Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004117.1 Corchorus capsularis cultivar CVL-1 contig04125, 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: 6833
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34


Found at i:38 original size:12 final size:12

Alignment explanation


    Indices: 8--38  Score: 55
    Period size: 12  Copynumber: 2.7  Consensus size: 12

          1 TGAGGTC

                        
          8 AAAAAAA-TTTT
          1 AAAAAAATTTTT

                        
         19 AAAAAAATTTTT
          1 AAAAAAATTTTT

                    
         31 AAAAAAAT
          1 AAAAAAAT

         39 GGCTTTGCCG


Statistics
Matches: 19,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  11    7  0.37
  12   12  0.63

ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32


Consensus pattern (12 bp):   
AAAAAAATTTTT

Found at i:5323 original size:14 final size:13

Alignment explanation


    Indices: 5281--5323  Score: 50
    Period size: 14  Copynumber: 3.1  Consensus size: 13

       5271 TTTTCATTAT

                          
       5281 TATTATATAGTATA
          1 TATTATATA-TATA

                 *        
       5295 TATTAAATATAATA
          1 TATTATATAT-ATA

                          
       5309 TCATTATATATATA
          1 T-ATTATATATATA

             
       5323 T
          1 T

       5324 TCATATTGTA


Statistics
Matches: 25,  Mismatches: 2, Indels: 4
        0.81            0.06        0.13

Matches are distributed among these distances:
  13    1  0.04
  14   16  0.64
  15    8  0.32

ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49


Consensus pattern (13 bp):   
TATTATATATATA

Found at i:6700 original size:2 final size:2

Alignment explanation


    Indices: 6695--6829  Score: 65
    Period size: 2  Copynumber: 72.5  Consensus size: 2

       6685 AATAAAAAAC

                                                   *   *          *      *
       6695 AT AT AT A- AT AT AT AT A- AT AT AT -T TT AA AT AT AT TT AT AG
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                *          *                                   *   *    * 
       6734 A- AA AT AT AT TT AT A- AT AT AT AT A- AT AT AT -T TT AA AT TT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                        *               *  *  *                           
       6772 AT AT AT AT TT AT AT AT AT AA AA AC AT AT AT AT A- AT AT AT -T
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

            *   *                       
       6812 TT AA AT AT AT AT -T AT AT A
          1 AT AT AT AT AT AT AT AT AT A

       6830 AAAA


Statistics
Matches: 101,  Mismatches: 22, Indels: 20
        0.71            0.15        0.14

Matches are distributed among these distances:
   1   10  0.10
   2   91  0.90

ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:6755 original size:46 final size:46

Alignment explanation


    Indices: 6669--6832  Score: 177
    Period size: 46  Copynumber: 3.5  Consensus size: 46

       6659 TTTAAAAATT

                   **     *         * *                   
       6669 TATTTTATTTATATATA-ATAAAAAACATATATAATATATATAATA
          1 TATTTTAAATATATTTATATAAAATATATATATAATATATATAATA

                               *         *                
       6714 TATTTTAAATATATTTATAGAAAATATATTTATAATATATATAATA
          1 TATTTTAAATATATTTATATAAAATATATATATAATATATATAATA

                      *   *      * *       * *              
       6760 TATTTTAAATTTATATATATTTATATATATAAAAACATATATATAATA
          1 TATTTTAAATATATTTATA-TAAAATATATATATA-ATATATATAATA

                                     
       6808 TATTTTAAATATATATTATATAAAA
          1 TATTTTAAATATAT-TTATATAAAA

       6833 A


Statistics
Matches: 96,  Mismatches: 19, Indels: 5
        0.80            0.16        0.04

Matches are distributed among these distances:
  45   14  0.15
  46   41  0.43
  47    9  0.09
  48   28  0.29
  49    4  0.04

ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47


Consensus pattern (46 bp):   
TATTTTAAATATATTTATATAAAATATATATATAATATATATAATA

Done.