Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013191.1 Corchorus olitorius cultivar O-4 contig13224, 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: 32739
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:10217 original size:12 final size:12
Alignment explanation
Indices: 10200--10224 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10190 AACTTTTTAT
10200 CTCTCACACACA
1 CTCTCACACACA
10212 CTCTCACACACA
1 CTCTCACACACA
10224 C
1 C
10225 AAAAAACCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.52, G:0.00, T:0.16
Consensus pattern (12 bp):
CTCTCACACACA
Found at i:12211 original size:19 final size:18
Alignment explanation
Indices: 12187--12231 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
12177 AGGAAATATT
12187 AATAATAATTATTCTGAAA
1 AATAATAATTATT-TGAAA
* *
12206 AATAATTATTATTTGATA
1 AATAATAATTATTTGAAA
*
12224 AATTATAA
1 AATAATAA
12232 ATAAATCTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.42
Consensus pattern (18 bp):
AATAATAATTATTTGAAA
Found at i:20232 original size:16 final size:15
Alignment explanation
Indices: 20194--20232 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
20184 ACAGAGATTG
*
20194 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
20209 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
20224 ACTAGAAAA
1 AC-AGAAAA
20233 AAAAGCAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.64, C:0.13, G:0.10, T:0.13
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:20992 original size:11 final size:11
Alignment explanation
Indices: 20976--21001 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
20966 CCTTTGCCTA
20976 AAAACTAGAAG
1 AAAACTAGAAG
20987 AAAACTAGAAG
1 AAAACTAGAAG
20998 AAAA
1 AAAA
21002 GAAATTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:25837 original size:3 final size:3
Alignment explanation
Indices: 25824--25862 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
25814 TTATATATAT
25824 ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
25863 GATAAGTTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:26413 original size:13 final size:13
Alignment explanation
Indices: 26395--26421 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
26385 ATTATGTCTT
26395 TAATAATACAAAA
1 TAATAATACAAAA
26408 TAATAATACAAAA
1 TAATAATACAAAA
26421 T
1 T
26422 GTTGTCATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (13 bp):
TAATAATACAAAA
Found at i:30002 original size:6 final size:6
Alignment explanation
Indices: 29993--30025 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
29983 AATGCTAGTT
29993 CAATTC CAATTC CAATTC CAATTC CAATTC CAA
1 CAATTC CAATTC CAATTC CAATTC CAATTC CAA
30026 AAATTAGTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (6 bp):
CAATTC
Found at i:30706 original size:15 final size:15
Alignment explanation
Indices: 30686--30717 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
30676 GTAGTAATTA
30686 ATATGTAGGTTAGAT
1 ATATGTAGGTTAGAT
30701 ATATGTAGGTTAGAT
1 ATATGTAGGTTAGAT
30716 AT
1 AT
30718 TGCCTAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.25, T:0.41
Consensus pattern (15 bp):
ATATGTAGGTTAGAT
Found at i:31948 original size:13 final size:14
Alignment explanation
Indices: 31930--31962 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
31920 ATATTGATTT
31930 AGTCAG-TTTTCTG
1 AGTCAGTTTTTCTG
*
31943 AGTCAGTTTTTTTG
1 AGTCAGTTTTTCTG
31957 AGTCAG
1 AGTCAG
31963 AGTTTGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.18, C:0.12, G:0.24, T:0.45
Consensus pattern (14 bp):
AGTCAGTTTTTCTG
Found at i:32714 original size:2 final size:2
Alignment explanation
Indices: 32707--32739 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
32697 TGGAAAACTT
32707 TA TA TA TA 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 TA TA TA TA T
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.