Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007019.1 Hibiscus syriacus cultivar Beakdansim tig00018132_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: 36429
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Found at i:4495 original size:29 final size:28
Alignment explanation
Indices: 4450--4505 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
4440 AAAAATTTCA
4450 AAAATATTAAATATAAATAATACTAAAAAT
1 AAAATATTAAATATAAAT--TACTAAAAAT
*
4480 AAAAT-TTAAATTTAAATTACTAAAAA
1 AAAATATTAAATATAAATTACTAAAAA
4506 ATTAAAAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 9 0.36
29 11 0.44
30 5 0.20
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (28 bp):
AAAATATTAAATATAAATTACTAAAAAT
Found at i:4722 original size:22 final size:25
Alignment explanation
Indices: 4675--4722 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 25
4665 AAATTGAATT
4675 AAATAAATATTATAAAATCTTATAA
1 AAATAAATATTATAAAATCTTATAA
*
4700 AAATAAA-ATT-TAAAA-GTTATAA
1 AAATAAATATTATAAAATCTTATAA
4722 A
1 A
4723 TTAAAACTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 7 0.32
23 5 0.23
24 3 0.14
25 7 0.32
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (25 bp):
AAATAAATATTATAAAATCTTATAA
Found at i:5533 original size:21 final size:21
Alignment explanation
Indices: 5507--5550 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
5497 ATTTAAATTA
*
5507 TGTATCGATGTACTGCTACAG
1 TGTATCGATGCACTGCTACAG
5528 TGTATCGATGCACTGCTACAG
1 TGTATCGATGCACTGCTACAG
5549 TG
1 TG
5551 ATTTCAGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (21 bp):
TGTATCGATGCACTGCTACAG
Found at i:6331 original size:31 final size:31
Alignment explanation
Indices: 6286--6426 Score: 201
Period size: 31 Copynumber: 4.5 Consensus size: 31
6276 TCCATAGATT
* * *
6286 CCGAAGAACCTAGGTAAACAGTTCATATGTC
1 CCGAAGAACATAGGTAAACAATCCATATGTC
* *
6317 CCGAATAACATAGGTAAACAATTCATATGTC
1 CCGAAGAACATAGGTAAACAATCCATATGTC
*
6348 CCGAAGAACATAGGTAAACAATCCATATATC
1 CCGAAGAACATAGGTAAACAATCCATATGTC
* *
6379 CCGAAGAACATAGGTAATCAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAATCCATATGTC
*
6410 TCGAAGAACATAGGTAA
1 CCGAAGAACATAGGTAA
6427 CCCTCGACTC
Statistics
Matches: 100, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 100 1.00
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.22
Consensus pattern (31 bp):
CCGAAGAACATAGGTAAACAATCCATATGTC
Found at i:8043 original size:6 final size:6
Alignment explanation
Indices: 8032--8060 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
8022 GGAGAAAATA
8032 TATCCT TATCCT TATCCT TATCCT TATCC
1 TATCCT TATCCT TATCCT TATCCT TATCC
8061 CCATACATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.34, G:0.00, T:0.48
Consensus pattern (6 bp):
TATCCT
Found at i:8257 original size:2 final size:2
Alignment explanation
Indices: 8250--8284 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
8240 TTGAGGATGT
8250 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 T
8285 TTTTAAGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:22783 original size:21 final size:20
Alignment explanation
Indices: 22746--22784 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
22736 TATAAATATA
*
22746 TTAAAAAATATTGACACCAT
1 TTAAAAAATATTCACACCAT
*
22766 TTAAAAATTAATTCACACC
1 TTAAAAAAT-ATTCACACC
22785 CTAAAACTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.49, C:0.18, G:0.03, T:0.31
Consensus pattern (20 bp):
TTAAAAAATATTCACACCAT
Found at i:25928 original size:42 final size:41
Alignment explanation
Indices: 25882--25999 Score: 166
Period size: 42 Copynumber: 2.8 Consensus size: 41
25872 AAATAAATAA
25882 ATAACATCATTAAGTCTCAATAAATCTAAAATAAATAACACC
1 ATAACA-CATTAAGTCTCAATAAATCTAAAATAAATAACACC
*
25924 ATAACACCATTAAGTCTCAATAAATCTAAAATAAATAACATC
1 ATAACA-CATTAAGTCTCAATAAATCTAAAATAAATAACACC
* * *
25966 ATAACACTAATAAGTCTCAACAAGTCT-AAATAAA
1 ATAACAC-ATTAAGTCTCAATAAATCTAAAATAAA
26000 ATCAACATCA
Statistics
Matches: 70, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
41 8 0.11
42 62 0.89
ACGTcount: A:0.53, C:0.19, G:0.03, T:0.25
Consensus pattern (41 bp):
ATAACACATTAAGTCTCAATAAATCTAAAATAAATAACACC
Found at i:27235 original size:19 final size:19
Alignment explanation
Indices: 27185--27241 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 19
27175 AATTCCCCTT
27185 CCTTCTTCCTTCT-TTCCAC
1 CCTT-TTCCTTCTCTTCCAC
*
27204 CCTTTTCCTTTCTCTT-CTC
1 CCTTTTCC-TTCTCTTCCAC
*
27223 CCTCTTTCCTTCTCCTCCA
1 CCT-TTTCCTTCTCTTCCA
27242 ACGACACCGA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
18 4 0.13
19 19 0.61
20 8 0.26
ACGTcount: A:0.04, C:0.47, G:0.00, T:0.49
Consensus pattern (19 bp):
CCTTTTCCTTCTCTTCCAC
Found at i:30871 original size:18 final size:18
Alignment explanation
Indices: 30848--30900 Score: 97
Period size: 18 Copynumber: 2.9 Consensus size: 18
30838 ACTAAATATT
30848 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
30866 TGTCCCGAAGGATCACTA
1 TGTCCCGAAGGACCACTA
30884 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
30901 GATAATCCCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.26, C:0.32, G:0.23, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Done.