Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015202.1 Corchorus capsularis cultivar CVL-1 contig15223, 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: 18297
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31


Found at i:1841 original size:21 final size:21

Alignment explanation


    Indices: 1815--1855  Score: 73
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       1805 GTAGTTTTTT

                                 
       1815 ATCACTATTGACGTGCAAAAA
          1 ATCACTATTGACGTGCAAAAA

                           *    
       1836 ATCACTATTGACGTGGAAAA
          1 ATCACTATTGACGTGCAAAA

       1856 TTGCACGTTG


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   19  1.00

ACGTcount: A:0.41, C:0.17, G:0.17, T:0.24


Consensus pattern (21 bp):   
ATCACTATTGACGTGCAAAAA

Found at i:13357 original size:15 final size:15

Alignment explanation


    Indices: 13337--13365  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

      13327 CTAATAGCAT

                           
      13337 AATAGCCTCTGCTAC
          1 AATAGCCTCTGCTAC

                          
      13352 AATAGCCTCTGCTA
          1 AATAGCCTCTGCTA

      13366 TAGAAGCAGT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.28, C:0.31, G:0.14, T:0.28


Consensus pattern (15 bp):   
AATAGCCTCTGCTAC

Found at i:15422 original size:33 final size:33

Alignment explanation


    Indices: 15385--15478  Score: 118
    Period size: 33  Copynumber: 2.8  Consensus size: 33

      15375 ATTTGTGACT

                                *             
      15385 GGCCACGCGACTTGGAGATGTCC-GCGCAACACC
          1 GGCCACGCGACTTGGAGATGCCCGGC-CAACACC

                 *                      *    
      15418 GGCCATGCGACTTGGAGATGCCCGGCCATCACC
          1 GGCCACGCGACTTGGAGATGCCCGGCCAACACC

                       *   **           
      15451 GGCCACGCGACATGGCCATGCCCGGCCA
          1 GGCCACGCGACTTGGAGATGCCCGGCCA

      15479 CATGACTCGG


Statistics
Matches: 53,  Mismatches: 7, Indels: 2
        0.85            0.11        0.03

Matches are distributed among these distances:
  33   51  0.96
  34    2  0.04

ACGTcount: A:0.19, C:0.38, G:0.31, T:0.12


Consensus pattern (33 bp):   
GGCCACGCGACTTGGAGATGCCCGGCCAACACC

Found at i:16558 original size:18 final size:19

Alignment explanation


    Indices: 16531--16567  Score: 67
    Period size: 18  Copynumber: 2.0  Consensus size: 19

      16521 AGTTATATCG

                               
      16531 AAAAATATAAAAAAAAAAT
          1 AAAAATATAAAAAAAAAAT

                               
      16550 AAAAA-ATAAAAAAAAAAT
          1 AAAAATATAAAAAAAAAAT

      16568 TCGACCAGAA


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  18   13  0.72
  19    5  0.28

ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14


Consensus pattern (19 bp):   
AAAAATATAAAAAAAAAAT
Done.