Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010068.1 Corchorus olitorius cultivar O-4 contig10100, 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: 3447
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32


Found at i:2019 original size:8 final size:8

Alignment explanation


    Indices: 2006--2050  Score: 72
    Period size: 8  Copynumber: 5.4  Consensus size: 8

       1996 ATTTTATATA

                    
       2006 ATAGTAAG
          1 ATAGTAAG

                    
       2014 ATAGTAAG
          1 ATAGTAAG

                      
       2022 ATAAGATAAG
          1 AT-AG-TAAG

                    
       2032 ATAGTAAG
          1 ATAGTAAG

                    
       2040 ATAGTAAG
          1 ATAGTAAG

               
       2048 ATA
          1 ATA

       2051 AGATATAGAT


Statistics
Matches: 35,  Mismatches: 0, Indels: 4
        0.90            0.00        0.10

Matches are distributed among these distances:
   8   25  0.71
   9    4  0.11
  10    6  0.17

ACGTcount: A:0.53, C:0.00, G:0.22, T:0.24


Consensus pattern (8 bp):   
ATAGTAAG

Found at i:2028 original size:13 final size:13

Alignment explanation


    Indices: 2010--2055  Score: 60
    Period size: 13  Copynumber: 3.5  Consensus size: 13

       2000 TATATAATAG

                         
       2010 TAAGATAGTAAGA
          1 TAAGATAGTAAGA

                           
       2023 TAAGATAAG-ATAG-
          1 TAAGAT-AGTA-AGA

                         
       2036 TAAGATAGTAAGA
          1 TAAGATAGTAAGA

                   
       2049 TAAGATA
          1 TAAGATA

       2056 TAGATATCTA


Statistics
Matches: 29,  Mismatches: 0, Indels: 8
        0.78            0.00        0.22

Matches are distributed among these distances:
  12    4  0.14
  13   21  0.72
  14    4  0.14

ACGTcount: A:0.54, C:0.00, G:0.22, T:0.24


Consensus pattern (13 bp):   
TAAGATAGTAAGA

Found at i:2033 original size:18 final size:16

Alignment explanation


    Indices: 2006--2050  Score: 72
    Period size: 18  Copynumber: 2.7  Consensus size: 16

       1996 ATTTTATATA

                            
       2006 ATAGTAAGATAGTAAG
          1 ATAGTAAGATAGTAAG

                              
       2022 ATAAGATAAGATAGTAAG
          1 AT-AG-TAAGATAGTAAG

                       
       2040 ATAGTAAGATA
          1 ATAGTAAGATA

       2051 AGATATAGAT


Statistics
Matches: 27,  Mismatches: 0, Indels: 4
        0.87            0.00        0.13

Matches are distributed among these distances:
  16    9  0.33
  17    4  0.15
  18   14  0.52

ACGTcount: A:0.53, C:0.00, G:0.22, T:0.24


Consensus pattern (16 bp):   
ATAGTAAGATAGTAAG

Found at i:2037 original size:26 final size:27

Alignment explanation


    Indices: 2001--2061  Score: 108
    Period size: 26  Copynumber: 2.3  Consensus size: 27

       1991 TCGTGATTTT

                                       
       2001 ATATA-ATAGTAAGATAGTAAGATAAG
          1 ATATAGATAGTAAGATAGTAAGATAAG

                                       
       2027 ATA-AGATAGTAAGATAGTAAGATAAG
          1 ATATAGATAGTAAGATAGTAAGATAAG

                     
       2053 ATATAGATA
          1 ATATAGATA

       2062 TCTATCAATT


Statistics
Matches: 33,  Mismatches: 0, Indels: 3
        0.92            0.00        0.08

Matches are distributed among these distances:
  25    1  0.03
  26   27  0.82
  27    5  0.15

ACGTcount: A:0.54, C:0.00, G:0.20, T:0.26


Consensus pattern (27 bp):   
ATATAGATAGTAAGATAGTAAGATAAG
Done.