Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012802.1 Corchorus olitorius cultivar O-4 contig12835, 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: 9114
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34


Found at i:4062 original size:14 final size:14

Alignment explanation


    Indices: 4043--4087  Score: 53
    Period size: 14  Copynumber: 3.4  Consensus size: 14

       4033 ATGATTTGAC

                          
       4043 AAAATGATATAATG
          1 AAAATGATATAATG

                          
       4057 AAAATGAT-T--TG
          1 AAAATGATATAATG

                           
       4068 ACAAATGATATAAT-
          1 A-AAATGATATAATG

                  
       4082 AAAATG
          1 AAAATG

       4088 TTTTGAATTT


Statistics
Matches: 27,  Mismatches: 0, Indels: 9
        0.75            0.00        0.25

Matches are distributed among these distances:
  11    3  0.11
  12    7  0.26
  13    7  0.26
  14    9  0.33
  15    1  0.04

ACGTcount: A:0.56, C:0.02, G:0.13, T:0.29


Consensus pattern (14 bp):   
AAAATGATATAATG

Found at i:4080 original size:26 final size:26

Alignment explanation


    Indices: 4032--4093  Score: 99
    Period size: 26  Copynumber: 2.4  Consensus size: 26

       4022 TGTGTCTCTT

                                       
       4032 AATGATTTGACAAAATGATATAATGAA
          1 AATGATTTGACAAAATGATATAAT-AA

                                      
       4059 AATGATTTGAC-AAATGATATAATAA
          1 AATGATTTGACAAAATGATATAATAA

                *     
       4084 AATGTTTTGA
          1 AATGATTTGA

       4094 ATTTGTTGTT


Statistics
Matches: 34,  Mismatches: 1, Indels: 2
        0.92            0.03        0.05

Matches are distributed among these distances:
  25   11  0.32
  26   12  0.35
  27   11  0.32

ACGTcount: A:0.48, C:0.03, G:0.15, T:0.34


Consensus pattern (26 bp):   
AATGATTTGACAAAATGATATAATAA

Found at i:4824 original size:23 final size:23

Alignment explanation


    Indices: 4793--4837  Score: 72
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       4783 ACTAACAATG

                     *             
       4793 TATTATATAGTATTCTTAAAATT
          1 TATTATATAATATTCTTAAAATT

                *                 
       4816 TATTGTATAATATTCTTAAAAT
          1 TATTATATAATATTCTTAAAAT

       4838 ATATAACTTT


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  23   20  1.00

ACGTcount: A:0.40, C:0.04, G:0.04, T:0.51


Consensus pattern (23 bp):   
TATTATATAATATTCTTAAAATT

Found at i:5049 original size:2 final size:2

Alignment explanation


    Indices: 5042--5070  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

       5032 AAATTACTAG

                                                       
       5042 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       5071 GCCAAATATT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:7198 original size:11 final size:10

Alignment explanation


    Indices: 7155--7200  Score: 51
    Period size: 10  Copynumber: 4.8  Consensus size: 10

       7145 TTTTTTCTAA

                      
       7155 CTTTTTTATT
          1 CTTTTTTATT

                  *  *
       7165 C-TTTTCA-C
          1 CTTTTTTATT

                      
       7173 CTTTTTTATT
          1 CTTTTTTATT

                      
       7183 CTTTTTTATT
          1 CTTTTTTATT

             *      
       7193 CGTTTTTA
          1 CTTTTTTA

       7201 GGCTTTTTAT


Statistics
Matches: 29,  Mismatches: 5, Indels: 4
        0.76            0.13        0.11

Matches are distributed among these distances:
   8    1  0.03
   9   10  0.34
  10   18  0.62

ACGTcount: A:0.11, C:0.15, G:0.02, T:0.72


Consensus pattern (10 bp):   
CTTTTTTATT
Done.