Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga07g00917.F2

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: 2139
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.29


Found at i:575 original size:16 final size:16

Alignment explanation


    Indices: 556--633  Score: 60
    Period size: 16  Copynumber: 5.2  Consensus size: 16

        546 TTCTTCCTTT

                            
        556 TTCTTAACTTTCCCAA
          1 TTCTTAACTTTCCCAA

                         ***
        572 TTCTT--C-TTCCTTT
          1 TTCTTAACTTTCCCAA

                            
        585 TTCTTAACTTTCCCAA
          1 TTCTTAACTTTCCCAA

                         ***
        601 TTCTT--C-TTCCTTT
          1 TTCTTAACTTTCCCAA

                            
        614 TTCTTAACTTTCCCAA
          1 TTCTTAACTTTCCCAA

                
        630 TTCT
          1 TTCT

        634 GATCAGCATA


Statistics
Matches: 44,  Mismatches: 12, Indels: 12
        0.65            0.18        0.18

Matches are distributed among these distances:
  13   18  0.41
  14    2  0.05
  15    2  0.05
  16   22  0.50

ACGTcount: A:0.15, C:0.31, G:0.00, T:0.54


Consensus pattern (16 bp):   
TTCTTAACTTTCCCAA

Found at i:585 original size:29 final size:29

Alignment explanation


    Indices: 546--633  Score: 176
    Period size: 29  Copynumber: 3.0  Consensus size: 29

        536 GTTATTTTAT

                                         
        546 TTCTTCCTTTTTCTTAACTTTCCCAATTC
          1 TTCTTCCTTTTTCTTAACTTTCCCAATTC

                                         
        575 TTCTTCCTTTTTCTTAACTTTCCCAATTC
          1 TTCTTCCTTTTTCTTAACTTTCCCAATTC

                                         
        604 TTCTTCCTTTTTCTTAACTTTCCCAATTC
          1 TTCTTCCTTTTTCTTAACTTTCCCAATTC

             
        633 T
          1 T

        634 GATCAGCATA


Statistics
Matches: 59,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  29   59  1.00

ACGTcount: A:0.14, C:0.31, G:0.00, T:0.56


Consensus pattern (29 bp):   
TTCTTCCTTTTTCTTAACTTTCCCAATTC

Found at i:1502 original size:24 final size:24

Alignment explanation


    Indices: 1474--1520  Score: 85
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       1464 CATTGGAAAT

                           *        
       1474 GATGATAAGAAGAATGTACAGGAA
          1 GATGATAAGAAGAATATACAGGAA

                                   
       1498 GATGATAAGAAGAATATACAGGA
          1 GATGATAAGAAGAATATACAGGA

       1521 TGAGTATCTT


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  24   22  1.00

ACGTcount: A:0.51, C:0.04, G:0.28, T:0.17


Consensus pattern (24 bp):   
GATGATAAGAAGAATATACAGGAA

Done.