Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020599.1 Corchorus olitorius cultivar O-4 contig20632, 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: 4033
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31


Found at i:1670 original size:22 final size:21

Alignment explanation


    Indices: 1645--1721  Score: 82
    Period size: 22  Copynumber: 3.6  Consensus size: 21

       1635 TATTCTTATG

                                 *
       1645 AAATTTTGATAATCACTCTATT
          1 AAATTTTGATAATCAC-CTATA

                        *        *
       1667 AAATTTTGATAACCACCATATG
          1 AAATTTTGATAATCACC-TATA

             *           *       
       1689 AGATTTTGATAATTACCTATA
          1 AAATTTTGATAATCACCTATA

                 *      
       1710 AAATTGTGATAA
          1 AAATTTTGATAA

       1722 ACTCCATAAG


Statistics
Matches: 46,  Mismatches: 8, Indels: 3
        0.81            0.14        0.05

Matches are distributed among these distances:
  21   14  0.30
  22   32  0.70

ACGTcount: A:0.40, C:0.12, G:0.09, T:0.39


Consensus pattern (21 bp):   
AAATTTTGATAATCACCTATA

Found at i:1729 original size:43 final size:44

Alignment explanation


    Indices: 1641--1743  Score: 127
    Period size: 43  Copynumber: 2.4  Consensus size: 44

       1631 TGAATATTCT

                                     *     *      *     
       1641 TATGAAATTTTGATAATCACTCTATTAAATTTTGATAACCACCA
          1 TATGAAATTTTGATAATCACTCTATAAAATTGTGATAAACACCA

                 *           *                      *   
       1685 TATGAGATTTTGATAATTAC-CTATAAAATTGTGATAAACTCCA
          1 TATGAAATTTTGATAATCACTCTATAAAATTGTGATAAACACCA

              *    *        
       1728 TAAGAAACTTTGATAA
          1 TATGAAATTTTGATAA

       1744 CCTAACTATG


Statistics
Matches: 50,  Mismatches: 9, Indels: 1
        0.83            0.15        0.02

Matches are distributed among these distances:
  43   32  0.64
  44   18  0.36

ACGTcount: A:0.41, C:0.13, G:0.10, T:0.37


Consensus pattern (44 bp):   
TATGAAATTTTGATAATCACTCTATAAAATTGTGATAAACACCA

Found at i:1797 original size:20 final size:21

Alignment explanation


    Indices: 1755--1811  Score: 62
    Period size: 20  Copynumber: 2.7  Consensus size: 21

       1745 CTAACTATGA

                  *    *          
       1755 AATTTTAATAAACTTTCCAATG
          1 AATTTTGATAATC-TTCCAATG

                             *   
       1777 AATTTTG-TAATCTTCCTATG
          1 AATTTTGATAATCTTCCAATG

             *             
       1797 ATTTTTGATAATCTT
          1 AATTTTGATAATCTT

       1812 TGTGTGAGAT


Statistics
Matches: 30,  Mismatches: 4, Indels: 3
        0.81            0.11        0.08

Matches are distributed among these distances:
  20   13  0.43
  21   11  0.37
  22    6  0.20

ACGTcount: A:0.32, C:0.12, G:0.07, T:0.49


Consensus pattern (21 bp):   
AATTTTGATAATCTTCCAATG

Done.