Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004969.1 Corchorus capsularis cultivar CVL-1 contig04987, 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: 12740
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33


Found at i:592 original size:2 final size:2

Alignment explanation


    Indices: 585--620  Score: 65
    Period size: 2  Copynumber: 18.5  Consensus size: 2

        575 TTATTTGATT

                                                                   
        585 TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

        621 GTTATAAAAC


Statistics
Matches: 33,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   32  0.97

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (2 bp):   
TA

Found at i:611 original size:17 final size:17

Alignment explanation


    Indices: 585--626  Score: 68
    Period size: 17  Copynumber: 2.5  Consensus size: 17

        575 TTATTTGATT

                             
        585 TATA-TATATATATATA
          1 TATATTATATATATATA

                             
        601 TATATTATATATATATA
          1 TATATTATATATATATA

               *     
        618 TATGTTATA
          1 TATATTATA

        627 AAACTAATGA


Statistics
Matches: 24,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  16    4  0.17
  17   20  0.83

ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52


Consensus pattern (17 bp):   
TATATTATATATATATA

Found at i:626 original size:15 final size:15

Alignment explanation


    Indices: 585--620  Score: 65
    Period size: 15  Copynumber: 2.5  Consensus size: 15

        575 TTATTTGATT

                           
        585 TATATA-TATATATA
          1 TATATATTATATATA

                           
        599 TATATATTATATATA
          1 TATATATTATATATA

                   
        614 TATATAT
          1 TATATAT

        621 GTTATAAAAC


Statistics
Matches: 21,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  14    6  0.29
  15   15  0.71

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (15 bp):   
TATATATTATATATA

Found at i:3805 original size:60 final size:61

Alignment explanation


    Indices: 3685--3807  Score: 185
    Period size: 62  Copynumber: 2.0  Consensus size: 61

       3675 CAGATCCGAA

                                  *      *    *                           
       3685 ATGGTACTAAATTGAGTTTTTTTAAAAACGTTTGGTATGTATATTTGAGCCTACAATTAGGT
          1 ATGGTACTAAATTGAGTTTTTTAAAAAACATTTGATATG-ATATTTGAGCCTACAATTAGGT

                                                                 **      
       3747 ATGGTACTAAATTGAGTTTTTTAAAAAACATTTGATATG-TATTTGAGCCTACTTTTAGGT
          1 ATGGTACTAAATTGAGTTTTTTAAAAAACATTTGATATGATATTTGAGCCTACAATTAGGT

             
       3807 A
          1 A

       3808 ATACGTTTGA


Statistics
Matches: 56,  Mismatches: 5, Indels: 2
        0.89            0.08        0.03

Matches are distributed among these distances:
  60   20  0.36
  62   36  0.64

ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42


Consensus pattern (61 bp):   
ATGGTACTAAATTGAGTTTTTTAAAAAACATTTGATATGATATTTGAGCCTACAATTAGGT
Done.