Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016906.1 Corchorus olitorius cultivar O-4 contig16939, 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: 15205
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:2357 original size:22 final size:22

Alignment explanation


    Indices: 2332--2387  Score: 103
    Period size: 22  Copynumber: 2.5  Consensus size: 22

       2322 AGCTCAAGTC

                                  
       2332 CTGGACAGGACTTGGCCAAGAT
          1 CTGGACAGGACTTGGCCAAGAT

                   *              
       2354 CTGGACATGACTTGGCCAAGAT
          1 CTGGACAGGACTTGGCCAAGAT

                        
       2376 CTGGACAGGACT
          1 CTGGACAGGACT

       2388 CATTCTAATT


Statistics
Matches: 32,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  22   32  1.00

ACGTcount: A:0.27, C:0.23, G:0.30, T:0.20


Consensus pattern (22 bp):   
CTGGACAGGACTTGGCCAAGAT

Found at i:3627 original size:22 final size:23

Alignment explanation


    Indices: 3602--3658  Score: 59
    Period size: 22  Copynumber: 2.7  Consensus size: 23

       3592 ACTATAGTAT

                     *     *       
       3602 CAAAAAT-TTATAGGGAGATTAA
          1 CAAAAATCTCATAGGAAGATTAA

                                  *
       3624 C-AAAATCTCATAGGAAGATTAT
          1 CAAAAATCTCATAGGAAGATTAA

                           
       3646 C-AAAA-CTCATAGG
          1 CAAAAATCTCATAGG

       3659 GAGGTTACAA


Statistics
Matches: 31,  Mismatches: 3, Indels: 3
        0.84            0.08        0.08

Matches are distributed among these distances:
  21   13  0.42
  22   18  0.58

ACGTcount: A:0.47, C:0.12, G:0.16, T:0.25


Consensus pattern (23 bp):   
CAAAAATCTCATAGGAAGATTAA

Found at i:3656 original size:21 final size:22

Alignment explanation


    Indices: 3611--3658  Score: 71
    Period size: 22  Copynumber: 2.2  Consensus size: 22

       3601 TCAAAAATTT

                 *                
       3611 ATAGGGAGATTAACAAAATCTC
          1 ATAGGAAGATTAACAAAATCTC

                        *         
       3633 ATAGGAAGATTATCAAAA-CTC
          1 ATAGGAAGATTAACAAAATCTC

                 
       3654 ATAGG
          1 ATAGG

       3659 GAGGTTACAA


Statistics
Matches: 24,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  21    8  0.33
  22   16  0.67

ACGTcount: A:0.46, C:0.12, G:0.19, T:0.23


Consensus pattern (22 bp):   
ATAGGAAGATTAACAAAATCTC

Found at i:7597 original size:35 final size:35

Alignment explanation


    Indices: 7555--7645  Score: 137
    Period size: 35  Copynumber: 2.6  Consensus size: 35

       7545 GTTCCTGAAC

                           *                   
       7555 ATTTATCTAAGACAATCTTCTAATATCTAATGTGA
          1 ATTTATCTAAGACAAACTTCTAATATCTAATGTGA

                    *                 *        
       7590 ATTTATCTGAGACAAACTTCTAATATGTAATGTGA
          1 ATTTATCTAAGACAAACTTCTAATATCTAATGTGA

                        * *      
       7625 ATTTATCTAAGATAGACTTCT
          1 ATTTATCTAAGACAAACTTCT

       7646 TGTTTTGTCT


Statistics
Matches: 50,  Mismatches: 6, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  35   50  1.00

ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40


Consensus pattern (35 bp):   
ATTTATCTAAGACAAACTTCTAATATCTAATGTGA
Done.