Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016018.1 Corchorus olitorius cultivar O-4 contig16051, 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: 13904
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33


Found at i:2480 original size:45 final size:45

Alignment explanation


    Indices: 2429--2555  Score: 227
    Period size: 45  Copynumber: 2.8  Consensus size: 45

       2419 AATTCTACTT

                            *                            
       2429 CATCTCTAGGTAATTCTTCAAAATAAAGCTAATATTATACTCCTC
          1 CATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTCCTC

                                                *        
       2474 CATCTCTAGGTAATTCATCAAAATAAAGCTAATATTCTACTCCTC
          1 CATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTCCTC

                                       *         
       2519 CATCTCTAGGTAATTCATCAAAATAAACCTAATATTA
          1 CATCTCTAGGTAATTCATCAAAATAAAGCTAATATTA

       2556 ATTGTTGCTT


Statistics
Matches: 78,  Mismatches: 4, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  45   78  1.00

ACGTcount: A:0.38, C:0.22, G:0.06, T:0.34


Consensus pattern (45 bp):   
CATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTCCTC

Found at i:3386 original size:13 final size:13

Alignment explanation


    Indices: 3354--3387  Score: 50
    Period size: 14  Copynumber: 2.5  Consensus size: 13

       3344 TAGTAAATTA

                      *  
       3354 CAAAAAAGGGCAG
          1 CAAAAAAGGGAAG

                          
       3367 CAGAAAAAGGGAAG
          1 CA-AAAAAGGGAAG

                   
       3381 CAAAAAA
          1 CAAAAAA

       3388 TTCATTGAGG


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  13    7  0.37
  14   12  0.63

ACGTcount: A:0.62, C:0.12, G:0.26, T:0.00


Consensus pattern (13 bp):   
CAAAAAAGGGAAG

Found at i:6331 original size:6 final size:6

Alignment explanation


    Indices: 6322--6413  Score: 177
    Period size: 6  Copynumber: 15.5  Consensus size: 6

       6312 TTATATATAT

                                                                   
       6322 ATACTA ATACTA ATACTA ATACTA ATACTA ATACTA ATACTA ATACTA
          1 ATACTA ATACTA ATACTA ATACTA ATACTA ATACTA ATACTA ATACTA

                                                                
       6370 ATACTA ATACT- ATACTA ATACTA ATACTA ATACTA ATACTA ATA
          1 ATACTA ATACTA ATACTA ATACTA ATACTA ATACTA ATACTA ATA

       6414 AACTAATAAA


Statistics
Matches: 85,  Mismatches: 0, Indels: 2
        0.98            0.00        0.02

Matches are distributed among these distances:
   5    5  0.06
   6   80  0.94

ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34


Consensus pattern (6 bp):   
ATACTA

Done.