Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024845.1 Corchorus olitorius cultivar O-4 contig24878, 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: 17130
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31


Found at i:3860 original size:19 final size:18

Alignment explanation


    Indices: 3830--3875  Score: 58
    Period size: 19  Copynumber: 2.6  Consensus size: 18

       3820 TATTTATTAA

                           *  
       3830 TTTT-TTTAATATTATAT
          1 TTTTATTTAATATTACAT

                               
       3847 TTTTATTTATATATTACAT
          1 TTTTATTTA-ATATTACAT

                 *    
       3866 TTTTACTTAA
          1 TTTTATTTAA

       3876 AAACTACTCA


Statistics
Matches: 25,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  17    4  0.16
  18    5  0.20
  19   16  0.64

ACGTcount: A:0.30, C:0.04, G:0.00, T:0.65


Consensus pattern (18 bp):   
TTTTATTTAATATTACAT

Found at i:8145 original size:20 final size:20

Alignment explanation


    Indices: 8120--8158  Score: 69
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       8110 CATATAAAAT

                          *     
       8120 AATAATAACTAATTTTTAAA
          1 AATAATAACTAATTATTAAA

                               
       8140 AATAATAACTAATTATTAA
          1 AATAATAACTAATTATTAA

       8159 TTTTTTTTAA


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

Matches are distributed among these distances:
  20   18  1.00

ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38


Consensus pattern (20 bp):   
AATAATAACTAATTATTAAA

Found at i:8513 original size:17 final size:18

Alignment explanation


    Indices: 8488--8534  Score: 53
    Period size: 17  Copynumber: 2.7  Consensus size: 18

       8478 ATTGAGGTTT

                *             
       8488 GAAAGTTTGAA-AATTGA
          1 GAAAATTTGAAGAATTGA

                               
       8505 GAAAATTTGAGAGAATTGA
          1 GAAAATTTGA-AGAATTGA

                *       
       8524 -AAATTTTGAAG
          1 GAAAATTTGAAG

       8535 TTTGAAGGAA


Statistics
Matches: 26,  Mismatches: 2, Indels: 4
        0.81            0.06        0.12

Matches are distributed among these distances:
  17   11  0.42
  18    9  0.35
  19    6  0.23

ACGTcount: A:0.47, C:0.00, G:0.23, T:0.30


Consensus pattern (18 bp):   
GAAAATTTGAAGAATTGA

Found at i:11589 original size:22 final size:24

Alignment explanation


    Indices: 11537--11590  Score: 69
    Period size: 22  Copynumber: 2.4  Consensus size: 24

      11527 GGCATTACTG

                                    
      11537 TTACAAAA-TACAAAATATAAAAT
          1 TTACAAAAGTACAAAATATAAAAT

              **                    
      11560 TTGGAAAAGTACAAAA-A-AAAAT
          1 TTACAAAAGTACAAAATATAAAAT

                     
      11582 TTACAAAAG
          1 TTACAAAAG

      11591 AATTCCTTTC


Statistics
Matches: 26,  Mismatches: 4, Indels: 3
        0.79            0.12        0.09

Matches are distributed among these distances:
  22   12  0.46
  23    7  0.27
  24    7  0.27

ACGTcount: A:0.63, C:0.07, G:0.07, T:0.22


Consensus pattern (24 bp):   
TTACAAAAGTACAAAATATAAAAT

Found at i:15093 original size:27 final size:28

Alignment explanation


    Indices: 15055--15127  Score: 112
    Period size: 29  Copynumber: 2.6  Consensus size: 28

      15045 TAAAAATTTA

                                        
      15055 TCAGGGGCATTTTGGTCA-TTTTTCACC
          1 TCAGGGGCATTTTGGTCATTTTTTCACC

                                      *  
      15082 TCAGGGGCATTTTGGTCATTTTTTTCGCC
          1 TCAGGGGCATTTTGGTCA-TTTTTTCACC

                        *    
      15111 TCAGGGGCATTTAGGTC
          1 TCAGGGGCATTTTGGTC

      15128 CAAATTACTG


Statistics
Matches: 42,  Mismatches: 2, Indels: 2
        0.91            0.04        0.04

Matches are distributed among these distances:
  27   18  0.43
  29   24  0.57

ACGTcount: A:0.14, C:0.21, G:0.26, T:0.40


Consensus pattern (28 bp):   
TCAGGGGCATTTTGGTCATTTTTTCACC

Done.