Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012153.1 Corchorus olitorius cultivar O-4 contig12186, 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: 6795
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33


Found at i:3502 original size:12 final size:12

Alignment explanation


    Indices: 3485--3509  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

       3475 CAACCTATAA

                        
       3485 ATATAAGACAAT
          1 ATATAAGACAAT

                        
       3497 ATATAAGACAAT
          1 ATATAAGACAAT

             
       3509 A
          1 A

       3510 CATATAGAAA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.60, C:0.08, G:0.08, T:0.24


Consensus pattern (12 bp):   
ATATAAGACAAT

Found at i:4557 original size:18 final size:17

Alignment explanation


    Indices: 4534--4578  Score: 56
    Period size: 16  Copynumber: 2.6  Consensus size: 17

       4524 ACCTGATGAA

                            * 
       4534 AACAAAAGAATGGAGAGC
          1 AACAAAAGAAT-GAGACC

                       *     
       4552 AACAAAAG-ATTAGACC
          1 AACAAAAGAATGAGACC

                       
       4568 AACAAAAGAAT
          1 AACAAAAGAAT

       4579 TTATATTGGA


Statistics
Matches: 24,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  16   12  0.50
  17    4  0.17
  18    8  0.33

ACGTcount: A:0.60, C:0.13, G:0.18, T:0.09


Consensus pattern (17 bp):   
AACAAAAGAATGAGACC

Found at i:6131 original size:23 final size:23

Alignment explanation


    Indices: 6102--6155  Score: 90
    Period size: 23  Copynumber: 2.3  Consensus size: 23

       6092 TGGAGCAAAA

                                   
       6102 GAATATAACGTTAATATTCAATG
          1 GAATATAACGTTAATATTCAATG

             *                    *
       6125 GTATATAACGTTAATATTCAATT
          1 GAATATAACGTTAATATTCAATG

                    
       6148 GAATATAA
          1 GAATATAA

       6156 TTGAAATTAA


Statistics
Matches: 28,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  23   28  1.00

ACGTcount: A:0.44, C:0.07, G:0.11, T:0.37


Consensus pattern (23 bp):   
GAATATAACGTTAATATTCAATG

Found at i:6340 original size:2 final size:2

Alignment explanation


    Indices: 6335--6359  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       6325 ACGCGCATAC

                                                 
       6335 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

       6360 ATACACTGTC


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

Done.