Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005369.1 Corchorus capsularis cultivar CVL-1 contig05387, 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: 9621
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.35


Found at i:4053 original size:3 final size:3

Alignment explanation


    Indices: 4045--4076  Score: 64
    Period size: 3  Copynumber: 10.7  Consensus size: 3

       4035 CCCTTTTCAT

                                                      
       4045 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
          1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA

       4077 CAATGGCCTT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   29  1.00

ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34


Consensus pattern (3 bp):   
TAA

Found at i:6731 original size:28 final size:28

Alignment explanation


    Indices: 6674--6732  Score: 75
    Period size: 29  Copynumber: 2.1  Consensus size: 28

       6664 GCTTCTACGA

                                    *    
       6674 TTTGGATATTTTGTCCCATAAATTTTAAT
          1 TTTGGATATTTTGT-CCATAAATTATAAT

                                 *       
       6703 TTTGGATATTTTGT-CATGAACTTATAAT
          1 TTTGGATATTTTGTCCAT-AAATTATAAT

              
       6731 TT
          1 TT

       6733 GGAGTCATAT


Statistics
Matches: 27,  Mismatches: 2, Indels: 3
        0.84            0.06        0.09

Matches are distributed among these distances:
  27    3  0.11
  28   10  0.37
  29   14  0.52

ACGTcount: A:0.27, C:0.08, G:0.12, T:0.53


Consensus pattern (28 bp):   
TTTGGATATTTTGTCCATAAATTATAAT

Found at i:6896 original size:29 final size:28

Alignment explanation


    Indices: 6863--6927  Score: 69
    Period size: 29  Copynumber: 2.2  Consensus size: 28

       6853 CTAACGTGGC

                                        * 
       6863 TCCAAATTGAAAATTTAGG-GAACAAAATG
          1 TCCAAATT-AAAATTTAGGAG-ACAAAACG

                        *    *           
       6892 TCCAAAATTAAAGTTTATGAGACAAAACG
          1 TCC-AAATTAAAATTTAGGAGACAAAACG

                   
       6921 TCCAAAT
          1 TCCAAAT

       6928 CTTATAAGGG


Statistics
Matches: 31,  Mismatches: 3, Indels: 5
        0.79            0.08        0.13

Matches are distributed among these distances:
  28    4  0.13
  29   21  0.68
  30    6  0.19

ACGTcount: A:0.48, C:0.14, G:0.14, T:0.25


Consensus pattern (28 bp):   
TCCAAATTAAAATTTAGGAGACAAAACG

Found at i:7732 original size:14 final size:13

Alignment explanation


    Indices: 7703--7738  Score: 63
    Period size: 13  Copynumber: 2.7  Consensus size: 13

       7693 GTTTCATATC

                          
       7703 AAATCCAATTTGAA
          1 AAAT-CAATTTGAA

                         
       7717 AAATCAATTTGAA
          1 AAATCAATTTGAA

                     
       7730 AAATCAATT
          1 AAATCAATT

       7739 AATTTTGATT


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  13   18  0.82
  14    4  0.18

ACGTcount: A:0.53, C:0.11, G:0.06, T:0.31


Consensus pattern (13 bp):   
AAATCAATTTGAA

Found at i:7943 original size:25 final size:25

Alignment explanation


    Indices: 7909--7958  Score: 91
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       7899 ATTGTTTATG

                      *              
       7909 GAAAGTAAATCATTATTGATTGATT
          1 GAAAGTAAATAATTATTGATTGATT

                                     
       7934 GAAAGTAAATAATTATTGATTGATT
          1 GAAAGTAAATAATTATTGATTGATT

       7959 ATTACTGATT


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

Matches are distributed among these distances:
  25   24  1.00

ACGTcount: A:0.42, C:0.02, G:0.16, T:0.40


Consensus pattern (25 bp):   
GAAAGTAAATAATTATTGATTGATT

Done.