Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010085.1 Corchorus olitorius cultivar O-4 contig10117, 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: 5850
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36


Found at i:732 original size:20 final size:20

Alignment explanation


    Indices: 689--732  Score: 52
    Period size: 20  Copynumber: 2.2  Consensus size: 20

        679 CAACAGACAC

                            *  *
        689 TTAAGTCGTTACGTTAGATC
          1 TTAAGTCGTTACGTTAAATA

                      **        
        709 TTAAGTCGTTGTGTTAAATA
          1 TTAAGTCGTTACGTTAAATA

                
        729 TTAA
          1 TTAA

        733 ACAACGGAAC


Statistics
Matches: 20,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.30, C:0.09, G:0.18, T:0.43


Consensus pattern (20 bp):   
TTAAGTCGTTACGTTAAATA

Found at i:2590 original size:22 final size:22

Alignment explanation


    Indices: 2563--2608  Score: 92
    Period size: 22  Copynumber: 2.1  Consensus size: 22

       2553 TATTTATAGC

                                  
       2563 AAAAGTAAATAATTACTGGTTT
          1 AAAAGTAAATAATTACTGGTTT

                                  
       2585 AAAAGTAAATAATTACTGGTTT
          1 AAAAGTAAATAATTACTGGTTT

              
       2607 AA
          1 AA

       2609 TTTTGGAGTA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   24  1.00

ACGTcount: A:0.48, C:0.04, G:0.13, T:0.35


Consensus pattern (22 bp):   
AAAAGTAAATAATTACTGGTTT

Found at i:3530 original size:20 final size:20

Alignment explanation


    Indices: 3489--3531  Score: 59
    Period size: 20  Copynumber: 2.1  Consensus size: 20

       3479 CTCTCACAAG

                        *    *  
       3489 TTTCTAGCCGTTGGAGCTCT
          1 TTTCTAGCCGTTCGAGCACT

                         *      
       3509 TTTCTAGCCGTTCTAGCACT
          1 TTTCTAGCCGTTCGAGCACT

               
       3529 TTT
          1 TTT

       3532 TCCACTTTTT


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.12, C:0.26, G:0.19, T:0.44


Consensus pattern (20 bp):   
TTTCTAGCCGTTCGAGCACT

Found at i:5803 original size:2 final size:2

Alignment explanation


    Indices: 5796--5821  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       5786 CTAATTAATC

                                                  
       5796 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

       5822 CTTACTATCT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

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


Consensus pattern (2 bp):   
AT

Done.