Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga03g01191.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: 5813
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37


Found at i:746 original size:22 final size:22

Alignment explanation


    Indices: 721--769  Score: 62
    Period size: 22  Copynumber: 2.2  Consensus size: 22

        711 TGTTTTTTCC

                                  
        721 TTATTTTGCTACAATTTTACTA
          1 TTATTTTGCTACAATTTTACTA

                *   *   *      *  
        743 TTATGTTGTTACTATTTTATTA
          1 TTATTTTGCTACAATTTTACTA

                 
        765 TTATT
          1 TTATT

        770 GTTTAGATAT


Statistics
Matches: 22,  Mismatches: 5, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  22   22  1.00

ACGTcount: A:0.24, C:0.08, G:0.06, T:0.61


Consensus pattern (22 bp):   
TTATTTTGCTACAATTTTACTA

Found at i:835 original size:30 final size:30

Alignment explanation


    Indices: 797--860  Score: 103
    Period size: 30  Copynumber: 2.2  Consensus size: 30

        787 AACTTATTTT

                                          
        797 ATTT-TTAATTTTGTTATTATTTTAAAGGC
          1 ATTTGTTAATTTTGTTATTATTTTAAAGGC

                                     *   *
        826 ATTTGTTAATTTTGTTATTATTTTAGAGGT
          1 ATTTGTTAATTTTGTTATTATTTTAAAGGC

                 
        856 ATTTG
          1 ATTTG

        861 CTTGTTAAGT


Statistics
Matches: 32,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  29    4  0.12
  30   28  0.88

ACGTcount: A:0.25, C:0.02, G:0.14, T:0.59


Consensus pattern (30 bp):   
ATTTGTTAATTTTGTTATTATTTTAAAGGC

Found at i:1867 original size:34 final size:34

Alignment explanation


    Indices: 1824--1891  Score: 136
    Period size: 34  Copynumber: 2.0  Consensus size: 34

       1814 TTAAACTTTT

                                              
       1824 GTACATTTTTCAATTTAGTCCCTATTATCATGTA
          1 GTACATTTTTCAATTTAGTCCCTATTATCATGTA

                                              
       1858 GTACATTTTTCAATTTAGTCCCTATTATCATGTA
          1 GTACATTTTTCAATTTAGTCCCTATTATCATGTA

       1892 ATTTATTTTT


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  34   34  1.00

ACGTcount: A:0.26, C:0.18, G:0.09, T:0.47


Consensus pattern (34 bp):   
GTACATTTTTCAATTTAGTCCCTATTATCATGTA

Found at i:1876 original size:17 final size:17

Alignment explanation


    Indices: 1824--1876  Score: 54
    Period size: 17  Copynumber: 3.1  Consensus size: 17

       1814 TTAAACTTTT

                             
       1824 GTACATTTTTCAATTTA
          1 GTACATTTTTCAATTTA

              * *    *     *  
       1841 GTCCCTATTATC-ATGTA
          1 GTACAT-TTTTCAATTTA

                             
       1858 GTACATTTTTCAATTTA
          1 GTACATTTTTCAATTTA

              
       1875 GT
          1 GT

       1877 CCCTATTATC


Statistics
Matches: 26,  Mismatches: 8, Indels: 4
        0.68            0.21        0.11

Matches are distributed among these distances:
  16    4  0.15
  17   18  0.69
  18    4  0.15

ACGTcount: A:0.26, C:0.15, G:0.09, T:0.49


Consensus pattern (17 bp):   
GTACATTTTTCAATTTA

Found at i:1900 original size:34 final size:34

Alignment explanation


    Indices: 1825--1903  Score: 131
    Period size: 34  Copynumber: 2.3  Consensus size: 34

       1815 TAAACTTTTG

                                             *
       1825 TACATTTTTCAATTTAGTCCCTATTATCATGTAG
          1 TACATTTTTCAATTTAGTCCCTATTATCATGTAA

                                              
       1859 TACATTTTTCAATTTAGTCCCTATTATCATGTAA
          1 TACATTTTTCAATTTAGTCCCTATTATCATGTAA

             **        
       1893 TTTATTTTTCA
          1 TACATTTTTCA

       1904 CCATATAAGC


Statistics
Matches: 42,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  34   42  1.00

ACGTcount: A:0.27, C:0.16, G:0.06, T:0.51


Consensus pattern (34 bp):   
TACATTTTTCAATTTAGTCCCTATTATCATGTAA

Found at i:3342 original size:2 final size:2

Alignment explanation


    Indices: 3332--3387  Score: 69
    Period size: 2  Copynumber: 28.0  Consensus size: 2

       3322 ATATGAATGC

                                                                     *  * 
       3332 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT CT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                 *               
       3373 AT GAC AT AT AT AT AT
          1 AT -AT AT AT AT AT AT

       3388 CTCCATTTGT


Statistics
Matches: 47,  Mismatches: 5, Indels: 4
        0.84            0.09        0.07

Matches are distributed among these distances:
   1    1  0.02
   2   45  0.96
   3    1  0.02

ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46


Consensus pattern (2 bp):   
AT

Done.