Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2420

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: 11535
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30


Found at i:1371 original size:27 final size:26

Alignment explanation


    Indices: 1354--1423  Score: 95
    Period size: 27  Copynumber: 2.6  Consensus size: 26

       1344 ATATTAAGTC

                                       
       1354 CGCACACTCAGTGCTATATAATCAACT
          1 CGCACACTCAGTGCTATAT-ATCAACT

                    *                   
       1381 CGCACACTTAGTGCTATATAATCAAACT
          1 CGCACACTCAGTGCTATAT-ATC-AACT

                    *      
       1409 CGCACACTTAGTGCT
          1 CGCACACTCAGTGCT

       1424 GTACAATTTA


Statistics
Matches: 41,  Mismatches: 1, Indels: 1
        0.95            0.02        0.02

Matches are distributed among these distances:
  27   22  0.54
  28   19  0.46

ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27


Consensus pattern (26 bp):   
CGCACACTCAGTGCTATATATCAACT

Found at i:1417 original size:28 final size:28

Alignment explanation


    Indices: 1354--1451  Score: 135
    Period size: 28  Copynumber: 3.5  Consensus size: 28

       1344 ATATTAAGTC

                    *                   
       1354 CGCACACTCAGTGCTATATAATC-AACT
          1 CGCACACTTAGTGCTATATAATCAAACT

                                        
       1381 CGCACACTTAGTGCTATATAATCAAACT
          1 CGCACACTTAGTGCTATATAATCAAACT

                           *  *    *    *
       1409 CGCACACTTAGTGCTGTACAATTTAAACC
          1 CGCACACTTAGTGCTATATAA-TCAAACT

                          
       1438 CGCACACTTAGTGC
          1 CGCACACTTAGTGC

       1452 CAATCTCATG


Statistics
Matches: 64,  Mismatches: 5, Indels: 2
        0.90            0.07        0.03

Matches are distributed among these distances:
  27   22  0.34
  28   23  0.36
  29   19  0.30

ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27


Consensus pattern (28 bp):   
CGCACACTTAGTGCTATATAATCAAACT

Found at i:9474 original size:28 final size:28

Alignment explanation


    Indices: 9431--9512  Score: 112
    Period size: 28  Copynumber: 2.9  Consensus size: 28

       9421 GCACACTCAG

                                        
       9431 TATAATC-AACTCGCACACTTAGTGCTA
          1 TATAATCAAACTCGCACACTTAGTGCTA

                                       *
       9458 TATAATCAAACTCGCACACTTAGTGCTG
          1 TATAATCAAACTCGCACACTTAGTGCTA

              *    *    *              
       9486 TACAATTTAAACCCGCACACTTAGTGC
          1 TATAA-TCAAACTCGCACACTTAGTGC

       9513 CAATCTCATG


Statistics
Matches: 49,  Mismatches: 4, Indels: 2
        0.89            0.07        0.04

Matches are distributed among these distances:
  27    7  0.14
  28   23  0.47
  29   19  0.39

ACGTcount: A:0.33, C:0.27, G:0.12, T:0.28


Consensus pattern (28 bp):   
TATAATCAAACTCGCACACTTAGTGCTA

Done.