Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010099.1 Corchorus olitorius cultivar O-4 contig10131, 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: 4549
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34


Found at i:787 original size:29 final size:30

Alignment explanation


    Indices: 721--792  Score: 78
    Period size: 29  Copynumber: 2.4  Consensus size: 30

        711 CGTTAGAAAA

                                         *
        721 GGGCTTATTTGGCATAATCTAAGAGTTCAT
          1 GGGCTTATTTGGCATAATCTAAGAGTTCAG

               *                         *  
        751 GGGTTTATTTGGC-TGCAAT-T-AGAGTTTAG
          1 GGGCTTATTTGGCAT--AATCTAAGAGTTCAG

                         
        780 GGGCTTATTTGGC
          1 GGGCTTATTTGGC

        793 CGTTTTGTGT


Statistics
Matches: 36,  Mismatches: 4, Indels: 5
        0.80            0.09        0.11

Matches are distributed among these distances:
  29   20  0.56
  30   13  0.36
  31    3  0.08

ACGTcount: A:0.21, C:0.11, G:0.29, T:0.39


Consensus pattern (30 bp):   
GGGCTTATTTGGCATAATCTAAGAGTTCAG

Found at i:1264 original size:2 final size:2

Alignment explanation


    Indices: 1257--1281  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       1247 TCCAAATCAT

                                                 
       1257 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 T

       1282 GAACTATGTT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:3737 original size:10 final size:10

Alignment explanation


    Indices: 3722--3776  Score: 71
    Period size: 10  Copynumber: 5.6  Consensus size: 10

       3712 TAACAATTTA

                      
       3722 AATTAATAAT
          1 AATTAATAAT

                       
       3732 AATTAATAATT
          1 AATTAATAA-T

                       
       3743 AA-TAATTAAT
          1 AATTAA-TAAT

                      
       3753 AATT-A-AAT
          1 AATTAATAAT

                      
       3761 AATTAATAAT
          1 AATTAATAAT

                  
       3771 AATTAA
          1 AATTAA

       3777 AAAATAAAAA


Statistics
Matches: 40,  Mismatches: 0, Indels: 10
        0.80            0.00        0.20

Matches are distributed among these distances:
   8    7  0.17
   9    1  0.03
  10   25  0.62
  11    7  0.17

ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40


Consensus pattern (10 bp):   
AATTAATAAT

Found at i:3737 original size:29 final size:29

Alignment explanation


    Indices: 3699--3772  Score: 80
    Period size: 29  Copynumber: 2.6  Consensus size: 29

       3689 TTTTGGTTTT

                *      *         *        
       3699 TAATTATTAATTATAACAATTTA-AATTAA
          1 TAATAATTAATAATAACAATTAATAATT-A

                             *            
       3728 TAATAATTAATAATTAATAATTAATAATTA
          1 TAATAATTAATAA-TAACAATTAATAATTA

                            
       3758 -AATAATTAATAATAA
          1 TAATAATTAATAATAA

       3773 TTAAAAAATA


Statistics
Matches: 39,  Mismatches: 4, Indels: 5
        0.81            0.08        0.10

Matches are distributed among these distances:
  28    3  0.08
  29   23  0.59
  30    9  0.23
  31    4  0.10

ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42


Consensus pattern (29 bp):   
TAATAATTAATAATAACAATTAATAATTA

Found at i:3740 original size:7 final size:7

Alignment explanation


    Indices: 3728--3770  Score: 77
    Period size: 7  Copynumber: 6.0  Consensus size: 7

       3718 TTTAAATTAA

                   
       3728 TAATAAT
          1 TAATAAT

                   
       3735 TAATAAT
          1 TAATAAT

                   
       3742 TAATAAT
          1 TAATAAT

                   
       3749 TAATAAT
          1 TAATAAT

                    
       3756 TAAATAAT
          1 T-AATAAT

                   
       3764 TAATAAT
          1 TAATAAT

       3771 AATTAAAAAA


Statistics
Matches: 35,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   7   28  0.80
   8    7  0.20

ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42


Consensus pattern (7 bp):   
TAATAAT

Found at i:3749 original size:39 final size:39

Alignment explanation


    Indices: 3698--3776  Score: 101
    Period size: 39  Copynumber: 2.1  Consensus size: 39

       3688 TTTTTGGTTT

                 *      *           *              
       3698 TTAATTATTAATTA-TAACAATT-TA-AATTAATAATAA
          1 TTAATAATTAATAATTAACAATTAAATAATTAATAATAA

                              *                    
       3734 TTAATAATTAATAATTAATAATTAAATAATTAATAATAA
          1 TTAATAATTAATAATTAACAATTAAATAATTAATAATAA

                
       3773 TTAA
          1 TTAA

       3777 AAAATAAAAA


Statistics
Matches: 36,  Mismatches: 4, Indels: 3
        0.84            0.09        0.07

Matches are distributed among these distances:
  36   12  0.33
  37    7  0.19
  38    1  0.03
  39   16  0.44

ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43


Consensus pattern (39 bp):   
TTAATAATTAATAATTAACAATTAAATAATTAATAATAA

Found at i:3897 original size:12 final size:12

Alignment explanation


    Indices: 3880--3904  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

       3870 CTACAAAATC

                        
       3880 CGACATGATTTT
          1 CGACATGATTTT

                        
       3892 CGACATGATTTT
          1 CGACATGATTTT

             
       3904 C
          1 C

       3905 TTCAAGATTG


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40


Consensus pattern (12 bp):   
CGACATGATTTT
Done.