Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023092.1 Corchorus olitorius cultivar O-4 contig23125, 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: 9837
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38


Found at i:8056 original size:16 final size:16

Alignment explanation


    Indices: 8035--8090  Score: 78
    Period size: 16  Copynumber: 3.6  Consensus size: 16

       8025 GTTACTTTCT

                            
       8035 AAGGAGAGTGCTCTCC
          1 AAGGAGAGTGCTCTCC

                      *     
       8051 AAGGAGAGTGAT-TCC
          1 AAGGAGAGTGCTCTCC

            *               
       8066 CAGGAGAGTGCTCTCC
          1 AAGGAGAGTGCTCTCC

             *       
       8082 ATGGAGAGT
          1 AAGGAGAGT

       8091 CATTCCAAGG


Statistics
Matches: 34,  Mismatches: 5, Indels: 2
        0.83            0.12        0.05

Matches are distributed among these distances:
  15   13  0.38
  16   21  0.62

ACGTcount: A:0.27, C:0.20, G:0.34, T:0.20


Consensus pattern (16 bp):   
AAGGAGAGTGCTCTCC

Found at i:8072 original size:15 final size:15

Alignment explanation


    Indices: 8036--8120  Score: 73
    Period size: 15  Copynumber: 5.5  Consensus size: 15

       8026 TTACTTTCTA

                     *     *
       8036 AGGAGAGTGCTCTCCA
          1 AGGAGAGTGAT-TCCC

                           
       8052 AGGAGAGTGATTCCC
          1 AGGAGAGTGATTCCC

                      *     
       8067 AGGAGAGTG-CTCTCC
          1 AGGAGAGTGATTC-CC

                     *     *
       8082 ATGGAGAGTCATTCCA
          1 A-GGAGAGTGATTCCC

                *          
       8098 AGGATAGTGATTCCC
          1 AGGAGAGTGATTCCC

             *      
       8113 AAGAGAGT
          1 AGGAGAGT

       8121 ACTTTCCATG


Statistics
Matches: 55,  Mismatches: 11, Indels: 7
        0.75            0.15        0.10

Matches are distributed among these distances:
  14    2  0.04
  15   32  0.58
  16   19  0.35
  17    2  0.04

ACGTcount: A:0.28, C:0.20, G:0.31, T:0.21


Consensus pattern (15 bp):   
AGGAGAGTGATTCCC

Found at i:8074 original size:31 final size:31

Alignment explanation


    Indices: 8035--8106  Score: 108
    Period size: 31  Copynumber: 2.3  Consensus size: 31

       8025 GTTACTTTCT

                                     *     
       8035 AAGGAGAGTGCTCTCCAAGGAGAGTGATTCC
          1 AAGGAGAGTGCTCTCCAAGGAGAGTCATTCC

            *                *             
       8066 CAGGAGAGTGCTCTCCATGGAGAGTCATTCC
          1 AAGGAGAGTGCTCTCCAAGGAGAGTCATTCC

                 *    
       8097 AAGGATAGTG
          1 AAGGAGAGTG

       8107 ATTCCCAAGA


Statistics
Matches: 36,  Mismatches: 5, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  31   36  1.00

ACGTcount: A:0.28, C:0.19, G:0.32, T:0.21


Consensus pattern (31 bp):   
AAGGAGAGTGCTCTCCAAGGAGAGTCATTCC

Found at i:8107 original size:46 final size:46

Alignment explanation


    Indices: 8048--8142  Score: 136
    Period size: 46  Copynumber: 2.1  Consensus size: 46

       8038 GAGAGTGCTC

                                *      *           *      
       8048 TCCAAGGAGAGTGATTCCCAGGAGAGTGCTCTCCATGGAGAGTCAT
          1 TCCAAGGAGAGTGATTCCCAAGAGAGTACTCTCCATGGAAAGTCAT

                    *                     *             * 
       8094 TCCAAGGATAGTGATTCCCAAGAGAGTACTTTCCATGGAAAGTCTT
          1 TCCAAGGAGAGTGATTCCCAAGAGAGTACTCTCCATGGAAAGTCAT

               
       8140 TCC
          1 TCC

       8143 CTATTCCCCC


Statistics
Matches: 43,  Mismatches: 6, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  46   43  1.00

ACGTcount: A:0.27, C:0.22, G:0.25, T:0.25


Consensus pattern (46 bp):   
TCCAAGGAGAGTGATTCCCAAGAGAGTACTCTCCATGGAAAGTCAT

Found at i:8674 original size:39 final size:39

Alignment explanation


    Indices: 8620--8696  Score: 136
    Period size: 39  Copynumber: 2.0  Consensus size: 39

       8610 AGTCTGCTCC

                                       *    *      
       8620 ATTTTGCTTCTGTTCTTTTTCTTTTCAGATTAGATTTGA
          1 ATTTTGCTTCTGTTCTTTTTCTTTTCAAATTACATTTGA

                                                  
       8659 ATTTTGCTTCTGTTCTTTTTCTTTTCAAATTACATTTG
          1 ATTTTGCTTCTGTTCTTTTTCTTTTCAAATTACATTTG

       8697 CCAAGCTGTC


Statistics
Matches: 36,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  39   36  1.00

ACGTcount: A:0.16, C:0.14, G:0.10, T:0.60


Consensus pattern (39 bp):   
ATTTTGCTTCTGTTCTTTTTCTTTTCAAATTACATTTGA
Done.