Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001938.1 Corchorus olitorius cultivar O-4 contig01938, 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: 8292
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34


Found at i:3460 original size:64 final size:64

Alignment explanation


    Indices: 3390--3510  Score: 156
    Period size: 64  Copynumber: 1.9  Consensus size: 64

       3380 TTTGACAACC

                                 *                               *           
       3390 TCGATTGCAA-TTTTGACAACTGCCCTAT-ATAATTATGATAATCATCCTTTGTAATTTAATAAT
          1 TCGATTG-AACTTTTGACAACCGCCCTATGA-AATTATGATAATCATCCTTTGGAATTTAATAAT

             
       3453 T
         64 T

                                   *          *       *   *          
       3454 TCGATTGAACTTTTGACAACCGCTCTATGAAATTTTGATAATTATCGTTTGGAATTT
          1 TCGATTGAACTTTTGACAACCGCCCTATGAAATTATGATAATCATCCTTTGGAATTT

       3511 TGAAAACTAC


Statistics
Matches: 49,  Mismatches: 6, Indels: 4
        0.83            0.10        0.07

Matches are distributed among these distances:
  63    2  0.04
  64   46  0.94
  65    1  0.02

ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42


Consensus pattern (64 bp):   
TCGATTGAACTTTTGACAACCGCCCTATGAAATTATGATAATCATCCTTTGGAATTTAATAATT

Found at i:3547 original size:22 final size:22

Alignment explanation


    Indices: 3522--3582  Score: 70
    Period size: 22  Copynumber: 2.8  Consensus size: 22

       3512 GAAAACTACC

                                 *
       3522 ATTTGAAATTTTAATAACCGCT
          1 ATTTGAAATTTTAATAACCGCG

                 *      *      *  
       3544 ATTTGTAATTTTGATAACCTCG
          1 ATTTGAAATTTTAATAACCGCG

                        *     
       3566 A-TTGAAATTTTTATAAC
          1 ATTTGAAATTTTAATAAC

       3583 GACCCTATAT


Statistics
Matches: 33,  Mismatches: 6, Indels: 1
        0.82            0.15        0.03

Matches are distributed among these distances:
  21   14  0.42
  22   19  0.58

ACGTcount: A:0.34, C:0.11, G:0.10, T:0.44


Consensus pattern (22 bp):   
ATTTGAAATTTTAATAACCGCG

Found at i:3596 original size:22 final size:22

Alignment explanation


    Indices: 3571--3647  Score: 84
    Period size: 22  Copynumber: 3.5  Consensus size: 22

       3561 CCTCGATTGA

                  *               
       3571 AATTTTTATAACGACCCTATAT
          1 AATTTTGATAACGACCCTATAT

                        *   *   * 
       3593 AATTTTGATAACCACCATATGT
          1 AATTTTGATAACGACCCTATAT

               *       *          
       3615 -ATATTGATAATGACCCTATAT
          1 AATTTTGATAACGACCCTATAT

                  *     
       3636 AATTTTAATAAC
          1 AATTTTGATAAC

       3648 CTCATTGAAA


Statistics
Matches: 42,  Mismatches: 12, Indels: 2
        0.75            0.21        0.04

Matches are distributed among these distances:
  21   16  0.38
  22   26  0.62

ACGTcount: A:0.39, C:0.16, G:0.06, T:0.39


Consensus pattern (22 bp):   
AATTTTGATAACGACCCTATAT

Found at i:3596 original size:43 final size:42

Alignment explanation


    Indices: 3549--3667  Score: 141
    Period size: 43  Copynumber: 2.8  Consensus size: 42

       3539 CCGCTATTTG

                                        *              
       3549 TAATTTTGATAACCTCGATTGAAATTTTTATAACGACCCTATA
          1 TAATTTTGATAACCTC-ATTGAAATTTTGATAACGACCCTATA

                           *       *  *       *         
       3592 TAATTTTGATAACCACCATATG-TATATTGATAATGACCCTATA
          1 TAATTTTGATAACC-TCAT-TGAAATTTTGATAACGACCCTATA

                   *                    *    
       3635 TAATTTTAATAACCTCATTGAAATTTTGGTAAC
          1 TAATTTTGATAACCTCATTGAAATTTTGATAAC

       3668 TATCTTTTGT


Statistics
Matches: 62,  Mismatches: 11, Indels: 7
        0.77            0.14        0.09

Matches are distributed among these distances:
  41    2  0.03
  42   11  0.18
  43   46  0.74
  44    3  0.05

ACGTcount: A:0.36, C:0.15, G:0.09, T:0.39


Consensus pattern (42 bp):   
TAATTTTGATAACCTCATTGAAATTTTGATAACGACCCTATA

Found at i:3825 original size:22 final size:23

Alignment explanation


    Indices: 3776--3830  Score: 85
    Period size: 23  Copynumber: 2.4  Consensus size: 23

       3766 TTATTACGAG

                                   
       3776 GTTTTGATAACAATCCTTTTGTA
          1 GTTTTGATAACAATCCTTTTGTA

            *                      
       3799 ATTTTGATAACAATCC-TTTGTA
          1 GTTTTGATAACAATCCTTTTGTA

                 *    
       3821 GTTTTTATAA
          1 GTTTTGATAA

       3831 GGATTTATAT


Statistics
Matches: 29,  Mismatches: 3, Indels: 1
        0.88            0.09        0.03

Matches are distributed among these distances:
  22   14  0.48
  23   15  0.52

ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49


Consensus pattern (23 bp):   
GTTTTGATAACAATCCTTTTGTA
Done.