Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000514.1 Corchorus olitorius cultivar O-4 contig00514, 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: 4870
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34


Found at i:1141 original size:22 final size:22

Alignment explanation


    Indices: 1097--1141  Score: 56
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       1087 AGGAAATTCC

                             **   
       1097 GGTGGCGGTGGCAGTTATGGTG
          1 GGTGGCGGTGGCAGTTACAGTG

                                   
       1119 GGTGGCGGTGGC-GTTGACAGTG
          1 GGTGGCGGTGGCAGTT-ACAGTG

             
       1141 G
          1 G

       1142 TTCCATGGTG


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  21    3  0.15
  22   17  0.85

ACGTcount: A:0.09, C:0.11, G:0.56, T:0.24


Consensus pattern (22 bp):   
GGTGGCGGTGGCAGTTACAGTG

Found at i:2087 original size:13 final size:14

Alignment explanation


    Indices: 2042--2094  Score: 63
    Period size: 14  Copynumber: 3.6  Consensus size: 14

       2032 GCAGATCGGC

                       *   
       2042 TTTGTTTATTTGGTT
          1 TTTGTTT-TTTTGTT

                            
       2057 GTTTGTTTGTTTTG-T
          1 -TTTGTTT-TTTTGTT

                          
       2072 TTTGTTTTTTTGTT
          1 TTTGTTTTTTTGTT

                     
       2086 TTTGTTTTT
          1 TTTGTTTTT

       2095 ATTTTCTTTT


Statistics
Matches: 34,  Mismatches: 2, Indels: 4
        0.85            0.05        0.10

Matches are distributed among these distances:
  13    5  0.15
  14   17  0.50
  15    1  0.03
  16   11  0.32

ACGTcount: A:0.02, C:0.00, G:0.19, T:0.79


Consensus pattern (14 bp):   
TTTGTTTTTTTGTT

Found at i:2855 original size:3 final size:3

Alignment explanation


    Indices: 2841--2872  Score: 55
    Period size: 3  Copynumber: 10.7  Consensus size: 3

       2831 GATTATATAA

                  *                                   
       2841 AAG AAA AAG AAG AAG AAG AAG AAG AAG AAG AA
          1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA

       2873 AAAAGAAAAT


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   3   27  1.00

ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00


Consensus pattern (3 bp):   
AAG

Found at i:4825 original size:19 final size:20

Alignment explanation


    Indices: 4801--4845  Score: 58
    Period size: 19  Copynumber: 2.4  Consensus size: 20

       4791 ATCAATTACT

                       *        
       4801 TTTTTTACT-TGATTTATTA
          1 TTTTTTACTCTAATTTATTA

                            *   
       4820 TTTTTT-CTCTAATTTTTTA
          1 TTTTTTACTCTAATTTATTA

                   
       4839 TTTTTTA
          1 TTTTTTA

       4846 TTCTTTTCTT


Statistics
Matches: 22,  Mismatches: 2, Indels: 3
        0.81            0.07        0.11

Matches are distributed among these distances:
  18    2  0.09
  19   20  0.91

ACGTcount: A:0.18, C:0.07, G:0.02, T:0.73


Consensus pattern (20 bp):   
TTTTTTACTCTAATTTATTA
Done.