Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015455.1 Corchorus capsularis cultivar CVL-1 contig15476, 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: 5912
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30


Found at i:548 original size:27 final size:24

Alignment explanation


    Indices: 498--571  Score: 69
    Period size: 23  Copynumber: 3.0  Consensus size: 24

        488 AGCACAAGTG

                    *         **    
        498 ACCGGCCACGCGACATGGCCATGC
          1 ACCGGCCATGCGACATGGAGATGC

                                       
        522 AAAACCGGCCATGCGACATGGAGATGC
          1 ---ACCGGCCATGCGACATGGAGATGC

                *         *         
        549 -CCGACCATGCGACTTGGAGATGC
          1 ACCGGCCATGCGACATGGAGATGC

        572 CCGTCCAACA


Statistics
Matches: 42,  Mismatches: 5, Indels: 4
        0.82            0.10        0.08

Matches are distributed among these distances:
  23   21  0.50
  27   21  0.50

ACGTcount: A:0.26, C:0.32, G:0.30, T:0.12


Consensus pattern (24 bp):   
ACCGGCCATGCGACATGGAGATGC

Found at i:556 original size:23 final size:23

Alignment explanation


    Indices: 530--574  Score: 81
    Period size: 23  Copynumber: 2.0  Consensus size: 23

        520 GCAAAACCGG

                                   
        530 CCATGCGACATGGAGATGCCCGA
          1 CCATGCGACATGGAGATGCCCGA

                     *            
        553 CCATGCGACTTGGAGATGCCCG
          1 CCATGCGACATGGAGATGCCCG

        575 TCCAACAACG


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  23   21  1.00

ACGTcount: A:0.22, C:0.31, G:0.31, T:0.16


Consensus pattern (23 bp):   
CCATGCGACATGGAGATGCCCGA

Found at i:621 original size:33 final size:33

Alignment explanation


    Indices: 553--645  Score: 107
    Period size: 33  Copynumber: 2.8  Consensus size: 33

        543 AGATGCCCGA

                     *            *          
        553 CCATGCGACTTGGAGATGCCCGTCCAACAACGG
          1 CCATGCGACATGGAGATGCCCGGCCAACAACGG

                                      *       
        586 CCATGCGACATGGAGATGCCCGGCCATC-ACTGG
          1 CCATGCGACATGGAGATGCCCGGCCAACAAC-GG

               *         **    *       
        619 CCACGCGACATGGCCATGCGCGGCCAA
          1 CCATGCGACATGGAGATGCCCGGCCAA

        646 ACCCGGCCAC


Statistics
Matches: 51,  Mismatches: 8, Indels: 2
        0.84            0.13        0.03

Matches are distributed among these distances:
  32    2  0.04
  33   49  0.96

ACGTcount: A:0.23, C:0.35, G:0.29, T:0.13


Consensus pattern (33 bp):   
CCATGCGACATGGAGATGCCCGGCCAACAACGG

Found at i:667 original size:33 final size:33

Alignment explanation


    Indices: 630--692  Score: 92
    Period size: 33  Copynumber: 1.9  Consensus size: 33

        620 CACGCGACAT

                    * *                       
        630 GGCCATGCGCGGCCA-AACCCGGCCACATGACTC
          1 GGCCATGCCCAGCCACAA-CCGGCCACATGACTC

                                          
        663 GGCCATGCCCAGCCACAACCGGCCACATGA
          1 GGCCATGCCCAGCCACAACCGGCCACATGA

        693 TCCTTTAGCT


Statistics
Matches: 27,  Mismatches: 2, Indels: 2
        0.87            0.06        0.06

Matches are distributed among these distances:
  33   25  0.93
  34    2  0.07

ACGTcount: A:0.24, C:0.43, G:0.25, T:0.08


Consensus pattern (33 bp):   
GGCCATGCCCAGCCACAACCGGCCACATGACTC

Found at i:4050 original size:11 final size:11

Alignment explanation


    Indices: 4034--4059  Score: 52
    Period size: 11  Copynumber: 2.4  Consensus size: 11

       4024 TTATGGTCGA

                       
       4034 ATTTTTTTTAT
          1 ATTTTTTTTAT

                       
       4045 ATTTTTTTTAT
          1 ATTTTTTTTAT

                
       4056 ATTT
          1 ATTT

       4060 GTTGATATAA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   15  1.00

ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81


Consensus pattern (11 bp):   
ATTTTTTTTAT
Done.