Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga08g00896.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: 23900
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33


Found at i:15123 original size:14 final size:14

Alignment explanation


    Indices: 15100--15129  Score: 51
    Period size: 14  Copynumber: 2.1  Consensus size: 14

      15090 CTTGAAATAT

                          
      15100 GTTGAATTGGATTG
          1 GTTGAATTGGATTG

                 *        
      15114 GTTGATTTGGATTG
          1 GTTGAATTGGATTG

              
      15128 GT
          1 GT

      15130 CTCGATGTAG


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  14   15  1.00

ACGTcount: A:0.17, C:0.00, G:0.37, T:0.47


Consensus pattern (14 bp):   
GTTGAATTGGATTG

Found at i:16010 original size:9 final size:9

Alignment explanation


    Indices: 15996--16063  Score: 93
    Period size: 9  Copynumber: 7.6  Consensus size: 9

      15986 ATAAGTATAA

                     
      15996 AATTAACCG
          1 AATTAACCG

                  *  
      16005 AATTAATCG
          1 AATTAACCG

                     
      16014 AATTAACCG
          1 AATTAACCG

                 *   
      16023 AATTACCCG
          1 AATTAACCG

                      
      16032 AATT-ACCTG
          1 AATTAACC-G

                     
      16041 AATTAACCG
          1 AATTAACCG

                  *  
      16050 AATTAATCG
          1 AATTAACCG

                 
      16059 AATTA
          1 AATTA

      16064 TTTGTATAAA


Statistics
Matches: 52,  Mismatches: 5, Indels: 4
        0.85            0.08        0.07

Matches are distributed among these distances:
   8    2  0.04
   9   47  0.90
  10    3  0.06

ACGTcount: A:0.43, C:0.19, G:0.10, T:0.28


Consensus pattern (9 bp):   
AATTAACCG

Found at i:16096 original size:5 final size:6

Alignment explanation


    Indices: 16081--16144  Score: 58
    Period size: 6  Copynumber: 10.2  Consensus size: 6

      16071 AAAATTATAT

                                       *                         **   
      16081 TTTTTA TTTTTA TTTTTA GTTTTAGA TTTTTA TTTTTA TTTATTA -AATTA
          1 TTTTTA TTTTTA TTTTTA -TTTT-TA TTTTTA TTTTTA TTT-TTA TTTTTA

                            
      16131 TTTTTAA TTTTTA T
          1 TTTTT-A TTTTTA T

      16145 GATTGGGTTG


Statistics
Matches: 47,  Mismatches: 6, Indels: 10
        0.75            0.10        0.16

Matches are distributed among these distances:
   5    3  0.06
   6   26  0.55
   7   17  0.36
   8    1  0.02

ACGTcount: A:0.23, C:0.00, G:0.03, T:0.73


Consensus pattern (6 bp):   
TTTTTA

Found at i:21794 original size:20 final size:21

Alignment explanation


    Indices: 21757--21796  Score: 55
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      21747 AAAATTTATA

                    *  *         
      21757 TAAAAAATTAACTGATATTTT
          1 TAAAAAATAAAATGATATTTT

                                
      21778 TAAAAAATAAAAT-ATATTT
          1 TAAAAAATAAAATGATATTT

      21797 AACAAAATTA


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  20    6  0.35
  21   11  0.65

ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40


Consensus pattern (21 bp):   
TAAAAAATAAAATGATATTTT

Found at i:21813 original size:19 final size:18

Alignment explanation


    Indices: 21734--21804  Score: 52
    Period size: 18  Copynumber: 3.7  Consensus size: 18

      21724 CGAAAAATAA

                    * *       
      21734 ATATTTAACATATAAAAT
          1 ATATTTAAAAAATAAAAT

            *   *             *  
      21752 TTATATAAAAAATTAACTGAT
          1 ATATTTAAAAAA-TAA--AAT

              *               
      21773 ATTTTTAAAAAATAAAAT
          1 ATATTTAAAAAATAAAAT

                          
      21791 ATATTTAACAAAAT
          1 ATATTTAA-AAAAT

      21805 TATATATATA


Statistics
Matches: 39,  Mismatches: 10, Indels: 7
        0.70            0.18        0.12

Matches are distributed among these distances:
  18   17  0.44
  19    8  0.21
  20    3  0.08
  21   11  0.28

ACGTcount: A:0.56, C:0.04, G:0.01, T:0.38


Consensus pattern (18 bp):   
ATATTTAAAAAATAAAAT
Done.