Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011728.1 Corchorus capsularis cultivar CVL-1 contig11749, 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: 7960
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35


Found at i:695 original size:21 final size:21

Alignment explanation


    Indices: 670--710  Score: 55
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        660 TTAATATATC

                                 
        670 AAATAATTAATTATCTTTTTA
          1 AAATAATTAATTATCTTTTTA

                 *   *    *     
        691 AAATATTTATTTATTTTTTT
          1 AAATAATTAATTATCTTTTT

        711 TGTTTAAGCA


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61


Consensus pattern (21 bp):   
AAATAATTAATTATCTTTTTA

Found at i:1912 original size:36 final size:35

Alignment explanation


    Indices: 1726--1960  Score: 337
    Period size: 35  Copynumber: 6.7  Consensus size: 35

       1716 TTCTAACTAA

                                *   *     *    
       1726 ACTTAATTACCCTGAATTAAATTGTTTA-TTACTT
          1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT

                                        *   *  
       1760 ACTTAATTACCCTGAATTAAGTTGATTATTGAATT
          1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT

            *                                 *
       1795 CCTTAATTACCCTGAATTAAGTTGATTACTGACTC
          1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT

                                              *
       1830 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
          1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT

                                   *       *    
       1865 ACTTAATTACCCTGAATTAAGTTTATTAACTTACTT
          1 ACTTAATTACCCTGAATTAAGTTGATT-ACTGACTT

                                                
       1901 ACTTAATTACCCTGAATTAAGTTGATTACTGACTTT
          1 ACTTAATTACCCTGAATTAAGTTGATTACTGAC-TT

              *                *    
       1937 ACCTAATTACCCTGAATTAGGTTG
          1 ACTTAATTACCCTGAATTAAGTTG

       1961 CTTATTATGA


Statistics
Matches: 182,  Mismatches: 16, Indels: 4
        0.90            0.08        0.02

Matches are distributed among these distances:
  34   26  0.14
  35  100  0.55
  36   56  0.31

ACGTcount: A:0.31, C:0.17, G:0.10, T:0.41


Consensus pattern (35 bp):   
ACTTAATTACCCTGAATTAAGTTGATTACTGACTT

Found at i:3715 original size:15 final size:15

Alignment explanation


    Indices: 3692--3725  Score: 50
    Period size: 15  Copynumber: 2.3  Consensus size: 15

       3682 CTCTCGGTAA

                *          
       3692 TTTTTTCTTACTCAC
          1 TTTTGTCTTACTCAC

                      *    
       3707 TTTTGTCTTATTCAC
          1 TTTTGTCTTACTCAC

                
       3722 TTTT
          1 TTTT

       3726 AATTTTGTTA


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.12, C:0.21, G:0.03, T:0.65


Consensus pattern (15 bp):   
TTTTGTCTTACTCAC

Found at i:6370 original size:31 final size:30

Alignment explanation


    Indices: 6332--6432  Score: 96
    Period size: 31  Copynumber: 3.3  Consensus size: 30

       6322 AAGTACCTAA

                     *                     
       6332 TTAGTCCCTATACTATGAAAAAAAGATCAAT
          1 TTAGTCCCTCTACTATG-AAAAAAGATCAAT

                      * *       ***       
       6363 TTAGTCCCTCCATTATGAAATCTG-TCAAT
          1 TTAGTCCCTCTACTATGAAAAAAGATCAAT

                             *    * *      
       6392 TTAGTCCCTCTACTATTTAAAAGATATCAAT
          1 TTAGTCCCTCTACTA-TGAAAAAAGATCAAT

                      
       6423 TTAGTCCCTC
          1 TTAGTCCCTC

       6433 CATGAAATGG


Statistics
Matches: 55,  Mismatches: 13, Indels: 4
        0.76            0.18        0.06

Matches are distributed among these distances:
  29   18  0.33
  30    8  0.15
  31   29  0.53

ACGTcount: A:0.34, C:0.22, G:0.09, T:0.36


Consensus pattern (30 bp):   
TTAGTCCCTCTACTATGAAAAAAGATCAAT
Done.