Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015812.1 Corchorus olitorius cultivar O-4 contig15845, 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: 10778
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30


Found at i:1603 original size:51 final size:50

Alignment explanation


    Indices: 1502--1603  Score: 127
    Period size: 51  Copynumber: 2.0  Consensus size: 50

       1492 GTTCTTCATA

                                                     * **     
       1502 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCTTTTAGTGT
          1 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT

                                            *                    
       1552 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGT
          1 TTTTC-CTTGTTT-AGATCTTGTCTCCGGACAAACAAACACTCGTACA-GTGT

             
       1603 T
          1 T

       1604 CTTCATTCAG


Statistics
Matches: 45,  Mismatches: 4, Indels: 5
        0.83            0.07        0.09

Matches are distributed among these distances:
  50    7  0.16
  51   37  0.82
  52    1  0.02

ACGTcount: A:0.22, C:0.24, G:0.14, T:0.41


Consensus pattern (50 bp):   
TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT

Found at i:4428 original size:22 final size:22

Alignment explanation


    Indices: 4378--4429  Score: 68
    Period size: 22  Copynumber: 2.4  Consensus size: 22

       4368 GAGGAAATCG

                 *   *            
       4378 CGGAGATTTCAGAGAAAAAGCA
          1 CGGAGCTTTGAGAGAAAAAGCA

                            *     
       4400 CGGAGCTTTGAGAGAATAAGCA
          1 CGGAGCTTTGAGAGAAAAAGCA

              *     
       4422 CGTAGCTT
          1 CGGAGCTT

       4430 GATTTTTTGC


Statistics
Matches: 26,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  22   26  1.00

ACGTcount: A:0.37, C:0.15, G:0.29, T:0.19


Consensus pattern (22 bp):   
CGGAGCTTTGAGAGAAAAAGCA

Found at i:4512 original size:24 final size:25

Alignment explanation


    Indices: 4485--4534  Score: 66
    Period size: 24  Copynumber: 2.0  Consensus size: 25

       4475 TGAAATTTGC

                         *           
       4485 ACTATCCAAAATCGAAA-CCGTTTA
          1 ACTATCCAAAATCCAAATCCGTTTA

                    **               
       4509 ACTATCCACTATCCAAATCCGTTTA
          1 ACTATCCAAAATCCAAATCCGTTTA

             
       4534 A
          1 A

       4535 AAACCGCTTA


Statistics
Matches: 22,  Mismatches: 3, Indels: 1
        0.85            0.12        0.04

Matches are distributed among these distances:
  24   14  0.64
  25    8  0.36

ACGTcount: A:0.38, C:0.28, G:0.06, T:0.28


Consensus pattern (25 bp):   
ACTATCCAAAATCCAAATCCGTTTA

Found at i:5668 original size:29 final size:29

Alignment explanation


    Indices: 5626--5682  Score: 96
    Period size: 29  Copynumber: 2.0  Consensus size: 29

       5616 GAAATCGCAT

                                         
       5626 GCCTCTAGCTAGGTAAATTCCACCAATTG
          1 GCCTCTAGCTAGGTAAATTCCACCAATTG

                          *       *     
       5655 GCCTCTAGCTAGGTCAATTCCAGCAATT
          1 GCCTCTAGCTAGGTAAATTCCACCAATT

       5683 TCGCCATTTT


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  29   26  1.00

ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28


Consensus pattern (29 bp):   
GCCTCTAGCTAGGTAAATTCCACCAATTG

Found at i:8469 original size:16 final size:15

Alignment explanation


    Indices: 8431--8472  Score: 75
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       8421 ACAGAGGTTG

                           
       8431 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                           
       8446 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
       8461 ACTAGAAAACAA
          1 AC-AGAAAACAA

       8473 AACAAAGTAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15   17  0.65
  16    9  0.35

ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA
Done.