Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016138.1 Corchorus olitorius cultivar O-4 contig16171, 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: 6254
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33


Found at i:1038 original size:20 final size:21

Alignment explanation


    Indices: 995--1038  Score: 54
    Period size: 20  Copynumber: 2.1  Consensus size: 21

        985 TTTTCTTTGC

                     *         * 
        995 ATTGTTTTGCTCTGATTGATT
          1 ATTGTTTTGATCTGATTGACT

                              *  
       1016 ATTGTTTTGAT-TGATTGCCT
          1 ATTGTTTTGATCTGATTGACT

               
       1036 ATT
          1 ATT

       1039 TCTTGATTTG


Statistics
Matches: 20,  Mismatches: 3, Indels: 1
        0.83            0.12        0.04

Matches are distributed among these distances:
  20   10  0.50
  21   10  0.50

ACGTcount: A:0.16, C:0.09, G:0.18, T:0.57


Consensus pattern (21 bp):   
ATTGTTTTGATCTGATTGACT

Found at i:1348 original size:25 final size:25

Alignment explanation


    Indices: 1314--1362  Score: 98
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       1304 TAGAGAGTCT

                                     
       1314 GCATGCATCATAATCTTAAAATATG
          1 GCATGCATCATAATCTTAAAATATG

                                    
       1339 GCATGCATCATAATCTTAAAATAT
          1 GCATGCATCATAATCTTAAAATAT

       1363 ACCATAATTT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  25   24  1.00

ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33


Consensus pattern (25 bp):   
GCATGCATCATAATCTTAAAATATG

Found at i:4179 original size:35 final size:35

Alignment explanation


    Indices: 4009--4173  Score: 190
    Period size: 34  Copynumber: 4.7  Consensus size: 35

       3999 TCAGTCTTCG

                                               
       4009 AAGTTTTCAAATTGGGAAAGTTCCCACCAGGTTTT
          1 AAGTTTTCAAATTGGGAAAGTTCCCACCAGGTTTT

                   *                    *  *    
       4044 -AGTTTTTAAATTGGGAAAGTTCCCAACAAGTTTTT
          1 AAGTTTTCAAATTGGGAAAGTTCCC-ACCAGGTTTT

                   *          *           *    
       4079 AAGTTTTAAAATTGGGAAGGTTCCCACCAGTTTTT
          1 AAGTTTTCAAATTGGGAAAGTTCCCACCAGGTTTT

                     *         *        *        
       4114 CAAAGTTTTTAAATTGGGAGAGTTCCCATCAGGTTTT
          1 --AAGTTTTCAAATTGGGAAAGTTCCCACCAGGTTTT

                      *             
       4151 -AGTTTTCAATTTAGGGAAAGTTC
          1 AAGTTTTCAAATT-GGGAAAGTTC

       4174 ACATCATTTT


Statistics
Matches: 111,  Mismatches: 14, Indels: 10
        0.82            0.10        0.07

Matches are distributed among these distances:
  34   33  0.30
  35   26  0.23
  36   22  0.20
  37   30  0.27

ACGTcount: A:0.29, C:0.13, G:0.20, T:0.38


Consensus pattern (35 bp):   
AAGTTTTCAAATTGGGAAAGTTCCCACCAGGTTTT
Done.