Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga08g00002.C3

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: 10676
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34


Found at i:2158 original size:78 final size:78

Alignment explanation


    Indices: 2016--2160  Score: 220
    Period size: 78  Copynumber: 1.9  Consensus size: 78

       2006 TATTCTACCG

                                          *                         *  *     
       2016 TTAAACCATGATCCCTTGATCTCACCAGCTGGGAGAGTCGGTGATCATGTTGATAATGATCACCA
          1 TTAAACCATGATCCCTTGATCTCACCAGCTAGGAGAGTCGGTGATCATGTTGATAACGACCACCA

                         
       2081 TGGAGTTCGACCA
         66 TGGAGTTCGACCA

                   *                               *                *        
       2094 TTAAACCCTGATCCCTTGATCTCATCC-GCTAGGAGAGTTGGTGATCATGTTGATAGCGACCACC
          1 TTAAACCATGATCCCTTGATCTCA-CCAGCTAGGAGAGTCGGTGATCATGTTGATAACGACCACC

               
       2158 ATG
         65 ATG

       2161 ACGTTGTGCA


Statistics
Matches: 60,  Mismatches: 6, Indels: 2
        0.88            0.09        0.03

Matches are distributed among these distances:
  78   58  0.97
  79    2  0.03

ACGTcount: A:0.26, C:0.24, G:0.23, T:0.28


Consensus pattern (78 bp):   
TTAAACCATGATCCCTTGATCTCACCAGCTAGGAGAGTCGGTGATCATGTTGATAACGACCACCA
TGGAGTTCGACCA

Found at i:3838 original size:39 final size:39

Alignment explanation


    Indices: 3793--3874  Score: 119
    Period size: 39  Copynumber: 2.1  Consensus size: 39

       3783 CACCGACCAC

                   *                               
       3793 CACCATCGTCGTTCACCAGTCAGGCAGTCACCACCGGTA
          1 CACCATCATCGTTCACCAGTCAGGCAGTCACCACCGGTA

                                 *  *        *    *
       3832 CACCATCATCGTTCACCAGTCTGGTAGTCACCATCGGTC
          1 CACCATCATCGTTCACCAGTCAGGCAGTCACCACCGGTA

                
       3871 CACC
          1 CACC

       3875 CGTCACCACG


Statistics
Matches: 38,  Mismatches: 5, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  39   38  1.00

ACGTcount: A:0.22, C:0.39, G:0.18, T:0.21


Consensus pattern (39 bp):   
CACCATCATCGTTCACCAGTCAGGCAGTCACCACCGGTA
Done.