Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009210.1 Corchorus capsularis cultivar CVL-1 contig09231, 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: 18291
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33


Found at i:5913 original size:2 final size:2

Alignment explanation


    Indices: 5906--5934  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

       5896 TTTTTAGTTC

                                                       
       5906 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       5935 ATTAGTAATG


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:7795 original size:7 final size:7

Alignment explanation


    Indices: 7783--7807  Score: 50
    Period size: 7  Copynumber: 3.6  Consensus size: 7

       7773 TTATTACCCA

                   
       7783 AAAAAAC
          1 AAAAAAC

                   
       7790 AAAAAAC
          1 AAAAAAC

                   
       7797 AAAAAAC
          1 AAAAAAC

                
       7804 AAAA
          1 AAAA

       7808 CAAATTAGGG


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   18  1.00

ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00


Consensus pattern (7 bp):   
AAAAAAC

Found at i:9011 original size:26 final size:26

Alignment explanation


    Indices: 8981--9034  Score: 99
    Period size: 26  Copynumber: 2.1  Consensus size: 26

       8971 CAAAATAGTT

                                      
       8981 AAAATACCTTCAAATTTGGAAATACA
          1 AAAATACCTTCAAATTTGGAAATACA

                      *               
       9007 AAAATACCTTGAAATTTGGAAATACA
          1 AAAATACCTTCAAATTTGGAAATACA

              
       9033 AA
          1 AA

       9035 GCTTCAGTAA


Statistics
Matches: 27,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  26   27  1.00

ACGTcount: A:0.52, C:0.13, G:0.09, T:0.26


Consensus pattern (26 bp):   
AAAATACCTTCAAATTTGGAAATACA

Found at i:15101 original size:20 final size:19

Alignment explanation


    Indices: 15076--15116  Score: 55
    Period size: 19  Copynumber: 2.1  Consensus size: 19

      15066 CCGTCCCTAG

                        *       
      15076 AACAACTCACTCTTTCTTAC
          1 AACAACT-ACTCCTTCTTAC

                   *           
      15096 AACAACTTCTCCTTCTTAC
          1 AACAACTACTCCTTCTTAC

              
      15115 AA
          1 AA

      15117 ATACCAGGTA


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  19   12  0.63
  20    7  0.37

ACGTcount: A:0.32, C:0.34, G:0.00, T:0.34


Consensus pattern (19 bp):   
AACAACTACTCCTTCTTAC

Found at i:16373 original size:1 final size:1

Alignment explanation


    Indices: 16367--16396  Score: 60
    Period size: 1  Copynumber: 30.0  Consensus size: 1

      16357 TTCTATATAT

                                          
      16367 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

      16397 TTAAGGAAGC


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

Matches are distributed among these distances:
   1   29  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Done.