Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017121.1 Corchorus olitorius cultivar O-4 contig17154, 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: 2090
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28


Found at i:1437 original size:54 final size:54

Alignment explanation


    Indices: 1364--1576  Score: 209
    Period size: 54  Copynumber: 3.9  Consensus size: 54

       1354 CAGATGTTTA

                  * *    *                       *                 
       1364 AGATGAGCTAGTGTGGTCTTTCATAGAAGTTTTTAGAAATCTA-AGTTGATCTTC
          1 AGATGACCCAGTGCGGTCTTTCATAGAAGTTTTTAGAGATC-AGAGTTGATCTTC

                     *    *                   *                    *
       1418 AGATGACCCTGTGCAGTCTTTCATAAGAAGTTTTCA-ATGATCAGAGTTGATCTTA
          1 AGATGACCCAGTGCGGTCTTTCAT-AGAAGTTTTTAGA-GATCAGAGTTGATCTTC

              *      *             *        *         *         * 
       1473 AGTTGACCCCGTGCGGTCTTTCAAAGAAGTTTGTAGAGATCATAGTTGATC-CC
          1 AGATGACCCAGTGCGGTCTTTCATAGAAGTTTTTAGAGATCAGAGTTGATCTTC

                  *             **                              
       1526 AGATGATCCAGTGCGGTCGTCCCA-AGAAGTTTTTAGAGATCAGAGTTGATC
          1 AGATGACCCAGTGCGGTC-TTTCATAGAAGTTTTTAGAGATCAGAGTTGATC

       1577 CCCAAGCTGT


Statistics
Matches: 130,  Mismatches: 24, Indels: 11
        0.79            0.15        0.07

Matches are distributed among these distances:
  53   40  0.31
  54   46  0.35
  55   44  0.34

ACGTcount: A:0.27, C:0.16, G:0.23, T:0.33


Consensus pattern (54 bp):   
AGATGACCCAGTGCGGTCTTTCATAGAAGTTTTTAGAGATCAGAGTTGATCTTC

Found at i:2037 original size:4 final size:4

Alignment explanation


    Indices: 2028--2090  Score: 58
    Period size: 4  Copynumber: 16.0  Consensus size: 4

       2018 TAAAAATAAT

                                *          *      *             *       
       2028 AATA AATA AATA AATA GAT- AATA ACTA AATT AATA AATA AAAA TAATA
          1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA -AATA

                  *            
       2076 AAT- AGTA AATA AATA
          1 AATA AATA AATA AATA


Statistics
Matches: 46,  Mismatches: 10, Indels: 6
        0.74            0.16        0.10

Matches are distributed among these distances:
   3    4  0.09
   4   39  0.85
   5    3  0.07

ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27


Consensus pattern (4 bp):   
AATA

Found at i:2084 original size:7 final size:7

Alignment explanation


    Indices: 2017--2087  Score: 69
    Period size: 7  Copynumber: 10.1  Consensus size: 7

       2007 AATAGGTAGC

                   
       2017 ATAAA-A
          1 ATAAATA

                   
       2023 AT-AATA
          1 ATAAATA

                    
       2029 ATAAATAA
          1 ATAAAT-A

                   
       2037 ATAAATA
          1 ATAAATA

                    
       2044 GAT-AATA
          1 -ATAAATA

                     
       2051 ACTAAATTA
          1 A-TAAA-TA

                   
       2060 ATAAATA
          1 ATAAATA

                   
       2067 A-AAATA
          1 ATAAATA

                   
       2073 ATAAATA
          1 ATAAATA

            *      
       2080 GTAAATA
          1 ATAAATA

             
       2087 A
          1 A

       2088 ATA


Statistics
Matches: 55,  Mismatches: 2, Indels: 15
        0.76            0.03        0.21

Matches are distributed among these distances:
   5    2  0.04
   6   12  0.22
   7   23  0.42
   8   15  0.27
   9    3  0.05

ACGTcount: A:0.69, C:0.01, G:0.03, T:0.27


Consensus pattern (7 bp):   
ATAAATA
Done.