Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014371.1 Corchorus capsularis cultivar CVL-1 contig14392, 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: 10375
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33


Found at i:11 original size:2 final size:2

Alignment explanation


    Indices: 5--40  Score: 72
    Period size: 2  Copynumber: 18.0  Consensus size: 2

          1 TACA

                                                                 
          5 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

         41 TTTCAATAGG


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   34  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:8412 original size:17 final size:16

Alignment explanation


    Indices: 8369--8428  Score: 102
    Period size: 16  Copynumber: 3.7  Consensus size: 16

       8359 GCCTGAACTT

                            
       8369 GAACCCGAAAAAACCC
          1 GAACCCGAAAAAACCC

                            
       8385 GAACCCGAAAAAACCC
          1 GAACCCGAAAAAACCC

                             
       8401 GAACCCGAAAAAAACCC
          1 GAACCCG-AAAAAACCC

               *       
       8418 GAATCCGAAAA
          1 GAACCCGAAAA

       8429 TTTACGAAAA


Statistics
Matches: 42,  Mismatches: 1, Indels: 2
        0.93            0.02        0.04

Matches are distributed among these distances:
  16   27  0.64
  17   15  0.36

ACGTcount: A:0.52, C:0.33, G:0.13, T:0.02


Consensus pattern (16 bp):   
GAACCCGAAAAAACCC

Found at i:8604 original size:32 final size:32

Alignment explanation


    Indices: 8568--8630  Score: 90
    Period size: 32  Copynumber: 2.0  Consensus size: 32

       8558 TGGCCAAAAC

                   *         *              
       8568 CCAAACAGAACCCGAACTCGAATTAACCTGAT
          1 CCAAACACAACCCGAACCCGAATTAACCTGAT

                 **                        
       8600 CCAAATTCAACCCGAACCCGAATTAACCTGA
          1 CCAAACACAACCCGAACCCGAATTAACCTGA

       8631 CCTAAATCCA


Statistics
Matches: 27,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  32   27  1.00

ACGTcount: A:0.40, C:0.33, G:0.11, T:0.16


Consensus pattern (32 bp):   
CCAAACACAACCCGAACCCGAATTAACCTGAT

Found at i:8627 original size:16 final size:16

Alignment explanation


    Indices: 8576--8627  Score: 52
    Period size: 16  Copynumber: 3.2  Consensus size: 16

       8566 ACCCAAACAG

                     *      
       8576 AACCCGAACTCGAATT
          1 AACCCGAACCCGAATT

                *   *  *    
       8592 AACCTG-ATCCAAATT
          1 AACCCGAACCCGAATT

                             
       8607 CAACCCGAACCCGAATT
          1 -AACCCGAACCCGAATT

                
       8624 AACC
          1 AACC

       8628 TGACCTAAAT


Statistics
Matches: 27,  Mismatches: 7, Indels: 4
        0.71            0.18        0.11

Matches are distributed among these distances:
  15    6  0.22
  16   14  0.52
  17    7  0.26

ACGTcount: A:0.38, C:0.35, G:0.10, T:0.17


Consensus pattern (16 bp):   
AACCCGAACCCGAATT
Done.