Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022776.1 Corchorus olitorius cultivar O-4 contig22809, 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: 43852
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1284 original size:21 final size:21
Alignment explanation
Indices: 1258--1304 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
1248 CCGCTGGGCG
1258 CCCAGGCGA-AATGCCTCAGCA
1 CCCAGGCGACAA-GCCTCAGCA
* *
1279 CCCAGGCGACAAGGCTCAGCG
1 CCCAGGCGACAAGCCTCAGCA
1300 CCCAG
1 CCCAG
1305 CTCGATCCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.26, C:0.40, G:0.28, T:0.06
Consensus pattern (21 bp):
CCCAGGCGACAAGCCTCAGCA
Found at i:15618 original size:20 final size:20
Alignment explanation
Indices: 15593--15633 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
15583 CACCTTTGCT
15593 TTTTGGCACACCCACCAATA
1 TTTTGGCACACCCACCAATA
*
15613 TTTTGGCACACCCACTAATA
1 TTTTGGCACACCCACCAATA
15633 T
1 T
15634 AGTGAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.32, G:0.10, T:0.29
Consensus pattern (20 bp):
TTTTGGCACACCCACCAATA
Found at i:17080 original size:41 final size:41
Alignment explanation
Indices: 17034--17115 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
17024 TTAGCCTTTA
17034 CCCTATATTTAAGACTAAACATTGGCCATACACATTAGCGG
1 CCCTATATTTAAGACTAAACATTGGCCATACACATTAGCGG
17075 CCCTATATTTAAGACTAAACATTGGCCATACACATTAGCGG
1 CCCTATATTTAAGACTAAACATTGGCCATACACATTAGCGG
17116 TTAGCCTGCC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (41 bp):
CCCTATATTTAAGACTAAACATTGGCCATACACATTAGCGG
Found at i:17518 original size:37 final size:37
Alignment explanation
Indices: 17475--17549 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
17465 TTGCCCTGAT
17475 ATTAATTTTTTAAGGGAAGGACCCATGGTAGCTTGCC
1 ATTAATTTTTTAAGGGAAGGACCCATGGTAGCTTGCC
17512 ATTAATTTTTTAAGGGAAGGACCCATGGTAGCTTGCC
1 ATTAATTTTTTAAGGGAAGGACCCATGGTAGCTTGCC
17549 A
1 A
17550 CTCTGGGTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (37 bp):
ATTAATTTTTTAAGGGAAGGACCCATGGTAGCTTGCC
Found at i:17714 original size:46 final size:47
Alignment explanation
Indices: 17658--17752 Score: 183
Period size: 46 Copynumber: 2.0 Consensus size: 47
17648 GTGACAAACG
17658 ATCTTGGCAAAAACAATTCCATTTAGTATG-AAAGTTGACAACTTCA
1 ATCTTGGCAAAAACAATTCCATTTAGTATGAAAAGTTGACAACTTCA
17704 ATCTTGGCAAAAACAATTCCATTTAGTATGAAAAGTTGACAACTTCA
1 ATCTTGGCAAAAACAATTCCATTTAGTATGAAAAGTTGACAACTTCA
17751 AT
1 AT
17753 TTCAGTCTAG
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 30 0.62
47 18 0.38
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.31
Consensus pattern (47 bp):
ATCTTGGCAAAAACAATTCCATTTAGTATGAAAAGTTGACAACTTCA
Found at i:30955 original size:10 final size:10
Alignment explanation
Indices: 30940--30979 Score: 71
Period size: 10 Copynumber: 4.0 Consensus size: 10
30930 CTAATGCAAT
*
30940 GAGAAAAGGA
1 GAGAAAAGAA
30950 GAGAAAAGAA
1 GAGAAAAGAA
30960 GAGAAAAGAA
1 GAGAAAAGAA
30970 GAGAAAAGAA
1 GAGAAAAGAA
30980 TGTCAATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.68, C:0.00, G:0.33, T:0.00
Consensus pattern (10 bp):
GAGAAAAGAA
Found at i:37020 original size:31 final size:31
Alignment explanation
Indices: 36944--37023 Score: 115
Period size: 31 Copynumber: 2.6 Consensus size: 31
36934 ATGTGGCGTG
*
36944 ACACGTGGTATGCCACGTGTCACTTTTTGGT
1 ACACGTGGCATGCCACGTGTCACTTTTTGGT
* * *
36975 ACATGTGGCGTGCCATGTGTCACTTTTTGGT
1 ACACGTGGCATGCCACGTGTCACTTTTTGGT
*
37006 ACACATGGCATGCCACGT
1 ACACGTGGCATGCCACGT
37024 CGGACACCAT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.17, C:0.24, G:0.26, T:0.33
Consensus pattern (31 bp):
ACACGTGGCATGCCACGTGTCACTTTTTGGT
Found at i:41029 original size:21 final size:21
Alignment explanation
Indices: 41005--41048 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
40995 AAAATGCATA
41005 AACAAGATTCTTGATAGAACT
1 AACAAGATTCTTGATAGAACT
41026 AACAAGATTCTTGATAGAACT
1 AACAAGATTCTTGATAGAACT
41047 AA
1 AA
41049 GATTGAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.27
Consensus pattern (21 bp):
AACAAGATTCTTGATAGAACT
Done.