Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1024

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: 10126
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.35


Found at i:46 original size:26 final size:25

Alignment explanation


    Indices: 1--51  Score: 75
    Period size: 26  Copynumber: 2.0  Consensus size: 25

                                     
          1 TTATATTAAATTAATATAAAAATTA
          1 TTATATTAAATTAATATAAAAATTA

                *           *         
         26 TTATTTTAATATTAATGTAAAAATTA
          1 TTATATTAA-ATTAATATAAAAATTA

         52 ATAACGAGAA


Statistics
Matches: 23,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  25    8  0.35
  26   15  0.65

ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47


Consensus pattern (25 bp):   
TTATATTAAATTAATATAAAAATTA

Found at i:7147 original size:2 final size:2

Alignment explanation


    Indices: 7136--7168  Score: 50
    Period size: 2  Copynumber: 17.0  Consensus size: 2

       7126 TGTTTATGTA

                                                      *       
       7136 AT AT -T AT AT AT AT AT AT AT AT AT AT AT GT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       7169 GTGATATGGC


Statistics
Matches: 28,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
   1    1  0.04
   2   27  0.96

ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52


Consensus pattern (2 bp):   
AT

Found at i:7783 original size:22 final size:21

Alignment explanation


    Indices: 7733--7787  Score: 69
    Period size: 20  Copynumber: 2.6  Consensus size: 21

       7723 ATATTTTAAA

                                 
       7733 ATTATATTAA-ATATTATATT
          1 ATTATATTAATATATTATATT

                *                 
       7753 ATTAAATTAATATATT-TATTT
          1 ATTATATTAATATATTATA-TT

                          
       7774 ATTTATATTAATAT
          1 A-TTATATTAATAT

       7788 TAAAAATATT


Statistics
Matches: 30,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
  20   11  0.37
  21    8  0.27
  22   11  0.37

ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56


Consensus pattern (21 bp):   
ATTATATTAATATATTATATT

Found at i:9602 original size:2 final size:2

Alignment explanation


    Indices: 9597--9628  Score: 55
    Period size: 2  Copynumber: 16.0  Consensus size: 2

       9587 CATATCATAC

                                                *          
       9597 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       9629 TTGATGCTTG


Statistics
Matches: 28,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   2   28  1.00

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (2 bp):   
AT

Found at i:9844 original size:20 final size:20

Alignment explanation


    Indices: 9819--9875  Score: 59
    Period size: 20  Copynumber: 3.0  Consensus size: 20

       9809 TTAAATTTAC

                                
       9819 TTATTAAAAATATATAAATA
          1 TTATTAAAAATATATAAATA

                  *             
       9839 TTATTATAAA-A-AT-AATA
          1 TTATTAAAAATATATAAATA

                   *             
       9856 TT-TTAATAATATAATAAATA
          1 TTATTAAAAATAT-ATAAATA

       9876 ATTAAATAAA


Statistics
Matches: 30,  Mismatches: 3, Indels: 8
        0.73            0.07        0.20

Matches are distributed among these distances:
  16    5  0.17
  17    7  0.23
  18    2  0.07
  19    3  0.10
  20   13  0.43

ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42


Consensus pattern (20 bp):   
TTATTAAAAATATATAAATA

Found at i:9856 original size:23 final size:23

Alignment explanation


    Indices: 9810--9852  Score: 63
    Period size: 22  Copynumber: 1.9  Consensus size: 23

       9800 ATATTTTATT

                                   
       9810 TAAATTTACTTATTAAAAATATA
          1 TAAATTTACTTATTAAAAATATA

                                  
       9833 TAAATATTA-TTA-TAAAAATA
          1 TAAAT-TTACTTATTAAAAATA

       9853 ATATTTTAAT


Statistics
Matches: 19,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  22    8  0.42
  23    8  0.42
  24    3  0.16

ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42


Consensus pattern (23 bp):   
TAAATTTACTTATTAAAAATATA
Done.