Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013074.1 Corchorus olitorius cultivar O-4 contig13107, 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: 44389
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33


Found at i:19464 original size:21 final size:21

Alignment explanation


    Indices: 19440--19483  Score: 88
    Period size: 21  Copynumber: 2.1  Consensus size: 21

      19430 ATGATGGAGT

                                 
      19440 CAAATCTGCTTGTGGATTTTG
          1 CAAATCTGCTTGTGGATTTTG

                                 
      19461 CAAATCTGCTTGTGGATTTTG
          1 CAAATCTGCTTGTGGATTTTG

              
      19482 CA
          1 CA

      19484 GACCAGGTTC


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   23  1.00

ACGTcount: A:0.20, C:0.16, G:0.23, T:0.41


Consensus pattern (21 bp):   
CAAATCTGCTTGTGGATTTTG

Found at i:23282 original size:2 final size:2

Alignment explanation


    Indices: 23275--23300  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

      23265 CCTTGTATTC

                                                  
      23275 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

      23301 CAACTTAAAG


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:34985 original size:21 final size:19

Alignment explanation


    Indices: 34940--34997  Score: 80
    Period size: 19  Copynumber: 2.9  Consensus size: 19

      34930 CTGTATAGTA

                               
      34940 ACTGTACAGATGAGATTAC
          1 ACTGTACAGATGAGATTAC

                       *        *
      34959 ACTGTACAGATTAGATTAGGT
          1 ACTGTACAGATGAGATTA--C

                              
      34980 ACTGTACAGATGAGATTA
          1 ACTGTACAGATGAGATTA

      34998 TTAGAACAGT


Statistics
Matches: 34,  Mismatches: 3, Indels: 2
        0.87            0.08        0.05

Matches are distributed among these distances:
  19   17  0.50
  21   17  0.50

ACGTcount: A:0.36, C:0.12, G:0.22, T:0.29


Consensus pattern (19 bp):   
ACTGTACAGATGAGATTAC

Found at i:42136 original size:19 final size:19

Alignment explanation


    Indices: 42108--42144  Score: 65
    Period size: 19  Copynumber: 1.9  Consensus size: 19

      42098 TTTGGACCCA

                 *             
      42108 AAACGGTAGTGAAACGGTC
          1 AAACGATAGTGAAACGGTC

                              
      42127 AAACGATAGTGAAACGGT
          1 AAACGATAGTGAAACGGT

      42145 TACAAATAAG


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  19   17  1.00

ACGTcount: A:0.41, C:0.14, G:0.30, T:0.16


Consensus pattern (19 bp):   
AAACGATAGTGAAACGGTC
Done.