Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017302.1 Corchorus olitorius cultivar O-4 contig17335, 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: 4896
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30


Found at i:133 original size:25 final size:24

Alignment explanation


    Indices: 96--142  Score: 69
    Period size: 26  Copynumber: 1.9  Consensus size: 24

         86 CTAGAAAATT

                                      
         96 TGAAAAACTTTGATGCATGAGATGGA
          1 TGAAAAACTTTGATG-AT-AGATGGA

                                  
        122 TGAAAAAC-TTGATGATAGATG
          1 TGAAAAACTTTGATGATAGATG

        143 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    2  0.10
  25    6  0.29
  26    8  0.38

ACGTcount: A:0.40, C:0.06, G:0.26, T:0.28


Consensus pattern (24 bp):   
TGAAAAACTTTGATGATAGATGGA

Found at i:1035 original size:21 final size:21

Alignment explanation


    Indices: 1011--1081  Score: 117
    Period size: 21  Copynumber: 3.4  Consensus size: 21

       1001 CTTAGGCAAT

                         *       
       1011 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                 
       1032 TCCAATGAGCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                  
       1053 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                    
       1074 TCCAATGA
          1 TCCAATGA

       1082 TCTCCTAGCA


Statistics
Matches: 48,  Mismatches: 1, Indels: 2
        0.94            0.02        0.04

Matches are distributed among these distances:
  20    3  0.06
  21   45  0.94

ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACCTTC

Found at i:4540 original size:13 final size:13

Alignment explanation


    Indices: 4522--4548  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

       4512 GAAAAACTTG

                         
       4522 ATGATAGATGAAT
          1 ATGATAGATGAAT

                         
       4535 ATGATAGATGAAT
          1 ATGATAGATGAAT

             
       4548 A
          1 A

       4549 GAAGGATAGA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.48, C:0.00, G:0.22, T:0.30


Consensus pattern (13 bp):   
ATGATAGATGAAT
Done.