Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022179.1 Corchorus olitorius cultivar O-4 contig22212, 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: 4753
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33


Found at i:537 original size:23 final size:23

Alignment explanation


    Indices: 511--586  Score: 77
    Period size: 23  Copynumber: 3.3  Consensus size: 23

        501 GATGGTGTGA

                                   
        511 AGAAATTTATACCATCAGGATGG
          1 AGAAATTTATACCATCAGGATGG

                   *     * *         
        534 AGAAATTGAT--CTTGATGG-TGTG
          1 AGAAATTTATACCATCA-GGATG-G

                                    
        556 AAGAAATTTATACCATCAGGATGG
          1 -AGAAATTTATACCATCAGGATGG

                   
        580 AGAAATT
          1 AGAAATT

        587 GATCCTGATG


Statistics
Matches: 41,  Mismatches: 6, Indels: 12
        0.69            0.10        0.20

Matches are distributed among these distances:
  21    5  0.12
  22    3  0.07
  23   25  0.61
  24    3  0.07
  25    5  0.12

ACGTcount: A:0.38, C:0.09, G:0.24, T:0.29


Consensus pattern (23 bp):   
AGAAATTTATACCATCAGGATGG

Found at i:550 original size:46 final size:46

Alignment explanation


    Indices: 491--677  Score: 295
    Period size: 46  Copynumber: 4.1  Consensus size: 46

        481 GGCAAAGCAG

                 *                                        
        491 AATTGGTCCTGATGGTGTGAAGAAATTTATACCATCAGGATGGAGA
          1 AATTGATCCTGATGGTGTGAAGAAATTTATACCATCAGGATGGAGA

                    *                                     
        537 AATTGATCTTGATGGTGTGAAGAAATTTATACCATCAGGATGGAGA
          1 AATTGATCCTGATGGTGTGAAGAAATTTATACCATCAGGATGGAGA

                                   *            *         
        583 AATTGATCCTGATGGTGTGAAGAGATTTATACCATCTGGATGGA-A
          1 AATTGATCCTGATGGTGTGAAGAAATTTATACCATCAGGATGGAGA

                  *                              *       * 
        628 ATATTGGTCCTGATGGTGTGAAGAAATTTATACCATCTGGATGGAAA
          1 A-ATTGATCCTGATGGTGTGAAGAAATTTATACCATCAGGATGGAGA

               
        675 AAT
          1 AAT

        678 CACAAAGAGC


Statistics
Matches: 132,  Mismatches: 7, Indels: 4
        0.92            0.05        0.03

Matches are distributed among these distances:
  45    2  0.02
  46  128  0.97
  47    2  0.02

ACGTcount: A:0.33, C:0.10, G:0.26, T:0.30


Consensus pattern (46 bp):   
AATTGATCCTGATGGTGTGAAGAAATTTATACCATCAGGATGGAGA

Found at i:1180 original size:27 final size:27

Alignment explanation


    Indices: 1150--1216  Score: 125
    Period size: 27  Copynumber: 2.5  Consensus size: 27

       1140 TCCAAAATTG

                 *                     
       1150 GATCCTGATGGTCGGGATGCCAAGGTT
          1 GATCCCGATGGTCGGGATGCCAAGGTT

                                       
       1177 GATCCCGATGGTCGGGATGCCAAGGTT
          1 GATCCCGATGGTCGGGATGCCAAGGTT

                         
       1204 GATCCCGATGGTC
          1 GATCCCGATGGTC

       1217 ATGAGATGAT


Statistics
Matches: 39,  Mismatches: 1, Indels: 0
        0.98            0.03        0.00

Matches are distributed among these distances:
  27   39  1.00

ACGTcount: A:0.18, C:0.22, G:0.36, T:0.24


Consensus pattern (27 bp):   
GATCCCGATGGTCGGGATGCCAAGGTT

Found at i:1429 original size:16 final size:16

Alignment explanation


    Indices: 1408--1438  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       1398 CATCAAGAAG

                            
       1408 CTTATCATCAGGACGA
          1 CTTATCATCAGGACGA

                    *      
       1424 CTTATCATTAGGACG
          1 CTTATCATCAGGACG

       1439 CTTTCCATCG


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29


Consensus pattern (16 bp):   
CTTATCATCAGGACGA

Found at i:3935 original size:15 final size:16

Alignment explanation


    Indices: 3899--3937  Score: 53
    Period size: 15  Copynumber: 2.5  Consensus size: 16

       3889 TACTTTGCTT

                            
       3899 TGTTTTCTAGTATAAA
          1 TGTTTTCTAGTATAAA

                       *   *
       3915 TGTTTTCT-GTTTAAC
          1 TGTTTTCTAGTATAAA

                    
       3930 TGTTTTCT
          1 TGTTTTCT

       3938 TTCAATCTCT


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  15   13  0.62
  16    8  0.38

ACGTcount: A:0.18, C:0.10, G:0.13, T:0.59


Consensus pattern (16 bp):   
TGTTTTCTAGTATAAA
Done.