Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016620.1 Corchorus olitorius cultivar O-4 contig16653, 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: 9512
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32


Found at i:1921 original size:20 final size:21

Alignment explanation


    Indices: 1896--1935  Score: 64
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       1886 AGTGGAGTTT

                      *          
       1896 ATAATTTT-TTTTTATATTTC
          1 ATAATTTTATATTTATATTTC

                                
       1916 ATAATTTTATATTTATATTT
          1 ATAATTTTATATTTATATTT

       1936 ATATTTGTTT


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  20    8  0.44
  21   10  0.56

ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68


Consensus pattern (21 bp):   
ATAATTTTATATTTATATTTC

Found at i:3599 original size:25 final size:26

Alignment explanation


    Indices: 3547--3596  Score: 68
    Period size: 24  Copynumber: 2.0  Consensus size: 26

       3537 AAGTCTACCC

                                      
       3547 ATTTTATTACTAATTAAATATATATT
          1 ATTTTATTACTAATTAAATATATATT

                     *         *      
       3573 ATTTT-TTATTAATT-AATTTATATT
          1 ATTTTATTACTAATTAAATATATATT

       3597 TATCTAATAA


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  24    9  0.41
  25    8  0.36
  26    5  0.23

ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60


Consensus pattern (26 bp):   
ATTTTATTACTAATTAAATATATATT

Found at i:4568 original size:22 final size:22

Alignment explanation


    Indices: 4538--4582  Score: 56
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       4528 TCCTGTCTAT

                                   
       4538 TAAGCAGATTAATGTTT-AATGA
          1 TAAGCAGA-TAATGTTTCAATGA

                *       *         
       4560 TAAGGAGATAATTTTTCAATGA
          1 TAAGCAGATAATGTTTCAATGA

             
       4582 T
          1 T

       4583 TGAAATGCTT


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  21    7  0.35
  22   13  0.65

ACGTcount: A:0.40, C:0.04, G:0.18, T:0.38


Consensus pattern (22 bp):   
TAAGCAGATAATGTTTCAATGA

Found at i:5432 original size:50 final size:47

Alignment explanation


    Indices: 5329--5472  Score: 155
    Period size: 49  Copynumber: 3.0  Consensus size: 47

       5319 CGAGCGTGCC

                         *                   *       *     
       5329 AATCAATTTTGTCAAAAAATTGATAAAAAGTGCGATGAAAATTAAAA
          1 AATCAATTTTGTCTAAAAATTGATAAAAAGTGCAATGAAAAATAAAA

                                     *                         
       5376 AATCAATTTTGTCTTTAAAAATTGAGAAAAAGATGCAA-GTAAAAATAAAA
          1 AATCAATTTTGTC--TAAAAATTGATAAAAAG-TGCAATG-AAAAATAAAA

            **           *                     *      *    
       5426 GTTCAATTTTGTAGTAAAAATTGATAAAAAGTGCAGTGAAAAGTAAA
          1 AATCAATTTTGT-CTAAAAATTGATAAAAAGTGCAATGAAAAATAAA

       5473 GGATTGCTTG


Statistics
Matches: 81,  Mismatches: 10, Indels: 11
        0.79            0.10        0.11

Matches are distributed among these distances:
  47   13  0.16
  48   12  0.15
  49   33  0.41
  50   23  0.28

ACGTcount: A:0.51, C:0.06, G:0.15, T:0.28


Consensus pattern (47 bp):   
AATCAATTTTGTCTAAAAATTGATAAAAAGTGCAATGAAAAATAAAA

Found at i:6768 original size:9 final size:9

Alignment explanation


    Indices: 6750--6787  Score: 60
    Period size: 9  Copynumber: 4.3  Consensus size: 9

       6740 TTAATTCATT

                     
       6750 TAATTT-CA
          1 TAATTTCCA

                     
       6758 TAATTTCCA
          1 TAATTTCCA

                    *
       6767 TAATTTCCT
          1 TAATTTCCA

                     
       6776 TAATTTCCA
          1 TAATTTCCA

               
       6785 TAA
          1 TAA

       6788 GTAATTTGGG


Statistics
Matches: 27,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
   8    6  0.22
   9   21  0.78

ACGTcount: A:0.34, C:0.18, G:0.00, T:0.47


Consensus pattern (9 bp):   
TAATTTCCA
Done.