Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022750.1 Corchorus olitorius cultivar O-4 contig22783, 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: 9736
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:4833 original size:19 final size:18
Alignment explanation
Indices: 4809--4844 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
4799 TGAAGATATA
4809 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
4828 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
4845 ATTATTTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:7747 original size:13 final size:13
Alignment explanation
Indices: 7729--7757 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
7719 GTGGCTGCTC
7729 TAATAATAATTTT
1 TAATAATAATTTT
7742 TAATAATAATTTT
1 TAATAATAATTTT
7755 TAA
1 TAA
7758 AGGCTGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TAATAATAATTTT
Found at i:8068 original size:11 final size:11
Alignment explanation
Indices: 8052--8093 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
8042 AAAACGATAA
8052 TTCTCTCTC-T
1 TTCTCTCTCTT
*
8062 TT-TCTCTCTG
1 TTCTCTCTCTT
8072 TTCTCTCTCTT
1 TTCTCTCTCTT
8083 TTCTCTCTCTT
1 TTCTCTCTCTT
8094 CGAACTCGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
9 6 0.21
10 4 0.14
11 18 0.64
ACGTcount: A:0.00, C:0.36, G:0.02, T:0.62
Consensus pattern (11 bp):
TTCTCTCTCTT
Found at i:8069 original size:9 final size:9
Alignment explanation
Indices: 8055--8090 Score: 54
Period size: 9 Copynumber: 3.8 Consensus size: 9
8045 ACGATAATTC
8055 TCTCTCTTT
1 TCTCTCTTT
8064 TCTCTCTGTT
1 TCTCTCT-TT
8074 CTCTCTCTTT
1 -TCTCTCTTT
8084 TCTCTCT
1 TCTCTCT
8091 CTTCGAACTC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 14 0.56
10 4 0.16
11 7 0.28
ACGTcount: A:0.00, C:0.36, G:0.03, T:0.61
Consensus pattern (9 bp):
TCTCTCTTT
Found at i:8077 original size:20 final size:20
Alignment explanation
Indices: 8052--8090 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
8042 AAAACGATAA
8052 TTCTCTCTCTTTTCTCTCTG
1 TTCTCTCTCTTTTCTCTCTG
8072 TTCTCTCTCTTTTCTCTCT
1 TTCTCTCTCTTTTCTCTCT
8091 CTTCGAACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.00, C:0.36, G:0.03, T:0.62
Consensus pattern (20 bp):
TTCTCTCTCTTTTCTCTCTG
Found at i:8476 original size:14 final size:15
Alignment explanation
Indices: 8457--8485 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
8447 TTTTTTATGG
8457 GTTTTCT-GGTTTGT
1 GTTTTCTGGGTTTGT
8471 GTTTTCTGGGTTTGT
1 GTTTTCTGGGTTTGT
8486 TCTATATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.00, C:0.07, G:0.31, T:0.62
Consensus pattern (15 bp):
GTTTTCTGGGTTTGT
Found at i:9261 original size:18 final size:18
Alignment explanation
Indices: 9240--9288 Score: 98
Period size: 18 Copynumber: 2.7 Consensus size: 18
9230 TGTTCACAGT
9240 GAGGATGAAGTTGAGGTG
1 GAGGATGAAGTTGAGGTG
9258 GAGGATGAAGTTGAGGTG
1 GAGGATGAAGTTGAGGTG
9276 GAGGATGAAGTTG
1 GAGGATGAAGTTG
9289 TCGATGGTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.29, C:0.00, G:0.49, T:0.22
Consensus pattern (18 bp):
GAGGATGAAGTTGAGGTG
Done.