Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1395
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: 14887
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1961 original size:13 final size:13
Alignment explanation
Indices: 1943--1969 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1933 CAATTTTTTG
1943 TTGTATCGATACA
1 TTGTATCGATACA
1956 TTGTATCGATACA
1 TTGTATCGATACA
1969 T
1 T
1970 ACTTTGTGTA
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1963 original size:34 final size:32
Alignment explanation
Indices: 1920--1987 Score: 100
Period size: 34 Copynumber: 2.1 Consensus size: 32
1910 CGTTACAAGC
**
1920 CATTGTATCGATACAATTTTTTGTTGTATCGATA
1 CATTGTATCGATAC-ATACTTTG-TGTATCGATA
1954 CATTGTATCGATACATACTTTGTGTATCGATA
1 CATTGTATCGATACATACTTTGTGTATCGATA
1986 CA
1 CA
1988 AGTTTGGCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 12 0.38
33 6 0.19
34 14 0.44
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.43
Consensus pattern (32 bp):
CATTGTATCGATACATACTTTGTGTATCGATA
Found at i:2661 original size:40 final size:41
Alignment explanation
Indices: 2617--2707 Score: 107
Period size: 39 Copynumber: 2.3 Consensus size: 41
2607 TTTTCTTTCT
*
2617 CCCTTAACTAAAG-TAATTTTAACAAATTCGTACATTCTCC
1 CCCTTAACTAAAGATAATTTTAACAAATTCATACATTCTCC
* * *
2657 CCCTTAA-T-AAGATAATTTTAGCAAATTTATGCATTCTCC
1 CCCTTAACTAAAGATAATTTTAACAAATTCATACATTCTCC
* *
2696 CCTTTTACTAAA
1 CCCTTAACTAAA
2708 AAAATCTCCC
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
38 3 0.07
39 29 0.69
40 8 0.19
41 2 0.05
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.37
Consensus pattern (41 bp):
CCCTTAACTAAAGATAATTTTAACAAATTCATACATTCTCC
Found at i:4566 original size:13 final size:13
Alignment explanation
Indices: 4548--4581 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
4538 ATAATCCCCC
4548 TGTATCGATACAG
1 TGTATCGATACAG
*
4561 TGTATCGATACAT
1 TGTATCGATACAG
4574 TGTATCGA
1 TGTATCGA
4582 ACAAAGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:8504 original size:21 final size:23
Alignment explanation
Indices: 8478--8526 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 23
8468 ATGCAAGTTT
*
8478 TTATTTTTC-TTAGCTAAC-TCA
1 TTATTTTTCATTAGCCAACTTCA
8499 TTA-TTTTCATTAGCCAACTTCA
1 TTATTTTTCATTAGCCAACTTCA
8521 TTATTT
1 TTATTT
8527 CAACTTGCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 5 0.21
21 11 0.46
22 6 0.25
23 2 0.08
ACGTcount: A:0.24, C:0.18, G:0.04, T:0.53
Consensus pattern (23 bp):
TTATTTTTCATTAGCCAACTTCA
Found at i:8528 original size:21 final size:21
Alignment explanation
Indices: 8482--8526 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
8472 AAGTTTTTAT
*
8482 TTTTC-TTAGCTAACTCATTA
1 TTTTCATTAGCCAACTCATTA
8502 TTTTCATTAGCCAACTTCATTA
1 TTTTCATTAGCCAAC-TCATTA
8524 TTT
1 TTT
8527 CAACTTGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.23
21 8 0.36
22 9 0.41
ACGTcount: A:0.24, C:0.20, G:0.04, T:0.51
Consensus pattern (21 bp):
TTTTCATTAGCCAACTCATTA
Found at i:10124 original size:13 final size:13
Alignment explanation
Indices: 10106--10131 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10096 CAATTTTTTG
10106 TGTATCGATACAT
1 TGTATCGATACAT
10119 TGTATCGATACAT
1 TGTATCGATACAT
10132 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:10143 original size:32 final size:33
Alignment explanation
Indices: 10083--10149 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 33
10073 CGTTACAAGC
**
10083 CATTGTATCGATACAATTTTTTGTGTATCGATA
1 CATTGTATCGATACAATACTTTGTGTATCGATA
10116 CATTGTATCGATAC-ATACTTTGTGTATCGATA
1 CATTGTATCGATACAATACTTTGTGTATCGATA
10148 CA
1 CA
10150 AGTTTGGCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.56
33 14 0.44
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (33 bp):
CATTGTATCGATACAATACTTTGTGTATCGATA
Done.