Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1863

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: 3017
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.35


Found at i:316 original size:13 final size:13

Alignment explanation


    Indices: 298--325  Score: 56
    Period size: 13  Copynumber: 2.2  Consensus size: 13

        288 ACATATTATA

                         
        298 AATATTTTGTGTT
          1 AATATTTTGTGTT

                         
        311 AATATTTTGTGTT
          1 AATATTTTGTGTT

              
        324 AA
          1 AA

        326 AATAATAAAA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   15  1.00

ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57


Consensus pattern (13 bp):   
AATATTTTGTGTT

Found at i:1818 original size:39 final size:40

Alignment explanation


    Indices: 1707--1829  Score: 166
    Period size: 39  Copynumber: 3.2  Consensus size: 40

       1697 GGACTAAGAT

                                 *                  
       1707 CCGAAGGCATTTGTGCTAGTTAC--TATCCGGGCTAAG-C
          1 CCGAAGGCATTTGTGCTAGTTGCTATATCCGGGCTAAGTC

                                   *                 
       1744 CCGAAGGCATTTGTGCTAG-TGATTATATCCGGGCTAAGTC
          1 CCGAAGGCATTTGTGCTAGTTG-CTATATCCGGGCTAAGTC

                            *                    *  
       1784 CCGAAGGCATTTGTGCGAGTTGCTATATCC-GGCTAAATC
          1 CCGAAGGCATTTGTGCTAGTTGCTATATCCGGGCTAAGTC

                   
       1823 CCGAAGG
          1 CCGAAGG

       1830 TACTTGGGTT


Statistics
Matches: 76,  Mismatches: 5, Indels: 8
        0.85            0.06        0.09

Matches are distributed among these distances:
  36    1  0.01
  37   19  0.25
  39   28  0.37
  40   26  0.34
  41    2  0.03

ACGTcount: A:0.23, C:0.23, G:0.28, T:0.27


Consensus pattern (40 bp):   
CCGAAGGCATTTGTGCTAGTTGCTATATCCGGGCTAAGTC
Done.