Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020074.1 Corchorus olitorius cultivar O-4 contig20107, 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: 12422
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33


Found at i:950 original size:29 final size:29

Alignment explanation


    Indices: 853--1007  Score: 244
    Period size: 28  Copynumber: 5.4  Consensus size: 29

        843 AAGGTACTTG

                   *               *     
        853 AAATGACTAAAATGCCCCTGGACGTGC-A
          1 AAATGACCAAAATGCCCCTGGACATGCAA

                  *          *           
        881 AAATGATCAAAATGCCCATGGACATGC-A
          1 AAATGACCAAAATGCCCCTGGACATGCAA

                               *         
        909 AAATGACCAAAATGCCCCTAGACATGCAA
          1 AAATGACCAAAATGCCCCTGGACATGCAA

                                         
        938 AAATGACCAAAATGCCCCT-GACATGCAA
          1 AAATGACCAAAATGCCCCTGGACATGCAA

                                         
        966 AAATGACCAAAATGCCCCTGGACATGCAA
          1 AAATGACCAAAATGCCCCTGGACATGCAA

                         
        995 AAATGACCAAAAT
          1 AAATGACCAAAAT

       1008 AAGAAATAAA


Statistics
Matches: 118,  Mismatches: 7, Indels: 3
        0.92            0.05        0.02

Matches are distributed among these distances:
  28   76  0.64
  29   42  0.36

ACGTcount: A:0.43, C:0.25, G:0.16, T:0.15


Consensus pattern (29 bp):   
AAATGACCAAAATGCCCCTGGACATGCAA

Found at i:969 original size:57 final size:57

Alignment explanation


    Indices: 853--1007  Score: 242
    Period size: 57  Copynumber: 2.7  Consensus size: 57

        843 AAGGTACTTG

                   *               *           *                     
        853 AAATGACTAAAATGCCCCTGGACGTGC-AAAATGATCAAAATGCCCATGGACATGCA
          1 AAATGACCAAAATGCCCCTGGACATGCAAAAATGACCAAAATGCCCATGGACATGCA

                               *                          *           
        909 AAATGACCAAAATGCCCCTAGACATGCAAAAATGACCAAAATGCCCCT-GACATGCAA
          1 AAATGACCAAAATGCCCCTGGACATGCAAAAATGACCAAAATGCCCATGGACATGC-A

                                                      
        966 AAATGACCAAAATGCCCCTGGACATGCAAAAATGACCAAAAT
          1 AAATGACCAAAATGCCCCTGGACATGCAAAAATGACCAAAAT

       1008 AAGAAATAAA


Statistics
Matches: 91,  Mismatches: 6, Indels: 3
        0.91            0.06        0.03

Matches are distributed among these distances:
  56   31  0.34
  57   60  0.66

ACGTcount: A:0.43, C:0.25, G:0.16, T:0.15


Consensus pattern (57 bp):   
AAATGACCAAAATGCCCCTGGACATGCAAAAATGACCAAAATGCCCATGGACATGCA

Found at i:11666 original size:25 final size:25

Alignment explanation


    Indices: 11638--11686  Score: 89
    Period size: 25  Copynumber: 2.0  Consensus size: 25

      11628 GCAATACCGG

                                     
      11638 TGATGAATAATTGGCTTCAATTTTA
          1 TGATGAATAATTGGCTTCAATTTTA

                *                   
      11663 TGATTAATAATTGGCTTCAATTTT
          1 TGATGAATAATTGGCTTCAATTTT

      11687 CTGGCCGAAT


Statistics
Matches: 23,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  25   23  1.00

ACGTcount: A:0.31, C:0.08, G:0.14, T:0.47


Consensus pattern (25 bp):   
TGATGAATAATTGGCTTCAATTTTA

Found at i:12164 original size:15 final size:14

Alignment explanation


    Indices: 12141--12170  Score: 51
    Period size: 15  Copynumber: 2.1  Consensus size: 14

      12131 TCTCTGATGC

                          
      12141 AAAAAAAAAAAGAA
          1 AAAAAAAAAAAGAA

                           
      12155 AAAAAGAAAAAAGAA
          1 AAAAA-AAAAAAGAA

             
      12170 A
          1 A

      12171 TAAGAATAAG


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

Matches are distributed among these distances:
  14    5  0.33
  15   10  0.67

ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00


Consensus pattern (14 bp):   
AAAAAAAAAAAGAA
Done.