Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004851.1 Corchorus capsularis cultivar CVL-1 contig04869, 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: 20700
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33


Found at i:2633 original size:11 final size:11

Alignment explanation


    Indices: 2603--2650  Score: 53
    Period size: 11  Copynumber: 4.4  Consensus size: 11

       2593 ATACATATAT

                    ** 
       2603 ATTTATAACAA
          1 ATTTATAATTA

                       
       2614 ATTTATAATTA
          1 ATTTATAATTA

                       
       2625 ATTTATAATT-
          1 ATTTATAATTA

                       *
       2635 ATTTGATAATTT
          1 ATTT-ATAATTA

                
       2647 ATTT
          1 ATTT

       2651 TATATATAGG


Statistics
Matches: 33,  Mismatches: 2, Indels: 3
        0.87            0.05        0.08

Matches are distributed among these distances:
  10    4  0.12
  11   25  0.76
  12    4  0.12

ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54


Consensus pattern (11 bp):   
ATTTATAATTA

Found at i:13326 original size:3 final size:3

Alignment explanation


    Indices: 13318--13347  Score: 60
    Period size: 3  Copynumber: 10.0  Consensus size: 3

      13308 TATTACTATG

                                                   
      13318 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
          1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT

      13348 GTTTAAAGCA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   27  1.00

ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67


Consensus pattern (3 bp):   
CTT

Found at i:13487 original size:2 final size:2

Alignment explanation


    Indices: 13480--13508  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

      13470 AATTGTAGAT

                                                       
      13480 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      13509 TCTGAAGTTC


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:17144 original size:1 final size:1

Alignment explanation


    Indices: 17138--17163  Score: 52
    Period size: 1  Copynumber: 26.0  Consensus size: 1

      17128 ACAAAATTTC

                                      
      17138 AAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAA

      17164 GAACCTTCCT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   25  1.00

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


Consensus pattern (1 bp):   
A

Found at i:19006 original size:11 final size:11

Alignment explanation


    Indices: 18992--19029  Score: 51
    Period size: 11  Copynumber: 3.5  Consensus size: 11

      18982 ATTCATAACA

                       
      18992 AATTTATAATT
          1 AATTTATAATT

                       
      19003 AATTTATAATT
          1 AATTTATAATT

                        
      19014 -ATTTGATAATT
          1 AATTT-ATAATT

            *    
      19025 TATTT
          1 AATTT

      19030 TATATAGGAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 3
        0.89            0.00        0.11

Matches are distributed among these distances:
  10    4  0.16
  11   17  0.68
  12    4  0.16

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


Consensus pattern (11 bp):   
AATTTATAATT
Done.