Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022391.1 Corchorus olitorius cultivar O-4 contig22424, 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: 9407
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29


Found at i:2614 original size:31 final size:31

Alignment explanation


    Indices: 2576--2637  Score: 124
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       2566 CTGATTCCCA

                                           
       2576 AGCCTGAAGAAAGTATTAGGAAGAGCGATAT
          1 AGCCTGAAGAAAGTATTAGGAAGAGCGATAT

                                           
       2607 AGCCTGAAGAAAGTATTAGGAAGAGCGATAT
          1 AGCCTGAAGAAAGTATTAGGAAGAGCGATAT

       2638 CCTTTATCTG


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  31   31  1.00

ACGTcount: A:0.42, C:0.10, G:0.29, T:0.19


Consensus pattern (31 bp):   
AGCCTGAAGAAAGTATTAGGAAGAGCGATAT

Found at i:3047 original size:21 final size:21

Alignment explanation


    Indices: 3021--3063  Score: 86
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       3011 TTTGGATAGG

                                 
       3021 TTCTTAACCTTCATACATAAA
          1 TTCTTAACCTTCATACATAAA

                                 
       3042 TTCTTAACCTTCATACATAAA
          1 TTCTTAACCTTCATACATAAA

             
       3063 T
          1 T

       3064 AAGGAAAAAC


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

Matches are distributed among these distances:
  21   22  1.00

ACGTcount: A:0.37, C:0.23, G:0.00, T:0.40


Consensus pattern (21 bp):   
TTCTTAACCTTCATACATAAA

Found at i:6263 original size:19 final size:19

Alignment explanation


    Indices: 6241--6291  Score: 54
    Period size: 19  Copynumber: 2.7  Consensus size: 19

       6231 AGGCTGAAAT

                               
       6241 TAATTAATTATTAATT-AA
          1 TAATTAATTATTAATTGAA

                          *      
       6259 GTAA-TAATTATTTTATTGAA
          1 -TAATTAATTA-TTAATTGAA

                          
       6279 TAATT-ATTATTAA
          1 TAATTAATTATTAA

       6292 GAATCTTATG


Statistics
Matches: 27,  Mismatches: 2, Indels: 7
        0.75            0.06        0.19

Matches are distributed among these distances:
  18    9  0.33
  19   15  0.56
  20    3  0.11

ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51


Consensus pattern (19 bp):   
TAATTAATTATTAATTGAA

Found at i:6295 original size:16 final size:16

Alignment explanation


    Indices: 6245--6295  Score: 59
    Period size: 16  Copynumber: 3.1  Consensus size: 16

       6235 TGAAATTAAT

                              
       6245 TAATTATTAATTAAGTAA
          1 TAATTATT-ATTAAG-AA

                         *   
       6263 TAATTATT-TTATTGAA
          1 TAATTATTATTA-AGAA

                            
       6279 TAATTATTATTAAGAA
          1 TAATTATTATTAAGAA

             
       6295 T
          1 T

       6296 CTTATGTGTG


Statistics
Matches: 29,  Mismatches: 2, Indels: 6
        0.78            0.05        0.16

Matches are distributed among these distances:
  16   17  0.59
  17    4  0.14
  18    8  0.28

ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49


Consensus pattern (16 bp):   
TAATTATTATTAAGAA

Found at i:8085 original size:27 final size:28

Alignment explanation


    Indices: 8035--8087  Score: 74
    Period size: 28  Copynumber: 1.9  Consensus size: 28

       8025 AGTAAGTTTC

                     *                  
       8035 TGTTTTGGTTTGTTTGATATTTGAATCT
          1 TGTTTTGGTGTGTTTGATATTTGAATCT

                                       
       8063 TGTTTTGGTGT-TTTGAGTA-TTGAAT
          1 TGTTTTGGTGTGTTTGA-TATTTGAAT

       8088 ATGTTTCGAG


Statistics
Matches: 23,  Mismatches: 1, Indels: 3
        0.85            0.04        0.11

Matches are distributed among these distances:
  27   11  0.48
  28   12  0.52

ACGTcount: A:0.15, C:0.02, G:0.25, T:0.58


Consensus pattern (28 bp):   
TGTTTTGGTGTGTTTGATATTTGAATCT
Done.