Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021713.1 Corchorus olitorius cultivar O-4 contig21746, 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: 10824
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31


Found at i:1584 original size:19 final size:19

Alignment explanation


    Indices: 1536--1585  Score: 55
    Period size: 19  Copynumber: 2.6  Consensus size: 19

       1526 CCTTTTGTCT

                  *           *
       1536 ACATTTTTGTAATTCTGTT
          1 ACATTTATGTAATTCTGTA

            *  *  *            
       1555 GCAATTCTGTAATTCTGTA
          1 ACATTTATGTAATTCTGTA

                        
       1574 ACATTTATGTAA
          1 ACATTTATGTAA

       1586 GTAATTCTGT


Statistics
Matches: 24,  Mismatches: 7, Indels: 0
        0.77            0.23        0.00

Matches are distributed among these distances:
  19   24  1.00

ACGTcount: A:0.28, C:0.12, G:0.12, T:0.48


Consensus pattern (19 bp):   
ACATTTATGTAATTCTGTA

Found at i:1878 original size:14 final size:14

Alignment explanation


    Indices: 1861--1888  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

       1851 GCTTTGGACT

                          
       1861 TTGGTAGTTGGTAC
          1 TTGGTAGTTGGTAC

                          
       1875 TTGGTAGTTGGTAC
          1 TTGGTAGTTGGTAC

       1889 AAATCTTTCT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.14, C:0.07, G:0.36, T:0.43


Consensus pattern (14 bp):   
TTGGTAGTTGGTAC

Found at i:2274 original size:2 final size:2

Alignment explanation


    Indices: 2267--2301  Score: 52
    Period size: 2  Copynumber: 17.5  Consensus size: 2

       2257 TTACACAGTC

                         *     *                                
       2267 AT AT AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       2302 GAGAGAGAGA


Statistics
Matches: 29,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43


Consensus pattern (2 bp):   
AT

Found at i:3256 original size:2 final size:2

Alignment explanation


    Indices: 3249--3294  Score: 67
    Period size: 2  Copynumber: 23.5  Consensus size: 2

       3239 TTGAGCATAC

                               *     *                                    
       3249 AT AT AT AT AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT A-
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                   
       3290 AT AT A
          1 AT AT A

       3295 CCCTAATTAG


Statistics
Matches: 39,  Mismatches: 4, Indels: 2
        0.87            0.09        0.04

Matches are distributed among these distances:
   1    1  0.03
   2   38  0.97

ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43


Consensus pattern (2 bp):   
AT

Done.