Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1689
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: 21282
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.31
Found at i:1630 original size:81 final size:80
Alignment explanation
Indices: 1495--1662 Score: 327
Period size: 81 Copynumber: 2.1 Consensus size: 80
1485 GTTTGTCAAA
1495 GTATTTTCCAATTTTATTCAATCTTTGTTTTATCAAAACTAAGATCCTAACAACATTTATCATTG
1 GTATTTTCCAATTTTATTCAATCTTTGTTTTATCAAAACTAAGATCCTAACAACATTTATCATTG
1560 TATCGATACATCTGGG
66 TATCGATACATCT-GG
1576 GTATTTTCCAATTTTATTCAATCTTTGTTTTATCAAAACTAAGATCCTAACAACATTTATCATTG
1 GTATTTTCCAATTTTATTCAATCTTTGTTTTATCAAAACTAAGATCCTAACAACATTTATCATTG
1641 TATCGATACATCTGG
66 TATCGATACATCTGG
1656 GTATTTT
1 GTATTTT
1663 ACCCAGAATG
Statistics
Matches: 87, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
80 9 0.10
81 78 0.90
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.43
Consensus pattern (80 bp):
GTATTTTCCAATTTTATTCAATCTTTGTTTTATCAAAACTAAGATCCTAACAACATTTATCATTG
TATCGATACATCTGG
Found at i:6899 original size:52 final size:52
Alignment explanation
Indices: 6829--6949 Score: 215
Period size: 52 Copynumber: 2.3 Consensus size: 52
6819 GAAAATTTAT
* *
6829 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATAAATCTGGGCAAATTTGC
*
6881 CTGCATGTATCGATACATTTTATAATGTATCGATAAATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATAAATCTGGGCAAATTTGC
6933 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
6950 AAGATCAGTG
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATAAATCTGGGCAAATTTGC
Found at i:6962 original size:52 final size:51
Alignment explanation
Indices: 6829--6967 Score: 199
Period size: 52 Copynumber: 2.7 Consensus size: 51
6819 GAAAATTTAT
*
6829 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATAAATCTGGGCAAATTTGC
* *
6881 CTGCATGTATCGATACATTTTATAATGTATCGATAAATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATAAATCTGGGCAAATTTGC
*
6933 CTGCATGTATCGATACA-AAGATCAGTGTATCGATA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATA
6968 CAATGTATCG
Statistics
Matches: 79, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.03
52 77 0.97
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATAAATCTGGGCAAATTTGC
Found at i:6976 original size:13 final size:13
Alignment explanation
Indices: 6958--6982 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6948 CAAAGATCAG
6958 TGTATCGATACAA
1 TGTATCGATACAA
6971 TGTATCGATACA
1 TGTATCGATACA
6983 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:7064 original size:13 final size:13
Alignment explanation
Indices: 7046--7070 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7036 ACAAAAAATA
7046 TGTATCGATACAT
1 TGTATCGATACAT
7059 TGTATCGATACA
1 TGTATCGATACA
7071 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:13175 original size:19 final size:19
Alignment explanation
Indices: 13123--13182 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 19
13113 GGAGAAGATA
13123 GAGATAATTGTTTAAGGGG
1 GAGATAATTGTTTAAGGGG
* * *
13142 GAGA-ATTTTTTTAAGGAG
1 GAGATAATTGTTTAAGGGG
*
13160 GAGATAATCGTTTAAGGGG
1 GAGATAATTGTTTAAGGGG
13179 GAGA
1 GAGA
13183 ATTTTTGAAG
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
18 15 0.45
19 18 0.55
ACGTcount: A:0.33, C:0.02, G:0.35, T:0.30
Consensus pattern (19 bp):
GAGATAATTGTTTAAGGGG
Found at i:13868 original size:13 final size:13
Alignment explanation
Indices: 13847--13877 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
13837 CGATACATGG
*
13847 TACAATGTATCGA
1 TACATTGTATCGA
13860 TACATTGTATCGA
1 TACATTGTATCGA
13873 TACAT
1 TACAT
13878 GAAGAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:13876 original size:33 final size:32
Alignment explanation
Indices: 13834--13897 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 32
13824 TCATTATTTT
13834 TATCGATACATG-GTACAATGTATCGATACATTG
1 TATCGATACATGAG-A-AATGTATCGATACATTG
13867 TATCGATACATGAAGAAATGTATCGATACAT
1 TATCGATACATG-AGAAATGTATCGATACAT
13898 AGCTTGTAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 27 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (32 bp):
TATCGATACATGAGAAATGTATCGATACATTG
Found at i:18337 original size:20 final size:20
Alignment explanation
Indices: 18308--18359 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
18298 TATTGATACT
*
18308 TATCAGTACATTCACAAATG
1 TATCAATACATTCACAAATG
* **
18328 TATCTATACATTCACTCATG
1 TATCAATACATTCACAAATG
18348 TATCAATACATT
1 TATCAATACATT
18360 TGTGTCTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.37, C:0.21, G:0.06, T:0.37
Consensus pattern (20 bp):
TATCAATACATTCACAAATG
Done.