Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011876.1 Corchorus olitorius cultivar O-4 contig11909, 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: 6497
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31


Found at i:1347 original size:13 final size:14

Alignment explanation


    Indices: 1331--1360  Score: 53
    Period size: 14  Copynumber: 2.2  Consensus size: 14

       1321 CAATTAAAGC

                          
       1331 AATAAT-CAAGGAA
          1 AATAATGCAAGGAA

                          
       1344 AATAATGCAAGGAA
          1 AATAATGCAAGGAA

               
       1358 AAT
          1 AAT

       1361 TAAAGAGATA


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13    6  0.38
  14   10  0.62

ACGTcount: A:0.60, C:0.07, G:0.17, T:0.17


Consensus pattern (14 bp):   
AATAATGCAAGGAA

Found at i:4943 original size:25 final size:25

Alignment explanation


    Indices: 4907--4963  Score: 73
    Period size: 26  Copynumber: 2.3  Consensus size: 25

       4897 AAACAAGAAA

                               *   * 
       4907 TTTTTTT-TTATGACGC-AGAAATT
          1 TTTTTTTATTATGACGCAAAAAACT

                                      
       4930 TTTTTTTATATATGACGCAAAAAACT
          1 TTTTTTTAT-TATGACGCAAAAAACT

                    
       4956 TTTTTTTA
          1 TTTTTTTA

       4964 AAAAATAACA


Statistics
Matches: 29,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  23    7  0.24
  24    1  0.03
  25    8  0.28
  26   13  0.45

ACGTcount: A:0.30, C:0.09, G:0.09, T:0.53


Consensus pattern (25 bp):   
TTTTTTTATTATGACGCAAAAAACT

Found at i:4998 original size:31 final size:29

Alignment explanation


    Indices: 4955--5021  Score: 82
    Period size: 31  Copynumber: 2.2  Consensus size: 29

       4945 CGCAAAAAAC

                           *               
       4955 TTTTTTTTAAAAAA-TAACACAAAAACTCTT
          1 TTTTTTTTAAAAAACCAACAC-AAAACT-TT

                                           
       4985 TTTTTTTTCAAAAAACGCAACACAAAACTTT
          1 TTTTTTTT-AAAAAAC-CAACACAAAACTTT

                  
       5016 TTTTTT
          1 TTTTTT

       5022 CTTTGACGCA


Statistics
Matches: 33,  Mismatches: 1, Indels: 5
        0.85            0.03        0.13

Matches are distributed among these distances:
  30    8  0.24
  31   14  0.42
  32    6  0.18
  33    5  0.15

ACGTcount: A:0.40, C:0.15, G:0.01, T:0.43


Consensus pattern (29 bp):   
TTTTTTTTAAAAAACCAACACAAAACTTT
Done.