Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008503.1 Corchorus olitorius cultivar O-4 contig08530, 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: 1998
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:1407 original size:124 final size:124

Alignment explanation


    Indices: 1187--1440  Score: 490
    Period size: 124  Copynumber: 2.0  Consensus size: 124

       1177 ACCAGCATAG

                                                                     *       
       1187 TACTACATCTTAACAAAACAACTAGAAATTAAGAGGCTCTCCTATTTGAGAGAACACTACAAACA
          1 TACTACATCTTAACAAAACAACTAGAAATTAAGAGGCTCTCCTATTTGAGAGAACACAACAAACA

                                                                       
       1252 CACACCTTAGGTGGAAAACCTTAGGTACCCAACACACAGACAAAGACATATGCCAAAGT
         66 CACACCTTAGGTGGAAAACCTTAGGTACCCAACACACAGACAAAGACATATGCCAAAGT

                                                                             
       1311 TACTACATCTTAACAAAACAACTAGAAATTAAGAGGCTCTCCTATTTGAGAGAACACAACAAACA
          1 TACTACATCTTAACAAAACAACTAGAAATTAAGAGGCTCTCCTATTTGAGAGAACACAACAAACA

                                                                       
       1376 CACACCTTAGGTGGAAAACCTTAGGTACCCAACACACAGACAAAGACATATGCCAAAGT
         66 CACACCTTAGGTGGAAAACCTTAGGTACCCAACACACAGACAAAGACATATGCCAAAGT

            *     
       1435 CACTAC
          1 TACTAC

       1441 TCCCTACCAA


Statistics
Matches: 128,  Mismatches: 2, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
 124  128  1.00

ACGTcount: A:0.43, C:0.25, G:0.13, T:0.19


Consensus pattern (124 bp):   
TACTACATCTTAACAAAACAACTAGAAATTAAGAGGCTCTCCTATTTGAGAGAACACAACAAACA
CACACCTTAGGTGGAAAACCTTAGGTACCCAACACACAGACAAAGACATATGCCAAAGT

Found at i:1517 original size:77 final size:77

Alignment explanation


    Indices: 1390--1539  Score: 275
    Period size: 77  Copynumber: 1.9  Consensus size: 77

       1380 CCTTAGGTGG

                       *                                                     
       1390 AAAACCTTAGGTACCCAACACACAGACAAAGACATATGCCAAAGTCACTACTCCCTACCAATGCA
          1 AAAACCTTAGGCACCCAACACACAGACAAAGACATATGCCAAAGTCACTACTCCCTACCAATGCA

                        
       1455 CAATGATCTGGA
         66 CAATGATCTGGA

                                                                             
       1467 AAAACCTTAGGCACCCAACACACAGA-AAGAGACATATGCCAAAGTCACTACTCCCTACCAATGC
          1 AAAACCTTAGGCACCCAACACACAGACAA-AGACATATGCCAAAGTCACTACTCCCTACCAATGC

                     
       1531 ACAATGATC
         65 ACAATGATC

       1540 CCAAGCTCAT


Statistics
Matches: 71,  Mismatches: 1, Indels: 2
        0.96            0.01        0.03

Matches are distributed among these distances:
  76    2  0.03
  77   69  0.97

ACGTcount: A:0.41, C:0.31, G:0.13, T:0.16


Consensus pattern (77 bp):   
AAAACCTTAGGCACCCAACACACAGACAAAGACATATGCCAAAGTCACTACTCCCTACCAATGCA
CAATGATCTGGA

Found at i:1960 original size:2 final size:2

Alignment explanation


    Indices: 1953--1978  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       1943 GCATTTGGAG

                                                  
       1953 AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT

       1979 GAGAGAGAGA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.