Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022025.1 Corchorus olitorius cultivar O-4 contig22058, 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: 18169
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34


Found at i:2478 original size:21 final size:21

Alignment explanation


    Indices: 2453--2535  Score: 64
    Period size: 22  Copynumber: 3.8  Consensus size: 21

       2443 TATCTTAGAT

                                  
       2453 ATAAT-ATATATTATTAAATAA
          1 ATAATAATATATT-TTAAATAA

                                  
       2474 ATAATAAATATATTTTAAAT-A
          1 ATAAT-AATATATTTTAAATAA

                        *  **      
       2495 ATAAATAATGA-GTTCAAAATAA
          1 AT-AATAAT-ATATTTTAAATAA

                               
       2517 ATAAATAATATATATTTAA
          1 AT-AATAATATAT-TTTAA

       2536 TTACTAAACG


Statistics
Matches: 49,  Mismatches: 6, Indels: 12
        0.73            0.09        0.18

Matches are distributed among these distances:
  21   18  0.37
  22   21  0.43
  23   10  0.20

ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39


Consensus pattern (21 bp):   
ATAATAATATATTTTAAATAA

Found at i:2486 original size:25 final size:25

Alignment explanation


    Indices: 2455--2503  Score: 64
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       2445 TCTTAGATAT

                        *             
       2455 AATATATATT-ATTAAATAAATAATA
          1 AATATATATTAAAT-AATAAATAATA

                   *                
       2480 AATATATTTTAAATAATAAATAAT
          1 AATATATATTAAATAATAAATAAT

       2504 GAGTTCAAAA


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  25   19  0.90
  26    2  0.10

ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41


Consensus pattern (25 bp):   
AATATATATTAAATAATAAATAATA

Found at i:4095 original size:29 final size:30

Alignment explanation


    Indices: 4026--4101  Score: 127
    Period size: 30  Copynumber: 2.6  Consensus size: 30

       4016 TTTATGAGTT

                                 *        
       4026 AAATAAGGGTTATTATTTTCCGGCCATAAA
          1 AAATAAGGGTTATTATTTTCCAGCCATAAA

              *                           
       4056 AAGTAAGGGTTATTATTTTCCAGCCA-AAA
          1 AAATAAGGGTTATTATTTTCCAGCCATAAA

                             
       4085 AAATAAGGGTTATTATT
          1 AAATAAGGGTTATTATT

       4102 AGTGCAATAA


Statistics
Matches: 43,  Mismatches: 3, Indels: 1
        0.91            0.06        0.02

Matches are distributed among these distances:
  29   19  0.44
  30   24  0.56

ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34


Consensus pattern (30 bp):   
AAATAAGGGTTATTATTTTCCAGCCATAAA

Found at i:6413 original size:29 final size:29

Alignment explanation


    Indices: 6376--6442  Score: 107
    Period size: 29  Copynumber: 2.3  Consensus size: 29

       6366 ATACAAACTT

                                 *       
       6376 TTAGACCTAATTAGATTCAATTTAAAGAA
          1 TTAGACCTAATTAGATTCAATCTAAAGAA

                *                     *  
       6405 TTAGGCCTAATTAGATTCAATCTAAATAA
          1 TTAGACCTAATTAGATTCAATCTAAAGAA

                     
       6434 TTAGACCTA
          1 TTAGACCTA

       6443 GTTTGAGTAT


Statistics
Matches: 34,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  29   34  1.00

ACGTcount: A:0.42, C:0.13, G:0.10, T:0.34


Consensus pattern (29 bp):   
TTAGACCTAATTAGATTCAATCTAAAGAA

Found at i:17405 original size:2 final size:2

Alignment explanation


    Indices: 17398--17439  Score: 50
    Period size: 2  Copynumber: 21.5  Consensus size: 2

      17388 TGTTAGAGTG

                         *        *                                *      
      17398 TA TA TA TA TG TA TA TG TA TA TA TA TA TA TA TA T- TA TC TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

             
      17439 T
          1 T

      17440 TCGGTTAGGT


Statistics
Matches: 33,  Mismatches: 6, Indels: 2
        0.80            0.15        0.05

Matches are distributed among these distances:
   1    1  0.03
   2   32  0.97

ACGTcount: A:0.40, C:0.02, G:0.05, T:0.52


Consensus pattern (2 bp):   
TA

Done.