Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024409.1 Corchorus olitorius cultivar O-4 contig24442, 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: 8440
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.35


Found at i:3346 original size:2 final size:2

Alignment explanation


    Indices: 3339--3363  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       3329 ATTTAAAACC

                                                 
       3339 AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT A

       3364 CTAGTTAATT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:3440 original size:58 final size:58

Alignment explanation


    Indices: 3316--3429  Score: 183
    Period size: 58  Copynumber: 1.9  Consensus size: 58

       3306 AACATGAGGC

                                                      * *      **     
       3316 AACATACTAGTTAATTTAAAACCATATATATATATATATATATATATACTAGTTAATT
          1 AACATACTAGTTAATTTAAAACCATATATATATATATATATACACATACTACATAATT

                                                                    
       3374 AACATACTAGTTAATTTAAAACCATATATATATATATATATACACATACATACATA
          1 AACATACTAGTTAATTTAAAACCATATATATATATATATATACACATAC-TACATA

       3430 CATACATACT


Statistics
Matches: 51,  Mismatches: 4, Indels: 1
        0.91            0.07        0.02

Matches are distributed among these distances:
  58   47  0.92
  59    4  0.08

ACGTcount: A:0.48, C:0.11, G:0.03, T:0.38


Consensus pattern (58 bp):   
AACATACTAGTTAATTTAAAACCATATATATATATATATATACACATACTACATAATT

Found at i:6569 original size:24 final size:26

Alignment explanation


    Indices: 6535--6586  Score: 72
    Period size: 25  Copynumber: 2.1  Consensus size: 26

       6525 ATTGGAGTAT

                                      
       6535 TTATTTATCTTG-TTACTTAATTTTA
          1 TTATTTATCTTGTTTACTTAATTTTA

                            *   *     
       6560 TTATTT-TCTTGTTTATTTATTTTTA
          1 TTATTTATCTTGTTTACTTAATTTTA

              
       6585 TT
          1 TT

       6587 GTTCCTTATT


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  24    5  0.21
  25   19  0.79

ACGTcount: A:0.19, C:0.06, G:0.04, T:0.71


Consensus pattern (26 bp):   
TTATTTATCTTGTTTACTTAATTTTA
Done.