Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015144.1 Corchorus olitorius cultivar O-4 contig15177, 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: 4451
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.37


Found at i:926 original size:13 final size:12

Alignment explanation


    Indices: 890--939  Score: 52
    Period size: 13  Copynumber: 4.3  Consensus size: 12

        880 AATTTCCTTA

                        
        890 TTTTC-CTT-TT
          1 TTTTCTCTTCTT

                      * 
        900 TTTTC-CTTCCT
          1 TTTTCTCTTCTT

                  *      
        911 TTTTCTTTTCTAT
          1 TTTTCTCTTCT-T

                        
        924 TTTTCTCTTCTT
          1 TTTTCTCTTCTT

                
        936 TTTT
          1 TTTT

        940 GGGCTAGGCC


Statistics
Matches: 33,  Mismatches: 4, Indels: 4
        0.80            0.10        0.10

Matches are distributed among these distances:
  10    8  0.24
  11    6  0.18
  12    8  0.24
  13   11  0.33

ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76


Consensus pattern (12 bp):   
TTTTCTCTTCTT

Found at i:1112 original size:46 final size:46

Alignment explanation


    Indices: 1039--1127  Score: 124
    Period size: 46  Copynumber: 1.9  Consensus size: 46

       1029 CTAGGACCCA

                                 **              *        
       1039 ACGCTGCCCATTGGCAGCAGCGTGGCCCAGCACTGGCTAGGCCCGC
          1 ACGCTGCCCATTGGCAGCAGCACGGCCCAGCACTGGCCAGGCCCGC

                             *  *          *           
       1085 ACGCTGCCCATTGGCAGTAGTACGGCCCAGCGCTGGCCAGGCC
          1 ACGCTGCCCATTGGCAGCAGCACGGCCCAGCACTGGCCAGGCC

       1128 TGCTTAGCAG


Statistics
Matches: 37,  Mismatches: 6, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  46   37  1.00

ACGTcount: A:0.16, C:0.38, G:0.33, T:0.13


Consensus pattern (46 bp):   
ACGCTGCCCATTGGCAGCAGCACGGCCCAGCACTGGCCAGGCCCGC

Found at i:1781 original size:1 final size:1

Alignment explanation


    Indices: 1775--1806  Score: 64
    Period size: 1  Copynumber: 32.0  Consensus size: 1

       1765 AATTTGTTAG

                                            
       1775 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

       1807 AATGCTTTAC


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   31  1.00

ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00


Consensus pattern (1 bp):   
T

Found at i:2630 original size:2 final size:2

Alignment explanation


    Indices: 2623--2652  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

       2613 GTTTGTAGTG

                                                        
       2623 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       2653 ATTGGAAACA


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:4201 original size:6 final size:6

Alignment explanation


    Indices: 4190--4240  Score: 70
    Period size: 6  Copynumber: 8.5  Consensus size: 6

       4180 CTTTTATTAG

                                                                     
       4190 TATCTA TATCTA TATCTA TATCTA TATCTA TATAC-A -ATCTA TATACTA
          1 TATCTA TATCTA TATCTA TATCTA TATCTA TAT-CTA TATCTA TAT-CTA

               
       4238 TAT
          1 TAT

       4241 AAGTCTAAAC


Statistics
Matches: 41,  Mismatches: 0, Indels: 7
        0.85            0.00        0.15

Matches are distributed among these distances:
   4    1  0.02
   5    3  0.07
   6   30  0.73
   7    7  0.17

ACGTcount: A:0.37, C:0.16, G:0.00, T:0.47


Consensus pattern (6 bp):   
TATCTA

Done.