Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000450.1 Corchorus capsularis cultivar CVL-1 contig00450, 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: 4252
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32


Found at i:679 original size:13 final size:13

Alignment explanation


    Indices: 661--685  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

        651 TCACTAACAG

                         
        661 CAGGTTGAGACAA
          1 CAGGTTGAGACAA

                        
        674 CAGGTTGAGACA
          1 CAGGTTGAGACA

        686 GGAAAATTTC


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16


Consensus pattern (13 bp):   
CAGGTTGAGACAA

Found at i:3566 original size:36 final size:35

Alignment explanation


    Indices: 3519--3593  Score: 123
    Period size: 36  Copynumber: 2.1  Consensus size: 35

       3509 ATTTTTTACT

                         *                     
       3519 TTTCATCACCCTTGTTTTTACAAGGTGTAATCTTG
          1 TTTCATCACCCTTATTTTTACAAGGTGTAATCTTG

                                 *              
       3554 TTTCATTCACCCTTATTTTTATAAGGTGTAATCTTG
          1 TTTCA-TCACCCTTATTTTTACAAGGTGTAATCTTG

                
       3590 TTTC
          1 TTTC

       3594 GGCAATTAGT


Statistics
Matches: 37,  Mismatches: 2, Indels: 1
        0.93            0.05        0.03

Matches are distributed among these distances:
  35    5  0.14
  36   32  0.86

ACGTcount: A:0.20, C:0.19, G:0.12, T:0.49


Consensus pattern (35 bp):   
TTTCATCACCCTTATTTTTACAAGGTGTAATCTTG

Found at i:4182 original size:19 final size:17

Alignment explanation


    Indices: 4148--4197  Score: 52
    Period size: 16  Copynumber: 3.0  Consensus size: 17

       4138 TAGACTAATA

                        *    
       4148 TATTAT-ATTACATATT
          1 TATTATAATTACGTATT

                               
       4164 TATTAGCTAATTACGTA-T
          1 TATTA--TAATTACGTATT

                             
       4182 TATTATAATTA-GTATT
          1 TATTATAATTACGTATT

       4198 GGAATTTAAT


Statistics
Matches: 29,  Mismatches: 1, Indels: 8
        0.76            0.03        0.21

Matches are distributed among these distances:
  15    3  0.10
  16   12  0.41
  18    7  0.24
  19    7  0.24

ACGTcount: A:0.36, C:0.06, G:0.06, T:0.52


Consensus pattern (17 bp):   
TATTATAATTACGTATT
Done.