Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1629

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: 6551
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:1303 original size:11 final size:12

Alignment explanation


    Indices: 1276--1302  Score: 54
    Period size: 12  Copynumber: 2.2  Consensus size: 12

       1266 AATAGAAAAC

                        
       1276 TTTTCATCACTT
          1 TTTTCATCACTT

                        
       1288 TTTTCATCACTT
          1 TTTTCATCACTT

               
       1300 TTT
          1 TTT

       1303 CTTTAGCCTC


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

Matches are distributed among these distances:
  12   15  1.00

ACGTcount: A:0.15, C:0.22, G:0.00, T:0.63


Consensus pattern (12 bp):   
TTTTCATCACTT

Found at i:3310 original size:16 final size:16

Alignment explanation


    Indices: 3285--3335  Score: 84
    Period size: 16  Copynumber: 3.2  Consensus size: 16

       3275 AGAAAGAGCC

                            
       3285 AAATACGCTAGTAAAT
          1 AAATACGCTAGTAAAT

            *    *          
       3301 GAATATGCTAGTAAAT
          1 AAATACGCTAGTAAAT

                            
       3317 AAATACGCTAGTAAAT
          1 AAATACGCTAGTAAAT

               
       3333 AAA
          1 AAA

       3336 ATACTAGAAA


Statistics
Matches: 31,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  16   31  1.00

ACGTcount: A:0.51, C:0.10, G:0.14, T:0.25


Consensus pattern (16 bp):   
AAATACGCTAGTAAAT

Found at i:3353 original size:32 final size:32

Alignment explanation


    Indices: 3285--3350  Score: 89
    Period size: 32  Copynumber: 2.1  Consensus size: 32

       3275 AGAAAGAGCC

                               *  *    *   *
       3285 AAATACGCTAGTAAATGAATATGCTAGTAAAT
          1 AAATACGCTAGTAAATGAAAATACTAGAAAAA

                                            
       3317 AAATACGCTAGTAAAT-AAAATACTAGAAAAA
          1 AAATACGCTAGTAAATGAAAATACTAGAAAAA

               
       3348 AAA
          1 AAA

       3351 ATAGGCTTTC


Statistics
Matches: 30,  Mismatches: 4, Indels: 1
        0.86            0.11        0.03

Matches are distributed among these distances:
  31   14  0.47
  32   16  0.53

ACGTcount: A:0.56, C:0.09, G:0.12, T:0.23


Consensus pattern (32 bp):   
AAATACGCTAGTAAATGAAAATACTAGAAAAA

Found at i:4951 original size:14 final size:14

Alignment explanation


    Indices: 4934--4962  Score: 58
    Period size: 14  Copynumber: 2.1  Consensus size: 14

       4924 ATAACTAAAG

                          
       4934 AAAAATAGATAGAT
          1 AAAAATAGATAGAT

                          
       4948 AAAAATAGATAGAT
          1 AAAAATAGATAGAT

             
       4962 A
          1 A

       4963 GATGAGAGAT


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

Matches are distributed among these distances:
  14   15  1.00

ACGTcount: A:0.66, C:0.00, G:0.14, T:0.21


Consensus pattern (14 bp):   
AAAAATAGATAGAT
Done.