Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014277.1 Corchorus olitorius cultivar O-4 contig14310, 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: 24033
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29


Found at i:3001 original size:11 final size:11

Alignment explanation


    Indices: 2985--3032  Score: 50
    Period size: 11  Copynumber: 4.7  Consensus size: 11

       2975 GAAGTTCGTG

                       
       2985 TTTGAAGACCA
          1 TTTGAAGACCA

                    ** 
       2996 TTTGAAGATAA
          1 TTTGAAGACCA

                       
       3007 TTTGAAGA-C-
          1 TTTGAAGACCA

                       
       3016 -TTGAAGACCA
          1 TTTGAAGACCA

                    
       3026 -TTGAAGA
          1 TTTGAAGA

       3033 TTTTGATGCC


Statistics
Matches: 32,  Mismatches: 3, Indels: 5
        0.80            0.08        0.12

Matches are distributed among these distances:
   8    7  0.22
   9    1  0.03
  10    7  0.22
  11   17  0.53

ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29


Consensus pattern (11 bp):   
TTTGAAGACCA

Found at i:4444 original size:15 final size:16

Alignment explanation


    Indices: 4414--4451  Score: 69
    Period size: 15  Copynumber: 2.4  Consensus size: 16

       4404 TTACTTTGCT

                            
       4414 TTGTTTTCTAGTTTAA
          1 TTGTTTTCTAGTTTAA

                            
       4430 TTGTTTTCT-GTTTAA
          1 TTGTTTTCTAGTTTAA

                   
       4445 TTGTTTT
          1 TTGTTTT

       4452 ATGTCAACCT


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15   13  0.59
  16    9  0.41

ACGTcount: A:0.13, C:0.05, G:0.13, T:0.68


Consensus pattern (16 bp):   
TTGTTTTCTAGTTTAA

Found at i:12007 original size:10 final size:10

Alignment explanation


    Indices: 11992--12024  Score: 66
    Period size: 10  Copynumber: 3.3  Consensus size: 10

      11982 CCAAATTCTC

                      
      11992 TCTTCCATTT
          1 TCTTCCATTT

                      
      12002 TCTTCCATTT
          1 TCTTCCATTT

                      
      12012 TCTTCCATTT
          1 TCTTCCATTT

               
      12022 TCT
          1 TCT

      12025 CTTCGACCCA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   23  1.00

ACGTcount: A:0.09, C:0.30, G:0.00, T:0.61


Consensus pattern (10 bp):   
TCTTCCATTT

Found at i:14097 original size:24 final size:24

Alignment explanation


    Indices: 14063--14179  Score: 189
    Period size: 24  Copynumber: 4.9  Consensus size: 24

      14053 GGTCAGAGAG

                       *            
      14063 AAAATGTTGGTCATGGTGGGGCTC
          1 AAAATGTTGGTAATGGTGGGGCTC

                  *                 
      14087 AAAATGCTGGTAATGGTGGGGCTC
          1 AAAATGTTGGTAATGGTGGGGCTC

                  *                 
      14111 AAAATGCTGGTAATGGTGGGGCTC
          1 AAAATGTTGGTAATGGTGGGGCTC

                                    
      14135 AAAATGTTGGTAATGGTGGGGCTC
          1 AAAATGTTGGTAATGGTGGGGCTC

                       *   *     
      14159 AAAATGTTGGTGATGTTGGGG
          1 AAAATGTTGGTAATGGTGGGG

      14180 GTGAGGCTGT


Statistics
Matches: 88,  Mismatches: 5, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  24   88  1.00

ACGTcount: A:0.24, C:0.09, G:0.38, T:0.28


Consensus pattern (24 bp):   
AAAATGTTGGTAATGGTGGGGCTC

Found at i:17302 original size:20 final size:20

Alignment explanation


    Indices: 17277--17318  Score: 84
    Period size: 20  Copynumber: 2.1  Consensus size: 20

      17267 TGAAACCAGT

                                
      17277 TTATGGTTGTTGTTTTAATG
          1 TTATGGTTGTTGTTTTAATG

                                
      17297 TTATGGTTGTTGTTTTAATG
          1 TTATGGTTGTTGTTTTAATG

              
      17317 TT
          1 TT

      17319 TATTTTGAAC


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   22  1.00

ACGTcount: A:0.14, C:0.00, G:0.24, T:0.62


Consensus pattern (20 bp):   
TTATGGTTGTTGTTTTAATG

Found at i:18210 original size:21 final size:21

Alignment explanation


    Indices: 18186--18232  Score: 67
    Period size: 21  Copynumber: 2.2  Consensus size: 21

      18176 AGACAAGGAT

                    *  *         
      18186 AAGAACGAGAAGAAGAAGAAG
          1 AAGAACGACAACAAGAAGAAG

                             *   
      18207 AAGAACGACAACAAGAATAAG
          1 AAGAACGACAACAAGAAGAAG

                 
      18228 AAGAA
          1 AAGAA

      18233 TAACAATAAA


Statistics
Matches: 23,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  21   23  1.00

ACGTcount: A:0.64, C:0.09, G:0.26, T:0.02


Consensus pattern (21 bp):   
AAGAACGACAACAAGAAGAAG

Found at i:18238 original size:21 final size:21

Alignment explanation


    Indices: 18198--18238  Score: 55
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      18188 GAACGAGAAG

                           *     
      18198 AAGAAGAAGAAGAACGACAAC
          1 AAGAAGAAGAAGAACAACAAC

                 *        *     
      18219 AAGAATAAGAAGAATAACAA
          1 AAGAAGAAGAAGAACAACAA

      18239 TAAACCCTAA


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.66, C:0.10, G:0.20, T:0.05


Consensus pattern (21 bp):   
AAGAAGAAGAAGAACAACAAC
Done.