Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017805.1 Corchorus olitorius cultivar O-4 contig17838, 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: 12126
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:2812 original size:7 final size:7
Alignment explanation
Indices: 2802--2846 Score: 72
Period size: 7 Copynumber: 6.3 Consensus size: 7
2792 AAAAGGAAAG
2802 GACTTGA
1 GACTTGA
2809 GACTTGA
1 GACTTGA
2816 GACTTGA
1 GACTTGA
2823 GACTTGA
1 GACTTGA
2830 GACTTGGA
1 GACTT-GA
*
2838 GAGTTGA
1 GACTTGA
2845 GA
1 GA
2847 ATAGAGCTGT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
7 30 0.83
8 6 0.17
ACGTcount: A:0.29, C:0.11, G:0.33, T:0.27
Consensus pattern (7 bp):
GACTTGA
Found at i:3011 original size:15 final size:15
Alignment explanation
Indices: 2991--3021 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2981 TTGAATTGAA
*
2991 TAAAATTTTGACTAT
1 TAAAATTTTGAATAT
3006 TAAAATTTTGAATAT
1 TAAAATTTTGAATAT
3021 T
1 T
3022 CCAGTATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (15 bp):
TAAAATTTTGAATAT
Found at i:3595 original size:2 final size:2
Alignment explanation
Indices: 3588--3615 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3578 TAAGCGTTAA
3588 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3616 TTGAGGGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7156 original size:11 final size:11
Alignment explanation
Indices: 7133--7166 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
7123 TATTTTCGGG
*
7133 TTTG-TTTTGT
1 TTTGTTTTTTT
7143 TTTGTTTTTTT
1 TTTGTTTTTTT
7154 TTTGTTTTTTT
1 TTTGTTTTTTT
7165 TT
1 TT
7167 CCAATCTGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 4 0.18
11 18 0.82
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (11 bp):
TTTGTTTTTTT
Found at i:7158 original size:16 final size:15
Alignment explanation
Indices: 7137--7166 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
7127 TTCGGGTTTG
7137 TTTTGTTTTGTTTTTT
1 TTTTGTTTT-TTTTTT
7153 TTTTGTTTTTTTTT
1 TTTTGTTTTTTTTT
7167 CCAATCTGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (15 bp):
TTTTGTTTTTTTTTT
Found at i:7166 original size:10 final size:10
Alignment explanation
Indices: 7133--7166 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
7123 TATTTTCGGG
*
7133 TTTGTTTTGT
1 TTTGTTTTTT
7143 TTTGTTTTTTT
1 TTTG-TTTTTT
7154 TTTGTTTTTT
1 TTTGTTTTTT
7164 TTT
1 TTT
7167 CCAATCTGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (10 bp):
TTTGTTTTTT
Found at i:11348 original size:8 final size:9
Alignment explanation
Indices: 11322--11350 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
11312 CCCAAATTAC
11322 TTATGGAAA
1 TTATGGAAA
11331 TTATGGAAA
1 TTATGGAAA
11340 TTA-GGAAA
1 TTATGGAAA
11348 TTA
1 TTA
11351 AATGAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (9 bp):
TTATGGAAA
Done.