Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_1006

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: 38723
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33


Found at i:8002 original size:20 final size:20

Alignment explanation


    Indices: 7947--8002  Score: 76
    Period size: 20  Copynumber: 2.8  Consensus size: 20

       7937 AGTTCATGCT

                     *     *    
       7947 AAGTAAATGAAATGGAAAGA
          1 AAGTAAATGGAATGGTAAGA

                   *            
       7967 AAGTAAACGGAATGGTAAGA
          1 AAGTAAATGGAATGGTAAGA

                       *    
       7987 AAGTAAATGGAGTGGT
          1 AAGTAAATGGAATGGT

       8003 TCATAGTATT


Statistics
Matches: 31,  Mismatches: 5, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  20   31  1.00

ACGTcount: A:0.50, C:0.02, G:0.30, T:0.18


Consensus pattern (20 bp):   
AAGTAAATGGAATGGTAAGA

Found at i:14799 original size:24 final size:24

Alignment explanation


    Indices: 14763--14821  Score: 73
    Period size: 24  Copynumber: 2.5  Consensus size: 24

      14753 GAGCCAACAT

                    *       * * *   
      14763 TGGCACTAAGTGTGCGTATTTGAA
          1 TGGCACTATGTGTGCGAAATCGAA

                                   *
      14787 TGGCACTATGTGTGCGAAATCGAT
          1 TGGCACTATGTGTGCGAAATCGAA

                       
      14811 TGGCACTATGT
          1 TGGCACTATGT

      14822 ATGATGGTTT


Statistics
Matches: 30,  Mismatches: 5, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  24   30  1.00

ACGTcount: A:0.24, C:0.15, G:0.29, T:0.32


Consensus pattern (24 bp):   
TGGCACTATGTGTGCGAAATCGAA

Found at i:23346 original size:45 final size:45

Alignment explanation


    Indices: 23184--23355  Score: 194
    Period size: 45  Copynumber: 3.8  Consensus size: 45

      23174 TGTAACCCGC

                                           *      *       
      23184 CCATAAGTGAACTCGGACTC-ACTCAACGAGCTCGG-CGTTCGCAT
          1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATT-GCAT

                                                          *   
      23228 CCA-AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
          1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTGCAT

                *  *                    *                
      23277 -C-TCA-CGAACTCGGACTCAACTCAACAAGTTCGGACATTGCAT
          1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTGCAT

                                                 
      23319 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
          1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA

      23356 TGCTCAACCA


Statistics
Matches: 107,  Mismatches: 10, Indels: 21
        0.78            0.07        0.15

Matches are distributed among these distances:
  42    5  0.05
  43   18  0.17
  44   20  0.19
  45   28  0.26
  47   28  0.26
  48    3  0.03
  49    3  0.03
  50    2  0.02

ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21


Consensus pattern (45 bp):   
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTGCAT

Found at i:23347 original size:92 final size:90

Alignment explanation


    Indices: 23192--23358  Score: 273
    Period size: 92  Copynumber: 1.8  Consensus size: 90

      23182 GCCCATAAGT

                               *        *                                    
      23192 GAACTCGGACTCACTCAACGAGCTCGGCGTTCGCATCCAAAGTGAACTCGGACTCAACTCAACGA
          1 GAACTCGGACTCACTCAACAAGCTCGGCATTCGCATCCAAAGTGAACTCGGACTCAACTCAACGA

                                     
      23257 GTTCGGATGCCTAGTTACATCTCAC
         66 GTTCGGATGCCTAGTTACATCTCAC

                                   *                                         
      23282 GAACTCGGACTCAACTCAACAAGTTCGGACATT-GCATCCATAAGTGAACTCGGACTCAACTCAA
          1 GAACTCGGACTC-ACTCAACAAGCTCGG-CATTCGCATCCA-AAGTGAACTCGGACTCAACTCAA

                         
      23346 CGAGTTCGGATGC
         63 CGAGTTCGGATGC

      23359 TCAACCATCC


Statistics
Matches: 71,  Mismatches: 3, Indels: 4
        0.91            0.04        0.05

Matches are distributed among these distances:
  90   12  0.17
  91   20  0.28
  92   39  0.55

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


Consensus pattern (90 bp):   
GAACTCGGACTCACTCAACAAGCTCGGCATTCGCATCCAAAGTGAACTCGGACTCAACTCAACGA
GTTCGGATGCCTAGTTACATCTCAC

Found at i:33820 original size:47 final size:46

Alignment explanation


    Indices: 33719--33843  Score: 178
    Period size: 47  Copynumber: 2.7  Consensus size: 46

      33709 GGTTGAGCAT

                                         *            *** 
      33719 CGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATACAAATGTC
          1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACAAACACC

                                                  * *      
      33765 CGAACTCGTTGAGTTGAGTCCGAGTTTCACTTATGGATGCGAACACC
          1 CGAACTCGTTGAGTTGAGTCCGAG-TTCACTTATGGATACAAACACC

               *                            
      33812 CGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
          1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTA

      33844 GGGGTGGGTT


Statistics
Matches: 71,  Mismatches: 7, Indels: 2
        0.89            0.09        0.03

Matches are distributed among these distances:
  46   32  0.45
  47   39  0.55

ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29


Consensus pattern (46 bp):   
CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACAAACACC
Done.