Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga04g01591.F1

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, 740

Length: 1234
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30


Found at i:47 original size:17 final size:17

Alignment explanation


    Indices: 27--77  Score: 59
    Period size: 17  Copynumber: 2.9  Consensus size: 17

         17 AAACCCTTAT

                             
         27 TTTCCCCTAAATCAAAA
          1 TTTCCCCTAAATCAAAA

                         *    *
         44 TTTCCCCTAAACCCCAAAT
          1 TTTCCCCTAAA--TCAAAA

                            
         63 TTTCCCC-AAATCAAA
          1 TTTCCCCTAAATCAAA

         78 CCCATTTGCC


Statistics
Matches: 29,  Mismatches: 3, Indels: 5
        0.78            0.08        0.14

Matches are distributed among these distances:
  16    4  0.14
  17   11  0.38
  18    3  0.10
  19   11  0.38

ACGTcount: A:0.37, C:0.35, G:0.00, T:0.27


Consensus pattern (17 bp):   
TTTCCCCTAAATCAAAA

Found at i:274 original size:25 final size:24

Alignment explanation


    Indices: 246--310  Score: 58
    Period size: 25  Copynumber: 2.6  Consensus size: 24

        236 GTAGTCTTTC

                              *      
        246 ACATCCTCGTCGGCAGCCTTCTGCT
          1 ACAT-CTCGTCGGCAGCCCTCTGCT

                 *       * *      *  
        271 ACATTTTCGTCGGTATCCCTCTTCT
          1 ACA-TCTCGTCGGCAGCCCTCTGCT

                           
        296 ACATCTCCGTCGGCA
          1 ACATCT-CGTCGGCA

        311 TTCCTCTGTT


Statistics
Matches: 31,  Mismatches: 7, Indels: 4
        0.74            0.17        0.10

Matches are distributed among these distances:
  24    2  0.06
  25   28  0.90
  26    1  0.03

ACGTcount: A:0.14, C:0.37, G:0.17, T:0.32


Consensus pattern (24 bp):   
ACATCTCGTCGGCAGCCCTCTGCT

Found at i:316 original size:25 final size:25

Alignment explanation


    Indices: 253--317  Score: 67
    Period size: 25  Copynumber: 2.6  Consensus size: 25

        243 TTCACATCCT

                    *  *   *      * *
        253 CGTCGGCAGCCTTCTGCTACATTTT
          1 CGTCGGCATCCCTCTTCTACATCTC

                  *                  
        278 CGTCGGTATCCCTCTTCTACATCTC
          1 CGTCGGCATCCCTCTTCTACATCTC

                     *     
        303 CGTCGGCATTCCTCT
          1 CGTCGGCATCCCTCT

        318 GTTGCTTCTC


Statistics
Matches: 32,  Mismatches: 8, Indels: 0
        0.80            0.20        0.00

Matches are distributed among these distances:
  25   32  1.00

ACGTcount: A:0.11, C:0.37, G:0.17, T:0.35


Consensus pattern (25 bp):   
CGTCGGCATCCCTCTTCTACATCTC

Found at i:994 original size:35 final size:35

Alignment explanation


    Indices: 948--1054  Score: 160
    Period size: 35  Copynumber: 3.0  Consensus size: 35

        938 ATAATCTTCA

                                                
        948 ATGATATGCAATCTTAGATATGATACAATCTTAGAT
          1 ATGAT-TGCAATCTTAGATATGATACAATCTTAGAT

                           *                   
        984 ATGATTGCAATCTTAAATATGATACAATCTTAGAT
          1 ATGATTGCAATCTTAGATATGATACAATCTTAGAT

                   *   *                        
       1019 ATGATTGTAATTTTAGATATGATATACAATCTTAGA
          1 ATGATTGCAATCTTAGATATG--ATACAATCTTAGA

       1055 AGATATGATT


Statistics
Matches: 65,  Mismatches: 4, Indels: 3
        0.90            0.06        0.04

Matches are distributed among these distances:
  35   47  0.72
  36    5  0.08
  37   13  0.20

ACGTcount: A:0.39, C:0.09, G:0.13, T:0.38


Consensus pattern (35 bp):   
ATGATTGCAATCTTAGATATGATACAATCTTAGAT

Found at i:996 original size:18 final size:18

Alignment explanation


    Indices: 956--1054  Score: 130
    Period size: 17  Copynumber: 5.6  Consensus size: 18

        946 CAATGATATG

                              
        956 CAATCTTAGATATGA-TA
          1 CAATCTTAGATATGATTA

                             *
        973 CAATCTTAGATATGATTG
          1 CAATCTTAGATATGATTA

                    *         
        991 CAATCTTAAATATGA-TA
          1 CAATCTTAGATATGATTA

                             *
       1008 CAATCTTAGATATGATTG
          1 CAATCTTAGATATGATTA

            *   *              
       1026 TAATTTTAGATATGATATA
          1 CAATCTTAGATATGAT-TA

                      
       1045 CAATCTTAGA
          1 CAATCTTAGA

       1055 AGATATGATT


Statistics
Matches: 69,  Mismatches: 10, Indels: 4
        0.83            0.12        0.05

Matches are distributed among these distances:
  17   30  0.43
  18   30  0.43
  19    9  0.13

ACGTcount: A:0.39, C:0.10, G:0.12, T:0.38


Consensus pattern (18 bp):   
CAATCTTAGATATGATTA
Done.