Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014406.1 Corchorus olitorius cultivar O-4 contig14439, 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: 13004
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Found at i:622 original size:2 final size:2
Alignment explanation
Indices: 609--649 Score: 73
Period size: 2 Copynumber: 20.0 Consensus size: 2
599 ACTAAAAATA
609 AT AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
650 GGGCTGACTA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5895 original size:15 final size:16
Alignment explanation
Indices: 5866--5899 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
5856 TTAAATAGAA
5866 CAATTAAAAAGAAAAG
1 CAATTAAAAAGAAAAG
*
5882 CAATT-AAAATAAAAG
1 CAATTAAAAAGAAAAG
5897 CAA
1 CAA
5900 ACTAAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.68, C:0.09, G:0.09, T:0.15
Consensus pattern (16 bp):
CAATTAAAAAGAAAAG
Found at i:7956 original size:13 final size:12
Alignment explanation
Indices: 7936--7988 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
7926 CCTGGCCCAA
7936 GCGCCAGGCCAG
1 GCGCCAGGCCAG
7948 GCGCGCAGGCCA-
1 GCGC-CAGGCCAG
**
7960 GCGCTTGGCCCAG
1 GCGCCAGG-CCAG
*
7973 GCGCCAGGCCTG
1 GCGCCAGGCCAG
7985 GCGC
1 GCGC
7989 GCGGGCCAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
11 2 0.06
12 18 0.55
13 13 0.39
ACGTcount: A:0.11, C:0.42, G:0.42, T:0.06
Consensus pattern (12 bp):
GCGCCAGGCCAG
Found at i:7971 original size:37 final size:37
Alignment explanation
Indices: 7928--8011 Score: 132
Period size: 37 Copynumber: 2.3 Consensus size: 37
7918 CAGCAAGGCC
*
7928 TGGCCCAAGCGCCAGGCCAGGCGCGCAGGCCAGCGCT
1 TGGCCCAAGCGCCAGGCCAGGCGCGCAGGCCAGAGCT
* * *
7965 TGGCCCAGGCGCCAGGCCTGGCGCGCGGGCCAGAGCT
1 TGGCCCAAGCGCCAGGCCAGGCGCGCAGGCCAGAGCT
8002 TGGCCCAAGC
1 TGGCCCAAGC
8012 TTGGGCCCCA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.14, C:0.39, G:0.39, T:0.07
Consensus pattern (37 bp):
TGGCCCAAGCGCCAGGCCAGGCGCGCAGGCCAGAGCT
Found at i:7997 original size:25 final size:25
Alignment explanation
Indices: 7942--7997 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
7932 CCAAGCGCCA
**
7942 GGCCAGGCGCGCAGGCCAGCGCTTG
1 GGCCAGGCGCGCAGGCCAGCGCGCG
* *
7967 GCCCAGGCGC-CAGGCCTGGCGCGCG
1 GGCCAGGCGCGCAGGCC-AGCGCGCG
7992 GGCCAG
1 GGCCAG
7998 AGCTTGGCCC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
24 6 0.24
25 19 0.76
ACGTcount: A:0.11, C:0.39, G:0.45, T:0.05
Consensus pattern (25 bp):
GGCCAGGCGCGCAGGCCAGCGCGCG
Found at i:8113 original size:18 final size:19
Alignment explanation
Indices: 8065--8105 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
8055 GCCCATTTTG
8065 GAATAAAGAAAA-GGAAAAA
1 GAATAAA-AAAAGGGAAAAA
8084 GAATAAAAAAAGGGAAAAA
1 GAATAAAAAAAGGGAAAAA
8103 GAA
1 GAA
8106 AATAAAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.73, C:0.00, G:0.22, T:0.05
Consensus pattern (19 bp):
GAATAAAAAAAGGGAAAAA
Found at i:12661 original size:3 final size:3
Alignment explanation
Indices: 12653--12678 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
12643 ACATATAGTG
12653 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
12679 TTATTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Done.