Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015470.1 Corchorus olitorius cultivar O-4 contig15503, 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: 19078
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32


Found at i:2671 original size:21 final size:21

Alignment explanation


    Indices: 2641--2680  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       2631 CTGTTTGGCA

                       *         
       2641 ACTGTACAGATTAGATTATGT
          1 ACTGTACAGATAAGATTATGT

                 *             
       2662 ACTGTTCAGATAAGATTAT
          1 ACTGTACAGATAAGATTAT

       2681 TTAAAACAGT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38


Consensus pattern (21 bp):   
ACTGTACAGATAAGATTATGT

Found at i:3613 original size:64 final size:64

Alignment explanation


    Indices: 3512--3672  Score: 274
    Period size: 64  Copynumber: 2.5  Consensus size: 64

       3502 AAACTTATTT

                                                                             
       3512 TGATAAGGATGGAAGTTCCTTCGTGA-AACAGAGTAATTTACAGAGGAAAAGAAACAGAGTAATC
          1 TGATAAGGATGGAAGTTCCTTCG-GATAACAGAGTAATTTACAGAGGAAAAGAAACAGAGTAATC

                                                                         *  
       3576 TGATAAGGATGGAAGTTCCTTCGGATAACAGAGTAATTTACAGAGGAAAAGAAACAGAGTATTC
          1 TGATAAGGATGGAAGTTCCTTCGGATAACAGAGTAATTTACAGAGGAAAAGAAACAGAGTAATC

                       *                       
       3640 TGATAAGGATGAAAGTTCCTTC-G-TAACAGAGTA
          1 TGATAAGGATGGAAGTTCCTTCGGATAACAGAGTA

       3673 GTAATTTAAG


Statistics
Matches: 94,  Mismatches: 2, Indels: 4
        0.94            0.02        0.04

Matches are distributed among these distances:
  62   10  0.11
  63    3  0.03
  64   81  0.86

ACGTcount: A:0.40, C:0.11, G:0.25, T:0.24


Consensus pattern (64 bp):   
TGATAAGGATGGAAGTTCCTTCGGATAACAGAGTAATTTACAGAGGAAAAGAAACAGAGTAATC

Found at i:3789 original size:36 final size:36

Alignment explanation


    Indices: 3742--3840  Score: 135
    Period size: 36  Copynumber: 2.7  Consensus size: 36

       3732 ACAGAGTTCG

                                             *  
       3742 ATGATGTAAGAATTATTCAATGCCATGACGTGAGCT
          1 ATGATGTAAGAATTATTCAATGCCATGACGTGAACT

                           *  *   *             
       3778 ATGATGTAAGAATTACTCGATGACATGACGTGAACT
          1 ATGATGTAAGAATTATTCAATGCCATGACGTGAACT

                          *     *      
       3814 ATGATGTAAGGAATCATTCAGTGCCAT
          1 ATGATGTAA-GAATTATTCAATGCCAT

       3841 TGGCGGCTTA


Statistics
Matches: 53,  Mismatches: 9, Indels: 1
        0.84            0.14        0.02

Matches are distributed among these distances:
  36   41  0.77
  37   12  0.23

ACGTcount: A:0.34, C:0.14, G:0.22, T:0.29


Consensus pattern (36 bp):   
ATGATGTAAGAATTATTCAATGCCATGACGTGAACT

Found at i:15112 original size:31 final size:31

Alignment explanation


    Indices: 15071--15156  Score: 113
    Period size: 29  Copynumber: 2.8  Consensus size: 31

      15061 GAGGGCTAAA

                             *          *  
      15071 TGCTCAATTTGGTCCTATACCTTTCACGGTC
          1 TGCTCAATTTGGTCCTAAACCTTTCACGATC

                 *                    *    
      15102 TGCTCGATTTGGTCCTAAACC-TTC-TGATC
          1 TGCTCAATTTGGTCCTAAACCTTTCACGATC

            *                         
      15131 GGCTCAATTTGGTCCTAAACCTTTCA
          1 TGCTCAATTTGGTCCTAAACCTTTCA

      15157 ATTTCTACTC


Statistics
Matches: 47,  Mismatches: 6, Indels: 4
        0.82            0.11        0.07

Matches are distributed among these distances:
  29   22  0.47
  30    6  0.13
  31   19  0.40

ACGTcount: A:0.19, C:0.28, G:0.16, T:0.37


Consensus pattern (31 bp):   
TGCTCAATTTGGTCCTAAACCTTTCACGATC

Done.