Multiple sequence alignment - TraesCS4A01G010600

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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 TraesCS4A01G010600 chr4A 100.000 3375 0 0 1 3375 6015513 6018887 0.000000e+00 6233
1 TraesCS4A01G010600 chr4A 93.170 776 52 1 2 777 89439458 89438684 0.000000e+00 1138
2 TraesCS4A01G010600 chr4A 78.007 582 104 19 1004 1573 6009452 6010021 8.970000e-91 344
3 TraesCS4A01G010600 chr4B 92.691 1587 93 8 941 2517 579408987 579407414 0.000000e+00 2266
4 TraesCS4A01G010600 chr4B 84.340 811 69 32 2589 3375 579407185 579406409 0.000000e+00 741
5 TraesCS4A01G010600 chr4B 78.692 535 88 17 1049 1573 579433705 579433187 1.940000e-87 333
6 TraesCS4A01G010600 chr4D 91.597 1547 98 10 955 2489 463678026 463676500 0.000000e+00 2108
7 TraesCS4A01G010600 chr4D 91.500 1000 66 6 909 1905 463467229 463466246 0.000000e+00 1358
8 TraesCS4A01G010600 chr4D 89.605 481 37 5 1930 2410 463466140 463465673 1.730000e-167 599
9 TraesCS4A01G010600 chr4D 90.994 322 16 4 3059 3371 463464934 463464617 4.030000e-114 422
10 TraesCS4A01G010600 chr4D 92.262 168 9 2 2881 3048 463465154 463464991 5.630000e-58 235
11 TraesCS4A01G010600 chr5D 93.436 777 46 2 1 777 318819333 318818562 0.000000e+00 1147
12 TraesCS4A01G010600 chr5D 93.050 777 54 0 1 777 552035215 552034439 0.000000e+00 1136
13 TraesCS4A01G010600 chr5D 92.793 777 56 0 1 777 269338443 269339219 0.000000e+00 1125
14 TraesCS4A01G010600 chr5D 92.793 777 50 3 1 777 539720273 539721043 0.000000e+00 1120
15 TraesCS4A01G010600 chr2D 92.811 779 54 2 1 777 538955635 538954857 0.000000e+00 1127
16 TraesCS4A01G010600 chr2D 92.535 777 55 1 1 777 620189549 620190322 0.000000e+00 1110
17 TraesCS4A01G010600 chr6D 92.674 778 54 3 1 777 42087911 42087136 0.000000e+00 1118
18 TraesCS4A01G010600 chr1D 92.407 777 59 0 1 777 413350398 413351174 0.000000e+00 1109


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 TraesCS4A01G010600 chr4A 6015513 6018887 3374 False 6233.0 6233 100.00000 1 3375 1 chr4A.!!$F2 3374
1 TraesCS4A01G010600 chr4A 89438684 89439458 774 True 1138.0 1138 93.17000 2 777 1 chr4A.!!$R1 775
2 TraesCS4A01G010600 chr4A 6009452 6010021 569 False 344.0 344 78.00700 1004 1573 1 chr4A.!!$F1 569
3 TraesCS4A01G010600 chr4B 579406409 579408987 2578 True 1503.5 2266 88.51550 941 3375 2 chr4B.!!$R2 2434
4 TraesCS4A01G010600 chr4B 579433187 579433705 518 True 333.0 333 78.69200 1049 1573 1 chr4B.!!$R1 524
5 TraesCS4A01G010600 chr4D 463676500 463678026 1526 True 2108.0 2108 91.59700 955 2489 1 chr4D.!!$R1 1534
6 TraesCS4A01G010600 chr4D 463464617 463467229 2612 True 653.5 1358 91.09025 909 3371 4 chr4D.!!$R2 2462
7 TraesCS4A01G010600 chr5D 318818562 318819333 771 True 1147.0 1147 93.43600 1 777 1 chr5D.!!$R1 776
8 TraesCS4A01G010600 chr5D 552034439 552035215 776 True 1136.0 1136 93.05000 1 777 1 chr5D.!!$R2 776
9 TraesCS4A01G010600 chr5D 269338443 269339219 776 False 1125.0 1125 92.79300 1 777 1 chr5D.!!$F1 776
10 TraesCS4A01G010600 chr5D 539720273 539721043 770 False 1120.0 1120 92.79300 1 777 1 chr5D.!!$F2 776
11 TraesCS4A01G010600 chr2D 538954857 538955635 778 True 1127.0 1127 92.81100 1 777 1 chr2D.!!$R1 776
12 TraesCS4A01G010600 chr2D 620189549 620190322 773 False 1110.0 1110 92.53500 1 777 1 chr2D.!!$F1 776
13 TraesCS4A01G010600 chr6D 42087136 42087911 775 True 1118.0 1118 92.67400 1 777 1 chr6D.!!$R1 776
14 TraesCS4A01G010600 chr1D 413350398 413351174 776 False 1109.0 1109 92.40700 1 777 1 chr1D.!!$F1 776

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
906 909 0.164647 GCATTGACGTGTCTGTGCTC 59.835 55.0 17.08 0.0 37.54 4.26 F
934 938 0.179029 ATGCGGCTATAACCACCCAC 60.179 55.0 0.00 0.0 0.00 4.61 F
939 943 0.465642 GCTATAACCACCCACCCAGC 60.466 60.0 0.00 0.0 0.00 4.85 F
2239 2348 0.523072 CCGATGGTTTCAGGTGCTTG 59.477 55.0 0.00 0.0 0.00 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2220 2329 0.523072 CAAGCACCTGAAACCATCGG 59.477 55.000 0.0 0.0 0.00 4.18 R
2221 2330 0.523072 CCAAGCACCTGAAACCATCG 59.477 55.000 0.0 0.0 0.00 3.84 R
2335 2444 1.202940 GGGGACTTTTGAGAGGCAAGT 60.203 52.381 0.0 0.0 37.87 3.16 R
3080 3460 1.145819 GAGGCAGAGGATGGTGCTC 59.854 63.158 0.0 0.0 39.76 4.26 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
21 22 3.200483 GGTGAACTTTACTGTCAACGGT 58.800 45.455 0.00 0.00 39.18 4.83
56 57 4.847990 AAGGGTATTATTTGGGTGACGA 57.152 40.909 0.00 0.00 0.00 4.20
159 160 5.486526 CAAGAGAGTGCTAGAAAGGATGTT 58.513 41.667 0.00 0.00 0.00 2.71
219 220 3.884693 TCGTTCGGTATCCTGCTAATACA 59.115 43.478 6.20 0.00 32.35 2.29
324 325 2.565391 TCTGTACGATCAAGGCTTCCAA 59.435 45.455 0.00 0.00 0.00 3.53
335 336 0.897621 GGCTTCCAATTTCAGGGTGG 59.102 55.000 0.00 0.00 0.00 4.61
378 379 1.068610 GTAGCGGCAACATTTGAGCAA 60.069 47.619 1.45 0.00 37.98 3.91
567 570 8.828688 AACTATACTATTTATTTGGACGGCTC 57.171 34.615 0.00 0.00 0.00 4.70
668 671 3.083848 ATATGGGTCGGCGCGTTGA 62.084 57.895 8.43 2.59 0.00 3.18
697 700 6.210078 GTTGTCGACCCATATGAAAAACAAA 58.790 36.000 14.12 0.00 0.00 2.83
703 706 6.353404 ACCCATATGAAAAACAAAACGGAT 57.647 33.333 3.65 0.00 0.00 4.18
708 711 4.617808 TGAAAAACAAAACGGATGTCGA 57.382 36.364 0.00 0.00 42.43 4.20
770 773 0.885596 CGTTTGTTTAGGTCGGCCCA 60.886 55.000 0.08 0.00 34.66 5.36
777 780 0.619255 TTAGGTCGGCCCATTGGAGA 60.619 55.000 0.08 0.00 34.66 3.71
778 781 0.619255 TAGGTCGGCCCATTGGAGAA 60.619 55.000 0.08 0.00 34.66 2.87
779 782 1.749258 GGTCGGCCCATTGGAGAAC 60.749 63.158 3.62 0.00 0.00 3.01
780 783 1.749258 GTCGGCCCATTGGAGAACC 60.749 63.158 3.62 0.00 0.00 3.62
781 784 2.440247 CGGCCCATTGGAGAACCC 60.440 66.667 3.62 0.00 34.81 4.11
782 785 2.440247 GGCCCATTGGAGAACCCG 60.440 66.667 3.62 0.00 37.93 5.28
783 786 2.440247 GCCCATTGGAGAACCCGG 60.440 66.667 3.62 0.00 37.93 5.73
784 787 2.978946 GCCCATTGGAGAACCCGGA 61.979 63.158 0.73 0.00 37.93 5.14
785 788 1.224592 CCCATTGGAGAACCCGGAG 59.775 63.158 0.73 0.00 37.93 4.63
799 802 3.602104 CGGAGGGAGGTAGTGGTAA 57.398 57.895 0.00 0.00 0.00 2.85
800 803 1.109609 CGGAGGGAGGTAGTGGTAAC 58.890 60.000 0.00 0.00 0.00 2.50
817 820 4.865925 TGGTAACATAATTCGTCGTTCTGG 59.134 41.667 0.00 0.00 46.17 3.86
818 821 4.269363 GGTAACATAATTCGTCGTTCTGGG 59.731 45.833 0.00 0.00 0.00 4.45
819 822 2.277084 ACATAATTCGTCGTTCTGGGC 58.723 47.619 0.00 0.00 0.00 5.36
820 823 2.276201 CATAATTCGTCGTTCTGGGCA 58.724 47.619 0.00 0.00 0.00 5.36
821 824 2.004583 TAATTCGTCGTTCTGGGCAG 57.995 50.000 0.00 0.00 0.00 4.85
822 825 1.298859 AATTCGTCGTTCTGGGCAGC 61.299 55.000 0.00 0.00 0.00 5.25
823 826 4.717629 TCGTCGTTCTGGGCAGCG 62.718 66.667 0.00 0.00 0.00 5.18
835 838 4.865761 GCAGCGCGTCGGTCCATA 62.866 66.667 8.43 0.00 34.62 2.74
836 839 2.655364 CAGCGCGTCGGTCCATAG 60.655 66.667 8.43 0.00 34.62 2.23
837 840 4.570663 AGCGCGTCGGTCCATAGC 62.571 66.667 8.43 0.00 29.31 2.97
839 842 4.201679 CGCGTCGGTCCATAGCCA 62.202 66.667 0.00 0.00 0.00 4.75
840 843 2.185867 GCGTCGGTCCATAGCCAA 59.814 61.111 0.00 0.00 0.00 4.52
841 844 1.448893 GCGTCGGTCCATAGCCAAA 60.449 57.895 0.00 0.00 0.00 3.28
842 845 1.429148 GCGTCGGTCCATAGCCAAAG 61.429 60.000 0.00 0.00 0.00 2.77
843 846 1.429148 CGTCGGTCCATAGCCAAAGC 61.429 60.000 0.00 0.00 40.32 3.51
844 847 1.095807 GTCGGTCCATAGCCAAAGCC 61.096 60.000 0.00 0.00 41.25 4.35
845 848 1.077787 CGGTCCATAGCCAAAGCCA 60.078 57.895 0.00 0.00 41.25 4.75
846 849 0.466189 CGGTCCATAGCCAAAGCCAT 60.466 55.000 0.00 0.00 41.25 4.40
847 850 1.202758 CGGTCCATAGCCAAAGCCATA 60.203 52.381 0.00 0.00 41.25 2.74
848 851 2.230660 GGTCCATAGCCAAAGCCATAC 58.769 52.381 0.00 0.00 41.25 2.39
849 852 2.158608 GGTCCATAGCCAAAGCCATACT 60.159 50.000 0.00 0.00 41.25 2.12
850 853 3.555966 GTCCATAGCCAAAGCCATACTT 58.444 45.455 0.00 0.00 41.70 2.24
851 854 3.316308 GTCCATAGCCAAAGCCATACTTG 59.684 47.826 0.00 0.00 39.09 3.16
852 855 3.053693 TCCATAGCCAAAGCCATACTTGT 60.054 43.478 0.00 0.00 39.09 3.16
853 856 4.165180 TCCATAGCCAAAGCCATACTTGTA 59.835 41.667 0.00 0.00 39.09 2.41
854 857 4.275936 CCATAGCCAAAGCCATACTTGTAC 59.724 45.833 0.00 0.00 39.09 2.90
855 858 3.721087 AGCCAAAGCCATACTTGTACT 57.279 42.857 0.00 0.00 39.09 2.73
856 859 3.347216 AGCCAAAGCCATACTTGTACTG 58.653 45.455 0.00 0.00 39.09 2.74
857 860 3.081804 GCCAAAGCCATACTTGTACTGT 58.918 45.455 0.00 0.00 39.09 3.55
858 861 4.019681 AGCCAAAGCCATACTTGTACTGTA 60.020 41.667 0.00 0.00 39.09 2.74
859 862 4.094442 GCCAAAGCCATACTTGTACTGTAC 59.906 45.833 10.98 10.98 39.09 2.90
860 863 4.328983 CCAAAGCCATACTTGTACTGTACG 59.671 45.833 12.87 2.80 39.09 3.67
861 864 4.796038 AAGCCATACTTGTACTGTACGT 57.204 40.909 12.87 8.29 37.17 3.57
862 865 5.902613 AAGCCATACTTGTACTGTACGTA 57.097 39.130 12.87 10.04 37.17 3.57
863 866 5.240713 AGCCATACTTGTACTGTACGTAC 57.759 43.478 18.90 18.90 46.94 3.67
870 873 1.790696 GTACTGTACGTACGTGAGCG 58.209 55.000 30.25 17.12 39.15 5.03
871 874 1.390123 GTACTGTACGTACGTGAGCGA 59.610 52.381 30.25 14.01 39.15 4.93
872 875 0.441533 ACTGTACGTACGTGAGCGAG 59.558 55.000 30.25 18.60 42.00 5.03
873 876 0.717784 CTGTACGTACGTGAGCGAGA 59.282 55.000 30.25 7.96 42.00 4.04
874 877 0.717784 TGTACGTACGTGAGCGAGAG 59.282 55.000 30.25 0.00 42.00 3.20
888 891 0.926846 CGAGAGCCGAGAGAATTTGC 59.073 55.000 0.00 0.00 41.76 3.68
889 892 1.737029 CGAGAGCCGAGAGAATTTGCA 60.737 52.381 0.00 0.00 41.76 4.08
890 893 2.559440 GAGAGCCGAGAGAATTTGCAT 58.441 47.619 0.00 0.00 0.00 3.96
891 894 2.941720 GAGAGCCGAGAGAATTTGCATT 59.058 45.455 0.00 0.00 0.00 3.56
892 895 2.681848 AGAGCCGAGAGAATTTGCATTG 59.318 45.455 0.00 0.00 0.00 2.82
893 896 2.679837 GAGCCGAGAGAATTTGCATTGA 59.320 45.455 0.00 0.00 0.00 2.57
894 897 2.421424 AGCCGAGAGAATTTGCATTGAC 59.579 45.455 0.00 0.00 0.00 3.18
895 898 2.789092 GCCGAGAGAATTTGCATTGACG 60.789 50.000 0.00 0.00 0.00 4.35
896 899 2.416547 CCGAGAGAATTTGCATTGACGT 59.583 45.455 0.00 0.00 0.00 4.34
897 900 3.410850 CGAGAGAATTTGCATTGACGTG 58.589 45.455 0.00 0.00 0.00 4.49
898 901 3.120546 CGAGAGAATTTGCATTGACGTGT 60.121 43.478 0.00 0.00 0.00 4.49
899 902 4.398247 GAGAGAATTTGCATTGACGTGTC 58.602 43.478 0.00 0.00 0.00 3.67
900 903 4.067896 AGAGAATTTGCATTGACGTGTCT 58.932 39.130 0.00 0.00 0.00 3.41
901 904 4.083643 AGAGAATTTGCATTGACGTGTCTG 60.084 41.667 0.00 0.00 0.00 3.51
902 905 3.565482 AGAATTTGCATTGACGTGTCTGT 59.435 39.130 0.00 0.00 0.00 3.41
903 906 2.753989 TTTGCATTGACGTGTCTGTG 57.246 45.000 0.00 1.86 0.00 3.66
904 907 0.307453 TTGCATTGACGTGTCTGTGC 59.693 50.000 17.34 17.34 39.40 4.57
905 908 0.532640 TGCATTGACGTGTCTGTGCT 60.533 50.000 21.60 0.00 39.55 4.40
906 909 0.164647 GCATTGACGTGTCTGTGCTC 59.835 55.000 17.08 0.00 37.54 4.26
907 910 0.436150 CATTGACGTGTCTGTGCTCG 59.564 55.000 0.00 0.00 0.00 5.03
934 938 0.179029 ATGCGGCTATAACCACCCAC 60.179 55.000 0.00 0.00 0.00 4.61
936 940 1.147600 CGGCTATAACCACCCACCC 59.852 63.158 0.00 0.00 0.00 4.61
939 943 0.465642 GCTATAACCACCCACCCAGC 60.466 60.000 0.00 0.00 0.00 4.85
952 956 2.027625 CCCAGCTCGTCCGTTTCAC 61.028 63.158 0.00 0.00 0.00 3.18
957 963 1.773496 CTCGTCCGTTTCACTTCGC 59.227 57.895 0.00 0.00 0.00 4.70
968 977 1.446099 CACTTCGCCGCTCAAGCTA 60.446 57.895 0.00 0.00 39.32 3.32
1038 1047 1.685180 CCCGTGATGGAGTACCTCTCA 60.685 57.143 0.00 0.00 44.40 3.27
1134 1149 1.278127 ACCCAAACGATCCACTACTGG 59.722 52.381 0.00 0.00 39.23 4.00
1135 1150 1.406887 CCCAAACGATCCACTACTGGG 60.407 57.143 0.00 0.00 38.25 4.45
1136 1151 1.369625 CAAACGATCCACTACTGGGC 58.630 55.000 0.00 0.00 38.25 5.36
1137 1152 1.066143 CAAACGATCCACTACTGGGCT 60.066 52.381 0.00 0.00 38.25 5.19
1138 1153 0.824759 AACGATCCACTACTGGGCTC 59.175 55.000 0.00 0.00 38.25 4.70
1139 1154 1.043673 ACGATCCACTACTGGGCTCC 61.044 60.000 0.00 0.00 38.25 4.70
1283 1298 4.749310 CCTGCTCTGCTTCGGCGT 62.749 66.667 6.85 0.00 45.37 5.68
1485 1503 1.538204 CCCGTGGTGATATCCAACTCG 60.538 57.143 0.00 4.34 45.82 4.18
1503 1521 2.435059 GACCTGCTCAAGACGGCC 60.435 66.667 0.00 0.00 0.00 6.13
1664 1682 1.412343 GGACTTCCTGATCAGAGAGGC 59.588 57.143 24.62 20.70 0.00 4.70
1692 1710 4.114997 GCCCGTCCATTGTTGCCG 62.115 66.667 0.00 0.00 0.00 5.69
1716 1734 4.133820 TGCACCACCCTAATAATTGATCG 58.866 43.478 0.00 0.00 0.00 3.69
1757 1775 4.694509 ACTGAGCAGTGATCTTGTCAATTC 59.305 41.667 10.19 0.00 40.75 2.17
1800 1818 0.673437 GGGAGGAGAAGATCGAGCTG 59.327 60.000 2.80 0.00 0.00 4.24
1824 1842 2.570386 AGGCCATAACTGTAGGGACT 57.430 50.000 5.01 0.00 45.09 3.85
1861 1879 1.627864 GCCCTTGGAGCAGGTAAAAA 58.372 50.000 0.00 0.00 30.96 1.94
1870 1888 4.761739 TGGAGCAGGTAAAAATCTGAACAG 59.238 41.667 0.00 0.00 33.11 3.16
1878 1896 8.025445 CAGGTAAAAATCTGAACAGAATGAAGG 58.975 37.037 8.59 0.00 41.36 3.46
1928 2012 7.421530 TTCTGTTTCTGAAATACAGTAGTGC 57.578 36.000 17.31 0.00 45.86 4.40
1930 2014 6.989759 TCTGTTTCTGAAATACAGTAGTGCAA 59.010 34.615 17.31 0.03 45.86 4.08
1933 2017 7.066404 TGTTTCTGAAATACAGTAGTGCAACAA 59.934 33.333 6.06 0.00 45.86 2.83
1935 2019 7.561021 TCTGAAATACAGTAGTGCAACAAAA 57.439 32.000 0.00 0.00 45.86 2.44
1936 2020 8.165239 TCTGAAATACAGTAGTGCAACAAAAT 57.835 30.769 0.00 0.00 45.86 1.82
1937 2021 9.278978 TCTGAAATACAGTAGTGCAACAAAATA 57.721 29.630 0.00 0.00 45.86 1.40
1952 2057 8.547069 TGCAACAAAATATTCTGTTAACTTTGC 58.453 29.630 6.83 6.89 34.04 3.68
2175 2284 4.056740 TGCCACACTGTAATGCAAATTTG 58.943 39.130 14.03 14.03 0.00 2.32
2176 2285 4.202192 TGCCACACTGTAATGCAAATTTGA 60.202 37.500 22.31 7.50 0.00 2.69
2220 2329 2.670414 CTGCTTACTGCTAGTGTGCTTC 59.330 50.000 0.00 0.00 43.37 3.86
2221 2330 2.003301 GCTTACTGCTAGTGTGCTTCC 58.997 52.381 0.00 0.00 38.95 3.46
2239 2348 0.523072 CCGATGGTTTCAGGTGCTTG 59.477 55.000 0.00 0.00 0.00 4.01
2335 2444 2.486982 CGAGGTCGTCTTGGACTTCTTA 59.513 50.000 3.84 0.00 39.94 2.10
2435 2544 4.698780 CAGAGCATTCCTGAACTTGAATGA 59.301 41.667 14.51 0.00 46.89 2.57
2450 2559 5.476945 ACTTGAATGACCCCATACAAAGTTC 59.523 40.000 0.00 0.00 31.43 3.01
2464 2573 3.122297 CAAAGTTCGCAGGAATTTTGCA 58.878 40.909 13.97 0.00 46.10 4.08
2475 2584 6.696583 CGCAGGAATTTTGCAATACATATGAA 59.303 34.615 10.38 0.00 41.59 2.57
2506 2615 6.544197 TCCAAGTTGTTCAGTAATGTTGCTAA 59.456 34.615 1.45 0.00 0.00 3.09
2560 2865 2.645838 TATGATTCAGCCCTTGAGCC 57.354 50.000 0.00 0.00 37.07 4.70
2577 2882 1.308069 GCCGGAAGAATGCTTGCAGA 61.308 55.000 5.05 0.00 41.99 4.26
2581 2886 2.289002 CGGAAGAATGCTTGCAGATACC 59.711 50.000 5.71 0.00 41.99 2.73
2585 2890 3.539604 AGAATGCTTGCAGATACCTGTC 58.460 45.455 0.87 0.00 42.35 3.51
2586 2891 3.199508 AGAATGCTTGCAGATACCTGTCT 59.800 43.478 0.87 0.00 42.35 3.41
2588 2893 2.182827 TGCTTGCAGATACCTGTCTCT 58.817 47.619 0.00 0.00 42.35 3.10
2643 2948 3.096092 CAGTAGCAGAGAAGAACCCTCT 58.904 50.000 0.00 0.00 41.35 3.69
2649 2954 4.020662 AGCAGAGAAGAACCCTCTAAACTG 60.021 45.833 0.00 0.00 38.84 3.16
2660 2965 3.318017 CCTCTAAACTGTGACCTTGTCG 58.682 50.000 0.00 0.00 34.95 4.35
2666 2971 3.746045 ACTGTGACCTTGTCGTGTAAT 57.254 42.857 0.00 0.00 34.95 1.89
2669 2974 4.879545 ACTGTGACCTTGTCGTGTAATTTT 59.120 37.500 0.00 0.00 34.95 1.82
2677 2982 5.856455 CCTTGTCGTGTAATTTTTGTGGATC 59.144 40.000 0.00 0.00 0.00 3.36
2679 2984 5.996219 TGTCGTGTAATTTTTGTGGATCTG 58.004 37.500 0.00 0.00 0.00 2.90
2684 2989 8.286800 TCGTGTAATTTTTGTGGATCTGTTTAG 58.713 33.333 0.00 0.00 0.00 1.85
2690 2995 9.883142 AATTTTTGTGGATCTGTTTAGAAAACA 57.117 25.926 5.22 5.22 36.32 2.83
2703 3008 9.853921 CTGTTTAGAAAACATTTTTCATTGAGC 57.146 29.630 12.63 0.99 0.00 4.26
2704 3009 9.376075 TGTTTAGAAAACATTTTTCATTGAGCA 57.624 25.926 12.63 2.98 0.00 4.26
2709 3014 9.715121 AGAAAACATTTTTCATTGAGCATACAT 57.285 25.926 12.63 0.00 0.00 2.29
2710 3015 9.962759 GAAAACATTTTTCATTGAGCATACATC 57.037 29.630 6.53 0.00 0.00 3.06
2711 3016 9.491675 AAAACATTTTTCATTGAGCATACATCA 57.508 25.926 0.00 0.00 0.00 3.07
2723 3028 7.466746 TGAGCATACATCATACTATGTGCTA 57.533 36.000 9.82 0.53 38.56 3.49
2724 3029 7.542025 TGAGCATACATCATACTATGTGCTAG 58.458 38.462 9.82 0.00 38.56 3.42
2727 3032 4.543590 ACATCATACTATGTGCTAGCCC 57.456 45.455 13.29 0.00 38.65 5.19
2735 3056 4.999310 ACTATGTGCTAGCCCTACAGATA 58.001 43.478 13.29 0.54 0.00 1.98
2737 3058 5.654650 ACTATGTGCTAGCCCTACAGATATC 59.345 44.000 13.29 0.00 0.00 1.63
2739 3060 3.165875 GTGCTAGCCCTACAGATATCCA 58.834 50.000 13.29 0.00 0.00 3.41
2742 3063 4.044191 TGCTAGCCCTACAGATATCCAGTA 59.956 45.833 13.29 2.50 0.00 2.74
2743 3064 4.399934 GCTAGCCCTACAGATATCCAGTAC 59.600 50.000 2.29 0.00 0.00 2.73
2745 3066 2.094649 GCCCTACAGATATCCAGTACGC 60.095 54.545 0.00 2.63 0.00 4.42
2762 3083 4.577283 AGTACGCCTTTGCTTCTTAAAACA 59.423 37.500 0.00 0.00 34.43 2.83
2766 3087 6.508777 ACGCCTTTGCTTCTTAAAACAAATA 58.491 32.000 0.00 0.00 31.85 1.40
2767 3088 7.151976 ACGCCTTTGCTTCTTAAAACAAATAT 58.848 30.769 0.00 0.00 31.85 1.28
2768 3089 7.116233 ACGCCTTTGCTTCTTAAAACAAATATG 59.884 33.333 0.00 0.00 31.85 1.78
2769 3090 7.116233 CGCCTTTGCTTCTTAAAACAAATATGT 59.884 33.333 0.00 0.00 36.94 2.29
2770 3091 8.223100 GCCTTTGCTTCTTAAAACAAATATGTG 58.777 33.333 0.00 0.00 35.48 3.21
2772 3093 8.654230 TTTGCTTCTTAAAACAAATATGTGCA 57.346 26.923 0.00 0.00 40.46 4.57
2801 3124 4.113354 GCTGTAGTTAACTTCCATCCTCG 58.887 47.826 14.49 0.98 0.00 4.63
2802 3125 4.113354 CTGTAGTTAACTTCCATCCTCGC 58.887 47.826 14.49 0.00 0.00 5.03
2806 3129 2.930682 GTTAACTTCCATCCTCGCAGAC 59.069 50.000 0.00 0.00 0.00 3.51
2816 3139 0.532573 CCTCGCAGACTTAGAAGCCA 59.467 55.000 0.00 0.00 0.00 4.75
2822 3145 2.095008 GCAGACTTAGAAGCCAAAAGCC 60.095 50.000 0.00 0.00 45.47 4.35
2825 3148 3.760684 AGACTTAGAAGCCAAAAGCCATG 59.239 43.478 0.00 0.00 45.47 3.66
2837 3160 5.477510 CCAAAAGCCATGTGTTGCTTAATA 58.522 37.500 7.26 0.00 46.58 0.98
2845 3173 9.533253 AGCCATGTGTTGCTTAATATTTATTTC 57.467 29.630 0.00 0.00 32.94 2.17
2852 3180 7.984617 TGTTGCTTAATATTTATTTCCCCTTGC 59.015 33.333 0.00 0.00 0.00 4.01
2855 3183 9.077885 TGCTTAATATTTATTTCCCCTTGCTAG 57.922 33.333 0.00 0.00 0.00 3.42
2856 3184 9.078990 GCTTAATATTTATTTCCCCTTGCTAGT 57.921 33.333 0.00 0.00 0.00 2.57
2859 3187 5.598416 ATTTATTTCCCCTTGCTAGTTGC 57.402 39.130 0.00 0.00 43.25 4.17
2860 3188 2.907458 ATTTCCCCTTGCTAGTTGCT 57.093 45.000 0.00 0.00 43.37 3.91
2863 3191 3.281727 TTCCCCTTGCTAGTTGCTATG 57.718 47.619 0.00 0.00 43.37 2.23
2864 3192 2.196595 TCCCCTTGCTAGTTGCTATGT 58.803 47.619 0.00 0.00 43.37 2.29
2865 3193 2.092968 TCCCCTTGCTAGTTGCTATGTG 60.093 50.000 0.00 0.00 43.37 3.21
2871 3199 3.334691 TGCTAGTTGCTATGTGTGGAAC 58.665 45.455 0.00 0.00 43.37 3.62
2872 3200 3.244387 TGCTAGTTGCTATGTGTGGAACA 60.244 43.478 0.00 0.00 44.26 3.18
2873 3201 4.565444 TGCTAGTTGCTATGTGTGGAACAT 60.565 41.667 0.00 0.00 46.73 2.71
2915 3243 4.046462 CACAAGCAATCAACAAAGTGAGG 58.954 43.478 0.00 0.00 0.00 3.86
2968 3296 2.023673 CAGTCAAGCAGTTTGGTTCCA 58.976 47.619 0.00 0.00 35.69 3.53
3032 3366 1.802069 TTCGACATGCCGAATGACAA 58.198 45.000 13.10 0.00 42.74 3.18
3033 3367 1.075542 TCGACATGCCGAATGACAAC 58.924 50.000 0.10 0.00 38.72 3.32
3042 3376 3.181482 TGCCGAATGACAACACACATTTT 60.181 39.130 0.00 0.00 36.94 1.82
3043 3377 3.182173 GCCGAATGACAACACACATTTTG 59.818 43.478 0.00 0.00 36.94 2.44
3044 3378 4.605968 CCGAATGACAACACACATTTTGA 58.394 39.130 0.00 0.00 36.94 2.69
3080 3460 0.101399 ATTGCACGAGTCTAGCGAGG 59.899 55.000 0.00 0.00 0.00 4.63
3132 3512 0.250081 GGCGGAATCTCCTCATCCAC 60.250 60.000 0.00 0.00 33.30 4.02
3163 3543 4.803426 CGGTGAGCTCGTCAGGGC 62.803 72.222 9.64 0.00 46.47 5.19
3309 3698 1.475280 CGGAAGATGTTCAGGTACGGA 59.525 52.381 4.83 0.00 33.93 4.69
3357 3746 4.818546 ACAACATCTTCAGAAAGTCACCAG 59.181 41.667 0.00 0.00 33.95 4.00
3368 3757 2.332063 AGTCACCAGACCAAACTGTG 57.668 50.000 0.00 0.00 46.15 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 4.877378 ATACCCTTTGTCGTAGTTGTGA 57.123 40.909 0.00 0.00 0.00 3.58
159 160 1.317613 AAACATCAAAGGCACGCTCA 58.682 45.000 0.00 0.00 0.00 4.26
219 220 2.679837 CCATAGTTTCTGCGTGCTTCAT 59.320 45.455 0.00 0.00 0.00 2.57
293 294 2.956987 CGTACAGACGTTCCGGGT 59.043 61.111 0.00 0.00 44.31 5.28
321 322 2.539302 ACATTCCCACCCTGAAATTGG 58.461 47.619 0.00 0.00 0.00 3.16
324 325 2.899256 CACAACATTCCCACCCTGAAAT 59.101 45.455 0.00 0.00 0.00 2.17
335 336 2.644887 TGCTCAGGCACAACATTCC 58.355 52.632 0.00 0.00 44.28 3.01
452 453 1.531149 GGTTGTCAACATGAGTCCACG 59.469 52.381 17.29 0.00 0.00 4.94
637 640 0.468585 CCCATATGTGCAGGCATGGT 60.469 55.000 15.63 0.00 36.92 3.55
641 644 1.153188 CGACCCATATGTGCAGGCA 60.153 57.895 1.24 0.00 0.00 4.75
668 671 0.108520 ATATGGGTCGACAACGCGTT 60.109 50.000 20.79 20.79 43.53 4.84
674 677 6.392625 TTTGTTTTTCATATGGGTCGACAA 57.607 33.333 18.91 5.15 0.00 3.18
697 700 2.125512 GCCTGCTCGACATCCGTT 60.126 61.111 0.00 0.00 39.75 4.44
728 731 4.448732 GGCGATTTCATCTGCTTTTTGTTT 59.551 37.500 0.00 0.00 0.00 2.83
770 773 0.983378 CTCCCTCCGGGTTCTCCAAT 60.983 60.000 0.00 0.00 44.74 3.16
777 780 1.305887 CACTACCTCCCTCCGGGTT 60.306 63.158 0.00 0.00 44.74 4.11
778 781 2.363361 CACTACCTCCCTCCGGGT 59.637 66.667 0.00 0.00 44.74 5.28
779 782 1.941403 TACCACTACCTCCCTCCGGG 61.941 65.000 0.00 0.00 46.11 5.73
780 783 0.032813 TTACCACTACCTCCCTCCGG 60.033 60.000 0.00 0.00 0.00 5.14
781 784 1.109609 GTTACCACTACCTCCCTCCG 58.890 60.000 0.00 0.00 0.00 4.63
782 785 2.242882 TGTTACCACTACCTCCCTCC 57.757 55.000 0.00 0.00 0.00 4.30
783 786 6.496144 AATTATGTTACCACTACCTCCCTC 57.504 41.667 0.00 0.00 0.00 4.30
784 787 5.070047 CGAATTATGTTACCACTACCTCCCT 59.930 44.000 0.00 0.00 0.00 4.20
785 788 5.163374 ACGAATTATGTTACCACTACCTCCC 60.163 44.000 0.00 0.00 0.00 4.30
786 789 5.910614 ACGAATTATGTTACCACTACCTCC 58.089 41.667 0.00 0.00 0.00 4.30
787 790 5.684626 CGACGAATTATGTTACCACTACCTC 59.315 44.000 0.00 0.00 0.00 3.85
788 791 5.126061 ACGACGAATTATGTTACCACTACCT 59.874 40.000 0.00 0.00 0.00 3.08
789 792 5.343249 ACGACGAATTATGTTACCACTACC 58.657 41.667 0.00 0.00 0.00 3.18
790 793 6.749118 AGAACGACGAATTATGTTACCACTAC 59.251 38.462 0.00 0.00 0.00 2.73
791 794 6.748658 CAGAACGACGAATTATGTTACCACTA 59.251 38.462 0.00 0.00 0.00 2.74
792 795 5.575606 CAGAACGACGAATTATGTTACCACT 59.424 40.000 0.00 0.00 0.00 4.00
793 796 5.220340 CCAGAACGACGAATTATGTTACCAC 60.220 44.000 0.00 0.00 0.00 4.16
794 797 4.865925 CCAGAACGACGAATTATGTTACCA 59.134 41.667 0.00 0.00 0.00 3.25
795 798 4.269363 CCCAGAACGACGAATTATGTTACC 59.731 45.833 0.00 0.00 0.00 2.85
796 799 4.260091 GCCCAGAACGACGAATTATGTTAC 60.260 45.833 0.00 0.00 0.00 2.50
797 800 3.866910 GCCCAGAACGACGAATTATGTTA 59.133 43.478 0.00 0.00 0.00 2.41
798 801 2.676342 GCCCAGAACGACGAATTATGTT 59.324 45.455 0.00 0.00 0.00 2.71
799 802 2.277084 GCCCAGAACGACGAATTATGT 58.723 47.619 0.00 0.00 0.00 2.29
800 803 2.276201 TGCCCAGAACGACGAATTATG 58.724 47.619 0.00 0.00 0.00 1.90
801 804 2.550978 CTGCCCAGAACGACGAATTAT 58.449 47.619 0.00 0.00 0.00 1.28
802 805 2.004583 CTGCCCAGAACGACGAATTA 57.995 50.000 0.00 0.00 0.00 1.40
803 806 1.298859 GCTGCCCAGAACGACGAATT 61.299 55.000 0.00 0.00 0.00 2.17
804 807 1.741770 GCTGCCCAGAACGACGAAT 60.742 57.895 0.00 0.00 0.00 3.34
805 808 2.357034 GCTGCCCAGAACGACGAA 60.357 61.111 0.00 0.00 0.00 3.85
806 809 4.717629 CGCTGCCCAGAACGACGA 62.718 66.667 0.00 0.00 0.00 4.20
818 821 4.865761 TATGGACCGACGCGCTGC 62.866 66.667 5.73 0.00 0.00 5.25
819 822 2.655364 CTATGGACCGACGCGCTG 60.655 66.667 5.73 1.02 0.00 5.18
820 823 4.570663 GCTATGGACCGACGCGCT 62.571 66.667 5.73 0.00 0.00 5.92
822 825 3.709880 TTGGCTATGGACCGACGCG 62.710 63.158 3.53 3.53 0.00 6.01
823 826 1.429148 CTTTGGCTATGGACCGACGC 61.429 60.000 0.00 0.00 0.00 5.19
824 827 1.429148 GCTTTGGCTATGGACCGACG 61.429 60.000 0.00 0.00 35.22 5.12
825 828 1.095807 GGCTTTGGCTATGGACCGAC 61.096 60.000 0.00 0.00 38.73 4.79
826 829 1.223487 GGCTTTGGCTATGGACCGA 59.777 57.895 0.00 0.00 38.73 4.69
827 830 0.466189 ATGGCTTTGGCTATGGACCG 60.466 55.000 0.00 0.00 38.23 4.79
828 831 2.158608 AGTATGGCTTTGGCTATGGACC 60.159 50.000 0.00 0.00 39.92 4.46
829 832 3.214696 AGTATGGCTTTGGCTATGGAC 57.785 47.619 0.00 0.00 39.92 4.02
830 833 3.053693 ACAAGTATGGCTTTGGCTATGGA 60.054 43.478 0.00 0.00 39.92 3.41
831 834 3.290710 ACAAGTATGGCTTTGGCTATGG 58.709 45.455 0.00 0.00 39.92 2.74
832 835 5.008019 CAGTACAAGTATGGCTTTGGCTATG 59.992 44.000 0.00 0.00 39.92 2.23
833 836 5.126067 CAGTACAAGTATGGCTTTGGCTAT 58.874 41.667 0.00 0.00 42.28 2.97
834 837 4.019681 ACAGTACAAGTATGGCTTTGGCTA 60.020 41.667 0.00 0.00 38.73 3.93
835 838 3.244911 ACAGTACAAGTATGGCTTTGGCT 60.245 43.478 0.00 0.00 38.73 4.75
836 839 3.081804 ACAGTACAAGTATGGCTTTGGC 58.918 45.455 0.00 0.00 34.69 4.52
837 840 4.328983 CGTACAGTACAAGTATGGCTTTGG 59.671 45.833 11.37 0.00 34.69 3.28
838 841 4.927425 ACGTACAGTACAAGTATGGCTTTG 59.073 41.667 11.37 0.00 34.69 2.77
839 842 5.143376 ACGTACAGTACAAGTATGGCTTT 57.857 39.130 11.37 0.30 34.69 3.51
840 843 4.796038 ACGTACAGTACAAGTATGGCTT 57.204 40.909 11.37 0.56 38.08 4.35
852 855 1.655597 CTCGCTCACGTACGTACAGTA 59.344 52.381 22.34 11.03 41.18 2.74
853 856 0.441533 CTCGCTCACGTACGTACAGT 59.558 55.000 22.34 19.05 41.18 3.55
854 857 0.717784 TCTCGCTCACGTACGTACAG 59.282 55.000 22.34 19.74 41.18 2.74
855 858 0.717784 CTCTCGCTCACGTACGTACA 59.282 55.000 22.34 9.82 41.18 2.90
856 859 0.586010 GCTCTCGCTCACGTACGTAC 60.586 60.000 22.34 15.90 41.18 3.67
857 860 1.699656 GGCTCTCGCTCACGTACGTA 61.700 60.000 22.34 8.85 41.18 3.57
858 861 2.479650 GCTCTCGCTCACGTACGT 59.520 61.111 16.72 16.72 41.18 3.57
859 862 2.277373 GGCTCTCGCTCACGTACG 60.277 66.667 15.01 15.01 41.18 3.67
860 863 2.277373 CGGCTCTCGCTCACGTAC 60.277 66.667 0.00 0.00 41.18 3.67
861 864 2.435410 TCGGCTCTCGCTCACGTA 60.435 61.111 0.00 0.00 41.18 3.57
862 865 3.805307 CTCGGCTCTCGCTCACGT 61.805 66.667 0.00 0.00 41.18 4.49
863 866 3.447634 CTCTCGGCTCTCGCTCACG 62.448 68.421 0.00 0.00 39.05 4.35
864 867 1.649390 TTCTCTCGGCTCTCGCTCAC 61.649 60.000 0.00 0.00 39.05 3.51
865 868 0.749818 ATTCTCTCGGCTCTCGCTCA 60.750 55.000 0.00 0.00 39.05 4.26
866 869 0.383949 AATTCTCTCGGCTCTCGCTC 59.616 55.000 0.00 0.00 39.05 5.03
867 870 0.820871 AAATTCTCTCGGCTCTCGCT 59.179 50.000 0.00 0.00 39.05 4.93
868 871 0.926846 CAAATTCTCTCGGCTCTCGC 59.073 55.000 0.00 0.00 39.05 5.03
869 872 0.926846 GCAAATTCTCTCGGCTCTCG 59.073 55.000 0.00 0.00 40.90 4.04
870 873 2.015736 TGCAAATTCTCTCGGCTCTC 57.984 50.000 0.00 0.00 0.00 3.20
871 874 2.681848 CAATGCAAATTCTCTCGGCTCT 59.318 45.455 0.00 0.00 0.00 4.09
872 875 2.679837 TCAATGCAAATTCTCTCGGCTC 59.320 45.455 0.00 0.00 0.00 4.70
873 876 2.421424 GTCAATGCAAATTCTCTCGGCT 59.579 45.455 0.00 0.00 0.00 5.52
874 877 2.789092 CGTCAATGCAAATTCTCTCGGC 60.789 50.000 0.00 0.00 0.00 5.54
875 878 2.416547 ACGTCAATGCAAATTCTCTCGG 59.583 45.455 0.00 0.00 0.00 4.63
876 879 3.120546 ACACGTCAATGCAAATTCTCTCG 60.121 43.478 0.00 0.00 0.00 4.04
877 880 4.153117 AGACACGTCAATGCAAATTCTCTC 59.847 41.667 0.00 0.00 0.00 3.20
878 881 4.067896 AGACACGTCAATGCAAATTCTCT 58.932 39.130 0.00 0.00 0.00 3.10
879 882 4.153986 CAGACACGTCAATGCAAATTCTC 58.846 43.478 0.00 0.00 0.00 2.87
880 883 3.565482 ACAGACACGTCAATGCAAATTCT 59.435 39.130 0.00 0.00 0.00 2.40
881 884 3.665409 CACAGACACGTCAATGCAAATTC 59.335 43.478 0.00 0.00 0.00 2.17
882 885 3.631144 CACAGACACGTCAATGCAAATT 58.369 40.909 0.00 0.00 0.00 1.82
883 886 2.605338 GCACAGACACGTCAATGCAAAT 60.605 45.455 16.43 0.00 40.36 2.32
884 887 1.268488 GCACAGACACGTCAATGCAAA 60.268 47.619 16.43 0.00 40.36 3.68
885 888 0.307453 GCACAGACACGTCAATGCAA 59.693 50.000 16.43 0.00 40.36 4.08
886 889 0.532640 AGCACAGACACGTCAATGCA 60.533 50.000 20.88 0.00 41.96 3.96
887 890 0.164647 GAGCACAGACACGTCAATGC 59.835 55.000 14.49 14.49 40.70 3.56
888 891 0.436150 CGAGCACAGACACGTCAATG 59.564 55.000 0.00 0.00 0.00 2.82
889 892 1.284982 GCGAGCACAGACACGTCAAT 61.285 55.000 0.00 0.00 0.00 2.57
890 893 1.949133 GCGAGCACAGACACGTCAA 60.949 57.895 0.00 0.00 0.00 3.18
891 894 2.354656 GCGAGCACAGACACGTCA 60.355 61.111 0.00 0.00 0.00 4.35
892 895 3.106407 GGCGAGCACAGACACGTC 61.106 66.667 0.00 0.00 0.00 4.34
914 917 0.107831 TGGGTGGTTATAGCCGCATC 59.892 55.000 19.34 11.76 41.09 3.91
917 920 1.525306 GGTGGGTGGTTATAGCCGC 60.525 63.158 10.51 10.51 45.49 6.53
925 928 3.953775 CGAGCTGGGTGGGTGGTT 61.954 66.667 0.00 0.00 0.00 3.67
927 930 4.394712 GACGAGCTGGGTGGGTGG 62.395 72.222 0.00 0.00 0.00 4.61
934 938 2.027625 GTGAAACGGACGAGCTGGG 61.028 63.158 0.00 0.00 0.00 4.45
936 940 0.784778 GAAGTGAAACGGACGAGCTG 59.215 55.000 0.00 0.00 45.86 4.24
939 943 1.615107 GGCGAAGTGAAACGGACGAG 61.615 60.000 0.00 0.00 45.86 4.18
947 951 1.841663 GCTTGAGCGGCGAAGTGAAA 61.842 55.000 12.98 0.00 0.00 2.69
968 977 2.588877 GAGCACGTGCACCAGTGT 60.589 61.111 39.21 19.41 45.16 3.55
1104 1116 4.660938 GTTTGGGTCCCGCTGCCT 62.661 66.667 2.65 0.00 0.00 4.75
1485 1503 2.435059 GCCGTCTTGAGCAGGTCC 60.435 66.667 0.00 0.00 0.00 4.46
1608 1626 1.139095 CTGCCTCCGGTAGAACGAC 59.861 63.158 0.00 0.00 37.63 4.34
1679 1697 2.126346 GCAGCGGCAACAATGGAC 60.126 61.111 3.18 0.00 40.72 4.02
1692 1710 3.287222 TCAATTATTAGGGTGGTGCAGC 58.713 45.455 9.47 9.47 0.00 5.25
1699 1717 8.184192 GGCATTTATCGATCAATTATTAGGGTG 58.816 37.037 0.00 0.00 0.00 4.61
1702 1720 8.950210 ACTGGCATTTATCGATCAATTATTAGG 58.050 33.333 0.00 0.00 0.00 2.69
1757 1775 5.164233 TCTTATCACTGAAAAGTCTCTGCG 58.836 41.667 0.00 0.00 0.00 5.18
1800 1818 3.391296 TCCCTACAGTTATGGCCTTCATC 59.609 47.826 3.32 0.00 37.30 2.92
1824 1842 2.614481 GGGCGTAAGTTGGAACTCATCA 60.614 50.000 0.00 0.00 38.57 3.07
1861 1879 3.726557 TGCCCTTCATTCTGTTCAGAT 57.273 42.857 3.28 0.00 0.00 2.90
1870 1888 2.785679 CGTCGAATTTGCCCTTCATTC 58.214 47.619 0.00 0.00 0.00 2.67
1878 1896 2.202479 GGCTGCGTCGAATTTGCC 60.202 61.111 0.00 5.27 0.00 4.52
1928 2012 8.751335 ACGCAAAGTTAACAGAATATTTTGTTG 58.249 29.630 26.42 14.94 37.98 3.33
1930 2014 8.865590 AACGCAAAGTTAACAGAATATTTTGT 57.134 26.923 8.61 5.82 42.14 2.83
1933 2017 7.577979 TCGAACGCAAAGTTAACAGAATATTT 58.422 30.769 8.61 0.00 44.35 1.40
1935 2019 6.715344 TCGAACGCAAAGTTAACAGAATAT 57.285 33.333 8.61 0.00 44.35 1.28
1936 2020 6.588756 AGATCGAACGCAAAGTTAACAGAATA 59.411 34.615 8.61 0.00 44.35 1.75
1937 2021 5.408604 AGATCGAACGCAAAGTTAACAGAAT 59.591 36.000 8.61 0.00 44.35 2.40
1938 2022 4.748102 AGATCGAACGCAAAGTTAACAGAA 59.252 37.500 8.61 0.00 44.35 3.02
1952 2057 3.185188 CCTGCCATTCATAAGATCGAACG 59.815 47.826 0.00 0.00 0.00 3.95
2000 2105 3.838244 TCCAAAGGGAATATCTGGTCG 57.162 47.619 0.00 0.00 41.32 4.79
2144 2249 6.207614 TGCATTACAGTGTGGCAATTTTACTA 59.792 34.615 14.28 0.00 0.00 1.82
2145 2250 5.010516 TGCATTACAGTGTGGCAATTTTACT 59.989 36.000 14.28 0.00 0.00 2.24
2175 2284 2.501316 AGGGGGTTATGCTGCAATTTTC 59.499 45.455 6.36 0.00 0.00 2.29
2176 2285 2.236893 CAGGGGGTTATGCTGCAATTTT 59.763 45.455 6.36 0.00 0.00 1.82
2220 2329 0.523072 CAAGCACCTGAAACCATCGG 59.477 55.000 0.00 0.00 0.00 4.18
2221 2330 0.523072 CCAAGCACCTGAAACCATCG 59.477 55.000 0.00 0.00 0.00 3.84
2239 2348 1.909302 TCCAACCTCACATTCTCTCCC 59.091 52.381 0.00 0.00 0.00 4.30
2335 2444 1.202940 GGGGACTTTTGAGAGGCAAGT 60.203 52.381 0.00 0.00 37.87 3.16
2435 2544 1.613255 CCTGCGAACTTTGTATGGGGT 60.613 52.381 0.00 0.00 0.00 4.95
2450 2559 6.207928 TCATATGTATTGCAAAATTCCTGCG 58.792 36.000 1.71 0.00 42.97 5.18
2464 2573 8.752187 ACAACTTGGAGCATTTTCATATGTATT 58.248 29.630 1.90 0.00 0.00 1.89
2475 2584 6.040842 ACATTACTGAACAACTTGGAGCATTT 59.959 34.615 0.00 0.00 0.00 2.32
2506 2615 7.658261 ACAACATACTATAGTGTACGATGCAT 58.342 34.615 15.90 0.00 0.00 3.96
2535 2803 6.467677 GCTCAAGGGCTGAATCATATACTAA 58.532 40.000 0.00 0.00 32.17 2.24
2560 2865 2.289002 GGTATCTGCAAGCATTCTTCCG 59.711 50.000 0.00 0.00 0.00 4.30
2577 2882 2.324541 GGATCCAGCAGAGACAGGTAT 58.675 52.381 6.95 0.00 0.00 2.73
2581 2886 2.169978 TGAATGGATCCAGCAGAGACAG 59.830 50.000 21.33 0.00 0.00 3.51
2585 2890 1.767088 TCCTGAATGGATCCAGCAGAG 59.233 52.381 33.10 25.62 40.56 3.35
2586 2891 1.883678 TCCTGAATGGATCCAGCAGA 58.116 50.000 33.10 22.11 40.56 4.26
2606 2911 6.152154 TCTGCTACTGTACTTGTTATACTGCA 59.848 38.462 0.00 0.00 0.00 4.41
2613 2918 7.368833 GTTCTTCTCTGCTACTGTACTTGTTA 58.631 38.462 0.00 0.00 0.00 2.41
2614 2919 6.217294 GTTCTTCTCTGCTACTGTACTTGTT 58.783 40.000 0.00 0.00 0.00 2.83
2615 2920 5.279056 GGTTCTTCTCTGCTACTGTACTTGT 60.279 44.000 0.00 0.00 0.00 3.16
2643 2948 3.530265 ACACGACAAGGTCACAGTTTA 57.470 42.857 0.00 0.00 32.09 2.01
2649 2954 5.454232 CACAAAAATTACACGACAAGGTCAC 59.546 40.000 0.00 0.00 32.09 3.67
2660 2965 9.959749 TTCTAAACAGATCCACAAAAATTACAC 57.040 29.630 0.00 0.00 0.00 2.90
2666 2971 9.883142 AATGTTTTCTAAACAGATCCACAAAAA 57.117 25.926 10.34 0.00 33.18 1.94
2669 2974 9.883142 AAAAATGTTTTCTAAACAGATCCACAA 57.117 25.926 10.34 0.00 33.18 3.33
2677 2982 9.853921 GCTCAATGAAAAATGTTTTCTAAACAG 57.146 29.630 13.09 5.74 33.18 3.16
2684 2989 9.962759 GATGTATGCTCAATGAAAAATGTTTTC 57.037 29.630 6.53 6.53 0.00 2.29
2702 3007 5.521735 GGCTAGCACATAGTATGATGTATGC 59.478 44.000 18.24 14.46 37.99 3.14
2703 3008 6.045318 GGGCTAGCACATAGTATGATGTATG 58.955 44.000 18.24 5.35 37.99 2.39
2704 3009 5.960811 AGGGCTAGCACATAGTATGATGTAT 59.039 40.000 21.39 7.25 37.99 2.29
2705 3010 5.333581 AGGGCTAGCACATAGTATGATGTA 58.666 41.667 21.39 4.05 37.99 2.29
2706 3011 4.163427 AGGGCTAGCACATAGTATGATGT 58.837 43.478 21.39 3.11 40.78 3.06
2707 3012 4.815533 AGGGCTAGCACATAGTATGATG 57.184 45.455 21.39 11.63 33.65 3.07
2708 3013 5.333581 TGTAGGGCTAGCACATAGTATGAT 58.666 41.667 21.39 0.00 33.65 2.45
2709 3014 4.736473 TGTAGGGCTAGCACATAGTATGA 58.264 43.478 21.39 0.00 33.65 2.15
2710 3015 4.767409 TCTGTAGGGCTAGCACATAGTATG 59.233 45.833 21.39 8.66 33.65 2.39
2711 3016 4.999310 TCTGTAGGGCTAGCACATAGTAT 58.001 43.478 21.39 0.00 33.65 2.12
2718 3023 3.165875 TGGATATCTGTAGGGCTAGCAC 58.834 50.000 18.24 14.32 0.00 4.40
2723 3028 3.422796 CGTACTGGATATCTGTAGGGCT 58.577 50.000 2.05 0.00 34.32 5.19
2724 3029 2.094649 GCGTACTGGATATCTGTAGGGC 60.095 54.545 19.89 16.00 36.68 5.19
2727 3032 5.223382 CAAAGGCGTACTGGATATCTGTAG 58.777 45.833 2.05 2.11 31.79 2.74
2739 3060 7.683463 ATTTGTTTTAAGAAGCAAAGGCGTACT 60.683 33.333 7.13 0.00 45.12 2.73
2742 3063 5.356426 ATTTGTTTTAAGAAGCAAAGGCGT 58.644 33.333 7.13 0.00 45.12 5.68
2743 3064 5.905480 ATTTGTTTTAAGAAGCAAAGGCG 57.095 34.783 7.13 0.00 45.12 5.52
2745 3066 8.223100 GCACATATTTGTTTTAAGAAGCAAAGG 58.777 33.333 7.13 3.24 45.12 3.11
2762 3083 4.981806 ACAGCCGTTTATGCACATATTT 57.018 36.364 0.00 0.00 0.00 1.40
2766 3087 2.985896 ACTACAGCCGTTTATGCACAT 58.014 42.857 0.00 0.00 0.00 3.21
2767 3088 2.465860 ACTACAGCCGTTTATGCACA 57.534 45.000 0.00 0.00 0.00 4.57
2768 3089 4.390909 AGTTAACTACAGCCGTTTATGCAC 59.609 41.667 6.26 0.00 0.00 4.57
2769 3090 4.571919 AGTTAACTACAGCCGTTTATGCA 58.428 39.130 6.26 0.00 0.00 3.96
2770 3091 5.446875 GGAAGTTAACTACAGCCGTTTATGC 60.447 44.000 8.92 0.00 0.00 3.14
2772 3093 5.797051 TGGAAGTTAACTACAGCCGTTTAT 58.203 37.500 8.92 0.00 0.00 1.40
2801 3124 2.095008 GGCTTTTGGCTTCTAAGTCTGC 60.095 50.000 0.00 0.00 42.31 4.26
2802 3125 3.149196 TGGCTTTTGGCTTCTAAGTCTG 58.851 45.455 0.00 0.00 46.20 3.51
2806 3129 3.256631 ACACATGGCTTTTGGCTTCTAAG 59.743 43.478 0.00 0.00 46.20 2.18
2822 3145 9.260002 GGGGAAATAAATATTAAGCAACACATG 57.740 33.333 0.00 0.00 0.00 3.21
2825 3148 9.313118 CAAGGGGAAATAAATATTAAGCAACAC 57.687 33.333 0.00 0.00 0.00 3.32
2837 3160 5.598416 GCAACTAGCAAGGGGAAATAAAT 57.402 39.130 0.00 0.00 44.79 1.40
2852 3180 4.333649 CCATGTTCCACACATAGCAACTAG 59.666 45.833 0.00 0.00 45.06 2.57
2855 3183 2.164219 CCCATGTTCCACACATAGCAAC 59.836 50.000 0.00 0.00 45.06 4.17
2856 3184 2.224992 ACCCATGTTCCACACATAGCAA 60.225 45.455 0.00 0.00 45.06 3.91
2859 3187 5.467035 AAAAACCCATGTTCCACACATAG 57.533 39.130 0.00 0.00 45.06 2.23
2915 3243 6.391227 TTTTTGGGTCTTTCTGATGAGTTC 57.609 37.500 0.00 0.00 0.00 3.01
2945 3273 3.251004 GGAACCAAACTGCTTGACTGTAG 59.749 47.826 0.00 0.00 37.17 2.74
2968 3296 9.778741 TTTTCTTCTTCTGAATGTGTATGTAGT 57.221 29.630 0.00 0.00 0.00 2.73
3032 3366 3.225104 AGTGCTCCATCAAAATGTGTGT 58.775 40.909 0.00 0.00 0.00 3.72
3033 3367 3.829948 GAGTGCTCCATCAAAATGTGTG 58.170 45.455 0.00 0.00 0.00 3.82
3067 3446 1.353804 GTGCTCCTCGCTAGACTCG 59.646 63.158 0.00 0.00 40.11 4.18
3080 3460 1.145819 GAGGCAGAGGATGGTGCTC 59.854 63.158 0.00 0.00 39.76 4.26
3085 3465 2.509916 GCAGGAGGCAGAGGATGG 59.490 66.667 0.00 0.00 43.97 3.51
3125 3505 1.630369 CCAACCAGAGGAAGTGGATGA 59.370 52.381 1.26 0.00 39.60 2.92
3132 3512 1.672356 CACCGCCAACCAGAGGAAG 60.672 63.158 0.00 0.00 0.00 3.46
3176 3556 4.033776 CCGAGCTCCCTGCCCAAA 62.034 66.667 8.47 0.00 44.23 3.28
3330 3719 7.173218 TGGTGACTTTCTGAAGATGTTGTTATC 59.827 37.037 0.00 0.00 36.69 1.75
3332 3721 6.353323 TGGTGACTTTCTGAAGATGTTGTTA 58.647 36.000 0.00 0.00 36.69 2.41


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

AutoCloner maintained by Alex Coulton.