Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013956.1 Corchorus olitorius cultivar O-4 contig13989, 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: 14562
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35


Found at i:4016 original size:15 final size:15

Alignment explanation


    Indices: 3984--4017  Score: 50
    Period size: 15  Copynumber: 2.3  Consensus size: 15

       3974 GCTAAACTTC

                         * 
       3984 ATTATATGAACAATT
          1 ATTATATGAACAAAT

                      *    
       3999 ATTATATGAATAAAT
          1 ATTATATGAACAAAT

                
       4014 ATTA
          1 ATTA

       4018 AATCTGTTAT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41


Consensus pattern (15 bp):   
ATTATATGAACAAAT

Found at i:4636 original size:20 final size:21

Alignment explanation


    Indices: 4606--4646  Score: 57
    Period size: 20  Copynumber: 2.0  Consensus size: 21

       4596 TTACTCTTCT

                                 
       4606 TTTTATTTTAAAAACTTTAAA
          1 TTTTATTTTAAAAACTTTAAA

                       **        
       4627 TTTT-TTTTAATTACTTTAAA
          1 TTTTATTTTAAAAACTTTAAA

       4647 AAATGATAAA


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  20   14  0.78
  21    4  0.22

ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59


Consensus pattern (21 bp):   
TTTTATTTTAAAAACTTTAAA

Found at i:8866 original size:19 final size:19

Alignment explanation


    Indices: 8842--8899  Score: 62
    Period size: 19  Copynumber: 2.9  Consensus size: 19

       8832 CTGTTTGGCA

                    *          
       8842 ACTGTACATATGAGATTAC
          1 ACTGTACAAATGAGATTAC

                       *        *
       8861 ACTGTACAAATTAGATTATGT
          1 ACTGTACAAATGAGATTA--C

                  *           
       8882 ACTGTATAAATGAGATTA
          1 ACTGTACAAATGAGATTA

       8900 TTAGAACAAC


Statistics
Matches: 32,  Mismatches: 5, Indels: 2
        0.82            0.13        0.05

Matches are distributed among these distances:
  19   16  0.50
  21   16  0.50

ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34


Consensus pattern (19 bp):   
ACTGTACAAATGAGATTAC

Found at i:8887 original size:21 final size:21

Alignment explanation


    Indices: 8842--8900  Score: 68
    Period size: 21  Copynumber: 2.9  Consensus size: 21

       8832 CTGTTTGGCA

                    *           *
       8842 ACTGTACATATGAGATTA--C
          1 ACTGTACAAATGAGATTATGT

                       *         
       8861 ACTGTACAAATTAGATTATGT
          1 ACTGTACAAATGAGATTATGT

                  *            
       8882 ACTGTATAAATGAGATTAT
          1 ACTGTACAAATGAGATTAT

       8901 TAGAACAACG


Statistics
Matches: 33,  Mismatches: 5, Indels: 2
        0.82            0.12        0.05

Matches are distributed among these distances:
  19   16  0.48
  21   17  0.52

ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36


Consensus pattern (21 bp):   
ACTGTACAAATGAGATTATGT

Found at i:8974 original size:19 final size:19

Alignment explanation


    Indices: 8950--8986  Score: 74
    Period size: 19  Copynumber: 1.9  Consensus size: 19

       8940 TTTGGTCCCA

                               
       8950 AAACGGTGATGAAACGGTC
          1 AAACGGTGATGAAACGGTC

                              
       8969 AAACGGTGATGAAACGGT
          1 AAACGGTGATGAAACGGT

       8987 TACAAATAAG


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   18  1.00

ACGTcount: A:0.38, C:0.14, G:0.32, T:0.16


Consensus pattern (19 bp):   
AAACGGTGATGAAACGGTC

Found at i:10030 original size:15 final size:15

Alignment explanation


    Indices: 10010--10043  Score: 50
    Period size: 15  Copynumber: 2.3  Consensus size: 15

      10000 TTTAAGAATG

                          *
      10010 TATTTTTAAAGGATT
          1 TATTTTTAAAGGATA

                   *       
      10025 TATTTTTGAAGGATA
          1 TATTTTTAAAGGATA

                
      10040 TATT
          1 TATT

      10044 ATGATGATAT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53


Consensus pattern (15 bp):   
TATTTTTAAAGGATA

Found at i:12081 original size:6 final size:6

Alignment explanation


    Indices: 12063--12123  Score: 81
    Period size: 6  Copynumber: 10.5  Consensus size: 6

      12053 CCAAGCCAGG

                                    *    * *                       
      12063 AAAAG- AAAA-A AAAAGA AAAGGA AGAGGA AAAAGA AAAAGA AAAAGA
          1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA

                             
      12109 AAAAGA AAAAGA AAA
          1 AAAAGA AAAAGA AAA

      12124 TAAAATAAAA


Statistics
Matches: 50,  Mismatches: 4, Indels: 3
        0.88            0.07        0.05

Matches are distributed among these distances:
   5    8  0.16
   6   42  0.84

ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00


Consensus pattern (6 bp):   
AAAAGA

Done.