Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013928.1 Corchorus capsularis cultivar CVL-1 contig13949, 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: 10662
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33


Found at i:276 original size:19 final size:17

Alignment explanation


    Indices: 242--283  Score: 57
    Period size: 19  Copynumber: 2.4  Consensus size: 17

        232 TTACATATAC

                             
        242 ATATTAATATTTGTATT
          1 ATATTAATATTTGTATT

                               
        259 ATATTATATATATTGTATT
          1 ATATTA-ATAT-TTGTATT

             *    
        278 AGATTA
          1 ATATTA

        284 GGAACTCCAA


Statistics
Matches: 22,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  17    6  0.27
  18    4  0.18
  19   12  0.55

ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55


Consensus pattern (17 bp):   
ATATTAATATTTGTATT

Found at i:1825 original size:35 final size:35

Alignment explanation


    Indices: 1786--1864  Score: 108
    Period size: 35  Copynumber: 2.3  Consensus size: 35

       1776 ATAAGAACTT

                                               
       1786 GATGAACAATGAAGAACGTTGCAAAGAAAAATTGA
          1 GATGAACAATGAAGAACGTTGCAAAGAAAAATTGA

                             *   * *      *    
       1821 GATGAACAATGAAGAACTTTGTAGAGAAAATTTGA
          1 GATGAACAATGAAGAACGTTGCAAAGAAAAATTGA

                       
       1856 GA-GAA-AATG
          1 GATGAACAATG

       1865 CTCAGGGCTT


Statistics
Matches: 40,  Mismatches: 4, Indels: 2
        0.87            0.09        0.04

Matches are distributed among these distances:
  33    4  0.10
  34    3  0.08
  35   33  0.82

ACGTcount: A:0.49, C:0.06, G:0.24, T:0.20


Consensus pattern (35 bp):   
GATGAACAATGAAGAACGTTGCAAAGAAAAATTGA

Found at i:3343 original size:36 final size:36

Alignment explanation


    Indices: 3296--3366  Score: 142
    Period size: 36  Copynumber: 2.0  Consensus size: 36

       3286 GTAAATTAAG

                                                
       3296 GTATAAACAGATGTGGAGCATTCCTATTAGCCACGA
          1 GTATAAACAGATGTGGAGCATTCCTATTAGCCACGA

                                               
       3332 GTATAAACAGATGTGGAGCATTCCTATTAGCCACG
          1 GTATAAACAGATGTGGAGCATTCCTATTAGCCACG

       3367 TTGGATTCTA


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  36   35  1.00

ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25


Consensus pattern (36 bp):   
GTATAAACAGATGTGGAGCATTCCTATTAGCCACGA

Found at i:4821 original size:2 final size:2

Alignment explanation


    Indices: 4814--4855  Score: 84
    Period size: 2  Copynumber: 21.0  Consensus size: 2

       4804 CTAGTACAAC

                                                                          
       4814 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       4856 CACCATCAGA


Statistics
Matches: 40,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   40  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:8545 original size:3 final size:3

Alignment explanation


    Indices: 8537--8568  Score: 64
    Period size: 3  Copynumber: 10.7  Consensus size: 3

       8527 ATTCAAAATA

                                                      
       8537 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA

       8569 AACCTACTAT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   29  1.00

ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66


Consensus pattern (3 bp):   
TAT

Done.