Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000730.1 Corchorus olitorius cultivar O-4 contig00730, 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: 6233
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.26


Found at i:341 original size:5 final size:5

Alignment explanation


    Indices: 325--357  Score: 57
    Period size: 5  Copynumber: 6.4  Consensus size: 5

        315 ATTGATAATC

                                                   
        325 TTATT CTTATT TTATT TTATT TTATT TTATT TT
          1 TTATT -TTATT TTATT TTATT TTATT TTATT TT

        358 TGCATCAGAG


Statistics
Matches: 27,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   5   22  0.81
   6    5  0.19

ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79


Consensus pattern (5 bp):   
TTATT

Found at i:1478 original size:2 final size:2

Alignment explanation


    Indices: 1473--1506  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

       1463 CAGAGGCGCG

                                                              
       1473 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
          1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA

       1507 TATATATATA


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00


Consensus pattern (2 bp):   
CA

Found at i:1511 original size:2 final size:2

Alignment explanation


    Indices: 1506--1554  Score: 62
    Period size: 2  Copynumber: 24.5  Consensus size: 2

       1496 ACACACACAC

                                                         **    *          
       1506 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GC AT GT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

               *      
       1548 AT CT AT A
          1 AT AT AT A

       1555 AAAGATCAGT


Statistics
Matches: 39,  Mismatches: 8, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
   2   39  1.00

ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47


Consensus pattern (2 bp):   
AT

Found at i:4578 original size:58 final size:58

Alignment explanation


    Indices: 4488--4604  Score: 209
    Period size: 58  Copynumber: 2.0  Consensus size: 58

       4478 TGACAAATCC

                                                                      
       4488 AAGTAAAAATAAAAGACATGAAACAACAGAGAGGTTAGCCTATCAAAGTATGAGCATA
          1 AAGTAAAAATAAAAGACATGAAACAACAGAGAGGTTAGCCTATCAAAGTATGAGCATA

                                                   *                   
       4546 AAGTAAAAA-AAACAGACATGAAACAACAGAGAGGTTAGTCTATCAAAGTATGAGCATA
          1 AAGTAAAAATAAA-AGACATGAAACAACAGAGAGGTTAGCCTATCAAAGTATGAGCATA

             
       4604 A
          1 A

       4605 CCATACTCAG


Statistics
Matches: 57,  Mismatches: 1, Indels: 2
        0.95            0.02        0.03

Matches are distributed among these distances:
  57    3  0.05
  58   54  0.95

ACGTcount: A:0.52, C:0.12, G:0.19, T:0.17


Consensus pattern (58 bp):   
AAGTAAAAATAAAAGACATGAAACAACAGAGAGGTTAGCCTATCAAAGTATGAGCATA

Found at i:4937 original size:14 final size:15

Alignment explanation


    Indices: 4904--4934  Score: 62
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       4894 AATTGACCAT

                           
       4904 AACAATTTAATCCAA
          1 AACAATTTAATCCAA

                           
       4919 AACAATTTAATCCAA
          1 AACAATTTAATCCAA

             
       4934 A
          1 A

       4935 CAAAAGCACC


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.55, C:0.19, G:0.00, T:0.26


Consensus pattern (15 bp):   
AACAATTTAATCCAA
Done.