Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011656.1 Corchorus capsularis cultivar CVL-1 contig11677, 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: 41118
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:978 original size:12 final size:12

Alignment explanation


    Indices: 961--1000  Score: 71
    Period size: 12  Copynumber: 3.3  Consensus size: 12

        951 CTTCCACTAC

                    *   
        961 TGCTGCTGCTGG
          1 TGCTGCTGTTGG

                        
        973 TGCTGCTGTTGG
          1 TGCTGCTGTTGG

                        
        985 TGCTGCTGTTGG
          1 TGCTGCTGTTGG

                
        997 TGCT
          1 TGCT

       1001 ACTCAACCCC


Statistics
Matches: 27,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  12   27  1.00

ACGTcount: A:0.00, C:0.20, G:0.40, T:0.40


Consensus pattern (12 bp):   
TGCTGCTGTTGG

Found at i:9992 original size:30 final size:30

Alignment explanation


    Indices: 9958--10019  Score: 115
    Period size: 30  Copynumber: 2.1  Consensus size: 30

       9948 GTGAATCGAA

                                     *    
       9958 TGAAACCTTGAAGCATGTGTTTTTTTAGTG
          1 TGAAACCTTGAAGCATGTGTTTTTTGAGTG

                                          
       9988 TGAAACCTTGAAGCATGTGTTTTTTGAGTG
          1 TGAAACCTTGAAGCATGTGTTTTTTGAGTG

              
      10018 TG
          1 TG

      10020 TGTATGCAAA


Statistics
Matches: 31,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  30   31  1.00

ACGTcount: A:0.23, C:0.10, G:0.26, T:0.42


Consensus pattern (30 bp):   
TGAAACCTTGAAGCATGTGTTTTTTGAGTG

Found at i:19093 original size:12 final size:12

Alignment explanation


    Indices: 19076--19115  Score: 55
    Period size: 12  Copynumber: 3.3  Consensus size: 12

      19066 TTGCTTTTGA

                        
      19076 AAAAAAACAAAC
          1 AAAAAAACAAAC

                        
      19088 AAAAAAACAAA-
          1 AAAAAAACAAAC

             *           
      19099 ACAAAAACAAAAC
          1 AAAAAAAC-AAAC

                
      19112 AAAA
          1 AAAA

      19116 GGACAACTAG


Statistics
Matches: 24,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  11    7  0.29
  12   14  0.58
  13    3  0.12

ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00


Consensus pattern (12 bp):   
AAAAAAACAAAC

Found at i:19093 original size:13 final size:14

Alignment explanation


    Indices: 19075--19115  Score: 50
    Period size: 16  Copynumber: 2.9  Consensus size: 14

      19065 TTTGCTTTTG

                          
      19075 AAAAAAAAC-AAAC
          1 AAAAAAAACAAAAC

                          
      19088 -AAAAAAACAAAAC
          1 AAAAAAAACAAAAC

                           
      19101 AAAAACAAAACAAAA
          1 -AAAA-AAAACAAAA

      19116 GGACAACTAG


Statistics
Matches: 24,  Mismatches: 0, Indels: 5
        0.83            0.00        0.17

Matches are distributed among these distances:
  12    8  0.33
  13    4  0.17
  15    3  0.12
  16    9  0.38

ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00


Consensus pattern (14 bp):   
AAAAAAAACAAAAC

Found at i:38091 original size:6 final size:6

Alignment explanation


    Indices: 38080--38109  Score: 60
    Period size: 6  Copynumber: 5.0  Consensus size: 6

      38070 ATCAGACATA

                                              
      38080 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG
          1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG

      38110 ATTATCTAAC


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.33, T:0.17


Consensus pattern (6 bp):   
TGAAAG

Done.