Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011186.1 Corchorus capsularis cultivar CVL-1 contig11207, 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: 36407
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34


Found at i:13739 original size:2 final size:2

Alignment explanation


    Indices: 13732--13762  Score: 53
    Period size: 2  Copynumber: 15.5  Consensus size: 2

      13722 AAACTTCTGA

                                          *               
      13732 AT AT AT AT AT AT AT AT AT AT CT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

      13763 AGATGAGAGT


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:20627 original size:13 final size:13

Alignment explanation


    Indices: 20609--20636  Score: 56
    Period size: 13  Copynumber: 2.2  Consensus size: 13

      20599 TTGGATAATA

                         
      20609 AGGTGGTCACTAT
          1 AGGTGGTCACTAT

                         
      20622 AGGTGGTCACTAT
          1 AGGTGGTCACTAT

              
      20635 AG
          1 AG

      20637 CTGATAATCC


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   15  1.00

ACGTcount: A:0.25, C:0.14, G:0.32, T:0.29


Consensus pattern (13 bp):   
AGGTGGTCACTAT

Found at i:25801 original size:30 final size:29

Alignment explanation


    Indices: 25739--25808  Score: 86
    Period size: 29  Copynumber: 2.4  Consensus size: 29

      25729 ATCGAACCGT

                                  ****   
      25739 CAAATAAGCCCCTGAACTATTATTTCAGC
          1 CAAATAAGCCCCTGAACTATTAAAAAAGC

                              *           
      25768 CAAATAAGCCCCTGAACTCTTAAAAAAAGC
          1 CAAATAAGCCCCTGAACTATT-AAAAAAGC

                       
      25798 CAAATAAGCCC
          1 CAAATAAGCCC

      25809 TATTGCCAAG


Statistics
Matches: 35,  Mismatches: 5, Indels: 1
        0.85            0.12        0.02

Matches are distributed among these distances:
  29   20  0.57
  30   15  0.43

ACGTcount: A:0.41, C:0.29, G:0.10, T:0.20


Consensus pattern (29 bp):   
CAAATAAGCCCCTGAACTATTAAAAAAGC

Found at i:27187 original size:31 final size:31

Alignment explanation


    Indices: 27015--27176  Score: 200
    Period size: 31  Copynumber: 5.2  Consensus size: 31

      27005 GACAAAAATG

                     *  *  *             ** 
      27015 ACACGTGGCATGCCAAATGTCACCTTTTTTTT
          1 ACACGTGGCGTGACACATGTCA-CTTTTTGGT

                    *      **              
      27047 ACACGTGGTGTGACATGTGTCAC-TTTTGGT
          1 ACACGTGGCGTGACACATGTCACTTTTTGGT

                           **              
      27077 ACACGTGGCGTGACATGTGTCACTTTTTGGT
          1 ACACGTGGCGTGACACATGTCACTTTTTGGT

                *                          
      27108 ACACATGGCGTGACACATGTCACTTTTTGGT
          1 ACACGTGGCGTGACACATGTCACTTTTTGGT

                        *                  
      27139 ACACGTGGCGTGCCACATGTCACTTTTTGGT
          1 ACACGTGGCGTGACACATGTCACTTTTTGGT

                   
      27170 ACACGTG
          1 ACACGTG

      27177 ACATGCCACA


Statistics
Matches: 116,  Mismatches: 13, Indels: 3
        0.88            0.10        0.02

Matches are distributed among these distances:
  30   27  0.23
  31   72  0.62
  32   17  0.15

ACGTcount: A:0.19, C:0.22, G:0.25, T:0.34


Consensus pattern (31 bp):   
ACACGTGGCGTGACACATGTCACTTTTTGGT

Found at i:27720 original size:11 final size:11

Alignment explanation


    Indices: 27706--27736  Score: 53
    Period size: 11  Copynumber: 2.8  Consensus size: 11

      27696 AATCTACTTA

                       
      27706 AATCTTCAGAT
          1 AATCTTCAGAT

                 *     
      27717 AATCTCCAGAT
          1 AATCTTCAGAT

                     
      27728 AATCTTCAG
          1 AATCTTCAG

      27737 TTGAAATCTT


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  11   18  1.00

ACGTcount: A:0.35, C:0.23, G:0.10, T:0.32


Consensus pattern (11 bp):   
AATCTTCAGAT

Found at i:32099 original size:41 final size:41

Alignment explanation


    Indices: 32038--32184  Score: 186
    Period size: 41  Copynumber: 3.6  Consensus size: 41

      32028 CTGGAGTAAC

                           *                         
      32038 ACTTCTGGTGTCAAAGGTAATTTTAATTTACCAAAGTGACA
          1 ACTTCTGGTGTCAAAAGTAATTTTAATTTACCAAAGTGACA

                                   *        * *      
      32079 ACTTCTGGTGTCAAAAGTAATTTCAATTTACCGAGGTGACA
          1 ACTTCTGGTGTCAAAAGTAATTTTAATTTACCAAAGTGACA

                  *      **            * *     *     
      32120 ACTTCTAGTGTCAGCAGTAATTTTAATATGCCAAAATGACA
          1 ACTTCTGGTGTCAAAAGTAATTTTAATTTACCAAAGTGACA

                       *   *        
      32161 ACTTCTGGTGTTAAAGGTAATTTT
          1 ACTTCTGGTGTCAAAAGTAATTTT

      32185 CAATATTATT


Statistics
Matches: 88,  Mismatches: 18, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  41   88  1.00

ACGTcount: A:0.33, C:0.15, G:0.18, T:0.35


Consensus pattern (41 bp):   
ACTTCTGGTGTCAAAAGTAATTTTAATTTACCAAAGTGACA
Done.