Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015264.1 Corchorus olitorius cultivar O-4 contig15297, 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: 11398
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31


Found at i:2842 original size:29 final size:29

Alignment explanation


    Indices: 2809--2868  Score: 111
    Period size: 29  Copynumber: 2.1  Consensus size: 29

       2799 AAACTATACG

                          *              
       2809 TGTTCTTGGTATGGGTTTAACATGGTGCT
          1 TGTTCTTGGTATGGATTTAACATGGTGCT

                                         
       2838 TGTTCTTGGTATGGATTTAACATGGTGCT
          1 TGTTCTTGGTATGGATTTAACATGGTGCT

              
       2867 TG
          1 TG

       2869 GTAAGAGTAG


Statistics
Matches: 30,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  29   30  1.00

ACGTcount: A:0.15, C:0.10, G:0.30, T:0.45


Consensus pattern (29 bp):   
TGTTCTTGGTATGGATTTAACATGGTGCT

Found at i:4022 original size:36 final size:36

Alignment explanation


    Indices: 3981--4085  Score: 95
    Period size: 36  Copynumber: 3.2  Consensus size: 36

       3971 AAAATGATAA

                                                
       3981 GAAGTAAAATAACAATAAATTTATAATTAACTGTAT
          1 GAAGTAAAATAACAATAAATTTATAATTAACTGTAT

                    *    **                    *
       4017 GAAGTAAAGT-A-TGT-AA--TAT-A-TAAC---AA
          1 GAAGTAAAATAACAATAAATTTATAATTAACTGTAT

                                          *     
       4043 GAAGTAAAATAACAATAAATTTATAATTAATTGTAT
          1 GAAGTAAAATAACAATAAATTTATAATTAACTGTAT

                   
       4079 GAAGTAA
          1 GAAGTAA

       4086 TGCATGTAAA


Statistics
Matches: 50,  Mismatches: 9, Indels: 20
        0.63            0.11        0.25

Matches are distributed among these distances:
  26   10  0.20
  27    1  0.02
  28    1  0.02
  29    6  0.12
  30    1  0.02
  31    6  0.12
  32    1  0.02
  33    5  0.10
  34    1  0.02
  35    1  0.02
  36   17  0.34

ACGTcount: A:0.53, C:0.04, G:0.11, T:0.31


Consensus pattern (36 bp):   
GAAGTAAAATAACAATAAATTTATAATTAACTGTAT

Found at i:4078 original size:62 final size:62

Alignment explanation


    Indices: 3979--4099  Score: 206
    Period size: 62  Copynumber: 2.0  Consensus size: 62

       3969 GAAAAATGAT

                                                           *      *       
       3979 AAGAAGTAAAATAACAATAAATTTATAATTAACTGTATGAAGTAAAGTATGTAATATATAAC
          1 AAGAAGTAAAATAACAATAAATTTATAATTAACTGTATGAAGTAAAGCATGTAAAATATAAC

                                            *            *             
       4041 AAGAAGTAAAATAACAATAAATTTATAATTAATTGTATGAAGTAATGCATGTAAAATAT
          1 AAGAAGTAAAATAACAATAAATTTATAATTAACTGTATGAAGTAAAGCATGTAAAATAT

       4100 TTTTTTCTTT


Statistics
Matches: 55,  Mismatches: 4, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  62   55  1.00

ACGTcount: A:0.53, C:0.04, G:0.12, T:0.31


Consensus pattern (62 bp):   
AAGAAGTAAAATAACAATAAATTTATAATTAACTGTATGAAGTAAAGCATGTAAAATATAAC

Found at i:4112 original size:5 final size:5

Alignment explanation


    Indices: 4102--4134  Score: 57
    Period size: 5  Copynumber: 6.6  Consensus size: 5

       4092 TAAAATATTT

                                 *                 
       4102 TTTTC TTTTC TTTTC TTTGC TTTTC TTTTC TTT
          1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTT

       4135 AATTAAGAAA


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   5   26  1.00

ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79


Consensus pattern (5 bp):   
TTTTC

Done.