Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020847.1 Corchorus olitorius cultivar O-4 contig20880, 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: 6897
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32


Found at i:478 original size:15 final size:15

Alignment explanation


    Indices: 445--503  Score: 57
    Period size: 15  Copynumber: 3.7  Consensus size: 15

        435 TTACTTTGTT

                        *   
        445 TTGTTTTCTAGTATAA
          1 TTGTTTTCT-GTTTAA

                           
        461 TTGTTTTCTGTTTAA
          1 TTGTTTTCTGTTTAA

               *           
        476 TTGCTTTCT-TTTAA
          1 TTGTTTTCTGTTTAA

                          
        490 CCTCTGTTTTCTGT
          1 --T-TGTTTTCTGT

        504 GTTTTGTTTT


Statistics
Matches: 36,  Mismatches: 3, Indels: 6
        0.80            0.07        0.13

Matches are distributed among these distances:
  14    5  0.14
  15   13  0.36
  16   10  0.28
  17    7  0.19
  18    1  0.03

ACGTcount: A:0.14, C:0.14, G:0.12, T:0.61


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA

Found at i:883 original size:21 final size:20

Alignment explanation


    Indices: 859--905  Score: 51
    Period size: 21  Copynumber: 2.3  Consensus size: 20

        849 TGCGTTAAAA

                           *     
        859 TTTTTTTTTTTAT-TTTTGCG
          1 TTTTTTTTTTT-TGTGTTGCG

                  *              
        879 TTTTTAATTTTTTGTGTTGCG
          1 TTTTT-TTTTTTTGTGTTGCG

                  
        900 TTTTTT
          1 TTTTTT

        906 AAAAAAAAAT


Statistics
Matches: 22,  Mismatches: 3, Indels: 4
        0.76            0.10        0.14

Matches are distributed among these distances:
  20    6  0.27
  21   16  0.73

ACGTcount: A:0.06, C:0.04, G:0.13, T:0.77


Consensus pattern (20 bp):   
TTTTTTTTTTTTGTGTTGCG

Found at i:4176 original size:21 final size:21

Alignment explanation


    Indices: 4152--4201  Score: 73
    Period size: 21  Copynumber: 2.4  Consensus size: 21

       4142 CGCCCATTCA

                           *     
       4152 CCGTGCCACCACCGGTCAAGC
          1 CCGTGCCACCACCGGCCAAGC

                              *  
       4173 CCGTGCCACCACCGGCCATGC
          1 CCGTGCCACCACCGGCCAAGC

             *      
       4194 CTGTGCCA
          1 CCGTGCCA

       4202 TCACAATTCC


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

Matches are distributed among these distances:
  21   26  1.00

ACGTcount: A:0.16, C:0.48, G:0.24, T:0.12


Consensus pattern (21 bp):   
CCGTGCCACCACCGGCCAAGC

Found at i:4776 original size:17 final size:17

Alignment explanation


    Indices: 4754--4792  Score: 69
    Period size: 17  Copynumber: 2.3  Consensus size: 17

       4744 TGGGGGAGAG

                             
       4754 AGTCTAGTCTAATAGAA
          1 AGTCTAGTCTAATAGAA

                            *
       4771 AGTCTAGTCTAATAGAG
          1 AGTCTAGTCTAATAGAA

                 
       4788 AGTCT
          1 AGTCT

       4793 GCATGCATCA


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

Matches are distributed among these distances:
  17   21  1.00

ACGTcount: A:0.36, C:0.13, G:0.21, T:0.31


Consensus pattern (17 bp):   
AGTCTAGTCTAATAGAA

Found at i:5138 original size:15 final size:16

Alignment explanation


    Indices: 5120--5152  Score: 50
    Period size: 15  Copynumber: 2.1  Consensus size: 16

       5110 AAAAGGGTAG

                       *    
       5120 TTAAAAAA-AATTGTT
          1 TTAAAAAAGAAGTGTT

                            
       5135 TTAAAAAAGAAGTGTT
          1 TTAAAAAAGAAGTGTT

              
       5151 TT
          1 TT

       5153 CATGCAAGAG


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  15    8  0.50
  16    8  0.50

ACGTcount: A:0.48, C:0.00, G:0.12, T:0.39


Consensus pattern (16 bp):   
TTAAAAAAGAAGTGTT
Done.