Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019359.1 Corchorus olitorius cultivar O-4 contig19392, 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: 3214
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.39


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--44  Score: 88
    Period size: 2  Copynumber: 22.0  Consensus size: 2

                                                                          
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

              
         43 AT
          1 AT

         45 GGAAACTCAT


Statistics
Matches: 42,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   42  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:69 original size:31 final size:32

Alignment explanation


    Indices: 31--91  Score: 115
    Period size: 31  Copynumber: 1.9  Consensus size: 32

         21 ATATATATAT

                                            
         31 ATATATATATATATGG-AAACTCATTATGGTC
          1 ATATATATATATATGGAAAACTCATTATGGTC

                                          
         62 ATATATATATATATGGAAAACTCATTATGG
          1 ATATATATATATATGGAAAACTCATTATGG

         92 AGTGACCGCT


Statistics
Matches: 29,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  31   16  0.55
  32   13  0.45

ACGTcount: A:0.41, C:0.08, G:0.13, T:0.38


Consensus pattern (32 bp):   
ATATATATATATATGGAAAACTCATTATGGTC

Found at i:2538 original size:129 final size:135

Alignment explanation


    Indices: 2389--2632  Score: 347
    Period size: 138  Copynumber: 1.8  Consensus size: 135

       2379 CATTGTTTAA

                   *       *                           *                     
       2389 ACTTTTATAGTTTTATTCAACTAAAAA-CTCTAATTTTATTTATTTAAATCTAATAT-C-T-T-T
          1 ACTTTTACAGTTTTACTCAACTAAAAATCTCTAATTTTATTTAATTAAATCTAATATCCTTATCT

                                                                             
       2449 A-TGATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATATATATTAGAATTTTTTA
         66 ATTGATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATATATATTAGAATTTTTTA

                 
       2513 AATAT
        131 AATAT

                                             *                               
       2518 ACTTTTACAGTTTTACTCAACTAAAAATCTCTATTTTTATTTAATTAAATCTAATATCCTTATAC
          1 ACTTTTACAGTTTTACTCAACTAAAAATCTCTAATTTTATTTAATTAAATCTAATATCCTTAT--

                  *               *       *  *                
       2583 CTATTTTATTTTTACCATTTTATTATTTTATTTCAAAAACTTATATATAT
         64 CTA-TTGATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATAT

       2633 TAGAATTTTT


Statistics
Matches: 98,  Mismatches: 8, Indels: 9
        0.85            0.07        0.08

Matches are distributed among these distances:
 129   25  0.26
 130   27  0.28
 131    1  0.01
 132    1  0.01
 133    1  0.01
 136    2  0.02
 138   41  0.42

ACGTcount: A:0.36, C:0.11, G:0.02, T:0.51


Consensus pattern (135 bp):   
ACTTTTACAGTTTTACTCAACTAAAAATCTCTAATTTTATTTAATTAAATCTAATATCCTTATCT
ATTGATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATATATATTAGAATTTTTTA
AATAT

Done.