Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007374.1 Corchorus olitorius cultivar O-4 contig07399, 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: 4776
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35


Found at i:693 original size:43 final size:44

Alignment explanation


    Indices: 631--723  Score: 145
    Period size: 43  Copynumber: 2.1  Consensus size: 44

        621 ATTAGGGATT

                                            *            
        631 ATATTTATAAATTATATATGTAATGAAA-TATTATTTAGAAAATA
          1 ATATTTATAAATTATATATGTAATGAAATTATAATTT-GAAAATA

                                                       *
        675 ATATTTA-AAATTATATATGTAATGAAATTATAATTTGAAAATC
          1 ATATTTATAAATTATATATGTAATGAAATTATAATTTGAAAATA

                  
        718 ATATTT
          1 ATATTT

        724 TTTTTGGGCA


Statistics
Matches: 46,  Mismatches: 2, Indels: 3
        0.90            0.04        0.06

Matches are distributed among these distances:
  43   32  0.70
  44   14  0.30

ACGTcount: A:0.48, C:0.01, G:0.06, T:0.44


Consensus pattern (44 bp):   
ATATTTATAAATTATATATGTAATGAAATTATAATTTGAAAATA

Found at i:704 original size:17 final size:16

Alignment explanation


    Indices: 630--706  Score: 51
    Period size: 14  Copynumber: 5.1  Consensus size: 16

        620 AATTAGGGAT

                  *         
        630 TATATTTAT-AAATTA
          1 TATATTAATGAAATTA

                             
        645 TATATGTAATGAAA-TA
          1 TATAT-TAATGAAATTA

                  *      *  
        661 T-TATTTA-GAAAATA
          1 TATATTAATGAAATTA

                     *      
        675 -ATATT--TAAAATTA
          1 TATATTAATGAAATTA

                             
        688 TATATGTAATGAAATTA
          1 TATAT-TAATGAAATTA

              
        705 TA
          1 TA

        707 ATTTGAAAAT


Statistics
Matches: 48,  Mismatches: 5, Indels: 16
        0.70            0.07        0.23

Matches are distributed among these distances:
  13    9  0.19
  14   12  0.25
  15    9  0.19
  16    6  0.12
  17   12  0.25

ACGTcount: A:0.49, C:0.00, G:0.06, T:0.44


Consensus pattern (16 bp):   
TATATTAATGAAATTA

Found at i:846 original size:13 final size:14

Alignment explanation


    Indices: 781--837  Score: 53
    Period size: 14  Copynumber: 3.9  Consensus size: 14

        771 GAAATTTTAT

                       *  
        781 TTAGAAAATAACAA
          1 TTAGAAAATAATAA

                     *     
        795 TTAG-AAATTATATA
          1 TTAGAAAATAATA-A

                *           
        809 TGTAAAGAAATAATAA
          1 T-TAGA-AAATAATAA

                         
        825 TTAGAAAATAATA
          1 TTAGAAAATAATA

        838 TTTATAAATT


Statistics
Matches: 34,  Mismatches: 5, Indels: 8
        0.72            0.11        0.17

Matches are distributed among these distances:
  13    6  0.18
  14   14  0.41
  15    5  0.15
  16    2  0.06
  17    7  0.21

ACGTcount: A:0.60, C:0.02, G:0.09, T:0.30


Consensus pattern (14 bp):   
TTAGAAAATAATAA
Done.