Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014583.1 Corchorus olitorius cultivar O-4 contig14616, 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: 52274
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33


Found at i:13862 original size:30 final size:30

Alignment explanation


    Indices: 13828--13892  Score: 130
    Period size: 30  Copynumber: 2.2  Consensus size: 30

      13818 AATGTGATTG

                                          
      13828 ACACTGTTTTGCAACTGTATAAATGAAATT
          1 ACACTGTTTTGCAACTGTATAAATGAAATT

                                          
      13858 ACACTGTTTTGCAACTGTATAAATGAAATT
          1 ACACTGTTTTGCAACTGTATAAATGAAATT

                 
      13888 ACACT
          1 ACACT

      13893 ATACATATTA


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  30   35  1.00

ACGTcount: A:0.37, C:0.15, G:0.12, T:0.35


Consensus pattern (30 bp):   
ACACTGTTTTGCAACTGTATAAATGAAATT

Found at i:36986 original size:1 final size:1

Alignment explanation


    Indices: 36980--37016  Score: 74
    Period size: 1  Copynumber: 37.0  Consensus size: 1

      36970 CTACTGTTGA

                                                 
      36980 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

      37017 GCACAAGTGT


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   36  1.00

ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00


Consensus pattern (1 bp):   
T

Found at i:39806 original size:16 final size:16

Alignment explanation


    Indices: 39781--39840  Score: 102
    Period size: 16  Copynumber: 3.7  Consensus size: 16

      39771 ATATATTTAG

                            
      39781 TTGTTTTTTTTAGTTT
          1 TTGTTTTTTTTAGTTT

               *             
      39797 TGTCTTTTTTTTAGTTT
          1 T-TGTTTTTTTTAGTTT

                            
      39814 TTGTTTTTTTTAGTTT
          1 TTGTTTTTTTTAGTTT

                       
      39830 TTGTTTTTTTT
          1 TTGTTTTTTTT

      39841 TTAGTTTTTC


Statistics
Matches: 41,  Mismatches: 2, Indels: 2
        0.91            0.04        0.04

Matches are distributed among these distances:
  16   26  0.63
  17   15  0.37

ACGTcount: A:0.05, C:0.02, G:0.12, T:0.82


Consensus pattern (16 bp):   
TTGTTTTTTTTAGTTT

Found at i:39806 original size:17 final size:17

Alignment explanation


    Indices: 39784--39848  Score: 96
    Period size: 17  Copynumber: 3.8  Consensus size: 17

      39774 TATTTAGTTG

                             
      39784 TTTTTTTTAGTTTTGTC
          1 TTTTTTTTAGTTTTGTC

                            *
      39801 TTTTTTTTAGTTTT-TG
          1 TTTTTTTTAGTTTTGTC

                             *
      39817 TTTTTTTTAGTTTTTGTT
          1 TTTTTTTTAG-TTTTGTC

                          
      39835 TTTTTTTTAGTTTT
          1 TTTTTTTTAGTTTT

      39849 TCTGAAATCT


Statistics
Matches: 44,  Mismatches: 2, Indels: 4
        0.88            0.04        0.08

Matches are distributed among these distances:
  16   11  0.25
  17   22  0.50
  18   11  0.25

ACGTcount: A:0.06, C:0.02, G:0.11, T:0.82


Consensus pattern (17 bp):   
TTTTTTTTAGTTTTGTC

Found at i:39820 original size:33 final size:34

Alignment explanation


    Indices: 39781--39849  Score: 122
    Period size: 34  Copynumber: 2.1  Consensus size: 34

      39771 ATATATTTAG

                                              
      39781 TTGTTTTTTTTAG-TTTTGTCTTTTTTTTAGTTT
          1 TTGTTTTTTTTAGTTTTTGTCTTTTTTTTAGTTT

                                *             
      39814 TTGTTTTTTTTAGTTTTTGTTTTTTTTTTAGTTT
          1 TTGTTTTTTTTAGTTTTTGTCTTTTTTTTAGTTT

              
      39848 TT
          1 TT

      39850 CTGAAATCTC


Statistics
Matches: 34,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
  33   13  0.38
  34   21  0.62

ACGTcount: A:0.06, C:0.01, G:0.12, T:0.81


Consensus pattern (34 bp):   
TTGTTTTTTTTAGTTTTTGTCTTTTTTTTAGTTT

Found at i:39849 original size:18 final size:17

Alignment explanation


    Indices: 39784--39849  Score: 100
    Period size: 18  Copynumber: 3.9  Consensus size: 17

      39774 TATTTAGTTG

                             
      39784 TTTTTTTTAG-TTTTGT
          1 TTTTTTTTAGTTTTTGT

                              
      39800 CTTTTTTTTAGTTTTTG-
          1 -TTTTTTTTAGTTTTTGT

                              
      39817 TTTTTTTTAGTTTTTGTT
          1 TTTTTTTTAGTTTTTG-T

                           
      39835 TTTTTTTTAGTTTTT
          1 TTTTTTTTAGTTTTT

      39850 CTGAAATCTC


Statistics
Matches: 46,  Mismatches: 0, Indels: 5
        0.90            0.00        0.10

Matches are distributed among these distances:
  16   16  0.35
  17   10  0.22
  18   20  0.43

ACGTcount: A:0.06, C:0.02, G:0.11, T:0.82


Consensus pattern (17 bp):   
TTTTTTTTAGTTTTTGT

Found at i:52242 original size:2 final size:2

Alignment explanation


    Indices: 52235--52274  Score: 80
    Period size: 2  Copynumber: 20.0  Consensus size: 2

      52225 AAAGTTACCT

                                                                       
      52235 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   38  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Done.