Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020913.1 Corchorus olitorius cultivar O-4 contig20946, 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: 3474
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.31


Found at i:384 original size:21 final size:21

Alignment explanation


    Indices: 360--409  Score: 64
    Period size: 21  Copynumber: 2.4  Consensus size: 21

        350 GGCCGGCTAT

                           *     
        360 GGCCTGACCATCCGCGCACCA
          1 GGCCTGACCATCCGCACACCA

                  *     *        
        381 GGCCTGGCCATCTGCACACCA
          1 GGCCTGACCATCCGCACACCA

            *       
        402 TGCCTGAC
          1 GGCCTGAC

        410 TAGGACCGGC


Statistics
Matches: 24,  Mismatches: 5, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  21   24  1.00

ACGTcount: A:0.18, C:0.44, G:0.24, T:0.14


Consensus pattern (21 bp):   
GGCCTGACCATCCGCACACCA

Found at i:1160 original size:21 final size:21

Alignment explanation


    Indices: 1136--1185  Score: 64
    Period size: 21  Copynumber: 2.4  Consensus size: 21

       1126 GGCCGGCTAT

                           *     
       1136 GGCCTGACCATCCGCGCACCA
          1 GGCCTGACCATCCGCACACCA

                  *     *        
       1157 GGCCTGGCCATCTGCACACCA
          1 GGCCTGACCATCCGCACACCA

            *       
       1178 TGCCTGAC
          1 GGCCTGAC

       1186 TAGGACCGGC


Statistics
Matches: 24,  Mismatches: 5, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  21   24  1.00

ACGTcount: A:0.18, C:0.44, G:0.24, T:0.14


Consensus pattern (21 bp):   
GGCCTGACCATCCGCACACCA

Found at i:1579 original size:15 final size:15

Alignment explanation


    Indices: 1556--1585  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       1546 TTTCACTAAC

                           
       1556 CTTTAATTTTTCTTT
          1 CTTTAATTTTTCTTT

                *          
       1571 CTTTTATTTTTCTTT
          1 CTTTAATTTTTCTTT

       1586 TTCTTTTTAG


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

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77


Consensus pattern (15 bp):   
CTTTAATTTTTCTTT

Found at i:3182 original size:18 final size:18

Alignment explanation


    Indices: 3159--3204  Score: 56
    Period size: 18  Copynumber: 2.6  Consensus size: 18

       3149 TGAAATTAAT

                              
       3159 TAATTATTAATTAAATAA
          1 TAATTATTAATTAAATAA

                    **  *     
       3177 TAATTATTTTTTGAATAA
          1 TAATTATTAATTAAATAA

             *        
       3195 TTATTATTAA
          1 TAATTATTAA

       3205 ATTTCTAGTG


Statistics
Matches: 22,  Mismatches: 6, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
  18   22  1.00

ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52


Consensus pattern (18 bp):   
TAATTATTAATTAAATAA
Done.