Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004440.1 Corchorus capsularis cultivar CVL-1 contig04448, 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, 796

Length: 1327
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29


Found at i:750 original size:17 final size:17

Alignment explanation


    Indices: 728--762  Score: 70
    Period size: 17  Copynumber: 2.1  Consensus size: 17

        718 ATAACAAAAC

                             
        728 ATTAGACATTATCTATA
          1 ATTAGACATTATCTATA

                             
        745 ATTAGACATTATCTATA
          1 ATTAGACATTATCTATA

             
        762 A
          1 A

        763 AAAATTAAGA


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

Matches are distributed among these distances:
  17   18  1.00

ACGTcount: A:0.43, C:0.11, G:0.06, T:0.40


Consensus pattern (17 bp):   
ATTAGACATTATCTATA

Found at i:775 original size:22 final size:21

Alignment explanation


    Indices: 723--786  Score: 82
    Period size: 22  Copynumber: 3.2  Consensus size: 21

        713 ACATTATAAC

                *                
        723 AAAACATTAGACATTATCTAT
          1 AAAAAATTAGACATTATCTAT

                                 
        744 ----AATTAGACATTATCTAT
          1 AAAAAATTAGACATTATCTAT

                                  
        761 AAAAAATTAAGACATTATCTAT
          1 AAAAAATT-AGACATTATCTAT

                
        783 AAAA
          1 AAAA

        787 GGAATCCATG


Statistics
Matches: 37,  Mismatches: 1, Indels: 9
        0.79            0.02        0.19

Matches are distributed among these distances:
  17   16  0.43
  21    4  0.11
  22   17  0.46

ACGTcount: A:0.52, C:0.11, G:0.05, T:0.33


Consensus pattern (21 bp):   
AAAAAATTAGACATTATCTAT

Found at i:844 original size:10 final size:10

Alignment explanation


    Indices: 829--868  Score: 57
    Period size: 10  Copynumber: 4.1  Consensus size: 10

        819 TATGTTTAAT

                      
        829 TACTTATATA
          1 TACTTATATA

                       
        839 TACTTATACT-
          1 TACTTATA-TA

                      
        849 TACTTATATA
          1 TACTTATATA

                      
        859 TA-TTATATA
          1 TACTTATATA

             
        868 T
          1 T

        869 TCAATATAGA


Statistics
Matches: 28,  Mismatches: 0, Indels: 5
        0.85            0.00        0.15

Matches are distributed among these distances:
   9    9  0.32
  10   18  0.64
  11    1  0.04

ACGTcount: A:0.38, C:0.10, G:0.00, T:0.53


Consensus pattern (10 bp):   
TACTTATATA

Found at i:853 original size:20 final size:19

Alignment explanation


    Indices: 828--865  Score: 67
    Period size: 20  Copynumber: 1.9  Consensus size: 19

        818 TTATGTTTAA

                                
        828 TTACTTATATATACTTATAC
          1 TTACTTATATATA-TTATAC

                              
        848 TTACTTATATATATTATA
          1 TTACTTATATATATTATA

        866 TATTCAATAT


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  19    5  0.28
  20   13  0.72

ACGTcount: A:0.37, C:0.11, G:0.00, T:0.53


Consensus pattern (19 bp):   
TTACTTATATATATTATAC
Done.