Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015699.1 Corchorus olitorius cultivar O-4 contig15732, 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: 15811
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33


Found at i:1441 original size:20 final size:22

Alignment explanation


    Indices: 1401--1442  Score: 61
    Period size: 20  Copynumber: 2.0  Consensus size: 22

       1391 CCAGATAAAG

                            *     
       1401 CATCATTTCTAACAATGATTAT
          1 CATCATTTCTAACAATAATTAT

                                  
       1423 CATCATTT-T-ACAATAATTAT
          1 CATCATTTCTAACAATAATTAT

       1443 ACTATCAGTT


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  20   10  0.53
  21    1  0.05
  22    8  0.42

ACGTcount: A:0.38, C:0.17, G:0.02, T:0.43


Consensus pattern (22 bp):   
CATCATTTCTAACAATAATTAT

Found at i:3537 original size:16 final size:16

Alignment explanation


    Indices: 3516--3548  Score: 66
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       3506 GACGTCGAAG

                            
       3516 AGCATCGACCAAAAAT
          1 AGCATCGACCAAAAAT

                            
       3532 AGCATCGACCAAAAAT
          1 AGCATCGACCAAAAAT

             
       3548 A
          1 A

       3549 TCACTGCTGT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   17  1.00

ACGTcount: A:0.52, C:0.24, G:0.12, T:0.12


Consensus pattern (16 bp):   
AGCATCGACCAAAAAT

Found at i:9851 original size:3 final size:3

Alignment explanation


    Indices: 9843--9874  Score: 64
    Period size: 3  Copynumber: 10.7  Consensus size: 3

       9833 GTATAATATC

                                                      
       9843 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
          1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT

       9875 ATGTGCAACA


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   29  1.00

ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69


Consensus pattern (3 bp):   
TTG

Found at i:14883 original size:48 final size:47

Alignment explanation


    Indices: 14808--14936  Score: 170
    Period size: 48  Copynumber: 2.7  Consensus size: 47

      14798 GAGCGTGCCA

                        *         *                         
      14808 ATCAATTTTGTCAAAAAATTGATAAAAAGTGCAATGAAAAT-TAAAAG
          1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAA-GAAAATATAAAAG

                                         *      *           
      14855 ATCAATTTTGTCTTAAAAATTGAGAAAAAATGCAAGTAAATATAAAAG
          1 ATCAATTTTGTC-TAAAAATTGAGAAAAAGTGCAAGAAAATATAAAAG

            *           *                     
      14903 TTCAATTTTGTAGTAAAAATTGAGAAAAAGTGCA
          1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCA

      14937 GTAAAAAGTA


Statistics
Matches: 72,  Mismatches: 7, Indels: 5
        0.86            0.08        0.06

Matches are distributed among these distances:
  47   17  0.24
  48   55  0.76

ACGTcount: A:0.50, C:0.06, G:0.14, T:0.29


Consensus pattern (47 bp):   
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAAGAAAATATAAAAG
Done.