Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001523.1 Corchorus capsularis cultivar CVL-1 contig01523, 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: 5766
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33


Found at i:2204 original size:66 final size:66

Alignment explanation


    Indices: 2095--2227  Score: 230
    Period size: 66  Copynumber: 2.0  Consensus size: 66

       2085 TGAATGGATT

                                              *                              
       2095 TAAACACTAATTCTTCCCATTGCACTTAAAAGTTTCGGGGTTGTCTTCTCAAACTATAACAAAAA
          1 TAAACACTAATTCTTCCCATTGCACTTAAAAGTTCCGGGGTTGTCTTCTCAAACTATAACAAAAA

             
       2160 G
         66 G

                            *    *                *                          
       2161 TAAACACTAATTCTTCTCATTTCACTTAAAAGTTCCGGTGTTGTCTTCTCAAACTATAACAAAAA
          1 TAAACACTAATTCTTCCCATTGCACTTAAAAGTTCCGGGGTTGTCTTCTCAAACTATAACAAAAA

             
       2226 G
         66 G

             
       2227 T
          1 T

       2228 TTTGAAGAGT


Statistics
Matches: 63,  Mismatches: 4, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  66   63  1.00

ACGTcount: A:0.35, C:0.21, G:0.11, T:0.34


Consensus pattern (66 bp):   
TAAACACTAATTCTTCCCATTGCACTTAAAAGTTCCGGGGTTGTCTTCTCAAACTATAACAAAAA
G

Found at i:4579 original size:31 final size:31

Alignment explanation


    Indices: 4535--4600  Score: 87
    Period size: 31  Copynumber: 2.1  Consensus size: 31

       4525 TAAAGTGGTA

                    *                   *  
       4535 AATTTAATTCATGTACTCACAAGATTGGGTC
          1 AATTTAATCCATGTACTCACAAGATTGGATC

                  *        *   *           
       4566 AATTTAGTCCATGTATTCATAAGATTGGATC
          1 AATTTAATCCATGTACTCACAAGATTGGATC

                
       4597 AATT
          1 AATT

       4601 GAGTTCTCAT


Statistics
Matches: 30,  Mismatches: 5, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  31   30  1.00

ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38


Consensus pattern (31 bp):   
AATTTAATCCATGTACTCACAAGATTGGATC

Found at i:5661 original size:2 final size:2

Alignment explanation


    Indices: 5648--5686  Score: 69
    Period size: 2  Copynumber: 19.0  Consensus size: 2

       5638 TTATACATAC

                                                                     
       5648 AT AT ACT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       5687 CTTACAATGA


Statistics
Matches: 36,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   2   34  0.94
   3    2  0.06

ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Done.