Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017349.1 Corchorus olitorius cultivar O-4 contig17382, 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: 4507
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.33


Found at i:168 original size:13 final size:13

Alignment explanation


    Indices: 126--170  Score: 56
    Period size: 12  Copynumber: 3.5  Consensus size: 13

        116 TCATGCACCC

                        * 
        126 AAAACAATTTATTT
          1 AAAACAATTTA-AT

                 *       
        140 AAAACCATTT-AT
          1 AAAACAATTTAAT

                         
        152 AAAACAATTTAAT
          1 AAAACAATTTAAT

                  
        165 AAAACA
          1 AAAACA

        171 GTAATAAAAT


Statistics
Matches: 27,  Mismatches: 3, Indels: 3
        0.82            0.09        0.09

Matches are distributed among these distances:
  12   10  0.37
  13    8  0.30
  14    9  0.33

ACGTcount: A:0.58, C:0.11, G:0.00, T:0.31


Consensus pattern (13 bp):   
AAAACAATTTAAT

Found at i:2463 original size:14 final size:14

Alignment explanation


    Indices: 2444--2470  Score: 54
    Period size: 14  Copynumber: 1.9  Consensus size: 14

       2434 TATCACATAA

                          
       2444 TTACTTAAATTTTT
          1 TTACTTAAATTTTT

                         
       2458 TTACTTAAATTTT
          1 TTACTTAAATTTT

       2471 GTTAAGCTGC


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   13  1.00

ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63


Consensus pattern (14 bp):   
TTACTTAAATTTTT

Found at i:3643 original size:25 final size:26

Alignment explanation


    Indices: 3609--3657  Score: 91
    Period size: 25  Copynumber: 1.9  Consensus size: 26

       3599 CCATCCGTTT

                                      
       3609 ATAATTATCCATTATATTCTTTAAAA
          1 ATAATTATCCATTATATTCTTTAAAA

                                    
       3635 ATAA-TATCCATTATATTCTTTAA
          1 ATAATTATCCATTATATTCTTTAA

       3658 TTATCTATTA


Statistics
Matches: 23,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  25   19  0.83
  26    4  0.17

ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47


Consensus pattern (26 bp):   
ATAATTATCCATTATATTCTTTAAAA

Found at i:3667 original size:20 final size:20

Alignment explanation


    Indices: 3610--3676  Score: 64
    Period size: 25  Copynumber: 3.1  Consensus size: 20

       3600 CATCCGTTTA

                                
       3610 TAATTATCCATTATATTCTT
          1 TAATTATCCATTATATTCTT

                                     
       3630 TAAAAATAATATCCATTATATTCTT
          1 T---AAT--TATCCATTATATTCTT

                    *     *     
       3655 TAATTATCTATTA-GTTCTT
          1 TAATTATCCATTATATTCTT

               
       3674 TAA
          1 TAA

       3677 CCTTAGATTA


Statistics
Matches: 40,  Mismatches: 2, Indels: 11
        0.75            0.04        0.21

Matches are distributed among these distances:
  19    8  0.20
  20    9  0.22
  22    3  0.08
  23    3  0.08
  25   17  0.43

ACGTcount: A:0.36, C:0.12, G:0.01, T:0.51


Consensus pattern (20 bp):   
TAATTATCCATTATATTCTT
Done.