Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012509.1 Corchorus olitorius cultivar O-4 contig12542, 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: 10377
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32


Found at i:648 original size:27 final size:27

Alignment explanation


    Indices: 570--641  Score: 126
    Period size: 27  Copynumber: 2.7  Consensus size: 27

        560 TGTCAACTTT

                     *                 
        570 AAAATGACCGAAATGCCCCTGAATGTA
          1 AAAATGACCAAAATGCCCCTGAATGTA

                          *            
        597 AAAATGACCAAAATACCCCTGAATGTA
          1 AAAATGACCAAAATGCCCCTGAATGTA

                              
        624 AAAATGACCAAAATGCCC
          1 AAAATGACCAAAATGCCC

        642 TTAAATGACC


Statistics
Matches: 42,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  27   42  1.00

ACGTcount: A:0.46, C:0.24, G:0.14, T:0.17


Consensus pattern (27 bp):   
AAAATGACCAAAATGCCCCTGAATGTA

Found at i:6974 original size:26 final size:25

Alignment explanation


    Indices: 6928--6979  Score: 59
    Period size: 26  Copynumber: 2.0  Consensus size: 25

       6918 GTTTCTAAGC

                                 *   
       6928 AAGCATTAAACAAAAAATTCAGTAT
          1 AAGCATTAAACAAAAAATTCAATAT

                         * * *        
       6953 AAGCAATTAAACACATACTTCAATAT
          1 AAGC-ATTAAACAAAAAATTCAATAT

             
       6979 A
          1 A

       6980 TAATTATATA


Statistics
Matches: 22,  Mismatches: 4, Indels: 1
        0.81            0.15        0.04

Matches are distributed among these distances:
  25    4  0.18
  26   18  0.82

ACGTcount: A:0.54, C:0.15, G:0.06, T:0.25


Consensus pattern (25 bp):   
AAGCATTAAACAAAAAATTCAATAT

Found at i:8401 original size:28 final size:27

Alignment explanation


    Indices: 8308--8404  Score: 113
    Period size: 28  Copynumber: 3.5  Consensus size: 27

       8298 ATCTAAGGGA

                                         
       8308 ATTTTGGGTCATTTTCAAAATCCAGGGGC
          1 ATTTT-GGTCATTTTC-AAATCCAGGGGC

                            *  *      *
       8337 ATTTTGGTCATTTTCATATTCAGGGGT
          1 ATTTTGGTCATTTTCAAATCCAGGGGC

                 *           *          
       8364 ATTTTAGTCATTTTGCACATCCAGGGGC
          1 ATTTTGGTCATTTT-CAAATCCAGGGGC

               *         
       8392 ATTGTGGTCATTT
          1 ATTTTGGTCATTT

       8405 CTACTCCATT


Statistics
Matches: 58,  Mismatches: 9, Indels: 3
        0.83            0.13        0.04

Matches are distributed among these distances:
  27   22  0.38
  28   31  0.53
  29    5  0.09

ACGTcount: A:0.21, C:0.15, G:0.23, T:0.41


Consensus pattern (27 bp):   
ATTTTGGTCATTTTCAAATCCAGGGGC
Done.