Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005232.1 Corchorus capsularis cultivar CVL-1 contig05250, 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: 4221
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33


Found at i:1531 original size:31 final size:31

Alignment explanation


    Indices: 1462--1550  Score: 110
    Period size: 31  Copynumber: 2.9  Consensus size: 31

       1452 AACTTTTTGT

                                     *     
       1462 AACCTTATATCCTGAATTGCATTTTCAAACA
          1 AACCTTATATCCTGAATTGCATTTTTAAACA

                                       **  
       1493 AACCTTATATCCTGAATTGCATTTTTAGGCA
          1 AACCTTATATCCTGAATTGCATTTTTAAACA

              *                 *        
       1524 AAGCTTATA-CCTTGAATT-TATTTTTAA
          1 AACCTTATATCC-TGAATTGCATTTTTAA

       1551 GCATAAAACA


Statistics
Matches: 51,  Mismatches: 6, Indels: 3
        0.85            0.10        0.05

Matches are distributed among these distances:
  30    9  0.18
  31   42  0.82

ACGTcount: A:0.33, C:0.18, G:0.09, T:0.40


Consensus pattern (31 bp):   
AACCTTATATCCTGAATTGCATTTTTAAACA

Found at i:3232 original size:28 final size:28

Alignment explanation


    Indices: 3176--3232  Score: 69
    Period size: 28  Copynumber: 2.0  Consensus size: 28

       3166 GCTCACCTTA

                               ***  *   
       3176 GAAATCGAAGCACAAAATCTGGAATTTC
          1 GAAATCGAAGCACAAAATCCCCAAATTC

                   *                    
       3204 GAAATCGTAGCACAAAATCCCCAAATTC
          1 GAAATCGAAGCACAAAATCCCCAAATTC

             
       3232 G
          1 G

       3233 CGATTTTAGT


Statistics
Matches: 24,  Mismatches: 5, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  28   24  1.00

ACGTcount: A:0.42, C:0.23, G:0.16, T:0.19


Consensus pattern (28 bp):   
GAAATCGAAGCACAAAATCCCCAAATTC

Found at i:3690 original size:31 final size:30

Alignment explanation


    Indices: 3655--3727  Score: 92
    Period size: 30  Copynumber: 2.4  Consensus size: 30

       3645 CGTCCAAATT

                  *           **   *       
       3655 TATCCTTAATTGTAACCTTTTCGTAACGTTA
          1 TATCCTGAATTGTAACCTCATC-AAACGTTA

                         *                
       3686 TATCCTGAATTGTCACCTCATCAAACGTTA
          1 TATCCTGAATTGTAACCTCATCAAACGTTA

                        
       3716 TATCCTGAATTG
          1 TATCCTGAATTG

       3728 GATTTTCGGG


Statistics
Matches: 37,  Mismatches: 5, Indels: 1
        0.86            0.12        0.02

Matches are distributed among these distances:
  30   19  0.51
  31   18  0.49

ACGTcount: A:0.27, C:0.22, G:0.11, T:0.40


Consensus pattern (30 bp):   
TATCCTGAATTGTAACCTCATCAAACGTTA
Done.