Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga12g00947.P2
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: 10052
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Found at i:1260 original size:37 final size:37
Alignment explanation
Indices: 1209--1289 Score: 103
Period size: 37 Copynumber: 2.2 Consensus size: 37
1199 GAAAATTACT
1209 AATATAT-ATTTAAAAATAA-TATACAATAAATAATAA
1 AATATATAATTTAAAAATAATTA-ACAATAAATAATAA
* * * *
1245 AATATATAATTTAAAATTAATTAATAATAACTTATAA
1 AATATATAATTTAAAAATAATTAACAATAAATAATAA
1282 AATATATA
1 AATATATA
1290 CAATATCAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
36 7 0.18
37 30 0.77
38 2 0.05
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (37 bp):
AATATATAATTTAAAAATAATTAACAATAAATAATAA
Found at i:4223 original size:21 final size:21
Alignment explanation
Indices: 4190--4245 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
4180 GTTGGGGCAG
*
4190 CTTGTTGAGTTGGGGTACCCT
1 CTTGCTGAGTTGGGGTACCCT
* *
4211 CTTGCTGATTTGGGGTAGCCT
1 CTTGCTGAGTTGGGGTACCCT
*
4232 GTTGCTGAGTTGGG
1 CTTGCTGAGTTGGG
4246 ACACCAACTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.09, C:0.16, G:0.38, T:0.38
Consensus pattern (21 bp):
CTTGCTGAGTTGGGGTACCCT
Found at i:4915 original size:40 final size:40
Alignment explanation
Indices: 4808--4915 Score: 171
Period size: 40 Copynumber: 2.7 Consensus size: 40
4798 AAAAAAATAC
**
4808 TCACTGCATGCATATTAAAAAATAGGCAACACACCAACAA
1 TCACTGCATGCATATTAAAAAATATTCAACACACCAACAA
4848 TCACTGCATGCATATTAAAAAATATTCAACACACCAACAA
1 TCACTGCATGCATATTAAAAAATATTCAACACACCAACAA
* * *
4888 TCAGTGTATGCATATTAAAAAACATTCA
1 TCACTGCATGCATATTAAAAAATATTCA
4916 CTAAAATAGC
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 63 1.00
ACGTcount: A:0.46, C:0.22, G:0.08, T:0.23
Consensus pattern (40 bp):
TCACTGCATGCATATTAAAAAATATTCAACACACCAACAA
Found at i:6584 original size:15 final size:15
Alignment explanation
Indices: 6566--6594 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
6556 ATGCATCACT
6566 ATCACTACCAGACAC
1 ATCACTACCAGACAC
6581 ATCACTACCAGACA
1 ATCACTACCAGACA
6595 TGTTTTCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.38, G:0.07, T:0.14
Consensus pattern (15 bp):
ATCACTACCAGACAC
Found at i:6972 original size:64 final size:64
Alignment explanation
Indices: 6902--7105 Score: 318
Period size: 64 Copynumber: 3.2 Consensus size: 64
6892 TAGGAGCTTG
* *
6902 GATACAAACAATGACATATATACACAATAAACATCAGTTTGATCATGGCATTCATACAATGGCA
1 GATACAAACAATGACAGATATACACAATAAACATCAGTTTGATAATGGCATTCATACAATGGCA
* *
6966 GATACAAACAATGACAGATATACACAATAAACATAAGTTTGATAATGGCATTTATACAATGGCA
1 GATACAAACAATGACAGATATACACAATAAACATCAGTTTGATAATGGCATTCATACAATGGCA
** * * *
7030 GATACAAACAATGGTAGATATACATAATAAGCATCAGTTTGATAATGGCATTCGTACAATGGCA
1 GATACAAACAATGACAGATATACACAATAAACATCAGTTTGATAATGGCATTCATACAATGGCA
*
7094 AATACAAACAAT
1 GATACAAACAAT
7106 AAAAATCATG
Statistics
Matches: 128, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 128 1.00
ACGTcount: A:0.45, C:0.16, G:0.14, T:0.25
Consensus pattern (64 bp):
GATACAAACAATGACAGATATACACAATAAACATCAGTTTGATAATGGCATTCATACAATGGCA
Found at i:7273 original size:18 final size:18
Alignment explanation
Indices: 7252--7292 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
7242 TTCTAATTTT
*
7252 AAATCGAGATCAAAATCG
1 AAATCGAAATCAAAATCG
* *
7270 AAATTGAAATCAAAATCT
1 AAATCGAAATCAAAATCG
7288 AAATC
1 AAATC
7293 AGAATCAGTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.54, C:0.15, G:0.10, T:0.22
Consensus pattern (18 bp):
AAATCGAAATCAAAATCG
Found at i:7298 original size:18 final size:17
Alignment explanation
Indices: 7251--7299 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
7241 ATTCTAATTT
7251 TAAATCGAGATCAAAATC
1 TAAATCGA-ATCAAAATC
* *
7269 GAAATTGAAATCAAAATC
1 TAAATCG-AATCAAAATC
7287 TAAATCAGAATCA
1 TAAATC-GAATCA
7300 GTGAGTGCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 23 0.92
19 2 0.08
ACGTcount: A:0.53, C:0.14, G:0.10, T:0.22
Consensus pattern (17 bp):
TAAATCGAATCAAAATC
Found at i:7330 original size:6 final size:6
Alignment explanation
Indices: 7319--7380 Score: 72
Period size: 6 Copynumber: 10.3 Consensus size: 6
7309 TCAAAATTGT
* *
7319 AATCAA AATCAA AAT-AGA AATCGA AATCAA AATCAA AATCAA AATCGA
1 AATCAA AATCAA AATCA-A AATCAA AATCAA AATCAA AATCAA AATCAA
* *
7367 AATTAA AATTAA AA
1 AATCAA AATCAA AA
7381 CCGAAATAAC
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
5 1 0.02
6 48 0.98
ACGTcount: A:0.65, C:0.11, G:0.05, T:0.19
Consensus pattern (6 bp):
AATCAA
Found at i:7332 original size:18 final size:18
Alignment explanation
Indices: 7309--7380 Score: 72
Period size: 18 Copynumber: 4.0 Consensus size: 18
7299 AGTGAGTGCT
*
7309 TCAAAATTGTAATCAAAA
1 TCAAAATTGAAATCAAAA
* *
7327 TCAAAATAGAAATCGAAA
1 TCAAAATTGAAATCAAAA
**
7345 TCAAAATCAAAATCAAAA
1 TCAAAATTGAAATCAAAA
* * *
7363 TCGAAATTAAAATTAAAA
1 TCAAAATTGAAATCAAAA
7381 CCGAAATAAC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.61, C:0.11, G:0.06, T:0.22
Consensus pattern (18 bp):
TCAAAATTGAAATCAAAA
Found at i:7339 original size:24 final size:24
Alignment explanation
Indices: 7319--7380 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
7309 TCAAAATTGT
7319 AATCAAAATCAAAATAGAAATCGA
1 AATCAAAATCAAAATAGAAATCGA
7343 AATCAAAATCAAAATCA-AAATCGA
1 AATCAAAATCAAAAT-AGAAATCGA
* *
7367 AATTAAAATTAAAA
1 AATCAAAATCAAAA
7381 CCGAAATAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
24 34 0.97
25 1 0.03
ACGTcount: A:0.65, C:0.11, G:0.05, T:0.19
Consensus pattern (24 bp):
AATCAAAATCAAAATAGAAATCGA
Found at i:7385 original size:18 final size:18
Alignment explanation
Indices: 7348--7387 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
7338 ATCGAAATCA
*
7348 AAATCAAAATCAAAATCG
1 AAATCAAAATCAAAACCG
* *
7366 AAATTAAAATTAAAACCG
1 AAATCAAAATCAAAACCG
7384 AAAT
1 AAAT
7388 AACCCTAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.62, C:0.12, G:0.05, T:0.20
Consensus pattern (18 bp):
AAATCAAAATCAAAACCG
Done.