Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010581.1 Corchorus olitorius cultivar O-4 contig10613, 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: 7050
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.36


Found at i:947 original size:24 final size:24

Alignment explanation


    Indices: 919--965  Score: 94
    Period size: 24  Copynumber: 2.0  Consensus size: 24

        909 CTTTTTAAAG

                                    
        919 ATTTATTTTTGTAAAAGGATTAGT
          1 ATTTATTTTTGTAAAAGGATTAGT

                                   
        943 ATTTATTTTTGTAAAAGGATTAG
          1 ATTTATTTTTGTAAAAGGATTAG

        966 GGTATATTAA


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

Matches are distributed among these distances:
  24   23  1.00

ACGTcount: A:0.34, C:0.00, G:0.17, T:0.49


Consensus pattern (24 bp):   
ATTTATTTTTGTAAAAGGATTAGT

Found at i:973 original size:24 final size:24

Alignment explanation


    Indices: 922--973  Score: 77
    Period size: 24  Copynumber: 2.2  Consensus size: 24

        912 TTTAAAGATT

                                *  *
        922 TATTTTTGTAAAAGGATTAGTATT
          1 TATTTTTGTAAAAGGATTAGGATA

                                 *  
        946 TATTTTTGTAAAAGGATTAGGGTA
          1 TATTTTTGTAAAAGGATTAGGATA

                
        970 TATT
          1 TATT

        974 AAGAGATTAA


Statistics
Matches: 25,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  24   25  1.00

ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48


Consensus pattern (24 bp):   
TATTTTTGTAAAAGGATTAGGATA

Found at i:1785 original size:23 final size:24

Alignment explanation


    Indices: 1745--1790  Score: 76
    Period size: 23  Copynumber: 2.0  Consensus size: 24

       1735 TTTTTTTAAG

                                    
       1745 ATTTATTATTGTAAAAGGATTAGT
          1 ATTTATTATTGTAAAAGGATTAGT

                      *            
       1769 ATTTATT-TTTTAAAAGGATTAG
          1 ATTTATTATTGTAAAAGGATTAG

       1791 GGTATATTAA


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  23   14  0.67
  24    7  0.33

ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48


Consensus pattern (24 bp):   
ATTTATTATTGTAAAAGGATTAGT

Found at i:3369 original size:23 final size:22

Alignment explanation


    Indices: 3339--3442  Score: 88
    Period size: 22  Copynumber: 4.7  Consensus size: 22

       3329 TCACATTGTG

                           *  * *  
       3339 AAATTTTGATAACCTTGAGTGTA
          1 AAATTTTGATAACCTCG-CTATA

                        *         
       3362 AAATTTTGATAATCTCGCTATA
          1 AAATTTTGATAACCTCGCTATA

                          * *     
       3384 AAATTTTGATAACCACACTATA
          1 AAATTTTGATAACCTCGCTATA

                    *     *         
       3406 AAA--TTGGTAATCGT-GCTATAA
          1 AAATTTTGATAA-CCTCGCTAT-A

                            
       3427 AAATTTTGATAACCTC
          1 AAATTTTGATAACCTC

       3443 CTCACAAATT


Statistics
Matches: 63,  Mismatches: 13, Indels: 10
        0.73            0.15        0.12

Matches are distributed among these distances:
  20   10  0.16
  21    5  0.08
  22   27  0.43
  23   21  0.33

ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37


Consensus pattern (22 bp):   
AAATTTTGATAACCTCGCTATA

Found at i:3410 original size:67 final size:67

Alignment explanation


    Indices: 3250--3410  Score: 157
    Period size: 67  Copynumber: 2.4  Consensus size: 67

       3240 TCCAACGTAG

                *                     *                 *                    
       3250 AAATATTGATAACCACACTGTGAAAAATTTGATAACCTCAATACGAAATTTCGATAATCTCCCTA
          1 AAATTTTGATAACCACACTGT-AAAATTTTGATAACCTCAATACAAAATTTCGATAATCTCCCTA

               
       3315 TGA
         65 TGA

                         *    *   *                * * **       *         *  
       3318 AAA-TTT-ATTAATCACATTGTGAAATTTTGATAACCTTGAGTGTAAAATTTTGATAATCTCGCT
          1 AAATTTTGA-TAACCACACTGTAAAATTTTGATAACC-TCAATACAAAATTTCGATAATCTCCCT

                
       3381 AT-A
         64 ATGA

                               *       
       3384 AAATTTTGATAACCACACTATAAAATT
          1 AAATTTTGATAACCACACTGTAAAATT

       3411 GGTAATCGTG


Statistics
Matches: 73,  Mismatches: 16, Indels: 9
        0.74            0.16        0.09

Matches are distributed among these distances:
  66   18  0.25
  67   51  0.70
  68    4  0.05

ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35


Consensus pattern (67 bp):   
AAATTTTGATAACCACACTGTAAAATTTTGATAACCTCAATACAAAATTTCGATAATCTCCCTAT
GA
Done.