Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013607.1 Corchorus olitorius cultivar O-4 contig13640, 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: 14645
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31


Found at i:270 original size:20 final size:20

Alignment explanation


    Indices: 245--284  Score: 80
    Period size: 20  Copynumber: 2.0  Consensus size: 20

        235 AGGGTATACC

                                
        245 AATGCAATGTTATAGCGACG
          1 AATGCAATGTTATAGCGACG

                                
        265 AATGCAATGTTATAGCGACG
          1 AATGCAATGTTATAGCGACG

        285 TCAAAACGGA


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

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25


Consensus pattern (20 bp):   
AATGCAATGTTATAGCGACG

Found at i:509 original size:26 final size:27

Alignment explanation


    Indices: 448--517  Score: 106
    Period size: 27  Copynumber: 2.6  Consensus size: 27

        438 CCAGTAATCT

                                       
        448 TGACCAAAATGCCCCTGAGGCGGAAAA
          1 TGACCAAAATGCCCCTGAGGCGGAAAA

                                    *  
        475 TGACCAAAATGCCCCTGAGGC-GAGAA
          1 TGACCAAAATGCCCCTGAGGCGGAAAA

                *     *      
        501 TGACAAAAATACCCCTG
          1 TGACCAAAATGCCCCTG

        518 GTAACTTCTT


Statistics
Matches: 40,  Mismatches: 3, Indels: 1
        0.91            0.07        0.02

Matches are distributed among these distances:
  26   19  0.47
  27   21  0.52

ACGTcount: A:0.37, C:0.27, G:0.23, T:0.13


Consensus pattern (27 bp):   
TGACCAAAATGCCCCTGAGGCGGAAAA

Found at i:6906 original size:15 final size:16

Alignment explanation


    Indices: 6880--6921  Score: 59
    Period size: 16  Copynumber: 2.6  Consensus size: 16

       6870 ACAGAGAGTT

                             
       6880 AAGAAGAACAATTAAA-
          1 AAGAA-AACAATTAAAC

                            
       6896 AAGAAAACAATTAAAC
          1 AAGAAAACAATTAAAC

            *         
       6912 TAGAAAACAA
          1 AAGAAAACAA

       6922 AGCAAAGTAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  15   10  0.42
  16   14  0.58

ACGTcount: A:0.69, C:0.10, G:0.10, T:0.12


Consensus pattern (16 bp):   
AAGAAAACAATTAAAC

Found at i:10573 original size:29 final size:31

Alignment explanation


    Indices: 10536--10595  Score: 88
    Period size: 29  Copynumber: 2.0  Consensus size: 31

      10526 AATTCTTTCC

                *      *                   
      10536 TCTTGAAATAATTCTTCAAT-A-TCTTCAAA
          1 TCTTCAAATAAGTCTTCAATGAGTCTTCAAA

                                           
      10565 TCTTCAAATAAGTCTTCAATGAGTCTTCAAA
          1 TCTTCAAATAAGTCTTCAATGAGTCTTCAAA

      10596 CACGAGCTTC


Statistics
Matches: 27,  Mismatches: 2, Indels: 2
        0.87            0.06        0.06

Matches are distributed among these distances:
  29   18  0.67
  30    1  0.04
  31    8  0.30

ACGTcount: A:0.37, C:0.18, G:0.07, T:0.38


Consensus pattern (31 bp):   
TCTTCAAATAAGTCTTCAATGAGTCTTCAAA

Found at i:12553 original size:22 final size:23

Alignment explanation


    Indices: 12525--12569  Score: 65
    Period size: 22  Copynumber: 2.0  Consensus size: 23

      12515 GATACATTTT

                   *        *      
      12525 AAGCTCGGGCTCG-TTTGAGCTC
          1 AAGCTCGAGCTCGATTGGAGCTC

                                   
      12547 AAGCTCGAGCTCGATTGGAGCTC
          1 AAGCTCGAGCTCGATTGGAGCTC

      12570 GAAAATTTTT


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  22   12  0.60
  23    8  0.40

ACGTcount: A:0.18, C:0.27, G:0.31, T:0.24


Consensus pattern (23 bp):   
AAGCTCGAGCTCGATTGGAGCTC
Done.