Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga05g01442.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: 5308
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.28
Found at i:3531 original size:21 final size:21
Alignment explanation
Indices: 3489--3531 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3479 GCAACTAGAT
* *
3489 CCACAACCACCACAGCAACAG
1 CCACAACAACCACAACAACAG
*
3510 CCACAACAACCACAACAGCAG
1 CCACAACAACCACAACAACAG
3531 C
1 C
3532 AGCAAAGTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.47, G:0.09, T:0.00
Consensus pattern (21 bp):
CCACAACAACCACAACAACAG
Found at i:3746 original size:15 final size:15
Alignment explanation
Indices: 3705--3760 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
3695 GATGATGCAA
*
3705 CAGCAGCAGCAGCAG
1 CAGCAGCAGCAACAG
* ***
3720 CGGCAATTGCAACAG
1 CAGCAGCAGCAACAG
3735 CAGCAGCAGCAACCA-
1 CAGCAGCAGCAA-CAG
3750 CAGCAGCAGCA
1 CAGCAGCAGCA
3761 GCAAATGCAG
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
15 29 0.94
16 2 0.06
ACGTcount: A:0.36, C:0.34, G:0.27, T:0.04
Consensus pattern (15 bp):
CAGCAGCAGCAACAG
Found at i:3756 original size:21 final size:21
Alignment explanation
Indices: 3708--3763 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
3698 GATGCAACAG
* ***
3708 CAGCAGCAGCAGCGGCAATTG
1 CAGCAGCAGCAGCAGCAACCA
*
3729 CAACAGCAGCAGCAGCAACCA
1 CAGCAGCAGCAGCAGCAACCA
3750 CAGCAGCAGCAGCA
1 CAGCAGCAGCAGCA
3764 AATGCAGAGG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.36, C:0.34, G:0.27, T:0.04
Consensus pattern (21 bp):
CAGCAGCAGCAGCAGCAACCA
Found at i:4251 original size:3 final size:3
Alignment explanation
Indices: 4236--4450 Score: 139
Period size: 3 Copynumber: 71.7 Consensus size: 3
4226 TTACATGAAC
* ** * **
4236 CAG CAG CAA CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG TTG CAA TTG
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
* * ** *
4284 CAG CAG CAG CAG CAA CAA CAG CAG CAG TTG CA- CTTG CAG CAG CAG
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG C-AG CAG CAG CAG
* * * ** **
4329 CAG CAG CAG CAG CAA CAA CAA CAG CAG CAG TTG CAG TTG CAG CAG CAG
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
** * * * * * * *
4377 TTG CAT CAT CAG CAA CAA CAG CTG CAG CAG CAG CAG TTA- CAA CAG
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG -CAG CAG CAG
4422 CAG CAG CCA- CAG CAG CAG CAG CAG CAG CA
1 CAG CAG -CAG CAG CAG CAG CAG CAG CAG CA
4451 AGAAACAACT
Statistics
Matches: 163, Mismatches: 43, Indels: 12
0.75 0.20 0.06
Matches are distributed among these distances:
2 4 0.02
3 155 0.95
4 4 0.02
ACGTcount: A:0.34, C:0.31, G:0.26, T:0.09
Consensus pattern (3 bp):
CAG
Found at i:4294 original size:36 final size:36
Alignment explanation
Indices: 4247--4448 Score: 179
Period size: 36 Copynumber: 5.8 Consensus size: 36
4237 AGCAGCAACA
4247 GCAGCAGCAGCAGCAGCAGCAGCAGCAGTTGCAATT
1 GCAGCAGCAGCAGCAGCAGCAGCAGCAGTTGCAATT
* * *
4283 GCAGCAGCAGCAGCAACAACAGCAGCAGTTGCACTT
1 GCAGCAGCAGCAGCAGCAGCAGCAGCAGTTGCAATT
* *
4319 GCAGCAGCAGCAGCAGCAGCAGCAACA---ACAA--
1 GCAGCAGCAGCAGCAGCAGCAGCAGCAGTTGCAATT
** **
4350 -CAGCAGCAGTTGCAGTTGCAGCAGCAGTTGC-ATCAT
1 GCAGCAGCAGCAGCAGCAGCAGCAGCAGTTGCAAT--T
* * * * **
4386 -CAGCAACAACAGCTGCAGCAGCAGCAGTTACAACA
1 GCAGCAGCAGCAGCAGCAGCAGCAGCAGTTGCAATT
4421 GCAGCAGCCA-CAGCAGCAGCAGCAGCAG
1 GCAGCAG-CAGCAGCAGCAGCAGCAGCAG
4449 CAAGAAACAA
Statistics
Matches: 130, Mismatches: 26, Indels: 20
0.74 0.15 0.11
Matches are distributed among these distances:
30 21 0.16
32 1 0.01
33 3 0.02
36 102 0.78
37 3 0.02
ACGTcount: A:0.34, C:0.30, G:0.27, T:0.09
Consensus pattern (36 bp):
GCAGCAGCAGCAGCAGCAGCAGCAGCAGTTGCAATT
Found at i:4307 original size:48 final size:46
Alignment explanation
Indices: 4236--4450 Score: 153
Period size: 48 Copynumber: 4.8 Consensus size: 46
4226 TTACATGAAC
* * *
4236 CAGCAGCAACAGCAGCAGCAGCAGCAGCAGCAGCAGCAGTTGCAATTG
1 CAGCAGCAGCAGCAACAACAGCAGCAGCAGCAGCAGCAGTTGCAA--G
** * **
4284 CAGCAGCAGCAGCAACAACAGCAGCAGTTGCA-CTTGCAGCAGC-AG
1 CAGCAGCAGCAGCAACAACAGCAGCAGCAGCAGC-AGCAGTTGCAAG
**
4329 CAGCAGCAGCAGCAACAACA--A-CAGCAGCAGTTGCAGTTGC-AG
1 CAGCAGCAGCAGCAACAACAGCAGCAGCAGCAGCAGCAGTTGCAAG
* * * * * *
4371 CAGCAGTTGCATCATCAGCAACAACAGCTGCAGCAGCAGCAGTTACAA-
1 CAGCA---GCAGCAGCAACAACAGCAGCAGCAGCAGCAGCAGTTGCAAG
*
4419 CAGCAGCAGC--C-ACAGCAGCAGCAGCAGCAGCA
1 CAGCAGCAGCAGCAACAACAGCAGCAGCAGCAGCA
4451 AGAAACAACT
Statistics
Matches: 133, Mismatches: 25, Indels: 24
0.73 0.14 0.13
Matches are distributed among these distances:
42 37 0.28
43 2 0.02
45 37 0.28
47 3 0.02
48 53 0.40
49 1 0.01
ACGTcount: A:0.34, C:0.31, G:0.26, T:0.09
Consensus pattern (46 bp):
CAGCAGCAGCAGCAACAACAGCAGCAGCAGCAGCAGCAGTTGCAAG
Found at i:4564 original size:24 final size:24
Alignment explanation
Indices: 4532--4587 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
4522 CACAATTGAA
4532 CCAGCAACCTCAGCAACTGCAGGC
1 CCAGCAACCTCAGCAACTGCAGGC
4556 CCAGCAACCTCAGCAACTGCAGGC
1 CCAGCAACCTCAGCAACTGCAGGC
4580 CCAGCAAC
1 CCAGCAAC
4588 AGGCCAGCCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.30, C:0.43, G:0.20, T:0.07
Consensus pattern (24 bp):
CCAGCAACCTCAGCAACTGCAGGC
Done.