Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008879.1 Corchorus capsularis cultivar CVL-1 contig08900, 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: 7962
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39


Found at i:556 original size:13 final size:13

Alignment explanation


    Indices: 538--565  Score: 56
    Period size: 13  Copynumber: 2.2  Consensus size: 13

        528 ATTTTCATTA

                         
        538 ATTAATATGTTAT
          1 ATTAATATGTTAT

                         
        551 ATTAATATGTTAT
          1 ATTAATATGTTAT

              
        564 AT
          1 AT

        566 AATCTTTTTA


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

Matches are distributed among these distances:
  13   15  1.00

ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54


Consensus pattern (13 bp):   
ATTAATATGTTAT

Found at i:614 original size:28 final size:26

Alignment explanation


    Indices: 583--644  Score: 74
    Period size: 24  Copynumber: 2.4  Consensus size: 26

        573 TTATTTTAGA

                          *             
        583 CAAACTCTTAACCATTTTTAATCTCAAC
          1 CAAACTCTT--CCAATTTTAATCTCAAC

                                      
        611 CAAACTC--CCAATTTTAATCTCAAC
          1 CAAACTCTTCCAATTTTAATCTCAAC

               *      
        635 CAATCTCTTC
          1 CAAACTCTTC

        645 AACATTACTT


Statistics
Matches: 30,  Mismatches: 2, Indels: 6
        0.79            0.05        0.16

Matches are distributed among these distances:
  24   22  0.73
  26    1  0.03
  28    7  0.23

ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34


Consensus pattern (26 bp):   
CAAACTCTTCCAATTTTAATCTCAAC

Found at i:749 original size:33 final size:33

Alignment explanation


    Indices: 699--762  Score: 85
    Period size: 33  Copynumber: 1.9  Consensus size: 33

        689 GATTACACTT

                     *                        
        699 AACCCGTAATATATAA-TTGCAATTGGACTAAGA
          1 AACCCGTAAAATATAATTTG-AATTGGACTAAGA

                        *            *     
        732 AACCCGTAAAATGTAATTTGAATTGTACTAA
          1 AACCCGTAAAATATAATTTGAATTGGACTAA

        763 TAAAATTCTA


Statistics
Matches: 27,  Mismatches: 3, Indels: 2
        0.84            0.09        0.06

Matches are distributed among these distances:
  33   24  0.89
  34    3  0.11

ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30


Consensus pattern (33 bp):   
AACCCGTAAAATATAATTTGAATTGGACTAAGA

Found at i:1991 original size:12 final size:12

Alignment explanation


    Indices: 1974--2003  Score: 51
    Period size: 12  Copynumber: 2.5  Consensus size: 12

       1964 GAATGAAGAT

                        
       1974 GATAAATTACTA
          1 GATAAATTACTA

                        
       1986 GATAAATTACTA
          1 GATAAATTACTA

            *     
       1998 AATAAA
          1 GATAAA

       2004 ACGGAGAAAC


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  12   17  1.00

ACGTcount: A:0.57, C:0.07, G:0.07, T:0.30


Consensus pattern (12 bp):   
GATAAATTACTA

Found at i:2848 original size:11 final size:12

Alignment explanation


    Indices: 2821--2853  Score: 50
    Period size: 12  Copynumber: 2.8  Consensus size: 12

       2811 GTTAATTCTG

                  *     
       2821 TTTTTTACTTCA
          1 TTTTTTGCTTCA

                        
       2833 TTTTTTGCTTCA
          1 TTTTTTGCTTCA

                      
       2845 -TTTTTGCTT
          1 TTTTTTGCTT

       2854 GACACGTGTC


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  11    9  0.45
  12   11  0.55

ACGTcount: A:0.09, C:0.15, G:0.06, T:0.70


Consensus pattern (12 bp):   
TTTTTTGCTTCA
Done.