Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019164.1 Corchorus olitorius cultivar O-4 contig19197, 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: 19134
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1172 original size:20 final size:20
Alignment explanation
Indices: 1131--1173 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1121 CTCTCACAAG
* *
1131 TTTCTAGCCGTTGGAGCTCT
1 TTTCTAGCCGTTAGAGCACT
*
1151 TTTCTAGCCGTTATAGCACT
1 TTTCTAGCCGTTAGAGCACT
1171 TTT
1 TTT
1174 TCCACTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (20 bp):
TTTCTAGCCGTTAGAGCACT
Found at i:3229 original size:29 final size:29
Alignment explanation
Indices: 3196--3251 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
3186 AATAAGCCCC
3196 TAAAATAAAAGTTCAGGGGCTTATTTGGT
1 TAAAATAAAAGTTCAGGGGCTTATTTGGT
*
3225 TAAAATAAAGGTTCAGGGGCTTATTTG
1 TAAAATAAAAGTTCAGGGGCTTATTTG
3252 ACCATTTGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.34, C:0.07, G:0.25, T:0.34
Consensus pattern (29 bp):
TAAAATAAAAGTTCAGGGGCTTATTTGGT
Found at i:10993 original size:24 final size:24
Alignment explanation
Indices: 10966--11018 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
10956 GTATTTTAAT
*
10966 TTTATAAATTATTATAAATATATA
1 TTTATAAATTATAATAAATATATA
* **
10990 TTTAAAAATTATAATTTATATATA
1 TTTATAAATTATAATAAATATATA
11014 TTTAT
1 TTTAT
11019 CTGATATATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
TTTATAAATTATAATAAATATATA
Found at i:11013 original size:2 final size:2
Alignment explanation
Indices: 11006--11058 Score: 56
Period size: 2 Copynumber: 27.0 Consensus size: 2
10996 AATTATAATT
* * *
11006 TA TA TA TA TT TA TC TGA TA TA T- TA TA TA TT TA TA TA TA TA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
11048 TA TA T- TA TA TA
1 TA TA TA TA TA TA
11059 AAAACGGCCG
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
1 2 0.05
2 39 0.93
3 1 0.02
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (2 bp):
TA
Found at i:11033 original size:20 final size:18
Alignment explanation
Indices: 11006--11058 Score: 72
Period size: 20 Copynumber: 2.9 Consensus size: 18
10996 AATTATAATT
*
11006 TATATATATTTATCTGATA
1 TATATATATTTATAT-ATA
11025 TATTATATATTTATATATA
1 TA-TATATATTTATATATA
11044 TATATATA-TTATATA
1 TATATATATTTATATA
11059 AAAACGGCCG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 7 0.22
18 6 0.19
19 7 0.22
20 12 0.38
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (18 bp):
TATATATATTTATATATA
Found at i:15986 original size:35 final size:35
Alignment explanation
Indices: 15938--16005 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
15928 GGATCCTCTT
* *
15938 TGATATTGGAGTTAGTAGGATATTAAGGTGTTTGG
1 TGATACTGAAGTTAGTAGGATATTAAGGTGTTTGG
* * *
15973 TGATACTGAAGTTAGTGGGGTTTTAAGGTGTTT
1 TGATACTGAAGTTAGTAGGATATTAAGGTGTTT
16006 AGAGAGCTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.24, C:0.01, G:0.34, T:0.41
Consensus pattern (35 bp):
TGATACTGAAGTTAGTAGGATATTAAGGTGTTTGG
Found at i:16975 original size:23 final size:22
Alignment explanation
Indices: 16917--16976 Score: 70
Period size: 20 Copynumber: 2.8 Consensus size: 22
16907 CACAGAGAGA
* *
16917 TTATCAAAAATCATAG-GAAGG
1 TTATCAAAATTCATAGTAAAGG
*
16938 TTA-CAAAATTCATAGTAAAGT
1 TTATCAAAATTCATAGTAAAGG
16959 TTATCAAAATTTCATAGT
1 TTATCAAAA-TTCATAGT
16977 TAGATTATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 11 0.33
21 9 0.27
22 5 0.15
23 8 0.24
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (22 bp):
TTATCAAAATTCATAGTAAAGG
Found at i:17008 original size:44 final size:43
Alignment explanation
Indices: 16956--17060 Score: 117
Period size: 44 Copynumber: 2.4 Consensus size: 43
16946 TTCATAGTAA
* **
16956 AGTTTATCAAAATTTCATAGTTAGATTA-TAAAAGTTTCTTATGG-
1 AGTTTATCAAAATTTCATAGGTA-ATTATTAAAA-TTTAATA-GGT
* *
17000 AGTTTATCACAATTTTATAGGTAATTATTAAAATTTAATAGGT
1 AGTTTATCAAAATTTCATAGGTAATTATTAAAATTTAATAGGT
17043 AG-TTATCAAAATTTCATA
1 AGTTTATCAAAATTTCATA
17061 AAACTATTCA
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
42 16 0.31
43 11 0.21
44 25 0.48
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.43
Consensus pattern (43 bp):
AGTTTATCAAAATTTCATAGGTAATTATTAAAATTTAATAGGT
Found at i:17036 original size:20 final size:21
Alignment explanation
Indices: 17003--17056 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
16993 CTTATGGAGT
* *
17003 TTATCACAATTTTATAGGTAA
1 TTATCAAAATTTAATAGGTAA
* *
17024 TTATTAAAATTTAATAGGTAG
1 TTATCAAAATTTAATAGGTAA
17045 TTATCAAAATTT
1 TTATCAAAATTT
17057 CATAAAACTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (21 bp):
TTATCAAAATTTAATAGGTAA
Done.