Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013682.1 Corchorus olitorius cultivar O-4 contig13715, 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: 18441
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31


Found at i:72 original size:21 final size:21

Alignment explanation


    Indices: 16--72  Score: 51
    Period size: 21  Copynumber: 2.7  Consensus size: 21

          6 TTTATAACAC

                 *               
         16 CTTGTTCCTGCCTCATCTCTT
          1 CTTGTGCCTGCCTCATCTCTT

            *   * **  *     *    
         37 ATTGCGAATGTCTCATTTCTT
          1 CTTGTGCCTGCCTCATCTCTT

                           
         58 CTTGTGCCTGCCTCA
          1 CTTGTGCCTGCCTCA

         73 GATGTTGGAT


Statistics
Matches: 24,  Mismatches: 12, Indels: 0
        0.67            0.33        0.00

Matches are distributed among these distances:
  21   24  1.00

ACGTcount: A:0.11, C:0.32, G:0.14, T:0.44


Consensus pattern (21 bp):   
CTTGTGCCTGCCTCATCTCTT

Found at i:7070 original size:54 final size:54

Alignment explanation


    Indices: 6988--7102  Score: 151
    Period size: 54  Copynumber: 2.1  Consensus size: 54

       6978 CGGCCATAGC

                   *                     * *             *         
       6988 TCGGCCATCCGACCCATCTGCCTGGCCACGCTCGGACTC-CTCCATGCACCACAA
          1 TCGGCCACCCGACCCATCTGCCTGGCCACACCCGGAC-CACTCCACGCACCACAA

                        *                          *              
       7042 TCGGCCACCCGAGCCATCTGCCTGGCCACACCCGGACCAGTCCACGCACCACAA
          1 TCGGCCACCCGACCCATCTGCCTGGCCACACCCGGACCACTCCACGCACCACAA

            *      
       7096 CCGGCCA
          1 TCGGCCA

       7103 TCCGCGCCGC


Statistics
Matches: 53,  Mismatches: 7, Indels: 2
        0.85            0.11        0.03

Matches are distributed among these distances:
  53    1  0.02
  54   52  0.98

ACGTcount: A:0.20, C:0.48, G:0.20, T:0.12


Consensus pattern (54 bp):   
TCGGCCACCCGACCCATCTGCCTGGCCACACCCGGACCACTCCACGCACCACAA

Found at i:7753 original size:9 final size:9

Alignment explanation


    Indices: 7739--7766  Score: 56
    Period size: 9  Copynumber: 3.1  Consensus size: 9

       7729 TTTGTCTTGA

                     
       7739 TTGATTGCT
          1 TTGATTGCT

                     
       7748 TTGATTGCT
          1 TTGATTGCT

                     
       7757 TTGATTGCT
          1 TTGATTGCT

             
       7766 T
          1 T

       7767 GCTTGTTCTT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   19  1.00

ACGTcount: A:0.11, C:0.11, G:0.21, T:0.57


Consensus pattern (9 bp):   
TTGATTGCT

Found at i:10658 original size:15 final size:16

Alignment explanation


    Indices: 10625--10664  Score: 55
    Period size: 15  Copynumber: 2.6  Consensus size: 16

      10615 TTACTTTGCT

                            
      10625 TTGTTTTCTAGTATAA
          1 TTGTTTTCTAGTATAA

                        *   
      10641 TTGTTTTCT-GTTTAA
          1 TTGTTTTCTAGTATAA

               *     
      10656 TTGCTTTCT
          1 TTGTTTTCT

      10665 TTCAACCTCT


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  15   13  0.59
  16    9  0.41

ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62


Consensus pattern (16 bp):   
TTGTTTTCTAGTATAA

Found at i:11304 original size:18 final size:19

Alignment explanation


    Indices: 11281--11320  Score: 64
    Period size: 19  Copynumber: 2.2  Consensus size: 19

      11271 TTCTTGAGAA

                               
      11281 AATTCTTC-AATGATCTTC
          1 AATTCTTCAAATGATCTTC

                        *      
      11299 AATTCTTCAAATTATCTTC
          1 AATTCTTCAAATGATCTTC

               
      11318 AAT
          1 AAT

      11321 AAATCTTCAA


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  18    8  0.40
  19   12  0.60

ACGTcount: A:0.33, C:0.20, G:0.03, T:0.45


Consensus pattern (19 bp):   
AATTCTTCAAATGATCTTC

Done.