Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008450.1 Corchorus olitorius cultivar O-4 contig08477, 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, 935

Length: 1559
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37


Found at i:522 original size:35 final size:33

Alignment explanation


    Indices: 447--550  Score: 133
    Period size: 35  Copynumber: 3.1  Consensus size: 33

        437 CTCATAATTT

                                    *       *
        447 AATGACAACCACACCTTAATTTTTGT--A-TTC
          1 AATGACAACCACACCTTAATTTTTATAAACTTA

                                              
        477 AATGACAACCACACCTTAATTTTGTATAAACTTA
          1 AATGACAACCACACCTTAATTTT-TATAAACTTA

                                                
        511 AATGAACAACCACACCTTAATTTTTCATAAACTTTA
          1 AATG-ACAACCACACCTTAATTTTT-ATAAAC-TTA

                
        547 AATG
          1 AATG

        551 GATTTGGCTT


Statistics
Matches: 65,  Mismatches: 2, Indels: 8
        0.87            0.03        0.11

Matches are distributed among these distances:
  30   23  0.35
  31    2  0.03
  33    1  0.02
  34    7  0.11
  35   25  0.38
  36    7  0.11

ACGTcount: A:0.39, C:0.21, G:0.06, T:0.34


Consensus pattern (33 bp):   
AATGACAACCACACCTTAATTTTTATAAACTTA

Found at i:944 original size:8 final size:8

Alignment explanation


    Indices: 928--960  Score: 57
    Period size: 8  Copynumber: 4.1  Consensus size: 8

        918 TACCATCTAC

                *   
        928 CAAAGAAA
          1 CAAATAAA

                    
        936 CAAATAAA
          1 CAAATAAA

                    
        944 CAAATAAA
          1 CAAATAAA

                    
        952 CAAATAAA
          1 CAAATAAA

             
        960 C
          1 C

        961 TAAAATTATA


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   8   24  1.00

ACGTcount: A:0.73, C:0.15, G:0.03, T:0.09


Consensus pattern (8 bp):   
CAAATAAA

Found at i:1492 original size:80 final size:81

Alignment explanation


    Indices: 1395--1559  Score: 289
    Period size: 83  Copynumber: 2.0  Consensus size: 81

       1385 TTTAATCCAT

                                                                  *          
       1395 AGACTATGCTACTAGTAATTTCTTTTT-GTGTTATTAATTACATTTATTCGTC-CAAAGAAAATA
          1 AGACTATGCTACTAGTAATTTCTTTTTGGTGTTATTAATTACATTTATTCGTCAAAAAGAAAATA

                            
       1458 CTATACTAGCATGCAG
         66 CTATACTAGCATGCAG

                                                                             
       1474 AGACTACTGCTACTAGTAATTTCTTTTTGGTGTTATTAATTACATTTATTCGTCATAAAAGAAAA
          1 AGACTA-TGCTACTAGTAATTTCTTTTTGGTGTTATTAATTACATTTATTCGTCA-AAAAGAAAA

                              
       1539 TACTATACTAGCATGCAG
         64 TACTATACTAGCATGCAG

               
       1557 AGA
          1 AGA


Statistics
Matches: 81,  Mismatches: 1, Indels: 4
        0.94            0.01        0.05

Matches are distributed among these distances:
  79    6  0.07
  80   21  0.26
  81   25  0.31
  83   29  0.36

ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38


Consensus pattern (81 bp):   
AGACTATGCTACTAGTAATTTCTTTTTGGTGTTATTAATTACATTTATTCGTCAAAAAGAAAATA
CTATACTAGCATGCAG

Done.