Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007852.1 Corchorus capsularis cultivar CVL-1 contig07873, 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: 3878
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36


Found at i:117 original size:2 final size:2

Alignment explanation


    Indices: 106--142  Score: 67
    Period size: 2  Copynumber: 19.0  Consensus size: 2

         96 ACAATTATGT

                                                                    
        106 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

        143 AACATAGGAT


Statistics
Matches: 34,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   33  0.97

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
TA

Found at i:681 original size:16 final size:16

Alignment explanation


    Indices: 660--691  Score: 64
    Period size: 16  Copynumber: 2.0  Consensus size: 16

        650 TTCTAGTCTT

                            
        660 AAACTTTCTATAGAAA
          1 AAACTTTCTATAGAAA

                            
        676 AAACTTTCTATAGAAA
          1 AAACTTTCTATAGAAA

        692 CTTCCAAACG


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.50, C:0.12, G:0.06, T:0.31


Consensus pattern (16 bp):   
AAACTTTCTATAGAAA

Found at i:763 original size:31 final size:31

Alignment explanation


    Indices: 722--780  Score: 100
    Period size: 31  Copynumber: 1.9  Consensus size: 31

        712 GGTCAACATT

                                           
        722 ATAAAACTTTCATTTTAATGGGATCAATACA
          1 ATAAAACTTTCATTTTAATGGGATCAATACA

                 *           *          
        753 ATAAATCTTTCATTTTAGTGGGATCAAT
          1 ATAAAACTTTCATTTTAATGGGATCAAT

        781 TATGAATTTT


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  31   26  1.00

ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39


Consensus pattern (31 bp):   
ATAAAACTTTCATTTTAATGGGATCAATACA

Found at i:1858 original size:12 final size:13

Alignment explanation


    Indices: 1833--1865  Score: 50
    Period size: 12  Copynumber: 2.6  Consensus size: 13

       1823 GCTACATCAC

                     *   
       1833 TTTTTTTATTAAT
          1 TTTTTTTATCAAT

                         
       1846 TTTTTTTA-CAAT
          1 TTTTTTTATCAAT

                    
       1858 TTTTTTTA
          1 TTTTTTTA

       1866 AAAAAATTTT


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  12   11  0.58
  13    8  0.42

ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76


Consensus pattern (13 bp):   
TTTTTTTATCAAT

Found at i:3469 original size:17 final size:17

Alignment explanation


    Indices: 3447--3482  Score: 72
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       3437 GACGGTTTCC

                             
       3447 TATTAAGTTGGATAAAT
          1 TATTAAGTTGGATAAAT

                             
       3464 TATTAAGTTGGATAAAT
          1 TATTAAGTTGGATAAAT

              
       3481 TA
          1 TA

       3483 GGATGTCGGT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   19  1.00

ACGTcount: A:0.42, C:0.00, G:0.17, T:0.42


Consensus pattern (17 bp):   
TATTAAGTTGGATAAAT

Done.