Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001340.1 Corchorus capsularis cultivar CVL-1 contig01340, 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: 8272
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30


Found at i:3367 original size:11 final size:11

Alignment explanation


    Indices: 3324--3361  Score: 51
    Period size: 11  Copynumber: 3.5  Consensus size: 11

       3314 TTCCTATATA

                *      
       3324 AAATAAATTAT
          1 AAATTAATTAT

                        
       3335 CAAA-TAATTAT
          1 -AAATTAATTAT

                       
       3346 AAATTAATTAT
          1 AAATTAATTAT

                 
       3357 AAATT
          1 AAATT

       3362 TGTTATGAAT


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  10    3  0.12
  11   18  0.75
  12    3  0.12

ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39


Consensus pattern (11 bp):   
AAATTAATTAT

Found at i:3570 original size:17 final size:18

Alignment explanation


    Indices: 3540--3577  Score: 51
    Period size: 17  Copynumber: 2.2  Consensus size: 18

       3530 AATGAGAACA

                          *   
       3540 ATTTCTCTTATTCTTCAT
          1 ATTTCTCTTATTCTCCAT

                     *        
       3558 ATTT-TCTTCTTCTCCAT
          1 ATTTCTCTTATTCTCCAT

               
       3575 ATT
          1 ATT

       3578 ATATTGTCTA


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  17   14  0.78
  18    4  0.22

ACGTcount: A:0.16, C:0.24, G:0.00, T:0.61


Consensus pattern (18 bp):   
ATTTCTCTTATTCTCCAT

Found at i:3731 original size:41 final size:42

Alignment explanation


    Indices: 3664--3747  Score: 134
    Period size: 41  Copynumber: 2.0  Consensus size: 42

       3654 ACAAAATTTC

                *         *                   *       
       3664 ATTTTTTAACTGAATTTTTCTTAAAAGAATTTATCAAATAAA
          1 ATTTCTTAACTGAAATTTTCTTAAAAGAATTTATAAAATAAA

                                                      
       3706 ATTTCTTAACT-AAATTTTCTTAAAAGAATTTATAAAATAAA
          1 ATTTCTTAACTGAAATTTTCTTAAAAGAATTTATAAAATAAA

             
       3747 A
          1 A

       3748 CAGCCGCACC


Statistics
Matches: 39,  Mismatches: 3, Indels: 1
        0.91            0.07        0.02

Matches are distributed among these distances:
  41   29  0.74
  42   10  0.26

ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43


Consensus pattern (42 bp):   
ATTTCTTAACTGAAATTTTCTTAAAAGAATTTATAAAATAAA

Found at i:8252 original size:1 final size:1

Alignment explanation


    Indices: 8246--8272  Score: 54
    Period size: 1  Copynumber: 27.0  Consensus size: 1

       8236 ACTAGTTTGG

                                       
       8246 AAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAA


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

Matches are distributed among these distances:
   1   26  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Done.