Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012457.1 Corchorus olitorius cultivar O-4 contig12490, 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: 8630
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30


Found at i:1904 original size:6 final size:6

Alignment explanation


    Indices: 1893--1923  Score: 53
    Period size: 6  Copynumber: 5.2  Consensus size: 6

       1883 AGGAACAAGC

                                      *         
       1893 AACACA AACACA AACACA AACACG AACACA A
          1 AACACA AACACA AACACA AACACA AACACA A

       1924 TGAGGCTACT


Statistics
Matches: 23,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
   6   23  1.00

ACGTcount: A:0.65, C:0.32, G:0.03, T:0.00


Consensus pattern (6 bp):   
AACACA

Found at i:4583 original size:21 final size:21

Alignment explanation


    Indices: 4557--4613  Score: 105
    Period size: 21  Copynumber: 2.7  Consensus size: 21

       4547 TTTCGCCTTC

                       *         
       4557 CCTTTCTTTGCGGACCCGGAT
          1 CCTTTCTTTGCAGACCCGGAT

                                 
       4578 CCTTTCTTTGCAGACCCGGAT
          1 CCTTTCTTTGCAGACCCGGAT

                           
       4599 CCTTTCTTTGCAGAC
          1 CCTTTCTTTGCAGAC

       4614 TTCTTATTAA


Statistics
Matches: 35,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  21   35  1.00

ACGTcount: A:0.12, C:0.33, G:0.19, T:0.35


Consensus pattern (21 bp):   
CCTTTCTTTGCAGACCCGGAT

Found at i:8056 original size:19 final size:19

Alignment explanation


    Indices: 8016--8052  Score: 67
    Period size: 19  Copynumber: 2.0  Consensus size: 19

       8006 GAGTAACAAG

                               
       8016 TAAAAATATAATATATAAA
          1 TAAAAATATAATATATAAA

                               
       8035 TAAAAATATAATA-ATAAA
          1 TAAAAATATAATATATAAA

       8053 ATAATTAATT


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  18    5  0.28
  19   13  0.72

ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30


Consensus pattern (19 bp):   
TAAAAATATAATATATAAA
Done.