Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001906.1 Hibiscus syriacus cultivar Beakdansim tig00003859_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: 63179
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:1408 original size:2 final size:2
Alignment explanation
Indices: 1403--1461 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
1393 CACACCTATT
1403 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1445 TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC T
1462 TTTTGTGTGT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1701 original size:24 final size:25
Alignment explanation
Indices: 1669--1716 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
1659 AAGTAAGCAT
*
1669 TTAATTTTTTTTATCTAATTATGTC
1 TTAATTTTTTTTATCTAATGATGTC
1694 TTAA-TTTTTTTATCTAATGATGT
1 TTAATTTTTTTTATCTAATGATGT
1717 TAACATCGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.62
Consensus pattern (25 bp):
TTAATTTTTTTTATCTAATGATGTC
Found at i:27633 original size:33 final size:31
Alignment explanation
Indices: 27565--27634 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 31
27555 ATTATGTGTT
** *
27565 TAATATATAAATTATTATTTTTATTTTATTT
1 TAATATATAAATTATTATTTTTAAATTATTA
27596 TAATATATAAATT-TTATTTTTTAAAATTATATA
1 TAATATATAAATTATTA-TTTTT-AAATTAT-TA
27629 TAATAT
1 TAATAT
27635 TTTCTTTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 3 0.09
31 18 0.55
32 5 0.15
33 7 0.21
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (31 bp):
TAATATATAAATTATTATTTTTAAATTATTA
Found at i:29377 original size:20 final size:20
Alignment explanation
Indices: 29352--29389 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
29342 AAAAAAAAAA
29352 AAAG-AAGAAGAAGAAGAAAG
1 AAAGAAAGAA-AAGAAGAAAG
29372 AAAGAAAGAAAAGAAGAA
1 AAAGAAAGAAAAGAAGAA
29390 GAAGCTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (20 bp):
AAAGAAAGAAAAGAAGAAAG
Found at i:33968 original size:5 final size:6
Alignment explanation
Indices: 33945--33974 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
33935 TTACAAGAAG
*
33945 ATAACA ATAAAA ATAAAA ATAAAA ATAAAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA
33975 GAAGCTTGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (6 bp):
ATAAAA
Found at i:34086 original size:56 final size:56
Alignment explanation
Indices: 34019--34125 Score: 153
Period size: 56 Copynumber: 1.9 Consensus size: 56
34009 TTATTGAGCG
* **
34019 ATCTCAATAGTAAAA-AGAAATGTTATTTTTAAAATCTGGATTATAATGATAAAATA
1 ATCTCAATAGTAAAAGA-AAATGTTATTTTCAAAATCTAAATTATAATGATAAAATA
* *
34075 ATCTCAGTAGTAAAAGAAAATTTTATTTTCAAAATCTAAATTATAATGATA
1 ATCTCAATAGTAAAAGAAAATGTTATTTTCAAAATCTAAATTATAATGATA
34126 GAGGATATCA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
56 44 0.98
57 1 0.02
ACGTcount: A:0.48, C:0.07, G:0.09, T:0.36
Consensus pattern (56 bp):
ATCTCAATAGTAAAAGAAAATGTTATTTTCAAAATCTAAATTATAATGATAAAATA
Found at i:44393 original size:68 final size:68
Alignment explanation
Indices: 44321--44451 Score: 253
Period size: 68 Copynumber: 1.9 Consensus size: 68
44311 TTTTAATCAC
44321 TCCAAATTAATTTAAAGAAAATTTAAGAGATAAAAACTTATAAAAATTTGAAGGATAAAAATATA
1 TCCAAATTAATTTAAAGAAAATTTAAGAGATAAAAACTTATAAAAATTTGAAGGATAAAAATATA
44386 TTG
66 TTG
*
44389 TCCAAATTAATTTAAAGAAAATTTAAGGGATAAAAACTTATAAAAATTTGAAGGATAAAAATA
1 TCCAAATTAATTTAAAGAAAATTTAAGAGATAAAAACTTATAAAAATTTGAAGGATAAAAATA
44452 AATTATCAAT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
68 62 1.00
ACGTcount: A:0.55, C:0.05, G:0.11, T:0.30
Consensus pattern (68 bp):
TCCAAATTAATTTAAAGAAAATTTAAGAGATAAAAACTTATAAAAATTTGAAGGATAAAAATATA
TTG
Found at i:46999 original size:48 final size:48
Alignment explanation
Indices: 46926--47022 Score: 185
Period size: 48 Copynumber: 2.0 Consensus size: 48
46916 CAATACGATT
46926 CTCCCAAGTTTCAATTCATAACTTCTGCATATCTGATCCAATGGAGTG
1 CTCCCAAGTTTCAATTCATAACTTCTGCATATCTGATCCAATGGAGTG
*
46974 CTCCCAAGTTTCAATTCATACCTTCTGCATATCTGATCCAATGGAGTG
1 CTCCCAAGTTTCAATTCATAACTTCTGCATATCTGATCCAATGGAGTG
47022 C
1 C
47023 GGTAATGATC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.26, C:0.27, G:0.14, T:0.33
Consensus pattern (48 bp):
CTCCCAAGTTTCAATTCATAACTTCTGCATATCTGATCCAATGGAGTG
Found at i:55393 original size:23 final size:23
Alignment explanation
Indices: 55367--55430 Score: 56
Period size: 23 Copynumber: 2.8 Consensus size: 23
55357 AAACAGGGCA
***
55367 TATGTTTTAAGAGAAATGAGTTT
1 TATGTTTTAAGAGAAATGAAAAT
* * * *
55390 TATGTCTCAAGGGAAATAAAAAT
1 TATGTTTTAAGAGAAATGAAAAT
*
55413 TATATTTTAAGAGAAATG
1 TATGTTTTAAGAGAAATG
55431 GTCTTAAGGA
Statistics
Matches: 29, Mismatches: 12, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.42, C:0.03, G:0.19, T:0.36
Consensus pattern (23 bp):
TATGTTTTAAGAGAAATGAAAAT
Found at i:57034 original size:18 final size:16
Alignment explanation
Indices: 57011--57050 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 16
57001 TTTATTAAAA
*
57011 AATATTATTTATTATCAT
1 AATATTAATTA-TAT-AT
57029 AATATTAATTATATAT
1 AATATTAATTATATAT
57045 AATATT
1 AATATT
57051 TCAAATCCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.38
17 3 0.14
18 10 0.48
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
AATATTAATTATATAT
Found at i:59065 original size:6 final size:6
Alignment explanation
Indices: 59056--59082 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
59046 ATCCTAGTCC
59056 TTTTAA TTTTAA TTTTAA TTTTAA TTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTT
59083 CAGACCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTTAA
Done.