Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016280.1 Corchorus olitorius cultivar O-4 contig16313, 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: 7688
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32


Found at i:5106 original size:25 final size:27

Alignment explanation


    Indices: 5073--5135  Score: 103
    Period size: 27  Copynumber: 2.4  Consensus size: 27

       5063 AGACTTAAGC

                                       
       5073 AAAATATGAAC-AAA-CATGGCCCCAG
          1 AAAATATGAACAAAATCATGGCCCCAG

                *                      
       5098 AAAACATGAACAAAATCATGGCCCCAG
          1 AAAATATGAACAAAATCATGGCCCCAG

                       
       5125 AAAATATGAAC
          1 AAAATATGAAC

       5136 TTTCCAGGTA


Statistics
Matches: 34,  Mismatches: 2, Indels: 2
        0.89            0.05        0.05

Matches are distributed among these distances:
  25   10  0.29
  26    3  0.09
  27   21  0.62

ACGTcount: A:0.51, C:0.22, G:0.14, T:0.13


Consensus pattern (27 bp):   
AAAATATGAACAAAATCATGGCCCCAG

Found at i:6402 original size:8 final size:8

Alignment explanation


    Indices: 6391--6425  Score: 52
    Period size: 8  Copynumber: 4.2  Consensus size: 8

       6381 ATTTTTCTAA

                    
       6391 ATCTTACT
          1 ATCTTACT

                    
       6399 ATCTTACT
          1 ATCTTACT

                     
       6407 ATCTTATCT
          1 ATCTTA-CT

            *       
       6416 TTCTTACT
          1 ATCTTACT

              
       6424 AT
          1 AT

       6426 ACTATATAAA


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
   8   17  0.71
   9    7  0.29

ACGTcount: A:0.23, C:0.23, G:0.00, T:0.54


Consensus pattern (8 bp):   
ATCTTACT

Found at i:6422 original size:17 final size:16

Alignment explanation


    Indices: 6391--6425  Score: 52
    Period size: 17  Copynumber: 2.1  Consensus size: 16

       6381 ATTTTTCTAA

                            
       6391 ATCTTACTATCTTACT
          1 ATCTTACTATCTTACT

                     *       
       6407 ATCTTATCTTTCTTACT
          1 ATCTTA-CTATCTTACT

              
       6424 AT
          1 AT

       6426 ACTATATAAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  16    6  0.35
  17   11  0.65

ACGTcount: A:0.23, C:0.23, G:0.00, T:0.54


Consensus pattern (16 bp):   
ATCTTACTATCTTACT

Found at i:6699 original size:15 final size:16

Alignment explanation


    Indices: 6674--6703  Score: 53
    Period size: 15  Copynumber: 1.9  Consensus size: 16

       6664 AATAATTATT

                            
       6674 TTTAGATTATAATATA
          1 TTTAGATTATAATATA

                           
       6690 TTTA-ATTATAATAT
          1 TTTAGATTATAATAT

       6704 TATATTATTA


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15   10  0.71
  16    4  0.29

ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53


Consensus pattern (16 bp):   
TTTAGATTATAATATA
Done.