Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013515.1 Corchorus capsularis cultivar CVL-1 contig13536, 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: 14866
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32


Found at i:3060 original size:24 final size:24

Alignment explanation


    Indices: 3016--3062  Score: 60
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       3006 ATATGCATAT

                           *        
       3016 ATTGATCGATTGATTTGATTTTTG
          1 ATTGATCGATTGATTAGATTTTTG

                        *           
       3040 ATTGAT-GATTGCTTAGAATTTTT
          1 ATTGATCGATTGATTAG-ATTTTT

       3063 AAGAATGTTT


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  23    8  0.40
  24   12  0.60

ACGTcount: A:0.23, C:0.04, G:0.19, T:0.53


Consensus pattern (24 bp):   
ATTGATCGATTGATTAGATTTTTG

Found at i:4191 original size:11 final size:10

Alignment explanation


    Indices: 4173--4206  Score: 50
    Period size: 11  Copynumber: 3.2  Consensus size: 10

       4163 GAAGTTCGTG

                      
       4173 TTTTGAAGAT
          1 TTTTGAAGAT

                       
       4183 TTCTTGAAGAT
          1 TT-TTGAAGAT

                       
       4194 ATTTTGAAGAT
          1 -TTTTGAAGAT

              
       4205 TT
          1 TT

       4207 GAAGACTATT


Statistics
Matches: 22,  Mismatches: 0, Indels: 4
        0.85            0.00        0.15

Matches are distributed among these distances:
  10    4  0.18
  11   16  0.73
  12    2  0.09

ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50


Consensus pattern (10 bp):   
TTTTGAAGAT

Found at i:14720 original size:16 final size:16

Alignment explanation


    Indices: 14677--14720  Score: 52
    Period size: 16  Copynumber: 2.8  Consensus size: 16

      14667 ACCCGCTCGA

                          * 
      14677 ACCCGAACCCGAAATT
          1 ACCCGAACCCGAAAAT

             * *            
      14693 ATCTGAACCCGAAAAT
          1 ACCCGAACCCGAAAAT

                   *    
      14709 ACCCGAATCCGA
          1 ACCCGAACCCGA

      14721 GGCAGCCCGA


Statistics
Matches: 22,  Mismatches: 6, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
  16   22  1.00

ACGTcount: A:0.39, C:0.34, G:0.14, T:0.14


Consensus pattern (16 bp):   
ACCCGAACCCGAAAAT

Found at i:14752 original size:23 final size:23

Alignment explanation


    Indices: 14724--14777  Score: 63
    Period size: 23  Copynumber: 2.3  Consensus size: 23

      14714 AATCCGAGGC

                       *   *       
      14724 AGCCCGAACCCGACCGGAGACCG
          1 AGCCCGAACCCAACCCGAGACCG

                   *           *   
      14747 AGCCCGATCCCAACCCGAGTCCG
          1 AGCCCGAACCCAACCCGAGACCG

             *      
      14770 AACCCGAA
          1 AGCCCGAA

      14778 ATAATTTGAA


Statistics
Matches: 25,  Mismatches: 6, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  23   25  1.00

ACGTcount: A:0.28, C:0.44, G:0.24, T:0.04


Consensus pattern (23 bp):   
AGCCCGAACCCAACCCGAGACCG
Done.