Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021098.1 Corchorus olitorius cultivar O-4 contig21131, 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: 1843
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.32

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:349 original size:3 final size:3

Alignment explanation


    Indices: 341--367  Score: 54
    Period size: 3  Copynumber: 9.0  Consensus size: 3

        331 GCCGGAAGGA

                                               
        341 AAG AAG AAG AAG AAG AAG AAG AAG AAG
          1 AAG AAG AAG AAG AAG AAG AAG AAG AAG

        368 GAAAAAAAAA


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

Matches are distributed among these distances:
   3   24  1.00

ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00


Consensus pattern (3 bp):   
AAG

Found at i:481 original size:23 final size:24

Alignment explanation


    Indices: 435--482  Score: 89
    Period size: 23  Copynumber: 2.0  Consensus size: 24

        425 CCAGGCCAGA

                                    
        435 CGCGGGCCAGCACATGGCCCAGCG
          1 CGCGGGCCAGCACATGGCCCAGCG

                                    
        459 CGCGGGCCAGC-CATGGCCCAGCG
          1 CGCGGGCCAGCACATGGCCCAGCG

             
        482 C
          1 C

        483 TCAAGCTTGG


Statistics
Matches: 24,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  23   13  0.54
  24   11  0.46

ACGTcount: A:0.15, C:0.44, G:0.38, T:0.04


Consensus pattern (24 bp):   
CGCGGGCCAGCACATGGCCCAGCG

Found at i:1435 original size:28 final size:29

Alignment explanation


    Indices: 1377--1440  Score: 71
    Period size: 28  Copynumber: 2.3  Consensus size: 29

       1367 CTTAGGACAT

                            *   *      * 
       1377 TAAAATTA-CATATTTTCCCTTGGTCGGC
          1 TAAAATTACCATATTTACCCCTGGTCGAC

                                     *   
       1405 TAAAATTACCAT-TTTACCCCTGGTTGAC
          1 TAAAATTACCATATTTACCCCTGGTCGAC

                     
       1433 T-AAATTAC
          1 TAAAATTAC

       1441 AGTTCTGCCC


Statistics
Matches: 31,  Mismatches: 4, Indels: 3
        0.82            0.11        0.08

Matches are distributed among these distances:
  27    7  0.23
  28   21  0.68
  29    3  0.10

ACGTcount: A:0.30, C:0.22, G:0.11, T:0.38


Consensus pattern (29 bp):   
TAAAATTACCATATTTACCCCTGGTCGAC
Done.