Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017413.1 Corchorus olitorius cultivar O-4 contig17446, 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: 7578
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38


Found at i:619 original size:21 final size:22

Alignment explanation


    Indices: 595--635  Score: 57
    Period size: 21  Copynumber: 1.9  Consensus size: 22

        585 GTTTATAATA

                *                 
        595 TTCTTGGGTCA-TCGGGTTATC
          1 TTCTCGGGTCATTCGGGTTATC

                     *          
        616 TTCTCGGGTTATTCGGGTTA
          1 TTCTCGGGTCATTCGGGTTA

        636 CGAGTTTGTC


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  21    9  0.53
  22    8  0.47

ACGTcount: A:0.10, C:0.17, G:0.29, T:0.44


Consensus pattern (22 bp):   
TTCTCGGGTCATTCGGGTTATC

Found at i:1198 original size:23 final size:23

Alignment explanation


    Indices: 1172--1216  Score: 56
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       1162 TCAAATATAA

                *                   
       1172 TATCCTTATACCT-ATTTTATTTT
          1 TATCATTATA-CTAATTTTATTTT

                   *              
       1195 TATCATTTTACTAATTTTATTT
          1 TATCATTATACTAATTTTATTT

       1217 AAAAACTTAG


Statistics
Matches: 19,  Mismatches: 2, Indels: 2
        0.83            0.09        0.09

Matches are distributed among these distances:
  22    2  0.11
  23   17  0.89

ACGTcount: A:0.24, C:0.13, G:0.00, T:0.62


Consensus pattern (23 bp):   
TATCATTATACTAATTTTATTTT

Found at i:4631 original size:14 final size:13

Alignment explanation


    Indices: 4607--4634  Score: 56
    Period size: 13  Copynumber: 2.2  Consensus size: 13

       4597 GCTCTGTTTA

                         
       4607 CTGTCTTTTTTTT
          1 CTGTCTTTTTTTT

                         
       4620 CTGTCTTTTTTTT
          1 CTGTCTTTTTTTT

              
       4633 CT
          1 CT

       4635 TATAATTTTA


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

Matches are distributed among these distances:
  13   15  1.00

ACGTcount: A:0.00, C:0.18, G:0.07, T:0.75


Consensus pattern (13 bp):   
CTGTCTTTTTTTT

Found at i:6445 original size:14 final size:14

Alignment explanation


    Indices: 6426--6459  Score: 59
    Period size: 14  Copynumber: 2.4  Consensus size: 14

       6416 TTTTATAACT

                          
       6426 ATTTTATTTTTACC
          1 ATTTTATTTTTACC

                         *
       6440 ATTTTATTTTTACT
          1 ATTTTATTTTTACC

                  
       6454 ATTTTA
          1 ATTTTA

       6460 ATTTAAAAGG


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  14   19  1.00

ACGTcount: A:0.24, C:0.09, G:0.00, T:0.68


Consensus pattern (14 bp):   
ATTTTATTTTTACC

Found at i:6510 original size:16 final size:16

Alignment explanation


    Indices: 6485--6516  Score: 55
    Period size: 16  Copynumber: 2.0  Consensus size: 16

       6475 GTGATTAACC

                            
       6485 TGTTTACTATTTGATA
          1 TGTTTACTATTTGATA

                 *          
       6501 TGTTTTCTATTTGATA
          1 TGTTTACTATTTGATA

       6517 GTTAATTGTA


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

Matches are distributed among these distances:
  16   15  1.00

ACGTcount: A:0.22, C:0.06, G:0.12, T:0.59


Consensus pattern (16 bp):   
TGTTTACTATTTGATA
Done.