Multiple sequence alignment - TraesCS3D01G502300

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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 TraesCS3D01G502300 chr3D 100.000 2405 0 0 544 2948 590830688 590828284 0.000000e+00 4442.0
1 TraesCS3D01G502300 chr3D 80.058 1379 162 58 809 2128 590704391 590703067 0.000000e+00 918.0
2 TraesCS3D01G502300 chr3D 84.615 143 16 3 654 796 590707578 590707442 1.420000e-28 137.0
3 TraesCS3D01G502300 chr3D 100.000 32 0 0 1 32 590831231 590831200 3.170000e-05 60.2
4 TraesCS3D01G502300 chr3B 91.073 2274 100 33 544 2754 790784623 790782390 0.000000e+00 2979.0
5 TraesCS3D01G502300 chr3B 81.146 838 93 25 810 1605 790635557 790634743 1.940000e-171 612.0
6 TraesCS3D01G502300 chr3B 77.566 682 75 46 1455 2098 790569877 790569236 1.010000e-89 340.0
7 TraesCS3D01G502300 chr3B 79.796 490 61 15 985 1438 790571123 790570636 3.670000e-84 322.0
8 TraesCS3D01G502300 chr3B 80.603 464 47 13 1687 2128 790634688 790634246 4.740000e-83 318.0
9 TraesCS3D01G502300 chr3B 78.824 510 68 26 912 1383 790640583 790640076 1.030000e-79 307.0
10 TraesCS3D01G502300 chr3B 91.150 113 5 3 2018 2129 790569241 790569133 6.580000e-32 148.0
11 TraesCS3D01G502300 chr3A 90.287 1709 80 30 545 2203 721296882 721295210 0.000000e+00 2158.0
12 TraesCS3D01G502300 chr3A 79.680 1373 149 54 809 2112 721241601 721240290 0.000000e+00 870.0
13 TraesCS3D01G502300 chr3A 91.150 113 3 1 2642 2754 721295175 721295070 2.370000e-31 147.0
14 TraesCS3D01G502300 chr4A 81.481 162 29 1 2130 2291 619723158 619722998 6.630000e-27 132.0
15 TraesCS3D01G502300 chr4A 89.583 48 5 0 2130 2177 598331032 598330985 8.820000e-06 62.1
16 TraesCS3D01G502300 chr1D 82.993 147 24 1 2130 2276 42037314 42037459 6.630000e-27 132.0
17 TraesCS3D01G502300 chr2B 82.000 150 25 2 2129 2278 405747017 405747164 3.080000e-25 126.0
18 TraesCS3D01G502300 chr6D 81.633 147 26 1 2130 2276 83061776 83061921 1.440000e-23 121.0
19 TraesCS3D01G502300 chr6D 100.000 28 0 0 5 32 116863646 116863673 5.000000e-03 52.8
20 TraesCS3D01G502300 chr5B 81.208 149 23 4 2130 2276 692918130 692918275 6.680000e-22 115.0
21 TraesCS3D01G502300 chr4D 89.583 48 5 0 2130 2177 354820144 354820097 8.820000e-06 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 TraesCS3D01G502300 chr3D 590828284 590831231 2947 True 2251.1 4442 100.000000 1 2948 2 chr3D.!!$R2 2947
1 TraesCS3D01G502300 chr3D 590703067 590707578 4511 True 527.5 918 82.336500 654 2128 2 chr3D.!!$R1 1474
2 TraesCS3D01G502300 chr3B 790782390 790784623 2233 True 2979.0 2979 91.073000 544 2754 1 chr3B.!!$R2 2210
3 TraesCS3D01G502300 chr3B 790634246 790635557 1311 True 465.0 612 80.874500 810 2128 2 chr3B.!!$R4 1318
4 TraesCS3D01G502300 chr3B 790640076 790640583 507 True 307.0 307 78.824000 912 1383 1 chr3B.!!$R1 471
5 TraesCS3D01G502300 chr3B 790569133 790571123 1990 True 270.0 340 82.837333 985 2129 3 chr3B.!!$R3 1144
6 TraesCS3D01G502300 chr3A 721295070 721296882 1812 True 1152.5 2158 90.718500 545 2754 2 chr3A.!!$R2 2209
7 TraesCS3D01G502300 chr3A 721240290 721241601 1311 True 870.0 870 79.680000 809 2112 1 chr3A.!!$R1 1303

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
842 3935 0.107643 GGGGAGACAGCTAATGAGGC 59.892 60.0 0.0 0.0 0.0 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2763 6817 0.036875 GGGCACTCAACCTTGTAGCT 59.963 55.0 0.0 0.0 0.0 3.32 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
25 26 6.843069 AAAAGCATATGTGTTCACAAAACC 57.157 33.333 9.68 0.52 0.00 3.27
26 27 4.519540 AGCATATGTGTTCACAAAACCC 57.480 40.909 9.68 0.00 0.00 4.11
27 28 3.894427 AGCATATGTGTTCACAAAACCCA 59.106 39.130 9.68 0.00 0.00 4.51
28 29 3.987220 GCATATGTGTTCACAAAACCCAC 59.013 43.478 9.68 0.00 0.00 4.61
29 30 4.261994 GCATATGTGTTCACAAAACCCACT 60.262 41.667 9.68 0.00 0.00 4.00
30 31 5.738783 GCATATGTGTTCACAAAACCCACTT 60.739 40.000 9.68 0.00 0.00 3.16
31 32 3.859411 TGTGTTCACAAAACCCACTTC 57.141 42.857 2.99 0.00 0.00 3.01
646 647 2.742116 GCCCCCTAGCGAATGGTCA 61.742 63.158 0.00 0.00 0.00 4.02
648 649 0.250467 CCCCCTAGCGAATGGTCATG 60.250 60.000 0.00 0.00 0.00 3.07
652 653 1.541233 CCTAGCGAATGGTCATGGGAC 60.541 57.143 0.00 0.00 43.55 4.46
841 3934 1.500474 TGGGGAGACAGCTAATGAGG 58.500 55.000 0.00 0.00 0.00 3.86
842 3935 0.107643 GGGGAGACAGCTAATGAGGC 59.892 60.000 0.00 0.00 0.00 4.70
843 3936 0.107643 GGGAGACAGCTAATGAGGCC 59.892 60.000 0.00 0.00 0.00 5.19
844 3937 1.127343 GGAGACAGCTAATGAGGCCT 58.873 55.000 3.86 3.86 0.00 5.19
845 3938 2.320781 GGAGACAGCTAATGAGGCCTA 58.679 52.381 4.42 0.00 0.00 3.93
848 3941 4.714308 GGAGACAGCTAATGAGGCCTATAT 59.286 45.833 4.42 0.00 0.00 0.86
849 3942 5.894393 GGAGACAGCTAATGAGGCCTATATA 59.106 44.000 4.42 0.00 0.00 0.86
850 3943 6.381420 GGAGACAGCTAATGAGGCCTATATAA 59.619 42.308 4.42 0.00 0.00 0.98
851 3944 7.093289 GGAGACAGCTAATGAGGCCTATATAAA 60.093 40.741 4.42 0.00 0.00 1.40
852 3945 8.386012 AGACAGCTAATGAGGCCTATATAAAT 57.614 34.615 4.42 0.00 0.00 1.40
853 3946 8.263640 AGACAGCTAATGAGGCCTATATAAATG 58.736 37.037 4.42 3.04 0.00 2.32
854 3947 7.922382 ACAGCTAATGAGGCCTATATAAATGT 58.078 34.615 4.42 3.76 0.00 2.71
855 3948 9.046846 ACAGCTAATGAGGCCTATATAAATGTA 57.953 33.333 4.42 0.00 0.00 2.29
856 3949 9.319143 CAGCTAATGAGGCCTATATAAATGTAC 57.681 37.037 4.42 0.00 0.00 2.90
857 3950 9.273137 AGCTAATGAGGCCTATATAAATGTACT 57.727 33.333 4.42 0.00 0.00 2.73
861 3954 7.729124 TGAGGCCTATATAAATGTACTACCC 57.271 40.000 4.42 0.00 0.00 3.69
898 3991 2.036346 GGTCTTGCCAAAATTGAGTGCT 59.964 45.455 0.00 0.00 37.17 4.40
1061 4160 6.036517 CCAAATCCAAACGAGAGAGAATACAG 59.963 42.308 0.00 0.00 0.00 2.74
1646 5568 1.237285 GGTGAGATGCCCACACACAC 61.237 60.000 0.00 0.00 36.31 3.82
1885 5833 1.532090 GCGACGTCTGTGATGAGTAGG 60.532 57.143 14.70 0.00 0.00 3.18
1980 5928 3.001838 TCTGTGTAAACGTGTGAACATGC 59.998 43.478 2.54 0.00 36.36 4.06
1981 5929 2.678336 TGTGTAAACGTGTGAACATGCA 59.322 40.909 2.54 0.00 36.36 3.96
1990 5960 4.142838 ACGTGTGAACATGCATGATTACTG 60.143 41.667 32.75 22.80 36.36 2.74
1993 5963 2.689471 TGAACATGCATGATTACTGCCC 59.311 45.455 32.75 8.06 38.89 5.36
2230 6276 5.175859 ACGTATTCAACACAGTATTCCTGG 58.824 41.667 0.00 0.00 46.06 4.45
2232 6278 3.788227 TTCAACACAGTATTCCTGGCT 57.212 42.857 0.00 0.00 46.06 4.75
2240 6286 3.898123 ACAGTATTCCTGGCTGTATCGAT 59.102 43.478 2.16 2.16 46.06 3.59
2263 6309 1.312815 GGAAAATGCGGGAGAGATGG 58.687 55.000 0.00 0.00 0.00 3.51
2291 6337 8.853230 ACATTTAATGTGACGGTGGTCGTTAAA 61.853 37.037 10.02 12.11 45.86 1.52
2298 6344 1.193874 CGGTGGTCGTTAAAGCAGTTC 59.806 52.381 0.00 0.00 0.00 3.01
2299 6345 1.534163 GGTGGTCGTTAAAGCAGTTCC 59.466 52.381 0.00 0.00 0.00 3.62
2315 6361 1.052124 TTCCGATGGCCCGTCCTTAT 61.052 55.000 0.00 0.00 35.26 1.73
2326 6372 1.687123 CCGTCCTTATCTTCCATCGGT 59.313 52.381 0.00 0.00 33.39 4.69
2378 6424 0.036732 AATCGCAGCTCCAAACCAGA 59.963 50.000 0.00 0.00 0.00 3.86
2392 6438 0.763223 ACCAGACTCCGGTTCAACCT 60.763 55.000 4.68 0.00 35.66 3.50
2412 6458 4.783621 GCCGCCATGACAGCCTCA 62.784 66.667 0.00 0.00 0.00 3.86
2414 6460 3.200593 CGCCATGACAGCCTCAGC 61.201 66.667 0.00 0.00 40.32 4.26
2431 6477 0.715987 AGCTTCTTCCTCCTCCTCCT 59.284 55.000 0.00 0.00 0.00 3.69
2477 6523 1.152963 CCCCCGGGACATGTTCATC 60.153 63.158 26.32 0.00 37.50 2.92
2533 6579 2.162681 CCCCCAGTTGAATCAGTTGAC 58.837 52.381 0.00 0.00 0.00 3.18
2541 6587 5.240183 CAGTTGAATCAGTTGACATTCCTGT 59.760 40.000 0.00 0.00 38.67 4.00
2548 6594 3.822735 CAGTTGACATTCCTGTTGTCCAT 59.177 43.478 1.73 0.00 42.25 3.41
2562 6608 1.067846 TGTCCATTCGTCAGGTTCGAG 60.068 52.381 0.00 0.00 38.52 4.04
2567 6613 2.163818 TTCGTCAGGTTCGAGCATTT 57.836 45.000 0.53 0.00 38.52 2.32
2593 6647 7.010771 AGTCCACCACATCAGTAGCTTATATA 58.989 38.462 0.00 0.00 0.00 0.86
2690 6744 2.601666 ACAGCACTCGCCTCCTCA 60.602 61.111 0.00 0.00 39.83 3.86
2691 6745 2.183811 CAGCACTCGCCTCCTCAG 59.816 66.667 0.00 0.00 39.83 3.35
2692 6746 2.283532 AGCACTCGCCTCCTCAGT 60.284 61.111 0.00 0.00 39.83 3.41
2693 6747 2.183046 GCACTCGCCTCCTCAGTC 59.817 66.667 0.00 0.00 0.00 3.51
2694 6748 2.888863 CACTCGCCTCCTCAGTCC 59.111 66.667 0.00 0.00 0.00 3.85
2695 6749 1.680651 CACTCGCCTCCTCAGTCCT 60.681 63.158 0.00 0.00 0.00 3.85
2696 6750 1.379309 ACTCGCCTCCTCAGTCCTC 60.379 63.158 0.00 0.00 0.00 3.71
2751 6805 1.457346 CCAAATTTGCTCGCTCTCCT 58.543 50.000 12.92 0.00 0.00 3.69
2754 6808 0.615331 AATTTGCTCGCTCTCCTCCA 59.385 50.000 0.00 0.00 0.00 3.86
2755 6809 0.835941 ATTTGCTCGCTCTCCTCCAT 59.164 50.000 0.00 0.00 0.00 3.41
2756 6810 1.485124 TTTGCTCGCTCTCCTCCATA 58.515 50.000 0.00 0.00 0.00 2.74
2757 6811 1.035923 TTGCTCGCTCTCCTCCATAG 58.964 55.000 0.00 0.00 0.00 2.23
2758 6812 1.288752 GCTCGCTCTCCTCCATAGC 59.711 63.158 0.00 0.00 0.00 2.97
2759 6813 1.963679 CTCGCTCTCCTCCATAGCC 59.036 63.158 0.00 0.00 32.50 3.93
2760 6814 0.539438 CTCGCTCTCCTCCATAGCCT 60.539 60.000 0.00 0.00 32.50 4.58
2761 6815 0.825425 TCGCTCTCCTCCATAGCCTG 60.825 60.000 0.00 0.00 32.50 4.85
2762 6816 1.370810 GCTCTCCTCCATAGCCTGC 59.629 63.158 0.00 0.00 0.00 4.85
2763 6817 1.406065 GCTCTCCTCCATAGCCTGCA 61.406 60.000 0.00 0.00 0.00 4.41
2764 6818 0.680618 CTCTCCTCCATAGCCTGCAG 59.319 60.000 6.78 6.78 0.00 4.41
2765 6819 1.071128 CTCCTCCATAGCCTGCAGC 59.929 63.158 8.66 3.91 44.25 5.25
2774 6828 4.404691 GCCTGCAGCTACAAGGTT 57.595 55.556 8.66 0.00 38.99 3.50
2775 6829 1.878775 GCCTGCAGCTACAAGGTTG 59.121 57.895 8.66 0.00 38.99 3.77
2776 6830 0.606401 GCCTGCAGCTACAAGGTTGA 60.606 55.000 8.66 0.00 38.99 3.18
2777 6831 1.446907 CCTGCAGCTACAAGGTTGAG 58.553 55.000 8.66 0.00 0.00 3.02
2778 6832 1.271054 CCTGCAGCTACAAGGTTGAGT 60.271 52.381 8.66 0.00 0.00 3.41
2779 6833 1.802960 CTGCAGCTACAAGGTTGAGTG 59.197 52.381 0.00 0.00 0.00 3.51
2780 6834 0.519077 GCAGCTACAAGGTTGAGTGC 59.481 55.000 0.00 0.00 0.00 4.40
2781 6835 1.160137 CAGCTACAAGGTTGAGTGCC 58.840 55.000 0.00 0.00 0.00 5.01
2782 6836 0.036875 AGCTACAAGGTTGAGTGCCC 59.963 55.000 0.00 0.00 0.00 5.36
2783 6837 1.298859 GCTACAAGGTTGAGTGCCCG 61.299 60.000 0.00 0.00 0.00 6.13
2784 6838 1.298859 CTACAAGGTTGAGTGCCCGC 61.299 60.000 0.00 0.00 0.00 6.13
2785 6839 2.046009 TACAAGGTTGAGTGCCCGCA 62.046 55.000 0.00 0.00 0.00 5.69
2786 6840 2.281761 AAGGTTGAGTGCCCGCAG 60.282 61.111 0.00 0.00 0.00 5.18
2799 6853 4.578913 CGCAGGTGAACGACTGAT 57.421 55.556 0.00 0.00 36.86 2.90
2800 6854 2.827604 CGCAGGTGAACGACTGATT 58.172 52.632 0.00 0.00 36.86 2.57
2801 6855 0.716108 CGCAGGTGAACGACTGATTC 59.284 55.000 0.00 0.00 36.86 2.52
2802 6856 1.795768 GCAGGTGAACGACTGATTCA 58.204 50.000 0.00 0.00 36.86 2.57
2817 6871 5.794726 CTGATTCACAGGATGATCTCTCT 57.205 43.478 0.00 0.00 42.39 3.10
2818 6872 5.532664 TGATTCACAGGATGATCTCTCTG 57.467 43.478 0.00 1.49 39.69 3.35
2819 6873 4.344390 TGATTCACAGGATGATCTCTCTGG 59.656 45.833 12.06 4.48 39.69 3.86
2820 6874 3.395054 TCACAGGATGATCTCTCTGGT 57.605 47.619 12.06 2.71 39.69 4.00
2821 6875 4.526438 TCACAGGATGATCTCTCTGGTA 57.474 45.455 12.06 1.04 39.69 3.25
2822 6876 4.871822 TCACAGGATGATCTCTCTGGTAA 58.128 43.478 12.06 0.00 39.69 2.85
2823 6877 5.462240 TCACAGGATGATCTCTCTGGTAAT 58.538 41.667 12.06 0.00 39.69 1.89
2824 6878 5.303845 TCACAGGATGATCTCTCTGGTAATG 59.696 44.000 12.06 4.40 39.69 1.90
2825 6879 4.040217 ACAGGATGATCTCTCTGGTAATGC 59.960 45.833 12.06 0.00 39.69 3.56
2826 6880 3.582208 AGGATGATCTCTCTGGTAATGCC 59.418 47.826 0.00 0.00 37.90 4.40
2827 6881 3.307339 GGATGATCTCTCTGGTAATGCCC 60.307 52.174 0.00 0.00 36.04 5.36
2828 6882 2.763039 TGATCTCTCTGGTAATGCCCA 58.237 47.619 0.00 0.00 36.04 5.36
2829 6883 3.114606 TGATCTCTCTGGTAATGCCCAA 58.885 45.455 0.00 0.00 33.07 4.12
2830 6884 3.135348 TGATCTCTCTGGTAATGCCCAAG 59.865 47.826 0.00 0.00 33.07 3.61
2831 6885 1.839994 TCTCTCTGGTAATGCCCAAGG 59.160 52.381 0.00 0.00 33.07 3.61
2832 6886 1.561542 CTCTCTGGTAATGCCCAAGGT 59.438 52.381 0.00 0.00 33.07 3.50
2833 6887 1.281867 TCTCTGGTAATGCCCAAGGTG 59.718 52.381 0.00 0.00 33.07 4.00
2834 6888 0.323360 TCTGGTAATGCCCAAGGTGC 60.323 55.000 0.00 0.00 33.07 5.01
2835 6889 1.304879 TGGTAATGCCCAAGGTGCC 60.305 57.895 0.00 0.00 36.04 5.01
2836 6890 2.058001 GGTAATGCCCAAGGTGCCC 61.058 63.158 0.00 0.00 0.00 5.36
2837 6891 1.304879 GTAATGCCCAAGGTGCCCA 60.305 57.895 0.00 0.00 0.00 5.36
2838 6892 1.304879 TAATGCCCAAGGTGCCCAC 60.305 57.895 0.00 0.00 0.00 4.61
2841 6895 4.338710 GCCCAAGGTGCCCACGTA 62.339 66.667 0.00 0.00 0.00 3.57
2842 6896 2.046314 CCCAAGGTGCCCACGTAG 60.046 66.667 0.00 0.00 0.00 3.51
2843 6897 2.589157 CCCAAGGTGCCCACGTAGA 61.589 63.158 0.00 0.00 0.00 2.59
2844 6898 1.373435 CCAAGGTGCCCACGTAGAA 59.627 57.895 0.00 0.00 0.00 2.10
2845 6899 0.953960 CCAAGGTGCCCACGTAGAAC 60.954 60.000 0.00 0.00 0.00 3.01
2846 6900 0.953960 CAAGGTGCCCACGTAGAACC 60.954 60.000 6.79 6.79 0.00 3.62
2847 6901 2.046604 GGTGCCCACGTAGAACCC 60.047 66.667 3.86 0.00 0.00 4.11
2848 6902 2.590114 GGTGCCCACGTAGAACCCT 61.590 63.158 3.86 0.00 0.00 4.34
2849 6903 1.375523 GTGCCCACGTAGAACCCTG 60.376 63.158 0.00 0.00 0.00 4.45
2850 6904 1.534476 TGCCCACGTAGAACCCTGA 60.534 57.895 0.00 0.00 0.00 3.86
2851 6905 1.218316 GCCCACGTAGAACCCTGAG 59.782 63.158 0.00 0.00 0.00 3.35
2852 6906 1.218316 CCCACGTAGAACCCTGAGC 59.782 63.158 0.00 0.00 0.00 4.26
2853 6907 1.541310 CCCACGTAGAACCCTGAGCA 61.541 60.000 0.00 0.00 0.00 4.26
2854 6908 0.537188 CCACGTAGAACCCTGAGCAT 59.463 55.000 0.00 0.00 0.00 3.79
2855 6909 1.471676 CCACGTAGAACCCTGAGCATC 60.472 57.143 0.00 0.00 0.00 3.91
2856 6910 1.478510 CACGTAGAACCCTGAGCATCT 59.521 52.381 0.00 0.00 34.92 2.90
2857 6911 1.751924 ACGTAGAACCCTGAGCATCTC 59.248 52.381 0.00 0.00 34.92 2.75
2858 6912 2.028130 CGTAGAACCCTGAGCATCTCT 58.972 52.381 0.00 0.00 34.92 3.10
2859 6913 2.428890 CGTAGAACCCTGAGCATCTCTT 59.571 50.000 0.00 0.00 34.92 2.85
2860 6914 3.632604 CGTAGAACCCTGAGCATCTCTTA 59.367 47.826 0.00 0.00 34.92 2.10
2861 6915 4.261405 CGTAGAACCCTGAGCATCTCTTAG 60.261 50.000 0.00 0.00 34.92 2.18
2862 6916 3.718723 AGAACCCTGAGCATCTCTTAGT 58.281 45.455 0.00 0.00 34.92 2.24
2863 6917 3.704061 AGAACCCTGAGCATCTCTTAGTC 59.296 47.826 0.00 0.00 34.92 2.59
2864 6918 2.393646 ACCCTGAGCATCTCTTAGTCC 58.606 52.381 0.00 0.00 34.92 3.85
2865 6919 2.292521 ACCCTGAGCATCTCTTAGTCCA 60.293 50.000 0.00 0.00 34.92 4.02
2866 6920 2.102252 CCCTGAGCATCTCTTAGTCCAC 59.898 54.545 0.00 0.00 34.92 4.02
2867 6921 2.762887 CCTGAGCATCTCTTAGTCCACA 59.237 50.000 0.00 0.00 34.92 4.17
2868 6922 3.181477 CCTGAGCATCTCTTAGTCCACAG 60.181 52.174 0.00 0.00 34.92 3.66
2869 6923 2.167281 TGAGCATCTCTTAGTCCACAGC 59.833 50.000 0.00 0.00 34.92 4.40
2870 6924 2.430332 GAGCATCTCTTAGTCCACAGCT 59.570 50.000 0.00 0.00 0.00 4.24
2871 6925 2.836981 AGCATCTCTTAGTCCACAGCTT 59.163 45.455 0.00 0.00 0.00 3.74
2872 6926 3.118811 AGCATCTCTTAGTCCACAGCTTC 60.119 47.826 0.00 0.00 0.00 3.86
2873 6927 3.368843 GCATCTCTTAGTCCACAGCTTCA 60.369 47.826 0.00 0.00 0.00 3.02
2874 6928 3.944055 TCTCTTAGTCCACAGCTTCAC 57.056 47.619 0.00 0.00 0.00 3.18
2875 6929 3.230976 TCTCTTAGTCCACAGCTTCACA 58.769 45.455 0.00 0.00 0.00 3.58
2876 6930 3.256879 TCTCTTAGTCCACAGCTTCACAG 59.743 47.826 0.00 0.00 0.00 3.66
2877 6931 2.965831 TCTTAGTCCACAGCTTCACAGT 59.034 45.455 0.00 0.00 0.00 3.55
2878 6932 2.820059 TAGTCCACAGCTTCACAGTG 57.180 50.000 0.00 0.00 35.64 3.66
2879 6933 0.833287 AGTCCACAGCTTCACAGTGT 59.167 50.000 0.00 0.00 34.12 3.55
2880 6934 0.940126 GTCCACAGCTTCACAGTGTG 59.060 55.000 17.53 17.53 41.09 3.82
2881 6935 0.815213 TCCACAGCTTCACAGTGTGC 60.815 55.000 18.80 7.19 40.26 4.57
2882 6936 1.650912 CACAGCTTCACAGTGTGCC 59.349 57.895 18.80 9.06 35.53 5.01
2883 6937 0.816825 CACAGCTTCACAGTGTGCCT 60.817 55.000 18.80 11.14 35.53 4.75
2884 6938 0.107017 ACAGCTTCACAGTGTGCCTT 60.107 50.000 18.80 1.22 32.98 4.35
2885 6939 1.027357 CAGCTTCACAGTGTGCCTTT 58.973 50.000 18.80 1.58 32.98 3.11
2886 6940 1.027357 AGCTTCACAGTGTGCCTTTG 58.973 50.000 18.80 7.29 32.98 2.77
2887 6941 0.595825 GCTTCACAGTGTGCCTTTGC 60.596 55.000 18.80 12.83 32.98 3.68
2888 6942 0.317269 CTTCACAGTGTGCCTTTGCG 60.317 55.000 18.80 0.00 41.78 4.85
2889 6943 1.723608 TTCACAGTGTGCCTTTGCGG 61.724 55.000 18.80 0.00 41.78 5.69
2890 6944 2.124320 ACAGTGTGCCTTTGCGGT 60.124 55.556 0.00 0.00 41.78 5.68
2891 6945 1.147376 ACAGTGTGCCTTTGCGGTA 59.853 52.632 0.00 0.00 41.78 4.02
2892 6946 0.250727 ACAGTGTGCCTTTGCGGTAT 60.251 50.000 0.00 0.00 41.78 2.73
2893 6947 0.881118 CAGTGTGCCTTTGCGGTATT 59.119 50.000 0.00 0.00 41.78 1.89
2894 6948 1.269448 CAGTGTGCCTTTGCGGTATTT 59.731 47.619 0.00 0.00 41.78 1.40
2895 6949 1.539827 AGTGTGCCTTTGCGGTATTTC 59.460 47.619 0.00 0.00 41.78 2.17
2896 6950 0.885196 TGTGCCTTTGCGGTATTTCC 59.115 50.000 0.00 0.00 41.78 3.13
2897 6951 1.173913 GTGCCTTTGCGGTATTTCCT 58.826 50.000 0.00 0.00 41.78 3.36
2898 6952 1.132453 GTGCCTTTGCGGTATTTCCTC 59.868 52.381 0.00 0.00 41.78 3.71
2899 6953 1.004277 TGCCTTTGCGGTATTTCCTCT 59.996 47.619 0.00 0.00 41.78 3.69
2900 6954 2.237643 TGCCTTTGCGGTATTTCCTCTA 59.762 45.455 0.00 0.00 41.78 2.43
2901 6955 2.872858 GCCTTTGCGGTATTTCCTCTAG 59.127 50.000 0.00 0.00 34.25 2.43
2902 6956 3.467803 CCTTTGCGGTATTTCCTCTAGG 58.532 50.000 0.00 0.00 0.00 3.02
2903 6957 3.118371 CCTTTGCGGTATTTCCTCTAGGT 60.118 47.826 0.00 0.00 36.34 3.08
2904 6958 4.514401 CTTTGCGGTATTTCCTCTAGGTT 58.486 43.478 0.00 0.00 36.34 3.50
2905 6959 3.814005 TGCGGTATTTCCTCTAGGTTC 57.186 47.619 0.00 0.00 36.34 3.62
2906 6960 3.101437 TGCGGTATTTCCTCTAGGTTCA 58.899 45.455 0.00 0.00 36.34 3.18
2907 6961 3.132289 TGCGGTATTTCCTCTAGGTTCAG 59.868 47.826 0.00 0.00 36.34 3.02
2908 6962 3.383825 GCGGTATTTCCTCTAGGTTCAGA 59.616 47.826 0.00 0.00 36.34 3.27
2909 6963 4.142004 GCGGTATTTCCTCTAGGTTCAGAA 60.142 45.833 0.00 0.00 36.34 3.02
2910 6964 5.349809 CGGTATTTCCTCTAGGTTCAGAAC 58.650 45.833 4.52 4.52 36.34 3.01
2911 6965 5.349809 GGTATTTCCTCTAGGTTCAGAACG 58.650 45.833 7.22 0.00 36.34 3.95
2912 6966 5.105432 GGTATTTCCTCTAGGTTCAGAACGT 60.105 44.000 12.94 12.94 36.34 3.99
2913 6967 4.516365 TTTCCTCTAGGTTCAGAACGTC 57.484 45.455 11.77 0.00 36.34 4.34
2914 6968 2.444421 TCCTCTAGGTTCAGAACGTCC 58.556 52.381 11.77 0.00 36.34 4.79
2915 6969 2.168496 CCTCTAGGTTCAGAACGTCCA 58.832 52.381 11.77 0.00 0.00 4.02
2916 6970 2.761208 CCTCTAGGTTCAGAACGTCCAT 59.239 50.000 11.77 0.00 0.00 3.41
2917 6971 3.195825 CCTCTAGGTTCAGAACGTCCATT 59.804 47.826 11.77 0.00 0.00 3.16
2918 6972 4.401519 CCTCTAGGTTCAGAACGTCCATTA 59.598 45.833 11.77 0.00 0.00 1.90
2919 6973 5.320549 TCTAGGTTCAGAACGTCCATTAC 57.679 43.478 11.77 0.00 0.00 1.89
2920 6974 3.329929 AGGTTCAGAACGTCCATTACC 57.670 47.619 7.22 0.00 0.00 2.85
2921 6975 2.904434 AGGTTCAGAACGTCCATTACCT 59.096 45.455 7.22 5.97 0.00 3.08
2922 6976 4.091549 AGGTTCAGAACGTCCATTACCTA 58.908 43.478 7.22 0.00 33.22 3.08
2923 6977 4.081807 AGGTTCAGAACGTCCATTACCTAC 60.082 45.833 7.22 0.00 33.22 3.18
2924 6978 4.322198 GGTTCAGAACGTCCATTACCTACA 60.322 45.833 7.22 0.00 0.00 2.74
2925 6979 5.416947 GTTCAGAACGTCCATTACCTACAT 58.583 41.667 0.00 0.00 0.00 2.29
2926 6980 5.006153 TCAGAACGTCCATTACCTACATG 57.994 43.478 0.00 0.00 0.00 3.21
2927 6981 4.119862 CAGAACGTCCATTACCTACATGG 58.880 47.826 0.00 0.00 42.51 3.66
2928 6982 2.614829 ACGTCCATTACCTACATGGC 57.385 50.000 0.00 0.00 41.10 4.40
2929 6983 1.834896 ACGTCCATTACCTACATGGCA 59.165 47.619 0.00 0.00 41.10 4.92
2930 6984 2.237643 ACGTCCATTACCTACATGGCAA 59.762 45.455 0.00 0.00 41.10 4.52
2931 6985 3.275143 CGTCCATTACCTACATGGCAAA 58.725 45.455 0.00 0.00 41.10 3.68
2932 6986 3.064820 CGTCCATTACCTACATGGCAAAC 59.935 47.826 0.00 0.00 41.10 2.93
2933 6987 4.013728 GTCCATTACCTACATGGCAAACA 58.986 43.478 0.00 0.00 41.10 2.83
2934 6988 4.461081 GTCCATTACCTACATGGCAAACAA 59.539 41.667 0.00 0.00 41.10 2.83
2935 6989 5.127031 GTCCATTACCTACATGGCAAACAAT 59.873 40.000 0.00 0.00 41.10 2.71
2936 6990 6.320164 GTCCATTACCTACATGGCAAACAATA 59.680 38.462 0.00 0.00 41.10 1.90
2937 6991 6.892456 TCCATTACCTACATGGCAAACAATAA 59.108 34.615 0.00 0.00 41.10 1.40
2938 6992 7.397476 TCCATTACCTACATGGCAAACAATAAA 59.603 33.333 0.00 0.00 41.10 1.40
2939 6993 7.491048 CCATTACCTACATGGCAAACAATAAAC 59.509 37.037 0.00 0.00 40.22 2.01
2940 6994 5.054390 ACCTACATGGCAAACAATAAACG 57.946 39.130 0.00 0.00 40.22 3.60
2941 6995 4.082463 ACCTACATGGCAAACAATAAACGG 60.082 41.667 0.00 0.00 40.22 4.44
2942 6996 4.082463 CCTACATGGCAAACAATAAACGGT 60.082 41.667 0.00 0.00 0.00 4.83
2943 6997 5.124138 CCTACATGGCAAACAATAAACGGTA 59.876 40.000 0.00 0.00 0.00 4.02
2944 6998 5.455056 ACATGGCAAACAATAAACGGTAA 57.545 34.783 0.00 0.00 0.00 2.85
2945 6999 5.844004 ACATGGCAAACAATAAACGGTAAA 58.156 33.333 0.00 0.00 0.00 2.01
2946 7000 5.692654 ACATGGCAAACAATAAACGGTAAAC 59.307 36.000 0.00 0.00 0.00 2.01
2947 7001 5.258456 TGGCAAACAATAAACGGTAAACA 57.742 34.783 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 6.259829 GGGTTTTGTGAACACATATGCTTTTT 59.740 34.615 8.46 0.00 41.52 1.94
2 3 5.757808 GGGTTTTGTGAACACATATGCTTTT 59.242 36.000 8.46 0.00 41.52 2.27
3 4 5.163364 TGGGTTTTGTGAACACATATGCTTT 60.163 36.000 8.46 0.00 41.52 3.51
4 5 4.343526 TGGGTTTTGTGAACACATATGCTT 59.656 37.500 8.46 0.00 41.52 3.91
5 6 3.894427 TGGGTTTTGTGAACACATATGCT 59.106 39.130 8.46 0.00 41.52 3.79
6 7 3.987220 GTGGGTTTTGTGAACACATATGC 59.013 43.478 8.46 1.51 41.52 3.14
7 8 5.452078 AGTGGGTTTTGTGAACACATATG 57.548 39.130 8.46 0.00 41.52 1.78
8 9 6.084326 GAAGTGGGTTTTGTGAACACATAT 57.916 37.500 8.46 0.00 41.52 1.78
9 10 5.508200 GAAGTGGGTTTTGTGAACACATA 57.492 39.130 8.46 1.41 41.52 2.29
10 11 4.385358 GAAGTGGGTTTTGTGAACACAT 57.615 40.909 8.46 0.00 41.52 3.21
11 12 3.859411 GAAGTGGGTTTTGTGAACACA 57.141 42.857 3.39 3.39 39.98 3.72
634 635 1.199615 TGTCCCATGACCATTCGCTA 58.800 50.000 0.00 0.00 41.01 4.26
646 647 9.347240 CATTTATCTAAGAGAATGTTGTCCCAT 57.653 33.333 0.00 0.00 0.00 4.00
648 649 7.993183 TCCATTTATCTAAGAGAATGTTGTCCC 59.007 37.037 0.00 0.00 0.00 4.46
824 3917 0.107643 GGCCTCATTAGCTGTCTCCC 59.892 60.000 0.00 0.00 0.00 4.30
841 3934 7.179694 TGTCCAGGGTAGTACATTTATATAGGC 59.820 40.741 2.06 0.00 0.00 3.93
842 3935 8.660295 TGTCCAGGGTAGTACATTTATATAGG 57.340 38.462 2.06 0.00 0.00 2.57
848 3941 7.037873 ACAGATTTGTCCAGGGTAGTACATTTA 60.038 37.037 2.06 0.00 29.46 1.40
849 3942 6.180472 CAGATTTGTCCAGGGTAGTACATTT 58.820 40.000 2.06 0.00 0.00 2.32
850 3943 5.250774 ACAGATTTGTCCAGGGTAGTACATT 59.749 40.000 2.06 0.00 29.46 2.71
851 3944 4.783227 ACAGATTTGTCCAGGGTAGTACAT 59.217 41.667 2.06 0.00 29.46 2.29
852 3945 4.164981 ACAGATTTGTCCAGGGTAGTACA 58.835 43.478 2.06 0.00 29.46 2.90
853 3946 4.820894 ACAGATTTGTCCAGGGTAGTAC 57.179 45.455 0.00 0.00 29.46 2.73
854 3947 5.514136 CCAAACAGATTTGTCCAGGGTAGTA 60.514 44.000 0.00 0.00 43.23 1.82
855 3948 4.398319 CAAACAGATTTGTCCAGGGTAGT 58.602 43.478 0.00 0.00 40.39 2.73
856 3949 3.758554 CCAAACAGATTTGTCCAGGGTAG 59.241 47.826 0.00 0.00 43.23 3.18
857 3950 3.139397 ACCAAACAGATTTGTCCAGGGTA 59.861 43.478 0.00 0.00 43.23 3.69
858 3951 2.091333 ACCAAACAGATTTGTCCAGGGT 60.091 45.455 0.00 0.00 43.23 4.34
859 3952 2.558359 GACCAAACAGATTTGTCCAGGG 59.442 50.000 0.00 0.00 43.23 4.45
860 3953 3.490348 AGACCAAACAGATTTGTCCAGG 58.510 45.455 0.00 0.00 43.23 4.45
861 3954 4.794003 GCAAGACCAAACAGATTTGTCCAG 60.794 45.833 0.00 0.00 43.23 3.86
1061 4160 1.774639 TACGTCCGTGCTCTTGTTTC 58.225 50.000 1.98 0.00 0.00 2.78
1112 4228 0.686789 TTCCTAGCAGCAGAAGCACA 59.313 50.000 0.00 0.00 45.49 4.57
1173 4302 2.544486 GGCTTGGCAAAAACAGAGAGTG 60.544 50.000 0.00 0.00 0.00 3.51
1174 4303 1.683385 GGCTTGGCAAAAACAGAGAGT 59.317 47.619 0.00 0.00 0.00 3.24
1706 5632 3.181440 TGTGCAGGTCTCTGAAAGGAAAT 60.181 43.478 0.00 0.00 43.49 2.17
1824 5753 3.148340 GGGGTAAACGCCAGTACAG 57.852 57.895 11.06 0.00 46.98 2.74
1885 5833 2.092374 TGCGATGCTGCATTGTCTC 58.908 52.632 26.20 13.51 40.62 3.36
1980 5928 6.866480 ACAAATTAACTGGGCAGTAATCATG 58.134 36.000 0.00 0.00 41.58 3.07
1981 5929 8.466798 GTTACAAATTAACTGGGCAGTAATCAT 58.533 33.333 0.00 0.00 41.58 2.45
1990 5960 3.253921 ACCACGTTACAAATTAACTGGGC 59.746 43.478 12.92 0.00 33.77 5.36
1993 5963 7.743520 AAACAACCACGTTACAAATTAACTG 57.256 32.000 0.00 0.00 0.00 3.16
2129 6175 2.936498 TCGGGCTCAGAATCGAATTTTC 59.064 45.455 0.00 0.00 0.00 2.29
2230 6276 3.058639 GCATTTTCCAGGATCGATACAGC 60.059 47.826 10.99 0.00 0.00 4.40
2232 6278 3.130633 CGCATTTTCCAGGATCGATACA 58.869 45.455 10.99 0.00 0.00 2.29
2240 6286 0.253044 CTCTCCCGCATTTTCCAGGA 59.747 55.000 0.00 0.00 0.00 3.86
2291 6337 4.473520 CGGGCCATCGGAACTGCT 62.474 66.667 4.39 0.00 0.00 4.24
2298 6344 1.004918 GATAAGGACGGGCCATCGG 60.005 63.158 4.39 0.00 40.02 4.18
2299 6345 0.393077 AAGATAAGGACGGGCCATCG 59.607 55.000 4.39 1.48 40.02 3.84
2315 6361 1.201647 GACGAACTGACCGATGGAAGA 59.798 52.381 0.00 0.00 0.00 2.87
2326 6372 2.513259 GGTGTGGGGGACGAACTGA 61.513 63.158 0.00 0.00 0.00 3.41
2378 6424 2.030562 CGCAGGTTGAACCGGAGT 59.969 61.111 18.66 0.00 44.90 3.85
2412 6458 0.715987 AGGAGGAGGAGGAAGAAGCT 59.284 55.000 0.00 0.00 0.00 3.74
2414 6460 1.788229 GGAGGAGGAGGAGGAAGAAG 58.212 60.000 0.00 0.00 0.00 2.85
2419 6465 2.691779 GGACGGAGGAGGAGGAGGA 61.692 68.421 0.00 0.00 0.00 3.71
2420 6466 2.123640 GGACGGAGGAGGAGGAGG 60.124 72.222 0.00 0.00 0.00 4.30
2421 6467 2.123640 GGGACGGAGGAGGAGGAG 60.124 72.222 0.00 0.00 0.00 3.69
2422 6468 3.752167 GGGGACGGAGGAGGAGGA 61.752 72.222 0.00 0.00 0.00 3.71
2431 6477 2.283676 GGTGAGTCTGGGGACGGA 60.284 66.667 0.00 0.00 46.29 4.69
2477 6523 0.745845 CAGCAGAATCGGTTGAGGGG 60.746 60.000 0.00 0.00 0.00 4.79
2502 6548 4.528039 CTGGGGGCGGCATTGGAT 62.528 66.667 12.47 0.00 0.00 3.41
2508 6554 3.936772 GATTCAACTGGGGGCGGCA 62.937 63.158 12.47 0.00 0.00 5.69
2533 6579 3.073678 TGACGAATGGACAACAGGAATG 58.926 45.455 0.00 0.00 0.00 2.67
2541 6587 1.341852 TCGAACCTGACGAATGGACAA 59.658 47.619 0.00 0.00 36.84 3.18
2548 6594 2.163818 AAATGCTCGAACCTGACGAA 57.836 45.000 0.00 0.00 39.23 3.85
2562 6608 3.347216 ACTGATGTGGTGGACTAAATGC 58.653 45.455 0.00 0.00 0.00 3.56
2567 6613 3.101643 AGCTACTGATGTGGTGGACTA 57.898 47.619 0.00 0.00 0.00 2.59
2690 6744 2.963371 GCGAGTTCGGTGAGGACT 59.037 61.111 3.50 0.00 40.23 3.85
2757 6811 0.606401 TCAACCTTGTAGCTGCAGGC 60.606 55.000 17.12 7.98 42.19 4.85
2758 6812 1.271054 ACTCAACCTTGTAGCTGCAGG 60.271 52.381 17.12 15.27 0.00 4.85
2759 6813 1.802960 CACTCAACCTTGTAGCTGCAG 59.197 52.381 10.11 10.11 0.00 4.41
2760 6814 1.882912 CACTCAACCTTGTAGCTGCA 58.117 50.000 0.00 0.00 0.00 4.41
2761 6815 0.519077 GCACTCAACCTTGTAGCTGC 59.481 55.000 0.00 0.00 0.00 5.25
2762 6816 1.160137 GGCACTCAACCTTGTAGCTG 58.840 55.000 0.00 0.00 0.00 4.24
2763 6817 0.036875 GGGCACTCAACCTTGTAGCT 59.963 55.000 0.00 0.00 0.00 3.32
2764 6818 1.298859 CGGGCACTCAACCTTGTAGC 61.299 60.000 0.00 0.00 0.00 3.58
2765 6819 1.298859 GCGGGCACTCAACCTTGTAG 61.299 60.000 0.00 0.00 0.00 2.74
2766 6820 1.302192 GCGGGCACTCAACCTTGTA 60.302 57.895 0.00 0.00 0.00 2.41
2767 6821 2.594592 GCGGGCACTCAACCTTGT 60.595 61.111 0.00 0.00 0.00 3.16
2768 6822 2.594303 TGCGGGCACTCAACCTTG 60.594 61.111 0.00 0.00 0.00 3.61
2769 6823 2.281761 CTGCGGGCACTCAACCTT 60.282 61.111 0.00 0.00 0.00 3.50
2770 6824 4.335647 CCTGCGGGCACTCAACCT 62.336 66.667 0.00 0.00 0.00 3.50
2771 6825 4.643387 ACCTGCGGGCACTCAACC 62.643 66.667 12.89 0.00 35.63 3.77
2772 6826 3.357079 CACCTGCGGGCACTCAAC 61.357 66.667 12.89 0.00 35.63 3.18
2773 6827 3.113514 TTCACCTGCGGGCACTCAA 62.114 57.895 12.89 0.00 35.63 3.02
2774 6828 3.555324 TTCACCTGCGGGCACTCA 61.555 61.111 12.89 0.00 35.63 3.41
2775 6829 3.050275 GTTCACCTGCGGGCACTC 61.050 66.667 12.89 0.00 35.63 3.51
2776 6830 4.988598 CGTTCACCTGCGGGCACT 62.989 66.667 12.89 0.00 35.63 4.40
2777 6831 4.980805 TCGTTCACCTGCGGGCAC 62.981 66.667 12.89 5.20 35.63 5.01
2778 6832 4.980805 GTCGTTCACCTGCGGGCA 62.981 66.667 12.89 0.00 35.63 5.36
2779 6833 4.681978 AGTCGTTCACCTGCGGGC 62.682 66.667 12.89 0.00 35.63 6.13
2780 6834 2.507110 ATCAGTCGTTCACCTGCGGG 62.507 60.000 11.02 11.02 38.88 6.13
2781 6835 0.670546 AATCAGTCGTTCACCTGCGG 60.671 55.000 0.00 0.00 0.00 5.69
2782 6836 0.716108 GAATCAGTCGTTCACCTGCG 59.284 55.000 0.00 0.00 0.00 5.18
2783 6837 1.461127 GTGAATCAGTCGTTCACCTGC 59.539 52.381 7.56 0.00 46.03 4.85
2788 6842 3.258123 TCATCCTGTGAATCAGTCGTTCA 59.742 43.478 0.00 0.00 42.19 3.18
2789 6843 3.849911 TCATCCTGTGAATCAGTCGTTC 58.150 45.455 0.00 0.00 42.19 3.95
2790 6844 3.961480 TCATCCTGTGAATCAGTCGTT 57.039 42.857 0.00 0.00 42.19 3.85
2791 6845 3.703556 AGATCATCCTGTGAATCAGTCGT 59.296 43.478 0.00 0.00 40.97 4.34
2792 6846 4.037803 AGAGATCATCCTGTGAATCAGTCG 59.962 45.833 0.00 0.00 40.97 4.18
2793 6847 5.302568 AGAGAGATCATCCTGTGAATCAGTC 59.697 44.000 0.00 0.00 40.97 3.51
2794 6848 5.069383 CAGAGAGATCATCCTGTGAATCAGT 59.931 44.000 0.00 0.00 40.97 3.41
2795 6849 5.510009 CCAGAGAGATCATCCTGTGAATCAG 60.510 48.000 0.00 0.00 40.97 2.90
2796 6850 4.344390 CCAGAGAGATCATCCTGTGAATCA 59.656 45.833 0.00 0.00 40.97 2.57
2797 6851 4.344679 ACCAGAGAGATCATCCTGTGAATC 59.655 45.833 0.00 0.00 40.97 2.52
2798 6852 4.296912 ACCAGAGAGATCATCCTGTGAAT 58.703 43.478 0.00 0.00 40.97 2.57
2799 6853 3.717576 ACCAGAGAGATCATCCTGTGAA 58.282 45.455 0.00 0.00 40.97 3.18
2800 6854 3.395054 ACCAGAGAGATCATCCTGTGA 57.605 47.619 0.00 0.00 42.06 3.58
2801 6855 5.539979 CATTACCAGAGAGATCATCCTGTG 58.460 45.833 0.00 0.00 0.00 3.66
2802 6856 4.040217 GCATTACCAGAGAGATCATCCTGT 59.960 45.833 0.00 0.00 0.00 4.00
2803 6857 4.563168 GGCATTACCAGAGAGATCATCCTG 60.563 50.000 0.00 0.00 38.86 3.86
2804 6858 3.582208 GGCATTACCAGAGAGATCATCCT 59.418 47.826 0.00 0.00 38.86 3.24
2805 6859 3.307339 GGGCATTACCAGAGAGATCATCC 60.307 52.174 0.00 0.00 42.05 3.51
2806 6860 3.326006 TGGGCATTACCAGAGAGATCATC 59.674 47.826 0.00 0.00 42.05 2.92
2807 6861 3.321039 TGGGCATTACCAGAGAGATCAT 58.679 45.455 0.00 0.00 42.05 2.45
2808 6862 2.763039 TGGGCATTACCAGAGAGATCA 58.237 47.619 0.00 0.00 42.05 2.92
2809 6863 3.495806 CCTTGGGCATTACCAGAGAGATC 60.496 52.174 0.00 0.00 42.47 2.75
2810 6864 2.441001 CCTTGGGCATTACCAGAGAGAT 59.559 50.000 0.00 0.00 42.47 2.75
2811 6865 1.839994 CCTTGGGCATTACCAGAGAGA 59.160 52.381 0.00 0.00 42.47 3.10
2812 6866 1.561542 ACCTTGGGCATTACCAGAGAG 59.438 52.381 0.00 0.00 42.47 3.20
2813 6867 1.281867 CACCTTGGGCATTACCAGAGA 59.718 52.381 0.00 0.00 42.47 3.10
2814 6868 1.755179 CACCTTGGGCATTACCAGAG 58.245 55.000 0.00 0.00 42.47 3.35
2815 6869 0.323360 GCACCTTGGGCATTACCAGA 60.323 55.000 0.00 0.00 42.47 3.86
2816 6870 1.322538 GGCACCTTGGGCATTACCAG 61.323 60.000 0.00 0.00 42.47 4.00
2817 6871 1.304879 GGCACCTTGGGCATTACCA 60.305 57.895 0.00 0.00 42.05 3.25
2818 6872 3.616086 GGCACCTTGGGCATTACC 58.384 61.111 0.00 0.00 30.93 2.85
2831 6885 1.375523 CAGGGTTCTACGTGGGCAC 60.376 63.158 0.00 0.00 0.00 5.01
2832 6886 1.534476 TCAGGGTTCTACGTGGGCA 60.534 57.895 0.00 0.00 0.00 5.36
2833 6887 1.218316 CTCAGGGTTCTACGTGGGC 59.782 63.158 0.00 0.00 0.00 5.36
2834 6888 1.218316 GCTCAGGGTTCTACGTGGG 59.782 63.158 0.00 0.00 0.00 4.61
2835 6889 0.537188 ATGCTCAGGGTTCTACGTGG 59.463 55.000 0.00 0.00 0.00 4.94
2836 6890 1.478510 AGATGCTCAGGGTTCTACGTG 59.521 52.381 0.00 0.00 0.00 4.49
2837 6891 1.751924 GAGATGCTCAGGGTTCTACGT 59.248 52.381 0.00 0.00 0.00 3.57
2838 6892 2.028130 AGAGATGCTCAGGGTTCTACG 58.972 52.381 0.00 0.00 32.06 3.51
2839 6893 4.647399 ACTAAGAGATGCTCAGGGTTCTAC 59.353 45.833 0.00 0.00 32.06 2.59
2840 6894 4.873010 ACTAAGAGATGCTCAGGGTTCTA 58.127 43.478 0.00 0.00 32.06 2.10
2841 6895 3.704061 GACTAAGAGATGCTCAGGGTTCT 59.296 47.826 0.00 0.00 32.06 3.01
2842 6896 3.181470 GGACTAAGAGATGCTCAGGGTTC 60.181 52.174 0.00 0.00 32.06 3.62
2843 6897 2.769095 GGACTAAGAGATGCTCAGGGTT 59.231 50.000 0.00 0.00 32.06 4.11
2844 6898 2.292521 TGGACTAAGAGATGCTCAGGGT 60.293 50.000 0.00 0.00 32.06 4.34
2845 6899 2.102252 GTGGACTAAGAGATGCTCAGGG 59.898 54.545 0.00 0.00 32.06 4.45
2846 6900 2.762887 TGTGGACTAAGAGATGCTCAGG 59.237 50.000 0.00 0.00 32.06 3.86
2847 6901 3.737663 GCTGTGGACTAAGAGATGCTCAG 60.738 52.174 0.00 0.00 32.06 3.35
2848 6902 2.167281 GCTGTGGACTAAGAGATGCTCA 59.833 50.000 0.00 0.00 32.06 4.26
2849 6903 2.430332 AGCTGTGGACTAAGAGATGCTC 59.570 50.000 0.00 0.00 0.00 4.26
2850 6904 2.465813 AGCTGTGGACTAAGAGATGCT 58.534 47.619 0.00 0.00 0.00 3.79
2851 6905 2.977772 AGCTGTGGACTAAGAGATGC 57.022 50.000 0.00 0.00 0.00 3.91
2852 6906 4.180057 GTGAAGCTGTGGACTAAGAGATG 58.820 47.826 0.00 0.00 0.00 2.90
2853 6907 3.834813 TGTGAAGCTGTGGACTAAGAGAT 59.165 43.478 0.00 0.00 0.00 2.75
2854 6908 3.230976 TGTGAAGCTGTGGACTAAGAGA 58.769 45.455 0.00 0.00 0.00 3.10
2855 6909 3.006323 ACTGTGAAGCTGTGGACTAAGAG 59.994 47.826 0.00 0.00 0.00 2.85
2856 6910 2.965831 ACTGTGAAGCTGTGGACTAAGA 59.034 45.455 0.00 0.00 0.00 2.10
2857 6911 3.062763 CACTGTGAAGCTGTGGACTAAG 58.937 50.000 0.32 0.00 41.50 2.18
2858 6912 2.434336 ACACTGTGAAGCTGTGGACTAA 59.566 45.455 15.86 0.00 46.95 2.24
2859 6913 2.039418 ACACTGTGAAGCTGTGGACTA 58.961 47.619 15.86 0.00 46.95 2.59
2860 6914 0.833287 ACACTGTGAAGCTGTGGACT 59.167 50.000 15.86 0.00 46.95 3.85
2861 6915 0.940126 CACACTGTGAAGCTGTGGAC 59.060 55.000 15.86 0.00 46.95 4.02
2862 6916 0.815213 GCACACTGTGAAGCTGTGGA 60.815 55.000 15.86 0.00 46.95 4.02
2863 6917 1.650912 GCACACTGTGAAGCTGTGG 59.349 57.895 15.86 0.00 46.95 4.17
2865 6919 0.107017 AAGGCACACTGTGAAGCTGT 60.107 50.000 15.86 7.09 35.23 4.40
2866 6920 1.027357 AAAGGCACACTGTGAAGCTG 58.973 50.000 15.86 3.18 35.23 4.24
2867 6921 1.027357 CAAAGGCACACTGTGAAGCT 58.973 50.000 15.86 5.66 36.45 3.74
2868 6922 0.595825 GCAAAGGCACACTGTGAAGC 60.596 55.000 15.86 16.71 36.45 3.86
2869 6923 0.317269 CGCAAAGGCACACTGTGAAG 60.317 55.000 15.86 7.67 36.45 3.02
2870 6924 1.723608 CCGCAAAGGCACACTGTGAA 61.724 55.000 15.86 0.00 36.45 3.18
2871 6925 2.186160 CCGCAAAGGCACACTGTGA 61.186 57.895 15.86 0.00 36.45 3.58
2872 6926 1.163420 TACCGCAAAGGCACACTGTG 61.163 55.000 6.19 6.19 46.52 3.66
2873 6927 0.250727 ATACCGCAAAGGCACACTGT 60.251 50.000 0.00 0.00 46.52 3.55
2874 6928 0.881118 AATACCGCAAAGGCACACTG 59.119 50.000 0.00 0.00 46.52 3.66
2875 6929 1.539827 GAAATACCGCAAAGGCACACT 59.460 47.619 0.00 0.00 46.52 3.55
2876 6930 1.402325 GGAAATACCGCAAAGGCACAC 60.402 52.381 0.00 0.00 46.52 3.82
2877 6931 0.885196 GGAAATACCGCAAAGGCACA 59.115 50.000 0.00 0.00 46.52 4.57
2878 6932 1.132453 GAGGAAATACCGCAAAGGCAC 59.868 52.381 0.00 0.00 46.52 5.01
2879 6933 1.004277 AGAGGAAATACCGCAAAGGCA 59.996 47.619 0.00 0.00 46.52 4.75
2880 6934 1.751437 AGAGGAAATACCGCAAAGGC 58.249 50.000 0.00 0.00 46.52 4.35
2881 6935 3.118371 ACCTAGAGGAAATACCGCAAAGG 60.118 47.826 1.60 0.00 43.79 3.11
2882 6936 4.138487 ACCTAGAGGAAATACCGCAAAG 57.862 45.455 1.60 0.00 44.74 2.77
2883 6937 4.020039 TGAACCTAGAGGAAATACCGCAAA 60.020 41.667 1.60 0.00 44.74 3.68
2884 6938 3.516300 TGAACCTAGAGGAAATACCGCAA 59.484 43.478 1.60 0.00 44.74 4.85
2885 6939 3.101437 TGAACCTAGAGGAAATACCGCA 58.899 45.455 1.60 0.00 44.74 5.69
2886 6940 3.383825 TCTGAACCTAGAGGAAATACCGC 59.616 47.826 1.60 0.00 44.74 5.68
2887 6941 5.349809 GTTCTGAACCTAGAGGAAATACCG 58.650 45.833 9.38 0.00 44.74 4.02
2888 6942 5.105432 ACGTTCTGAACCTAGAGGAAATACC 60.105 44.000 14.48 0.00 38.94 2.73
2889 6943 5.963594 ACGTTCTGAACCTAGAGGAAATAC 58.036 41.667 14.48 0.00 38.94 1.89
2890 6944 5.126707 GGACGTTCTGAACCTAGAGGAAATA 59.873 44.000 14.48 0.00 38.94 1.40
2891 6945 4.081586 GGACGTTCTGAACCTAGAGGAAAT 60.082 45.833 14.48 0.00 38.94 2.17
2892 6946 3.257624 GGACGTTCTGAACCTAGAGGAAA 59.742 47.826 14.48 0.00 38.94 3.13
2893 6947 2.824341 GGACGTTCTGAACCTAGAGGAA 59.176 50.000 14.48 0.00 38.94 3.36
2894 6948 2.224942 TGGACGTTCTGAACCTAGAGGA 60.225 50.000 14.48 0.00 38.94 3.71
2895 6949 2.168496 TGGACGTTCTGAACCTAGAGG 58.832 52.381 14.48 2.55 42.17 3.69
2896 6950 4.457834 AATGGACGTTCTGAACCTAGAG 57.542 45.455 14.48 3.23 0.00 2.43
2897 6951 4.159135 GGTAATGGACGTTCTGAACCTAGA 59.841 45.833 14.48 0.00 0.00 2.43
2898 6952 4.159879 AGGTAATGGACGTTCTGAACCTAG 59.840 45.833 14.48 3.92 34.40 3.02
2899 6953 4.091549 AGGTAATGGACGTTCTGAACCTA 58.908 43.478 14.48 0.55 34.40 3.08
2900 6954 2.904434 AGGTAATGGACGTTCTGAACCT 59.096 45.455 14.48 8.30 0.00 3.50
2901 6955 3.329929 AGGTAATGGACGTTCTGAACC 57.670 47.619 14.48 0.00 0.00 3.62
2902 6956 4.813027 TGTAGGTAATGGACGTTCTGAAC 58.187 43.478 10.48 10.48 0.00 3.18
2903 6957 5.416083 CATGTAGGTAATGGACGTTCTGAA 58.584 41.667 0.00 0.00 0.00 3.02
2904 6958 4.142026 CCATGTAGGTAATGGACGTTCTGA 60.142 45.833 0.00 0.00 46.44 3.27
2905 6959 4.119862 CCATGTAGGTAATGGACGTTCTG 58.880 47.826 0.00 0.00 46.44 3.02
2906 6960 3.431766 GCCATGTAGGTAATGGACGTTCT 60.432 47.826 6.63 0.00 46.44 3.01
2907 6961 2.870411 GCCATGTAGGTAATGGACGTTC 59.130 50.000 6.63 0.00 46.44 3.95
2908 6962 2.237643 TGCCATGTAGGTAATGGACGTT 59.762 45.455 6.63 0.00 46.44 3.99
2909 6963 1.834896 TGCCATGTAGGTAATGGACGT 59.165 47.619 6.63 0.00 46.44 4.34
2910 6964 2.613026 TGCCATGTAGGTAATGGACG 57.387 50.000 6.63 0.00 46.44 4.79
2911 6965 4.013728 TGTTTGCCATGTAGGTAATGGAC 58.986 43.478 6.63 0.00 46.44 4.02
2912 6966 4.308526 TGTTTGCCATGTAGGTAATGGA 57.691 40.909 6.63 0.00 46.44 3.41
2913 6967 5.596836 ATTGTTTGCCATGTAGGTAATGG 57.403 39.130 0.00 0.00 46.29 3.16
2914 6968 7.219917 CGTTTATTGTTTGCCATGTAGGTAATG 59.780 37.037 0.00 0.00 41.89 1.90
2915 6969 7.254852 CGTTTATTGTTTGCCATGTAGGTAAT 58.745 34.615 0.00 0.00 41.89 1.89
2916 6970 6.349445 CCGTTTATTGTTTGCCATGTAGGTAA 60.349 38.462 0.00 0.00 40.51 2.85
2917 6971 5.124138 CCGTTTATTGTTTGCCATGTAGGTA 59.876 40.000 0.00 0.00 40.61 3.08
2918 6972 4.082463 CCGTTTATTGTTTGCCATGTAGGT 60.082 41.667 0.00 0.00 40.61 3.08
2919 6973 4.082463 ACCGTTTATTGTTTGCCATGTAGG 60.082 41.667 0.00 0.00 41.84 3.18
2920 6974 5.054390 ACCGTTTATTGTTTGCCATGTAG 57.946 39.130 0.00 0.00 0.00 2.74
2921 6975 6.570672 TTACCGTTTATTGTTTGCCATGTA 57.429 33.333 0.00 0.00 0.00 2.29
2922 6976 5.455056 TTACCGTTTATTGTTTGCCATGT 57.545 34.783 0.00 0.00 0.00 3.21
2923 6977 5.692204 TGTTTACCGTTTATTGTTTGCCATG 59.308 36.000 0.00 0.00 0.00 3.66
2924 6978 5.844004 TGTTTACCGTTTATTGTTTGCCAT 58.156 33.333 0.00 0.00 0.00 4.40
2925 6979 5.258456 TGTTTACCGTTTATTGTTTGCCA 57.742 34.783 0.00 0.00 0.00 4.92


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

AutoCloner maintained by Alex Coulton.