Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022844.1 Corchorus olitorius cultivar O-4 contig22877, 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: 17449
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:17 original size:2 final size:2

Alignment explanation


    Indices: 11--42  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

          1 GACTAAACTA

                                                           
         11 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

         43 TATCCACCAA


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:8589 original size:31 final size:31

Alignment explanation


    Indices: 8543--8643  Score: 184
    Period size: 31  Copynumber: 3.2  Consensus size: 31

       8533 TGTTTCAGTT

                     *                      
       8543 CAAAAACGCGACAAAATAGTGGCATTTTGATG
          1 CAAAAA-GCCACAAAATAGTGGCATTTTGATG

                                           
       8575 CAAAAAGCCACAAAATAGTGGCATTTTGATG
          1 CAAAAAGCCACAAAATAGTGGCATTTTGATG

                                           
       8606 CAAAAAGCCACAAAATAGTGGCATTTTGATG
          1 CAAAAAGCCACAAAATAGTGGCATTTTGATG

                   
       8637 CAAAAAG
          1 CAAAAAG

       8644 GCGGTTATGT


Statistics
Matches: 68,  Mismatches: 1, Indels: 1
        0.97            0.01        0.01

Matches are distributed among these distances:
  31   62  0.91
  32    6  0.09

ACGTcount: A:0.44, C:0.16, G:0.20, T:0.21


Consensus pattern (31 bp):   
CAAAAAGCCACAAAATAGTGGCATTTTGATG

Found at i:10293 original size:30 final size:30

Alignment explanation


    Indices: 10236--10293  Score: 73
    Period size: 30  Copynumber: 1.9  Consensus size: 30

      10226 ACCGGAAATG

                 *         *      *       
      10236 GGAACTTTCCCTTCTTATAAAACTAAAAAA
          1 GGAACATTCCCTTCTGATAAAAATAAAAAA

                                         
      10266 GGAACATTCCCTT-TGATGAAAAATAAAA
          1 GGAACATTCCCTTCTGAT-AAAAATAAAA

      10294 CTTGGTTGAA


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  29    3  0.12
  30   21  0.88

ACGTcount: A:0.45, C:0.17, G:0.10, T:0.28


Consensus pattern (30 bp):   
GGAACATTCCCTTCTGATAAAAATAAAAAA

Found at i:13558 original size:16 final size:17

Alignment explanation


    Indices: 13537--13568  Score: 57
    Period size: 16  Copynumber: 1.9  Consensus size: 17

      13527 GAGATTGCGT

                             
      13537 TTTATTTTTCT-TTTTC
          1 TTTATTTTTCTATTTTC

                            
      13553 TTTATTTTTCTATTTT
          1 TTTATTTTTCTATTTT

      13569 AATTTGCACT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  16   11  0.73
  17    4  0.27

ACGTcount: A:0.09, C:0.09, G:0.00, T:0.81


Consensus pattern (17 bp):   
TTTATTTTTCTATTTTC
Done.