Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3349

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: 45049
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31


Found at i:14026 original size:27 final size:27

Alignment explanation


    Indices: 13987--14041  Score: 101
    Period size: 27  Copynumber: 2.0  Consensus size: 27

      13977 TAAAATAGAT

                    *                  
      13987 ATTACCACCTTTCAAAAGATATAATAA
          1 ATTACCACATTTCAAAAGATATAATAA

                                       
      14014 ATTACCACATTTCAAAAGATATAATAA
          1 ATTACCACATTTCAAAAGATATAATAA

             
      14041 A
          1 A

      14042 CATAAATTTT


Statistics
Matches: 27,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  27   27  1.00

ACGTcount: A:0.51, C:0.16, G:0.04, T:0.29


Consensus pattern (27 bp):   
ATTACCACATTTCAAAAGATATAATAA

Found at i:28071 original size:27 final size:27

Alignment explanation


    Indices: 28012--28077  Score: 87
    Period size: 27  Copynumber: 2.4  Consensus size: 27

      28002 CCTAAACTGA

                     *                 
      28012 TATAAAATGGCTGTTATGCCCCCACGT
          1 TATAAAATGACTGTTATGCCCCCACGT

            **                    * *  
      28039 GGTAAAATGACTGTTATGCCCCTATGT
          1 TATAAAATGACTGTTATGCCCCCACGT

                        
      28066 TATAAAATGACT
          1 TATAAAATGACT

      28078 ACATGCTCTA


Statistics
Matches: 32,  Mismatches: 7, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  27   32  1.00

ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32


Consensus pattern (27 bp):   
TATAAAATGACTGTTATGCCCCCACGT

Found at i:30229 original size:3 final size:3

Alignment explanation


    Indices: 30221--30268  Score: 51
    Period size: 3  Copynumber: 15.7  Consensus size: 3

      30211 AAGGGCTCAA

                          *       *      *                *             
      30221 ATT ATT ATT ATC ATT ATC ATT ACT ATT ATT ATT AAAT ATT ATT ATT
          1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT

              
      30267 AT
          1 AT

      30269 CTTTTTTTAC


Statistics
Matches: 36,  Mismatches: 8, Indels: 2
        0.78            0.17        0.04

Matches are distributed among these distances:
   3   34  0.94
   4    2  0.06

ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56


Consensus pattern (3 bp):   
ATT

Found at i:30476 original size:21 final size:21

Alignment explanation


    Indices: 30426--30477  Score: 56
    Period size: 21  Copynumber: 2.6  Consensus size: 21

      30416 ATTTCGAAAT

                                 
      30426 AAAACTTTGA--TTTTTAAAG
          1 AAAACTTTGATTTTTTTAAAG

                *  *              
      30445 -AAAGTAGTGATTTTTTTAAAG
          1 AAAACT-TTGATTTTTTTAAAG

                        
      30466 AAAACTTTGATT
          1 AAAACTTTGATT

      30478 CCACAAAAAA


Statistics
Matches: 25,  Mismatches: 4, Indels: 6
        0.71            0.11        0.17

Matches are distributed among these distances:
  18    4  0.16
  19    3  0.12
  21   14  0.56
  22    4  0.16

ACGTcount: A:0.40, C:0.04, G:0.13, T:0.42


Consensus pattern (21 bp):   
AAAACTTTGATTTTTTTAAAG
Done.