Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017162.1 Corchorus olitorius cultivar O-4 contig17195, 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: 31790
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:490 original size:2 final size:2

Alignment explanation


    Indices: 483--515  Score: 57
    Period size: 2  Copynumber: 16.5  Consensus size: 2

        473 ACCCACTTCC

                                                      *      
        483 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

        516 ATTAATACAT


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

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:1137 original size:20 final size:20

Alignment explanation


    Indices: 1114--1154  Score: 82
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       1104 AGTCATAGAT

                                
       1114 TTTTTTTTATCAGAAGTAAG
          1 TTTTTTTTATCAGAAGTAAG

                                
       1134 TTTTTTTTATCAGAAGTAAG
          1 TTTTTTTTATCAGAAGTAAG

             
       1154 T
          1 T

       1155 CATAGATTCG


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   21  1.00

ACGTcount: A:0.29, C:0.05, G:0.15, T:0.51


Consensus pattern (20 bp):   
TTTTTTTTATCAGAAGTAAG

Found at i:1325 original size:2 final size:2

Alignment explanation


    Indices: 1318--1353  Score: 72
    Period size: 2  Copynumber: 18.0  Consensus size: 2

       1308 AAATAAATGC

                                                                 
       1318 AT AT 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 AT AT

       1354 GGTGATGATG


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:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:20928 original size:62 final size:62

Alignment explanation


    Indices: 20831--20954  Score: 230
    Period size: 62  Copynumber: 2.0  Consensus size: 62

      20821 AAGGGCGTGG

                                                                    *     
      20831 GTTCAAATCCCACACTCCACATTCAGACCATTTTTTCCTCTTTTTCCAAGAGACCCTATCTT
          1 GTTCAAATCCCACACTCCACATTCAGACCATTTTTTCCTCTTTTTCCAAGAGACCCCATCTT

                                                   *                      
      20893 GTTCAAATCCCACACTCCACATTCAGACCATTTTTTCCTGTTTTTCCAAGAGACCCCATCTT
          1 GTTCAAATCCCACACTCCACATTCAGACCATTTTTTCCTCTTTTTCCAAGAGACCCCATCTT

      20955 TTTGGACAAT


Statistics
Matches: 60,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  62   60  1.00

ACGTcount: A:0.24, C:0.34, G:0.07, T:0.35


Consensus pattern (62 bp):   
GTTCAAATCCCACACTCCACATTCAGACCATTTTTTCCTCTTTTTCCAAGAGACCCCATCTT

Found at i:30061 original size:14 final size:15

Alignment explanation


    Indices: 30042--30075  Score: 52
    Period size: 15  Copynumber: 2.3  Consensus size: 15

      30032 TTGCTTTGCC

                           
      30042 TTTTTTA-ATATAAA
          1 TTTTTTAGATATAAA

                    *      
      30056 TTTTTTAGTTATAAA
          1 TTTTTTAGATATAAA

                 
      30071 TTTTT
          1 TTTTT

      30076 AAAAAATAAT


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

Matches are distributed among these distances:
  14    7  0.39
  15   11  0.61

ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65


Consensus pattern (15 bp):   
TTTTTTAGATATAAA
Done.