Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015367.1 Corchorus olitorius cultivar O-4 contig15400, 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: 14618
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29


Found at i:100 original size:62 final size:62

Alignment explanation


    Indices: 1--329  Score: 588
    Period size: 62  Copynumber: 5.3  Consensus size: 62

                                            *                             
          1 ATGACAACTTCTGGTGTCAAGATAATAATTTGCTATGACAACTTCTGGTGTCAAAAATTTTC
          1 ATGACAACTTCTGGTGTCAAGATAATAATTTGATATGACAACTTCTGGTGTCAAAAATTTTC

                                                                  *       
         63 ATGACAACTTCTGGTGTCAAGATAATAATTTGATATGACAACTTCTGGTGTCAATAATTTTC
          1 ATGACAACTTCTGGTGTCAAGATAATAATTTGATATGACAACTTCTGGTGTCAAAAATTTTC

                                            *             *               
        125 ATGACAACTTCTGGTGTCAAGATAATAATTTGCTATGACAACTTCTAGTGTCAAAAATTTTC
          1 ATGACAACTTCTGGTGTCAAGATAATAATTTGATATGACAACTTCTGGTGTCAAAAATTTTC

                                                                          
        187 ATGACAACTTCTGGTGTCAAGATAATAATTTGATATGACAACTTCTGGTGTCAAAAATTTTC
          1 ATGACAACTTCTGGTGTCAAGATAATAATTTGATATGACAACTTCTGGTGTCAAAAATTTTC

                                                                  *       
        249 ATGACAACTTCTGGTGTCAAGATAATAATTTGATATGACAACTTCTGGTGTCAATAA-TTTC
          1 ATGACAACTTCTGGTGTCAAGATAATAATTTGATATGACAACTTCTGGTGTCAAAAATTTTC

             *                  
        310 TGTGACAACTTCTGGTGTCA
          1 -ATGACAACTTCTGGTGTCA

        330 TTTGTAAGAC


Statistics
Matches: 257,  Mismatches: 9, Indels: 2
        0.96            0.03        0.01

Matches are distributed among these distances:
  61    4  0.02
  62  253  0.98

ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36


Consensus pattern (62 bp):   
ATGACAACTTCTGGTGTCAAGATAATAATTTGATATGACAACTTCTGGTGTCAAAAATTTTC

Found at i:348 original size:30 final size:28

Alignment explanation


    Indices: 312--391  Score: 105
    Period size: 30  Copynumber: 2.9  Consensus size: 28

        302 ATAATTTCTG

                                          
        312 TGACAACTTCTGGTGTCATTTGTAAGACCA
          1 TGACAACTTCTGGTGTCATTTGTAAGA--A

                              *         
        342 TGACAACTTCTGGTGTCAATTGT---AA
          1 TGACAACTTCTGGTGTCATTTGTAAGAA

                                      
        367 -GACAACTTCTGGTGTCATTTGTAAG
          1 TGACAACTTCTGGTGTCATTTGTAAG

        392 TAGAATAAAT


Statistics
Matches: 45,  Mismatches: 2, Indels: 9
        0.80            0.04        0.16

Matches are distributed among these distances:
  24   21  0.47
  25    1  0.02
  27    1  0.02
  30   22  0.49

ACGTcount: A:0.26, C:0.17, G:0.21, T:0.35


Consensus pattern (28 bp):   
TGACAACTTCTGGTGTCATTTGTAAGAA

Found at i:375 original size:24 final size:24

Alignment explanation


    Indices: 343--391  Score: 89
    Period size: 24  Copynumber: 2.0  Consensus size: 24

        333 GTAAGACCAT

                                    
        343 GACAACTTCTGGTGTCAATTGTAA
          1 GACAACTTCTGGTGTCAATTGTAA

                             *      
        367 GACAACTTCTGGTGTCATTTGTAA
          1 GACAACTTCTGGTGTCAATTGTAA

             
        391 G
          1 G

        392 TAGAATAAAT


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  24   24  1.00

ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35


Consensus pattern (24 bp):   
GACAACTTCTGGTGTCAATTGTAA

Found at i:4341 original size:16 final size:18

Alignment explanation


    Indices: 4304--4350  Score: 64
    Period size: 16  Copynumber: 2.8  Consensus size: 18

       4294 CAGAAATTAT

                              
       4304 TAATTATTTATTAAGTAA
          1 TAATTATTTATTAAGTAA

                        *     
       4322 TAATTATTT-TTCAG-AA
          1 TAATTATTTATTAAGTAA

                          
       4338 TAATTA-TTATTAA
          1 TAATTATTTATTAA

       4351 AATTCCCTTC


Statistics
Matches: 26,  Mismatches: 2, Indels: 4
        0.81            0.06        0.12

Matches are distributed among these distances:
  15    2  0.08
  16   11  0.42
  17    4  0.15
  18    9  0.35

ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51


Consensus pattern (18 bp):   
TAATTATTTATTAAGTAA

Found at i:8180 original size:21 final size:21

Alignment explanation


    Indices: 8124--8183  Score: 57
    Period size: 21  Copynumber: 2.9  Consensus size: 21

       8114 TGGAGATGCT

                             **  
       8124 TCCTACCTCCCAGGAGATGCC
          1 TCCTACCTCCCAGGAGACACC

              *   *** *          
       8145 TCTTACAAACAAGGAGACACC
          1 TCCTACCTCCCAGGAGACACC

                              
       8166 TCCTACCTCCCAGGAGAC
          1 TCCTACCTCCCAGGAGAC

       8184 GTCACCTGCA


Statistics
Matches: 27,  Mismatches: 12, Indels: 0
        0.69            0.31        0.00

Matches are distributed among these distances:
  21   27  1.00

ACGTcount: A:0.28, C:0.38, G:0.17, T:0.17


Consensus pattern (21 bp):   
TCCTACCTCCCAGGAGACACC

Found at i:13422 original size:16 final size:15

Alignment explanation


    Indices: 13384--13425  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

      13374 ACAGAGATTG

                   *       
      13384 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                           
      13399 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
      13414 ACTAGAAAACAA
          1 AC-AGAAAACAA

      13426 AGTAAAGTAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA
Done.