Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015505.1 Corchorus olitorius cultivar O-4 contig15538, 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: 10038
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.32


Found at i:2800 original size:22 final size:23

Alignment explanation


    Indices: 2744--2811  Score: 72
    Period size: 22  Copynumber: 3.0  Consensus size: 23

       2734 TTTAGTAATT

                                    *
       2744 AAATATATATTATTTATTTATTTTG
          1 AAATATAT-TTATTTATTTA-TTTA

              *                    
       2769 AACTA-A-TTATTTA-TTATTTA
          1 AAATATATTTATTTATTTATTTA

                                   
       2789 AAATATATTTA-TTATTTATTTA
          1 AAATATATTTATTTATTTATTTA

             
       2811 A
          1 A

       2812 TAGTATATAT


Statistics
Matches: 37,  Mismatches: 3, Indels: 9
        0.76            0.06        0.18

Matches are distributed among these distances:
  20    7  0.19
  21    7  0.19
  22   18  0.49
  24    1  0.03
  25    4  0.11

ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57


Consensus pattern (23 bp):   
AAATATATTTATTTATTTATTTA

Found at i:3599 original size:24 final size:22

Alignment explanation


    Indices: 3572--3619  Score: 62
    Period size: 24  Copynumber: 2.1  Consensus size: 22

       3562 TCTTCCTAAA

                                     
       3572 ATTTAGGCACAAA-TTTAGCACCAG
          1 ATTTAGGC-CAAAGTTT--CACCAG

                                  
       3596 ATTTAGGCCAAAGTTTCACCAG
          1 ATTTAGGCCAAAGTTTCACCAG

              
       3618 AT
          1 AT

       3620 GAGATTTGCA


Statistics
Matches: 23,  Mismatches: 0, Indels: 4
        0.85            0.00        0.15

Matches are distributed among these distances:
  22    8  0.35
  23    4  0.17
  24   11  0.48

ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27


Consensus pattern (22 bp):   
ATTTAGGCCAAAGTTTCACCAG

Found at i:5185 original size:15 final size:16

Alignment explanation


    Indices: 5165--5207  Score: 70
    Period size: 15  Copynumber: 2.7  Consensus size: 16

       5155 ACAGAGGTTG

                            
       5165 ACAGAAAACAA-TTAA
          1 ACAGAAAACAATTTAA

                            
       5180 ACAGAAAACAATTTAA
          1 ACAGAAAACAATTTAA

                        
       5196 ACTAGAAAACAA
          1 AC-AGAAAACAA

       5208 AGCAAAGTAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
  15   11  0.42
  16    6  0.23
  17    9  0.35

ACGTcount: A:0.65, C:0.14, G:0.07, T:0.14


Consensus pattern (16 bp):   
ACAGAAAACAATTTAA

Found at i:8060 original size:14 final size:15

Alignment explanation


    Indices: 8041--8070  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       8031 CAATCAAAGT

                           
       8041 AATAAT-CAAGGAAA
          1 AATAATGCAAGGAAA

                           
       8055 AATAATGCAAGGAAA
          1 AATAATGCAAGGAAA

             
       8070 A
          1 A

       8071 TTAAAAAGAT


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

Done.