Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015665.1 Corchorus capsularis cultivar CVL-1 contig15686, 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: 7551
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:2768 original size:2 final size:2
Alignment explanation
Indices: 2763--2801 Score: 53
Period size: 2 Copynumber: 19.0 Consensus size: 2
2753 AAAGTGTTGC
2763 AT AT AT AGT AT -T CAT 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
2802 CTGCTGTTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 1 0.03
2 30 0.88
3 3 0.09
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5924 original size:42 final size:43
Alignment explanation
Indices: 5859--5941 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 43
5849 CGTGTTTGGC
5859 TTATCGTGTCTCGTGTCTGAATCGTGTC-AGACACGATTAAAA
1 TTATCGTGTCTCGTGTCTGAATCGTGTCAAGACACGATTAAAA
*
5901 TTATCGTGTTTCGTGTC-GTAATCGTGTCAAGACACGATTAA
1 TTATCGTGTCTCGTGTCTG-AATCGTGTCAAGACACGATTAA
5942 CACGTTTAAG
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
41 1 0.03
42 25 0.66
43 12 0.32
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (43 bp):
TTATCGTGTCTCGTGTCTGAATCGTGTCAAGACACGATTAAAA
Found at i:5954 original size:20 final size:21
Alignment explanation
Indices: 5929--5971 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
5919 TAATCGTGTC
*
5929 AAGACACGATTAACACG-TTT
1 AAGACACGAGTAACACGCTTT
*
5949 AAGACACGAGTGACACGCTTT
1 AAGACACGAGTAACACGCTTT
5970 AA
1 AA
5972 TTAACGGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (21 bp):
AAGACACGAGTAACACGCTTT
Found at i:6130 original size:14 final size:14
Alignment explanation
Indices: 6111--6138 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6101 CAATTATCTT
6111 TAATTATATATATA
1 TAATTATATATATA
6125 TAATTATATATATA
1 TAATTATATATATA
6139 GTTTAGTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TAATTATATATATA
Found at i:6365 original size:12 final size:12
Alignment explanation
Indices: 6348--6378 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
6338 TACCCTATGT
*
6348 AAACACGACACG
1 AAACACGACACA
6360 AAACACGACACA
1 AAACACGACACA
6372 AAACACG
1 AAACACG
6379 GATTGCCAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.55, C:0.32, G:0.13, T:0.00
Consensus pattern (12 bp):
AAACACGACACA
Found at i:6776 original size:21 final size:22
Alignment explanation
Indices: 6750--6791 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
6740 GAAGAAAAAA
* *
6750 AAAGCAA-AAATAAGAAAAGCC
1 AAAGCAAGAAAGAACAAAAGCC
6771 AAAGCAAGAAAGAACAAAAGC
1 AAAGCAAGAAAGAACAAAAGC
6792 AATAATCAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.67, C:0.14, G:0.17, T:0.02
Consensus pattern (22 bp):
AAAGCAAGAAAGAACAAAAGCC
Found at i:7289 original size:2 final size:2
Alignment explanation
Indices: 7282--7306 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7272 TTAAATTAAT
7282 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
7307 CTTGTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.