Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022705.1 Corchorus olitorius cultivar O-4 contig22738, 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: 22843
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Found at i:1991 original size:11 final size:11
Alignment explanation
Indices: 1961--2016 Score: 67
Period size: 11 Copynumber: 4.8 Consensus size: 11
1951 ACTTATGCCC
1961 AAAACATTTATT
1 AAAACATTTA-T
1973 AAAACATTTAT
1 AAAACATTTAT
*
1984 AAAGCATTTAT
1 AAAACATTTAT
*
1995 ATAAAGCAGTTAT
1 A-AAA-CATTTAT
2008 AAAACATTT
1 AAAACATTT
2017 CCTCAACGGG
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
11 16 0.42
12 15 0.39
13 7 0.18
ACGTcount: A:0.50, C:0.09, G:0.05, T:0.36
Consensus pattern (11 bp):
AAAACATTTAT
Found at i:1999 original size:13 final size:13
Alignment explanation
Indices: 1965--2016 Score: 51
Period size: 13 Copynumber: 4.4 Consensus size: 13
1955 ATGCCCAAAA
*
1965 CATTTAT-TAAAA
1 CATTTATATAAAG
1977 CA-TT-TATAAAG
1 CATTTATATAAAG
1988 CATTTATATAAAG
1 CATTTATATAAAG
*
2001 CAGTTATA-AAA-
1 CATTTATATAAAG
2012 CATTT
1 CATTT
2017 CCTCAACGGG
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
10 1 0.03
11 12 0.35
12 7 0.21
13 14 0.41
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (13 bp):
CATTTATATAAAG
Found at i:2007 original size:24 final size:23
Alignment explanation
Indices: 1961--2016 Score: 76
Period size: 24 Copynumber: 2.4 Consensus size: 23
1951 ACTTATGCCC
*
1961 AAAACATTTATTAAAACATTTAT
1 AAAACATTTATTAAAACAGTTAT
* *
1984 AAAGCATTTATATAAAGCAGTTAT
1 AAAACATTTAT-TAAAACAGTTAT
2008 AAAACATTT
1 AAAACATTT
2017 CCTCAACGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 10 0.36
24 18 0.64
ACGTcount: A:0.50, C:0.09, G:0.05, T:0.36
Consensus pattern (23 bp):
AAAACATTTATTAAAACAGTTAT
Found at i:3247 original size:15 final size:14
Alignment explanation
Indices: 3221--3288 Score: 63
Period size: 14 Copynumber: 5.1 Consensus size: 14
3211 CCTTATTTCC
3221 TTCTT-CTTTTTTT
1 TTCTTCCTTTTTTT
3234 TTCTTCCTTTTTTT
1 TTCTTCCTTTTTTT
* **
3248 TTCTTTCTTTTCCT
1 TTCTTCCTTTTTTT
* *
3262 TTC-T-ATTTTTCT
1 TTCTTCCTTTTTTT
3274 TT-TTCCTTTTTTT
1 TTCTTCCTTTTTTT
3287 TT
1 TT
3289 GGACCAAGCC
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
12 9 0.20
13 14 0.31
14 22 0.49
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.79
Consensus pattern (14 bp):
TTCTTCCTTTTTTT
Found at i:3270 original size:24 final size:24
Alignment explanation
Indices: 3224--3271 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3214 TATTTCCTTC
* * *
3224 TTCTTTTTTTTTCTTCCTTTTTTT
1 TTCTTTCTTTTCCTTCCTATTTTT
*
3248 TTCTTTCTTTTCCTTTCTATTTTT
1 TTCTTTCTTTTCCTTCCTATTTTT
3272 CTTTTTCCTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (24 bp):
TTCTTTCTTTTCCTTCCTATTTTT
Found at i:3278 original size:24 final size:22
Alignment explanation
Indices: 3224--3283 Score: 59
Period size: 25 Copynumber: 2.6 Consensus size: 22
3214 TATTTCCTTC
3224 TTCTTTTT-TTTTCTTCCTTTT
1 TTCTTTTTCTTTTCTTCCTTTT
* *
3245 TTTTTCTTTCTTTTCCTTTCTATTT
1 TTCTT-TTTCTTTT-CTTCCT-TTT
3270 TTCTTTTTCCTTTT
1 TTCTTTTT-CTTTT
3284 TTTTTGGACC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 4 0.13
22 3 0.10
23 4 0.13
24 8 0.26
25 12 0.39
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (22 bp):
TTCTTTTTCTTTTCTTCCTTTT
Found at i:4435 original size:58 final size:57
Alignment explanation
Indices: 4345--4458 Score: 165
Period size: 58 Copynumber: 2.0 Consensus size: 57
4335 ATAGCATCAT
*
4345 GCCTTGGTCCTAAAACGTCTTTTTTAGGCATCTAATAAAAAAACATGTCACTCGATAA
1 GCCTTGGTCCGAAAACGTCTTTTTTAGGCATCTAAT-AAAAAACATGTCACTCGATAA
* * * * *
4403 GCCTTGGTCCGAAAACTTTTTTTTTATGCATCTAATAAAGAACATGTCACTTGATA
1 GCCTTGGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAACATGTCACTCGATA
4459 TTTGATTAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
57 18 0.36
58 32 0.64
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.34
Consensus pattern (57 bp):
GCCTTGGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAACATGTCACTCGATAA
Found at i:5917 original size:2 final size:2
Alignment explanation
Indices: 5910--5944 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5900 AGCGCACGTG
5910 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
5945 TTTATACTTA
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:8956 original size:1 final size:1
Alignment explanation
Indices: 8950--8976 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
8940 GTGTGCATTA
8950 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
8977 GCAATAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:16753 original size:12 final size:12
Alignment explanation
Indices: 16732--16778 Score: 85
Period size: 12 Copynumber: 3.9 Consensus size: 12
16722 TTTAGACCCG
16732 AAACCGACCGAA
1 AAACCGACCGAA
*
16744 AAACCAACCGAA
1 AAACCGACCGAA
16756 AAACCGACCGAA
1 AAACCGACCGAA
16768 AAACCGACCGA
1 AAACCGACCGA
16779 CCCATATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.51, C:0.34, G:0.15, T:0.00
Consensus pattern (12 bp):
AAACCGACCGAA
Found at i:18640 original size:27 final size:28
Alignment explanation
Indices: 18610--18663 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
18600 CTTGAGGGAA
18610 ACTATAC-TAGGATCAAGTAATAAATAT
1 ACTATACATAGGATCAAGTAATAAATAT
* *
18637 ACTATGCTATATGATCAAGTAATAAAT
1 ACTATAC-ATAGGATCAAGTAATAAAT
18664 TCTAATTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 6 0.26
29 17 0.74
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.31
Consensus pattern (28 bp):
ACTATACATAGGATCAAGTAATAAATAT
Done.