Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013326.1 Corchorus capsularis cultivar CVL-1 contig13347, 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: 28013
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31


Found at i:3685 original size:25 final size:25

Alignment explanation


    Indices: 3657--3707  Score: 102
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       3647 GTAATCTGAT

                                     
       3657 TCCCACAAGAACAAGAAATGTATAC
          1 TCCCACAAGAACAAGAAATGTATAC

                                     
       3682 TCCCACAAGAACAAGAAATGTATAC
          1 TCCCACAAGAACAAGAAATGTATAC

             
       3707 T
          1 T

       3708 TTCCCACTAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  25   26  1.00

ACGTcount: A:0.47, C:0.24, G:0.12, T:0.18


Consensus pattern (25 bp):   
TCCCACAAGAACAAGAAATGTATAC

Found at i:11875 original size:14 final size:14

Alignment explanation


    Indices: 11856--11884  Score: 58
    Period size: 14  Copynumber: 2.1  Consensus size: 14

      11846 AAGCAAGACT

                          
      11856 ACCCACTTTTACAC
          1 ACCCACTTTTACAC

                          
      11870 ACCCACTTTTACAC
          1 ACCCACTTTTACAC

             
      11884 A
          1 A

      11885 TTCGCATCCT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   15  1.00

ACGTcount: A:0.31, C:0.41, G:0.00, T:0.28


Consensus pattern (14 bp):   
ACCCACTTTTACAC

Found at i:24260 original size:21 final size:20

Alignment explanation


    Indices: 24224--24263  Score: 62
    Period size: 20  Copynumber: 1.9  Consensus size: 20

      24214 AGCAAAATTA

                                
      24224 CTAATATAATATATCTTATC
          1 CTAATATAATATATCTTATC

                 *              
      24244 CTAATCTAATAATATCTTAT
          1 CTAATATAAT-ATATCTTAT

      24264 TCCAATATTT


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  20    9  0.50
  21    9  0.50

ACGTcount: A:0.40, C:0.15, G:0.00, T:0.45


Consensus pattern (20 bp):   
CTAATATAATATATCTTATC

Found at i:25212 original size:15 final size:15

Alignment explanation


    Indices: 25192--25222  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

      25182 CCAAGCTTAC

                      *    
      25192 ACCTGGCGGCTTGTA
          1 ACCTGGCGGCCTGTA

                           
      25207 ACCTGGCGGCCTGTA
          1 ACCTGGCGGCCTGTA

             
      25222 A
          1 A

      25223 TTAACACCTG


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.16, C:0.29, G:0.32, T:0.23


Consensus pattern (15 bp):   
ACCTGGCGGCCTGTA

Found at i:26265 original size:30 final size:31

Alignment explanation


    Indices: 26206--26268  Score: 85
    Period size: 31  Copynumber: 2.1  Consensus size: 31

      26196 TGTTATGTGC

                            *     *        
      26206 TTCTGTTATTGTGCCCTTTTGGGTTATTTTG
          1 TTCTGTTATTGTGCCCCTTTGGATTATTTTG

                                            
      26237 TTCTGTTATTG-GCACCCTTT-GATTATTTTG
          1 TTCTGTTATTGTGC-CCCTTTGGATTATTTTG

              
      26267 TT
          1 TT

      26269 TTCCACTTTT


Statistics
Matches: 29,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  30   13  0.45
  31   16  0.55

ACGTcount: A:0.10, C:0.14, G:0.19, T:0.57


Consensus pattern (31 bp):   
TTCTGTTATTGTGCCCCTTTGGATTATTTTG
Done.