Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_717 ID=scaffold_717-JGI_221_v2.0
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: 5297
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.22
Warning! 952 characters in sequence are not A, C, G, or T
Found at i:87 original size:17 final size:17
Alignment explanation
Indices: 65--125 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
55 AATCTTAGAG
65 TTCTAATTGTATACAGT
1 TTCTAATTGTATACAGT
* *
82 TTCTAATTATGTCTTAGAG-
1 TTCTAA-T-TGT-ATACAGT
101 TTCTAATTGTATACAGCT
1 TTCTAATTGTATACAG-T
119 TT-TAATT
1 TTCTAATT
126 ATAGCCTTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
16 4 0.11
17 14 0.40
18 4 0.11
19 9 0.26
20 4 0.11
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.49
Consensus pattern (17 bp):
TTCTAATTGTATACAGT
Found at i:98 original size:36 final size:36
Alignment explanation
Indices: 57--127 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
47 GATTATTTAA
57 TCTTAGAGTTCTAATTGTATACAG-TTTCTAATTATG
1 TCTTAGAGTTCTAATTGTATACAGCTTT-TAATTATG
93 TCTTAGAGTTCTAATTGTATACAGCTTTTAATTAT
1 TCTTAGAGTTCTAATTGTATACAGCTTTTAATTAT
128 AGCCTTTGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
36 31 0.91
37 3 0.09
ACGTcount: A:0.28, C:0.11, G:0.13, T:0.48
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTGTATACAGCTTTTAATTATG
Found at i:106 original size:19 final size:18
Alignment explanation
Indices: 57--108 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
47 GATTATTTAA
57 TCTTAGAGTTCTAA-TTG
1 TCTTAGAGTTCTAATTTG
* *
74 T-ATACAGTTTCTAATTATG
1 TCTTAGAG-TTCTAATT-TG
93 TCTTAGAGTTCTAATT
1 TCTTAGAGTTCTAATT
109 GTATACAGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
16 4 0.15
17 7 0.26
18 1 0.04
19 11 0.41
20 4 0.15
ACGTcount: A:0.27, C:0.12, G:0.13, T:0.48
Consensus pattern (18 bp):
TCTTAGAGTTCTAATTTG
Found at i:5193 original size:17 final size:17
Alignment explanation
Indices: 5171--5231 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
5161 AATCTTAGAG
5171 TTCTAATTGTATACAGT
1 TTCTAATTGTATACAGT
* *
5188 TTCTAATTATGTCTTAGAG-
1 TTCTAA-T-TGT-ATACAGT
5207 TTCTAATTGTATACAGCT
1 TTCTAATTGTATACAG-T
5225 TT-TAATT
1 TTCTAATT
5232 ATAGCCTTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
16 4 0.11
17 14 0.40
18 4 0.11
19 9 0.26
20 4 0.11
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.49
Consensus pattern (17 bp):
TTCTAATTGTATACAGT
Found at i:5204 original size:36 final size:36
Alignment explanation
Indices: 5163--5233 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
5153 GATTATTTAA
5163 TCTTAGAGTTCTAATTGTATACAG-TTTCTAATTATG
1 TCTTAGAGTTCTAATTGTATACAGCTTT-TAATTATG
5199 TCTTAGAGTTCTAATTGTATACAGCTTTTAATTAT
1 TCTTAGAGTTCTAATTGTATACAGCTTTTAATTAT
5234 AGCCTTTGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
36 31 0.91
37 3 0.09
ACGTcount: A:0.28, C:0.11, G:0.13, T:0.48
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTGTATACAGCTTTTAATTATG
Found at i:5212 original size:19 final size:18
Alignment explanation
Indices: 5163--5214 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
5153 GATTATTTAA
5163 TCTTAGAGTTCTAA-TTG
1 TCTTAGAGTTCTAATTTG
* *
5180 T-ATACAGTTTCTAATTATG
1 TCTTAGAG-TTCTAATT-TG
5199 TCTTAGAGTTCTAATT
1 TCTTAGAGTTCTAATT
5215 GTATACAGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
16 4 0.15
17 7 0.26
18 1 0.04
19 11 0.41
20 4 0.15
ACGTcount: A:0.27, C:0.12, G:0.13, T:0.48
Consensus pattern (18 bp):
TCTTAGAGTTCTAATTTG
Done.