Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008168.1 Corchorus capsularis cultivar CVL-1 contig08189, 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: 8567
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35


Found at i:2561 original size:55 final size:54

Alignment explanation


    Indices: 2484--2622  Score: 154
    Period size: 54  Copynumber: 2.6  Consensus size: 54

       2474 TACCATAATT

                *          * *       *               *   *         
       2484 CTTTGGGGTTTGACCGTACATGTACGATGATGTTTTTTGTGTTTTGACTATCAAA
          1 CTTTCGGGTTTGACCATGCATGTACAATGATG-TTTTTGTGGTTTAACTATCAAA

                         *               *                    *   
       2539 CTTTCGGGTTTGAGCATGCATGTACAATGTTGTTTTTGTGGTTTAACTATTAAA
          1 CTTTCGGGTTTGACCATGCATGTACAATGATGTTTTTGTGGTTTAACTATCAAA

                *   *                      
       2593 -TTTTGAGATTTGACCATGCATGTACAATGA
          1 CTTTCG-GGTTTGACCATGCATGTACAATGA

       2623 AATACTTTTT


Statistics
Matches: 70,  Mismatches: 13, Indels: 3
        0.81            0.15        0.03

Matches are distributed among these distances:
  53    4  0.06
  54   40  0.57
  55   26  0.37

ACGTcount: A:0.23, C:0.12, G:0.22, T:0.42


Consensus pattern (54 bp):   
CTTTCGGGTTTGACCATGCATGTACAATGATGTTTTTGTGGTTTAACTATCAAA

Found at i:8465 original size:16 final size:16

Alignment explanation


    Indices: 8445--8560  Score: 117
    Period size: 16  Copynumber: 7.2  Consensus size: 16

       8435 TCATTTGAGT

                           *
       8445 TCGGGTCAATCGGGTT
          1 TCGGGTCAATCGGGTC

                            
       8461 TCGGGTCAATCGGGTC
          1 TCGGGTCAATCGGGTC

                  * * *     
       8477 TCGGGTTATTTGGGTC
          1 TCGGGTCAATCGGGTC

                     *       
       8493 TCGGG-CTATTCGGGTC
          1 TCGGGTC-AATCGGGTC

                  *        *
       8509 TCGGGTTAATCGGGTT
          1 TCGGGTCAATCGGGTC

                    *    *  
       8525 TCGGGTCATTCGGTTC
          1 TCGGGTCAATCGGGTC

             *    *         
       8541 TTGGGTTAATCGGGTC
          1 TCGGGTCAATCGGGTC

                
       8557 TCGG
          1 TCGG

       8561 ATTTTCG


Statistics
Matches: 80,  Mismatches: 18, Indels: 4
        0.78            0.18        0.04

Matches are distributed among these distances:
  16   80  1.00

ACGTcount: A:0.09, C:0.19, G:0.37, T:0.34


Consensus pattern (16 bp):   
TCGGGTCAATCGGGTC

Found at i:8497 original size:32 final size:32

Alignment explanation


    Indices: 8445--8560  Score: 144
    Period size: 32  Copynumber: 3.6  Consensus size: 32

       8435 TCATTTGAGT

                  *        *        *       
       8445 TCGGGTCAATCGGGTTTCGGGTCAATCGGGTC
          1 TCGGGTTAATCGGGTCTCGGGTCATTCGGGTC

                    * *                      
       8477 TCGGGTTATTTGGGTCTCGGG-CTATTCGGGTC
          1 TCGGGTTAATCGGGTCTCGGGTC-ATTCGGGTC

                           *             *  
       8509 TCGGGTTAATCGGGTTTCGGGTCATTCGGTTC
          1 TCGGGTTAATCGGGTCTCGGGTCATTCGGGTC

             *                  
       8541 TTGGGTTAATCGGGTCTCGG
          1 TCGGGTTAATCGGGTCTCGG

       8561 ATTTTCG


Statistics
Matches: 71,  Mismatches: 11, Indels: 4
        0.83            0.13        0.05

Matches are distributed among these distances:
  31    1  0.01
  32   69  0.97
  33    1  0.01

ACGTcount: A:0.09, C:0.19, G:0.37, T:0.34


Consensus pattern (32 bp):   
TCGGGTTAATCGGGTCTCGGGTCATTCGGGTC

Found at i:8513 original size:48 final size:48

Alignment explanation


    Indices: 8452--8560  Score: 137
    Period size: 48  Copynumber: 2.3  Consensus size: 48

       8442 AGTTCGGGTC

                    *                      *   *            
       8452 AATCGGGTTTCGGGTCAATCGGGTCTCGGGTTATTTGGGTCTCGGGCT
          1 AATCGGGTCTCGGGTCAATCGGGTCTCGGGTCATTCGGGTCTCGGGCT

             *             *        *             *   *   * 
       8500 ATTCGGGTCTCGGGTTAATCGGGTTTCGGGTCATTCGGTTCTTGGGTT
          1 AATCGGGTCTCGGGTCAATCGGGTCTCGGGTCATTCGGGTCTCGGGCT

                         
       8548 AATCGGGTCTCGG
          1 AATCGGGTCTCGG

       8561 ATTTTCG


Statistics
Matches: 51,  Mismatches: 10, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  48   51  1.00

ACGTcount: A:0.10, C:0.18, G:0.37, T:0.35


Consensus pattern (48 bp):   
AATCGGGTCTCGGGTCAATCGGGTCTCGGGTCATTCGGGTCTCGGGCT
Done.