Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_62 ID=scaffold_62-JGI_221_v2.0
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: 18335
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Found at i:125 original size:17 final size:18
Alignment explanation
Indices: 84--125 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
74 TTTACTAACC
* *
84 ATTAATACAATTTTTTGA
1 ATTAATACAATTTTATCA
*
102 CTTAATACAA-TTTATCA
1 ATTAATACAATTTTATCA
119 ATTAATA
1 ATTAATA
126 ATTTCACAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTAATACAATTTTATCA
Found at i:3437 original size:126 final size:126
Alignment explanation
Indices: 3138--3490 Score: 555
Period size: 126 Copynumber: 2.8 Consensus size: 126
3128 CCCAAACATG
* * * *
3138 CTACTGTAGCAAAAGCGCGTCCACAAGGGCGCAATTTCACAAATTCTTCTCAAATAGTATCCTAC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
*
3203 TAGAAGCGATTTTATATTATTTGCTCAGAAACGTC-AAAAAATAATTATTTCTTACATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTTACATGAC
* * * *
3263 CTACTGTAGCAAAAGCGCGTCTACGAGGCCGCGATTTCATAAATTCTTCTCAAATAACATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
*
3328 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTTCCATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTTACATGAC
* * *
3389 CTACTGTAGCAAAAGCACGTCCACGAGGGCGTGATTTCACAAATTCTTCTCAAATAGCATTCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
** *
3454 TAGAAGCGATTTTATACTATTTTATCAGAAACATCAA
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAA
3491 CTTGAAATTA
Statistics
Matches: 207, Mismatches: 20, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
125 91 0.44
126 116 0.56
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Consensus pattern (126 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTTACATGAC
Found at i:7003 original size:46 final size:46
Alignment explanation
Indices: 6950--7043 Score: 152
Period size: 46 Copynumber: 2.0 Consensus size: 46
6940 ACAATGCTAT
* * *
6950 AACTCAGTATGGTTTCCTTCATTGAAATATCATACCTACTTTTCAC
1 AACTCAGTATGGTTTCCTTCACTGAAACACCATACCTACTTTTCAC
*
6996 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTCCTTCACTGAAACACCATACCTACTTTTCAC
7042 AA
1 AA
7044 TTTGACTTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.36
Consensus pattern (46 bp):
AACTCAGTATGGTTTCCTTCACTGAAACACCATACCTACTTTTCAC
Found at i:10954 original size:7 final size:7
Alignment explanation
Indices: 10942--10972 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
10932 CACAAGACTG
10942 GTGGAGA
1 GTGGAGA
10949 GTGGAGA
1 GTGGAGA
10956 GTGGAGA
1 GTGGAGA
10963 GTGGAGA
1 GTGGAGA
10970 GTG
1 GTG
10973 AACGTAGATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.00, G:0.58, T:0.16
Consensus pattern (7 bp):
GTGGAGA
Found at i:16274 original size:22 final size:22
Alignment explanation
Indices: 16244--16299 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
16234 ATTTCCTCTC
16244 AATTACTCTCAATTTCCTTCCAA
1 AATT-CTCTCAATTTCCTTCCAA
16267 AATTCTCTCAATTTCCTTCCAA
1 AATTCTCTCAATTTCCTTCCAA
16289 AATTCTCTCAA
1 AATTCTCTCAA
16300 ATCCATATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 29 0.88
23 4 0.12
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTCTCTCAATTTCCTTCCAA
Found at i:18173 original size:18 final size:18
Alignment explanation
Indices: 18147--18181 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
18137 AGGTGCGTTT
*
18147 CCTAGCCCTTATATGTAC
1 CCTAACCCTTATATGTAC
18165 CCTAACCCTTATATGTA
1 CCTAACCCTTATATGTA
18182 TCATTTTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.31, G:0.09, T:0.34
Consensus pattern (18 bp):
CCTAACCCTTATATGTAC
Done.