Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002419.1 Corchorus olitorius cultivar O-4 contig02419, 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: 3693
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.35


Found at i:1830 original size:29 final size:29

Alignment explanation


    Indices: 1798--1859  Score: 72
    Period size: 29  Copynumber: 2.1  Consensus size: 29

       1788 TATAAGGATA

                                          
       1798 TTAGATTTATTT-AAATAAAAATAGAGTTT
          1 TTAGATTTATTTGAAA-AAAAATAGAGTTT

                *   *    **              
       1827 TTAGTTTTTTTTGCCAAAAAATAGAGTTT
          1 TTAGATTTATTTGAAAAAAAATAGAGTTT

                
       1856 TTAG
          1 TTAG

       1860 TTGAGTAAAA


Statistics
Matches: 28,  Mismatches: 4, Indels: 2
        0.82            0.12        0.06

Matches are distributed among these distances:
  29   27  0.96
  30    1  0.04

ACGTcount: A:0.37, C:0.03, G:0.13, T:0.47


Consensus pattern (29 bp):   
TTAGATTTATTTGAAAAAAAATAGAGTTT

Found at i:2528 original size:19 final size:20

Alignment explanation


    Indices: 2506--2555  Score: 59
    Period size: 19  Copynumber: 2.5  Consensus size: 20

       2496 TTGATCATTG

                                 
       2506 TTTGGTGTAAT-G-ATTCTTT
          1 TTTGGTGTAATAGTA-TCTTT

                  *             
       2525 TTTGGTTTAATAGTATCTTT
          1 TTTGGTGTAATAGTATCTTT

                       
       2545 TTTGAGTGTAA
          1 TTTG-GTGTAA

       2556 CAAAAAATCT


Statistics
Matches: 26,  Mismatches: 2, Indels: 4
        0.81            0.06        0.12

Matches are distributed among these distances:
  19   10  0.38
  20   10  0.38
  21    6  0.23

ACGTcount: A:0.20, C:0.04, G:0.20, T:0.56


Consensus pattern (20 bp):   
TTTGGTGTAATAGTATCTTT

Found at i:3426 original size:2 final size:2

Alignment explanation


    Indices: 3419--3456  Score: 76
    Period size: 2  Copynumber: 19.0  Consensus size: 2

       3409 GAACTACCTA

                                                                    
       3419 AT AT AT AT AT AT 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 AT AT AT AT AT AT

       3457 TGTATGCATC


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   36  1.00

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


Consensus pattern (2 bp):   
AT

Done.