Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold4017
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, 363
Length: 605
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.40
Found at i:79 original size:22 final size:20
Alignment explanation
Indices: 29--136 Score: 78
Period size: 22 Copynumber: 5.2 Consensus size: 20
19 CCGGTAGAGG
* *
29 TTTTTTTT-CTCTTATTTTT
1 TTTTTTTTGCTTTTTTTTTT
* *
48 TTATTTTT--TTATTTTTTT
1 TTTTTTTTGCTTTTTTTTTT
* *
66 GTTTTTTTGCTTTTGTTTTCTCG
1 TTTTTTTTGCTTTT-TTTT-T-T
*
89 TTTTTTTTGCTTTCTTTTTTAC
1 TTTTTTTTGCTTT-TTTTTT-T
111 TTTTTTTTGCTTTTTTTCTTT
1 TTTTTTTTGCTTTTTTT-TTT
132 TTTTT
1 TTTTT
137 GTTTTTTTGT
Statistics
Matches: 70, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
18 13 0.19
19 7 0.10
20 3 0.04
21 13 0.19
22 17 0.24
23 16 0.23
24 1 0.01
ACGTcount: A:0.04, C:0.09, G:0.06, T:0.81
Consensus pattern (20 bp):
TTTTTTTTGCTTTTTTTTTT
Found at i:106 original size:12 final size:11
Alignment explanation
Indices: 67--127 Score: 63
Period size: 11 Copynumber: 5.5 Consensus size: 11
57 TATTTTTTTG
67 TTTTTTTGCTT
1 TTTTTTTGCTT
*
78 TTGTTTTCT-CGT
1 TT-TTTT-TGCTT
90 TTTTTTTGCTT
1 TTTTTTTGCTT
*
101 TCTTTTTTAC-T
1 T-TTTTTTGCTT
112 TTTTTTTGCTT
1 TTTTTTTGCTT
123 TTTTT
1 TTTTT
128 CTTTTTTTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
10 8 0.20
11 17 0.41
12 15 0.37
13 1 0.02
ACGTcount: A:0.02, C:0.11, G:0.08, T:0.79
Consensus pattern (11 bp):
TTTTTTTGCTT
Found at i:141 original size:7 final size:8
Alignment explanation
Indices: 43--150 Score: 71
Period size: 8 Copynumber: 13.6 Consensus size: 8
33 TTTTCTCTTA
*
43 TTTTTTTA
1 TTTTTTTG
*
51 TTTTTTTA
1 TTTTTTTG
59 TTTTTTTG
1 TTTTTTTG
67 TTTTTTTG
1 TTTTTTTG
*
75 --CTTTTG
1 TTTTTTTG
* *
81 TTTTCTCG
1 TTTTTTTG
89 TTTTTTTTG
1 -TTTTTTTG
* *
98 CTTTCTT-
1 TTTTTTTG
**
105 TTTTACT-
1 TTTTTTTG
112 TTTTTTTG
1 TTTTTTTG
*
120 CTTTTTTTCT
1 -TTTTTTT-G
130 TTTTTTTG
1 TTTTTTTG
138 TTTTTTTG
1 TTTTTTTG
146 TTTTT
1 TTTTT
151 GCCTCCACTG
Statistics
Matches: 78, Mismatches: 16, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
6 5 0.06
7 9 0.12
8 44 0.56
9 20 0.26
ACGTcount: A:0.03, C:0.07, G:0.07, T:0.82
Consensus pattern (8 bp):
TTTTTTTG
Found at i:149 original size:22 final size:22
Alignment explanation
Indices: 59--149 Score: 67
Period size: 22 Copynumber: 3.9 Consensus size: 22
49 TATTTTTTTA
*
59 TTTTTTTGTTTTTTTGCTTTT-G
1 TTTTTTTGTTTTTTTG-TTTTCT
* * *
81 TTTTCTCGTTTTTTTTGCTTTCT
1 TTTTTTTG-TTTTTTTGTTTTCT
* *
104 TTTTTACTTTTTTTTGCTTTTTTTCT
1 TTTTT--TTGTTTTT--TTGTTTTCT
130 TTTTTTTGTTTTTTTGTTTT
1 TTTTTTTGTTTTTTTGTTTT
150 TGCCTCCACT
Statistics
Matches: 52, Mismatches: 11, Indels: 12
0.69 0.15 0.16
Matches are distributed among these distances:
22 15 0.29
23 12 0.23
24 12 0.23
25 1 0.02
26 12 0.23
ACGTcount: A:0.01, C:0.09, G:0.09, T:0.81
Consensus pattern (22 bp):
TTTTTTTGTTTTTTTGTTTTCT
Done.