Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001309.1 Corchorus olitorius cultivar O-4 contig01309, 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: 1917
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34


Found at i:685 original size:38 final size:38

Alignment explanation


    Indices: 634--709  Score: 143
    Period size: 38  Copynumber: 2.0  Consensus size: 38

        624 GATCATGTTT

                                      *           
        634 AGTGCACCGATTCACCGGTCGTTTGGTCGGTGCACCGG
          1 AGTGCACCGATTCACCGGTCGTTTGGCCGGTGCACCGG

                                                  
        672 AGTGCACCGATTCACCGGTCGTTTGGCCGGTGCACCGG
          1 AGTGCACCGATTCACCGGTCGTTTGGCCGGTGCACCGG

        710 TCAAATGGAG


Statistics
Matches: 37,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  38   37  1.00

ACGTcount: A:0.13, C:0.30, G:0.34, T:0.22


Consensus pattern (38 bp):   
AGTGCACCGATTCACCGGTCGTTTGGCCGGTGCACCGG

Found at i:709 original size:20 final size:20

Alignment explanation


    Indices: 646--711  Score: 57
    Period size: 20  Copynumber: 3.4  Consensus size: 20

        636 TGCACCGATT

                          *     
        646 CACCGGTCGTTTGGTCGGTG
          1 CACCGGTCGTTTGGCCGGTG

                   *      *   * *
        666 CACCGG-AG--TGCACCGATT
          1 CACCGGTCGTTTG-GCCGGTG

                                
        684 CACCGGTCGTTTGGCCGGTG
          1 CACCGGTCGTTTGGCCGGTG

                    
        704 CACCGGTC
          1 CACCGGTC

        712 AAATGGAGGT


Statistics
Matches: 33,  Mismatches: 9, Indels: 8
        0.66            0.18        0.16

Matches are distributed among these distances:
  17    2  0.06
  18    9  0.27
  19    2  0.06
  20   18  0.55
  21    2  0.06

ACGTcount: A:0.11, C:0.32, G:0.35, T:0.23


Consensus pattern (20 bp):   
CACCGGTCGTTTGGCCGGTG

Found at i:801 original size:19 final size:19

Alignment explanation


    Indices: 777--813  Score: 65
    Period size: 19  Copynumber: 1.9  Consensus size: 19

        767 GTACAATACC

                               
        777 TAATCTAATCTGTACAGTG
          1 TAATCTAATCTGTACAGTG

                  *           
        796 TAATCTCATCTGTACAGT
          1 TAATCTAATCTGTACAGT

        814 TGCTAAACAG


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

Matches are distributed among these distances:
  19   17  1.00

ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38


Consensus pattern (19 bp):   
TAATCTAATCTGTACAGTG

Found at i:1563 original size:13 final size:13

Alignment explanation


    Indices: 1545--1570  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       1535 AAACCAAATC

                         
       1545 GTTATTTTTATTT
          1 GTTATTTTTATTT

                         
       1558 GTTATTTTTATTT
          1 GTTATTTTTATTT

       1571 ATTCAGGAAA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77


Consensus pattern (13 bp):   
GTTATTTTTATTT
Done.