Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017774.1 Corchorus olitorius cultivar O-4 contig17807, 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: 21217
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32


Found at i:1035 original size:18 final size:18

Alignment explanation


    Indices: 981--1026  Score: 58
    Period size: 18  Copynumber: 2.6  Consensus size: 18

        971 AATTAGTTTG

                           *  
        981 AGATTAATTT-CTAAGTT
          1 AGATTAATTTACTAAATT

              *         *     
        998 AGCTTAATTTACAAAATT
          1 AGATTAATTTACTAAATT

                       
       1016 AGATTAATTTA
          1 AGATTAATTTA

       1027 GTAATTTAGT


Statistics
Matches: 24,  Mismatches: 4, Indels: 1
        0.83            0.14        0.03

Matches are distributed among these distances:
  17    9  0.38
  18   15  0.62

ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43


Consensus pattern (18 bp):   
AGATTAATTTACTAAATT

Found at i:9623 original size:17 final size:17

Alignment explanation


    Indices: 9601--9635  Score: 70
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       9591 TGAGGACGGC

                             
       9601 AAATATTACTTACAAAA
          1 AAATATTACTTACAAAA

                             
       9618 AAATATTACTTACAAAA
          1 AAATATTACTTACAAAA

             
       9635 A
          1 A

       9636 TAACATGCAC


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   18  1.00

ACGTcount: A:0.60, C:0.11, G:0.00, T:0.29


Consensus pattern (17 bp):   
AAATATTACTTACAAAA

Found at i:9697 original size:25 final size:26

Alignment explanation


    Indices: 9650--9699  Score: 68
    Period size: 25  Copynumber: 2.0  Consensus size: 26

       9640 ATGCACTAAT

                              *       
       9650 AATTAACATACAAAATTACTTACAAA
          1 AATTAACATACAAAATTAATTACAAA

                                      
       9676 AATT-ACATACAATAA-TAATTACAA
          1 AATTAACATACAA-AATTAATTACAA

       9700 TCATGTCTCT


Statistics
Matches: 22,  Mismatches: 1, Indels: 3
        0.85            0.04        0.12

Matches are distributed among these distances:
  25   16  0.73
  26    6  0.27

ACGTcount: A:0.58, C:0.14, G:0.00, T:0.28


Consensus pattern (26 bp):   
AATTAACATACAAAATTAATTACAAA

Found at i:18774 original size:24 final size:23

Alignment explanation


    Indices: 18733--18778  Score: 65
    Period size: 24  Copynumber: 2.0  Consensus size: 23

      18723 TCGAAGTTCG

                                   
      18733 AAATGAAATAAAAAAAATAGAAT
          1 AAATGAAATAAAAAAAATAGAAT

                         **        
      18756 AAATGAAAATAAATGAAATAGAA
          1 AAATG-AAATAAAAAAAATAGAA

      18779 ATATTCGAAA


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

Matches are distributed among these distances:
  23    5  0.25
  24   15  0.75

ACGTcount: A:0.72, C:0.00, G:0.11, T:0.17


Consensus pattern (23 bp):   
AAATGAAATAAAAAAAATAGAAT

Found at i:19179 original size:29 final size:28

Alignment explanation


    Indices: 19137--19191  Score: 101
    Period size: 29  Copynumber: 1.9  Consensus size: 28

      19127 GACAAAATGG

                                         
      19137 TAATATTAGATCAAAGAGAGCTATATGAT
          1 TAATATTAGATCAAAGAG-GCTATATGAT

                                      
      19166 TAATATTAGATCAAAGAGGCTATATG
          1 TAATATTAGATCAAAGAGGCTATATG

      19192 CCTGGGAAAG


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  28    8  0.31
  29   18  0.69

ACGTcount: A:0.44, C:0.07, G:0.18, T:0.31


Consensus pattern (28 bp):   
TAATATTAGATCAAAGAGGCTATATGAT
Done.