Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008867.1 Corchorus capsularis cultivar CVL-1 contig08888, 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: 20149
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31


Found at i:4792 original size:27 final size:27

Alignment explanation


    Indices: 4754--4808  Score: 110
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       4744 CGTCTAGGTT

                                       
       4754 CGTAGTGGCAGATTCTTGCTCTTTCTC
          1 CGTAGTGGCAGATTCTTGCTCTTTCTC

                                       
       4781 CGTAGTGGCAGATTCTTGCTCTTTCTC
          1 CGTAGTGGCAGATTCTTGCTCTTTCTC

             
       4808 C
          1 C

       4809 TCACAAGCAG


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  27   28  1.00

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


Consensus pattern (27 bp):   
CGTAGTGGCAGATTCTTGCTCTTTCTC

Found at i:4818 original size:27 final size:27

Alignment explanation


    Indices: 4761--4818  Score: 73
    Period size: 27  Copynumber: 2.1  Consensus size: 27

       4751 GTTCGTAGTG

                                    ***
       4761 GCAGATTCTTGCTCTTTCTCCGTAGTG
          1 GCAGATTCTTGCTCTTTCTCCGTACAA

                                        
       4788 GCAGATTCTTGCTCTTTCTCC-TCACAA
          1 GCAGATTCTTGCTCTTTCTCCGT-ACAA

                
       4815 GCAG
          1 GCAG

       4819 CAGCCAACGC


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

Matches are distributed among these distances:
  26    1  0.04
  27   26  0.96

ACGTcount: A:0.16, C:0.29, G:0.19, T:0.36


Consensus pattern (27 bp):   
GCAGATTCTTGCTCTTTCTCCGTACAA

Found at i:7407 original size:2 final size:2

Alignment explanation


    Indices: 7400--7433  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

       7390 ATTATATGAA

                                                              
       7400 AT AT AT AT AT 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

       7434 GAATCACTTT


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:14423 original size:17 final size:17

Alignment explanation


    Indices: 14401--14450  Score: 54
    Period size: 17  Copynumber: 3.1  Consensus size: 17

      14391 TGAGTATGAC

                             
      14401 GGATTGTTTCAATTTAA
          1 GGATTGTTTCAATTTAA

                            * 
      14418 GGATTGTTT--ATGTTTA
          1 GGATTGTTTCAAT-TTAA

                             
      14434 --ATTGTTTCAATTTAA
          1 GGATTGTTTCAATTTAA

              
      14449 GG
          1 GG

      14451 CCTGCTTGTT


Statistics
Matches: 26,  Mismatches: 2, Indels: 10
        0.68            0.05        0.26

Matches are distributed among these distances:
  14    7  0.27
  15    5  0.19
  16    5  0.19
  17    9  0.35

ACGTcount: A:0.26, C:0.04, G:0.20, T:0.50


Consensus pattern (17 bp):   
GGATTGTTTCAATTTAA

Found at i:16892 original size:10 final size:10

Alignment explanation


    Indices: 16877--16925  Score: 55
    Period size: 10  Copynumber: 4.7  Consensus size: 10

      16867 TTCAAAATTG

                      
      16877 TAATTAATAA
          1 TAATTAATAA

                      
      16887 TAATTAATAA
          1 TAATTAATAA

                *       
      16897 TTAAATAATTAA
          1 -TAATTAA-TAA

                       
      16909 TAA-TAATCAA
          1 TAATTAAT-AA

                   
      16919 TAATTAA
          1 TAATTAA

      16926 AGCTTTTCAA


Statistics
Matches: 34,  Mismatches: 1, Indels: 7
        0.81            0.02        0.17

Matches are distributed among these distances:
   9    1  0.03
  10   18  0.53
  11   12  0.35
  12    3  0.09

ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39


Consensus pattern (10 bp):   
TAATTAATAA

Found at i:16908 original size:25 final size:25

Alignment explanation


    Indices: 16877--16926  Score: 91
    Period size: 25  Copynumber: 2.0  Consensus size: 25

      16867 TTCAAAATTG

                          *          
      16877 TAATTAATAATAATTAATAATTAAA
          1 TAATTAATAATAATCAATAATTAAA

                                     
      16902 TAATTAATAATAATCAATAATTAAA
          1 TAATTAATAATAATCAATAATTAAA

      16927 GCTTTTCAAA


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:0.60, C:0.02, G:0.00, T:0.38


Consensus pattern (25 bp):   
TAATTAATAATAATCAATAATTAAA
Done.