Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013632.1 Corchorus olitorius cultivar O-4 contig13665, 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: 30645
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:1324 original size:21 final size:21

Alignment explanation


    Indices: 1298--1368  Score: 117
    Period size: 21  Copynumber: 3.4  Consensus size: 21

       1288 TGCTAGGAGA

                                  
       1298 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                                 
       1319 TCATTGGAGAAGGTTCCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                           *     
       1340 TCATTGGAGAAGGTTTCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                    
       1361 TCATTGGA
          1 TCATTGGA

       1369 ATTTCCTAAG


Statistics
Matches: 48,  Mismatches: 1, Indels: 2
        0.94            0.02        0.04

Matches are distributed among these distances:
  20    2  0.04
  21   46  0.96

ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27


Consensus pattern (21 bp):   
TCATTGGAGAAGGTTCCAAGC

Found at i:5576 original size:24 final size:26

Alignment explanation


    Indices: 5547--5602  Score: 64
    Period size: 27  Copynumber: 2.2  Consensus size: 26

       5537 AAGCCCAATT

                                       
       5547 AATAAT-T-ATGAT-GCAGTAATTTCC
          1 AATAATCTGATGATCGCA-TAATTTCC

                            *          
       5571 AATAATCCTGATGATCTCATAATTTCC
          1 AATAAT-CTGATGATCGCATAATTTCC

                 
       5598 AATAA
          1 AATAA

       5603 GTAATCCCCT


Statistics
Matches: 27,  Mismatches: 1, Indels: 5
        0.82            0.03        0.15

Matches are distributed among these distances:
  24    6  0.22
  26    1  0.04
  27   18  0.67
  28    2  0.07

ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36


Consensus pattern (26 bp):   
AATAATCTGATGATCGCATAATTTCC

Found at i:17187 original size:11 final size:11

Alignment explanation


    Indices: 17141--17180  Score: 64
    Period size: 11  Copynumber: 3.6  Consensus size: 11

      17131 GCTAGCTCGG

                       
      17141 CCGGCTAATGC
          1 CCGGCTAATGC

                       
      17152 CCGGCTAATGC
          1 CCGGCTAATGC

                        
      17163 CCGGCT-ATGGC
          1 CCGGCTAAT-GC

                   
      17174 CCGGCTA
          1 CCGGCTA

      17181 TGGCCCGACC


Statistics
Matches: 27,  Mismatches: 0, Indels: 3
        0.90            0.00        0.10

Matches are distributed among these distances:
  10    2  0.07
  11   25  0.93

ACGTcount: A:0.15, C:0.38, G:0.30, T:0.17


Consensus pattern (11 bp):   
CCGGCTAATGC

Found at i:22230 original size:26 final size:26

Alignment explanation


    Indices: 22201--22254  Score: 90
    Period size: 26  Copynumber: 2.1  Consensus size: 26

      22191 TGATAATATG

                                      
      22201 AACATCAAGTAATCAAAACCAAAACC
          1 AACATCAAGTAATCAAAACCAAAACC

                      *           *   
      22227 AACATCAAGTCATCAAAACCAATACC
          1 AACATCAAGTAATCAAAACCAAAACC

              
      22253 AA
          1 AA

      22255 ATCCAACATC


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  26   26  1.00

ACGTcount: A:0.56, C:0.28, G:0.04, T:0.13


Consensus pattern (26 bp):   
AACATCAAGTAATCAAAACCAAAACC
Done.