Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010951.1 Corchorus olitorius cultivar O-4 contig10983, 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: 4162
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:1320 original size:11 final size:11
Alignment explanation
Indices: 1304--1333 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
1294 TTATGCTTAA
1304 ATATGTTAAAT
1 ATATGTTAAAT
1315 ATATGTTAAAT
1 ATATGTTAAAT
1326 ATATGTTA
1 ATATGTTA
1334 TTTTATTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (11 bp):
ATATGTTAAAT
Found at i:3122 original size:76 final size:73
Alignment explanation
Indices: 2991--3136 Score: 193
Period size: 76 Copynumber: 2.0 Consensus size: 73
2981 ATTTGGACTA
* * **
2991 TGAGCAAAGGAATGATGAGTTTTAATCAAAAATCTTCAAAATCAGTTTTAATCAAAGCTTTGATT
1 TGAGCAAAGGAATGAGGAGTTTTAATCAAAAATCTTCAAAATCAGTTTTAATCAAAACAATGATT
3056 TCGAGTTG
66 TCGAGTTG
* * **
3064 TGAGCAAAGGAATGACGGTGTTTTAATCAAAAGATGTTTCAAAATCAGTTTTGGTCAAAACAATG
1 TGAGCAAAGGAATGA-GGAGTTTTAATCAAAA-AT-CTTCAAAATCAGTTTTAATCAAAACAATG
3129 ATTTCGAG
63 ATTTCGAG
3137 GTGACTGAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
73 15 0.24
74 14 0.23
75 2 0.03
76 31 0.50
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.32
Consensus pattern (73 bp):
TGAGCAAAGGAATGAGGAGTTTTAATCAAAAATCTTCAAAATCAGTTTTAATCAAAACAATGATT
TCGAGTTG
Found at i:3558 original size:7 final size:8
Alignment explanation
Indices: 3534--3558 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
3524 AAAAAAAATG
3534 AAATGAAA
1 AAATGAAA
3542 AAATGAAA
1 AAATGAAA
3550 AAATGAAA
1 AAATGAAA
3558 A
1 A
3559 TAAAGGCACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AAATGAAA
Found at i:3953 original size:20 final size:20
Alignment explanation
Indices: 3928--3969 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
3918 CCACTCCATC
*
3928 AAGAAATTTAAAAAAAAAGA
1 AAGAAATTCAAAAAAAAAGA
*
3948 AAGAAATTCAAAAGAAAAGA
1 AAGAAATTCAAAAAAAAAGA
3968 AA
1 AA
3970 AAAAAGAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.74, C:0.02, G:0.12, T:0.12
Consensus pattern (20 bp):
AAGAAATTCAAAAAAAAAGA
Found at i:4020 original size:21 final size:22
Alignment explanation
Indices: 3979--4042 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 22
3969 AAAAAAGAAG
*
3979 AAAAAAAATCAATCAATCAAAAATTA
1 AAAAAAAATC-A--AATCAAAAA-CA
4005 AAAAAAAA-CAAA-CAAAAACA
1 AAAAAAAATCAAATCAAAAACA
4025 AAAAAAAATCAAATCAAA
1 AAAAAAAATCAAATCAAA
4043 TCAAAATCAA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
20 9 0.26
21 10 0.29
22 6 0.17
24 1 0.03
25 1 0.03
26 8 0.23
ACGTcount: A:0.77, C:0.12, G:0.00, T:0.11
Consensus pattern (22 bp):
AAAAAAAATCAAATCAAAAACA
Found at i:4042 original size:16 final size:16
Alignment explanation
Indices: 3979--4053 Score: 50
Period size: 16 Copynumber: 4.8 Consensus size: 16
3969 AAAAAAGAAG
3979 AAAAAAAATC-AATCA
1 AAAAAAAATCAAATCA
** *
3994 ATCAAAAATTAAA--A
1 AAAAAAAATCAAATCA
*
4008 AAAAACAAA-CAAAAACA
1 AAAAA-AAATC-AAATCA
4025 AAAAAAAATCAAATCA
1 AAAAAAAATCAAATCA
**
4041 AATCAAAATCAAA
1 AAAAAAAATCAAA
4054 AGAGAATGGA
Statistics
Matches: 45, Mismatches: 9, Indels: 11
0.69 0.14 0.17
Matches are distributed among these distances:
14 4 0.09
15 13 0.29
16 21 0.47
17 7 0.16
ACGTcount: A:0.75, C:0.13, G:0.00, T:0.12
Consensus pattern (16 bp):
AAAAAAAATCAAATCA
Found at i:4047 original size:21 final size:20
Alignment explanation
Indices: 3998--4048 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
3988 CAATCAATCA
*
3998 AAAATTAAAAAAAAACAAAC
1 AAAATCAAAAAAAAACAAAC
*
4018 AAAAACAAAAAAAAATCAAATC
1 AAAATCAAAAAAAAA-CAAA-C
4040 -AAATCAAAA
1 AAAATCAAAA
4049 TCAAAAGAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 13 0.50
21 12 0.46
22 1 0.04
ACGTcount: A:0.78, C:0.12, G:0.00, T:0.10
Consensus pattern (20 bp):
AAAATCAAAAAAAAACAAAC
Done.