Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2219
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: 10435
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.33
Found at i:64 original size:13 final size:13
Alignment explanation
Indices: 46--71 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
36 TACACCAAGT
46 ATGTATCGATACA
1 ATGTATCGATACA
59 ATGTATCGATACA
1 ATGTATCGATACA
72 CCAAAAATTG
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:65 original size:32 final size:33
Alignment explanation
Indices: 28--91 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
18 TAGCCAAACT
**
28 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACCAAAAATTGTATCGATACAA
60 TGTATCGATACACCAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAATTGTATCGATACA
92 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACCAAAAATTGTATCGATACAA
Found at i:156 original size:20 final size:21
Alignment explanation
Indices: 126--164 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
116 CTATATTTTC
126 AAATATGTATCGATACATTAA
1 AAATATGTATCGATACATTAA
147 AAAT-TGTATCGATACATT
1 AAATATGTATCGATACATT
165 TACACGGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (21 bp):
AAATATGTATCGATACATTAA
Found at i:2271 original size:83 final size:83
Alignment explanation
Indices: 2113--2271 Score: 182
Period size: 83 Copynumber: 1.9 Consensus size: 83
2103 ACTCAAAGAA
* * * * *
2113 GAAATAAATCAATAAGTGTAGAGAATCATATTCTTGAAAAGAAATTAAGTGAATTAGATAAGAGT
1 GAAATAAATCAATAAGTGTAGAGAAACATATTCTTAAAAAGAAAATAAATGAATTAGATAAGAGA
*
2178 ATGAAAGAGTTACAAAAT
66 AAGAAAGAGTTACAAAAT
* *
2196 GAAATAAATCAATGAGTTTAGA-AAACA-ATTCTTTTAAAAAGAAAATAAATGAATTAG--AAGA
1 GAAATAAATCAATAAGTGTAGAGAAACATATTC--TTAAAAAGAAAATAAATGAATTAGATAAGA
2257 GAAAAGAAATGAGTT
64 G-AAAGAAA-GAGTT
2272 GCAAGTGGAA
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
81 9 0.14
82 9 0.14
83 46 0.72
ACGTcount: A:0.53, C:0.04, G:0.17, T:0.26
Consensus pattern (83 bp):
GAAATAAATCAATAAGTGTAGAGAAACATATTCTTAAAAAGAAAATAAATGAATTAGATAAGAGA
AAGAAAGAGTTACAAAAT
Found at i:3804 original size:13 final size:13
Alignment explanation
Indices: 3776--3814 Score: 69
Period size: 13 Copynumber: 2.9 Consensus size: 13
3766 TTTTCCAGAT
3776 TGTATCGATAACAA
1 TGTATCGAT-ACAA
3790 TGTATCGATACAA
1 TGTATCGATACAA
3803 TGTATCGATACA
1 TGTATCGATACA
3815 TTGCTTCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 16 0.64
14 9 0.36
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5754 original size:13 final size:13
Alignment explanation
Indices: 5736--5761 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5726 TACACCAAGT
5736 ATGTATCGATACA
1 ATGTATCGATACA
5749 ATGTATCGATACA
1 ATGTATCGATACA
5762 CCAAAAATTG
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:5759 original size:32 final size:33
Alignment explanation
Indices: 5718--5781 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
5708 AGCCCAAACT
**
5718 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACCAAAAATTGTATCGATACAA
5750 TGTATCGATACACCAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAATTGTATCGATACA
5782 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACCAAAAATTGTATCGATACAA
Found at i:5833 original size:21 final size:20
Alignment explanation
Indices: 5807--5854 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
5797 TAGAAACGGC
*
5807 TACATTTCAAATATGTATCGA
1 TACATTTAAAAT-TGTATCGA
5828 TACA-TTAAAATTGTATCGA
1 TACATTTAAAATTGTATCGA
*
5847 TGCATTTA
1 TACATTTA
5855 CACGGGAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 11 0.46
20 9 0.38
21 4 0.17
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (20 bp):
TACATTTAAAATTGTATCGA
Found at i:8818 original size:3 final size:3
Alignment explanation
Indices: 8800--8833 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
8790 AACCATCAAG
* *
8800 GAT GAT GAA GAC GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
8834 GTAATCAGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.03, G:0.35, T:0.26
Consensus pattern (3 bp):
GAT
Done.