Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013296.1 Corchorus olitorius cultivar O-4 contig13329, 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: 22850
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


Found at i:1354 original size:2 final size:2

Alignment explanation


    Indices: 1349--1387  Score: 78
    Period size: 2  Copynumber: 19.5  Consensus size: 2

       1339 TCACACACAC

                                                                      
       1349 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       1388 GATAAGAAAG


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   37  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:2675 original size:19 final size:19

Alignment explanation


    Indices: 2651--2698  Score: 96
    Period size: 19  Copynumber: 2.5  Consensus size: 19

       2641 ATAAGTTACC

                               
       2651 CCTTTGTCTTTGATGACAA
          1 CCTTTGTCTTTGATGACAA

                               
       2670 CCTTTGTCTTTGATGACAA
          1 CCTTTGTCTTTGATGACAA

                      
       2689 CCTTTGTCTT
          1 CCTTTGTCTT

       2699 AAACAAGCGA


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   29  1.00

ACGTcount: A:0.17, C:0.23, G:0.15, T:0.46


Consensus pattern (19 bp):   
CCTTTGTCTTTGATGACAA

Found at i:3401 original size:2 final size:2

Alignment explanation


    Indices: 3394--3421  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

       3384 TACTATTTAG

                                                     
       3394 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

       3422 ATAGATTGAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:15055 original size:17 final size:17

Alignment explanation


    Indices: 15016--15064  Score: 57
    Period size: 17  Copynumber: 2.9  Consensus size: 17

      15006 TGCCTGAATT

                             *
      15016 TTTATTATACTATATATG
          1 TTTATTATA-TATATATA

            *                
      15034 GTTATTATATATATATA
          1 TTTATTATATATATATA

                            
      15051 TTTA-TATA-ATATAT
          1 TTTATTATATATATAT

      15065 GTGCTTCAAT


Statistics
Matches: 28,  Mismatches: 3, Indels: 3
        0.82            0.09        0.09

Matches are distributed among these distances:
  15    6  0.21
  16    4  0.14
  17   10  0.36
  18    8  0.29

ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55


Consensus pattern (17 bp):   
TTTATTATATATATATA

Found at i:21462 original size:29 final size:30

Alignment explanation


    Indices: 21400--21472  Score: 103
    Period size: 29  Copynumber: 2.5  Consensus size: 30

      21390 TTGAGAGGAG

                                    *    *
      21400 GCAAAACGTCCAAAATTGAGAGTTTAGGGG
          1 GCAAAACGTCCAAAATTGAGAGTTAAGGGA

                  *   *                   
      21430 GCAAAATGTCTAAAATTGA-AGTTAAGGGA
          1 GCAAAACGTCCAAAATTGAGAGTTAAGGGA

                          
      21459 GCAAAACGTCCAAA
          1 GCAAAACGTCCAAA

      21473 CGCTACAAGT


Statistics
Matches: 37,  Mismatches: 6, Indels: 1
        0.84            0.14        0.02

Matches are distributed among these distances:
  29   20  0.54
  30   17  0.46

ACGTcount: A:0.42, C:0.14, G:0.25, T:0.19


Consensus pattern (30 bp):   
GCAAAACGTCCAAAATTGAGAGTTAAGGGA

Found at i:21601 original size:29 final size:30

Alignment explanation


    Indices: 21564--21625  Score: 90
    Period size: 30  Copynumber: 2.1  Consensus size: 30

      21554 CGTTTGGAAG

                                          
      21564 TTTCTATAGAAAG-TAAAAATTAGAAAGTT
          1 TTTCTATAGAAAGTTAAAAATTAGAAAGTT

                           * **           
      21593 TTTCTATAGAAAGTTTAGGATTAGAAAGTT
          1 TTTCTATAGAAAGTTAAAAATTAGAAAGTT

               
      21623 TTT
          1 TTT

      21626 TTCTTAAGAA


Statistics
Matches: 29,  Mismatches: 3, Indels: 1
        0.88            0.09        0.03

Matches are distributed among these distances:
  29   13  0.45
  30   16  0.55

ACGTcount: A:0.40, C:0.03, G:0.16, T:0.40


Consensus pattern (30 bp):   
TTTCTATAGAAAGTTAAAAATTAGAAAGTT

Done.