Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011121.1 Corchorus olitorius cultivar O-4 contig11154, 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: 28972
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30


Found at i:4756 original size:61 final size:61

Alignment explanation


    Indices: 4637--4756  Score: 143
    Period size: 61  Copynumber: 2.0  Consensus size: 61

       4627 GTCGGATATC

                *          *       *      * *   *                        
       4637 AAGGGACTTTTCCTCCTTTGGAGTCCGATGTAGTTCCACTTCAAACTAATCGGGATTGTCT
          1 AAGGAACTTTTCCTCATTTGGAGGCCGATGCAATTCAACTTCAAACTAATCGGGATTGTCT

                                                      *   *  *          
       4698 AAGGAACTTTTCCTCATTT-GAGGCCTGATGCAATTCAACTTTAAATTAGTCGGGATTGT
          1 AAGGAACTTTTCCTCATTTGGAGGCC-GATGCAATTCAACTTCAAACTAATCGGGATTGT

       4757 GGATACTAAG


Statistics
Matches: 49,  Mismatches: 9, Indels: 2
        0.82            0.15        0.03

Matches are distributed among these distances:
  60    5  0.10
  61   44  0.90

ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35


Consensus pattern (61 bp):   
AAGGAACTTTTCCTCATTTGGAGGCCGATGCAATTCAACTTCAAACTAATCGGGATTGTCT

Found at i:14771 original size:18 final size:18

Alignment explanation


    Indices: 14743--14783  Score: 75
    Period size: 18  Copynumber: 2.3  Consensus size: 18

      14733 CATTGGCTTG

                              
      14743 AGTTT-GCCTCTAATGAT
          1 AGTTTCGCCTCTAATGAT

                              
      14760 AGTTTCGCCTCTAATGAT
          1 AGTTTCGCCTCTAATGAT

                  
      14778 AGTTTC
          1 AGTTTC

      14784 AAATGGTTAA


Statistics
Matches: 23,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  17    5  0.22
  18   18  0.78

ACGTcount: A:0.22, C:0.20, G:0.17, T:0.41


Consensus pattern (18 bp):   
AGTTTCGCCTCTAATGAT

Found at i:17654 original size:2 final size:2

Alignment explanation


    Indices: 17649--17683  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

      17639 CATGTCGTTA

                                                                
      17649 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A

      17684 CCTCCAGACT


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00


Consensus pattern (2 bp):   
AG

Found at i:19831 original size:2 final size:2

Alignment explanation


    Indices: 19824--19860  Score: 60
    Period size: 2  Copynumber: 19.5  Consensus size: 2

      19814 AGCAACCAAC

                                                                      
      19824 AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G A- AG AG AG A
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A

      19861 CGTACCTTAT


Statistics
Matches: 33,  Mismatches: 0, Indels: 4
        0.89            0.00        0.11

Matches are distributed among these distances:
   1    2  0.06
   2   31  0.94

ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00


Consensus pattern (2 bp):   
AG

Found at i:24153 original size:15 final size:15

Alignment explanation


    Indices: 24133--24174  Score: 66
    Period size: 15  Copynumber: 2.8  Consensus size: 15

      24123 ATAGAAAAAA

                           
      24133 ATATACTTCCTACCG
          1 ATATACTTCCTACCG

                    **     
      24148 ATATACTTGATACCG
          1 ATATACTTCCTACCG

                        
      24163 ATATACTTCCTA
          1 ATATACTTCCTA

      24175 ACTTTGACCT


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  15   23  1.00

ACGTcount: A:0.31, C:0.26, G:0.07, T:0.36


Consensus pattern (15 bp):   
ATATACTTCCTACCG

Found at i:24351 original size:20 final size:20

Alignment explanation


    Indices: 24326--24366  Score: 82
    Period size: 20  Copynumber: 2.0  Consensus size: 20

      24316 ATGTATGATT

                                
      24326 GGTTTGACCCAAAAGGAACA
          1 GGTTTGACCCAAAAGGAACA

                                
      24346 GGTTTGACCCAAAAGGAACA
          1 GGTTTGACCCAAAAGGAACA

             
      24366 G
          1 G

      24367 ATAATATGAG


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   21  1.00

ACGTcount: A:0.39, C:0.20, G:0.27, T:0.15


Consensus pattern (20 bp):   
GGTTTGACCCAAAAGGAACA
Done.