Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023095.1 Corchorus olitorius cultivar O-4 contig23128, 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: 5047
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39


Found at i:873 original size:51 final size:50

Alignment explanation


    Indices: 772--873  Score: 127
    Period size: 51  Copynumber: 2.0  Consensus size: 50

        762 GTTCTTCATA

                                                     * **     
        772 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCTTTTAGTGT
          1 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT

                                            *                    
        822 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGT
          1 TTTTC-CTTGTTT-AGATCTTGTCTCCGGACAAACAAACACTCGTACA-GTGT

             
        873 T
          1 T

        874 CTTCATTCAG


Statistics
Matches: 45,  Mismatches: 4, Indels: 5
        0.83            0.07        0.09

Matches are distributed among these distances:
  50    7  0.16
  51   37  0.82
  52    1  0.02

ACGTcount: A:0.22, C:0.24, G:0.14, T:0.41


Consensus pattern (50 bp):   
TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT

Found at i:1852 original size:2 final size:2

Alignment explanation


    Indices: 1845--1872  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

       1835 CAATATAATC

                                                     
       1845 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

       1873 TAATAACAAT


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:4476 original size:2 final size:2

Alignment explanation


    Indices: 4471--4502  Score: 55
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       4461 TTTTTTTATG

                                                           
       4471 AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A

       4503 CTACATATTA


Statistics
Matches: 29,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   2   27  0.93
   3    2  0.07

ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47


Consensus pattern (2 bp):   
AT

Done.