Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga08g00002.M6

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: 10198
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33


Found at i:171 original size:39 final size:39

Alignment explanation


    Indices: 121--199  Score: 104
    Period size: 39  Copynumber: 2.0  Consensus size: 39

        111 CCGGCCACCC

                 *            *               *    
        121 CCATCGTCGTTCACCAGTTAGGCAGTCACCACCGTTCCA
          1 CCATCATCGTTCACCAGTCAGGCAGTCACCACCGGTCCA

                        *         *        *       
        160 CCATCATCGTTCTCCAGTCAGGTAGTCACCATCGGTCCA
          1 CCATCATCGTTCACCAGTCAGGCAGTCACCACCGGTCCA

             
        199 C
          1 C

        200 GCGTCACCAC


Statistics
Matches: 34,  Mismatches: 6, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  39   34  1.00

ACGTcount: A:0.20, C:0.38, G:0.18, T:0.24


Consensus pattern (39 bp):   
CCATCATCGTTCACCAGTCAGGCAGTCACCACCGGTCCA

Found at i:2261 original size:78 final size:78

Alignment explanation


    Indices: 2119--2263  Score: 220
    Period size: 78  Copynumber: 1.9  Consensus size: 78

       2109 TATTCTACCG

                                          *                         *  *     
       2119 TTAAACCATGATCCCTTGATCTCACCAGCTGGGAGAGTCGGTGATCATGTTGATAATGATCACCA
          1 TTAAACCATGATCCCTTGATCTCACCAGCTAGGAGAGTCGGTGATCATGTTGATAACGACCACCA

                         
       2184 TGGAGTTCGACCA
         66 TGGAGTTCGACCA

                   *                               *                *        
       2197 TTAAACCCTGATCCCTTGATCTCATCC-GCTAGGAGAGTTGGTGATCATGTTGATAGCGACCACC
          1 TTAAACCATGATCCCTTGATCTCA-CCAGCTAGGAGAGTCGGTGATCATGTTGATAACGACCACC

               
       2261 ATG
         65 ATG

       2264 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:3837 original size:39 final size:39

Alignment explanation


    Indices: 3792--3873  Score: 119
    Period size: 39  Copynumber: 2.1  Consensus size: 39

       3782 CACCGACCAC

                   *                               
       3792 CACCATCGTCGTTCACCAGTCAGGCAGTCACCACCGGTA
          1 CACCATCATCGTTCACCAGTCAGGCAGTCACCACCGGTA

                                 *  *        *    *
       3831 CACCATCATCGTTCACCAGTCTGGTAGTCACCATCGGTC
          1 CACCATCATCGTTCACCAGTCAGGCAGTCACCACCGGTA

                
       3870 CACC
          1 CACC

       3874 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.