Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014944.1 Corchorus olitorius cultivar O-4 contig14977, 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: 33735
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30


Found at i:17649 original size:11 final size:11

Alignment explanation


    Indices: 17633--17659  Score: 54
    Period size: 11  Copynumber: 2.5  Consensus size: 11

      17623 AATGCCAATA

                       
      17633 ATTTTATTTTT
          1 ATTTTATTTTT

                       
      17644 ATTTTATTTTT
          1 ATTTTATTTTT

                 
      17655 ATTTT
          1 ATTTT

      17660 TTACAAAAAA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   16  1.00

ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81


Consensus pattern (11 bp):   
ATTTTATTTTT

Found at i:19430 original size:32 final size:32

Alignment explanation


    Indices: 19394--19460  Score: 125
    Period size: 32  Copynumber: 2.1  Consensus size: 32

      19384 AACAATCGCA

                               *            
      19394 TCGGATTTAGACTAATTTAGAGTCAAATCGTG
          1 TCGGATTTAGACTAATTTAAAGTCAAATCGTG

                                            
      19426 TCGGATTTAGACTAATTTAAAGTCAAATCGTG
          1 TCGGATTTAGACTAATTTAAAGTCAAATCGTG

               
      19458 TCG
          1 TCG

      19461 ACTAATTTAG


Statistics
Matches: 34,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  32   34  1.00

ACGTcount: A:0.31, C:0.13, G:0.21, T:0.34


Consensus pattern (32 bp):   
TCGGATTTAGACTAATTTAAAGTCAAATCGTG

Found at i:19469 original size:25 final size:25

Alignment explanation


    Indices: 19435--19484  Score: 82
    Period size: 25  Copynumber: 2.0  Consensus size: 25

      19425 GTCGGATTTA

                                     
      19435 GACTAATTTAAAGTCAAATCGTGTC
          1 GACTAATTTAAAGTCAAATCGTGTC

                      *        *     
      19460 GACTAATTTAGAGTCAAATTGTGTC
          1 GACTAATTTAAAGTCAAATCGTGTC

      19485 AAACTTCAAA


Statistics
Matches: 23,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  25   23  1.00

ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34


Consensus pattern (25 bp):   
GACTAATTTAAAGTCAAATCGTGTC

Found at i:19506 original size:23 final size:23

Alignment explanation


    Indices: 19475--19521  Score: 76
    Period size: 23  Copynumber: 2.0  Consensus size: 23

      19465 ATTTAGAGTC

                *                  
      19475 AAATTGTGTCAAACTTCAAACAT
          1 AAATCGTGTCAAACTTCAAACAT

                      *            
      19498 AAATCGTGTCGAACTTCAAACAT
          1 AAATCGTGTCAAACTTCAAACAT

             
      19521 A
          1 A

      19522 CGACGTTTTC


Statistics
Matches: 22,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  23   22  1.00

ACGTcount: A:0.43, C:0.19, G:0.11, T:0.28


Consensus pattern (23 bp):   
AAATCGTGTCAAACTTCAAACAT

Found at i:22064 original size:21 final size:21

Alignment explanation


    Indices: 21999--22068  Score: 63
    Period size: 21  Copynumber: 3.4  Consensus size: 21

      21989 ACGAAAAAAA

                 *               
      21999 AATTAGAAAGATAATACTCAT
          1 AATTACAAAGATAATACTCAT

            *    *  **           *
      22020 GATTATAATTATAAATA-T-AA
          1 AATTACAAAGAT-AATACTCAT

                                 
      22040 AATTACAAAGATAATACTCAT
          1 AATTACAAAGATAATACTCAT

                    
      22061 AATTACAA
          1 AATTACAA

      22069 TGAATTGAGA


Statistics
Matches: 36,  Mismatches: 10, Indels: 6
        0.69            0.19        0.12

Matches are distributed among these distances:
  19    4  0.11
  20   10  0.28
  21   18  0.50
  22    4  0.11

ACGTcount: A:0.54, C:0.09, G:0.06, T:0.31


Consensus pattern (21 bp):   
AATTACAAAGATAATACTCAT
Done.