Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019570.1 Corchorus olitorius cultivar O-4 contig19603, 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: 16147
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34


Found at i:2671 original size:11 final size:11

Alignment explanation


    Indices: 2651--2681  Score: 53
    Period size: 11  Copynumber: 2.8  Consensus size: 11

       2641 TTGACAGCGT

                       
       2651 AACAAAAACGA
          1 AACAAAAACGA

               *       
       2662 AACGAAAACGA
          1 AACAAAAACGA

                     
       2673 AACAAAAAC
          1 AACAAAAAC

       2682 AAAAAACAGA


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  11   18  1.00

ACGTcount: A:0.71, C:0.19, G:0.10, T:0.00


Consensus pattern (11 bp):   
AACAAAAACGA

Found at i:2917 original size:29 final size:29

Alignment explanation


    Indices: 2875--2938  Score: 101
    Period size: 29  Copynumber: 2.2  Consensus size: 29

       2865 AGATTTATAA

                           * *          *
       2875 GGAATTATGTAGCACGTTTATTGGTAGAT
          1 GGAATTATGTAGCACATATATTGGTAGAC

                                         
       2904 GGAATTATGTAGCACATATATTGGTAGAC
          1 GGAATTATGTAGCACATATATTGGTAGAC

                  
       2933 GGAATT
          1 GGAATT

       2939 TTAATGATTA


Statistics
Matches: 32,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  29   32  1.00

ACGTcount: A:0.31, C:0.08, G:0.27, T:0.34


Consensus pattern (29 bp):   
GGAATTATGTAGCACATATATTGGTAGAC

Found at i:2990 original size:2 final size:2

Alignment explanation


    Indices: 2983--3017  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

       2973 CATAATACTA

                                                                
       2983 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       3018 CGGTAATGAT


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:3153 original size:21 final size:20

Alignment explanation


    Indices: 3120--3163  Score: 52
    Period size: 20  Copynumber: 2.1  Consensus size: 20

       3110 TAAATCATAT

                            *    
       3120 AAAATAAAAATAAATGTTATC
          1 AAAATAAAAAT-AATGCTATC

                   **           
       3141 AAAATAACTATAATGCTATC
          1 AAAATAAAAATAATGCTATC

               
       3161 AAA
          1 AAA

       3164 TAAGTTTTAA


Statistics
Matches: 20,  Mismatches: 3, Indels: 1
        0.83            0.12        0.04

Matches are distributed among these distances:
  20   11  0.55
  21    9  0.45

ACGTcount: A:0.59, C:0.09, G:0.05, T:0.27


Consensus pattern (20 bp):   
AAAATAAAAATAATGCTATC

Found at i:5141 original size:13 final size:13

Alignment explanation


    Indices: 5117--5149  Score: 57
    Period size: 13  Copynumber: 2.5  Consensus size: 13

       5107 AAAGAAGATT

                          
       5117 ATATATTTTATTTA
          1 ATATA-TTTATTTA

                         
       5131 ATATATTTATTTA
          1 ATATATTTATTTA

                  
       5144 ATATAT
          1 ATATAT

       5150 GACATATAAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  13   14  0.74
  14    5  0.26

ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61


Consensus pattern (13 bp):   
ATATATTTATTTA

Found at i:5278 original size:2 final size:2

Alignment explanation


    Indices: 5271--5295  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       5261 GGTAGACTAT

                                                 
       5271 TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA T

       5296 GTATTGAATT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Done.