Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016920.1 Corchorus olitorius cultivar O-4 contig16953, 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: 3510
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36


Found at i:2860 original size:42 final size:43

Alignment explanation


    Indices: 2813--2896  Score: 127
    Period size: 42  Copynumber: 2.0  Consensus size: 43

       2803 CGTGTTTGGC

                                                        
       2813 TTATCGTGTCTCGTGTCGA-AATCGTGTCG-GACACGATTAAGA
          1 TTATCGTGTCTCGTGTC-ATAATCGTGTCGTGACACGATTAAGA

                     *                                
       2855 TTATCGTGTTTCGTGTCATAATCGTGTCGTTGACACGATTAA
          1 TTATCGTGTCTCGTGTCATAATCGTGTCG-TGACACGATTAA

       2897 CACGTTTAAA


Statistics
Matches: 38,  Mismatches: 1, Indels: 4
        0.88            0.02        0.09

Matches are distributed among these distances:
  41    1  0.03
  42   26  0.68
  44   11  0.29

ACGTcount: A:0.23, C:0.18, G:0.24, T:0.36


Consensus pattern (43 bp):   
TTATCGTGTCTCGTGTCATAATCGTGTCGTGACACGATTAAGA

Found at i:3034 original size:13 final size:13

Alignment explanation


    Indices: 3016--3042  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

       3006 AATTTATGAT

                         
       3016 ATACCCAACCCAA
          1 ATACCCAACCCAA

                         
       3029 ATACCCAACCCAA
          1 ATACCCAACCCAA

             
       3042 A
          1 A

       3043 GCCCAAAGCC


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.48, C:0.44, G:0.00, T:0.07


Consensus pattern (13 bp):   
ATACCCAACCCAA

Found at i:3049 original size:7 final size:7

Alignment explanation


    Indices: 3037--3068  Score: 57
    Period size: 7  Copynumber: 4.7  Consensus size: 7

       3027 AAATACCCAA

                   
       3037 CCCAAAG
          1 CCCAAAG

                   
       3044 CCCAAAG
          1 CCCAAAG

                   
       3051 CCCAAAG
          1 CCCAAAG

                   
       3058 CCCAAA-
          1 CCCAAAG

                 
       3064 CCCAA
          1 CCCAA

       3069 TTAATTAAAT


Statistics
Matches: 25,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   6    5  0.20
   7   20  0.80

ACGTcount: A:0.44, C:0.47, G:0.09, T:0.00


Consensus pattern (7 bp):   
CCCAAAG

Found at i:3056 original size:14 final size:13

Alignment explanation


    Indices: 3022--3068  Score: 60
    Period size: 13  Copynumber: 3.5  Consensus size: 13

       3012 TGATATACCC

                     *    
       3022 AACCCAAATACCC-
          1 AACCCAAA-GCCCA

                         
       3035 AACCCAAAGCCCA
          1 AACCCAAAGCCCA

                          
       3048 AAGCCCAAAGCCCA
          1 AA-CCCAAAGCCCA

                   
       3062 AACCCAA
          1 AACCCAA

       3069 TTAATTAAAT


Statistics
Matches: 31,  Mismatches: 1, Indels: 4
        0.86            0.03        0.11

Matches are distributed among these distances:
  12    3  0.10
  13   15  0.48
  14   13  0.42

ACGTcount: A:0.47, C:0.45, G:0.06, T:0.02


Consensus pattern (13 bp):   
AACCCAAAGCCCA
Done.