Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017525.1 Corchorus olitorius cultivar O-4 contig17558, 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: 8646
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32


Found at i:686 original size:23 final size:21

Alignment explanation


    Indices: 645--706  Score: 83
    Period size: 22  Copynumber: 2.9  Consensus size: 21

        635 TTTGATTTGA

                                  
        645 TTTTTTTATTTTTTTGTTTGTG
          1 TTTTTTT-TTTTTTTGTTTGTG

                                   
        667 TTTTGTTTTTTGTTTTGTTT-TG
          1 TTTT-TTTTTT-TTTTGTTTGTG

                               
        689 TTTTTTTTTTTTTT-TTTG
          1 TTTTTTTTTTTTTTGTTTG

        707 GATTGATTGA


Statistics
Matches: 37,  Mismatches: 0, Indels: 8
        0.82            0.00        0.18

Matches are distributed among these distances:
  19    3  0.08
  20    4  0.11
  21    6  0.16
  22   13  0.35
  23   11  0.30

ACGTcount: A:0.02, C:0.00, G:0.13, T:0.85


Consensus pattern (21 bp):   
TTTTTTTTTTTTTTGTTTGTG

Found at i:695 original size:18 final size:18

Alignment explanation


    Indices: 648--706  Score: 75
    Period size: 18  Copynumber: 3.3  Consensus size: 18

        638 GATTTGATTT

                *              
        648 TTTTATTTTTTTGTTTGTG
          1 TTTTGTTTTTTTGTTT-TG

                              
        667 TTTTG-TTTTTTGTTTTG
          1 TTTTGTTTTTTTGTTTTG

                        *    *
        684 TTTTGTTTTTTTTTTTTT
          1 TTTTGTTTTTTTGTTTTG

                 
        702 TTTTG
          1 TTTTG

        707 GATTGATTGA


Statistics
Matches: 36,  Mismatches: 3, Indels: 3
        0.86            0.07        0.07

Matches are distributed among these distances:
  17    7  0.19
  18   25  0.69
  19    4  0.11

ACGTcount: A:0.02, C:0.00, G:0.14, T:0.85


Consensus pattern (18 bp):   
TTTTGTTTTTTTGTTTTG

Found at i:721 original size:45 final size:46

Alignment explanation


    Indices: 623--733  Score: 110
    Period size: 44  Copynumber: 2.5  Consensus size: 46

        613 ATCCATTCTC

                 *            *                           
        623 TTTTGATTTTT-A-TTTGATTTGATTTTTTTATTTTTTTGTTTGTG
          1 TTTTGTTTTTTGATTTTGTTTTGATTTTTTTATTTTTTTGTTTGTG

                                                          
        667 TTTTGTTTTTTG-TTTTGTTTTG-TTTTTTT-TTTTTTT-TTTG-G
          1 TTTTGTTTTTTGATTTTGTTTTGATTTTTTTATTTTTTTGTTTGTG

                                 *    
        708 ATTGATTGATTTTTTGATTTTTTTTT
          1 -TT--TTG-TTTTTTGATTTTGTTTT

        734 TTGAATTTCT


Statistics
Matches: 57,  Mismatches: 3, Indels: 12
        0.79            0.04        0.17

Matches are distributed among these distances:
  41    1  0.02
  42    6  0.11
  43    7  0.12
  44   20  0.35
  45   15  0.26
  46    8  0.14

ACGTcount: A:0.08, C:0.00, G:0.14, T:0.78


Consensus pattern (46 bp):   
TTTTGTTTTTTGATTTTGTTTTGATTTTTTTATTTTTTTGTTTGTG

Found at i:722 original size:1 final size:1

Alignment explanation


    Indices: 645--705  Score: 50
    Period size: 1  Copynumber: 61.0  Consensus size: 1

        635 TTTGATTTGA

                   *       *   * *    *      *    *    *                 
        645 TTTTTTTATTTTTTTGTTTGTGTTTTGTTTTTTGTTTTGTTTTGTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

        706 GGATTGATTG


Statistics
Matches: 44,  Mismatches: 16, Indels: 0
        0.73            0.27        0.00

Matches are distributed among these distances:
   1   44  1.00

ACGTcount: A:0.02, C:0.00, G:0.11, T:0.87


Consensus pattern (1 bp):   
T

Found at i:3195 original size:21 final size:21

Alignment explanation


    Indices: 3160--3205  Score: 67
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       3150 TGAAGGTTTA

                                  
       3160 ATGGAATGCATGAATGAATGCC
          1 ATGGAATGCATGAATGAATG-C

                *                
       3182 ATGGCATG-ATGAATGAATGC
          1 ATGGAATGCATGAATGAATGC

                
       3202 ATGG
          1 ATGG

       3206 GGCGAAAATG


Statistics
Matches: 23,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  20    5  0.22
  21   11  0.48
  22    7  0.30

ACGTcount: A:0.35, C:0.11, G:0.30, T:0.24


Consensus pattern (21 bp):   
ATGGAATGCATGAATGAATGC
Done.