Multiple sequence alignment - TraesCS3B01G170000

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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 TraesCS3B01G170000 chr3B 100.000 4745 0 0 1 4745 169836768 169832024 0.000000e+00 8763.0
1 TraesCS3B01G170000 chr3B 95.497 1932 73 12 1075 2994 169693883 169691954 0.000000e+00 3073.0
2 TraesCS3B01G170000 chr3B 96.727 611 17 2 3726 4336 169690863 169690256 0.000000e+00 1014.0
3 TraesCS3B01G170000 chr3B 99.565 460 2 0 2992 3451 169691796 169691337 0.000000e+00 839.0
4 TraesCS3B01G170000 chr3B 93.250 400 8 2 4365 4745 169690254 169689855 5.330000e-159 571.0
5 TraesCS3B01G170000 chr3B 96.416 279 8 2 3452 3730 169691300 169691024 4.330000e-125 459.0
6 TraesCS3B01G170000 chr3D 94.904 2453 75 21 1012 3451 116163118 116160703 0.000000e+00 3792.0
7 TraesCS3B01G170000 chr3D 96.970 528 13 3 3452 3979 116160666 116160142 0.000000e+00 883.0
8 TraesCS3B01G170000 chr3D 88.983 118 12 1 4162 4278 116159962 116159845 1.380000e-30 145.0
9 TraesCS3B01G170000 chr3A 94.242 2275 97 16 1201 3451 125094963 125092699 0.000000e+00 3445.0
10 TraesCS3B01G170000 chr3A 96.491 456 12 4 3452 3907 125092662 125092211 0.000000e+00 750.0
11 TraesCS3B01G170000 chr3A 89.899 198 18 2 4083 4278 125091868 125091671 2.190000e-63 254.0
12 TraesCS3B01G170000 chr4D 95.140 823 40 0 1 823 3576893 3577715 0.000000e+00 1299.0
13 TraesCS3B01G170000 chr2D 95.128 821 36 2 1 821 39292163 39291347 0.000000e+00 1291.0
14 TraesCS3B01G170000 chr5B 88.712 815 76 11 1 815 129148713 129147915 0.000000e+00 981.0
15 TraesCS3B01G170000 chr5B 97.222 36 0 1 427 461 129148259 129148224 5.130000e-05 60.2
16 TraesCS3B01G170000 chr5D 88.571 70 7 1 4004 4072 539674255 539674186 3.040000e-12 84.2
17 TraesCS3B01G170000 chrUn 83.750 80 11 2 6 84 46065729 46065807 1.830000e-09 75.0


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 TraesCS3B01G170000 chr3B 169832024 169836768 4744 True 8763.000000 8763 100.000 1 4745 1 chr3B.!!$R1 4744
1 TraesCS3B01G170000 chr3B 169689855 169693883 4028 True 1191.200000 3073 96.291 1075 4745 5 chr3B.!!$R2 3670
2 TraesCS3B01G170000 chr3D 116159845 116163118 3273 True 1606.666667 3792 93.619 1012 4278 3 chr3D.!!$R1 3266
3 TraesCS3B01G170000 chr3A 125091671 125094963 3292 True 1483.000000 3445 93.544 1201 4278 3 chr3A.!!$R1 3077
4 TraesCS3B01G170000 chr4D 3576893 3577715 822 False 1299.000000 1299 95.140 1 823 1 chr4D.!!$F1 822
5 TraesCS3B01G170000 chr2D 39291347 39292163 816 True 1291.000000 1291 95.128 1 821 1 chr2D.!!$R1 820
6 TraesCS3B01G170000 chr5B 129147915 129148713 798 True 520.600000 981 92.967 1 815 2 chr5B.!!$R1 814

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
425 426 0.037139 GCATTTGGCTGCAACCATCA 60.037 50.000 10.21 0.0 41.87 3.07 F
1310 1317 0.036306 CACCCCTTTACTTCCACGCT 59.964 55.000 0.00 0.0 0.00 5.07 F
1311 1318 0.323957 ACCCCTTTACTTCCACGCTC 59.676 55.000 0.00 0.0 0.00 5.03 F
2031 2069 1.278985 CCAGTAAGTGCCACTCATCCA 59.721 52.381 0.00 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1626 1645 1.210155 GCCATTGCAGTTGTCGTCC 59.790 57.895 0.00 0.00 37.47 4.79 R
2746 2785 5.123344 AGCTTGCTGGTTTAAGTTATAACCG 59.877 40.000 12.05 13.06 45.40 4.44 R
2949 2988 5.643777 AGTACAAACTCACATAAGACATGCC 59.356 40.000 0.00 0.00 0.00 4.40 R
3778 4178 0.799534 GCACGCATTGAGCATGTTCC 60.800 55.000 7.13 0.00 46.13 3.62 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
57 58 2.124109 TGCAACCGTTGAGGCCAA 60.124 55.556 15.63 0.00 46.52 4.52
194 195 1.896220 TCCAGCACAAAATCTCGCTT 58.104 45.000 0.00 0.00 30.72 4.68
281 282 0.179097 GGTTCCAGGATCTGCGAGAC 60.179 60.000 0.00 0.00 0.00 3.36
282 283 0.532573 GTTCCAGGATCTGCGAGACA 59.467 55.000 0.00 0.00 0.00 3.41
291 292 1.300620 CTGCGAGACACGGTTCCAA 60.301 57.895 0.00 0.00 42.83 3.53
304 305 2.742053 CGGTTCCAACAAATCATCTCGT 59.258 45.455 0.00 0.00 0.00 4.18
391 392 4.752879 GAACCGGCAGCCGCACTA 62.753 66.667 29.55 0.00 46.86 2.74
412 413 0.039978 TACAACCGTTGGCGCATTTG 60.040 50.000 15.60 5.07 36.67 2.32
425 426 0.037139 GCATTTGGCTGCAACCATCA 60.037 50.000 10.21 0.00 41.87 3.07
476 477 3.595758 GCACCAAGCTGCAACGGT 61.596 61.111 1.02 1.76 41.15 4.83
542 543 2.288213 GGCAACTTTCCTGCAACCTTAC 60.288 50.000 0.00 0.00 41.78 2.34
567 568 2.174685 TGAAGCTACTAGGCCATGGA 57.825 50.000 18.40 0.00 0.00 3.41
677 682 3.047877 GCCAAGTCCCACGTTCCG 61.048 66.667 0.00 0.00 0.00 4.30
774 779 1.369091 CCTAATCAAACGGCTGCGCT 61.369 55.000 9.73 0.00 0.00 5.92
818 823 2.362120 ACCGGCGCCTAGTACTGT 60.362 61.111 26.68 6.90 0.00 3.55
823 828 1.396653 GGCGCCTAGTACTGTCCTAA 58.603 55.000 22.15 0.00 0.00 2.69
824 829 1.066757 GGCGCCTAGTACTGTCCTAAC 59.933 57.143 22.15 0.00 0.00 2.34
825 830 1.747355 GCGCCTAGTACTGTCCTAACA 59.253 52.381 5.39 0.00 0.00 2.41
826 831 2.165030 GCGCCTAGTACTGTCCTAACAA 59.835 50.000 5.39 0.00 34.24 2.83
827 832 3.367703 GCGCCTAGTACTGTCCTAACAAA 60.368 47.826 5.39 0.00 34.24 2.83
828 833 4.813027 CGCCTAGTACTGTCCTAACAAAA 58.187 43.478 5.39 0.00 34.24 2.44
829 834 5.416947 CGCCTAGTACTGTCCTAACAAAAT 58.583 41.667 5.39 0.00 34.24 1.82
830 835 5.873164 CGCCTAGTACTGTCCTAACAAAATT 59.127 40.000 5.39 0.00 34.24 1.82
831 836 6.370718 CGCCTAGTACTGTCCTAACAAAATTT 59.629 38.462 5.39 0.00 34.24 1.82
832 837 7.546667 CGCCTAGTACTGTCCTAACAAAATTTA 59.453 37.037 5.39 0.00 34.24 1.40
833 838 8.663025 GCCTAGTACTGTCCTAACAAAATTTAC 58.337 37.037 5.39 0.00 34.24 2.01
834 839 9.715121 CCTAGTACTGTCCTAACAAAATTTACA 57.285 33.333 5.39 0.00 34.24 2.41
836 841 8.387190 AGTACTGTCCTAACAAAATTTACACC 57.613 34.615 0.00 0.00 34.24 4.16
837 842 6.308371 ACTGTCCTAACAAAATTTACACCG 57.692 37.500 0.00 0.00 34.24 4.94
838 843 6.056884 ACTGTCCTAACAAAATTTACACCGA 58.943 36.000 0.00 0.00 34.24 4.69
839 844 6.543100 ACTGTCCTAACAAAATTTACACCGAA 59.457 34.615 0.00 0.00 34.24 4.30
840 845 7.067251 ACTGTCCTAACAAAATTTACACCGAAA 59.933 33.333 0.00 0.00 34.24 3.46
841 846 7.419204 TGTCCTAACAAAATTTACACCGAAAG 58.581 34.615 0.00 0.00 30.70 2.62
842 847 7.282675 TGTCCTAACAAAATTTACACCGAAAGA 59.717 33.333 0.00 0.00 30.70 2.52
843 848 7.801783 GTCCTAACAAAATTTACACCGAAAGAG 59.198 37.037 0.00 0.00 0.00 2.85
844 849 7.499895 TCCTAACAAAATTTACACCGAAAGAGT 59.500 33.333 0.00 0.00 0.00 3.24
845 850 8.132995 CCTAACAAAATTTACACCGAAAGAGTT 58.867 33.333 0.00 0.00 0.00 3.01
848 853 9.511144 AACAAAATTTACACCGAAAGAGTTAAG 57.489 29.630 0.00 0.00 0.00 1.85
849 854 8.680001 ACAAAATTTACACCGAAAGAGTTAAGT 58.320 29.630 0.00 0.00 0.00 2.24
850 855 9.166126 CAAAATTTACACCGAAAGAGTTAAGTC 57.834 33.333 1.75 1.75 0.00 3.01
851 856 8.441312 AAATTTACACCGAAAGAGTTAAGTCA 57.559 30.769 12.77 0.00 0.00 3.41
852 857 6.833342 TTTACACCGAAAGAGTTAAGTCAC 57.167 37.500 12.77 3.22 0.00 3.67
853 858 3.725490 ACACCGAAAGAGTTAAGTCACC 58.275 45.455 12.77 0.70 0.00 4.02
854 859 3.133362 ACACCGAAAGAGTTAAGTCACCA 59.867 43.478 12.77 0.00 0.00 4.17
855 860 3.493503 CACCGAAAGAGTTAAGTCACCAC 59.506 47.826 12.77 1.01 0.00 4.16
856 861 3.133362 ACCGAAAGAGTTAAGTCACCACA 59.867 43.478 12.77 0.00 0.00 4.17
857 862 4.124238 CCGAAAGAGTTAAGTCACCACAA 58.876 43.478 12.77 0.00 0.00 3.33
858 863 4.573201 CCGAAAGAGTTAAGTCACCACAAA 59.427 41.667 12.77 0.00 0.00 2.83
859 864 5.065474 CCGAAAGAGTTAAGTCACCACAAAA 59.935 40.000 12.77 0.00 0.00 2.44
860 865 6.238648 CCGAAAGAGTTAAGTCACCACAAAAT 60.239 38.462 12.77 0.00 0.00 1.82
861 866 7.193595 CGAAAGAGTTAAGTCACCACAAAATT 58.806 34.615 12.77 0.00 0.00 1.82
862 867 7.165812 CGAAAGAGTTAAGTCACCACAAAATTG 59.834 37.037 12.77 0.00 0.00 2.32
863 868 7.404671 AAGAGTTAAGTCACCACAAAATTGT 57.595 32.000 12.77 0.00 43.36 2.71
864 869 8.514330 AAGAGTTAAGTCACCACAAAATTGTA 57.486 30.769 12.77 0.00 39.91 2.41
865 870 7.927048 AGAGTTAAGTCACCACAAAATTGTAC 58.073 34.615 12.77 0.00 39.91 2.90
866 871 7.773690 AGAGTTAAGTCACCACAAAATTGTACT 59.226 33.333 12.77 0.00 39.91 2.73
867 872 8.967664 AGTTAAGTCACCACAAAATTGTACTA 57.032 30.769 0.00 0.00 39.91 1.82
868 873 9.398538 AGTTAAGTCACCACAAAATTGTACTAA 57.601 29.630 0.00 0.00 39.91 2.24
872 877 7.581476 AGTCACCACAAAATTGTACTAAATCG 58.419 34.615 0.00 0.00 39.91 3.34
873 878 6.304683 GTCACCACAAAATTGTACTAAATCGC 59.695 38.462 0.00 0.00 39.91 4.58
874 879 6.017026 TCACCACAAAATTGTACTAAATCGCA 60.017 34.615 0.00 0.00 39.91 5.10
875 880 6.305399 CACCACAAAATTGTACTAAATCGCAG 59.695 38.462 0.00 0.00 39.91 5.18
876 881 5.286082 CCACAAAATTGTACTAAATCGCAGC 59.714 40.000 0.00 0.00 39.91 5.25
877 882 5.855925 CACAAAATTGTACTAAATCGCAGCA 59.144 36.000 0.00 0.00 39.91 4.41
878 883 6.032775 CACAAAATTGTACTAAATCGCAGCAG 59.967 38.462 0.00 0.00 39.91 4.24
879 884 4.882671 AATTGTACTAAATCGCAGCAGG 57.117 40.909 0.00 0.00 0.00 4.85
880 885 3.603158 TTGTACTAAATCGCAGCAGGA 57.397 42.857 0.00 0.00 0.00 3.86
881 886 3.165058 TGTACTAAATCGCAGCAGGAG 57.835 47.619 0.00 0.00 0.00 3.69
882 887 1.861575 GTACTAAATCGCAGCAGGAGC 59.138 52.381 0.00 0.00 42.56 4.70
883 888 0.462759 ACTAAATCGCAGCAGGAGCC 60.463 55.000 0.00 0.00 43.56 4.70
884 889 1.153168 TAAATCGCAGCAGGAGCCC 60.153 57.895 0.00 0.00 43.56 5.19
885 890 1.909459 TAAATCGCAGCAGGAGCCCA 61.909 55.000 0.00 0.00 43.56 5.36
886 891 2.769652 AAATCGCAGCAGGAGCCCAA 62.770 55.000 0.00 0.00 43.56 4.12
887 892 2.769652 AATCGCAGCAGGAGCCCAAA 62.770 55.000 0.00 0.00 43.56 3.28
888 893 2.563013 ATCGCAGCAGGAGCCCAAAT 62.563 55.000 0.00 0.00 43.56 2.32
889 894 2.345760 CGCAGCAGGAGCCCAAATT 61.346 57.895 0.00 0.00 43.56 1.82
890 895 1.031571 CGCAGCAGGAGCCCAAATTA 61.032 55.000 0.00 0.00 43.56 1.40
891 896 1.185315 GCAGCAGGAGCCCAAATTAA 58.815 50.000 0.00 0.00 43.56 1.40
892 897 1.758862 GCAGCAGGAGCCCAAATTAAT 59.241 47.619 0.00 0.00 43.56 1.40
893 898 2.958355 GCAGCAGGAGCCCAAATTAATA 59.042 45.455 0.00 0.00 43.56 0.98
894 899 3.243535 GCAGCAGGAGCCCAAATTAATAC 60.244 47.826 0.00 0.00 43.56 1.89
895 900 3.953612 CAGCAGGAGCCCAAATTAATACA 59.046 43.478 0.00 0.00 43.56 2.29
896 901 3.954258 AGCAGGAGCCCAAATTAATACAC 59.046 43.478 0.00 0.00 43.56 2.90
897 902 3.243068 GCAGGAGCCCAAATTAATACACG 60.243 47.826 0.00 0.00 33.58 4.49
898 903 3.945285 CAGGAGCCCAAATTAATACACGT 59.055 43.478 0.00 0.00 0.00 4.49
899 904 3.945285 AGGAGCCCAAATTAATACACGTG 59.055 43.478 15.48 15.48 0.00 4.49
900 905 3.488553 GGAGCCCAAATTAATACACGTGC 60.489 47.826 17.22 0.00 0.00 5.34
901 906 2.425668 AGCCCAAATTAATACACGTGCC 59.574 45.455 17.22 0.00 0.00 5.01
902 907 2.425668 GCCCAAATTAATACACGTGCCT 59.574 45.455 17.22 2.35 0.00 4.75
903 908 3.733684 GCCCAAATTAATACACGTGCCTG 60.734 47.826 17.22 1.42 0.00 4.85
904 909 3.434637 CCAAATTAATACACGTGCCTGC 58.565 45.455 17.22 0.00 0.00 4.85
905 910 3.119673 CCAAATTAATACACGTGCCTGCA 60.120 43.478 17.22 0.00 0.00 4.41
906 911 3.757745 AATTAATACACGTGCCTGCAC 57.242 42.857 17.22 12.18 43.01 4.57
907 912 2.465860 TTAATACACGTGCCTGCACT 57.534 45.000 17.22 4.41 44.16 4.40
908 913 2.004583 TAATACACGTGCCTGCACTC 57.995 50.000 17.22 0.00 44.16 3.51
909 914 1.014044 AATACACGTGCCTGCACTCG 61.014 55.000 17.22 12.28 44.16 4.18
910 915 1.873270 ATACACGTGCCTGCACTCGA 61.873 55.000 17.22 3.56 44.16 4.04
911 916 1.873270 TACACGTGCCTGCACTCGAT 61.873 55.000 17.22 5.74 44.16 3.59
912 917 1.153842 CACGTGCCTGCACTCGATA 60.154 57.895 19.07 0.00 44.16 2.92
913 918 1.139734 ACGTGCCTGCACTCGATAG 59.860 57.895 19.07 5.96 44.16 2.08
914 919 1.589993 CGTGCCTGCACTCGATAGG 60.590 63.158 19.07 0.00 44.16 2.57
915 920 1.517832 GTGCCTGCACTCGATAGGT 59.482 57.895 14.77 0.00 43.12 3.08
916 921 0.108138 GTGCCTGCACTCGATAGGTT 60.108 55.000 14.77 0.00 43.12 3.50
917 922 0.175760 TGCCTGCACTCGATAGGTTC 59.824 55.000 6.92 0.00 34.06 3.62
918 923 0.175760 GCCTGCACTCGATAGGTTCA 59.824 55.000 6.92 0.00 34.06 3.18
919 924 1.927895 CCTGCACTCGATAGGTTCAC 58.072 55.000 0.00 0.00 0.00 3.18
920 925 1.204704 CCTGCACTCGATAGGTTCACA 59.795 52.381 0.00 0.00 0.00 3.58
921 926 2.353704 CCTGCACTCGATAGGTTCACAA 60.354 50.000 0.00 0.00 0.00 3.33
922 927 2.926200 CTGCACTCGATAGGTTCACAAG 59.074 50.000 0.00 0.00 0.00 3.16
923 928 2.299013 TGCACTCGATAGGTTCACAAGT 59.701 45.455 0.00 0.00 0.00 3.16
924 929 3.244078 TGCACTCGATAGGTTCACAAGTT 60.244 43.478 0.00 0.00 0.00 2.66
925 930 3.123621 GCACTCGATAGGTTCACAAGTTG 59.876 47.826 0.00 0.00 0.00 3.16
926 931 3.123621 CACTCGATAGGTTCACAAGTTGC 59.876 47.826 1.81 0.00 0.00 4.17
927 932 3.244078 ACTCGATAGGTTCACAAGTTGCA 60.244 43.478 1.81 0.00 0.00 4.08
928 933 3.734463 TCGATAGGTTCACAAGTTGCAA 58.266 40.909 1.81 0.00 0.00 4.08
929 934 4.323417 TCGATAGGTTCACAAGTTGCAAT 58.677 39.130 0.59 0.00 0.00 3.56
930 935 4.391830 TCGATAGGTTCACAAGTTGCAATC 59.608 41.667 0.59 0.00 0.00 2.67
931 936 4.154015 CGATAGGTTCACAAGTTGCAATCA 59.846 41.667 0.59 0.00 0.00 2.57
932 937 5.334802 CGATAGGTTCACAAGTTGCAATCAA 60.335 40.000 0.59 0.00 0.00 2.57
951 956 2.029743 CCAAGTGGTGAAACGTGGG 58.970 57.895 0.00 0.00 43.52 4.61
952 957 0.750182 CCAAGTGGTGAAACGTGGGT 60.750 55.000 0.00 0.00 43.52 4.51
953 958 0.380378 CAAGTGGTGAAACGTGGGTG 59.620 55.000 0.00 0.00 38.12 4.61
954 959 1.381165 AAGTGGTGAAACGTGGGTGC 61.381 55.000 0.00 0.00 38.12 5.01
955 960 2.897846 TGGTGAAACGTGGGTGCG 60.898 61.111 0.00 0.00 38.12 5.34
956 961 2.589442 GGTGAAACGTGGGTGCGA 60.589 61.111 0.00 0.00 38.12 5.10
957 962 2.181521 GGTGAAACGTGGGTGCGAA 61.182 57.895 0.00 0.00 38.12 4.70
958 963 1.278637 GTGAAACGTGGGTGCGAAG 59.721 57.895 0.00 0.00 35.59 3.79
959 964 1.153329 TGAAACGTGGGTGCGAAGT 60.153 52.632 0.00 0.00 35.59 3.01
960 965 1.155424 TGAAACGTGGGTGCGAAGTC 61.155 55.000 0.00 0.00 35.59 3.01
961 966 0.878961 GAAACGTGGGTGCGAAGTCT 60.879 55.000 0.00 0.00 35.59 3.24
962 967 0.463116 AAACGTGGGTGCGAAGTCTT 60.463 50.000 0.00 0.00 35.59 3.01
963 968 1.157870 AACGTGGGTGCGAAGTCTTG 61.158 55.000 0.00 0.00 35.59 3.02
964 969 1.300620 CGTGGGTGCGAAGTCTTGA 60.301 57.895 0.00 0.00 0.00 3.02
965 970 0.670546 CGTGGGTGCGAAGTCTTGAT 60.671 55.000 0.00 0.00 0.00 2.57
966 971 1.523758 GTGGGTGCGAAGTCTTGATT 58.476 50.000 0.00 0.00 0.00 2.57
967 972 2.695359 GTGGGTGCGAAGTCTTGATTA 58.305 47.619 0.00 0.00 0.00 1.75
968 973 2.673368 GTGGGTGCGAAGTCTTGATTAG 59.327 50.000 0.00 0.00 0.00 1.73
969 974 2.565391 TGGGTGCGAAGTCTTGATTAGA 59.435 45.455 0.00 0.00 0.00 2.10
970 975 3.007506 TGGGTGCGAAGTCTTGATTAGAA 59.992 43.478 0.00 0.00 33.81 2.10
971 976 4.000988 GGGTGCGAAGTCTTGATTAGAAA 58.999 43.478 0.00 0.00 33.81 2.52
972 977 4.636206 GGGTGCGAAGTCTTGATTAGAAAT 59.364 41.667 0.00 0.00 33.81 2.17
973 978 5.815740 GGGTGCGAAGTCTTGATTAGAAATA 59.184 40.000 0.00 0.00 33.81 1.40
974 979 6.018669 GGGTGCGAAGTCTTGATTAGAAATAG 60.019 42.308 0.00 0.00 33.81 1.73
975 980 6.018669 GGTGCGAAGTCTTGATTAGAAATAGG 60.019 42.308 0.00 0.00 33.81 2.57
976 981 6.018669 GTGCGAAGTCTTGATTAGAAATAGGG 60.019 42.308 0.00 0.00 33.81 3.53
977 982 5.467063 GCGAAGTCTTGATTAGAAATAGGGG 59.533 44.000 0.00 0.00 33.81 4.79
978 983 6.583562 CGAAGTCTTGATTAGAAATAGGGGT 58.416 40.000 0.00 0.00 33.81 4.95
979 984 7.048512 CGAAGTCTTGATTAGAAATAGGGGTT 58.951 38.462 0.00 0.00 33.81 4.11
980 985 7.553044 CGAAGTCTTGATTAGAAATAGGGGTTT 59.447 37.037 0.00 0.00 33.81 3.27
981 986 9.244292 GAAGTCTTGATTAGAAATAGGGGTTTT 57.756 33.333 0.00 0.00 33.81 2.43
982 987 8.581253 AGTCTTGATTAGAAATAGGGGTTTTG 57.419 34.615 0.00 0.00 33.81 2.44
983 988 7.615757 AGTCTTGATTAGAAATAGGGGTTTTGG 59.384 37.037 0.00 0.00 33.81 3.28
984 989 7.396339 GTCTTGATTAGAAATAGGGGTTTTGGT 59.604 37.037 0.00 0.00 33.81 3.67
985 990 8.616598 TCTTGATTAGAAATAGGGGTTTTGGTA 58.383 33.333 0.00 0.00 0.00 3.25
986 991 9.421399 CTTGATTAGAAATAGGGGTTTTGGTAT 57.579 33.333 0.00 0.00 0.00 2.73
987 992 8.760980 TGATTAGAAATAGGGGTTTTGGTATG 57.239 34.615 0.00 0.00 0.00 2.39
988 993 8.340757 TGATTAGAAATAGGGGTTTTGGTATGT 58.659 33.333 0.00 0.00 0.00 2.29
989 994 8.762481 ATTAGAAATAGGGGTTTTGGTATGTC 57.238 34.615 0.00 0.00 0.00 3.06
990 995 6.402981 AGAAATAGGGGTTTTGGTATGTCT 57.597 37.500 0.00 0.00 0.00 3.41
991 996 6.424032 AGAAATAGGGGTTTTGGTATGTCTC 58.576 40.000 0.00 0.00 0.00 3.36
992 997 4.790718 ATAGGGGTTTTGGTATGTCTCC 57.209 45.455 0.00 0.00 0.00 3.71
993 998 2.644151 AGGGGTTTTGGTATGTCTCCT 58.356 47.619 0.00 0.00 0.00 3.69
994 999 2.993863 AGGGGTTTTGGTATGTCTCCTT 59.006 45.455 0.00 0.00 0.00 3.36
995 1000 3.089284 GGGGTTTTGGTATGTCTCCTTG 58.911 50.000 0.00 0.00 0.00 3.61
996 1001 3.499745 GGGGTTTTGGTATGTCTCCTTGT 60.500 47.826 0.00 0.00 0.00 3.16
997 1002 4.263594 GGGGTTTTGGTATGTCTCCTTGTA 60.264 45.833 0.00 0.00 0.00 2.41
998 1003 5.318630 GGGTTTTGGTATGTCTCCTTGTAA 58.681 41.667 0.00 0.00 0.00 2.41
999 1004 5.182570 GGGTTTTGGTATGTCTCCTTGTAAC 59.817 44.000 0.00 0.00 0.00 2.50
1000 1005 5.766174 GGTTTTGGTATGTCTCCTTGTAACA 59.234 40.000 0.00 0.00 0.00 2.41
1001 1006 6.433093 GGTTTTGGTATGTCTCCTTGTAACAT 59.567 38.462 0.00 0.00 37.40 2.71
1002 1007 7.608761 GGTTTTGGTATGTCTCCTTGTAACATA 59.391 37.037 0.00 0.00 35.38 2.29
1003 1008 9.005777 GTTTTGGTATGTCTCCTTGTAACATAA 57.994 33.333 0.00 0.00 37.56 1.90
1004 1009 8.556213 TTTGGTATGTCTCCTTGTAACATAAC 57.444 34.615 3.44 3.44 41.71 1.89
1005 1010 7.490657 TGGTATGTCTCCTTGTAACATAACT 57.509 36.000 10.19 0.00 41.83 2.24
1006 1011 7.553334 TGGTATGTCTCCTTGTAACATAACTC 58.447 38.462 10.19 0.25 41.83 3.01
1007 1012 6.696148 GGTATGTCTCCTTGTAACATAACTCG 59.304 42.308 3.21 0.00 39.43 4.18
1008 1013 5.970317 TGTCTCCTTGTAACATAACTCGA 57.030 39.130 0.00 0.00 0.00 4.04
1009 1014 5.950883 TGTCTCCTTGTAACATAACTCGAG 58.049 41.667 11.84 11.84 0.00 4.04
1010 1015 5.475909 TGTCTCCTTGTAACATAACTCGAGT 59.524 40.000 13.58 13.58 0.00 4.18
1016 1021 9.146984 TCCTTGTAACATAACTCGAGTATTTTG 57.853 33.333 20.39 15.51 0.00 2.44
1021 1026 9.750882 GTAACATAACTCGAGTATTTTGTTTCC 57.249 33.333 26.30 18.54 0.00 3.13
1110 1115 4.660938 GAACCCCTGGCGGTTGCT 62.661 66.667 20.02 1.52 46.35 3.91
1140 1145 0.459237 CTGAGAAGCGATTCTGCCGT 60.459 55.000 22.47 0.00 34.65 5.68
1156 1161 0.255890 CCGTGGATCAGGGGAAACAT 59.744 55.000 0.00 0.00 35.96 2.71
1196 1201 2.273449 CTACCCCAGCCCTTGCAG 59.727 66.667 0.00 0.00 41.13 4.41
1305 1312 2.215942 ATGTGCACCCCTTTACTTCC 57.784 50.000 15.69 0.00 0.00 3.46
1306 1313 0.847373 TGTGCACCCCTTTACTTCCA 59.153 50.000 15.69 0.00 0.00 3.53
1307 1314 1.244816 GTGCACCCCTTTACTTCCAC 58.755 55.000 5.22 0.00 0.00 4.02
1308 1315 0.250553 TGCACCCCTTTACTTCCACG 60.251 55.000 0.00 0.00 0.00 4.94
1309 1316 1.583495 GCACCCCTTTACTTCCACGC 61.583 60.000 0.00 0.00 0.00 5.34
1310 1317 0.036306 CACCCCTTTACTTCCACGCT 59.964 55.000 0.00 0.00 0.00 5.07
1311 1318 0.323957 ACCCCTTTACTTCCACGCTC 59.676 55.000 0.00 0.00 0.00 5.03
1496 1508 2.978824 CCGAGTGATTGACGGGGT 59.021 61.111 0.00 0.00 42.48 4.95
1522 1538 5.224441 AGAAAGATTGCCCAGGTACCTATA 58.776 41.667 15.80 0.00 0.00 1.31
1563 1579 3.088532 TCCCCGAAATTTCAACCATGAG 58.911 45.455 17.99 0.00 36.78 2.90
1578 1594 6.043938 TCAACCATGAGTAAGTTAACTTCCCT 59.956 38.462 23.76 19.46 37.40 4.20
1618 1634 1.938577 CAGGGAATGAAGCAGTCGATG 59.061 52.381 0.00 0.00 28.47 3.84
1626 1645 2.200067 GAAGCAGTCGATGGTGATGAG 58.800 52.381 0.00 0.00 40.26 2.90
1672 1706 4.925054 TCGTTTACGAGGACAATAAACCAG 59.075 41.667 0.03 0.00 44.22 4.00
1699 1733 4.621747 CGAAGATAATCTGCCCAGGTATCC 60.622 50.000 12.37 0.00 31.71 2.59
1820 1855 2.015587 GCAGAGGAAATTGAGCTGGAG 58.984 52.381 0.00 0.00 0.00 3.86
1859 1894 3.181456 GCAAGCAGATGGGAGAATACTCT 60.181 47.826 0.00 0.00 42.28 3.24
2029 2067 2.770164 ACCAGTAAGTGCCACTCATC 57.230 50.000 0.00 0.00 0.00 2.92
2031 2069 1.278985 CCAGTAAGTGCCACTCATCCA 59.721 52.381 0.00 0.00 0.00 3.41
2158 2196 5.362556 TGCTACAGTTCTTTTCAATGAGC 57.637 39.130 0.00 0.00 0.00 4.26
2311 2349 9.423061 CAGGTAAATAAAGCTTGCTTTGTTTAT 57.577 29.630 31.97 22.77 39.86 1.40
2361 2400 6.935167 TGTTCAACAGCTCAACTCTATGATA 58.065 36.000 0.00 0.00 0.00 2.15
2746 2785 6.518493 TGGGAACGAGACATGGTAATAATAC 58.482 40.000 0.00 0.00 0.00 1.89
2885 2924 2.356125 CCGAGATGAATGGGGTCAAAGT 60.356 50.000 0.00 0.00 0.00 2.66
2949 2988 7.910162 CACCCAATATTTGATTTAGACGAACAG 59.090 37.037 0.00 0.00 0.00 3.16
2971 3010 5.643348 CAGGCATGTCTTATGTGAGTTTGTA 59.357 40.000 0.00 0.00 0.00 2.41
3346 3545 2.201732 TCACGTGAAGTTCACTGCTTC 58.798 47.619 28.53 6.64 44.85 3.86
3500 3735 1.095600 TCAGTTCTCCCGATGACTCG 58.904 55.000 0.00 0.00 44.62 4.18
3585 3820 4.697756 CGCCGGCCTCCTGACAAA 62.698 66.667 23.46 0.00 0.00 2.83
3586 3821 3.056328 GCCGGCCTCCTGACAAAC 61.056 66.667 18.11 0.00 0.00 2.93
3587 3822 2.359975 CCGGCCTCCTGACAAACC 60.360 66.667 0.00 0.00 0.00 3.27
3588 3823 2.742372 CGGCCTCCTGACAAACCG 60.742 66.667 0.00 0.00 0.00 4.44
3589 3824 3.056328 GGCCTCCTGACAAACCGC 61.056 66.667 0.00 0.00 0.00 5.68
3590 3825 3.423154 GCCTCCTGACAAACCGCG 61.423 66.667 0.00 0.00 0.00 6.46
3591 3826 2.342279 CCTCCTGACAAACCGCGA 59.658 61.111 8.23 0.00 0.00 5.87
3592 3827 1.079127 CCTCCTGACAAACCGCGAT 60.079 57.895 8.23 0.00 0.00 4.58
3607 3842 2.279136 CCGCGATTTAAGTGAAGACTCG 59.721 50.000 8.23 0.00 0.00 4.18
3608 3843 3.168963 CGCGATTTAAGTGAAGACTCGA 58.831 45.455 0.00 0.00 0.00 4.04
3610 3845 4.086025 CGCGATTTAAGTGAAGACTCGATC 60.086 45.833 0.00 0.00 0.00 3.69
3617 3852 3.426615 AGTGAAGACTCGATCCTTCAGT 58.573 45.455 22.21 21.97 46.33 3.41
3629 3864 2.745968 TCCTTCAGTTTGGCCAGTTTT 58.254 42.857 5.11 0.00 0.00 2.43
3740 4140 6.183360 CCTGTGCCTTCTACTTAGTATAGCAA 60.183 42.308 7.14 0.89 0.00 3.91
3778 4178 2.218603 AGTTGAACCGCTGTAAACCTG 58.781 47.619 0.00 0.00 0.00 4.00
3970 4370 2.432510 AGGTGTCCTATGCTGTTCTAGC 59.567 50.000 0.00 0.00 42.15 3.42
4001 4401 7.519057 ACTCAGCAGTATTATACTACCTCTGA 58.481 38.462 4.41 12.69 37.23 3.27
4068 4468 7.639113 AATAATCTTACATTTTGAGGCGGAA 57.361 32.000 0.00 0.00 0.00 4.30
4069 4469 5.567138 AATCTTACATTTTGAGGCGGAAG 57.433 39.130 0.00 0.00 0.00 3.46
4088 4655 6.571150 GCGGAAGAGGAGTAGTAGTTTTAACA 60.571 42.308 0.00 0.00 0.00 2.41
4221 4872 0.966875 GGTGGTTGATGATGCTGCCA 60.967 55.000 0.00 0.00 0.00 4.92
4287 4939 2.095853 AGTGCGTTTTGATAGGCAATCG 59.904 45.455 0.00 0.00 40.20 3.34
4322 4974 7.465900 AAAATTCCCAAGTAGGATATCCTCA 57.534 36.000 27.86 11.63 44.77 3.86
4324 4976 7.654287 AATTCCCAAGTAGGATATCCTCAAT 57.346 36.000 27.86 12.09 44.77 2.57
4336 4988 5.766670 GGATATCCTCAATGCTGTTCATCAA 59.233 40.000 14.97 0.00 33.40 2.57
4337 4989 6.263842 GGATATCCTCAATGCTGTTCATCAAA 59.736 38.462 14.97 0.00 33.40 2.69
4338 4990 7.039923 GGATATCCTCAATGCTGTTCATCAAAT 60.040 37.037 14.97 0.00 33.40 2.32
4339 4991 5.571784 TCCTCAATGCTGTTCATCAAATC 57.428 39.130 0.00 0.00 33.40 2.17
4340 4992 5.011586 TCCTCAATGCTGTTCATCAAATCA 58.988 37.500 0.00 0.00 33.40 2.57
4341 4993 5.124936 TCCTCAATGCTGTTCATCAAATCAG 59.875 40.000 0.00 0.00 33.40 2.90
4342 4994 5.124936 CCTCAATGCTGTTCATCAAATCAGA 59.875 40.000 0.00 0.00 33.40 3.27
4343 4995 5.946298 TCAATGCTGTTCATCAAATCAGAC 58.054 37.500 0.00 0.00 33.40 3.51
4344 4996 5.474189 TCAATGCTGTTCATCAAATCAGACA 59.526 36.000 0.00 0.00 33.40 3.41
4345 4997 4.754372 TGCTGTTCATCAAATCAGACAC 57.246 40.909 0.00 0.00 0.00 3.67
4346 4998 3.503363 TGCTGTTCATCAAATCAGACACC 59.497 43.478 0.00 0.00 0.00 4.16
4347 4999 3.119708 GCTGTTCATCAAATCAGACACCC 60.120 47.826 0.00 0.00 0.00 4.61
4348 5000 4.074259 CTGTTCATCAAATCAGACACCCA 58.926 43.478 0.00 0.00 0.00 4.51
4349 5001 4.468713 TGTTCATCAAATCAGACACCCAA 58.531 39.130 0.00 0.00 0.00 4.12
4350 5002 4.892345 TGTTCATCAAATCAGACACCCAAA 59.108 37.500 0.00 0.00 0.00 3.28
4351 5003 5.362143 TGTTCATCAAATCAGACACCCAAAA 59.638 36.000 0.00 0.00 0.00 2.44
4352 5004 5.452078 TCATCAAATCAGACACCCAAAAC 57.548 39.130 0.00 0.00 0.00 2.43
4353 5005 3.980646 TCAAATCAGACACCCAAAACG 57.019 42.857 0.00 0.00 0.00 3.60
4354 5006 3.283751 TCAAATCAGACACCCAAAACGT 58.716 40.909 0.00 0.00 0.00 3.99
4355 5007 3.314080 TCAAATCAGACACCCAAAACGTC 59.686 43.478 0.00 0.00 0.00 4.34
4356 5008 2.930826 ATCAGACACCCAAAACGTCT 57.069 45.000 0.00 0.00 40.60 4.18
4357 5009 4.345859 AATCAGACACCCAAAACGTCTA 57.654 40.909 0.00 0.00 37.92 2.59
4358 5010 4.553330 ATCAGACACCCAAAACGTCTAT 57.447 40.909 0.00 0.00 37.92 1.98
4359 5011 5.670792 ATCAGACACCCAAAACGTCTATA 57.329 39.130 0.00 0.00 37.92 1.31
4360 5012 5.068234 TCAGACACCCAAAACGTCTATAG 57.932 43.478 0.00 0.00 37.92 1.31
4361 5013 4.768448 TCAGACACCCAAAACGTCTATAGA 59.232 41.667 0.00 0.00 37.92 1.98
4362 5014 4.863131 CAGACACCCAAAACGTCTATAGAC 59.137 45.833 21.00 21.00 37.92 2.59
4363 5015 4.525487 AGACACCCAAAACGTCTATAGACA 59.475 41.667 28.00 0.00 44.99 3.41
4471 5141 6.468543 TGCAATGAACAAGGTACACTATGTA 58.531 36.000 0.00 0.00 0.00 2.29
4525 5196 9.474313 AGGAAAACATTTAGAGGCATTACATTA 57.526 29.630 0.00 0.00 0.00 1.90
4681 5352 2.397777 TGTTGTATTGCGCACAGTTG 57.602 45.000 11.12 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 1.270907 CTGACAGGGGTTGTAGCTCT 58.729 55.000 0.00 0.00 41.05 4.09
270 271 0.802607 GGAACCGTGTCTCGCAGATC 60.803 60.000 0.00 0.00 38.35 2.75
281 282 3.424829 CGAGATGATTTGTTGGAACCGTG 60.425 47.826 0.00 0.00 0.00 4.94
282 283 2.742053 CGAGATGATTTGTTGGAACCGT 59.258 45.455 0.00 0.00 0.00 4.83
291 292 3.750371 TGGAACCAACGAGATGATTTGT 58.250 40.909 0.00 0.00 0.00 2.83
304 305 4.342378 TCGATGGAAAAATGTTGGAACCAA 59.658 37.500 1.83 1.83 0.00 3.67
347 348 0.040499 AATAACCATGCCCCCACGTT 59.960 50.000 0.00 0.00 0.00 3.99
391 392 0.887387 AATGCGCCAACGGTTGTAGT 60.887 50.000 18.73 0.37 40.57 2.73
412 413 1.503542 CTCGTTGATGGTTGCAGCC 59.496 57.895 13.50 13.50 0.00 4.85
425 426 1.267806 CATTGCAGCTTTGTCCTCGTT 59.732 47.619 0.00 0.00 0.00 3.85
542 543 1.269831 GGCCTAGTAGCTTCATCCGTG 60.270 57.143 0.00 0.00 0.00 4.94
677 682 1.153784 CAACGCAATCCATGGCCAC 60.154 57.895 8.16 0.00 0.00 5.01
746 751 0.808755 GTTTGATTAGGCCCACACCG 59.191 55.000 0.00 0.00 33.69 4.94
774 779 1.519751 CCGAATTTTGGCCGGTCACA 61.520 55.000 9.15 0.00 38.55 3.58
818 823 7.499895 ACTCTTTCGGTGTAAATTTTGTTAGGA 59.500 33.333 0.00 0.00 0.00 2.94
823 828 8.680001 ACTTAACTCTTTCGGTGTAAATTTTGT 58.320 29.630 0.00 0.00 0.00 2.83
824 829 9.166126 GACTTAACTCTTTCGGTGTAAATTTTG 57.834 33.333 0.00 0.00 0.00 2.44
825 830 8.895737 TGACTTAACTCTTTCGGTGTAAATTTT 58.104 29.630 0.00 0.00 0.00 1.82
826 831 8.340443 GTGACTTAACTCTTTCGGTGTAAATTT 58.660 33.333 0.00 0.00 0.00 1.82
827 832 7.041576 GGTGACTTAACTCTTTCGGTGTAAATT 60.042 37.037 0.00 0.00 0.00 1.82
828 833 6.426025 GGTGACTTAACTCTTTCGGTGTAAAT 59.574 38.462 0.00 0.00 0.00 1.40
829 834 5.754890 GGTGACTTAACTCTTTCGGTGTAAA 59.245 40.000 0.00 0.00 0.00 2.01
830 835 5.163426 TGGTGACTTAACTCTTTCGGTGTAA 60.163 40.000 0.00 0.00 0.00 2.41
831 836 4.341806 TGGTGACTTAACTCTTTCGGTGTA 59.658 41.667 0.00 0.00 0.00 2.90
832 837 3.133362 TGGTGACTTAACTCTTTCGGTGT 59.867 43.478 0.00 0.00 0.00 4.16
833 838 3.493503 GTGGTGACTTAACTCTTTCGGTG 59.506 47.826 0.00 0.00 0.00 4.94
834 839 3.133362 TGTGGTGACTTAACTCTTTCGGT 59.867 43.478 0.00 0.00 0.00 4.69
835 840 3.724374 TGTGGTGACTTAACTCTTTCGG 58.276 45.455 0.00 0.00 0.00 4.30
836 841 5.728351 TTTGTGGTGACTTAACTCTTTCG 57.272 39.130 0.00 0.00 0.00 3.46
837 842 7.973944 ACAATTTTGTGGTGACTTAACTCTTTC 59.026 33.333 0.00 0.00 40.49 2.62
838 843 7.836842 ACAATTTTGTGGTGACTTAACTCTTT 58.163 30.769 0.00 0.00 40.49 2.52
839 844 7.404671 ACAATTTTGTGGTGACTTAACTCTT 57.595 32.000 0.00 0.00 40.49 2.85
840 845 7.773690 AGTACAATTTTGTGGTGACTTAACTCT 59.226 33.333 6.21 0.00 42.31 3.24
841 846 7.927048 AGTACAATTTTGTGGTGACTTAACTC 58.073 34.615 6.21 0.00 42.31 3.01
842 847 7.875327 AGTACAATTTTGTGGTGACTTAACT 57.125 32.000 6.21 0.00 42.31 2.24
846 851 8.073768 CGATTTAGTACAATTTTGTGGTGACTT 58.926 33.333 6.21 0.00 42.31 3.01
847 852 7.581476 CGATTTAGTACAATTTTGTGGTGACT 58.419 34.615 6.21 4.40 42.31 3.41
848 853 6.304683 GCGATTTAGTACAATTTTGTGGTGAC 59.695 38.462 6.21 0.00 42.31 3.67
849 854 6.017026 TGCGATTTAGTACAATTTTGTGGTGA 60.017 34.615 6.21 0.00 42.31 4.02
850 855 6.146216 TGCGATTTAGTACAATTTTGTGGTG 58.854 36.000 6.21 0.00 42.31 4.17
851 856 6.320494 TGCGATTTAGTACAATTTTGTGGT 57.680 33.333 6.21 0.00 42.31 4.16
852 857 5.286082 GCTGCGATTTAGTACAATTTTGTGG 59.714 40.000 6.21 0.00 42.31 4.17
853 858 5.855925 TGCTGCGATTTAGTACAATTTTGTG 59.144 36.000 6.21 0.00 42.31 3.33
854 859 6.007936 TGCTGCGATTTAGTACAATTTTGT 57.992 33.333 1.08 1.08 44.86 2.83
855 860 5.512788 CCTGCTGCGATTTAGTACAATTTTG 59.487 40.000 0.00 0.00 0.00 2.44
856 861 5.414454 TCCTGCTGCGATTTAGTACAATTTT 59.586 36.000 0.00 0.00 0.00 1.82
857 862 4.941263 TCCTGCTGCGATTTAGTACAATTT 59.059 37.500 0.00 0.00 0.00 1.82
858 863 4.513442 TCCTGCTGCGATTTAGTACAATT 58.487 39.130 0.00 0.00 0.00 2.32
859 864 4.122776 CTCCTGCTGCGATTTAGTACAAT 58.877 43.478 0.00 0.00 0.00 2.71
860 865 3.521560 CTCCTGCTGCGATTTAGTACAA 58.478 45.455 0.00 0.00 0.00 2.41
861 866 2.738643 GCTCCTGCTGCGATTTAGTACA 60.739 50.000 0.00 0.00 36.03 2.90
862 867 1.861575 GCTCCTGCTGCGATTTAGTAC 59.138 52.381 0.00 0.00 36.03 2.73
863 868 1.202533 GGCTCCTGCTGCGATTTAGTA 60.203 52.381 0.00 0.00 39.59 1.82
864 869 0.462759 GGCTCCTGCTGCGATTTAGT 60.463 55.000 0.00 0.00 39.59 2.24
865 870 1.162800 GGGCTCCTGCTGCGATTTAG 61.163 60.000 0.00 0.00 39.59 1.85
866 871 1.153168 GGGCTCCTGCTGCGATTTA 60.153 57.895 0.00 0.00 39.59 1.40
867 872 2.439156 GGGCTCCTGCTGCGATTT 60.439 61.111 0.00 0.00 39.59 2.17
868 873 2.769652 TTTGGGCTCCTGCTGCGATT 62.770 55.000 0.00 0.00 39.59 3.34
869 874 2.563013 ATTTGGGCTCCTGCTGCGAT 62.563 55.000 0.00 0.00 39.59 4.58
870 875 2.769652 AATTTGGGCTCCTGCTGCGA 62.770 55.000 0.00 0.00 39.59 5.10
871 876 1.031571 TAATTTGGGCTCCTGCTGCG 61.032 55.000 0.00 0.00 39.59 5.18
872 877 1.185315 TTAATTTGGGCTCCTGCTGC 58.815 50.000 0.00 0.00 39.59 5.25
873 878 3.953612 TGTATTAATTTGGGCTCCTGCTG 59.046 43.478 0.00 0.00 39.59 4.41
874 879 3.954258 GTGTATTAATTTGGGCTCCTGCT 59.046 43.478 0.00 0.00 39.59 4.24
875 880 3.243068 CGTGTATTAATTTGGGCTCCTGC 60.243 47.826 0.00 0.00 38.76 4.85
876 881 3.945285 ACGTGTATTAATTTGGGCTCCTG 59.055 43.478 0.00 0.00 0.00 3.86
877 882 3.945285 CACGTGTATTAATTTGGGCTCCT 59.055 43.478 7.58 0.00 0.00 3.69
878 883 3.488553 GCACGTGTATTAATTTGGGCTCC 60.489 47.826 18.38 0.00 0.00 4.70
879 884 3.488553 GGCACGTGTATTAATTTGGGCTC 60.489 47.826 18.38 0.00 0.00 4.70
880 885 2.425668 GGCACGTGTATTAATTTGGGCT 59.574 45.455 18.38 0.00 0.00 5.19
881 886 2.425668 AGGCACGTGTATTAATTTGGGC 59.574 45.455 18.38 0.00 0.00 5.36
882 887 3.733684 GCAGGCACGTGTATTAATTTGGG 60.734 47.826 18.38 0.00 0.00 4.12
883 888 3.119673 TGCAGGCACGTGTATTAATTTGG 60.120 43.478 18.38 0.00 0.00 3.28
884 889 3.851403 GTGCAGGCACGTGTATTAATTTG 59.149 43.478 18.38 5.56 37.19 2.32
885 890 4.091453 GTGCAGGCACGTGTATTAATTT 57.909 40.909 18.38 0.00 37.19 1.82
886 891 3.757745 GTGCAGGCACGTGTATTAATT 57.242 42.857 18.38 0.00 37.19 1.40
897 902 0.108138 AACCTATCGAGTGCAGGCAC 60.108 55.000 16.29 16.29 46.50 5.01
898 903 0.175760 GAACCTATCGAGTGCAGGCA 59.824 55.000 0.00 0.00 32.31 4.75
899 904 0.175760 TGAACCTATCGAGTGCAGGC 59.824 55.000 0.00 0.00 32.31 4.85
900 905 1.204704 TGTGAACCTATCGAGTGCAGG 59.795 52.381 0.00 0.00 35.45 4.85
901 906 2.654749 TGTGAACCTATCGAGTGCAG 57.345 50.000 0.00 0.00 0.00 4.41
902 907 2.299013 ACTTGTGAACCTATCGAGTGCA 59.701 45.455 0.00 0.00 0.00 4.57
903 908 2.960819 ACTTGTGAACCTATCGAGTGC 58.039 47.619 0.00 0.00 0.00 4.40
904 909 3.123621 GCAACTTGTGAACCTATCGAGTG 59.876 47.826 0.00 0.00 0.00 3.51
905 910 3.244078 TGCAACTTGTGAACCTATCGAGT 60.244 43.478 0.00 0.00 0.00 4.18
906 911 3.325870 TGCAACTTGTGAACCTATCGAG 58.674 45.455 0.00 0.00 0.00 4.04
907 912 3.394674 TGCAACTTGTGAACCTATCGA 57.605 42.857 0.00 0.00 0.00 3.59
908 913 4.154015 TGATTGCAACTTGTGAACCTATCG 59.846 41.667 0.00 0.00 0.00 2.92
909 914 5.627499 TGATTGCAACTTGTGAACCTATC 57.373 39.130 0.00 0.00 0.00 2.08
933 938 0.750182 ACCCACGTTTCACCACTTGG 60.750 55.000 0.00 0.00 36.13 3.61
934 939 0.380378 CACCCACGTTTCACCACTTG 59.620 55.000 0.00 0.00 0.00 3.16
935 940 1.381165 GCACCCACGTTTCACCACTT 61.381 55.000 0.00 0.00 0.00 3.16
936 941 1.822186 GCACCCACGTTTCACCACT 60.822 57.895 0.00 0.00 0.00 4.00
937 942 2.719354 GCACCCACGTTTCACCAC 59.281 61.111 0.00 0.00 0.00 4.16
938 943 2.871216 TTCGCACCCACGTTTCACCA 62.871 55.000 0.00 0.00 0.00 4.17
939 944 2.113131 CTTCGCACCCACGTTTCACC 62.113 60.000 0.00 0.00 0.00 4.02
940 945 1.278637 CTTCGCACCCACGTTTCAC 59.721 57.895 0.00 0.00 0.00 3.18
941 946 1.153329 ACTTCGCACCCACGTTTCA 60.153 52.632 0.00 0.00 0.00 2.69
942 947 0.878961 AGACTTCGCACCCACGTTTC 60.879 55.000 0.00 0.00 0.00 2.78
943 948 0.463116 AAGACTTCGCACCCACGTTT 60.463 50.000 0.00 0.00 0.00 3.60
944 949 1.145377 AAGACTTCGCACCCACGTT 59.855 52.632 0.00 0.00 0.00 3.99
945 950 1.594293 CAAGACTTCGCACCCACGT 60.594 57.895 0.00 0.00 0.00 4.49
946 951 0.670546 ATCAAGACTTCGCACCCACG 60.671 55.000 0.00 0.00 0.00 4.94
947 952 1.523758 AATCAAGACTTCGCACCCAC 58.476 50.000 0.00 0.00 0.00 4.61
948 953 2.565391 TCTAATCAAGACTTCGCACCCA 59.435 45.455 0.00 0.00 0.00 4.51
949 954 3.247006 TCTAATCAAGACTTCGCACCC 57.753 47.619 0.00 0.00 0.00 4.61
950 955 5.803020 ATTTCTAATCAAGACTTCGCACC 57.197 39.130 0.00 0.00 32.51 5.01
951 956 6.018669 CCCTATTTCTAATCAAGACTTCGCAC 60.019 42.308 0.00 0.00 32.51 5.34
952 957 6.049149 CCCTATTTCTAATCAAGACTTCGCA 58.951 40.000 0.00 0.00 32.51 5.10
953 958 5.467063 CCCCTATTTCTAATCAAGACTTCGC 59.533 44.000 0.00 0.00 32.51 4.70
954 959 6.583562 ACCCCTATTTCTAATCAAGACTTCG 58.416 40.000 0.00 0.00 32.51 3.79
955 960 8.809468 AAACCCCTATTTCTAATCAAGACTTC 57.191 34.615 0.00 0.00 32.51 3.01
956 961 9.025041 CAAAACCCCTATTTCTAATCAAGACTT 57.975 33.333 0.00 0.00 32.51 3.01
957 962 7.615757 CCAAAACCCCTATTTCTAATCAAGACT 59.384 37.037 0.00 0.00 32.51 3.24
958 963 7.396339 ACCAAAACCCCTATTTCTAATCAAGAC 59.604 37.037 0.00 0.00 32.51 3.01
959 964 7.475299 ACCAAAACCCCTATTTCTAATCAAGA 58.525 34.615 0.00 0.00 0.00 3.02
960 965 7.718334 ACCAAAACCCCTATTTCTAATCAAG 57.282 36.000 0.00 0.00 0.00 3.02
961 966 9.196139 CATACCAAAACCCCTATTTCTAATCAA 57.804 33.333 0.00 0.00 0.00 2.57
962 967 8.340757 ACATACCAAAACCCCTATTTCTAATCA 58.659 33.333 0.00 0.00 0.00 2.57
963 968 8.762481 ACATACCAAAACCCCTATTTCTAATC 57.238 34.615 0.00 0.00 0.00 1.75
964 969 8.566109 AGACATACCAAAACCCCTATTTCTAAT 58.434 33.333 0.00 0.00 0.00 1.73
965 970 7.935405 AGACATACCAAAACCCCTATTTCTAA 58.065 34.615 0.00 0.00 0.00 2.10
966 971 7.366191 GGAGACATACCAAAACCCCTATTTCTA 60.366 40.741 0.00 0.00 0.00 2.10
967 972 6.402981 AGACATACCAAAACCCCTATTTCT 57.597 37.500 0.00 0.00 0.00 2.52
968 973 5.593095 GGAGACATACCAAAACCCCTATTTC 59.407 44.000 0.00 0.00 0.00 2.17
969 974 5.255443 AGGAGACATACCAAAACCCCTATTT 59.745 40.000 0.00 0.00 0.00 1.40
970 975 4.794067 AGGAGACATACCAAAACCCCTATT 59.206 41.667 0.00 0.00 0.00 1.73
971 976 4.380791 AGGAGACATACCAAAACCCCTAT 58.619 43.478 0.00 0.00 0.00 2.57
972 977 3.810623 AGGAGACATACCAAAACCCCTA 58.189 45.455 0.00 0.00 0.00 3.53
973 978 2.644151 AGGAGACATACCAAAACCCCT 58.356 47.619 0.00 0.00 0.00 4.79
974 979 3.089284 CAAGGAGACATACCAAAACCCC 58.911 50.000 0.00 0.00 0.00 4.95
975 980 3.763057 ACAAGGAGACATACCAAAACCC 58.237 45.455 0.00 0.00 0.00 4.11
976 981 5.766174 TGTTACAAGGAGACATACCAAAACC 59.234 40.000 0.00 0.00 0.00 3.27
977 982 6.870971 TGTTACAAGGAGACATACCAAAAC 57.129 37.500 0.00 0.00 0.00 2.43
978 983 9.005777 GTTATGTTACAAGGAGACATACCAAAA 57.994 33.333 0.00 0.00 36.35 2.44
979 984 8.380099 AGTTATGTTACAAGGAGACATACCAAA 58.620 33.333 0.00 0.00 36.35 3.28
980 985 7.913789 AGTTATGTTACAAGGAGACATACCAA 58.086 34.615 0.00 0.00 36.35 3.67
981 986 7.490657 AGTTATGTTACAAGGAGACATACCA 57.509 36.000 0.00 0.00 36.35 3.25
982 987 6.696148 CGAGTTATGTTACAAGGAGACATACC 59.304 42.308 0.00 0.00 36.35 2.73
983 988 7.478322 TCGAGTTATGTTACAAGGAGACATAC 58.522 38.462 0.00 0.00 36.35 2.39
984 989 7.338703 ACTCGAGTTATGTTACAAGGAGACATA 59.661 37.037 13.58 0.00 35.72 2.29
985 990 6.153000 ACTCGAGTTATGTTACAAGGAGACAT 59.847 38.462 13.58 0.00 37.70 3.06
986 991 5.475909 ACTCGAGTTATGTTACAAGGAGACA 59.524 40.000 13.58 0.00 0.00 3.41
987 992 5.952033 ACTCGAGTTATGTTACAAGGAGAC 58.048 41.667 13.58 0.00 0.00 3.36
988 993 7.876936 ATACTCGAGTTATGTTACAAGGAGA 57.123 36.000 25.44 0.00 0.00 3.71
989 994 8.928270 AAATACTCGAGTTATGTTACAAGGAG 57.072 34.615 25.44 0.00 0.00 3.69
990 995 9.146984 CAAAATACTCGAGTTATGTTACAAGGA 57.853 33.333 25.44 0.11 0.00 3.36
991 996 8.932791 ACAAAATACTCGAGTTATGTTACAAGG 58.067 33.333 25.44 6.93 0.00 3.61
995 1000 9.750882 GGAAACAAAATACTCGAGTTATGTTAC 57.249 33.333 25.44 18.58 0.00 2.50
996 1001 8.938906 GGGAAACAAAATACTCGAGTTATGTTA 58.061 33.333 25.44 4.38 0.00 2.41
997 1002 7.664318 AGGGAAACAAAATACTCGAGTTATGTT 59.336 33.333 25.44 23.06 0.00 2.71
998 1003 7.166167 AGGGAAACAAAATACTCGAGTTATGT 58.834 34.615 25.44 19.05 0.00 2.29
999 1004 7.611213 AGGGAAACAAAATACTCGAGTTATG 57.389 36.000 25.44 18.43 0.00 1.90
1000 1005 9.729281 TTTAGGGAAACAAAATACTCGAGTTAT 57.271 29.630 25.44 10.28 0.00 1.89
1001 1006 9.558396 TTTTAGGGAAACAAAATACTCGAGTTA 57.442 29.630 25.44 10.18 0.00 2.24
1002 1007 8.454570 TTTTAGGGAAACAAAATACTCGAGTT 57.545 30.769 25.44 8.91 0.00 3.01
1003 1008 8.454570 TTTTTAGGGAAACAAAATACTCGAGT 57.545 30.769 23.66 23.66 0.00 4.18
1096 1101 2.516930 CATAGCAACCGCCAGGGG 60.517 66.667 0.00 0.00 43.47 4.79
1100 1105 4.402528 ACGCCATAGCAACCGCCA 62.403 61.111 0.00 0.00 39.83 5.69
1101 1106 3.573491 GACGCCATAGCAACCGCC 61.573 66.667 0.00 0.00 39.83 6.13
1103 1108 2.461110 GGTGACGCCATAGCAACCG 61.461 63.158 0.00 0.00 39.83 4.44
1104 1109 1.078426 AGGTGACGCCATAGCAACC 60.078 57.895 7.99 0.00 40.61 3.77
1110 1115 0.175760 GCTTCTCAGGTGACGCCATA 59.824 55.000 7.99 0.00 40.61 2.74
1140 1145 1.006998 CCCAATGTTTCCCCTGATCCA 59.993 52.381 0.00 0.00 0.00 3.41
1156 1161 2.029964 GGCGTGAGACGAACCCAA 59.970 61.111 0.00 0.00 46.05 4.12
1208 1213 0.103208 CACCTCCTCCAGCGTATCAC 59.897 60.000 0.00 0.00 0.00 3.06
1311 1318 4.760047 CTTCCCCGTGGAGCGTGG 62.760 72.222 0.00 0.00 43.07 4.94
1321 1333 1.451387 CCATCCGAAACCTTCCCCG 60.451 63.158 0.00 0.00 0.00 5.73
1496 1508 2.978156 ACCTGGGCAATCTTTCTTCA 57.022 45.000 0.00 0.00 0.00 3.02
1522 1538 6.002082 GGGGAAATTTAATCTAGCGGTACAT 58.998 40.000 0.00 0.00 0.00 2.29
1563 1579 5.646793 GTGGAATCCAGGGAAGTTAACTTAC 59.353 44.000 20.60 20.60 32.74 2.34
1578 1594 5.500234 CCTGAAGAATTAGTGTGGAATCCA 58.500 41.667 0.00 0.00 0.00 3.41
1610 1626 1.534805 CGTCCTCATCACCATCGACTG 60.535 57.143 0.00 0.00 0.00 3.51
1618 1634 1.714794 CAGTTGTCGTCCTCATCACC 58.285 55.000 0.00 0.00 0.00 4.02
1626 1645 1.210155 GCCATTGCAGTTGTCGTCC 59.790 57.895 0.00 0.00 37.47 4.79
1665 1699 5.810587 GCAGATTATCTTCGTGTCTGGTTTA 59.189 40.000 0.00 0.00 37.39 2.01
1672 1706 3.126831 CTGGGCAGATTATCTTCGTGTC 58.873 50.000 0.00 0.00 0.00 3.67
1727 1762 1.833630 GATGATCTCTGGGTGGTGACA 59.166 52.381 0.00 0.00 38.70 3.58
1730 1765 2.616634 CAGATGATCTCTGGGTGGTG 57.383 55.000 12.00 0.00 46.52 4.17
1820 1855 3.265791 CTTGCAGTACCTCTCAATCCAC 58.734 50.000 0.00 0.00 0.00 4.02
1859 1894 5.048083 GGCCAGAATGTCATCAAACAGTTTA 60.048 40.000 0.00 0.00 31.50 2.01
1991 2029 6.441222 ACTGGTAGAAGTATCATGGGTCTTA 58.559 40.000 0.00 0.00 0.00 2.10
2746 2785 5.123344 AGCTTGCTGGTTTAAGTTATAACCG 59.877 40.000 12.05 13.06 45.40 4.44
2885 2924 9.571810 GCATGTGACTTTAATGTCATTTTATCA 57.428 29.630 22.61 16.11 46.77 2.15
2949 2988 5.643777 AGTACAAACTCACATAAGACATGCC 59.356 40.000 0.00 0.00 0.00 4.40
3500 3735 3.567478 AACTGGCCATACTGAAGGATC 57.433 47.619 5.51 0.00 0.00 3.36
3581 3816 3.810941 TCTTCACTTAAATCGCGGTTTGT 59.189 39.130 26.87 14.43 0.00 2.83
3582 3817 4.084013 AGTCTTCACTTAAATCGCGGTTTG 60.084 41.667 26.87 13.75 0.00 2.93
3585 3820 3.251571 GAGTCTTCACTTAAATCGCGGT 58.748 45.455 6.13 0.00 30.63 5.68
3586 3821 2.279136 CGAGTCTTCACTTAAATCGCGG 59.721 50.000 6.13 0.00 30.63 6.46
3587 3822 3.168963 TCGAGTCTTCACTTAAATCGCG 58.831 45.455 0.00 0.00 30.63 5.87
3588 3823 4.207429 GGATCGAGTCTTCACTTAAATCGC 59.793 45.833 0.00 0.00 30.63 4.58
3589 3824 5.583495 AGGATCGAGTCTTCACTTAAATCG 58.417 41.667 0.00 0.00 30.63 3.34
3590 3825 7.036220 TGAAGGATCGAGTCTTCACTTAAATC 58.964 38.462 21.74 0.00 42.81 2.17
3591 3826 6.936279 TGAAGGATCGAGTCTTCACTTAAAT 58.064 36.000 21.74 0.00 42.81 1.40
3592 3827 6.015350 ACTGAAGGATCGAGTCTTCACTTAAA 60.015 38.462 21.74 7.20 42.81 1.52
3607 3842 2.206576 ACTGGCCAAACTGAAGGATC 57.793 50.000 7.01 0.00 0.00 3.36
3608 3843 2.683211 AACTGGCCAAACTGAAGGAT 57.317 45.000 7.01 0.00 0.00 3.24
3610 3845 3.541996 AAAAACTGGCCAAACTGAAGG 57.458 42.857 7.01 0.00 0.00 3.46
3629 3864 1.133823 TCTTTGGAGCAGCCTCACAAA 60.134 47.619 0.00 0.00 39.96 2.83
3740 4140 7.822822 GGTTCAACTTAACACACTGGACTATAT 59.177 37.037 0.00 0.00 0.00 0.86
3778 4178 0.799534 GCACGCATTGAGCATGTTCC 60.800 55.000 7.13 0.00 46.13 3.62
3970 4370 8.732531 GGTAGTATAATACTGCTGAGTAGAAGG 58.267 40.741 4.11 0.00 40.63 3.46
4068 4468 8.247666 ACAACTGTTAAAACTACTACTCCTCT 57.752 34.615 0.00 0.00 0.00 3.69
4069 4469 9.971922 TTACAACTGTTAAAACTACTACTCCTC 57.028 33.333 0.00 0.00 0.00 3.71
4088 4655 4.655963 AGAGCATGGTCATGTTTACAACT 58.344 39.130 25.71 0.00 40.80 3.16
4221 4872 5.149973 TGTGCATATGCCAAAGTTTCAAT 57.850 34.783 24.54 0.00 41.18 2.57
4309 4961 6.471146 ATGAACAGCATTGAGGATATCCTAC 58.529 40.000 24.58 17.14 39.55 3.18
4312 4964 5.311265 TGATGAACAGCATTGAGGATATCC 58.689 41.667 14.41 14.41 37.34 2.59
4315 4967 6.829811 TGATTTGATGAACAGCATTGAGGATA 59.170 34.615 0.00 0.00 37.34 2.59
4322 4974 5.336213 GGTGTCTGATTTGATGAACAGCATT 60.336 40.000 0.00 0.00 37.34 3.56
4324 4976 3.503363 GGTGTCTGATTTGATGAACAGCA 59.497 43.478 0.00 0.00 0.00 4.41
4336 4988 3.208747 AGACGTTTTGGGTGTCTGATT 57.791 42.857 0.00 0.00 41.21 2.57
4337 4989 2.930826 AGACGTTTTGGGTGTCTGAT 57.069 45.000 0.00 0.00 41.21 2.90
4338 4990 4.768448 TCTATAGACGTTTTGGGTGTCTGA 59.232 41.667 0.00 0.00 42.59 3.27
4339 4991 4.863131 GTCTATAGACGTTTTGGGTGTCTG 59.137 45.833 16.87 0.00 42.59 3.51
4340 4992 5.069501 GTCTATAGACGTTTTGGGTGTCT 57.930 43.478 16.87 0.00 44.63 3.41
4353 5005 1.658673 CCGCCCCGTGTCTATAGAC 59.341 63.158 23.53 23.53 44.97 2.59
4354 5006 2.198287 GCCGCCCCGTGTCTATAGA 61.198 63.158 0.00 0.00 0.00 1.98
4355 5007 2.338984 GCCGCCCCGTGTCTATAG 59.661 66.667 0.00 0.00 0.00 1.31
4356 5008 3.228759 GGCCGCCCCGTGTCTATA 61.229 66.667 0.00 0.00 0.00 1.31
4489 5159 8.817100 CCTCTAAATGTTTTCCTTTTGTGTTTC 58.183 33.333 0.00 0.00 0.00 2.78
4637 5308 0.839946 GAGTAGACCATGTGCCCCAT 59.160 55.000 0.00 0.00 0.00 4.00
4681 5352 1.069258 CGGGATCTAAAGGTCGGGC 59.931 63.158 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.