Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga05g01460.P1

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: 6045
ACGTcount: A:0.32, C:0.13, G:0.22, T:0.33


Found at i:1233 original size:46 final size:45

Alignment explanation


    Indices: 1182--1348  Score: 212
    Period size: 46  Copynumber: 3.7  Consensus size: 45

       1172 GACGAGGGCT

                                                          
       1182 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGTATGAGAGCC
          1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAG-ATGAGAGCC

                                        *   *        *    
       1228 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGATAGCC
          1 AGTGTAAGACATGTCTGGGACATGCATCAGCCAC-AGATGAGAGCC

                 *                   *     *          *  *
       1274 AGTGTCAGACATGTCTGGGACATGCGTCAGCTAC-GA-GATGTGCT
          1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGATGA-GAGCC

                                     *     
       1318 AGTGTAAGACATGTCTGGGACATGCGTCAGC
          1 AGTGTAAGACATGTCTGGGACATGCATCAGC

       1349 ACGGTTACAT


Statistics
Matches: 107,  Mismatches: 12, Indels: 6
        0.86            0.10        0.05

Matches are distributed among these distances:
  43    2  0.02
  44   34  0.32
  46   69  0.64
  47    2  0.02

ACGTcount: A:0.26, C:0.21, G:0.31, T:0.22


Consensus pattern (45 bp):   
AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGATGAGAGCC

Found at i:1278 original size:92 final size:90

Alignment explanation


    Indices: 1131--1342  Score: 255
    Period size: 92  Copynumber: 2.3  Consensus size: 90

       1121 GATTGTGTGT

                              *  *                *        *  *              
       1131 GCCAGTGTAAGACCATGTATGAGACATGGCATCGGCATTGAGACGAGGGCTAGTGTAAGACATGT
          1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATCGAGACGAGAGCCAGTGTAAGACATGT

                                          
       1196 CTGGGACATGCATCAGCCAC-AGTATGAGA
         64 CTGGGACATGCATCAGCCACGAG-AT--GA

                                              *      *  *         *          
       1225 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGATAGCCAGTGTCAGACATGTCT
          1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGACGAGAGCCAGTGTAAGACATGTCT

                     *     *        *
       1290 GGGACATGCGTCAGCTACGAGATGT
         66 GGGACATGCATCAGCCACGAGATGA

              *                         
       1315 GCTAGTGTAAGACATGTCTGGGACATGC
          1 GCCAGTGTAAGACATGTCTGGGACATGC

       1343 GTCAGCACGG


Statistics
Matches: 104,  Mismatches: 13, Indels: 6
        0.85            0.11        0.05

Matches are distributed among these distances:
  90   28  0.27
  92   50  0.48
  93   14  0.13
  94   12  0.12

ACGTcount: A:0.27, C:0.20, G:0.31, T:0.22


Consensus pattern (90 bp):   
GCCAGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGACGAGAGCCAGTGTAAGACATGTCT
GGGACATGCATCAGCCACGAGATGA

Found at i:1379 original size:46 final size:43

Alignment explanation


    Indices: 1182--1385  Score: 180
    Period size: 46  Copynumber: 4.5  Consensus size: 43

       1172 GACGAGGGCT

                                     *     *     *     *   
       1182 AGTGTAAGACATGTCTGGGACATGCATCAGCCAC-AGTATGAGAGCC
          1 AGTGTAAGACATGTCTGGGACATGCGTCAGCTACGA-CAT--GTG-C

                                     *  *        *         
       1228 AGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGATGATAGCC
          1 AGTGTAAGACATGTCTGGGACATGCGTCAG-CTACGACATG-T-G-C

                 *                              *      
       1274 AGTGTCAGACATGTCTGGGACATGCGTCAGCTACGAGATGTGC
          1 AGTGTAAGACATGTCTGGGACATGCGTCAGCTACGACATGTGC

                                                            
       1317 TAGTGTAAGACATGTCTGGGACATGCGTCAGC-ACGGTTACATGTGTC
          1 -AGTGTAAGACATGTCTGGGACATGCGTCAGCTAC-G--ACATGTG-C

                      *           
       1364 AGTGTAAGACCTGTCTGGGACA
          1 AGTGTAAGACATGTCTGGGACA

       1386 CGGCATCGAC


Statistics
Matches: 138,  Mismatches: 10, Indels: 20
        0.82            0.06        0.12

Matches are distributed among these distances:
  43    3  0.02
  44   33  0.24
  45    3  0.02
  46   96  0.70
  47    3  0.02

ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23


Consensus pattern (43 bp):   
AGTGTAAGACATGTCTGGGACATGCGTCAGCTACGACATGTGC

Done.