Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012603.1 Corchorus olitorius cultivar O-4 contig12636, 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: 10622
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:4685 original size:26 final size:27

Alignment explanation


    Indices: 4656--4731  Score: 100
    Period size: 26  Copynumber: 2.8  Consensus size: 27

       4646 CAGATTTTTC

                    *               *  
       4656 TTTTTTTGGAAAACGCAAAAAC-ACTT
          1 TTTTTTTGAAAAACGCAAAAACAAATT

                   *                   
       4682 TTTTTTTCAAAAACGCAAAAACAAATT
          1 TTTTTTTGAAAAACGCAAAAACAAATT

                                   
       4709 TTTTTTTAGTAAAAACGCAAAAA
          1 TTTTTTT-G-AAAAACGCAAAAA

       4732 AGAAATATTC


Statistics
Matches: 43,  Mismatches: 4, Indels: 3
        0.86            0.08        0.06

Matches are distributed among these distances:
  26   20  0.47
  27   10  0.23
  29   13  0.30

ACGTcount: A:0.45, C:0.13, G:0.08, T:0.34


Consensus pattern (27 bp):   
TTTTTTTGAAAAACGCAAAAACAAATT

Found at i:8135 original size:14 final size:14

Alignment explanation


    Indices: 8112--8141  Score: 51
    Period size: 14  Copynumber: 2.1  Consensus size: 14

       8102 CCACCAGTGA

                          
       8112 AAGAAATAATATTG
          1 AAGAAATAATATTG

                 *        
       8126 AAGAAGTAATATTG
          1 AAGAAATAATATTG

              
       8140 AA
          1 AA

       8142 TAATTTCAAT


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

Matches are distributed among these distances:
  14   15  1.00

ACGTcount: A:0.57, C:0.00, G:0.17, T:0.27


Consensus pattern (14 bp):   
AAGAAATAATATTG

Found at i:8680 original size:25 final size:25

Alignment explanation


    Indices: 8650--8724  Score: 87
    Period size: 25  Copynumber: 3.0  Consensus size: 25

       8640 TGTGTTTTCC

                         *           
       8650 AAACGCAAGCACATGCTCGTTTGCT
          1 AAACGCAAGCACAAGCTCGTTTGCT

             *             *      *  
       8675 ATACGCAAGCACAAGTTCGTTTTCT
          1 AAACGCAAGCACAAGCTCGTTTGCT

               *         *  *        
       8700 AAATGCAAGCACAGGCGCGTTTGCT
          1 AAACGCAAGCACAAGCTCGTTTGCT

       8725 CAGCGCACGC


Statistics
Matches: 40,  Mismatches: 10, Indels: 0
        0.80            0.20        0.00

Matches are distributed among these distances:
  25   40  1.00

ACGTcount: A:0.28, C:0.25, G:0.21, T:0.25


Consensus pattern (25 bp):   
AAACGCAAGCACAAGCTCGTTTGCT
Done.