Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018865.1 Corchorus olitorius cultivar O-4 contig18898, 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: 3989
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.31


Found at i:2458 original size:25 final size:24

Alignment explanation


    Indices: 2421--2467  Score: 69
    Period size: 26  Copynumber: 1.9  Consensus size: 24

       2411 CTAGAAAATT

                                      
       2421 TGAAAAACTTTGATGGATGAGATGGA
          1 TGAAAAACTTTGAT-GAT-AGATGGA

                                  
       2447 TGAAAAAC-TTGATGATAGATG
          1 TGAAAAACTTTGATGATAGATG

       2468 AATAGAAGGA


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  23    5  0.24
  24    3  0.14
  25    5  0.24
  26    8  0.38

ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28


Consensus pattern (24 bp):   
TGAAAAACTTTGATGATAGATGGA

Found at i:3330 original size:21 final size:21

Alignment explanation


    Indices: 3306--3481  Score: 291
    Period size: 21  Copynumber: 8.4  Consensus size: 21

       3296 CTTAGGCAAT

                         *       
       3306 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                              *  
       3327 TCCAATGAGCTTGGAACCATC
          1 TCCAATGAGCTTGGAACCTTC

                                 
       3348 TCCAATGAGCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                 
       3369 TCCAATGAGCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

               *           *     
       3390 TCCTATGAGCTTGGAGCCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *            
       3411 TCCAATGACCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                 
       3432 TCCAATGAGCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                  
       3453 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                    
       3474 TCCAATGA
          1 TCCAATGA

       3482 TCTCCTAGCA


Statistics
Matches: 145,  Mismatches: 9, Indels: 2
        0.93            0.06        0.01

Matches are distributed among these distances:
  20    3  0.02
  21  142  0.98

ACGTcount: A:0.24, C:0.28, G:0.19, T:0.28


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACCTTC

Done.