Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Gorai.009G145100.10-JGI_221_v2.1

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: 4895
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27


Found at i:3163 original size:21 final size:21

Alignment explanation


    Indices: 3121--3163  Score: 50
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       3111 GCAACTAGAT

                   *      *      
       3121 CCACAACCACCACAGCAACAG
          1 CCACAACAACCACAACAACAG

                       *     *   
       3142 CCACAACAACCGCAACAGCAG
          1 CCACAACAACCACAACAACAG

             
       3163 C
          1 C

       3164 AGCAAAGTCA


Statistics
Matches: 18,  Mismatches: 4, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.42, C:0.47, G:0.12, T:0.00


Consensus pattern (21 bp):   
CCACAACAACCACAACAACAG

Found at i:3876 original size:3 final size:3

Alignment explanation


    Indices: 3868--4054  Score: 74
    Period size: 3  Copynumber: 62.7  Consensus size: 3

       3858 TTACATGAAC

                                            **    * **            *   *    
       3868 CAG CAG CAG CAG CAG CAG CAG CAG TTG CAA TTG CAG CAG CAA CAA CAG
          1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG

                    **      **                            *   *   *        
       3916 CAG CAG TTG CAG TTG CAG CAG CAG CAG CAG CAG CAA CAA CAA CAG CAG
          1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG

                **      **              **    *   *       *   *       *    
       3964 CAG TTG CAG TTG CAG CAG CAG TTG CAT CAT CAG CAA CAA CAG C-T CAG
          1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG

                       * *     *   *                                    
       4011 CAG CAG CAAT TA- CAA CAA CAG CAG CCA- CAG CAG CAG CAG CAG CA
          1 CAG CAG C-AG CAG CAG CAG CAG CAG -CAG CAG CAG CAG CAG CAG CA

       4055 AGAAACAACT


Statistics
Matches: 135,  Mismatches: 44, Indels: 10
        0.71            0.23        0.05

Matches are distributed among these distances:
   2    4  0.03
   3  128  0.95
   4    3  0.02

ACGTcount: A:0.35, C:0.30, G:0.25, T:0.10


Consensus pattern (3 bp):   
CAG

Found at i:3906 original size:30 final size:30

Alignment explanation


    Indices: 3870--3950  Score: 135
    Period size: 30  Copynumber: 2.7  Consensus size: 30

       3860 ACATGAACCA

                                          
       3870 GCAGCAGCAGCAGCAGCAGCAGTTGCAATT
          1 GCAGCAGCAGCAGCAGCAGCAGTTGCAATT

                     *  *              *  
       3900 GCAGCAGCAACAACAGCAGCAGTTGCAGTT
          1 GCAGCAGCAGCAGCAGCAGCAGTTGCAATT

                                 
       3930 GCAGCAGCAGCAGCAGCAGCA
          1 GCAGCAGCAGCAGCAGCAGCA

       3951 ACAACAACAG


Statistics
Matches: 46,  Mismatches: 5, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  30   46  1.00

ACGTcount: A:0.32, C:0.28, G:0.30, T:0.10


Consensus pattern (30 bp):   
GCAGCAGCAGCAGCAGCAGCAGTTGCAATT

Found at i:4001 original size:45 final size:45

Alignment explanation


    Indices: 3882--4006  Score: 178
    Period size: 45  Copynumber: 2.7  Consensus size: 45

       3872 AGCAGCAGCA

                                                            
       3882 GCAGCAGCAGTTGCAATTGCAGCAGCAACAACAGCAGCAGTTGCAGTT
          1 GCAGCAGCAGTTGC-A-T-CAGCAGCAACAACAGCAGCAGTTGCAGTT

                      **   *     *                       
       3930 GCAGCAGCAGCAGCAGCAGCAACAACAACAGCAGCAGTTGCAGTT
          1 GCAGCAGCAGTTGCATCAGCAGCAACAACAGCAGCAGTTGCAGTT

                              *             
       3975 GCAGCAGCAGTTGCATCATCAGCAACAACAGC
          1 GCAGCAGCAGTTGCATCAGCAGCAACAACAGC

       4007 TCAGCAGCAG


Statistics
Matches: 68,  Mismatches: 9, Indels: 3
        0.85            0.11        0.04

Matches are distributed among these distances:
  45   55  0.81
  47    1  0.01
  48   12  0.18

ACGTcount: A:0.34, C:0.28, G:0.26, T:0.13


Consensus pattern (45 bp):   
GCAGCAGCAGTTGCATCAGCAGCAACAACAGCAGCAGTTGCAGTT
Done.