Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012011.1 Corchorus olitorius cultivar O-4 contig12044, 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: 23205
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--32  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

                                                           
          1 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

         33 TACTGTCATC


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:9061 original size:3 final size:3

Alignment explanation


    Indices: 9053--9082  Score: 51
    Period size: 3  Copynumber: 9.7  Consensus size: 3

       9043 AAACACACAA

                                                   
       9053 TTG TTG TTG TTG TTG TTG TTG TTTG TTG TT
          1 TTG TTG TTG TTG TTG TTG TTG -TTG TTG TT

       9083 AAACTGTGTT


Statistics
Matches: 26,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   3   23  0.88
   4    3  0.12

ACGTcount: A:0.00, C:0.00, G:0.30, T:0.70


Consensus pattern (3 bp):   
TTG

Found at i:11133 original size:33 final size:33

Alignment explanation


    Indices: 11085--11147  Score: 92
    Period size: 33  Copynumber: 1.9  Consensus size: 33

      11075 TGTAAAACTT

                              *              
      11085 TTGAATCGACTATTATACTCGTATTTTTTCTAA
          1 TTGAATCGACTATTATACCCGTATTTTTTCTAA

                                 *         
      11118 TTGAATCGA-TCATTATACCCTTATTTTTTC
          1 TTGAATCGACT-ATTATACCCGTATTTTTTC

      11148 AAACATATTT


Statistics
Matches: 27,  Mismatches: 2, Indels: 2
        0.87            0.06        0.06

Matches are distributed among these distances:
  32    1  0.04
  33   26  0.96

ACGTcount: A:0.25, C:0.17, G:0.08, T:0.49


Consensus pattern (33 bp):   
TTGAATCGACTATTATACCCGTATTTTTTCTAA

Found at i:17541 original size:9 final size:9

Alignment explanation


    Indices: 17527--17556  Score: 53
    Period size: 9  Copynumber: 3.4  Consensus size: 9

      17517 TCCTAGCTTT

                     
      17527 TTTTATTTA
          1 TTTTATTTA

                     
      17536 TTTTATTTA
          1 TTTTATTTA

                     
      17545 -TTTATTTA
          1 TTTTATTTA

                
      17553 TTTT
          1 TTTT

      17557 CTTATGATTA


Statistics
Matches: 20,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
   8    8  0.40
   9   12  0.60

ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80


Consensus pattern (9 bp):   
TTTTATTTA
Done.