Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006365.1 Corchorus olitorius cultivar O-4 contig06390, 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: 4348
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.34


Found at i:1059 original size:12 final size:12

Alignment explanation


    Indices: 1042--1067  Score: 52
    Period size: 12  Copynumber: 2.2  Consensus size: 12

       1032 AAGTTTGGCT

                        
       1042 TTTTTTTTCCTA
          1 TTTTTTTTCCTA

                        
       1054 TTTTTTTTCCTA
          1 TTTTTTTTCCTA

              
       1066 TT
          1 TT

       1068 ACAAACATCT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   14  1.00

ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77


Consensus pattern (12 bp):   
TTTTTTTTCCTA

Found at i:2156 original size:21 final size:21

Alignment explanation


    Indices: 2118--2157  Score: 53
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       2108 AAACATCCCA

                         *       
       2118 AATATTATAATACCATATTGC
          1 AATATTATAATACAATATTGC

                    **         
       2139 AATATTATCCTACAATATT
          1 AATATTATAATACAATATT

       2158 ATATGAATTA


Statistics
Matches: 16,  Mismatches: 3, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  21   16  1.00

ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40


Consensus pattern (21 bp):   
AATATTATAATACAATATTGC

Found at i:2243 original size:3 final size:3

Alignment explanation


    Indices: 2237--2272  Score: 72
    Period size: 3  Copynumber: 12.0  Consensus size: 3

       2227 AAAAAAATAA

                                                           
       2237 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
          1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG

       2273 GAGTACAAAA


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   33  1.00

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


Consensus pattern (3 bp):   
AAG

Found at i:3850 original size:45 final size:45

Alignment explanation


    Indices: 3786--3877  Score: 175
    Period size: 45  Copynumber: 2.0  Consensus size: 45

       3776 AAGGGGGTAT

                                                         
       3786 CAAATAAGTAAATCATCCTATTACAATGTTTCTGCCAATAAATAA
          1 CAAATAAGTAAATCATCCTATTACAATGTTTCTGCCAATAAATAA

                         *                               
       3831 CAAATAAGTAAATTATCCTATTACAATGTTTCTGCCAATAAATAA
          1 CAAATAAGTAAATCATCCTATTACAATGTTTCTGCCAATAAATAA

              
       3876 CA
          1 CA

       3878 GACAAGAATA


Statistics
Matches: 46,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  45   46  1.00

ACGTcount: A:0.45, C:0.17, G:0.07, T:0.32


Consensus pattern (45 bp):   
CAAATAAGTAAATCATCCTATTACAATGTTTCTGCCAATAAATAA
Done.