Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018623.1 Corchorus olitorius cultivar O-4 contig18656, 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: 2339
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.40


Found at i:853 original size:21 final size:21

Alignment explanation


    Indices: 829--892  Score: 64
    Period size: 17  Copynumber: 3.2  Consensus size: 21

        819 GTAATATATA

                                 
        829 TAATAACTAAAATACTTACAT
          1 TAATAACTAAAATACTTACAT

                   * **           
        850 TAATTAAATGTAATAC-T--A-
          1 TAA-TAACTAAAATACTTACAT

                                 
        868 TAATAACTAAAATACTTACAT
          1 TAATAACTAAAATACTTACAT

                
        889 TAAT
          1 TAAT

        893 TAAATTCTTA


Statistics
Matches: 32,  Mismatches: 6, Indels: 10
        0.67            0.12        0.21

Matches are distributed among these distances:
  17    9  0.28
  18    4  0.12
  19    1  0.03
  20    1  0.03
  21    8  0.25
  22    9  0.28

ACGTcount: A:0.52, C:0.11, G:0.02, T:0.36


Consensus pattern (21 bp):   
TAATAACTAAAATACTTACAT

Found at i:857 original size:18 final size:18

Alignment explanation


    Indices: 836--896  Score: 54
    Period size: 18  Copynumber: 3.2  Consensus size: 18

        826 ATATAATAAC

                              
        836 TAAAATACTTACATTAAT
          1 TAAAATACTTACATTAAT

                                  *
        854 TAAATGTAATACTATA-A-TAAC
          1 T-AA---AATACT-TACATTAAT

                              
        875 TAAAATACTTACATTAAT
          1 TAAAATACTTACATTAAT

                
        893 TAAA
          1 TAAA

        897 TTCTTAGGTA


Statistics
Matches: 34,  Mismatches: 2, Indels: 14
        0.68            0.04        0.28

Matches are distributed among these distances:
  16    2  0.06
  17    7  0.21
  18    8  0.24
  19    2  0.06
  20    2  0.06
  21    4  0.12
  22    7  0.21
  23    2  0.06

ACGTcount: A:0.52, C:0.10, G:0.02, T:0.36


Consensus pattern (18 bp):   
TAAAATACTTACATTAAT

Found at i:873 original size:39 final size:40

Alignment explanation


    Indices: 817--897  Score: 146
    Period size: 39  Copynumber: 2.0  Consensus size: 40

        807 TTTAATTCCT

                                                    
        817 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
          1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA

                     *                              
        857 ATGTAATA-CTATAATAACTAAAATACTTACATTAATTAA
          1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA

              
        896 AT
          1 AT

        898 TCTTAGGTAT


Statistics
Matches: 40,  Mismatches: 1, Indels: 1
        0.95            0.02        0.02

Matches are distributed among these distances:
  39   32  0.80
  40    8  0.20

ACGTcount: A:0.52, C:0.09, G:0.02, T:0.37


Consensus pattern (40 bp):   
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA

Found at i:924 original size:25 final size:24

Alignment explanation


    Indices: 888--934  Score: 85
    Period size: 25  Copynumber: 1.9  Consensus size: 24

        878 AATACTTACA

                                    
        888 TTAATTAAATTCTTAGGTATTTTT
          1 TTAATTAAATTCTTAGGTATTTTT

                                   
        912 TTAATTCAAATTCTTAGGTATTT
          1 TTAATT-AAATTCTTAGGTATTT

        935 GTGCAAATGT


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  24    6  0.27
  25   16  0.73

ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55


Consensus pattern (24 bp):   
TTAATTAAATTCTTAGGTATTTTT

Found at i:1986 original size:36 final size:36

Alignment explanation


    Indices: 1932--2001  Score: 104
    Period size: 36  Copynumber: 1.9  Consensus size: 36

       1922 GAGATTTTGG

                       * *      *               
       1932 AGAAATATGATTATCAAAATTACAAAAAATGTAATA
          1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA

                                       *      
       1968 AGAAATATGATAACCAAAATCACAAAAGATGTAA
          1 AGAAATATGATAACCAAAATCACAAAAAATGTAA

       2002 GCTTATTGAA


Statistics
Matches: 30,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  36   30  1.00

ACGTcount: A:0.59, C:0.09, G:0.10, T:0.23


Consensus pattern (36 bp):   
AGAAATATGATAACCAAAATCACAAAAAATGTAATA
Done.