Multiple sequence alignment - TraesCS4A01G018200

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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 TraesCS4A01G018200 chr4A 100.000 2881 0 0 1 2881 11818489 11815609 0.000000e+00 5321.0
1 TraesCS4A01G018200 chr4A 95.897 853 30 5 1 849 11828407 11827556 0.000000e+00 1376.0
2 TraesCS4A01G018200 chr4A 95.986 847 29 5 1 843 12576296 12577141 0.000000e+00 1371.0
3 TraesCS4A01G018200 chr4A 95.868 847 31 4 1 843 133208477 133209323 0.000000e+00 1367.0
4 TraesCS4A01G018200 chr4A 95.863 846 29 6 1 843 246358419 246357577 0.000000e+00 1363.0
5 TraesCS4A01G018200 chr4A 95.540 852 33 4 1 849 300184838 300183989 0.000000e+00 1358.0
6 TraesCS4A01G018200 chr7A 95.981 846 29 5 1 842 323262299 323263143 0.000000e+00 1369.0
7 TraesCS4A01G018200 chr7A 95.858 845 32 3 1 842 84253456 84254300 0.000000e+00 1363.0
8 TraesCS4A01G018200 chr5A 95.863 846 30 5 1 842 264453128 264453972 0.000000e+00 1363.0
9 TraesCS4A01G018200 chr5A 84.848 132 15 3 2174 2304 42739290 42739163 8.380000e-26 128.0
10 TraesCS4A01G018200 chr6A 95.550 854 32 5 1 849 77762555 77761703 0.000000e+00 1362.0
11 TraesCS4A01G018200 chr6A 82.342 555 64 18 1113 1652 564276057 564276592 4.380000e-123 451.0
12 TraesCS4A01G018200 chr6A 83.401 247 32 5 1678 1915 565342684 565342438 1.340000e-53 220.0
13 TraesCS4A01G018200 chr6A 85.039 127 14 3 2179 2304 98891371 98891493 1.080000e-24 124.0
14 TraesCS4A01G018200 chr6A 90.625 64 3 1 1653 1713 564277069 564277132 6.620000e-12 82.4
15 TraesCS4A01G018200 chr3B 98.172 711 9 1 2175 2881 643852229 643852939 0.000000e+00 1238.0
16 TraesCS4A01G018200 chr2A 94.405 697 30 5 2187 2879 134281633 134282324 0.000000e+00 1062.0
17 TraesCS4A01G018200 chr2A 82.667 150 18 7 2185 2331 763163608 763163464 3.010000e-25 126.0
18 TraesCS4A01G018200 chr4D 93.352 707 39 1 1224 1930 455740118 455740816 0.000000e+00 1038.0
19 TraesCS4A01G018200 chr4D 94.086 186 7 1 1047 1228 455739901 455740086 2.190000e-71 279.0
20 TraesCS4A01G018200 chr2B 89.972 708 53 12 2186 2881 767779861 767779160 0.000000e+00 898.0
21 TraesCS4A01G018200 chr2B 78.541 233 28 21 2615 2832 754882039 754882264 1.800000e-27 134.0
22 TraesCS4A01G018200 chr2B 83.916 143 17 4 2713 2850 715946046 715945905 6.480000e-27 132.0
23 TraesCS4A01G018200 chr2B 84.800 125 13 6 2174 2293 184112290 184112413 1.400000e-23 121.0
24 TraesCS4A01G018200 chrUn 89.097 642 51 13 2252 2881 137865324 137865958 0.000000e+00 780.0
25 TraesCS4A01G018200 chr6D 83.024 754 88 27 1113 1849 421463219 421463949 0.000000e+00 647.0
26 TraesCS4A01G018200 chr6D 82.620 748 100 18 1113 1849 421697156 421696428 4.050000e-178 634.0
27 TraesCS4A01G018200 chr6D 84.921 630 80 8 1228 1849 421664612 421663990 8.770000e-175 623.0
28 TraesCS4A01G018200 chr6D 82.258 744 97 24 1121 1849 421682687 421681964 6.820000e-171 610.0
29 TraesCS4A01G018200 chr6D 83.055 419 63 4 1461 1872 422217928 422217511 9.750000e-100 374.0
30 TraesCS4A01G018200 chr6D 89.899 198 16 2 842 1039 70537133 70537326 4.770000e-63 252.0
31 TraesCS4A01G018200 chr6B 81.280 828 112 26 1113 1915 634501498 634502307 5.240000e-177 630.0
32 TraesCS4A01G018200 chr5D 89.691 194 15 5 852 1043 467215764 467215954 2.870000e-60 243.0
33 TraesCS4A01G018200 chr5D 90.374 187 12 6 855 1039 513048168 513048350 1.030000e-59 241.0
34 TraesCS4A01G018200 chr5D 80.198 202 29 10 2655 2850 256007860 256007664 1.080000e-29 141.0
35 TraesCS4A01G018200 chr3A 91.111 180 13 2 863 1039 113691220 113691399 1.030000e-59 241.0
36 TraesCS4A01G018200 chr3A 88.095 126 12 2 2727 2850 9130261 9130137 2.310000e-31 147.0
37 TraesCS4A01G018200 chr5B 89.175 194 17 3 848 1039 670938076 670938267 3.710000e-59 239.0
38 TraesCS4A01G018200 chr5B 83.217 143 18 4 2713 2850 596062245 596062386 3.010000e-25 126.0
39 TraesCS4A01G018200 chr7B 90.217 184 14 4 857 1039 612980190 612980010 1.330000e-58 237.0
40 TraesCS4A01G018200 chr7B 87.603 121 11 2 2185 2304 60856507 60856390 1.390000e-28 137.0
41 TraesCS4A01G018200 chr2D 89.840 187 13 5 855 1039 646599326 646599144 4.800000e-58 235.0
42 TraesCS4A01G018200 chr2D 88.776 196 14 7 848 1039 552578315 552578124 1.730000e-57 233.0
43 TraesCS4A01G018200 chr2D 92.254 142 7 2 1854 1994 343131906 343131768 6.300000e-47 198.0
44 TraesCS4A01G018200 chr2D 87.705 122 10 3 2185 2304 314390367 314390249 1.390000e-28 137.0
45 TraesCS4A01G018200 chr1A 89.474 190 15 5 852 1039 593703440 593703626 4.800000e-58 235.0


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 TraesCS4A01G018200 chr4A 11815609 11818489 2880 True 5321.0 5321 100.0000 1 2881 1 chr4A.!!$R1 2880
1 TraesCS4A01G018200 chr4A 11827556 11828407 851 True 1376.0 1376 95.8970 1 849 1 chr4A.!!$R2 848
2 TraesCS4A01G018200 chr4A 12576296 12577141 845 False 1371.0 1371 95.9860 1 843 1 chr4A.!!$F1 842
3 TraesCS4A01G018200 chr4A 133208477 133209323 846 False 1367.0 1367 95.8680 1 843 1 chr4A.!!$F2 842
4 TraesCS4A01G018200 chr4A 246357577 246358419 842 True 1363.0 1363 95.8630 1 843 1 chr4A.!!$R3 842
5 TraesCS4A01G018200 chr4A 300183989 300184838 849 True 1358.0 1358 95.5400 1 849 1 chr4A.!!$R4 848
6 TraesCS4A01G018200 chr7A 323262299 323263143 844 False 1369.0 1369 95.9810 1 842 1 chr7A.!!$F2 841
7 TraesCS4A01G018200 chr7A 84253456 84254300 844 False 1363.0 1363 95.8580 1 842 1 chr7A.!!$F1 841
8 TraesCS4A01G018200 chr5A 264453128 264453972 844 False 1363.0 1363 95.8630 1 842 1 chr5A.!!$F1 841
9 TraesCS4A01G018200 chr6A 77761703 77762555 852 True 1362.0 1362 95.5500 1 849 1 chr6A.!!$R1 848
10 TraesCS4A01G018200 chr6A 564276057 564277132 1075 False 266.7 451 86.4835 1113 1713 2 chr6A.!!$F2 600
11 TraesCS4A01G018200 chr3B 643852229 643852939 710 False 1238.0 1238 98.1720 2175 2881 1 chr3B.!!$F1 706
12 TraesCS4A01G018200 chr2A 134281633 134282324 691 False 1062.0 1062 94.4050 2187 2879 1 chr2A.!!$F1 692
13 TraesCS4A01G018200 chr4D 455739901 455740816 915 False 658.5 1038 93.7190 1047 1930 2 chr4D.!!$F1 883
14 TraesCS4A01G018200 chr2B 767779160 767779861 701 True 898.0 898 89.9720 2186 2881 1 chr2B.!!$R2 695
15 TraesCS4A01G018200 chrUn 137865324 137865958 634 False 780.0 780 89.0970 2252 2881 1 chrUn.!!$F1 629
16 TraesCS4A01G018200 chr6D 421463219 421463949 730 False 647.0 647 83.0240 1113 1849 1 chr6D.!!$F2 736
17 TraesCS4A01G018200 chr6D 421696428 421697156 728 True 634.0 634 82.6200 1113 1849 1 chr6D.!!$R3 736
18 TraesCS4A01G018200 chr6D 421663990 421664612 622 True 623.0 623 84.9210 1228 1849 1 chr6D.!!$R1 621
19 TraesCS4A01G018200 chr6D 421681964 421682687 723 True 610.0 610 82.2580 1121 1849 1 chr6D.!!$R2 728
20 TraesCS4A01G018200 chr6B 634501498 634502307 809 False 630.0 630 81.2800 1113 1915 1 chr6B.!!$F1 802

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
951 962 0.036732 TGAGTGGTTGACATCCAGCC 59.963 55.0 5.44 2.05 45.32 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2164 2737 0.042581 TCACTGGATGCTACCTCCCA 59.957 55.0 0.0 0.0 31.32 4.37 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
59 60 5.131475 ACGGAAACTAAGGGATATTAAGGCA 59.869 40.000 0.00 0.00 0.00 4.75
82 83 6.486993 GCATCCTTTTAATAGAGAACCGGAAT 59.513 38.462 9.46 0.00 0.00 3.01
415 416 1.003355 CCATCACCGTCCAGCAAGT 60.003 57.895 0.00 0.00 0.00 3.16
505 506 2.325393 GATGGCGACGGATTCCCCTT 62.325 60.000 0.00 0.00 0.00 3.95
646 651 1.747444 ATGGAGGTGGAGTTGGAGTT 58.253 50.000 0.00 0.00 0.00 3.01
810 821 3.071023 AGTTTCAGGTCATTCCGAGAACA 59.929 43.478 0.00 0.00 41.99 3.18
817 828 3.191371 GGTCATTCCGAGAACATTTGCTT 59.809 43.478 0.00 0.00 0.00 3.91
843 854 5.592282 TGCACATAAATAACACCATGGTAGG 59.408 40.000 19.28 9.08 0.00 3.18
851 862 1.002134 ACCATGGTAGGTGTGCAGC 60.002 57.895 18.10 0.00 41.30 5.25
852 863 2.108514 CCATGGTAGGTGTGCAGCG 61.109 63.158 2.57 0.00 0.00 5.18
853 864 1.375908 CATGGTAGGTGTGCAGCGT 60.376 57.895 0.00 0.00 0.00 5.07
854 865 1.375908 ATGGTAGGTGTGCAGCGTG 60.376 57.895 0.00 0.00 0.00 5.34
855 866 3.423154 GGTAGGTGTGCAGCGTGC 61.423 66.667 0.00 3.44 45.29 5.34
900 911 4.857251 CCGAACCCTGGCTGATAC 57.143 61.111 0.00 0.00 0.00 2.24
901 912 1.146263 CCGAACCCTGGCTGATACC 59.854 63.158 0.00 0.00 0.00 2.73
902 913 1.622607 CCGAACCCTGGCTGATACCA 61.623 60.000 0.00 0.00 38.29 3.25
911 922 2.790433 TGGCTGATACCAGGTTGAAAC 58.210 47.619 0.00 0.00 40.72 2.78
912 923 2.107378 TGGCTGATACCAGGTTGAAACA 59.893 45.455 0.00 0.00 40.72 2.83
913 924 2.488153 GGCTGATACCAGGTTGAAACAC 59.512 50.000 0.00 0.00 40.72 3.32
914 925 3.146066 GCTGATACCAGGTTGAAACACA 58.854 45.455 0.00 0.00 40.72 3.72
915 926 3.189287 GCTGATACCAGGTTGAAACACAG 59.811 47.826 0.00 0.00 40.72 3.66
916 927 3.750371 TGATACCAGGTTGAAACACAGG 58.250 45.455 0.00 0.00 0.00 4.00
917 928 3.392947 TGATACCAGGTTGAAACACAGGA 59.607 43.478 0.00 0.00 0.00 3.86
918 929 4.042809 TGATACCAGGTTGAAACACAGGAT 59.957 41.667 0.00 0.00 0.00 3.24
919 930 3.312736 ACCAGGTTGAAACACAGGATT 57.687 42.857 0.00 0.00 0.00 3.01
920 931 3.642141 ACCAGGTTGAAACACAGGATTT 58.358 40.909 0.00 0.00 0.00 2.17
921 932 4.798882 ACCAGGTTGAAACACAGGATTTA 58.201 39.130 0.00 0.00 0.00 1.40
922 933 4.827284 ACCAGGTTGAAACACAGGATTTAG 59.173 41.667 0.00 0.00 0.00 1.85
923 934 4.218417 CCAGGTTGAAACACAGGATTTAGG 59.782 45.833 0.00 0.00 0.00 2.69
924 935 4.218417 CAGGTTGAAACACAGGATTTAGGG 59.782 45.833 0.00 0.00 0.00 3.53
925 936 4.141018 AGGTTGAAACACAGGATTTAGGGT 60.141 41.667 0.00 0.00 0.00 4.34
926 937 4.587262 GGTTGAAACACAGGATTTAGGGTT 59.413 41.667 0.00 0.00 0.00 4.11
927 938 5.069914 GGTTGAAACACAGGATTTAGGGTTT 59.930 40.000 0.00 0.00 0.00 3.27
928 939 6.407639 GGTTGAAACACAGGATTTAGGGTTTT 60.408 38.462 0.00 0.00 0.00 2.43
929 940 6.155475 TGAAACACAGGATTTAGGGTTTTG 57.845 37.500 0.00 0.00 0.00 2.44
930 941 4.600692 AACACAGGATTTAGGGTTTTGC 57.399 40.909 0.00 0.00 0.00 3.68
931 942 2.556622 ACACAGGATTTAGGGTTTTGCG 59.443 45.455 0.00 0.00 0.00 4.85
932 943 2.556622 CACAGGATTTAGGGTTTTGCGT 59.443 45.455 0.00 0.00 0.00 5.24
933 944 2.556622 ACAGGATTTAGGGTTTTGCGTG 59.443 45.455 0.00 0.00 0.00 5.34
934 945 2.817258 CAGGATTTAGGGTTTTGCGTGA 59.183 45.455 0.00 0.00 0.00 4.35
935 946 3.081804 AGGATTTAGGGTTTTGCGTGAG 58.918 45.455 0.00 0.00 0.00 3.51
936 947 2.817844 GGATTTAGGGTTTTGCGTGAGT 59.182 45.455 0.00 0.00 0.00 3.41
937 948 3.365969 GGATTTAGGGTTTTGCGTGAGTG 60.366 47.826 0.00 0.00 0.00 3.51
938 949 1.600023 TTAGGGTTTTGCGTGAGTGG 58.400 50.000 0.00 0.00 0.00 4.00
939 950 0.470766 TAGGGTTTTGCGTGAGTGGT 59.529 50.000 0.00 0.00 0.00 4.16
940 951 0.395173 AGGGTTTTGCGTGAGTGGTT 60.395 50.000 0.00 0.00 0.00 3.67
941 952 0.248866 GGGTTTTGCGTGAGTGGTTG 60.249 55.000 0.00 0.00 0.00 3.77
942 953 0.736053 GGTTTTGCGTGAGTGGTTGA 59.264 50.000 0.00 0.00 0.00 3.18
943 954 1.533129 GGTTTTGCGTGAGTGGTTGAC 60.533 52.381 0.00 0.00 0.00 3.18
944 955 1.131504 GTTTTGCGTGAGTGGTTGACA 59.868 47.619 0.00 0.00 0.00 3.58
945 956 1.674359 TTTGCGTGAGTGGTTGACAT 58.326 45.000 0.00 0.00 0.00 3.06
946 957 1.225855 TTGCGTGAGTGGTTGACATC 58.774 50.000 0.00 0.00 0.00 3.06
947 958 0.602638 TGCGTGAGTGGTTGACATCC 60.603 55.000 0.00 0.00 0.00 3.51
948 959 0.602638 GCGTGAGTGGTTGACATCCA 60.603 55.000 0.82 0.82 0.00 3.41
949 960 1.432514 CGTGAGTGGTTGACATCCAG 58.567 55.000 5.44 0.00 35.49 3.86
950 961 1.160137 GTGAGTGGTTGACATCCAGC 58.840 55.000 5.44 2.54 35.49 4.85
951 962 0.036732 TGAGTGGTTGACATCCAGCC 59.963 55.000 5.44 2.05 45.32 4.85
952 963 0.326264 GAGTGGTTGACATCCAGCCT 59.674 55.000 5.44 0.81 45.33 4.58
953 964 0.326264 AGTGGTTGACATCCAGCCTC 59.674 55.000 5.44 0.00 45.33 4.70
954 965 0.036732 GTGGTTGACATCCAGCCTCA 59.963 55.000 5.44 0.00 45.33 3.86
955 966 0.036732 TGGTTGACATCCAGCCTCAC 59.963 55.000 0.82 0.00 45.33 3.51
956 967 1.021390 GGTTGACATCCAGCCTCACG 61.021 60.000 0.00 0.00 42.24 4.35
957 968 0.320771 GTTGACATCCAGCCTCACGT 60.321 55.000 0.00 0.00 0.00 4.49
958 969 0.037326 TTGACATCCAGCCTCACGTC 60.037 55.000 0.00 0.00 0.00 4.34
959 970 0.900182 TGACATCCAGCCTCACGTCT 60.900 55.000 0.00 0.00 0.00 4.18
960 971 0.179124 GACATCCAGCCTCACGTCTC 60.179 60.000 0.00 0.00 0.00 3.36
961 972 0.900182 ACATCCAGCCTCACGTCTCA 60.900 55.000 0.00 0.00 0.00 3.27
962 973 0.247460 CATCCAGCCTCACGTCTCAA 59.753 55.000 0.00 0.00 0.00 3.02
963 974 1.134580 CATCCAGCCTCACGTCTCAAT 60.135 52.381 0.00 0.00 0.00 2.57
964 975 1.847328 TCCAGCCTCACGTCTCAATA 58.153 50.000 0.00 0.00 0.00 1.90
965 976 2.388735 TCCAGCCTCACGTCTCAATAT 58.611 47.619 0.00 0.00 0.00 1.28
966 977 3.562182 TCCAGCCTCACGTCTCAATATA 58.438 45.455 0.00 0.00 0.00 0.86
967 978 4.152647 TCCAGCCTCACGTCTCAATATAT 58.847 43.478 0.00 0.00 0.00 0.86
968 979 5.321927 TCCAGCCTCACGTCTCAATATATA 58.678 41.667 0.00 0.00 0.00 0.86
969 980 5.416013 TCCAGCCTCACGTCTCAATATATAG 59.584 44.000 0.00 0.00 0.00 1.31
970 981 5.416013 CCAGCCTCACGTCTCAATATATAGA 59.584 44.000 0.00 0.00 0.00 1.98
971 982 6.096141 CCAGCCTCACGTCTCAATATATAGAT 59.904 42.308 0.00 0.00 0.00 1.98
972 983 6.971756 CAGCCTCACGTCTCAATATATAGATG 59.028 42.308 3.96 3.96 35.32 2.90
973 984 6.887002 AGCCTCACGTCTCAATATATAGATGA 59.113 38.462 10.46 0.00 33.74 2.92
974 985 7.559533 AGCCTCACGTCTCAATATATAGATGAT 59.440 37.037 10.46 0.00 33.74 2.45
975 986 7.860373 GCCTCACGTCTCAATATATAGATGATC 59.140 40.741 10.46 0.00 33.74 2.92
976 987 8.897752 CCTCACGTCTCAATATATAGATGATCA 58.102 37.037 10.46 0.00 33.74 2.92
977 988 9.715123 CTCACGTCTCAATATATAGATGATCAC 57.285 37.037 0.00 0.00 33.74 3.06
978 989 9.231297 TCACGTCTCAATATATAGATGATCACA 57.769 33.333 0.00 0.00 33.74 3.58
979 990 9.846248 CACGTCTCAATATATAGATGATCACAA 57.154 33.333 0.00 0.00 33.74 3.33
1030 1041 8.639761 ACATGTATAAGGACAATGTACTAGACC 58.360 37.037 0.00 0.00 31.83 3.85
1031 1042 7.592885 TGTATAAGGACAATGTACTAGACCC 57.407 40.000 0.00 0.00 0.00 4.46
1032 1043 7.359849 TGTATAAGGACAATGTACTAGACCCT 58.640 38.462 0.00 0.00 0.00 4.34
1033 1044 8.505246 TGTATAAGGACAATGTACTAGACCCTA 58.495 37.037 0.00 0.00 0.00 3.53
1034 1045 7.836479 ATAAGGACAATGTACTAGACCCTAC 57.164 40.000 0.00 0.00 0.00 3.18
1035 1046 5.469210 AGGACAATGTACTAGACCCTACT 57.531 43.478 0.00 0.00 0.00 2.57
1036 1047 5.840081 AGGACAATGTACTAGACCCTACTT 58.160 41.667 0.00 0.00 0.00 2.24
1037 1048 6.262207 AGGACAATGTACTAGACCCTACTTT 58.738 40.000 0.00 0.00 0.00 2.66
1038 1049 7.416731 AGGACAATGTACTAGACCCTACTTTA 58.583 38.462 0.00 0.00 0.00 1.85
1039 1050 8.066247 AGGACAATGTACTAGACCCTACTTTAT 58.934 37.037 0.00 0.00 0.00 1.40
1040 1051 9.359653 GGACAATGTACTAGACCCTACTTTATA 57.640 37.037 0.00 0.00 0.00 0.98
1079 1090 2.487086 GGGGCAAACTGGCAAAGAAAAT 60.487 45.455 2.45 0.00 45.76 1.82
1084 1095 3.934457 AACTGGCAAAGAAAATACGGG 57.066 42.857 0.00 0.00 0.00 5.28
1184 1216 4.681978 GGCTCCGTGTGGCTTCGT 62.682 66.667 0.00 0.00 34.14 3.85
1368 1451 3.958147 CTTCGATGCTGCCGGGTGT 62.958 63.158 2.18 0.00 0.00 4.16
1745 2307 1.605058 AACTACGAGGAGCCATGCGT 61.605 55.000 0.00 0.00 40.42 5.24
1812 2374 3.104512 TCTGGACCAGAACATCGGTATT 58.895 45.455 22.30 0.00 37.57 1.89
1874 2440 6.647895 ACCATATATTTATTCGTGTTCCCGTC 59.352 38.462 0.00 0.00 0.00 4.79
1960 2533 9.465199 TGTAGTGATGTATAGTAAGGTACAACA 57.535 33.333 0.00 0.00 34.77 3.33
1964 2537 9.811995 GTGATGTATAGTAAGGTACAACAATCA 57.188 33.333 0.00 0.00 36.03 2.57
1966 2539 9.477484 GATGTATAGTAAGGTACAACAATCAGG 57.523 37.037 0.00 0.00 34.77 3.86
1967 2540 8.598202 TGTATAGTAAGGTACAACAATCAGGA 57.402 34.615 0.00 0.00 0.00 3.86
1968 2541 8.692710 TGTATAGTAAGGTACAACAATCAGGAG 58.307 37.037 0.00 0.00 0.00 3.69
1969 2542 7.735326 ATAGTAAGGTACAACAATCAGGAGT 57.265 36.000 0.00 0.00 0.00 3.85
1970 2543 6.435292 AGTAAGGTACAACAATCAGGAGTT 57.565 37.500 0.00 0.00 0.00 3.01
1972 2545 3.412386 AGGTACAACAATCAGGAGTTGC 58.588 45.455 5.31 0.00 46.79 4.17
1973 2546 3.146066 GGTACAACAATCAGGAGTTGCA 58.854 45.455 5.31 0.00 46.79 4.08
1974 2547 3.758554 GGTACAACAATCAGGAGTTGCAT 59.241 43.478 5.31 0.00 46.79 3.96
1975 2548 4.142600 GGTACAACAATCAGGAGTTGCATC 60.143 45.833 5.31 0.00 46.79 3.91
1976 2549 3.489355 ACAACAATCAGGAGTTGCATCA 58.511 40.909 5.31 0.00 46.79 3.07
1977 2550 3.890756 ACAACAATCAGGAGTTGCATCAA 59.109 39.130 5.31 0.00 46.79 2.57
1978 2551 4.022589 ACAACAATCAGGAGTTGCATCAAG 60.023 41.667 5.31 0.00 46.79 3.02
1979 2552 2.490903 ACAATCAGGAGTTGCATCAAGC 59.509 45.455 0.00 0.00 45.96 4.01
1997 2570 9.237846 GCATCAAGCATAAATAAAAGTTACTCC 57.762 33.333 0.00 0.00 44.79 3.85
1998 2571 9.736023 CATCAAGCATAAATAAAAGTTACTCCC 57.264 33.333 0.00 0.00 0.00 4.30
1999 2572 9.700831 ATCAAGCATAAATAAAAGTTACTCCCT 57.299 29.630 0.00 0.00 0.00 4.20
2000 2573 9.174166 TCAAGCATAAATAAAAGTTACTCCCTC 57.826 33.333 0.00 0.00 0.00 4.30
2001 2574 8.406297 CAAGCATAAATAAAAGTTACTCCCTCC 58.594 37.037 0.00 0.00 0.00 4.30
2002 2575 7.873195 AGCATAAATAAAAGTTACTCCCTCCT 58.127 34.615 0.00 0.00 0.00 3.69
2003 2576 8.336987 AGCATAAATAAAAGTTACTCCCTCCTT 58.663 33.333 0.00 0.00 0.00 3.36
2004 2577 8.622157 GCATAAATAAAAGTTACTCCCTCCTTC 58.378 37.037 0.00 0.00 0.00 3.46
2005 2578 9.907229 CATAAATAAAAGTTACTCCCTCCTTCT 57.093 33.333 0.00 0.00 0.00 2.85
2007 2580 7.569599 AATAAAAGTTACTCCCTCCTTCTCA 57.430 36.000 0.00 0.00 0.00 3.27
2008 2581 7.757242 ATAAAAGTTACTCCCTCCTTCTCAT 57.243 36.000 0.00 0.00 0.00 2.90
2009 2582 8.855804 ATAAAAGTTACTCCCTCCTTCTCATA 57.144 34.615 0.00 0.00 0.00 2.15
2010 2583 7.569599 AAAAGTTACTCCCTCCTTCTCATAA 57.430 36.000 0.00 0.00 0.00 1.90
2011 2584 7.757242 AAAGTTACTCCCTCCTTCTCATAAT 57.243 36.000 0.00 0.00 0.00 1.28
2012 2585 6.739331 AGTTACTCCCTCCTTCTCATAATG 57.261 41.667 0.00 0.00 0.00 1.90
2013 2586 6.206042 AGTTACTCCCTCCTTCTCATAATGT 58.794 40.000 0.00 0.00 0.00 2.71
2014 2587 7.363031 AGTTACTCCCTCCTTCTCATAATGTA 58.637 38.462 0.00 0.00 0.00 2.29
2015 2588 7.844779 AGTTACTCCCTCCTTCTCATAATGTAA 59.155 37.037 0.00 0.00 0.00 2.41
2016 2589 8.483758 GTTACTCCCTCCTTCTCATAATGTAAA 58.516 37.037 0.00 0.00 0.00 2.01
2017 2590 7.510675 ACTCCCTCCTTCTCATAATGTAAAA 57.489 36.000 0.00 0.00 0.00 1.52
2018 2591 7.339482 ACTCCCTCCTTCTCATAATGTAAAAC 58.661 38.462 0.00 0.00 0.00 2.43
2019 2592 6.346096 TCCCTCCTTCTCATAATGTAAAACG 58.654 40.000 0.00 0.00 0.00 3.60
2020 2593 6.070424 TCCCTCCTTCTCATAATGTAAAACGT 60.070 38.462 0.00 0.00 0.00 3.99
2021 2594 6.598064 CCCTCCTTCTCATAATGTAAAACGTT 59.402 38.462 0.00 0.00 0.00 3.99
2022 2595 7.120726 CCCTCCTTCTCATAATGTAAAACGTTT 59.879 37.037 7.96 7.96 0.00 3.60
2023 2596 8.512138 CCTCCTTCTCATAATGTAAAACGTTTT 58.488 33.333 27.65 27.65 0.00 2.43
2024 2597 9.893305 CTCCTTCTCATAATGTAAAACGTTTTT 57.107 29.630 29.42 15.16 0.00 1.94
2064 2637 8.827177 AAAAACATCTTACGTTATGAGACAGA 57.173 30.769 10.95 0.00 0.00 3.41
2065 2638 8.467402 AAAACATCTTACGTTATGAGACAGAG 57.533 34.615 10.95 0.00 0.00 3.35
2066 2639 6.761099 ACATCTTACGTTATGAGACAGAGT 57.239 37.500 10.95 0.00 0.00 3.24
2067 2640 6.556212 ACATCTTACGTTATGAGACAGAGTG 58.444 40.000 10.95 1.56 0.00 3.51
2068 2641 5.562506 TCTTACGTTATGAGACAGAGTGG 57.437 43.478 0.00 0.00 0.00 4.00
2069 2642 5.008331 TCTTACGTTATGAGACAGAGTGGT 58.992 41.667 0.00 0.00 0.00 4.16
2070 2643 6.175471 TCTTACGTTATGAGACAGAGTGGTA 58.825 40.000 0.00 0.00 0.00 3.25
2071 2644 4.698583 ACGTTATGAGACAGAGTGGTAC 57.301 45.455 0.00 0.00 0.00 3.34
2072 2645 3.126514 ACGTTATGAGACAGAGTGGTACG 59.873 47.826 0.00 0.00 0.00 3.67
2073 2646 3.126514 CGTTATGAGACAGAGTGGTACGT 59.873 47.826 0.00 0.00 0.00 3.57
2074 2647 4.330894 CGTTATGAGACAGAGTGGTACGTA 59.669 45.833 0.00 0.00 0.00 3.57
2075 2648 5.163824 CGTTATGAGACAGAGTGGTACGTAA 60.164 44.000 0.00 0.00 0.00 3.18
2076 2649 6.457934 CGTTATGAGACAGAGTGGTACGTAAT 60.458 42.308 0.00 0.00 0.00 1.89
2077 2650 7.254556 CGTTATGAGACAGAGTGGTACGTAATA 60.255 40.741 0.00 0.00 0.00 0.98
2078 2651 8.400947 GTTATGAGACAGAGTGGTACGTAATAA 58.599 37.037 0.00 0.00 0.00 1.40
2079 2652 6.822667 TGAGACAGAGTGGTACGTAATAAA 57.177 37.500 0.00 0.00 0.00 1.40
2080 2653 6.849502 TGAGACAGAGTGGTACGTAATAAAG 58.150 40.000 0.00 0.00 0.00 1.85
2081 2654 6.432162 TGAGACAGAGTGGTACGTAATAAAGT 59.568 38.462 0.00 0.00 0.00 2.66
2082 2655 7.607607 TGAGACAGAGTGGTACGTAATAAAGTA 59.392 37.037 0.00 0.00 0.00 2.24
2083 2656 8.517062 AGACAGAGTGGTACGTAATAAAGTAT 57.483 34.615 0.00 0.00 0.00 2.12
2084 2657 8.964772 AGACAGAGTGGTACGTAATAAAGTATT 58.035 33.333 0.00 0.00 0.00 1.89
2085 2658 9.578439 GACAGAGTGGTACGTAATAAAGTATTT 57.422 33.333 0.00 0.00 43.42 1.40
2103 2676 8.658499 AAGTATTTACTATACCTTGGCGAAAG 57.342 34.615 0.00 0.00 34.99 2.62
2104 2677 8.015185 AGTATTTACTATACCTTGGCGAAAGA 57.985 34.615 0.00 0.00 34.61 2.52
2105 2678 8.480501 AGTATTTACTATACCTTGGCGAAAGAA 58.519 33.333 0.00 0.00 34.61 2.52
2106 2679 9.269453 GTATTTACTATACCTTGGCGAAAGAAT 57.731 33.333 0.00 0.00 38.24 2.40
2107 2680 7.548196 TTTACTATACCTTGGCGAAAGAATG 57.452 36.000 0.00 0.00 38.24 2.67
2108 2681 5.099042 ACTATACCTTGGCGAAAGAATGT 57.901 39.130 0.00 0.00 38.24 2.71
2109 2682 5.497474 ACTATACCTTGGCGAAAGAATGTT 58.503 37.500 0.00 0.00 38.24 2.71
2110 2683 4.965119 ATACCTTGGCGAAAGAATGTTC 57.035 40.909 0.00 0.00 38.24 3.18
2111 2684 2.582052 ACCTTGGCGAAAGAATGTTCA 58.418 42.857 0.00 0.00 38.24 3.18
2112 2685 2.554032 ACCTTGGCGAAAGAATGTTCAG 59.446 45.455 0.00 0.00 38.24 3.02
2113 2686 2.589014 CTTGGCGAAAGAATGTTCAGC 58.411 47.619 0.00 0.00 38.24 4.26
2114 2687 0.881118 TGGCGAAAGAATGTTCAGCC 59.119 50.000 11.35 11.35 42.46 4.85
2115 2688 0.881118 GGCGAAAGAATGTTCAGCCA 59.119 50.000 12.62 0.00 42.08 4.75
2116 2689 1.269448 GGCGAAAGAATGTTCAGCCAA 59.731 47.619 12.62 0.00 42.08 4.52
2117 2690 2.319472 GCGAAAGAATGTTCAGCCAAC 58.681 47.619 0.00 0.00 35.28 3.77
2118 2691 2.922335 GCGAAAGAATGTTCAGCCAACC 60.922 50.000 0.00 0.00 33.51 3.77
2119 2692 2.554032 CGAAAGAATGTTCAGCCAACCT 59.446 45.455 0.00 0.00 33.51 3.50
2120 2693 3.365364 CGAAAGAATGTTCAGCCAACCTC 60.365 47.826 0.00 0.00 33.51 3.85
2121 2694 2.957402 AGAATGTTCAGCCAACCTCA 57.043 45.000 0.00 0.00 33.51 3.86
2122 2695 3.228188 AGAATGTTCAGCCAACCTCAA 57.772 42.857 0.00 0.00 33.51 3.02
2123 2696 3.771216 AGAATGTTCAGCCAACCTCAAT 58.229 40.909 0.00 0.00 33.51 2.57
2124 2697 4.154942 AGAATGTTCAGCCAACCTCAATT 58.845 39.130 0.00 0.00 33.51 2.32
2125 2698 3.947910 ATGTTCAGCCAACCTCAATTG 57.052 42.857 0.00 0.00 33.51 2.32
2126 2699 1.340889 TGTTCAGCCAACCTCAATTGC 59.659 47.619 0.00 0.00 33.51 3.56
2127 2700 0.968405 TTCAGCCAACCTCAATTGCC 59.032 50.000 0.00 0.00 0.00 4.52
2128 2701 0.178967 TCAGCCAACCTCAATTGCCA 60.179 50.000 0.00 0.00 0.00 4.92
2129 2702 0.245539 CAGCCAACCTCAATTGCCAG 59.754 55.000 0.00 0.00 0.00 4.85
2130 2703 1.079612 GCCAACCTCAATTGCCAGC 60.080 57.895 0.00 0.00 0.00 4.85
2131 2704 1.818959 GCCAACCTCAATTGCCAGCA 61.819 55.000 0.00 0.00 0.00 4.41
2132 2705 0.680618 CCAACCTCAATTGCCAGCAA 59.319 50.000 7.64 7.64 40.47 3.91
2145 2718 5.835113 TTGCCAGCAATTTCCTTCTATAC 57.165 39.130 0.00 0.00 0.00 1.47
2146 2719 4.854173 TGCCAGCAATTTCCTTCTATACA 58.146 39.130 0.00 0.00 0.00 2.29
2147 2720 5.260424 TGCCAGCAATTTCCTTCTATACAA 58.740 37.500 0.00 0.00 0.00 2.41
2148 2721 5.893255 TGCCAGCAATTTCCTTCTATACAAT 59.107 36.000 0.00 0.00 0.00 2.71
2149 2722 7.059788 TGCCAGCAATTTCCTTCTATACAATA 58.940 34.615 0.00 0.00 0.00 1.90
2150 2723 7.559533 TGCCAGCAATTTCCTTCTATACAATAA 59.440 33.333 0.00 0.00 0.00 1.40
2151 2724 8.413229 GCCAGCAATTTCCTTCTATACAATAAA 58.587 33.333 0.00 0.00 0.00 1.40
2168 2741 9.713684 ATACAATAAAAATCCTCTCAATTGGGA 57.286 29.630 8.00 8.00 0.00 4.37
2169 2742 8.071177 ACAATAAAAATCCTCTCAATTGGGAG 57.929 34.615 25.89 25.89 36.21 4.30
2171 2744 4.682021 AAAATCCTCTCAATTGGGAGGT 57.318 40.909 40.68 29.38 46.56 3.85
2172 2745 5.796502 AAAATCCTCTCAATTGGGAGGTA 57.203 39.130 40.68 30.73 46.56 3.08
2173 2746 5.379706 AAATCCTCTCAATTGGGAGGTAG 57.620 43.478 40.68 23.82 46.56 3.18
2174 2747 2.119495 TCCTCTCAATTGGGAGGTAGC 58.881 52.381 40.68 0.00 46.56 3.58
2175 2748 1.839994 CCTCTCAATTGGGAGGTAGCA 59.160 52.381 36.92 3.41 42.86 3.49
2176 2749 2.441001 CCTCTCAATTGGGAGGTAGCAT 59.559 50.000 36.92 0.00 42.86 3.79
2183 2756 0.042581 TGGGAGGTAGCATCCAGTGA 59.957 55.000 11.05 0.00 38.70 3.41
2200 2773 1.982938 GACGGAGCTACAGGGTGGT 60.983 63.158 0.00 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
199 200 6.150140 GTGTTCTTGATCCTATCTTGCAAGTT 59.850 38.462 25.19 19.51 37.71 2.66
335 336 2.509964 GGGTTTGATCCCTAGTGTCCAT 59.490 50.000 0.00 0.00 43.85 3.41
388 389 0.035439 GACGGTGATGGGTTGGATGT 60.035 55.000 0.00 0.00 0.00 3.06
415 416 3.547413 CGCGTGAGTAATTCCATCGTAGA 60.547 47.826 0.00 0.00 45.75 2.59
505 506 2.602267 TCCGTTCAGGGCTCCGAA 60.602 61.111 0.00 0.00 41.52 4.30
646 651 2.935481 CCCCCTGTTGCCTCTCCA 60.935 66.667 0.00 0.00 0.00 3.86
736 747 4.322057 AATACCTGCCAAAGATGAAGGT 57.678 40.909 0.00 0.00 42.56 3.50
817 828 5.260424 ACCATGGTGTTATTTATGTGCAGA 58.740 37.500 18.99 0.00 0.00 4.26
883 894 1.146263 GGTATCAGCCAGGGTTCGG 59.854 63.158 0.00 0.00 0.00 4.30
884 895 1.904771 TGGTATCAGCCAGGGTTCG 59.095 57.895 0.00 0.00 33.97 3.95
891 902 2.107378 TGTTTCAACCTGGTATCAGCCA 59.893 45.455 0.00 0.00 39.61 4.75
892 903 2.488153 GTGTTTCAACCTGGTATCAGCC 59.512 50.000 0.00 0.00 39.61 4.85
893 904 3.146066 TGTGTTTCAACCTGGTATCAGC 58.854 45.455 0.00 0.00 39.61 4.26
894 905 3.753272 CCTGTGTTTCAACCTGGTATCAG 59.247 47.826 0.00 0.00 40.59 2.90
895 906 3.392947 TCCTGTGTTTCAACCTGGTATCA 59.607 43.478 0.00 0.00 0.00 2.15
896 907 4.015872 TCCTGTGTTTCAACCTGGTATC 57.984 45.455 0.00 0.00 0.00 2.24
897 908 4.657814 ATCCTGTGTTTCAACCTGGTAT 57.342 40.909 0.00 0.00 0.00 2.73
898 909 4.447138 AATCCTGTGTTTCAACCTGGTA 57.553 40.909 0.00 0.00 0.00 3.25
899 910 3.312736 AATCCTGTGTTTCAACCTGGT 57.687 42.857 0.00 0.00 0.00 4.00
900 911 4.218417 CCTAAATCCTGTGTTTCAACCTGG 59.782 45.833 0.00 0.00 0.00 4.45
901 912 4.218417 CCCTAAATCCTGTGTTTCAACCTG 59.782 45.833 0.00 0.00 0.00 4.00
902 913 4.141018 ACCCTAAATCCTGTGTTTCAACCT 60.141 41.667 0.00 0.00 0.00 3.50
903 914 4.149598 ACCCTAAATCCTGTGTTTCAACC 58.850 43.478 0.00 0.00 0.00 3.77
904 915 5.784578 AACCCTAAATCCTGTGTTTCAAC 57.215 39.130 0.00 0.00 0.00 3.18
905 916 6.578023 CAAAACCCTAAATCCTGTGTTTCAA 58.422 36.000 0.00 0.00 0.00 2.69
906 917 5.452636 GCAAAACCCTAAATCCTGTGTTTCA 60.453 40.000 0.00 0.00 0.00 2.69
907 918 4.988540 GCAAAACCCTAAATCCTGTGTTTC 59.011 41.667 0.00 0.00 0.00 2.78
908 919 4.500716 CGCAAAACCCTAAATCCTGTGTTT 60.501 41.667 0.00 0.00 0.00 2.83
909 920 3.005367 CGCAAAACCCTAAATCCTGTGTT 59.995 43.478 0.00 0.00 0.00 3.32
910 921 2.556622 CGCAAAACCCTAAATCCTGTGT 59.443 45.455 0.00 0.00 0.00 3.72
911 922 2.556622 ACGCAAAACCCTAAATCCTGTG 59.443 45.455 0.00 0.00 0.00 3.66
912 923 2.556622 CACGCAAAACCCTAAATCCTGT 59.443 45.455 0.00 0.00 0.00 4.00
913 924 2.817258 TCACGCAAAACCCTAAATCCTG 59.183 45.455 0.00 0.00 0.00 3.86
914 925 3.081804 CTCACGCAAAACCCTAAATCCT 58.918 45.455 0.00 0.00 0.00 3.24
915 926 2.817844 ACTCACGCAAAACCCTAAATCC 59.182 45.455 0.00 0.00 0.00 3.01
916 927 3.365969 CCACTCACGCAAAACCCTAAATC 60.366 47.826 0.00 0.00 0.00 2.17
917 928 2.556622 CCACTCACGCAAAACCCTAAAT 59.443 45.455 0.00 0.00 0.00 1.40
918 929 1.950909 CCACTCACGCAAAACCCTAAA 59.049 47.619 0.00 0.00 0.00 1.85
919 930 1.134037 ACCACTCACGCAAAACCCTAA 60.134 47.619 0.00 0.00 0.00 2.69
920 931 0.470766 ACCACTCACGCAAAACCCTA 59.529 50.000 0.00 0.00 0.00 3.53
921 932 0.395173 AACCACTCACGCAAAACCCT 60.395 50.000 0.00 0.00 0.00 4.34
922 933 0.248866 CAACCACTCACGCAAAACCC 60.249 55.000 0.00 0.00 0.00 4.11
923 934 0.736053 TCAACCACTCACGCAAAACC 59.264 50.000 0.00 0.00 0.00 3.27
924 935 1.131504 TGTCAACCACTCACGCAAAAC 59.868 47.619 0.00 0.00 0.00 2.43
925 936 1.454201 TGTCAACCACTCACGCAAAA 58.546 45.000 0.00 0.00 0.00 2.44
926 937 1.601903 GATGTCAACCACTCACGCAAA 59.398 47.619 0.00 0.00 0.00 3.68
927 938 1.225855 GATGTCAACCACTCACGCAA 58.774 50.000 0.00 0.00 0.00 4.85
928 939 0.602638 GGATGTCAACCACTCACGCA 60.603 55.000 0.00 0.00 0.00 5.24
929 940 0.602638 TGGATGTCAACCACTCACGC 60.603 55.000 0.00 0.00 32.03 5.34
930 941 1.432514 CTGGATGTCAACCACTCACG 58.567 55.000 0.00 0.00 33.57 4.35
931 942 1.160137 GCTGGATGTCAACCACTCAC 58.840 55.000 0.00 0.00 33.57 3.51
932 943 0.036732 GGCTGGATGTCAACCACTCA 59.963 55.000 0.00 0.00 32.02 3.41
933 944 0.326264 AGGCTGGATGTCAACCACTC 59.674 55.000 0.00 0.00 34.12 3.51
934 945 0.326264 GAGGCTGGATGTCAACCACT 59.674 55.000 0.00 0.00 34.12 4.00
935 946 0.036732 TGAGGCTGGATGTCAACCAC 59.963 55.000 0.00 0.00 34.12 4.16
936 947 0.036732 GTGAGGCTGGATGTCAACCA 59.963 55.000 1.38 1.38 34.12 3.67
937 948 1.021390 CGTGAGGCTGGATGTCAACC 61.021 60.000 0.00 0.00 31.85 3.77
938 949 0.320771 ACGTGAGGCTGGATGTCAAC 60.321 55.000 0.00 0.00 0.00 3.18
939 950 0.037326 GACGTGAGGCTGGATGTCAA 60.037 55.000 0.00 0.00 34.96 3.18
940 951 1.591703 GACGTGAGGCTGGATGTCA 59.408 57.895 0.00 0.00 34.96 3.58
941 952 4.504132 GACGTGAGGCTGGATGTC 57.496 61.111 0.00 0.00 34.96 3.06
949 960 7.089770 TCATCTATATATTGAGACGTGAGGC 57.910 40.000 0.00 0.00 42.06 4.70
950 961 8.897752 TGATCATCTATATATTGAGACGTGAGG 58.102 37.037 0.00 0.00 0.00 3.86
951 962 9.715123 GTGATCATCTATATATTGAGACGTGAG 57.285 37.037 0.00 0.00 0.00 3.51
952 963 9.231297 TGTGATCATCTATATATTGAGACGTGA 57.769 33.333 0.00 2.70 0.00 4.35
953 964 9.846248 TTGTGATCATCTATATATTGAGACGTG 57.154 33.333 0.00 0.00 0.00 4.49
1004 1015 8.639761 GGTCTAGTACATTGTCCTTATACATGT 58.360 37.037 2.69 2.69 0.00 3.21
1005 1016 8.088981 GGGTCTAGTACATTGTCCTTATACATG 58.911 40.741 0.00 0.00 0.00 3.21
1006 1017 8.011290 AGGGTCTAGTACATTGTCCTTATACAT 58.989 37.037 0.00 0.00 0.00 2.29
1007 1018 7.359849 AGGGTCTAGTACATTGTCCTTATACA 58.640 38.462 0.00 0.00 0.00 2.29
1008 1019 7.836479 AGGGTCTAGTACATTGTCCTTATAC 57.164 40.000 0.00 0.00 0.00 1.47
1009 1020 8.730948 AGTAGGGTCTAGTACATTGTCCTTATA 58.269 37.037 0.00 0.00 0.00 0.98
1010 1021 7.593653 AGTAGGGTCTAGTACATTGTCCTTAT 58.406 38.462 0.00 0.00 0.00 1.73
1011 1022 6.978261 AGTAGGGTCTAGTACATTGTCCTTA 58.022 40.000 0.00 0.00 0.00 2.69
1012 1023 5.840081 AGTAGGGTCTAGTACATTGTCCTT 58.160 41.667 0.00 0.00 0.00 3.36
1013 1024 5.469210 AGTAGGGTCTAGTACATTGTCCT 57.531 43.478 0.00 0.00 0.00 3.85
1014 1025 6.541934 AAAGTAGGGTCTAGTACATTGTCC 57.458 41.667 0.00 0.00 0.00 4.02
1037 1048 9.610104 TGCCCCTTGAAAATAGTAGAGTATATA 57.390 33.333 0.00 0.00 0.00 0.86
1038 1049 8.506196 TGCCCCTTGAAAATAGTAGAGTATAT 57.494 34.615 0.00 0.00 0.00 0.86
1039 1050 7.924358 TGCCCCTTGAAAATAGTAGAGTATA 57.076 36.000 0.00 0.00 0.00 1.47
1040 1051 6.824958 TGCCCCTTGAAAATAGTAGAGTAT 57.175 37.500 0.00 0.00 0.00 2.12
1041 1052 6.630203 TTGCCCCTTGAAAATAGTAGAGTA 57.370 37.500 0.00 0.00 0.00 2.59
1042 1053 5.514500 TTGCCCCTTGAAAATAGTAGAGT 57.486 39.130 0.00 0.00 0.00 3.24
1043 1054 5.946377 AGTTTGCCCCTTGAAAATAGTAGAG 59.054 40.000 0.00 0.00 0.00 2.43
1044 1055 5.710099 CAGTTTGCCCCTTGAAAATAGTAGA 59.290 40.000 0.00 0.00 0.00 2.59
1045 1056 5.105756 CCAGTTTGCCCCTTGAAAATAGTAG 60.106 44.000 0.00 0.00 0.00 2.57
1079 1090 1.761449 TGATACTTACACCGCCCGTA 58.239 50.000 0.00 0.00 0.00 4.02
1084 1095 5.734855 ATTCACATTGATACTTACACCGC 57.265 39.130 0.00 0.00 0.00 5.68
1184 1216 3.459232 GCATAGGCATATATGAGCGGA 57.541 47.619 17.10 0.00 40.72 5.54
1519 1602 1.078848 CTCCGTCCTTGCCCTTCTG 60.079 63.158 0.00 0.00 0.00 3.02
1541 1624 2.632544 TTGTCGCACTCGGACGGAT 61.633 57.895 0.00 0.00 36.13 4.18
1639 1722 1.217882 CCCTTCGCGGTAATCATGAC 58.782 55.000 6.13 0.00 0.00 3.06
1643 1726 1.219664 CCACCCTTCGCGGTAATCA 59.780 57.895 6.13 0.00 33.67 2.57
1716 2278 1.080772 CTCGTAGTTGTGCTCGGCA 60.081 57.895 0.00 0.00 35.60 5.69
1934 2507 9.465199 TGTTGTACCTTACTATACATCACTACA 57.535 33.333 0.00 0.00 31.55 2.74
1938 2511 9.811995 TGATTGTTGTACCTTACTATACATCAC 57.188 33.333 0.00 0.00 33.08 3.06
1940 2513 9.477484 CCTGATTGTTGTACCTTACTATACATC 57.523 37.037 0.00 0.00 31.55 3.06
1941 2514 9.209048 TCCTGATTGTTGTACCTTACTATACAT 57.791 33.333 0.00 0.00 31.55 2.29
1942 2515 8.598202 TCCTGATTGTTGTACCTTACTATACA 57.402 34.615 0.00 0.00 0.00 2.29
1943 2516 8.693625 ACTCCTGATTGTTGTACCTTACTATAC 58.306 37.037 0.00 0.00 0.00 1.47
1944 2517 8.834004 ACTCCTGATTGTTGTACCTTACTATA 57.166 34.615 0.00 0.00 0.00 1.31
1945 2518 7.735326 ACTCCTGATTGTTGTACCTTACTAT 57.265 36.000 0.00 0.00 0.00 2.12
1946 2519 7.383687 CAACTCCTGATTGTTGTACCTTACTA 58.616 38.462 0.00 0.00 38.81 1.82
1947 2520 6.231211 CAACTCCTGATTGTTGTACCTTACT 58.769 40.000 0.00 0.00 38.81 2.24
1948 2521 5.106673 GCAACTCCTGATTGTTGTACCTTAC 60.107 44.000 0.00 0.00 43.66 2.34
1949 2522 5.001232 GCAACTCCTGATTGTTGTACCTTA 58.999 41.667 0.00 0.00 43.66 2.69
1950 2523 3.821033 GCAACTCCTGATTGTTGTACCTT 59.179 43.478 0.00 0.00 43.66 3.50
1951 2524 3.181445 TGCAACTCCTGATTGTTGTACCT 60.181 43.478 0.00 0.00 43.66 3.08
1952 2525 3.146066 TGCAACTCCTGATTGTTGTACC 58.854 45.455 0.00 0.00 43.66 3.34
1953 2526 4.455533 TGATGCAACTCCTGATTGTTGTAC 59.544 41.667 0.00 0.00 43.66 2.90
1954 2527 4.650734 TGATGCAACTCCTGATTGTTGTA 58.349 39.130 0.00 0.00 43.66 2.41
1955 2528 3.489355 TGATGCAACTCCTGATTGTTGT 58.511 40.909 0.00 0.00 43.66 3.32
1956 2529 4.482386 CTTGATGCAACTCCTGATTGTTG 58.518 43.478 0.00 0.00 44.33 3.33
1957 2530 3.057033 GCTTGATGCAACTCCTGATTGTT 60.057 43.478 0.00 0.00 42.31 2.83
1958 2531 2.490903 GCTTGATGCAACTCCTGATTGT 59.509 45.455 0.00 0.00 42.31 2.71
1959 2532 3.146618 GCTTGATGCAACTCCTGATTG 57.853 47.619 0.00 0.00 42.31 2.67
1971 2544 9.237846 GGAGTAACTTTTATTTATGCTTGATGC 57.762 33.333 0.00 0.00 43.25 3.91
1972 2545 9.736023 GGGAGTAACTTTTATTTATGCTTGATG 57.264 33.333 0.00 0.00 0.00 3.07
1973 2546 9.700831 AGGGAGTAACTTTTATTTATGCTTGAT 57.299 29.630 0.00 0.00 0.00 2.57
1974 2547 9.174166 GAGGGAGTAACTTTTATTTATGCTTGA 57.826 33.333 0.00 0.00 0.00 3.02
1975 2548 8.406297 GGAGGGAGTAACTTTTATTTATGCTTG 58.594 37.037 0.00 0.00 0.00 4.01
1976 2549 8.336987 AGGAGGGAGTAACTTTTATTTATGCTT 58.663 33.333 0.00 0.00 0.00 3.91
1977 2550 7.873195 AGGAGGGAGTAACTTTTATTTATGCT 58.127 34.615 0.00 0.00 0.00 3.79
1978 2551 8.521170 AAGGAGGGAGTAACTTTTATTTATGC 57.479 34.615 0.00 0.00 0.00 3.14
1979 2552 9.907229 AGAAGGAGGGAGTAACTTTTATTTATG 57.093 33.333 0.00 0.00 0.00 1.90
1981 2554 9.108111 TGAGAAGGAGGGAGTAACTTTTATTTA 57.892 33.333 0.00 0.00 0.00 1.40
1982 2555 7.985589 TGAGAAGGAGGGAGTAACTTTTATTT 58.014 34.615 0.00 0.00 0.00 1.40
1983 2556 7.569599 TGAGAAGGAGGGAGTAACTTTTATT 57.430 36.000 0.00 0.00 0.00 1.40
1984 2557 7.757242 ATGAGAAGGAGGGAGTAACTTTTAT 57.243 36.000 0.00 0.00 0.00 1.40
1985 2558 8.674925 TTATGAGAAGGAGGGAGTAACTTTTA 57.325 34.615 0.00 0.00 0.00 1.52
1986 2559 7.569599 TTATGAGAAGGAGGGAGTAACTTTT 57.430 36.000 0.00 0.00 0.00 2.27
1987 2560 7.182930 ACATTATGAGAAGGAGGGAGTAACTTT 59.817 37.037 0.00 0.00 0.00 2.66
1988 2561 6.674419 ACATTATGAGAAGGAGGGAGTAACTT 59.326 38.462 0.00 0.00 0.00 2.66
1989 2562 6.206042 ACATTATGAGAAGGAGGGAGTAACT 58.794 40.000 0.00 0.00 0.00 2.24
1990 2563 6.487299 ACATTATGAGAAGGAGGGAGTAAC 57.513 41.667 0.00 0.00 0.00 2.50
1991 2564 8.618240 TTTACATTATGAGAAGGAGGGAGTAA 57.382 34.615 0.00 0.00 0.00 2.24
1992 2565 8.483758 GTTTTACATTATGAGAAGGAGGGAGTA 58.516 37.037 0.00 0.00 0.00 2.59
1993 2566 7.339482 GTTTTACATTATGAGAAGGAGGGAGT 58.661 38.462 0.00 0.00 0.00 3.85
1994 2567 6.480320 CGTTTTACATTATGAGAAGGAGGGAG 59.520 42.308 0.00 0.00 0.00 4.30
1995 2568 6.070424 ACGTTTTACATTATGAGAAGGAGGGA 60.070 38.462 0.00 0.00 0.00 4.20
1996 2569 6.113411 ACGTTTTACATTATGAGAAGGAGGG 58.887 40.000 0.00 0.00 0.00 4.30
1997 2570 7.611213 AACGTTTTACATTATGAGAAGGAGG 57.389 36.000 0.00 0.00 0.00 4.30
1998 2571 9.893305 AAAAACGTTTTACATTATGAGAAGGAG 57.107 29.630 25.44 0.00 0.00 3.69
2039 2612 8.827177 TCTGTCTCATAACGTAAGATGTTTTT 57.173 30.769 0.00 0.00 43.62 1.94
2040 2613 8.088981 ACTCTGTCTCATAACGTAAGATGTTTT 58.911 33.333 0.00 0.00 43.62 2.43
2041 2614 7.542477 CACTCTGTCTCATAACGTAAGATGTTT 59.458 37.037 0.00 0.00 43.62 2.83
2042 2615 7.030165 CACTCTGTCTCATAACGTAAGATGTT 58.970 38.462 0.00 0.00 43.62 2.71
2043 2616 6.404844 CCACTCTGTCTCATAACGTAAGATGT 60.405 42.308 0.00 0.00 43.62 3.06
2044 2617 5.974158 CCACTCTGTCTCATAACGTAAGATG 59.026 44.000 0.00 0.00 43.62 2.90
2045 2618 5.652891 ACCACTCTGTCTCATAACGTAAGAT 59.347 40.000 0.00 0.00 43.62 2.40
2046 2619 5.008331 ACCACTCTGTCTCATAACGTAAGA 58.992 41.667 0.00 0.00 43.62 2.10
2047 2620 9.209970 ACGTACCACTCTGTCTCATAACGTAAG 62.210 44.444 0.00 0.00 37.99 2.34
2048 2621 5.163824 CGTACCACTCTGTCTCATAACGTAA 60.164 44.000 0.00 0.00 0.00 3.18
2049 2622 4.330894 CGTACCACTCTGTCTCATAACGTA 59.669 45.833 0.00 0.00 0.00 3.57
2050 2623 3.126514 CGTACCACTCTGTCTCATAACGT 59.873 47.826 0.00 0.00 0.00 3.99
2051 2624 3.126514 ACGTACCACTCTGTCTCATAACG 59.873 47.826 0.00 0.00 0.00 3.18
2052 2625 4.698583 ACGTACCACTCTGTCTCATAAC 57.301 45.455 0.00 0.00 0.00 1.89
2053 2626 8.510243 TTATTACGTACCACTCTGTCTCATAA 57.490 34.615 0.00 0.00 0.00 1.90
2054 2627 8.510243 TTTATTACGTACCACTCTGTCTCATA 57.490 34.615 0.00 0.00 0.00 2.15
2055 2628 7.122353 ACTTTATTACGTACCACTCTGTCTCAT 59.878 37.037 0.00 0.00 0.00 2.90
2056 2629 6.432162 ACTTTATTACGTACCACTCTGTCTCA 59.568 38.462 0.00 0.00 0.00 3.27
2057 2630 6.850555 ACTTTATTACGTACCACTCTGTCTC 58.149 40.000 0.00 0.00 0.00 3.36
2058 2631 6.830873 ACTTTATTACGTACCACTCTGTCT 57.169 37.500 0.00 0.00 0.00 3.41
2059 2632 9.578439 AAATACTTTATTACGTACCACTCTGTC 57.422 33.333 0.00 0.00 0.00 3.51
2077 2650 9.106070 CTTTCGCCAAGGTATAGTAAATACTTT 57.894 33.333 0.00 0.00 37.73 2.66
2078 2651 8.480501 TCTTTCGCCAAGGTATAGTAAATACTT 58.519 33.333 0.00 0.00 34.05 2.24
2079 2652 8.015185 TCTTTCGCCAAGGTATAGTAAATACT 57.985 34.615 0.00 0.00 35.37 2.12
2080 2653 8.652810 TTCTTTCGCCAAGGTATAGTAAATAC 57.347 34.615 0.00 0.00 32.64 1.89
2081 2654 9.268268 CATTCTTTCGCCAAGGTATAGTAAATA 57.732 33.333 0.00 0.00 32.64 1.40
2082 2655 7.773690 ACATTCTTTCGCCAAGGTATAGTAAAT 59.226 33.333 0.00 0.00 32.64 1.40
2083 2656 7.107542 ACATTCTTTCGCCAAGGTATAGTAAA 58.892 34.615 0.00 0.00 32.64 2.01
2084 2657 6.646267 ACATTCTTTCGCCAAGGTATAGTAA 58.354 36.000 0.00 0.00 32.64 2.24
2085 2658 6.229936 ACATTCTTTCGCCAAGGTATAGTA 57.770 37.500 0.00 0.00 32.64 1.82
2086 2659 5.099042 ACATTCTTTCGCCAAGGTATAGT 57.901 39.130 0.00 0.00 32.64 2.12
2087 2660 5.584649 TGAACATTCTTTCGCCAAGGTATAG 59.415 40.000 0.00 0.00 32.64 1.31
2088 2661 5.492895 TGAACATTCTTTCGCCAAGGTATA 58.507 37.500 0.00 0.00 32.64 1.47
2089 2662 4.331968 TGAACATTCTTTCGCCAAGGTAT 58.668 39.130 0.00 0.00 32.64 2.73
2090 2663 3.745799 TGAACATTCTTTCGCCAAGGTA 58.254 40.909 0.00 0.00 32.64 3.08
2091 2664 2.554032 CTGAACATTCTTTCGCCAAGGT 59.446 45.455 0.00 0.00 32.64 3.50
2092 2665 2.669391 GCTGAACATTCTTTCGCCAAGG 60.669 50.000 0.00 0.00 32.64 3.61
2093 2666 2.589014 GCTGAACATTCTTTCGCCAAG 58.411 47.619 0.00 0.00 0.00 3.61
2094 2667 1.269448 GGCTGAACATTCTTTCGCCAA 59.731 47.619 11.35 0.00 41.17 4.52
2095 2668 0.881118 GGCTGAACATTCTTTCGCCA 59.119 50.000 11.35 0.00 41.17 5.69
2096 2669 0.881118 TGGCTGAACATTCTTTCGCC 59.119 50.000 10.05 10.05 41.53 5.54
2097 2670 2.319472 GTTGGCTGAACATTCTTTCGC 58.681 47.619 0.00 0.00 34.35 4.70
2098 2671 2.554032 AGGTTGGCTGAACATTCTTTCG 59.446 45.455 2.29 0.00 36.12 3.46
2099 2672 3.569701 TGAGGTTGGCTGAACATTCTTTC 59.430 43.478 2.29 0.00 36.12 2.62
2100 2673 3.565307 TGAGGTTGGCTGAACATTCTTT 58.435 40.909 2.29 0.00 36.12 2.52
2101 2674 3.228188 TGAGGTTGGCTGAACATTCTT 57.772 42.857 2.29 0.00 36.12 2.52
2102 2675 2.957402 TGAGGTTGGCTGAACATTCT 57.043 45.000 2.29 0.00 36.12 2.40
2103 2676 4.240096 CAATTGAGGTTGGCTGAACATTC 58.760 43.478 0.00 0.00 36.12 2.67
2104 2677 3.555586 GCAATTGAGGTTGGCTGAACATT 60.556 43.478 10.34 0.00 36.12 2.71
2105 2678 2.028748 GCAATTGAGGTTGGCTGAACAT 60.029 45.455 10.34 0.00 36.12 2.71
2106 2679 1.340889 GCAATTGAGGTTGGCTGAACA 59.659 47.619 10.34 0.00 36.12 3.18
2107 2680 2.070262 GCAATTGAGGTTGGCTGAAC 57.930 50.000 10.34 0.00 0.00 3.18
2113 2686 0.680618 TTGCTGGCAATTGAGGTTGG 59.319 50.000 10.34 0.00 0.00 3.77
2114 2687 2.754946 ATTGCTGGCAATTGAGGTTG 57.245 45.000 10.34 0.00 43.32 3.77
2123 2696 5.260424 TGTATAGAAGGAAATTGCTGGCAA 58.740 37.500 10.48 10.48 40.47 4.52
2124 2697 4.854173 TGTATAGAAGGAAATTGCTGGCA 58.146 39.130 0.00 0.00 0.00 4.92
2125 2698 5.835113 TTGTATAGAAGGAAATTGCTGGC 57.165 39.130 0.00 0.00 0.00 4.85
2142 2715 9.713684 TCCCAATTGAGAGGATTTTTATTGTAT 57.286 29.630 7.12 0.00 0.00 2.29
2143 2716 9.189156 CTCCCAATTGAGAGGATTTTTATTGTA 57.811 33.333 9.03 0.00 34.11 2.41
2144 2717 8.071177 CTCCCAATTGAGAGGATTTTTATTGT 57.929 34.615 9.03 0.00 34.11 2.71
2156 2729 3.495806 GGATGCTACCTCCCAATTGAGAG 60.496 52.174 9.89 9.89 34.11 3.20
2157 2730 2.439507 GGATGCTACCTCCCAATTGAGA 59.560 50.000 7.12 0.00 34.11 3.27
2158 2731 2.173356 TGGATGCTACCTCCCAATTGAG 59.827 50.000 7.12 0.00 31.32 3.02
2159 2732 2.173356 CTGGATGCTACCTCCCAATTGA 59.827 50.000 7.12 0.00 31.32 2.57
2160 2733 2.092212 ACTGGATGCTACCTCCCAATTG 60.092 50.000 0.00 0.00 31.32 2.32
2161 2734 2.092212 CACTGGATGCTACCTCCCAATT 60.092 50.000 0.00 0.00 31.32 2.32
2162 2735 1.492176 CACTGGATGCTACCTCCCAAT 59.508 52.381 0.00 0.00 31.32 3.16
2163 2736 0.911769 CACTGGATGCTACCTCCCAA 59.088 55.000 0.00 0.00 31.32 4.12
2164 2737 0.042581 TCACTGGATGCTACCTCCCA 59.957 55.000 0.00 0.00 31.32 4.37
2165 2738 0.466124 GTCACTGGATGCTACCTCCC 59.534 60.000 0.00 0.00 31.32 4.30
2166 2739 0.103208 CGTCACTGGATGCTACCTCC 59.897 60.000 0.00 0.00 0.00 4.30
2167 2740 0.103208 CCGTCACTGGATGCTACCTC 59.897 60.000 0.00 0.00 0.00 3.85
2168 2741 0.324368 TCCGTCACTGGATGCTACCT 60.324 55.000 0.00 0.00 31.53 3.08
2169 2742 0.103208 CTCCGTCACTGGATGCTACC 59.897 60.000 0.00 0.00 37.41 3.18
2170 2743 0.528684 GCTCCGTCACTGGATGCTAC 60.529 60.000 0.00 0.00 37.41 3.58
2171 2744 0.684479 AGCTCCGTCACTGGATGCTA 60.684 55.000 9.28 0.00 39.29 3.49
2172 2745 0.684479 TAGCTCCGTCACTGGATGCT 60.684 55.000 0.00 13.04 41.86 3.79
2173 2746 0.528684 GTAGCTCCGTCACTGGATGC 60.529 60.000 0.00 0.00 37.41 3.91
2174 2747 0.817654 TGTAGCTCCGTCACTGGATG 59.182 55.000 0.00 0.00 37.41 3.51
2175 2748 1.107114 CTGTAGCTCCGTCACTGGAT 58.893 55.000 0.00 0.00 37.41 3.41
2176 2749 0.965866 CCTGTAGCTCCGTCACTGGA 60.966 60.000 3.97 0.00 34.24 3.86
2183 2756 1.982938 GACCACCCTGTAGCTCCGT 60.983 63.158 0.00 0.00 0.00 4.69
2682 3265 8.503573 TGGTCGGTTCATCTATAGGATAGATAT 58.496 37.037 8.34 0.00 33.34 1.63


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

AutoCloner maintained by Alex Coulton.