Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000047.1 Corchorus olitorius cultivar O-4 contig00047, 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: 3051
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.30


Found at i:698 original size:9 final size:9

Alignment explanation


    Indices: 686--710  Score: 50
    Period size: 9  Copynumber: 2.8  Consensus size: 9

        676 AAAATTAGAA

                     
        686 AAAAAAAAC
          1 AAAAAAAAC

                     
        695 AAAAAAAAC
          1 AAAAAAAAC

                   
        704 AAAAAAA
          1 AAAAAAA

        711 CATTTATTCG


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   16  1.00

ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00


Consensus pattern (9 bp):   
AAAAAAAAC

Found at i:1450 original size:13 final size:13

Alignment explanation


    Indices: 1434--1460  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

       1424 TTATATAGTG

                         
       1434 ATAAGATAAGATA
          1 ATAAGATAAGATA

                         
       1447 ATAAGATAAGATA
          1 ATAAGATAAGATA

             
       1460 A
          1 A

       1461 ATTATATAAT


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:0.63, C:0.00, G:0.15, T:0.22


Consensus pattern (13 bp):   
ATAAGATAAGATA

Found at i:2030 original size:38 final size:38

Alignment explanation


    Indices: 1979--2053  Score: 150
    Period size: 38  Copynumber: 2.0  Consensus size: 38

       1969 TAGACTATTA

                                                  
       1979 ATCAACTTTTTCAAGTTTTATCTGATGTAATTAGATTG
          1 ATCAACTTTTTCAAGTTTTATCTGATGTAATTAGATTG

                                                 
       2017 ATCAACTTTTTCAAGTTTTATCTGATGTAATTAGATT
          1 ATCAACTTTTTCAAGTTTTATCTGATGTAATTAGATT

       2054 TAGGTTATAT


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  38   37  1.00

ACGTcount: A:0.29, C:0.11, G:0.12, T:0.48


Consensus pattern (38 bp):   
ATCAACTTTTTCAAGTTTTATCTGATGTAATTAGATTG

Found at i:2594 original size:44 final size:42

Alignment explanation


    Indices: 2544--2631  Score: 122
    Period size: 44  Copynumber: 2.0  Consensus size: 42

       2534 AAGCACATCG

                                                 *      
       2544 GACATGGAATGATCCAACAAAACTTTGAATATATGATTAAAAGA
          1 GACATGGAATGATCCAACAAAACTTTG-A-ATATGATCAAAAGA

                      *   *     *                     
       2588 GACATGGAATTATCTAACAAGACTTTGAATATGATCAAAAGA
          1 GACATGGAATGATCCAACAAAACTTTGAATATGATCAAAAGA

              
       2630 GA
          1 GA

       2632 AAGTCCCTGG


Statistics
Matches: 40,  Mismatches: 4, Indels: 2
        0.87            0.09        0.04

Matches are distributed among these distances:
  42   15  0.38
  43    1  0.03
  44   24  0.60

ACGTcount: A:0.47, C:0.11, G:0.17, T:0.25


Consensus pattern (42 bp):   
GACATGGAATGATCCAACAAAACTTTGAATATGATCAAAAGA
Done.