Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011850.1 Corchorus olitorius cultivar O-4 contig11883, 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: 30001
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30


Found at i:4057 original size:25 final size:25

Alignment explanation


    Indices: 4029--4079  Score: 93
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       4019 AGAAGAGAGC

                            *        
       4029 ATATTTATAGGGGGAGTGTAGTTAA
          1 ATATTTATAGGGGGAGAGTAGTTAA

                                     
       4054 ATATTTATAGGGGGAGAGTAGTTAA
          1 ATATTTATAGGGGGAGAGTAGTTAA

             
       4079 A
          1 A

       4080 GGGTTTGTGT


Statistics
Matches: 25,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  25   25  1.00

ACGTcount: A:0.35, C:0.00, G:0.31, T:0.33


Consensus pattern (25 bp):   
ATATTTATAGGGGGAGAGTAGTTAA

Found at i:8078 original size:18 final size:18

Alignment explanation


    Indices: 8055--8091  Score: 74
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       8045 AATCGCACAC

                              
       8055 CCCTAGCGGGGACACGGA
          1 CCCTAGCGGGGACACGGA

                              
       8073 CCCTAGCGGGGACACGGA
          1 CCCTAGCGGGGACACGGA

             
       8091 C
          1 C

       8092 ACCAGGTTTA


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   19  1.00

ACGTcount: A:0.22, C:0.35, G:0.38, T:0.05


Consensus pattern (18 bp):   
CCCTAGCGGGGACACGGA

Found at i:11266 original size:15 final size:16

Alignment explanation


    Indices: 11239--11268  Score: 53
    Period size: 15  Copynumber: 1.9  Consensus size: 16

      11229 TTAGCACTGA

                            
      11239 CAAGTTGATTGATGAG
          1 CAAGTTGATTGATGAG

                           
      11255 CAAGTT-ATTGATGA
          1 CAAGTTGATTGATGA

      11269 ATATGGTATG


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    8  0.57
  16    6  0.43

ACGTcount: A:0.33, C:0.07, G:0.27, T:0.33


Consensus pattern (16 bp):   
CAAGTTGATTGATGAG

Found at i:22463 original size:13 final size:13

Alignment explanation


    Indices: 22445--22471  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

      22435 CAAAATTGCC

                         
      22445 TAATTAATATAAA
          1 TAATTAATATAAA

                         
      22458 TAATTAATATAAA
          1 TAATTAATATAAA

             
      22471 T
          1 T

      22472 GGTATGGGGT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41


Consensus pattern (13 bp):   
TAATTAATATAAA

Found at i:24378 original size:20 final size:20

Alignment explanation


    Indices: 24350--24390  Score: 73
    Period size: 20  Copynumber: 2.0  Consensus size: 20

      24340 TTCTAAAAAT

                *               
      24350 AATATTTTATGAAAACTCCC
          1 AATACTTTATGAAAACTCCC

                                
      24370 AATACTTTATGAAAACTCCC
          1 AATACTTTATGAAAACTCCC

             
      24390 A
          1 A

      24391 TATAAATTTC


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.41, C:0.22, G:0.05, T:0.32


Consensus pattern (20 bp):   
AATACTTTATGAAAACTCCC

Found at i:26129 original size:15 final size:16

Alignment explanation


    Indices: 26109--26152  Score: 56
    Period size: 15  Copynumber: 2.8  Consensus size: 16

      26099 GCAAAGTTAA

                            
      26109 GAAAAACACAAAA-AC
          1 GAAAAACACAAAATAC

                            
      26124 GAAAAACA-AAAATAC
          1 GAAAAACACAAAATAC

                   *      
      26139 GAAACAAAACAAAA
          1 GAAA-AACACAAAA

      26153 CAAAACTAAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 4
        0.83            0.03        0.13

Matches are distributed among these distances:
  14    4  0.16
  15   14  0.56
  16    3  0.12
  17    4  0.16

ACGTcount: A:0.75, C:0.16, G:0.07, T:0.02


Consensus pattern (16 bp):   
GAAAAACACAAAATAC
Done.