Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga06g01374.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: 5272
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.34


Found at i:1537 original size:46 final size:46

Alignment explanation


    Indices: 1481--1647  Score: 179
    Period size: 46  Copynumber: 3.7  Consensus size: 46

       1471 TGGTTGAGCA

                                                          
       1481 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
          1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG

                                             *        *       
       1527 TCCGAACTCGTTGAGTTGAGTCCGAGTT---C-GTGAGATG-TAACTAGG
          1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATG-GATGCGAA-T--G

                                             *            * 
       1572 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
          1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG

                 *                         
       1620 --CGAGCTCGTTGAGTTGAGT-CGAGTTCAC
          1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCAC

       1648 TTAGGGGCGG


Statistics
Matches: 103,  Mismatches: 7, Indels: 25
        0.76            0.05        0.19

Matches are distributed among these distances:
  42    4  0.04
  43   15  0.15
  44   18  0.17
  45    1  0.01
  46   28  0.27
  47   28  0.27
  48    1  0.01
  50    4  0.04
  51    4  0.04

ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28


Consensus pattern (46 bp):   
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG

Found at i:3880 original size:47 final size:47

Alignment explanation


    Indices: 3810--4030  Score: 197
    Period size: 47  Copynumber: 4.7  Consensus size: 47

       3800 TTTGTGTGCC

                             *            *                 
       3810 AGTGTAAGACCATGTCTAGGACATGGCATCAGCATTGAAACGAGAGCT
          1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCA-TGAAACGAGAGCT

                           *                               * 
       3858 AGTGTAAGA-CATGTTTGGGACAT-GCATCGGC-T---ACGAGATGTGT
          1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATGAAACGAGA-G-CT

                              *                        *  *    
       3901 CAGTGTAAGACCATGTCTAGGACATGGCATCGGCATGAAAATGTGAAAGCT
          1 -AGTGTAAGACCATGTCTGGGACATGGCATCGGCATG-AAA--CGAGAGCT

                                           ***     *        *
       3952 AGTGTAAGACCATGTCTGGGACATGGCATCGATTTGATGGAC-A-AGCC
          1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATGA--AACGAGAGCT

                                            
       3999 AGTGTAAGACCATGTCTGGGACATGGCATCGG
          1 AGTGTAAGACCATGTCTGGGACATGGCATCGG

       4031 TATTATACCC


Statistics
Matches: 142,  Mismatches: 17, Indels: 29
        0.76            0.09        0.15

Matches are distributed among these distances:
  41    6  0.04
  42    1  0.01
  43    1  0.01
  44   10  0.07
  45   12  0.08
  46   15  0.11
  47   47  0.33
  48   10  0.07
  49    1  0.01
  50   32  0.23
  51    3  0.02
  52    1  0.01
  53    3  0.02

ACGTcount: A:0.29, C:0.18, G:0.30, T:0.23


Consensus pattern (47 bp):   
AGTGTAAGACCATGTCTGGGACATGGCATCGGCATGAAACGAGAGCT
Done.