Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019554.1 Corchorus olitorius cultivar O-4 contig19587, 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: 7916
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32


Found at i:1546 original size:13 final size:13

Alignment explanation


    Indices: 1528--1552  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       1518 TTATCAGTTC

                         
       1528 TAAATATTATTTA
          1 TAAATATTATTTA

                        
       1541 TAAATATTATTT
          1 TAAATATTATTT

       1553 GGAATTTCAA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56


Consensus pattern (13 bp):   
TAAATATTATTTA

Found at i:3495 original size:55 final size:55

Alignment explanation


    Indices: 3433--3551  Score: 220
    Period size: 55  Copynumber: 2.2  Consensus size: 55

       3423 TGCGCGCTAG

                                                                   
       3433 CTGGCCCAGTGCGCTGGCCATGCTGACCAGGCCAGCCTAGCGGACCTGGCACGCA
          1 CTGGCCCAGTGCGCTGGCCATGCTGACCAGGCCAGCCTAGCGGACCTGGCACGCA

                                                       *           
       3488 CTGGCCCAGTGCGCTGGCCATGCTGACCAGGCCAGCCTAGCGGGCCTGGCACGCA
          1 CTGGCCCAGTGCGCTGGCCATGCTGACCAGGCCAGCCTAGCGGACCTGGCACGCA

                *    
       3543 CTGGGCCAG
          1 CTGGCCCAG

       3552 CTAGCGCGCT


Statistics
Matches: 62,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  55   62  1.00

ACGTcount: A:0.15, C:0.38, G:0.34, T:0.13


Consensus pattern (55 bp):   
CTGGCCCAGTGCGCTGGCCATGCTGACCAGGCCAGCCTAGCGGACCTGGCACGCA

Found at i:3565 original size:17 final size:17

Alignment explanation


    Indices: 3543--3576  Score: 59
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       3533 CTGGCACGCA

                             
       3543 CTGGGCCAGCTAGCGCG
          1 CTGGGCCAGCTAGCGCG

                       *     
       3560 CTGGGCCAGCTGGCGCG
          1 CTGGGCCAGCTAGCGCG

       3577 GGCCTGAGCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.09, C:0.35, G:0.44, T:0.12


Consensus pattern (17 bp):   
CTGGGCCAGCTAGCGCG

Found at i:3640 original size:23 final size:23

Alignment explanation


    Indices: 3609--3654  Score: 67
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       3599 TGGGCCCAAC

                                    
       3609 AAAAAAAAAG-AAGACAAGAAAAG
          1 AAAAAAAAAGAAAGA-AAGAAAAG

                *                  
       3632 AAAAGAAAAGAAAGAAAGAAAAG
          1 AAAAAAAAAGAAAGAAAGAAAAG

       3655 GGACTTGGCC


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  23   17  0.81
  24    4  0.19

ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00


Consensus pattern (23 bp):   
AAAAAAAAAGAAAGAAAGAAAAG
Done.