Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012084.1 Corchorus olitorius cultivar O-4 contig12117, 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: 15941
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31


Found at i:12347 original size:19 final size:19

Alignment explanation


    Indices: 12297--12347  Score: 61
    Period size: 19  Copynumber: 2.7  Consensus size: 19

      12287 CATAAGATTT

                               
      12297 TTAATAA-TAATTATTCAA
          1 TTAATAATTAATTATTCAA

              *              *  
      12315 TAAAATAATT-ATTATTTAA
          1 T-TAATAATTAATTATTCAA

                          
      12334 TTAATAATTAATTA
          1 TTAATAATTAATTA

      12348 ATTTCAGCCC


Statistics
Matches: 27,  Mismatches: 3, Indels: 5
        0.77            0.09        0.14

Matches are distributed among these distances:
  18    8  0.30
  19   18  0.67
  20    1  0.04

ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47


Consensus pattern (19 bp):   
TTAATAATTAATTATTCAA

Found at i:13588 original size:54 final size:54

Alignment explanation


    Indices: 13476--13589  Score: 174
    Period size: 54  Copynumber: 2.1  Consensus size: 54

      13466 AGGGGGTTAT

                    *                                         *  *
      13476 GGAGGGTATGGTGGACGTGGAGGTAATGGAGGGTACGGTGGACGTGGAGGTTAT
          1 GGAGGGTACGGTGGACGTGGAGGTAATGGAGGGTACGGTGGACGTGGAGGCTAC

                                    *                *     *      
      13530 GGAGGGTACGGTGGACGTGGAGGTTATGGAGGGTACGGTGGCCGTGGTGGCTAC
          1 GGAGGGTACGGTGGACGTGGAGGTAATGGAGGGTACGGTGGACGTGGAGGCTAC

                  
      13584 GGAGGG
          1 GGAGGG

      13590 CGTGGTGGAT


Statistics
Matches: 54,  Mismatches: 6, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  54   54  1.00

ACGTcount: A:0.18, C:0.09, G:0.54, T:0.20


Consensus pattern (54 bp):   
GGAGGGTACGGTGGACGTGGAGGTAATGGAGGGTACGGTGGACGTGGAGGCTAC

Found at i:13589 original size:27 final size:27

Alignment explanation


    Indices: 13470--13576  Score: 187
    Period size: 27  Copynumber: 4.0  Consensus size: 27

      13460 AAACCAAGGG

                          *            
      13470 GGTTATGGAGGGTATGGTGGACGTGGA
          1 GGTTATGGAGGGTACGGTGGACGTGGA

               *                       
      13497 GGTAATGGAGGGTACGGTGGACGTGGA
          1 GGTTATGGAGGGTACGGTGGACGTGGA

                                       
      13524 GGTTATGGAGGGTACGGTGGACGTGGA
          1 GGTTATGGAGGGTACGGTGGACGTGGA

                                *     
      13551 GGTTATGGAGGGTACGGTGGCCGTGG
          1 GGTTATGGAGGGTACGGTGGACGTGG

      13577 TGGCTACGGA


Statistics
Matches: 76,  Mismatches: 4, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  27   76  1.00

ACGTcount: A:0.18, C:0.07, G:0.52, T:0.22


Consensus pattern (27 bp):   
GGTTATGGAGGGTACGGTGGACGTGGA

Found at i:15909 original size:2 final size:2

Alignment explanation


    Indices: 15902--15941  Score: 80
    Period size: 2  Copynumber: 20.0  Consensus size: 2

      15892 AACAGAAGGG

                                                                       
      15902 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   38  1.00

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


Consensus pattern (2 bp):   
AT

Done.