Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006965.1 Corchorus capsularis cultivar CVL-1 contig06986, 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: 5717
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.33


Found at i:2974 original size:33 final size:34

Alignment explanation


    Indices: 2937--3010  Score: 107
    Period size: 33  Copynumber: 2.2  Consensus size: 34

       2927 CCGAGTCGTT

                                *          *  
       2937 TGGCCGGTTG-TAGCCGGACTTGTCCATGTCGCG
          1 TGGCCGGTTGATAGCCGGACATGTCCATGTCACG

                        *                     
       2970 TGGCCGG-TGATGGCCGGACATGTCCATGTCACG
          1 TGGCCGGTTGATAGCCGGACATGTCCATGTCACG

                    
       3003 TGGCCGGT
          1 TGGCCGGT

       3011 CTTGTGGCCG


Statistics
Matches: 36,  Mismatches: 3, Indels: 3
        0.86            0.07        0.07

Matches are distributed among these distances:
  32    2  0.06
  33   34  0.94

ACGTcount: A:0.11, C:0.27, G:0.38, T:0.24


Consensus pattern (34 bp):   
TGGCCGGTTGATAGCCGGACATGTCCATGTCACG

Found at i:4021 original size:18 final size:19

Alignment explanation


    Indices: 3998--4035  Score: 60
    Period size: 18  Copynumber: 2.1  Consensus size: 19

       3988 GTGCATGGGC

                      *        
       3998 TGCATGGAG-GCATGGAGA
          1 TGCATGGAGACCATGGAGA

                               
       4016 TGCATGGAGACCATGGAGA
          1 TGCATGGAGACCATGGAGA

             
       4035 T
          1 T

       4036 AACGATGGAC


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  18    9  0.50
  19    9  0.50

ACGTcount: A:0.29, C:0.13, G:0.39, T:0.18


Consensus pattern (19 bp):   
TGCATGGAGACCATGGAGA

Found at i:4332 original size:11 final size:11

Alignment explanation


    Indices: 4316--4341  Score: 52
    Period size: 11  Copynumber: 2.4  Consensus size: 11

       4306 GCATTAGTTT

                       
       4316 GCTTTGTGTGG
          1 GCTTTGTGTGG

                       
       4327 GCTTTGTGTGG
          1 GCTTTGTGTGG

                
       4338 GCTT
          1 GCTT

       4342 AATTATATCT


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:0.00, C:0.12, G:0.42, T:0.46


Consensus pattern (11 bp):   
GCTTTGTGTGG
Done.