Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001533.1 Corchorus capsularis cultivar CVL-1 contig01533, 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, 603

Length: 1006
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33


Found at i:646 original size:18 final size:18

Alignment explanation


    Indices: 623--657  Score: 70
    Period size: 18  Copynumber: 1.9  Consensus size: 18

        613 ATCATTATTG

                              
        623 ATTATTATATGATAATTA
          1 ATTATTATATGATAATTA

                             
        641 ATTATTATATGATAATT
          1 ATTATTATATGATAATT

        658 CATTTTTAGA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51


Consensus pattern (18 bp):   
ATTATTATATGATAATTA

Found at i:686 original size:25 final size:24

Alignment explanation


    Indices: 657--740  Score: 66
    Period size: 25  Copynumber: 3.4  Consensus size: 24

        647 ATATGATAAT

                                     
        657 TCATTTTTAGAAATTTAGAATTTCA
          1 TCATTTTT-GAAATTTAGAATTTCA

                 *     *             * 
        682 TCATTATTGATTATTATATG-A--TAA
          1 TCATTTTTGA-AATT-TA-GAATTTCA

                                     
        706 TTCATTTTTGAAATTTAGAATTTCA
          1 -TCATTTTTGAAATTTAGAATTTCA

                 *    
        731 TCATTATTGA
          1 TCATTTTTGA

        741 TTATTATATG


Statistics
Matches: 45,  Mismatches: 7, Indels: 15
        0.67            0.10        0.22

Matches are distributed among these distances:
  22    1  0.02
  23    3  0.07
  24   16  0.36
  25   21  0.47
  26    3  0.07
  27    1  0.02

ACGTcount: A:0.35, C:0.07, G:0.08, T:0.50


Consensus pattern (24 bp):   
TCATTTTTGAAATTTAGAATTTCA

Found at i:738 original size:49 final size:49

Alignment explanation


    Indices: 641--766  Score: 243
    Period size: 49  Copynumber: 2.6  Consensus size: 49

        631 ATGATAATTA

                                                              
        641 ATTATTATATGATAATTCATTTTTAGAAATTTAGAATTTCATCATTATTG
          1 ATTATTATATGATAATTCATTTTT-GAAATTTAGAATTTCATCATTATTG

                                                             
        691 ATTATTATATGATAATTCATTTTTGAAATTTAGAATTTCATCATTATTG
          1 ATTATTATATGATAATTCATTTTTGAAATTTAGAATTTCATCATTATTG

                                       
        740 ATTATTATATGATAATTCATTTTTGAA
          1 ATTATTATATGATAATTCATTTTTGAA

        767 TGATGATTTT


Statistics
Matches: 76,  Mismatches: 0, Indels: 1
        0.99            0.00        0.01

Matches are distributed among these distances:
  49   52  0.68
  50   24  0.32

ACGTcount: A:0.36, C:0.06, G:0.08, T:0.51


Consensus pattern (49 bp):   
ATTATTATATGATAATTCATTTTTGAAATTTAGAATTTCATCATTATTG

Found at i:759 original size:25 final size:25

Alignment explanation


    Indices: 682--765  Score: 77
    Period size: 25  Copynumber: 3.4  Consensus size: 25

        672 TAGAATTTCA

                                     
        682 TCATTATTGATTATTATATGATAAT
          1 TCATTATTGATTATTATATGATAAT

                 *     *            * 
        707 TCATTTTTGA-AATT-TA-GA-ATTT
          1 TCATTATTGATTATTATATGATA-AT

                                       
        729 CATCATTATTGATTATTATATGATAAT
          1 --TCATTATTGATTATTATATGATAAT

                 *    
        756 TCATTTTTGA
          1 TCATTATTGA

        766 ATGATGATTT


Statistics
Matches: 45,  Mismatches: 7, Indels: 14
        0.68            0.11        0.21

Matches are distributed among these distances:
  21    1  0.02
  22    3  0.07
  23    2  0.04
  24   12  0.27
  25   21  0.47
  26    2  0.04
  27    3  0.07
  28    1  0.02

ACGTcount: A:0.33, C:0.06, G:0.08, T:0.52


Consensus pattern (25 bp):   
TCATTATTGATTATTATATGATAAT
Done.