Multiple sequence alignment - TraesCS1B01G246500

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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 TraesCS1B01G246500 chr1B 100.000 4160 0 0 1 4160 436300667 436296508 0.000000e+00 7683.0
1 TraesCS1B01G246500 chr1D 95.680 3009 75 8 1171 4160 323945497 323942525 0.000000e+00 4785.0
2 TraesCS1B01G246500 chr1D 89.474 912 78 10 1 899 337102902 337101996 0.000000e+00 1136.0
3 TraesCS1B01G246500 chr1D 89.231 910 84 8 2 899 356043425 356044332 0.000000e+00 1125.0
4 TraesCS1B01G246500 chr1D 86.777 121 5 4 1043 1153 323945602 323945483 1.570000e-24 124.0
5 TraesCS1B01G246500 chr1A 96.942 2191 65 2 1171 3361 423922919 423920731 0.000000e+00 3674.0
6 TraesCS1B01G246500 chr1A 91.546 828 28 10 3357 4160 423918130 423917321 0.000000e+00 1103.0
7 TraesCS1B01G246500 chr1A 91.667 60 0 3 1043 1100 94784028 94784084 1.240000e-10 78.7
8 TraesCS1B01G246500 chr6A 89.836 915 79 8 1 903 5349631 5348719 0.000000e+00 1162.0
9 TraesCS1B01G246500 chr7D 89.912 912 75 11 1 899 172150855 172149948 0.000000e+00 1158.0
10 TraesCS1B01G246500 chr3D 89.803 912 80 7 1 899 164906281 164907192 0.000000e+00 1157.0
11 TraesCS1B01G246500 chr4D 89.791 911 80 7 1 899 258155032 258155941 0.000000e+00 1155.0
12 TraesCS1B01G246500 chr4D 91.667 60 0 3 1043 1100 123424434 123424490 1.240000e-10 78.7
13 TraesCS1B01G246500 chr2D 89.462 911 84 6 1 899 603811348 603810438 0.000000e+00 1140.0
14 TraesCS1B01G246500 chr2D 89.121 910 88 5 1 899 478984510 478985419 0.000000e+00 1122.0
15 TraesCS1B01G246500 chr6D 89.183 906 86 5 6 899 300715105 300716010 0.000000e+00 1120.0
16 TraesCS1B01G246500 chr6D 91.667 60 0 3 1043 1100 168767508 168767564 1.240000e-10 78.7
17 TraesCS1B01G246500 chrUn 91.667 60 0 3 1043 1100 260203007 260202951 1.240000e-10 78.7
18 TraesCS1B01G246500 chrUn 91.667 60 0 3 1043 1100 270908502 270908446 1.240000e-10 78.7
19 TraesCS1B01G246500 chrUn 91.667 60 0 3 1043 1100 282363976 282363920 1.240000e-10 78.7
20 TraesCS1B01G246500 chrUn 91.667 60 0 3 1043 1100 397470752 397470696 1.240000e-10 78.7
21 TraesCS1B01G246500 chr5D 91.667 60 0 3 1043 1100 324420923 324420979 1.240000e-10 78.7


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 TraesCS1B01G246500 chr1B 436296508 436300667 4159 True 7683.0 7683 100.0000 1 4160 1 chr1B.!!$R1 4159
1 TraesCS1B01G246500 chr1D 323942525 323945602 3077 True 2454.5 4785 91.2285 1043 4160 2 chr1D.!!$R2 3117
2 TraesCS1B01G246500 chr1D 337101996 337102902 906 True 1136.0 1136 89.4740 1 899 1 chr1D.!!$R1 898
3 TraesCS1B01G246500 chr1D 356043425 356044332 907 False 1125.0 1125 89.2310 2 899 1 chr1D.!!$F1 897
4 TraesCS1B01G246500 chr1A 423917321 423922919 5598 True 2388.5 3674 94.2440 1171 4160 2 chr1A.!!$R1 2989
5 TraesCS1B01G246500 chr6A 5348719 5349631 912 True 1162.0 1162 89.8360 1 903 1 chr6A.!!$R1 902
6 TraesCS1B01G246500 chr7D 172149948 172150855 907 True 1158.0 1158 89.9120 1 899 1 chr7D.!!$R1 898
7 TraesCS1B01G246500 chr3D 164906281 164907192 911 False 1157.0 1157 89.8030 1 899 1 chr3D.!!$F1 898
8 TraesCS1B01G246500 chr4D 258155032 258155941 909 False 1155.0 1155 89.7910 1 899 1 chr4D.!!$F2 898
9 TraesCS1B01G246500 chr2D 603810438 603811348 910 True 1140.0 1140 89.4620 1 899 1 chr2D.!!$R1 898
10 TraesCS1B01G246500 chr2D 478984510 478985419 909 False 1122.0 1122 89.1210 1 899 1 chr2D.!!$F1 898
11 TraesCS1B01G246500 chr6D 300715105 300716010 905 False 1120.0 1120 89.1830 6 899 1 chr6D.!!$F2 893

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
989 1004 0.956633 TTGCTTACTCTCGGACACGT 59.043 50.0 0.0 0.0 41.85 4.49 F
1147 1170 0.106335 CAACCAAGCCAATGTGCCAA 59.894 50.0 0.0 0.0 0.00 4.52 F
1148 1171 0.106521 AACCAAGCCAATGTGCCAAC 59.893 50.0 0.0 0.0 0.00 3.77 F
2197 2220 0.258774 AAAGTGTGGCAAGGTCAGGT 59.741 50.0 0.0 0.0 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2595 2618 0.108804 CTGCGACTTCGGCTAGGAAA 60.109 55.000 0.02 0.00 40.23 3.13 R
2934 2957 1.596260 CTGTGCACAGCAAGGATATCG 59.404 52.381 32.39 6.92 41.47 2.92 R
3105 3128 5.935945 TCCTTGAAGTGATGAAACCTGTTA 58.064 37.500 0.00 0.00 0.00 2.41 R
4010 6662 1.002430 GGGTCATGTCTGCACAAGAGA 59.998 52.381 0.00 0.00 35.64 3.10 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
80 81 2.520549 AGGTAGTGGCTCCTCCTCTAAT 59.479 50.000 0.00 0.00 41.21 1.73
86 87 1.323412 GCTCCTCCTCTAATCGCTCA 58.677 55.000 0.00 0.00 0.00 4.26
155 157 2.512515 GCTCGGTGCTAGCCCAAG 60.513 66.667 13.29 8.96 38.95 3.61
189 191 3.331150 CACCGTTGCCACTCATTAAGTA 58.669 45.455 0.00 0.00 36.07 2.24
262 264 2.304470 TCTCGGATGGGTGTTCATCAAA 59.696 45.455 7.08 0.00 43.82 2.69
273 275 4.621034 GGTGTTCATCAAATGCTTAAACGG 59.379 41.667 0.00 0.00 0.00 4.44
274 276 4.089923 GTGTTCATCAAATGCTTAAACGGC 59.910 41.667 0.00 0.00 0.00 5.68
336 338 8.228464 GGATTTGACTAGTTGTGCTAACTTAAC 58.772 37.037 11.26 5.41 0.00 2.01
375 377 8.584157 AGAATGAATGCAAGTTTTGGTATTGTA 58.416 29.630 0.00 0.00 0.00 2.41
513 515 3.701542 ACATGAGACTAGATGCGAGGAAA 59.298 43.478 0.00 0.00 0.00 3.13
581 587 1.938577 CCTCCGCAGATCAACAATGAG 59.061 52.381 0.00 0.00 39.39 2.90
618 624 5.245531 CACTAATCCAACTTACAGGAGCAA 58.754 41.667 0.00 0.00 37.34 3.91
668 674 9.665719 AAATGTATTCTTGTGGTTCTTGTTTTT 57.334 25.926 0.00 0.00 0.00 1.94
833 848 1.228862 GGACACAACCCCATTGCCT 60.229 57.895 0.00 0.00 42.62 4.75
836 851 2.456577 GACACAACCCCATTGCCTTAT 58.543 47.619 0.00 0.00 42.62 1.73
889 904 1.279527 CGTTTAAGGTCGTGCGCTGA 61.280 55.000 9.73 3.44 0.00 4.26
899 914 1.671054 GTGCGCTGAAGTTGGCCTA 60.671 57.895 9.73 0.00 0.00 3.93
903 918 1.079503 CGCTGAAGTTGGCCTAAGAC 58.920 55.000 3.32 0.00 0.00 3.01
904 919 1.454201 GCTGAAGTTGGCCTAAGACC 58.546 55.000 3.32 0.00 0.00 3.85
905 920 1.003696 GCTGAAGTTGGCCTAAGACCT 59.996 52.381 3.32 0.00 0.00 3.85
906 921 2.704572 CTGAAGTTGGCCTAAGACCTG 58.295 52.381 3.32 0.00 0.00 4.00
907 922 1.351017 TGAAGTTGGCCTAAGACCTGG 59.649 52.381 3.32 0.00 0.00 4.45
916 931 4.625607 GCCTAAGACCTGGCTAATACAT 57.374 45.455 0.00 0.00 45.26 2.29
917 932 4.570930 GCCTAAGACCTGGCTAATACATC 58.429 47.826 0.00 0.00 45.26 3.06
918 933 4.040461 GCCTAAGACCTGGCTAATACATCA 59.960 45.833 0.00 0.00 45.26 3.07
919 934 5.280215 GCCTAAGACCTGGCTAATACATCAT 60.280 44.000 0.00 0.00 45.26 2.45
920 935 6.402222 CCTAAGACCTGGCTAATACATCATC 58.598 44.000 0.00 0.00 0.00 2.92
921 936 4.527509 AGACCTGGCTAATACATCATCG 57.472 45.455 0.00 0.00 0.00 3.84
922 937 4.152647 AGACCTGGCTAATACATCATCGA 58.847 43.478 0.00 0.00 0.00 3.59
923 938 4.021894 AGACCTGGCTAATACATCATCGAC 60.022 45.833 0.00 0.00 0.00 4.20
924 939 3.641436 ACCTGGCTAATACATCATCGACA 59.359 43.478 0.00 0.00 0.00 4.35
925 940 4.100963 ACCTGGCTAATACATCATCGACAA 59.899 41.667 0.00 0.00 0.00 3.18
926 941 5.221722 ACCTGGCTAATACATCATCGACAAT 60.222 40.000 0.00 0.00 0.00 2.71
927 942 5.121298 CCTGGCTAATACATCATCGACAATG 59.879 44.000 7.19 7.19 36.65 2.82
928 943 4.996758 TGGCTAATACATCATCGACAATGG 59.003 41.667 12.14 0.00 35.94 3.16
929 944 5.221621 TGGCTAATACATCATCGACAATGGA 60.222 40.000 12.14 5.25 35.94 3.41
930 945 5.349817 GGCTAATACATCATCGACAATGGAG 59.650 44.000 12.14 6.12 35.94 3.86
931 946 6.159293 GCTAATACATCATCGACAATGGAGA 58.841 40.000 12.14 0.29 35.94 3.71
932 947 6.090088 GCTAATACATCATCGACAATGGAGAC 59.910 42.308 12.14 0.00 35.94 3.36
949 964 6.544928 TGGAGACATAACTGAGATTTAGCA 57.455 37.500 0.00 0.00 33.40 3.49
950 965 6.946340 TGGAGACATAACTGAGATTTAGCAA 58.054 36.000 0.00 0.00 33.40 3.91
951 966 7.044181 TGGAGACATAACTGAGATTTAGCAAG 58.956 38.462 0.00 0.00 33.40 4.01
952 967 7.093333 TGGAGACATAACTGAGATTTAGCAAGA 60.093 37.037 0.00 0.00 33.40 3.02
953 968 7.437862 GGAGACATAACTGAGATTTAGCAAGAG 59.562 40.741 0.00 0.00 0.00 2.85
954 969 7.846066 AGACATAACTGAGATTTAGCAAGAGT 58.154 34.615 0.00 0.00 0.00 3.24
955 970 7.763528 AGACATAACTGAGATTTAGCAAGAGTG 59.236 37.037 0.00 0.00 0.00 3.51
956 971 7.615403 ACATAACTGAGATTTAGCAAGAGTGA 58.385 34.615 0.00 0.00 0.00 3.41
957 972 8.263640 ACATAACTGAGATTTAGCAAGAGTGAT 58.736 33.333 0.00 0.00 0.00 3.06
958 973 9.107177 CATAACTGAGATTTAGCAAGAGTGATT 57.893 33.333 0.00 0.00 0.00 2.57
960 975 8.715191 AACTGAGATTTAGCAAGAGTGATTAG 57.285 34.615 0.00 0.00 0.00 1.73
961 976 8.072321 ACTGAGATTTAGCAAGAGTGATTAGA 57.928 34.615 0.00 0.00 0.00 2.10
962 977 8.535335 ACTGAGATTTAGCAAGAGTGATTAGAA 58.465 33.333 0.00 0.00 0.00 2.10
963 978 9.376075 CTGAGATTTAGCAAGAGTGATTAGAAA 57.624 33.333 0.00 0.00 0.00 2.52
964 979 9.725019 TGAGATTTAGCAAGAGTGATTAGAAAA 57.275 29.630 0.00 0.00 0.00 2.29
966 981 9.171877 AGATTTAGCAAGAGTGATTAGAAAAGG 57.828 33.333 0.00 0.00 0.00 3.11
967 982 7.687941 TTTAGCAAGAGTGATTAGAAAAGGG 57.312 36.000 0.00 0.00 0.00 3.95
968 983 4.593956 AGCAAGAGTGATTAGAAAAGGGG 58.406 43.478 0.00 0.00 0.00 4.79
969 984 4.289672 AGCAAGAGTGATTAGAAAAGGGGA 59.710 41.667 0.00 0.00 0.00 4.81
970 985 5.044550 AGCAAGAGTGATTAGAAAAGGGGAT 60.045 40.000 0.00 0.00 0.00 3.85
971 986 5.654209 GCAAGAGTGATTAGAAAAGGGGATT 59.346 40.000 0.00 0.00 0.00 3.01
972 987 6.405176 GCAAGAGTGATTAGAAAAGGGGATTG 60.405 42.308 0.00 0.00 0.00 2.67
973 988 5.196695 AGAGTGATTAGAAAAGGGGATTGC 58.803 41.667 0.00 0.00 0.00 3.56
974 989 5.044550 AGAGTGATTAGAAAAGGGGATTGCT 60.045 40.000 0.00 0.00 0.00 3.91
975 990 5.583932 AGTGATTAGAAAAGGGGATTGCTT 58.416 37.500 0.00 0.00 0.00 3.91
976 991 6.731467 AGTGATTAGAAAAGGGGATTGCTTA 58.269 36.000 0.00 0.00 0.00 3.09
977 992 6.603599 AGTGATTAGAAAAGGGGATTGCTTAC 59.396 38.462 0.00 0.00 0.00 2.34
978 993 6.603599 GTGATTAGAAAAGGGGATTGCTTACT 59.396 38.462 0.00 0.00 0.00 2.24
979 994 6.828785 TGATTAGAAAAGGGGATTGCTTACTC 59.171 38.462 0.00 0.00 0.00 2.59
980 995 4.936685 AGAAAAGGGGATTGCTTACTCT 57.063 40.909 0.00 0.00 0.00 3.24
981 996 4.849518 AGAAAAGGGGATTGCTTACTCTC 58.150 43.478 0.00 0.00 0.00 3.20
982 997 2.990066 AAGGGGATTGCTTACTCTCG 57.010 50.000 0.00 0.00 0.00 4.04
983 998 1.123928 AGGGGATTGCTTACTCTCGG 58.876 55.000 0.00 0.00 0.00 4.63
984 999 1.120530 GGGGATTGCTTACTCTCGGA 58.879 55.000 0.00 0.00 0.00 4.55
985 1000 1.202545 GGGGATTGCTTACTCTCGGAC 60.203 57.143 0.00 0.00 0.00 4.79
986 1001 1.480954 GGGATTGCTTACTCTCGGACA 59.519 52.381 0.00 0.00 0.00 4.02
987 1002 2.541556 GGATTGCTTACTCTCGGACAC 58.458 52.381 0.00 0.00 0.00 3.67
988 1003 2.186076 GATTGCTTACTCTCGGACACG 58.814 52.381 0.00 0.00 42.74 4.49
989 1004 0.956633 TTGCTTACTCTCGGACACGT 59.043 50.000 0.00 0.00 41.85 4.49
990 1005 0.956633 TGCTTACTCTCGGACACGTT 59.043 50.000 0.00 0.00 41.85 3.99
991 1006 1.338973 TGCTTACTCTCGGACACGTTT 59.661 47.619 0.00 0.00 41.85 3.60
992 1007 2.223876 TGCTTACTCTCGGACACGTTTT 60.224 45.455 0.00 0.00 41.85 2.43
993 1008 2.407696 GCTTACTCTCGGACACGTTTTC 59.592 50.000 0.00 0.00 41.85 2.29
994 1009 3.635331 CTTACTCTCGGACACGTTTTCA 58.365 45.455 0.00 0.00 41.85 2.69
995 1010 1.849097 ACTCTCGGACACGTTTTCAC 58.151 50.000 0.00 0.00 41.85 3.18
996 1011 1.407979 ACTCTCGGACACGTTTTCACT 59.592 47.619 0.00 0.00 41.85 3.41
997 1012 2.159142 ACTCTCGGACACGTTTTCACTT 60.159 45.455 0.00 0.00 41.85 3.16
998 1013 2.864343 CTCTCGGACACGTTTTCACTTT 59.136 45.455 0.00 0.00 41.85 2.66
999 1014 3.264104 TCTCGGACACGTTTTCACTTTT 58.736 40.909 0.00 0.00 41.85 2.27
1000 1015 4.431809 TCTCGGACACGTTTTCACTTTTA 58.568 39.130 0.00 0.00 41.85 1.52
1001 1016 5.051816 TCTCGGACACGTTTTCACTTTTAT 58.948 37.500 0.00 0.00 41.85 1.40
1002 1017 5.050634 TCTCGGACACGTTTTCACTTTTATG 60.051 40.000 0.00 0.00 41.85 1.90
1003 1018 3.662186 CGGACACGTTTTCACTTTTATGC 59.338 43.478 0.00 0.00 34.81 3.14
1004 1019 4.553938 CGGACACGTTTTCACTTTTATGCT 60.554 41.667 0.00 0.00 34.81 3.79
1005 1020 5.278604 GGACACGTTTTCACTTTTATGCTT 58.721 37.500 0.00 0.00 0.00 3.91
1006 1021 6.432107 GGACACGTTTTCACTTTTATGCTTA 58.568 36.000 0.00 0.00 0.00 3.09
1007 1022 6.577427 GGACACGTTTTCACTTTTATGCTTAG 59.423 38.462 0.00 0.00 0.00 2.18
1008 1023 7.023197 ACACGTTTTCACTTTTATGCTTAGT 57.977 32.000 0.00 0.00 0.00 2.24
1009 1024 7.130269 ACACGTTTTCACTTTTATGCTTAGTC 58.870 34.615 0.00 0.00 0.00 2.59
1010 1025 7.129622 CACGTTTTCACTTTTATGCTTAGTCA 58.870 34.615 0.00 0.00 0.00 3.41
1011 1026 7.642194 CACGTTTTCACTTTTATGCTTAGTCAA 59.358 33.333 0.00 0.00 0.00 3.18
1012 1027 7.855904 ACGTTTTCACTTTTATGCTTAGTCAAG 59.144 33.333 0.00 0.00 34.66 3.02
1013 1028 7.855904 CGTTTTCACTTTTATGCTTAGTCAAGT 59.144 33.333 0.00 0.00 34.00 3.16
1014 1029 8.958043 GTTTTCACTTTTATGCTTAGTCAAGTG 58.042 33.333 15.36 15.36 41.57 3.16
1015 1030 8.445275 TTTCACTTTTATGCTTAGTCAAGTGA 57.555 30.769 17.88 17.88 45.19 3.41
1016 1031 7.658179 TCACTTTTATGCTTAGTCAAGTGAG 57.342 36.000 17.88 4.62 43.15 3.51
1017 1032 7.217200 TCACTTTTATGCTTAGTCAAGTGAGT 58.783 34.615 17.88 0.00 43.15 3.41
1018 1033 7.715249 TCACTTTTATGCTTAGTCAAGTGAGTT 59.285 33.333 17.88 0.00 43.15 3.01
1019 1034 8.012241 CACTTTTATGCTTAGTCAAGTGAGTTC 58.988 37.037 15.95 0.00 42.41 3.01
1020 1035 7.173390 ACTTTTATGCTTAGTCAAGTGAGTTCC 59.827 37.037 0.00 0.00 34.00 3.62
1021 1036 4.623932 ATGCTTAGTCAAGTGAGTTCCA 57.376 40.909 0.00 0.00 34.00 3.53
1022 1037 4.623932 TGCTTAGTCAAGTGAGTTCCAT 57.376 40.909 0.00 0.00 34.00 3.41
1023 1038 4.973168 TGCTTAGTCAAGTGAGTTCCATT 58.027 39.130 0.00 0.00 34.00 3.16
1024 1039 4.997395 TGCTTAGTCAAGTGAGTTCCATTC 59.003 41.667 0.00 0.00 34.00 2.67
1025 1040 4.997395 GCTTAGTCAAGTGAGTTCCATTCA 59.003 41.667 0.00 0.00 34.00 2.57
1026 1041 5.106908 GCTTAGTCAAGTGAGTTCCATTCAC 60.107 44.000 0.00 0.00 44.09 3.18
1027 1042 3.744660 AGTCAAGTGAGTTCCATTCACC 58.255 45.455 2.04 0.00 44.68 4.02
1028 1043 2.814336 GTCAAGTGAGTTCCATTCACCC 59.186 50.000 2.04 0.00 44.68 4.61
1029 1044 2.162681 CAAGTGAGTTCCATTCACCCC 58.837 52.381 2.04 0.00 44.68 4.95
1030 1045 0.324943 AGTGAGTTCCATTCACCCCG 59.675 55.000 2.04 0.00 44.68 5.73
1031 1046 0.323629 GTGAGTTCCATTCACCCCGA 59.676 55.000 0.00 0.00 39.17 5.14
1032 1047 1.060729 TGAGTTCCATTCACCCCGAA 58.939 50.000 0.00 0.00 38.22 4.30
1033 1048 1.422024 TGAGTTCCATTCACCCCGAAA 59.578 47.619 0.00 0.00 37.12 3.46
1034 1049 2.158593 TGAGTTCCATTCACCCCGAAAA 60.159 45.455 0.00 0.00 37.12 2.29
1035 1050 2.888414 GAGTTCCATTCACCCCGAAAAA 59.112 45.455 0.00 0.00 37.12 1.94
1065 1080 5.465724 ACAAGTGAGTTCCATTCGAAGTAAC 59.534 40.000 3.35 7.86 35.98 2.50
1066 1081 4.235360 AGTGAGTTCCATTCGAAGTAACG 58.765 43.478 3.35 0.00 39.49 3.18
1067 1082 3.985925 GTGAGTTCCATTCGAAGTAACGT 59.014 43.478 3.35 0.00 34.09 3.99
1096 1116 3.823304 AGGAGCACCATCTTCAAAACTTC 59.177 43.478 2.07 0.00 38.94 3.01
1107 1127 5.529791 TCTTCAAAACTTCTCGAGTCGATT 58.470 37.500 16.94 4.35 37.72 3.34
1138 1161 0.553819 ACCAAGTACCAACCAAGCCA 59.446 50.000 0.00 0.00 0.00 4.75
1139 1162 1.063567 ACCAAGTACCAACCAAGCCAA 60.064 47.619 0.00 0.00 0.00 4.52
1140 1163 2.247358 CCAAGTACCAACCAAGCCAAT 58.753 47.619 0.00 0.00 0.00 3.16
1141 1164 2.029110 CCAAGTACCAACCAAGCCAATG 60.029 50.000 0.00 0.00 0.00 2.82
1142 1165 2.627699 CAAGTACCAACCAAGCCAATGT 59.372 45.455 0.00 0.00 0.00 2.71
1143 1166 2.238521 AGTACCAACCAAGCCAATGTG 58.761 47.619 0.00 0.00 0.00 3.21
1144 1167 0.965439 TACCAACCAAGCCAATGTGC 59.035 50.000 0.00 0.00 0.00 4.57
1145 1168 1.004679 CCAACCAAGCCAATGTGCC 60.005 57.895 0.00 0.00 0.00 5.01
1146 1169 1.747145 CAACCAAGCCAATGTGCCA 59.253 52.632 0.00 0.00 0.00 4.92
1147 1170 0.106335 CAACCAAGCCAATGTGCCAA 59.894 50.000 0.00 0.00 0.00 4.52
1148 1171 0.106521 AACCAAGCCAATGTGCCAAC 59.893 50.000 0.00 0.00 0.00 3.77
1149 1172 1.047596 ACCAAGCCAATGTGCCAACA 61.048 50.000 0.00 0.00 41.58 3.33
1159 1182 2.632643 GTGCCAACACTCATGCTCA 58.367 52.632 0.00 0.00 43.85 4.26
1160 1183 0.953727 GTGCCAACACTCATGCTCAA 59.046 50.000 0.00 0.00 43.85 3.02
1161 1184 1.337703 GTGCCAACACTCATGCTCAAA 59.662 47.619 0.00 0.00 43.85 2.69
1162 1185 2.030371 TGCCAACACTCATGCTCAAAA 58.970 42.857 0.00 0.00 0.00 2.44
1163 1186 2.429971 TGCCAACACTCATGCTCAAAAA 59.570 40.909 0.00 0.00 0.00 1.94
1194 1217 1.455383 GCCAACACTCCAACACCCTG 61.455 60.000 0.00 0.00 0.00 4.45
1230 1253 3.155167 GTCTCCTTCCCGCCGGAT 61.155 66.667 5.05 0.00 38.24 4.18
1265 1288 3.120385 CGCGCTCAAGTCATGCCA 61.120 61.111 5.56 0.00 0.00 4.92
1360 1383 0.965866 CTCGCTCCTCCACACCTACA 60.966 60.000 0.00 0.00 0.00 2.74
1464 1487 1.585006 CGGTTACTCTGCACGAGGT 59.415 57.895 14.88 6.07 44.33 3.85
1758 1781 0.321919 ATGTGGTCACTGCGCTCATT 60.322 50.000 9.73 0.00 0.00 2.57
1995 2018 1.893137 GGGAAAGATTTGGAAGCGGTT 59.107 47.619 0.00 0.00 0.00 4.44
2127 2150 5.885912 AGCACACTGTTTTTCTCTTAGGAAA 59.114 36.000 0.00 0.00 33.98 3.13
2197 2220 0.258774 AAAGTGTGGCAAGGTCAGGT 59.741 50.000 0.00 0.00 0.00 4.00
2256 2279 0.446222 CGGTTTCGTGGAATGCGATT 59.554 50.000 0.00 0.00 38.21 3.34
2352 2375 1.276622 AGCCCGACCTAGTCACATTT 58.723 50.000 0.00 0.00 32.09 2.32
2365 2388 7.038587 ACCTAGTCACATTTACCTGTGTCATTA 60.039 37.037 4.33 0.00 45.40 1.90
2405 2428 2.680352 GACAGAGGAGGGGCGTCA 60.680 66.667 0.00 0.00 33.89 4.35
2574 2597 3.334054 GGGTCCTTGCTGGGCTCT 61.334 66.667 1.34 0.00 38.09 4.09
2595 2618 4.837860 TCTTGCAGGGTTTATGGAAATGTT 59.162 37.500 0.00 0.00 0.00 2.71
2601 2624 6.071051 GCAGGGTTTATGGAAATGTTTTCCTA 60.071 38.462 17.39 6.97 39.31 2.94
2798 2821 2.358898 AGAACAAGGTGCACATGTTGTC 59.641 45.455 32.22 23.05 37.41 3.18
2832 2855 0.322726 CACACCCCATGATGACTGCA 60.323 55.000 0.00 0.00 0.00 4.41
2907 2930 1.466167 CCGAGCACAGATTTTGTCCTG 59.534 52.381 0.00 0.00 38.16 3.86
2934 2957 5.299279 TGATGTGGAAGAACAAGAAAAGGAC 59.701 40.000 0.00 0.00 32.81 3.85
3105 3128 6.274322 AGGGAGATATCTGTTAGAGACACT 57.726 41.667 10.74 0.00 33.82 3.55
3164 3187 4.746466 TGTGGGGATTACTGGTGATTTTT 58.254 39.130 0.00 0.00 0.00 1.94
3171 3194 1.632589 ACTGGTGATTTTTCCTGCCC 58.367 50.000 0.00 0.00 0.00 5.36
3187 3210 2.826128 CTGCCCTGACTTACTGTCTGTA 59.174 50.000 0.00 0.00 45.54 2.74
3234 3257 1.227102 GCATGCATGTCCCCCTACA 59.773 57.895 26.79 0.00 0.00 2.74
3238 3261 3.815396 GCATGCATGTCCCCCTACATTAT 60.815 47.826 26.79 0.00 38.01 1.28
3468 6097 5.817296 TGATCTACAACACACCATTATCTGC 59.183 40.000 0.00 0.00 0.00 4.26
3540 6188 6.910972 GCTTCACCTTGAGTTAGTTGTTTTAC 59.089 38.462 0.00 0.00 0.00 2.01
3645 6293 6.594159 ACCCTATGAATTTTGTAGTCGTTCAG 59.406 38.462 0.00 0.00 32.93 3.02
3668 6316 5.655532 AGCCTGCAGATTTCAGAAATACATT 59.344 36.000 17.39 0.00 33.54 2.71
3676 6324 7.972277 CAGATTTCAGAAATACATTTGGTGGAG 59.028 37.037 8.45 0.00 0.00 3.86
3714 6362 4.654262 AGACTCAGTTGGAACTTGGAGTTA 59.346 41.667 11.69 0.00 40.36 2.24
3780 6428 1.620819 AGACACATCAGCTTTCGGAGT 59.379 47.619 0.00 0.00 0.00 3.85
3841 6493 1.953559 ACACGTGACACTTGCTGAAT 58.046 45.000 25.01 0.00 0.00 2.57
3853 6505 7.042797 ACACTTGCTGAATGAACTTAACATT 57.957 32.000 0.00 0.00 40.08 2.71
3880 6532 9.736023 CCTTGTTTTAAGTTAATAGCATCATCC 57.264 33.333 0.00 0.00 0.00 3.51
3884 6536 9.221775 GTTTTAAGTTAATAGCATCATCCGTTG 57.778 33.333 0.00 0.00 0.00 4.10
3939 6591 6.669125 TTCACCAAATGAATGATCCAGTTT 57.331 33.333 0.00 0.00 42.62 2.66
3940 6592 6.271488 TCACCAAATGAATGATCCAGTTTC 57.729 37.500 0.00 0.00 33.02 2.78
3941 6593 5.185635 TCACCAAATGAATGATCCAGTTTCC 59.814 40.000 0.00 0.00 33.02 3.13
3942 6594 5.047164 CACCAAATGAATGATCCAGTTTCCA 60.047 40.000 0.00 0.00 0.00 3.53
3943 6595 5.186409 ACCAAATGAATGATCCAGTTTCCAG 59.814 40.000 0.00 0.00 0.00 3.86
3944 6596 5.186409 CCAAATGAATGATCCAGTTTCCAGT 59.814 40.000 0.00 0.00 0.00 4.00
3945 6597 6.295462 CCAAATGAATGATCCAGTTTCCAGTT 60.295 38.462 0.00 0.00 0.00 3.16
3946 6598 6.923199 AATGAATGATCCAGTTTCCAGTTT 57.077 33.333 0.00 0.00 0.00 2.66
3947 6599 6.923199 ATGAATGATCCAGTTTCCAGTTTT 57.077 33.333 0.00 0.00 0.00 2.43
4010 6662 1.904865 CCGCTATGGGCATGCCATT 60.905 57.895 36.56 24.86 41.91 3.16
4097 6749 4.737855 TCTCCGAGGGATTTTTAGACAG 57.262 45.455 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 1.015109 GACGGTGTAGATCTGAGCGA 58.985 55.000 25.77 0.00 34.77 4.93
189 191 0.600255 CTTCTTTGGGCAGTCGTCGT 60.600 55.000 0.00 0.00 0.00 4.34
262 264 0.181824 ATACCCCGCCGTTTAAGCAT 59.818 50.000 0.00 0.00 0.00 3.79
273 275 2.480845 CTAAAGTAGCACATACCCCGC 58.519 52.381 0.00 0.00 34.67 6.13
355 357 9.260002 CTTCTTTACAATACCAAAACTTGCATT 57.740 29.630 0.00 0.00 0.00 3.56
483 485 4.280677 GCATCTAGTCTCATGTCTAGCCTT 59.719 45.833 13.35 3.83 33.82 4.35
513 515 5.008019 TCGAGTGTAAAGAAGTAGACGTTGT 59.992 40.000 0.00 0.00 0.00 3.32
737 747 5.240121 ACATTTTTCTTTGCAAGCCCATAG 58.760 37.500 0.00 0.00 0.00 2.23
794 804 2.531428 TCTGGGATGTGGTGGCCA 60.531 61.111 0.00 0.00 0.00 5.36
875 890 1.227556 AACTTCAGCGCACGACCTT 60.228 52.632 11.47 0.00 0.00 3.50
876 891 1.956170 CAACTTCAGCGCACGACCT 60.956 57.895 11.47 0.00 0.00 3.85
889 904 0.038310 GCCAGGTCTTAGGCCAACTT 59.962 55.000 5.39 0.00 45.18 2.66
899 914 4.588951 TCGATGATGTATTAGCCAGGTCTT 59.411 41.667 0.00 0.00 0.00 3.01
903 918 4.257267 TGTCGATGATGTATTAGCCAGG 57.743 45.455 0.00 0.00 0.00 4.45
904 919 5.121298 CCATTGTCGATGATGTATTAGCCAG 59.879 44.000 1.19 0.00 38.03 4.85
905 920 4.996758 CCATTGTCGATGATGTATTAGCCA 59.003 41.667 1.19 0.00 38.03 4.75
906 921 5.237815 TCCATTGTCGATGATGTATTAGCC 58.762 41.667 1.19 0.00 38.03 3.93
907 922 6.090088 GTCTCCATTGTCGATGATGTATTAGC 59.910 42.308 1.19 0.00 38.03 3.09
908 923 7.147976 TGTCTCCATTGTCGATGATGTATTAG 58.852 38.462 1.19 3.48 38.03 1.73
909 924 7.049799 TGTCTCCATTGTCGATGATGTATTA 57.950 36.000 1.19 0.00 38.03 0.98
910 925 5.917462 TGTCTCCATTGTCGATGATGTATT 58.083 37.500 1.19 0.00 38.03 1.89
911 926 5.535753 TGTCTCCATTGTCGATGATGTAT 57.464 39.130 1.19 0.00 38.03 2.29
912 927 5.535753 ATGTCTCCATTGTCGATGATGTA 57.464 39.130 1.19 0.00 38.03 2.29
913 928 3.893326 TGTCTCCATTGTCGATGATGT 57.107 42.857 1.19 0.00 38.03 3.06
914 929 5.987953 AGTTATGTCTCCATTGTCGATGATG 59.012 40.000 1.19 0.00 38.03 3.07
915 930 5.987953 CAGTTATGTCTCCATTGTCGATGAT 59.012 40.000 1.19 0.00 38.03 2.45
916 931 5.127031 TCAGTTATGTCTCCATTGTCGATGA 59.873 40.000 1.19 0.00 38.03 2.92
917 932 5.351458 TCAGTTATGTCTCCATTGTCGATG 58.649 41.667 0.00 0.00 35.42 3.84
918 933 5.360999 TCTCAGTTATGTCTCCATTGTCGAT 59.639 40.000 0.00 0.00 32.29 3.59
919 934 4.705023 TCTCAGTTATGTCTCCATTGTCGA 59.295 41.667 0.00 0.00 32.29 4.20
920 935 4.998788 TCTCAGTTATGTCTCCATTGTCG 58.001 43.478 0.00 0.00 32.29 4.35
921 936 7.856145 AAATCTCAGTTATGTCTCCATTGTC 57.144 36.000 0.00 0.00 32.29 3.18
922 937 7.497249 GCTAAATCTCAGTTATGTCTCCATTGT 59.503 37.037 0.00 0.00 32.29 2.71
923 938 7.496920 TGCTAAATCTCAGTTATGTCTCCATTG 59.503 37.037 0.00 0.00 32.29 2.82
924 939 7.568349 TGCTAAATCTCAGTTATGTCTCCATT 58.432 34.615 0.00 0.00 32.29 3.16
925 940 7.129457 TGCTAAATCTCAGTTATGTCTCCAT 57.871 36.000 0.00 0.00 34.97 3.41
926 941 6.544928 TGCTAAATCTCAGTTATGTCTCCA 57.455 37.500 0.00 0.00 0.00 3.86
927 942 7.268586 TCTTGCTAAATCTCAGTTATGTCTCC 58.731 38.462 0.00 0.00 0.00 3.71
928 943 7.978975 ACTCTTGCTAAATCTCAGTTATGTCTC 59.021 37.037 0.00 0.00 0.00 3.36
929 944 7.763528 CACTCTTGCTAAATCTCAGTTATGTCT 59.236 37.037 0.00 0.00 0.00 3.41
930 945 7.761704 TCACTCTTGCTAAATCTCAGTTATGTC 59.238 37.037 0.00 0.00 0.00 3.06
931 946 7.615403 TCACTCTTGCTAAATCTCAGTTATGT 58.385 34.615 0.00 0.00 0.00 2.29
932 947 8.659925 ATCACTCTTGCTAAATCTCAGTTATG 57.340 34.615 0.00 0.00 0.00 1.90
934 949 9.809096 CTAATCACTCTTGCTAAATCTCAGTTA 57.191 33.333 0.00 0.00 0.00 2.24
935 950 8.535335 TCTAATCACTCTTGCTAAATCTCAGTT 58.465 33.333 0.00 0.00 0.00 3.16
936 951 8.072321 TCTAATCACTCTTGCTAAATCTCAGT 57.928 34.615 0.00 0.00 0.00 3.41
937 952 8.939201 TTCTAATCACTCTTGCTAAATCTCAG 57.061 34.615 0.00 0.00 0.00 3.35
938 953 9.725019 TTTTCTAATCACTCTTGCTAAATCTCA 57.275 29.630 0.00 0.00 0.00 3.27
940 955 9.171877 CCTTTTCTAATCACTCTTGCTAAATCT 57.828 33.333 0.00 0.00 0.00 2.40
941 956 8.401709 CCCTTTTCTAATCACTCTTGCTAAATC 58.598 37.037 0.00 0.00 0.00 2.17
942 957 7.340487 CCCCTTTTCTAATCACTCTTGCTAAAT 59.660 37.037 0.00 0.00 0.00 1.40
943 958 6.659242 CCCCTTTTCTAATCACTCTTGCTAAA 59.341 38.462 0.00 0.00 0.00 1.85
944 959 6.012858 TCCCCTTTTCTAATCACTCTTGCTAA 60.013 38.462 0.00 0.00 0.00 3.09
945 960 5.487488 TCCCCTTTTCTAATCACTCTTGCTA 59.513 40.000 0.00 0.00 0.00 3.49
946 961 4.289672 TCCCCTTTTCTAATCACTCTTGCT 59.710 41.667 0.00 0.00 0.00 3.91
947 962 4.589908 TCCCCTTTTCTAATCACTCTTGC 58.410 43.478 0.00 0.00 0.00 4.01
948 963 6.405176 GCAATCCCCTTTTCTAATCACTCTTG 60.405 42.308 0.00 0.00 0.00 3.02
949 964 5.654209 GCAATCCCCTTTTCTAATCACTCTT 59.346 40.000 0.00 0.00 0.00 2.85
950 965 5.044550 AGCAATCCCCTTTTCTAATCACTCT 60.045 40.000 0.00 0.00 0.00 3.24
951 966 5.196695 AGCAATCCCCTTTTCTAATCACTC 58.803 41.667 0.00 0.00 0.00 3.51
952 967 5.198602 AGCAATCCCCTTTTCTAATCACT 57.801 39.130 0.00 0.00 0.00 3.41
953 968 5.921962 AAGCAATCCCCTTTTCTAATCAC 57.078 39.130 0.00 0.00 0.00 3.06
954 969 6.731467 AGTAAGCAATCCCCTTTTCTAATCA 58.269 36.000 0.00 0.00 0.00 2.57
955 970 7.057264 AGAGTAAGCAATCCCCTTTTCTAATC 58.943 38.462 0.00 0.00 0.00 1.75
956 971 6.974795 AGAGTAAGCAATCCCCTTTTCTAAT 58.025 36.000 0.00 0.00 0.00 1.73
957 972 6.388619 AGAGTAAGCAATCCCCTTTTCTAA 57.611 37.500 0.00 0.00 0.00 2.10
958 973 5.395324 CGAGAGTAAGCAATCCCCTTTTCTA 60.395 44.000 0.00 0.00 0.00 2.10
959 974 4.624125 CGAGAGTAAGCAATCCCCTTTTCT 60.624 45.833 0.00 0.00 0.00 2.52
960 975 3.623510 CGAGAGTAAGCAATCCCCTTTTC 59.376 47.826 0.00 0.00 0.00 2.29
961 976 3.610911 CGAGAGTAAGCAATCCCCTTTT 58.389 45.455 0.00 0.00 0.00 2.27
962 977 2.092914 CCGAGAGTAAGCAATCCCCTTT 60.093 50.000 0.00 0.00 0.00 3.11
963 978 1.486726 CCGAGAGTAAGCAATCCCCTT 59.513 52.381 0.00 0.00 0.00 3.95
964 979 1.123928 CCGAGAGTAAGCAATCCCCT 58.876 55.000 0.00 0.00 0.00 4.79
965 980 1.120530 TCCGAGAGTAAGCAATCCCC 58.879 55.000 0.00 0.00 0.00 4.81
966 981 1.480954 TGTCCGAGAGTAAGCAATCCC 59.519 52.381 0.00 0.00 0.00 3.85
967 982 2.541556 GTGTCCGAGAGTAAGCAATCC 58.458 52.381 0.00 0.00 0.00 3.01
968 983 2.186076 CGTGTCCGAGAGTAAGCAATC 58.814 52.381 0.00 0.00 35.63 2.67
969 984 1.544691 ACGTGTCCGAGAGTAAGCAAT 59.455 47.619 0.00 0.00 37.88 3.56
970 985 0.956633 ACGTGTCCGAGAGTAAGCAA 59.043 50.000 0.00 0.00 37.88 3.91
971 986 0.956633 AACGTGTCCGAGAGTAAGCA 59.043 50.000 0.00 0.00 37.88 3.91
972 987 2.061740 AAACGTGTCCGAGAGTAAGC 57.938 50.000 0.00 0.00 37.88 3.09
973 988 3.424529 GTGAAAACGTGTCCGAGAGTAAG 59.575 47.826 0.00 0.00 37.88 2.34
974 989 3.067180 AGTGAAAACGTGTCCGAGAGTAA 59.933 43.478 0.00 0.00 37.88 2.24
975 990 2.620115 AGTGAAAACGTGTCCGAGAGTA 59.380 45.455 0.00 0.00 37.88 2.59
976 991 1.407979 AGTGAAAACGTGTCCGAGAGT 59.592 47.619 0.00 0.00 37.88 3.24
977 992 2.135664 AGTGAAAACGTGTCCGAGAG 57.864 50.000 0.00 0.00 37.88 3.20
978 993 2.589798 AAGTGAAAACGTGTCCGAGA 57.410 45.000 0.00 0.00 37.88 4.04
979 994 3.668596 AAAAGTGAAAACGTGTCCGAG 57.331 42.857 0.00 0.00 37.88 4.63
980 995 4.553156 GCATAAAAGTGAAAACGTGTCCGA 60.553 41.667 0.00 0.00 37.88 4.55
981 996 3.662186 GCATAAAAGTGAAAACGTGTCCG 59.338 43.478 0.00 0.00 40.83 4.79
982 997 4.855531 AGCATAAAAGTGAAAACGTGTCC 58.144 39.130 0.00 0.00 0.00 4.02
983 998 7.130269 ACTAAGCATAAAAGTGAAAACGTGTC 58.870 34.615 0.00 0.00 0.00 3.67
984 999 7.023197 ACTAAGCATAAAAGTGAAAACGTGT 57.977 32.000 0.00 0.00 0.00 4.49
985 1000 7.129622 TGACTAAGCATAAAAGTGAAAACGTG 58.870 34.615 0.00 0.00 0.00 4.49
986 1001 7.254227 TGACTAAGCATAAAAGTGAAAACGT 57.746 32.000 0.00 0.00 0.00 3.99
987 1002 7.855904 ACTTGACTAAGCATAAAAGTGAAAACG 59.144 33.333 0.00 0.00 37.43 3.60
988 1003 8.958043 CACTTGACTAAGCATAAAAGTGAAAAC 58.042 33.333 7.42 0.00 44.53 2.43
989 1004 8.898761 TCACTTGACTAAGCATAAAAGTGAAAA 58.101 29.630 12.28 0.00 46.21 2.29
990 1005 8.445275 TCACTTGACTAAGCATAAAAGTGAAA 57.555 30.769 12.28 0.00 46.21 2.69
992 1007 7.217200 ACTCACTTGACTAAGCATAAAAGTGA 58.783 34.615 13.58 13.58 46.71 3.41
993 1008 7.426929 ACTCACTTGACTAAGCATAAAAGTG 57.573 36.000 6.95 6.95 43.62 3.16
994 1009 7.173390 GGAACTCACTTGACTAAGCATAAAAGT 59.827 37.037 0.00 0.00 37.43 2.66
995 1010 7.173218 TGGAACTCACTTGACTAAGCATAAAAG 59.827 37.037 0.00 0.00 37.43 2.27
996 1011 6.995686 TGGAACTCACTTGACTAAGCATAAAA 59.004 34.615 0.00 0.00 37.43 1.52
997 1012 6.530120 TGGAACTCACTTGACTAAGCATAAA 58.470 36.000 0.00 0.00 37.43 1.40
998 1013 6.109156 TGGAACTCACTTGACTAAGCATAA 57.891 37.500 0.00 0.00 37.43 1.90
999 1014 5.738619 TGGAACTCACTTGACTAAGCATA 57.261 39.130 0.00 0.00 37.43 3.14
1000 1015 4.623932 TGGAACTCACTTGACTAAGCAT 57.376 40.909 0.00 0.00 37.43 3.79
1001 1016 4.623932 ATGGAACTCACTTGACTAAGCA 57.376 40.909 0.00 0.00 37.43 3.91
1002 1017 4.997395 TGAATGGAACTCACTTGACTAAGC 59.003 41.667 0.00 0.00 37.43 3.09
1003 1018 5.409826 GGTGAATGGAACTCACTTGACTAAG 59.590 44.000 3.24 0.00 39.86 2.18
1004 1019 5.305585 GGTGAATGGAACTCACTTGACTAA 58.694 41.667 3.24 0.00 35.00 2.24
1005 1020 4.262894 GGGTGAATGGAACTCACTTGACTA 60.263 45.833 3.24 0.00 35.00 2.59
1006 1021 3.496870 GGGTGAATGGAACTCACTTGACT 60.497 47.826 3.24 0.00 35.00 3.41
1007 1022 2.814336 GGGTGAATGGAACTCACTTGAC 59.186 50.000 3.24 0.00 35.00 3.18
1008 1023 2.224769 GGGGTGAATGGAACTCACTTGA 60.225 50.000 3.24 0.00 35.00 3.02
1009 1024 2.162681 GGGGTGAATGGAACTCACTTG 58.837 52.381 3.24 0.00 35.00 3.16
1010 1025 1.271379 CGGGGTGAATGGAACTCACTT 60.271 52.381 3.24 0.00 35.00 3.16
1011 1026 0.324943 CGGGGTGAATGGAACTCACT 59.675 55.000 3.24 0.00 35.00 3.41
1012 1027 0.323629 TCGGGGTGAATGGAACTCAC 59.676 55.000 0.00 0.00 0.00 3.51
1013 1028 1.060729 TTCGGGGTGAATGGAACTCA 58.939 50.000 0.00 0.00 0.00 3.41
1014 1029 2.194201 TTTCGGGGTGAATGGAACTC 57.806 50.000 0.00 0.00 36.22 3.01
1015 1030 2.668144 TTTTCGGGGTGAATGGAACT 57.332 45.000 0.00 0.00 36.22 3.01
1037 1052 5.828299 TCGAATGGAACTCACTTGTTTTT 57.172 34.783 0.00 0.00 0.00 1.94
1038 1053 5.357032 ACTTCGAATGGAACTCACTTGTTTT 59.643 36.000 0.00 0.00 0.00 2.43
1039 1054 4.881850 ACTTCGAATGGAACTCACTTGTTT 59.118 37.500 0.00 0.00 0.00 2.83
1040 1055 4.451900 ACTTCGAATGGAACTCACTTGTT 58.548 39.130 0.00 0.00 0.00 2.83
1041 1056 4.073293 ACTTCGAATGGAACTCACTTGT 57.927 40.909 0.00 0.00 0.00 3.16
1042 1057 5.388475 CGTTACTTCGAATGGAACTCACTTG 60.388 44.000 15.89 0.00 0.00 3.16
1043 1058 4.684703 CGTTACTTCGAATGGAACTCACTT 59.315 41.667 15.89 0.00 0.00 3.16
1044 1059 4.235360 CGTTACTTCGAATGGAACTCACT 58.765 43.478 15.89 0.00 0.00 3.41
1045 1060 3.985925 ACGTTACTTCGAATGGAACTCAC 59.014 43.478 15.89 0.24 34.70 3.51
1046 1061 4.247267 ACGTTACTTCGAATGGAACTCA 57.753 40.909 15.89 0.00 34.70 3.41
1047 1062 5.630680 TGTTACGTTACTTCGAATGGAACTC 59.369 40.000 15.89 8.08 39.15 3.01
1048 1063 5.531634 TGTTACGTTACTTCGAATGGAACT 58.468 37.500 15.89 8.98 39.15 3.01
1058 1073 4.053295 TGCTCCTGTTGTTACGTTACTTC 58.947 43.478 6.24 0.21 0.00 3.01
1065 1080 1.732259 GATGGTGCTCCTGTTGTTACG 59.268 52.381 6.34 0.00 34.23 3.18
1066 1081 3.059352 AGATGGTGCTCCTGTTGTTAC 57.941 47.619 6.34 0.00 34.23 2.50
1067 1082 3.072330 TGAAGATGGTGCTCCTGTTGTTA 59.928 43.478 6.34 0.00 34.23 2.41
1096 1116 3.304257 CCAGCTGATTAATCGACTCGAG 58.696 50.000 17.39 11.84 39.91 4.04
1107 1127 2.355716 GGTACTTGGTGCCAGCTGATTA 60.356 50.000 17.39 0.00 38.20 1.75
1141 1164 0.953727 TTGAGCATGAGTGTTGGCAC 59.046 50.000 0.00 0.00 45.57 5.01
1142 1165 1.689984 TTTGAGCATGAGTGTTGGCA 58.310 45.000 0.00 0.00 0.00 4.92
1143 1166 2.798976 TTTTGAGCATGAGTGTTGGC 57.201 45.000 0.00 0.00 0.00 4.52
1194 1217 4.704833 TGGCGGAGGAAGTGCAGC 62.705 66.667 0.00 0.00 0.00 5.25
1382 1405 4.368808 CGAACACAACGCGGGCAG 62.369 66.667 12.47 0.00 0.00 4.85
1383 1406 4.893601 TCGAACACAACGCGGGCA 62.894 61.111 12.47 0.00 0.00 5.36
1391 1414 1.265635 CCGGCATTCTTTCGAACACAA 59.734 47.619 0.00 0.00 30.67 3.33
1425 1448 4.479993 ATGAGTGCGCTCCAGCCC 62.480 66.667 23.96 0.00 40.95 5.19
1509 1532 1.303236 CACATTTGGCTCGACCCCA 60.303 57.895 0.00 0.00 37.83 4.96
1512 1535 1.398390 GTGATCACATTTGGCTCGACC 59.602 52.381 21.07 0.00 39.84 4.79
1515 1538 1.399440 CAGGTGATCACATTTGGCTCG 59.601 52.381 26.47 2.83 0.00 5.03
1626 1649 3.681835 GAGACACCGGTGGCGTCT 61.682 66.667 36.47 29.02 46.24 4.18
1758 1781 1.507562 CACACTTGCCGTACATGTCA 58.492 50.000 0.00 0.00 34.59 3.58
1807 1830 1.878211 TCCATGTGGCTGGACTCATA 58.122 50.000 0.00 0.00 40.43 2.15
1995 2018 4.914983 ACTGCATCTTCCTGAAAAGATCA 58.085 39.130 0.00 0.00 42.68 2.92
2127 2150 5.779806 CGTAAACGTCATGAAGAAATCCT 57.220 39.130 15.90 0.00 34.11 3.24
2197 2220 1.589803 TCGAAGATCGTCCTCGCATA 58.410 50.000 2.90 0.00 41.35 3.14
2256 2279 2.664015 TGCATTGCATAGCCACCAATA 58.336 42.857 7.38 0.00 31.71 1.90
2352 2375 2.903784 ACAGGCACTAATGACACAGGTA 59.096 45.455 0.00 0.00 35.60 3.08
2405 2428 5.909621 ATGCTGCATTTCATTGAAGTAGT 57.090 34.783 9.81 0.00 0.00 2.73
2574 2597 5.559148 AAACATTTCCATAAACCCTGCAA 57.441 34.783 0.00 0.00 0.00 4.08
2595 2618 0.108804 CTGCGACTTCGGCTAGGAAA 60.109 55.000 0.02 0.00 40.23 3.13
2601 2624 2.715532 TTTCTGCTGCGACTTCGGCT 62.716 55.000 0.02 0.00 40.23 5.52
2810 2833 2.086869 CAGTCATCATGGGGTGTGAAC 58.913 52.381 0.00 0.00 0.00 3.18
2832 2855 5.246307 AGCTGCTTTAGTTTCTCCGTTATT 58.754 37.500 0.00 0.00 0.00 1.40
2907 2930 4.771590 TTCTTGTTCTTCCACATCATGC 57.228 40.909 0.00 0.00 0.00 4.06
2934 2957 1.596260 CTGTGCACAGCAAGGATATCG 59.404 52.381 32.39 6.92 41.47 2.92
3105 3128 5.935945 TCCTTGAAGTGATGAAACCTGTTA 58.064 37.500 0.00 0.00 0.00 2.41
3164 3187 1.267121 GACAGTAAGTCAGGGCAGGA 58.733 55.000 0.00 0.00 46.77 3.86
3187 3210 3.053917 ACCTTCCTACACCAAGTTGTTGT 60.054 43.478 11.08 11.08 30.95 3.32
3203 3226 1.466856 TGCATGCTCATTCACCTTCC 58.533 50.000 20.33 0.00 0.00 3.46
3234 3257 8.863086 CCTCATGAAAACAATATCCACCATAAT 58.137 33.333 0.00 0.00 0.00 1.28
3238 3261 5.579047 ACCTCATGAAAACAATATCCACCA 58.421 37.500 0.00 0.00 0.00 4.17
3280 3303 7.038154 TGTTGGATTCTGTTTCTTACTTTGG 57.962 36.000 0.00 0.00 0.00 3.28
3281 3304 7.115378 GCATGTTGGATTCTGTTTCTTACTTTG 59.885 37.037 0.00 0.00 0.00 2.77
3468 6097 9.249457 GAAATAAAGTTCTCCTTTGGAAAACAG 57.751 33.333 5.72 0.00 43.27 3.16
3540 6188 5.510520 GCTTGGATACCAATCAGTCTCTAGG 60.511 48.000 3.65 0.00 43.07 3.02
3645 6293 4.970662 TGTATTTCTGAAATCTGCAGGC 57.029 40.909 18.22 1.87 34.20 4.85
3676 6324 4.464597 ACTGAGTCTCTCCAATGGAAGTAC 59.535 45.833 2.61 1.49 0.00 2.73
3749 6397 3.618263 GCTGATGTGTCTCACTTCCATGA 60.618 47.826 0.00 0.00 37.62 3.07
3799 6448 8.175716 GTGTAAACAGAAGCATGTAAAGATACC 58.824 37.037 0.00 0.00 31.70 2.73
3800 6449 7.898309 CGTGTAAACAGAAGCATGTAAAGATAC 59.102 37.037 0.00 0.00 31.70 2.24
3801 6450 7.601130 ACGTGTAAACAGAAGCATGTAAAGATA 59.399 33.333 0.00 0.00 31.70 1.98
3802 6451 6.426937 ACGTGTAAACAGAAGCATGTAAAGAT 59.573 34.615 0.00 0.00 31.70 2.40
3804 6453 5.845953 CACGTGTAAACAGAAGCATGTAAAG 59.154 40.000 7.58 0.00 31.70 1.85
4010 6662 1.002430 GGGTCATGTCTGCACAAGAGA 59.998 52.381 0.00 0.00 35.64 3.10
4097 6749 6.734104 AAGATATGCTGAAGAAGTTGTCAC 57.266 37.500 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.