Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga05g01389.F1
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: 5444
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Found at i:752 original size:14 final size:15
Alignment explanation
Indices: 726--754 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
716 TCAAGTTTTG
726 GAAGGTACAAGAAAA
1 GAAGGTACAAGAAAA
741 GAAGGT-CAAGAAAA
1 GAAGGTACAAGAAAA
755 TTTCAGACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.59, C:0.07, G:0.28, T:0.07
Consensus pattern (15 bp):
GAAGGTACAAGAAAA
Found at i:1866 original size:253 final size:254
Alignment explanation
Indices: 1417--1925 Score: 912
Period size: 253 Copynumber: 2.0 Consensus size: 254
1407 GAACATAGGC
* *
1417 CATAGGTATTCTTCATTCTTCAGCTACGTTATTTGGACCTGGATCAGGTTTCTGATATGGGTATG
1 CATAGGTATTCTTCATTCTTCAGCAACGTTATATGGACCTGGATCAGGTTTCTGATATGGGTATG
*
1482 AATTTAAGGGTCAGATTCTTCTTTTTCTTAAAGTTGTGGAAACTCAAGTGATTTAGAAACTGTCC
66 AATTTAAGGGTCAGATTCTTCTTTTTCTTAAACTTGTGGAAACTCAAGTGATTTAGAAACTGTCC
* *
1547 TGACATAGTATATAGAAATTCGAGTGATTTAAATACTTAAATTCAAATATATTTGTCGTTAATGT
131 TGACATAGTATATAGAAATTCGAGTGATTTAAATACTTAAATTCAAATATATTTATAGTTAATGT
*
1612 TAGTATTAAATATTTGTATTTTGGCTATCTTAAATCCCCGATATTATTTGTTATATGAT
196 TAGTATTAAATATTTGTATTTTGGCTATCTTAAATCCCCGATATTATATGTTATATGAT
*
1671 CATAGGTATTCTTCATTCTTCAGCAATGTTATATGGACCTGGATCAGGTTTCTGATATGGGTATG
1 CATAGGTATTCTTCATTCTTCAGCAACGTTATATGGACCTGGATCAGGTTTCTGATATGGGTATG
*
1736 AATTTAAGGGTCAGATTCTT-TTTTTCTTAAACTTGTGGAAATTCAAGTGATTTAGAAACTGTCC
66 AATTTAAGGGTCAGATTCTTCTTTTTCTTAAACTTGTGGAAACTCAAGTGATTTAGAAACTGTCC
*
1800 TGACATGGTATATAGAAATTCGAGTGATTTAAATACTTAAATTCAAATATATTTATAGTTAATGT
131 TGACATAGTATATAGAAATTCGAGTGATTTAAATACTTAAATTCAAATATATTTATAGTTAATGT
**
1865 TAGTATTAAATATTTGTATTTTGGCTATCTTAAATCCTTGATATTATATGTTATATGAT
196 TAGTATTAAATATTTGTATTTTGGCTATCTTAAATCCCCGATATTATATGTTATATGAT
1924 CA
1 CA
1926 ATTGAAAGCC
Statistics
Matches: 244, Mismatches: 11, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
253 162 0.66
254 82 0.34
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.42
Consensus pattern (254 bp):
CATAGGTATTCTTCATTCTTCAGCAACGTTATATGGACCTGGATCAGGTTTCTGATATGGGTATG
AATTTAAGGGTCAGATTCTTCTTTTTCTTAAACTTGTGGAAACTCAAGTGATTTAGAAACTGTCC
TGACATAGTATATAGAAATTCGAGTGATTTAAATACTTAAATTCAAATATATTTATAGTTAATGT
TAGTATTAAATATTTGTATTTTGGCTATCTTAAATCCCCGATATTATATGTTATATGAT
Found at i:2013 original size:22 final size:22
Alignment explanation
Indices: 1988--2029 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1978 GGCCAGTCAA
1988 TTTTCCTCTACATTCTTTTCTT
1 TTTTCCTCTACATTCTTTTCTT
* * *
2010 TTTTTCTCTTCTTTCTTTTC
1 TTTTCCTCTACATTCTTTTC
2030 CTCCTTTTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.05, C:0.26, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTTCCTCTACATTCTTTTCTT
Found at i:2045 original size:9 final size:9
Alignment explanation
Indices: 2004--2056 Score: 54
Period size: 9 Copynumber: 5.9 Consensus size: 9
1994 TCTACATTCT
2004 TTTCTTTT-
1 TTTCTTTTC
*
2012 TTTCTCTTC
1 TTTCTTTTC
2021 TTTCTTTTC
1 TTTCTTTTC
* * *
2030 CTCCTTTTA
1 TTTCTTTTC
2039 TTTCTTTTC
1 TTTCTTTTC
2048 TTTTCTTTT
1 -TTTCTTTT
2057 TTTTTTAAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
8 7 0.20
9 20 0.57
10 8 0.23
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTCTTTTC
Found at i:2059 original size:13 final size:13
Alignment explanation
Indices: 2000--2051 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
1990 TTCCTCTACA
*
2000 TTCTTTTCTTTTT
1 TTCTCTTCTTTTT
2013 TTCTCTTCTTTCTT
1 TTCTCTTCTTT-TT
*
2027 TTC-CTCCTTTTAT
1 TTCTCTTCTTTT-T
*
2040 TTCTTTTCTTTT
1 TTCTCTTCTTTT
2052 CTTTTTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
12 1 0.03
13 20 0.62
14 11 0.34
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (13 bp):
TTCTCTTCTTTTT
Found at i:4017 original size:2 final size:2
Alignment explanation
Indices: 4010--4034 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4000 TTATATGAGA
4010 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
4035 TTGAAAACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Done.