Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001608.1 Corchorus capsularis cultivar CVL-1 contig01608, 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: 4970
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--28  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

                                                     
          1 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

         29 GAGATTTTGT


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:468 original size:47 final size:47

Alignment explanation


    Indices: 399--509  Score: 213
    Period size: 47  Copynumber: 2.4  Consensus size: 47

        389 GTGGATAACA

                                                           
        399 AGTCATCTTTACTCTTTTTTATGTTTCTTTTCTTTTGGGGAACATTT
          1 AGTCATCTTTACTCTTTTTTATGTTTCTTTTCTTTTGGGGAACATTT

                                                           
        446 AGTCATCTTTACTCTTTTTTATGTTTCTTTTCTTTTGGGGAACATTT
          1 AGTCATCTTTACTCTTTTTTATGTTTCTTTTCTTTTGGGGAACATTT

                        *    
        493 AGTCATCTTTACACTTT
          1 AGTCATCTTTACTCTTT

        510 AAGTTATTTT


Statistics
Matches: 63,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  47   63  1.00

ACGTcount: A:0.16, C:0.16, G:0.12, T:0.56


Consensus pattern (47 bp):   
AGTCATCTTTACTCTTTTTTATGTTTCTTTTCTTTTGGGGAACATTT

Found at i:3065 original size:34 final size:35

Alignment explanation


    Indices: 3022--3108  Score: 167
    Period size: 35  Copynumber: 2.5  Consensus size: 35

       3012 GTTCTTTATT

                                               
       3022 AACTTTATGTAGAAAAATTTTCACC-AAAAAAAAA
          1 AACTTTATGTAGAAAAATTTTCACCAAAAAAAAAA

                                               
       3056 AACTTTATGTAGAAAAATTTTCACCAAAAAAAAAA
          1 AACTTTATGTAGAAAAATTTTCACCAAAAAAAAAA

                              
       3091 AACTTTATGTAGAAAAAT
          1 AACTTTATGTAGAAAAAT

       3109 ACTCCTTACA


Statistics
Matches: 52,  Mismatches: 0, Indels: 1
        0.98            0.00        0.02

Matches are distributed among these distances:
  34   25  0.48
  35   27  0.52

ACGTcount: A:0.55, C:0.10, G:0.07, T:0.28


Consensus pattern (35 bp):   
AACTTTATGTAGAAAAATTTTCACCAAAAAAAAAA

Found at i:4869 original size:2 final size:2

Alignment explanation


    Indices: 4862--4893  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

       4852 AATATTTTCA

                                                           
       4862 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

       4894 TATCTAGGAA


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

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


Consensus pattern (2 bp):   
AT

Done.