Multiple sequence alignment - TraesCS3B01G208700

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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 TraesCS3B01G208700 chr3B 100.000 2768 0 0 1 2768 244663610 244660843 0.000000e+00 5112
1 TraesCS3B01G208700 chr3B 90.544 772 71 2 71 840 377139734 377138963 0.000000e+00 1020
2 TraesCS3B01G208700 chr3A 93.667 979 35 10 1109 2077 197437322 197436361 0.000000e+00 1439
3 TraesCS3B01G208700 chr3A 91.761 704 27 7 2085 2768 197436151 197435459 0.000000e+00 950
4 TraesCS3B01G208700 chr3A 75.372 471 86 22 1295 1743 163910127 163910589 1.680000e-47 200
5 TraesCS3B01G208700 chr1B 96.370 799 27 2 98 894 49618358 49619156 0.000000e+00 1314
6 TraesCS3B01G208700 chr7B 93.515 879 42 8 1264 2137 568390293 568391161 0.000000e+00 1293
7 TraesCS3B01G208700 chr7B 91.549 71 6 0 7 77 189481210 189481280 6.310000e-17 99
8 TraesCS3B01G208700 chr2B 95.068 811 36 3 77 883 89649810 89649000 0.000000e+00 1273
9 TraesCS3B01G208700 chr2B 98.571 70 1 0 8 77 756696401 756696470 1.040000e-24 124
10 TraesCS3B01G208700 chr2B 92.958 71 5 0 7 77 159330744 159330674 1.360000e-18 104
11 TraesCS3B01G208700 chr2D 94.634 820 42 2 77 894 481449557 481448738 0.000000e+00 1269
12 TraesCS3B01G208700 chr3D 90.308 908 57 20 1878 2768 169792289 169791396 0.000000e+00 1160
13 TraesCS3B01G208700 chr3D 90.873 756 57 4 133 887 255449847 255449103 0.000000e+00 1003
14 TraesCS3B01G208700 chr3D 96.255 267 8 2 1051 1317 169792553 169792289 1.180000e-118 436
15 TraesCS3B01G208700 chr3D 74.260 676 120 31 1110 1743 144249988 144250651 4.610000e-58 235
16 TraesCS3B01G208700 chr3D 95.652 69 3 0 7 75 8251044 8250976 8.100000e-21 111
17 TraesCS3B01G208700 chr5B 87.798 672 72 8 70 739 532595895 532596558 0.000000e+00 778
18 TraesCS3B01G208700 chr5B 94.595 74 4 0 7 80 448291620 448291547 6.260000e-22 115
19 TraesCS3B01G208700 chr5B 92.958 71 5 0 7 77 513973639 513973709 1.360000e-18 104
20 TraesCS3B01G208700 chrUn 89.837 551 44 3 71 618 119877325 119876784 0.000000e+00 697
21 TraesCS3B01G208700 chrUn 89.674 552 44 4 71 618 222915874 222915332 0.000000e+00 691
22 TraesCS3B01G208700 chr6B 95.775 71 3 0 7 77 232757180 232757110 6.260000e-22 115
23 TraesCS3B01G208700 chr4B 93.243 74 5 0 7 80 456918106 456918033 2.910000e-20 110
24 TraesCS3B01G208700 chr4B 93.939 66 4 0 12 77 608976062 608976127 1.750000e-17 100


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 TraesCS3B01G208700 chr3B 244660843 244663610 2767 True 5112.0 5112 100.0000 1 2768 1 chr3B.!!$R1 2767
1 TraesCS3B01G208700 chr3B 377138963 377139734 771 True 1020.0 1020 90.5440 71 840 1 chr3B.!!$R2 769
2 TraesCS3B01G208700 chr3A 197435459 197437322 1863 True 1194.5 1439 92.7140 1109 2768 2 chr3A.!!$R1 1659
3 TraesCS3B01G208700 chr1B 49618358 49619156 798 False 1314.0 1314 96.3700 98 894 1 chr1B.!!$F1 796
4 TraesCS3B01G208700 chr7B 568390293 568391161 868 False 1293.0 1293 93.5150 1264 2137 1 chr7B.!!$F2 873
5 TraesCS3B01G208700 chr2B 89649000 89649810 810 True 1273.0 1273 95.0680 77 883 1 chr2B.!!$R1 806
6 TraesCS3B01G208700 chr2D 481448738 481449557 819 True 1269.0 1269 94.6340 77 894 1 chr2D.!!$R1 817
7 TraesCS3B01G208700 chr3D 255449103 255449847 744 True 1003.0 1003 90.8730 133 887 1 chr3D.!!$R2 754
8 TraesCS3B01G208700 chr3D 169791396 169792553 1157 True 798.0 1160 93.2815 1051 2768 2 chr3D.!!$R3 1717
9 TraesCS3B01G208700 chr3D 144249988 144250651 663 False 235.0 235 74.2600 1110 1743 1 chr3D.!!$F1 633
10 TraesCS3B01G208700 chr5B 532595895 532596558 663 False 778.0 778 87.7980 70 739 1 chr5B.!!$F2 669
11 TraesCS3B01G208700 chrUn 119876784 119877325 541 True 697.0 697 89.8370 71 618 1 chrUn.!!$R1 547
12 TraesCS3B01G208700 chrUn 222915332 222915874 542 True 691.0 691 89.6740 71 618 1 chrUn.!!$R2 547

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
926 934 0.034059 CTGTCCGTTGGAGTTGCTCT 59.966 55.0 0.0 0.0 29.39 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2045 2104 1.205179 ACGATACCGCACATTGTACCA 59.795 47.619 0.0 0.0 39.95 3.25 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
31 32 3.837669 CGACCCAAACGGACAAAAG 57.162 52.632 0.00 0.00 34.64 2.27
32 33 1.018910 CGACCCAAACGGACAAAAGT 58.981 50.000 0.00 0.00 34.64 2.66
33 34 1.003223 CGACCCAAACGGACAAAAGTC 60.003 52.381 0.00 0.00 34.64 3.01
34 35 1.003223 GACCCAAACGGACAAAAGTCG 60.003 52.381 0.00 0.00 34.64 4.18
35 36 0.309612 CCCAAACGGACAAAAGTCGG 59.690 55.000 0.00 0.00 0.00 4.79
36 37 1.301423 CCAAACGGACAAAAGTCGGA 58.699 50.000 9.67 0.00 0.00 4.55
37 38 1.003223 CCAAACGGACAAAAGTCGGAC 60.003 52.381 9.67 0.00 0.00 4.79
38 39 1.666700 CAAACGGACAAAAGTCGGACA 59.333 47.619 11.27 0.00 0.00 4.02
39 40 2.027003 AACGGACAAAAGTCGGACAA 57.973 45.000 11.27 0.00 0.00 3.18
40 41 2.027003 ACGGACAAAAGTCGGACAAA 57.973 45.000 11.27 0.00 0.00 2.83
41 42 2.567985 ACGGACAAAAGTCGGACAAAT 58.432 42.857 11.27 0.00 0.00 2.32
42 43 2.289547 ACGGACAAAAGTCGGACAAATG 59.710 45.455 11.27 8.04 0.00 2.32
43 44 2.661594 GGACAAAAGTCGGACAAATGC 58.338 47.619 11.27 2.89 0.00 3.56
44 45 2.307049 GACAAAAGTCGGACAAATGCG 58.693 47.619 11.27 0.00 41.78 4.73
45 46 1.052287 CAAAAGTCGGACAAATGCGC 58.948 50.000 11.27 0.00 39.93 6.09
46 47 0.039527 AAAAGTCGGACAAATGCGCC 60.040 50.000 11.27 0.00 39.93 6.53
47 48 2.182614 AAAGTCGGACAAATGCGCCG 62.183 55.000 11.27 0.00 46.08 6.46
48 49 3.419759 GTCGGACAAATGCGCCGT 61.420 61.111 4.18 0.00 45.02 5.68
49 50 3.115892 TCGGACAAATGCGCCGTC 61.116 61.111 4.18 6.37 45.02 4.79
50 51 4.160635 CGGACAAATGCGCCGTCC 62.161 66.667 19.71 19.71 44.79 4.79
51 52 4.160635 GGACAAATGCGCCGTCCG 62.161 66.667 16.42 0.29 39.86 4.79
52 53 3.419759 GACAAATGCGCCGTCCGT 61.420 61.111 4.18 0.00 39.71 4.69
53 54 2.961669 GACAAATGCGCCGTCCGTT 61.962 57.895 4.18 0.00 39.71 4.44
54 55 2.254051 CAAATGCGCCGTCCGTTT 59.746 55.556 4.18 0.00 39.71 3.60
55 56 2.080062 CAAATGCGCCGTCCGTTTG 61.080 57.895 4.18 3.18 39.71 2.93
56 57 3.262142 AAATGCGCCGTCCGTTTGG 62.262 57.895 4.18 0.00 39.71 3.28
57 58 4.690719 ATGCGCCGTCCGTTTGGA 62.691 61.111 4.18 0.00 43.88 3.53
65 66 2.360600 TCCGTTTGGATTGGCCCG 60.361 61.111 0.00 0.00 40.17 6.13
66 67 2.675075 CCGTTTGGATTGGCCCGT 60.675 61.111 0.00 0.00 37.49 5.28
67 68 2.272447 CCGTTTGGATTGGCCCGTT 61.272 57.895 0.00 0.00 37.49 4.44
68 69 1.080839 CGTTTGGATTGGCCCGTTG 60.081 57.895 0.00 0.00 34.97 4.10
69 70 1.291906 GTTTGGATTGGCCCGTTGG 59.708 57.895 0.00 0.00 34.97 3.77
74 75 1.595093 GGATTGGCCCGTTGGAGTTG 61.595 60.000 0.00 0.00 0.00 3.16
101 103 1.611519 TTGAACAAACTAAGGGCCCG 58.388 50.000 18.44 4.53 0.00 6.13
136 138 3.631227 AGCTGCATTGATTAGAAAGGAGC 59.369 43.478 1.02 0.00 0.00 4.70
354 359 0.917533 ACTCCAGGATGAAGCTGCAT 59.082 50.000 6.99 6.99 39.69 3.96
418 423 2.755650 CCATTCGGTTAGAGGATTCGG 58.244 52.381 0.00 0.00 0.00 4.30
534 539 0.820871 CCTCTCTTCCTCCTTCACCG 59.179 60.000 0.00 0.00 0.00 4.94
612 618 2.561733 CGAGCTTATTCGTGGAGTCA 57.438 50.000 0.00 0.00 35.91 3.41
629 635 3.953775 ACCGGCAACCCACTCCTG 61.954 66.667 0.00 0.00 0.00 3.86
894 902 2.035442 GGGGCGCTCTCTGTTGTTC 61.035 63.158 7.48 0.00 0.00 3.18
895 903 1.301716 GGGCGCTCTCTGTTGTTCA 60.302 57.895 7.64 0.00 0.00 3.18
896 904 1.294659 GGGCGCTCTCTGTTGTTCAG 61.295 60.000 7.64 0.00 44.85 3.02
897 905 0.601311 GGCGCTCTCTGTTGTTCAGT 60.601 55.000 7.64 0.00 43.97 3.41
898 906 1.221414 GCGCTCTCTGTTGTTCAGTT 58.779 50.000 0.00 0.00 43.97 3.16
899 907 1.193426 GCGCTCTCTGTTGTTCAGTTC 59.807 52.381 0.00 0.00 43.97 3.01
900 908 2.473816 CGCTCTCTGTTGTTCAGTTCA 58.526 47.619 0.00 0.00 43.97 3.18
901 909 2.474359 CGCTCTCTGTTGTTCAGTTCAG 59.526 50.000 0.00 0.00 43.97 3.02
902 910 3.722147 GCTCTCTGTTGTTCAGTTCAGA 58.278 45.455 0.00 0.00 43.97 3.27
903 911 4.314121 GCTCTCTGTTGTTCAGTTCAGAT 58.686 43.478 0.00 0.00 43.97 2.90
904 912 4.152045 GCTCTCTGTTGTTCAGTTCAGATG 59.848 45.833 0.00 0.00 43.97 2.90
905 913 5.282055 TCTCTGTTGTTCAGTTCAGATGT 57.718 39.130 0.00 0.00 43.97 3.06
906 914 5.052481 TCTCTGTTGTTCAGTTCAGATGTG 58.948 41.667 0.00 0.00 43.97 3.21
907 915 3.561310 TCTGTTGTTCAGTTCAGATGTGC 59.439 43.478 0.00 0.00 43.97 4.57
908 916 3.544684 TGTTGTTCAGTTCAGATGTGCT 58.455 40.909 0.00 0.00 0.00 4.40
909 917 3.313249 TGTTGTTCAGTTCAGATGTGCTG 59.687 43.478 0.00 0.00 46.31 4.41
910 918 3.198409 TGTTCAGTTCAGATGTGCTGT 57.802 42.857 0.00 0.00 45.14 4.40
911 919 3.133691 TGTTCAGTTCAGATGTGCTGTC 58.866 45.455 0.00 0.00 45.14 3.51
912 920 2.462456 TCAGTTCAGATGTGCTGTCC 57.538 50.000 0.00 0.00 45.14 4.02
913 921 1.073964 CAGTTCAGATGTGCTGTCCG 58.926 55.000 0.00 0.00 45.14 4.79
914 922 0.681733 AGTTCAGATGTGCTGTCCGT 59.318 50.000 0.00 0.00 45.14 4.69
915 923 1.070758 AGTTCAGATGTGCTGTCCGTT 59.929 47.619 0.00 0.00 45.14 4.44
916 924 1.195448 GTTCAGATGTGCTGTCCGTTG 59.805 52.381 0.00 0.00 45.14 4.10
917 925 0.320683 TCAGATGTGCTGTCCGTTGG 60.321 55.000 0.00 0.00 45.14 3.77
918 926 0.320683 CAGATGTGCTGTCCGTTGGA 60.321 55.000 0.00 0.00 39.85 3.53
919 927 0.036952 AGATGTGCTGTCCGTTGGAG 60.037 55.000 0.00 0.00 29.39 3.86
920 928 0.320771 GATGTGCTGTCCGTTGGAGT 60.321 55.000 0.00 0.00 29.39 3.85
921 929 0.108585 ATGTGCTGTCCGTTGGAGTT 59.891 50.000 0.00 0.00 29.39 3.01
922 930 0.813610 TGTGCTGTCCGTTGGAGTTG 60.814 55.000 0.00 0.00 29.39 3.16
923 931 1.891919 TGCTGTCCGTTGGAGTTGC 60.892 57.895 0.00 0.00 29.39 4.17
924 932 1.598130 GCTGTCCGTTGGAGTTGCT 60.598 57.895 0.00 0.00 29.39 3.91
925 933 1.569479 GCTGTCCGTTGGAGTTGCTC 61.569 60.000 0.00 0.00 29.39 4.26
926 934 0.034059 CTGTCCGTTGGAGTTGCTCT 59.966 55.000 0.00 0.00 29.39 4.09
927 935 1.272490 CTGTCCGTTGGAGTTGCTCTA 59.728 52.381 0.00 0.00 29.39 2.43
928 936 1.689813 TGTCCGTTGGAGTTGCTCTAA 59.310 47.619 0.00 0.00 29.39 2.10
929 937 2.067013 GTCCGTTGGAGTTGCTCTAAC 58.933 52.381 13.14 13.14 44.66 2.34
934 942 3.890128 GTTGGAGTTGCTCTAACAAAGC 58.110 45.455 16.75 0.00 46.43 3.51
935 943 3.315191 GTTGGAGTTGCTCTAACAAAGCA 59.685 43.478 16.75 0.00 46.43 3.91
957 965 4.972514 AAAAAGATAGTTGCAGCCTAGC 57.027 40.909 0.00 0.00 0.00 3.42
958 966 3.922171 AAAGATAGTTGCAGCCTAGCT 57.078 42.857 7.27 7.27 40.77 3.32
959 967 5.359194 AAAAGATAGTTGCAGCCTAGCTA 57.641 39.130 12.04 0.00 36.40 3.32
960 968 4.599047 AAGATAGTTGCAGCCTAGCTAG 57.401 45.455 14.20 14.20 36.40 3.42
961 969 2.896685 AGATAGTTGCAGCCTAGCTAGG 59.103 50.000 32.12 32.12 46.42 3.02
962 970 2.454336 TAGTTGCAGCCTAGCTAGGA 57.546 50.000 38.74 18.50 46.63 2.94
963 971 1.573108 AGTTGCAGCCTAGCTAGGAA 58.427 50.000 38.74 22.95 46.63 3.36
964 972 2.122768 AGTTGCAGCCTAGCTAGGAAT 58.877 47.619 38.74 24.77 46.63 3.01
965 973 3.309296 AGTTGCAGCCTAGCTAGGAATA 58.691 45.455 38.74 20.19 46.63 1.75
966 974 3.906846 AGTTGCAGCCTAGCTAGGAATAT 59.093 43.478 38.74 20.02 46.63 1.28
967 975 5.087323 AGTTGCAGCCTAGCTAGGAATATA 58.913 41.667 38.74 19.40 46.63 0.86
968 976 5.723887 AGTTGCAGCCTAGCTAGGAATATAT 59.276 40.000 38.74 17.63 46.63 0.86
969 977 6.897966 AGTTGCAGCCTAGCTAGGAATATATA 59.102 38.462 38.74 16.80 46.63 0.86
970 978 7.566879 AGTTGCAGCCTAGCTAGGAATATATAT 59.433 37.037 38.74 17.03 46.63 0.86
971 979 7.295322 TGCAGCCTAGCTAGGAATATATATG 57.705 40.000 38.74 22.53 46.63 1.78
972 980 6.162777 GCAGCCTAGCTAGGAATATATATGC 58.837 44.000 38.74 26.67 46.63 3.14
973 981 6.014669 GCAGCCTAGCTAGGAATATATATGCT 60.015 42.308 38.74 22.36 46.63 3.79
974 982 7.472663 GCAGCCTAGCTAGGAATATATATGCTT 60.473 40.741 38.74 9.80 46.63 3.91
975 983 8.428063 CAGCCTAGCTAGGAATATATATGCTTT 58.572 37.037 38.74 5.74 46.63 3.51
976 984 8.428063 AGCCTAGCTAGGAATATATATGCTTTG 58.572 37.037 38.74 10.19 46.63 2.77
977 985 7.659390 GCCTAGCTAGGAATATATATGCTTTGG 59.341 40.741 38.74 10.88 46.63 3.28
978 986 8.709308 CCTAGCTAGGAATATATATGCTTTGGT 58.291 37.037 32.79 6.92 46.63 3.67
979 987 9.539825 CTAGCTAGGAATATATATGCTTTGGTG 57.460 37.037 13.32 0.00 0.00 4.17
980 988 8.150827 AGCTAGGAATATATATGCTTTGGTGA 57.849 34.615 0.57 0.00 0.00 4.02
981 989 8.605947 AGCTAGGAATATATATGCTTTGGTGAA 58.394 33.333 0.57 0.00 0.00 3.18
982 990 8.887717 GCTAGGAATATATATGCTTTGGTGAAG 58.112 37.037 0.57 0.00 38.45 3.02
983 991 9.950496 CTAGGAATATATATGCTTTGGTGAAGT 57.050 33.333 0.57 0.00 37.69 3.01
984 992 8.854614 AGGAATATATATGCTTTGGTGAAGTC 57.145 34.615 0.57 0.00 37.69 3.01
985 993 7.604164 AGGAATATATATGCTTTGGTGAAGTCG 59.396 37.037 0.57 0.00 37.69 4.18
986 994 7.148407 GGAATATATATGCTTTGGTGAAGTCGG 60.148 40.741 0.57 0.00 37.69 4.79
987 995 3.627395 ATATGCTTTGGTGAAGTCGGA 57.373 42.857 0.00 0.00 37.69 4.55
988 996 1.523758 ATGCTTTGGTGAAGTCGGAC 58.476 50.000 0.00 0.00 37.69 4.79
989 997 0.534203 TGCTTTGGTGAAGTCGGACC 60.534 55.000 4.14 0.00 37.69 4.46
990 998 1.235281 GCTTTGGTGAAGTCGGACCC 61.235 60.000 4.14 0.00 37.69 4.46
991 999 0.949105 CTTTGGTGAAGTCGGACCCG 60.949 60.000 4.14 1.31 41.35 5.28
992 1000 1.688269 TTTGGTGAAGTCGGACCCGT 61.688 55.000 8.42 0.00 40.74 5.28
993 1001 0.827089 TTGGTGAAGTCGGACCCGTA 60.827 55.000 8.42 0.00 40.74 4.02
994 1002 0.827089 TGGTGAAGTCGGACCCGTAA 60.827 55.000 8.42 0.00 40.74 3.18
995 1003 0.318120 GGTGAAGTCGGACCCGTAAA 59.682 55.000 8.42 0.00 40.74 2.01
996 1004 1.066645 GGTGAAGTCGGACCCGTAAAT 60.067 52.381 8.42 0.00 40.74 1.40
997 1005 2.166254 GGTGAAGTCGGACCCGTAAATA 59.834 50.000 8.42 0.00 40.74 1.40
998 1006 3.368323 GGTGAAGTCGGACCCGTAAATAA 60.368 47.826 8.42 0.00 40.74 1.40
999 1007 3.861689 GTGAAGTCGGACCCGTAAATAAG 59.138 47.826 8.42 0.00 40.74 1.73
1000 1008 2.591571 AGTCGGACCCGTAAATAAGC 57.408 50.000 8.42 0.00 40.74 3.09
1001 1009 2.105766 AGTCGGACCCGTAAATAAGCT 58.894 47.619 8.42 0.00 40.74 3.74
1002 1010 3.290710 AGTCGGACCCGTAAATAAGCTA 58.709 45.455 8.42 0.00 40.74 3.32
1003 1011 3.893813 AGTCGGACCCGTAAATAAGCTAT 59.106 43.478 8.42 0.00 40.74 2.97
1004 1012 5.072741 AGTCGGACCCGTAAATAAGCTATA 58.927 41.667 8.42 0.00 40.74 1.31
1005 1013 5.713861 AGTCGGACCCGTAAATAAGCTATAT 59.286 40.000 8.42 0.00 40.74 0.86
1006 1014 6.886459 AGTCGGACCCGTAAATAAGCTATATA 59.114 38.462 8.42 0.00 40.74 0.86
1007 1015 7.559170 AGTCGGACCCGTAAATAAGCTATATAT 59.441 37.037 8.42 0.00 40.74 0.86
1008 1016 8.840321 GTCGGACCCGTAAATAAGCTATATATA 58.160 37.037 8.42 0.00 40.74 0.86
1009 1017 9.578576 TCGGACCCGTAAATAAGCTATATATAT 57.421 33.333 8.42 0.00 40.74 0.86
1031 1039 4.844349 ATATGCTTTGGTGTCCTGTAGT 57.156 40.909 0.00 0.00 0.00 2.73
1032 1040 5.950544 ATATGCTTTGGTGTCCTGTAGTA 57.049 39.130 0.00 0.00 0.00 1.82
1033 1041 4.844349 ATGCTTTGGTGTCCTGTAGTAT 57.156 40.909 0.00 0.00 0.00 2.12
1034 1042 5.950544 ATGCTTTGGTGTCCTGTAGTATA 57.049 39.130 0.00 0.00 0.00 1.47
1035 1043 5.950544 TGCTTTGGTGTCCTGTAGTATAT 57.049 39.130 0.00 0.00 0.00 0.86
1036 1044 5.670485 TGCTTTGGTGTCCTGTAGTATATG 58.330 41.667 0.00 0.00 0.00 1.78
1037 1045 4.511826 GCTTTGGTGTCCTGTAGTATATGC 59.488 45.833 0.00 0.00 0.00 3.14
1038 1046 4.682778 TTGGTGTCCTGTAGTATATGCC 57.317 45.455 0.00 0.00 0.00 4.40
1039 1047 3.648739 TGGTGTCCTGTAGTATATGCCA 58.351 45.455 0.00 0.00 0.00 4.92
1040 1048 4.231273 TGGTGTCCTGTAGTATATGCCAT 58.769 43.478 0.00 0.00 0.00 4.40
1041 1049 4.283467 TGGTGTCCTGTAGTATATGCCATC 59.717 45.833 0.00 0.00 0.00 3.51
1042 1050 4.486090 GTGTCCTGTAGTATATGCCATCG 58.514 47.826 0.00 0.00 0.00 3.84
1043 1051 4.022242 GTGTCCTGTAGTATATGCCATCGT 60.022 45.833 0.00 0.00 0.00 3.73
1044 1052 4.217767 TGTCCTGTAGTATATGCCATCGTC 59.782 45.833 0.00 0.00 0.00 4.20
1045 1053 4.459685 GTCCTGTAGTATATGCCATCGTCT 59.540 45.833 0.00 0.00 0.00 4.18
1046 1054 4.700692 TCCTGTAGTATATGCCATCGTCTC 59.299 45.833 0.00 0.00 0.00 3.36
1047 1055 4.142359 CCTGTAGTATATGCCATCGTCTCC 60.142 50.000 0.00 0.00 0.00 3.71
1048 1056 4.663334 TGTAGTATATGCCATCGTCTCCT 58.337 43.478 0.00 0.00 0.00 3.69
1049 1057 4.459337 TGTAGTATATGCCATCGTCTCCTG 59.541 45.833 0.00 0.00 0.00 3.86
1050 1058 2.828520 AGTATATGCCATCGTCTCCTGG 59.171 50.000 0.00 0.00 35.53 4.45
1051 1059 1.722034 ATATGCCATCGTCTCCTGGT 58.278 50.000 0.00 0.00 34.86 4.00
1052 1060 1.040646 TATGCCATCGTCTCCTGGTC 58.959 55.000 0.00 0.00 34.86 4.02
1053 1061 0.689080 ATGCCATCGTCTCCTGGTCT 60.689 55.000 0.00 0.00 34.86 3.85
1054 1062 1.323271 TGCCATCGTCTCCTGGTCTC 61.323 60.000 0.00 0.00 34.86 3.36
1055 1063 1.040339 GCCATCGTCTCCTGGTCTCT 61.040 60.000 0.00 0.00 34.86 3.10
1056 1064 0.743688 CCATCGTCTCCTGGTCTCTG 59.256 60.000 0.00 0.00 0.00 3.35
1057 1065 0.102120 CATCGTCTCCTGGTCTCTGC 59.898 60.000 0.00 0.00 0.00 4.26
1058 1066 0.323816 ATCGTCTCCTGGTCTCTGCA 60.324 55.000 0.00 0.00 0.00 4.41
1059 1067 0.323816 TCGTCTCCTGGTCTCTGCAT 60.324 55.000 0.00 0.00 0.00 3.96
1060 1068 1.064685 TCGTCTCCTGGTCTCTGCATA 60.065 52.381 0.00 0.00 0.00 3.14
1061 1069 1.959985 CGTCTCCTGGTCTCTGCATAT 59.040 52.381 0.00 0.00 0.00 1.78
1062 1070 3.149981 CGTCTCCTGGTCTCTGCATATA 58.850 50.000 0.00 0.00 0.00 0.86
1063 1071 3.057876 CGTCTCCTGGTCTCTGCATATAC 60.058 52.174 0.00 0.00 0.00 1.47
1064 1072 3.257127 GTCTCCTGGTCTCTGCATATACC 59.743 52.174 0.17 0.17 0.00 2.73
1065 1073 2.564947 CTCCTGGTCTCTGCATATACCC 59.435 54.545 4.48 0.00 0.00 3.69
1066 1074 1.273606 CCTGGTCTCTGCATATACCCG 59.726 57.143 4.48 0.00 0.00 5.28
1170 1178 2.045536 GGGACAGCTTCTGCCTGG 60.046 66.667 0.00 0.00 40.80 4.45
1171 1179 2.596851 GGGACAGCTTCTGCCTGGA 61.597 63.158 0.00 0.00 40.80 3.86
1233 1241 4.178169 ACCGTGGGCCGTTTCACA 62.178 61.111 10.04 0.00 33.83 3.58
1256 1270 3.122971 ATCTCCGTCGACGTCGCA 61.123 61.111 33.49 18.37 39.60 5.10
1613 1669 4.107051 GCGCAGTGTCATGCCCAC 62.107 66.667 0.30 7.12 43.49 4.61
1761 1817 8.635765 ACAAATCCATCACTAAAATGTACTGT 57.364 30.769 0.00 0.00 0.00 3.55
1762 1818 9.077885 ACAAATCCATCACTAAAATGTACTGTT 57.922 29.630 0.00 0.00 0.00 3.16
1763 1819 9.345517 CAAATCCATCACTAAAATGTACTGTTG 57.654 33.333 0.00 0.00 0.00 3.33
1764 1820 7.630242 ATCCATCACTAAAATGTACTGTTGG 57.370 36.000 0.00 0.00 0.00 3.77
1768 1824 5.133941 TCACTAAAATGTACTGTTGGCCAA 58.866 37.500 16.05 16.05 0.00 4.52
1769 1825 5.772672 TCACTAAAATGTACTGTTGGCCAAT 59.227 36.000 23.66 8.57 0.00 3.16
1771 1827 7.613801 TCACTAAAATGTACTGTTGGCCAATAT 59.386 33.333 23.66 12.69 0.00 1.28
1772 1828 8.898761 CACTAAAATGTACTGTTGGCCAATATA 58.101 33.333 23.66 11.62 0.00 0.86
1773 1829 8.899771 ACTAAAATGTACTGTTGGCCAATATAC 58.100 33.333 23.66 22.11 0.00 1.47
1774 1830 7.954666 AAAATGTACTGTTGGCCAATATACT 57.045 32.000 23.66 6.93 0.00 2.12
1776 1832 8.677148 AAATGTACTGTTGGCCAATATACTAG 57.323 34.615 23.66 14.77 0.00 2.57
1778 1834 7.901283 TGTACTGTTGGCCAATATACTAGTA 57.099 36.000 23.66 18.22 0.00 1.82
1779 1835 7.948357 TGTACTGTTGGCCAATATACTAGTAG 58.052 38.462 23.66 6.87 0.00 2.57
1783 1839 7.783596 ACTGTTGGCCAATATACTAGTAGTAGT 59.216 37.037 23.66 14.57 42.49 2.73
1892 1948 3.746492 GCTTCGTCTTTGTACTCCAACAT 59.254 43.478 0.00 0.00 31.20 2.71
1900 1956 1.479323 TGTACTCCAACATACTCCGGC 59.521 52.381 0.00 0.00 0.00 6.13
2217 2482 2.046314 GCCTAACGCCAAGCTCCA 60.046 61.111 0.00 0.00 0.00 3.86
2399 2664 6.072286 CCACATTGTATATCTTCCTGGCATTC 60.072 42.308 0.00 0.00 0.00 2.67
2412 2677 3.925913 CCTGGCATTCAAATGGTTAAACG 59.074 43.478 4.98 0.00 36.90 3.60
2414 2679 4.950050 TGGCATTCAAATGGTTAAACGTT 58.050 34.783 0.00 0.00 36.90 3.99
2429 2695 8.798402 TGGTTAAACGTTGGAAATCAATTATCT 58.202 29.630 0.00 0.00 37.73 1.98
2434 2700 7.687941 ACGTTGGAAATCAATTATCTGTCTT 57.312 32.000 0.00 0.00 37.73 3.01
2437 2703 7.413000 CGTTGGAAATCAATTATCTGTCTTCGT 60.413 37.037 0.00 0.00 37.73 3.85
2441 2707 8.012241 GGAAATCAATTATCTGTCTTCGTATGC 58.988 37.037 0.00 0.00 0.00 3.14
2456 2722 3.670203 CGTATGCACGGTCATTTTTCTC 58.330 45.455 0.00 0.00 44.59 2.87
2494 2775 7.347508 ACATAAGCTTACAAAACGTGACTAG 57.652 36.000 8.70 0.00 0.00 2.57
2496 2777 7.654520 ACATAAGCTTACAAAACGTGACTAGAA 59.345 33.333 8.70 0.00 0.00 2.10
2509 2790 6.561614 ACGTGACTAGAACATGTATGGTAAG 58.438 40.000 0.00 0.00 36.01 2.34
2512 2793 6.979238 GTGACTAGAACATGTATGGTAAGACC 59.021 42.308 0.00 0.00 39.22 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 4.629523 TGTCCGTTTGGGTCGGCC 62.630 66.667 0.00 0.00 46.49 6.13
11 12 1.726533 TTTTGTCCGTTTGGGTCGGC 61.727 55.000 0.00 0.00 46.49 5.54
14 15 1.003223 CGACTTTTGTCCGTTTGGGTC 60.003 52.381 0.00 0.00 46.25 4.46
15 16 1.018910 CGACTTTTGTCCGTTTGGGT 58.981 50.000 0.00 0.00 46.25 4.51
16 17 0.309612 CCGACTTTTGTCCGTTTGGG 59.690 55.000 0.00 0.00 46.25 4.12
17 18 1.003223 GTCCGACTTTTGTCCGTTTGG 60.003 52.381 0.00 0.00 46.25 3.28
18 19 1.666700 TGTCCGACTTTTGTCCGTTTG 59.333 47.619 0.00 0.00 46.25 2.93
19 20 2.027003 TGTCCGACTTTTGTCCGTTT 57.973 45.000 0.00 0.00 46.25 3.60
20 21 2.027003 TTGTCCGACTTTTGTCCGTT 57.973 45.000 0.00 0.00 46.25 4.44
21 22 2.027003 TTTGTCCGACTTTTGTCCGT 57.973 45.000 0.00 0.00 46.25 4.69
22 23 2.916111 CATTTGTCCGACTTTTGTCCG 58.084 47.619 0.00 0.00 46.25 4.79
23 24 2.661594 GCATTTGTCCGACTTTTGTCC 58.338 47.619 0.00 0.00 46.25 4.02
24 25 2.307049 CGCATTTGTCCGACTTTTGTC 58.693 47.619 0.00 0.00 45.55 3.18
25 26 1.599419 GCGCATTTGTCCGACTTTTGT 60.599 47.619 0.30 0.00 0.00 2.83
26 27 1.052287 GCGCATTTGTCCGACTTTTG 58.948 50.000 0.30 0.00 0.00 2.44
27 28 0.039527 GGCGCATTTGTCCGACTTTT 60.040 50.000 10.83 0.00 0.00 2.27
28 29 1.579429 GGCGCATTTGTCCGACTTT 59.421 52.632 10.83 0.00 0.00 2.66
29 30 2.677003 CGGCGCATTTGTCCGACTT 61.677 57.895 10.83 0.00 45.53 3.01
30 31 3.118454 CGGCGCATTTGTCCGACT 61.118 61.111 10.83 0.00 45.53 4.18
31 32 3.362851 GACGGCGCATTTGTCCGAC 62.363 63.158 10.83 0.00 45.53 4.79
32 33 3.115892 GACGGCGCATTTGTCCGA 61.116 61.111 10.83 0.00 45.53 4.55
34 35 4.160635 CGGACGGCGCATTTGTCC 62.161 66.667 22.73 22.73 46.91 4.02
35 36 2.452366 AAACGGACGGCGCATTTGTC 62.452 55.000 10.83 11.19 0.00 3.18
36 37 2.548295 AAACGGACGGCGCATTTGT 61.548 52.632 10.83 0.74 0.00 2.83
37 38 2.080062 CAAACGGACGGCGCATTTG 61.080 57.895 10.83 9.01 0.00 2.32
38 39 2.254051 CAAACGGACGGCGCATTT 59.746 55.556 10.83 0.00 0.00 2.32
39 40 3.732892 CCAAACGGACGGCGCATT 61.733 61.111 10.83 0.00 0.00 3.56
40 41 3.969250 ATCCAAACGGACGGCGCAT 62.969 57.895 10.83 0.00 34.62 4.73
41 42 4.690719 ATCCAAACGGACGGCGCA 62.691 61.111 10.83 0.00 34.62 6.09
42 43 3.428282 AATCCAAACGGACGGCGC 61.428 61.111 6.90 0.00 34.62 6.53
43 44 2.478746 CAATCCAAACGGACGGCG 59.521 61.111 4.80 4.80 34.62 6.46
44 45 2.874751 CCAATCCAAACGGACGGC 59.125 61.111 0.00 0.00 34.62 5.68
45 46 2.696759 GGCCAATCCAAACGGACGG 61.697 63.158 0.00 0.00 34.62 4.79
46 47 2.696759 GGGCCAATCCAAACGGACG 61.697 63.158 4.39 0.00 34.62 4.79
47 48 2.696759 CGGGCCAATCCAAACGGAC 61.697 63.158 4.39 0.00 34.62 4.79
48 49 2.360600 CGGGCCAATCCAAACGGA 60.361 61.111 4.39 0.00 36.85 4.69
49 50 2.272447 AACGGGCCAATCCAAACGG 61.272 57.895 4.39 0.00 36.21 4.44
50 51 1.080839 CAACGGGCCAATCCAAACG 60.081 57.895 4.39 0.00 36.21 3.60
51 52 1.182385 TCCAACGGGCCAATCCAAAC 61.182 55.000 4.39 0.00 36.21 2.93
52 53 0.897863 CTCCAACGGGCCAATCCAAA 60.898 55.000 4.39 0.00 36.21 3.28
53 54 1.304052 CTCCAACGGGCCAATCCAA 60.304 57.895 4.39 0.00 36.21 3.53
54 55 2.075355 AACTCCAACGGGCCAATCCA 62.075 55.000 4.39 0.00 36.21 3.41
55 56 1.304134 AACTCCAACGGGCCAATCC 60.304 57.895 4.39 0.00 0.00 3.01
56 57 1.883021 CAACTCCAACGGGCCAATC 59.117 57.895 4.39 0.00 0.00 2.67
57 58 2.275380 GCAACTCCAACGGGCCAAT 61.275 57.895 4.39 0.00 0.00 3.16
58 59 2.909965 GCAACTCCAACGGGCCAA 60.910 61.111 4.39 0.00 0.00 4.52
59 60 2.920076 AAAGCAACTCCAACGGGCCA 62.920 55.000 4.39 0.00 0.00 5.36
60 61 1.744320 AAAAGCAACTCCAACGGGCC 61.744 55.000 0.00 0.00 0.00 5.80
61 62 0.104120 AAAAAGCAACTCCAACGGGC 59.896 50.000 0.00 0.00 0.00 6.13
101 103 2.269241 CAGCTTCGGGGTCCTTCC 59.731 66.667 0.00 0.00 0.00 3.46
136 138 3.615056 TGATGTAAAATCGCCGTGTACTG 59.385 43.478 0.00 0.00 0.00 2.74
332 337 1.649664 CAGCTTCATCCTGGAGTTCG 58.350 55.000 1.52 0.00 0.00 3.95
469 474 0.753479 AGCTCATCACCGACGGAGAT 60.753 55.000 23.38 21.21 33.47 2.75
534 539 0.817654 GCTTCCAAGGTTACCATGGC 59.182 55.000 19.78 5.76 41.64 4.40
612 618 3.953775 CAGGAGTGGGTTGCCGGT 61.954 66.667 1.90 0.00 0.00 5.28
629 635 1.360192 GGTGTGCCAGTTGCTTGTC 59.640 57.895 0.00 0.00 42.00 3.18
894 902 1.073964 CGGACAGCACATCTGAACTG 58.926 55.000 0.00 0.00 45.72 3.16
895 903 0.681733 ACGGACAGCACATCTGAACT 59.318 50.000 0.00 0.00 45.72 3.01
896 904 1.195448 CAACGGACAGCACATCTGAAC 59.805 52.381 0.00 0.00 45.72 3.18
897 905 1.511850 CAACGGACAGCACATCTGAA 58.488 50.000 0.00 0.00 45.72 3.02
898 906 0.320683 CCAACGGACAGCACATCTGA 60.321 55.000 0.00 0.00 45.72 3.27
900 908 0.036952 CTCCAACGGACAGCACATCT 60.037 55.000 0.00 0.00 0.00 2.90
901 909 0.320771 ACTCCAACGGACAGCACATC 60.321 55.000 0.00 0.00 0.00 3.06
902 910 0.108585 AACTCCAACGGACAGCACAT 59.891 50.000 0.00 0.00 0.00 3.21
903 911 0.813610 CAACTCCAACGGACAGCACA 60.814 55.000 0.00 0.00 0.00 4.57
904 912 1.941812 CAACTCCAACGGACAGCAC 59.058 57.895 0.00 0.00 0.00 4.40
905 913 1.891919 GCAACTCCAACGGACAGCA 60.892 57.895 0.00 0.00 0.00 4.41
906 914 1.569479 GAGCAACTCCAACGGACAGC 61.569 60.000 0.00 0.00 0.00 4.40
907 915 0.034059 AGAGCAACTCCAACGGACAG 59.966 55.000 0.00 0.00 0.00 3.51
908 916 1.334160 TAGAGCAACTCCAACGGACA 58.666 50.000 0.00 0.00 0.00 4.02
909 917 2.067013 GTTAGAGCAACTCCAACGGAC 58.933 52.381 0.00 0.00 34.06 4.79
910 918 1.689813 TGTTAGAGCAACTCCAACGGA 59.310 47.619 2.34 0.00 35.48 4.69
911 919 2.163818 TGTTAGAGCAACTCCAACGG 57.836 50.000 2.34 0.00 35.48 4.44
912 920 3.607078 GCTTTGTTAGAGCAACTCCAACG 60.607 47.826 2.34 0.00 35.48 4.10
913 921 3.315191 TGCTTTGTTAGAGCAACTCCAAC 59.685 43.478 0.00 0.00 46.35 3.77
914 922 3.550820 TGCTTTGTTAGAGCAACTCCAA 58.449 40.909 0.00 0.00 46.35 3.53
915 923 3.207265 TGCTTTGTTAGAGCAACTCCA 57.793 42.857 0.00 0.00 46.35 3.86
936 944 4.593956 AGCTAGGCTGCAACTATCTTTTT 58.406 39.130 0.50 0.00 37.57 1.94
937 945 4.227864 AGCTAGGCTGCAACTATCTTTT 57.772 40.909 0.50 0.00 37.57 2.27
938 946 3.922171 AGCTAGGCTGCAACTATCTTT 57.078 42.857 0.50 0.00 37.57 2.52
939 947 3.323403 CCTAGCTAGGCTGCAACTATCTT 59.677 47.826 26.62 0.00 40.10 2.40
940 948 2.896685 CCTAGCTAGGCTGCAACTATCT 59.103 50.000 26.62 6.67 40.10 1.98
941 949 2.894126 TCCTAGCTAGGCTGCAACTATC 59.106 50.000 31.76 0.00 43.31 2.08
942 950 2.964209 TCCTAGCTAGGCTGCAACTAT 58.036 47.619 31.76 0.00 43.31 2.12
943 951 2.454336 TCCTAGCTAGGCTGCAACTA 57.546 50.000 31.76 11.84 43.31 2.24
944 952 1.573108 TTCCTAGCTAGGCTGCAACT 58.427 50.000 31.76 0.00 43.31 3.16
945 953 2.629336 ATTCCTAGCTAGGCTGCAAC 57.371 50.000 31.76 0.00 43.31 4.17
946 954 7.687837 GCATATATATTCCTAGCTAGGCTGCAA 60.688 40.741 31.76 21.71 43.31 4.08
947 955 6.239430 GCATATATATTCCTAGCTAGGCTGCA 60.239 42.308 31.76 17.79 43.31 4.41
948 956 6.014669 AGCATATATATTCCTAGCTAGGCTGC 60.015 42.308 31.76 24.63 43.31 5.25
949 957 7.537596 AGCATATATATTCCTAGCTAGGCTG 57.462 40.000 31.76 18.24 43.31 4.85
950 958 8.428063 CAAAGCATATATATTCCTAGCTAGGCT 58.572 37.037 31.76 23.15 43.31 4.58
951 959 7.659390 CCAAAGCATATATATTCCTAGCTAGGC 59.341 40.741 31.76 17.06 43.31 3.93
952 960 8.709308 ACCAAAGCATATATATTCCTAGCTAGG 58.291 37.037 30.94 30.94 45.02 3.02
953 961 9.539825 CACCAAAGCATATATATTCCTAGCTAG 57.460 37.037 14.20 14.20 0.00 3.42
954 962 9.267071 TCACCAAAGCATATATATTCCTAGCTA 57.733 33.333 5.26 0.00 0.00 3.32
955 963 8.150827 TCACCAAAGCATATATATTCCTAGCT 57.849 34.615 0.00 0.00 0.00 3.32
956 964 8.792830 TTCACCAAAGCATATATATTCCTAGC 57.207 34.615 0.00 0.00 0.00 3.42
957 965 9.950496 ACTTCACCAAAGCATATATATTCCTAG 57.050 33.333 0.00 0.00 38.67 3.02
958 966 9.944376 GACTTCACCAAAGCATATATATTCCTA 57.056 33.333 0.00 0.00 38.67 2.94
959 967 7.604164 CGACTTCACCAAAGCATATATATTCCT 59.396 37.037 0.00 0.00 38.67 3.36
960 968 7.148407 CCGACTTCACCAAAGCATATATATTCC 60.148 40.741 0.00 0.00 38.67 3.01
961 969 7.602644 TCCGACTTCACCAAAGCATATATATTC 59.397 37.037 0.00 0.00 38.67 1.75
962 970 7.387948 GTCCGACTTCACCAAAGCATATATATT 59.612 37.037 0.00 0.00 38.67 1.28
963 971 6.874134 GTCCGACTTCACCAAAGCATATATAT 59.126 38.462 0.00 0.00 38.67 0.86
964 972 6.220930 GTCCGACTTCACCAAAGCATATATA 58.779 40.000 0.00 0.00 38.67 0.86
965 973 5.057149 GTCCGACTTCACCAAAGCATATAT 58.943 41.667 0.00 0.00 38.67 0.86
966 974 4.439057 GTCCGACTTCACCAAAGCATATA 58.561 43.478 0.00 0.00 38.67 0.86
967 975 3.270877 GTCCGACTTCACCAAAGCATAT 58.729 45.455 0.00 0.00 38.67 1.78
968 976 2.614481 GGTCCGACTTCACCAAAGCATA 60.614 50.000 0.00 0.00 38.67 3.14
969 977 1.523758 GTCCGACTTCACCAAAGCAT 58.476 50.000 0.00 0.00 38.67 3.79
970 978 0.534203 GGTCCGACTTCACCAAAGCA 60.534 55.000 0.00 0.00 38.67 3.91
971 979 1.235281 GGGTCCGACTTCACCAAAGC 61.235 60.000 0.00 0.00 38.67 3.51
972 980 0.949105 CGGGTCCGACTTCACCAAAG 60.949 60.000 2.83 0.00 42.83 2.77
973 981 1.070105 CGGGTCCGACTTCACCAAA 59.930 57.895 2.83 0.00 42.83 3.28
974 982 0.827089 TACGGGTCCGACTTCACCAA 60.827 55.000 16.90 0.00 42.83 3.67
975 983 0.827089 TTACGGGTCCGACTTCACCA 60.827 55.000 16.90 0.00 42.83 4.17
976 984 0.318120 TTTACGGGTCCGACTTCACC 59.682 55.000 16.90 0.00 42.83 4.02
977 985 2.375173 ATTTACGGGTCCGACTTCAC 57.625 50.000 16.90 0.00 42.83 3.18
978 986 3.676873 GCTTATTTACGGGTCCGACTTCA 60.677 47.826 16.90 0.00 42.83 3.02
979 987 2.862536 GCTTATTTACGGGTCCGACTTC 59.137 50.000 16.90 0.00 42.83 3.01
980 988 2.498885 AGCTTATTTACGGGTCCGACTT 59.501 45.455 16.90 0.00 42.83 3.01
981 989 2.105766 AGCTTATTTACGGGTCCGACT 58.894 47.619 16.90 0.00 42.83 4.18
982 990 2.591571 AGCTTATTTACGGGTCCGAC 57.408 50.000 16.90 0.00 42.83 4.79
983 991 7.886629 ATATATAGCTTATTTACGGGTCCGA 57.113 36.000 16.90 0.00 42.83 4.55
1005 1013 9.321532 ACTACAGGACACCAAAGCATATATATA 57.678 33.333 0.00 0.00 0.00 0.86
1006 1014 8.207350 ACTACAGGACACCAAAGCATATATAT 57.793 34.615 0.00 0.00 0.00 0.86
1007 1015 7.612065 ACTACAGGACACCAAAGCATATATA 57.388 36.000 0.00 0.00 0.00 0.86
1008 1016 6.500589 ACTACAGGACACCAAAGCATATAT 57.499 37.500 0.00 0.00 0.00 0.86
1009 1017 5.950544 ACTACAGGACACCAAAGCATATA 57.049 39.130 0.00 0.00 0.00 0.86
1010 1018 4.844349 ACTACAGGACACCAAAGCATAT 57.156 40.909 0.00 0.00 0.00 1.78
1011 1019 5.950544 ATACTACAGGACACCAAAGCATA 57.049 39.130 0.00 0.00 0.00 3.14
1012 1020 4.844349 ATACTACAGGACACCAAAGCAT 57.156 40.909 0.00 0.00 0.00 3.79
1013 1021 5.670485 CATATACTACAGGACACCAAAGCA 58.330 41.667 0.00 0.00 0.00 3.91
1014 1022 4.511826 GCATATACTACAGGACACCAAAGC 59.488 45.833 0.00 0.00 0.00 3.51
1015 1023 5.057149 GGCATATACTACAGGACACCAAAG 58.943 45.833 0.00 0.00 0.00 2.77
1016 1024 4.471747 TGGCATATACTACAGGACACCAAA 59.528 41.667 0.00 0.00 0.00 3.28
1017 1025 4.034410 TGGCATATACTACAGGACACCAA 58.966 43.478 0.00 0.00 0.00 3.67
1018 1026 3.648739 TGGCATATACTACAGGACACCA 58.351 45.455 0.00 0.00 0.00 4.17
1019 1027 4.618460 CGATGGCATATACTACAGGACACC 60.618 50.000 0.00 0.00 0.00 4.16
1020 1028 4.022242 ACGATGGCATATACTACAGGACAC 60.022 45.833 0.00 0.00 0.00 3.67
1021 1029 4.149598 ACGATGGCATATACTACAGGACA 58.850 43.478 0.00 0.00 0.00 4.02
1022 1030 4.459685 AGACGATGGCATATACTACAGGAC 59.540 45.833 0.00 0.00 0.00 3.85
1023 1031 4.663334 AGACGATGGCATATACTACAGGA 58.337 43.478 0.00 0.00 0.00 3.86
1024 1032 4.142359 GGAGACGATGGCATATACTACAGG 60.142 50.000 0.00 0.00 0.00 4.00
1025 1033 4.702612 AGGAGACGATGGCATATACTACAG 59.297 45.833 0.00 0.00 0.00 2.74
1026 1034 4.459337 CAGGAGACGATGGCATATACTACA 59.541 45.833 0.00 0.00 0.00 2.74
1027 1035 4.142359 CCAGGAGACGATGGCATATACTAC 60.142 50.000 0.00 0.56 0.00 2.73
1028 1036 4.017126 CCAGGAGACGATGGCATATACTA 58.983 47.826 0.00 0.00 0.00 1.82
1029 1037 2.828520 CCAGGAGACGATGGCATATACT 59.171 50.000 0.00 0.00 0.00 2.12
1030 1038 2.563179 ACCAGGAGACGATGGCATATAC 59.437 50.000 0.00 0.00 40.45 1.47
1031 1039 2.826128 GACCAGGAGACGATGGCATATA 59.174 50.000 0.00 0.00 40.45 0.86
1032 1040 1.620819 GACCAGGAGACGATGGCATAT 59.379 52.381 0.00 0.00 40.45 1.78
1033 1041 1.040646 GACCAGGAGACGATGGCATA 58.959 55.000 0.00 0.00 40.45 3.14
1034 1042 0.689080 AGACCAGGAGACGATGGCAT 60.689 55.000 0.00 0.00 40.45 4.40
1035 1043 1.305297 AGACCAGGAGACGATGGCA 60.305 57.895 0.00 0.00 40.45 4.92
1036 1044 1.040339 AGAGACCAGGAGACGATGGC 61.040 60.000 0.00 0.00 40.45 4.40
1037 1045 0.743688 CAGAGACCAGGAGACGATGG 59.256 60.000 0.00 0.00 42.60 3.51
1038 1046 0.102120 GCAGAGACCAGGAGACGATG 59.898 60.000 0.00 0.00 0.00 3.84
1039 1047 0.323816 TGCAGAGACCAGGAGACGAT 60.324 55.000 0.00 0.00 0.00 3.73
1040 1048 0.323816 ATGCAGAGACCAGGAGACGA 60.324 55.000 0.00 0.00 0.00 4.20
1041 1049 1.393603 TATGCAGAGACCAGGAGACG 58.606 55.000 0.00 0.00 0.00 4.18
1042 1050 3.257127 GGTATATGCAGAGACCAGGAGAC 59.743 52.174 19.87 0.00 31.89 3.36
1043 1051 3.501349 GGTATATGCAGAGACCAGGAGA 58.499 50.000 19.87 0.00 31.89 3.71
1044 1052 2.564947 GGGTATATGCAGAGACCAGGAG 59.435 54.545 25.21 0.00 33.33 3.69
1045 1053 2.609747 GGGTATATGCAGAGACCAGGA 58.390 52.381 25.21 0.00 33.33 3.86
1046 1054 1.273606 CGGGTATATGCAGAGACCAGG 59.726 57.143 25.21 13.33 33.33 4.45
1047 1055 1.337260 GCGGGTATATGCAGAGACCAG 60.337 57.143 25.21 22.12 33.33 4.00
1048 1056 0.679505 GCGGGTATATGCAGAGACCA 59.320 55.000 25.21 0.00 33.33 4.02
1049 1057 0.037232 GGCGGGTATATGCAGAGACC 60.037 60.000 16.77 16.77 0.00 3.85
1050 1058 0.679505 TGGCGGGTATATGCAGAGAC 59.320 55.000 0.00 0.00 0.00 3.36
1051 1059 0.679505 GTGGCGGGTATATGCAGAGA 59.320 55.000 0.00 0.00 0.00 3.10
1052 1060 0.392706 TGTGGCGGGTATATGCAGAG 59.607 55.000 0.00 0.00 0.00 3.35
1053 1061 1.001974 GATGTGGCGGGTATATGCAGA 59.998 52.381 0.00 0.00 0.00 4.26
1054 1062 1.442769 GATGTGGCGGGTATATGCAG 58.557 55.000 0.00 0.00 0.00 4.41
1055 1063 0.320334 CGATGTGGCGGGTATATGCA 60.320 55.000 0.00 0.00 0.00 3.96
1056 1064 1.635663 GCGATGTGGCGGGTATATGC 61.636 60.000 0.00 0.00 0.00 3.14
1057 1065 2.456000 GCGATGTGGCGGGTATATG 58.544 57.895 0.00 0.00 0.00 1.78
1170 1178 1.004440 AGAAGGCGTGGAAGCAGTC 60.004 57.895 0.00 0.00 39.27 3.51
1171 1179 1.302033 CAGAAGGCGTGGAAGCAGT 60.302 57.895 0.00 0.00 39.27 4.40
1233 1241 3.823330 GTCGACGGAGATGGCGGT 61.823 66.667 0.00 0.00 0.00 5.68
1237 1245 2.022902 CGACGTCGACGGAGATGG 59.977 66.667 37.89 17.24 44.95 3.51
1613 1669 4.504596 TAATGCCAGCCCGCCCAG 62.505 66.667 0.00 0.00 0.00 4.45
1761 1817 8.800332 GCTAACTACTACTAGTATATTGGCCAA 58.200 37.037 23.00 23.00 32.23 4.52
1762 1818 8.168725 AGCTAACTACTACTAGTATATTGGCCA 58.831 37.037 0.00 0.00 35.58 5.36
1763 1819 8.460428 CAGCTAACTACTACTAGTATATTGGCC 58.540 40.741 16.90 0.00 35.58 5.36
1764 1820 9.012161 ACAGCTAACTACTACTAGTATATTGGC 57.988 37.037 2.33 14.68 35.40 4.52
1783 1839 8.745590 GGGAAAATGAAAATAACCTACAGCTAA 58.254 33.333 0.00 0.00 0.00 3.09
1813 1869 2.092699 GCCAGAGAGGGAGCAATTACTT 60.093 50.000 0.00 0.00 38.09 2.24
1814 1870 1.488393 GCCAGAGAGGGAGCAATTACT 59.512 52.381 0.00 0.00 38.09 2.24
1865 1921 4.039488 TGGAGTACAAAGACGAAGCCTAAA 59.961 41.667 0.00 0.00 0.00 1.85
1892 1948 3.562182 TGAATCAGTAGATGCCGGAGTA 58.438 45.455 5.05 0.00 33.90 2.59
1900 1956 8.366401 ACTAGATGTCCATTGAATCAGTAGATG 58.634 37.037 0.00 0.00 33.90 2.90
1996 2055 5.068460 CCCAAGGAATATTTTGCCGAATGTA 59.932 40.000 0.00 0.00 0.00 2.29
1997 2056 4.141959 CCCAAGGAATATTTTGCCGAATGT 60.142 41.667 0.00 0.00 0.00 2.71
1998 2057 4.099266 TCCCAAGGAATATTTTGCCGAATG 59.901 41.667 0.00 0.00 0.00 2.67
1999 2058 4.285863 TCCCAAGGAATATTTTGCCGAAT 58.714 39.130 0.00 0.00 0.00 3.34
2042 2101 3.527533 GATACCGCACATTGTACCAGAA 58.472 45.455 0.00 0.00 0.00 3.02
2045 2104 1.205179 ACGATACCGCACATTGTACCA 59.795 47.619 0.00 0.00 39.95 3.25
2210 2475 1.594331 GTCGGTTGAAACTGGAGCTT 58.406 50.000 2.29 0.00 35.96 3.74
2217 2482 5.425630 GGTATCTAATGGTCGGTTGAAACT 58.574 41.667 0.00 0.00 0.00 2.66
2297 2562 8.789767 TGATAGAGAAAAGATACCCTGATCTT 57.210 34.615 0.00 0.00 46.02 2.40
2399 2664 7.470289 TTGATTTCCAACGTTTAACCATTTG 57.530 32.000 0.00 0.00 0.00 2.32
2412 2677 7.752695 ACGAAGACAGATAATTGATTTCCAAC 58.247 34.615 0.00 0.00 37.63 3.77
2414 2679 9.045223 CATACGAAGACAGATAATTGATTTCCA 57.955 33.333 0.00 0.00 0.00 3.53
2437 2703 3.591023 TCGAGAAAAATGACCGTGCATA 58.409 40.909 0.00 0.00 0.00 3.14
2441 2707 7.222031 TCAGTATAATCGAGAAAAATGACCGTG 59.778 37.037 0.00 0.00 0.00 4.94
2494 2775 6.920569 ATTTCGGTCTTACCATACATGTTC 57.079 37.500 2.30 0.00 38.47 3.18
2496 2777 7.732025 TCATATTTCGGTCTTACCATACATGT 58.268 34.615 2.69 2.69 38.47 3.21
2509 2790 6.077838 GTGTGTTCAACTTCATATTTCGGTC 58.922 40.000 0.00 0.00 0.00 4.79
2512 2793 5.079406 CCGTGTGTTCAACTTCATATTTCG 58.921 41.667 0.00 0.00 0.00 3.46
2595 2876 6.869388 GTCCTCTTCGTTTGTATTTCTCTCTT 59.131 38.462 0.00 0.00 0.00 2.85
2678 2960 4.209452 TGAGTCTTCACGCAATTTTCAC 57.791 40.909 0.00 0.00 27.98 3.18


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

AutoCloner maintained by Alex Coulton.