCTCGTGAATTAGC 57.378 33.333 0.00 0.00 39.08 3.09


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

AutoCloner maintained by Alex Coulton.