Multiple sequence alignment - TraesCS2B01G625700

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 TraesCS2B01G625700 chr2B 100.000 2702 0 0 1 2702 798293672 798296373 0.000000e+00 4990.0
1 TraesCS2B01G625700 chr2B 97.917 864 15 3 1 863 17221014 17221875 0.000000e+00 1493.0
2 TraesCS2B01G625700 chr2B 94.316 651 35 2 1007 1656 798702764 798702115 0.000000e+00 996.0
3 TraesCS2B01G625700 chr2B 80.526 837 69 37 1834 2628 798686994 798686210 8.450000e-155 556.0
4 TraesCS2B01G625700 chr2B 88.235 119 8 3 1621 1733 798702114 798701996 1.300000e-28 137.0
5 TraesCS2B01G625700 chr2B 89.796 49 5 0 1608 1656 206897020 206896972 2.250000e-06 63.9
6 TraesCS2B01G625700 chr2B 89.796 49 3 2 1609 1656 375779904 375779857 8.080000e-06 62.1
7 TraesCS2B01G625700 chr7A 97.890 853 17 1 1 852 126047478 126046626 0.000000e+00 1474.0
8 TraesCS2B01G625700 chr7A 85.781 647 87 4 963 1607 424534659 424535302 0.000000e+00 680.0
9 TraesCS2B01G625700 chrUn 97.655 853 16 3 1 852 16896574 16895725 0.000000e+00 1461.0
10 TraesCS2B01G625700 chrUn 95.513 156 7 0 1 156 278597751 278597906 1.610000e-62 250.0
11 TraesCS2B01G625700 chrUn 84.211 152 22 2 1 152 27270795 27270646 2.170000e-31 147.0
12 TraesCS2B01G625700 chr3A 97.655 853 17 3 1 852 50962926 50963776 0.000000e+00 1461.0
13 TraesCS2B01G625700 chr3A 80.099 608 93 21 1001 1600 449656928 449656341 6.910000e-116 427.0
14 TraesCS2B01G625700 chr1B 97.304 853 21 2 1 852 312611115 312611966 0.000000e+00 1447.0
15 TraesCS2B01G625700 chr1B 97.083 857 23 2 1 856 451561233 451560378 0.000000e+00 1443.0
16 TraesCS2B01G625700 chr1B 91.111 45 4 0 1609 1653 59237029 59237073 8.080000e-06 62.1
17 TraesCS2B01G625700 chr2A 97.186 853 21 2 1 852 200335517 200334667 0.000000e+00 1439.0
18 TraesCS2B01G625700 chr2A 91.216 740 60 3 995 1733 764913449 764914184 0.000000e+00 1002.0
19 TraesCS2B01G625700 chr2A 85.959 584 36 11 1834 2385 764914252 764914821 1.390000e-162 582.0
20 TraesCS2B01G625700 chr2A 81.588 277 31 11 2390 2660 764916743 764917005 7.580000e-51 211.0
21 TraesCS2B01G625700 chr4A 95.170 704 28 5 151 852 11752950 11752251 0.000000e+00 1107.0
22 TraesCS2B01G625700 chr4A 87.520 617 77 0 988 1604 17887867 17888483 0.000000e+00 713.0
23 TraesCS2B01G625700 chr5B 94.209 708 36 5 151 856 444766068 444765364 0.000000e+00 1075.0
24 TraesCS2B01G625700 chr5B 88.168 262 29 2 1001 1262 6869408 6869667 7.260000e-81 311.0
25 TraesCS2B01G625700 chr7D 87.302 630 77 3 984 1612 376941109 376941736 0.000000e+00 717.0
26 TraesCS2B01G625700 chr5A 87.034 617 80 0 988 1604 4080750 4081366 0.000000e+00 697.0
27 TraesCS2B01G625700 chr7B 86.741 626 79 3 984 1607 372008133 372008756 0.000000e+00 693.0
28 TraesCS2B01G625700 chr7B 91.667 48 2 2 1607 1653 627273883 627273837 6.240000e-07 65.8
29 TraesCS2B01G625700 chr7B 91.111 45 4 0 1609 1653 306223631 306223587 8.080000e-06 62.1
30 TraesCS2B01G625700 chr3D 80.165 605 98 16 1001 1600 332327014 332326427 1.490000e-117 433.0
31 TraesCS2B01G625700 chr4B 90.000 50 1 4 1608 1653 111565457 111565506 8.080000e-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 TraesCS2B01G625700 chr2B 798293672 798296373 2701 False 4990.000000 4990 100.000000 1 2702 1 chr2B.!!$F2 2701
1 TraesCS2B01G625700 chr2B 17221014 17221875 861 False 1493.000000 1493 97.917000 1 863 1 chr2B.!!$F1 862
2 TraesCS2B01G625700 chr2B 798701996 798702764 768 True 566.500000 996 91.275500 1007 1733 2 chr2B.!!$R4 726
3 TraesCS2B01G625700 chr2B 798686210 798686994 784 True 556.000000 556 80.526000 1834 2628 1 chr2B.!!$R3 794
4 TraesCS2B01G625700 chr7A 126046626 126047478 852 True 1474.000000 1474 97.890000 1 852 1 chr7A.!!$R1 851
5 TraesCS2B01G625700 chr7A 424534659 424535302 643 False 680.000000 680 85.781000 963 1607 1 chr7A.!!$F1 644
6 TraesCS2B01G625700 chrUn 16895725 16896574 849 True 1461.000000 1461 97.655000 1 852 1 chrUn.!!$R1 851
7 TraesCS2B01G625700 chr3A 50962926 50963776 850 False 1461.000000 1461 97.655000 1 852 1 chr3A.!!$F1 851
8 TraesCS2B01G625700 chr3A 449656341 449656928 587 True 427.000000 427 80.099000 1001 1600 1 chr3A.!!$R1 599
9 TraesCS2B01G625700 chr1B 312611115 312611966 851 False 1447.000000 1447 97.304000 1 852 1 chr1B.!!$F2 851
10 TraesCS2B01G625700 chr1B 451560378 451561233 855 True 1443.000000 1443 97.083000 1 856 1 chr1B.!!$R1 855
11 TraesCS2B01G625700 chr2A 200334667 200335517 850 True 1439.000000 1439 97.186000 1 852 1 chr2A.!!$R1 851
12 TraesCS2B01G625700 chr2A 764913449 764917005 3556 False 598.333333 1002 86.254333 995 2660 3 chr2A.!!$F1 1665
13 TraesCS2B01G625700 chr4A 11752251 11752950 699 True 1107.000000 1107 95.170000 151 852 1 chr4A.!!$R1 701
14 TraesCS2B01G625700 chr4A 17887867 17888483 616 False 713.000000 713 87.520000 988 1604 1 chr4A.!!$F1 616
15 TraesCS2B01G625700 chr5B 444765364 444766068 704 True 1075.000000 1075 94.209000 151 856 1 chr5B.!!$R1 705
16 TraesCS2B01G625700 chr7D 376941109 376941736 627 False 717.000000 717 87.302000 984 1612 1 chr7D.!!$F1 628
17 TraesCS2B01G625700 chr5A 4080750 4081366 616 False 697.000000 697 87.034000 988 1604 1 chr5A.!!$F1 616
18 TraesCS2B01G625700 chr7B 372008133 372008756 623 False 693.000000 693 86.741000 984 1607 1 chr7B.!!$F1 623
19 TraesCS2B01G625700 chr3D 332326427 332327014 587 True 433.000000 433 80.165000 1001 1600 1 chr3D.!!$R1 599

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
993 997 0.105964 TCGTCCAAGGTCCAACACAG 59.894 55.0 0.0 0.0 0.0 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2508 4553 0.099791 AACAAGCACCGTTTTGACCG 59.9 50.0 0.0 0.0 0.0 4.79 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
92 93 2.817844 GACGGGATTTTTGCTACAACCT 59.182 45.455 0.00 0.00 0.00 3.50
200 201 7.160726 ACCGTAGTTAATTTTTGCTACTACCA 58.839 34.615 0.00 0.00 38.48 3.25
325 326 1.440938 TTTTGCTACAACCGCTGCGT 61.441 50.000 21.59 6.30 0.00 5.24
664 667 4.812476 CGACGAGGATGGCCGCAA 62.812 66.667 0.00 0.00 39.96 4.85
780 784 1.377725 CCAGATCCAAAGGCTGCGT 60.378 57.895 0.00 0.00 0.00 5.24
857 861 1.610624 CGCCTATCGGTGCCCATAATT 60.611 52.381 0.00 0.00 33.35 1.40
858 862 2.354303 CGCCTATCGGTGCCCATAATTA 60.354 50.000 0.00 0.00 33.35 1.40
860 864 4.076394 GCCTATCGGTGCCCATAATTAAA 58.924 43.478 0.00 0.00 0.00 1.52
862 866 5.185056 GCCTATCGGTGCCCATAATTAAATT 59.815 40.000 0.00 0.00 0.00 1.82
863 867 6.376018 GCCTATCGGTGCCCATAATTAAATTA 59.624 38.462 0.00 0.00 0.00 1.40
864 868 7.627726 GCCTATCGGTGCCCATAATTAAATTAC 60.628 40.741 0.00 0.00 0.00 1.89
865 869 7.610305 CCTATCGGTGCCCATAATTAAATTACT 59.390 37.037 0.00 0.00 0.00 2.24
866 870 9.661563 CTATCGGTGCCCATAATTAAATTACTA 57.338 33.333 0.00 0.00 0.00 1.82
867 871 8.927675 ATCGGTGCCCATAATTAAATTACTAA 57.072 30.769 0.00 0.00 0.00 2.24
868 872 8.749026 TCGGTGCCCATAATTAAATTACTAAA 57.251 30.769 0.00 0.00 0.00 1.85
869 873 9.357161 TCGGTGCCCATAATTAAATTACTAAAT 57.643 29.630 0.00 0.00 0.00 1.40
889 893 9.530633 ACTAAATACCAAATAGATGTCTCGTTC 57.469 33.333 0.00 0.00 0.00 3.95
890 894 7.464830 AAATACCAAATAGATGTCTCGTTCG 57.535 36.000 0.00 0.00 0.00 3.95
891 895 3.187700 ACCAAATAGATGTCTCGTTCGC 58.812 45.455 0.00 0.00 0.00 4.70
892 896 3.119101 ACCAAATAGATGTCTCGTTCGCT 60.119 43.478 0.00 0.00 0.00 4.93
893 897 3.865745 CCAAATAGATGTCTCGTTCGCTT 59.134 43.478 0.00 0.00 0.00 4.68
894 898 4.259970 CCAAATAGATGTCTCGTTCGCTTG 60.260 45.833 0.00 0.00 0.00 4.01
895 899 2.561733 TAGATGTCTCGTTCGCTTGG 57.438 50.000 0.00 0.00 0.00 3.61
896 900 0.603569 AGATGTCTCGTTCGCTTGGT 59.396 50.000 0.00 0.00 0.00 3.67
897 901 0.716108 GATGTCTCGTTCGCTTGGTG 59.284 55.000 0.00 0.00 0.00 4.17
898 902 0.317160 ATGTCTCGTTCGCTTGGTGA 59.683 50.000 0.00 0.00 0.00 4.02
899 903 0.317160 TGTCTCGTTCGCTTGGTGAT 59.683 50.000 0.00 0.00 0.00 3.06
900 904 0.992802 GTCTCGTTCGCTTGGTGATC 59.007 55.000 0.00 0.00 0.00 2.92
901 905 0.888619 TCTCGTTCGCTTGGTGATCT 59.111 50.000 0.00 0.00 0.00 2.75
902 906 1.135373 TCTCGTTCGCTTGGTGATCTC 60.135 52.381 0.00 0.00 0.00 2.75
903 907 0.888619 TCGTTCGCTTGGTGATCTCT 59.111 50.000 0.00 0.00 0.00 3.10
904 908 1.272490 TCGTTCGCTTGGTGATCTCTT 59.728 47.619 0.00 0.00 0.00 2.85
905 909 1.656095 CGTTCGCTTGGTGATCTCTTC 59.344 52.381 0.00 0.00 0.00 2.87
906 910 2.003301 GTTCGCTTGGTGATCTCTTCC 58.997 52.381 0.00 0.00 0.00 3.46
907 911 1.561643 TCGCTTGGTGATCTCTTCCT 58.438 50.000 0.00 0.00 0.00 3.36
908 912 1.478510 TCGCTTGGTGATCTCTTCCTC 59.521 52.381 0.00 0.00 0.00 3.71
909 913 1.480137 CGCTTGGTGATCTCTTCCTCT 59.520 52.381 0.00 0.00 0.00 3.69
910 914 2.738000 CGCTTGGTGATCTCTTCCTCTG 60.738 54.545 0.00 0.00 0.00 3.35
911 915 2.235898 GCTTGGTGATCTCTTCCTCTGT 59.764 50.000 0.00 0.00 0.00 3.41
912 916 3.307339 GCTTGGTGATCTCTTCCTCTGTT 60.307 47.826 0.00 0.00 0.00 3.16
913 917 4.805609 GCTTGGTGATCTCTTCCTCTGTTT 60.806 45.833 0.00 0.00 0.00 2.83
914 918 4.277515 TGGTGATCTCTTCCTCTGTTTG 57.722 45.455 0.00 0.00 0.00 2.93
915 919 3.006247 GGTGATCTCTTCCTCTGTTTGC 58.994 50.000 0.00 0.00 0.00 3.68
916 920 2.670414 GTGATCTCTTCCTCTGTTTGCG 59.330 50.000 0.00 0.00 0.00 4.85
917 921 1.663135 GATCTCTTCCTCTGTTTGCGC 59.337 52.381 0.00 0.00 0.00 6.09
918 922 0.392706 TCTCTTCCTCTGTTTGCGCA 59.607 50.000 5.66 5.66 0.00 6.09
919 923 1.002430 TCTCTTCCTCTGTTTGCGCAT 59.998 47.619 12.75 0.00 0.00 4.73
920 924 1.396301 CTCTTCCTCTGTTTGCGCATC 59.604 52.381 12.75 8.68 0.00 3.91
921 925 1.159285 CTTCCTCTGTTTGCGCATCA 58.841 50.000 12.75 13.29 0.00 3.07
922 926 1.741706 CTTCCTCTGTTTGCGCATCAT 59.258 47.619 12.75 0.00 0.00 2.45
923 927 1.372582 TCCTCTGTTTGCGCATCATC 58.627 50.000 12.75 2.61 0.00 2.92
924 928 1.065926 TCCTCTGTTTGCGCATCATCT 60.066 47.619 12.75 0.00 0.00 2.90
925 929 1.329906 CCTCTGTTTGCGCATCATCTC 59.670 52.381 12.75 0.00 0.00 2.75
926 930 2.277969 CTCTGTTTGCGCATCATCTCT 58.722 47.619 12.75 0.00 0.00 3.10
927 931 2.676839 CTCTGTTTGCGCATCATCTCTT 59.323 45.455 12.75 0.00 0.00 2.85
928 932 2.674852 TCTGTTTGCGCATCATCTCTTC 59.325 45.455 12.75 0.00 0.00 2.87
929 933 1.739466 TGTTTGCGCATCATCTCTTCC 59.261 47.619 12.75 0.00 0.00 3.46
930 934 1.064654 GTTTGCGCATCATCTCTTCCC 59.935 52.381 12.75 0.00 0.00 3.97
931 935 0.252761 TTGCGCATCATCTCTTCCCA 59.747 50.000 12.75 0.00 0.00 4.37
932 936 0.179065 TGCGCATCATCTCTTCCCAG 60.179 55.000 5.66 0.00 0.00 4.45
933 937 1.505477 GCGCATCATCTCTTCCCAGC 61.505 60.000 0.30 0.00 0.00 4.85
934 938 0.883814 CGCATCATCTCTTCCCAGCC 60.884 60.000 0.00 0.00 0.00 4.85
935 939 0.182061 GCATCATCTCTTCCCAGCCA 59.818 55.000 0.00 0.00 0.00 4.75
936 940 1.409241 GCATCATCTCTTCCCAGCCAA 60.409 52.381 0.00 0.00 0.00 4.52
937 941 2.295885 CATCATCTCTTCCCAGCCAAC 58.704 52.381 0.00 0.00 0.00 3.77
938 942 1.661463 TCATCTCTTCCCAGCCAACT 58.339 50.000 0.00 0.00 0.00 3.16
939 943 1.556911 TCATCTCTTCCCAGCCAACTC 59.443 52.381 0.00 0.00 0.00 3.01
940 944 0.915364 ATCTCTTCCCAGCCAACTCC 59.085 55.000 0.00 0.00 0.00 3.85
941 945 1.201429 TCTCTTCCCAGCCAACTCCC 61.201 60.000 0.00 0.00 0.00 4.30
942 946 2.203549 CTCTTCCCAGCCAACTCCCC 62.204 65.000 0.00 0.00 0.00 4.81
943 947 3.628646 CTTCCCAGCCAACTCCCCG 62.629 68.421 0.00 0.00 0.00 5.73
944 948 4.974438 TCCCAGCCAACTCCCCGT 62.974 66.667 0.00 0.00 0.00 5.28
945 949 3.006728 CCCAGCCAACTCCCCGTA 61.007 66.667 0.00 0.00 0.00 4.02
946 950 2.584608 CCAGCCAACTCCCCGTAG 59.415 66.667 0.00 0.00 0.00 3.51
947 951 2.125106 CAGCCAACTCCCCGTAGC 60.125 66.667 0.00 0.00 0.00 3.58
948 952 2.284699 AGCCAACTCCCCGTAGCT 60.285 61.111 0.00 0.00 32.29 3.32
949 953 1.001248 AGCCAACTCCCCGTAGCTA 59.999 57.895 0.00 0.00 34.60 3.32
950 954 1.043673 AGCCAACTCCCCGTAGCTAG 61.044 60.000 0.00 0.00 34.60 3.42
951 955 1.442148 CCAACTCCCCGTAGCTAGC 59.558 63.158 6.62 6.62 0.00 3.42
952 956 1.043673 CCAACTCCCCGTAGCTAGCT 61.044 60.000 23.12 23.12 0.00 3.32
953 957 1.688772 CAACTCCCCGTAGCTAGCTA 58.311 55.000 20.67 20.67 0.00 3.32
954 958 1.609555 CAACTCCCCGTAGCTAGCTAG 59.390 57.143 24.78 16.84 0.00 3.42
967 971 1.392710 TAGCTAGCTTGAGGGACCGC 61.393 60.000 24.88 0.00 0.00 5.68
981 985 4.717629 CCGCTGTCGCTCGTCCAA 62.718 66.667 0.00 0.00 0.00 3.53
982 986 3.175240 CGCTGTCGCTCGTCCAAG 61.175 66.667 0.00 0.00 0.00 3.61
993 997 0.105964 TCGTCCAAGGTCCAACACAG 59.894 55.000 0.00 0.00 0.00 3.66
1052 1056 2.087344 TCGAGGACGACGTGATCAG 58.913 57.895 4.58 0.45 43.81 2.90
1238 1242 2.203126 CCGCTGCCTCATCTTCCC 60.203 66.667 0.00 0.00 0.00 3.97
1260 1264 2.564975 CTCCACGCGGACTACGTT 59.435 61.111 12.47 0.00 42.96 3.99
1284 1288 1.383248 GGCCCTGGAGAGCTTCCTA 60.383 63.158 13.76 3.20 46.92 2.94
1448 1452 1.528824 CCGGGCTCAAGGACATCAT 59.471 57.895 0.00 0.00 0.00 2.45
1575 1579 1.419374 CGTTCGTCTCCTTTGAGGTG 58.581 55.000 0.00 0.00 39.23 4.00
1614 1618 1.107945 GTGACTACTCCTGCTCCTCC 58.892 60.000 0.00 0.00 0.00 4.30
1615 1619 1.003646 TGACTACTCCTGCTCCTCCT 58.996 55.000 0.00 0.00 0.00 3.69
1616 1620 1.064314 TGACTACTCCTGCTCCTCCTC 60.064 57.143 0.00 0.00 0.00 3.71
1617 1621 0.260523 ACTACTCCTGCTCCTCCTCC 59.739 60.000 0.00 0.00 0.00 4.30
1618 1622 0.555769 CTACTCCTGCTCCTCCTCCT 59.444 60.000 0.00 0.00 0.00 3.69
1668 1714 5.445964 GAAGAAGATGACTCCTACTCCTCT 58.554 45.833 0.00 0.00 0.00 3.69
1687 1733 3.229293 TCTGATGAGTATGGCTCCTCTG 58.771 50.000 0.00 0.00 43.48 3.35
1688 1734 3.117360 TCTGATGAGTATGGCTCCTCTGA 60.117 47.826 0.00 0.00 43.48 3.27
1689 1735 3.229293 TGATGAGTATGGCTCCTCTGAG 58.771 50.000 0.00 0.00 43.48 3.35
1707 1756 2.291024 TGAGGAGGACTACTGAGGTGAC 60.291 54.545 0.00 0.00 0.00 3.67
1719 1768 4.077184 GGTGACCGATGGCCGTCA 62.077 66.667 24.56 15.76 36.31 4.35
1728 1777 2.869503 GATGGCCGTCATCCCGTGTT 62.870 60.000 20.55 0.00 44.92 3.32
1733 1782 1.374125 CGTCATCCCGTGTTCTGCA 60.374 57.895 0.00 0.00 0.00 4.41
1743 1792 2.997485 GTGTTCTGCACAGGGAATTC 57.003 50.000 0.00 0.00 46.91 2.17
1744 1793 2.508526 GTGTTCTGCACAGGGAATTCT 58.491 47.619 5.23 0.00 46.91 2.40
1745 1794 3.674997 GTGTTCTGCACAGGGAATTCTA 58.325 45.455 5.23 0.00 46.91 2.10
1746 1795 3.437049 GTGTTCTGCACAGGGAATTCTAC 59.563 47.826 5.23 0.00 46.91 2.59
1747 1796 3.010420 GTTCTGCACAGGGAATTCTACC 58.990 50.000 5.23 0.00 0.00 3.18
1748 1797 2.265367 TCTGCACAGGGAATTCTACCA 58.735 47.619 5.23 0.00 0.00 3.25
1749 1798 2.237143 TCTGCACAGGGAATTCTACCAG 59.763 50.000 5.23 0.00 0.00 4.00
1750 1799 1.340017 TGCACAGGGAATTCTACCAGC 60.340 52.381 5.23 5.71 0.00 4.85
1751 1800 1.065126 GCACAGGGAATTCTACCAGCT 60.065 52.381 5.23 0.00 0.00 4.24
1752 1801 2.911484 CACAGGGAATTCTACCAGCTC 58.089 52.381 5.23 0.00 0.00 4.09
1753 1802 1.840635 ACAGGGAATTCTACCAGCTCC 59.159 52.381 5.23 0.00 0.00 4.70
1754 1803 1.839994 CAGGGAATTCTACCAGCTCCA 59.160 52.381 5.23 0.00 0.00 3.86
1755 1804 2.239654 CAGGGAATTCTACCAGCTCCAA 59.760 50.000 5.23 0.00 0.00 3.53
1756 1805 2.507471 AGGGAATTCTACCAGCTCCAAG 59.493 50.000 5.23 0.00 0.00 3.61
1757 1806 2.293170 GGAATTCTACCAGCTCCAAGC 58.707 52.381 5.23 0.00 42.84 4.01
1758 1807 2.356125 GGAATTCTACCAGCTCCAAGCA 60.356 50.000 5.23 0.00 45.56 3.91
1759 1808 3.347216 GAATTCTACCAGCTCCAAGCAA 58.653 45.455 0.00 0.00 45.56 3.91
1760 1809 2.479566 TTCTACCAGCTCCAAGCAAG 57.520 50.000 1.29 0.00 45.56 4.01
1761 1810 1.352083 TCTACCAGCTCCAAGCAAGT 58.648 50.000 1.29 0.89 45.56 3.16
1762 1811 2.536066 TCTACCAGCTCCAAGCAAGTA 58.464 47.619 1.29 1.99 45.56 2.24
1763 1812 2.233922 TCTACCAGCTCCAAGCAAGTAC 59.766 50.000 1.29 0.00 45.56 2.73
1764 1813 1.059913 ACCAGCTCCAAGCAAGTACT 58.940 50.000 1.29 0.00 45.56 2.73
1765 1814 2.257207 ACCAGCTCCAAGCAAGTACTA 58.743 47.619 0.00 0.00 45.56 1.82
1766 1815 2.234908 ACCAGCTCCAAGCAAGTACTAG 59.765 50.000 0.00 0.00 45.56 2.57
1767 1816 2.234908 CCAGCTCCAAGCAAGTACTAGT 59.765 50.000 0.00 0.00 45.56 2.57
1768 1817 3.257393 CAGCTCCAAGCAAGTACTAGTG 58.743 50.000 5.39 0.00 45.56 2.74
1769 1818 2.003301 GCTCCAAGCAAGTACTAGTGC 58.997 52.381 10.95 10.95 41.89 4.40
1770 1819 2.612972 GCTCCAAGCAAGTACTAGTGCA 60.613 50.000 19.15 0.79 43.42 4.57
1771 1820 3.866651 CTCCAAGCAAGTACTAGTGCAT 58.133 45.455 19.15 6.86 43.42 3.96
1784 1833 3.927142 ACTAGTGCATGCGTTTAGACTTC 59.073 43.478 22.18 2.53 0.00 3.01
1785 1834 1.726791 AGTGCATGCGTTTAGACTTCG 59.273 47.619 14.09 0.00 0.00 3.79
1787 1836 2.096417 GTGCATGCGTTTAGACTTCGTT 60.096 45.455 14.09 0.00 0.00 3.85
1789 1838 2.495939 CATGCGTTTAGACTTCGTTGC 58.504 47.619 0.00 0.00 0.00 4.17
1791 1840 1.525197 TGCGTTTAGACTTCGTTGCTG 59.475 47.619 0.00 0.00 0.00 4.41
1792 1841 1.721804 GCGTTTAGACTTCGTTGCTGC 60.722 52.381 0.00 0.00 0.00 5.25
1793 1842 1.792949 CGTTTAGACTTCGTTGCTGCT 59.207 47.619 0.00 0.00 0.00 4.24
1794 1843 2.159960 CGTTTAGACTTCGTTGCTGCTC 60.160 50.000 0.00 0.00 0.00 4.26
1808 1857 1.584308 GCTGCTCGTTGATCTCGTAAC 59.416 52.381 9.75 0.00 0.00 2.50
1812 1861 2.026507 GCTCGTTGATCTCGTAACGTTG 59.973 50.000 11.99 10.01 46.90 4.10
1813 1862 1.980844 TCGTTGATCTCGTAACGTTGC 59.019 47.619 11.99 9.00 46.90 4.17
1815 1872 2.026507 CGTTGATCTCGTAACGTTGCTC 59.973 50.000 11.99 3.70 43.23 4.26
1830 1887 5.526010 CGTTGCTCGTTTATTAGGAGTTT 57.474 39.130 0.00 0.00 40.19 2.66
1831 1888 6.636666 CGTTGCTCGTTTATTAGGAGTTTA 57.363 37.500 0.00 0.00 40.19 2.01
1832 1889 6.464311 CGTTGCTCGTTTATTAGGAGTTTAC 58.536 40.000 0.00 0.00 40.19 2.01
1849 1906 5.734720 AGTTTACTACCTGTCATGGTGATG 58.265 41.667 0.00 0.00 41.05 3.07
1979 2047 4.051922 GGAGTAGTACCATTCTTGCGATG 58.948 47.826 0.00 0.00 0.00 3.84
2039 2107 6.094603 AGTCCTTGCTGCAAACAATATCTAAG 59.905 38.462 16.74 0.00 0.00 2.18
2040 2108 5.039333 CCTTGCTGCAAACAATATCTAAGC 58.961 41.667 16.74 0.00 0.00 3.09
2041 2109 5.163581 CCTTGCTGCAAACAATATCTAAGCT 60.164 40.000 16.74 0.00 0.00 3.74
2042 2110 6.038603 CCTTGCTGCAAACAATATCTAAGCTA 59.961 38.462 16.74 0.00 0.00 3.32
2043 2111 7.389803 TTGCTGCAAACAATATCTAAGCTAA 57.610 32.000 13.51 0.00 0.00 3.09
2044 2112 7.389803 TGCTGCAAACAATATCTAAGCTAAA 57.610 32.000 0.00 0.00 0.00 1.85
2045 2113 7.999679 TGCTGCAAACAATATCTAAGCTAAAT 58.000 30.769 0.00 0.00 0.00 1.40
2046 2114 9.119418 TGCTGCAAACAATATCTAAGCTAAATA 57.881 29.630 0.00 0.00 0.00 1.40
2080 2148 6.423604 GGTAGTGCGTTAAGGTTGTTTAGTAA 59.576 38.462 0.00 0.00 0.00 2.24
2085 2159 7.118245 GTGCGTTAAGGTTGTTTAGTAATAGGT 59.882 37.037 0.00 0.00 0.00 3.08
2121 2195 4.005650 TGTTGAAGAATCAGCCAGACATC 58.994 43.478 0.00 0.00 36.07 3.06
2122 2196 2.897436 TGAAGAATCAGCCAGACATCG 58.103 47.619 0.00 0.00 0.00 3.84
2133 2207 2.549563 GCCAGACATCGGTGATGATGAT 60.550 50.000 13.36 0.00 46.98 2.45
2138 2212 4.100653 AGACATCGGTGATGATGATGAGTT 59.899 41.667 13.36 0.00 46.98 3.01
2140 2214 3.183793 TCGGTGATGATGATGAGTTGG 57.816 47.619 0.00 0.00 0.00 3.77
2141 2215 1.600957 CGGTGATGATGATGAGTTGGC 59.399 52.381 0.00 0.00 0.00 4.52
2145 2219 2.169144 TGATGATGATGAGTTGGCGACT 59.831 45.455 7.22 7.22 42.70 4.18
2190 2268 0.179000 ATGGCAACTCCTTCGGCTAG 59.821 55.000 0.00 0.00 35.26 3.42
2221 2299 4.927978 TTTGTTACAAATGTCCACCAGG 57.072 40.909 6.41 0.00 0.00 4.45
2242 2320 3.335579 GGTTAGCTTTGATCTTGACGGT 58.664 45.455 0.00 0.00 0.00 4.83
2245 2328 2.154462 AGCTTTGATCTTGACGGTTGG 58.846 47.619 0.00 0.00 0.00 3.77
2263 2346 4.355437 GTTGGTCGACTACATCATCTCTG 58.645 47.826 16.46 0.00 0.00 3.35
2273 2356 5.873712 ACTACATCATCTCTGAAAGTGCAAG 59.126 40.000 0.00 0.00 34.37 4.01
2290 2373 1.144093 CAAGGGGACTAAACACACCCA 59.856 52.381 0.00 0.00 43.96 4.51
2311 2398 5.509670 CCCATTATCATGTCAAGTCTCGCTA 60.510 44.000 0.00 0.00 0.00 4.26
2315 2402 4.783764 TCATGTCAAGTCTCGCTAAGAA 57.216 40.909 0.00 0.00 35.21 2.52
2323 2410 5.120830 TCAAGTCTCGCTAAGAAAGATTTGC 59.879 40.000 0.00 0.00 36.95 3.68
2333 2420 5.757850 AAGAAAGATTTGCGATATGGGTC 57.242 39.130 0.00 0.00 0.00 4.46
2340 2427 1.080434 GCGATATGGGTCGAGGAGC 60.080 63.158 0.00 0.00 44.06 4.70
2342 2429 0.673985 CGATATGGGTCGAGGAGCAA 59.326 55.000 0.00 0.00 44.06 3.91
2345 2432 0.824109 TATGGGTCGAGGAGCAACAG 59.176 55.000 0.00 0.00 0.00 3.16
2346 2433 0.904865 ATGGGTCGAGGAGCAACAGA 60.905 55.000 0.00 0.00 0.00 3.41
2347 2434 1.079750 GGGTCGAGGAGCAACAGAC 60.080 63.158 0.00 0.00 0.00 3.51
2348 2435 1.079750 GGTCGAGGAGCAACAGACC 60.080 63.158 8.64 8.64 43.55 3.85
2365 2458 0.921896 ACCATTATCAGCAGCAGGGT 59.078 50.000 0.00 0.00 0.00 4.34
2385 2478 4.876679 GGGTAGTTTCTCAGTCCATTTAGC 59.123 45.833 0.00 0.00 0.00 3.09
2386 2479 5.488341 GGTAGTTTCTCAGTCCATTTAGCA 58.512 41.667 0.00 0.00 0.00 3.49
2387 2480 6.116126 GGTAGTTTCTCAGTCCATTTAGCAT 58.884 40.000 0.00 0.00 0.00 3.79
2389 2482 7.769044 GGTAGTTTCTCAGTCCATTTAGCATAA 59.231 37.037 0.00 0.00 0.00 1.90
2390 2483 7.856145 AGTTTCTCAGTCCATTTAGCATAAG 57.144 36.000 0.00 0.00 0.00 1.73
2391 2484 6.317391 AGTTTCTCAGTCCATTTAGCATAAGC 59.683 38.462 0.00 0.00 42.56 3.09
2415 4426 1.470098 CTAATTGCGGTGCAGAAAGCT 59.530 47.619 0.00 0.00 45.94 3.74
2416 4427 1.533625 AATTGCGGTGCAGAAAGCTA 58.466 45.000 0.00 0.00 45.94 3.32
2417 4428 0.804989 ATTGCGGTGCAGAAAGCTAC 59.195 50.000 0.00 0.00 45.94 3.58
2418 4429 1.565156 TTGCGGTGCAGAAAGCTACG 61.565 55.000 0.00 0.00 45.94 3.51
2419 4430 2.027625 GCGGTGCAGAAAGCTACGT 61.028 57.895 0.00 0.00 45.94 3.57
2420 4431 0.734942 GCGGTGCAGAAAGCTACGTA 60.735 55.000 0.00 0.00 45.94 3.57
2421 4432 0.989890 CGGTGCAGAAAGCTACGTAC 59.010 55.000 0.00 0.00 45.94 3.67
2422 4433 1.356938 GGTGCAGAAAGCTACGTACC 58.643 55.000 0.00 0.00 45.94 3.34
2423 4434 1.067071 GGTGCAGAAAGCTACGTACCT 60.067 52.381 0.00 0.00 45.94 3.08
2424 4435 2.165030 GGTGCAGAAAGCTACGTACCTA 59.835 50.000 0.00 0.00 45.94 3.08
2425 4436 3.181478 GGTGCAGAAAGCTACGTACCTAT 60.181 47.826 0.00 0.00 45.94 2.57
2426 4437 4.430908 GTGCAGAAAGCTACGTACCTATT 58.569 43.478 0.00 0.00 45.94 1.73
2427 4438 5.450965 GGTGCAGAAAGCTACGTACCTATTA 60.451 44.000 0.00 0.00 45.94 0.98
2428 4439 5.686397 GTGCAGAAAGCTACGTACCTATTAG 59.314 44.000 0.00 0.00 45.94 1.73
2438 4449 4.979335 ACGTACCTATTAGGACCTAGGTC 58.021 47.826 30.72 30.72 43.36 3.85
2464 4492 3.069729 CAGTAGGTGTAGGCATTAGGTCC 59.930 52.174 0.00 0.00 0.00 4.46
2465 4493 1.508256 AGGTGTAGGCATTAGGTCCC 58.492 55.000 0.00 0.00 0.00 4.46
2466 4494 1.009675 AGGTGTAGGCATTAGGTCCCT 59.990 52.381 0.00 0.00 0.00 4.20
2480 4525 0.176910 GTCCCTTACAGCAGAGGAGC 59.823 60.000 0.00 0.00 34.91 4.70
2488 4533 0.037882 CAGCAGAGGAGCGAAAGACA 60.038 55.000 0.00 0.00 40.15 3.41
2494 4539 0.318762 AGGAGCGAAAGACAGGTCAC 59.681 55.000 1.84 0.00 36.68 3.67
2516 4561 2.088423 AGCTGTGAAACACGGTCAAAA 58.912 42.857 11.48 0.00 45.67 2.44
2549 4595 3.515502 TGTACTTGGCTGCTCACTATTCT 59.484 43.478 0.00 0.00 0.00 2.40
2614 4660 0.727122 AGTCGTTTCTTCGTACGCCG 60.727 55.000 11.24 3.72 37.66 6.46
2631 4677 2.093783 CGCCGGATGACAAAAGTTCTAC 59.906 50.000 5.05 0.00 0.00 2.59
2674 4720 6.855763 AAAATGGAATAGCTGGAATTCACA 57.144 33.333 7.93 2.28 35.46 3.58
2675 4721 6.855763 AAATGGAATAGCTGGAATTCACAA 57.144 33.333 7.93 0.00 35.46 3.33
2676 4722 6.855763 AATGGAATAGCTGGAATTCACAAA 57.144 33.333 7.93 0.00 35.46 2.83
2677 4723 7.427989 AATGGAATAGCTGGAATTCACAAAT 57.572 32.000 7.93 0.00 35.46 2.32
2678 4724 6.455360 TGGAATAGCTGGAATTCACAAATC 57.545 37.500 7.93 0.00 35.46 2.17
2679 4725 5.360714 TGGAATAGCTGGAATTCACAAATCC 59.639 40.000 7.93 6.42 35.46 3.01
2680 4726 5.505173 AATAGCTGGAATTCACAAATCCG 57.495 39.130 7.93 0.00 0.00 4.18
2681 4727 2.094675 AGCTGGAATTCACAAATCCGG 58.905 47.619 7.93 0.00 0.00 5.14
2682 4728 1.469767 GCTGGAATTCACAAATCCGGC 60.470 52.381 7.93 8.91 44.26 6.13
2683 4729 1.818060 CTGGAATTCACAAATCCGGCA 59.182 47.619 7.93 0.00 0.00 5.69
2684 4730 1.543802 TGGAATTCACAAATCCGGCAC 59.456 47.619 7.93 0.00 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 76 7.158697 ACCAATAAAGGTTGTAGCAAAAATCC 58.841 34.615 0.00 0.00 39.34 3.01
92 93 6.568844 CGCTGGTAGTAGCAAAAACCAATAAA 60.569 38.462 3.25 0.00 43.87 1.40
200 201 3.805422 TCGATGTAGCACAAAACTTCGTT 59.195 39.130 9.56 0.00 41.41 3.85
325 326 2.748647 TCGTCATCGTCGCAGGGA 60.749 61.111 0.00 0.00 38.33 4.20
556 558 4.082523 CACCATCACCGGCCGTCT 62.083 66.667 26.12 5.40 0.00 4.18
705 708 2.065789 TCAGGCCAGATCCGCATCA 61.066 57.895 5.01 0.00 0.00 3.07
780 784 2.359850 GCCGTTGGATGTGAGCCA 60.360 61.111 0.00 0.00 0.00 4.75
863 867 9.530633 GAACGAGACATCTATTTGGTATTTAGT 57.469 33.333 0.00 0.00 0.00 2.24
864 868 8.691727 CGAACGAGACATCTATTTGGTATTTAG 58.308 37.037 0.00 0.00 0.00 1.85
865 869 7.168637 GCGAACGAGACATCTATTTGGTATTTA 59.831 37.037 0.00 0.00 0.00 1.40
866 870 6.018994 GCGAACGAGACATCTATTTGGTATTT 60.019 38.462 0.00 0.00 0.00 1.40
867 871 5.462398 GCGAACGAGACATCTATTTGGTATT 59.538 40.000 0.00 0.00 0.00 1.89
868 872 4.982916 GCGAACGAGACATCTATTTGGTAT 59.017 41.667 0.00 0.00 0.00 2.73
869 873 4.097437 AGCGAACGAGACATCTATTTGGTA 59.903 41.667 0.00 0.00 0.00 3.25
870 874 3.119101 AGCGAACGAGACATCTATTTGGT 60.119 43.478 0.00 0.00 0.00 3.67
871 875 3.448686 AGCGAACGAGACATCTATTTGG 58.551 45.455 0.00 0.00 0.00 3.28
872 876 4.259970 CCAAGCGAACGAGACATCTATTTG 60.260 45.833 0.00 0.00 0.00 2.32
873 877 3.865745 CCAAGCGAACGAGACATCTATTT 59.134 43.478 0.00 0.00 0.00 1.40
874 878 3.119101 ACCAAGCGAACGAGACATCTATT 60.119 43.478 0.00 0.00 0.00 1.73
875 879 2.427453 ACCAAGCGAACGAGACATCTAT 59.573 45.455 0.00 0.00 0.00 1.98
876 880 1.816835 ACCAAGCGAACGAGACATCTA 59.183 47.619 0.00 0.00 0.00 1.98
877 881 0.603569 ACCAAGCGAACGAGACATCT 59.396 50.000 0.00 0.00 0.00 2.90
878 882 0.716108 CACCAAGCGAACGAGACATC 59.284 55.000 0.00 0.00 0.00 3.06
879 883 0.317160 TCACCAAGCGAACGAGACAT 59.683 50.000 0.00 0.00 0.00 3.06
880 884 0.317160 ATCACCAAGCGAACGAGACA 59.683 50.000 0.00 0.00 0.00 3.41
881 885 0.992802 GATCACCAAGCGAACGAGAC 59.007 55.000 0.00 0.00 0.00 3.36
882 886 0.888619 AGATCACCAAGCGAACGAGA 59.111 50.000 0.00 0.00 0.00 4.04
883 887 1.135257 AGAGATCACCAAGCGAACGAG 60.135 52.381 0.00 0.00 0.00 4.18
884 888 0.888619 AGAGATCACCAAGCGAACGA 59.111 50.000 0.00 0.00 0.00 3.85
885 889 1.656095 GAAGAGATCACCAAGCGAACG 59.344 52.381 0.00 0.00 0.00 3.95
886 890 2.003301 GGAAGAGATCACCAAGCGAAC 58.997 52.381 0.00 0.00 0.00 3.95
887 891 1.902508 AGGAAGAGATCACCAAGCGAA 59.097 47.619 0.00 0.00 0.00 4.70
888 892 1.478510 GAGGAAGAGATCACCAAGCGA 59.521 52.381 0.00 0.00 0.00 4.93
889 893 1.480137 AGAGGAAGAGATCACCAAGCG 59.520 52.381 0.00 0.00 0.00 4.68
890 894 2.235898 ACAGAGGAAGAGATCACCAAGC 59.764 50.000 0.00 0.00 0.00 4.01
891 895 4.550076 AACAGAGGAAGAGATCACCAAG 57.450 45.455 0.00 0.00 0.00 3.61
892 896 4.645535 CAAACAGAGGAAGAGATCACCAA 58.354 43.478 0.00 0.00 0.00 3.67
893 897 3.557898 GCAAACAGAGGAAGAGATCACCA 60.558 47.826 0.00 0.00 0.00 4.17
894 898 3.006247 GCAAACAGAGGAAGAGATCACC 58.994 50.000 0.00 0.00 0.00 4.02
895 899 2.670414 CGCAAACAGAGGAAGAGATCAC 59.330 50.000 0.00 0.00 0.00 3.06
896 900 2.932622 GCGCAAACAGAGGAAGAGATCA 60.933 50.000 0.30 0.00 0.00 2.92
897 901 1.663135 GCGCAAACAGAGGAAGAGATC 59.337 52.381 0.30 0.00 0.00 2.75
898 902 1.002430 TGCGCAAACAGAGGAAGAGAT 59.998 47.619 8.16 0.00 0.00 2.75
899 903 0.392706 TGCGCAAACAGAGGAAGAGA 59.607 50.000 8.16 0.00 0.00 3.10
900 904 1.396301 GATGCGCAAACAGAGGAAGAG 59.604 52.381 17.11 0.00 0.00 2.85
901 905 1.270785 TGATGCGCAAACAGAGGAAGA 60.271 47.619 17.11 0.00 0.00 2.87
902 906 1.159285 TGATGCGCAAACAGAGGAAG 58.841 50.000 17.11 0.00 0.00 3.46
903 907 1.739466 GATGATGCGCAAACAGAGGAA 59.261 47.619 17.11 0.00 0.00 3.36
904 908 1.065926 AGATGATGCGCAAACAGAGGA 60.066 47.619 17.11 0.00 0.00 3.71
905 909 1.329906 GAGATGATGCGCAAACAGAGG 59.670 52.381 17.11 0.00 0.00 3.69
906 910 2.277969 AGAGATGATGCGCAAACAGAG 58.722 47.619 17.11 0.00 0.00 3.35
907 911 2.391616 AGAGATGATGCGCAAACAGA 57.608 45.000 17.11 0.00 0.00 3.41
908 912 2.223203 GGAAGAGATGATGCGCAAACAG 60.223 50.000 17.11 0.00 0.00 3.16
909 913 1.739466 GGAAGAGATGATGCGCAAACA 59.261 47.619 17.11 18.71 0.00 2.83
910 914 1.064654 GGGAAGAGATGATGCGCAAAC 59.935 52.381 17.11 12.90 0.00 2.93
911 915 1.339920 TGGGAAGAGATGATGCGCAAA 60.340 47.619 17.11 6.35 0.00 3.68
912 916 0.252761 TGGGAAGAGATGATGCGCAA 59.747 50.000 17.11 0.00 0.00 4.85
913 917 0.179065 CTGGGAAGAGATGATGCGCA 60.179 55.000 14.96 14.96 0.00 6.09
914 918 1.505477 GCTGGGAAGAGATGATGCGC 61.505 60.000 0.00 0.00 0.00 6.09
915 919 0.883814 GGCTGGGAAGAGATGATGCG 60.884 60.000 0.00 0.00 0.00 4.73
916 920 0.182061 TGGCTGGGAAGAGATGATGC 59.818 55.000 0.00 0.00 0.00 3.91
917 921 2.092538 AGTTGGCTGGGAAGAGATGATG 60.093 50.000 0.00 0.00 0.00 3.07
918 922 2.172293 GAGTTGGCTGGGAAGAGATGAT 59.828 50.000 0.00 0.00 0.00 2.45
919 923 1.556911 GAGTTGGCTGGGAAGAGATGA 59.443 52.381 0.00 0.00 0.00 2.92
920 924 1.407989 GGAGTTGGCTGGGAAGAGATG 60.408 57.143 0.00 0.00 0.00 2.90
921 925 0.915364 GGAGTTGGCTGGGAAGAGAT 59.085 55.000 0.00 0.00 0.00 2.75
922 926 1.201429 GGGAGTTGGCTGGGAAGAGA 61.201 60.000 0.00 0.00 0.00 3.10
923 927 1.301293 GGGAGTTGGCTGGGAAGAG 59.699 63.158 0.00 0.00 0.00 2.85
924 928 2.231380 GGGGAGTTGGCTGGGAAGA 61.231 63.158 0.00 0.00 0.00 2.87
925 929 2.356667 GGGGAGTTGGCTGGGAAG 59.643 66.667 0.00 0.00 0.00 3.46
926 930 3.646715 CGGGGAGTTGGCTGGGAA 61.647 66.667 0.00 0.00 0.00 3.97
927 931 3.549433 TACGGGGAGTTGGCTGGGA 62.549 63.158 0.00 0.00 0.00 4.37
928 932 3.006728 TACGGGGAGTTGGCTGGG 61.007 66.667 0.00 0.00 0.00 4.45
929 933 2.584608 CTACGGGGAGTTGGCTGG 59.415 66.667 0.00 0.00 0.00 4.85
930 934 1.327690 TAGCTACGGGGAGTTGGCTG 61.328 60.000 0.00 0.00 39.62 4.85
931 935 1.001248 TAGCTACGGGGAGTTGGCT 59.999 57.895 0.00 0.00 41.22 4.75
932 936 1.442148 CTAGCTACGGGGAGTTGGC 59.558 63.158 0.00 0.00 0.00 4.52
933 937 1.043673 AGCTAGCTACGGGGAGTTGG 61.044 60.000 17.69 0.00 0.00 3.77
934 938 1.609555 CTAGCTAGCTACGGGGAGTTG 59.390 57.143 20.67 4.00 0.00 3.16
935 939 1.984066 CTAGCTAGCTACGGGGAGTT 58.016 55.000 20.67 0.00 0.00 3.01
936 940 0.537828 GCTAGCTAGCTACGGGGAGT 60.538 60.000 33.71 0.00 45.62 3.85
937 941 2.259281 GCTAGCTAGCTACGGGGAG 58.741 63.158 33.71 12.62 45.62 4.30
938 942 4.496429 GCTAGCTAGCTACGGGGA 57.504 61.111 33.71 1.02 45.62 4.81
947 951 0.671251 CGGTCCCTCAAGCTAGCTAG 59.329 60.000 19.70 16.84 0.00 3.42
948 952 1.392710 GCGGTCCCTCAAGCTAGCTA 61.393 60.000 19.70 1.64 0.00 3.32
949 953 2.726351 GCGGTCCCTCAAGCTAGCT 61.726 63.158 12.68 12.68 0.00 3.32
950 954 2.202946 GCGGTCCCTCAAGCTAGC 60.203 66.667 6.62 6.62 0.00 3.42
951 955 1.142748 CAGCGGTCCCTCAAGCTAG 59.857 63.158 0.00 0.00 37.94 3.42
952 956 1.605058 GACAGCGGTCCCTCAAGCTA 61.605 60.000 5.60 0.00 37.94 3.32
953 957 2.925170 ACAGCGGTCCCTCAAGCT 60.925 61.111 0.00 0.00 41.07 3.74
954 958 2.435059 GACAGCGGTCCCTCAAGC 60.435 66.667 5.60 0.00 38.12 4.01
955 959 2.125912 CGACAGCGGTCCCTCAAG 60.126 66.667 11.54 0.00 41.13 3.02
956 960 4.373116 GCGACAGCGGTCCCTCAA 62.373 66.667 11.54 0.00 41.13 3.02
967 971 1.444553 GACCTTGGACGAGCGACAG 60.445 63.158 0.00 0.00 0.00 3.51
976 980 2.427506 GATCTGTGTTGGACCTTGGAC 58.572 52.381 0.00 0.00 0.00 4.02
977 981 1.001974 CGATCTGTGTTGGACCTTGGA 59.998 52.381 0.00 0.00 0.00 3.53
978 982 1.442769 CGATCTGTGTTGGACCTTGG 58.557 55.000 0.00 0.00 0.00 3.61
980 984 0.396435 TGCGATCTGTGTTGGACCTT 59.604 50.000 0.00 0.00 0.00 3.50
981 985 0.396435 TTGCGATCTGTGTTGGACCT 59.604 50.000 0.00 0.00 0.00 3.85
982 986 1.131126 CATTGCGATCTGTGTTGGACC 59.869 52.381 0.00 0.00 0.00 4.46
993 997 2.513666 TCGGTGCCCATTGCGATC 60.514 61.111 0.00 0.00 45.60 3.69
1052 1056 4.295119 AGGACGTGACGGTGGTGC 62.295 66.667 10.66 0.00 0.00 5.01
1519 1523 2.842496 ACTTGATCTGCTCATGGGAGAA 59.158 45.455 0.00 0.00 45.21 2.87
1575 1579 4.475135 GTGAGGAGCTTCCGGCCC 62.475 72.222 0.00 0.00 42.75 5.80
1617 1621 4.833938 TCCTCTTCCTCATCATCATCAGAG 59.166 45.833 0.00 0.00 0.00 3.35
1618 1622 4.812653 TCCTCTTCCTCATCATCATCAGA 58.187 43.478 0.00 0.00 0.00 3.27
1635 1669 3.272020 AGTCATCTTCTTCCTCCTCCTCT 59.728 47.826 0.00 0.00 0.00 3.69
1687 1733 2.371306 GTCACCTCAGTAGTCCTCCTC 58.629 57.143 0.00 0.00 0.00 3.71
1688 1734 1.006162 GGTCACCTCAGTAGTCCTCCT 59.994 57.143 0.00 0.00 0.00 3.69
1689 1735 1.476477 GGTCACCTCAGTAGTCCTCC 58.524 60.000 0.00 0.00 0.00 4.30
1728 1777 2.237143 CTGGTAGAATTCCCTGTGCAGA 59.763 50.000 0.65 0.00 0.00 4.26
1733 1782 1.840635 GGAGCTGGTAGAATTCCCTGT 59.159 52.381 0.65 0.00 0.00 4.00
1735 1784 2.270434 TGGAGCTGGTAGAATTCCCT 57.730 50.000 0.65 0.00 0.00 4.20
1736 1785 2.924421 CTTGGAGCTGGTAGAATTCCC 58.076 52.381 0.65 0.00 0.00 3.97
1737 1786 2.293170 GCTTGGAGCTGGTAGAATTCC 58.707 52.381 0.65 0.00 38.45 3.01
1738 1787 2.991250 TGCTTGGAGCTGGTAGAATTC 58.009 47.619 0.00 0.00 42.97 2.17
1739 1788 3.245052 ACTTGCTTGGAGCTGGTAGAATT 60.245 43.478 0.00 0.00 42.97 2.17
1740 1789 2.307098 ACTTGCTTGGAGCTGGTAGAAT 59.693 45.455 0.00 0.00 42.97 2.40
1741 1790 1.699634 ACTTGCTTGGAGCTGGTAGAA 59.300 47.619 0.00 0.00 42.97 2.10
1742 1791 1.352083 ACTTGCTTGGAGCTGGTAGA 58.648 50.000 0.00 0.00 42.97 2.59
1743 1792 2.234908 AGTACTTGCTTGGAGCTGGTAG 59.765 50.000 0.00 0.00 42.97 3.18
1744 1793 2.257207 AGTACTTGCTTGGAGCTGGTA 58.743 47.619 0.00 2.36 42.97 3.25
1745 1794 1.059913 AGTACTTGCTTGGAGCTGGT 58.940 50.000 0.00 3.21 42.97 4.00
1746 1795 2.234908 ACTAGTACTTGCTTGGAGCTGG 59.765 50.000 0.00 0.00 42.97 4.85
1747 1796 3.257393 CACTAGTACTTGCTTGGAGCTG 58.743 50.000 0.00 0.00 42.97 4.24
1748 1797 2.354203 GCACTAGTACTTGCTTGGAGCT 60.354 50.000 11.53 0.00 42.97 4.09
1749 1798 2.003301 GCACTAGTACTTGCTTGGAGC 58.997 52.381 11.53 0.00 42.82 4.70
1750 1799 3.319137 TGCACTAGTACTTGCTTGGAG 57.681 47.619 18.00 3.44 39.62 3.86
1751 1800 3.599343 CATGCACTAGTACTTGCTTGGA 58.401 45.455 20.09 8.80 39.19 3.53
1752 1801 2.096496 GCATGCACTAGTACTTGCTTGG 59.904 50.000 25.14 14.72 41.72 3.61
1753 1802 2.222886 CGCATGCACTAGTACTTGCTTG 60.223 50.000 23.93 22.13 43.36 4.01
1754 1803 2.002586 CGCATGCACTAGTACTTGCTT 58.997 47.619 23.93 10.65 39.62 3.91
1755 1804 1.066858 ACGCATGCACTAGTACTTGCT 60.067 47.619 23.93 13.07 39.62 3.91
1756 1805 1.359848 ACGCATGCACTAGTACTTGC 58.640 50.000 19.57 19.31 39.33 4.01
1757 1806 4.862574 TCTAAACGCATGCACTAGTACTTG 59.137 41.667 19.57 0.59 0.00 3.16
1758 1807 4.863131 GTCTAAACGCATGCACTAGTACTT 59.137 41.667 19.57 2.39 0.00 2.24
1759 1808 4.158025 AGTCTAAACGCATGCACTAGTACT 59.842 41.667 19.57 10.83 0.00 2.73
1760 1809 4.421948 AGTCTAAACGCATGCACTAGTAC 58.578 43.478 19.57 8.66 0.00 2.73
1761 1810 4.713824 AGTCTAAACGCATGCACTAGTA 57.286 40.909 19.57 1.15 0.00 1.82
1762 1811 3.594603 AGTCTAAACGCATGCACTAGT 57.405 42.857 19.57 4.10 0.00 2.57
1763 1812 3.000674 CGAAGTCTAAACGCATGCACTAG 60.001 47.826 19.57 13.96 0.00 2.57
1764 1813 2.921121 CGAAGTCTAAACGCATGCACTA 59.079 45.455 19.57 4.40 0.00 2.74
1765 1814 1.726791 CGAAGTCTAAACGCATGCACT 59.273 47.619 19.57 9.45 0.00 4.40
1766 1815 1.459592 ACGAAGTCTAAACGCATGCAC 59.540 47.619 19.57 7.01 29.74 4.57
1767 1816 1.790755 ACGAAGTCTAAACGCATGCA 58.209 45.000 19.57 0.00 29.74 3.96
1768 1817 2.495939 CAACGAAGTCTAAACGCATGC 58.504 47.619 7.91 7.91 45.00 4.06
1769 1818 2.157668 AGCAACGAAGTCTAAACGCATG 59.842 45.455 0.00 0.00 45.00 4.06
1770 1819 2.157668 CAGCAACGAAGTCTAAACGCAT 59.842 45.455 0.00 0.00 45.00 4.73
1771 1820 1.525197 CAGCAACGAAGTCTAAACGCA 59.475 47.619 0.00 0.00 45.00 5.24
1784 1833 0.368227 GAGATCAACGAGCAGCAACG 59.632 55.000 9.85 9.85 0.00 4.10
1785 1834 0.368227 CGAGATCAACGAGCAGCAAC 59.632 55.000 6.49 0.00 0.00 4.17
1787 1836 0.808755 TACGAGATCAACGAGCAGCA 59.191 50.000 16.73 0.00 34.70 4.41
1812 1861 7.434602 CAGGTAGTAAACTCCTAATAAACGAGC 59.565 40.741 0.00 0.00 0.00 5.03
1813 1862 8.465201 ACAGGTAGTAAACTCCTAATAAACGAG 58.535 37.037 0.00 0.00 0.00 4.18
1815 1872 8.246180 TGACAGGTAGTAAACTCCTAATAAACG 58.754 37.037 0.00 0.00 0.00 3.60
1821 1878 6.021030 ACCATGACAGGTAGTAAACTCCTAA 58.979 40.000 0.00 0.00 40.98 2.69
1822 1879 5.421056 CACCATGACAGGTAGTAAACTCCTA 59.579 44.000 0.00 0.00 40.77 2.94
1825 1882 5.401531 TCACCATGACAGGTAGTAAACTC 57.598 43.478 0.00 0.00 40.77 3.01
1828 1885 6.156083 TCATCATCACCATGACAGGTAGTAAA 59.844 38.462 0.00 0.00 42.05 2.01
1829 1886 5.660864 TCATCATCACCATGACAGGTAGTAA 59.339 40.000 0.00 0.00 42.05 2.24
1830 1887 5.208121 TCATCATCACCATGACAGGTAGTA 58.792 41.667 0.00 0.00 42.05 1.82
1831 1888 4.033009 TCATCATCACCATGACAGGTAGT 58.967 43.478 0.00 0.00 42.05 2.73
1832 1889 4.677673 TCATCATCACCATGACAGGTAG 57.322 45.455 0.00 0.00 42.05 3.18
1849 1906 5.982516 CCACAAGAAGCTACTAGTCATCATC 59.017 44.000 0.00 0.00 0.00 2.92
2040 2108 8.813643 AACGCACTACCTAATTAGCTATTTAG 57.186 34.615 21.04 21.04 0.00 1.85
2042 2110 9.257651 CTTAACGCACTACCTAATTAGCTATTT 57.742 33.333 6.99 6.17 0.00 1.40
2043 2111 7.871463 CCTTAACGCACTACCTAATTAGCTATT 59.129 37.037 6.99 0.00 0.00 1.73
2044 2112 7.015001 ACCTTAACGCACTACCTAATTAGCTAT 59.985 37.037 6.99 0.00 0.00 2.97
2045 2113 6.322201 ACCTTAACGCACTACCTAATTAGCTA 59.678 38.462 6.99 0.00 0.00 3.32
2046 2114 5.128335 ACCTTAACGCACTACCTAATTAGCT 59.872 40.000 6.99 0.00 0.00 3.32
2080 2148 7.915293 TCAACACAAATCGATAAACACCTAT 57.085 32.000 0.00 0.00 0.00 2.57
2085 2159 8.563732 TGATTCTTCAACACAAATCGATAAACA 58.436 29.630 0.00 0.00 32.09 2.83
2121 2195 1.600957 GCCAACTCATCATCATCACCG 59.399 52.381 0.00 0.00 0.00 4.94
2122 2196 1.600957 CGCCAACTCATCATCATCACC 59.399 52.381 0.00 0.00 0.00 4.02
2133 2207 0.106708 AGAAAGCAGTCGCCAACTCA 59.893 50.000 0.00 0.00 39.83 3.41
2138 2212 2.831685 TTAGAAGAAAGCAGTCGCCA 57.168 45.000 0.00 0.00 39.83 5.69
2140 2214 3.369451 CCTCTTTAGAAGAAAGCAGTCGC 59.631 47.826 0.00 0.00 37.02 5.19
2141 2215 4.387256 CACCTCTTTAGAAGAAAGCAGTCG 59.613 45.833 0.00 0.00 37.02 4.18
2145 2219 5.248640 CCATCACCTCTTTAGAAGAAAGCA 58.751 41.667 0.00 0.00 37.02 3.91
2190 2268 7.870445 TGGACATTTGTAACAAAATTAAGGCTC 59.130 33.333 0.00 0.00 0.00 4.70
2197 2275 6.287525 CCTGGTGGACATTTGTAACAAAATT 58.712 36.000 0.00 0.00 34.57 1.82
2198 2276 5.221621 CCCTGGTGGACATTTGTAACAAAAT 60.222 40.000 0.00 0.00 35.39 1.82
2199 2277 4.100189 CCCTGGTGGACATTTGTAACAAAA 59.900 41.667 0.00 0.00 35.39 2.44
2200 2278 3.639094 CCCTGGTGGACATTTGTAACAAA 59.361 43.478 0.00 0.00 35.39 2.83
2201 2279 3.226777 CCCTGGTGGACATTTGTAACAA 58.773 45.455 0.00 0.00 35.39 2.83
2202 2280 2.175931 ACCCTGGTGGACATTTGTAACA 59.824 45.455 0.00 0.00 38.00 2.41
2203 2281 2.871453 ACCCTGGTGGACATTTGTAAC 58.129 47.619 0.00 0.00 38.00 2.50
2204 2282 3.603965 AACCCTGGTGGACATTTGTAA 57.396 42.857 0.00 0.00 38.00 2.41
2221 2299 3.335579 ACCGTCAAGATCAAAGCTAACC 58.664 45.455 0.00 0.00 0.00 2.85
2242 2320 4.270008 TCAGAGATGATGTAGTCGACCAA 58.730 43.478 13.01 0.00 0.00 3.67
2245 2328 5.741510 CACTTTCAGAGATGATGTAGTCGAC 59.258 44.000 7.70 7.70 0.00 4.20
2263 2346 3.004419 GTGTTTAGTCCCCTTGCACTTTC 59.996 47.826 0.00 0.00 0.00 2.62
2273 2356 2.597578 AATGGGTGTGTTTAGTCCCC 57.402 50.000 0.00 0.00 39.20 4.81
2290 2373 7.043961 TCTTAGCGAGACTTGACATGATAAT 57.956 36.000 0.00 0.00 0.00 1.28
2311 2398 4.273480 CGACCCATATCGCAAATCTTTCTT 59.727 41.667 0.00 0.00 34.90 2.52
2315 2402 3.393800 CTCGACCCATATCGCAAATCTT 58.606 45.455 0.00 0.00 41.97 2.40
2323 2410 0.673985 TTGCTCCTCGACCCATATCG 59.326 55.000 0.00 0.00 43.63 2.92
2333 2420 2.672961 TAATGGTCTGTTGCTCCTCG 57.327 50.000 0.00 0.00 0.00 4.63
2340 2427 3.011818 TGCTGCTGATAATGGTCTGTTG 58.988 45.455 0.00 0.00 0.00 3.33
2342 2429 2.421107 CCTGCTGCTGATAATGGTCTGT 60.421 50.000 8.20 0.00 0.00 3.41
2345 2432 1.133976 ACCCTGCTGCTGATAATGGTC 60.134 52.381 8.20 0.00 0.00 4.02
2346 2433 0.921896 ACCCTGCTGCTGATAATGGT 59.078 50.000 8.20 3.57 0.00 3.55
2347 2434 2.105477 ACTACCCTGCTGCTGATAATGG 59.895 50.000 8.20 2.94 0.00 3.16
2348 2435 3.482156 ACTACCCTGCTGCTGATAATG 57.518 47.619 8.20 0.00 0.00 1.90
2365 2458 7.495934 GCTTATGCTAAATGGACTGAGAAACTA 59.504 37.037 0.00 0.00 36.03 2.24
2392 2485 1.086696 TTCTGCACCGCAATTAGAGC 58.913 50.000 0.00 0.00 38.41 4.09
2409 4420 5.534278 AGGTCCTAATAGGTACGTAGCTTTC 59.466 44.000 30.17 11.44 36.53 2.62
2421 4432 5.222171 ACTGCTAGACCTAGGTCCTAATAGG 60.222 48.000 33.81 20.84 45.59 2.57
2422 4433 5.883180 ACTGCTAGACCTAGGTCCTAATAG 58.117 45.833 33.81 27.55 45.59 1.73
2423 4434 5.926580 ACTGCTAGACCTAGGTCCTAATA 57.073 43.478 33.81 20.26 45.59 0.98
2424 4435 4.817874 ACTGCTAGACCTAGGTCCTAAT 57.182 45.455 33.81 20.23 45.59 1.73
2425 4436 4.104420 CCTACTGCTAGACCTAGGTCCTAA 59.896 50.000 33.81 20.49 45.59 2.69
2426 4437 3.651904 CCTACTGCTAGACCTAGGTCCTA 59.348 52.174 33.81 23.56 45.59 2.94
2427 4438 2.444010 CCTACTGCTAGACCTAGGTCCT 59.556 54.545 33.81 23.70 45.59 3.85
2428 4439 2.175284 ACCTACTGCTAGACCTAGGTCC 59.825 54.545 33.81 21.17 45.59 4.46
2438 4449 4.021894 CCTAATGCCTACACCTACTGCTAG 60.022 50.000 0.00 0.00 0.00 3.42
2464 4492 0.532573 TTCGCTCCTCTGCTGTAAGG 59.467 55.000 0.00 0.00 0.00 2.69
2465 4493 2.094494 TCTTTCGCTCCTCTGCTGTAAG 60.094 50.000 0.00 0.00 0.00 2.34
2466 4494 1.893137 TCTTTCGCTCCTCTGCTGTAA 59.107 47.619 0.00 0.00 0.00 2.41
2480 4525 2.029828 ACAGCTAGTGACCTGTCTTTCG 60.030 50.000 0.00 0.00 37.77 3.46
2494 4539 2.148916 TGACCGTGTTTCACAGCTAG 57.851 50.000 0.00 0.00 33.40 3.42
2500 4545 1.130938 ACCGTTTTGACCGTGTTTCAC 59.869 47.619 0.00 0.00 0.00 3.18
2501 4546 1.130749 CACCGTTTTGACCGTGTTTCA 59.869 47.619 0.00 0.00 0.00 2.69
2502 4547 1.817609 CACCGTTTTGACCGTGTTTC 58.182 50.000 0.00 0.00 0.00 2.78
2503 4548 0.179158 GCACCGTTTTGACCGTGTTT 60.179 50.000 0.00 0.00 0.00 2.83
2504 4549 1.027792 AGCACCGTTTTGACCGTGTT 61.028 50.000 0.00 0.00 0.00 3.32
2505 4550 1.027792 AAGCACCGTTTTGACCGTGT 61.028 50.000 0.00 0.00 0.00 4.49
2506 4551 0.591236 CAAGCACCGTTTTGACCGTG 60.591 55.000 0.00 0.00 0.00 4.94
2507 4552 1.027792 ACAAGCACCGTTTTGACCGT 61.028 50.000 0.00 0.00 0.00 4.83
2508 4553 0.099791 AACAAGCACCGTTTTGACCG 59.900 50.000 0.00 0.00 0.00 4.79
2509 4554 1.135228 ACAACAAGCACCGTTTTGACC 60.135 47.619 0.00 0.00 0.00 4.02
2516 4561 1.305201 CCAAGTACAACAAGCACCGT 58.695 50.000 0.00 0.00 0.00 4.83
2549 4595 1.078072 ACACGACAACACCCTGCAA 60.078 52.632 0.00 0.00 0.00 4.08
2614 4660 3.435671 CGTGGGTAGAACTTTTGTCATCC 59.564 47.826 0.00 0.00 0.00 3.51
2654 4700 6.041296 GGATTTGTGAATTCCAGCTATTCCAT 59.959 38.462 2.27 0.00 32.29 3.41
2655 4701 5.360714 GGATTTGTGAATTCCAGCTATTCCA 59.639 40.000 2.27 1.56 32.29 3.53
2657 4703 5.506317 CCGGATTTGTGAATTCCAGCTATTC 60.506 44.000 0.00 1.40 33.58 1.75
2659 4705 3.885297 CCGGATTTGTGAATTCCAGCTAT 59.115 43.478 0.00 0.00 0.00 2.97
2660 4706 3.278574 CCGGATTTGTGAATTCCAGCTA 58.721 45.455 0.00 0.00 0.00 3.32
2661 4707 2.094675 CCGGATTTGTGAATTCCAGCT 58.905 47.619 0.00 0.00 0.00 4.24
2662 4708 1.469767 GCCGGATTTGTGAATTCCAGC 60.470 52.381 5.05 0.00 0.00 4.85
2663 4709 1.818060 TGCCGGATTTGTGAATTCCAG 59.182 47.619 5.05 0.00 0.00 3.86
2664 4710 1.543802 GTGCCGGATTTGTGAATTCCA 59.456 47.619 5.05 0.00 0.00 3.53
2665 4711 1.467374 CGTGCCGGATTTGTGAATTCC 60.467 52.381 5.05 0.00 0.00 3.01
2666 4712 1.199097 ACGTGCCGGATTTGTGAATTC 59.801 47.619 5.05 0.00 0.00 2.17
2667 4713 1.199097 GACGTGCCGGATTTGTGAATT 59.801 47.619 5.05 0.00 0.00 2.17
2668 4714 0.802494 GACGTGCCGGATTTGTGAAT 59.198 50.000 5.05 0.00 0.00 2.57
2669 4715 1.231958 GGACGTGCCGGATTTGTGAA 61.232 55.000 5.05 0.00 0.00 3.18
2670 4716 1.669760 GGACGTGCCGGATTTGTGA 60.670 57.895 5.05 0.00 0.00 3.58
2671 4717 2.867472 GGACGTGCCGGATTTGTG 59.133 61.111 5.05 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.