Multiple sequence alignment - TraesCS2D01G193400

Loading Multiple Alignment...

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 TraesCS2D01G193400 chr2D 100.000 2846 0 0 1 2846 138517685 138514840 0.000000e+00 5256
1 TraesCS2D01G193400 chr2A 93.762 2693 83 29 1 2650 163096670 163099320 0.000000e+00 3964
2 TraesCS2D01G193400 chr2B 95.554 2294 70 13 373 2655 196542258 196539986 0.000000e+00 3642
3 TraesCS2D01G193400 chr2B 94.795 365 8 4 1 361 196543757 196543400 2.480000e-155 558
4 TraesCS2D01G193400 chr4D 82.500 200 34 1 1038 1237 51616881 51616683 1.050000e-39 174
5 TraesCS2D01G193400 chr4A 82.500 200 34 1 1038 1237 544953077 544953275 1.050000e-39 174


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 TraesCS2D01G193400 chr2D 138514840 138517685 2845 True 5256 5256 100.0000 1 2846 1 chr2D.!!$R1 2845
1 TraesCS2D01G193400 chr2A 163096670 163099320 2650 False 3964 3964 93.7620 1 2650 1 chr2A.!!$F1 2649
2 TraesCS2D01G193400 chr2B 196539986 196543757 3771 True 2100 3642 95.1745 1 2655 2 chr2B.!!$R1 2654

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
109 114 1.260544 AACAGAAAGCCAAGATGCCC 58.739 50.0 0.0 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2090 3252 0.973632 TAGTAGTGGTGGTGGTGCTG 59.026 55.0 0.0 0.0 0.0 4.41 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
109 114 1.260544 AACAGAAAGCCAAGATGCCC 58.739 50.000 0.00 0.00 0.00 5.36
265 274 3.162499 ACAAGAATTTGTGCGTGCG 57.838 47.368 0.00 0.00 45.54 5.34
338 347 4.795970 ATTCTTGGTTATAGCTTTCGCG 57.204 40.909 0.00 0.00 42.32 5.87
352 361 1.721664 TTCGCGAGGTATCCCGTCAG 61.722 60.000 9.59 0.00 35.12 3.51
424 1563 3.573772 TTGCGACTGCTCGGTCCAG 62.574 63.158 3.48 0.00 43.34 3.86
479 1618 2.626780 GCAAAAGCGGTGGAGGGTC 61.627 63.158 0.00 0.00 0.00 4.46
480 1619 1.971695 CAAAAGCGGTGGAGGGTCC 60.972 63.158 0.00 0.00 36.96 4.46
481 1620 2.457323 AAAAGCGGTGGAGGGTCCA 61.457 57.895 0.00 0.00 45.98 4.02
530 1669 9.045223 GGAGCAATTTTATTTTTGTGAGAAAGT 57.955 29.630 0.00 0.00 0.00 2.66
915 2055 1.614525 GTTACCTCCCGACCCCCTT 60.615 63.158 0.00 0.00 0.00 3.95
1405 2554 3.000819 ATCAACCCGGTGAGCGGA 61.001 61.111 26.22 4.36 0.00 5.54
2090 3252 4.617645 CGATAATAGTACCGCTGCTTTCTC 59.382 45.833 0.00 0.00 0.00 2.87
2102 3264 2.633860 CTTTCTCAGCACCACCACC 58.366 57.895 0.00 0.00 0.00 4.61
2219 3383 2.367241 TGCTAATACGCCATTGCTCCTA 59.633 45.455 0.00 0.00 34.43 2.94
2236 3400 4.528920 CTCCTACAGGCTACAGTACTCTT 58.471 47.826 0.00 0.00 34.44 2.85
2253 3417 7.384115 CAGTACTCTTCCGATTGTGTTTCTTTA 59.616 37.037 0.00 0.00 0.00 1.85
2668 3849 8.400947 GCATCAGCATATAGTATTGTTATTGGG 58.599 37.037 0.00 0.00 41.58 4.12
2669 3850 7.921786 TCAGCATATAGTATTGTTATTGGGC 57.078 36.000 0.00 0.00 0.00 5.36
2670 3851 7.689299 TCAGCATATAGTATTGTTATTGGGCT 58.311 34.615 0.00 0.00 0.00 5.19
2671 3852 8.163408 TCAGCATATAGTATTGTTATTGGGCTT 58.837 33.333 0.00 0.00 0.00 4.35
2672 3853 8.796475 CAGCATATAGTATTGTTATTGGGCTTT 58.204 33.333 0.00 0.00 0.00 3.51
2684 3865 9.743057 TTGTTATTGGGCTTTATTATTCATTCG 57.257 29.630 0.00 0.00 0.00 3.34
2685 3866 8.908903 TGTTATTGGGCTTTATTATTCATTCGT 58.091 29.630 0.00 0.00 0.00 3.85
2686 3867 9.744468 GTTATTGGGCTTTATTATTCATTCGTT 57.256 29.630 0.00 0.00 0.00 3.85
2687 3868 9.743057 TTATTGGGCTTTATTATTCATTCGTTG 57.257 29.630 0.00 0.00 0.00 4.10
2688 3869 6.142818 TGGGCTTTATTATTCATTCGTTGG 57.857 37.500 0.00 0.00 0.00 3.77
2689 3870 5.068460 TGGGCTTTATTATTCATTCGTTGGG 59.932 40.000 0.00 0.00 0.00 4.12
2690 3871 5.300792 GGGCTTTATTATTCATTCGTTGGGA 59.699 40.000 0.00 0.00 0.00 4.37
2691 3872 6.183360 GGGCTTTATTATTCATTCGTTGGGAA 60.183 38.462 0.00 0.00 39.42 3.97
2692 3873 7.262048 GGCTTTATTATTCATTCGTTGGGAAA 58.738 34.615 0.00 0.00 38.36 3.13
2693 3874 7.762159 GGCTTTATTATTCATTCGTTGGGAAAA 59.238 33.333 0.00 0.00 38.36 2.29
2694 3875 9.145865 GCTTTATTATTCATTCGTTGGGAAAAA 57.854 29.630 0.00 0.00 38.36 1.94
2709 3890 3.000815 AAAAACGAGAAGAGCGCCA 57.999 47.368 2.29 0.00 0.00 5.69
2710 3891 1.305201 AAAAACGAGAAGAGCGCCAA 58.695 45.000 2.29 0.00 0.00 4.52
2711 3892 1.305201 AAAACGAGAAGAGCGCCAAA 58.695 45.000 2.29 0.00 0.00 3.28
2712 3893 1.305201 AAACGAGAAGAGCGCCAAAA 58.695 45.000 2.29 0.00 0.00 2.44
2713 3894 0.586802 AACGAGAAGAGCGCCAAAAC 59.413 50.000 2.29 0.00 0.00 2.43
2714 3895 1.130613 CGAGAAGAGCGCCAAAACG 59.869 57.895 2.29 0.00 0.00 3.60
2715 3896 1.557443 CGAGAAGAGCGCCAAAACGT 61.557 55.000 2.29 0.00 34.88 3.99
2716 3897 0.586802 GAGAAGAGCGCCAAAACGTT 59.413 50.000 2.29 0.00 34.88 3.99
2717 3898 1.796459 GAGAAGAGCGCCAAAACGTTA 59.204 47.619 2.29 0.00 34.88 3.18
2718 3899 1.529865 AGAAGAGCGCCAAAACGTTAC 59.470 47.619 2.29 0.00 34.88 2.50
2719 3900 1.529865 GAAGAGCGCCAAAACGTTACT 59.470 47.619 2.29 0.00 34.88 2.24
2720 3901 2.443887 AGAGCGCCAAAACGTTACTA 57.556 45.000 2.29 0.00 34.88 1.82
2721 3902 2.334838 AGAGCGCCAAAACGTTACTAG 58.665 47.619 2.29 0.00 34.88 2.57
2722 3903 0.794473 AGCGCCAAAACGTTACTAGC 59.206 50.000 2.29 4.39 34.88 3.42
2723 3904 0.517742 GCGCCAAAACGTTACTAGCG 60.518 55.000 22.62 22.62 44.54 4.26
2724 3905 1.062258 CGCCAAAACGTTACTAGCGA 58.938 50.000 22.54 0.00 44.51 4.93
2725 3906 1.201736 CGCCAAAACGTTACTAGCGAC 60.202 52.381 22.54 0.52 44.51 5.19
2726 3907 1.127397 GCCAAAACGTTACTAGCGACC 59.873 52.381 0.00 0.00 0.00 4.79
2727 3908 1.387756 CCAAAACGTTACTAGCGACCG 59.612 52.381 0.00 0.00 0.00 4.79
2728 3909 1.387756 CAAAACGTTACTAGCGACCGG 59.612 52.381 0.00 0.00 0.00 5.28
2729 3910 0.598065 AAACGTTACTAGCGACCGGT 59.402 50.000 6.92 6.92 0.00 5.28
2730 3911 0.598065 AACGTTACTAGCGACCGGTT 59.402 50.000 9.42 0.00 0.00 4.44
2731 3912 0.109597 ACGTTACTAGCGACCGGTTG 60.110 55.000 18.24 18.24 0.00 3.77
2732 3913 0.109597 CGTTACTAGCGACCGGTTGT 60.110 55.000 22.97 12.16 35.91 3.32
2733 3914 1.666888 CGTTACTAGCGACCGGTTGTT 60.667 52.381 22.97 19.59 34.05 2.83
2734 3915 2.407090 GTTACTAGCGACCGGTTGTTT 58.593 47.619 22.97 13.93 34.05 2.83
2735 3916 2.802247 GTTACTAGCGACCGGTTGTTTT 59.198 45.455 22.97 11.54 34.05 2.43
2736 3917 1.505425 ACTAGCGACCGGTTGTTTTC 58.495 50.000 22.97 6.39 0.00 2.29
2737 3918 1.069668 ACTAGCGACCGGTTGTTTTCT 59.930 47.619 22.97 13.47 0.00 2.52
2738 3919 1.725164 CTAGCGACCGGTTGTTTTCTC 59.275 52.381 22.97 5.26 0.00 2.87
2739 3920 0.883370 AGCGACCGGTTGTTTTCTCC 60.883 55.000 22.97 4.53 0.00 3.71
2740 3921 0.883370 GCGACCGGTTGTTTTCTCCT 60.883 55.000 22.97 0.00 0.00 3.69
2741 3922 1.589803 CGACCGGTTGTTTTCTCCTT 58.410 50.000 9.42 0.00 0.00 3.36
2742 3923 1.263217 CGACCGGTTGTTTTCTCCTTG 59.737 52.381 9.42 0.00 0.00 3.61
2743 3924 2.567985 GACCGGTTGTTTTCTCCTTGA 58.432 47.619 9.42 0.00 0.00 3.02
2744 3925 2.946990 GACCGGTTGTTTTCTCCTTGAA 59.053 45.455 9.42 0.00 0.00 2.69
2745 3926 3.358118 ACCGGTTGTTTTCTCCTTGAAA 58.642 40.909 0.00 0.00 42.33 2.69
2765 3946 1.379527 AAAATCCCGAGCAATCGTCC 58.620 50.000 0.00 0.00 0.00 4.79
2766 3947 0.251916 AAATCCCGAGCAATCGTCCA 59.748 50.000 0.00 0.00 0.00 4.02
2767 3948 0.251916 AATCCCGAGCAATCGTCCAA 59.748 50.000 0.00 0.00 0.00 3.53
2768 3949 0.251916 ATCCCGAGCAATCGTCCAAA 59.748 50.000 0.00 0.00 0.00 3.28
2769 3950 0.035598 TCCCGAGCAATCGTCCAAAA 59.964 50.000 0.00 0.00 0.00 2.44
2770 3951 0.878416 CCCGAGCAATCGTCCAAAAA 59.122 50.000 0.00 0.00 0.00 1.94
2794 3975 4.390341 AGGGTGATCCTCCTCTGC 57.610 61.111 0.00 0.00 44.06 4.26
2795 3976 1.393746 AGGGTGATCCTCCTCTGCA 59.606 57.895 0.00 0.00 44.06 4.41
2796 3977 0.030297 AGGGTGATCCTCCTCTGCAT 60.030 55.000 0.00 0.00 44.06 3.96
2797 3978 0.108207 GGGTGATCCTCCTCTGCATG 59.892 60.000 0.00 0.00 0.00 4.06
2798 3979 0.534652 GGTGATCCTCCTCTGCATGC 60.535 60.000 11.82 11.82 0.00 4.06
2799 3980 0.534652 GTGATCCTCCTCTGCATGCC 60.535 60.000 16.68 0.00 0.00 4.40
2800 3981 0.984432 TGATCCTCCTCTGCATGCCA 60.984 55.000 16.68 0.00 0.00 4.92
2801 3982 0.534652 GATCCTCCTCTGCATGCCAC 60.535 60.000 16.68 0.00 0.00 5.01
2802 3983 2.321263 ATCCTCCTCTGCATGCCACG 62.321 60.000 16.68 3.68 0.00 4.94
2803 3984 3.200593 CTCCTCTGCATGCCACGC 61.201 66.667 16.68 0.00 0.00 5.34
2806 3987 4.156622 CTCTGCATGCCACGCGTG 62.157 66.667 31.77 31.77 46.98 5.34
2812 3993 4.451150 ATGCCACGCGTGATCCGT 62.451 61.111 39.10 23.63 39.91 4.69
2814 3995 4.796231 GCCACGCGTGATCCGTCT 62.796 66.667 39.10 0.00 36.69 4.18
2815 3996 2.579787 CCACGCGTGATCCGTCTC 60.580 66.667 39.10 0.00 36.69 3.36
2816 3997 2.579787 CACGCGTGATCCGTCTCC 60.580 66.667 34.93 0.00 36.69 3.71
2817 3998 2.750637 ACGCGTGATCCGTCTCCT 60.751 61.111 12.93 0.00 39.32 3.69
2818 3999 2.024871 CGCGTGATCCGTCTCCTC 59.975 66.667 0.00 0.00 39.32 3.71
2819 4000 2.024871 GCGTGATCCGTCTCCTCG 59.975 66.667 5.66 0.00 39.32 4.63
2820 4001 2.470362 GCGTGATCCGTCTCCTCGA 61.470 63.158 5.66 0.00 39.32 4.04
2821 4002 1.644372 CGTGATCCGTCTCCTCGAG 59.356 63.158 5.13 5.13 0.00 4.04
2822 4003 1.090625 CGTGATCCGTCTCCTCGAGT 61.091 60.000 12.31 0.00 0.00 4.18
2823 4004 1.805495 CGTGATCCGTCTCCTCGAGTA 60.805 57.143 12.31 0.00 0.00 2.59
2824 4005 1.868498 GTGATCCGTCTCCTCGAGTAG 59.132 57.143 12.31 4.95 0.00 2.57
2825 4006 1.761198 TGATCCGTCTCCTCGAGTAGA 59.239 52.381 12.31 7.79 0.00 2.59
2826 4007 2.369203 TGATCCGTCTCCTCGAGTAGAT 59.631 50.000 11.19 3.74 0.00 1.98
2827 4008 3.181453 TGATCCGTCTCCTCGAGTAGATT 60.181 47.826 11.19 0.00 0.00 2.40
2828 4009 3.278668 TCCGTCTCCTCGAGTAGATTT 57.721 47.619 11.19 0.00 0.00 2.17
2829 4010 3.204526 TCCGTCTCCTCGAGTAGATTTC 58.795 50.000 11.19 0.00 0.00 2.17
2830 4011 2.943690 CCGTCTCCTCGAGTAGATTTCA 59.056 50.000 11.19 0.00 0.00 2.69
2831 4012 3.566322 CCGTCTCCTCGAGTAGATTTCAT 59.434 47.826 11.19 0.00 0.00 2.57
2832 4013 4.532276 CGTCTCCTCGAGTAGATTTCATG 58.468 47.826 11.19 0.00 0.00 3.07
2833 4014 4.295051 GTCTCCTCGAGTAGATTTCATGC 58.705 47.826 11.19 0.00 0.00 4.06
2834 4015 3.003793 TCTCCTCGAGTAGATTTCATGCG 59.996 47.826 12.31 0.00 0.00 4.73
2835 4016 2.688446 TCCTCGAGTAGATTTCATGCGT 59.312 45.455 12.31 0.00 0.00 5.24
2836 4017 2.791560 CCTCGAGTAGATTTCATGCGTG 59.208 50.000 12.31 0.00 0.00 5.34
2837 4018 3.439293 CTCGAGTAGATTTCATGCGTGT 58.561 45.455 3.62 0.00 0.00 4.49
2838 4019 3.179048 TCGAGTAGATTTCATGCGTGTG 58.821 45.455 5.68 0.00 0.00 3.82
2839 4020 3.119637 TCGAGTAGATTTCATGCGTGTGA 60.120 43.478 5.68 0.00 0.00 3.58
2840 4021 3.798878 CGAGTAGATTTCATGCGTGTGAT 59.201 43.478 5.68 1.19 0.00 3.06
2841 4022 4.976116 CGAGTAGATTTCATGCGTGTGATA 59.024 41.667 5.68 0.00 0.00 2.15
2842 4023 5.458779 CGAGTAGATTTCATGCGTGTGATAA 59.541 40.000 5.68 0.00 0.00 1.75
2843 4024 6.144563 CGAGTAGATTTCATGCGTGTGATAAT 59.855 38.462 5.68 2.42 0.00 1.28
2844 4025 7.306807 CGAGTAGATTTCATGCGTGTGATAATT 60.307 37.037 5.68 0.00 0.00 1.40
2845 4026 8.213518 AGTAGATTTCATGCGTGTGATAATTT 57.786 30.769 5.68 1.15 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
109 114 0.031178 GAGTGGTGCAAGTTGCCAAG 59.969 55.000 24.59 0.00 44.23 3.61
113 118 2.186826 ACGGAGTGGTGCAAGTTGC 61.187 57.895 21.17 21.17 42.51 4.17
174 183 2.736995 CCTTTTCTCGTCGCCGCA 60.737 61.111 0.00 0.00 0.00 5.69
175 184 1.838568 AAACCTTTTCTCGTCGCCGC 61.839 55.000 0.00 0.00 0.00 6.53
176 185 0.110823 CAAACCTTTTCTCGTCGCCG 60.111 55.000 0.00 0.00 0.00 6.46
177 186 0.385598 GCAAACCTTTTCTCGTCGCC 60.386 55.000 0.00 0.00 0.00 5.54
178 187 0.306533 TGCAAACCTTTTCTCGTCGC 59.693 50.000 0.00 0.00 0.00 5.19
265 274 1.983605 CGTCGTCGCATATTATCACCC 59.016 52.381 0.00 0.00 0.00 4.61
363 372 9.787626 CGTTGTCCGTTTATGTGTATATTTATC 57.212 33.333 0.00 0.00 0.00 1.75
367 1506 7.830940 TTCGTTGTCCGTTTATGTGTATATT 57.169 32.000 0.00 0.00 37.94 1.28
371 1510 5.228665 TCATTCGTTGTCCGTTTATGTGTA 58.771 37.500 0.00 0.00 37.94 2.90
380 1519 1.375523 GGGCTCATTCGTTGTCCGT 60.376 57.895 0.00 0.00 37.94 4.69
424 1563 2.570181 GTGCAGCATCAAGGCCAC 59.430 61.111 5.01 0.00 0.00 5.01
458 1597 2.256461 CTCCACCGCTTTTGCTGC 59.744 61.111 0.00 0.00 44.80 5.25
479 1618 4.552365 AGGCGCATGGACGGATGG 62.552 66.667 10.83 0.00 0.00 3.51
480 1619 3.274586 CAGGCGCATGGACGGATG 61.275 66.667 15.54 0.00 0.00 3.51
481 1620 4.552365 CCAGGCGCATGGACGGAT 62.552 66.667 36.51 0.00 43.57 4.18
514 1653 7.093354 TGCACACAAACTTTCTCACAAAAATA 58.907 30.769 0.00 0.00 0.00 1.40
724 1863 2.668632 GATTGGACAGCGGGTGGA 59.331 61.111 12.33 0.00 0.00 4.02
907 2047 2.764547 CCGAGGAGGAAGGGGGTC 60.765 72.222 0.00 0.00 45.00 4.46
915 2055 2.798445 TAACCAGCAGCCGAGGAGGA 62.798 60.000 3.28 0.00 45.00 3.71
971 2117 1.539827 CAACCAACCCCGATCAAGAAC 59.460 52.381 0.00 0.00 0.00 3.01
1312 2461 2.798283 CAAACAGCATGCAAACTTCAGG 59.202 45.455 21.98 0.00 42.53 3.86
1548 2697 2.364317 CCCGCCTGGAAGAGGAGA 60.364 66.667 0.00 0.00 46.33 3.71
1787 2945 4.847444 GGGCTCCTTCTCGCCTGC 62.847 72.222 0.00 0.00 45.57 4.85
1788 2946 4.521062 CGGGCTCCTTCTCGCCTG 62.521 72.222 0.00 0.00 45.57 4.85
1789 2947 4.761058 TCGGGCTCCTTCTCGCCT 62.761 66.667 0.00 0.00 45.57 5.52
1804 2962 3.549299 ACAAAAAGATTCAGCAGCTCG 57.451 42.857 0.00 0.00 0.00 5.03
1929 3087 2.412089 CGAGAGGCTACCAAAAAGTTCG 59.588 50.000 0.00 0.00 0.00 3.95
2090 3252 0.973632 TAGTAGTGGTGGTGGTGCTG 59.026 55.000 0.00 0.00 0.00 4.41
2130 3292 4.948608 TCAGAGAGCTTTAGTGTACTCG 57.051 45.455 0.00 0.00 34.31 4.18
2219 3383 2.093106 CGGAAGAGTACTGTAGCCTGT 58.907 52.381 0.00 0.00 0.00 4.00
2236 3400 5.800296 TCTCCATAAAGAAACACAATCGGA 58.200 37.500 0.00 0.00 0.00 4.55
2253 3417 1.411977 CACGGAAGAGCAGATCTCCAT 59.588 52.381 0.00 0.00 42.90 3.41
2658 3839 9.743057 CGAATGAATAATAAAGCCCAATAACAA 57.257 29.630 0.00 0.00 0.00 2.83
2659 3840 8.908903 ACGAATGAATAATAAAGCCCAATAACA 58.091 29.630 0.00 0.00 0.00 2.41
2660 3841 9.744468 AACGAATGAATAATAAAGCCCAATAAC 57.256 29.630 0.00 0.00 0.00 1.89
2661 3842 9.743057 CAACGAATGAATAATAAAGCCCAATAA 57.257 29.630 0.00 0.00 0.00 1.40
2662 3843 8.356657 CCAACGAATGAATAATAAAGCCCAATA 58.643 33.333 0.00 0.00 0.00 1.90
2663 3844 7.209475 CCAACGAATGAATAATAAAGCCCAAT 58.791 34.615 0.00 0.00 0.00 3.16
2664 3845 6.406400 CCCAACGAATGAATAATAAAGCCCAA 60.406 38.462 0.00 0.00 0.00 4.12
2665 3846 5.068460 CCCAACGAATGAATAATAAAGCCCA 59.932 40.000 0.00 0.00 0.00 5.36
2666 3847 5.300792 TCCCAACGAATGAATAATAAAGCCC 59.699 40.000 0.00 0.00 0.00 5.19
2667 3848 6.385649 TCCCAACGAATGAATAATAAAGCC 57.614 37.500 0.00 0.00 0.00 4.35
2668 3849 8.696410 TTTTCCCAACGAATGAATAATAAAGC 57.304 30.769 0.00 0.00 0.00 3.51
2691 3872 1.305201 TTGGCGCTCTTCTCGTTTTT 58.695 45.000 7.64 0.00 0.00 1.94
2692 3873 1.305201 TTTGGCGCTCTTCTCGTTTT 58.695 45.000 7.64 0.00 0.00 2.43
2693 3874 1.002792 GTTTTGGCGCTCTTCTCGTTT 60.003 47.619 7.64 0.00 0.00 3.60
2694 3875 0.586802 GTTTTGGCGCTCTTCTCGTT 59.413 50.000 7.64 0.00 0.00 3.85
2695 3876 1.557443 CGTTTTGGCGCTCTTCTCGT 61.557 55.000 7.64 0.00 0.00 4.18
2696 3877 1.130613 CGTTTTGGCGCTCTTCTCG 59.869 57.895 7.64 2.11 0.00 4.04
2697 3878 0.586802 AACGTTTTGGCGCTCTTCTC 59.413 50.000 7.64 0.00 34.88 2.87
2698 3879 1.529865 GTAACGTTTTGGCGCTCTTCT 59.470 47.619 5.91 0.00 34.88 2.85
2699 3880 1.529865 AGTAACGTTTTGGCGCTCTTC 59.470 47.619 5.91 0.00 34.88 2.87
2700 3881 1.589803 AGTAACGTTTTGGCGCTCTT 58.410 45.000 5.91 0.00 34.88 2.85
2701 3882 2.334838 CTAGTAACGTTTTGGCGCTCT 58.665 47.619 5.91 0.00 34.88 4.09
2702 3883 1.201888 GCTAGTAACGTTTTGGCGCTC 60.202 52.381 5.91 0.00 34.88 5.03
2703 3884 0.794473 GCTAGTAACGTTTTGGCGCT 59.206 50.000 5.91 0.00 34.88 5.92
2704 3885 0.517742 CGCTAGTAACGTTTTGGCGC 60.518 55.000 22.70 0.00 35.13 6.53
2705 3886 1.062258 TCGCTAGTAACGTTTTGGCG 58.938 50.000 25.98 25.98 42.00 5.69
2706 3887 1.127397 GGTCGCTAGTAACGTTTTGGC 59.873 52.381 5.91 8.40 0.00 4.52
2707 3888 1.387756 CGGTCGCTAGTAACGTTTTGG 59.612 52.381 5.91 0.00 0.00 3.28
2708 3889 1.387756 CCGGTCGCTAGTAACGTTTTG 59.612 52.381 5.91 0.00 0.00 2.44
2709 3890 1.000274 ACCGGTCGCTAGTAACGTTTT 60.000 47.619 5.91 0.00 0.00 2.43
2710 3891 0.598065 ACCGGTCGCTAGTAACGTTT 59.402 50.000 5.91 0.00 0.00 3.60
2711 3892 0.598065 AACCGGTCGCTAGTAACGTT 59.402 50.000 8.04 5.88 0.00 3.99
2712 3893 0.109597 CAACCGGTCGCTAGTAACGT 60.110 55.000 8.04 0.00 0.00 3.99
2713 3894 0.109597 ACAACCGGTCGCTAGTAACG 60.110 55.000 8.04 0.00 0.00 3.18
2714 3895 2.070262 AACAACCGGTCGCTAGTAAC 57.930 50.000 8.04 0.00 0.00 2.50
2715 3896 2.818130 AAACAACCGGTCGCTAGTAA 57.182 45.000 8.04 0.00 0.00 2.24
2716 3897 2.297033 AGAAAACAACCGGTCGCTAGTA 59.703 45.455 8.04 0.00 0.00 1.82
2717 3898 1.069668 AGAAAACAACCGGTCGCTAGT 59.930 47.619 8.04 0.00 0.00 2.57
2718 3899 1.725164 GAGAAAACAACCGGTCGCTAG 59.275 52.381 8.04 0.00 0.00 3.42
2719 3900 1.606224 GGAGAAAACAACCGGTCGCTA 60.606 52.381 8.04 0.00 0.00 4.26
2720 3901 0.883370 GGAGAAAACAACCGGTCGCT 60.883 55.000 8.04 0.00 0.00 4.93
2721 3902 0.883370 AGGAGAAAACAACCGGTCGC 60.883 55.000 8.04 0.00 0.00 5.19
2722 3903 1.263217 CAAGGAGAAAACAACCGGTCG 59.737 52.381 8.04 0.00 0.00 4.79
2723 3904 2.567985 TCAAGGAGAAAACAACCGGTC 58.432 47.619 8.04 0.00 0.00 4.79
2724 3905 2.721425 TCAAGGAGAAAACAACCGGT 57.279 45.000 0.00 0.00 0.00 5.28
2778 3959 0.108207 CATGCAGAGGAGGATCACCC 59.892 60.000 0.00 0.00 36.25 4.61
2779 3960 0.534652 GCATGCAGAGGAGGATCACC 60.535 60.000 14.21 0.00 36.25 4.02
2780 3961 0.534652 GGCATGCAGAGGAGGATCAC 60.535 60.000 21.36 0.00 36.25 3.06
2781 3962 0.984432 TGGCATGCAGAGGAGGATCA 60.984 55.000 21.36 0.48 36.25 2.92
2782 3963 0.534652 GTGGCATGCAGAGGAGGATC 60.535 60.000 21.36 0.00 0.00 3.36
2783 3964 1.530771 GTGGCATGCAGAGGAGGAT 59.469 57.895 21.36 0.00 0.00 3.24
2784 3965 2.993008 GTGGCATGCAGAGGAGGA 59.007 61.111 21.36 0.00 0.00 3.71
2785 3966 2.513204 CGTGGCATGCAGAGGAGG 60.513 66.667 21.36 0.00 0.00 4.30
2786 3967 3.200593 GCGTGGCATGCAGAGGAG 61.201 66.667 26.05 5.30 0.00 3.69
2789 3970 4.156622 CACGCGTGGCATGCAGAG 62.157 66.667 31.15 16.63 0.00 3.35
2790 3971 3.956305 ATCACGCGTGGCATGCAGA 62.956 57.895 36.41 24.97 0.00 4.26
2791 3972 3.444717 GATCACGCGTGGCATGCAG 62.445 63.158 36.41 22.92 0.00 4.41
2792 3973 3.498834 GATCACGCGTGGCATGCA 61.499 61.111 36.41 18.59 0.00 3.96
2793 3974 4.241999 GGATCACGCGTGGCATGC 62.242 66.667 36.41 25.03 0.00 4.06
2794 3975 3.928769 CGGATCACGCGTGGCATG 61.929 66.667 36.41 21.12 34.82 4.06
2803 3984 1.090625 ACTCGAGGAGACGGATCACG 61.091 60.000 18.41 0.00 39.89 4.35
2804 3985 1.868498 CTACTCGAGGAGACGGATCAC 59.132 57.143 20.78 0.00 33.32 3.06
2805 3986 1.761198 TCTACTCGAGGAGACGGATCA 59.239 52.381 23.88 0.00 33.32 2.92
2806 3987 2.529780 TCTACTCGAGGAGACGGATC 57.470 55.000 23.88 0.00 33.32 3.36
2807 3988 3.495434 AATCTACTCGAGGAGACGGAT 57.505 47.619 29.59 11.24 33.32 4.18
2808 3989 3.204526 GAAATCTACTCGAGGAGACGGA 58.795 50.000 29.59 8.25 33.32 4.69
2809 3990 2.943690 TGAAATCTACTCGAGGAGACGG 59.056 50.000 29.59 1.85 33.32 4.79
2810 3991 4.532276 CATGAAATCTACTCGAGGAGACG 58.468 47.826 29.59 10.10 33.32 4.18
2811 3992 4.295051 GCATGAAATCTACTCGAGGAGAC 58.705 47.826 29.59 17.27 33.32 3.36
2812 3993 3.003793 CGCATGAAATCTACTCGAGGAGA 59.996 47.826 29.18 29.18 33.32 3.71
2813 3994 3.243234 ACGCATGAAATCTACTCGAGGAG 60.243 47.826 19.33 19.33 35.52 3.69
2814 3995 2.688446 ACGCATGAAATCTACTCGAGGA 59.312 45.455 18.41 7.44 0.00 3.71
2815 3996 2.791560 CACGCATGAAATCTACTCGAGG 59.208 50.000 18.41 0.00 0.00 4.63
2816 3997 3.241553 CACACGCATGAAATCTACTCGAG 59.758 47.826 11.84 11.84 0.00 4.04
2817 3998 3.119637 TCACACGCATGAAATCTACTCGA 60.120 43.478 0.00 0.00 0.00 4.04
2818 3999 3.179048 TCACACGCATGAAATCTACTCG 58.821 45.455 0.00 0.00 0.00 4.18
2819 4000 6.828502 TTATCACACGCATGAAATCTACTC 57.171 37.500 0.00 0.00 30.82 2.59
2820 4001 7.792374 AATTATCACACGCATGAAATCTACT 57.208 32.000 0.00 0.00 30.82 2.57


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

AutoCloner maintained by Alex Coulton.