Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020654.1 Corchorus olitorius cultivar O-4 contig20687, 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: 3359
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35


Found at i:1251 original size:37 final size:37

Alignment explanation


    Indices: 1201--1275  Score: 150
    Period size: 37  Copynumber: 2.0  Consensus size: 37

       1191 TCCTAACAGG

                                                 
       1201 ATTAGGATTCAGGCGCAGTTTTGGTAGAAAAATCATA
          1 ATTAGGATTCAGGCGCAGTTTTGGTAGAAAAATCATA

                                                 
       1238 ATTAGGATTCAGGCGCAGTTTTGGTAGAAAAATCATA
          1 ATTAGGATTCAGGCGCAGTTTTGGTAGAAAAATCATA

             
       1275 A
          1 A

       1276 CTTTCTTCTC


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  37   38  1.00

ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29


Consensus pattern (37 bp):   
ATTAGGATTCAGGCGCAGTTTTGGTAGAAAAATCATA

Found at i:2705 original size:31 final size:33

Alignment explanation


    Indices: 2639--2714  Score: 111
    Period size: 31  Copynumber: 2.4  Consensus size: 33

       2629 GAATTTTTCT

                           *              *  
       2639 TTTTTGCGTTTTTTCTAAAGAAAAAAAAAATTG
          1 TTTTTGCGTTTTTTCGAAAGAAAAAAAAAAGTG

                                  *          
       2672 TTTTTGCGTTTTTT-GAAA-AACAAAAAAAGTG
          1 TTTTTGCGTTTTTTCGAAAGAAAAAAAAAAGTG

                        
       2703 TTTTTGCGTTTT
          1 TTTTTGCGTTTT

       2715 CCAAAATTAA


Statistics
Matches: 40,  Mismatches: 3, Indels: 2
        0.89            0.07        0.04

Matches are distributed among these distances:
  31   23  0.57
  32    3  0.08
  33   14  0.35

ACGTcount: A:0.33, C:0.07, G:0.14, T:0.46


Consensus pattern (33 bp):   
TTTTTGCGTTTTTTCGAAAGAAAAAAAAAAGTG

Found at i:2727 original size:30 final size:31

Alignment explanation


    Indices: 2639--2729  Score: 94
    Period size: 31  Copynumber: 2.9  Consensus size: 31

       2629 GAATTTTTCT

                           *      *       *  
       2639 TTTTTGCGTTTTTTCTAAAGAAAAAAAAAATTG
          1 TTTTTGCG-TTTTTCCAAA-AACAAAAAAAGTG

                         **                
       2672 TTTTTGCGTTTTTTGAAAAACAAAAAAAGTG
          1 TTTTTGCGTTTTTCCAAAAACAAAAAAAGTG

                               **       
       2703 TTTTTGCG-TTTTCCAAAATTAAAAAAA
          1 TTTTTGCGTTTTTCCAAAAACAAAAAAA

       2730 AAATCTGCGT


Statistics
Matches: 50,  Mismatches: 8, Indels: 3
        0.82            0.13        0.05

Matches are distributed among these distances:
  30   15  0.30
  31   19  0.38
  32    8  0.16
  33    8  0.16

ACGTcount: A:0.40, C:0.08, G:0.12, T:0.41


Consensus pattern (31 bp):   
TTTTTGCGTTTTTCCAAAAACAAAAAAAGTG

Done.