Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01002750.1 Corchorus capsularis cultivar CVL-1 contig02758, 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: 1871
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38


Found at i:523 original size:32 final size:31

Alignment explanation


    Indices: 487--548  Score: 79
    Period size: 31  Copynumber: 2.0  Consensus size: 31

        477 CATTAAAGCC

                    *           *           
        487 CTCAAACATTTAAATTATATGCAATTTAGTCT
          1 CTCAAACACTT-AATTATATACAATTTAGTCT

                  *        *              
        519 CTCAAATACTTAATTCTATACAATTTAGTC
          1 CTCAAACACTTAATTATATACAATTTAGTC

        549 CTTAAACTTG


Statistics
Matches: 26,  Mismatches: 4, Indels: 1
        0.84            0.13        0.03

Matches are distributed among these distances:
  31   17  0.65
  32    9  0.35

ACGTcount: A:0.37, C:0.18, G:0.05, T:0.40


Consensus pattern (31 bp):   
CTCAAACACTTAATTATATACAATTTAGTCT

Found at i:698 original size:17 final size:19

Alignment explanation


    Indices: 658--699  Score: 61
    Period size: 20  Copynumber: 2.3  Consensus size: 19

        648 GTGCGGGGGA

                                
        658 ATTTTCTAGTATATATGGTT
          1 ATTTTCTAGTATATAT-GTT

                               
        678 ATTTTCTAGTA-ATAT-TT
          1 ATTTTCTAGTATATATGTT

                 
        695 ATTTT
          1 ATTTT

        700 TGGTTTCTAA


Statistics
Matches: 22,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  17    7  0.32
  19    4  0.18
  20   11  0.50

ACGTcount: A:0.26, C:0.05, G:0.10, T:0.60


Consensus pattern (19 bp):   
ATTTTCTAGTATATATGTT

Found at i:761 original size:57 final size:57

Alignment explanation


    Indices: 687--821  Score: 202
    Period size: 57  Copynumber: 2.4  Consensus size: 57

        677 TATTTTCTAG

                                                        *              
        687 TAATATTTATTTTTGGTTTCTAATTACA-GATCTACTCTCTTTTTATAT-ATACTATAC
          1 TAATATTTATTTTTGGTTTCTAATTACATG-TCTACTCTCTTTTAAT-TCATACTATAC

                                              * *              *     
        744 TAATATTTATTTTTGGTTTCTAATTACATGTCTATTTTCTTTTAATTCATATTATAC
          1 TAATATTTATTTTTGGTTTCTAATTACATGTCTACTCTCTTTTAATTCATACTATAC

                                 
        801 TAATATTTATTTTTGGTTTCT
          1 TAATATTTATTTTTGGTTTCT

        822 TCTAATTATA


Statistics
Matches: 72,  Mismatches: 4, Indels: 4
        0.90            0.05        0.05

Matches are distributed among these distances:
  56    1  0.01
  57   70  0.97
  58    1  0.01

ACGTcount: A:0.26, C:0.11, G:0.06, T:0.57


Consensus pattern (57 bp):   
TAATATTTATTTTTGGTTTCTAATTACATGTCTACTCTCTTTTAATTCATACTATAC

Found at i:1813 original size:50 final size:49

Alignment explanation


    Indices: 1737--1832  Score: 129
    Period size: 50  Copynumber: 1.9  Consensus size: 49

       1727 CACTTCGCTA

                    * *                **    **              
       1737 TTTCCATTTGGTATTTTAGTTTTAGTGTGTTGGGTTAGTTTATTTAGCT
          1 TTTCCATTAGATATTTTAGTTTTAGTGAATTGGACTAGTTTATTTAGCT

                                                           
       1786 TTTCCATTAGATATTTTTAGTTTTAGTGAATTGGACTAGTTTATTTA
          1 TTTCCATTAGATA-TTTTAGTTTTAGTGAATTGGACTAGTTTATTTA

       1833 ACTCTGGGCT


Statistics
Matches: 40,  Mismatches: 6, Indels: 1
        0.85            0.13        0.02

Matches are distributed among these distances:
  49   11  0.28
  50   29  0.73

ACGTcount: A:0.20, C:0.06, G:0.19, T:0.55


Consensus pattern (49 bp):   
TTTCCATTAGATATTTTAGTTTTAGTGAATTGGACTAGTTTATTTAGCT
Done.