Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003579.1 Hibiscus syriacus cultivar Beakdansim tig00007554_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: 34852
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:3383 original size:21 final size:21
Alignment explanation
Indices: 3357--3406 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
3347 TGTACGTTGA
3357 TGACATGCTCGTTGCAGGCTC
1 TGACATGCTCGTTGCAGGCTC
3378 TGACATGCTCGTTGCAGGCTC
1 TGACATGCTCGTTGCAGGCTC
3399 TGACATGC
1 TGACATGC
3407 AAGAGATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.16, C:0.28, G:0.28, T:0.28
Consensus pattern (21 bp):
TGACATGCTCGTTGCAGGCTC
Found at i:3443 original size:15 final size:15
Alignment explanation
Indices: 3423--3458 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
3413 TTATAAACTT
3423 GAAGCAAAAATTGTC
1 GAAGCAAAAATTGTC
3438 GAAGCAAAAATTGTC
1 GAAGCAAAAATTGTC
3453 GAAGCA
1 GAAGCA
3459 GTTTGCTATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.47, C:0.14, G:0.22, T:0.17
Consensus pattern (15 bp):
GAAGCAAAAATTGTC
Found at i:8945 original size:16 final size:18
Alignment explanation
Indices: 8924--8961 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
8914 CTATATTATT
*
8924 TTTTATTT-TTTGAAT-A
1 TTTTATTTATTTAAATAA
8940 TTTTATTTATTTAAATAA
1 TTTTATTTATTTAAATAA
8958 TTTT
1 TTTT
8962 TGAAATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (18 bp):
TTTTATTTATTTAAATAA
Found at i:10398 original size:16 final size:16
Alignment explanation
Indices: 10379--10412 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
10369 TTGAACTGGT
*
10379 TTGATATTTACCTGAC
1 TTGATACTTACCTGAC
*
10395 TTGATACTTACCTTAC
1 TTGATACTTACCTGAC
10411 TT
1 TT
10413 ATAAGTTACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.21, G:0.09, T:0.47
Consensus pattern (16 bp):
TTGATACTTACCTGAC
Found at i:11353 original size:20 final size:21
Alignment explanation
Indices: 11318--11357 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
11308 GCGCGCATAC
11318 ATTATACATATATACTTATAT
1 ATTATACATATATACTTATAT
*
11339 ATTATAC-TTTATACTTATA
1 ATTATACATATATACTTATA
11358 AAGTTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTATACATATATACTTATAT
Found at i:11655 original size:19 final size:19
Alignment explanation
Indices: 11631--11678 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
11621 AAACTTATAT
*
11631 TCATACTTATATACATACA
1 TCATACATATATACATACA
*
11650 TCATACATATGTACATACA
1 TCATACATATATACATACA
*
11669 TCATATATAT
1 TCATACATAT
11679 TTTATTATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.42, C:0.19, G:0.02, T:0.38
Consensus pattern (19 bp):
TCATACATATATACATACA
Found at i:12568 original size:8 final size:8
Alignment explanation
Indices: 12557--12628 Score: 67
Period size: 8 Copynumber: 9.0 Consensus size: 8
12547 AACTCTGCAT
*
12557 CTCTTAAA
1 CTCTCAAA
12565 CTCTCAAA
1 CTCTCAAA
*
12573 TTCTCAAA
1 CTCTCAAA
*
12581 CTTTCAAA
1 CTCTCAAA
12589 CTCTCAATA
1 CTCTCAA-A
*
12598 -TCTGAAA
1 CTCTCAAA
*
12605 CTCTAAAA
1 CTCTCAAA
12613 CTCTCAATA
1 CTCTCAA-A
12622 -TCTCAAA
1 CTCTCAAA
12629 GTGGCTCGTA
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
7 2 0.04
8 49 0.92
9 2 0.04
ACGTcount: A:0.39, C:0.28, G:0.01, T:0.32
Consensus pattern (8 bp):
CTCTCAAA
Found at i:12594 original size:24 final size:24
Alignment explanation
Indices: 12557--12628 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
12547 AACTCTGCAT
*
12557 CTCTTAAACTCTCAA-ATTCTCAAA
1 CTCTAAAACTCTCAATA-TCTCAAA
* * *
12581 CTTTCAAACTCTCAATATCTGAAA
1 CTCTAAAACTCTCAATATCTCAAA
12605 CTCTAAAACTCTCAATATCTCAAA
1 CTCTAAAACTCTCAATATCTCAAA
12629 GTGGCTCGTA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
24 40 0.98
25 1 0.02
ACGTcount: A:0.39, C:0.28, G:0.01, T:0.32
Consensus pattern (24 bp):
CTCTAAAACTCTCAATATCTCAAA
Found at i:21157 original size:24 final size:23
Alignment explanation
Indices: 21107--21157 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
21097 GCTTCAACTT
* *
21107 TTTGGATTGTTTGATTTTGTGAC
1 TTTGGATTGTTTGATGTTGTGAA
21130 TTTGGATTTGTTTGGATGTT-TGAA
1 TTTGGA-TTGTTT-GATGTTGTGAA
21154 TTTG
1 TTTG
21158 TGGATTGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 6 0.25
24 13 0.54
25 5 0.21
ACGTcount: A:0.14, C:0.02, G:0.27, T:0.57
Consensus pattern (23 bp):
TTTGGATTGTTTGATGTTGTGAA
Found at i:22079 original size:14 final size:14
Alignment explanation
Indices: 22062--22101 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
22052 GAACGTTCGA
*
22062 TTATGTTCGTTTGT
1 TTATGTTCGTTTGG
*
22076 TTATGTTCGTTCGG
1 TTATGTTCGTTTGG
22090 TTATGTTCGTTT
1 TTATGTTCGTTT
22102 ATGTTCATTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.07, C:0.10, G:0.23, T:0.60
Consensus pattern (14 bp):
TTATGTTCGTTTGG
Found at i:22117 original size:24 final size:24
Alignment explanation
Indices: 22074--22120 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
22064 ATGTTCGTTT
* *
22074 GTTTATGTTCGTTCGGTTATGTTC
1 GTTTATGTTCATTCAGTTATGTTC
*
22098 GTTTATGTTCATTCATTTATGTT
1 GTTTATGTTCATTCAGTTATGTT
22121 TAACCCAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.13, C:0.11, G:0.19, T:0.57
Consensus pattern (24 bp):
GTTTATGTTCATTCAGTTATGTTC
Found at i:23201 original size:16 final size:16
Alignment explanation
Indices: 23180--23246 Score: 75
Period size: 16 Copynumber: 4.3 Consensus size: 16
23170 GTCTCCAACG
23180 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
* *
23196 TTTATGTTAGTGTTCG
1 TTTATGTTCGTGTTCA
** *
23212 TTTATGTTCGTGCGCG
1 TTTATGTTCGTGTTCA
23228 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
23242 TTTAT
1 TTTAT
23247 TAAATGAACG
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
14 5 0.12
16 38 0.88
ACGTcount: A:0.12, C:0.10, G:0.21, T:0.57
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:25225 original size:29 final size:29
Alignment explanation
Indices: 25192--25252 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
25182 GTCATTATAA
25192 AACTACACAACGAGTGGGATTTATCTTAC
1 AACTACACAACGAGTGGGATTTATCTTAC
*
25221 AACTACACAATGAGTGGGATTTATCTTAC
1 AACTACACAACGAGTGGGATTTATCTTAC
25250 AAC
1 AAC
25253 GAGCTACACA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (29 bp):
AACTACACAACGAGTGGGATTTATCTTAC
Found at i:26806 original size:2 final size:2
Alignment explanation
Indices: 26799--26835 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
26789 CGTTTTCTTT
26799 TA TA TA 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 TA TA TA T
26836 TGCAATCTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:27032 original size:16 final size:15
Alignment explanation
Indices: 26982--27033 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
26972 ATAAAAACCA
26982 TAACCCTAAACTATTC
1 TAACCCTAAAC-ATTC
* * *
26998 TAA-CATAAAAATCC
1 TAACCCTAAACATTC
27012 TAACCCTAAATCATTC
1 TAACCCTAAA-CATTC
27028 TAACCC
1 TAACCC
27034 AAAAAACCCT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
14 6 0.21
15 10 0.36
16 12 0.43
ACGTcount: A:0.42, C:0.31, G:0.00, T:0.27
Consensus pattern (15 bp):
TAACCCTAAACATTC
Found at i:27045 original size:31 final size:30
Alignment explanation
Indices: 26955--27045 Score: 98
Period size: 30 Copynumber: 3.0 Consensus size: 30
26945 ACTTTAAGAC
* *
26955 CCCTAAACCT-TTATAACATAAAAACCATAA
1 CCCTAAA-CTATTCTAACATAAAAACCCTAA
*
26985 CCCTAAACTATTCTAACATAAAAATCCTAA
1 CCCTAAACTATTCTAACATAAAAACCCTAA
27015 CCCTAAA-TCATTCTAACCCA-AAAAACCCTAA
1 CCCTAAACT-ATTCTAA--CATAAAAACCCTAA
27046 ACGAGAAATC
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
29 3 0.06
30 38 0.72
31 10 0.19
32 2 0.04
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (30 bp):
CCCTAAACTATTCTAACATAAAAACCCTAA
Done.