Multiple sequence alignment - TraesCS7A01G410900

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 TraesCS7A01G410900 chr7A 100.000 6035 0 0 1 6035 598355355 598349321 0.000000e+00 11145.0
1 TraesCS7A01G410900 chr7B 96.728 4920 132 18 1013 5922 554193696 554188796 0.000000e+00 8167.0
2 TraesCS7A01G410900 chr7B 90.311 867 57 12 948 1812 554339838 554338997 0.000000e+00 1110.0
3 TraesCS7A01G410900 chr7B 87.548 787 95 3 1 787 639868927 639869710 0.000000e+00 907.0
4 TraesCS7A01G410900 chr7B 88.837 430 31 9 955 1384 554355552 554355140 4.170000e-141 512.0
5 TraesCS7A01G410900 chr7B 94.068 118 5 2 5920 6035 554188747 554188630 1.730000e-40 178.0
6 TraesCS7A01G410900 chr7D 97.355 4613 100 14 1316 5922 520865159 520860563 0.000000e+00 7823.0
7 TraesCS7A01G410900 chr7D 88.396 586 45 14 955 1539 520872334 520871771 0.000000e+00 684.0
8 TraesCS7A01G410900 chr7D 93.966 116 6 1 5920 6035 520860515 520860401 2.240000e-39 174.0
9 TraesCS7A01G410900 chr7D 81.461 178 5 9 948 1112 520865763 520865601 2.950000e-23 121.0
10 TraesCS7A01G410900 chr3B 86.224 784 106 2 1 784 763272806 763272025 0.000000e+00 848.0
11 TraesCS7A01G410900 chr3B 84.949 784 116 2 1 784 774793728 774792947 0.000000e+00 793.0
12 TraesCS7A01G410900 chr3B 84.724 779 117 1 1 779 750201612 750202388 0.000000e+00 778.0
13 TraesCS7A01G410900 chr3B 83.549 772 123 3 1 771 457597057 457596289 0.000000e+00 719.0
14 TraesCS7A01G410900 chr5B 85.842 784 109 2 1 784 623557601 623556820 0.000000e+00 832.0
15 TraesCS7A01G410900 chr5B 85.842 784 109 2 1 784 627155835 627155054 0.000000e+00 832.0
16 TraesCS7A01G410900 chr4A 85.077 784 113 3 1 784 196568343 196567564 0.000000e+00 797.0
17 TraesCS7A01G410900 chr4D 82.803 785 132 2 1 784 446170652 446169870 0.000000e+00 699.0
18 TraesCS7A01G410900 chrUn 86.957 138 18 0 2411 2548 22142955 22142818 8.100000e-34 156.0
19 TraesCS7A01G410900 chrUn 98.438 64 1 0 2545 2608 22142269 22142206 4.940000e-21 113.0
20 TraesCS7A01G410900 chr2A 86.957 138 18 0 2411 2548 681091991 681092128 8.100000e-34 156.0
21 TraesCS7A01G410900 chr2B 80.172 232 22 7 1417 1648 17597010 17596803 1.050000e-32 152.0
22 TraesCS7A01G410900 chr2D 98.438 64 1 0 2545 2608 538669336 538669399 4.940000e-21 113.0
23 TraesCS7A01G410900 chr3D 97.143 35 1 0 5494 5528 37073516 37073550 6.530000e-05 60.2
24 TraesCS7A01G410900 chr3D 100.000 28 0 0 5500 5527 37073501 37073474 1.100000e-02 52.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G410900 chr7A 598349321 598355355 6034 True 11145.0 11145 100.000000 1 6035 1 chr7A.!!$R1 6034
1 TraesCS7A01G410900 chr7B 554188630 554193696 5066 True 4172.5 8167 95.398000 1013 6035 2 chr7B.!!$R3 5022
2 TraesCS7A01G410900 chr7B 554338997 554339838 841 True 1110.0 1110 90.311000 948 1812 1 chr7B.!!$R1 864
3 TraesCS7A01G410900 chr7B 639868927 639869710 783 False 907.0 907 87.548000 1 787 1 chr7B.!!$F1 786
4 TraesCS7A01G410900 chr7D 520860401 520865763 5362 True 2706.0 7823 90.927333 948 6035 3 chr7D.!!$R2 5087
5 TraesCS7A01G410900 chr7D 520871771 520872334 563 True 684.0 684 88.396000 955 1539 1 chr7D.!!$R1 584
6 TraesCS7A01G410900 chr3B 763272025 763272806 781 True 848.0 848 86.224000 1 784 1 chr3B.!!$R2 783
7 TraesCS7A01G410900 chr3B 774792947 774793728 781 True 793.0 793 84.949000 1 784 1 chr3B.!!$R3 783
8 TraesCS7A01G410900 chr3B 750201612 750202388 776 False 778.0 778 84.724000 1 779 1 chr3B.!!$F1 778
9 TraesCS7A01G410900 chr3B 457596289 457597057 768 True 719.0 719 83.549000 1 771 1 chr3B.!!$R1 770
10 TraesCS7A01G410900 chr5B 623556820 623557601 781 True 832.0 832 85.842000 1 784 1 chr5B.!!$R1 783
11 TraesCS7A01G410900 chr5B 627155054 627155835 781 True 832.0 832 85.842000 1 784 1 chr5B.!!$R2 783
12 TraesCS7A01G410900 chr4A 196567564 196568343 779 True 797.0 797 85.077000 1 784 1 chr4A.!!$R1 783
13 TraesCS7A01G410900 chr4D 446169870 446170652 782 True 699.0 699 82.803000 1 784 1 chr4D.!!$R1 783


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
255 257 0.036010 ACCTTGTCATTGAGGCCGAG 60.036 55.000 0.00 0.0 36.48 4.63 F
2034 2293 0.037590 AAGGGCGTACAATTGCTGGA 59.962 50.000 5.05 0.0 0.00 3.86 F
2750 3009 1.277842 TGTTGAGCTCCTATCGGCAAA 59.722 47.619 12.15 0.0 0.00 3.68 F
4446 4705 1.754803 CTATCTGGTGCTTCCACGGTA 59.245 52.381 0.00 0.0 43.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2193 2452 0.038744 CTGTGATCCCAGTGGCCTTT 59.961 55.000 3.32 0.0 0.00 3.11 R
3072 3331 0.391263 GCTGGACCTCCGTAACCTTG 60.391 60.000 0.00 0.0 39.43 3.61 R
4708 4967 0.178964 CCTTCCCCAGTTTTGCCAGA 60.179 55.000 0.00 0.0 0.00 3.86 R
5910 6176 1.455408 GTTTAAGCGCAACAATGGCAC 59.545 47.619 11.47 0.0 0.00 5.01 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
48 50 0.890542 TGTTGCAATCGCCTTCAGCT 60.891 50.000 0.59 0.00 40.39 4.24
93 95 2.925966 TTGCCATGATTTCCTCCCTT 57.074 45.000 0.00 0.00 0.00 3.95
101 103 5.308825 CATGATTTCCTCCCTTTACGCTAT 58.691 41.667 0.00 0.00 0.00 2.97
127 129 5.296780 TCAATCAAGCGATCCATAACCTTTC 59.703 40.000 0.00 0.00 0.00 2.62
255 257 0.036010 ACCTTGTCATTGAGGCCGAG 60.036 55.000 0.00 0.00 36.48 4.63
279 281 1.474478 TCTTGCAACTTGTTCGCCAAA 59.526 42.857 0.00 0.00 31.20 3.28
280 282 2.094494 TCTTGCAACTTGTTCGCCAAAA 60.094 40.909 0.00 0.00 31.20 2.44
300 303 3.807538 GCTAGTGTCGTCGCCGGA 61.808 66.667 5.05 0.00 33.95 5.14
307 310 1.957695 GTCGTCGCCGGACCTTTTT 60.958 57.895 5.05 0.00 40.17 1.94
435 438 1.227089 CGTCTTGAGCAGGATCGGG 60.227 63.158 0.00 0.00 0.00 5.14
456 459 2.354103 GCTGTGATCACTCTTGGCTACA 60.354 50.000 25.55 1.46 0.00 2.74
471 474 2.166664 GGCTACAGTCAGGTGTTCTAGG 59.833 54.545 0.00 0.00 31.46 3.02
551 554 1.535204 CCCTGCAATGTTGACCACCC 61.535 60.000 0.00 0.00 0.00 4.61
587 590 4.523943 TCAAAAGTCCAATCAAGACCCATG 59.476 41.667 0.00 0.00 34.67 3.66
757 760 5.280727 CCCTCCTCAACCTCTTCATAGTTTT 60.281 44.000 0.00 0.00 0.00 2.43
784 787 2.596904 TTATACCGCAAGCTCCTGTC 57.403 50.000 0.00 0.00 0.00 3.51
786 789 0.905357 ATACCGCAAGCTCCTGTCTT 59.095 50.000 0.00 0.00 0.00 3.01
787 790 1.552578 TACCGCAAGCTCCTGTCTTA 58.447 50.000 0.00 0.00 0.00 2.10
788 791 0.905357 ACCGCAAGCTCCTGTCTTAT 59.095 50.000 0.00 0.00 0.00 1.73
789 792 1.134670 ACCGCAAGCTCCTGTCTTATC 60.135 52.381 0.00 0.00 0.00 1.75
790 793 1.134699 CCGCAAGCTCCTGTCTTATCA 60.135 52.381 0.00 0.00 0.00 2.15
791 794 2.621338 CGCAAGCTCCTGTCTTATCAA 58.379 47.619 0.00 0.00 0.00 2.57
792 795 3.201290 CGCAAGCTCCTGTCTTATCAAT 58.799 45.455 0.00 0.00 0.00 2.57
793 796 3.247173 CGCAAGCTCCTGTCTTATCAATC 59.753 47.826 0.00 0.00 0.00 2.67
794 797 4.194640 GCAAGCTCCTGTCTTATCAATCA 58.805 43.478 0.00 0.00 0.00 2.57
795 798 4.820716 GCAAGCTCCTGTCTTATCAATCAT 59.179 41.667 0.00 0.00 0.00 2.45
796 799 5.298777 GCAAGCTCCTGTCTTATCAATCATT 59.701 40.000 0.00 0.00 0.00 2.57
797 800 6.726230 CAAGCTCCTGTCTTATCAATCATTG 58.274 40.000 0.00 0.00 0.00 2.82
798 801 5.999044 AGCTCCTGTCTTATCAATCATTGT 58.001 37.500 0.00 0.00 0.00 2.71
799 802 5.821470 AGCTCCTGTCTTATCAATCATTGTG 59.179 40.000 0.00 0.00 0.00 3.33
800 803 5.505324 GCTCCTGTCTTATCAATCATTGTGC 60.505 44.000 0.00 0.00 0.00 4.57
801 804 4.883585 TCCTGTCTTATCAATCATTGTGCC 59.116 41.667 0.00 0.00 0.00 5.01
802 805 4.885907 CCTGTCTTATCAATCATTGTGCCT 59.114 41.667 0.00 0.00 0.00 4.75
803 806 6.057533 CCTGTCTTATCAATCATTGTGCCTA 58.942 40.000 0.00 0.00 0.00 3.93
804 807 6.543465 CCTGTCTTATCAATCATTGTGCCTAA 59.457 38.462 0.00 0.00 0.00 2.69
805 808 7.255035 CCTGTCTTATCAATCATTGTGCCTAAG 60.255 40.741 0.00 2.33 0.00 2.18
806 809 6.543465 TGTCTTATCAATCATTGTGCCTAAGG 59.457 38.462 0.00 0.00 0.00 2.69
816 819 4.858680 GCCTAAGGCCGGCCAGAC 62.859 72.222 45.13 25.21 44.06 3.51
817 820 4.176752 CCTAAGGCCGGCCAGACC 62.177 72.222 45.13 20.27 38.92 3.85
818 821 3.083997 CTAAGGCCGGCCAGACCT 61.084 66.667 45.13 24.03 38.92 3.85
819 822 2.609610 TAAGGCCGGCCAGACCTT 60.610 61.111 45.13 31.69 45.62 3.50
820 823 2.198304 CTAAGGCCGGCCAGACCTTT 62.198 60.000 45.13 30.97 40.98 3.11
821 824 1.785353 TAAGGCCGGCCAGACCTTTT 61.785 55.000 45.13 30.25 40.98 2.27
822 825 2.600470 GGCCGGCCAGACCTTTTT 60.600 61.111 40.73 0.00 35.61 1.94
823 826 1.303806 GGCCGGCCAGACCTTTTTA 60.304 57.895 40.73 0.00 35.61 1.52
824 827 1.592400 GGCCGGCCAGACCTTTTTAC 61.592 60.000 40.73 7.78 35.61 2.01
825 828 1.918868 GCCGGCCAGACCTTTTTACG 61.919 60.000 18.11 0.00 35.61 3.18
826 829 1.303091 CCGGCCAGACCTTTTTACGG 61.303 60.000 2.24 0.00 35.61 4.02
827 830 0.604511 CGGCCAGACCTTTTTACGGT 60.605 55.000 2.24 0.00 37.50 4.83
828 831 1.612676 GGCCAGACCTTTTTACGGTT 58.387 50.000 0.00 0.00 34.19 4.44
829 832 1.538512 GGCCAGACCTTTTTACGGTTC 59.461 52.381 0.00 0.00 34.19 3.62
830 833 2.501261 GCCAGACCTTTTTACGGTTCT 58.499 47.619 0.00 0.00 34.19 3.01
831 834 2.225727 GCCAGACCTTTTTACGGTTCTG 59.774 50.000 0.00 0.00 34.19 3.02
832 835 2.812011 CCAGACCTTTTTACGGTTCTGG 59.188 50.000 8.04 8.04 40.28 3.86
833 836 3.473625 CAGACCTTTTTACGGTTCTGGT 58.526 45.455 0.00 0.00 34.19 4.00
834 837 4.503643 CCAGACCTTTTTACGGTTCTGGTA 60.504 45.833 12.51 0.00 40.75 3.25
835 838 5.243207 CAGACCTTTTTACGGTTCTGGTAT 58.757 41.667 0.00 0.00 34.19 2.73
836 839 5.121768 CAGACCTTTTTACGGTTCTGGTATG 59.878 44.000 0.00 0.00 34.19 2.39
837 840 4.976864 ACCTTTTTACGGTTCTGGTATGT 58.023 39.130 0.00 0.00 0.00 2.29
838 841 6.014327 AGACCTTTTTACGGTTCTGGTATGTA 60.014 38.462 0.00 0.00 34.19 2.29
839 842 6.168389 ACCTTTTTACGGTTCTGGTATGTAG 58.832 40.000 0.00 0.00 0.00 2.74
840 843 5.583457 CCTTTTTACGGTTCTGGTATGTAGG 59.417 44.000 0.00 0.00 0.00 3.18
841 844 4.741321 TTTACGGTTCTGGTATGTAGGG 57.259 45.455 0.00 0.00 0.00 3.53
842 845 2.242882 ACGGTTCTGGTATGTAGGGT 57.757 50.000 0.00 0.00 0.00 4.34
843 846 2.105766 ACGGTTCTGGTATGTAGGGTC 58.894 52.381 0.00 0.00 0.00 4.46
844 847 2.292061 ACGGTTCTGGTATGTAGGGTCT 60.292 50.000 0.00 0.00 0.00 3.85
845 848 2.100916 CGGTTCTGGTATGTAGGGTCTG 59.899 54.545 0.00 0.00 0.00 3.51
846 849 2.158943 GGTTCTGGTATGTAGGGTCTGC 60.159 54.545 0.00 0.00 0.00 4.26
847 850 2.766828 GTTCTGGTATGTAGGGTCTGCT 59.233 50.000 0.00 0.00 0.00 4.24
848 851 2.667470 TCTGGTATGTAGGGTCTGCTC 58.333 52.381 0.00 0.00 0.00 4.26
849 852 1.338337 CTGGTATGTAGGGTCTGCTCG 59.662 57.143 0.00 0.00 0.00 5.03
850 853 1.064240 TGGTATGTAGGGTCTGCTCGA 60.064 52.381 0.00 0.00 0.00 4.04
851 854 1.337387 GGTATGTAGGGTCTGCTCGAC 59.663 57.143 0.00 0.00 42.07 4.20
852 855 2.299521 GTATGTAGGGTCTGCTCGACT 58.700 52.381 6.67 0.00 42.44 4.18
853 856 1.107114 ATGTAGGGTCTGCTCGACTG 58.893 55.000 6.67 0.00 42.44 3.51
854 857 1.139947 GTAGGGTCTGCTCGACTGC 59.860 63.158 6.67 0.00 42.44 4.40
855 858 1.304134 TAGGGTCTGCTCGACTGCA 60.304 57.895 0.00 0.00 42.44 4.41
861 864 2.048784 TGCTCGACTGCAGCTCAC 60.049 61.111 15.27 2.11 38.12 3.51
862 865 3.177920 GCTCGACTGCAGCTCACG 61.178 66.667 15.27 14.48 33.75 4.35
863 866 3.177920 CTCGACTGCAGCTCACGC 61.178 66.667 15.27 0.00 0.00 5.34
864 867 4.724602 TCGACTGCAGCTCACGCC 62.725 66.667 15.27 0.00 36.60 5.68
866 869 3.117171 GACTGCAGCTCACGCCAG 61.117 66.667 15.27 0.00 36.60 4.85
874 877 2.979676 CTCACGCCAGCCTGCAAA 60.980 61.111 0.00 0.00 0.00 3.68
875 878 2.974489 CTCACGCCAGCCTGCAAAG 61.974 63.158 0.00 0.00 0.00 2.77
876 879 4.712425 CACGCCAGCCTGCAAAGC 62.712 66.667 0.04 0.04 0.00 3.51
880 883 3.297620 CCAGCCTGCAAAGCCGTT 61.298 61.111 4.82 0.00 0.00 4.44
881 884 2.730094 CAGCCTGCAAAGCCGTTT 59.270 55.556 4.82 0.00 0.00 3.60
882 885 1.067916 CAGCCTGCAAAGCCGTTTT 59.932 52.632 4.82 0.00 0.00 2.43
883 886 0.313672 CAGCCTGCAAAGCCGTTTTA 59.686 50.000 4.82 0.00 0.00 1.52
884 887 0.313987 AGCCTGCAAAGCCGTTTTAC 59.686 50.000 4.82 0.00 0.00 2.01
885 888 0.666274 GCCTGCAAAGCCGTTTTACC 60.666 55.000 0.00 0.00 0.00 2.85
886 889 0.386731 CCTGCAAAGCCGTTTTACCG 60.387 55.000 0.00 0.00 0.00 4.02
887 890 1.001745 CTGCAAAGCCGTTTTACCGC 61.002 55.000 0.00 0.00 0.00 5.68
888 891 2.078341 GCAAAGCCGTTTTACCGCG 61.078 57.895 0.00 0.00 0.00 6.46
889 892 1.570475 CAAAGCCGTTTTACCGCGA 59.430 52.632 8.23 0.00 0.00 5.87
890 893 0.041135 CAAAGCCGTTTTACCGCGAA 60.041 50.000 8.23 0.00 0.00 4.70
891 894 0.041047 AAAGCCGTTTTACCGCGAAC 60.041 50.000 8.23 2.38 0.00 3.95
892 895 0.881600 AAGCCGTTTTACCGCGAACT 60.882 50.000 8.23 0.00 0.00 3.01
893 896 1.154543 GCCGTTTTACCGCGAACTG 60.155 57.895 8.23 1.06 0.00 3.16
894 897 1.834458 GCCGTTTTACCGCGAACTGT 61.834 55.000 8.23 0.00 0.00 3.55
895 898 1.417372 CCGTTTTACCGCGAACTGTA 58.583 50.000 8.23 0.00 0.00 2.74
896 899 1.791785 CCGTTTTACCGCGAACTGTAA 59.208 47.619 8.23 4.40 0.00 2.41
897 900 2.220593 CCGTTTTACCGCGAACTGTAAA 59.779 45.455 8.23 11.04 34.77 2.01
898 901 3.120580 CCGTTTTACCGCGAACTGTAAAT 60.121 43.478 8.23 0.00 36.00 1.40
899 902 4.456914 CGTTTTACCGCGAACTGTAAATT 58.543 39.130 8.23 0.00 36.00 1.82
900 903 5.389307 CCGTTTTACCGCGAACTGTAAATTA 60.389 40.000 8.23 0.00 36.00 1.40
901 904 5.724859 CGTTTTACCGCGAACTGTAAATTAG 59.275 40.000 8.23 4.77 36.00 1.73
902 905 6.593072 GTTTTACCGCGAACTGTAAATTAGT 58.407 36.000 8.23 0.00 36.00 2.24
903 906 6.783892 TTTACCGCGAACTGTAAATTAGTT 57.216 33.333 8.23 0.00 40.84 2.24
904 907 6.783892 TTACCGCGAACTGTAAATTAGTTT 57.216 33.333 8.23 0.00 38.42 2.66
905 908 5.678132 ACCGCGAACTGTAAATTAGTTTT 57.322 34.783 8.23 0.00 38.42 2.43
906 909 5.445845 ACCGCGAACTGTAAATTAGTTTTG 58.554 37.500 8.23 0.00 38.42 2.44
907 910 4.319901 CCGCGAACTGTAAATTAGTTTTGC 59.680 41.667 8.23 0.00 38.42 3.68
908 911 4.907010 CGCGAACTGTAAATTAGTTTTGCA 59.093 37.500 0.00 0.00 38.42 4.08
915 918 5.992729 TGTAAATTAGTTTTGCAGGTCGAC 58.007 37.500 7.13 7.13 35.35 4.20
916 919 3.806316 AATTAGTTTTGCAGGTCGACG 57.194 42.857 9.92 0.00 0.00 5.12
917 920 2.512485 TTAGTTTTGCAGGTCGACGA 57.488 45.000 9.92 0.00 0.00 4.20
918 921 2.736144 TAGTTTTGCAGGTCGACGAT 57.264 45.000 9.92 0.00 0.00 3.73
919 922 2.736144 AGTTTTGCAGGTCGACGATA 57.264 45.000 9.92 0.00 0.00 2.92
920 923 2.334838 AGTTTTGCAGGTCGACGATAC 58.665 47.619 9.92 0.00 0.00 2.24
921 924 2.063266 GTTTTGCAGGTCGACGATACA 58.937 47.619 9.92 2.21 0.00 2.29
922 925 1.705256 TTTGCAGGTCGACGATACAC 58.295 50.000 9.92 0.00 0.00 2.90
935 938 3.815337 CGATACACGGGTCTGATAGAG 57.185 52.381 0.00 0.00 38.46 2.43
936 939 3.400255 CGATACACGGGTCTGATAGAGA 58.600 50.000 0.00 0.00 38.46 3.10
937 940 5.275052 ACGATACACGGGTCTGATAGAGAC 61.275 50.000 0.00 0.00 46.37 3.36
1006 1019 2.030371 TCTTCTCGATCAGCATGCTCT 58.970 47.619 19.68 8.29 34.76 4.09
1007 1020 2.034432 TCTTCTCGATCAGCATGCTCTC 59.966 50.000 19.68 16.33 34.76 3.20
1008 1021 0.672889 TCTCGATCAGCATGCTCTCC 59.327 55.000 19.68 8.43 34.76 3.71
1009 1022 0.388294 CTCGATCAGCATGCTCTCCA 59.612 55.000 19.68 5.59 34.76 3.86
1010 1023 0.103755 TCGATCAGCATGCTCTCCAC 59.896 55.000 19.68 7.00 34.76 4.02
1011 1024 1.213733 CGATCAGCATGCTCTCCACG 61.214 60.000 19.68 14.96 34.76 4.94
1082 1100 0.462759 CCACTGCCGAAATCCTCTCC 60.463 60.000 0.00 0.00 0.00 3.71
1083 1101 0.807667 CACTGCCGAAATCCTCTCCG 60.808 60.000 0.00 0.00 0.00 4.63
1084 1102 1.227380 CTGCCGAAATCCTCTCCGG 60.227 63.158 0.00 0.00 44.34 5.14
1086 1104 3.221222 CCGAAATCCTCTCCGGCT 58.779 61.111 0.00 0.00 35.29 5.52
1087 1105 1.068250 CCGAAATCCTCTCCGGCTC 59.932 63.158 0.00 0.00 35.29 4.70
1088 1106 1.395826 CCGAAATCCTCTCCGGCTCT 61.396 60.000 0.00 0.00 35.29 4.09
1629 1885 2.589540 CCGCACATGCCCTTCCTA 59.410 61.111 0.00 0.00 37.91 2.94
1670 1929 4.839706 GCCGATGGCCCCAATGGT 62.840 66.667 0.00 0.00 44.06 3.55
1734 1993 2.437343 CGTTGAGCGCGAGGAAGAC 61.437 63.158 12.10 0.00 0.00 3.01
1785 2044 2.829120 GGACTATAGGCCTCCTAAGCTG 59.171 54.545 18.25 0.00 39.77 4.24
1865 2124 3.100671 AGCCTCCTGAACCTACTTACAG 58.899 50.000 0.00 0.00 0.00 2.74
2034 2293 0.037590 AAGGGCGTACAATTGCTGGA 59.962 50.000 5.05 0.00 0.00 3.86
2055 2314 3.454719 TTGATCTGGGAGAATTGGCAA 57.545 42.857 0.68 0.68 0.00 4.52
2122 2381 2.687700 ATATGATGCCCGCAGAGATC 57.312 50.000 0.00 0.00 0.00 2.75
2193 2452 6.325028 AGCTGCCATATTCTAAGTTAGACTCA 59.675 38.462 12.25 0.00 33.84 3.41
2727 2986 3.766545 AGCTGAATTTTGGGCTGAGTTA 58.233 40.909 0.00 0.00 33.50 2.24
2750 3009 1.277842 TGTTGAGCTCCTATCGGCAAA 59.722 47.619 12.15 0.00 0.00 3.68
2867 3126 2.948979 CAAAGGTACCTGCTGTTGTGAA 59.051 45.455 17.14 0.00 0.00 3.18
3072 3331 2.838736 TGTTCTCAGCAAGGTGAAGAC 58.161 47.619 3.39 5.76 0.00 3.01
4134 4393 3.867493 TCATCACTAGATCAAAAGCTGCG 59.133 43.478 0.00 0.00 30.20 5.18
4428 4687 3.762288 AGACAGTTCACGTTGATAGCCTA 59.238 43.478 0.00 0.00 0.00 3.93
4446 4705 1.754803 CTATCTGGTGCTTCCACGGTA 59.245 52.381 0.00 0.00 43.00 4.02
4470 4729 4.062293 TGTTCACTCTTACAATTGACCGG 58.938 43.478 13.59 0.00 0.00 5.28
4542 4801 3.734463 TGGTGCGTGTTCTTCTAATGAA 58.266 40.909 0.00 0.00 0.00 2.57
4708 4967 2.180276 AGTACAAGAAGGCCTCATCGT 58.820 47.619 5.23 4.20 0.00 3.73
4712 4971 0.539051 AAGAAGGCCTCATCGTCTGG 59.461 55.000 5.23 0.00 0.00 3.86
4965 5224 0.916086 ACCATCGGATTGTTGGGCTA 59.084 50.000 0.84 0.00 41.07 3.93
4986 5245 2.880890 AGTCATTCCAAACACAGCAGTC 59.119 45.455 0.00 0.00 0.00 3.51
4992 5251 1.570813 CAAACACAGCAGTCGAGTCA 58.429 50.000 0.00 0.00 0.00 3.41
5084 5343 2.234300 TTCTTCGGTCTGGTGTTGTC 57.766 50.000 0.00 0.00 0.00 3.18
5085 5344 1.410004 TCTTCGGTCTGGTGTTGTCT 58.590 50.000 0.00 0.00 0.00 3.41
5298 5558 1.152567 CCCACAAGTTGAAGGGCCA 60.153 57.895 20.05 0.00 31.79 5.36
5377 5639 9.860898 AAACTGCTTGTTTTTGGAAGATATATC 57.139 29.630 4.42 4.42 45.69 1.63
5424 5686 0.668535 GTTTGGGGACTTGCACTGTC 59.331 55.000 9.78 9.78 0.00 3.51
5467 5729 3.584406 ACTGTGTTTGATCTCTGGGATGA 59.416 43.478 0.00 0.00 34.33 2.92
5506 5768 2.892784 ACTCCCTACTAAATCAGCGC 57.107 50.000 0.00 0.00 0.00 5.92
5559 5821 8.362464 TCTGATAACCTTTTCAGTAGAGCTTA 57.638 34.615 0.00 0.00 40.22 3.09
5585 5847 2.952310 TCTGTGGTATGATCCTGAGTCG 59.048 50.000 0.00 0.00 0.00 4.18
5604 5866 6.038382 TGAGTCGATAGCTAAGTCTGGTTTAG 59.962 42.308 0.00 0.00 0.00 1.85
5606 5868 6.038492 AGTCGATAGCTAAGTCTGGTTTAGTC 59.962 42.308 0.00 0.00 32.09 2.59
5667 5929 1.142262 GGGGGTGTAGTCTTTGTGTGT 59.858 52.381 0.00 0.00 0.00 3.72
5769 6031 3.534357 TTTTGTGGCCTCTATCCCAAA 57.466 42.857 3.32 0.00 31.90 3.28
5777 6039 5.067805 GTGGCCTCTATCCCAAAATAAAGTG 59.932 44.000 3.32 0.00 31.90 3.16
5813 6075 7.402862 ACATTATGGCTAAACCTCTTTAGTGT 58.597 34.615 0.00 0.00 40.73 3.55
5865 6131 3.953612 TCCTCTGTTTGAGTGCATTGTTT 59.046 39.130 0.00 0.00 41.11 2.83
5867 6133 5.105392 TCCTCTGTTTGAGTGCATTGTTTTT 60.105 36.000 0.00 0.00 41.11 1.94
5868 6134 6.096141 TCCTCTGTTTGAGTGCATTGTTTTTA 59.904 34.615 0.00 0.00 41.11 1.52
5869 6135 6.198966 CCTCTGTTTGAGTGCATTGTTTTTAC 59.801 38.462 0.00 0.00 41.11 2.01
5887 6153 4.837093 TTACTAGGACAGTTTGGGATGG 57.163 45.455 0.00 0.00 38.80 3.51
5989 6306 4.661222 TGAAACAGGTTTGGCATCTGATA 58.339 39.130 16.31 0.00 32.11 2.15
5990 6307 4.458989 TGAAACAGGTTTGGCATCTGATAC 59.541 41.667 16.31 9.08 32.11 2.24
6013 6331 1.597461 GGCTACCTGGTGGAGTGTC 59.403 63.158 15.03 0.00 37.04 3.67
6025 6343 2.554893 GTGGAGTGTCGAGGGATCTATC 59.445 54.545 0.00 0.00 0.00 2.08
6026 6344 2.443632 TGGAGTGTCGAGGGATCTATCT 59.556 50.000 0.00 0.00 0.00 1.98
6027 6345 3.651423 TGGAGTGTCGAGGGATCTATCTA 59.349 47.826 0.00 0.00 0.00 1.98
6028 6346 4.004982 GGAGTGTCGAGGGATCTATCTAC 58.995 52.174 0.00 0.00 0.00 2.59
6030 6348 3.394940 AGTGTCGAGGGATCTATCTACCA 59.605 47.826 0.00 0.00 0.00 3.25
6031 6349 3.502979 GTGTCGAGGGATCTATCTACCAC 59.497 52.174 0.00 0.00 0.00 4.16
6032 6350 3.394940 TGTCGAGGGATCTATCTACCACT 59.605 47.826 0.00 0.00 0.00 4.00
6033 6351 4.004982 GTCGAGGGATCTATCTACCACTC 58.995 52.174 0.00 0.00 0.00 3.51
6034 6352 3.651423 TCGAGGGATCTATCTACCACTCA 59.349 47.826 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 50 2.809446 CGTTCTCGAATCATGTGGCTA 58.191 47.619 0.00 0.00 39.71 3.93
101 103 4.101585 AGGTTATGGATCGCTTGATTGAGA 59.898 41.667 0.00 0.00 30.70 3.27
255 257 2.310577 GCGAACAAGTTGCAAGATGTC 58.689 47.619 15.27 9.42 0.00 3.06
279 281 1.080705 GGCGACGACACTAGCTGTT 60.081 57.895 0.00 0.00 31.03 3.16
280 282 2.567049 GGCGACGACACTAGCTGT 59.433 61.111 0.00 0.00 34.96 4.40
300 303 3.636764 ACGAAGCTTGGAATGAAAAAGGT 59.363 39.130 16.00 0.00 33.28 3.50
307 310 1.610624 GGTGGACGAAGCTTGGAATGA 60.611 52.381 16.00 0.00 0.00 2.57
435 438 2.275318 GTAGCCAAGAGTGATCACAGC 58.725 52.381 27.02 19.31 0.00 4.40
456 459 1.348036 GCAACCCTAGAACACCTGACT 59.652 52.381 0.00 0.00 0.00 3.41
490 493 3.793144 CGCCGAGCTGGTCTTTGC 61.793 66.667 5.23 4.36 41.21 3.68
491 494 2.048222 TCGCCGAGCTGGTCTTTG 60.048 61.111 5.23 0.00 41.21 2.77
551 554 3.280775 GACTTTTGAAAAGCGAGTGACG 58.719 45.455 16.96 0.00 45.66 4.35
587 590 3.746492 GTGGCTTGTCGGATATTGGATAC 59.254 47.826 0.00 0.00 0.00 2.24
736 739 5.309543 TGGAAAACTATGAAGAGGTTGAGGA 59.690 40.000 0.00 0.00 0.00 3.71
757 760 3.616219 AGCTTGCGGTATAAAACATGGA 58.384 40.909 0.00 0.00 0.00 3.41
800 803 4.176752 GGTCTGGCCGGCCTTAGG 62.177 72.222 43.34 29.01 36.94 2.69
801 804 2.198304 AAAGGTCTGGCCGGCCTTAG 62.198 60.000 43.34 33.30 41.31 2.18
802 805 1.785353 AAAAGGTCTGGCCGGCCTTA 61.785 55.000 43.34 29.37 41.31 2.69
803 806 2.656698 AAAAAGGTCTGGCCGGCCTT 62.657 55.000 43.34 27.69 43.75 4.35
804 807 1.785353 TAAAAAGGTCTGGCCGGCCT 61.785 55.000 43.34 23.22 43.70 5.19
805 808 1.303806 TAAAAAGGTCTGGCCGGCC 60.304 57.895 39.40 39.40 43.70 6.13
806 809 1.880894 GTAAAAAGGTCTGGCCGGC 59.119 57.895 21.18 21.18 43.70 6.13
807 810 1.303091 CCGTAAAAAGGTCTGGCCGG 61.303 60.000 4.71 4.71 43.70 6.13
808 811 0.604511 ACCGTAAAAAGGTCTGGCCG 60.605 55.000 0.00 0.00 43.70 6.13
809 812 1.538512 GAACCGTAAAAAGGTCTGGCC 59.461 52.381 0.00 0.00 41.95 5.36
810 813 2.225727 CAGAACCGTAAAAAGGTCTGGC 59.774 50.000 0.00 0.00 41.95 4.85
811 814 2.812011 CCAGAACCGTAAAAAGGTCTGG 59.188 50.000 9.54 9.54 43.54 3.86
812 815 3.473625 ACCAGAACCGTAAAAAGGTCTG 58.526 45.455 0.00 0.00 41.95 3.51
813 816 3.851458 ACCAGAACCGTAAAAAGGTCT 57.149 42.857 0.00 0.00 41.95 3.85
814 817 4.999311 ACATACCAGAACCGTAAAAAGGTC 59.001 41.667 0.00 0.00 41.95 3.85
815 818 4.976864 ACATACCAGAACCGTAAAAAGGT 58.023 39.130 0.00 0.00 45.29 3.50
816 819 5.583457 CCTACATACCAGAACCGTAAAAAGG 59.417 44.000 0.00 0.00 0.00 3.11
817 820 5.583457 CCCTACATACCAGAACCGTAAAAAG 59.417 44.000 0.00 0.00 0.00 2.27
818 821 5.012975 ACCCTACATACCAGAACCGTAAAAA 59.987 40.000 0.00 0.00 0.00 1.94
819 822 4.531732 ACCCTACATACCAGAACCGTAAAA 59.468 41.667 0.00 0.00 0.00 1.52
820 823 4.095946 ACCCTACATACCAGAACCGTAAA 58.904 43.478 0.00 0.00 0.00 2.01
821 824 3.701040 GACCCTACATACCAGAACCGTAA 59.299 47.826 0.00 0.00 0.00 3.18
822 825 3.053395 AGACCCTACATACCAGAACCGTA 60.053 47.826 0.00 0.00 0.00 4.02
823 826 2.105766 GACCCTACATACCAGAACCGT 58.894 52.381 0.00 0.00 0.00 4.83
824 827 2.100916 CAGACCCTACATACCAGAACCG 59.899 54.545 0.00 0.00 0.00 4.44
825 828 2.158943 GCAGACCCTACATACCAGAACC 60.159 54.545 0.00 0.00 0.00 3.62
826 829 2.766828 AGCAGACCCTACATACCAGAAC 59.233 50.000 0.00 0.00 0.00 3.01
827 830 3.031736 GAGCAGACCCTACATACCAGAA 58.968 50.000 0.00 0.00 0.00 3.02
828 831 2.667470 GAGCAGACCCTACATACCAGA 58.333 52.381 0.00 0.00 0.00 3.86
829 832 1.338337 CGAGCAGACCCTACATACCAG 59.662 57.143 0.00 0.00 0.00 4.00
830 833 1.064240 TCGAGCAGACCCTACATACCA 60.064 52.381 0.00 0.00 0.00 3.25
831 834 1.337387 GTCGAGCAGACCCTACATACC 59.663 57.143 1.39 0.00 43.95 2.73
832 835 2.778187 GTCGAGCAGACCCTACATAC 57.222 55.000 1.39 0.00 43.95 2.39
844 847 2.048784 GTGAGCTGCAGTCGAGCA 60.049 61.111 16.64 3.91 43.35 4.26
845 848 3.177920 CGTGAGCTGCAGTCGAGC 61.178 66.667 16.64 0.26 36.65 5.03
857 860 2.974489 CTTTGCAGGCTGGCGTGAG 61.974 63.158 17.64 4.23 36.28 3.51
858 861 2.979676 CTTTGCAGGCTGGCGTGA 60.980 61.111 17.64 2.30 36.28 4.35
859 862 4.712425 GCTTTGCAGGCTGGCGTG 62.712 66.667 17.64 10.40 36.28 5.34
863 866 2.367868 AAAACGGCTTTGCAGGCTGG 62.368 55.000 17.64 12.74 43.69 4.85
864 867 0.313672 TAAAACGGCTTTGCAGGCTG 59.686 50.000 10.94 10.94 43.69 4.85
865 868 0.313987 GTAAAACGGCTTTGCAGGCT 59.686 50.000 12.30 0.00 43.69 4.58
866 869 0.666274 GGTAAAACGGCTTTGCAGGC 60.666 55.000 5.35 5.35 42.39 4.85
867 870 0.386731 CGGTAAAACGGCTTTGCAGG 60.387 55.000 0.00 0.00 31.68 4.85
868 871 1.001745 GCGGTAAAACGGCTTTGCAG 61.002 55.000 2.71 0.00 40.69 4.41
869 872 1.008309 GCGGTAAAACGGCTTTGCA 60.008 52.632 2.71 0.00 40.69 4.08
870 873 2.078341 CGCGGTAAAACGGCTTTGC 61.078 57.895 0.00 0.00 41.55 3.68
871 874 0.041135 TTCGCGGTAAAACGGCTTTG 60.041 50.000 6.13 0.00 41.55 2.77
872 875 0.041047 GTTCGCGGTAAAACGGCTTT 60.041 50.000 6.13 0.00 41.55 3.51
873 876 0.881600 AGTTCGCGGTAAAACGGCTT 60.882 50.000 6.13 0.00 41.55 4.35
874 877 1.301165 AGTTCGCGGTAAAACGGCT 60.301 52.632 6.13 0.00 41.55 5.52
875 878 1.154543 CAGTTCGCGGTAAAACGGC 60.155 57.895 6.13 0.00 40.50 5.68
876 879 1.417372 TACAGTTCGCGGTAAAACGG 58.583 50.000 6.13 6.64 0.00 4.44
877 880 3.502256 TTTACAGTTCGCGGTAAAACG 57.498 42.857 6.13 2.76 42.00 3.60
878 881 6.593072 ACTAATTTACAGTTCGCGGTAAAAC 58.407 36.000 17.99 10.56 45.62 2.43
879 882 6.783892 ACTAATTTACAGTTCGCGGTAAAA 57.216 33.333 17.99 7.26 45.62 1.52
880 883 6.783892 AACTAATTTACAGTTCGCGGTAAA 57.216 33.333 16.89 16.89 46.18 2.01
881 884 6.783892 AAACTAATTTACAGTTCGCGGTAA 57.216 33.333 6.13 3.69 35.19 2.85
882 885 6.592166 CAAAACTAATTTACAGTTCGCGGTA 58.408 36.000 6.13 0.00 35.19 4.02
883 886 5.445845 CAAAACTAATTTACAGTTCGCGGT 58.554 37.500 6.13 0.00 35.19 5.68
884 887 4.319901 GCAAAACTAATTTACAGTTCGCGG 59.680 41.667 6.13 0.00 35.19 6.46
885 888 4.907010 TGCAAAACTAATTTACAGTTCGCG 59.093 37.500 0.00 0.00 37.24 5.87
886 889 5.342259 CCTGCAAAACTAATTTACAGTTCGC 59.658 40.000 0.00 6.86 35.19 4.70
887 890 6.435428 ACCTGCAAAACTAATTTACAGTTCG 58.565 36.000 0.00 0.00 35.19 3.95
888 891 6.577427 CGACCTGCAAAACTAATTTACAGTTC 59.423 38.462 0.00 0.00 35.19 3.01
889 892 6.261381 TCGACCTGCAAAACTAATTTACAGTT 59.739 34.615 0.00 0.00 37.85 3.16
890 893 5.761234 TCGACCTGCAAAACTAATTTACAGT 59.239 36.000 0.00 0.00 33.36 3.55
891 894 6.077838 GTCGACCTGCAAAACTAATTTACAG 58.922 40.000 3.51 0.00 34.28 2.74
892 895 5.333492 CGTCGACCTGCAAAACTAATTTACA 60.333 40.000 10.58 0.00 0.00 2.41
893 896 5.077424 CGTCGACCTGCAAAACTAATTTAC 58.923 41.667 10.58 0.00 0.00 2.01
894 897 4.989797 TCGTCGACCTGCAAAACTAATTTA 59.010 37.500 10.58 0.00 0.00 1.40
895 898 3.810941 TCGTCGACCTGCAAAACTAATTT 59.189 39.130 10.58 0.00 0.00 1.82
896 899 3.395639 TCGTCGACCTGCAAAACTAATT 58.604 40.909 10.58 0.00 0.00 1.40
897 900 3.034721 TCGTCGACCTGCAAAACTAAT 57.965 42.857 10.58 0.00 0.00 1.73
898 901 2.512485 TCGTCGACCTGCAAAACTAA 57.488 45.000 10.58 0.00 0.00 2.24
899 902 2.736144 ATCGTCGACCTGCAAAACTA 57.264 45.000 10.58 0.00 0.00 2.24
900 903 2.288579 TGTATCGTCGACCTGCAAAACT 60.289 45.455 10.58 0.00 0.00 2.66
901 904 2.063266 TGTATCGTCGACCTGCAAAAC 58.937 47.619 10.58 0.00 0.00 2.43
902 905 2.063266 GTGTATCGTCGACCTGCAAAA 58.937 47.619 10.58 0.00 0.00 2.44
903 906 1.705256 GTGTATCGTCGACCTGCAAA 58.295 50.000 10.58 0.00 0.00 3.68
904 907 0.455464 CGTGTATCGTCGACCTGCAA 60.455 55.000 10.58 0.00 34.52 4.08
905 908 1.135939 CGTGTATCGTCGACCTGCA 59.864 57.895 10.58 4.72 34.52 4.41
906 909 1.585521 CCGTGTATCGTCGACCTGC 60.586 63.158 10.58 1.88 37.94 4.85
907 910 1.063649 CCCGTGTATCGTCGACCTG 59.936 63.158 10.58 0.00 37.94 4.00
908 911 1.372087 GACCCGTGTATCGTCGACCT 61.372 60.000 10.58 0.00 37.94 3.85
909 912 1.063166 GACCCGTGTATCGTCGACC 59.937 63.158 10.58 0.00 37.94 4.79
910 913 0.247974 CAGACCCGTGTATCGTCGAC 60.248 60.000 5.18 5.18 37.94 4.20
911 914 0.391528 TCAGACCCGTGTATCGTCGA 60.392 55.000 0.00 0.00 37.94 4.20
912 915 0.661552 ATCAGACCCGTGTATCGTCG 59.338 55.000 0.00 0.00 37.94 5.12
913 916 3.136763 TCTATCAGACCCGTGTATCGTC 58.863 50.000 0.00 0.00 37.94 4.20
914 917 3.139850 CTCTATCAGACCCGTGTATCGT 58.860 50.000 0.00 0.00 37.94 3.73
915 918 3.186817 GTCTCTATCAGACCCGTGTATCG 59.813 52.174 0.00 0.00 45.47 2.92
916 919 4.752661 GTCTCTATCAGACCCGTGTATC 57.247 50.000 0.00 0.00 45.47 2.24
938 941 1.887707 ATACAGGCCGCGCTTAAGC 60.888 57.895 17.83 17.83 37.78 3.09
939 942 1.498865 CCATACAGGCCGCGCTTAAG 61.499 60.000 5.56 0.00 0.00 1.85
940 943 1.522806 CCATACAGGCCGCGCTTAA 60.523 57.895 5.56 0.00 0.00 1.85
941 944 2.108157 CCATACAGGCCGCGCTTA 59.892 61.111 5.56 0.00 0.00 3.09
952 955 1.271871 CCACTCAAACCTGGCCATACA 60.272 52.381 5.51 0.00 0.00 2.29
987 1000 2.396601 GAGAGCATGCTGATCGAGAAG 58.603 52.381 28.27 0.00 37.94 2.85
988 1001 1.068281 GGAGAGCATGCTGATCGAGAA 59.932 52.381 28.27 0.00 37.94 2.87
989 1002 0.672889 GGAGAGCATGCTGATCGAGA 59.327 55.000 28.27 0.00 37.94 4.04
990 1003 0.388294 TGGAGAGCATGCTGATCGAG 59.612 55.000 28.27 0.00 37.94 4.04
998 1011 2.103042 GTGGACGTGGAGAGCATGC 61.103 63.158 10.51 10.51 0.00 4.06
1006 1019 3.968837 ATAGGGCCGTGGACGTGGA 62.969 63.158 8.57 0.00 37.74 4.02
1007 1020 2.530958 AAATAGGGCCGTGGACGTGG 62.531 60.000 8.57 0.00 37.74 4.94
1008 1021 0.675522 AAAATAGGGCCGTGGACGTG 60.676 55.000 8.57 0.00 37.74 4.49
1009 1022 0.392060 GAAAATAGGGCCGTGGACGT 60.392 55.000 8.57 0.00 37.74 4.34
1010 1023 0.107848 AGAAAATAGGGCCGTGGACG 60.108 55.000 8.57 0.00 39.44 4.79
1011 1024 2.124277 AAGAAAATAGGGCCGTGGAC 57.876 50.000 8.57 0.00 0.00 4.02
1022 1035 5.538433 CAGGAGGGTTTGGTGAAAGAAAATA 59.462 40.000 0.00 0.00 0.00 1.40
1067 1085 2.900273 CCGGAGAGGATTTCGGCA 59.100 61.111 0.00 0.00 45.00 5.69
1082 1100 3.474570 CAGGAAGGGGGAGAGCCG 61.475 72.222 0.00 0.00 33.83 5.52
1083 1101 3.803162 GCAGGAAGGGGGAGAGCC 61.803 72.222 0.00 0.00 0.00 4.70
1084 1102 4.168291 CGCAGGAAGGGGGAGAGC 62.168 72.222 0.00 0.00 0.00 4.09
1085 1103 1.764054 ATCGCAGGAAGGGGGAGAG 60.764 63.158 0.00 0.00 0.00 3.20
1086 1104 2.066393 CATCGCAGGAAGGGGGAGA 61.066 63.158 0.00 0.00 0.00 3.71
1087 1105 2.507944 CATCGCAGGAAGGGGGAG 59.492 66.667 0.00 0.00 0.00 4.30
1088 1106 3.089874 CCATCGCAGGAAGGGGGA 61.090 66.667 0.00 0.00 0.00 4.81
1254 1272 2.817056 GGAGGAGGGCATGAGCTCC 61.817 68.421 12.15 0.00 44.52 4.70
1314 1570 1.383803 CTGAGGAGGAAGGGGAGGG 60.384 68.421 0.00 0.00 0.00 4.30
1734 1993 0.937304 CACCAACAGTGTCACCTTCG 59.063 55.000 0.00 0.00 41.93 3.79
1785 2044 2.159170 CGGATGAGGAAGACCAAGAGAC 60.159 54.545 0.00 0.00 38.94 3.36
1865 2124 4.159135 CCAATTCATCCATAATAGCCAGGC 59.841 45.833 1.84 1.84 0.00 4.85
2034 2293 3.675348 TGCCAATTCTCCCAGATCAAT 57.325 42.857 0.00 0.00 0.00 2.57
2055 2314 0.995675 ATGCCTTATGCCTCCCCTGT 60.996 55.000 0.00 0.00 40.16 4.00
2122 2381 3.663995 TTTTGCACCAACATCATCCAG 57.336 42.857 0.00 0.00 0.00 3.86
2193 2452 0.038744 CTGTGATCCCAGTGGCCTTT 59.961 55.000 3.32 0.00 0.00 3.11
2750 3009 6.682611 GCTCTTGTCTTCTGCATAGTACTCAT 60.683 42.308 0.00 0.00 0.00 2.90
2867 3126 2.553247 GCTAAGGCTTCCTTCACCAACT 60.553 50.000 1.30 0.00 43.57 3.16
3072 3331 0.391263 GCTGGACCTCCGTAACCTTG 60.391 60.000 0.00 0.00 39.43 3.61
3900 4159 2.029200 TGCCACAATTGATGCAAATCGT 60.029 40.909 19.32 0.00 0.00 3.73
4017 4276 2.292267 CTGTACATCAATGTCAGGGCC 58.708 52.381 0.00 0.00 41.97 5.80
4027 4286 6.158871 TGTTCCATTATACCCCTGTACATCAA 59.841 38.462 0.00 0.00 0.00 2.57
4134 4393 5.066505 CCTGATAATTCCAACTGCCACTAAC 59.933 44.000 0.00 0.00 0.00 2.34
4446 4705 5.181245 CCGGTCAATTGTAAGAGTGAACAAT 59.819 40.000 5.13 0.00 45.75 2.71
4470 4729 0.535797 CCGACTCCCAAGTAACTCCC 59.464 60.000 0.00 0.00 35.28 4.30
4542 4801 0.542702 TCCGGGACTCGTAAAACCCT 60.543 55.000 0.00 0.00 40.12 4.34
4590 4849 2.143925 GTTGAGCCTTCAAACGCTAGT 58.856 47.619 0.00 0.00 44.49 2.57
4708 4967 0.178964 CCTTCCCCAGTTTTGCCAGA 60.179 55.000 0.00 0.00 0.00 3.86
4712 4971 1.667722 CAGCCTTCCCCAGTTTTGC 59.332 57.895 0.00 0.00 0.00 3.68
4965 5224 2.880890 GACTGCTGTGTTTGGAATGACT 59.119 45.455 0.00 0.00 0.00 3.41
4986 5245 3.827625 CAGACCTTCTAACACTGACTCG 58.172 50.000 0.00 0.00 0.00 4.18
4992 5251 2.037772 CCACTGCAGACCTTCTAACACT 59.962 50.000 23.35 0.00 0.00 3.55
5039 5298 7.446769 TGTGCAGAGAAATAACCTGTAGTTTA 58.553 34.615 0.00 0.00 40.05 2.01
5084 5343 6.763610 CCTCCTTAGCTACAGAAATTTGGTAG 59.236 42.308 16.74 16.74 38.00 3.18
5085 5344 6.214819 ACCTCCTTAGCTACAGAAATTTGGTA 59.785 38.462 0.00 0.00 0.00 3.25
5239 5499 4.929781 AGCAAGACTTGAGCAAGAAAAAG 58.070 39.130 19.51 4.27 40.79 2.27
5298 5558 9.075678 GGGAATCACTATTCTTCATTCATTGAT 57.924 33.333 0.00 0.00 41.18 2.57
5377 5639 3.447229 AGCTAATGGGGAATTTCCAAACG 59.553 43.478 17.08 1.87 38.64 3.60
5446 5708 4.081254 TCTCATCCCAGAGATCAAACACAG 60.081 45.833 0.00 0.00 39.62 3.66
5467 5729 8.504409 AGGGAGTACTACATCTTAACTGTATCT 58.496 37.037 7.57 0.00 0.00 1.98
5490 5752 2.325583 TTGGCGCTGATTTAGTAGGG 57.674 50.000 7.64 0.00 0.00 3.53
5506 5768 5.179452 ACCCTCCGATCCATATTAATTGG 57.821 43.478 0.00 1.98 35.45 3.16
5559 5821 4.550669 TCAGGATCATACCACAGACTCAT 58.449 43.478 0.00 0.00 0.00 2.90
5585 5847 5.298777 TCCGACTAAACCAGACTTAGCTATC 59.701 44.000 0.00 0.00 30.79 2.08
5604 5866 6.986904 ATTAAAGAATCTTCCTGTTCCGAC 57.013 37.500 0.00 0.00 0.00 4.79
5606 5868 8.345565 CCATAATTAAAGAATCTTCCTGTTCCG 58.654 37.037 0.00 0.00 0.00 4.30
5667 5929 8.573035 GTTGGACACCTCTAAAATTAACAATGA 58.427 33.333 0.00 0.00 0.00 2.57
5777 6039 8.454106 GGTTTAGCCATAATGTCATATGTCATC 58.546 37.037 14.54 3.84 37.17 2.92
5813 6075 9.685276 ATTGATTCAATTTCAGTACAGTGGATA 57.315 29.630 6.06 0.00 28.76 2.59
5865 6131 4.600111 ACCATCCCAAACTGTCCTAGTAAA 59.400 41.667 0.00 0.00 39.18 2.01
5867 6133 3.517901 CACCATCCCAAACTGTCCTAGTA 59.482 47.826 0.00 0.00 39.18 1.82
5868 6134 2.305927 CACCATCCCAAACTGTCCTAGT 59.694 50.000 0.00 0.00 42.89 2.57
5869 6135 2.305927 ACACCATCCCAAACTGTCCTAG 59.694 50.000 0.00 0.00 0.00 3.02
5910 6176 1.455408 GTTTAAGCGCAACAATGGCAC 59.545 47.619 11.47 0.00 0.00 5.01
5989 6306 2.610859 CACCAGGTAGCCCCCAGT 60.611 66.667 0.00 0.00 0.00 4.00
5990 6307 3.411517 CCACCAGGTAGCCCCCAG 61.412 72.222 0.00 0.00 0.00 4.45
6013 6331 4.022413 TGAGTGGTAGATAGATCCCTCG 57.978 50.000 0.00 0.00 0.00 4.63



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

AutoCloner maintained by Alex Coulton.