Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022695.1 Corchorus olitorius cultivar O-4 contig22728, 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: 2460
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36


Found at i:2424 original size:62 final size:61

Alignment explanation


    Indices: 2300--2451  Score: 209
    Period size: 67  Copynumber: 2.4  Consensus size: 61

       2290 AATTCCAATC

                *                                                            
       2300 TTGGGATGACAACTTCTGGTGTCAATAATTTCCTCAGCATGACAACTTCTGGTGTCAAGATAATA
          1 TTGGTATGACAACTTCTGGTGTCAATAATTT-CT-A-CATGACAACTTCTGGTGTCAAG---ATA

              
       2365 AT
         60 AT

                                                                         
       2367 TTGGTATGACAACTTCTGGTGTCAATAATTT-T-CATGACAACTTCTGGTGTCAAGATAAT
          1 TTGGTATGACAACTTCTGGTGTCAATAATTTCTACATGACAACTTCTGGTGTCAAGATAAT

              **                      
       2426 TTAATATGACAACTTCTGGTGTCAAT
          1 TTGGTATGACAACTTCTGGTGTCAAT

       2452 TAAATTTAA


Statistics
Matches: 82,  Mismatches: 3, Indels: 8
        0.88            0.03        0.09

Matches are distributed among these distances:
  59   29  0.35
  62   22  0.27
  65    1  0.01
  67   30  0.37

ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36


Consensus pattern (61 bp):   
TTGGTATGACAACTTCTGGTGTCAATAATTTCTACATGACAACTTCTGGTGTCAAGATAAT

Found at i:2449 original size:59 final size:62

Alignment explanation


    Indices: 2305--2451  Score: 210
    Period size: 59  Copynumber: 2.3  Consensus size: 62

       2295 CAATCTTGGG

                                                                            *
       2305 ATGACAACTTCTGGTGTCAATAATTTCCTCAGCATGACAACTTCTGGTGTCAAGATAATAATTTG
          1 ATGACAACTTCTGGTGTCAATAATTT-CT-A-CATGACAACTTCTGGTGTCAAG--AATAATTTA

            * 
       2370 GT
         61 AT

                                                                          
       2372 ATGACAACTTCTGGTGTCAATAATTT-T-CATGACAACTTCTGGTGTCAAG-ATAATTTAAT
          1 ATGACAACTTCTGGTGTCAATAATTTCTACATGACAACTTCTGGTGTCAAGAATAATTTAAT

                                 
       2431 ATGACAACTTCTGGTGTCAAT
          1 ATGACAACTTCTGGTGTCAAT

       2452 TAAATTTAA


Statistics
Matches: 78,  Mismatches: 2, Indels: 8
        0.89            0.02        0.09

Matches are distributed among these distances:
  59   29  0.37
  62   22  0.28
  65    1  0.01
  67   26  0.33

ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35


Consensus pattern (62 bp):   
ATGACAACTTCTGGTGTCAATAATTTCTACATGACAACTTCTGGTGTCAAGAATAATTTAAT

Found at i:2458 original size:31 final size:30

Alignment explanation


    Indices: 2305--2460  Score: 147
    Period size: 31  Copynumber: 5.0  Consensus size: 30

       2295 CAATCTTGGG

                                   *       **
       2305 ATGACAACTTCTGGTGTCAATAATTTCCTCAGC
          1 ATGACAACTTCTGGTGTCAATAAATT--T-AAT

                                           ** 
       2338 ATGACAACTTCTGGTGTCAAGATAATAATTTGGT
          1 ATGACAACTTCTGGTGTC-A-AT-A-AATTTAAT

                                          
       2372 ATGACAACTTCTGGTGTCAAT-AATTT--T
          1 ATGACAACTTCTGGTGTCAATAAATTTAAT

                                 *          
       2399 CATGACAACTTCTGGTGTCAAGATAATTTAAT
          1 -ATGACAACTTCTGGTGTCAATA-AATTTAAT

                                          
       2431 ATGACAACTTCTGGTGTCAATTAAATTTAA
          1 ATGACAACTTCTGGTGTCAA-TAAATTTAA


Statistics
Matches: 108,  Mismatches: 5, Indels: 22
        0.80            0.04        0.16

Matches are distributed among these distances:
  27    1  0.01
  28   20  0.19
  29    5  0.05
  30    5  0.05
  31   27  0.25
  32    4  0.04
  33   19  0.18
  34   20  0.19
  35    3  0.03
  36    1  0.01
  37    3  0.03

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


Consensus pattern (30 bp):   
ATGACAACTTCTGGTGTCAATAAATTTAAT
Done.