Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009077.1 Corchorus capsularis cultivar CVL-1 contig09098, 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: 14619
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30


Found at i:10445 original size:5 final size:5

Alignment explanation


    Indices: 10435--10460  Score: 52
    Period size: 5  Copynumber: 5.2  Consensus size: 5

      10425 CTTGTAAACA

                                           
      10435 TAAGT TAAGT TAAGT TAAGT TAAGT T
          1 TAAGT TAAGT TAAGT TAAGT TAAGT T

      10461 TTTAATAAAG


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   21  1.00

ACGTcount: A:0.38, C:0.00, G:0.19, T:0.42


Consensus pattern (5 bp):   
TAAGT

Found at i:13759 original size:17 final size:17

Alignment explanation


    Indices: 13737--13777  Score: 73
    Period size: 17  Copynumber: 2.4  Consensus size: 17

      13727 ATCACCCCCT

                             
      13737 AGATCACTAGTGATCTA
          1 AGATCACTAGTGATCTA

                          *  
      13754 AGATCACTAGTGATGTA
          1 AGATCACTAGTGATCTA

                   
      13771 AGATCAC
          1 AGATCAC

      13778 CGGTGATTAA


Statistics
Matches: 23,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  17   23  1.00

ACGTcount: A:0.37, C:0.17, G:0.20, T:0.27


Consensus pattern (17 bp):   
AGATCACTAGTGATCTA

Found at i:13783 original size:17 final size:17

Alignment explanation


    Indices: 13737--13784  Score: 60
    Period size: 17  Copynumber: 2.8  Consensus size: 17

      13727 ATCACCCCCT

                   *         
      13737 AGATCACTAGTGATCTA
          1 AGATCACCAGTGATCTA

                   *      *  
      13754 AGATCACTAGTGATGTA
          1 AGATCACCAGTGATCTA

                    *     
      13771 AGATCACCGGTGAT
          1 AGATCACCAGTGAT

      13785 TAAAGATTAC


Statistics
Matches: 28,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  17   28  1.00

ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27


Consensus pattern (17 bp):   
AGATCACCAGTGATCTA

Found at i:14410 original size:16 final size:16

Alignment explanation


    Indices: 14368--14496  Score: 117
    Period size: 16  Copynumber: 8.1  Consensus size: 16

      14358 GAACCCGCCC

                             
      14368 GACCCGAATGACCCGCA
          1 GACCCGAATGACCCG-A

                 *          
      14385 -A-CCAAATGACCCGA
          1 GACCCGAATGACCCGA

                             
      14399 GACCCGAATGACCCGTA
          1 GACCCGAATGACCCG-A

                             
      14416 -ACCC-AGATGACCCGA
          1 GACCCGA-ATGACCCGA

            *               
      14431 AACCCGAATGACCC-A
          1 GACCCGAATGACCCGA

             *      *        
      14446 TAACCCGAGTGACCCGA
          1 -GACCCGAATGACCCGA

                             
      14463 GACCC-ATATGACCCGA
          1 GACCCGA-ATGACCCGA

            *        *      
      14479 AACCCGAATAACCCGA
          1 GACCCGAATGACCCGA

              
      14495 GA
          1 GA

      14497 AGTTAACCCG


Statistics
Matches: 94,  Mismatches: 8, Indels: 21
        0.76            0.07        0.17

Matches are distributed among these distances:
  14    1  0.01
  15   16  0.17
  16   73  0.78
  17    4  0.04

ACGTcount: A:0.35, C:0.37, G:0.19, T:0.09


Consensus pattern (16 bp):   
GACCCGAATGACCCGA

Found at i:14436 original size:32 final size:32

Alignment explanation


    Indices: 14368--14496  Score: 149
    Period size: 32  Copynumber: 4.1  Consensus size: 32

      14358 GAACCCGCCC

                           *      *         
      14368 GACCCGAATGACCCGCAA-CCAAATGACCCGA
          1 GACCCGAATGACCCGTAACCCAGATGACCCGA

                                            
      14399 GACCCGAATGACCCGTAACCCAGATGACCCGA
          1 GACCCGAATGACCCGTAACCCAGATGACCCGA

            *             *                  
      14431 AACCCGAATGACCCATAACCC-GAGTGACCCGA
          1 GACCCGAATGACCCGTAACCCAGA-TGACCCGA

                            *          *      
      14463 GACCC-ATATGACCCGAAACCC-GAATAACCCGA
          1 GACCCGA-ATGACCCGTAACCCAG-ATGACCCGA

              
      14495 GA
          1 GA

      14497 AGTTAACCCG


Statistics
Matches: 86,  Mismatches: 8, Indels: 7
        0.85            0.08        0.07

Matches are distributed among these distances:
  31   20  0.23
  32   65  0.76
  33    1  0.01

ACGTcount: A:0.35, C:0.37, G:0.19, T:0.09


Consensus pattern (32 bp):   
GACCCGAATGACCCGTAACCCAGATGACCCGA

Found at i:14444 original size:48 final size:48

Alignment explanation


    Indices: 14375--14496  Score: 151
    Period size: 48  Copynumber: 2.6  Consensus size: 48

      14365 CCCGACCCGA

                    *     *                                  
      14375 ATGACCCGCAA-CCAAATGACCCGAGACCCGAATGACCCGTA-ACCCAG
          1 ATGACCCGAAACCCGAATGACCCGAGACCCGAATGACCCG-AGACCCAG

                                      *      *              *
      14422 ATGACCCGAAACCCGAATGACCC-ATAACCCGAGTGACCCGAGACCCAT
          1 ATGACCCGAAACCCGAATGACCCGA-GACCCGAATGACCCGAGACCCAG

                              *        
      14470 ATGACCCGAAACCCGAATAACCCGAGA
          1 ATGACCCGAAACCCGAATGACCCGAGA

      14497 AGTTAACCCG


Statistics
Matches: 64,  Mismatches: 7, Indels: 7
        0.82            0.09        0.09

Matches are distributed among these distances:
  47   12  0.19
  48   51  0.80
  49    1  0.02

ACGTcount: A:0.35, C:0.37, G:0.19, T:0.09


Consensus pattern (48 bp):   
ATGACCCGAAACCCGAATGACCCGAGACCCGAATGACCCGAGACCCAG
Done.