Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006260.1 Corchorus capsularis cultivar CVL-1 contig06279, 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: 5339
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.30


Found at i:523 original size:33 final size:33

Alignment explanation


    Indices: 473--596  Score: 137
    Period size: 33  Copynumber: 3.7  Consensus size: 33

        463 CCGCGCAACA

                                               
        473 CCGGCCACAAGACCGGCCACGCGACATGGACATGT
          1 CCGGCCAC-A-ACCGGCCACGCGACATGGACATGT

                                              
        508 CCGGCCATC-ACCGGCCACGCGACATGGACATGT
          1 CCGGCCA-CAACCGGCCACGCGACATGGACATGT

             *   *           **         *     
        541 CTGGCTACAACCGGCCAAACGAC-TCGGCCATG-
          1 CCGGCCACAACCGGCCACGCGACAT-GGACATGT

                                    
        573 CCTGGCCACAACCGGCCACGCGAC
          1 CC-GGCCACAACCGGCCACGCGAC

        597 CCTTTGTCTA


Statistics
Matches: 76,  Mismatches: 9, Indels: 10
        0.80            0.09        0.11

Matches are distributed among these distances:
  32    3  0.04
  33   65  0.86
  35    7  0.09
  36    1  0.01

ACGTcount: A:0.23, C:0.40, G:0.27, T:0.10


Consensus pattern (33 bp):   
CCGGCCACAACCGGCCACGCGACATGGACATGT

Found at i:1511 original size:8 final size:8

Alignment explanation


    Indices: 1498--1531  Score: 50
    Period size: 8  Copynumber: 4.1  Consensus size: 8

       1488 CACCTTCTTG

                    
       1498 AAAAATTC
          1 AAAAATTC

                    
       1506 AAAAATTC
          1 AAAAATTC

                 *   
       1514 AGAAACTTC
          1 A-AAAATTC

                    
       1523 AAAAATTC
          1 AAAAATTC

             
       1531 A
          1 A

       1532 TAGCTGATTC


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
   8   16  0.70
   9    7  0.30

ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24


Consensus pattern (8 bp):   
AAAAATTC

Found at i:1624 original size:15 final size:14

Alignment explanation


    Indices: 1604--1638  Score: 52
    Period size: 14  Copynumber: 2.4  Consensus size: 14

       1594 AGTTATATCG

                     *     
       1604 AAAAATATATATAAA
          1 AAAAATA-AAATAAA

                          
       1619 AAAAATAAAATAAA
          1 AAAAATAAAATAAA

                  
       1633 AAAAAT
          1 AAAAAT

       1639 TTTCGACCAG


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  14   12  0.63
  15    7  0.37

ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20


Consensus pattern (14 bp):   
AAAAATAAAATAAA
Done.