Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023515.1 Corchorus olitorius cultivar O-4 contig23548, 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: 26223
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33


Found at i:3895 original size:3 final size:3

Alignment explanation


    Indices: 3887--3918  Score: 64
    Period size: 3  Copynumber: 10.7  Consensus size: 3

       3877 AGATGGCCTT

                                                      
       3887 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
          1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT

       3919 TTGCCTTCTT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   29  1.00

ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69


Consensus pattern (3 bp):   
TTC

Found at i:9964 original size:13 final size:13

Alignment explanation


    Indices: 9948--9972  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       9938 GATGGTGGAT

                         
       9948 TATCATGGTTAAG
          1 TATCATGGTTAAG

                        
       9961 TATCATGGTTAA
          1 TATCATGGTTAA

       9973 TGGTGGATTA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40


Consensus pattern (13 bp):   
TATCATGGTTAAG

Found at i:18038 original size:19 final size:20

Alignment explanation


    Indices: 18014--18071  Score: 73
    Period size: 19  Copynumber: 2.9  Consensus size: 20

      18004 CTGTTTAATA

                                
      18014 ACTGTACAGATGAGATTA-C
          1 ACTGTACAGATGAGATTAGC

                    *  *        *
      18033 ACTGTACATATTAGATTAGGT
          1 ACTGTACAGATGAGATTA-GC

                              
      18054 ACTGTACAGATGAGATTA
          1 ACTGTACAGATGAGATTA

      18072 TTAGAGCAGC


Statistics
Matches: 32,  Mismatches: 5, Indels: 2
        0.82            0.13        0.05

Matches are distributed among these distances:
  19   16  0.50
  21   16  0.50

ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31


Consensus pattern (20 bp):   
ACTGTACAGATGAGATTAGC

Found at i:18702 original size:21 final size:21

Alignment explanation


    Indices: 18672--18714  Score: 77
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      18662 CTACTTGAGA

                                 
      18672 AATGGCGGTTACAGTCTAAGC
          1 AATGGCGGTTACAGTCTAAGC

                 *               
      18693 AATGGTGGTTACAGTCTAAGC
          1 AATGGCGGTTACAGTCTAAGC

             
      18714 A
          1 A

      18715 TCTTCGCCAT


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26


Consensus pattern (21 bp):   
AATGGCGGTTACAGTCTAAGC

Found at i:21008 original size:12 final size:13

Alignment explanation


    Indices: 20993--21022  Score: 53
    Period size: 12  Copynumber: 2.4  Consensus size: 13

      20983 ATCCTTCCCA

                         
      20993 TTTTCCTCCTT-T
          1 TTTTCCTCCTTCT

                         
      21005 TTTTCCTCCTTCT
          1 TTTTCCTCCTTCT

                 
      21018 TTTTC
          1 TTTTC

      21023 ACTGTAATGG


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  12   11  0.65
  13    6  0.35

ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67


Consensus pattern (13 bp):   
TTTTCCTCCTTCT
Done.