Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2642
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: 23783
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:4013 original size:13 final size:13
Alignment explanation
Indices: 3995--4019 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3985 TTTTTTGGTG
3995 GTATCGATACATT
1 GTATCGATACATT
4008 GTATCGATACAT
1 GTATCGATACAT
4020 AATTGGTGTA
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):
GTATCGATACATT
Found at i:4118 original size:20 final size:20
Alignment explanation
Indices: 4092--4148 Score: 82
Period size: 20 Copynumber: 2.9 Consensus size: 20
4082 ACATCTTTTT
4092 TCATGTATCGATACTTTGCAA
1 TCATGTATCGATACTTTG-AA
4113 -CATGTATCGATACTTTGAA
1 TCATGTATCGATACTTTGAA
4132 TTC-TGTATCGATACTTT
1 -TCATGTATCGATACTTT
4149 TAAGGGTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
19 2 0.06
20 31 0.91
21 1 0.03
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (20 bp):
TCATGTATCGATACTTTGAA
Found at i:6114 original size:21 final size:20
Alignment explanation
Indices: 6085--6124 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
6075 GGCTAGTGTG
*
6085 GGGACTGCCCGGTTGCGACCT
1 GGGACTG-CCGGTCGCGACCT
*
6106 GGGAGTGCCGGTCGCGACC
1 GGGACTGCCGGTCGCGACC
6125 GGGTGGGTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.10, C:0.33, G:0.42, T:0.15
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:6583 original size:13 final size:13
Alignment explanation
Indices: 6565--6602 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
6555 ATAATCCCCC
*
6565 TGTATCGATACAG
1 TGTATCGATACAA
*
6578 TGTATCAATACAA
1 TGTATCGATACAA
6591 TGTATCGATACA
1 TGTATCGATACA
6603 TTGAATTTCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:12810 original size:32 final size:34
Alignment explanation
Indices: 12744--12812 Score: 97
Period size: 32 Copynumber: 2.1 Consensus size: 34
12734 CGTTACAAGC
** *
12744 CAATGTATCGATACAATTTTTTGGTGTATTGATA
1 CAATGTATCGATACAATTACTTGGTGTATCGATA
12778 CAATGTATCGATAC-A-TACTTGGTGTATCGATA
1 CAATGTATCGATACAATTACTTGGTGTATCGATA
12810 CAA
1 CAA
12813 GTTTGGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 17 0.53
33 1 0.03
34 14 0.44
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (34 bp):
CAATGTATCGATACAATTACTTGGTGTATCGATA
Found at i:13926 original size:51 final size:51
Alignment explanation
Indices: 13869--14011 Score: 223
Period size: 51 Copynumber: 2.8 Consensus size: 51
13859 TTTTAACTAG
* * *
13869 ATGTATCAATACATTGAAAAATGTATCGATACATCCGGGTAAAAAGACAGA
1 ATGTATCGATACATTGAAGAATGTATCGATACATCTGGGTAAAAAGACAGA
* * *
13920 ATGTATCGATACATTGAAGAATATATCGATACATCTGGGTAAAAGGATAGA
1 ATGTATCGATACATTGAAGAATGTATCGATACATCTGGGTAAAAAGACAGA
*
13971 ATGTATCGATACATTGAAGAATGTTTCGATACATCTGGGTA
1 ATGTATCGATACATTGAAGAATGTATCGATACATCTGGGTA
14012 CCTTTCCATA
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 84 1.00
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (51 bp):
ATGTATCGATACATTGAAGAATGTATCGATACATCTGGGTAAAAAGACAGA
Found at i:16160 original size:33 final size:32
Alignment explanation
Indices: 16097--16164 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 32
16087 CCTTAACTGT
*
16097 TTGTATCGATACATACAAGATGTATCGATACA
1 TTGTATAGATACATACAAGATGTATCGATACA
*
16129 TTGTATAGATACATGACCAA-ATGTATTGATACA
1 TTGTATAGATACAT-A-CAAGATGTATCGATACA
16162 TTG
1 TTG
16165 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
32 13 0.41
33 16 0.50
34 3 0.09
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (32 bp):
TTGTATAGATACATACAAGATGTATCGATACA
Found at i:23014 original size:13 final size:13
Alignment explanation
Indices: 22992--23022 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
22982 TTCTCTGTCA
*
22992 ATACATTGTATCG
1 ATACAGTGTATCG
23005 ATACAGTGTATCG
1 ATACAGTGTATCG
23018 ATACA
1 ATACA
23023 AAAGGTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATACAGTGTATCG
Done.