Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold304
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: 184049
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:156598 original size:33 final size:32
Alignment explanation
Indices: 156556--156619 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
156546 TACAAGCCAA
*
156556 TGTATCGATACATTTTGCGGTGTATCGATACAT
1 TGTATCGATACATCTTG-GGTGTATCGATACAT
*
156589 TGTATCGATACATCTTGTGTGTATCGATACA
1 TGTATCGATACATCTTGGGTGTATCGATACA
156620 AACAGTTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATCTTGGGTGTATCGATACAT
Found at i:156719 original size:13 final size:13
Alignment explanation
Indices: 156701--156725 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
156691 ACATTTGGTC
156701 ATGTATCGATACA
1 ATGTATCGATACA
156714 ATGTATCGATAC
1 ATGTATCGATAC
156726 TGTGCAATCT
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):
ATGTATCGATACA
Found at i:160996 original size:13 final size:13
Alignment explanation
Indices: 160978--161004 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
160968 TGAAAGTTGC
160978 CAAGATGGATTCA
1 CAAGATGGATTCA
160991 CAAGATGGATTCA
1 CAAGATGGATTCA
161004 C
1 C
161005 TTTGCTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (13 bp):
CAAGATGGATTCA
Found at i:163460 original size:2 final size:2
Alignment explanation
Indices: 163449--163487 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
163439 ACATTGAAAC
163449 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
163488 GAGAGAGAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:163528 original size:2 final size:2
Alignment explanation
Indices: 163487--163518 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
163477 ATATATATAT
163487 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
163519 GGGTAGAGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:166904 original size:2 final size:2
Alignment explanation
Indices: 166897--166922 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
166887 AGAAAACTTG
166897 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
166923 GATGAAAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:168019 original size:61 final size:60
Alignment explanation
Indices: 167924--168039 Score: 196
Period size: 61 Copynumber: 1.9 Consensus size: 60
167914 AGAGTACATT
*
167924 TTTTGAATCTATTTCAATTTCTTGTGAAAATGAAATAATGTTATGACATCTTAGGCTATTG
1 TTTTGAATCTATTTCAATTTCTGGTGAAAATGAAATAATGTTATGACATC-TAGGCTATTG
* *
167985 TTTTGAATCTATTTCTATTTCTGGTGAAAATGAAATAATGTTATGGCATCTAGGC
1 TTTTGAATCTATTTCAATTTCTGGTGAAAATGAAATAATGTTATGACATCTAGGC
168040 AATGCTGTCC
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
60 5 0.10
61 47 0.90
ACGTcount: A:0.30, C:0.10, G:0.16, T:0.43
Consensus pattern (60 bp):
TTTTGAATCTATTTCAATTTCTGGTGAAAATGAAATAATGTTATGACATCTAGGCTATTG
Found at i:168662 original size:24 final size:25
Alignment explanation
Indices: 168618--168665 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 25
168608 TTGATATGGC
168618 ATCAGAGCCATAAAAATCTGGTATT
1 ATCAGAGCCATAAAAATCTGGTATT
168643 ATCAGAGCCAT-AAAATCTGGTAT
1 ATCAGAGCCATAAAAATCTGGTAT
168666 ATATAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.27
Consensus pattern (25 bp):
ATCAGAGCCATAAAAATCTGGTATT
Found at i:172819 original size:2 final size:2
Alignment explanation
Indices: 172812--172845 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
172802 TTAATCATAA
*
172812 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
172846 AAAGTATTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:172921 original size:25 final size:25
Alignment explanation
Indices: 172888--172936 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
172878 AATTAGATCT
*
172888 AATAGCATAATTTAATAAATATATC
1 AATAACATAATTTAATAAATATATC
172913 AATAACATAATTTAATAAATATAT
1 AATAACATAATTTAATAAATATAT
172937 TTTATTTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.37
Consensus pattern (25 bp):
AATAACATAATTTAATAAATATATC
Found at i:172938 original size:13 final size:13
Alignment explanation
Indices: 172897--172938 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
172887 TAATAGCATA
172897 ATTTAATAAATAT
1 ATTTAATAAATAT
*
172910 A-TCAATAACATA-
1 ATTTAATAA-ATAT
172922 ATTTAATAAATAT
1 ATTTAATAAATAT
172935 ATTT
1 ATTT
172939 TATTTTGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
12 10 0.42
13 14 0.58
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (13 bp):
ATTTAATAAATAT
Done.