Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012372.1 Corchorus olitorius cultivar O-4 contig12405, 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: 6296
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34


Found at i:3080 original size:20 final size:19

Alignment explanation


    Indices: 3057--3103  Score: 60
    Period size: 19  Copynumber: 2.5  Consensus size: 19

       3047 AATTTGAGTA

                        *       
       3057 TGTTATTAATCATTTTTTAT
          1 TGTTATT-ATCAATTTTTAT

                     *         
       3077 TGTTATTATTAATTTTTAT
          1 TGTTATTATCAATTTTTAT

                     
       3096 TGTT-TTAT
          1 TGTTATTAT

       3104 TATCTCTTAT


Statistics
Matches: 25,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  18    4  0.16
  19   14  0.56
  20    7  0.28

ACGTcount: A:0.23, C:0.02, G:0.06, T:0.68


Consensus pattern (19 bp):   
TGTTATTATCAATTTTTAT

Found at i:3094 original size:19 final size:18

Alignment explanation


    Indices: 3070--3105  Score: 63
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       3060 TATTAATCAT

                               
       3070 TTTTTATTGTTATTATTAA
          1 TTTTTATTGTT-TTATTAA

                             
       3089 TTTTTATTGTTTTATTA
          1 TTTTTATTGTTTTATTA

       3106 TCTCTTATTT


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  18    6  0.35
  19   11  0.65

ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72


Consensus pattern (18 bp):   
TTTTTATTGTTTTATTAA

Found at i:3113 original size:18 final size:19

Alignment explanation


    Indices: 3073--3114  Score: 52
    Period size: 18  Copynumber: 2.3  Consensus size: 19

       3063 TAATCATTTT

                              *
       3073 TTATTGTTATTATTAATTT
          1 TTATTGTTATTATTAATTC

                                
       3092 TTATTGTT-TTATT-ATCTC
          1 TTATTGTTATTATTAAT-TC

                 
       3110 TTATT
          1 TTATT

       3115 TCCCTCGCAC


Statistics
Matches: 21,  Mismatches: 1, Indels: 3
        0.84            0.04        0.12

Matches are distributed among these distances:
  17    2  0.10
  18   11  0.52
  19    8  0.38

ACGTcount: A:0.21, C:0.05, G:0.05, T:0.69


Consensus pattern (19 bp):   
TTATTGTTATTATTAATTC

Found at i:5008 original size:19 final size:19

Alignment explanation


    Indices: 4988--5024  Score: 67
    Period size: 19  Copynumber: 2.0  Consensus size: 19

       4978 AATTAATTAT

                               
       4988 TTTA-ATATTAAATTTTTA
          1 TTTATATATTAAATTTTTA

                               
       5006 TTTATATATTAAATTTTTA
          1 TTTATATATTAAATTTTTA

       5025 CTTAAAAATT


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  18    4  0.22
  19   14  0.78

ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62


Consensus pattern (19 bp):   
TTTATATATTAAATTTTTA

Found at i:5035 original size:19 final size:19

Alignment explanation


    Indices: 4994--5035  Score: 57
    Period size: 19  Copynumber: 2.2  Consensus size: 19

       4984 TTATTTTAAT

                        *   * *
       4994 ATTAAATTTTTATTTATAT
          1 ATTAAATTTTTACTTAAAA

                               
       5013 ATTAAATTTTTACTTAAAA
          1 ATTAAATTTTTACTTAAAA

                
       5032 ATTA
          1 ATTA

       5036 CTCCTATTTA


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  19   20  1.00

ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55


Consensus pattern (19 bp):   
ATTAAATTTTTACTTAAAA
Done.