Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023403.1 Corchorus olitorius cultivar O-4 contig23436, 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: 7726
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31


Found at i:233 original size:10 final size:10

Alignment explanation


    Indices: 212--240  Score: 51
    Period size: 10  Copynumber: 3.0  Consensus size: 10

        202 TTAAAAAAGG

                      
        212 AAATAAAA-T
          1 AAATAAAATT

                      
        221 AAATAAAATT
          1 AAATAAAATT

                      
        231 AAATAAAATT
          1 AAATAAAATT

        241 GTTAATATGG


Statistics
Matches: 19,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
   9    8  0.42
  10   11  0.58

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


Consensus pattern (10 bp):   
AAATAAAATT

Found at i:1515 original size:19 final size:19

Alignment explanation


    Indices: 1493--1549  Score: 64
    Period size: 19  Copynumber: 3.0  Consensus size: 19

       1483 ATAAATGAAT

                               
       1493 ACATTAATAAATAATAATA
          1 ACATTAATAAATAATAATA

                               *
       1512 ACATTAAT-AATAA-ATATT
          1 ACATTAATAAATAATA-ATA

                *               
       1530 ACGACTAATAAATAATAATA
          1 AC-ATTAATAAATAATAATA

       1550 CCACTTGTTG


Statistics
Matches: 31,  Mismatches: 3, Indels: 7
        0.76            0.07        0.17

Matches are distributed among these distances:
  17    1  0.03
  18    9  0.29
  19   13  0.42
  20    7  0.23
  21    1  0.03

ACGTcount: A:0.60, C:0.07, G:0.02, T:0.32


Consensus pattern (19 bp):   
ACATTAATAAATAATAATA

Found at i:2937 original size:10 final size:10

Alignment explanation


    Indices: 2922--2949  Score: 56
    Period size: 10  Copynumber: 2.8  Consensus size: 10

       2912 AATTAGAAAT

                      
       2922 GTTCTTGAGC
          1 GTTCTTGAGC

                      
       2932 GTTCTTGAGC
          1 GTTCTTGAGC

                    
       2942 GTTCTTGA
          1 GTTCTTGA

       2950 AGATTGCAGA


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   18  1.00

ACGTcount: A:0.11, C:0.18, G:0.29, T:0.43


Consensus pattern (10 bp):   
GTTCTTGAGC
Done.