Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005350.1 Hibiscus syriacus cultivar Beakdansim tig00012146_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 53749
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:13406 original size:28 final size:28
Alignment explanation
Indices: 13374--13437 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
13364 TCCATAACAA
* *
13374 AGTTTTGACTATTAGTTTCCGGACCTTG
1 AGTTTTGACTATTAGTTCCCGGACCTAG
13402 AGTTTTGACTATTAGTTCCCGGACCTAG
1 AGTTTTGACTATTAGTTCCCGGACCTAG
13430 AGTTTTGA
1 AGTTTTGA
13438 TGTTTGAGCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.41
Consensus pattern (28 bp):
AGTTTTGACTATTAGTTCCCGGACCTAG
Found at i:15814 original size:34 final size:32
Alignment explanation
Indices: 15751--15812 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
15741 AAATGATGAT
15751 ATAATATGTACTAAATTATCTAAAATAATAAC
1 ATAATATGTACTAAATTATCTAAAATAATAAC
* * *
15783 ATAATATGT-GTACATTATCTAAAATGATAA
1 ATAATATGTACTAAATTATCTAAAATAATAA
15813 TATGATATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 18 0.67
32 9 0.33
ACGTcount: A:0.50, C:0.08, G:0.06, T:0.35
Consensus pattern (32 bp):
ATAATATGTACTAAATTATCTAAAATAATAAC
Found at i:17829 original size:21 final size:22
Alignment explanation
Indices: 17792--17833 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
17782 TGCTTATTTT
17792 TTAAAAAAAAATAATAATATAG
1 TTAAAAAAAAATAATAATATAG
*
17814 TTAATAAAAAAT-ATAATATA
1 TTAAAAAAAAATAATAATATA
17834 TAAAATATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (22 bp):
TTAAAAAAAAATAATAATATAG
Found at i:17840 original size:21 final size:22
Alignment explanation
Indices: 17793--17837 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
17783 GCTTATTTTT
17793 TAAA-AAAAAATAATAATATAG
1 TAAATAAAAAATAATAATATAG
*
17814 TTAATAAAAAAT-ATAATATA-
1 TAAATAAAAAATAATAATATAG
17834 TAAA
1 TAAA
17838 ATATGCTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
20 3 0.14
21 11 0.52
22 7 0.33
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (22 bp):
TAAATAAAAAATAATAATATAG
Found at i:18009 original size:16 final size:16
Alignment explanation
Indices: 17990--18025 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
17980 AATTCAATGT
17990 GATATAAATTAATAAA
1 GATATAAATTAATAAA
18006 GATATAAATTAATAAA
1 GATATAAATTAATAAA
18022 GATA
1 GATA
18026 AATTTGACGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.31
Consensus pattern (16 bp):
GATATAAATTAATAAA
Found at i:18063 original size:17 final size:16
Alignment explanation
Indices: 18041--18093 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 16
18031 GACGGTCAAC
18041 GGTCAACGGTCGGGTCG
1 GGTCAAC-GTCGGGTCG
*
18058 GGTCAA--T--AGTCG
1 GGTCAACGTCGGGTCG
18070 GGTCAACAGTCGGGTCG
1 GGTCAAC-GTCGGGTCG
18087 GGTCAAC
1 GGTCAAC
18094 CCGGTTTAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
12 10 0.34
14 1 0.03
15 1 0.03
17 17 0.59
ACGTcount: A:0.19, C:0.23, G:0.40, T:0.19
Consensus pattern (16 bp):
GGTCAACGTCGGGTCG
Found at i:18069 original size:12 final size:12
Alignment explanation
Indices: 18054--18085 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
18044 CAACGGTCGG
*
18054 GTCGGGTCAATA
1 GTCGGGTCAACA
18066 GTCGGGTCAACA
1 GTCGGGTCAACA
18078 GTCGGGTC
1 GTCGGGTC
18086 GGGTCAACCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.22, G:0.38, T:0.22
Consensus pattern (12 bp):
GTCGGGTCAACA
Found at i:18111 original size:19 final size:19
Alignment explanation
Indices: 18087--18157 Score: 99
Period size: 19 Copynumber: 3.7 Consensus size: 19
18077 AGTCGGGTCG
*
18087 GGTCAACCCGGTTTAGACC
1 GGTCAAACCGGTTTAGACC
*
18106 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTTAGACC
*
18125 GGTCAAACCGG-TTCGAACC
1 GGTCAAACCGGTTTAG-ACC
18144 GGTCAAACCGGTTT
1 GGTCAAACCGGTTT
18158 TCCAGCAGCT
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
18 2 0.04
19 42 0.91
20 2 0.04
ACGTcount: A:0.24, C:0.30, G:0.27, T:0.20
Consensus pattern (19 bp):
GGTCAAACCGGTTTAGACC
Found at i:18117 original size:9 final size:9
Alignment explanation
Indices: 18103--18155 Score: 70
Period size: 9 Copynumber: 5.7 Consensus size: 9
18093 CCCGGTTTAG
18103 ACCGGTCAA
1 ACCGGTCAA
*
18112 ACCGGTTCAG
1 ACCGG-TCAA
18122 ACCGGTCAA
1 ACCGGTCAA
*
18131 ACCGGTTCGA
1 ACCGG-TCAA
18141 ACCGGTCAA
1 ACCGGTCAA
18150 ACCGGT
1 ACCGGT
18156 TTTCCAGCAG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
9 22 0.58
10 16 0.42
ACGTcount: A:0.26, C:0.32, G:0.26, T:0.15
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:18873 original size:4 final size:4
Alignment explanation
Indices: 18864--19334 Score: 928
Period size: 4 Copynumber: 118.2 Consensus size: 4
18854 AATTTTATAA
18864 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
18912 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
18960 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
19008 ATGT ATGT ATGT ATGT A--T ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
19054 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
19102 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
19150 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
19198 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
19246 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
19294 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
19335 ACCCCCTAGA
Statistics
Matches: 465, Mismatches: 0, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
2 2 0.00
4 463 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:20868 original size:7 final size:7
Alignment explanation
Indices: 20848--20884 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
20838 GTCAAAGAAA
20848 GTCAACG
1 GTCAACG
20855 GTC-ACG
1 GTCAACG
20861 GTCAACG
1 GTCAACG
20868 GTCAACG
1 GTCAACG
20875 GTCAACG
1 GTCAACG
20882 GTC
1 GTC
20885 GGGTCGGGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:20896 original size:17 final size:17
Alignment explanation
Indices: 20874--20914 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
20864 AACGGTCAAC
*
20874 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
20891 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
20908 GGTCAAC
1 GGTCAAC
20915 CCGGTTTAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.17, C:0.24, G:0.41, T:0.17
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:20932 original size:19 final size:19
Alignment explanation
Indices: 20908--20977 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
20898 AGTCGGGTCG
* *
20908 GGTCAACCCGGTTTAGACC
1 GGTCAAACCGGTTCAGACC
20927 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
*
20946 GGTCAAACCGGTTC-GAACT
1 GGTCAAACCGGTTCAG-ACC
*
20965 GATCAAACCGGTT
1 GGTCAAACCGGTT
20978 TTCCAGCAGC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
18 1 0.02
19 45 0.98
ACGTcount: A:0.26, C:0.29, G:0.26, T:0.20
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:20946 original size:10 final size:10
Alignment explanation
Indices: 20910--20977 Score: 52
Period size: 9 Copynumber: 7.1 Consensus size: 10
20900 TCGGGTCGGG
*
20910 TCAACCCGGT
1 TCAAACCGGT
* *
20920 TTAGACCGG-
1 TCAAACCGGT
20929 TCAAACCGGT
1 TCAAACCGGT
*
20939 TCAGACCGG-
1 TCAAACCGGT
20948 TCAAACCGGT
1 TCAAACCGGT
* * *
20958 TCGAA-CTGA
1 TCAAACCGGT
20967 TCAAACCGGT
1 TCAAACCGGT
20977 T
1 T
20978 TTCCAGCAGC
Statistics
Matches: 42, Mismatches: 13, Indels: 6
0.69 0.21 0.10
Matches are distributed among these distances:
9 21 0.50
10 21 0.50
ACGTcount: A:0.26, C:0.29, G:0.24, T:0.21
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:22969 original size:17 final size:16
Alignment explanation
Indices: 22947--22999 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 16
22937 AACGGTCAAC
22947 GGTCAACGGTCGGGTCG
1 GGTCAAC-GTCGGGTCG
*
22964 GGTCAA--T--AGTCG
1 GGTCAACGTCGGGTCG
22976 GGTCAACAGTCGGGTCG
1 GGTCAAC-GTCGGGTCG
22993 GGTCAAC
1 GGTCAAC
23000 CCGGTTTAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
12 10 0.34
14 1 0.03
15 1 0.03
17 17 0.59
ACGTcount: A:0.19, C:0.23, G:0.40, T:0.19
Consensus pattern (16 bp):
GGTCAACGTCGGGTCG
Found at i:22975 original size:12 final size:12
Alignment explanation
Indices: 22960--22991 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
22950 CAACGGTCGG
*
22960 GTCGGGTCAATA
1 GTCGGGTCAACA
22972 GTCGGGTCAACA
1 GTCGGGTCAACA
22984 GTCGGGTC
1 GTCGGGTC
22992 GGGTCAACCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.22, G:0.38, T:0.22
Consensus pattern (12 bp):
GTCGGGTCAACA
Found at i:23022 original size:19 final size:19
Alignment explanation
Indices: 22993--23063 Score: 90
Period size: 19 Copynumber: 3.7 Consensus size: 19
22983 AGTCGGGTCG
*
22993 GGTCAACCCGGTTTAGACC
1 GGTCAAACCGGTTTAGACC
* *
23012 AGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTTAGACC
*
23031 GGTCAAACCGG-TTCGAACC
1 GGTCAAACCGGTTTAG-ACC
23050 GGTCAAACCGGTTT
1 GGTCAAACCGGTTT
23064 TCCAGCAGCT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
18 2 0.05
19 40 0.91
20 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.25, T:0.20
Consensus pattern (19 bp):
GGTCAAACCGGTTTAGACC
Found at i:23042 original size:9 final size:9
Alignment explanation
Indices: 23013--23061 Score: 62
Period size: 9 Copynumber: 5.2 Consensus size: 9
23003 GTTTAGACCA
23013 GTCAAACCG
1 GTCAAACCG
*
23022 GTTCAGACCG
1 G-TCAAACCG
23032 GTCAAACCG
1 GTCAAACCG
*
23041 GTTCGAACCG
1 G-TCAAACCG
23051 GTCAAACCG
1 GTCAAACCG
23060 GT
1 GT
23062 TTTCCAGCAG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
9 18 0.53
10 16 0.47
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.16
Consensus pattern (9 bp):
GTCAAACCG
Found at i:23792 original size:4 final size:4
Alignment explanation
Indices: 23783--24868 Score: 2144
Period size: 4 Copynumber: 272.5 Consensus size: 4
23773 GGTTGTTACA
23783 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
23831 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
23879 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
23927 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
23975 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A--T
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
24021 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
24069 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
24117 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
24165 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
24213 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
24261 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
24309 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
24357 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
24405 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
24453 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
24501 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
24549 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
24597 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
24645 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
24693 ATGT ATGT ATGT ATGT ATGT ATGT A--T ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
24739 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
24787 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
24835 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
24869 TGCCTGCATG
Statistics
Matches: 1078, Mismatches: 0, Indels: 8
0.99 0.00 0.01
Matches are distributed among these distances:
2 4 0.00
4 1074 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:25522 original size:12 final size:12
Alignment explanation
Indices: 25505--25532 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
25495 GGACTTTTTG
25505 GAAAATTGAGAA
1 GAAAATTGAGAA
25517 GAAAATTGAGAA
1 GAAAATTGAGAA
25529 GAAA
1 GAAA
25533 TGGAGTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.25, T:0.14
Consensus pattern (12 bp):
GAAAATTGAGAA
Found at i:28606 original size:22 final size:22
Alignment explanation
Indices: 28581--28632 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
28571 AAAACATTAA
*
28581 AAAAATAATATATATAATTTA-T
1 AAAAATAAAATAT-TAATTTATT
*
28603 AAAAATAAAATATTTATTTATTT
1 AAAAATAAAATATTAATTTA-TT
28626 AAAAATA
1 AAAAATA
28633 TCAGAAAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 6 0.23
22 12 0.46
23 8 0.31
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAAATAAAATATTAATTTATT
Found at i:28813 original size:3 final size:3
Alignment explanation
Indices: 28805--28840 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
28795 ATATCTGTAG
*
28805 TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
28841 ATAAATAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:30415 original size:3 final size:3
Alignment explanation
Indices: 30407--30463 Score: 78
Period size: 3 Copynumber: 18.3 Consensus size: 3
30397 TATATGTATT
* *
30407 TAA TAA TAA TAAA TAA TAA TAA TAA TAA TAA TAA TATA TTA TAT TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
30454 TAA TAA TAA T
1 TAA TAA TAA T
30464 TATTATATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
3 43 0.90
4 5 0.10
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:30435 original size:22 final size:24
Alignment explanation
Indices: 30408--30471 Score: 80
Period size: 25 Copynumber: 2.8 Consensus size: 24
30398 ATATGTATTT
30408 AATAATAATAA-ATA-ATAATAAT
1 AATAATAATAATATATATAATAAT
*
30430 AATAATAATAATATATTATATTAAT
1 AATAATAATAATATA-TATAATAAT
*
30455 AATAATAATTAT-TATAT
1 AATAATAATAATATATAT
30472 TTATGAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
22 11 0.30
23 6 0.16
24 2 0.05
25 18 0.49
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
AATAATAATAATATATATAATAAT
Found at i:30646 original size:46 final size:46
Alignment explanation
Indices: 30571--31018 Score: 772
Period size: 46 Copynumber: 9.8 Consensus size: 46
30561 GACGAAAATG
* * *
30571 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACTCAAAGGTT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
*
30617 TTTGAAAACATCATGCACTAAAGGACTTACAGATGACCCGAAGGTT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
*
30663 TTTGAAAACATCATGCTCTGAAGGACTTACAGATGACCCGAAGGTT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
30709 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
30755 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
*
30801 TTTGAAAACATCATGCACTGAAGAACTTACAGATGACCCGAAGGTT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
30847 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
* * *
30893 TTTGAAAACATCATGTACTAAAAGACTTACAGATGACCCGAAGGTT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
* *
30939 TTTGAAAACATCATACACTGAAGG-CTTACAAATGACCCGAAGGTT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
* *
30984 TTTGAAAACATCATGTACTGAAAGACTTACAGATG
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATG
31019 CGAGAAATAG
Statistics
Matches: 380, Mismatches: 21, Indels: 2
0.94 0.05 0.00
Matches are distributed among these distances:
45 41 0.11
46 339 0.89
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (46 bp):
TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
Found at i:31571 original size:25 final size:25
Alignment explanation
Indices: 31537--31597 Score: 122
Period size: 25 Copynumber: 2.4 Consensus size: 25
31527 CTTGTATATT
31537 TGTTTCATTTAAGTCTCAGAAGAAA
1 TGTTTCATTTAAGTCTCAGAAGAAA
31562 TGTTTCATTTAAGTCTCAGAAGAAA
1 TGTTTCATTTAAGTCTCAGAAGAAA
31587 TGTTTCATTTA
1 TGTTTCATTTA
31598 TGGAACTCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (25 bp):
TGTTTCATTTAAGTCTCAGAAGAAA
Found at i:37904 original size:370 final size:371
Alignment explanation
Indices: 37222--37967 Score: 1476
Period size: 370 Copynumber: 2.0 Consensus size: 371
37212 TGAAAAAGAA
37222 TATTTAATGTACTTGATATTCAAAAATTTCAAGATTAAAATTTAATTCCTTGTTCATAACTATAA
1 TATTTAATGTACTTGATATTCAAAAATTTCAAGATTAAAATTTAATTCCTTGTTCATAACTATAA
37287 AAGCAACACATGTTTATTTATTGCACAAAAAGCGGAGAAAGGAACAACAAAAAAAAAGTTCAAAC
66 AAGCAACACATGTTTATTTATTGCACAAAAAGCGGAGAAAGGAACAACAAAAAAAAAGTTCAAAC
37352 AAGATGCTGAAAATAGAAAAGTACTACAGTGGTAGATAACACTTCCACTTGTTTATGCATCATTA
131 AAGATGCTGAAAATAGAAAAGTACTACAGTGGTAGATAACACTTCCACTTGTTTATGCATCATTA
37417 CTCCTCTAATGTTGGGTGTGTAATAGGATCAGGGTCATTATCCTCATTTGCCCCTCATTTCTTGA
196 CTCCTCTAATGTTGGGTGTGTAATAGGATCAGGGTCATTATCCTCATTTGCCCCTCATTTCTTGA
37482 TCATTTCTTGCGTCAAGACTCCCTTGTCAACAAGCATCTTTATTTCTTTTAATAGTGGCCAATAA
261 TCATTTCTTGCGTCAAGACTCCCTTGTCAACAAGCATCTTTATTTCTTTTAATAGTGGCCAATAA
37547 TTCCCTGTTGAATGCCCCTTCACCCCCAAGTGAAACTTGCAGAAAC
326 TTCCCTGTTGAATGCCCCTTCACCCCCAAGTGAAACTTGCAGAAAC
37593 TATTTAATGTACTTGATATTCAAAAATTTCAAGATTAAAATTTAATTCCTTGTTCATAACTATAA
1 TATTTAATGTACTTGATATTCAAAAATTTCAAGATTAAAATTTAATTCCTTGTTCATAACTATAA
*
37658 AAGCAACACATGTTTATTTATTGCACAAAAAGCGGAGAAAGGAACAACAACAAAAAAGTTCAAAC
66 AAGCAACACATGTTTATTTATTGCACAAAAAGCGGAGAAAGGAACAACAAAAAAAAAGTTCAAAC
37723 AAGATGCTG-AAATAGAAAAGTACTACAGTGGTAGATAACACTTCCACTTGTTTATGCATCATTA
131 AAGATGCTGAAAATAGAAAAGTACTACAGTGGTAGATAACACTTCCACTTGTTTATGCATCATTA
37787 CTCCTCTAATGTTGGGTGTGTAATAGGATCAGGGTCATTATCCTCATTTGCCCCTCATTTCTTGA
196 CTCCTCTAATGTTGGGTGTGTAATAGGATCAGGGTCATTATCCTCATTTGCCCCTCATTTCTTGA
37852 TCATTTCTTGCGTCAAGACTCCCTTGTCAACAAGCATCTTTATTTCTTTTAATAGTGGCCAATAA
261 TCATTTCTTGCGTCAAGACTCCCTTGTCAACAAGCATCTTTATTTCTTTTAATAGTGGCCAATAA
37917 TTCCCTGTTGAATGCCCCTTCACCCCCAAGTGAAACTTGCAGAAAC
326 TTCCCTGTTGAATGCCCCTTCACCCCCAAGTGAAACTTGCAGAAAC
37963 TATTT
1 TATTT
37968 TGATCATAGC
Statistics
Matches: 374, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
370 236 0.63
371 138 0.37
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (371 bp):
TATTTAATGTACTTGATATTCAAAAATTTCAAGATTAAAATTTAATTCCTTGTTCATAACTATAA
AAGCAACACATGTTTATTTATTGCACAAAAAGCGGAGAAAGGAACAACAAAAAAAAAGTTCAAAC
AAGATGCTGAAAATAGAAAAGTACTACAGTGGTAGATAACACTTCCACTTGTTTATGCATCATTA
CTCCTCTAATGTTGGGTGTGTAATAGGATCAGGGTCATTATCCTCATTTGCCCCTCATTTCTTGA
TCATTTCTTGCGTCAAGACTCCCTTGTCAACAAGCATCTTTATTTCTTTTAATAGTGGCCAATAA
TTCCCTGTTGAATGCCCCTTCACCCCCAAGTGAAACTTGCAGAAAC
Found at i:39232 original size:14 final size:14
Alignment explanation
Indices: 39213--39243 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
39203 TTAACAAATA
39213 AAAAATGTAAATGT
1 AAAAATGTAAATGT
39227 AAAAATGTAAATGT
1 AAAAATGTAAATGT
39241 AAA
1 AAA
39244 TTATTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.13, T:0.26
Consensus pattern (14 bp):
AAAAATGTAAATGT
Found at i:42411 original size:31 final size:31
Alignment explanation
Indices: 42354--42412 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
42344 CATTTCTTAA
42354 TAAAAAAAATAAATAAATGTTAATAAAACAT
1 TAAAAAAAATAAATAAATGTTAATAAAACAT
*
42385 TAAAAAATAATATATATAAT-TT-ATAAAA
1 TAAAAAA-AATAAATA-AATGTTAATAAAA
42413 ATAAAATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
31 13 0.52
32 9 0.36
33 3 0.12
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (31 bp):
TAAAAAAAATAAATAAATGTTAATAAAACAT
Found at i:42415 original size:22 final size:22
Alignment explanation
Indices: 42387--42438 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
42377 TAAAACATTA
*
42387 AAAAATAATATATATAATTTA-T
1 AAAAATAAAATAT-TAATTTATT
*
42409 AAAAATAAAATATTTATTTATTT
1 AAAAATAAAATATTAATTTA-TT
42432 AAAAATA
1 AAAAATA
42439 TCAGAAAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 6 0.23
22 12 0.46
23 8 0.31
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAAATAAAATATTAATTTATT
Found at i:42606 original size:3 final size:3
Alignment explanation
Indices: 42600--42626 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
42590 ATATATATTG
42600 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
42627 ATAAATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:44158 original size:21 final size:21
Alignment explanation
Indices: 44133--44175 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
44123 TAATAAATAA
44133 TAATAATAA-TATATATTATAT
1 TAATAATAATTAT-TATTATAT
*
44154 TAATAATTATTATTATTATAT
1 TAATAATAATTATTATTATAT
44175 T
1 T
44176 TATGAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TAATAATAATTATTATTATAT
Found at i:46367 original size:2 final size:2
Alignment explanation
Indices: 46360--46390 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
46350 ATAGGTCATC
46360 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
46391 CTACATGACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:47615 original size:41 final size:40
Alignment explanation
Indices: 47552--47664 Score: 192
Period size: 41 Copynumber: 2.8 Consensus size: 40
47542 ACCCCAAAGG
* *
47552 CCCAAAC-ACAACAAAACACACACAAACACCCATACATAC
1 CCCAAACTACAACAAAACTCACACCAACACCCATACATAC
47591 CCCAAACTACAACAAAAACTCACACCAACACCCATACATAC
1 CCCAAACTACAAC-AAAACTCACACCAACACCCATACATAC
47632 CCCAAACTACAACAAAACTCACACCAACACCCA
1 CCCAAACTACAACAAAACTCACACCAACACCCA
47665 ATGACAACGA
Statistics
Matches: 70, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
39 7 0.10
40 25 0.36
41 38 0.54
ACGTcount: A:0.50, C:0.42, G:0.00, T:0.07
Consensus pattern (40 bp):
CCCAAACTACAACAAAACTCACACCAACACCCATACATAC
Done.