Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015265.1 Corchorus olitorius cultivar O-4 contig15298, 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: 19871
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30


Found at i:3225 original size:3 final size:3

Alignment explanation


    Indices: 3217--3244  Score: 56
    Period size: 3  Copynumber: 9.3  Consensus size: 3

       3207 CTCGACACTG

                                                 
       3217 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
          1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C

       3245 CTATCTTTGC


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   25  1.00

ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64


Consensus pattern (3 bp):   
CTT

Found at i:4597 original size:15 final size:15

Alignment explanation


    Indices: 4577--4606  Score: 60
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       4567 CAAATTTGAC

                           
       4577 ATACAAGTTTTATAT
          1 ATACAAGTTTTATAT

                           
       4592 ATACAAGTTTTATAT
          1 ATACAAGTTTTATAT

       4607 GATTAATTAA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47


Consensus pattern (15 bp):   
ATACAAGTTTTATAT

Found at i:8499 original size:14 final size:13

Alignment explanation


    Indices: 8469--8502  Score: 52
    Period size: 13  Copynumber: 2.6  Consensus size: 13

       8459 AGCACTCTTG

                         
       8469 AAAAA-AAAAAGA
          1 AAAAAGAAAAAGA

                         
       8481 AAAAAGAAAAAGA
          1 AAAAAGAAAAAGA

                     
       8494 ATAAAAGAA
          1 A-AAAAGAA

       8503 TCATAGTAGG


Statistics
Matches: 20,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  12    5  0.25
  13    8  0.40
  14    7  0.35

ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03


Consensus pattern (13 bp):   
AAAAAGAAAAAGA

Found at i:12586 original size:14 final size:14

Alignment explanation


    Indices: 12569--12598  Score: 51
    Period size: 14  Copynumber: 2.1  Consensus size: 14

      12559 TACCCTTGAT

                          
      12569 CCTTGAGCCTTTAG
          1 CCTTGAGCCTTTAG

                *         
      12583 CCTTTAGCCTTTAG
          1 CCTTGAGCCTTTAG

              
      12597 CC
          1 CC

      12599 AACGAGAGAG


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

Matches are distributed among these distances:
  14   15  1.00

ACGTcount: A:0.13, C:0.33, G:0.17, T:0.37


Consensus pattern (14 bp):   
CCTTGAGCCTTTAG

Found at i:16488 original size:15 final size:15

Alignment explanation


    Indices: 16468--16504  Score: 56
    Period size: 15  Copynumber: 2.5  Consensus size: 15

      16458 CCTTCAAATT

                       *   
      16468 TTCTTCATTAGTTTG
          1 TTCTTCATTAGCTTG

                           
      16483 TTCTTCATTAGCTTG
          1 TTCTTCATTAGCTTG

            *      
      16498 ATCTTCA
          1 TTCTTCA

      16505 CCAAGAGGGC


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  15   20  1.00

ACGTcount: A:0.16, C:0.19, G:0.11, T:0.54


Consensus pattern (15 bp):   
TTCTTCATTAGCTTG
Done.