Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008480.1 Corchorus capsularis cultivar CVL-1 contig08501, 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: 13592
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32


Found at i:836 original size:20 final size:21

Alignment explanation


    Indices: 803--842  Score: 55
    Period size: 20  Copynumber: 2.0  Consensus size: 21

        793 TTCAACTTCA

                   * *           
        803 ATACTATTACTTTA-TAGTTT
          1 ATACTATAAATTTACTAGTTT

                                
        823 ATACTATAAATTTACTAGTT
          1 ATACTATAAATTTACTAGTT

        843 AAATAAGGTG


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  20   12  0.71
  21    5  0.29

ACGTcount: A:0.35, C:0.10, G:0.05, T:0.50


Consensus pattern (21 bp):   
ATACTATAAATTTACTAGTTT

Found at i:2134 original size:13 final size:13

Alignment explanation


    Indices: 2113--2143  Score: 53
    Period size: 13  Copynumber: 2.4  Consensus size: 13

       2103 GCATAAAGAC

                *        
       2113 TTAAATAATAAAA
          1 TTAATTAATAAAA

                         
       2126 TTAATTAATAAAA
          1 TTAATTAATAAAA

                 
       2139 TTAAT
          1 TTAAT

       2144 AAACTCAAAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  13   17  1.00

ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39


Consensus pattern (13 bp):   
TTAATTAATAAAA

Found at i:6489 original size:65 final size:65

Alignment explanation


    Indices: 6407--6612  Score: 205
    Period size: 77  Copynumber: 3.0  Consensus size: 65

       6397 ATTACTAACC

                                      * *                 *            *     
       6407 CTCTCATATTCGTTGATCACATTAGATCTCGACTACTCCGGATTTAGGCCGCATCGGACTTGAAA
          1 CTCTCATATTCGTTGATCACATTAGACCCCGACTACTCCGGATTTAAGCCGCATCGGACCTGAAA

                      *                                                      
       6472 CTCTCATATTTGTTGATCACATTAGACCCCGACTACTCCGGATTTAAGCTGCGTCGGACCTGAAA
          1 CTCTCATATTCGTTGATCACATTAGACCCCGACTACTCCGGATTTAAGC--CG-C--A--T----

               * *      
       6537 CCGAAACTGAAA
         55 -CGGACCTGAAA

                       *                                   * *  *           
       6549 CTCTCATATTCATTGATCACATTAGACCCCGACTACTCCGGATTTAAACTGCGTCGGACCTGAA
          1 CTCTCATATTCGTTGATCACATTAGACCCCGACTACTCCGGATTTAAGCCGCATCGGACCTGAA

       6613 GCCGAAACTG


Statistics
Matches: 115,  Mismatches: 14, Indels: 24
        0.75            0.09        0.16

Matches are distributed among these distances:
  65   53  0.46
  67    2  0.02
  68    1  0.01
  70    2  0.02
  72    1  0.01
  74    1  0.01
  75    1  0.01
  77   54  0.47

ACGTcount: A:0.27, C:0.28, G:0.17, T:0.28


Consensus pattern (65 bp):   
CTCTCATATTCGTTGATCACATTAGACCCCGACTACTCCGGATTTAAGCCGCATCGGACCTGAAA

Found at i:6594 original size:77 final size:77

Alignment explanation


    Indices: 6467--6627  Score: 286
    Period size: 77  Copynumber: 2.1  Consensus size: 77

       6457 GCATCGGACT

                           **                                   *            
       6467 TGAAACTCTCATATTTGTTGATCACATTAGACCCCGACTACTCCGGATTTAAGCTGCGTCGGACC
          1 TGAAACTCTCATATTCATTGATCACATTAGACCCCGACTACTCCGGATTTAAACTGCGTCGGACC

                        
       6532 TGAAACCGAAAC
         66 TGAAACCGAAAC

                                                                             
       6544 TGAAACTCTCATATTCATTGATCACATTAGACCCCGACTACTCCGGATTTAAACTGCGTCGGACC
          1 TGAAACTCTCATATTCATTGATCACATTAGACCCCGACTACTCCGGATTTAAACTGCGTCGGACC

                *       
       6609 TGAAGCCGAAAC
         66 TGAAACCGAAAC

                   
       6621 TGAAACT
          1 TGAAACT

       6628 GAGGCAATCA


Statistics
Matches: 80,  Mismatches: 4, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  77   80  1.00

ACGTcount: A:0.30, C:0.27, G:0.17, T:0.25


Consensus pattern (77 bp):   
TGAAACTCTCATATTCATTGATCACATTAGACCCCGACTACTCCGGATTTAAACTGCGTCGGACC
TGAAACCGAAAC

Found at i:9702 original size:64 final size:65

Alignment explanation


    Indices: 9600--9766  Score: 187
    Period size: 64  Copynumber: 2.6  Consensus size: 65

       9590 AAGTAGTCTC

                     * *              *             *                *     * 
       9600 TCACTTATTTCTCTAAAATAAGGTCTTGAGTTCGAGTTTTGTAAAT-GAATGG-TC-GGTTCGGG
          1 TCACTTATTCCCCTAAAATAAGGTCTCGAGTTCGAGTTTTATAAATAG-ATGGTTCAAGTT-GCG

              
       9662 TG
         64 TG

                          *            *     *        *     *                
       9664 TCACTTATTCCCCTGAAATAAGGTCTCAAGTTCAAGTTTTATGAATAGTTGGTTCAAGTTGCGTG
          1 TCACTTATTCCCCTAAAATAAGGTCTCGAGTTCGAGTTTTATAAATAGATGGTTCAAGTTGCGTG

                 *                                
       9729 TCACTAATTCCCCTAAAATAAGGTCTCGAGTTCGAGTT
          1 TCACTTATTCCCCTAAAATAAGGTCTCGAGTTCGAGTT

       9767 CGAGTTTTAG


Statistics
Matches: 85,  Mismatches: 15, Indels: 5
        0.81            0.14        0.05

Matches are distributed among these distances:
  64   41  0.48
  65   41  0.48
  66    3  0.04

ACGTcount: A:0.26, C:0.17, G:0.21, T:0.37


Consensus pattern (65 bp):   
TCACTTATTCCCCTAAAATAAGGTCTCGAGTTCGAGTTTTATAAATAGATGGTTCAAGTTGCGTG
Done.