Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01005689.1 Corchorus olitorius cultivar O-4 contig05713, 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, 718

Length: 1198
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.37


Found at i:184 original size:13 final size:13

Alignment explanation


    Indices: 168--194  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

        158 TTTTTTCCCC

                         
        168 TCTTTTTTTTATT
          1 TCTTTTTTTTATT

                         
        181 TCTTTTTTTTATT
          1 TCTTTTTTTTATT

             
        194 T
          1 T

        195 TATTCCCTTC


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.07, C:0.07, G:0.00, T:0.85


Consensus pattern (13 bp):   
TCTTTTTTTTATT

Found at i:721 original size:15 final size:15

Alignment explanation


    Indices: 701--730  Score: 60
    Period size: 15  Copynumber: 2.0  Consensus size: 15

        691 TATATTAGTA

                           
        701 TTTTTCTATTCTATT
          1 TTTTTCTATTCTATT

                           
        716 TTTTTCTATTCTATT
          1 TTTTTCTATTCTATT

        731 AGTATTAGAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.13, C:0.13, G:0.00, T:0.73


Consensus pattern (15 bp):   
TTTTTCTATTCTATT

Found at i:742 original size:5 final size:6

Alignment explanation


    Indices: 727--788  Score: 71
    Period size: 6  Copynumber: 11.2  Consensus size: 6

        717 TTTTCTATTC

                                      *      *                     
        727 TATTAG TATTAG -ATTAG TATT-C TATT-C TATTAG TATTAG -ATTAG
          1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG

                                  
        771 TATTAG -ATTAG TATTAG T
          1 TATTAG TATTAG TATTAG T

        789 TAGTGATCCC


Statistics
Matches: 50,  Mismatches: 2, Indels: 8
        0.83            0.03        0.13

Matches are distributed among these distances:
   5   24  0.48
   6   26  0.52

ACGTcount: A:0.32, C:0.03, G:0.15, T:0.50


Consensus pattern (6 bp):   
TATTAG

Found at i:742 original size:11 final size:11

Alignment explanation


    Indices: 728--792  Score: 54
    Period size: 11  Copynumber: 6.5  Consensus size: 11

        718 TTTCTATTCT

                       
        728 ATTAGTATTAG
          1 ATTAGTATTAG

                     **
        739 ATTAGTATTCT
          1 ATTAGTATTAG

                *      
        750 ATT-CTATTAG
          1 ATTAGTATTAG

                       
        760 --TA-T--TAG
          1 ATTAGTATTAG

                       
        766 ATTAGTATTAG
          1 ATTAGTATTAG

                       
        777 ATTAGTATTAG
          1 ATTAGTATTAG

                  
        788 -TTAGT
          1 ATTAGT

        793 GATCCCGGCT


Statistics
Matches: 43,  Mismatches: 5, Indels: 13
        0.70            0.08        0.21

Matches are distributed among these distances:
   6    3  0.07
   8    4  0.09
   9    1  0.02
  10    9  0.21
  11   26  0.60

ACGTcount: A:0.32, C:0.03, G:0.15, T:0.49


Consensus pattern (11 bp):   
ATTAGTATTAG

Found at i:749 original size:27 final size:27

Alignment explanation


    Indices: 719--774  Score: 112
    Period size: 27  Copynumber: 2.1  Consensus size: 27

        709 TTCTATTTTT

                                       
        719 TTCTATTCTATTAGTATTAGATTAGTA
          1 TTCTATTCTATTAGTATTAGATTAGTA

                                       
        746 TTCTATTCTATTAGTATTAGATTAGTA
          1 TTCTATTCTATTAGTATTAGATTAGTA

              
        773 TT
          1 TT

        775 AGATTAGTAT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  27   29  1.00

ACGTcount: A:0.29, C:0.07, G:0.11, T:0.54


Consensus pattern (27 bp):   
TTCTATTCTATTAGTATTAGATTAGTA

Found at i:750 original size:22 final size:22

Alignment explanation


    Indices: 722--792  Score: 72
    Period size: 27  Copynumber: 3.0  Consensus size: 22

        712 TATTTTTTTC

                                  
        722 TATTCTATTAGTATTAGATTAG
          1 TATTCTATTAGTATTAGATTAG

                                       
        744 TATTCTATTCTATTAGTATTAGATTAG
          1 -----TATTCTATTAGTATTAGATTAG

                **                
        771 TATTAGATTAGTATTAG-TTAG
          1 TATTCTATTAGTATTAGATTAG

             
        792 T
          1 T

        793 GATCCCGGCT


Statistics
Matches: 42,  Mismatches: 2, Indels: 6
        0.84            0.04        0.12

Matches are distributed among these distances:
  21    5  0.12
  22   15  0.36
  27   22  0.52

ACGTcount: A:0.31, C:0.04, G:0.14, T:0.51


Consensus pattern (22 bp):   
TATTCTATTAGTATTAGATTAG
Done.