Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008009.1 Corchorus olitorius cultivar O-4 contig08036, 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: 8505
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34


Found at i:3095 original size:13 final size:13

Alignment explanation


    Indices: 3076--3109  Score: 52
    Period size: 13  Copynumber: 2.6  Consensus size: 13

       3066 AAAAGTTACA

                         
       3076 AGTACTAAAG-AT
          1 AGTACTAAAGAAT

                          
       3088 ATGTACTAAAGAAT
          1 A-GTACTAAAGAAT

                    
       3102 AGTACTAA
          1 AGTACTAA

       3110 CACTTTTTTA


Statistics
Matches: 20,  Mismatches: 0, Indels: 3
        0.87            0.00        0.13

Matches are distributed among these distances:
  12    1  0.05
  13   16  0.80
  14    3  0.15

ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26


Consensus pattern (13 bp):   
AGTACTAAAGAAT

Found at i:7471 original size:32 final size:32

Alignment explanation


    Indices: 7430--7494  Score: 130
    Period size: 32  Copynumber: 2.0  Consensus size: 32

       7420 CAGTCTACCT

                                            
       7430 AGACCATGAGGTCTTAGGTTCAACTCTCACGG
          1 AGACCATGAGGTCTTAGGTTCAACTCTCACGG

                                            
       7462 AGACCATGAGGTCTTAGGTTCAACTCTCACGG
          1 AGACCATGAGGTCTTAGGTTCAACTCTCACGG

             
       7494 A
          1 A

       7495 ATGTGAGTTT


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

Matches are distributed among these distances:
  32   33  1.00

ACGTcount: A:0.26, C:0.25, G:0.25, T:0.25


Consensus pattern (32 bp):   
AGACCATGAGGTCTTAGGTTCAACTCTCACGG

Found at i:7781 original size:2 final size:2

Alignment explanation


    Indices: 7774--7815  Score: 57
    Period size: 2  Copynumber: 20.5  Consensus size: 2

       7764 TATCTCAAAA

                                             *        *                   
       7774 AT AT AT AT AT AT AT AT AT AT AT CT AT AT CT AT AT ACT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A

       7816 AGTCTAAACT


Statistics
Matches: 35,  Mismatches: 4, Indels: 2
        0.85            0.10        0.05

Matches are distributed among these distances:
   2   33  0.94
   3    2  0.06

ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:8143 original size:30 final size:27

Alignment explanation


    Indices: 8093--8175  Score: 112
    Period size: 30  Copynumber: 3.0  Consensus size: 27

       8083 GTTAATTTAG

                                       
       8093 ACTTATTATTATTATAATAATTATTAA
          1 ACTTATTATTATTATAATAATTATTAA

                              *           
       8120 ACTTATTATTAGTGGTATTATAATTATTAA
          1 ACTTATTATTA-T--TATAATAATTATTAA

                     *  *             
       8150 ACTTATTATAATAATAATAATTATTA
          1 ACTTATTATTATTATAATAATTATTA

       8176 TTAGTAATAT


Statistics
Matches: 49,  Mismatches: 4, Indels: 6
        0.83            0.07        0.10

Matches are distributed among these distances:
  27   23  0.47
  28    1  0.02
  29    1  0.02
  30   24  0.49

ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49


Consensus pattern (27 bp):   
ACTTATTATTATTATAATAATTATTAA

Found at i:8147 original size:9 final size:9

Alignment explanation


    Indices: 8095--8176  Score: 60
    Period size: 9  Copynumber: 8.8  Consensus size: 9

       8085 TAATTTAGAC

                   * 
       8095 TTATTATTA
          1 TTATTATAA

                *    
       8104 TTATAATAA
          1 TTATTATAA

                     
       8113 TTATTA-AA
          1 TTATTATAA

                      *
       8121 CTTATTATTAG
          1 -TTATTA-TAA

                       
       8132 TGGTATTATAA
          1 T--TATTATAA

                     
       8143 TTATTA-AA
          1 TTATTATAA

                      
       8151 CTTATTATAA
          1 -TTATTATAA

             *  *    
       8161 TAATAATAA
          1 TTATTATAA

                   
       8170 TTATTAT
          1 TTATTAT

       8177 TAGTAATATG


Statistics
Matches: 57,  Mismatches: 9, Indels: 14
        0.71            0.11        0.17

Matches are distributed among these distances:
   8    4  0.07
   9   41  0.72
  10    3  0.05
  11    4  0.07
  12    5  0.09

ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51


Consensus pattern (9 bp):   
TTATTATAA

Done.