Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002300.1 Corchorus olitorius cultivar O-4 contig02300, 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: 2337
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38


Found at i:254 original size:7 final size:7

Alignment explanation


    Indices: 230--262  Score: 52
    Period size: 7  Copynumber: 5.0  Consensus size: 7

        220 TGTTATCATT

                   
        230 ATATAT-
          1 ATATATG

                   
        236 ATATAT-
          1 ATATATG

                   
        242 ATATATG
          1 ATATATG

                   
        249 ATATATG
          1 ATATATG

                   
        256 ATATATG
          1 ATATATG

        263 GTGACAAAAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   6   12  0.46
   7   14  0.54

ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45


Consensus pattern (7 bp):   
ATATATG

Found at i:1255 original size:29 final size:29

Alignment explanation


    Indices: 1222--1344  Score: 219
    Period size: 29  Copynumber: 4.2  Consensus size: 29

       1212 CTTTTTCAAA

                   *                     
       1222 AGTTCAGGGGCTTATTTGGCTACAATTAG
          1 AGTTCAGAGGCTTATTTGGCTACAATTAG

                                         
       1251 AGTTCAGAGGCTTATTTGGCTACAATTAG
          1 AGTTCAGAGGCTTATTTGGCTACAATTAG

                *             *          
       1280 AGTTTAGAGGCTTATTTGACTACAATTAG
          1 AGTTCAGAGGCTTATTTGGCTACAATTAG

                                         
       1309 AGTTCAGAGGCTTATTTGGCTACAATTAG
          1 AGTTCAGAGGCTTATTTGGCTACAATTAG

                   
       1338 AGTTCAG
          1 AGTTCAG

       1345 GGGCCTTTTG


Statistics
Matches: 89,  Mismatches: 5, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  29   89  1.00

ACGTcount: A:0.28, C:0.13, G:0.24, T:0.35


Consensus pattern (29 bp):   
AGTTCAGAGGCTTATTTGGCTACAATTAG

Found at i:2291 original size:3 final size:3

Alignment explanation


    Indices: 2283--2321  Score: 78
    Period size: 3  Copynumber: 13.0  Consensus size: 3

       2273 TTATATAAAT

                                                               
       2283 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
          1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA

       2322 TATTATTATT


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   36  1.00

ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33


Consensus pattern (3 bp):   
ATA

Done.