Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016495.1 Corchorus olitorius cultivar O-4 contig16528, 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: 15726
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29


Found at i:132 original size:15 final size:14

Alignment explanation


    Indices: 114--165  Score: 50
    Period size: 15  Copynumber: 3.5  Consensus size: 14

        104 TATAAAAAGT

                           
        114 AAATAATTAAATTAA
          1 AAATAA-TAAATTAA

                          *
        129 AAATAATAAATGTAT
          1 AAATAATAAAT-TAA

              *      *    
        144 AATTAATAATTTAA
          1 AAATAATAAATTAA

                    
        158 TAAATAAT
          1 -AAATAAT

        166 TGAAAATCAT


Statistics
Matches: 30,  Mismatches: 5, Indels: 4
        0.77            0.13        0.10

Matches are distributed among these distances:
  14    7  0.23
  15   23  0.77

ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37


Consensus pattern (14 bp):   
AAATAATAAATTAA

Found at i:6061 original size:35 final size:35

Alignment explanation


    Indices: 6018--6105  Score: 176
    Period size: 35  Copynumber: 2.5  Consensus size: 35

       6008 TTGGTCAATT

                                               
       6018 TTTGGTCAATTTTCGATAAGCTTGCCTCTAAGCAA
          1 TTTGGTCAATTTTCGATAAGCTTGCCTCTAAGCAA

                                               
       6053 TTTGGTCAATTTTCGATAAGCTTGCCTCTAAGCAA
          1 TTTGGTCAATTTTCGATAAGCTTGCCTCTAAGCAA

                              
       6088 TTTGGTCAATTTTCGATA
          1 TTTGGTCAATTTTCGATA

       6106 TCTCAACCAG


Statistics
Matches: 53,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  35   53  1.00

ACGTcount: A:0.25, C:0.18, G:0.17, T:0.40


Consensus pattern (35 bp):   
TTTGGTCAATTTTCGATAAGCTTGCCTCTAAGCAA

Found at i:6356 original size:7 final size:7

Alignment explanation


    Indices: 6344--6368  Score: 50
    Period size: 7  Copynumber: 3.6  Consensus size: 7

       6334 ATTTCAGTGG

                   
       6344 CAAGGCA
          1 CAAGGCA

                   
       6351 CAAGGCA
          1 CAAGGCA

                   
       6358 CAAGGCA
          1 CAAGGCA

                
       6365 CAAG
          1 CAAG

       6369 ATACAAGATA


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   18  1.00

ACGTcount: A:0.44, C:0.28, G:0.28, T:0.00


Consensus pattern (7 bp):   
CAAGGCA

Found at i:14073 original size:4 final size:4

Alignment explanation


    Indices: 14064--14089  Score: 52
    Period size: 4  Copynumber: 6.5  Consensus size: 4

      14054 TGGTTCTTTA

                                            
      14064 AAAT AAAT AAAT AAAT AAAT AAAT AA
          1 AAAT AAAT AAAT AAAT AAAT AAAT AA

      14090 TAGGATCATT


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

Matches are distributed among these distances:
   4   22  1.00

ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23


Consensus pattern (4 bp):   
AAAT

Found at i:14362 original size:16 final size:16

Alignment explanation


    Indices: 14341--14371  Score: 62
    Period size: 16  Copynumber: 1.9  Consensus size: 16

      14331 CCTTTATTTA

                            
      14341 TTCAGAAAACATAAAT
          1 TTCAGAAAACATAAAT

                           
      14357 TTCAGAAAACATAAA
          1 TTCAGAAAACATAAA

      14372 ACAAAATATA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   15  1.00

ACGTcount: A:0.58, C:0.13, G:0.06, T:0.23


Consensus pattern (16 bp):   
TTCAGAAAACATAAAT

Found at i:14406 original size:20 final size:20

Alignment explanation


    Indices: 14367--14407  Score: 57
    Period size: 20  Copynumber: 2.0  Consensus size: 20

      14357 TTCAGAAAAC

                           *    
      14367 ATAAAACAAAATATATTATT
          1 ATAAAACAAAATATACTATT

                                 
      14387 ATAAAA-AAAATAATACTATT
          1 ATAAAACAAAAT-ATACTATT

             
      14407 A
          1 A

      14408 GAGCGGGTGA


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  19    5  0.26
  20   14  0.74

ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32


Consensus pattern (20 bp):   
ATAAAACAAAATATACTATT
Done.