Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1383
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: 13363
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.36
Found at i:231 original size:23 final size:22
Alignment explanation
Indices: 169--232 Score: 60
Period size: 23 Copynumber: 2.9 Consensus size: 22
159 AATTGAGGCC
169 AAAAA-AT-TAAAAAATTATTTT
1 AAAAATATATAAAAAATT-TTTT
* **
190 AAAAATGAAATAAGTAATTTTTT
1 AAAAAT-ATATAAAAAATTTTTT
213 AAAAAATATATAAAAAATTT
1 -AAAAATATATAAAAAATTT
233 ATATCATTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
21 5 0.15
23 15 0.45
24 13 0.39
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (22 bp):
AAAAATATATAAAAAATTTTTT
Found at i:270 original size:21 final size:21
Alignment explanation
Indices: 232--299 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
222 ATAAAAAATT
232 TATATCATTAA-T-AATATTAA
1 TATAT-ATTAATTAAATATTAA
252 TATATATTAATTAAATATTAA
1 TATATATTAATTAAATATTAA
* * *
273 TTTA-ATTATATCAAATATAAA
1 TATATATTA-ATTAAATATTAA
*
294 TCTATA
1 TATATA
300 CGTACCAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
19 5 0.12
20 10 0.25
21 24 0.60
22 1 0.03
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (21 bp):
TATATATTAATTAAATATTAA
Found at i:920 original size:31 final size:32
Alignment explanation
Indices: 859--926 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 32
849 AATGAATATG
859 ATAAACAAAATTAAAAAAAAAGAAAGATTTTT
1 ATAAACAAAATTAAAAAAAAAGAAAGATTTTT
* * *
891 TTAAA-AAAATTATAAAAAAAA-TAATATTTTT
1 ATAAACAAAATTA-AAAAAAAAGAAAGATTTTT
922 ATAAA
1 ATAAA
927 TGGTAGTACA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
31 19 0.61
32 12 0.39
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (32 bp):
ATAAACAAAATTAAAAAAAAAGAAAGATTTTT
Found at i:1862 original size:31 final size:32
Alignment explanation
Indices: 1809--1892 Score: 118
Period size: 31 Copynumber: 2.7 Consensus size: 32
1799 ATTTCAATGA
*
1809 GTTGT-TCCATACAATGTATCGATACATAAGT
1 GTTGTATCGATACAATGTATCGATACATAAGT
1840 GTTGTATCGATACAATGT-TCGATACATAAGT
1 GTTGTATCGATACAATGTATCGATACATAAGT
* *
1871 TTTGTATCGATTCAATGGTATC
1 GTTGTATCGATACAAT-GTATC
1893 ACTACAAAGC
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
31 32 0.68
32 13 0.28
33 2 0.04
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (32 bp):
GTTGTATCGATACAATGTATCGATACATAAGT
Found at i:1955 original size:13 final size:13
Alignment explanation
Indices: 1937--1961 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1927 ATTACTCAAA
1937 TGTATCGATACAT
1 TGTATCGATACAT
1950 TGTATCGATACA
1 TGTATCGATACA
1962 CTGATCTTTG
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:2027 original size:53 final size:52
Alignment explanation
Indices: 1970--2095 Score: 182
Period size: 52 Copynumber: 2.4 Consensus size: 52
1960 CACTGATCTT
1970 TGTATCGATACATGCAGGCAAATTTGTCCCAGATGGTAT-GATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTG-CCCAGAT-GTATCGATACACTATGAAA
* ** * *
2023 TGTATCAATACATATAGGCCAATTTGCCCAGATGTATCGGTACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
2075 TGTATCGATACATGCAGGCAA
1 TGTATCGATACATGCAGGCAA
2096 TTTTAAATAT
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
51 4 0.06
52 37 0.59
53 22 0.35
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:5624 original size:20 final size:20
Alignment explanation
Indices: 5599--5649 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
5589 ATGGAAAAAT
*
5599 TGTATCGATACATAAGTAAA
1 TGTATCGATACATAACTAAA
* **
5619 TGTATCAATA-ATTTCTAAA
1 TGTATCGATACATAACTAAA
5638 TGTATCGATACA
1 TGTATCGATACA
5650 ACTTACTTTG
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (20 bp):
TGTATCGATACATAACTAAA
Found at i:8088 original size:24 final size:26
Alignment explanation
Indices: 8061--8109 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
8051 ATCAAAATTT
8061 ATTTATCG-G-GGATACTCCAACCTC
1 ATTTATCGAGAGGATACTCCAACCTC
*
8085 ATTTTTCGAGAGGATACTCCAACCT
1 ATTTATCGAGAGGATACTCCAACCT
8110 TACTTTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
25 1 0.05
26 14 0.64
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.31
Consensus pattern (26 bp):
ATTTATCGAGAGGATACTCCAACCTC
Done.