Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold363
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: 774241
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 50831 characters in sequence are not A, C, G, or T
File 4 of 4
Found at i:768832 original size:14 final size:14
Alignment explanation
Indices: 768819--768874 Score: 96
Period size: 14 Copynumber: 4.1 Consensus size: 14
768809 GAGAGAAAGG
*
768819 AGAAGAAGAGAAGG
1 AGAAGAAGAGAAGA
768833 AGAAGAAGAGAAGA
1 AGAAGAAGAGAAGA
768847 AGAAGAAGAGAAGA
1 AGAAGAAGAGAAGA
768861 AGAAGAAGA-AAGA
1 AGAAGAAGAGAAGA
768874 A
1 A
768875 AAAAAAAGGT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
13 5 0.12
14 36 0.88
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (14 bp):
AGAAGAAGAGAAGA
Found at i:768838 original size:11 final size:11
Alignment explanation
Indices: 768822--768866 Score: 58
Period size: 11 Copynumber: 4.1 Consensus size: 11
768812 AGAAAGGAGA
768822 AGAAG-AGAAGG
1 AGAAGAAGAA-G
768833 AGAAGAAG-AG
1 AGAAGAAGAAG
768843 AAGAAGAAGAAG
1 -AGAAGAAGAAG
768855 AGAAGAAGAAG
1 AGAAGAAGAAG
768866 A
1 A
768867 AGAAAGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
10 1 0.03
11 26 0.84
12 4 0.13
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (11 bp):
AGAAGAAGAAG
Found at i:769041 original size:19 final size:19
Alignment explanation
Indices: 769017--769058 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
769007 TTTGGATTAG
769017 AATTTTGTATGAATATTGT
1 AATTTTGTATGAATATTGT
*
769036 AATTTTTTATGAATATTGT
1 AATTTTGTATGAATATTGT
769055 AATT
1 AATT
769059 ATTTTATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (19 bp):
AATTTTGTATGAATATTGT
Found at i:771279 original size:18 final size:18
Alignment explanation
Indices: 771258--771292 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
771248 GCATCATGCA
*
771258 CCAGAGCCAGAGCCAGTG
1 CCAGAGCCAGAGACAGTG
*
771276 CCAGTGCCAGAGACAGT
1 CCAGAGCCAGAGACAGT
771293 ACTACATTCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.31, G:0.31, T:0.09
Consensus pattern (18 bp):
CCAGAGCCAGAGACAGTG
Found at i:771658 original size:28 final size:28
Alignment explanation
Indices: 771613--771681 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
771603 ACCTCATATT
771613 TAATGG-TTTTTTATGTAAATAAAATTA
1 TAATGGTTTTTTTATGTAAATAAAATTA
771640 TAATGGTTTTTTTATGTAAATAAAATTA
1 TAATGGTTTTTTTATGTAAATAAAATTA
*
771668 TAATGTTTTTTTTA
1 TAATGGTTTTTTTA
771682 ATTTTGTAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 6 0.15
28 34 0.85
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.54
Consensus pattern (28 bp):
TAATGGTTTTTTTATGTAAATAAAATTA
Done.