Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010230.1 Corchorus olitorius cultivar O-4 contig10262, 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: 2376
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.37


Found at i:371 original size:1 final size:1

Alignment explanation


    Indices: 365--399  Score: 61
    Period size: 1  Copynumber: 35.0  Consensus size: 1

        355 TTAGTAACGA

                                         *     
        365 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

        400 GCTCCAAGTT


Statistics
Matches: 32,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   1   32  1.00

ACGTcount: A:0.03, C:0.00, G:0.00, T:0.97


Consensus pattern (1 bp):   
T

Found at i:933 original size:6 final size:6

Alignment explanation


    Indices: 922--980  Score: 73
    Period size: 6  Copynumber: 9.8  Consensus size: 6

        912 ATTTCTTATT

                          *           *            *       *       
        922 GGACTC GGACTC AGACTC GGACTT GGACTC GGACCC GGACTT GGACTC
          1 GGACTC GGACTC GGACTC GGACTC GGACTC GGACTC GGACTC GGACTC

                   *    
        970 GGACTC AGACT
          1 GGACTC GGACT

        981 TGAGAGTAGG


Statistics
Matches: 44,  Mismatches: 9, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
   6   44  1.00

ACGTcount: A:0.20, C:0.31, G:0.31, T:0.19


Consensus pattern (6 bp):   
GGACTC

Found at i:949 original size:18 final size:18

Alignment explanation


    Indices: 922--982  Score: 86
    Period size: 18  Copynumber: 3.4  Consensus size: 18

        912 ATTTCTTATT

                 *      *     
        922 GGACTCGGACTCAGACTC
          1 GGACTTGGACTCGGACTC

                            * 
        940 GGACTTGGACTCGGACCC
          1 GGACTTGGACTCGGACTC

                              
        958 GGACTTGGACTCGGACTC
          1 GGACTTGGACTCGGACTC

            *      
        976 AGACTTG
          1 GGACTTG

        983 AGAGTAGGGA


Statistics
Matches: 38,  Mismatches: 5, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   38  1.00

ACGTcount: A:0.20, C:0.30, G:0.31, T:0.20


Consensus pattern (18 bp):   
GGACTTGGACTCGGACTC

Found at i:1594 original size:11 final size:11

Alignment explanation


    Indices: 1566--1596  Score: 55
    Period size: 10  Copynumber: 2.9  Consensus size: 11

       1556 AAAGCTGCTG

                       
       1566 GTATTCTTTAT
          1 GTATTCTTTAT

                       
       1577 GTA-TCTTTAT
          1 GTATTCTTTAT

                      
       1587 GTATTCTTTA
          1 GTATTCTTTA

       1597 ATCCAAATTC


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

Matches are distributed among these distances:
  10   10  0.53
  11    9  0.47

ACGTcount: A:0.19, C:0.10, G:0.10, T:0.61


Consensus pattern (11 bp):   
GTATTCTTTAT
Done.