Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013819.1 Corchorus olitorius cultivar O-4 contig13852, 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: 16680
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31


Found at i:1100 original size:16 final size:15

Alignment explanation


    Indices: 1062--1103  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       1052 ACAGAGGTTG

                   *       
       1062 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                           
       1077 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
       1092 ACTAGAAAACAA
          1 AC-AGAAAACAA

       1104 AACAAAGTAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA

Found at i:4716 original size:22 final size:21

Alignment explanation


    Indices: 4691--4744  Score: 60
    Period size: 19  Copynumber: 2.6  Consensus size: 21

       4681 GAAGTTCGTG

                                  
       4691 TTTGAAGACTTATTGAAGATAA
          1 TTTGAAGA-TTATTGAAGATAA

                               * 
       4713 TTTGAAGA-T-TTGAAGATCA
          1 TTTGAAGATTATTGAAGATAA

                          
       4732 -TTGAAGAATTATT
          1 TTTGAAG-ATTATT

       4745 TCGAGAAGCA


Statistics
Matches: 28,  Mismatches: 1, Indels: 7
        0.78            0.03        0.19

Matches are distributed among these distances:
  18    6  0.21
  19   10  0.36
  20    2  0.07
  21    2  0.07
  22    8  0.29

ACGTcount: A:0.39, C:0.04, G:0.19, T:0.39


Consensus pattern (21 bp):   
TTTGAAGATTATTGAAGATAA

Found at i:16405 original size:31 final size:30

Alignment explanation


    Indices: 16367--16467  Score: 105
    Period size: 31  Copynumber: 3.3  Consensus size: 30

      16357 AAGTACCTAA

                     *                     
      16367 TTAGTCCCTGTATTATAGAAAAAAGATCAAT
          1 TTAGTCCCTCTATTAT-GAAAAAAGATCAAT

                      *     *   ***       
      16398 TTAGTCCCTCCATTATCAAATCTG-TCAAT
          1 TTAGTCCCTCTATTATGAAAAAAGATCAAT

                        *         *        
      16427 TTAGTCCCTCTACTATTGAAAAGAGATCAAT
          1 TTAGTCCCTCTATTA-TGAAAAAAGATCAAT

                      
      16458 TTAGTCCCTC
          1 TTAGTCCCTC

      16468 CGTGAAATGG


Statistics
Matches: 56,  Mismatches: 12, Indels: 4
        0.78            0.17        0.06

Matches are distributed among these distances:
  29   18  0.32
  30    9  0.16
  31   29  0.52

ACGTcount: A:0.33, C:0.22, G:0.11, T:0.35


Consensus pattern (30 bp):   
TTAGTCCCTCTATTATGAAAAAAGATCAAT
Done.