Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2732
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: 27275
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:4585 original size:18 final size:18
Alignment explanation
Indices: 4549--4587 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
4539 AAACTTTTGC
**
4549 AATTTGAATAACTTGAAT
1 AATTTGAATAACTCAAAT
4567 AATTTGAATAACTCAAAT
1 AATTTGAATAACTCAAAT
4585 AAT
1 AAT
4588 AGATGGATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.36
Consensus pattern (18 bp):
AATTTGAATAACTCAAAT
Found at i:4869 original size:16 final size:16
Alignment explanation
Indices: 4850--4880 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4840 TTGAAAAAGT
4850 TTTCAAATATATATGG
1 TTTCAAATATATATGG
*
4866 TTTCAAATTTATATG
1 TTTCAAATATATATG
4881 CAGTAAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGG
Found at i:5570 original size:27 final size:28
Alignment explanation
Indices: 5547--5602 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
5537 AAACAATTTT
*
5547 ACTTT-GAGTTTTATTTCACTCAATCGA
1 ACTTTAGAGTTGTATTTCACTCAATCGA
*
5574 ATTTTAGAGTTGTATTTCACTCAATCGA
1 ACTTTAGAGTTGTATTTCACTCAATCGA
5602 A
1 A
5603 TTCTTGATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 4 0.15
28 22 0.85
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (28 bp):
ACTTTAGAGTTGTATTTCACTCAATCGA
Found at i:5754 original size:34 final size:33
Alignment explanation
Indices: 5716--5793 Score: 93
Period size: 34 Copynumber: 2.3 Consensus size: 33
5706 CAAATACATG
* *
5716 TTAAGCATGTTTATTGATACCGTATTAATCTGGT
1 TTAAGCATGTTTATTGATACCATATTAATC-CGT
* * *
5750 TTAAGCATATTTATTGTTACCATATTGATCCGT
1 TTAAGCATGTTTATTGATACCATATTAATCCGT
5783 TATAAGCATGT
1 T-TAAGCATGT
5794 CATATTGTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
33 3 0.08
34 34 0.92
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (33 bp):
TTAAGCATGTTTATTGATACCATATTAATCCGT
Found at i:9176 original size:66 final size:66
Alignment explanation
Indices: 9094--9238 Score: 164
Period size: 66 Copynumber: 2.2 Consensus size: 66
9084 TTTCACACAT
* * * * * * *
9094 CATATAGGCTCACATGTACCTAGGGTTCGCATACATATTGACTCGCTTATTCCTAGGGTTTGTAT
1 CATATAGGCTCACATGTACCGAGGGTTCGAATACATATAGACTCACTTATTCATAGGGTTCGCAT
9159 A
66 A
* * * * * *
9160 CATATAGGCTCTCATGTATCGGGGGTTCTAATGCATATAGGCTCACTTATTCATAGGGTTCGCAT
1 CATATAGGCTCACATGTACCGAGGGTTCGAATACATATAGACTCACTTATTCATAGGGTTCGCAT
*
9225 G
66 A
9226 CATATAGGCTCAC
1 CATATAGGCTCAC
9239 TTATAATAAA
Statistics
Matches: 64, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.33
Consensus pattern (66 bp):
CATATAGGCTCACATGTACCGAGGGTTCGAATACATATAGACTCACTTATTCATAGGGTTCGCAT
A
Found at i:9280 original size:36 final size:36
Alignment explanation
Indices: 9232--9318 Score: 129
Period size: 36 Copynumber: 2.4 Consensus size: 36
9222 CATGCATATA
* *
9232 GGCTCACTTATAATAAACACATGGTTTGCATAACAT
1 GGCTCACATATAATAAACACATGGTTCGCATAACAT
*
9268 GGCTCACATATAATAAACACATGGTTCGCGTAACAT
1 GGCTCACATATAATAAACACATGGTTCGCATAACAT
* *
9304 GGCTCGCACATAATA
1 GGCTCACATATAATA
9319 TCATATAAGT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (36 bp):
GGCTCACATATAATAAACACATGGTTCGCATAACAT
Found at i:12033 original size:20 final size:20
Alignment explanation
Indices: 12008--12057 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
11998 TGGCTTAAAA
12008 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
12028 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
12045 GTGGTAGTGGATT
1 TTGGTAGTGGATT
12058 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:16661 original size:20 final size:20
Alignment explanation
Indices: 16636--16685 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
16626 TGGCTTAAAA
16636 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
16656 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
16673 GTGGTAGTGGATT
1 TTGGTAGTGGATT
16686 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:19236 original size:13 final size:13
Alignment explanation
Indices: 19218--19242 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19208 TTGATCTTCA
19218 ACTAAGTTGTCAT
1 ACTAAGTTGTCAT
19231 ACTAAGTTGTCA
1 ACTAAGTTGTCA
19243 CGACAACTTC
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):
ACTAAGTTGTCAT
Done.