Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017716.1 Corchorus olitorius cultivar O-4 contig17749, 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: 25602
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36


Found at i:1424 original size:3 final size:3

Alignment explanation


    Indices: 1383--1415  Score: 66
    Period size: 3  Copynumber: 11.0  Consensus size: 3

       1373 CTTCCACAGT

                                                       
       1383 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
          1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC

       1416 AGCTTCTTCG


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   30  1.00

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


Consensus pattern (3 bp):   
TTC

Found at i:8887 original size:24 final size:24

Alignment explanation


    Indices: 8840--8887  Score: 60
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       8830 AGTTACAATC

                            * **    
       8840 AAAACCTACAAGATGATGTGCCAA
          1 AAAACCTACAAGATGACGCCCCAA

                           *        
       8864 AAAACCTACAAGATGCCGCCCCAA
          1 AAAACCTACAAGATGACGCCCCAA

       8888 TCTATCAAAT


Statistics
Matches: 20,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  24   20  1.00

ACGTcount: A:0.44, C:0.29, G:0.15, T:0.12


Consensus pattern (24 bp):   
AAAACCTACAAGATGACGCCCCAA

Found at i:20231 original size:6 final size:6

Alignment explanation


    Indices: 20220--20255  Score: 72
    Period size: 6  Copynumber: 6.0  Consensus size: 6

      20210 AAAGTTTGTT

                                                     
      20220 CCTTGA CCTTGA CCTTGA CCTTGA CCTTGA CCTTGA
          1 CCTTGA CCTTGA CCTTGA CCTTGA CCTTGA CCTTGA

      20256 GCATCAAATC


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   30  1.00

ACGTcount: A:0.17, C:0.33, G:0.17, T:0.33


Consensus pattern (6 bp):   
CCTTGA

Found at i:21015 original size:12 final size:12

Alignment explanation


    Indices: 21000--21056  Score: 69
    Period size: 12  Copynumber: 4.5  Consensus size: 12

      20990 GAGATGGATA

                *       
      21000 TTTATATTCCGT
          1 TTTAAATTCCGT

                         
      21012 TTTAAATTCCGTT
          1 TTTAAATTCCG-T

                          
      21025 TTTAAACTTTCCGT
          1 TTTAAA--TTCCGT

              *         
      21039 TTGAAATTCCGT
          1 TTTAAATTCCGT

                  
      21051 TTTAAA
          1 TTTAAA

      21057 CTCAGATAAA


Statistics
Matches: 39,  Mismatches: 3, Indels: 6
        0.81            0.06        0.12

Matches are distributed among these distances:
  12   21  0.54
  13    7  0.18
  14    6  0.15
  15    5  0.13

ACGTcount: A:0.25, C:0.16, G:0.09, T:0.51


Consensus pattern (12 bp):   
TTTAAATTCCGT

Found at i:21039 original size:27 final size:26

Alignment explanation


    Indices: 21006--21058  Score: 88
    Period size: 27  Copynumber: 2.0  Consensus size: 26

      20996 GATATTTATA

                    *                  
      21006 TTCCGTTTTAAATTCCGTTTTTAAACT
          1 TTCCGTTTGAAATTCCG-TTTTAAACT

                                      
      21033 TTCCGTTTGAAATTCCGTTTTAAACT
          1 TTCCGTTTGAAATTCCGTTTTAAACT

      21059 CAGATAAATT


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  26    9  0.36
  27   16  0.64

ACGTcount: A:0.23, C:0.19, G:0.09, T:0.49


Consensus pattern (26 bp):   
TTCCGTTTGAAATTCCGTTTTAAACT
Done.