Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga12g01813.N1

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, 693

Length: 1155
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.33


Found at i:437 original size:28 final size:26

Alignment explanation


    Indices: 406--481  Score: 80
    Period size: 26  Copynumber: 2.8  Consensus size: 26

        396 AAAAGCAGCT

                                      * 
        406 AAATTACTATAATACCCCTATGTGTGGA
          1 AAATTACTATAATACCCCTA-G-GTGCA

                    * *               
        434 AAATTACTGTTATACCCCTAGGTGCA
          1 AAATTACTATAATACCCCTAGGTGCA

                   ** *           
        460 AAATTACCGTTATACCCCTAGG
          1 AAATTACTATAATACCCCTAGG

        482 GTTAATTTTG


Statistics
Matches: 44,  Mismatches: 4, Indels: 2
        0.88            0.08        0.04

Matches are distributed among these distances:
  26   25  0.57
  27    1  0.02
  28   18  0.41

ACGTcount: A:0.33, C:0.22, G:0.14, T:0.30


Consensus pattern (26 bp):   
AAATTACTATAATACCCCTAGGTGCA

Found at i:471 original size:26 final size:26

Alignment explanation


    Indices: 417--481  Score: 94
    Period size: 26  Copynumber: 2.4  Consensus size: 26

        407 AATTACTATA

                           *        *   
        417 ATACCCCTATGTGTGGAAAATTACTGTT
          1 ATACCCCTA-G-GTGCAAAATTACCGTT

                                      
        445 ATACCCCTAGGTGCAAAATTACCGTT
          1 ATACCCCTAGGTGCAAAATTACCGTT

                       
        471 ATACCCCTAGG
          1 ATACCCCTAGG

        482 GTTAATTTTG


Statistics
Matches: 35,  Mismatches: 2, Indels: 2
        0.90            0.05        0.05

Matches are distributed among these distances:
  26   25  0.71
  27    1  0.03
  28    9  0.26

ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29


Consensus pattern (26 bp):   
ATACCCCTAGGTGCAAAATTACCGTT

Found at i:628 original size:27 final size:27

Alignment explanation


    Indices: 585--709  Score: 146
    Period size: 27  Copynumber: 4.6  Consensus size: 27

        575 AGGAAGCGTC

                     *  *               
        585 CTGGTGGCTATGTCACA-ATTATCTGAT
          1 CTGGTGGCTCTGCCACATA-TATCTGAT

              *                      * 
        612 CTAGTGGCTCTGCCACATATATCTGTT
          1 CTGGTGGCTCTGCCACATATATCTGAT

                     *                  
        639 CTGGTGGCTATGCCACGAT-TATCTGAT
          1 CTGGTGGCTCTGCCAC-ATATATCTGAT

                       *             * 
        666 CTGGTGGCTCTACCACATATATCTGTT
          1 CTGGTGGCTCTGCCACATATATCTGAT

                        *    
        693 CTGGTGGCTCTGTCACA
          1 CTGGTGGCTCTGCCACA

        710 ATAACTATAT


Statistics
Matches: 83,  Mismatches: 12, Indels: 6
        0.82            0.12        0.06

Matches are distributed among these distances:
  26    2  0.02
  27   78  0.94
  28    3  0.04

ACGTcount: A:0.18, C:0.24, G:0.22, T:0.35


Consensus pattern (27 bp):   
CTGGTGGCTCTGCCACATATATCTGAT

Found at i:667 original size:54 final size:54

Alignment explanation


    Indices: 585--711  Score: 200
    Period size: 54  Copynumber: 2.4  Consensus size: 54

        575 AGGAAGCGTC

                        *                         *               
        585 CTGGTGGCTATGTCACAATTATCTGATCTAGTGGCTCTGCCACATATATCTGTT
          1 CTGGTGGCTATGCCACAATTATCTGATCTAGTGGCTCTACCACATATATCTGTT

                            *            *                        
        639 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTACCACATATATCTGTT
          1 CTGGTGGCTATGCCACAATTATCTGATCTAGTGGCTCTACCACATATATCTGTT

                     *  *      
        693 CTGGTGGCTCTGTCACAAT
          1 CTGGTGGCTATGCCACAAT

        712 AACTATATTT


Statistics
Matches: 66,  Mismatches: 7, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  54   66  1.00

ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35


Consensus pattern (54 bp):   
CTGGTGGCTATGCCACAATTATCTGATCTAGTGGCTCTACCACATATATCTGTT

Done.