Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012646.1 Corchorus olitorius cultivar O-4 contig12679, 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: 43883
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30


Found at i:3630 original size:20 final size:20

Alignment explanation


    Indices: 3589--3642  Score: 76
    Period size: 20  Copynumber: 2.8  Consensus size: 20

       3579 GTGATTTTAT

                          *     
       3589 ATAGTATATAATAATATATA
          1 ATAGTATATAATAAAATATA

                                 
       3609 ATA-TATATAATAAAATTATA
          1 ATAGTATATAATAAAA-TATA

                           
       3629 ATAGTA-ATAATAAA
          1 ATAGTATATAATAAA

       3643 TCATATATAC


Statistics
Matches: 31,  Mismatches: 1, Indels: 4
        0.86            0.03        0.11

Matches are distributed among these distances:
  19   11  0.35
  20   18  0.58
  21    2  0.06

ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37


Consensus pattern (20 bp):   
ATAGTATATAATAAAATATA

Found at i:3902 original size:42 final size:43

Alignment explanation


    Indices: 3851--3944  Score: 129
    Period size: 45  Copynumber: 2.2  Consensus size: 43

       3841 AGTGTATTAC

                                    *                  
       3851 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAA
          1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA

                                *                       *
       3892 CTAATATTCTACTCCTCCATTTCTAGATAATTCATCAAAATAAAG
          1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAA

                    
       3937 CTAATATT
          1 CTAATATT

       3945 AATTGTTGCT


Statistics
Matches: 46,  Mismatches: 3, Indels: 4
        0.87            0.06        0.08

Matches are distributed among these distances:
  41    4  0.09
  42    6  0.13
  45   36  0.78

ACGTcount: A:0.39, C:0.21, G:0.04, T:0.35


Consensus pattern (43 bp):   
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA

Found at i:5152 original size:15 final size:16

Alignment explanation


    Indices: 5132--5161  Score: 53
    Period size: 15  Copynumber: 1.9  Consensus size: 16

       5122 ATAATAGTAA

                            
       5132 TAGTAAGA-AAGATAT
          1 TAGTAAGATAAGATAT

                           
       5147 TAGTAAGATAAGATA
          1 TAGTAAGATAAGATA

       5162 AGGTAGGTTT


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    8  0.57
  16    6  0.43

ACGTcount: A:0.53, C:0.00, G:0.20, T:0.27


Consensus pattern (16 bp):   
TAGTAAGATAAGATAT

Found at i:7595 original size:12 final size:10

Alignment explanation


    Indices: 7565--7594  Score: 51
    Period size: 10  Copynumber: 2.9  Consensus size: 10

       7555 ATTGATGAAA

                      
       7565 TATATAAAAT
          1 TATATAAAAT

                      
       7575 TATATAAAAT
          1 TATATAAAAT

                      
       7585 TATATCAAAA
          1 TATAT-AAAA

       7595 AAGTTGATAC


Statistics
Matches: 19,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  10   15  0.79
  11    4  0.21

ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37


Consensus pattern (10 bp):   
TATATAAAAT

Found at i:27130 original size:19 final size:19

Alignment explanation


    Indices: 27106--27146  Score: 73
    Period size: 19  Copynumber: 2.2  Consensus size: 19

      27096 TTCACATGCT

                               
      27106 AAAAGATCCAACAATGACA
          1 AAAAGATCCAACAATGACA

                       *       
      27125 AAAAGATCCAATAATGACA
          1 AAAAGATCCAACAATGACA

               
      27144 AAA
          1 AAA

      27147 TAAAAACGAA


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  19   21  1.00

ACGTcount: A:0.61, C:0.17, G:0.10, T:0.12


Consensus pattern (19 bp):   
AAAAGATCCAACAATGACA

Found at i:27792 original size:63 final size:62

Alignment explanation


    Indices: 27719--27843  Score: 232
    Period size: 63  Copynumber: 2.0  Consensus size: 62

      27709 CGTAGGTGAG

                                                                           
      27719 TAAACCAACCTTCATTTACTTGAAACAATAACTTAGATCTGTTAAATTCCATAGAACAAAGCC
          1 TAAACCAACCTTCATTTACTTGAAACAATAACTTAGATCTGTTAAA-TCCATAGAACAAAGCC

                                                                    *     
      27782 TAAACCAACCTTCATTTACTTGAAACAATAACTTAGATCTGTTAAATCCATAGAACTAAGCC
          1 TAAACCAACCTTCATTTACTTGAAACAATAACTTAGATCTGTTAAATCCATAGAACAAAGCC

      27844 ATACCTTTGG


Statistics
Matches: 61,  Mismatches: 1, Indels: 1
        0.97            0.02        0.02

Matches are distributed among these distances:
  62   15  0.25
  63   46  0.75

ACGTcount: A:0.41, C:0.22, G:0.08, T:0.29


Consensus pattern (62 bp):   
TAAACCAACCTTCATTTACTTGAAACAATAACTTAGATCTGTTAAATCCATAGAACAAAGCC

Found at i:32923 original size:31 final size:28

Alignment explanation


    Indices: 32888--32951  Score: 74
    Period size: 29  Copynumber: 2.2  Consensus size: 28

      32878 TGTGAATTTT

                                           
      32888 TTTTTTGCGCTAAAAGAAAAGCTTGTTAACC
          1 TTTTTTGCGCT-AAA-AAAAGCTTGTTAA-C

                  *  *      *           
      32919 TTTTTTTCGGTAAAAATAGCTTGTTAAC
          1 TTTTTTGCGCTAAAAAAAGCTTGTTAAC

                 
      32947 TTTTT
          1 TTTTT

      32952 GCTTGATGGT


Statistics
Matches: 30,  Mismatches: 3, Indels: 3
        0.83            0.08        0.08

Matches are distributed among these distances:
  28    6  0.20
  29   12  0.40
  30    3  0.10
  31    9  0.30

ACGTcount: A:0.28, C:0.12, G:0.14, T:0.45


Consensus pattern (28 bp):   
TTTTTTGCGCTAAAAAAAGCTTGTTAAC
Done.