Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024879.1 Corchorus olitorius cultivar O-4 contig24912, 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: 7755
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:2704 original size:6 final size:6

Alignment explanation


    Indices: 2693--2727  Score: 54
    Period size: 6  Copynumber: 6.0  Consensus size: 6

       2683 CACCTCTAGT

                                             *       
       2693 TTTTTG TTTTTG TTTTTG TTTTT- TTTTTT TTTTTG
          1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG

       2728 CCATACTTAT


Statistics
Matches: 27,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
   5    5  0.19
   6   22  0.81

ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89


Consensus pattern (6 bp):   
TTTTTG

Found at i:2714 original size:17 final size:17

Alignment explanation


    Indices: 2694--2727  Score: 50
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       2684 ACCTCTAGTT

                             
       2694 TTTTGTTTTTGTTTTTG
          1 TTTTGTTTTTGTTTTTG

                *     *      
       2711 TTTTTTTTTTTTTTTTG
          1 TTTTGTTTTTGTTTTTG

       2728 CCATACTTAT


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  17   15  1.00

ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88


Consensus pattern (17 bp):   
TTTTGTTTTTGTTTTTG

Found at i:2972 original size:51 final size:51

Alignment explanation


    Indices: 2896--2997  Score: 204
    Period size: 51  Copynumber: 2.0  Consensus size: 51

       2886 ATCAGTCCAA

                                                               
       2896 AAAAGAAGAAATTAAGAAAACAAATGTAGCAGACTAATGTAAGATCTTAAT
          1 AAAAGAAGAAATTAAGAAAACAAATGTAGCAGACTAATGTAAGATCTTAAT

                                                               
       2947 AAAAGAAGAAATTAAGAAAACAAATGTAGCAGACTAATGTAAGATCTTAAT
          1 AAAAGAAGAAATTAAGAAAACAAATGTAGCAGACTAATGTAAGATCTTAAT

       2998 TGAACAAAAA


Statistics
Matches: 51,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  51   51  1.00

ACGTcount: A:0.55, C:0.08, G:0.16, T:0.22


Consensus pattern (51 bp):   
AAAAGAAGAAATTAAGAAAACAAATGTAGCAGACTAATGTAAGATCTTAAT

Found at i:3105 original size:23 final size:23

Alignment explanation


    Indices: 3075--3122  Score: 87
    Period size: 23  Copynumber: 2.1  Consensus size: 23

       3065 AAATATGATA

                          *        
       3075 TACAAAGATGAGTCGAACCAAGT
          1 TACAAAGATGAGTCAAACCAAGT

                                   
       3098 TACAAAGATGAGTCAAACCAAGT
          1 TACAAAGATGAGTCAAACCAAGT

              
       3121 TA
          1 TA

       3123 AAGGGACGAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  23   24  1.00

ACGTcount: A:0.46, C:0.17, G:0.19, T:0.19


Consensus pattern (23 bp):   
TACAAAGATGAGTCAAACCAAGT

Found at i:6918 original size:27 final size:27

Alignment explanation


    Indices: 6878--6941  Score: 80
    Period size: 27  Copynumber: 2.4  Consensus size: 27

       6868 TCTAAATTTC

                                          
       6878 TATTATTTTAATAATTGAATAA-TTA-AAA
          1 TATTA-TTTAATAA-TG-ATAATTTAGAAA

                                       
       6906 TATTATTTAATAATGATAATTTAGAAA
          1 TATTATTTAATAATGATAATTTAGAAA

                      
       6933 TA-TATTTAA
          1 TATTATTTAA

       6942 AATAAAAGGG


Statistics
Matches: 34,  Mismatches: 0, Indels: 6
        0.85            0.00        0.15

Matches are distributed among these distances:
  25    4  0.12
  26   12  0.35
  27   13  0.38
  28    5  0.15

ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47


Consensus pattern (27 bp):   
TATTATTTAATAATGATAATTTAGAAA
Done.