Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018874.1 Corchorus olitorius cultivar O-4 contig18907, 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: 21463
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31


Found at i:14855 original size:15 final size:15

Alignment explanation


    Indices: 14835--14872  Score: 67
    Period size: 15  Copynumber: 2.5  Consensus size: 15

      14825 ACAGAGGTTG

                           
      14835 ACAGAAAGCAATTAA
          1 ACAGAAAGCAATTAA

                           
      14850 ACAGAAAGCAATTAA
          1 ACAGAAAGCAATTAA

                    
      14865 ACTAGAAA
          1 AC-AGAAA

      14873 ACAAAGCAAA


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15   17  0.77
  16    5  0.23

ACGTcount: A:0.61, C:0.13, G:0.13, T:0.13


Consensus pattern (15 bp):   
ACAGAAAGCAATTAA

Found at i:17752 original size:14 final size:15

Alignment explanation


    Indices: 17733--17762  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

      17723 CAATCAAAGC

                           
      17733 AATAAT-CAAGGAAA
          1 AATAATGCAAGGAAA

                           
      17747 AATAATGCAAGGAAA
          1 AATAATGCAAGGAAA

             
      17762 A
          1 A

      17763 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:18157 original size:21 final size:21

Alignment explanation


    Indices: 18114--18162  Score: 62
    Period size: 21  Copynumber: 2.3  Consensus size: 21

      18104 GGCTTGGAAT

                *            **  
      18114 GGTGATGGCACGGGCATGGCC
          1 GGTGGTGGCACGGGCATAACC

                           *     
      18135 GGTGGTGGCACGGGCTTAACC
          1 GGTGGTGGCACGGGCATAACC

                   
      18156 GGTGGTG
          1 GGTGGTG

      18163 TGGCAATCGG


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:18450 original size:54 final size:54

Alignment explanation


    Indices: 18392--18508  Score: 216
    Period size: 54  Copynumber: 2.2  Consensus size: 54

      18382 GTAGCGCGGA

                   *                                              
      18392 TGGCCGGTCGGATGGCGCGGATGAGGTCTAGCATGACCGGGTAGATGGCTCGGG
          1 TGGCCGGGCGGATGGCGCGGATGAGGTCTAGCATGACCGGGTAGATGGCTCGGG

                                         *                        
      18446 TGGCCGGGCGGATGGCGCGGATGAGGTCTGGCATGACCGGGTAGATGGCTCGGG
          1 TGGCCGGGCGGATGGCGCGGATGAGGTCTAGCATGACCGGGTAGATGGCTCGGG

                     
      18500 TGGCCGGGC
          1 TGGCCGGGC

      18509 CATGGCCGGG


Statistics
Matches: 61,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  54   61  1.00

ACGTcount: A:0.13, C:0.21, G:0.49, T:0.17


Consensus pattern (54 bp):   
TGGCCGGGCGGATGGCGCGGATGAGGTCTAGCATGACCGGGTAGATGGCTCGGG
Done.