Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015559.1 Corchorus capsularis cultivar CVL-1 contig15580, 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: 4005
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:1728 original size:21 final size:21

Alignment explanation


    Indices: 1687--1728  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       1677 GAATGTGACA

                           *     
       1687 CATGAAGTGCACGTGTACACG
          1 CATGAAGTGCACGTGCACACG

                       *    *    
       1708 CATGAAGTGCATGTGCCCACG
          1 CATGAAGTGCACGTGCACACG

       1729 TGCTTTCGCT


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.26, C:0.26, G:0.29, T:0.19


Consensus pattern (21 bp):   
CATGAAGTGCACGTGCACACG

Found at i:3776 original size:14 final size:15

Alignment explanation


    Indices: 3750--3781  Score: 57
    Period size: 14  Copynumber: 2.2  Consensus size: 15

       3740 CGCCCCACTT

                           
       3750 TTTATACTTTTACCC
          1 TTTATACTTTTACCC

                           
       3765 TTTATA-TTTTACCC
          1 TTTATACTTTTACCC

               
       3779 TTT
          1 TTT

       3782 TTACACTAAG


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14   11  0.65
  15    6  0.35

ACGTcount: A:0.19, C:0.22, G:0.00, T:0.59


Consensus pattern (15 bp):   
TTTATACTTTTACCC

Found at i:3844 original size:33 final size:33

Alignment explanation


    Indices: 3793--3867  Score: 116
    Period size: 33  Copynumber: 2.3  Consensus size: 33

       3783 TACACTAAGT

                                *            
       3793 CTCCCCACTAGGACGACTCAGCCACGGCGGAGC
          1 CTCCCCACTAGGACGACTCAACCACGGCGGAGC

                *                             
       3826 CTCCTCACTAGGGA-GACTCAACCACGGCGGAGC
          1 CTCCCCACTA-GGACGACTCAACCACGGCGGAGC

                     
       3859 CTCCCCACT
          1 CTCCCCACT

       3868 GGGGCGGCTT


Statistics
Matches: 38,  Mismatches: 3, Indels: 2
        0.88            0.07        0.05

Matches are distributed among these distances:
  33   35  0.92
  34    3  0.08

ACGTcount: A:0.21, C:0.43, G:0.24, T:0.12


Consensus pattern (33 bp):   
CTCCCCACTAGGACGACTCAACCACGGCGGAGC

Found at i:3926 original size:32 final size:32

Alignment explanation


    Indices: 3867--4005  Score: 226
    Period size: 32  Copynumber: 4.3  Consensus size: 32

       3857 GCCTCCCCAC

                        *    *               
       3867 TGGGGCGGCTTCACCATGGGCAGGCCGCCC-CA
          1 TGGGGCGGCTTCGCCA-CGGCAGGCCGCCCTCA

               *                             
       3899 CTGAGGCGGCTTCGCCACGGCAGGCCGCCCTCA
          1 -TGGGGCGGCTTCGCCACGGCAGGCCGCCCTCA

                                            
       3932 TGGGGCGGCTTCGCCACGGCAGGCCGCCCTCA
          1 TGGGGCGGCTTCGCCACGGCAGGCCGCCCTCA

                                            
       3964 TGGGGCGGCTTCGCCACGGCAGGCCGCCCTCA
          1 TGGGGCGGCTTCGCCACGGCAGGCCGCCCTCA

                      
       3996 TGGGGCGGCT
          1 TGGGGCGGCT


Statistics
Matches: 101,  Mismatches: 4, Indels: 3
        0.94            0.04        0.03

Matches are distributed among these distances:
  32   85  0.84
  33   16  0.16

ACGTcount: A:0.10, C:0.39, G:0.38, T:0.13


Consensus pattern (32 bp):   
TGGGGCGGCTTCGCCACGGCAGGCCGCCCTCA

Done.