Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020669.1 Corchorus olitorius cultivar O-4 contig20702, 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: 2865
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34


Found at i:1320 original size:15 final size:16

Alignment explanation


    Indices: 1295--1324  Score: 53
    Period size: 15  Copynumber: 1.9  Consensus size: 16

       1285 AATAATTATT

                            
       1295 TTTAGATTATAATATA
          1 TTTAGATTATAATATA

                           
       1311 TTTA-ATTATAATAT
          1 TTTAGATTATAATAT

       1325 TATTATTTAT


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15   10  0.71
  16    4  0.29

ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53


Consensus pattern (16 bp):   
TTTAGATTATAATATA

Found at i:1793 original size:10 final size:10

Alignment explanation


    Indices: 1778--1804  Score: 54
    Period size: 10  Copynumber: 2.7  Consensus size: 10

       1768 AACTCAACGT

                      
       1778 CCCGAACCCG
          1 CCCGAACCCG

                      
       1788 CCCGAACCCG
          1 CCCGAACCCG

                   
       1798 CCCGAAC
          1 CCCGAAC

       1805 GTGAACCCGA


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

Matches are distributed among these distances:
  10   17  1.00

ACGTcount: A:0.22, C:0.59, G:0.19, T:0.00


Consensus pattern (10 bp):   
CCCGAACCCG

Found at i:2084 original size:10 final size:10

Alignment explanation


    Indices: 2069--2108  Score: 50
    Period size: 10  Copynumber: 4.2  Consensus size: 10

       2059 AACTACTAAA

                      
       2069 TATATATAAT
          1 TATATATAAT

                      
       2079 TATATAT-A-
          1 TATATATAAT

                       
       2087 TATATATAACT
          1 TATATATAA-T

                      
       2098 TATATA-AAT
          1 TATATATAAT

              
       2107 TA
          1 TA

       2109 AAGCAAAAGA


Statistics
Matches: 27,  Mismatches: 0, Indels: 7
        0.79            0.00        0.21

Matches are distributed among these distances:
   8    7  0.26
   9    5  0.19
  10    9  0.33
  11    6  0.22

ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47


Consensus pattern (10 bp):   
TATATATAAT

Found at i:2404 original size:31 final size:31

Alignment explanation


    Indices: 2333--2404  Score: 78
    Period size: 31  Copynumber: 2.3  Consensus size: 31

       2323 GTCTATCAGC

                                      *    
       2333 TTTTAATTTGTTTAATTTAAGACTTTCATTT
          1 TTTTAATTTGTTTAATTTAAGACTTTAATTT

              *                              
       2364 TAATT-ATTTGTTTAATTTAATG-C-TTAATTT
          1 T-TTTAATTTGTTTAATTTAA-GACTTTAATTT

                       
       2394 GTTTTAATTTG
          1 -TTTTAATTTG

       2405 CAATAATTTA


Statistics
Matches: 34,  Mismatches: 3, Indels: 8
        0.76            0.07        0.18

Matches are distributed among these distances:
  30    8  0.24
  31   23  0.68
  32    3  0.09

ACGTcount: A:0.26, C:0.04, G:0.08, T:0.61


Consensus pattern (31 bp):   
TTTTAATTTGTTTAATTTAAGACTTTAATTT

Found at i:2692 original size:8 final size:8

Alignment explanation


    Indices: 2679--2712  Score: 52
    Period size: 8  Copynumber: 4.4  Consensus size: 8

       2669 AATAATGTTA

                    
       2679 TATTATAT
          1 TATTATAT

                    
       2687 TATTATAT
          1 TATTATAT

                    
       2695 TATTATAT
          1 TATTATAT

            *       
       2703 CA-TATAT
          1 TATTATAT

               
       2710 TAT
          1 TAT

       2713 CAATAAACTT


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
   7    6  0.26
   8   17  0.74

ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59


Consensus pattern (8 bp):   
TATTATAT
Done.