Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019926.1 Corchorus olitorius cultivar O-4 contig19959, 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: 9337
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36


Found at i:1157 original size:16 final size:16

Alignment explanation


    Indices: 1132--1165  Score: 52
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       1122 GTTGCTTAAT

                            
       1132 TTTATTATTTTT-TTG
          1 TTTATTATTTTTATTG

                             
       1147 TTTATTTATTTTTATTG
          1 TTTA-TTATTTTTATTG

              
       1164 TT
          1 TT

       1166 CTCTCTATTC


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  15    4  0.24
  16    8  0.47
  17    5  0.29

ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79


Consensus pattern (16 bp):   
TTTATTATTTTTATTG

Found at i:2019 original size:22 final size:22

Alignment explanation


    Indices: 1991--2036  Score: 67
    Period size: 22  Copynumber: 2.1  Consensus size: 22

       1981 AAAATCTCCT

                                   
       1991 AATTCAACC-TCTGGAGAGGTCG
          1 AATTCAACCTTC-GGAGAGGTCG

                         *        
       2013 AATTCAACCTTCGTAGAGGTCG
          1 AATTCAACCTTCGGAGAGGTCG

              
       2035 AA
          1 AA

       2037 ACAACAACTT


Statistics
Matches: 22,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  22   20  0.91
  23    2  0.09

ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24


Consensus pattern (22 bp):   
AATTCAACCTTCGGAGAGGTCG

Found at i:2751 original size:21 final size:21

Alignment explanation


    Indices: 2713--2781  Score: 66
    Period size: 21  Copynumber: 3.2  Consensus size: 21

       2703 GCGGCAAGGC

                         *       
       2713 CCCCTTGACGAGAACGGGGAG
          1 CCCCTTGACGAGAGCGGGGAG

                      **      *   
       2734 CCCCTTGACGCCAGCGGGAAGG
          1 CCCCTTGACGAGAGCGGGGA-G

              *        *          
       2756 TCACCTTGACGTGAGCGGGGAG
          1 -CCCCTTGACGAGAGCGGGGAG

                
       2778 CCCC
          1 CCCC

       2782 AGATCCTTCG


Statistics
Matches: 37,  Mismatches: 9, Indels: 4
        0.74            0.18        0.08

Matches are distributed among these distances:
  21   19  0.51
  22    2  0.05
  23   16  0.43

ACGTcount: A:0.19, C:0.33, G:0.36, T:0.12


Consensus pattern (21 bp):   
CCCCTTGACGAGAGCGGGGAG

Found at i:5559 original size:24 final size:25

Alignment explanation


    Indices: 5513--5560  Score: 62
    Period size: 24  Copynumber: 2.0  Consensus size: 25

       5503 ATTGGAGTAT

                           *         
       5513 TTATTTATCTTGTTGCTTAATTTTA
          1 TTATTTATCTTGTTGATTAATTTTA

                          *   *     
       5538 TTATTT-TCTTGTTTATTTATTTT
          1 TTATTTATCTTGTTGATTAATTTT

       5561 TATTGTTCTC


Statistics
Matches: 20,  Mismatches: 3, Indels: 1
        0.83            0.12        0.04

Matches are distributed among these distances:
  24   14  0.70
  25    6  0.30

ACGTcount: A:0.17, C:0.06, G:0.06, T:0.71


Consensus pattern (25 bp):   
TTATTTATCTTGTTGATTAATTTTA
Done.