Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014998.1 Corchorus olitorius cultivar O-4 contig15031, 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: 14644
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31


Found at i:4857 original size:16 final size:16

Alignment explanation


    Indices: 4836--4866  Score: 62
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       4826 ATACCCAATA

                            
       4836 ACCACATTGAATCTCG
          1 ACCACATTGAATCTCG

                           
       4852 ACCACATTGAATCTC
          1 ACCACATTGAATCTC

       4867 TGTATCTGAT


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

Matches are distributed among these distances:
  16   15  1.00

ACGTcount: A:0.32, C:0.32, G:0.10, T:0.26


Consensus pattern (16 bp):   
ACCACATTGAATCTCG

Found at i:5091 original size:13 final size:13

Alignment explanation


    Indices: 5073--5104  Score: 55
    Period size: 13  Copynumber: 2.5  Consensus size: 13

       5063 AGATTTGAAG

                      *  
       5073 AAAAATTATATAA
          1 AAAAATTATAAAA

                         
       5086 AAAAATTATAAAA
          1 AAAAATTATAAAA

                  
       5099 AAAAAT
          1 AAAAAT

       5105 ACAAAAGGAA


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

Matches are distributed among these distances:
  13   18  1.00

ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25


Consensus pattern (13 bp):   
AAAAATTATAAAA

Found at i:7397 original size:14 final size:14

Alignment explanation


    Indices: 7374--7407  Score: 52
    Period size: 13  Copynumber: 2.4  Consensus size: 14

       7364 GTTCGCACCA

                           
       7374 ACCCAACCCCCCCCC
          1 ACCC-ACCCCCCCCC

                          
       7389 -CCCACCCCCCCCC
          1 ACCCACCCCCCCCC

                  
       7402 ACCCAC
          1 ACCCAC

       7408 ACACACACTC


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

Matches are distributed among these distances:
  13   10  0.56
  14    8  0.44

ACGTcount: A:0.18, C:0.82, G:0.00, T:0.00


Consensus pattern (14 bp):   
ACCCACCCCCCCCC

Found at i:9929 original size:15 final size:14

Alignment explanation


    Indices: 9906--9935  Score: 51
    Period size: 15  Copynumber: 2.1  Consensus size: 14

       9896 ATAAAAATTA

                          
       9906 AATATTTTTATTTT
          1 AATATTTTTATTTT

                           
       9920 AATATATTTTATTTT
          1 AATAT-TTTTATTTT

             
       9935 A
          1 A

       9936 TTGAAATTTA


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

Matches are distributed among these distances:
  14    5  0.33
  15   10  0.67

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (14 bp):   
AATATTTTTATTTT

Found at i:11265 original size:15 final size:15

Alignment explanation


    Indices: 11245--11288  Score: 56
    Period size: 15  Copynumber: 3.0  Consensus size: 15

      11235 TTATTTTTTA

                            
      11245 AAAATAAAAT-TCAAT
          1 AAAATAAAATAT-AAT

                         * 
      11260 AAAATAAAATATATT
          1 AAAATAAAATATAAT

                           
      11275 AAAATAAAA-ATAAT
          1 AAAATAAAATATAAT

      11289 TAATTTTTAT


Statistics
Matches: 26,  Mismatches: 2, Indels: 3
        0.84            0.06        0.10

Matches are distributed among these distances:
  14    4  0.15
  15   21  0.81
  16    1  0.04

ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27


Consensus pattern (15 bp):   
AAAATAAAATATAAT

Done.