Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024874.1 Corchorus olitorius cultivar O-4 contig24907, 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: 18779
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35


Found at i:695 original size:27 final size:28

Alignment explanation


    Indices: 628--701  Score: 82
    Period size: 28  Copynumber: 2.7  Consensus size: 28

        618 TAGGATGTTA

                                     *   
        628 AAATTAC-GTATTTGCCCTTGGTCGGCTG
          1 AAATTACAGT-TTTGCCCTTGGTCGACTG

                          *        *     
        656 AAATTACCA-TTTTACCCTTGGTTGACT-
          1 AAATTA-CAGTTTTGCCCTTGGTCGACTG

                               
        683 AAATTACAGTTTTGCCCTT
          1 AAATTACAGTTTTGCCCTT

        702 AAACATCGGA


Statistics
Matches: 39,  Mismatches: 4, Indels: 7
        0.78            0.08        0.14

Matches are distributed among these distances:
  26    2  0.05
  27   15  0.38
  28   20  0.51
  29    2  0.05

ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39


Consensus pattern (28 bp):   
AAATTACAGTTTTGCCCTTGGTCGACTG

Found at i:6770 original size:27 final size:28

Alignment explanation


    Indices: 6701--6776  Score: 95
    Period size: 28  Copynumber: 2.8  Consensus size: 28

       6691 CTTAGGATGT

                                         
       6701 TAAAATTAC-GTATTTGCCCTTGGTTGAA
          1 TAAAATTACAGT-TTTGCCCTTGGTTGAA

                            *           *
       6729 TAAAATTACCA-TTTTACCCTTGGTTGAC
          1 TAAAATTA-CAGTTTTGCCCTTGGTTGAA

                                 
       6757 T-AAATTACAGTTTTGCCCTT
          1 TAAAATTACAGTTTTGCCCTT

       6777 AAACATCGGA


Statistics
Matches: 42,  Mismatches: 3, Indels: 7
        0.81            0.06        0.13

Matches are distributed among these distances:
  26    2  0.05
  27   15  0.36
  28   23  0.55
  29    2  0.05

ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41


Consensus pattern (28 bp):   
TAAAATTACAGTTTTGCCCTTGGTTGAA

Found at i:8981 original size:23 final size:23

Alignment explanation


    Indices: 8953--8996  Score: 79
    Period size: 23  Copynumber: 1.9  Consensus size: 23

       8943 TAATTTCTAC

                                   
       8953 TTTTTTGCTTCAATTTAGTCATA
          1 TTTTTTGCTTCAATTTAGTCATA

                       *         
       8976 TTTTTTGCTTCTATTTAGTCA
          1 TTTTTTGCTTCAATTTAGTCA

       8997 ATCAAGAGAG


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  23   20  1.00

ACGTcount: A:0.18, C:0.14, G:0.09, T:0.59


Consensus pattern (23 bp):   
TTTTTTGCTTCAATTTAGTCATA

Found at i:12436 original size:8 final size:8

Alignment explanation


    Indices: 12420--12454  Score: 52
    Period size: 8  Copynumber: 4.4  Consensus size: 8

      12410 CAGGCCCACT

                *   
      12420 TTTTTTTC
          1 TTTTCTTC

                    
      12428 TTTTCTTC
          1 TTTTCTTC

                    
      12436 TTTTCTTC
          1 TTTTCTTC

              *     
      12444 TTCTCTTC
          1 TTTTCTTC

               
      12452 TTT
          1 TTT

      12455 CCTTTTTTTT


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

Matches are distributed among these distances:
   8   24  1.00

ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77


Consensus pattern (8 bp):   
TTTTCTTC

Done.