Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010265.1 Corchorus olitorius cultivar O-4 contig10297, 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: 2740
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.34


Found at i:525 original size:14 final size:15

Alignment explanation


    Indices: 506--535  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

        496 CAATCAAAGC

                           
        506 AATAAT-CAAGGAAA
          1 AATAATGCAAGGAAA

                           
        520 AATAATGCAAGGAAA
          1 AATAATGCAAGGAAA

             
        535 A
          1 A

        536 TTAAAGAGAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    6  0.40
  15    9  0.60

ACGTcount: A:0.63, C:0.07, G:0.17, T:0.13


Consensus pattern (15 bp):   
AATAATGCAAGGAAA

Found at i:958 original size:22 final size:21

Alignment explanation


    Indices: 916--958  Score: 59
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        906 TTGGAATGGC

                       *         
        916 GATGGCACGGGCATGGCCGGT
          1 GATGGCACGGGAATGGCCGGT

                             *    
        937 GATGGCACGGTGAATGGGCGGT
          1 GATGGCACGG-GAATGGCCGGT

        959 AATGACTTGG


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  21   10  0.53
  22    9  0.47

ACGTcount: A:0.16, C:0.19, G:0.49, T:0.16


Consensus pattern (21 bp):   
GATGGCACGGGAATGGCCGGT

Found at i:1083 original size:42 final size:42

Alignment explanation


    Indices: 1037--1127  Score: 119
    Period size: 42  Copynumber: 2.2  Consensus size: 42

       1027 GCCGGTCCTA

                      *   *   *   *          *        
       1037 GCCGGGCATGTGGCTCGGGTGAGGCTTGAGATGGCGGGCATG
          1 GCCGGGCATGAGGCGCGGCTGAAGCTTGAGATGCCGGGCATG

                                        * *           
       1079 GCCGGGCATGAGGCGCGGCTGAAGCTTGTGTTGCCGGGCATG
          1 GCCGGGCATGAGGCGCGGCTGAAGCTTGAGATGCCGGGCATG

                   
       1121 GCCGGGC
          1 GCCGGGC

       1128 GTGATACTCG


Statistics
Matches: 42,  Mismatches: 7, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  42   42  1.00

ACGTcount: A:0.11, C:0.23, G:0.48, T:0.18


Consensus pattern (42 bp):   
GCCGGGCATGAGGCGCGGCTGAAGCTTGAGATGCCGGGCATG

Found at i:2484 original size:11 final size:11

Alignment explanation


    Indices: 2468--2492  Score: 50
    Period size: 11  Copynumber: 2.3  Consensus size: 11

       2458 AGAAAATTGT

                       
       2468 TTGTTTTTGGA
          1 TTGTTTTTGGA

                       
       2479 TTGTTTTTGGA
          1 TTGTTTTTGGA

               
       2490 TTG
          1 TTG

       2493 ATTATTCCCC


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

Matches are distributed among these distances:
  11   14  1.00

ACGTcount: A:0.08, C:0.00, G:0.28, T:0.64


Consensus pattern (11 bp):   
TTGTTTTTGGA
Done.