Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021508.1 Corchorus olitorius cultivar O-4 contig21541, 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: 28397
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33


Found at i:493 original size:14 final size:14

Alignment explanation


    Indices: 474--506  Score: 57
    Period size: 14  Copynumber: 2.4  Consensus size: 14

        464 CTAATTCTGT

                          
        474 AATTCTGTTTTTGC
          1 AATTCTGTTTTTGC

                         *
        488 AATTCTGTTTTTGT
          1 AATTCTGTTTTTGC

                 
        502 AATTC
          1 AATTC

        507 AGTAATTCTG


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  14   18  1.00

ACGTcount: A:0.18, C:0.12, G:0.12, T:0.58


Consensus pattern (14 bp):   
AATTCTGTTTTTGC

Found at i:5224 original size:17 final size:17

Alignment explanation


    Indices: 5202--5237  Score: 63
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       5192 CTTTTTCTGA

                             
       5202 GCTCAGTTACGGTTGGT
          1 GCTCAGTTACGGTTGGT

                     *       
       5219 GCTCAGTTATGGTTGGT
          1 GCTCAGTTACGGTTGGT

              
       5236 GC
          1 GC

       5238 GGGTGTGACA


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  17   18  1.00

ACGTcount: A:0.11, C:0.17, G:0.36, T:0.36


Consensus pattern (17 bp):   
GCTCAGTTACGGTTGGT

Found at i:6065 original size:11 final size:11

Alignment explanation


    Indices: 6033--6071  Score: 51
    Period size: 11  Copynumber: 3.5  Consensus size: 11

       6023 TCACGGCCTA

                    *  
       6033 TTTTTTATAAT
          1 TTTTTTATTAT

                *       
       6044 TTGTATTATTAT
          1 TT-TTTTATTAT

                       
       6056 TTTTTTATTAT
          1 TTTTTTATTAT

                 
       6067 TTTTT
          1 TTTTT

       6072 AATGTAAAAT


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  11   15  0.62
  12    9  0.38

ACGTcount: A:0.21, C:0.00, G:0.03, T:0.77


Consensus pattern (11 bp):   
TTTTTTATTAT

Found at i:6144 original size:3 final size:3

Alignment explanation


    Indices: 6136--6191  Score: 112
    Period size: 3  Copynumber: 18.7  Consensus size: 3

       6126 TTTTGTTTTG

                                                                           
       6136 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA

                      
       6184 TTA TTA TT
          1 TTA TTA TT

       6192 TTTAAGCTAG


Statistics
Matches: 53,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   53  1.00

ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68


Consensus pattern (3 bp):   
TTA

Found at i:6408 original size:28 final size:28

Alignment explanation


    Indices: 6376--6432  Score: 105
    Period size: 28  Copynumber: 2.0  Consensus size: 28

       6366 AATTGGGTCC

                                        
       6376 AATTGAAGCAAAATTAGCCCAAGAAGCA
          1 AATTGAAGCAAAATTAGCCCAAGAAGCA

                           *            
       6404 AATTGAAGCAAAATTGGCCCAAGAAGCA
          1 AATTGAAGCAAAATTAGCCCAAGAAGCA

             
       6432 A
          1 A

       6433 TGCCCAAAAG


Statistics
Matches: 28,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  28   28  1.00

ACGTcount: A:0.49, C:0.18, G:0.19, T:0.14


Consensus pattern (28 bp):   
AATTGAAGCAAAATTAGCCCAAGAAGCA

Found at i:19246 original size:18 final size:20

Alignment explanation


    Indices: 19225--19263  Score: 55
    Period size: 20  Copynumber: 2.0  Consensus size: 20

      19215 GTAGAAACAT

                                
      19225 AGAGA-AAAG-AGAGTTTTC
          1 AGAGAGAAAGTAGAGTTTTC

                          *     
      19243 AGAGAGAAAGTAGATTTTTC
          1 AGAGAGAAAGTAGAGTTTTC

             
      19263 A
          1 A

      19264 TTAATTAAAA


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  18    5  0.28
  19    4  0.22
  20    9  0.50

ACGTcount: A:0.44, C:0.05, G:0.26, T:0.26


Consensus pattern (20 bp):   
AGAGAGAAAGTAGAGTTTTC

Done.