Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga11g01286.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, 519
Length: 866
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.21
Found at i:114 original size:9 final size:9
Alignment explanation
Indices: 102--135 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
92 GAGGACGAGG
102 AGGACAAGA
1 AGGACAAGA
*
111 AGGACAAAA
1 AGGACAAGA
120 AGGACAAGA
1 AGGACAAGA
*
129 AAGACAA
1 AGGACAA
136 AGATCACAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.62, C:0.12, G:0.26, T:0.00
Consensus pattern (9 bp):
AGGACAAGA
Found at i:114 original size:18 final size:18
Alignment explanation
Indices: 102--136 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
92 GAGGACGAGG
102 AGGACAAGAAGGACAAAA
1 AGGACAAGAAGGACAAAA
*
120 AGGACAAGAAAGACAAA
1 AGGACAAGAAGGACAAA
137 GATCACAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.63, C:0.11, G:0.26, T:0.00
Consensus pattern (18 bp):
AGGACAAGAAGGACAAAA
Found at i:144 original size:18 final size:18
Alignment explanation
Indices: 123--159 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
113 GACAAAAAGG
123 ACAAGAAAGACAAAGATC
1 ACAAGAAAGACAAAGATC
*
141 ACAAGAAAGGCAAAGATC
1 ACAAGAAAGACAAAGATC
159 A
1 A
160 TAAAGATGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.59, C:0.16, G:0.19, T:0.05
Consensus pattern (18 bp):
ACAAGAAAGACAAAGATC
Found at i:347 original size:21 final size:21
Alignment explanation
Indices: 323--364 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
313 CACTGGTGAT
*
323 AAAGATGACGATAAGCACAAG
1 AAAGATGACCATAAGCACAAG
344 AAAGATGACCATAAGCACAAG
1 AAAGATGACCATAAGCACAAG
365 GAACGCAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.52, C:0.17, G:0.21, T:0.10
Consensus pattern (21 bp):
AAAGATGACCATAAGCACAAG
Found at i:402 original size:105 final size:105
Alignment explanation
Indices: 168--394 Score: 402
Period size: 105 Copynumber: 2.2 Consensus size: 105
158 CATAAAGATG
*
168 ACAAAGATGAAGGGATGATGGATAAAATCAAGGACATGATCACGGGTGATAAAGATGACGATAAG
1 ACAAGGATGAAGGGATGATGGATAAAATCAAGGACATGATCACGGGTGATAAAGATGACGATAAG
* *
233 CATAAGAAAGATGACCATAAGCACAAGGACAGCAAAGACC
66 CACAAGAAAGATGACCATAAGCACAAGGACAGCAAAGAAC
*
273 ACAAGGATGAAGGGATGATGGATAAAATCAAGGACATGATCACTGGTGATAAAGATGACGATAAG
1 ACAAGGATGAAGGGATGATGGATAAAATCAAGGACATGATCACGGGTGATAAAGATGACGATAAG
338 CACAAGAAAGATGACCATAAGCACAAGGA-ACGCAAAGAAC
66 CACAAGAAAGATGACCATAAGCACAAGGACA-GCAAAGAAC
378 ACAAGGATGAAGGGATG
1 ACAAGGATGAAGGGATG
395 CTAGATAAGA
Statistics
Matches: 117, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
104 1 0.01
105 116 0.99
ACGTcount: A:0.46, C:0.14, G:0.27, T:0.13
Consensus pattern (105 bp):
ACAAGGATGAAGGGATGATGGATAAAATCAAGGACATGATCACGGGTGATAAAGATGACGATAAG
CACAAGAAAGATGACCATAAGCACAAGGACAGCAAAGAAC
Found at i:601 original size:15 final size:16
Alignment explanation
Indices: 564--601 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
554 AGTGATGACG
564 AGAAG-AAGAAAAAGA
1 AGAAGAAAGAAAAAGA
*
579 AGAAGAAAGGAAAA-A
1 AGAAGAAAGAAAAAGA
594 AGAAGAAA
1 AGAAGAAA
602 CACGATGGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (16 bp):
AGAAGAAAGAAAAAGA
Done.