Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016803.1 Corchorus olitorius cultivar O-4 contig16836, 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: 2880
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31


Found at i:1079 original size:12 final size:12

Alignment explanation


    Indices: 1062--1105  Score: 88
    Period size: 12  Copynumber: 3.7  Consensus size: 12

       1052 ACTCATCCGC

                        
       1062 GCCATCCGACCG
          1 GCCATCCGACCG

                        
       1074 GCCATCCGACCG
          1 GCCATCCGACCG

                        
       1086 GCCATCCGACCG
          1 GCCATCCGACCG

                    
       1098 GCCATCCG
          1 GCCATCCG

       1106 CGCCGCCTGC


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   32  1.00

ACGTcount: A:0.16, C:0.50, G:0.25, T:0.09


Consensus pattern (12 bp):   
GCCATCCGACCG

Found at i:1343 original size:21 final size:21

Alignment explanation


    Indices: 1317--1371  Score: 74
    Period size: 21  Copynumber: 2.6  Consensus size: 21

       1307 CGGCCATTCA

                           **    
       1317 CCGTGCCACCACCGGTTAAGC
          1 CCGTGCCACCACCGGCCAAGC

                              *  
       1338 CCGTGCCACCACCGGCCATGC
          1 CCGTGCCACCACCGGCCAAGC

                    *    
       1359 CCGTGCCATCACC
          1 CCGTGCCACCACC

       1372 ATTCCAAGCC


Statistics
Matches: 30,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  21   30  1.00

ACGTcount: A:0.16, C:0.49, G:0.22, T:0.13


Consensus pattern (21 bp):   
CCGTGCCACCACCGGCCAAGC

Found at i:1703 original size:15 final size:14

Alignment explanation


    Indices: 1683--1712  Score: 51
    Period size: 15  Copynumber: 2.1  Consensus size: 14

       1673 ATCTTTTTAA

                           
       1683 TTTTCCTTGCATTAT
          1 TTTTCCTTG-ATTAT

                          
       1698 TTTTCCTTGATTAT
          1 TTTTCCTTGATTAT

             
       1712 T
          1 T

       1713 GCTTTGATTG


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    6  0.40
  15    9  0.60

ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63


Consensus pattern (14 bp):   
TTTTCCTTGATTAT

Found at i:2233 original size:15 final size:16

Alignment explanation


    Indices: 2215--2247  Score: 50
    Period size: 15  Copynumber: 2.1  Consensus size: 16

       2205 AAAAGGGTAG

                       *    
       2215 TTAAAAAA-AATTGTT
          1 TTAAAAAAGAAGTGTT

                            
       2230 TTAAAAAAGAAGTGTT
          1 TTAAAAAAGAAGTGTT

              
       2246 TT
          1 TT

       2248 CATGCAAGAG


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  15    8  0.50
  16    8  0.50

ACGTcount: A:0.48, C:0.00, G:0.12, T:0.39


Consensus pattern (16 bp):   
TTAAAAAAGAAGTGTT
Done.