Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010919.1 Corchorus capsularis cultivar CVL-1 contig10940, 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: 10452
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33


Found at i:136 original size:2 final size:2

Alignment explanation


    Indices: 129--161  Score: 57
    Period size: 2  Copynumber: 16.5  Consensus size: 2

        119 TTCCCTGCTC

                                             *               
        129 TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

        162 TTCTTTCTAT


Statistics
Matches: 29,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48


Consensus pattern (2 bp):   
TA

Found at i:4107 original size:27 final size:27

Alignment explanation


    Indices: 4073--4126  Score: 81
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       4063 ACATCCATTT

                       *      *        
       4073 AACACCGTTAATTTTAATTTTGGGTTA
          1 AACACCGTTAACTTTAATGTTGGGTTA

                      *                
       4100 AACACCGTTAGCTTTAATGTTGGGTTA
          1 AACACCGTTAACTTTAATGTTGGGTTA

       4127 GAATCCTTTT


Statistics
Matches: 24,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  27   24  1.00

ACGTcount: A:0.28, C:0.13, G:0.19, T:0.41


Consensus pattern (27 bp):   
AACACCGTTAACTTTAATGTTGGGTTA

Found at i:8296 original size:48 final size:50

Alignment explanation


    Indices: 8240--8334  Score: 176
    Period size: 50  Copynumber: 1.9  Consensus size: 50

       8230 AAATAATGAA

                                                              
       8240 GTTCAGAGGCAAAATCAC-A-ATGTTAAACTATAATATTATCATCATCGT
          1 GTTCAGAGGCAAAATCACAATATGTTAAACTATAATATTATCATCATCGT

                                                           
       8288 GTTCAGAGGCAAAATCACAATATGTTAAACTATAATATTATCATCAT
          1 GTTCAGAGGCAAAATCACAATATGTTAAACTATAATATTATCATCAT

       8335 TGTGATTGCT


Statistics
Matches: 45,  Mismatches: 0, Indels: 2
        0.96            0.00        0.04

Matches are distributed among these distances:
  48   18  0.40
  49    1  0.02
  50   26  0.58

ACGTcount: A:0.41, C:0.16, G:0.12, T:0.32


Consensus pattern (50 bp):   
GTTCAGAGGCAAAATCACAATATGTTAAACTATAATATTATCATCATCGT

Found at i:10419 original size:2 final size:2

Alignment explanation


    Indices: 10414--10447  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

      10404 ACACACACAC

                                                              
      10414 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      10448 TACTC


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.