Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold2060

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, 676

Length: 1127
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30


Found at i:455 original size:70 final size:70

Alignment explanation


    Indices: 337--473  Score: 247
    Period size: 70  Copynumber: 2.0  Consensus size: 70

        327 TTGCATGCCC

                                                                             
        337 AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCAGCCAACACCTCCTTTATTGCTGC
          1 AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCAGCCAACACCTCCTTTATTGCTGC

                 
        402 TGTTG
         66 TGTTG

                *          *                         *                       
        407 AACATCACCTTAAATGCATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
          1 AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCAGCCAACACCTCCTTTATTGCTGC

              
        472 TG
         66 TG

        474 ATTTAATTCA


Statistics
Matches: 64,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  70   64  1.00

ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34


Consensus pattern (70 bp):   
AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCAGCCAACACCTCCTTTATTGCTGC
TGTTG

Found at i:1013 original size:20 final size:19

Alignment explanation


    Indices: 984--1021  Score: 67
    Period size: 20  Copynumber: 1.9  Consensus size: 19

        974 AGCTAATAAC

                               
        984 GAGCTCAATGAGCTGAATT
          1 GAGCTCAATGAGCTGAATT

                               
       1003 GAGCTCGAATGAGCTGAAT
          1 GAGCTC-AATGAGCTGAAT

       1022 CAAAAATGTT


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  19    6  0.33
  20   12  0.67

ACGTcount: A:0.32, C:0.16, G:0.29, T:0.24


Consensus pattern (19 bp):   
GAGCTCAATGAGCTGAATT
Done.