Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Gorai.009G145100.1-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: 4988
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27


Found at i:3201 original size:21 final size:21

Alignment explanation


    Indices: 3159--3201  Score: 50
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       3149 GCAACTAGAT

                   *      *      
       3159 CCACAACCACCACAGCAACAG
          1 CCACAACAACCACAACAACAG

                       *     *   
       3180 CCACAACAACCGCAACAGCAG
          1 CCACAACAACCACAACAACAG

             
       3201 C
          1 C

       3202 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:3914 original size:3 final size:3

Alignment explanation


    Indices: 3906--4147  Score: 112
    Period size: 3  Copynumber: 80.7  Consensus size: 3

       3896 TTACATGAAC

                                            **    * **            *   *    
       3906 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

                    **      **                            *   *   *        
       3954 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

                **      **              **    *   *       *   *      *    *
       4002 CAG TTG CAG TTG CAG CAG CAG TTG CAT CAT CAG CAA CAA CAG CTG CAA
          1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG

                                       * *         *   *      *    *    
       4050 CAG CAG CAG CAG CAG CAG CAAT TA- CAG CAA CAA CAG CTG CAA CAG
          1 CAG CAG CAG CAG CAG CAG C-AG CAG CAG CAG CAG CAG CAG CAG CAG

                                   * *     *   *                         
       4095 CAG CAG CAG CAG CAG CAAT TA- CAA CAA CAG CAG CCA- CAG CAG CAG
          1 CAG CAG CAG CAG CAG C-AG CAG CAG CAG CAG CAG -CAG CAG CAG CAG

                      
       4140 CAG CAG CA
          1 CAG CAG CA

       4148 AGAAACAACT


Statistics
Matches: 178,  Mismatches: 55, Indels: 12
        0.73            0.22        0.05

Matches are distributed among these distances:
   2    4  0.02
   3  170  0.96
   4    4  0.02

ACGTcount: A:0.36, C:0.30, G:0.24, T:0.09


Consensus pattern (3 bp):   
CAG

Found at i:3944 original size:30 final size:30

Alignment explanation


    Indices: 3908--3988  Score: 135
    Period size: 30  Copynumber: 2.7  Consensus size: 30

       3898 ACATGAACCA

                                          
       3908 GCAGCAGCAGCAGCAGCAGCAGTTGCAATT
          1 GCAGCAGCAGCAGCAGCAGCAGTTGCAATT

                     *  *              *  
       3938 GCAGCAGCAACAACAGCAGCAGTTGCAGTT
          1 GCAGCAGCAGCAGCAGCAGCAGTTGCAATT

                                 
       3968 GCAGCAGCAGCAGCAGCAGCA
          1 GCAGCAGCAGCAGCAGCAGCA

       3989 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:4039 original size:45 final size:45

Alignment explanation


    Indices: 3920--4044  Score: 178
    Period size: 45  Copynumber: 2.7  Consensus size: 45

       3910 AGCAGCAGCA

                                                            
       3920 GCAGCAGCAGTTGCAATTGCAGCAGCAACAACAGCAGCAGTTGCAGTT
          1 GCAGCAGCAGTTGC-A-T-CAGCAGCAACAACAGCAGCAGTTGCAGTT

                      **   *     *                       
       3968 GCAGCAGCAGCAGCAGCAGCAACAACAACAGCAGCAGTTGCAGTT
          1 GCAGCAGCAGTTGCATCAGCAGCAACAACAGCAGCAGTTGCAGTT

                              *             
       4013 GCAGCAGCAGTTGCATCATCAGCAACAACAGC
          1 GCAGCAGCAGTTGCATCAGCAGCAACAACAGC

       4045 TGCAACAGCA


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

Found at i:4059 original size:42 final size:41

Alignment explanation


    Indices: 3969--4147  Score: 179
    Period size: 42  Copynumber: 4.4  Consensus size: 41

       3959 GTTGCAGTTG

                                     *     *    * ***
       3969 CAGCAGCAGCAGCAGCAGCA-A-CAACAACAGCAGCAGTTG
          1 CAGCAGCAGCAGCAGCAGCATATCAGCAACAACAGCTGCAA

               **          **                         
       4008 CAGTTGCAGCAGCAGTTGCATCATCAGCAACAACAGCTGCAA
          1 CAGCAGCAGCAGCAGCAGCAT-ATCAGCAACAACAGCTGCAA

                                                       
       4050 CAGCAGCAGCAGCAGCAGCA-ATTACAGCAACAACAGCTGCAA
          1 CAGCAGCAGCAGCAGCAGCATA-T-CAGCAACAACAGCTGCAA

                                   *            *  * 
       4092 CAGCAGCAGCAGCAGCAGCA-ATTA-CAACAACAGCAGCCA
          1 CAGCAGCAGCAGCAGCAGCATATCAGCAACAACAGCTGCAA

                             
       4131 CAGCAGCAGCAGCAGCA
          1 CAGCAGCAGCAGCAGCA

       4148 AGAAACAACT


Statistics
Matches: 118,  Mismatches: 17, Indels: 10
        0.81            0.12        0.07

Matches are distributed among these distances:
  39   46  0.39
  40    2  0.02
  41    3  0.03
  42   67  0.57

ACGTcount: A:0.38, C:0.31, G:0.23, T:0.08


Consensus pattern (41 bp):   
CAGCAGCAGCAGCAGCAGCATATCAGCAACAACAGCTGCAA
Done.