Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016715.1 Corchorus olitorius cultivar O-4 contig16748, 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: 25185
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Found at i:1828 original size:21 final size:21
Alignment explanation
Indices: 1804--1848 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1794 GGCGCCCACA
* *
1804 TGGTTTCCTTGAGCACCCATG
1 TGGTTTCCTTGAGAACCCAGG
*
1825 TGGTTTGCTTGAGAACCCAGG
1 TGGTTTCCTTGAGAACCCAGG
1846 TGG
1 TGG
1849 GCAGTGTCAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.22, G:0.31, T:0.31
Consensus pattern (21 bp):
TGGTTTCCTTGAGAACCCAGG
Found at i:3003 original size:25 final size:25
Alignment explanation
Indices: 2953--3004 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
2943 ATTACAATAT
** *
2953 ATAAAATTGACATTATTGGAATTTA
1 ATAAAATTGACATTATTAAAAATTA
*
2978 ATAAAATTGCCATTATTAAAAATTA
1 ATAAAATTGACATTATTAAAAATTA
3003 AT
1 AT
3005 TTTCAATTCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.48, C:0.06, G:0.08, T:0.38
Consensus pattern (25 bp):
ATAAAATTGACATTATTAAAAATTA
Found at i:5615 original size:3 final size:3
Alignment explanation
Indices: 5607--5634 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5597 AGTCTAGTTA
5607 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
5635 TAAAATCAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:10795 original size:13 final size:13
Alignment explanation
Indices: 10779--10803 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10769 TTAACCATTC
10779 TCTTTAGATTTTA
1 TCTTTAGATTTTA
10792 TCTTTAGATTTT
1 TCTTTAGATTTT
10804 GACCATCTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.08, G:0.08, T:0.64
Consensus pattern (13 bp):
TCTTTAGATTTTA
Found at i:14641 original size:17 final size:17
Alignment explanation
Indices: 14621--14654 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
14611 GCTAATAATA
14621 ATTATGAAATAATTATT
1 ATTATGAAATAATTATT
**
14638 ATTATTCAATAATTATT
1 ATTATGAAATAATTATT
14655 CCTTAATTTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (17 bp):
ATTATGAAATAATTATT
Found at i:16722 original size:42 final size:37
Alignment explanation
Indices: 16634--16707 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
16624 ATTAAATATA
16634 AATTTAAAATACTGAAGTTTTCAAATCAAAGTAAATG
1 AATTTAAAATACTGAAGTTTTCAAATCAAAGTAAATG
16671 AATTTAAAATACTGAAGTTTTCAAATCAAAGTAAATG
1 AATTTAAAATACTGAAGTTTTCAAATCAAAGTAAATG
16708 CGGATTCATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.49, C:0.08, G:0.11, T:0.32
Consensus pattern (37 bp):
AATTTAAAATACTGAAGTTTTCAAATCAAAGTAAATG
Found at i:25154 original size:2 final size:2
Alignment explanation
Indices: 25147--25185 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
25137 GGAGCATTGA
25147 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Done.