Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga11g02405.P2

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: 2898
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33


Found at i:482 original size:46 final size:46

Alignment explanation


    Indices: 432--605  Score: 187
    Period size: 46  Copynumber: 3.8  Consensus size: 46

        422 GTTGAGCATC

                                                          
        432 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTT
          1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTT

                               *                    *          
        478 CGAACTCGTTGAGTTGAGTTCGAGTT--C-T-TGAGATG-TAACTAGGTAT
          1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATGCGAA-T--GT-T

                *  *                                   * **
        524 CCGAGCTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCC
          1 -CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTT

               *                               
        571 CGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
          1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG

        606 GCGGGTTACA


Statistics
Matches: 107,  Mismatches: 10, Indels: 22
        0.77            0.07        0.16

Matches are distributed among these distances:
  42    4  0.04
  43    6  0.06
  44    1  0.01
  45    2  0.02
  46   60  0.56
  47   23  0.21
  48    1  0.01
  49    1  0.01
  50    5  0.05
  51    4  0.04

ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32


Consensus pattern (46 bp):   
CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTT

Found at i:588 original size:93 final size:93

Alignment explanation


    Indices: 429--597  Score: 275
    Period size: 93  Copynumber: 1.8  Consensus size: 93

        419 ATGGTTGAGC

                                                         * **                
        429 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTTCGAACTCGTTGAGTTG
          1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGTTG

               *                        
        494 AGTTCGAGTTCTTGAGATGTAACTAGGT
         66 AGTCCGAGTTCTTGAGATGTAACTAGGT

                  *  *                                          *            
        522 ATCCGAGCTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGTTG
          1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGTTG

                       
        587 AGTCCGAGTTC
         66 AGTCCGAGTTC

        598 ACTTATGGGC


Statistics
Matches: 69,  Mismatches: 7, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  93   69  1.00

ACGTcount: A:0.21, C:0.19, G:0.29, T:0.31


Consensus pattern (93 bp):   
ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGTTG
AGTCCGAGTTCTTGAGATGTAACTAGGT

Found at i:1777 original size:14 final size:14

Alignment explanation


    Indices: 1758--1789  Score: 64
    Period size: 14  Copynumber: 2.3  Consensus size: 14

       1748 TACCCCCCTC

                          
       1758 TTCTTTCCCATGTT
          1 TTCTTTCCCATGTT

                          
       1772 TTCTTTCCCATGTT
          1 TTCTTTCCCATGTT

                
       1786 TTCT
          1 TTCT

       1790 AGAGTTTCCA


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   18  1.00

ACGTcount: A:0.06, C:0.28, G:0.06, T:0.59


Consensus pattern (14 bp):   
TTCTTTCCCATGTT
Done.