Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019125.1 Corchorus olitorius cultivar O-4 contig19158, 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: 11967
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31


Found at i:2016 original size:15 final size:15

Alignment explanation


    Indices: 1998--2031  Score: 59
    Period size: 15  Copynumber: 2.3  Consensus size: 15

       1988 ACCGCCACGA

                           
       1998 GAGGAGGAAGAAGAG
          1 GAGGAGGAAGAAGAG

                       *   
       2013 GAGGAGGAAGAGGAG
          1 GAGGAGGAAGAAGAG

                
       2028 GAGG
          1 GAGG

       2032 GAATAGAGGG


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  15   18  1.00

ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00


Consensus pattern (15 bp):   
GAGGAGGAAGAAGAG

Found at i:2040 original size:15 final size:12

Alignment explanation


    Indices: 1997--2031  Score: 61
    Period size: 12  Copynumber: 2.9  Consensus size: 12

       1987 CACCGCCACG

                     *  
       1997 AGAGGAGGAAGA
          1 AGAGGAGGAGGA

                        
       2009 AGAGGAGGAGGA
          1 AGAGGAGGAGGA

                       
       2021 AGAGGAGGAGG
          1 AGAGGAGGAGG

       2032 GAATAGAGGG


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  12   22  1.00

ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00


Consensus pattern (12 bp):   
AGAGGAGGAGGA

Found at i:3474 original size:33 final size:33

Alignment explanation


    Indices: 3432--3535  Score: 115
    Period size: 33  Copynumber: 3.2  Consensus size: 33

       3422 TAAATGACAT

                                             
       3432 GTGGCATGCCACGTGTTAAAATGCAATGTCCAC
          1 GTGGCATGCCACGTGTTAAAATGCAATGTCCAC

                              **   *     *  *
       3465 GTGGCATGCCACGTG-TACCAT-AAATG-ACAT
          1 GTGGCATGCCACGTGTTAAAATGCAATGTCCAC

                                      **     
       3495 GTGGCATGCCACGTGTTAAAATGCAACATCCAC
          1 GTGGCATGCCACGTGTTAAAATGCAATGTCCAC

            *       
       3528 ATGGCATG
          1 GTGGCATG

       3536 TCATGTGTCA


Statistics
Matches: 55,  Mismatches: 13, Indels: 6
        0.74            0.18        0.08

Matches are distributed among these distances:
  30   17  0.31
  31    8  0.15
  32    6  0.11
  33   24  0.44

ACGTcount: A:0.29, C:0.24, G:0.24, T:0.23


Consensus pattern (33 bp):   
GTGGCATGCCACGTGTTAAAATGCAATGTCCAC

Found at i:3501 original size:30 final size:30

Alignment explanation


    Indices: 3419--3510  Score: 112
    Period size: 30  Copynumber: 3.0  Consensus size: 30

       3409 ATGATTTGTG

                                           
       3419 CCATAAATGACATGTGGCATGCCACGTGTTA
          1 CCATAAATGACATGTGGCATGCCACGTG-TA

            **   *     *  *                 
       3450 AAATGCAATGTCCACGTGGCATGCCACGTGTA
          1 CCAT-AAATG-ACATGTGGCATGCCACGTGTA

                                         
       3482 CCATAAATGACATGTGGCATGCCACGTGT
          1 CCATAAATGACATGTGGCATGCCACGTGT

       3511 TAAAATGCAA


Statistics
Matches: 49,  Mismatches: 10, Indels: 5
        0.77            0.16        0.08

Matches are distributed among these distances:
  30   18  0.37
  31    6  0.12
  32    8  0.16
  33   17  0.35

ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24


Consensus pattern (30 bp):   
CCATAAATGACATGTGGCATGCCACGTGTA

Found at i:4726 original size:2 final size:2

Alignment explanation


    Indices: 4719--4746  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

       4709 ATCTTGAATT

                                                     
       4719 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

       4747 CACCATACAT


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

Matches are distributed among these distances:
   2   26  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:7811 original size:13 final size:13

Alignment explanation


    Indices: 7793--7818  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       7783 TTTGGCTCAT

                         
       7793 GTAAATCTAGTTG
          1 GTAAATCTAGTTG

                         
       7806 GTAAATCTAGTTG
          1 GTAAATCTAGTTG

       7819 CTTATTTTTG


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38


Consensus pattern (13 bp):   
GTAAATCTAGTTG
Done.