Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023356.1 Corchorus olitorius cultivar O-4 contig23389, 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: 12194
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34


Found at i:2776 original size:24 final size:24

Alignment explanation


    Indices: 2744--2798  Score: 74
    Period size: 24  Copynumber: 2.3  Consensus size: 24

       2734 ACTTGACAAG

                *                   
       2744 GATAAGAAGACCATGAACACAATT
          1 GATATGAAGACCATGAACACAATT

                           *   *    
       2768 GATATGAAGACCATGCACATAATT
          1 GATATGAAGACCATGAACACAATT

              *    
       2792 GAGATGA
          1 GATATGA

       2799 TCAATGGGAA


Statistics
Matches: 27,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  24   27  1.00

ACGTcount: A:0.45, C:0.15, G:0.20, T:0.20


Consensus pattern (24 bp):   
GATATGAAGACCATGAACACAATT

Found at i:3081 original size:28 final size:28

Alignment explanation


    Indices: 3043--3118  Score: 107
    Period size: 28  Copynumber: 2.7  Consensus size: 28

       3033 AGTGCATTTG

                                   **    
       3043 AAATGACCCAAAATGCCCCTGGATGTGCA
          1 AAATGA-CCAAAATGCCCCTGGACATGCA

                                      * 
       3072 AAATGACCAAAATGCCCCTGGACATGTA
          1 AAATGACCAAAATGCCCCTGGACATGCA

                     *         
       3100 AAATGACCAGAATGCCCCT
          1 AAATGACCAAAATGCCCCT

       3119 TAAGTGATCC


Statistics
Matches: 43,  Mismatches: 4, Indels: 1
        0.90            0.08        0.02

Matches are distributed among these distances:
  28   37  0.86
  29    6  0.14

ACGTcount: A:0.37, C:0.28, G:0.18, T:0.17


Consensus pattern (28 bp):   
AAATGACCAAAATGCCCCTGGACATGCA

Found at i:3767 original size:16 final size:15

Alignment explanation


    Indices: 3748--3784  Score: 56
    Period size: 16  Copynumber: 2.3  Consensus size: 15

       3738 TGATTTTAGA

                            
       3748 GTTGTTGTTCTGTGTT
          1 GTTGTTGTTCT-TGTT

                            
       3764 GTTGGTTGTTCTTGTT
          1 GTT-GTTGTTCTTGTT

                 
       3780 GTTGT
          1 GTTGT

       3785 CTTCATTTAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 3
        0.87            0.00        0.13

Matches are distributed among these distances:
  15    2  0.10
  16   10  0.50
  17    8  0.40

ACGTcount: A:0.00, C:0.05, G:0.32, T:0.62


Consensus pattern (15 bp):   
GTTGTTGTTCTTGTT

Found at i:6728 original size:41 final size:41

Alignment explanation


    Indices: 6677--6771  Score: 118
    Period size: 41  Copynumber: 2.3  Consensus size: 41

       6667 AGAAAAATAA

                          *         *                
       6677 GGACCAAATTGAATTAAATAGTAACTAGAATCCCAAATCAG
          1 GGACCAAATTGAATCAAATAGTAAATAGAATCCCAAATCAG

                *      *              *      *    *  
       6718 GGACTAAATTGTATCAAATAGTAAATGGAATCCTAAATTAG
          1 GGACCAAATTGAATCAAATAGTAAATAGAATCCCAAATCAG

                  *      
       6759 GGACCATATTGAA
          1 GGACCAAATTGAA

       6772 CACGGAAACA


Statistics
Matches: 44,  Mismatches: 10, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  41   44  1.00

ACGTcount: A:0.44, C:0.14, G:0.17, T:0.25


Consensus pattern (41 bp):   
GGACCAAATTGAATCAAATAGTAAATAGAATCCCAAATCAG

Found at i:10433 original size:20 final size:21

Alignment explanation


    Indices: 10391--10433  Score: 52
    Period size: 21  Copynumber: 2.1  Consensus size: 21

      10381 TCCTTTGTTG

                         *       
      10391 ATGATCTCCAATGGGCTTCAA
          1 ATGATCTCCAATGAGCTTCAA

                     *        *  
      10412 ATGATCTCCGAT-AGCTTTAA
          1 ATGATCTCCAATGAGCTTCAA

              
      10432 AT
          1 AT

      10434 TCTTCAAGAT


Statistics
Matches: 19,  Mismatches: 3, Indels: 1
        0.83            0.13        0.04

Matches are distributed among these distances:
  20    8  0.42
  21   11  0.58

ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33


Consensus pattern (21 bp):   
ATGATCTCCAATGAGCTTCAA

Found at i:11029 original size:26 final size:23

Alignment explanation


    Indices: 10983--11029  Score: 58
    Period size: 26  Copynumber: 1.9  Consensus size: 23

      10973 TCCTTCTATT

                                   
      10983 CATCTATCATCAAGTTATTCATC
          1 CATCTATCATCAAGTTATTCATC

                               *    
      11006 CATCTCATCCATCAAAGTTTTTCA
          1 CATCT-AT-CATC-AAGTTATTCA

      11030 AATTTTCTAG


Statistics
Matches: 20,  Mismatches: 1, Indels: 3
        0.83            0.04        0.12

Matches are distributed among these distances:
  23    5  0.25
  24    2  0.10
  25    4  0.20
  26    9  0.45

ACGTcount: A:0.30, C:0.28, G:0.04, T:0.38


Consensus pattern (23 bp):   
CATCTATCATCAAGTTATTCATC
Done.