Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000828.1 Corchorus capsularis cultivar CVL-1 contig00828, 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: 4119
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34


Found at i:690 original size:106 final size:106

Alignment explanation


    Indices: 505--718  Score: 428
    Period size: 106  Copynumber: 2.0  Consensus size: 106

        495 TAGCTACTCA

                                                                             
        505 TTACCTGCTGCACCTATAGTCCTATGTGATAACTTAAGTGCGACCTACACGTGTGCTAATCCTGT
          1 TTACCTGCTGCACCTATAGTCCTATGTGATAACTTAAGTGCGACCTACACGTGTGCTAATCCTGT

                                                     
        570 TTTTCATACCAGGATGAAACATTTAGCTCTTGATTACTTCT
         66 TTTTCATACCAGGATGAAACATTTAGCTCTTGATTACTTCT

                                                                             
        611 TTACCTGCTGCACCTATAGTCCTATGTGATAACTTAAGTGCGACCTACACGTGTGCTAATCCTGT
          1 TTACCTGCTGCACCTATAGTCCTATGTGATAACTTAAGTGCGACCTACACGTGTGCTAATCCTGT

                                                     
        676 TTTTCATACCAGGATGAAACATTTAGCTCTTGATTACTTCT
         66 TTTTCATACCAGGATGAAACATTTAGCTCTTGATTACTTCT

              
        717 TT
          1 TT

        719 GTCCGAGAAA


Statistics
Matches: 108,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
 106  108  1.00

ACGTcount: A:0.24, C:0.23, G:0.16, T:0.36


Consensus pattern (106 bp):   
TTACCTGCTGCACCTATAGTCCTATGTGATAACTTAAGTGCGACCTACACGTGTGCTAATCCTGT
TTTTCATACCAGGATGAAACATTTAGCTCTTGATTACTTCT

Found at i:1712 original size:16 final size:16

Alignment explanation


    Indices: 1691--1729  Score: 78
    Period size: 16  Copynumber: 2.4  Consensus size: 16

       1681 GTGTGAAAAC

                            
       1691 TTGAACCTGTACATCT
          1 TTGAACCTGTACATCT

                            
       1707 TTGAACCTGTACATCT
          1 TTGAACCTGTACATCT

                   
       1723 TTGAACC
          1 TTGAACC

       1730 AATTGAATTA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   23  1.00

ACGTcount: A:0.26, C:0.26, G:0.13, T:0.36


Consensus pattern (16 bp):   
TTGAACCTGTACATCT

Found at i:3401 original size:30 final size:28

Alignment explanation


    Indices: 3336--3398  Score: 103
    Period size: 26  Copynumber: 2.3  Consensus size: 28

       3326 AATTATGCTT

                          *             
       3336 TAAACAAACTACCTGCCTAACAAATACA
          1 TAAACAAACTACCTACCTAACAAATACA

                                        
       3364 TAAACAAAC-A-CTACCTAACAAATACA
          1 TAAACAAACTACCTACCTAACAAATACA

                     
       3390 TAAACAAAC
          1 TAAACAAAC

       3399 AAATTACAAA


Statistics
Matches: 34,  Mismatches: 1, Indels: 2
        0.92            0.03        0.05

Matches are distributed among these distances:
  26   24  0.71
  27    1  0.03
  28    9  0.26

ACGTcount: A:0.56, C:0.27, G:0.02, T:0.16


Consensus pattern (28 bp):   
TAAACAAACTACCTACCTAACAAATACA
Done.