Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022956.1 Corchorus olitorius cultivar O-4 contig22989, 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: 36708
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33


Found at i:3561 original size:24 final size:24

Alignment explanation


    Indices: 3529--3581  Score: 79
    Period size: 24  Copynumber: 2.2  Consensus size: 24

       3519 CCATGGAAAC

                         *          
       3529 TTAAACATCCATGTAAATAAAAAG
          1 TTAAACATCCATGCAAATAAAAAG

                              *   * 
       3553 TTAAACATCCATGCAAATCAAATG
          1 TTAAACATCCATGCAAATAAAAAG

                 
       3577 TTAAA
          1 TTAAA

       3582 TATTGTTCCA


Statistics
Matches: 26,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  24   26  1.00

ACGTcount: A:0.51, C:0.15, G:0.08, T:0.26


Consensus pattern (24 bp):   
TTAAACATCCATGCAAATAAAAAG

Found at i:7077 original size:17 final size:17

Alignment explanation


    Indices: 7055--7087  Score: 57
    Period size: 17  Copynumber: 1.9  Consensus size: 17

       7045 GGCGGCGCGG

                   *         
       7055 GACCTTGTTAGGGTTTC
          1 GACCTTGGTAGGGTTTC

                            
       7072 GACCTTGGTAGGGTTT
          1 GACCTTGGTAGGGTTT

       7088 GAAGTTGGAA


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

Matches are distributed among these distances:
  17   15  1.00

ACGTcount: A:0.12, C:0.15, G:0.33, T:0.39


Consensus pattern (17 bp):   
GACCTTGGTAGGGTTTC

Found at i:12118 original size:2 final size:2

Alignment explanation


    Indices: 12111--12142  Score: 57
    Period size: 2  Copynumber: 16.5  Consensus size: 2

      12101 GTAAGAAGGA

                                                             
      12111 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

      12143 CCCAATTAAT


Statistics
Matches: 29,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   28  0.97

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:15972 original size:34 final size:34

Alignment explanation


    Indices: 15933--16000  Score: 127
    Period size: 34  Copynumber: 2.0  Consensus size: 34

      15923 TCAATTTTGA

                          *                   
      15933 GATCTGGTGCAGTTGTTTTTGGATAATATAATTT
          1 GATCTGGTGCAGTTATTTTTGGATAATATAATTT

                                              
      15967 GATCTGGTGCAGTTATTTTTGGATAATATAATTT
          1 GATCTGGTGCAGTTATTTTTGGATAATATAATTT

      16001 TTTAGGTTCT


Statistics
Matches: 33,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  34   33  1.00

ACGTcount: A:0.25, C:0.06, G:0.22, T:0.47


Consensus pattern (34 bp):   
GATCTGGTGCAGTTATTTTTGGATAATATAATTT

Found at i:16371 original size:2 final size:2

Alignment explanation


    Indices: 16364--16388  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

      16354 TATGTTAATA

                                                 
      16364 AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT A

      16389 AAAGAAAGAT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:17093 original size:31 final size:31

Alignment explanation


    Indices: 17058--17129  Score: 78
    Period size: 31  Copynumber: 2.3  Consensus size: 31

      17048 TAAATTATTG

                            *                
      17058 CAAATTAAAACAAAT-TAAG-CATTAAATTAAA
          1 CAAATTAAAA-AAATGAAAGTC-TTAAATTAAA

                     *                      
      17089 CAAA-TAATTAAAATGAAAGTCTTAAATTAAA
          1 CAAATTAA-AAAAATGAAAGTCTTAAATTAAA

                      
      17120 CAAATTAAAA
          1 CAAATTAAAA

      17130 GCTGATAGAC


Statistics
Matches: 34,  Mismatches: 3, Indels: 8
        0.76            0.07        0.18

Matches are distributed among these distances:
  30    7  0.21
  31   23  0.68
  32    4  0.12

ACGTcount: A:0.61, C:0.08, G:0.04, T:0.26


Consensus pattern (31 bp):   
CAAATTAAAAAAATGAAAGTCTTAAATTAAA

Found at i:22942 original size:19 final size:18

Alignment explanation


    Indices: 22909--22944  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      22899 TGAAAATAAT

                              
      22909 TCTTCAATGGTCTTCAAA
          1 TCTTCAATGGTCTTCAAA

                     *        
      22927 TCTTCAAATTGTCTTCAA
          1 TCTTC-AATGGTCTTCAA

      22945 TAAGTCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGGTCTTCAAA
Done.