Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3467

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: 11679
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.33


Found at i:498 original size:31 final size:32

Alignment explanation


    Indices: 463--522  Score: 86
    Period size: 31  Copynumber: 1.9  Consensus size: 32

        453 CTTTAATACG

                                            
        463 AACTTTGGCAAAATTAC-CATTTTGCCCCCTA
          1 AACTTTGGCAAAATTACACATTTTGCCCCCTA

                  *   *        *         
        494 AACTTTTGCATAATTACACTTTTTGCCCC
          1 AACTTTGGCAAAATTACACATTTTGCCCC

        523 TAGGCTCGGA


Statistics
Matches: 25,  Mismatches: 3, Indels: 1
        0.86            0.10        0.03

Matches are distributed among these distances:
  31   15  0.60
  32   10  0.40

ACGTcount: A:0.27, C:0.28, G:0.08, T:0.37


Consensus pattern (32 bp):   
AACTTTGGCAAAATTACACATTTTGCCCCCTA

Found at i:3879 original size:47 final size:47

Alignment explanation


    Indices: 3765--3934  Score: 169
    Period size: 45  Copynumber: 3.7  Consensus size: 47

       3755 CCCCCTAAGT

                                   *         *   *          *
       3765 GAACTCGGACTCAACTCAACGAGCTCGG--G-CGTTCGCATCCATAAGT
          1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACATCC--AAGC

                                                              
       3811 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACATCTC-A-C
          1 GAACTCGGACTCAACTCAACGAGTTCGGATGCC-A-TTCACATC-CAAGC

                                                 *         *
       3858 GAACTCGGACTCAACTCAACGAGTTCGGA---CATTCGCATCCATAGT
          1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACATCCA-AGC

                                            
       3903 GAACTCGGACTCAACTCAACGAGTTCGGATGC
          1 GAACTCGGACTCAACTCAACGAGTTCGGATGC

       3935 TCAACCATCC


Statistics
Matches: 105,  Mismatches: 6, Indels: 24
        0.78            0.04        0.18

Matches are distributed among these distances:
  42    3  0.03
  43    5  0.05
  44    2  0.02
  45   29  0.28
  46   27  0.26
  47   29  0.28
  48    2  0.02
  49    1  0.01
  50    4  0.04
  51    3  0.03

ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21


Consensus pattern (47 bp):   
GAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACATCCAAGC

Found at i:3934 original size:92 final size:93

Alignment explanation


    Indices: 3765--3934  Score: 306
    Period size: 93  Copynumber: 1.8  Consensus size: 93

       3755 CCCCCTAAGT

                                        * *                                  
       3765 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
          1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA

                                        
       3830 CGAGTTCGGATGCCTAGTTACATCTCAC
         66 CGAGTTCGGATGCCTAGTTACATCTCAC

                                   *                                         
       3858 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT-AGTGAACTCGGACTCAACTCAA
          1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA

                         
       3922 CGAGTTCGGATGC
         66 CGAGTTCGGATGC

       3935 TCAACCATCC


Statistics
Matches: 74,  Mismatches: 3, Indels: 1
        0.95            0.04        0.01

Matches are distributed among these distances:
  92   35  0.47
  93   39  0.53

ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21


Consensus pattern (93 bp):   
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC

Found at i:10394 original size:90 final size:90

Alignment explanation


    Indices: 10261--10425  Score: 271
    Period size: 90  Copynumber: 1.8  Consensus size: 90

      10251 GCCCCTAAGT

                                      **                                     
      10261 GAACTCGACTCAACTCAACGAGCTCGGGTTCGCATCCATAAGTGAACTCGGACTCAA-TCAACGA
          1 GAACTCGACTCAACTCAACGAGCTCGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAACGA

                                     
      10325 GTTC-GATGCCTAGTTACATCTCAC
         66 GTTCGGATGCCTAGTTACATCTCAC

                                   *                                         
      10349 GAACTCGGACTCAACTCAACGAGTTCGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
          1 GAACTC-GACTCAACTCAACGAGCTCG-CATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC

                        
      10414 GAGTTCGGATGC
         64 GAGTTCGGATGC

      10426 TCAACCATCC


Statistics
Matches: 70,  Mismatches: 3, Indels: 4
        0.91            0.04        0.05

Matches are distributed among these distances:
  88    6  0.09
  89   19  0.27
  90   29  0.41
  91   11  0.16
  92    5  0.07

ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22


Consensus pattern (90 bp):   
GAACTCGACTCAACTCAACGAGCTCGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAACGA
GTTCGGATGCCTAGTTACATCTCAC

Found at i:10398 original size:45 final size:45

Alignment explanation


    Indices: 10256--10420  Score: 182
    Period size: 45  Copynumber: 3.7  Consensus size: 45

      10246 AACCCGCCCC

                                        *    **          
      10256 TAAGTGAACTC-GACTCAACTCAACGAGCTCG-GGTTCGCATCCA
          1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGACATTCGCATCCA

                                                       *      
      10299 TAAGTGAACTCGGACTCAA-TCAACGAGTTCGATGCCTAGTT-ACAT-C-
          1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGA---C-A-TTCGCATCCA

             *  *                                        
      10345 TCA-CGAACTCGGACTCAACTCAACGAGTTCGACATTCGCATCCA
          1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGACATTCGCATCCA

                                            
      10389 TAAGTGAACTCGGACTCAACTCAACGAGTTCG
          1 TAAGTGAACTCGGACTCAACTCAACGAGTTCG

      10421 GATGCTCAAC


Statistics
Matches: 101,  Mismatches: 9, Indels: 22
        0.77            0.07        0.17

Matches are distributed among these distances:
  41    2  0.02
  42    4  0.04
  43   24  0.24
  44    9  0.09
  45   41  0.41
  46   15  0.15
  47    1  0.01
  48    3  0.03
  49    2  0.02

ACGTcount: A:0.30, C:0.28, G:0.19, T:0.22


Consensus pattern (45 bp):   
TAAGTGAACTCGGACTCAACTCAACGAGTTCGACATTCGCATCCA
Done.