Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga11g02668.P1
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: 3505
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.33
Found at i:1078 original size:19 final size:17
Alignment explanation
Indices: 1052--1110 Score: 57
Period size: 17 Copynumber: 3.2 Consensus size: 17
1042 CTATATAATA
1052 TTTTAGTTTTCTTCTAT
1 TTTTAGTTTTCTTCTAT
*
1069 TTTTAAAG-TTTCTATATAAT
1 TTTT--AGTTTTCT-TCT-AT
1089 ATTTTAGTTTTCTTCTAT
1 -TTTTAGTTTTCTTCTAT
1107 TTTT
1 TTTT
1111 TTGGTAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
17 8 0.24
18 7 0.21
19 8 0.24
20 7 0.21
21 4 0.12
ACGTcount: A:0.20, C:0.08, G:0.05, T:0.66
Consensus pattern (17 bp):
TTTTAGTTTTCTTCTAT
Found at i:1084 original size:38 final size:38
Alignment explanation
Indices: 1033--1110 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
1023 TTTGGTCTTG
1033 TTAAAGTTTCTATATAATATTTTAGTTTTCTTCTATTT
1 TTAAAGTTTCTATATAATATTTTAGTTTTCTTCTATTT
1071 TTAAAGTTTCTATATAATATTTTAGTTTTCTTCTATTT
1 TTAAAGTTTCTATATAATATTTTAGTTTTCTTCTATTT
1109 TT
1 TT
1111 TTGGTAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.26, C:0.08, G:0.05, T:0.62
Consensus pattern (38 bp):
TTAAAGTTTCTATATAATATTTTAGTTTTCTTCTATTT
Found at i:1112 original size:19 final size:19
Alignment explanation
Indices: 1052--1112 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
1042 CTATATAATA
1052 TTTTAGTTTTCTTCTATTT
1 TTTTAGTTTTCTTCTATTT
** * * *
1071 TTAAAG-TTTCTATATAATA
1 TTTTAGTTTTCT-TCTATTT
1090 TTTTAGTTTTCTTCTATTT
1 TTTTAGTTTTCTTCTATTT
1109 TTTT
1 TTTT
1113 GGTAAAAAGT
Statistics
Matches: 30, Mismatches: 10, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
18 5 0.17
19 20 0.67
20 5 0.17
ACGTcount: A:0.20, C:0.08, G:0.05, T:0.67
Consensus pattern (19 bp):
TTTTAGTTTTCTTCTATTT
Found at i:1712 original size:6 final size:6
Alignment explanation
Indices: 1701--1727 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1691 TCTGCATTGC
1701 TTTATT TTTATT TTTATT TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTT
1728 TGGTTTCATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Done.