Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015295.1 Corchorus capsularis cultivar CVL-1 contig15316, 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: 43138
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31


Found at i:30594 original size:2 final size:2

Alignment explanation


    Indices: 30589--30628  Score: 64
    Period size: 2  Copynumber: 20.0  Consensus size: 2

      30579 ATAAACACAC

                                                                        
      30589 AT AT AT AT AT A- AT CAT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT

      30629 TCTATAAGAG


Statistics
Matches: 36,  Mismatches: 0, Indels: 4
        0.90            0.00        0.10

Matches are distributed among these distances:
   1    1  0.03
   2   33  0.92
   3    2  0.06

ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47


Consensus pattern (2 bp):   
AT

Found at i:31566 original size:33 final size:33

Alignment explanation


    Indices: 31524--31589  Score: 114
    Period size: 33  Copynumber: 2.0  Consensus size: 33

      31514 CGCATGGGGG

                        *                    
      31524 AACCGGCCACAATCGACCATCGCATGGGGCATC
          1 AACCGGCCACAACCGACCATCGCATGGGGCATC

                           *                 
      31557 AACCGGCCACAACCGGCCATCGCATGGGGCATC
          1 AACCGGCCACAACCGACCATCGCATGGGGCATC

      31590 CGCGCACAAC


Statistics
Matches: 31,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  33   31  1.00

ACGTcount: A:0.26, C:0.38, G:0.26, T:0.11


Consensus pattern (33 bp):   
AACCGGCCACAACCGACCATCGCATGGGGCATC

Found at i:31600 original size:30 final size:31

Alignment explanation


    Indices: 31509--31606  Score: 112
    Period size: 30  Copynumber: 3.2  Consensus size: 31

      31499 CATCGCATGC

                          * *           *  
      31509 GCCATCGCATGGGGGAACCG-GCCACAATCG
          1 GCCATCGCATGGGGCATCCGCGCCACAACCG

            *                                 
      31539 ACCATCGCATGGGGCATCAAC-CGGCCACAACCG
          1 GCCATCGCATGGGGCATC--CGC-GCCACAACCG

                                           
      31572 GCCATCGCATGGGGCATCCGCG-CACAACCG
          1 GCCATCGCATGGGGCATCCGCGCCACAACCG

                 
      31602 GCCAT
          1 GCCAT

      31607 TGGATCCTTT


Statistics
Matches: 58,  Mismatches: 5, Indels: 10
        0.79            0.07        0.14

Matches are distributed among these distances:
  30   28  0.48
  31    2  0.03
  32    2  0.03
  33   26  0.45

ACGTcount: A:0.23, C:0.38, G:0.29, T:0.10


Consensus pattern (31 bp):   
GCCATCGCATGGGGCATCCGCGCCACAACCG

Found at i:38846 original size:6 final size:7

Alignment explanation


    Indices: 38817--38851  Score: 56
    Period size: 7  Copynumber: 5.3  Consensus size: 7

      38807 TGTGAAAATA

                   
      38817 ATTCATT
          1 ATTCATT

                   
      38824 ATTCATT
          1 ATTCATT

                   
      38831 ATTCATT
          1 ATTCATT

                   
      38838 ATT-ATT
          1 ATTCATT

                   
      38844 ATT-ATT
          1 ATTCATT

              
      38850 AT
          1 AT

      38852 ATATAAACTA


Statistics
Matches: 28,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
   6   11  0.39
   7   17  0.61

ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60


Consensus pattern (7 bp):   
ATTCATT

Found at i:40099 original size:13 final size:13

Alignment explanation


    Indices: 40083--40114  Score: 57
    Period size: 13  Copynumber: 2.5  Consensus size: 13

      40073 ATATATATAT

                         
      40083 CACTTATAAATTG
          1 CACTTATAAATTG

                         
      40096 CACTTATAAATTG
          1 CACTTATAAATTG

                   
      40109 CA-TTAT
          1 CACTTAT

      40115 GCATAATCAT


Statistics
Matches: 19,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  12    4  0.21
  13   15  0.79

ACGTcount: A:0.38, C:0.16, G:0.06, T:0.41


Consensus pattern (13 bp):   
CACTTATAAATTG
Done.