Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013669.1 Corchorus olitorius cultivar O-4 contig13702, 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: 26626
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.32


Found at i:1409 original size:19 final size:18

Alignment explanation


    Indices: 1376--1411  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       1366 TGAAAATAAT

                              
       1376 TCTTCAATGGTCTTCAAA
          1 TCTTCAATGGTCTTCAAA

                     *        
       1394 TCTTCAAATTGTCTTCAA
          1 TCTTC-AATGGTCTTCAA

       1412 TAAGTCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGGTCTTCAAA

Found at i:12469 original size:2 final size:2

Alignment explanation


    Indices: 12462--12493  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

      12452 GAAGATGTGA

                                                           
      12462 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      12494 TAAGAAAATA


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:15883 original size:32 final size:32

Alignment explanation


    Indices: 15847--15969  Score: 147
    Period size: 32  Copynumber: 3.8  Consensus size: 32

      15837 TTTGTGGTTT

                            *             * 
      15847 TAGTGGCATTTTGTTCTTGAAACGCCCTAAAA
          1 TAGTGGCATTTTGTTCATGAAACGCCCTAATA

                  **            *      *    
      15879 TAGTGGTGTTTTGTTCATGATACGCCCCAATA
          1 TAGTGGCATTTTGTTCATGAAACGCCCTAATA

                                *           
      15911 TAGTGGCATTTTGTTCATGATACGCCCTAATA
          1 TAGTGGCATTTTGTTCATGAAACGCCCTAATA

              *   **          *        
      15943 TAATGGTGTTTTGTTCATTAAACGCCC
          1 TAGTGGCATTTTGTTCATGAAACGCCC

      15970 CAATTTTGGT


Statistics
Matches: 77,  Mismatches: 14, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  32   77  1.00

ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37


Consensus pattern (32 bp):   
TAGTGGCATTTTGTTCATGAAACGCCCTAATA

Found at i:15918 original size:64 final size:64

Alignment explanation


    Indices: 15847--15973  Score: 200
    Period size: 64  Copynumber: 2.0  Consensus size: 64

      15837 TTTGTGGTTT

                            *                 *                 *           
      15847 TAGTGGCATTTTGTTCTTGAAACGCCCTAAAATAGTGGTGTTTTGTTCATGATACGCCCCAATA
          1 TAGTGGCATTTTGTTCATGAAACGCCCTAAAATAATGGTGTTTTGTTCATGAAACGCCCCAATA

                                *         *                   *            
      15911 TAGTGGCATTTTGTTCATGATACGCCCTAATATAATGGTGTTTTGTTCATTAAACGCCCCAAT
          1 TAGTGGCATTTTGTTCATGAAACGCCCTAAAATAATGGTGTTTTGTTCATGAAACGCCCCAAT

      15974 TTTGGTATAT


Statistics
Matches: 57,  Mismatches: 6, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  64   57  1.00

ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37


Consensus pattern (64 bp):   
TAGTGGCATTTTGTTCATGAAACGCCCTAAAATAATGGTGTTTTGTTCATGAAACGCCCCAATA

Found at i:18409 original size:21 final size:21

Alignment explanation


    Indices: 18380--18425  Score: 65
    Period size: 21  Copynumber: 2.2  Consensus size: 21

      18370 CACCTGGGCG

                               * 
      18380 CCCACATGGTTTCCTTGAGCA
          1 CCCACATGGTTTCCTTGAGAA

                *       *        
      18401 CCCATATGGTTTGCTTGAGAA
          1 CCCACATGGTTTCCTTGAGAA

                
      18422 CCCA
          1 CCCA

      18426 GGTGGGCAGT


Statistics
Matches: 22,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  21   22  1.00

ACGTcount: A:0.22, C:0.30, G:0.20, T:0.28


Consensus pattern (21 bp):   
CCCACATGGTTTCCTTGAGAA

Found at i:24948 original size:23 final size:24

Alignment explanation


    Indices: 24921--24976  Score: 69
    Period size: 26  Copynumber: 2.3  Consensus size: 24

      24911 GCCCAAAACA

                  *              *  
      24921 CAACAACTA-CACCAAATTTATCT
          1 CAACAAATAGCACCAAATTTAGCT

                                      
      24944 CAACAAAAATAGCACCAAATTTAGCT
          1 CAAC--AAATAGCACCAAATTTAGCT

                   
      24970 CAACAAA
          1 CAACAAA

      24977 AACAGACCAA


Statistics
Matches: 28,  Mismatches: 2, Indels: 5
        0.80            0.06        0.14

Matches are distributed among these distances:
  23    4  0.14
  24    3  0.11
  25    4  0.14
  26   17  0.61

ACGTcount: A:0.50, C:0.27, G:0.04, T:0.20


Consensus pattern (24 bp):   
CAACAAATAGCACCAAATTTAGCT

Found at i:24985 original size:25 final size:26

Alignment explanation


    Indices: 24930--24986  Score: 89
    Period size: 26  Copynumber: 2.2  Consensus size: 26

      24920 ACAACAACTA

                       *           *  
      24930 CACCAAATTTATCTCAACAAAAATAG
          1 CACCAAATTTAGCTCAACAAAAACAG

                                      
      24956 CACCAAATTTAGCTCAACAAAAACAG
          1 CACCAAATTTAGCTCAACAAAAACAG

                  
      24982 -ACCAA
          1 CACCAA

      24987 GACAATTTCT


Statistics
Matches: 29,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  25    5  0.17
  26   24  0.83

ACGTcount: A:0.51, C:0.26, G:0.05, T:0.18


Consensus pattern (26 bp):   
CACCAAATTTAGCTCAACAAAAACAG
Done.