Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013582.1 Corchorus olitorius cultivar O-4 contig13615, 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: 30195
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34


Found at i:1569 original size:18 final size:18

Alignment explanation


    Indices: 1529--1569  Score: 55
    Period size: 18  Copynumber: 2.3  Consensus size: 18

       1519 TATTATCCAG

                            **
       1529 ATTATTCACATTGTTCGG
          1 ATTATTCACATTGTTCAA

            *                 
       1547 GTTATTCACATTGTTCAA
          1 ATTATTCACATTGTTCAA

                 
       1565 ATTAT
          1 ATTAT

       1570 CTCCCATCGC


Statistics
Matches: 19,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  18   19  1.00

ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46


Consensus pattern (18 bp):   
ATTATTCACATTGTTCAA

Found at i:13374 original size:6 final size:6

Alignment explanation


    Indices: 13363--13388  Score: 52
    Period size: 6  Copynumber: 4.3  Consensus size: 6

      13353 GATTGGAGAT

                                          
      13363 CCAGAA CCAGAA CCAGAA CCAGAA CC
          1 CCAGAA CCAGAA CCAGAA CCAGAA CC

      13389 TTGGTAATAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   20  1.00

ACGTcount: A:0.46, C:0.38, G:0.15, T:0.00


Consensus pattern (6 bp):   
CCAGAA

Found at i:21151 original size:19 final size:19

Alignment explanation


    Indices: 21127--21170  Score: 61
    Period size: 19  Copynumber: 2.3  Consensus size: 19

      21117 AGTAATAATA

                  *     *      
      21127 ATTAAGTAACTTTTATCTC
          1 ATTAAGCAACTTCTATCTC

                               
      21146 ATTAAGCAACTTCTATCTC
          1 ATTAAGCAACTTCTATCTC

            *     
      21165 CTTAAG
          1 ATTAAG

      21171 AGTCAAAATA


Statistics
Matches: 22,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  19   22  1.00

ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41


Consensus pattern (19 bp):   
ATTAAGCAACTTCTATCTC

Found at i:27581 original size:44 final size:44

Alignment explanation


    Indices: 27518--27606  Score: 178
    Period size: 44  Copynumber: 2.0  Consensus size: 44

      27508 TCTCCCGCCA

                                                        
      27518 GTCCCCTTATTTGGGGTTTTTTTTGCTTAAGTTTGGTAGCTCTG
          1 GTCCCCTTATTTGGGGTTTTTTTTGCTTAAGTTTGGTAGCTCTG

                                                        
      27562 GTCCCCTTATTTGGGGTTTTTTTTGCTTAAGTTTGGTAGCTCTG
          1 GTCCCCTTATTTGGGGTTTTTTTTGCTTAAGTTTGGTAGCTCTG

             
      27606 G
          1 G

      27607 CCCATTTATA


Statistics
Matches: 45,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  44   45  1.00

ACGTcount: A:0.09, C:0.16, G:0.26, T:0.49


Consensus pattern (44 bp):   
GTCCCCTTATTTGGGGTTTTTTTTGCTTAAGTTTGGTAGCTCTG

Found at i:29700 original size:29 final size:29

Alignment explanation


    Indices: 29662--29717  Score: 76
    Period size: 29  Copynumber: 1.9  Consensus size: 29

      29652 CTAGTTTTGG

                                         
      29662 TTTAAGGATTTTTAAATTTTATTATTTAA
          1 TTTAAGGATTTTTAAATTTTATTATTTAA

                 *       * *    *      
      29691 TTTAATGATTTTTTAGTTTTTTTATTT
          1 TTTAAGGATTTTTAAATTTTATTATTT

      29718 TTTATTCTGA


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  29   23  1.00

ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66


Consensus pattern (29 bp):   
TTTAAGGATTTTTAAATTTTATTATTTAA
Done.