Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009735.1 Corchorus capsularis cultivar CVL-1 contig09756, 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: 27385
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.31


Found at i:2125 original size:18 final size:17

Alignment explanation


    Indices: 2094--2127  Score: 50
    Period size: 18  Copynumber: 1.9  Consensus size: 17

       2084 TAGCATTATG

                     *       
       2094 CCTTTGGCATCCTTGAA
          1 CCTTTGGCAACCTTGAA

                             
       2111 CCTTTCGGCAACCTTGA
          1 CCTTT-GGCAACCTTGA

       2128 CATATGCGGT


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  17    5  0.33
  18   10  0.67

ACGTcount: A:0.18, C:0.32, G:0.18, T:0.32


Consensus pattern (17 bp):   
CCTTTGGCAACCTTGAA

Found at i:11574 original size:36 final size:36

Alignment explanation


    Indices: 11532--11604  Score: 146
    Period size: 36  Copynumber: 2.0  Consensus size: 36

      11522 TTAACTTTCC

                                                
      11532 CACCCTTTTAGGTGGGAATGCCATTCCCACCACTTT
          1 CACCCTTTTAGGTGGGAATGCCATTCCCACCACTTT

                                                
      11568 CACCCTTTTAGGTGGGAATGCCATTCCCACCACTTT
          1 CACCCTTTTAGGTGGGAATGCCATTCCCACCACTTT

             
      11604 C
          1 C

      11605 CCACTTAAAT


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  36   37  1.00

ACGTcount: A:0.19, C:0.34, G:0.16, T:0.30


Consensus pattern (36 bp):   
CACCCTTTTAGGTGGGAATGCCATTCCCACCACTTT

Found at i:12801 original size:32 final size:31

Alignment explanation


    Indices: 12752--12863  Score: 118
    Period size: 32  Copynumber: 3.5  Consensus size: 31

      12742 AAAATAGCCG

                       *             *       
      12752 AGCCGCCCCACCTGGGCGGCCTGCCGTGGCT-A
          1 AGCCGCCCCA-GTGGGCGGCCTGCCATGG-TGA

                                   **        
      12784 AGCCGCCCCAGTGGGGCGGCCTTTTCATGGTGA
          1 AGCCGCCCCAGT-GGGCGGCC-TGCCATGGTGA

              *     *                       
      12817 AGACGCCCTAGTGGGCGGCCTGCCCATGGTGA
          1 AGCCGCCCCAGTGGGCGGCCTG-CCATGGTGA

                           
      12849 AGCCGCCCCAGTGGG
          1 AGCCGCCCCAGTGGG

      12864 GCCTCCCAAG


Statistics
Matches: 66,  Mismatches: 10, Indels: 8
        0.79            0.12        0.10

Matches are distributed among these distances:
  31    2  0.03
  32   48  0.73
  33   16  0.24

ACGTcount: A:0.12, C:0.36, G:0.37, T:0.15


Consensus pattern (31 bp):   
AGCCGCCCCAGTGGGCGGCCTGCCATGGTGA

Found at i:16638 original size:15 final size:15

Alignment explanation


    Indices: 16618--16648  Score: 62
    Period size: 15  Copynumber: 2.1  Consensus size: 15

      16608 TTGACATAAA

                           
      16618 ATACCCCAATTGCTC
          1 ATACCCCAATTGCTC

                           
      16633 ATACCCCAATTGCTC
          1 ATACCCCAATTGCTC

             
      16648 A
          1 A

      16649 CTCCCAATTA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.29, C:0.39, G:0.06, T:0.26


Consensus pattern (15 bp):   
ATACCCCAATTGCTC
Done.