Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000100.1 Corchorus capsularis cultivar CVL-1 contig00100, 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: 1905
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:669 original size:2 final size:2

Alignment explanation


    Indices: 645--777  Score: 83
    Period size: 2  Copynumber: 67.5  Consensus size: 2

        635 GAATGTACAA

                              *   *     *           *     *    *          
        645 AT AT AT A- AT AT CT AC AT AC AT AT AT AC AT AC AT GT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                                      *                *  *  *  *  *       
        686 AT AT AT AT -T CAT AT AT AC AT AT AT AT AT TT GT GT GT GT AT AT
          1 AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                              *        *                    *        *    
        728 AT AT AT AT AT AT CT AT AT GT AT A- AT AT AT AT GT AT AT CT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

               *         
        769 AT GT AT AT A
          1 AT AT AT AT A

        778 CAATAGGCAT


Statistics
Matches: 100,  Mismatches: 27, Indels: 8
        0.74            0.20        0.06

Matches are distributed among these distances:
   1    3  0.03
   2   96  0.96
   3    1  0.01

ACGTcount: A:0.41, C:0.07, G:0.06, T:0.46


Consensus pattern (2 bp):   
AT

Found at i:763 original size:25 final size:25

Alignment explanation


    Indices: 679--775  Score: 97
    Period size: 26  Copynumber: 3.8  Consensus size: 25

        669 TACATACATG

                     *               * 
        679 TATATATATATATAT-TCATATATACA
          1 TATATATATCTATATGT-ATA-ATATA

                     * * *   *        
        705 TATATATATTTGTGTGTGTATATATA
          1 TATATATATCTATATGTATA-ATATA

                                     
        731 TATATATATCTATATGTATAATATA
          1 TATATATATCTATATGTATAATATA

               *                
        756 TATGTATATCTATATGTATA
          1 TATATATATCTATATGTATA

        776 TACAATAGGC


Statistics
Matches: 60,  Mismatches: 10, Indels: 3
        0.82            0.14        0.04

Matches are distributed among these distances:
  25   24  0.40
  26   35  0.58
  27    1  0.02

ACGTcount: A:0.39, C:0.04, G:0.07, T:0.49


Consensus pattern (25 bp):   
TATATATATCTATATGTATAATATA

Found at i:980 original size:20 final size:20

Alignment explanation


    Indices: 955--996  Score: 66
    Period size: 20  Copynumber: 2.1  Consensus size: 20

        945 ACAATCTGGA

                                
        955 TTGCTAAACACCGCCCCATT
          1 TTGCTAAACACCGCCCCATT

                  **            
        975 TTGCTATTCACCGCCCCATT
          1 TTGCTAAACACCGCCCCATT

              
        995 TT
          1 TT

        997 TTACGCTTTT


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.19, C:0.38, G:0.10, T:0.33


Consensus pattern (20 bp):   
TTGCTAAACACCGCCCCATT

Found at i:1339 original size:32 final size:32

Alignment explanation


    Indices: 1298--1359  Score: 97
    Period size: 32  Copynumber: 1.9  Consensus size: 32

       1288 ATTTTGGTCT

                          *                 
       1298 AGCCGCCCCACCAGGGCGGCCTGCCGTGGCGA
          1 AGCCGCCCCACCAGCGCGGCCTGCCGTGGCGA

                      **                  
       1330 AGCCGCCCCATGAGCGCGGCCTGCCGTGGC
          1 AGCCGCCCCACCAGCGCGGCCTGCCGTGGC

       1360 TGAACCGTCC


Statistics
Matches: 27,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  32   27  1.00

ACGTcount: A:0.11, C:0.44, G:0.37, T:0.08


Consensus pattern (32 bp):   
AGCCGCCCCACCAGCGCGGCCTGCCGTGGCGA
Done.