Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019342.1 Corchorus olitorius cultivar O-4 contig19375, 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: 3821
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.31


Found at i:1766 original size:19 final size:19

Alignment explanation


    Indices: 1715--1766  Score: 61
    Period size: 19  Copynumber: 2.7  Consensus size: 19

       1705 TTATTTTTGG

                                
       1715 TCGGACCGGGCCAAACCCGT
          1 TCGGACC-GGCCAAACCCGT

                *   *           
       1735 TCGGTCCGACCAAA-CCGAT
          1 TCGGACCGGCCAAACCCG-T

                         
       1754 TCGGACCGGCCAA
          1 TCGGACCGGCCAA

       1767 GCCGGCTGGC


Statistics
Matches: 27,  Mismatches: 4, Indels: 3
        0.79            0.12        0.09

Matches are distributed among these distances:
  18    3  0.11
  19   18  0.67
  20    6  0.22

ACGTcount: A:0.23, C:0.38, G:0.27, T:0.12


Consensus pattern (19 bp):   
TCGGACCGGCCAAACCCGT

Found at i:2847 original size:22 final size:23

Alignment explanation


    Indices: 2819--2877  Score: 77
    Period size: 22  Copynumber: 2.7  Consensus size: 23

       2809 GGAGTCTAAG

                             *     
       2819 AAATTTTGATAACCT-TTTTATA
          1 AAATTTTGATAACCTATATTATA

                                  *
       2841 AAATTTTGATAA-CTATATTATG
          1 AAATTTTGATAACCTATATTATA

              *            
       2863 AAGTTTTGATAACCT
          1 AAATTTTGATAACCT

       2878 CCATATGAAA


Statistics
Matches: 32,  Mismatches: 3, Indels: 3
        0.84            0.08        0.08

Matches are distributed among these distances:
  21    2  0.06
  22   28  0.88
  23    2  0.06

ACGTcount: A:0.37, C:0.08, G:0.08, T:0.46


Consensus pattern (23 bp):   
AAATTTTGATAACCTATATTATA

Found at i:3548 original size:31 final size:30

Alignment explanation


    Indices: 3513--3571  Score: 84
    Period size: 31  Copynumber: 1.9  Consensus size: 30

       3503 ATTGACTCCA

                                            
       3513 CTAAAATTG-AAGTTTTACAATATTAACCCTT
          1 CTAAAA-TGAAAGTTTTA-AATATTAACCCTT

                             *          
       3544 CTAAAATGAAAGTTTTATATATTAACCC
          1 CTAAAATGAAAGTTTTAAATATTAACCC

       3572 CATTAAAATC


Statistics
Matches: 26,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  30   12  0.46
  31   14  0.54

ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37


Consensus pattern (30 bp):   
CTAAAATGAAAGTTTTAAATATTAACCCTT

Found at i:3568 original size:30 final size:30

Alignment explanation


    Indices: 3513--3610  Score: 92
    Period size: 30  Copynumber: 3.2  Consensus size: 30

       3503 ATTGACTCCA

                               *            
       3513 CTAAAATTG-AAGTTTTACAATATTAACCCTT
          1 CTAAAA-TGAAAGTTTTA-TATATTAACCCTT

                                         * 
       3544 CTAAAATGAAAGTTTTATATATTAACCCCAT
          1 CTAAAATGAAAGTTTTATATATTAA-CCCTT

                   *   *            *     *
       3575 -TAAAATCAAAATTTTATAGTATTGACCCTA
          1 CTAAAATGAAAGTTTTATA-TATTAACCCTT

                  
       3605 CTAAAA
          1 CTAAAA

       3611 ATGTTGAATC


Statistics
Matches: 56,  Mismatches: 7, Indels: 8
        0.79            0.10        0.11

Matches are distributed among these distances:
  30   28  0.50
  31   28  0.50

ACGTcount: A:0.43, C:0.15, G:0.06, T:0.36


Consensus pattern (30 bp):   
CTAAAATGAAAGTTTTATATATTAACCCTT
Done.