Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017334.1 Corchorus olitorius cultivar O-4 contig17367, 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: 4557
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34


Found at i:156 original size:25 final size:26

Alignment explanation


    Indices: 127--183  Score: 64
    Period size: 25  Copynumber: 2.3  Consensus size: 26

        117 GGCTTTTTTT

                                      
        127 TTATTTTTTAAAAATT-AATTATTAG
          1 TTATTTTTTAAAAATTGAATTATTAG

                  *   ** *            
        152 TTA-TTATTATTACTTGAATTATTAG
          1 TTATTTTTTAAAAATTGAATTATTAG

                   
        177 TTATTTT
          1 TTATTTT

        184 GGCCATAGAT


Statistics
Matches: 25,  Mismatches: 5, Indels: 3
        0.76            0.15        0.09

Matches are distributed among these distances:
  24    8  0.32
  25   15  0.60
  26    2  0.08

ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60


Consensus pattern (26 bp):   
TTATTTTTTAAAAATTGAATTATTAG

Found at i:1017 original size:25 final size:25

Alignment explanation


    Indices: 983--1032  Score: 100
    Period size: 25  Copynumber: 2.0  Consensus size: 25

        973 TTAGCCACTC

                                     
        983 ATAACTTTATTTATATATATAACTA
          1 ATAACTTTATTTATATATATAACTA

                                     
       1008 ATAACTTTATTTATATATATAACTA
          1 ATAACTTTATTTATATATATAACTA

       1033 GCAAAATGTC


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  25   25  1.00

ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48


Consensus pattern (25 bp):   
ATAACTTTATTTATATATATAACTA

Found at i:3549 original size:58 final size:58

Alignment explanation


    Indices: 3455--3573  Score: 184
    Period size: 58  Copynumber: 2.1  Consensus size: 58

       3445 GTCCCAATGG

                               *    *      *                          
       3455 AAACATGTACAATACTACATATATTGCATCATATCTTTACTTTATAAAAAATGTAGAA
          1 AAACATGTACAATACTACAAATATCGCATCACATCTTTACTTTATAAAAAATGTAGAA

                       *                          *    *              
       3513 AAACATGTACACTACTACAAATATCGCATCACATCTTTGCTTTTTAAAAAATGTAGAA
          1 AAACATGTACAATACTACAAATATCGCATCACATCTTTACTTTATAAAAAATGTAGAA

               
       3571 AAA
          1 AAA

       3574 AATATATATT


Statistics
Matches: 55,  Mismatches: 6, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  58   55  1.00

ACGTcount: A:0.45, C:0.16, G:0.08, T:0.32


Consensus pattern (58 bp):   
AAACATGTACAATACTACAAATATCGCATCACATCTTTACTTTATAAAAAATGTAGAA

Found at i:4254 original size:58 final size:58

Alignment explanation


    Indices: 4160--4278  Score: 193
    Period size: 58  Copynumber: 2.1  Consensus size: 58

       4150 GTCCCAATGG

                                    *      *                          
       4160 AAACATGTACAATACTACAAATATTGCATCATATCTTTGCTTTATAAAAAATGTAGAA
          1 AAACATGTACAATACTACAAATATCGCATCACATCTTTGCTTTATAAAAAATGTAGAA

                       *     *                         *              
       4218 AAACATGTACACTACTAGAAATATCGCATCACATCTTTGCTTTTTAAAAAATGTAGAA
          1 AAACATGTACAATACTACAAATATCGCATCACATCTTTGCTTTATAAAAAATGTAGAA

               
       4276 AAA
          1 AAA

       4279 AATATATATT


Statistics
Matches: 56,  Mismatches: 5, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  58   56  1.00

ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31


Consensus pattern (58 bp):   
AAACATGTACAATACTACAAATATCGCATCACATCTTTGCTTTATAAAAAATGTAGAA
Done.