Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005739.1 Corchorus capsularis cultivar CVL-1 contig05757, 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: 6708
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31


Found at i:1387 original size:30 final size:30

Alignment explanation


    Indices: 1351--1407  Score: 96
    Period size: 30  Copynumber: 1.9  Consensus size: 30

       1341 CAAAGGATCA

                         *                
       1351 AATGGCATCTTTGGTGCGATTCCTCCACCC
          1 AATGGCATCTTTGCTGCGATTCCTCCACCC

                            *          
       1381 AATGGCATCTTTGCTGTGATTCCTCCA
          1 AATGGCATCTTTGCTGCGATTCCTCCA

       1408 TCCATTAATG


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  30   25  1.00

ACGTcount: A:0.18, C:0.30, G:0.19, T:0.33


Consensus pattern (30 bp):   
AATGGCATCTTTGCTGCGATTCCTCCACCC

Found at i:1995 original size:18 final size:16

Alignment explanation


    Indices: 1972--2026  Score: 58
    Period size: 17  Copynumber: 3.2  Consensus size: 16

       1962 GCCATGTCAG

                              
       1972 ATTTTTTATTAAAAAATA
          1 ATTTTTT-TTAAAAAA-A

                            
       1990 A-TTTTTTTAAAAAAA
          1 ATTTTTTTTAAAAAAA

                        *     
       2005 ATGTTTTTTTAGGAAAAA
          1 AT-TTTTTTTA-AAAAAA

                
       2023 ATTT
          1 ATTT

       2027 CGAAAAAAAC


Statistics
Matches: 33,  Mismatches: 1, Indels: 7
        0.80            0.02        0.17

Matches are distributed among these distances:
  15    2  0.06
  16    8  0.24
  17   15  0.45
  18    8  0.24

ACGTcount: A:0.45, C:0.00, G:0.05, T:0.49


Consensus pattern (16 bp):   
ATTTTTTTTAAAAAAA

Found at i:2011 original size:15 final size:16

Alignment explanation


    Indices: 1980--2012  Score: 50
    Period size: 15  Copynumber: 2.1  Consensus size: 16

       1970 AGATTTTTTA

                        *   
       1980 TTAAAAAATAATTTTT
          1 TTAAAAAATAATGTTT

                            
       1996 TTAAAAAA-AATGTTT
          1 TTAAAAAATAATGTTT

              
       2011 TT
          1 TT

       2013 TTAGGAAAAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  15    8  0.50
  16    8  0.50

ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48


Consensus pattern (16 bp):   
TTAAAAAATAATGTTT

Found at i:2015 original size:17 final size:16

Alignment explanation


    Indices: 1974--2013  Score: 55
    Period size: 16  Copynumber: 2.4  Consensus size: 16

       1964 CATGTCAGAT

                             
       1974 TTTTTATTAAAAAATAA
          1 TTTTT-TTAAAAAATAA

                            
       1991 TTTTTTTAAAAAA-AA
          1 TTTTTTTAAAAAATAA

                    
       2006 TGTTTTTT
          1 T-TTTTTT

       2014 TAGGAAAAAA


Statistics
Matches: 22,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  15    3  0.14
  16   14  0.64
  17    5  0.23

ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55


Consensus pattern (16 bp):   
TTTTTTTAAAAAATAA

Found at i:6586 original size:33 final size:33

Alignment explanation


    Indices: 6540--6614  Score: 116
    Period size: 33  Copynumber: 2.3  Consensus size: 33

       6530 TTTTTACACT

                    *                  *      
       6540 GAGCCTCCTCACTA-GGACGGCTCAACTACGGCG
          1 GAGCCTCCCCACTAGGGA-GGCTCAACCACGGCG

                                             
       6573 GAGCCTCCCCACTAGGGAGGCTCAACCACGGCG
          1 GAGCCTCCCCACTAGGGAGGCTCAACCACGGCG

                     
       6606 GAGCCTCCC
          1 GAGCCTCCC

       6615 TACTGGGGCG


Statistics
Matches: 39,  Mismatches: 2, Indels: 2
        0.91            0.05        0.05

Matches are distributed among these distances:
  33   36  0.92
  34    3  0.08

ACGTcount: A:0.20, C:0.40, G:0.28, T:0.12


Consensus pattern (33 bp):   
GAGCCTCCCCACTAGGGAGGCTCAACCACGGCG

Found at i:6655 original size:33 final size:32

Alignment explanation


    Indices: 6618--6692  Score: 105
    Period size: 32  Copynumber: 2.3  Consensus size: 32

       6608 GCCTCCCTAC

                            *                
       6618 TGGGGCGGCTTCACCATGAGCAGGCCGCCCCAA
          1 TGGGGCGGCTTCACCACGA-CAGGCCGCCCCAA

                   *                      **
       6651 TGGGGCGACTTCACCACGACAGGCCGCCCCGG
          1 TGGGGCGGCTTCACCACGACAGGCCGCCCCAA

                      
       6683 TGGGGCGGCT
          1 TGGGGCGGCT

       6693 AGACCAAAAT


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

Matches are distributed among these distances:
  32   20  0.54
  33   17  0.46

ACGTcount: A:0.15, C:0.36, G:0.37, T:0.12


Consensus pattern (32 bp):   
TGGGGCGGCTTCACCACGACAGGCCGCCCCAA

Done.