Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019569.1 Corchorus olitorius cultivar O-4 contig19602, 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: 10381
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34


Found at i:550 original size:3 final size:3

Alignment explanation


    Indices: 542--598  Score: 114
    Period size: 3  Copynumber: 19.0  Consensus size: 3

        532 AATTACGAAA

                                                                           
        542 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT

                       
        590 AAT AAT AAT
          1 AAT AAT AAT

        599 TTAGTATTAA


Statistics
Matches: 54,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   54  1.00

ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33


Consensus pattern (3 bp):   
AAT

Found at i:1646 original size:10 final size:11

Alignment explanation


    Indices: 1626--1651  Score: 52
    Period size: 11  Copynumber: 2.4  Consensus size: 11

       1616 ACAGCCACAA

                       
       1626 TTTTTCTTTTT
          1 TTTTTCTTTTT

                       
       1637 TTTTTCTTTTT
          1 TTTTTCTTTTT

                
       1648 TTTT
          1 TTTT

       1652 GGGAAAATAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   15  1.00

ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92


Consensus pattern (11 bp):   
TTTTTCTTTTT

Found at i:10057 original size:6 final size:6

Alignment explanation


    Indices: 10046--10089  Score: 61
    Period size: 6  Copynumber: 6.8  Consensus size: 6

      10036 TGTTGCATAA

                                                              
      10046 TATATC TATATC TATATAC TATATATC TATATC TATATC TATAT
          1 TATATC TATATC TATAT-C --TATATC TATATC TATATC TATAT

      10090 ATTATATAAG


Statistics
Matches: 35,  Mismatches: 0, Indels: 6
        0.85            0.00        0.15

Matches are distributed among these distances:
   6   28  0.80
   7    1  0.03
   8    1  0.03
   9    5  0.14

ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50


Consensus pattern (6 bp):   
TATATC

Found at i:10070 original size:21 final size:20

Alignment explanation


    Indices: 10045--10096  Score: 88
    Period size: 21  Copynumber: 2.6  Consensus size: 20

      10035 TTGTTGCATA

                                 
      10045 ATATATCTATATCTATATACT
          1 ATATATCTATATCTATAT-CT

                                
      10066 ATATATCTATATCTATATCT
          1 ATATATCTATATCTATATCT

                        
      10086 ATATAT-TATAT
          1 ATATATCTATAT

      10097 AAGTCTAAAT


Statistics
Matches: 31,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
  19    5  0.16
  20    8  0.26
  21   18  0.58

ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50


Consensus pattern (20 bp):   
ATATATCTATATCTATATCT

Found at i:10084 original size:27 final size:27

Alignment explanation


    Indices: 10046--10097  Score: 95
    Period size: 27  Copynumber: 1.9  Consensus size: 27

      10036 TGTTGCATAA

                                       
      10046 TATATCTATATCTATATACTATATATC
          1 TATATCTATATCTATATACTATATATC

                              *      
      10073 TATATCTATATCTATATATTATATA
          1 TATATCTATATCTATATACTATATA

      10098 AGTCTAAATT


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  27   24  1.00

ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50


Consensus pattern (27 bp):   
TATATCTATATCTATATACTATATATC
Done.