Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008708.1 Corchorus olitorius cultivar O-4 contig08735, 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, 631

Length: 1053
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.31


Found at i:290 original size:25 final size:26

Alignment explanation


    Indices: 262--333  Score: 96
    Period size: 25  Copynumber: 2.8  Consensus size: 26

        252 ATGCAAAAAC

                                        
        262 TTTTTTTTTATGACGCAGAAACA-AATT
          1 TTTTTTTTTATGACGCA-AAACATAA-T

                                      
        289 TTTTTTTTTATGACGCAAAA-ATAAT
          1 TTTTTTTTTATGACGCAAAACATAAT

                                 
        314 TTTTTTTTT-TCGACGCAAAA
          1 TTTTTTTTTAT-GACGCAAAA

        334 ACACAAAACC


Statistics
Matches: 43,  Mismatches: 0, Indels: 6
        0.88            0.00        0.12

Matches are distributed among these distances:
  24    1  0.02
  25   20  0.47
  26    5  0.12
  27   17  0.40

ACGTcount: A:0.32, C:0.11, G:0.10, T:0.47


Consensus pattern (26 bp):   
TTTTTTTTTATGACGCAAAACATAAT

Found at i:292 original size:27 final size:27

Alignment explanation


    Indices: 262--333  Score: 105
    Period size: 27  Copynumber: 2.7  Consensus size: 27

        252 ATGCAAAAAC

                                        
        262 TTTTTTTTTATGACGCAGAAACA-AATT
          1 TTTTTTTTTATGACGCA-AAACATAATT

                                       
        289 TTTTTTTTTATGACGCAAAA-ATAATT
          1 TTTTTTTTTATGACGCAAAACATAATT

                      *         
        315 TTTTTTTTT-CGACGCAAAA
          1 TTTTTTTTTATGACGCAAAA

        334 ACACAAAACC


Statistics
Matches: 43,  Mismatches: 1, Indels: 4
        0.90            0.02        0.08

Matches are distributed among these distances:
  25   10  0.23
  26   16  0.37
  27   17  0.40

ACGTcount: A:0.32, C:0.11, G:0.10, T:0.47


Consensus pattern (27 bp):   
TTTTTTTTTATGACGCAAAACATAATT

Found at i:495 original size:89 final size:85

Alignment explanation


    Indices: 301--500  Score: 219
    Period size: 89  Copynumber: 2.3  Consensus size: 85

        291 TTTTTTTATG

                                                      **              *      
        301 ACGCAAAAATAATTTTTTTTTTTCGACGCAAAAACACAAAACCCTTTTTTTTTTTCTTTGACGCA
          1 ACGCAAAAATAATTTTTTTTTTTCGACGCAAAAACACAAAACAATTTTTTTTTTTCTTCGACGCA

                *               
        366 AGACTCAAAAAAAATTAAAA
         66 AGACACAAAAAAAATTAAAA

                        *                                                    
        386 ACGCAAAAGAAAAAGATTTTTTTTTTTCGACGCAAAAACACAAAACAATTTTTTTTTTT-TTCAA
          1 ACGC--AA-AAATA-ATTTTTTTTTTTCGACGCAAAAACACAAAACAATTTTTTTTTTTCTT---

                             * *          
        450 AAACGACGCAA-A-ACACACAAAATTAAAA
         59 ---CGACGCAAGACACAAAAAAAATTAAAA

                                    
        478 ACGC-AAAATAATTTTTTTTTTTC
          1 ACGCAAAAATAATTTTTTTTTTTC

        501 AGATAAAAAA


Statistics
Matches: 97,  Mismatches: 8, Indels: 18
        0.79            0.07        0.15

Matches are distributed among these distances:
  85    4  0.04
  87   15  0.15
  88   10  0.10
  89   43  0.44
  92   17  0.18
  93    1  0.01
  94    7  0.07

ACGTcount: A:0.43, C:0.17, G:0.07, T:0.34


Consensus pattern (85 bp):   
ACGCAAAAATAATTTTTTTTTTTCGACGCAAAAACACAAAACAATTTTTTTTTTTCTTCGACGCA
AGACACAAAAAAAATTAAAA

Found at i:817 original size:16 final size:15

Alignment explanation


    Indices: 779--820  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

        769 ACAGAGATTG

                   *       
        779 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                           
        794 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
        809 ACTAGAAAACAA
          1 AC-AGAAAACAA

        821 AGCAAAGTAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA
Done.