Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011017.1 Corchorus capsularis cultivar CVL-1 contig11038, 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: 37961
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33


Found at i:8668 original size:30 final size:30

Alignment explanation


    Indices: 8628--8699  Score: 135
    Period size: 30  Copynumber: 2.4  Consensus size: 30

       8618 ATGATCCAGA

                                          
       8628 AAGGAAAAGTGGGTTTAGTGAAGCAGAGCC
          1 AAGGAAAAGTGGGTTTAGTGAAGCAGAGCC

                 *                        
       8658 AAGGAGAAGTGGGTTTAGTGAAGCAGAGCC
          1 AAGGAAAAGTGGGTTTAGTGAAGCAGAGCC

                        
       8688 AAGGAAAAGTGG
          1 AAGGAAAAGTGG

       8700 TGGTGGTTTG


Statistics
Matches: 40,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  30   40  1.00

ACGTcount: A:0.38, C:0.08, G:0.39, T:0.15


Consensus pattern (30 bp):   
AAGGAAAAGTGGGTTTAGTGAAGCAGAGCC

Found at i:11599 original size:6 final size:6

Alignment explanation


    Indices: 11588--11612  Score: 50
    Period size: 6  Copynumber: 4.2  Consensus size: 6

      11578 TTTTATGTTA

                                         
      11588 CAATTT CAATTT CAATTT CAATTT C
          1 CAATTT CAATTT CAATTT CAATTT C

      11613 TTTAGGTAAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   19  1.00

ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48


Consensus pattern (6 bp):   
CAATTT

Found at i:16147 original size:17 final size:16

Alignment explanation


    Indices: 16125--16158  Score: 50
    Period size: 16  Copynumber: 2.1  Consensus size: 16

      16115 AGCAATTTGC

                       *     
      16125 TTATTATATATTAATTT
          1 TTATTATA-ATAAATTT

                            
      16142 TTATTATAATAAATTT
          1 TTATTATAATAAATTT

             
      16158 T
          1 T

      16159 AAAAATGAAT


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

Matches are distributed among these distances:
  16    8  0.50
  17    8  0.50

ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62


Consensus pattern (16 bp):   
TTATTATAATAAATTT

Found at i:22529 original size:19 final size:18

Alignment explanation


    Indices: 22501--22542  Score: 57
    Period size: 19  Copynumber: 2.3  Consensus size: 18

      22491 AATTAATTGT

                              
      22501 TTTAATATTAAATTTTTA
          1 TTTAATATTAAATTTTTA

                       *       
      22519 TTTATATATTATATTTTTA
          1 TTTA-ATATTAAATTTTTA

            *    
      22538 CTTAA
          1 TTTAA

      22543 AAATTACTCA


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  18    5  0.24
  19   16  0.76

ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62


Consensus pattern (18 bp):   
TTTAATATTAAATTTTTA

Found at i:28810 original size:15 final size:15

Alignment explanation


    Indices: 28787--28832  Score: 51
    Period size: 15  Copynumber: 3.1  Consensus size: 15

      28777 AGGTAATTTA

                           
      28787 TAATATTTTATCAAG
          1 TAATATTTTATCAAG

                            
      28802 TAAT-TTTT-TCTAAG
          1 TAATATTTTATC-AAG

                  *         
      28816 ATAATACTTTATCAAG
          1 -TAATATTTTATCAAG

             
      28832 T
          1 T

      28833 TTGTCTAATA


Statistics
Matches: 26,  Mismatches: 1, Indels: 8
        0.74            0.03        0.23

Matches are distributed among these distances:
  13    2  0.08
  14    7  0.27
  15    9  0.35
  16    6  0.23
  17    2  0.08

ACGTcount: A:0.37, C:0.09, G:0.07, T:0.48


Consensus pattern (15 bp):   
TAATATTTTATCAAG
Done.