Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015665.1 Corchorus olitorius cultivar O-4 contig15698, 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: 5964
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32


Found at i:261 original size:14 final size:14

Alignment explanation


    Indices: 225--274  Score: 55
    Period size: 14  Copynumber: 3.4  Consensus size: 14

        215 AAAGATAATA

                *         
        225 TTTTCAAAATTATT
          1 TTTTAAAAATTATT

               *          
        239 TTTAAAAAATTATT
          1 TTTTAAAAATTATT

                      *    
        253 TTTTGAAAAAATATT
          1 TTTT-AAAAATTATT

                   
        268 CTTTTAA
          1 -TTTTAA

        275 TAAAAAATGT


Statistics
Matches: 30,  Mismatches: 4, Indels: 3
        0.81            0.11        0.08

Matches are distributed among these distances:
  14   15  0.50
  15   11  0.37
  16    4  0.13

ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52


Consensus pattern (14 bp):   
TTTTAAAAATTATT

Found at i:272 original size:16 final size:16

Alignment explanation


    Indices: 230--264  Score: 56
    Period size: 14  Copynumber: 2.3  Consensus size: 16

        220 TAATATTTTC

                            
        230 AAAATTA-TTTTT-AA
          1 AAAATTATTTTTTGAA

                            
        244 AAAATTATTTTTTGAA
          1 AAAATTATTTTTTGAA

                 
        260 AAAAT
          1 AAAAT

        265 ATTCTTTTAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  14    7  0.37
  15    5  0.26
  16    7  0.37

ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46


Consensus pattern (16 bp):   
AAAATTATTTTTTGAA

Found at i:279 original size:16 final size:15

Alignment explanation


    Indices: 230--279  Score: 59
    Period size: 16  Copynumber: 3.3  Consensus size: 15

        220 TAATATTTTC

                           
        230 AAAATTA-TTTTTAA
          1 AAAATTATTTTTTAA

                            
        244 AAAATTATTTTTTGAA
          1 AAAATTATTTTTT-AA

                            
        260 AAAA-TATTCTTTTAA
          1 AAAATTATT-TTTTAA

                 
        275 TAAAA
          1 -AAAA

        280 AATGTGATGT


Statistics
Matches: 32,  Mismatches: 0, Indels: 6
        0.84            0.00        0.16

Matches are distributed among these distances:
  14    7  0.22
  15   11  0.34
  16   14  0.44

ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46


Consensus pattern (15 bp):   
AAAATTATTTTTTAA

Found at i:4764 original size:89 final size:89

Alignment explanation


    Indices: 4613--4795  Score: 325
    Period size: 89  Copynumber: 2.1  Consensus size: 89

       4603 CACTTTTTTT

                                                                             
       4613 TTAGGGAAATGAAATTGTCACTTTTAATTCTCAAAATTAGTACAAAAATTTGTCAAAAACAGAAC
          1 TTAGGGAAATGAAATTGTCACTTTTAATTCTCAAAATTAGTACAAAAATTTGTCAAAAACAGAAC

              *                     
       4678 ATGCAATCATCAATAGATATCAAG
         66 ATCCAATCATCAATAGATATCAAG

                                                                             
       4702 TTAGGGAAATGAAATTGTCACTTTTAATTCTCAAAATTAGAGTA-AAAAA-TTGTCAAAAACAGA
          1 TTAGGGAAATGAAATTGTCACTTTTAATTCTCAAAATT--AGTACAAAAATTTGTCAAAAACAGA

                                      
       4765 ACATCCAATCATCAATAGATATCAAG
         64 ACATCCAATCATCAATAGATATCAAG

                 
       4791 TTAGG
          1 TTAGG

       4796 AACAAAAAAA


Statistics
Matches: 91,  Mismatches: 1, Indels: 4
        0.95            0.01        0.04

Matches are distributed among these distances:
  89   82  0.90
  90    5  0.05
  91    4  0.04

ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29


Consensus pattern (89 bp):   
TTAGGGAAATGAAATTGTCACTTTTAATTCTCAAAATTAGTACAAAAATTTGTCAAAAACAGAAC
ATCCAATCATCAATAGATATCAAG
Done.