Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003529.1 Corchorus capsularis cultivar CVL-1 contig03537, 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, 610

Length: 1018
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.38


Found at i:113 original size:5 final size:5

Alignment explanation


    Indices: 103--128  Score: 52
    Period size: 5  Copynumber: 5.2  Consensus size: 5

         93 TTTTGAGAAC

                                           
        103 TTGAT TTGAT TTGAT TTGAT TTGAT T
          1 TTGAT TTGAT TTGAT TTGAT TTGAT T

        129 CAAGGGTCGA


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

Matches are distributed among these distances:
   5   21  1.00

ACGTcount: A:0.19, C:0.00, G:0.19, T:0.62


Consensus pattern (5 bp):   
TTGAT

Found at i:170 original size:40 final size:41

Alignment explanation


    Indices: 121--200  Score: 108
    Period size: 41  Copynumber: 2.0  Consensus size: 41

        111 ATTTGATTTG

                *               *   *  *             
        121 ATTTGATTCAAGGGTC-GAATGACTTGGTCTTGAATTGATA
          1 ATTTAATTCAAGGGTCTGAACGACGTGATCTTGAATTGATA

                              *                     
        161 ATTTAATTCAAGGGTCTGGACGACGTGATCTTGAATTGAT
          1 ATTTAATTCAAGGGTCTGAACGACGTGATCTTGAATTGAT

        201 GACTTGGGAA


Statistics
Matches: 34,  Mismatches: 5, Indels: 1
        0.85            0.12        0.03

Matches are distributed among these distances:
  40   15  0.44
  41   19  0.56

ACGTcount: A:0.28, C:0.11, G:0.25, T:0.36


Consensus pattern (41 bp):   
ATTTAATTCAAGGGTCTGAACGACGTGATCTTGAATTGATA

Found at i:276 original size:104 final size:98

Alignment explanation


    Indices: 111--297  Score: 232
    Period size: 99  Copynumber: 1.8  Consensus size: 98

        101 ACTTGATTTG

                         *                      *   *                        
        111 ATTTGATTTGATTTGATTCAAGGGTCGAATGACTTGGTCTTGAATTGATAATTTAATTCAAGGGT
          1 ATTTGATTTGATTCGATTCAAGGGTCGAATGACTTGATCTCGAATTGATAATTTAATTCAAGGGT

               *                              
        176 CTGGACGACGTGATCTTGAATTGATGACTTGGGA
         66 C-GAACGACGTGATCTTGAATTGATGACTTGGGA

                               *                                        *    
        210 ATTTGATTTGATTCGATTCGAGGGTCTTTG-ATGACTTGATCTCGAATTGATGATAATTTGATTC
          1 ATTTGATTTGATTCGATTCAAGGGTC---GAATGACTTGATCTCGAA-T--TGATAATTTAATTC

                      *   *         
        274 AAGGGTCGAATGACTTGATCTTGA
         60 AAGGGTCGAACGACGTGATCTTGA

        298 GCGAACACAA


Statistics
Matches: 74,  Mismatches: 8, Indels: 8
        0.82            0.09        0.09

Matches are distributed among these distances:
  99   24  0.32
 101   14  0.19
 102    2  0.03
 103   14  0.19
 104   20  0.27

ACGTcount: A:0.26, C:0.11, G:0.25, T:0.39


Consensus pattern (98 bp):   
ATTTGATTTGATTCGATTCAAGGGTCGAATGACTTGATCTCGAATTGATAATTTAATTCAAGGGT
CGAACGACGTGATCTTGAATTGATGACTTGGGA

Found at i:612 original size:16 final size:16

Alignment explanation


    Indices: 591--622  Score: 64
    Period size: 16  Copynumber: 2.0  Consensus size: 16

        581 AAAATACTTC

                            
        591 AGAGCTTTTCTGCTTT
          1 AGAGCTTTTCTGCTTT

                            
        607 AGAGCTTTTCTGCTTT
          1 AGAGCTTTTCTGCTTT

        623 CTGAATTGTG


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.12, C:0.19, G:0.19, T:0.50


Consensus pattern (16 bp):   
AGAGCTTTTCTGCTTT
Done.