Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019087.1 Corchorus olitorius cultivar O-4 contig19120, 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: 12560
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Found at i:3589 original size:24 final size:24
Alignment explanation
Indices: 3557--3605 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
3547 CATGTGCTAG
3557 CACCGTGCTAGCACAATCCCTTGT
1 CACCGTGCTAGCACAATCCCTTGT
3581 CACCGTGCTAGCACAATCCCTTGT
1 CACCGTGCTAGCACAATCCCTTGT
3605 C
1 C
3606 CTTTTATCCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.39, G:0.16, T:0.24
Consensus pattern (24 bp):
CACCGTGCTAGCACAATCCCTTGT
Found at i:5665 original size:29 final size:31
Alignment explanation
Indices: 5633--5700 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 31
5623 ATGCAATTTG
5633 GGATATAACGTTAC-AAAA-CAAGCAATTAA
1 GGATATAACGTTACAAAAAGCAAGCAATTAA
*
5662 GGATATAACGTTACGAAAAAGCGAGCAATTAA
1 GGATATAACGTTAC-AAAAAGCAAGCAATTAA
*
5694 GAATATA
1 GGATATA
5701 GTCCGTTAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 14 0.41
31 4 0.12
32 16 0.47
ACGTcount: A:0.50, C:0.12, G:0.18, T:0.21
Consensus pattern (31 bp):
GGATATAACGTTACAAAAAGCAAGCAATTAA
Found at i:5867 original size:31 final size:31
Alignment explanation
Indices: 5832--5910 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
5822 CTAACTGATT
**
5832 ATATCCTTAATTGCTTGAAATCGAAAACGCC
1 ATATCCTTAATTGCTTGAAATAAAAAACGCC
* * *
5863 ATATCCTTAATTGCATGAAATAAAAAATGTC
1 ATATCCTTAATTGCTTGAAATAAAAAACGCC
5894 ATATCCTTAATTGCTTG
1 ATATCCTTAATTGCTTG
5911 TTTTGTAACG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (31 bp):
ATATCCTTAATTGCTTGAAATAAAAAACGCC
Found at i:6022 original size:16 final size:16
Alignment explanation
Indices: 6001--6033 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5991 TATTCAGAAG
6001 AAAATAATTTT-TTTAA
1 AAAAT-ATTTTATTTAA
6017 AAAATATTTTATTTAA
1 AAAATATTTTATTTAA
6033 A
1 A
6034 TAACTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AAAATATTTTATTTAA
Found at i:6136 original size:16 final size:16
Alignment explanation
Indices: 6096--6129 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
6086 AAGGCATTGC
6096 TTAGTAGAAAAATGTA
1 TTAGTAGAAAAATGTA
6112 TTAGTAGAAAAATGTA
1 TTAGTAGAAAAATGTA
6128 TT
1 TT
6130 CTTAGAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35
Consensus pattern (16 bp):
TTAGTAGAAAAATGTA
Found at i:7020 original size:31 final size:31
Alignment explanation
Indices: 6980--7060 Score: 126
Period size: 31 Copynumber: 2.6 Consensus size: 31
6970 TTTGCTGCCA
* **
6980 CAAGTAATTAAGGATATAACGTTTTTTATTT
1 CAAGCAATTAAGGATATAACGTTTTCGATTT
*
7011 CAAGCAATTAAGGATATGACGTTTTCGATTT
1 CAAGCAATTAAGGATATAACGTTTTCGATTT
7042 CAAGCAATTAAGGATATAA
1 CAAGCAATTAAGGATATAA
7061 TCAGTTAGGG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (31 bp):
CAAGCAATTAAGGATATAACGTTTTCGATTT
Found at i:7234 original size:29 final size:31
Alignment explanation
Indices: 7167--7234 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
7157 ATTTAACGGA
*
7167 TTATATCTTTAATTGCTCGTTTTTCGTAACG
1 TTATATCCTTAATTGCTCGTTTTTCGTAACG
*
7198 TTATATCCTTAATTGCTTG-TTTT-GTAACG
1 TTATATCCTTAATTGCTCGTTTTTCGTAACG
7227 TTATATCC
1 TTATATCC
7235 CAAATTGCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 14 0.40
30 4 0.11
31 17 0.49
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (31 bp):
TTATATCCTTAATTGCTCGTTTTTCGTAACG
Found at i:7240 original size:29 final size:31
Alignment explanation
Indices: 7177--7242 Score: 91
Period size: 29 Copynumber: 2.2 Consensus size: 31
7167 TTATATCTTT
**
7177 AATTGCTCGTTTTTCGTAACGTTATATCCTT
1 AATTGCTCGTTTTTCGTAACGTTATATCCCA
*
7208 AATTGCTTG-TTTT-GTAACGTTATATCCCA
1 AATTGCTCGTTTTTCGTAACGTTATATCCCA
7237 AATTGC
1 AATTGC
7243 ATTTTGGGGC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 20 0.62
30 4 0.12
31 8 0.25
ACGTcount: A:0.23, C:0.18, G:0.14, T:0.45
Consensus pattern (31 bp):
AATTGCTCGTTTTTCGTAACGTTATATCCCA
Found at i:10290 original size:19 final size:19
Alignment explanation
Indices: 10262--10302 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
10252 TATTTGCTCC
* *
10262 AGTATTGTTCCGTTTCGGT
1 AGTATCGTTCCATTTCGGT
*
10281 AGTATCGTTCCATTTCGTT
1 AGTATCGTTCCATTTCGGT
10300 AGT
1 AGT
10303 TCAACGGAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.15, C:0.17, G:0.22, T:0.46
Consensus pattern (19 bp):
AGTATCGTTCCATTTCGGT
Done.