Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016258.1 Corchorus olitorius cultivar O-4 contig16291, 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: 8099
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34


Found at i:1208 original size:11 final size:11

Alignment explanation


    Indices: 1192--1216  Score: 50
    Period size: 11  Copynumber: 2.3  Consensus size: 11

       1182 GGATCAACAT

                       
       1192 ACTACAATTTA
          1 ACTACAATTTA

                       
       1203 ACTACAATTTA
          1 ACTACAATTTA

               
       1214 ACT
          1 ACT

       1217 TTAACAATAA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   14  1.00

ACGTcount: A:0.44, C:0.20, G:0.00, T:0.36


Consensus pattern (11 bp):   
ACTACAATTTA

Found at i:4906 original size:14 final size:14

Alignment explanation


    Indices: 4887--4915  Score: 58
    Period size: 14  Copynumber: 2.1  Consensus size: 14

       4877 CTAGGTAATT

                          
       4887 AATTTCTAAAACAG
          1 AATTTCTAAAACAG

                          
       4901 AATTTCTAAAACAG
          1 AATTTCTAAAACAG

             
       4915 A
          1 A

       4916 GATCCTTAAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   15  1.00

ACGTcount: A:0.52, C:0.14, G:0.07, T:0.28


Consensus pattern (14 bp):   
AATTTCTAAAACAG

Found at i:7057 original size:28 final size:28

Alignment explanation


    Indices: 7017--7075  Score: 102
    Period size: 28  Copynumber: 2.1  Consensus size: 28

       7007 CAAATTACAC

                                         
       7017 AAACATGAATAAG-TACTTTTTTTTTAAG
          1 AAACATGAATAAGTTA-TTTTTTTTTAAG

                                        
       7045 AAACATGAATAAGTTATTTTTTTTTAAG
          1 AAACATGAATAAGTTATTTTTTTTTAAG

               
       7073 AAA
          1 AAA

       7076 GCTAGCTAGA


Statistics
Matches: 30,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
  28   28  0.93
  29    2  0.07

ACGTcount: A:0.42, C:0.05, G:0.10, T:0.42


Consensus pattern (28 bp):   
AAACATGAATAAGTTATTTTTTTTTAAG

Found at i:7505 original size:89 final size:89

Alignment explanation


    Indices: 7354--7532  Score: 358
    Period size: 89  Copynumber: 2.0  Consensus size: 89

       7344 TACGTAAAAA

                                                                             
       7354 CAAATCCTTATATCCAATGTGGCTTAGTGACAAGCTCTAAACTATCCGCAAGCGCACGAAATCGC
          1 CAAATCCTTATATCCAATGTGGCTTAGTGACAAGCTCTAAACTATCCGCAAGCGCACGAAATCGC

                                    
       7419 TGTAGTGCAACCCAAGTGTCGTAT
         66 TGTAGTGCAACCCAAGTGTCGTAT

                                                                             
       7443 CAAATCCTTATATCCAATGTGGCTTAGTGACAAGCTCTAAACTATCCGCAAGCGCACGAAATCGC
          1 CAAATCCTTATATCCAATGTGGCTTAGTGACAAGCTCTAAACTATCCGCAAGCGCACGAAATCGC

                                    
       7508 TGTAGTGCAACCCAAGTGTCGTAT
         66 TGTAGTGCAACCCAAGTGTCGTAT

             
       7532 C
          1 C

       7533 CACAAAGACA


Statistics
Matches: 90,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  89   90  1.00

ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25


Consensus pattern (89 bp):   
CAAATCCTTATATCCAATGTGGCTTAGTGACAAGCTCTAAACTATCCGCAAGCGCACGAAATCGC
TGTAGTGCAACCCAAGTGTCGTAT
Done.