Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1931
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: 19190
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.30
Found at i:2938 original size:20 final size:20
Alignment explanation
Indices: 2915--2987 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2905 ACAATTCAAA
2915 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
2935 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
2956 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
2976 GTATCGATACAT
1 GTATCGATACAT
2988 AAAAAGGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:2959 original size:21 final size:21
Alignment explanation
Indices: 2933--3008 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 21
2923 ACATGTTGCA
2933 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
2954 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
2974 ATGTATCGATACAT-AAAAAGG
1 ATGTATCGATACATGAAAAA-G
2995 ATGTATCGATACAT
1 ATGTATCGATACAT
3009 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
19 1 0.02
20 14 0.31
21 30 0.67
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:2966 original size:41 final size:41
Alignment explanation
Indices: 2915--3008 Score: 172
Period size: 41 Copynumber: 2.3 Consensus size: 41
2905 ACAATTCAAA
2915 GTATCGATACATGTTGCAATGTATCGATACATGAAAAA-GAT
1 GTATCGATACATGTTGCAATGTATCGATACAT-AAAAAGGAT
2956 GTATCGATACATGTTGCAATGTATCGATACATAAAAAGGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAGGAT
2997 GTATCGATACAT
1 GTATCGATACAT
3009 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
40 5 0.10
41 47 0.90
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAGGAT
Found at i:3065 original size:13 final size:13
Alignment explanation
Indices: 3047--3072 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3037 TACAGCAAGT
3047 ATGTATCGATACA
1 ATGTATCGATACA
3060 ATGTATCGATACA
1 ATGTATCGATACA
3073 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:5306 original size:21 final size:21
Alignment explanation
Indices: 5273--5317 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
5263 TTGCAAGTTG
*
5273 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
5295 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
5315 AAA
1 AAA
5318 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:9241 original size:20 final size:20
Alignment explanation
Indices: 9162--9242 Score: 81
Period size: 20 Copynumber: 3.8 Consensus size: 20
9152 AATGTCCAAA
*
9162 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
9182 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
9207 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
9227 TTGTATCGATACATTT
1 ATGTATCGATACATTT
9243 ATCGATACAC
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
20 32 0.64
24 1 0.02
25 17 0.34
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:9247 original size:12 final size:13
Alignment explanation
Indices: 9228--9264 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
9218 CATTTTTCTT
9228 TGTATCGATACA-
1 TGTATCGATACAC
*
9240 TTTATCGATACAC
1 TGTATCGATACAC
9253 TGTATCGATACA
1 TGTATCGATACA
9265 GGGTGATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:11739 original size:20 final size:20
Alignment explanation
Indices: 11716--11789 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
11706 ACAATTCAAA
11716 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
11736 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
11757 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
11777 GTATCGATACATG
1 GTATCGATACATG
11790 AAAAAGATGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:11760 original size:21 final size:21
Alignment explanation
Indices: 11734--11809 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
11724 ACATGTTGCA
11734 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
11755 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
11775 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
11796 ATGTATCGATACAT
1 ATGTATCGATACAT
11810 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:11767 original size:41 final size:41
Alignment explanation
Indices: 11716--11809 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
11706 ACAATTCAAA
11716 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
11757 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
11798 GTATCGATACAT
1 GTATCGATACAT
11810 TTCTTGGCAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
Found at i:11866 original size:13 final size:13
Alignment explanation
Indices: 11848--11873 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11838 TACAGCAAGT
11848 ATGTATCGATACA
1 ATGTATCGATACA
11861 ATGTATCGATACA
1 ATGTATCGATACA
11874 CAAAAATTGT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:11871 original size:32 final size:32
Alignment explanation
Indices: 11830--11892 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
11820 TAGCCAAACT
**
11830 TGTATCGATACAGCAAGTA-TGTATCGATACAA
1 TGTATCGATACA-CAAAAATTGTATCGATACAA
11862 TGTATCGATACACAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAATTGTATCGATACA
11893 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 4 0.14
32 24 0.86
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.29
Consensus pattern (32 bp):
TGTATCGATACACAAAAATTGTATCGATACAA
Found at i:13009 original size:17 final size:17
Alignment explanation
Indices: 12983--13024 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
12973 GTATCGATAC
*
12983 AAATTGTAGAAATTTGA
1 AAATTTTAGAAATTTGA
13000 AAATTTTAGAAATTTGA
1 AAATTTTAGAAATTTGA
13017 AAATTTTA
1 AAATTTTA
13025 ACCATTGGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (17 bp):
AAATTTTAGAAATTTGA
Found at i:16030 original size:21 final size:21
Alignment explanation
Indices: 15997--16042 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
15987 TTGCAAGTTG
*
15997 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
16019 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
16039 AAAT
1 AAAT
16043 GAAAACTTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 6 0.27
21 9 0.41
22 7 0.32
ACGTcount: A:0.52, C:0.04, G:0.20, T:0.24
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Done.