Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold3217

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, 469

Length: 782
ACGTcount: A:0.42, C:0.23, G:0.03, T:0.32


Found at i:294 original size:29 final size:29

Alignment explanation


    Indices: 256--323  Score: 118
    Period size: 29  Copynumber: 2.3  Consensus size: 29

        246 ACCTTTGAAA

                                   *     
        256 CCCTAAACCCTAAACCCCAAATCTATTAC
          1 CCCTAAACCCTAAACCCCAAATCCATTAC

                            *            
        285 CCCTAAACCCTAAACCTCAAATCCATTAC
          1 CCCTAAACCCTAAACCCCAAATCCATTAC

                      
        314 CCCTAAACCC
          1 CCCTAAACCC

        324 GATCCTGAAT


Statistics
Matches: 37,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  29   37  1.00

ACGTcount: A:0.37, C:0.44, G:0.00, T:0.19


Consensus pattern (29 bp):   
CCCTAAACCCTAAACCCCAAATCCATTAC

Found at i:470 original size:12 final size:12

Alignment explanation


    Indices: 453--491  Score: 51
    Period size: 12  Copynumber: 3.1  Consensus size: 12

        443 CTCTTAACAT

                        
        453 CTAACCCCTAAC
          1 CTAACCCCTAAC

                          
        465 CTAACCCCTAACCC
          1 CTAACCCCTAA--C

                   *    
        479 CTAACCCTTAAC
          1 CTAACCCCTAAC

             
        491 C
          1 C

        492 CATAAACCTT


Statistics
Matches: 24,  Mismatches: 1, Indels: 4
        0.83            0.03        0.14

Matches are distributed among these distances:
  12   13  0.54
  14   11  0.46

ACGTcount: A:0.31, C:0.51, G:0.00, T:0.18


Consensus pattern (12 bp):   
CTAACCCCTAAC

Found at i:492 original size:14 final size:14

Alignment explanation


    Indices: 464--503  Score: 53
    Period size: 14  Copynumber: 2.9  Consensus size: 14

        454 TAACCCCTAA

                    *     
        464 CCTAACCCCTAACC
          1 CCTAACCCTTAACC

                          
        478 CCTAACCCTTAACC
          1 CCTAACCCTTAACC

             *   *      
        492 CATAAACCTTAA
          1 CCTAACCCTTAA

        504 ATCACATTAA


Statistics
Matches: 23,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  14   23  1.00

ACGTcount: A:0.35, C:0.45, G:0.00, T:0.20


Consensus pattern (14 bp):   
CCTAACCCTTAACC

Found at i:549 original size:14 final size:14

Alignment explanation


    Indices: 484--558  Score: 60
    Period size: 14  Copynumber: 5.1  Consensus size: 14

        474 AACCCCTAAC

                  *      *
        484 CCTTAACCCATAAA
          1 CCTTAATCCATAAT

                            *
        498 CCTTAAATCACATTAAC
          1 CCTT-AATC-CA-TAAT

                  *   *   
        515 CCTTAAACCAGAAT
          1 CCTTAATCCATAAT

              *           
        529 CCCTAATCCATAAT
          1 CCTTAATCCATAAT

                           
        543 CCTTAATTCCATAAT
          1 CCTTAA-TCCATAAT

             
        558 C
          1 C

        559 TATAAAACTT


Statistics
Matches: 48,  Mismatches: 9, Indels: 7
        0.75            0.14        0.11

Matches are distributed among these distances:
  14   22  0.46
  15   14  0.29
  16    5  0.10
  17    7  0.15

ACGTcount: A:0.39, C:0.32, G:0.01, T:0.28


Consensus pattern (14 bp):   
CCTTAATCCATAAT
Done.