Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020356.1 Corchorus olitorius cultivar O-4 contig20389, 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: 27134
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--36  Score: 72
    Period size: 2  Copynumber: 18.0  Consensus size: 2

                                                                 
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC

         37 ATTGATGCTA


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   34  1.00

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


Consensus pattern (2 bp):   
TC

Found at i:18039 original size:12 final size:12

Alignment explanation


    Indices: 18022--18048  Score: 54
    Period size: 12  Copynumber: 2.2  Consensus size: 12

      18012 TTGTTTGATT

                        
      18022 GTTGCCTTTATA
          1 GTTGCCTTTATA

                        
      18034 GTTGCCTTTATA
          1 GTTGCCTTTATA

               
      18046 GTT
          1 GTT

      18049 TATACATTGT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   15  1.00

ACGTcount: A:0.15, C:0.15, G:0.19, T:0.52


Consensus pattern (12 bp):   
GTTGCCTTTATA

Found at i:18702 original size:22 final size:22

Alignment explanation


    Indices: 18677--18719  Score: 70
    Period size: 22  Copynumber: 2.0  Consensus size: 22

      18667 TAGGGCTAAA

                                   
      18677 CAGAATTAAG-AACAGCTATTGT
          1 CAGAATTAAGTAA-AGCTATTGT

                                 
      18699 CAGAATTAAGTAAAGCTATTG
          1 CAGAATTAAGTAAAGCTATTG

      18720 GAAGTTTGGA


Statistics
Matches: 20,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  22   18  0.90
  23    2  0.10

ACGTcount: A:0.42, C:0.12, G:0.19, T:0.28


Consensus pattern (22 bp):   
CAGAATTAAGTAAAGCTATTGT

Found at i:19505 original size:21 final size:18

Alignment explanation


    Indices: 19466--19502  Score: 74
    Period size: 18  Copynumber: 2.1  Consensus size: 18

      19456 CACGTGACAC

                              
      19466 ATGATTTGCAAATAAAAA
          1 ATGATTTGCAAATAAAAA

                              
      19484 ATGATTTGCAAATAAAAA
          1 ATGATTTGCAAATAAAAA

             
      19502 A
          1 A

      19503 AAACATAACC


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   19  1.00

ACGTcount: A:0.57, C:0.05, G:0.11, T:0.27


Consensus pattern (18 bp):   
ATGATTTGCAAATAAAAA

Found at i:25035 original size:58 final size:58

Alignment explanation


    Indices: 24933--25042  Score: 150
    Period size: 58  Copynumber: 1.9  Consensus size: 58

      24923 ATTAATCAAA

                                                          *           
      24933 TATCAAGTGACATGTTATTTATTAGATGCATAAAAAAAGACGTTTTCGGACCAAGACT
          1 TATCAAGTGACATGTTATTTATTAGATGCATAAAAAAAGACGTTTTAGGACCAAGACT

                *            *            *    *    *            
      24991 TATCGAGTGACATGTTTTTTTATTAGATGCCT-AAGAAAGGCGTTTTAGGACC
          1 TATCAAGTGACATG-TTATTTATTAGATGCATAAAAAAAGACGTTTTAGGACC

      25043 GAGGCATGAT


Statistics
Matches: 45,  Mismatches: 6, Indels: 2
        0.85            0.11        0.04

Matches are distributed among these distances:
  58   30  0.67
  59   15  0.33

ACGTcount: A:0.33, C:0.14, G:0.20, T:0.34


Consensus pattern (58 bp):   
TATCAAGTGACATGTTATTTATTAGATGCATAAAAAAAGACGTTTTAGGACCAAGACT

Found at i:26358 original size:36 final size:36

Alignment explanation


    Indices: 26311--26380  Score: 106
    Period size: 36  Copynumber: 1.9  Consensus size: 36

      26301 TTCAATAACC

                         *                       
      26311 TTACATCTTTTGTGATTTT-AGTTATCATATTTCTTA
          1 TTACATCTTTTGTAATTTTGA-TTATCATATTTCTTA

                  *                           
      26347 TTACATTTTTTGTAATTTTGATTATCATATTTCT
          1 TTACATCTTTTGTAATTTTGATTATCATATTTCT

      26381 CCAAAATCTC


Statistics
Matches: 31,  Mismatches: 2, Indels: 2
        0.89            0.06        0.06

Matches are distributed among these distances:
  36   30  0.97
  37    1  0.03

ACGTcount: A:0.23, C:0.10, G:0.07, T:0.60


Consensus pattern (36 bp):   
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Done.