Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019905.1 Corchorus olitorius cultivar O-4 contig19938, 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: 10511
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34


Found at i:688 original size:20 final size:20

Alignment explanation


    Indices: 663--703  Score: 82
    Period size: 20  Copynumber: 2.0  Consensus size: 20

        653 ATGAAAGTCT

                                
        663 AAGGCCCAAGGATGCAAATA
          1 AAGGCCCAAGGATGCAAATA

                                
        683 AAGGCCCAAGGATGCAAATA
          1 AAGGCCCAAGGATGCAAATA

             
        703 A
          1 A

        704 TTAAACAAGG


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:0.46, C:0.20, G:0.24, T:0.10


Consensus pattern (20 bp):   
AAGGCCCAAGGATGCAAATA

Found at i:1127 original size:27 final size:28

Alignment explanation


    Indices: 1096--1169  Score: 96
    Period size: 27  Copynumber: 2.7  Consensus size: 28

       1086 AAGTGAACCT

                              *         
       1096 AAAATGACCAAAATGCCCTTAGAT-GTG
          1 AAAATGACCAAAATGCCCCTAGATCGTG

            *       *           *    *  
       1123 CAAATGACTAAAATGCCCCTGGATCTTG
          1 AAAATGACCAAAATGCCCCTAGATCGTG

                               
       1151 AAAATGACCAAAATGCCCC
          1 AAAATGACCAAAATGCCCC

       1170 CTAGTTGATC


Statistics
Matches: 39,  Mismatches: 7, Indels: 1
        0.83            0.15        0.02

Matches are distributed among these distances:
  27   20  0.51
  28   19  0.49

ACGTcount: A:0.39, C:0.24, G:0.16, T:0.20


Consensus pattern (28 bp):   
AAAATGACCAAAATGCCCCTAGATCGTG

Found at i:1674 original size:26 final size:26

Alignment explanation


    Indices: 1638--1718  Score: 108
    Period size: 26  Copynumber: 3.1  Consensus size: 26

       1628 AAACTAGTAA

                *                      
       1638 TGAATTAAAAATGACTAAAAGTGCCCC
          1 TGAAGTAAAAATGACTAAAA-TGCCCC

                           *  *      *
       1665 TGAAGTAAAAATGACCAAGATGCCCT
          1 TGAAGTAAAAATGACTAAAATGCCCC

                   *                  
       1691 TGAAGTACAAATGACTAAAATGCCCC
          1 TGAAGTAAAAATGACTAAAATGCCCC

              
       1717 TG
          1 TG

       1719 GATGACTTTA


Statistics
Matches: 46,  Mismatches: 8, Indels: 1
        0.84            0.15        0.02

Matches are distributed among these distances:
  26   29  0.63
  27   17  0.37

ACGTcount: A:0.42, C:0.20, G:0.17, T:0.21


Consensus pattern (26 bp):   
TGAAGTAAAAATGACTAAAATGCCCC

Found at i:6096 original size:11 final size:11

Alignment explanation


    Indices: 6080--6111  Score: 55
    Period size: 11  Copynumber: 2.9  Consensus size: 11

       6070 CCATTGATCA

                       
       6080 ATTCTGTTTCG
          1 ATTCTGTTTCG

                       
       6091 ATTCTGTTTCG
          1 ATTCTGTTTCG

                 *    
       6102 ATTCTCTTTC
          1 ATTCTGTTTC

       6112 ACTGTTTATT


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  11   20  1.00

ACGTcount: A:0.09, C:0.22, G:0.12, T:0.56


Consensus pattern (11 bp):   
ATTCTGTTTCG

Found at i:7182 original size:16 final size:15

Alignment explanation


    Indices: 7142--7183  Score: 50
    Period size: 15  Copynumber: 2.8  Consensus size: 15

       7132 TCAGGAAAGT

                        *  
       7142 AAAAAC-ATAATTTG
          1 AAAAACAATAATATG

                *          
       7156 AAAATCAATAATATG
          1 AAAAACAATAATATG

                         
       7171 AATAAACAATAAT
          1 AA-AAACAATAAT

       7184 TATAGAATTT


Statistics
Matches: 23,  Mismatches: 3, Indels: 2
        0.82            0.11        0.07

Matches are distributed among these distances:
  14    5  0.22
  15    9  0.39
  16    9  0.39

ACGTcount: A:0.62, C:0.07, G:0.05, T:0.26


Consensus pattern (15 bp):   
AAAAACAATAATATG
Done.