Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017740.1 Corchorus olitorius cultivar O-4 contig17773, 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: 35515
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32


Found at i:2929 original size:40 final size:40

Alignment explanation


    Indices: 2874--2970  Score: 176
    Period size: 40  Copynumber: 2.4  Consensus size: 40

       2864 CGATAACAAT

                                                    
       2874 ACATACATGCATTAGAATCAGAAAGGGAAATAGAAGGTGA
          1 ACATACATGCATTAGAATCAGAAAGGGAAATAGAAGGTGA

                                *        *          
       2914 ACATACATGCATTAGAATCATAAAGGGAATTAGAAGGTGA
          1 ACATACATGCATTAGAATCAGAAAGGGAAATAGAAGGTGA

                             
       2954 ACATACATGCATTAGAA
          1 ACATACATGCATTAGAA

       2971 GGTGATTTAG


Statistics
Matches: 55,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  40   55  1.00

ACGTcount: A:0.46, C:0.11, G:0.22, T:0.21


Consensus pattern (40 bp):   
ACATACATGCATTAGAATCAGAAAGGGAAATAGAAGGTGA

Found at i:2967 original size:22 final size:22

Alignment explanation


    Indices: 2904--2975  Score: 73
    Period size: 22  Copynumber: 3.5  Consensus size: 22

       2894 GAAAGGGAAA

                                  
       2904 TAGAAGGTGAACATACATGCAT
          1 TAGAAGGTGAACATACATGCAT

                           *  * *  
       2926 TAGAA--T---CATAAAGGGAAT
          1 TAGAAGGTGAACATACA-TGCAT

                                  
       2944 TAGAAGGTGAACATACATGCAT
          1 TAGAAGGTGAACATACATGCAT

                      
       2966 TAGAAGGTGA
          1 TAGAAGGTGA

       2976 TTTAGGACCC


Statistics
Matches: 38,  Mismatches: 6, Indels: 12
        0.68            0.11        0.21

Matches are distributed among these distances:
  17    5  0.13
  18    8  0.21
  20    2  0.05
  22   18  0.47
  23    5  0.13

ACGTcount: A:0.43, C:0.10, G:0.25, T:0.22


Consensus pattern (22 bp):   
TAGAAGGTGAACATACATGCAT

Found at i:14310 original size:30 final size:27

Alignment explanation


    Indices: 14276--14335  Score: 84
    Period size: 30  Copynumber: 2.1  Consensus size: 27

      14266 CCTGGAGCCA

                         *                
      14276 TTGACATTGGGCTTGGAGCTGCCATTGGAG
          1 TTGACATTGGGCTAGGAG-T--CATTGGAG

                                       
      14306 TTGACATTGGGCTAGGAGTCATTGGAG
          1 TTGACATTGGGCTAGGAGTCATTGGAG

               
      14333 TTG
          1 TTG

      14336 TTGTTGGAGC


Statistics
Matches: 29,  Mismatches: 1, Indels: 3
        0.88            0.03        0.09

Matches are distributed among these distances:
  27   11  0.38
  29    1  0.03
  30   17  0.59

ACGTcount: A:0.18, C:0.13, G:0.37, T:0.32


Consensus pattern (27 bp):   
TTGACATTGGGCTAGGAGTCATTGGAG

Found at i:14370 original size:21 final size:21

Alignment explanation


    Indices: 14346--14413  Score: 61
    Period size: 21  Copynumber: 3.2  Consensus size: 21

      14336 TTGTTGGAGC

                                 
      14346 CATGGAAGGAGGAGGGCTGGA
          1 CATGGAAGGAGGAGGGCTGGA

                     *  *          *
      14367 CATGGTCGACGGTGGA-GG-T-GC
          1 CAT-G--GAAGGAGGAGGGCTGGA

                                 
      14388 CATGGAAGGAGGAGGGCTGGA
          1 CATGGAAGGAGGAGGGCTGGA

                 
      14409 CATGG
          1 CATGG

      14414 TCGACGGTGG


Statistics
Matches: 35,  Mismatches: 6, Indels: 12
        0.66            0.11        0.23

Matches are distributed among these distances:
  18    7  0.20
  19    2  0.06
  20    2  0.06
  21   13  0.37
  22    2  0.06
  23    2  0.06
  24    7  0.20

ACGTcount: A:0.24, C:0.13, G:0.50, T:0.13


Consensus pattern (21 bp):   
CATGGAAGGAGGAGGGCTGGA

Found at i:14391 original size:42 final size:42

Alignment explanation


    Indices: 14344--14434  Score: 182
    Period size: 42  Copynumber: 2.2  Consensus size: 42

      14334 TGTTGTTGGA

                                                      
      14344 GCCATGGAAGGAGGAGGGCTGGACATGGTCGACGGTGGAGGT
          1 GCCATGGAAGGAGGAGGGCTGGACATGGTCGACGGTGGAGGT

                                                      
      14386 GCCATGGAAGGAGGAGGGCTGGACATGGTCGACGGTGGAGGT
          1 GCCATGGAAGGAGGAGGGCTGGACATGGTCGACGGTGGAGGT

                   
      14428 GCCATGG
          1 GCCATGG

      14435 TGGTTGTCGG


Statistics
Matches: 49,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  42   49  1.00

ACGTcount: A:0.21, C:0.15, G:0.49, T:0.14


Consensus pattern (42 bp):   
GCCATGGAAGGAGGAGGGCTGGACATGGTCGACGGTGGAGGT

Found at i:14433 original size:21 final size:21

Alignment explanation


    Indices: 14367--14435  Score: 63
    Period size: 21  Copynumber: 3.3  Consensus size: 21

      14357 GAGGGCTGGA

                                 
      14367 CATGGTCGACGGTGGAGGTGC
          1 CATGGTCGACGGTGGAGGTGC

                     *  *          *
      14388 CAT-G--GAAGGAGGAGGGCTGGA
          1 CATGGTCGACGGTGGA-GG-T-GC

                                 
      14409 CATGGTCGACGGTGGAGGTGC
          1 CATGGTCGACGGTGGAGGTGC

                  
      14430 CATGGT
          1 CATGGT

      14436 GGTTGTCGGC


Statistics
Matches: 36,  Mismatches: 6, Indels: 12
        0.67            0.11        0.22

Matches are distributed among these distances:
  18    7  0.19
  19    2  0.06
  20    2  0.06
  21   14  0.39
  22    2  0.06
  23    2  0.06
  24    7  0.19

ACGTcount: A:0.19, C:0.16, G:0.48, T:0.17


Consensus pattern (21 bp):   
CATGGTCGACGGTGGAGGTGC
Done.