Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018710.1 Corchorus olitorius cultivar O-4 contig18743, 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: 6139
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35


Found at i:330 original size:20 final size:20

Alignment explanation


    Indices: 307--355  Score: 64
    Period size: 19  Copynumber: 2.5  Consensus size: 20

        297 TAAAAAGGTT

                                
        307 TTACAAAAAACCCAAAAAAA
          1 TTACAAAAAACCCAAAAAAA

                      **        
        327 TTAC-AAAAATTCAAAAAAA
          1 TTACAAAAAACCCAAAAAAA

            *         
        346 ATACAAAAAA
          1 TTACAAAAAA

        356 GAATTTCACT


Statistics
Matches: 25,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  19   16  0.64
  20    9  0.36

ACGTcount: A:0.71, C:0.14, G:0.00, T:0.14


Consensus pattern (20 bp):   
TTACAAAAAACCCAAAAAAA

Found at i:2545 original size:14 final size:14

Alignment explanation


    Indices: 2526--2552  Score: 54
    Period size: 14  Copynumber: 1.9  Consensus size: 14

       2516 CAATTAGACA

                          
       2526 TAATAAATATATTG
          1 TAATAAATATATTG

                         
       2540 TAATAAATATATT
          1 TAATAAATATATT

       2553 TTATAACTTG


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

Matches are distributed among these distances:
  14   13  1.00

ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44


Consensus pattern (14 bp):   
TAATAAATATATTG

Found at i:4927 original size:4 final size:4

Alignment explanation


    Indices: 4751--4913  Score: 139
    Period size: 4  Copynumber: 40.5  Consensus size: 4

       4741 AATTATACCT

                                                       *              *
       4751 TACA TACA TACA TACA TACA TACA TACA TACA TACT TACA TACA TACT
          1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA

                                                 *   **    *   **  *   
       4799 TACA TACA TACA TACA TACA TACA TACA TATA TTTA TAGA TGTA AAC-
          1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA

                **   *       *      *    *    *  *                *      
       4846 TAGTTT TATA TACA CACA TATA TATA TATA CACA TACA TACA TATA TACA
          1 TA--CA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA

                                  
       4896 TACA TACA TACA TACA TA
          1 TACA TACA TACA TACA TA

       4914 TATTTATATA


Statistics
Matches: 131,  Mismatches: 25, Indels: 6
        0.81            0.15        0.04

Matches are distributed among these distances:
   3    1  0.01
   4  128  0.98
   6    2  0.02

ACGTcount: A:0.47, C:0.20, G:0.02, T:0.32


Consensus pattern (4 bp):   
TACA

Found at i:5292 original size:21 final size:21

Alignment explanation


    Indices: 5268--5308  Score: 55
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       5258 ATCATGAACA

                 *  *     *      
       5268 AAGTCTTGTCCAGATCTTGGC
          1 AAGTCCTGCCCAGAACTTGGC

                                
       5289 AAGTCCTGCCCAGAACTTGG
          1 AAGTCCTGCCCAGAACTTGG

       5309 GCTGTTGAGG


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27


Consensus pattern (21 bp):   
AAGTCCTGCCCAGAACTTGGC
Done.