Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022988.1 Corchorus olitorius cultivar O-4 contig23021, 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: 11124
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35


Found at i:43 original size:1 final size:1

Alignment explanation


    Indices: 37--62  Score: 52
    Period size: 1  Copynumber: 26.0  Consensus size: 1

         27 CGCATATGCG

                                      
         37 AAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAA

         63 CTCAGAAGTG


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   25  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:4670 original size:18 final size:18

Alignment explanation


    Indices: 4647--4681  Score: 70
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       4637 TTTTCTATCA

                              
       4647 TGTTTTCCATATGCAGAT
          1 TGTTTTCCATATGCAGAT

                             
       4665 TGTTTTCCATATGCAGA
          1 TGTTTTCCATATGCAGA

       4682 AACCTATCGT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43


Consensus pattern (18 bp):   
TGTTTTCCATATGCAGAT

Found at i:7356 original size:31 final size:31

Alignment explanation


    Indices: 7318--7380  Score: 108
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       7308 AAAAAAAAAT

                                           
       7318 CTAAATTGATCCAACTTTGAAACGTTTAGTA
          1 CTAAATTGATCCAACTTTGAAACGTTTAGTA

                      *   *                
       7349 CTAAATTGATTCAATTTTGAAACGTTTAGTA
          1 CTAAATTGATCCAACTTTGAAACGTTTAGTA

             
       7380 C
          1 C

       7381 CTATTTGAGC


Statistics
Matches: 30,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  31   30  1.00

ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38


Consensus pattern (31 bp):   
CTAAATTGATCCAACTTTGAAACGTTTAGTA

Found at i:7412 original size:10 final size:9

Alignment explanation


    Indices: 7395--7443  Score: 59
    Period size: 9  Copynumber: 5.8  Consensus size: 9

       7385 TTGAGCCGGT

                     
       7395 TTAAAAATA
          1 TTAAAAATA

                     
       7404 TTAAAAA-A
          1 TTAAAAATA

                     
       7412 -TAAAAATA
          1 TTAAAAATA

              *      
       7420 TTTAAAA-A
          1 TTAAAAATA

                     
       7428 TTAAAAATA
          1 TTAAAAATA

            *      
       7437 ATAAAAA
          1 TTAAAAA

       7444 AATATTTAAA


Statistics
Matches: 34,  Mismatches: 3, Indels: 6
        0.79            0.07        0.14

Matches are distributed among these distances:
   7    6  0.18
   8    9  0.26
   9   19  0.56

ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29


Consensus pattern (9 bp):   
TTAAAAATA

Found at i:7424 original size:17 final size:16

Alignment explanation


    Indices: 7396--7444  Score: 71
    Period size: 17  Copynumber: 3.0  Consensus size: 16

       7386 TGAGCCGGTT

                            
       7396 TAAAAATATTAAAAAA
          1 TAAAAATATTAAAAAA

                            *
       7412 TAAAAATATTTAAAAAT
          1 TAAAAATA-TTAAAAAA

                    *       
       7429 TAAAAATAATAAAAAA
          1 TAAAAATATTAAAAAA

       7445 ATATTTAAAA


Statistics
Matches: 29,  Mismatches: 3, Indels: 2
        0.85            0.09        0.06

Matches are distributed among these distances:
  16   14  0.48
  17   15  0.52

ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27


Consensus pattern (16 bp):   
TAAAAATATTAAAAAA

Found at i:7439 original size:26 final size:27

Alignment explanation


    Indices: 7394--7455  Score: 83
    Period size: 28  Copynumber: 2.3  Consensus size: 27

       7384 TTTGAGCCGG

                       *               
       7394 TTTAAAAATATTAAAAAAT-AAAAATA
          1 TTTAAAAATATAAAAAAATAAAAAATA

                                         
       7420 TTTAAAAAT-TAAAAATAATAAAAAAATA
          1 TTTAAAAATATAAAAA-AAT-AAAAAATA

                    
       7448 TTTAAAAA
          1 TTTAAAAA

       7456 AACCACGTAG


Statistics
Matches: 32,  Mismatches: 1, Indels: 4
        0.86            0.03        0.11

Matches are distributed among these distances:
  25    5  0.16
  26   12  0.38
  28   15  0.47

ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31


Consensus pattern (27 bp):   
TTTAAAAATATAAAAAAATAAAAAATA

Found at i:8918 original size:12 final size:12

Alignment explanation


    Indices: 8901--8926  Score: 52
    Period size: 12  Copynumber: 2.2  Consensus size: 12

       8891 TGAGCTTATG

                        
       8901 ATTAAATTATTA
          1 ATTAAATTATTA

                        
       8913 ATTAAATTATTA
          1 ATTAAATTATTA

              
       8925 AT
          1 AT

       8927 ATGTATTTTT


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:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (12 bp):   
ATTAAATTATTA

Found at i:11104 original size:2 final size:2

Alignment explanation


    Indices: 11097--11122  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

      11087 TCCTGAAAAT

                                                  
      11097 TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA

      11123 AT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

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


Consensus pattern (2 bp):   
TA

Done.