Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023673.1 Corchorus olitorius cultivar O-4 contig23706, 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: 15506
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31


Found at i:103 original size:16 final size:15

Alignment explanation


    Indices: 65--106  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

         55 ACAGAGGTTG

                   *       
         65 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                           
         80 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
         95 ACTAGAAAACAA
          1 AC-AGAAAACAA

        107 AGCAAAGTAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA

Found at i:3408 original size:21 final size:21

Alignment explanation


    Indices: 3365--3413  Score: 62
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       3355 GGCACTAAAT

                *            **  
       3365 GGTGATGGCACGGGCATGGCC
          1 GGTGGTGGCACGGGCATAACC

                           *     
       3386 GGTGGTGGCACGGGCTTAACC
          1 GGTGGTGGCACGGGCATAACC

                   
       3407 GGTGGTG
          1 GGTGGTG

       3414 TCATGGTGAA


Statistics
Matches: 24,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  21   24  1.00

ACGTcount: A:0.12, C:0.20, G:0.49, T:0.18


Consensus pattern (21 bp):   
GGTGGTGGCACGGGCATAACC

Found at i:6472 original size:16 final size:15

Alignment explanation


    Indices: 6434--6475  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       6424 ACAGAGGTTG

                   *       
       6434 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                           
       6449 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
       6464 ACTAGAAAACAA
          1 AC-AGAAAACAA

       6476 AGCAAAGTAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA
Done.