Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_5690

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: 10010
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33


Found at i:656 original size:21 final size:22

Alignment explanation


    Indices: 615--657  Score: 61
    Period size: 22  Copynumber: 2.0  Consensus size: 22

        605 AATTAGTTTC

                    *             
        615 GGCTAAGGTATAACATTCATAT
          1 GGCTAAGGAATAACATTCATAT

                  *               
        637 GGCTAATGAATAAC-TTCATAT
          1 GGCTAAGGAATAACATTCATAT

        658 ATGCACATTT


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  21    7  0.37
  22   12  0.63

ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33


Consensus pattern (22 bp):   
GGCTAAGGAATAACATTCATAT

Found at i:962 original size:38 final size:39

Alignment explanation


    Indices: 920--1094  Score: 175
    Period size: 39  Copynumber: 4.6  Consensus size: 39

        910 CTCGCACAAG

                                    *               
        920 GCCTTCGGGTCTTAGCCCGGA-ATGGTCACTAGC-TAAAT
          1 GCCTTC-GGTCTTAGCCCGGATATAGTCACTAGCATAAAT

                    *                  *      *    
        958 GCCTTCGGAC-TAG-CCGGATATAGTCGCTAGCACAAAT
          1 GCCTTCGGTCTTAGCCCGGATATAGTCACTAGCATAAAT

                                     **     *  *    
        995 GCCTTCTGGTCTTAGCCCGGATATAACCACT-CCACAAAT
          1 GCCTTC-GGTCTTAGCCCGGATATAGTCACTAGCATAAAT

                           *                       *
       1034 GCCTTCGGATCTTAGTCC-GATATAGTCACTAGCATAAAA
          1 GCCTTCGG-TCTTAGCCCGGATATAGTCACTAGCATAAAT

                    *              
       1073 GCCTTCGGACTTAGCCC-GATAT
          1 GCCTTCGGTCTTAGCCCGGATAT

       1095 CATTCGATAA


Statistics
Matches: 113,  Mismatches: 17, Indels: 14
        0.78            0.12        0.10

Matches are distributed among these distances:
  35    5  0.04
  36   13  0.12
  37   13  0.12
  38   33  0.29
  39   37  0.33
  40   12  0.11

ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26


Consensus pattern (39 bp):   
GCCTTCGGTCTTAGCCCGGATATAGTCACTAGCATAAAT

Found at i:1031 original size:39 final size:37

Alignment explanation


    Indices: 893--1094  Score: 119
    Period size: 38  Copynumber: 5.3  Consensus size: 37

        883 ATCTCGGAAT

                                       *           
        893 TTAGCCGGATATAACCACTCGCAC-AAGGCCTTCGGGTC
          1 TTAGCCGGATATAACCACTC-CACAAATGCCTTC-GGTC

                         ***                      * 
        931 TTAGCCCGGA-ATGGTCACT--AGCTAAATGCCTTCGGAC
          1 TTAG-CCGGATATAACCACTCCA-C-AAATGCCTTCGGTC

                         ** *   *                  
        968 -TAGCCGGATATAGTCGCTAGCACAAATGCCTTCTGGTC
          1 TTAGCCGGATATAACCACT-CCACAAATGCCTTC-GGTC

                                                   
       1006 TTAGCCCGGATATAACCACTCCACAAATGCCTTCGGATC
          1 TTAG-CCGGATATAACCACTCCACAAATGCCTTCGG-TC

                          **     *  *   *        * 
       1045 TTAGTCC-GATATAGTCACTAGCATAAAAGCCTTCGGAC
          1 TTAG-CCGGATATAACCACT-CCACAAATGCCTTCGGTC

                  *     
       1083 TTAGCCCGATAT
          1 TTAGCCGGATAT

       1095 CATTCGATAA


Statistics
Matches: 131,  Mismatches: 19, Indels: 28
        0.74            0.11        0.16

Matches are distributed among these distances:
  35    6  0.05
  36   11  0.08
  37   15  0.11
  38   44  0.34
  39   43  0.33
  40   12  0.09

ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25


Consensus pattern (37 bp):   
TTAGCCGGATATAACCACTCCACAAATGCCTTCGGTC

Found at i:1077 original size:78 final size:74

Alignment explanation


    Indices: 954--1094  Score: 194
    Period size: 78  Copynumber: 1.9  Consensus size: 74

        944 GTCACTAGCT

                                         *          *         *              
        954 AAATGCCTTCGGACTAGCCGGATATAGTCGCTAGCACAAATGCCTTCTGGTCTTAGCCCGGATAT
          1 AAATGCCTTCGGACTAGCCGGATATAGTCACTAGCACAAAAGCCTTC-GGACTTAGCCC-GATAT

                       
       1019 AACCACTCCAC
         64 AACCACTCCAC

                                                   *                         
       1030 AAATGCCTTCGGATCTTAGTCC-GATATAGTCACTAGCATAAAAGCCTTCGGACTTAGCCCGATA
          1 AAATGCCTTCGGA-C-TAG-CCGGATATAGTCACTAGCACAAAAGCCTTCGGACTTAGCCCGATA

             
       1094 T
         63 T

       1095 CATTCGATAA


Statistics
Matches: 58,  Mismatches: 4, Indels: 6
        0.85            0.06        0.09

Matches are distributed among these distances:
  76   18  0.31
  77   11  0.19
  78   27  0.47
  79    2  0.03

ACGTcount: A:0.28, C:0.28, G:0.19, T:0.26


Consensus pattern (74 bp):   
AAATGCCTTCGGACTAGCCGGATATAGTCACTAGCACAAAAGCCTTCGGACTTAGCCCGATATAA
CCACTCCAC

Found at i:6009 original size:46 final size:45

Alignment explanation


    Indices: 5866--6025  Score: 193
    Period size: 44  Copynumber: 3.6  Consensus size: 45

       5856 TTCCGATACT

                              *        *                 
       5866 TGATTTCGTGTAAG-CCATGTCTGGG-CGTTGGCATCGATATATG
          1 TGATTTCGTGTAAGACCACGTCTGGGATGTTGGCATCGATATATG

                   *  *                 *                
       5909 TGATTTCATGCAAGACCACGTCTGGGATATTGGCAT-GATATATG
          1 TGATTTCGTGTAAGACCACGTCTGGGATGTTGGCATCGATATATG

                                                           
       5953 TGATTTCGTGTAAGACCACGTTCTGGGATGTT-GCATCGCATATATG
          1 TGATTTCGTGTAAGACCACG-TCTGGGATGTTGGCATCG-ATATATG

              *  *            *  *     
       5999 TGGTTACGTGTAAGACCATGTATGGGA
          1 TGATTTCGTGTAAGACCACGTCTGGGA

       6026 CATCAGAAAT


Statistics
Matches: 100,  Mismatches: 12, Indels: 8
        0.83            0.10        0.07

Matches are distributed among these distances:
  43   12  0.12
  44   40  0.40
  45   24  0.24
  46   24  0.24

ACGTcount: A:0.23, C:0.16, G:0.28, T:0.33


Consensus pattern (45 bp):   
TGATTTCGTGTAAGACCACGTCTGGGATGTTGGCATCGATATATG
Done.