Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023683.1 Corchorus olitorius cultivar O-4 contig23716, 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: 19306
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32


Found at i:648 original size:16 final size:15

Alignment explanation


    Indices: 627--669  Score: 68
    Period size: 16  Copynumber: 2.7  Consensus size: 15

        617 TTATTTTGTT

                            
        627 TTGTTTTCTAGTTTAA
          1 TTGTTTTCT-GTTTAA

                            
        643 TTGTTTTTCTGTTTAA
          1 TTG-TTTTCTGTTTAA

                       
        659 TTGTTTTCTGT
          1 TTGTTTTCTGT

        670 CAACCTCTGT


Statistics
Matches: 26,  Mismatches: 0, Indels: 3
        0.90            0.00        0.10

Matches are distributed among these distances:
  15    8  0.31
  16   12  0.46
  17    6  0.23

ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA

Found at i:3992 original size:21 final size:21

Alignment explanation


    Indices: 3968--4022  Score: 67
    Period size: 21  Copynumber: 2.6  Consensus size: 21

       3958 CCGCCCATTA

                       *          
       3968 CCGTGCCACCATCGG-TCAAGC
          1 CCGTGCCACCACCGGCT-AAGC

                              *  
       3989 CCGTGCCACCACCGGCTATGC
          1 CCGTGCCACCACCGGCTAAGC

                    *    
       4010 CCGTGCCATCACC
          1 CCGTGCCACCACC

       4023 ATTCACTGCC


Statistics
Matches: 30,  Mismatches: 3, Indels: 2
        0.86            0.09        0.06

Matches are distributed among these distances:
  21   29  0.97
  22    1  0.03

ACGTcount: A:0.16, C:0.47, G:0.22, T:0.15


Consensus pattern (21 bp):   
CCGTGCCACCACCGGCTAAGC

Found at i:7284 original size:15 final size:15

Alignment explanation


    Indices: 7254--7295  Score: 75
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       7244 TTACTTTGTT

                            
       7254 TTGTTTTCTAGTTTAA
          1 TTGTTTTCT-GTTTAA

                           
       7270 TTGTTTTCTGTTTAA
          1 TTGTTTTCTGTTTAA

                       
       7285 TTGTTTTCTGT
          1 TTGTTTTCTGT

       7296 CAAGCTCTGT


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15   17  0.65
  16    9  0.35

ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA

Found at i:11978 original size:15 final size:16

Alignment explanation


    Indices: 11954--11993  Score: 55
    Period size: 15  Copynumber: 2.6  Consensus size: 16

      11944 AGAAATAGAA

                 *          
      11954 AGAAAGCAATTAAAC-
          1 AGAAAACAATTAAACT

                        *   
      11969 AGAAAACAATTATACT
          1 AGAAAACAATTAAACT

                     
      11985 AGAAAACAA
          1 AGAAAACAA

      11994 AACAAAGTAA


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  15   13  0.59
  16    9  0.41

ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15


Consensus pattern (16 bp):   
AGAAAACAATTAAACT

Found at i:13303 original size:9 final size:10

Alignment explanation


    Indices: 13281--13311  Score: 55
    Period size: 10  Copynumber: 3.2  Consensus size: 10

      13271 CTTCCCATAT

                      
      13281 AAAATATCCA
          1 AAAATATCCA

                      
      13291 AAAATATCCA
          1 AAAATATCCA

                      
      13301 AAAATA-CCA
          1 AAAATATCCA

              
      13310 AA
          1 AA

      13312 GCTTAAAGGC


Statistics
Matches: 21,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
   9    5  0.24
  10   16  0.76

ACGTcount: A:0.65, C:0.19, G:0.00, T:0.16


Consensus pattern (10 bp):   
AAAATATCCA
Done.