Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1294

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: 4509
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31


Found at i:972 original size:6 final size:6

Alignment explanation


    Indices: 955--1002  Score: 51
    Period size: 6  Copynumber: 7.8  Consensus size: 6

        945 AAAATAATAA

                                *  *   *    *                      
        955 ATATATG ATATAG ATATAT AGATAT ATAGAG ATATAG ATATAG ATATA
          1 ATATA-G ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATA

       1003 AAAAAACGAT


Statistics
Matches: 35,  Mismatches: 6, Indels: 1
        0.83            0.14        0.02

Matches are distributed among these distances:
   6   30  0.86
   7    5  0.14

ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35


Consensus pattern (6 bp):   
ATATAG

Found at i:975 original size:8 final size:8

Alignment explanation


    Indices: 962--996  Score: 61
    Period size: 8  Copynumber: 4.4  Consensus size: 8

        952 TAAATATATG

                    
        962 ATATAGAT
          1 ATATAGAT

                    
        970 ATATAGAT
          1 ATATAGAT

                   *
        978 ATATAGAG
          1 ATATAGAT

                    
        986 ATATAGAT
          1 ATATAGAT

               
        994 ATA
          1 ATA

        997 GATATAAAAA


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   8   25  1.00

ACGTcount: A:0.51, C:0.00, G:0.14, T:0.34


Consensus pattern (8 bp):   
ATATAGAT

Found at i:2463 original size:2 final size:2

Alignment explanation


    Indices: 2456--2486  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       2446 AAATGAGAAT

                                                          
       2456 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
          1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G

       2487 TATGGTGTGA


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00


Consensus pattern (2 bp):   
GA

Found at i:4358 original size:20 final size:20

Alignment explanation


    Indices: 4335--4372  Score: 58
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       4325 TCACGTATCA

                                
       4335 ATACAATATATCGATACATT
          1 ATACAATATATCGATACATT

                *  *          
       4355 ATACCATGTATCGATACA
          1 ATACAATATATCGATACA

       4373 AATAGTGATA


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  20   16  1.00

ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32


Consensus pattern (20 bp):   
ATACAATATATCGATACATT

Found at i:4447 original size:19 final size:19

Alignment explanation


    Indices: 4402--4458  Score: 78
    Period size: 19  Copynumber: 2.9  Consensus size: 19

       4392 CTACCAGTTT

                               **
       4402 CATGTATCGATACAATTTGTC
          1 CATGTATCGATACAA--TGAA

                               
       4423 CATGTATCGATACAATGAA
          1 CATGTATCGATACAATGAA

                             
       4442 CATGTATCGATACAATG
          1 CATGTATCGATACAATG

       4459 CATCGATACA


Statistics
Matches: 34,  Mismatches: 2, Indels: 2
        0.89            0.05        0.05

Matches are distributed among these distances:
  19   19  0.56
  21   15  0.44

ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32


Consensus pattern (19 bp):   
CATGTATCGATACAATGAA
Done.