Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023255.1 Corchorus olitorius cultivar O-4 contig23288, 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: 14136
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33


Found at i:4066 original size:62 final size:62

Alignment explanation


    Indices: 3941--4066  Score: 164
    Period size: 62  Copynumber: 2.0  Consensus size: 62

       3931 ATTTTCATCC

                          *                           *                   
       3941 AAAATCAGGGACTACATCGCATGGAAACAAAGGTAAGATCCTCAATCAACATAAATATAAAA
          1 AAAATCAGGGACTAAATCGCATGGAAACAAAGGTAAGATCCTAAATCAACATAAATATAAAA

                                      *   *    **            *              
       4003 AAAATCAGGGACTAAATCGCAT-GAATCTAGAGGTTTGAGTCCTAAATCGACATAAATATAAAA
          1 AAAATCAGGGACTAAATCGCATGGAAAC-AAAGGTAAGA-TCCTAAATCAACATAAATATAAAA

             
       4066 A
          1 A

       4067 CCACAGCGCA


Statistics
Matches: 55,  Mismatches: 7, Indels: 3
        0.85            0.11        0.05

Matches are distributed among these distances:
  61    4  0.07
  62   28  0.51
  63   23  0.42

ACGTcount: A:0.48, C:0.16, G:0.16, T:0.21


Consensus pattern (62 bp):   
AAAATCAGGGACTAAATCGCATGGAAACAAAGGTAAGATCCTAAATCAACATAAATATAAAA

Found at i:10185 original size:121 final size:121

Alignment explanation


    Indices: 9966--10204  Score: 406
    Period size: 121  Copynumber: 2.0  Consensus size: 121

       9956 AATGTCAATG

                *                                                            
       9966 GTCAGAAAGGCCTAGAAAACACTTAGTTAAGCATGCTTATAGCCTATCTTACTTGAAAGACATAA
          1 GTCAAAAAGGCCTAGAAAACACTTAGTTAAGCATGCTTATAGCCTATCTTACTTGAAAGACATAA

              *          *                                          
      10031 TAGCAGCCTTATTGAACTAAAACTCTAAGTACCACAAATCTGACTCACCAAATTTT
         66 TAACAGCCTTATTAAACTAAAACTCTAAGTACCACAAATCTGACTCACCAAATTTT

                                                      *    *                 
      10087 GTCAAAAAGGCCTAGAAAACACTTAGTTAAGCATGCTTATAGTCTATTTTACTTGAAAGACATAA
          1 GTCAAAAAGGCCTAGAAAACACTTAGTTAAGCATGCTTATAGCCTATCTTACTTGAAAGACATAA

                 **              *                               
      10152 TAACATTCTTATTAAACTAAAGCTCTAAGTACCACAAATCTGACTCACCAAAT
         66 TAACAGCCTTATTAAACTAAAACTCTAAGTACCACAAATCTGACTCACCAAAT

      10205 CATGTATGAC


Statistics
Matches: 110,  Mismatches: 8, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
 121  110  1.00

ACGTcount: A:0.39, C:0.21, G:0.12, T:0.28


Consensus pattern (121 bp):   
GTCAAAAAGGCCTAGAAAACACTTAGTTAAGCATGCTTATAGCCTATCTTACTTGAAAGACATAA
TAACAGCCTTATTAAACTAAAACTCTAAGTACCACAAATCTGACTCACCAAATTTT

Found at i:10427 original size:10 final size:11

Alignment explanation


    Indices: 10412--10440  Score: 51
    Period size: 11  Copynumber: 2.7  Consensus size: 11

      10402 AGGTGTTCAT

                       
      10412 GGGCCGGG-TC
          1 GGGCCGGGTTC

                       
      10422 GGGCCGGGTTC
          1 GGGCCGGGTTC

                    
      10433 GGGCCGGG
          1 GGGCCGGG

      10441 CCCAAGCTTT


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  10    8  0.44
  11   10  0.56

ACGTcount: A:0.00, C:0.28, G:0.62, T:0.10


Consensus pattern (11 bp):   
GGGCCGGGTTC

Found at i:10607 original size:21 final size:24

Alignment explanation


    Indices: 10578--10628  Score: 72
    Period size: 22  Copynumber: 2.2  Consensus size: 24

      10568 TTTTGAACTC

                                     
      10578 ATTATT-TATTATTTAA-AATATAT
          1 ATTATTAT-TTATTTAATAATATAT

                                    
      10601 -TTATTATTTATTTAATAATATAT
          1 ATTATTATTTATTTAATAATATAT

                 
      10624 ATTAT
          1 ATTAT

      10629 ATCTAAGATA


Statistics
Matches: 25,  Mismatches: 0, Indels: 5
        0.83            0.00        0.17

Matches are distributed among these distances:
  22   13  0.52
  23    8  0.32
  24    4  0.16

ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59


Consensus pattern (24 bp):   
ATTATTATTTATTTAATAATATAT

Found at i:10623 original size:25 final size:25

Alignment explanation


    Indices: 10578--10626  Score: 64
    Period size: 25  Copynumber: 2.0  Consensus size: 25

      10568 TTTTGAACTC

                        *            
      10578 ATTATTTATTATTTAAAATATATTT
          1 ATTATTTATTATATAAAATATATTT

                             *       
      10603 ATTATTTATT-TAATAATATATATT
          1 ATTATTTATTAT-ATAAAATATATT

      10627 ATATCTAAGA


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  24    1  0.05
  25   20  0.95

ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59


Consensus pattern (25 bp):   
ATTATTTATTATATAAAATATATTT

Found at i:12407 original size:2 final size:2

Alignment explanation


    Indices: 12400--12432  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

      12390 CGTCAGAGCC

                                                             
      12400 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      12433 TGAAGTCCAA


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   31  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Done.