Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009629.1 Corchorus capsularis cultivar CVL-1 contig09650, 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: 2973
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34


Found at i:1927 original size:9 final size:9

Alignment explanation


    Indices: 1900--1935  Score: 54
    Period size: 9  Copynumber: 3.8  Consensus size: 9

       1890 TACACCCAAA

                     
       1900 AAAAAAAAG
          1 AAAAAAAAG

                       
       1909 AAAAAGAAAAG
          1 -AAAA-AAAAG

                     
       1920 AAAAAAAAG
          1 AAAAAAAAG

                   
       1929 AAAAAAA
          1 AAAAAAA

       1936 GAAGCATATG


Statistics
Matches: 25,  Mismatches: 0, Indels: 3
        0.89            0.00        0.11

Matches are distributed among these distances:
   9   12  0.48
  10    8  0.32
  11    5  0.20

ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00


Consensus pattern (9 bp):   
AAAAAAAAG

Found at i:1934 original size:11 final size:11

Alignment explanation


    Indices: 1898--1935  Score: 53
    Period size: 11  Copynumber: 3.6  Consensus size: 11

       1888 ACTACACCCA

                       
       1898 AAAAAAAAAAG
          1 AAAAAAAAAAG

                 *     
       1909 AAAAAGAAAAG
          1 AAAAAAAAAAG

                       
       1920 --AAAAAAAAG
          1 AAAAAAAAAAG

                   
       1929 AAAAAAA
          1 AAAAAAA

       1936 GAAGCATATG


Statistics
Matches: 23,  Mismatches: 2, Indels: 4
        0.79            0.07        0.14

Matches are distributed among these distances:
   9    8  0.35
  11   15  0.65

ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00


Consensus pattern (11 bp):   
AAAAAAAAAAG

Found at i:2590 original size:27 final size:27

Alignment explanation


    Indices: 2552--2622  Score: 124
    Period size: 27  Copynumber: 2.6  Consensus size: 27

       2542 ACCATATTGC

                                   *   
       2552 CCAGGTCCAAACTGCCCTATACGTTGT
          1 CCAGGTCCAAACTGCCCTATACGGTGT

                                       
       2579 CCAGGTCCAAACTGCCCTATACGGTGT
          1 CCAGGTCCAAACTGCCCTATACGGTGT

                 *           
       2606 CCAGGACCAAACTGCCC
          1 CCAGGTCCAAACTGCCC

       2623 AATATTGGGA


Statistics
Matches: 42,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  27   42  1.00

ACGTcount: A:0.24, C:0.37, G:0.20, T:0.20


Consensus pattern (27 bp):   
CCAGGTCCAAACTGCCCTATACGGTGT
Done.