Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002296.1 Corchorus olitorius cultivar O-4 contig02296, 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: 4313
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33


Found at i:743 original size:17 final size:18

Alignment explanation


    Indices: 714--748  Score: 54
    Period size: 17  Copynumber: 2.0  Consensus size: 18

        704 AAAATCCTTC

                              
        714 CAAATCGAAACCCAAAAT
          1 CAAATCGAAACCCAAAAT

                         *    
        732 CAAATC-AAACCCTAAAT
          1 CAAATCGAAACCCAAAAT

        749 TGGCCTTTGA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  17   10  0.62
  18    6  0.38

ACGTcount: A:0.54, C:0.29, G:0.03, T:0.14


Consensus pattern (18 bp):   
CAAATCGAAACCCAAAAT

Found at i:2009 original size:15 final size:14

Alignment explanation


    Indices: 1989--2029  Score: 55
    Period size: 15  Copynumber: 2.7  Consensus size: 14

       1979 GATGGAAGTA

                           
       1989 GGGAGGAAAAAAATT
          1 GGGAGGAAAAAAA-T

                           
       2004 GGGAGGAAGAAAAAT
          1 GGGAGGAA-AAAAAT

                       
       2019 GGGAGAGAAAA
          1 GGGAG-GAAAA

       2030 CAAGAGAAAT


Statistics
Matches: 24,  Mismatches: 0, Indels: 4
        0.86            0.00        0.14

Matches are distributed among these distances:
  15   16  0.67
  16    8  0.33

ACGTcount: A:0.54, C:0.00, G:0.39, T:0.07


Consensus pattern (14 bp):   
GGGAGGAAAAAAAT

Found at i:3208 original size:20 final size:21

Alignment explanation


    Indices: 3169--3211  Score: 61
    Period size: 23  Copynumber: 2.0  Consensus size: 21

       3159 CACATCACAT

                                   
       3169 CGTTTACTTTGACTAATTAGTAG
          1 CGTTTACTTTGA--AATTAGTAG

                                 
       3192 CGTTTACTTTG-AATTAGTAG
          1 CGTTTACTTTGAAATTAGTAG

       3212 AGAGTACAAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 3
        0.87            0.00        0.13

Matches are distributed among these distances:
  20    9  0.45
  23   11  0.55

ACGTcount: A:0.26, C:0.12, G:0.19, T:0.44


Consensus pattern (21 bp):   
CGTTTACTTTGAAATTAGTAG
Done.