Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022658.1 Corchorus olitorius cultivar O-4 contig22691, 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: 31546
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33


Found at i:7465 original size:2 final size:2

Alignment explanation


    Indices: 7458--7489  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

       7448 AAAGAATGTC

                                                           
       7458 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       7490 TGGAATTAGT


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:17569 original size:15 final size:16

Alignment explanation


    Indices: 17544--17578  Score: 54
    Period size: 15  Copynumber: 2.2  Consensus size: 16

      17534 TCAAGAAAAT

                         *  
      17544 TAAAGAAAACAGTTAA
          1 TAAAGAAAACAGTGAA

                            
      17560 TAAA-AAAACAGTGAA
          1 TAAAGAAAACAGTGAA

                
      17575 TAAA
          1 TAAA

      17579 CTAGAGAATA


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  15   14  0.78
  16    4  0.22

ACGTcount: A:0.66, C:0.06, G:0.11, T:0.17


Consensus pattern (16 bp):   
TAAAGAAAACAGTGAA

Found at i:20692 original size:20 final size:20

Alignment explanation


    Indices: 20669--20717  Score: 55
    Period size: 20  Copynumber: 2.5  Consensus size: 20

      20659 TACAACTAAT

                      *    *    
      20669 TCAAATCAAGGAATAGGCAA
          1 TCAAATCAAGCAATAAGCAA

                             *   
      20689 TC-AATCAAAGCAATAATCAA
          1 TCAAATC-AAGCAATAAGCAA

                     
      20709 TCAAATCAA
          1 TCAAATCAA

      20718 ATCAAAAGAA


Statistics
Matches: 24,  Mismatches: 3, Indels: 4
        0.77            0.10        0.13

Matches are distributed among these distances:
  19    4  0.17
  20   16  0.67
  21    4  0.17

ACGTcount: A:0.53, C:0.18, G:0.10, T:0.18


Consensus pattern (20 bp):   
TCAAATCAAGCAATAAGCAA

Found at i:30852 original size:28 final size:27

Alignment explanation


    Indices: 30810--30864  Score: 76
    Period size: 28  Copynumber: 2.0  Consensus size: 27

      30800 TTTTTATTTG

                            *          
      30810 AGTTTGTTTTTGAGTCGGTTT-GAGTC
          1 AGTTTGTTTTTGAGTCAGTTTCGAGTC

                                         
      30836 AGTTTGTTTTTTCGAGTCAGTTTCGAGTC
          1 AGTTTG-TTTTT-GAGTCAGTTTCGAGTC

      30865 TAGTCTCAGT


Statistics
Matches: 25,  Mismatches: 1, Indels: 3
        0.86            0.03        0.10

Matches are distributed among these distances:
  26    6  0.24
  27    5  0.20
  28    9  0.36
  29    5  0.20

ACGTcount: A:0.13, C:0.11, G:0.27, T:0.49


Consensus pattern (27 bp):   
AGTTTGTTTTTGAGTCAGTTTCGAGTC
Done.