Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3436

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: 8530
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34


Found at i:1916 original size:44 final size:45

Alignment explanation


    Indices: 1754--1927  Score: 221
    Period size: 44  Copynumber: 3.8  Consensus size: 45

       1744 TGGTTGAGCA

                                                        * 
       1754 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
          1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAACG

                                          * *       *       
       1800 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
          1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAAC---G

                                                           
       1845 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAACG
          1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAACG

                 *                               
       1892 -CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
          1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG

       1928 GCGGGTTACA


Statistics
Matches: 112,  Mismatches: 8, Indels: 18
        0.81            0.06        0.13

Matches are distributed among these distances:
  42    2  0.02
  43    4  0.04
  44   35  0.31
  45    3  0.03
  46   29  0.26
  47   30  0.27
  48    2  0.02
  50    7  0.06

ACGTcount: A:0.21, C:0.20, G:0.29, T:0.29


Consensus pattern (45 bp):   
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAACG

Found at i:4880 original size:13 final size:15

Alignment explanation


    Indices: 4831--4880  Score: 59
    Period size: 16  Copynumber: 3.4  Consensus size: 15

       4821 GTATCTTGGG

                     *     
       4831 TTTCTTTATCCTGGA
          1 TTTCTTTATTCTGGA

             *              
       4846 TCTCTTTTATTCTGGA
          1 TTTC-TTTATTCTGGA

                           
       4862 TTTCTTTATTC-GG-
          1 TTTCTTTATTCTGGA

                  
       4875 TTTCTT
          1 TTTCTT

       4881 GTTATCTTTG


Statistics
Matches: 31,  Mismatches: 3, Indels: 4
        0.82            0.08        0.11

Matches are distributed among these distances:
  13    6  0.19
  14    2  0.06
  15   10  0.32
  16   13  0.42

ACGTcount: A:0.10, C:0.18, G:0.12, T:0.60


Consensus pattern (15 bp):   
TTTCTTTATTCTGGA
Done.