Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018242.1 Corchorus olitorius cultivar O-4 contig18275, 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: 6133
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32


Found at i:545 original size:16 final size:15

Alignment explanation


    Indices: 507--548  Score: 75
    Period size: 15  Copynumber: 2.7  Consensus size: 15

        497 ACAGAGGTTG

                           
        507 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                           
        522 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
        537 ACTAGAAAACAA
          1 AC-AGAAAACAA

        549 AACAAAGTAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15   17  0.65
  16    9  0.35

ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA

Found at i:3412 original size:14 final size:15

Alignment explanation


    Indices: 3393--3422  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       3383 CAATTAAAGC

                           
       3393 AATAAT-CAAGGAAA
          1 AATAATGCAAGGAAA

                           
       3407 AATAATGCAAGGAAA
          1 AATAATGCAAGGAAA

             
       3422 A
          1 A

       3423 TTAAAGAGAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    6  0.40
  15    9  0.60

ACGTcount: A:0.63, C:0.07, G:0.17, T:0.13


Consensus pattern (15 bp):   
AATAATGCAAGGAAA

Found at i:3820 original size:22 final size:21

Alignment explanation


    Indices: 3778--3820  Score: 59
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       3768 TTGGAATGGC

                       *         
       3778 GATGGCACGGGCATGGCCGGT
          1 GATGGCACGGGAATGGCCGGT

                             *    
       3799 GATGGCACGGTGAATGGGCGGT
          1 GATGGCACGG-GAATGGCCGGT

       3821 AATGACTTGG


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  21   10  0.53
  22    9  0.47

ACGTcount: A:0.16, C:0.19, G:0.49, T:0.16


Consensus pattern (21 bp):   
GATGGCACGGGAATGGCCGGT
Done.