Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014661.1 Corchorus olitorius cultivar O-4 contig14694, 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: 20732
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:530 original size:2 final size:2

Alignment explanation


    Indices: 518--555  Score: 53
    Period size: 2  Copynumber: 20.0  Consensus size: 2

        508 ACGATGTATG

                                                 *                     
        518 AT AT A- AT AT AT AT AT AT AT AT AT AC AT AT AT AT -T AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

        556 CCATTTTCTT


Statistics
Matches: 32,  Mismatches: 2, Indels: 4
        0.84            0.05        0.11

Matches are distributed among these distances:
   1    2  0.06
   2   30  0.94

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


Consensus pattern (2 bp):   
AT

Found at i:1506 original size:32 final size:32

Alignment explanation


    Indices: 1443--1509  Score: 84
    Period size: 32  Copynumber: 2.1  Consensus size: 32

       1433 GGGCTTAATC

                              *   *         
       1443 ATTCATATAGTTTATTTTTTTCTACATAATTA
          1 ATTCATATAGTTTATTTTATTCAACATAATTA

                                              
       1475 ATTCATATAGTTTATTTTAATT-AAC-TAAATTA
          1 ATTCATATAGTTTATTTT-ATTCAACAT-AATTA

               
       1507 ATT
          1 ATT

       1510 AAGGTAAATT


Statistics
Matches: 31,  Mismatches: 2, Indels: 4
        0.84            0.05        0.11

Matches are distributed among these distances:
  31    1  0.03
  32   28  0.90
  33    2  0.06

ACGTcount: A:0.36, C:0.07, G:0.03, T:0.54


Consensus pattern (32 bp):   
ATTCATATAGTTTATTTTATTCAACATAATTA

Found at i:2987 original size:7 final size:7

Alignment explanation


    Indices: 2975--2999  Score: 50
    Period size: 7  Copynumber: 3.6  Consensus size: 7

       2965 TGGCCATGCC

                   
       2975 ACTTCCA
          1 ACTTCCA

                   
       2982 ACTTCCA
          1 ACTTCCA

                   
       2989 ACTTCCA
          1 ACTTCCA

                
       2996 ACTT
          1 ACTT

       3000 GCATAATGGG


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   18  1.00

ACGTcount: A:0.28, C:0.40, G:0.00, T:0.32


Consensus pattern (7 bp):   
ACTTCCA

Found at i:20567 original size:2 final size:2

Alignment explanation


    Indices: 20560--20594  Score: 63
    Period size: 2  Copynumber: 18.0  Consensus size: 2

      20550 TTATTATTAT

                                                                 
      20560 TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      20595 AACAAACAAT


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

Matches are distributed among these distances:
   1    1  0.03
   2   31  0.97

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
TA

Done.