Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001307.1 Corchorus capsularis cultivar CVL-1 contig01307, 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: 8542
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34


Found at i:1693 original size:15 final size:15

Alignment explanation


    Indices: 1673--1705  Score: 66
    Period size: 15  Copynumber: 2.2  Consensus size: 15

       1663 TTAAGAAATG

                           
       1673 CAAAGAGATTAACCA
          1 CAAAGAGATTAACCA

                           
       1688 CAAAGAGATTAACCA
          1 CAAAGAGATTAACCA

               
       1703 CAA
          1 CAA

       1706 TAATGTCTTT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   18  1.00

ACGTcount: A:0.55, C:0.21, G:0.12, T:0.12


Consensus pattern (15 bp):   
CAAAGAGATTAACCA

Found at i:7485 original size:27 final size:24

Alignment explanation


    Indices: 7439--7488  Score: 64
    Period size: 27  Copynumber: 2.0  Consensus size: 24

       7429 CATATTTTAA

                                    
       7439 TATTTATATAAATAAAAATATAAT
          1 TATTTATATAAATAAAAATATAAT

                              *       
       7463 TATTATATATATAATATATAATATAA
          1 TATT-TATATA-AATA-AAAATATAA

       7489 ACGAACATAA


Statistics
Matches: 22,  Mismatches: 1, Indels: 3
        0.85            0.04        0.12

Matches are distributed among these distances:
  24    4  0.18
  25    6  0.27
  26    4  0.18
  27    8  0.36

ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44


Consensus pattern (24 bp):   
TATTTATATAAATAAAAATATAAT

Found at i:7531 original size:22 final size:22

Alignment explanation


    Indices: 7486--7532  Score: 60
    Period size: 22  Copynumber: 2.1  Consensus size: 22

       7476 ATATATAATA

                             *    
       7486 TAAACGAACATAAACGATCTAT
          1 TAAACGAACATAAACGAACTAT

                *                  
       7508 TAAATGAACACTAAACGAAC-AT
          1 TAAACGAACA-TAAACGAACTAT

               
       7530 TAA
          1 TAA

       7533 TCGAGCTTGT


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  22   14  0.64
  23    8  0.36

ACGTcount: A:0.53, C:0.17, G:0.09, T:0.21


Consensus pattern (22 bp):   
TAAACGAACATAAACGAACTAT
Done.