Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008765.1 Corchorus capsularis cultivar CVL-1 contig08786, 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: 39951
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.32
Found at i:12219 original size:30 final size:30
Alignment explanation
Indices: 12185--12255 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
12175 CCGGTTGTGC
** *
12185 CCGGTCTTGTGCGATTGGC-CCATGCCATGG
1 CCGGTCTTGTGCGA-TCCCTCCATGCAATGG
* *
12215 CCGGTCATGTGTGATCCCTCCATGCAATGG
1 CCGGTCTTGTGCGATCCCTCCATGCAATGG
12245 CCGGTCTTGTG
1 CCGGTCTTGTG
12256 TGATGGCATC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 2 0.06
30 32 0.94
ACGTcount: A:0.11, C:0.30, G:0.31, T:0.28
Consensus pattern (30 bp):
CCGGTCTTGTGCGATCCCTCCATGCAATGG
Found at i:18879 original size:15 final size:15
Alignment explanation
Indices: 18859--18888 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
18849 TCCATCCCTC
18859 ATATATGAACCGCAT
1 ATATATGAACCGCAT
18874 ATATATGAACCGCAT
1 ATATATGAACCGCAT
18889 TTATTATGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (15 bp):
ATATATGAACCGCAT
Found at i:19843 original size:11 final size:11
Alignment explanation
Indices: 19827--19858 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
19817 GAAGTTCTGG
19827 TTTGAAGATTA
1 TTTGAAGATTA
*
19838 TTTGAAGATAA
1 TTTGAAGATTA
19849 TTTGAAGATT
1 TTTGAAGATT
19859 TGAAGACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44
Consensus pattern (11 bp):
TTTGAAGATTA
Found at i:19855 original size:22 final size:22
Alignment explanation
Indices: 19827--19886 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
19817 GAAGTTCTGG
*
19827 TTTGAAGATTATTTGAAGATAA
1 TTTGAAGATTATTTGAAGACAA
19849 TTTGAAG---ATTTGAAGACAA
1 TTTGAAGATTATTTGAAGACAA
*
19868 -TTGAAGAATTATTTCAAGA
1 TTTGAAG-ATTATTTGAAGA
19887 AGCAAGAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 6 0.19
19 11 0.34
22 15 0.47
ACGTcount: A:0.42, C:0.03, G:0.18, T:0.37
Consensus pattern (22 bp):
TTTGAAGATTATTTGAAGACAA
Found at i:19861 original size:19 final size:18
Alignment explanation
Indices: 19837--19874 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
19827 TTTGAAGATT
*
19837 ATTTGAAGATAATTTGAAG
1 ATTTGAAGACAA-TTGAAG
19856 ATTTGAAGACAATTGAAG
1 ATTTGAAGACAATTGAAG
19874 A
1 A
19875 ATTATTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.32
Consensus pattern (18 bp):
ATTTGAAGACAATTGAAG
Found at i:21227 original size:6 final size:6
Alignment explanation
Indices: 21216--21252 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
21206 ATAATTGCCA
21216 TAGATT TAGATT TAGATT TAGATT TAGATT TA-ATT TA
1 TAGATT TAGATT TAGATT TAGATT TAGATT TAGATT TA
21253 CTTTGCTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (6 bp):
TAGATT
Found at i:21586 original size:16 final size:16
Alignment explanation
Indices: 21565--21607 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
21555 CGTTTTTTCT
21565 AAAAAAAAATTGCGTC
1 AAAAAAAAATTGCGTC
*
21581 AAAAAAAAATTGTGTC
1 AAAAAAAAATTGCGTC
* *
21597 GAAAATAAATT
1 AAAAAAAAATT
21608 TAGGGTTTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.58, C:0.07, G:0.12, T:0.23
Consensus pattern (16 bp):
AAAAAAAAATTGCGTC
Found at i:22709 original size:15 final size:15
Alignment explanation
Indices: 22689--22729 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
22679 CCTTGCTAAG
22689 CCAGAAGATGAGCCA
1 CCAGAAGATGAGCCA
*
22704 CCAGAAGATGAGCTA
1 CCAGAAGATGAGCCA
*
22719 CAAGAAGATGA
1 CCAGAAGATGA
22730 ACAACTTGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.44, C:0.20, G:0.27, T:0.10
Consensus pattern (15 bp):
CCAGAAGATGAGCCA
Found at i:24133 original size:6 final size:6
Alignment explanation
Indices: 24122--24158 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
24112 ATAATTGCCA
24122 TAGATT TAGATT TAGATT TAGATT TAGATT TA-ATT TA
1 TAGATT TAGATT TAGATT TAGATT TAGATT TAGATT TA
24159 CTTTGCTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (6 bp):
TAGATT
Found at i:28189 original size:16 final size:17
Alignment explanation
Indices: 28168--28201 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
28158 ATTTGGGAAA
28168 ATTAATC-CTCAACTTT
1 ATTAATCACTCAACTTT
28184 ATTAATCAACTCAACTTT
1 ATTAATC-ACTCAACTTT
28202 TGTTTACAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
18 9 0.56
ACGTcount: A:0.35, C:0.24, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTAATCACTCAACTTT
Done.