Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013359.1 Corchorus olitorius cultivar O-4 contig13392, 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: 10557
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36


Found at i:1458 original size:12 final size:13

Alignment explanation


    Indices: 1441--1473  Score: 50
    Period size: 12  Copynumber: 2.5  Consensus size: 13

       1431 ACTCACATGC

                         
       1441 TTTTTAA-TTTTT
          1 TTTTTAACTTTTT

                         
       1453 TTTTTAACTTTTT
          1 TTTTTAACTTTTT

                    
       1466 TTATTTAA
          1 TT-TTTAA

       1474 AAACATCCAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  12    7  0.37
  13    7  0.37
  14    5  0.26

ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76


Consensus pattern (13 bp):   
TTTTTAACTTTTT

Found at i:1548 original size:11 final size:11

Alignment explanation


    Indices: 1532--1566  Score: 61
    Period size: 11  Copynumber: 3.2  Consensus size: 11

       1522 TTGATAGCGC

                       
       1532 AACAAAAACAA
          1 AACAAAAACAA

                     * 
       1543 AACAAAAACGA
          1 AACAAAAACAA

                       
       1554 AACAAAAACAA
          1 AACAAAAACAA

              
       1565 AA
          1 AA

       1567 AAACGAAAAC


Statistics
Matches: 22,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  11   22  1.00

ACGTcount: A:0.80, C:0.17, G:0.03, T:0.00


Consensus pattern (11 bp):   
AACAAAAACAA

Found at i:5299 original size:2 final size:2

Alignment explanation


    Indices: 5292--5323  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

       5282 ATTTGGGGTG

                                                           
       5292 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

       5324 CATAGTAGAT


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:8077 original size:2 final size:2

Alignment explanation


    Indices: 8070--8104  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

       8060 CCAATTAGTT

                                                                
       8070 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       8105 GTAGGCAATG


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Done.