Multiple sequence alignment - TraesCS1A01G313200

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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 TraesCS1A01G313200 chr1A 100.000 4375 0 0 1 4375 505267172 505271546 0.000000e+00 8080.0
1 TraesCS1A01G313200 chr1A 79.156 806 153 13 15 815 22636038 22635243 1.070000e-150 544.0
2 TraesCS1A01G313200 chr1A 95.238 231 8 1 2734 2964 505269680 505269907 3.220000e-96 363.0
3 TraesCS1A01G313200 chr1A 95.238 231 8 1 2509 2736 505269905 505270135 3.220000e-96 363.0
4 TraesCS1A01G313200 chr1B 94.155 2361 85 29 2060 4373 551009257 551011611 0.000000e+00 3546.0
5 TraesCS1A01G313200 chr1B 94.604 556 22 6 1030 1581 551008288 551008839 0.000000e+00 854.0
6 TraesCS1A01G313200 chr1B 93.151 292 15 2 1579 1869 551008962 551009249 1.450000e-114 424.0
7 TraesCS1A01G313200 chr1B 96.104 231 6 1 2509 2736 551009931 551010161 1.490000e-99 374.0
8 TraesCS1A01G313200 chr1B 93.074 231 13 1 2734 2964 551009706 551009933 7.010000e-88 335.0
9 TraesCS1A01G313200 chr1D 95.707 1654 54 11 2734 4375 409048059 409049707 0.000000e+00 2645.0
10 TraesCS1A01G313200 chr1D 93.471 1164 42 11 1590 2736 409047143 409048289 0.000000e+00 1698.0
11 TraesCS1A01G313200 chr1D 90.449 534 21 8 1030 1537 409046514 409047043 0.000000e+00 676.0
12 TraesCS1A01G313200 chr1D 93.333 45 3 0 1030 1074 409016843 409016887 2.820000e-07 67.6
13 TraesCS1A01G313200 chr1D 83.824 68 2 3 971 1029 409016756 409016823 6.110000e-04 56.5
14 TraesCS1A01G313200 chr5D 94.657 861 39 4 1 861 307098653 307097800 0.000000e+00 1328.0
15 TraesCS1A01G313200 chr4B 95.417 720 28 2 141 860 129003906 129004620 0.000000e+00 1142.0
16 TraesCS1A01G313200 chrUn 88.367 851 50 21 1050 1868 446351496 446352329 0.000000e+00 977.0
17 TraesCS1A01G313200 chr3B 78.453 724 144 10 15 734 237636773 237636058 3.080000e-126 462.0
18 TraesCS1A01G313200 chr2A 76.309 401 95 0 15 415 613429976 613429576 9.530000e-52 215.0
19 TraesCS1A01G313200 chr3A 96.154 52 0 2 810 861 689502211 689502260 2.800000e-12 84.2


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 TraesCS1A01G313200 chr1A 505267172 505271546 4374 False 2935.333333 8080 96.825333 1 4375 3 chr1A.!!$F1 4374
1 TraesCS1A01G313200 chr1A 22635243 22636038 795 True 544.000000 544 79.156000 15 815 1 chr1A.!!$R1 800
2 TraesCS1A01G313200 chr1B 551008288 551011611 3323 False 1106.600000 3546 94.217600 1030 4373 5 chr1B.!!$F1 3343
3 TraesCS1A01G313200 chr1D 409046514 409049707 3193 False 1673.000000 2645 93.209000 1030 4375 3 chr1D.!!$F2 3345
4 TraesCS1A01G313200 chr5D 307097800 307098653 853 True 1328.000000 1328 94.657000 1 861 1 chr5D.!!$R1 860
5 TraesCS1A01G313200 chr4B 129003906 129004620 714 False 1142.000000 1142 95.417000 141 860 1 chr4B.!!$F1 719
6 TraesCS1A01G313200 chrUn 446351496 446352329 833 False 977.000000 977 88.367000 1050 1868 1 chrUn.!!$F1 818
7 TraesCS1A01G313200 chr3B 237636058 237636773 715 True 462.000000 462 78.453000 15 734 1 chr3B.!!$R1 719

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
956 958 0.108186 TCCTGCTCCTGCGTATTGTG 60.108 55.0 0.00 0.00 43.34 3.33 F
1696 1909 0.107703 ACATCACCTACCATGGCACG 60.108 55.0 13.04 0.73 0.00 5.34 F
2743 2972 0.106519 CCTAATCAAGGCAGGGGTGG 60.107 60.0 0.00 0.00 38.97 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1932 2161 0.178903 ACCCAGTTCTCTGTAGGGCA 60.179 55.0 0.0 0.0 39.82 5.36 R
3069 3299 0.250467 GCTGAAAGGAGGCACTGACA 60.250 55.0 0.0 0.0 41.55 3.58 R
3752 4025 0.675633 ACTTTGTGGATGCCTGTTGC 59.324 50.0 0.0 0.0 41.77 4.17 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
45 46 3.093814 TGATGCATGCTCTTGTCCATTT 58.906 40.909 20.33 0.00 0.00 2.32
113 114 1.883275 TGAAACTACCCCGTTTGCATG 59.117 47.619 0.00 0.00 37.24 4.06
115 117 1.582610 AACTACCCCGTTTGCATGCG 61.583 55.000 14.09 0.00 0.00 4.73
129 131 0.320683 CATGCGGAGACTTGGACACA 60.321 55.000 0.00 0.00 0.00 3.72
179 181 7.811713 TCAACGAATCAGATAGATGCAAGATAG 59.188 37.037 0.00 0.00 36.96 2.08
213 215 2.080286 ACAATCCGGAGTTCACGAAG 57.920 50.000 11.34 0.00 0.00 3.79
282 284 1.270732 GCAAGCGGGAGATGATCTGAT 60.271 52.381 0.00 0.00 0.00 2.90
351 353 2.359169 GGCGTCCACCTGATCCTGA 61.359 63.158 0.00 0.00 0.00 3.86
364 366 3.689347 TGATCCTGACTGGGTGAAAATG 58.311 45.455 0.00 0.00 36.20 2.32
517 519 0.957395 AAGCAATGCGAGAGGGTGTG 60.957 55.000 0.00 0.00 0.00 3.82
534 536 3.431486 GGTGTGATTTTTGCCCAACTCAA 60.431 43.478 0.00 0.00 0.00 3.02
584 586 7.502226 AGATTGATTGTTTAGAGGTTGTCAACA 59.498 33.333 17.29 0.00 0.00 3.33
585 587 6.371809 TGATTGTTTAGAGGTTGTCAACAC 57.628 37.500 17.29 10.35 0.00 3.32
607 609 0.874607 GGTTCTCGCGTCACAACACT 60.875 55.000 5.77 0.00 0.00 3.55
681 683 1.461888 CGCTTCTTTTACGGTTCAGCG 60.462 52.381 0.00 0.00 42.24 5.18
705 707 1.228245 CCAGGGATGGTAATGGCCG 60.228 63.158 0.00 0.00 0.00 6.13
714 716 2.110213 TAATGGCCGTGCGGATCC 59.890 61.111 15.45 0.00 37.50 3.36
780 782 0.980423 GACAGCTGTCCTTCCTTCCT 59.020 55.000 32.55 0.00 39.07 3.36
781 783 1.349357 GACAGCTGTCCTTCCTTCCTT 59.651 52.381 32.55 0.00 39.07 3.36
782 784 1.349357 ACAGCTGTCCTTCCTTCCTTC 59.651 52.381 15.25 0.00 0.00 3.46
783 785 0.988063 AGCTGTCCTTCCTTCCTTCC 59.012 55.000 0.00 0.00 0.00 3.46
855 857 2.798847 AGTCCTAAGTTTCGCGTCAAAC 59.201 45.455 13.78 13.78 36.64 2.93
859 861 4.094590 TCCTAAGTTTCGCGTCAAACAAAA 59.905 37.500 21.07 4.72 38.53 2.44
860 862 4.794246 CCTAAGTTTCGCGTCAAACAAAAA 59.206 37.500 21.07 4.04 38.53 1.94
883 885 4.351874 AAAAGGTCGTGAGAGGATTTCA 57.648 40.909 0.00 0.00 43.49 2.69
884 886 4.559862 AAAGGTCGTGAGAGGATTTCAT 57.440 40.909 0.00 0.00 43.49 2.57
885 887 3.533606 AGGTCGTGAGAGGATTTCATG 57.466 47.619 0.00 0.00 43.49 3.07
886 888 2.169352 AGGTCGTGAGAGGATTTCATGG 59.831 50.000 0.00 0.00 43.49 3.66
887 889 1.936547 GTCGTGAGAGGATTTCATGGC 59.063 52.381 0.00 0.00 43.49 4.40
888 890 1.134401 TCGTGAGAGGATTTCATGGCC 60.134 52.381 0.00 0.00 33.41 5.36
889 891 1.303309 GTGAGAGGATTTCATGGCCG 58.697 55.000 0.00 0.00 0.00 6.13
890 892 0.911769 TGAGAGGATTTCATGGCCGT 59.088 50.000 0.00 0.00 0.00 5.68
891 893 1.281867 TGAGAGGATTTCATGGCCGTT 59.718 47.619 0.00 0.00 0.00 4.44
892 894 2.503765 TGAGAGGATTTCATGGCCGTTA 59.496 45.455 0.00 0.00 0.00 3.18
893 895 3.054728 TGAGAGGATTTCATGGCCGTTAA 60.055 43.478 0.00 0.00 0.00 2.01
894 896 3.945285 GAGAGGATTTCATGGCCGTTAAA 59.055 43.478 6.77 6.77 0.00 1.52
895 897 4.340617 AGAGGATTTCATGGCCGTTAAAA 58.659 39.130 8.35 6.57 0.00 1.52
896 898 4.399303 AGAGGATTTCATGGCCGTTAAAAG 59.601 41.667 8.35 0.00 0.00 2.27
897 899 4.340617 AGGATTTCATGGCCGTTAAAAGA 58.659 39.130 8.35 0.00 0.00 2.52
898 900 4.399303 AGGATTTCATGGCCGTTAAAAGAG 59.601 41.667 8.35 0.00 0.00 2.85
899 901 4.398044 GGATTTCATGGCCGTTAAAAGAGA 59.602 41.667 8.35 0.00 0.00 3.10
900 902 5.105917 GGATTTCATGGCCGTTAAAAGAGAA 60.106 40.000 8.35 0.00 0.00 2.87
901 903 4.759516 TTCATGGCCGTTAAAAGAGAAC 57.240 40.909 0.00 0.00 0.00 3.01
902 904 3.078837 TCATGGCCGTTAAAAGAGAACC 58.921 45.455 0.00 0.00 0.00 3.62
903 905 1.900245 TGGCCGTTAAAAGAGAACCC 58.100 50.000 0.00 0.00 0.00 4.11
904 906 1.171308 GGCCGTTAAAAGAGAACCCC 58.829 55.000 0.00 0.00 0.00 4.95
905 907 1.271762 GGCCGTTAAAAGAGAACCCCT 60.272 52.381 0.00 0.00 0.00 4.79
906 908 2.082231 GCCGTTAAAAGAGAACCCCTC 58.918 52.381 0.00 0.00 42.28 4.30
918 920 4.720046 GAGAACCCCTCTTTTTCTGAACT 58.280 43.478 0.00 0.00 38.86 3.01
919 921 5.130705 AGAACCCCTCTTTTTCTGAACTT 57.869 39.130 0.00 0.00 0.00 2.66
920 922 5.519808 AGAACCCCTCTTTTTCTGAACTTT 58.480 37.500 0.00 0.00 0.00 2.66
921 923 5.594725 AGAACCCCTCTTTTTCTGAACTTTC 59.405 40.000 0.00 0.00 0.00 2.62
922 924 5.130705 ACCCCTCTTTTTCTGAACTTTCT 57.869 39.130 0.00 0.00 0.00 2.52
923 925 4.889995 ACCCCTCTTTTTCTGAACTTTCTG 59.110 41.667 0.00 0.00 0.00 3.02
924 926 5.133221 CCCCTCTTTTTCTGAACTTTCTGA 58.867 41.667 0.00 0.00 34.02 3.27
925 927 5.594317 CCCCTCTTTTTCTGAACTTTCTGAA 59.406 40.000 7.08 7.08 41.41 3.02
926 928 6.238869 CCCCTCTTTTTCTGAACTTTCTGAAG 60.239 42.308 10.16 2.11 43.07 3.02
927 929 6.205071 CCTCTTTTTCTGAACTTTCTGAAGC 58.795 40.000 10.16 0.00 43.07 3.86
928 930 6.039159 CCTCTTTTTCTGAACTTTCTGAAGCT 59.961 38.462 10.16 0.00 43.07 3.74
929 931 7.227512 CCTCTTTTTCTGAACTTTCTGAAGCTA 59.772 37.037 10.16 0.00 43.07 3.32
930 932 7.920738 TCTTTTTCTGAACTTTCTGAAGCTAC 58.079 34.615 10.16 0.00 43.07 3.58
931 933 7.552687 TCTTTTTCTGAACTTTCTGAAGCTACA 59.447 33.333 10.16 0.00 43.07 2.74
932 934 7.807977 TTTTCTGAACTTTCTGAAGCTACAT 57.192 32.000 10.16 0.00 43.07 2.29
933 935 6.791887 TTCTGAACTTTCTGAAGCTACATG 57.208 37.500 7.08 0.00 39.29 3.21
934 936 5.858381 TCTGAACTTTCTGAAGCTACATGT 58.142 37.500 2.69 2.69 36.29 3.21
935 937 6.291377 TCTGAACTTTCTGAAGCTACATGTT 58.709 36.000 2.30 0.00 36.29 2.71
936 938 6.767902 TCTGAACTTTCTGAAGCTACATGTTT 59.232 34.615 2.30 0.00 36.29 2.83
937 939 7.283127 TCTGAACTTTCTGAAGCTACATGTTTT 59.717 33.333 2.30 0.00 36.29 2.43
938 940 7.417612 TGAACTTTCTGAAGCTACATGTTTTC 58.582 34.615 2.30 7.05 36.29 2.29
939 941 6.319141 ACTTTCTGAAGCTACATGTTTTCC 57.681 37.500 2.30 0.00 36.29 3.13
940 942 6.064717 ACTTTCTGAAGCTACATGTTTTCCT 58.935 36.000 2.30 0.00 36.29 3.36
941 943 5.947228 TTCTGAAGCTACATGTTTTCCTG 57.053 39.130 2.30 3.14 0.00 3.86
942 944 3.753272 TCTGAAGCTACATGTTTTCCTGC 59.247 43.478 2.30 0.00 0.00 4.85
943 945 3.754965 TGAAGCTACATGTTTTCCTGCT 58.245 40.909 2.30 2.16 0.00 4.24
944 946 3.753272 TGAAGCTACATGTTTTCCTGCTC 59.247 43.478 2.30 1.35 0.00 4.26
945 947 2.716217 AGCTACATGTTTTCCTGCTCC 58.284 47.619 2.30 0.00 0.00 4.70
946 948 2.307098 AGCTACATGTTTTCCTGCTCCT 59.693 45.455 2.30 0.00 0.00 3.69
947 949 2.421424 GCTACATGTTTTCCTGCTCCTG 59.579 50.000 2.30 0.00 0.00 3.86
948 950 1.251251 ACATGTTTTCCTGCTCCTGC 58.749 50.000 0.00 0.00 40.20 4.85
949 951 0.169672 CATGTTTTCCTGCTCCTGCG 59.830 55.000 0.00 0.00 43.34 5.18
950 952 0.250901 ATGTTTTCCTGCTCCTGCGT 60.251 50.000 0.00 0.00 43.34 5.24
951 953 0.394938 TGTTTTCCTGCTCCTGCGTA 59.605 50.000 0.00 0.00 43.34 4.42
952 954 1.003118 TGTTTTCCTGCTCCTGCGTAT 59.997 47.619 0.00 0.00 43.34 3.06
953 955 2.084546 GTTTTCCTGCTCCTGCGTATT 58.915 47.619 0.00 0.00 43.34 1.89
954 956 1.737838 TTTCCTGCTCCTGCGTATTG 58.262 50.000 0.00 0.00 43.34 1.90
955 957 0.613260 TTCCTGCTCCTGCGTATTGT 59.387 50.000 0.00 0.00 43.34 2.71
956 958 0.108186 TCCTGCTCCTGCGTATTGTG 60.108 55.000 0.00 0.00 43.34 3.33
957 959 1.709147 CCTGCTCCTGCGTATTGTGC 61.709 60.000 0.00 0.00 43.34 4.57
958 960 2.028766 CTGCTCCTGCGTATTGTGCG 62.029 60.000 0.00 0.00 43.34 5.34
959 961 1.809619 GCTCCTGCGTATTGTGCGA 60.810 57.895 0.00 0.00 34.24 5.10
960 962 1.154205 GCTCCTGCGTATTGTGCGAT 61.154 55.000 0.00 0.00 34.24 4.58
961 963 0.578683 CTCCTGCGTATTGTGCGATG 59.421 55.000 0.00 0.00 34.24 3.84
962 964 0.174617 TCCTGCGTATTGTGCGATGA 59.825 50.000 0.00 0.00 34.24 2.92
963 965 0.301687 CCTGCGTATTGTGCGATGAC 59.698 55.000 0.00 0.00 34.24 3.06
964 966 0.998669 CTGCGTATTGTGCGATGACA 59.001 50.000 0.00 0.00 34.24 3.58
965 967 1.393196 CTGCGTATTGTGCGATGACAA 59.607 47.619 0.00 0.00 40.08 3.18
966 968 1.801178 TGCGTATTGTGCGATGACAAA 59.199 42.857 0.00 0.00 39.25 2.83
967 969 2.418280 TGCGTATTGTGCGATGACAAAT 59.582 40.909 0.00 0.00 39.25 2.32
968 970 3.619038 TGCGTATTGTGCGATGACAAATA 59.381 39.130 0.00 0.00 39.25 1.40
969 971 4.203828 GCGTATTGTGCGATGACAAATAG 58.796 43.478 0.00 0.00 39.25 1.73
970 972 4.260212 GCGTATTGTGCGATGACAAATAGT 60.260 41.667 0.00 0.00 39.25 2.12
971 973 5.051307 GCGTATTGTGCGATGACAAATAGTA 60.051 40.000 0.00 0.00 39.25 1.82
972 974 6.344800 CGTATTGTGCGATGACAAATAGTAC 58.655 40.000 0.00 0.00 39.25 2.73
973 975 6.020201 CGTATTGTGCGATGACAAATAGTACA 60.020 38.462 0.00 0.00 39.25 2.90
974 976 6.735678 ATTGTGCGATGACAAATAGTACAA 57.264 33.333 0.00 5.04 39.25 2.41
975 977 6.546972 TTGTGCGATGACAAATAGTACAAA 57.453 33.333 0.00 0.00 35.24 2.83
976 978 5.922546 TGTGCGATGACAAATAGTACAAAC 58.077 37.500 0.00 0.00 0.00 2.93
977 979 5.013236 GTGCGATGACAAATAGTACAAACG 58.987 41.667 0.00 0.00 0.00 3.60
978 980 4.019867 GCGATGACAAATAGTACAAACGC 58.980 43.478 0.00 0.00 34.37 4.84
979 981 4.434989 GCGATGACAAATAGTACAAACGCA 60.435 41.667 0.00 0.00 37.26 5.24
980 982 5.613812 CGATGACAAATAGTACAAACGCAA 58.386 37.500 0.00 0.00 0.00 4.85
981 983 9.860567 TGCGATGACAAATAGTACAAACGCAAG 62.861 40.741 0.00 0.00 39.89 4.01
982 984 5.351233 TGACAAATAGTACAAACGCAAGG 57.649 39.130 0.00 0.00 46.39 3.61
983 985 4.214545 TGACAAATAGTACAAACGCAAGGG 59.785 41.667 0.00 0.00 46.39 3.95
984 986 4.139038 ACAAATAGTACAAACGCAAGGGT 58.861 39.130 0.00 0.00 46.39 4.34
985 987 4.581409 ACAAATAGTACAAACGCAAGGGTT 59.419 37.500 0.00 0.00 46.39 4.11
986 988 5.764192 ACAAATAGTACAAACGCAAGGGTTA 59.236 36.000 2.84 0.00 46.39 2.85
987 989 5.868043 AATAGTACAAACGCAAGGGTTAC 57.132 39.130 2.84 0.00 46.39 2.50
988 990 3.480505 AGTACAAACGCAAGGGTTACT 57.519 42.857 2.84 1.18 46.39 2.24
989 991 3.396560 AGTACAAACGCAAGGGTTACTC 58.603 45.455 2.84 0.00 46.39 2.59
990 992 2.632987 ACAAACGCAAGGGTTACTCT 57.367 45.000 2.84 0.00 46.39 3.24
991 993 2.927028 ACAAACGCAAGGGTTACTCTT 58.073 42.857 2.84 0.00 46.39 2.85
992 994 2.876550 ACAAACGCAAGGGTTACTCTTC 59.123 45.455 0.00 0.00 46.39 2.87
993 995 3.139077 CAAACGCAAGGGTTACTCTTCT 58.861 45.455 0.00 0.00 46.39 2.85
994 996 2.745515 ACGCAAGGGTTACTCTTCTC 57.254 50.000 0.00 0.00 46.39 2.87
995 997 2.249139 ACGCAAGGGTTACTCTTCTCT 58.751 47.619 0.00 0.00 46.39 3.10
996 998 2.028930 ACGCAAGGGTTACTCTTCTCTG 60.029 50.000 0.00 0.00 46.39 3.35
997 999 2.231478 CGCAAGGGTTACTCTTCTCTGA 59.769 50.000 0.00 0.00 0.00 3.27
998 1000 3.306088 CGCAAGGGTTACTCTTCTCTGAA 60.306 47.826 0.00 0.00 0.00 3.02
999 1001 3.997681 GCAAGGGTTACTCTTCTCTGAAC 59.002 47.826 0.00 0.00 0.00 3.18
1000 1002 4.570930 CAAGGGTTACTCTTCTCTGAACC 58.429 47.826 0.00 0.00 39.09 3.62
1003 1005 4.618920 GGTTACTCTTCTCTGAACCCAA 57.381 45.455 0.00 0.00 34.67 4.12
1004 1006 4.570930 GGTTACTCTTCTCTGAACCCAAG 58.429 47.826 0.00 0.00 34.67 3.61
1005 1007 2.849294 ACTCTTCTCTGAACCCAAGC 57.151 50.000 0.00 0.00 0.00 4.01
1006 1008 1.001406 ACTCTTCTCTGAACCCAAGCG 59.999 52.381 0.00 0.00 0.00 4.68
1007 1009 0.321671 TCTTCTCTGAACCCAAGCGG 59.678 55.000 0.00 0.00 37.81 5.52
1008 1010 1.301677 CTTCTCTGAACCCAAGCGGC 61.302 60.000 0.00 0.00 33.26 6.53
1009 1011 2.747855 CTCTGAACCCAAGCGGCC 60.748 66.667 0.00 0.00 33.26 6.13
1010 1012 4.697756 TCTGAACCCAAGCGGCCG 62.698 66.667 24.05 24.05 33.26 6.13
1011 1013 4.697756 CTGAACCCAAGCGGCCGA 62.698 66.667 33.48 2.57 33.26 5.54
1012 1014 4.697756 TGAACCCAAGCGGCCGAG 62.698 66.667 33.48 17.79 33.26 4.63
1398 1406 2.350057 GGTATTGCCCCTCTTCTTCC 57.650 55.000 0.00 0.00 0.00 3.46
1423 1435 7.661847 CCCTTCCTGATGTTTATTGTATACTCC 59.338 40.741 4.17 0.00 0.00 3.85
1524 1562 4.623886 GCAGTTCCATTGATCCAGACAGTA 60.624 45.833 0.00 0.00 0.00 2.74
1660 1873 4.998033 GTGGTCCTTTTAGGTTGAAGAGAG 59.002 45.833 0.00 0.00 36.53 3.20
1696 1909 0.107703 ACATCACCTACCATGGCACG 60.108 55.000 13.04 0.73 0.00 5.34
1702 1915 1.602237 CTACCATGGCACGGAAGGT 59.398 57.895 13.04 4.61 36.40 3.50
1725 1938 7.775561 AGGTTGATTAAGAGAACACTTTTGACT 59.224 33.333 0.00 0.00 0.00 3.41
1830 2045 3.507622 AGAAATCCAGCTACTGTTTTGGC 59.492 43.478 0.00 0.00 0.00 4.52
1863 2078 5.843673 TCCTGCAAAATGTGAAAACTACA 57.156 34.783 0.00 0.00 0.00 2.74
1878 2107 7.750903 GTGAAAACTACAATCATGTTTCTAGCC 59.249 37.037 0.00 0.00 41.05 3.93
1879 2108 7.446931 TGAAAACTACAATCATGTTTCTAGCCA 59.553 33.333 0.00 0.00 41.05 4.75
1891 2120 6.554334 TGTTTCTAGCCAAACATAACTGTC 57.446 37.500 5.81 0.00 40.57 3.51
1895 2124 8.780249 GTTTCTAGCCAAACATAACTGTCTTAA 58.220 33.333 2.92 0.00 36.44 1.85
1914 2143 8.277713 TGTCTTAACGTATTGTTTACTCTTTGC 58.722 33.333 0.00 0.00 42.09 3.68
1932 2161 7.119846 ACTCTTTGCGTTGATCTTAGCTAAATT 59.880 33.333 7.74 0.00 0.00 1.82
1933 2162 7.243487 TCTTTGCGTTGATCTTAGCTAAATTG 58.757 34.615 7.74 0.00 0.00 2.32
1941 2170 6.291377 TGATCTTAGCTAAATTGCCCTACAG 58.709 40.000 7.74 0.00 0.00 2.74
1960 2189 3.165875 CAGAGAACTGGGTTAGTCAGGA 58.834 50.000 0.00 0.00 39.18 3.86
1998 2227 9.796120 GTAATTATTACAGTTTTAAGCCATGCA 57.204 29.630 9.94 0.00 36.17 3.96
2008 2237 4.707030 TTAAGCCATGCATCTGTTTGAG 57.293 40.909 0.00 0.00 0.00 3.02
2009 2238 2.502142 AGCCATGCATCTGTTTGAGA 57.498 45.000 0.00 0.00 34.25 3.27
2016 2245 4.168922 TGCATCTGTTTGAGATTTGCAG 57.831 40.909 0.00 0.00 40.34 4.41
2305 2534 3.862642 GCTCAAGATCCGTATCCACATCC 60.863 52.174 0.00 0.00 31.98 3.51
2458 2687 4.675976 TGAGTTACGAACCAAGAGGAAA 57.324 40.909 0.00 0.00 38.69 3.13
2531 2760 2.761208 CAGGGGTGAGAACTACTACCAG 59.239 54.545 0.00 0.00 34.89 4.00
2624 2853 4.559862 CTTCTACAGGAAGTCCATGGTT 57.440 45.455 12.58 0.00 44.59 3.67
2669 2898 2.963101 ACCTATCGTTGGCAGCATACTA 59.037 45.455 1.39 0.00 0.00 1.82
2681 2910 2.300152 CAGCATACTACCCATCGATGGT 59.700 50.000 36.09 26.97 46.65 3.55
2687 2916 0.180171 TACCCATCGATGGTGCCAAG 59.820 55.000 36.09 24.32 46.65 3.61
2709 2938 3.254629 TGGCTTCCAGAGTCATTGC 57.745 52.632 0.00 0.00 34.36 3.56
2743 2972 0.106519 CCTAATCAAGGCAGGGGTGG 60.107 60.000 0.00 0.00 38.97 4.61
2747 2976 1.224003 ATCAAGGCAGGGGTGGGAAT 61.224 55.000 0.00 0.00 0.00 3.01
2749 2978 0.545071 CAAGGCAGGGGTGGGAATTT 60.545 55.000 0.00 0.00 0.00 1.82
2909 3138 3.199946 ACATACTGAAACCCATCGATGGT 59.800 43.478 36.09 23.98 46.65 3.55
2912 3141 1.024046 TGAAACCCATCGATGGTGCG 61.024 55.000 36.09 25.60 46.65 5.34
2990 3219 7.201723 CGAACAATATCAAATCCAACATCAGGA 60.202 37.037 0.00 0.00 39.97 3.86
3069 3299 1.067212 AGACGTGACGTGAGCTCTTTT 59.933 47.619 18.09 0.00 41.37 2.27
3070 3300 1.190323 GACGTGACGTGAGCTCTTTTG 59.810 52.381 18.09 4.48 41.37 2.44
3071 3301 1.209128 CGTGACGTGAGCTCTTTTGT 58.791 50.000 16.19 7.80 0.00 2.83
3072 3302 1.190323 CGTGACGTGAGCTCTTTTGTC 59.810 52.381 16.19 16.19 0.00 3.18
3073 3303 2.201732 GTGACGTGAGCTCTTTTGTCA 58.798 47.619 16.19 18.36 34.27 3.58
3075 3305 2.159099 TGACGTGAGCTCTTTTGTCAGT 60.159 45.455 16.19 3.27 32.96 3.41
3076 3306 2.205074 ACGTGAGCTCTTTTGTCAGTG 58.795 47.619 16.19 0.00 0.00 3.66
3077 3307 1.070309 CGTGAGCTCTTTTGTCAGTGC 60.070 52.381 16.19 0.00 34.15 4.40
3078 3308 1.265365 GTGAGCTCTTTTGTCAGTGCC 59.735 52.381 16.19 0.00 34.42 5.01
3085 3315 3.214328 TCTTTTGTCAGTGCCTCCTTTC 58.786 45.455 0.00 0.00 0.00 2.62
3128 3359 1.271597 GGATTGCTGGTGTTCCTCAGT 60.272 52.381 0.00 0.00 33.81 3.41
3222 3478 6.296365 ACATTTTGATCTGCGATATCTGTG 57.704 37.500 0.34 0.00 0.00 3.66
3238 3494 4.344359 TCTGTGGTACTGTTTATGCACA 57.656 40.909 0.00 0.00 0.00 4.57
3309 3567 8.341173 CCTTTGAGCTTGTATTGTCTATCATTC 58.659 37.037 0.00 0.00 0.00 2.67
3313 3571 4.444388 GCTTGTATTGTCTATCATTCGCGA 59.556 41.667 3.71 3.71 0.00 5.87
3345 3603 9.912634 TTTCATGAGCTAAACCTAAATTTTGAG 57.087 29.630 0.00 0.00 0.00 3.02
3363 3621 2.636403 TGAGATATCATGGAGCCAGGTG 59.364 50.000 5.32 0.00 0.00 4.00
3366 3624 2.487746 TATCATGGAGCCAGGTGGTA 57.512 50.000 0.73 0.00 37.57 3.25
3381 3639 2.584791 GTGGTAAAATTGCACGCTGAG 58.415 47.619 0.00 0.00 0.00 3.35
3465 3730 1.963515 GCCCACAATGAAGAAACACCT 59.036 47.619 0.00 0.00 0.00 4.00
3682 3955 6.589523 CCGTCAAATTTATGCTGAAATTGGAA 59.410 34.615 12.53 1.16 39.39 3.53
3713 3986 2.273370 GCATGTCTGCTTGTTCCATG 57.727 50.000 0.00 0.00 45.32 3.66
3903 4177 4.141733 TGCTGGTGCTAATTATGTGAGCTA 60.142 41.667 0.00 0.00 40.48 3.32
3909 4183 7.280876 TGGTGCTAATTATGTGAGCTAAGAAAG 59.719 37.037 0.00 0.00 37.12 2.62
4003 4278 4.174762 GGTCTCTTACATTTCGAGTGGTC 58.825 47.826 5.11 0.00 0.00 4.02
4042 4317 1.270550 GAGGACAACATGGCAGGTTTG 59.729 52.381 15.73 12.92 0.00 2.93
4071 4346 6.038161 CGGTACATGAAAGGAATTAAGATGCA 59.962 38.462 0.00 0.00 0.00 3.96
4321 4597 3.052869 TGCAATAGACTACAGGAGAGGGA 60.053 47.826 0.00 0.00 0.00 4.20
4366 4642 8.755696 TGTGCAAATTTGTTCCATAATAGAAC 57.244 30.769 19.03 0.00 43.20 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 7.525759 GTTTCAGAAACTTTTTGCATGGAAAA 58.474 30.769 19.76 19.76 38.35 2.29
48 49 4.803088 CGTTTCAGAAACTTTTTGCATGGA 59.197 37.500 21.24 0.00 39.23 3.41
64 65 0.030101 TTTCCTTTGCCGCGTTTCAG 59.970 50.000 4.92 0.00 0.00 3.02
67 68 0.958822 AGATTTCCTTTGCCGCGTTT 59.041 45.000 4.92 0.00 0.00 3.60
113 114 0.033504 TCTTGTGTCCAAGTCTCCGC 59.966 55.000 2.69 0.00 46.70 5.54
115 117 3.971245 AGATCTTGTGTCCAAGTCTCC 57.029 47.619 0.00 0.00 46.70 3.71
129 131 9.725019 TGAACATACTGTCAACAATAAGATCTT 57.275 29.630 13.56 13.56 0.00 2.40
179 181 7.817962 ACTCCGGATTGTATGCATAATAGTTAC 59.182 37.037 8.28 0.00 0.00 2.50
200 202 1.153823 ATCGGCTTCGTGAACTCCG 60.154 57.895 10.56 10.56 41.30 4.63
213 215 0.604780 CTCATCATGGGTCCATCGGC 60.605 60.000 0.00 0.00 33.90 5.54
269 271 7.725251 AGTTCTAACAAGATCAGATCATCTCC 58.275 38.462 13.14 0.00 31.44 3.71
282 284 9.924650 GATGAGTTTTAGGTAGTTCTAACAAGA 57.075 33.333 0.00 0.00 0.00 3.02
364 366 3.932710 TGTCAATAGCTTCATCGGTGTTC 59.067 43.478 0.00 0.00 0.00 3.18
375 377 2.038952 TGTGCCTGAGTGTCAATAGCTT 59.961 45.455 0.00 0.00 0.00 3.74
517 519 3.402110 CCCTTTGAGTTGGGCAAAAATC 58.598 45.455 0.00 0.00 36.61 2.17
534 536 1.346395 TGACAACATGCGAGTACCCTT 59.654 47.619 0.00 0.00 0.00 3.95
560 562 7.285401 AGTGTTGACAACCTCTAAACAATCAAT 59.715 33.333 15.59 0.00 32.92 2.57
584 586 0.179094 TTGTGACGCGAGAACCAAGT 60.179 50.000 15.93 0.00 0.00 3.16
585 587 0.232303 GTTGTGACGCGAGAACCAAG 59.768 55.000 15.93 0.00 0.00 3.61
607 609 3.324846 AGATAGGCGCCAACAATGATCTA 59.675 43.478 31.54 8.32 0.00 1.98
681 683 3.747708 GCCATTACCATCCCTGGAACTAC 60.748 52.174 0.00 0.00 46.37 2.73
705 707 1.130561 GTTTAGCACAAGGATCCGCAC 59.869 52.381 5.98 0.00 0.00 5.34
780 782 2.553028 CCAAGAGGCTGCTTACAAGGAA 60.553 50.000 0.00 0.00 0.00 3.36
781 783 1.003580 CCAAGAGGCTGCTTACAAGGA 59.996 52.381 0.00 0.00 0.00 3.36
782 784 1.457346 CCAAGAGGCTGCTTACAAGG 58.543 55.000 0.00 0.00 0.00 3.61
861 863 4.714632 TGAAATCCTCTCACGACCTTTTT 58.285 39.130 0.00 0.00 0.00 1.94
862 864 4.351874 TGAAATCCTCTCACGACCTTTT 57.648 40.909 0.00 0.00 0.00 2.27
863 865 4.256920 CATGAAATCCTCTCACGACCTTT 58.743 43.478 0.00 0.00 0.00 3.11
864 866 3.369892 CCATGAAATCCTCTCACGACCTT 60.370 47.826 0.00 0.00 0.00 3.50
865 867 2.169352 CCATGAAATCCTCTCACGACCT 59.831 50.000 0.00 0.00 0.00 3.85
866 868 2.555199 CCATGAAATCCTCTCACGACC 58.445 52.381 0.00 0.00 0.00 4.79
867 869 1.936547 GCCATGAAATCCTCTCACGAC 59.063 52.381 0.00 0.00 0.00 4.34
868 870 1.134401 GGCCATGAAATCCTCTCACGA 60.134 52.381 0.00 0.00 0.00 4.35
869 871 1.303309 GGCCATGAAATCCTCTCACG 58.697 55.000 0.00 0.00 0.00 4.35
870 872 1.303309 CGGCCATGAAATCCTCTCAC 58.697 55.000 2.24 0.00 0.00 3.51
871 873 0.911769 ACGGCCATGAAATCCTCTCA 59.088 50.000 2.24 0.00 0.00 3.27
872 874 2.044123 AACGGCCATGAAATCCTCTC 57.956 50.000 2.24 0.00 0.00 3.20
873 875 3.644966 TTAACGGCCATGAAATCCTCT 57.355 42.857 2.24 0.00 0.00 3.69
874 876 4.398044 TCTTTTAACGGCCATGAAATCCTC 59.602 41.667 2.24 0.00 0.00 3.71
875 877 4.340617 TCTTTTAACGGCCATGAAATCCT 58.659 39.130 2.24 0.00 0.00 3.24
876 878 4.398044 TCTCTTTTAACGGCCATGAAATCC 59.602 41.667 2.24 0.00 0.00 3.01
877 879 5.560966 TCTCTTTTAACGGCCATGAAATC 57.439 39.130 2.24 0.00 0.00 2.17
878 880 5.336451 GGTTCTCTTTTAACGGCCATGAAAT 60.336 40.000 2.24 0.00 0.00 2.17
879 881 4.022676 GGTTCTCTTTTAACGGCCATGAAA 60.023 41.667 2.24 0.00 0.00 2.69
880 882 3.504520 GGTTCTCTTTTAACGGCCATGAA 59.495 43.478 2.24 0.00 0.00 2.57
881 883 3.078837 GGTTCTCTTTTAACGGCCATGA 58.921 45.455 2.24 0.00 0.00 3.07
882 884 2.163613 GGGTTCTCTTTTAACGGCCATG 59.836 50.000 2.24 0.00 0.00 3.66
883 885 2.443416 GGGTTCTCTTTTAACGGCCAT 58.557 47.619 2.24 0.00 0.00 4.40
884 886 1.546099 GGGGTTCTCTTTTAACGGCCA 60.546 52.381 2.24 0.00 0.00 5.36
885 887 1.171308 GGGGTTCTCTTTTAACGGCC 58.829 55.000 0.00 0.00 0.00 6.13
886 888 2.082231 GAGGGGTTCTCTTTTAACGGC 58.918 52.381 0.00 0.00 39.38 5.68
896 898 4.720046 AGTTCAGAAAAAGAGGGGTTCTC 58.280 43.478 0.00 0.00 42.75 2.87
897 899 4.797912 AGTTCAGAAAAAGAGGGGTTCT 57.202 40.909 0.00 0.00 37.93 3.01
898 900 5.594725 AGAAAGTTCAGAAAAAGAGGGGTTC 59.405 40.000 0.00 0.00 0.00 3.62
899 901 5.360999 CAGAAAGTTCAGAAAAAGAGGGGTT 59.639 40.000 0.00 0.00 0.00 4.11
900 902 4.889995 CAGAAAGTTCAGAAAAAGAGGGGT 59.110 41.667 0.00 0.00 0.00 4.95
901 903 5.133221 TCAGAAAGTTCAGAAAAAGAGGGG 58.867 41.667 0.00 0.00 0.00 4.79
902 904 6.699575 TTCAGAAAGTTCAGAAAAAGAGGG 57.300 37.500 0.00 0.00 31.06 4.30
903 905 6.039159 AGCTTCAGAAAGTTCAGAAAAAGAGG 59.961 38.462 1.29 0.00 33.25 3.69
904 906 7.025485 AGCTTCAGAAAGTTCAGAAAAAGAG 57.975 36.000 1.29 0.00 33.25 2.85
905 907 7.552687 TGTAGCTTCAGAAAGTTCAGAAAAAGA 59.447 33.333 0.00 0.00 33.25 2.52
906 908 7.697691 TGTAGCTTCAGAAAGTTCAGAAAAAG 58.302 34.615 0.00 0.00 33.25 2.27
907 909 7.624360 TGTAGCTTCAGAAAGTTCAGAAAAA 57.376 32.000 0.00 0.00 33.25 1.94
908 910 7.283127 ACATGTAGCTTCAGAAAGTTCAGAAAA 59.717 33.333 0.00 0.00 33.25 2.29
909 911 6.767902 ACATGTAGCTTCAGAAAGTTCAGAAA 59.232 34.615 0.00 0.00 33.25 2.52
910 912 6.291377 ACATGTAGCTTCAGAAAGTTCAGAA 58.709 36.000 0.00 0.00 34.79 3.02
911 913 5.858381 ACATGTAGCTTCAGAAAGTTCAGA 58.142 37.500 0.00 0.00 34.79 3.27
912 914 6.551385 AACATGTAGCTTCAGAAAGTTCAG 57.449 37.500 0.00 0.00 34.79 3.02
913 915 6.942532 AAACATGTAGCTTCAGAAAGTTCA 57.057 33.333 0.00 0.00 34.79 3.18
914 916 6.858478 GGAAAACATGTAGCTTCAGAAAGTTC 59.142 38.462 0.00 0.00 34.79 3.01
915 917 6.547510 AGGAAAACATGTAGCTTCAGAAAGTT 59.452 34.615 0.00 0.00 34.79 2.66
916 918 6.016777 CAGGAAAACATGTAGCTTCAGAAAGT 60.017 38.462 0.00 0.00 34.79 2.66
917 919 6.376978 CAGGAAAACATGTAGCTTCAGAAAG 58.623 40.000 0.00 0.00 35.47 2.62
918 920 5.278463 GCAGGAAAACATGTAGCTTCAGAAA 60.278 40.000 0.00 0.00 0.00 2.52
919 921 4.216257 GCAGGAAAACATGTAGCTTCAGAA 59.784 41.667 0.00 0.00 0.00 3.02
920 922 3.753272 GCAGGAAAACATGTAGCTTCAGA 59.247 43.478 0.00 0.00 0.00 3.27
921 923 3.755378 AGCAGGAAAACATGTAGCTTCAG 59.245 43.478 0.00 1.45 0.00 3.02
922 924 3.753272 GAGCAGGAAAACATGTAGCTTCA 59.247 43.478 0.00 0.00 0.00 3.02
923 925 3.127721 GGAGCAGGAAAACATGTAGCTTC 59.872 47.826 0.00 2.74 0.00 3.86
924 926 3.084786 GGAGCAGGAAAACATGTAGCTT 58.915 45.455 0.00 0.00 0.00 3.74
925 927 2.307098 AGGAGCAGGAAAACATGTAGCT 59.693 45.455 0.00 2.12 0.00 3.32
926 928 2.421424 CAGGAGCAGGAAAACATGTAGC 59.579 50.000 0.00 0.00 0.00 3.58
927 929 2.421424 GCAGGAGCAGGAAAACATGTAG 59.579 50.000 0.00 0.00 41.58 2.74
928 930 2.436417 GCAGGAGCAGGAAAACATGTA 58.564 47.619 0.00 0.00 41.58 2.29
929 931 1.251251 GCAGGAGCAGGAAAACATGT 58.749 50.000 0.00 0.00 41.58 3.21
930 932 0.169672 CGCAGGAGCAGGAAAACATG 59.830 55.000 0.00 0.00 42.27 3.21
931 933 0.250901 ACGCAGGAGCAGGAAAACAT 60.251 50.000 0.00 0.00 42.27 2.71
932 934 0.394938 TACGCAGGAGCAGGAAAACA 59.605 50.000 0.00 0.00 42.27 2.83
933 935 1.739067 ATACGCAGGAGCAGGAAAAC 58.261 50.000 0.00 0.00 42.27 2.43
934 936 2.083774 CAATACGCAGGAGCAGGAAAA 58.916 47.619 0.00 0.00 42.27 2.29
935 937 1.003118 ACAATACGCAGGAGCAGGAAA 59.997 47.619 0.00 0.00 42.27 3.13
936 938 0.613260 ACAATACGCAGGAGCAGGAA 59.387 50.000 0.00 0.00 42.27 3.36
937 939 0.108186 CACAATACGCAGGAGCAGGA 60.108 55.000 0.00 0.00 42.27 3.86
938 940 1.709147 GCACAATACGCAGGAGCAGG 61.709 60.000 0.00 0.00 42.27 4.85
939 941 1.717937 GCACAATACGCAGGAGCAG 59.282 57.895 0.00 0.00 42.27 4.24
940 942 2.100031 CGCACAATACGCAGGAGCA 61.100 57.895 0.00 0.00 42.27 4.26
941 943 1.154205 ATCGCACAATACGCAGGAGC 61.154 55.000 0.00 0.00 37.42 4.70
942 944 0.578683 CATCGCACAATACGCAGGAG 59.421 55.000 0.00 0.00 0.00 3.69
943 945 0.174617 TCATCGCACAATACGCAGGA 59.825 50.000 0.00 0.00 0.00 3.86
944 946 0.301687 GTCATCGCACAATACGCAGG 59.698 55.000 0.00 0.00 0.00 4.85
945 947 0.998669 TGTCATCGCACAATACGCAG 59.001 50.000 0.00 0.00 0.00 5.18
946 948 1.433534 TTGTCATCGCACAATACGCA 58.566 45.000 0.00 0.00 31.08 5.24
947 949 2.519002 TTTGTCATCGCACAATACGC 57.481 45.000 0.00 0.00 36.16 4.42
948 950 5.389642 ACTATTTGTCATCGCACAATACG 57.610 39.130 0.00 0.00 36.16 3.06
949 951 7.229228 TGTACTATTTGTCATCGCACAATAC 57.771 36.000 0.00 0.00 36.16 1.89
950 952 7.835634 TTGTACTATTTGTCATCGCACAATA 57.164 32.000 0.00 0.00 36.16 1.90
951 953 6.735678 TTGTACTATTTGTCATCGCACAAT 57.264 33.333 0.00 0.00 36.16 2.71
952 954 6.367421 GTTTGTACTATTTGTCATCGCACAA 58.633 36.000 0.00 0.00 34.36 3.33
953 955 5.388994 CGTTTGTACTATTTGTCATCGCACA 60.389 40.000 0.00 0.00 0.00 4.57
954 956 5.013236 CGTTTGTACTATTTGTCATCGCAC 58.987 41.667 0.00 0.00 0.00 5.34
955 957 4.434989 GCGTTTGTACTATTTGTCATCGCA 60.435 41.667 0.00 0.00 34.44 5.10
956 958 4.019867 GCGTTTGTACTATTTGTCATCGC 58.980 43.478 0.00 0.00 0.00 4.58
957 959 5.198116 TGCGTTTGTACTATTTGTCATCG 57.802 39.130 0.00 0.00 0.00 3.84
958 960 6.021596 CCTTGCGTTTGTACTATTTGTCATC 58.978 40.000 0.00 0.00 0.00 2.92
959 961 5.106317 CCCTTGCGTTTGTACTATTTGTCAT 60.106 40.000 0.00 0.00 0.00 3.06
960 962 4.214545 CCCTTGCGTTTGTACTATTTGTCA 59.785 41.667 0.00 0.00 0.00 3.58
961 963 4.214758 ACCCTTGCGTTTGTACTATTTGTC 59.785 41.667 0.00 0.00 0.00 3.18
962 964 4.139038 ACCCTTGCGTTTGTACTATTTGT 58.861 39.130 0.00 0.00 0.00 2.83
963 965 4.759516 ACCCTTGCGTTTGTACTATTTG 57.240 40.909 0.00 0.00 0.00 2.32
964 966 5.999600 AGTAACCCTTGCGTTTGTACTATTT 59.000 36.000 0.00 0.00 0.00 1.40
965 967 5.554070 AGTAACCCTTGCGTTTGTACTATT 58.446 37.500 0.00 0.00 0.00 1.73
966 968 5.046807 AGAGTAACCCTTGCGTTTGTACTAT 60.047 40.000 0.00 0.00 0.00 2.12
967 969 4.281688 AGAGTAACCCTTGCGTTTGTACTA 59.718 41.667 0.00 0.00 0.00 1.82
968 970 3.070590 AGAGTAACCCTTGCGTTTGTACT 59.929 43.478 0.00 0.00 0.00 2.73
969 971 3.396560 AGAGTAACCCTTGCGTTTGTAC 58.603 45.455 0.00 0.00 0.00 2.90
970 972 3.756933 AGAGTAACCCTTGCGTTTGTA 57.243 42.857 0.00 0.00 0.00 2.41
971 973 2.632987 AGAGTAACCCTTGCGTTTGT 57.367 45.000 0.00 0.00 0.00 2.83
972 974 3.139077 AGAAGAGTAACCCTTGCGTTTG 58.861 45.455 0.00 0.00 0.00 2.93
973 975 3.071167 AGAGAAGAGTAACCCTTGCGTTT 59.929 43.478 0.00 0.00 0.00 3.60
974 976 2.633481 AGAGAAGAGTAACCCTTGCGTT 59.367 45.455 0.00 0.00 0.00 4.84
975 977 2.028930 CAGAGAAGAGTAACCCTTGCGT 60.029 50.000 0.00 0.00 0.00 5.24
976 978 2.231478 TCAGAGAAGAGTAACCCTTGCG 59.769 50.000 0.00 0.00 0.00 4.85
977 979 3.963428 TCAGAGAAGAGTAACCCTTGC 57.037 47.619 0.00 0.00 0.00 4.01
978 980 4.570930 GGTTCAGAGAAGAGTAACCCTTG 58.429 47.826 0.00 0.00 34.75 3.61
979 981 4.893829 GGTTCAGAGAAGAGTAACCCTT 57.106 45.455 0.00 0.00 34.75 3.95
982 984 4.570930 CTTGGGTTCAGAGAAGAGTAACC 58.429 47.826 0.00 0.00 39.09 2.85
983 985 3.997681 GCTTGGGTTCAGAGAAGAGTAAC 59.002 47.826 0.00 0.00 0.00 2.50
984 986 3.306088 CGCTTGGGTTCAGAGAAGAGTAA 60.306 47.826 0.00 0.00 0.00 2.24
985 987 2.231478 CGCTTGGGTTCAGAGAAGAGTA 59.769 50.000 0.00 0.00 0.00 2.59
986 988 1.001406 CGCTTGGGTTCAGAGAAGAGT 59.999 52.381 0.00 0.00 0.00 3.24
987 989 1.674221 CCGCTTGGGTTCAGAGAAGAG 60.674 57.143 0.00 0.00 0.00 2.85
988 990 0.321671 CCGCTTGGGTTCAGAGAAGA 59.678 55.000 0.00 0.00 0.00 2.87
989 991 1.301677 GCCGCTTGGGTTCAGAGAAG 61.302 60.000 0.00 0.00 38.44 2.85
990 992 1.302511 GCCGCTTGGGTTCAGAGAA 60.303 57.895 0.00 0.00 38.44 2.87
991 993 2.347490 GCCGCTTGGGTTCAGAGA 59.653 61.111 0.00 0.00 38.44 3.10
992 994 2.747855 GGCCGCTTGGGTTCAGAG 60.748 66.667 0.00 0.00 38.44 3.35
993 995 4.697756 CGGCCGCTTGGGTTCAGA 62.698 66.667 14.67 0.00 38.44 3.27
994 996 4.697756 TCGGCCGCTTGGGTTCAG 62.698 66.667 23.51 0.00 38.44 3.02
995 997 4.697756 CTCGGCCGCTTGGGTTCA 62.698 66.667 23.51 0.00 38.44 3.18
1018 1020 2.862347 GATTGCTGCTTGCCTGCGAC 62.862 60.000 0.00 0.00 40.88 5.19
1019 1021 2.674033 ATTGCTGCTTGCCTGCGA 60.674 55.556 0.00 0.00 40.88 5.10
1020 1022 2.202570 GATTGCTGCTTGCCTGCG 60.203 61.111 0.00 0.00 40.88 5.18
1021 1023 2.183555 GGATTGCTGCTTGCCTGC 59.816 61.111 0.00 1.83 42.00 4.85
1022 1024 1.945354 CTGGGATTGCTGCTTGCCTG 61.945 60.000 13.00 9.62 42.00 4.85
1023 1025 1.681327 CTGGGATTGCTGCTTGCCT 60.681 57.895 13.00 0.00 42.00 4.75
1024 1026 1.041447 ATCTGGGATTGCTGCTTGCC 61.041 55.000 0.00 3.98 42.00 4.52
1025 1027 0.102481 CATCTGGGATTGCTGCTTGC 59.898 55.000 0.00 0.00 43.25 4.01
1026 1028 0.744874 CCATCTGGGATTGCTGCTTG 59.255 55.000 0.00 0.00 40.01 4.01
1027 1029 0.627451 TCCATCTGGGATTGCTGCTT 59.373 50.000 0.00 0.00 42.15 3.91
1028 1030 2.314402 TCCATCTGGGATTGCTGCT 58.686 52.632 0.00 0.00 42.15 4.24
1029 1031 4.993307 TCCATCTGGGATTGCTGC 57.007 55.556 0.00 0.00 42.15 5.25
1269 1271 4.214327 GCGGAGGAGGAGAAGGCG 62.214 72.222 0.00 0.00 0.00 5.52
1398 1406 7.385205 CGGAGTATACAATAAACATCAGGAAGG 59.615 40.741 5.50 0.00 0.00 3.46
1423 1435 0.247736 AACCTAGAAGCACAGGAGCG 59.752 55.000 0.00 0.00 40.15 5.03
1480 1518 6.317642 ACTGCTACGAATTATGCCAACAATAA 59.682 34.615 0.00 0.00 0.00 1.40
1489 1527 5.007626 TCAATGGAACTGCTACGAATTATGC 59.992 40.000 0.00 0.00 0.00 3.14
1498 1536 3.873952 GTCTGGATCAATGGAACTGCTAC 59.126 47.826 0.00 0.00 0.00 3.58
1524 1562 2.376855 AGCTTAAGCCCAGGAAAACTCT 59.623 45.455 23.71 0.00 43.38 3.24
1696 1909 7.511959 AAAGTGTTCTCTTAATCAACCTTCC 57.488 36.000 0.00 0.00 0.00 3.46
1702 1915 8.964476 AGAGTCAAAAGTGTTCTCTTAATCAA 57.036 30.769 0.00 0.00 35.38 2.57
1735 1948 6.005823 ACTAGCCAGTTTTTAAACCGGTATT 58.994 36.000 8.00 7.41 38.45 1.89
1736 1949 5.563592 ACTAGCCAGTTTTTAAACCGGTAT 58.436 37.500 8.00 0.00 38.45 2.73
1737 1950 4.971939 ACTAGCCAGTTTTTAAACCGGTA 58.028 39.130 8.00 0.00 38.45 4.02
1738 1951 3.824133 ACTAGCCAGTTTTTAAACCGGT 58.176 40.909 0.00 0.00 38.45 5.28
1769 1984 6.071334 AGCTACAAGTAATCACTAAGCAGTCA 60.071 38.462 0.00 0.00 37.50 3.41
1859 2074 7.144722 TGTTTGGCTAGAAACATGATTGTAG 57.855 36.000 13.59 13.59 40.18 2.74
1878 2107 9.872757 AACAATACGTTAAGACAGTTATGTTTG 57.127 29.630 0.00 0.00 36.35 2.93
1891 2120 7.285788 ACGCAAAGAGTAAACAATACGTTAAG 58.714 34.615 0.00 0.00 36.59 1.85
1895 2124 5.234757 TCAACGCAAAGAGTAAACAATACGT 59.765 36.000 0.00 0.00 0.00 3.57
1905 2134 5.073311 AGCTAAGATCAACGCAAAGAGTA 57.927 39.130 0.00 0.00 0.00 2.59
1914 2143 4.576463 AGGGCAATTTAGCTAAGATCAACG 59.424 41.667 6.24 0.00 34.17 4.10
1932 2161 0.178903 ACCCAGTTCTCTGTAGGGCA 60.179 55.000 0.00 0.00 39.82 5.36
1933 2162 0.984995 AACCCAGTTCTCTGTAGGGC 59.015 55.000 0.00 0.00 39.82 5.19
1941 2170 4.202172 GCTATCCTGACTAACCCAGTTCTC 60.202 50.000 0.00 0.00 37.72 2.87
1982 2211 4.445452 ACAGATGCATGGCTTAAAACTG 57.555 40.909 2.46 4.18 0.00 3.16
1983 2212 5.010922 TCAAACAGATGCATGGCTTAAAACT 59.989 36.000 2.46 0.00 0.00 2.66
1984 2213 5.229423 TCAAACAGATGCATGGCTTAAAAC 58.771 37.500 2.46 0.00 0.00 2.43
1985 2214 5.243507 TCTCAAACAGATGCATGGCTTAAAA 59.756 36.000 2.46 0.00 0.00 1.52
1986 2215 4.766373 TCTCAAACAGATGCATGGCTTAAA 59.234 37.500 2.46 0.00 0.00 1.52
1987 2216 4.334552 TCTCAAACAGATGCATGGCTTAA 58.665 39.130 2.46 0.00 0.00 1.85
1988 2217 3.954200 TCTCAAACAGATGCATGGCTTA 58.046 40.909 2.46 0.00 0.00 3.09
1989 2218 2.799017 TCTCAAACAGATGCATGGCTT 58.201 42.857 2.46 0.00 0.00 4.35
1990 2219 2.502142 TCTCAAACAGATGCATGGCT 57.498 45.000 2.46 0.00 0.00 4.75
1991 2220 3.795623 AATCTCAAACAGATGCATGGC 57.204 42.857 2.46 0.00 41.47 4.40
1992 2221 3.863424 GCAAATCTCAAACAGATGCATGG 59.137 43.478 2.46 0.00 41.47 3.66
1998 2227 7.275888 TGTAAACTGCAAATCTCAAACAGAT 57.724 32.000 0.00 0.00 44.56 2.90
2050 2279 6.349611 CCAATGATCAGGGTGAAACTTTGTAG 60.350 42.308 0.09 0.00 36.74 2.74
2193 2422 1.834263 AGTCTGGAACTGCATAGGACC 59.166 52.381 0.00 0.00 36.65 4.46
2435 2664 4.884668 TCCTCTTGGTTCGTAACTCATT 57.115 40.909 0.00 0.00 34.23 2.57
2458 2687 2.537633 TGGTACATAACTCCTCGGGT 57.462 50.000 0.00 0.00 0.00 5.28
2516 2745 2.042569 TGGGCTCTGGTAGTAGTTCTCA 59.957 50.000 0.00 0.00 0.00 3.27
2531 2760 1.258445 TTCCTCTCGAACCTGGGCTC 61.258 60.000 0.00 0.00 0.00 4.70
2709 2938 3.751175 TGATTAGGTGTCTCCTTTTTGCG 59.249 43.478 0.00 0.00 45.67 4.85
2741 2970 1.005450 GGGCTGTGGTAGAAATTCCCA 59.995 52.381 0.00 0.00 32.89 4.37
2743 2972 2.369394 CTGGGCTGTGGTAGAAATTCC 58.631 52.381 0.00 0.00 0.00 3.01
2747 2976 1.073284 GAACCTGGGCTGTGGTAGAAA 59.927 52.381 0.00 0.00 35.17 2.52
2749 2978 1.541310 CGAACCTGGGCTGTGGTAGA 61.541 60.000 0.00 0.00 35.17 2.59
2810 3039 3.450457 AGAAGTTCCTCTGATCTTGCGAT 59.550 43.478 0.00 0.00 32.06 4.58
2909 3138 2.347490 GGAAGCCAGGACTTCGCA 59.653 61.111 14.08 0.00 45.78 5.10
2929 3158 1.952990 TCTCCTTTTTGCGCAATGACA 59.047 42.857 25.64 5.79 0.00 3.58
2990 3219 3.181471 CGAGGTATTCTGCCAGACTCAAT 60.181 47.826 9.81 0.00 0.00 2.57
3069 3299 0.250467 GCTGAAAGGAGGCACTGACA 60.250 55.000 0.00 0.00 41.55 3.58
3070 3300 0.250467 TGCTGAAAGGAGGCACTGAC 60.250 55.000 0.00 0.00 41.55 3.51
3071 3301 0.694771 ATGCTGAAAGGAGGCACTGA 59.305 50.000 0.00 0.00 38.10 3.41
3072 3302 2.408271 TATGCTGAAAGGAGGCACTG 57.592 50.000 0.00 0.00 38.10 3.66
3073 3303 3.084786 GTTTATGCTGAAAGGAGGCACT 58.915 45.455 0.00 0.00 38.10 4.40
3075 3305 3.439857 AGTTTATGCTGAAAGGAGGCA 57.560 42.857 0.00 0.00 38.10 4.75
3076 3306 4.790765 AAAGTTTATGCTGAAAGGAGGC 57.209 40.909 0.00 0.00 38.10 4.70
3077 3307 6.089249 ACAAAAGTTTATGCTGAAAGGAGG 57.911 37.500 0.00 0.00 38.10 4.30
3078 3308 7.084486 GGTACAAAAGTTTATGCTGAAAGGAG 58.916 38.462 0.00 0.00 38.10 3.69
3222 3478 4.732784 CCACAATGTGCATAAACAGTACC 58.267 43.478 8.05 0.00 32.52 3.34
3238 3494 3.091545 CAAGGTACAAGATGGCCACAAT 58.908 45.455 8.16 0.00 0.00 2.71
3309 3567 6.955963 GGTTTAGCTCATGAAAATATATCGCG 59.044 38.462 0.00 0.00 0.00 5.87
3345 3603 1.701847 ACCACCTGGCTCCATGATATC 59.298 52.381 0.00 0.00 39.32 1.63
3348 3606 1.595311 TTACCACCTGGCTCCATGAT 58.405 50.000 0.00 0.00 39.32 2.45
3349 3607 1.367346 TTTACCACCTGGCTCCATGA 58.633 50.000 0.00 0.00 39.32 3.07
3350 3608 2.214376 TTTTACCACCTGGCTCCATG 57.786 50.000 0.00 0.00 39.32 3.66
3351 3609 3.099141 CAATTTTACCACCTGGCTCCAT 58.901 45.455 0.00 0.00 39.32 3.41
3363 3621 2.979813 CAACTCAGCGTGCAATTTTACC 59.020 45.455 0.00 0.00 0.00 2.85
3366 3624 1.408702 ACCAACTCAGCGTGCAATTTT 59.591 42.857 0.00 0.00 0.00 1.82
3381 3639 2.159114 ACCACACAAGAATGCAACCAAC 60.159 45.455 0.00 0.00 0.00 3.77
3465 3730 5.049886 GCATCATGAAGAGCGATATCACAAA 60.050 40.000 0.00 0.00 0.00 2.83
3682 3955 2.719739 CAGACATGCTCACCTTCCATT 58.280 47.619 0.00 0.00 0.00 3.16
3712 3985 2.489971 GGTTCATGTCGAAGTTCACCA 58.510 47.619 3.32 0.00 33.09 4.17
3713 3986 1.459592 CGGTTCATGTCGAAGTTCACC 59.540 52.381 3.32 0.13 33.09 4.02
3752 4025 0.675633 ACTTTGTGGATGCCTGTTGC 59.324 50.000 0.00 0.00 41.77 4.17
3903 4177 3.217626 CTCACTTGAGTTGCCCTTTCTT 58.782 45.455 0.00 0.00 37.40 2.52
3909 4183 0.819259 TGTGCTCACTTGAGTTGCCC 60.819 55.000 8.04 0.00 43.85 5.36
4003 4278 1.071605 CCCTCTTTTGCTCGTCTTCG 58.928 55.000 0.00 0.00 38.55 3.79
4042 4317 6.596497 TCTTAATTCCTTTCATGTACCGTTCC 59.404 38.462 0.00 0.00 0.00 3.62


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

AutoCloner maintained by Alex Coulton.