Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011825.1 Corchorus olitorius cultivar O-4 contig11858, 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: 33086
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Found at i:5070 original size:28 final size:27
Alignment explanation
Indices: 5005--5073 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
4995 AGTAGACTTT
*
5005 AAATGACCAAAACACCACTGAACGTGC
1 AAATGACCAAAATACCACTGAACGTGC
* * *
5032 AAATGACCAAAATACCCCTGGACTTGC
1 AAATGACCAAAATACCACTGAACGTGC
5059 AAAATGACCAAAATA
1 -AAATGACCAAAATA
5074 AGGAGTAACT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 23 0.62
28 14 0.38
ACGTcount: A:0.46, C:0.26, G:0.13, T:0.14
Consensus pattern (27 bp):
AAATGACCAAAATACCACTGAACGTGC
Found at i:7457 original size:17 final size:17
Alignment explanation
Indices: 7435--7482 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
7425 TCGGTCCTTC
7435 CGTGATTCCTGCTGTCA
1 CGTGATTCCTGCTGTCA
* **
7452 CGTGATTCCTGTTGTTG
1 CGTGATTCCTGCTGTCA
*
7469 CGCGATTCCTGCTG
1 CGTGATTCCTGCTG
7483 CCGGAATCAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.08, C:0.27, G:0.27, T:0.38
Consensus pattern (17 bp):
CGTGATTCCTGCTGTCA
Found at i:8294 original size:50 final size:50
Alignment explanation
Indices: 8228--8363 Score: 254
Period size: 50 Copynumber: 2.7 Consensus size: 50
8218 CACCTTTGAT
*
8228 AGATTGCCCTTGTGTTACATGTGTTTAGGGGCTTTGTATGTTTGAGAGAG
1 AGATTGCCCTTGTGTTACATGTGTTTAGGGACTTTGTATGTTTGAGAGAG
*
8278 AGATTGCCCTTTTGTTACATGTGTTTAGGGACTTTGTATGTTTGAGAGAG
1 AGATTGCCCTTGTGTTACATGTGTTTAGGGACTTTGTATGTTTGAGAGAG
8328 AGATTGCCCTTGTGTTACATGTGTTTAGGGACTTTG
1 AGATTGCCCTTGTGTTACATGTGTTTAGGGACTTTG
8364 GTTATTGGGA
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 83 1.00
ACGTcount: A:0.18, C:0.11, G:0.29, T:0.41
Consensus pattern (50 bp):
AGATTGCCCTTGTGTTACATGTGTTTAGGGACTTTGTATGTTTGAGAGAG
Found at i:17309 original size:55 final size:55
Alignment explanation
Indices: 17225--17345 Score: 242
Period size: 55 Copynumber: 2.2 Consensus size: 55
17215 CAGACAAGTT
17225 TGGCCAAGGCTGGCGGGTAGATCTTTCCAATAAGATCAATTGCCCATCCTCTAAA
1 TGGCCAAGGCTGGCGGGTAGATCTTTCCAATAAGATCAATTGCCCATCCTCTAAA
17280 TGGCCAAGGCTGGCGGGTAGATCTTTCCAATAAGATCAATTGCCCATCCTCTAAA
1 TGGCCAAGGCTGGCGGGTAGATCTTTCCAATAAGATCAATTGCCCATCCTCTAAA
17335 TGGCCAAGGCT
1 TGGCCAAGGCT
17346 TTATTATAGA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 66 1.00
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (55 bp):
TGGCCAAGGCTGGCGGGTAGATCTTTCCAATAAGATCAATTGCCCATCCTCTAAA
Found at i:28908 original size:31 final size:31
Alignment explanation
Indices: 28872--28945 Score: 148
Period size: 31 Copynumber: 2.4 Consensus size: 31
28862 CTATTCCTTA
28872 CTTCCCCGGCAAAAACCAGGAGAAAGTTTTC
1 CTTCCCCGGCAAAAACCAGGAGAAAGTTTTC
28903 CTTCCCCGGCAAAAACCAGGAGAAAGTTTTC
1 CTTCCCCGGCAAAAACCAGGAGAAAGTTTTC
28934 CTTCCCCGGCAA
1 CTTCCCCGGCAA
28946 CGGCGCCAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.30, C:0.32, G:0.19, T:0.19
Consensus pattern (31 bp):
CTTCCCCGGCAAAAACCAGGAGAAAGTTTTC
Done.