Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001393.1 Corchorus capsularis cultivar CVL-1 contig01393, whole genome shotgun sequence

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: 6793
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34


Found at i:84 original size:26 final size:26

Alignment explanation


    Indices: 55--122  Score: 93
    Period size: 26  Copynumber: 2.6  Consensus size: 26

         45 TATTTAGTTT

                                      
         55 ATTAGTTTATGTTTAATTAATATCTA
          1 ATTAGTTTATGTTTAATTAATATCTA

                                *   *  
         81 ATTAGTTTAT-TATTAATTAGTATTTA
          1 ATTAGTTTATGT-TTAATTAATATCTA

                       *    
        107 ATTAGTTTATGATTAA
          1 ATTAGTTTATGTTTAA

        123 AATGAAGGAA


Statistics
Matches: 37,  Mismatches: 3, Indels: 4
        0.84            0.07        0.09

Matches are distributed among these distances:
  25    1  0.03
  26   36  0.97

ACGTcount: A:0.35, C:0.01, G:0.09, T:0.54


Consensus pattern (26 bp):   
ATTAGTTTATGTTTAATTAATATCTA

Found at i:99 original size:15 final size:15

Alignment explanation


    Indices: 79--122  Score: 51
    Period size: 15  Copynumber: 3.2  Consensus size: 15

         69 AATTAATATC

                           
         79 TAATTAGTTTATTAT
          1 TAATTAGTTTATTAT

                           
         94 TAATTAG--TA-T-T
          1 TAATTAGTTTATTAT

                        *  
        105 TAATTAGTTTATGAT
          1 TAATTAGTTTATTAT

               
        120 TAA
          1 TAA

        123 AATGAAGGAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 8
        0.73            0.03        0.24

Matches are distributed among these distances:
  11    8  0.33
  12    1  0.04
  13    4  0.17
  15   11  0.46

ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55


Consensus pattern (15 bp):   
TAATTAGTTTATTAT

Found at i:107 original size:37 final size:33

Alignment explanation


    Indices: 34--110  Score: 82
    Period size: 34  Copynumber: 2.2  Consensus size: 33

         24 TTTTAATTAG

                         *                 * 
         34 TTAATTAAAATTATTTAGTTTATTAGTTTATGT
          1 TTAATTAAAATTAATTAGTTTATTAGTTTATAT

                    *                 *          
         67 TTAATTAATATCTAATTAGTTTATTATTAATTAGTAT
          1 TTAATTAAAAT-TAATTAGTTTATTAGT--TTA-TAT

                   
        104 TTAATTA
          1 TTAATTA

        111 GTTTATGATT


Statistics
Matches: 36,  Mismatches: 4, Indels: 4
        0.82            0.09        0.09

Matches are distributed among these distances:
  33   10  0.28
  34   14  0.39
  36    3  0.08
  37    9  0.25

ACGTcount: A:0.36, C:0.01, G:0.06, T:0.56


Consensus pattern (33 bp):   
TTAATTAAAATTAATTAGTTTATTAGTTTATAT

Found at i:167 original size:24 final size:25

Alignment explanation


    Indices: 131--190  Score: 79
    Period size: 25  Copynumber: 2.5  Consensus size: 25

        121 AAAATGAAGG

                              *      
        131 AAAATGAA-TTTGAAG-ATTTGTTA
          1 AAAATGAAGTTTGAAGAAGTTGTTA

                 *                   
        154 AAAATAAAGTTTGAAGAAGTTGTTA
          1 AAAATGAAGTTTGAAGAAGTTGTTA

            *           
        179 GAAATGAAGTTT
          1 AAAATGAAGTTT

        191 AGGGTTTGAA


Statistics
Matches: 31,  Mismatches: 4, Indels: 2
        0.84            0.11        0.05

Matches are distributed among these distances:
  23    7  0.23
  24    7  0.23
  25   17  0.55

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


Consensus pattern (25 bp):   
AAAATGAAGTTTGAAGAAGTTGTTA

Found at i:1876 original size:24 final size:25

Alignment explanation


    Indices: 1842--1892  Score: 77
    Period size: 24  Copynumber: 2.1  Consensus size: 25

       1832 ATTGGATTAT

                        *            
       1842 TTATTTATCTTGTTTATTAATTTTA
          1 TTATTTATCTTGCTTATTAATTTTA

                              *      
       1867 TTATTT-TCTTGCTTATTTATTTTA
          1 TTATTTATCTTGCTTATTAATTTTA

              
       1891 TT
          1 TT

       1893 GTTCCTTATT


Statistics
Matches: 24,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  24   18  0.75
  25    6  0.25

ACGTcount: A:0.20, C:0.06, G:0.04, T:0.71


Consensus pattern (25 bp):   
TTATTTATCTTGCTTATTAATTTTA
Done.