Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004933.1 Hibiscus syriacus cultivar Beakdansim tig00011099_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: 67110
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:211 original size:25 final size:26
Alignment explanation
Indices: 175--240 Score: 116
Period size: 25 Copynumber: 2.6 Consensus size: 26
165 ATCTTTTTCT
*
175 TAACCTTTTCTATCCTACCCCTATCA
1 TAACCATTTCTATCCTACCCCTATCA
201 TAACCA-TTCTATCCTACCCCTATCA
1 TAACCATTTCTATCCTACCCCTATCA
226 TAACCATTTCTATCC
1 TAACCATTTCTATCC
241 CTAACCATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
25 25 0.66
26 13 0.34
ACGTcount: A:0.26, C:0.38, G:0.00, T:0.36
Consensus pattern (26 bp):
TAACCATTTCTATCCTACCCCTATCA
Found at i:5615 original size:36 final size:37
Alignment explanation
Indices: 5575--5648 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 37
5565 CAAAAAGGAA
5575 CAAAAAAAAGAAAGTAG-AGCACTCATTAAAAATTCT
1 CAAAAAAAAGAAAGTAGAAGCACTCATTAAAAATTCT
* * *
5611 C-AAAAGAAGAAAGTTGAAGCACTCGTTAAAAATTCT
1 CAAAAAAAAGAAAGTAGAAGCACTCATTAAAAATTCT
5647 CA
1 CA
5649 TCACCAAGCC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
35 13 0.39
36 20 0.61
ACGTcount: A:0.51, C:0.15, G:0.14, T:0.20
Consensus pattern (37 bp):
CAAAAAAAAGAAAGTAGAAGCACTCATTAAAAATTCT
Found at i:14694 original size:13 final size:13
Alignment explanation
Indices: 14672--14707 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
14662 AAAGCAACAA
14672 AAAG-AGAAAAAT
1 AAAGAAGAAAAAT
14684 AAAGAAGAAAAAT
1 AAAGAAGAAAAAT
14697 AAAGAA-AAAAA
1 AAAGAAGAAAAA
14708 GAAAAGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 9 0.39
13 14 0.61
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.06
Consensus pattern (13 bp):
AAAGAAGAAAAAT
Found at i:14713 original size:13 final size:12
Alignment explanation
Indices: 14670--14717 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
14660 CAAAAGCAAC
*
14670 AAAAAGAGAAAA
1 AAAAAGAAAAAA
*
14682 ATAAAGAAGAAAA
1 AAAAAGAA-AAAA
*
14695 ATAAAGAAAAAA
1 AAAAAGAAAAAA
14707 AGAAAAGAAAA
1 A-AAAAGAAAA
14718 TGACTCCTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
12 11 0.35
13 20 0.65
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (12 bp):
AAAAAGAAAAAA
Found at i:21839 original size:11 final size:11
Alignment explanation
Indices: 21813--21847 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
21803 AATTCTTATC
21813 TTTATTATTCCA
1 TTTATTATT-CA
21825 TTTATTATTCA
1 TTTATTATTCA
*
21836 TTTATTAATCA
1 TTTATTATTCA
21847 T
1 T
21848 ATTCCTTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 13 0.59
12 9 0.41
ACGTcount: A:0.29, C:0.11, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTATTATTCA
Found at i:23189 original size:24 final size:24
Alignment explanation
Indices: 23138--23192 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
23128 CTTTCTTTCT
* * *
23138 TTTTCATCTTTTTGAGTGCTTAAG
1 TTTTCTTCTTTTGGAGTGCTTAAC
*
23162 TTTTCTTCTTTTGGAGTGCTTGAC
1 TTTTCTTCTTTTGGAGTGCTTAAC
23186 TTTTCTT
1 TTTTCTT
23193 TGCTGATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.11, C:0.15, G:0.16, T:0.58
Consensus pattern (24 bp):
TTTTCTTCTTTTGGAGTGCTTAAC
Found at i:33086 original size:19 final size:20
Alignment explanation
Indices: 33048--33097 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
33038 GAAACCCCTT
33048 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTTAA
*
33068 TGAAAATGCATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
33087 TGAAGATACAT
1 TGAAAATACAT
33098 TCTCTTGGCC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.36
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:37378 original size:16 final size:16
Alignment explanation
Indices: 37357--37388 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
37347 TTATACAAAT
37357 GGGTAAAGAAAAGCAA
1 GGGTAAAGAAAAGCAA
37373 GGGTAAAGAAAAGCAA
1 GGGTAAAGAAAAGCAA
37389 ACCAGCACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.06, G:0.31, T:0.06
Consensus pattern (16 bp):
GGGTAAAGAAAAGCAA
Found at i:53123 original size:11 final size:12
Alignment explanation
Indices: 53107--53135 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
53097 GGATGTTTCT
53107 ATGGTGAT-GAA
1 ATGGTGATGGAA
53118 ATGGTGATGGAA
1 ATGGTGATGGAA
53130 ATGGTG
1 ATGGTG
53136 TAGGTGCAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 8 0.47
12 9 0.53
ACGTcount: A:0.31, C:0.00, G:0.41, T:0.28
Consensus pattern (12 bp):
ATGGTGATGGAA
Found at i:53559 original size:19 final size:20
Alignment explanation
Indices: 53509--53550 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
53499 GAAACCCCTT
53509 TGAAAATACATGATTTCTAA
1 TGAAAATACATGATTTCTAA
53529 TGAAAATACATGATTT-TAA
1 TGAAAATACATGATTTCTAA
53548 TGA
1 TGA
53551 TGATGCATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.36
Consensus pattern (20 bp):
TGAAAATACATGATTTCTAA
Found at i:53950 original size:39 final size:39
Alignment explanation
Indices: 53907--53998 Score: 148
Period size: 39 Copynumber: 2.4 Consensus size: 39
53897 AACTCAAGCT
*
53907 AGTTAGCTTTAGTCTTCTCAGCTCCTCAGCTACTCTGCC
1 AGTTAGCTTTAGTCTTCTCAGCTCCTCAGCTACTCTCCC
*
53946 AGTTAGCTTTGGTCTTCTCAGCTCCTCAGCTACTCTCCC
1 AGTTAGCTTTAGTCTTCTCAGCTCCTCAGCTACTCTCCC
* *
53985 AGCTACCTTTAGTC
1 AGTTAGCTTTAGTC
53999 CACTTTTCAG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.15, C:0.34, G:0.15, T:0.36
Consensus pattern (39 bp):
AGTTAGCTTTAGTCTTCTCAGCTCCTCAGCTACTCTCCC
Found at i:61365 original size:13 final size:13
Alignment explanation
Indices: 61347--61378 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
61337 TATTTTTTTC
61347 AAAAAAAACAACA
1 AAAAAAAACAACA
61360 AAAAAAAACAACA
1 AAAAAAAACAACA
61373 AAAAAA
1 AAAAAA
61379 GAGGCAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAACAACA
Found at i:66065 original size:11 final size:11
Alignment explanation
Indices: 66049--66097 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
66039 TATTTTTTTC
66049 AAAAAAAACAA
1 AAAAAAAACAA
*
66060 AAAAAAGAGGC-A
1 AAAAAA-A-ACAA
*
66072 AAAACAAACAA
1 AAAAAAAACAA
66083 AAAAAAAACAA
1 AAAAAAAACAA
66094 AAAA
1 AAAA
66098 TCCAAAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
10 1 0.03
11 22 0.71
12 7 0.23
13 1 0.03
ACGTcount: A:0.84, C:0.10, G:0.06, T:0.00
Consensus pattern (11 bp):
AAAAAAAACAA
Done.