Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018195.1 Corchorus olitorius cultivar O-4 contig18228, 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: 17248
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.30


Found at i:7844 original size:13 final size:13

Alignment explanation


    Indices: 7811--7836  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       7801 GAGGAACAAC

                         
       7811 AAGGAACAACCAA
          1 AAGGAACAACCAA

                         
       7824 AAGGAACAACCAA
          1 AAGGAACAACCAA

       7837 CATGAACATC


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.62, C:0.23, G:0.15, T:0.00


Consensus pattern (13 bp):   
AAGGAACAACCAA

Found at i:8448 original size:2 final size:2

Alignment explanation


    Indices: 8441--8479  Score: 50
    Period size: 2  Copynumber: 21.5  Consensus size: 2

       8431 TGAAAACTAT

                                                                          
       8441 TA TA TA TA -A TA TA TA T- TA -A TA -A TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

             
       8479 T
          1 T

       8480 TAAAAAGGTC


Statistics
Matches: 33,  Mismatches: 0, Indels: 8
        0.80            0.00        0.20

Matches are distributed among these distances:
   1    4  0.12
   2   29  0.88

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
TA

Found at i:16071 original size:33 final size:31

Alignment explanation


    Indices: 15946--16075  Score: 107
    Period size: 33  Copynumber: 4.0  Consensus size: 31

      15936 ATTAGCATCC

                        * *      *           
      15946 AAAACAGAATTTGTTTCATCAAAAACAACACCT
          1 AAAACAG-ATTTATGTCATCACAAACAACA-CT

                  *                         
      15979 AAAACAAATTTATGTCATCACAAACAACACTT
          1 AAAACAGATTTATGTCATCACAAACAACAC-T

               **  *      *       *          
      16011 AAATTAGGTTTAATATCATCACTAACAACATCT
          1 AAAACAGATTT-ATGTCATCACAAACAACA-CT

                               **           
      16044 AAAACAGATTTCATGTCATTGCAAACAACACT
          1 AAAACAGATTT-ATGTCATCACAAACAACACT

      16076 CAAATCAGGT


Statistics
Matches: 76,  Mismatches: 18, Indels: 7
        0.75            0.18        0.07

Matches are distributed among these distances:
  31    1  0.01
  32   29  0.38
  33   45  0.59
  34    1  0.01

ACGTcount: A:0.46, C:0.21, G:0.06, T:0.27


Consensus pattern (31 bp):   
AAAACAGATTTATGTCATCACAAACAACACT

Found at i:16692 original size:15 final size:15

Alignment explanation


    Indices: 16672--16703  Score: 64
    Period size: 15  Copynumber: 2.1  Consensus size: 15

      16662 AAACTAAGTG

                           
      16672 GAGCTTGTTGATTTT
          1 GAGCTTGTTGATTTT

                           
      16687 GAGCTTGTTGATTTT
          1 GAGCTTGTTGATTTT

              
      16702 GA
          1 GA

      16704 ACCCCCAAGG


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.16, C:0.06, G:0.28, T:0.50


Consensus pattern (15 bp):   
GAGCTTGTTGATTTT
Done.