Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009127.1 Corchorus capsularis cultivar CVL-1 contig09148, 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: 27297
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--37  Score: 74
    Period size: 2  Copynumber: 18.5  Consensus size: 2

                                                                   
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

         38 GATGCAGCAC


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   35  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:8764 original size:1 final size:1

Alignment explanation


    Indices: 8758--8788  Score: 62
    Period size: 1  Copynumber: 31.0  Consensus size: 1

       8748 TGAGAGAGGG

                                           
       8758 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

       8789 GGCACATGAG


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   30  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:19316 original size:22 final size:22

Alignment explanation


    Indices: 19291--19341  Score: 59
    Period size: 21  Copynumber: 2.4  Consensus size: 22

      19281 TAACTGACTT

                                  
      19291 ACATATATGTCATAACATTTAA
          1 ACATATATGTCATAACATTTAA

                      *  *  *   * 
      19313 ACATATA-GTTATTACGTTTGA
          1 ACATATATGTCATAACATTTAA

                    
      19334 ACATATAT
          1 ACATATAT

      19342 CCACTATTCA


Statistics
Matches: 24,  Mismatches: 4, Indels: 2
        0.80            0.13        0.07

Matches are distributed among these distances:
  21   17  0.71
  22    7  0.29

ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39


Consensus pattern (22 bp):   
ACATATATGTCATAACATTTAA

Found at i:20950 original size:12 final size:12

Alignment explanation


    Indices: 20922--20958  Score: 56
    Period size: 12  Copynumber: 3.0  Consensus size: 12

      20912 TTCTTCTTCT

                        *
      20922 CTTCTTTTATCTC
          1 CTTCTTTTA-CTG

                        
      20935 CTTCTTTTACTG
          1 CTTCTTTTACTG

                        
      20947 CTTCTTTTACTG
          1 CTTCTTTTACTG

      20959 GTTTAGACAA


Statistics
Matches: 23,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  12   14  0.61
  13    9  0.39

ACGTcount: A:0.08, C:0.27, G:0.05, T:0.59


Consensus pattern (12 bp):   
CTTCTTTTACTG
Done.