Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014023.1 Corchorus capsularis cultivar CVL-1 contig14044, 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: 18461
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32


Found at i:227 original size:2 final size:2

Alignment explanation


    Indices: 220--249  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

        210 AAAATGGTCC

                                                        
        220 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

        250 TCCTAAATAT


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:15646 original size:20 final size:21

Alignment explanation


    Indices: 15612--15651  Score: 57
    Period size: 20  Copynumber: 2.0  Consensus size: 21

      15602 CTTTTCAAAG

                                 
      15612 TTATATATGATTATG-ATATT
          1 TTATATATGATTATGTATATT

                                 
      15632 TTATATAT-ATGTATGTATAT
          1 TTATATATGAT-TATGTATAT

      15652 AATGTGTATA


Statistics
Matches: 18,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  19    2  0.11
  20   12  0.67
  21    4  0.22

ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55


Consensus pattern (21 bp):   
TTATATATGATTATGTATATT

Found at i:17308 original size:10 final size:10

Alignment explanation


    Indices: 17293--17325  Score: 50
    Period size: 10  Copynumber: 3.4  Consensus size: 10

      17283 CCCTATTACA

                      
      17293 TATATCTATC
          1 TATATCTATC

                      
      17303 TATATCTATC
          1 TATATCTATC

                     *
      17313 TATA-CTATA
          1 TATATCTATC

                
      17322 TATA
          1 TATA

      17326 AAAGTACGAG


Statistics
Matches: 22,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
   9    8  0.36
  10   14  0.64

ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48


Consensus pattern (10 bp):   
TATATCTATC

Found at i:17385 original size:31 final size:31

Alignment explanation


    Indices: 17344--17412  Score: 102
    Period size: 31  Copynumber: 2.2  Consensus size: 31

      17334 AGTTTTGTAA

                                           
      17344 AACTTTTGAAACACCTATTATACCCTTATTT
          1 AACTTTTGAAACACCTATTATACCCTTATTT

              *        *          * *      
      17375 AATTTTTGAAATACCTATTATATCTTTATTT
          1 AACTTTTGAAACACCTATTATACCCTTATTT

                   
      17406 AACTTTT
          1 AACTTTT

      17413 ACAGTTTTTA


Statistics
Matches: 33,  Mismatches: 5, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  31   33  1.00

ACGTcount: A:0.32, C:0.16, G:0.03, T:0.49


Consensus pattern (31 bp):   
AACTTTTGAAACACCTATTATACCCTTATTT
Done.