Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006200.1 Corchorus olitorius cultivar O-4 contig06225, 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: 2375
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36


Found at i:237 original size:57 final size:58

Alignment explanation


    Indices: 134--250  Score: 209
    Period size: 57  Copynumber: 2.0  Consensus size: 58

        124 TTTATTTTGT

                                 *                             *      
        134 AGAATAATTAAGTAGAGATATGGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
          1 AGAATAATTAAGTAGAGATATAGGGGGATAGGATTTATTATAACATTTATTATGTGAA

                                                                      
        192 AGAATAATTAAGTAGAGATA-AGGGGGATAGGATTTATTATAACATTTATTATGTGAA
          1 AGAATAATTAAGTAGAGATATAGGGGGATAGGATTTATTATAACATTTATTATGTGAA

              
        249 AG
          1 AG

        251 GAAACAGATA


Statistics
Matches: 57,  Mismatches: 2, Indels: 1
        0.95            0.03        0.02

Matches are distributed among these distances:
  57   37  0.65
  58   20  0.35

ACGTcount: A:0.40, C:0.02, G:0.25, T:0.33


Consensus pattern (58 bp):   
AGAATAATTAAGTAGAGATATAGGGGGATAGGATTTATTATAACATTTATTATGTGAA

Found at i:443 original size:2 final size:2

Alignment explanation


    Indices: 436--472  Score: 60
    Period size: 2  Copynumber: 19.5  Consensus size: 2

        426 TAATATGTAG

                                                                      
        436 TA TA TA TA -A TA TA -A TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

        473 TGGCTGAATT


Statistics
Matches: 33,  Mismatches: 0, Indels: 4
        0.89            0.00        0.11

Matches are distributed among these distances:
   1    2  0.06
   2   31  0.94

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
TA

Found at i:446 original size:16 final size:14

Alignment explanation


    Indices: 425--471  Score: 51
    Period size: 14  Copynumber: 3.2  Consensus size: 14

        415 GGTGTTTCAA

                            
        425 ATAATATGTAGTATAT
          1 ATAATAT-TA-TATAT

                   *      
        441 ATAATATAATATAT
          1 ATAATATTATATAT

                           
        455 AT-ATATATATATAT
          1 ATAATAT-TATATAT

               
        469 ATA
          1 ATA

        472 TTGGCTGAAT


Statistics
Matches: 27,  Mismatches: 2, Indels: 5
        0.79            0.06        0.15

Matches are distributed among these distances:
  13    4  0.15
  14   15  0.56
  15    1  0.04
  16    7  0.26

ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45


Consensus pattern (14 bp):   
ATAATATTATATAT

Found at i:1126 original size:15 final size:15

Alignment explanation


    Indices: 1105--1137  Score: 50
    Period size: 14  Copynumber: 2.3  Consensus size: 15

       1095 TCTTCTAACC

                     *     
       1105 CTTTTTTTTATT-CT
          1 CTTTTTTTTTTTACT

                           
       1119 CTTTTTTTTTTTACT
          1 CTTTTTTTTTTTACT

                
       1134 CTTT
          1 CTTT

       1138 CTTTAACACT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  14   11  0.65
  15    6  0.35

ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79


Consensus pattern (15 bp):   
CTTTTTTTTTTTACT
Done.