Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015022.1 Corchorus capsularis cultivar CVL-1 contig15043, 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: 21538
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33


Found at i:2507 original size:24 final size:24

Alignment explanation


    Indices: 2480--2526  Score: 58
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       2470 TCAAATGCTG

                    * *             
       2480 ATTCTATTTCTTGTAATAATGTTT
          1 ATTCTATTCCCTGTAATAATGTTT

                 *           *     
       2504 ATTCTGTTCCCTGTAATGATGTT
          1 ATTCTATTCCCTGTAATAATGTT

       2527 AATTATGTTT


Statistics
Matches: 19,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  24   19  1.00

ACGTcount: A:0.21, C:0.13, G:0.13, T:0.53


Consensus pattern (24 bp):   
ATTCTATTCCCTGTAATAATGTTT

Found at i:5377 original size:4 final size:4

Alignment explanation


    Indices: 5368--5392  Score: 50
    Period size: 4  Copynumber: 6.2  Consensus size: 4

       5358 TTTGTACTCA

                                           
       5368 AAAT AAAT AAAT AAAT AAAT AAAT A
          1 AAAT AAAT AAAT AAAT AAAT AAAT A

       5393 TATATATATA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   21  1.00

ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24


Consensus pattern (4 bp):   
AAAT

Found at i:5828 original size:22 final size:22

Alignment explanation


    Indices: 5788--5830  Score: 61
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       5778 AAAATTCTTA

                                  
       5788 AACAGAGTTTCTATAACCCATC
          1 AACAGAGTTTCTATAACCCATC

                           *      
       5810 AACAGA-TTTCTTATTACCCAT
          1 AACAGAGTTTC-TATAACCCAT

       5831 AAAACCATGT


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

Matches are distributed among these distances:
  21    4  0.21
  22   15  0.79

ACGTcount: A:0.35, C:0.26, G:0.07, T:0.33


Consensus pattern (22 bp):   
AACAGAGTTTCTATAACCCATC

Found at i:10332 original size:24 final size:24

Alignment explanation


    Indices: 10300--10348  Score: 71
    Period size: 24  Copynumber: 2.0  Consensus size: 24

      10290 TCATGTCAAG

                           *        
      10300 ATATATATATATATAGATACATGA
          1 ATATATATATATATAAATACATGA

                *             *     
      10324 ATATCTATATATATAAATCCATGA
          1 ATATATATATATATAAATACATGA

             
      10348 A
          1 A

      10349 ATTATTTAAT


Statistics
Matches: 22,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  24   22  1.00

ACGTcount: A:0.49, C:0.08, G:0.06, T:0.37


Consensus pattern (24 bp):   
ATATATATATATATAAATACATGA

Found at i:15410 original size:29 final size:31

Alignment explanation


    Indices: 15377--15444  Score: 86
    Period size: 29  Copynumber: 2.3  Consensus size: 31

      15367 TTGCATTAAA

                     **                    
      15377 AACATTTTGTTCCCTAAACTT-CAAA-TCAG
          1 AACATTTTGCCCCCTAAACTTCCAAATTCAG

                           *               
      15406 AACATTTTGCCCCCTGAACTTCCAAATTCAG
          1 AACATTTTGCCCCCTAAACTTCCAAATTCAG

            *       
      15437 GACATTTT
          1 AACATTTT

      15445 ACCTGCTGAC


Statistics
Matches: 33,  Mismatches: 4, Indels: 2
        0.85            0.10        0.05

Matches are distributed among these distances:
  29   18  0.55
  30    4  0.12
  31   11  0.33

ACGTcount: A:0.31, C:0.26, G:0.09, T:0.34


Consensus pattern (31 bp):   
AACATTTTGCCCCCTAAACTTCCAAATTCAG
Done.