Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013825.1 Corchorus olitorius cultivar O-4 contig13858, 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: 12311
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33


Found at i:1401 original size:3 final size:3

Alignment explanation


    Indices: 1395--1448  Score: 83
    Period size: 3  Copynumber: 17.7  Consensus size: 3

       1385 TATAATAATA

                                                                         
       1395 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT ATATT TAT
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TA-T TAT

                      
       1442 TA- TAT TA
          1 TAT TAT TA

       1449 AAGTTATACC


Statistics
Matches: 48,  Mismatches: 0, Indels: 6
        0.89            0.00        0.11

Matches are distributed among these distances:
   2    2  0.04
   3   41  0.85
   4    4  0.08
   5    1  0.02

ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65


Consensus pattern (3 bp):   
TAT

Found at i:3805 original size:22 final size:22

Alignment explanation


    Indices: 3780--3826  Score: 58
    Period size: 22  Copynumber: 2.1  Consensus size: 22

       3770 TAACATAATA

                *   *     *       
       3780 AAAGCAAACGAAAACGAAAAAG
          1 AAAGAAAAAGAAAAAGAAAAAG

                                * 
       3802 AAAGAAAAAGAAAAAGAAAACG
          1 AAAGAAAAAGAAAAAGAAAAAG

               
       3824 AAA
          1 AAA

       3827 ACATGTCAAA


Statistics
Matches: 21,  Mismatches: 4, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  22   21  1.00

ACGTcount: A:0.74, C:0.09, G:0.17, T:0.00


Consensus pattern (22 bp):   
AAAGAAAAAGAAAAAGAAAAAG

Found at i:3814 original size:16 final size:17

Alignment explanation


    Indices: 3779--3827  Score: 64
    Period size: 16  Copynumber: 2.8  Consensus size: 17

       3769 ATAACATAAT

                           *  
       3779 AAAAGCAAACGAAAACGA
          1 AAAAG-AAACGAAAAAGA

                             
       3797 AAAAGAAA-GAAAAAGA
          1 AAAAGAAACGAAAAAGA

                           
       3813 AAAAGAAAACGAAAA
          1 AAAAG-AAACGAAAA

       3828 CATGTCAAAC


Statistics
Matches: 28,  Mismatches: 1, Indels: 4
        0.85            0.03        0.12

Matches are distributed among these distances:
  16   12  0.43
  17    6  0.21
  18   10  0.36

ACGTcount: A:0.76, C:0.08, G:0.16, T:0.00


Consensus pattern (17 bp):   
AAAAGAAACGAAAAAGA
Done.