Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014043.1 Corchorus olitorius cultivar O-4 contig14076, 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: 7027
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29


Found at i:27 original size:21 final size:21

Alignment explanation


    Indices: 1--40  Score: 80
    Period size: 21  Copynumber: 1.9  Consensus size: 21

                                 
          1 TTGGAACTTGCTCCAATGAGC
          1 TTGGAACTTGCTCCAATGAGC

                               
         22 TTGGAACTTGCTCCAATGA
          1 TTGGAACTTGCTCCAATGA

         41 ACTTCTATCA


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   19  1.00

ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30


Consensus pattern (21 bp):   
TTGGAACTTGCTCCAATGAGC

Found at i:1918 original size:33 final size:33

Alignment explanation


    Indices: 1848--1949  Score: 111
    Period size: 33  Copynumber: 3.1  Consensus size: 33

       1838 ATGATCAACC

                                     ** *      
       1848 AAAACAG-ATTTGTTTTCATCACAATTAGCATCC-
          1 AAAACAGAATTTG-TTTCATCACAAACAACA-CCT

                                             
       1881 AAAACAGAATTTGTTTCATCACAAACAACACCT
          1 AAAACAGAATTTGTTTCATCACAAACAACACCT

                           *                * 
       1914 AAAACA-AATTTAGTGTCATCACAAACAACACTT
          1 AAAACAGAATTT-GTTTCATCACAAACAACACCT

               
       1947 AAA
          1 AAA

       1950 TTAGGTTTAG


Statistics
Matches: 61,  Mismatches: 5, Indels: 6
        0.85            0.07        0.08

Matches are distributed among these distances:
  32    7  0.11
  33   49  0.80
  34    5  0.08

ACGTcount: A:0.45, C:0.22, G:0.07, T:0.26


Consensus pattern (33 bp):   
AAAACAGAATTTGTTTCATCACAAACAACACCT

Found at i:1959 original size:33 final size:33

Alignment explanation


    Indices: 1881--1990  Score: 105
    Period size: 33  Copynumber: 3.3  Consensus size: 33

       1871 ATTAGCATCC

                           *                  
       1881 AAAACAGAATTT-GTTTCATCACAAACAACACCT
          1 AAAACA-AATTTAGTATCATCACAAACAACACCT

                          *                * 
       1914 AAAACAAATTTAGTGTCATCACAAACAACACTT
          1 AAAACAAATTTAGTATCATCACAAACAACACCT

               ** **              * *     *  
       1947 AAATTAGGTTTAGTATCATCACTAGCAACATCT
          1 AAAACAAATTTAGTATCATCACAAACAACACCT

                  *    
       1980 AAAACAGATTT
          1 AAAACAAATTT

       1991 CATGTCATTG


Statistics
Matches: 62,  Mismatches: 14, Indels: 2
        0.79            0.18        0.03

Matches are distributed among these distances:
  32    5  0.08
  33   57  0.92

ACGTcount: A:0.45, C:0.20, G:0.08, T:0.27


Consensus pattern (33 bp):   
AAAACAAATTTAGTATCATCACAAACAACACCT

Found at i:1968 original size:66 final size:66

Alignment explanation


    Indices: 1896--2022  Score: 166
    Period size: 66  Copynumber: 1.9  Consensus size: 66

       1886 AGAATTTGTT

                                                               *    *        
       1896 TCATCACAAACAACACCTAAAACAAATTT-AGTGTCATCACAAACAACACTTAAATTAGGTTTAG
          1 TCATCACAAACAACACCTAAAACAAATTTCA-TGTCATCACAAACAACACTCAAATCAGGTTTAG

              
       1960 TA
         65 TA

                   * *     *        *            **                      
       1962 TCATCACTAGCAACATCTAAAACAGATTTCATGTCATTGCAAACAACACTCAAATCAGGTT
          1 TCATCACAAACAACACCTAAAACAAATTTCATGTCATCACAAACAACACTCAAATCAGGTT

       2023 CAGAATTACT


Statistics
Matches: 52,  Mismatches: 8, Indels: 2
        0.84            0.13        0.03

Matches are distributed among these distances:
  66   51  0.98
  67    1  0.02

ACGTcount: A:0.43, C:0.23, G:0.09, T:0.26


Consensus pattern (66 bp):   
TCATCACAAACAACACCTAAAACAAATTTCATGTCATCACAAACAACACTCAAATCAGGTTTAGT
A

Found at i:2638 original size:15 final size:16

Alignment explanation


    Indices: 2608--2640  Score: 50
    Period size: 15  Copynumber: 2.1  Consensus size: 16

       2598 AAACTAAGTG

                            
       2608 GAGCTTGTACGATTTT
          1 GAGCTTGTACGATTTT

                     *      
       2624 GAGCTTGT-TGATTTT
          1 GAGCTTGTACGATTTT

              
       2639 GA
          1 GA

       2641 ACCCCCAAGG


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  15    8  0.50
  16    8  0.50

ACGTcount: A:0.18, C:0.09, G:0.27, T:0.45


Consensus pattern (16 bp):   
GAGCTTGTACGATTTT

Found at i:6369 original size:33 final size:33

Alignment explanation


    Indices: 6309--6437  Score: 129
    Period size: 33  Copynumber: 3.9  Consensus size: 33

       6299 ATGATCAACC

                          *   *              
       6309 AAAACAGATTT-GTTTCAGCACAAACAACACCT
          1 AAAACAGATTTAGTGTCATCACAAACAACACCT

                                             
       6341 AAAACAGATTTAGTGTCATCACAAACAACA-CT
          1 AAAACAGATTTAGTGTCATCACAAACAACACCT

                **  *      *     *         *  
       6373 CAAATTAGGTTTAGTATCATCGCAAACAACATCT
          1 -AAAACAGATTTAGTGTCATCACAAACAACACCT

                                **          
       6407 AAAACAGATTTCA-TGTCATTGCAAACAACAC
          1 AAAACAGATTT-AGTGTCATCACAAACAACAC

       6438 TCAAATCAGG


Statistics
Matches: 80,  Mismatches: 13, Indels: 7
        0.80            0.13        0.07

Matches are distributed among these distances:
  32   13  0.16
  33   64  0.80
  34    3  0.04

ACGTcount: A:0.43, C:0.22, G:0.10, T:0.24


Consensus pattern (33 bp):   
AAAACAGATTTAGTGTCATCACAAACAACACCT
Done.