Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021047.1 Corchorus olitorius cultivar O-4 contig21080, 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: 11464
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.32


Found at i:797 original size:13 final size:12

Alignment explanation


    Indices: 774--811  Score: 51
    Period size: 11  Copynumber: 3.2  Consensus size: 12

        764 TGTCAGTCTA

                        
        774 AACCAAGATAAT
          1 AACCAAGATAAT

                   *     
        786 ATACCAATATAA-
          1 A-ACCAAGATAAT

                        
        798 AACCAAGATAAT
          1 AACCAAGATAAT

              
        810 AA
          1 AA

        812 ACGAAAATAC


Statistics
Matches: 22,  Mismatches: 2, Indels: 4
        0.79            0.07        0.14

Matches are distributed among these distances:
  11    9  0.41
  12    4  0.18
  13    9  0.41

ACGTcount: A:0.61, C:0.16, G:0.05, T:0.18


Consensus pattern (12 bp):   
AACCAAGATAAT

Found at i:813 original size:13 final size:13

Alignment explanation


    Indices: 772--813  Score: 52
    Period size: 13  Copynumber: 3.4  Consensus size: 13

        762 CTTGTCAGTC

                         
        772 TAAACCAAGATAA
          1 TAAACCAAGATAA

              *     *    
        785 TATACCAATAT-A
          1 TAAACCAAGATAA

                         
        797 -AAACCAAGATAA
          1 TAAACCAAGATAA

                 
        809 TAAAC
          1 TAAAC

        814 GAAAATACCA


Statistics
Matches: 23,  Mismatches: 4, Indels: 4
        0.74            0.13        0.13

Matches are distributed among these distances:
  11    8  0.35
  12    2  0.09
  13   13  0.57

ACGTcount: A:0.60, C:0.17, G:0.05, T:0.19


Consensus pattern (13 bp):   
TAAACCAAGATAA

Found at i:3266 original size:29 final size:29

Alignment explanation


    Indices: 3224--3307  Score: 141
    Period size: 29  Copynumber: 2.9  Consensus size: 29

       3214 TTTGTTTTCT

                *                        
       3224 TTCAGATTTCACAACTTCAAGAAATTCCC
          1 TTCATATTTCACAACTTCAAGAAATTCCC

                                     *   
       3253 TTCATATTTCACAACTTCAAGAAATCCCC
          1 TTCATATTTCACAACTTCAAGAAATTCCC

                      *               
       3282 TTCATATTTCCCAACTTCAAGAAATT
          1 TTCATATTTCACAACTTCAAGAAATT

       3308 GGCTGCAAAC


Statistics
Matches: 51,  Mismatches: 4, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  29   51  1.00

ACGTcount: A:0.35, C:0.27, G:0.05, T:0.33


Consensus pattern (29 bp):   
TTCATATTTCACAACTTCAAGAAATTCCC

Found at i:3961 original size:25 final size:25

Alignment explanation


    Indices: 3933--4008  Score: 64
    Period size: 25  Copynumber: 3.0  Consensus size: 25

       3923 TTGCCAGGAA

                                     
       3933 TTTATTAGTTCAACATTCAAGATAG
          1 TTTATTAGTTCAACATTCAAGATAG

                *  ** *  * *         *
       3958 TTTAATAAATAAATAATCAGAGA-AT
          1 TTTATTAGTTCAACATTCA-AGATAG

                              *      
       3983 TTTATTAGTTCAACATTCGAGATAG
          1 TTTATTAGTTCAACATTCAAGATAG

             
       4008 T
          1 T

       4009 GATAAGCATT


Statistics
Matches: 34,  Mismatches: 15, Indels: 4
        0.64            0.28        0.08

Matches are distributed among these distances:
  24    3  0.09
  25   28  0.82
  26    3  0.09

ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38


Consensus pattern (25 bp):   
TTTATTAGTTCAACATTCAAGATAG
Done.