Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000884.1 Corchorus capsularis cultivar CVL-1 contig00884, 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: 4097
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35


Found at i:345 original size:78 final size:77

Alignment explanation


    Indices: 263--501  Score: 352
    Period size: 78  Copynumber: 3.2  Consensus size: 77

        253 TTTTTTTAAC

                                                                             
        263 TAAAATAGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAACT-G
          1 TAAAATAGTAAAA-TGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAA-TAG

                          
        327 AGTTTTTAGTTGAG
         64 AGTTTTTAGTTGAG

                                                                             
        341 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
          1 TAAAATAGTAAAAT-GTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA

                         
        406 GTTTTTAGTTGAG
         65 GTTTTTAGTTGAG

                                              *       *         *            
        419 TAAAATAGTAAAA--T-AAA-AT-A-A-TTATAAAGATATTATATTTAATTAAATAAAAATAGAG
          1 TAAAATAGTAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAG

                        
        477 TTTTTAGTTGAG
         66 TTTTTAGTTGAG

                          
        489 TAAAACTA-TAAAA
          1 TAAAA-TAGTAAAA

        502 ACCTAAACAA


Statistics
Matches: 155,  Mismatches: 3, Indels: 14
        0.90            0.02        0.08

Matches are distributed among these distances:
  70   56  0.36
  71    3  0.02
  72    1  0.01
  73    2  0.01
  74    3  0.02
  75    1  0.01
  77    2  0.01
  78   87  0.56

ACGTcount: A:0.50, C:0.01, G:0.13, T:0.37


Consensus pattern (77 bp):   
TAAAATAGTAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAG
TTTTTAGTTGAG

Found at i:352 original size:70 final size:71

Alignment explanation


    Indices: 269--501  Score: 303
    Period size: 70  Copynumber: 3.2  Consensus size: 71

        259 TAACTAAAAT

                     *                                                       
        269 AGTAAAA-TTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAACT-GAGTTT
          1 AGTAAAACTAGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAA-TAGAGTTT

                   
        332 TTAGTTG
         65 TTAGTTG

                     *                                                       
        339 AGTAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATA
          1 AGT-AAA-ACT---A--GTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATA

                         
        404 GAGTTTTTAGTTG
         59 GAGTTTTTAGTTG

                              *    *      *       *         *                
        417 AGTAAAA-TAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTT
          1 AGTAAAACTAGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTT

                  
        481 TAGTTG
         66 TAGTTG

                            
        487 AGTAAAACTA-TAAAA
          1 AGTAAAACTAGTAAAA

        502 ACCTAAACAA


Statistics
Matches: 147,  Mismatches: 6, Indels: 20
        0.85            0.03        0.12

Matches are distributed among these distances:
  70   71  0.48
  71    5  0.03
  72    2  0.01
  73    1  0.01
  75    1  0.01
  76    1  0.01
  77    4  0.03
  78   62  0.42

ACGTcount: A:0.49, C:0.01, G:0.13, T:0.37


Consensus pattern (71 bp):   
AGTAAAACTAGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTT
TAGTTG

Found at i:610 original size:10 final size:10

Alignment explanation


    Indices: 591--640  Score: 55
    Period size: 10  Copynumber: 4.7  Consensus size: 10

        581 ACTTTTTAAC

                       
        591 ATAGTATAGAT
          1 ATAG-ATAGAT

             * *      
        602 AGATATAGAT
          1 ATAGATAGAT

                      
        612 ATAGATAGAT
          1 ATAGATAGAT

                        
        622 ATAGATATAGAT
          1 ATAG--ATAGAT

                   
        634 ATAGATA
          1 ATAGATA

        641 TAGATATTTA


Statistics
Matches: 33,  Mismatches: 4, Indels: 5
        0.79            0.10        0.12

Matches are distributed among these distances:
  10   21  0.64
  11    2  0.06
  12   10  0.30

ACGTcount: A:0.50, C:0.00, G:0.18, T:0.32


Consensus pattern (10 bp):   
ATAGATAGAT

Found at i:611 original size:6 final size:6

Alignment explanation


    Indices: 600--647  Score: 82
    Period size: 6  Copynumber: 8.3  Consensus size: 6

        590 CATAGTATAG

                                                                   
        600 ATAGAT ATAGAT ATAG-- ATAGAT ATAGAT ATAGAT ATAGAT ATAGAT
          1 ATAGAT ATAGAT ATAGAT ATAGAT ATAGAT ATAGAT ATAGAT ATAGAT

              
        646 AT
          1 AT

        648 TTATTGTGTT


Statistics
Matches: 40,  Mismatches: 0, Indels: 4
        0.91            0.00        0.09

Matches are distributed among these distances:
   4    4  0.10
   6   36  0.90

ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33


Consensus pattern (6 bp):   
ATAGAT

Found at i:616 original size:16 final size:16

Alignment explanation


    Indices: 591--647  Score: 89
    Period size: 16  Copynumber: 3.5  Consensus size: 16

        581 ACTTTTTAAC

                            
        591 ATAG-TATAGATAGAT
          1 ATAGATATAGATAGAT

                            
        606 ATAGATATAGATAGAT
          1 ATAGATATAGATAGAT

                              
        622 ATAGATATAGATATAGAT
          1 ATAGATATAG--ATAGAT

                    
        640 ATAGATAT
          1 ATAGATAT

        648 TTATTGTGTT


Statistics
Matches: 39,  Mismatches: 0, Indels: 3
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    4  0.10
  16   21  0.54
  18   14  0.36

ACGTcount: A:0.49, C:0.00, G:0.18, T:0.33


Consensus pattern (16 bp):   
ATAGATATAGATAGAT

Done.