Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015398.1 Corchorus olitorius cultivar O-4 contig15431, 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: 10725
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--84  Score: 168
    Period size: 2  Copynumber: 42.0  Consensus size: 2

                                                                          
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC

                                                                          
         43 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC

         85 CCCTAATATC


Statistics
Matches: 82,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   82  1.00

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


Consensus pattern (2 bp):   
TC

Found at i:5354 original size:6 final size:6

Alignment explanation


    Indices: 5345--5378  Score: 50
    Period size: 6  Copynumber: 5.7  Consensus size: 6

       5335 CAACTTCAAC

                               *      *            
       5345 TTCAGT TTCAGT TTCAGC TTCAGC TTCAGT TTCA
          1 TTCAGT TTCAGT TTCAGT TTCAGT TTCAGT TTCA

       5379 TTACCATCAA


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   6   26  1.00

ACGTcount: A:0.18, C:0.24, G:0.15, T:0.44


Consensus pattern (6 bp):   
TTCAGT

Found at i:5360 original size:12 final size:12

Alignment explanation


    Indices: 5339--5378  Score: 53
    Period size: 12  Copynumber: 3.3  Consensus size: 12

       5329 GTTCAACAAC

                *       
       5339 TTCAACTTCAGT
          1 TTCAGCTTCAGT

                 *     *
       5351 TTCAGTTTCAGC
          1 TTCAGCTTCAGT

                        
       5363 TTCAGCTTCAGT
          1 TTCAGCTTCAGT

                
       5375 TTCA
          1 TTCA

       5379 TTACCATCAA


Statistics
Matches: 23,  Mismatches: 5, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  12   23  1.00

ACGTcount: A:0.20, C:0.25, G:0.12, T:0.42


Consensus pattern (12 bp):   
TTCAGCTTCAGT

Found at i:5365 original size:18 final size:18

Alignment explanation


    Indices: 5339--5378  Score: 62
    Period size: 18  Copynumber: 2.2  Consensus size: 18

       5329 GTTCAACAAC

                       *      
       5339 TTCAACTTCAGTTTCAGT
          1 TTCAACTTCAGCTTCAGT

                *             
       5357 TTCAGCTTCAGCTTCAGT
          1 TTCAACTTCAGCTTCAGT

                
       5375 TTCA
          1 TTCA

       5379 TTACCATCAA


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  18   20  1.00

ACGTcount: A:0.20, C:0.25, G:0.12, T:0.42


Consensus pattern (18 bp):   
TTCAACTTCAGCTTCAGT

Found at i:9476 original size:19 final size:20

Alignment explanation


    Indices: 9452--9509  Score: 73
    Period size: 19  Copynumber: 2.9  Consensus size: 20

       9442 TTGTTTGGCA

                                
       9452 ACTGTACAGATGAGATTA-C
          1 ACTGTACAGATGAGATTAGC

                       *        *
       9471 ACTGTACAGATTAGATTAGGT
          1 ACTGTACAGATGAGATTA-GC

             *                
       9492 ATTGTACAGATGAGATTA
          1 ACTGTACAGATGAGATTA

       9510 TTAGAGCAGC


Statistics
Matches: 33,  Mismatches: 4, Indels: 2
        0.85            0.10        0.05

Matches are distributed among these distances:
  19   17  0.52
  21   16  0.48

ACGTcount: A:0.36, C:0.10, G:0.22, T:0.31


Consensus pattern (20 bp):   
ACTGTACAGATGAGATTAGC
Done.