Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015009.1 Corchorus olitorius cultivar O-4 contig15042, 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: 30211
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31


Found at i:126 original size:16 final size:16

Alignment explanation


    Indices: 86--116  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

         76 TTGGCCTTAG

                *           
         86 GTCACTCGGGTTTTGA
          1 GTCATTCGGGTTTTGA

                           
        102 GTCATTCGGGTTTTG
          1 GTCATTCGGGTTTTG

        117 GGTTTTTCGG


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.10, C:0.16, G:0.32, T:0.42


Consensus pattern (16 bp):   
GTCATTCGGGTTTTGA

Found at i:7318 original size:28 final size:30

Alignment explanation


    Indices: 7286--7344  Score: 77
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       7276 TGTTTGTAGG

                      *                   
       7286 AGAAAAAAACTA-TTTCA-ATTTTTTTAAA
          1 AGAAAAAAACAATTTTCATATTTTTTTAAA

                  *         *             
       7314 AGAAAATAACAATTTTTATATTTTTTTAAA
          1 AGAAAAAAACAATTTTCATATTTTTTTAAA

             
       7344 A
          1 A

       7345 AATTTCTGAT


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  28   10  0.38
  29    4  0.15
  30   12  0.46

ACGTcount: A:0.49, C:0.05, G:0.03, T:0.42


Consensus pattern (30 bp):   
AGAAAAAAACAATTTTCATATTTTTTTAAA

Found at i:13272 original size:2 final size:2

Alignment explanation


    Indices: 13265--13295  Score: 55
    Period size: 2  Copynumber: 16.0  Consensus size: 2

      13255 ACTTTTAGGG

                                                           
      13265 AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      13296 GGGGTAAACG


Statistics
Matches: 28,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   1    1  0.04
   2   27  0.96

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
AT

Found at i:21922 original size:30 final size:30

Alignment explanation


    Indices: 21888--21955  Score: 118
    Period size: 30  Copynumber: 2.3  Consensus size: 30

      21878 GGGATTGAGC

                                          
      21888 TAGGTGGCAGAGGAGGGCTGGGGACGGATG
          1 TAGGTGGCAGAGGAGGGCTGGGGACGGATG

                      *                *  
      21918 TAGGTGGCAGGGGAGGGCTGGGGACGGCTG
          1 TAGGTGGCAGAGGAGGGCTGGGGACGGATG

                    
      21948 TAGGTGGC
          1 TAGGTGGC

      21956 GTGGGCTGAT


Statistics
Matches: 36,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  30   36  1.00

ACGTcount: A:0.16, C:0.12, G:0.57, T:0.15


Consensus pattern (30 bp):   
TAGGTGGCAGAGGAGGGCTGGGGACGGATG

Found at i:23424 original size:13 final size:13

Alignment explanation


    Indices: 23406--23430  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

      23396 TCAGAATTCC

                         
      23406 AAATAATATTTAT
          1 AAATAATATTTAT

                        
      23419 AAATAATATTTA
          1 AAATAATATTTA

      23431 GAACATTGAA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44


Consensus pattern (13 bp):   
AAATAATATTTAT
Done.