Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga13g02522.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: 5257
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35


Found at i:1181 original size:39 final size:39

Alignment explanation


    Indices: 1074--1208  Score: 121
    Period size: 39  Copynumber: 3.4  Consensus size: 39

       1064 GACCTCGAGT

                                *      *      *     *
       1074 CGATGAGACACTGGGTGTCACTATATTTCTTCGGATAGATT
          1 CGATGAGACACTGGGTGTCAAT-TATTACTTCGGCTAG-TC

                   **       **   *               * 
       1115 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
          1 CGATGAGACACTGGGTGTCAATTATTACTTCGGCTAGTC

                                             *      
       1153 CGATGAGACACTGGGTGTCAATTATTACTTCGAACTA-TC
          1 CGATGAGACACTGGGTGTCAATTATTACTTCG-GCTAGTC

                   *         
       1192 CGATGAGGCACTGGGTG
          1 CGATGAGACACTGGGTG

       1209 CCATATTGGT


Statistics
Matches: 74,  Mismatches: 18, Indels: 6
        0.76            0.18        0.06

Matches are distributed among these distances:
  38   18  0.24
  39   36  0.49
  40    4  0.05
  41   16  0.22

ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29


Consensus pattern (39 bp):   
CGATGAGACACTGGGTGTCAATTATTACTTCGGCTAGTC

Found at i:3021 original size:39 final size:39

Alignment explanation


    Indices: 2978--3112  Score: 114
    Period size: 39  Copynumber: 3.4  Consensus size: 39

       2968 ACCAATATGG

                                   *               
       2978 CACCCAGTGCCTCATCGGATAGTTCGAAGTAATAATTGA
          1 CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAATTGA

                     *         *               *   *
       3017 CACCCAGTGTCTCATCGGCCTAG-CCGAAGTAA-AGTTGG
          1 CACCCAGTGCCTCATCGG-ATAGTCCGAAGTAATAATTGA

            *       *        *             *      *   
       3055 TACCCAGTACCTCATCGAATCTA-TCCGAAGAAATATAGTGA
          1 CACCCAGTGCCTCATCGGA--TAGTCCGAAGTAATA-ATTGA

                     *       
       3096 CACCCAGTGTCTCATCG
          1 CACCCAGTGCCTCATCG

       3113 ACTCGAGGTC


Statistics
Matches: 73,  Mismatches: 17, Indels: 10
        0.73            0.17        0.10

Matches are distributed among these distances:
  38   18  0.25
  39   35  0.48
  40    4  0.05
  41   16  0.22

ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24


Consensus pattern (39 bp):   
CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAATTGA

Found at i:4651 original size:17 final size:17

Alignment explanation


    Indices: 4629--4663  Score: 52
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       4619 GAATGCTCTC

                       *     
       4629 TGTTTCTTATTCTTCTT
          1 TGTTTCTTATTATTCTT

                    *        
       4646 TGTTTCTTTTTATTCTT
          1 TGTTTCTTATTATTCTT

             
       4663 T
          1 T

       4664 TTCTTCATTT


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.06, C:0.14, G:0.06, T:0.74


Consensus pattern (17 bp):   
TGTTTCTTATTATTCTT

Found at i:4733 original size:13 final size:13

Alignment explanation


    Indices: 4693--4726  Score: 50
    Period size: 13  Copynumber: 2.6  Consensus size: 13

       4683 ACATATATAT

                  *  *   
       4693 ATAATATTATTTA
          1 ATAATAATAGTTA

                         
       4706 ATAATAATAGTTA
          1 ATAATAATAGTTA

                    
       4719 ATAATAAT
          1 ATAATAAT

       4727 TTATAATTTA


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  13   19  1.00

ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44


Consensus pattern (13 bp):   
ATAATAATAGTTA
Done.