Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011137.1 Corchorus olitorius cultivar O-4 contig11170, 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: 4343
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30


Found at i:995 original size:31 final size:31

Alignment explanation


    Indices: 960--1021  Score: 115
    Period size: 31  Copynumber: 2.0  Consensus size: 31

        950 ATTAATCCTA

                            *              
        960 GCTGATGGGATAGAGGGGTTGTTCTATCTAT
          1 GCTGATGGGATAGAGGAGTTGTTCTATCTAT

                                           
        991 GCTGATGGGATAGAGGAGTTGTTCTATCTAT
          1 GCTGATGGGATAGAGGAGTTGTTCTATCTAT

       1022 CTGTGGAAGG


Statistics
Matches: 30,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  31   30  1.00

ACGTcount: A:0.21, C:0.10, G:0.34, T:0.35


Consensus pattern (31 bp):   
GCTGATGGGATAGAGGAGTTGTTCTATCTAT

Found at i:1558 original size:7 final size:8

Alignment explanation


    Indices: 1541--1606  Score: 54
    Period size: 7  Copynumber: 8.8  Consensus size: 8

       1531 CCGCCATCTA

                    
       1541 ATTGAAT-
          1 ATTGAATG

                    
       1548 ATTG-ATG
          1 ATTGAATG

                    *
       1555 ATTGAAGTA
          1 ATTGAA-TG

                    
       1564 ATTGAAT-
          1 ATTGAATG

                    
       1571 ATTG-ATG
          1 ATTGAATG

                    *
       1578 ATTGAAGTA
          1 ATTGAA-TG

                    
       1587 ATTGAAT-
          1 ATTGAATG

                    
       1594 ATTG-ATG
          1 ATTGAATG

                  
       1601 ATTGAA
          1 ATTGAA

       1607 GATGAGAGTA


Statistics
Matches: 49,  Mismatches: 2, Indels: 15
        0.74            0.03        0.23

Matches are distributed among these distances:
   6    6  0.12
   7   24  0.49
   8    5  0.10
   9   14  0.29

ACGTcount: A:0.39, C:0.00, G:0.21, T:0.39


Consensus pattern (8 bp):   
ATTGAATG

Found at i:1569 original size:23 final size:23

Alignment explanation


    Indices: 1539--1607  Score: 138
    Period size: 23  Copynumber: 3.0  Consensus size: 23

       1529 AACCGCCATC

                                   
       1539 TAATTGAATATTGATGATTGAAG
          1 TAATTGAATATTGATGATTGAAG

                                   
       1562 TAATTGAATATTGATGATTGAAG
          1 TAATTGAATATTGATGATTGAAG

                                   
       1585 TAATTGAATATTGATGATTGAAG
          1 TAATTGAATATTGATGATTGAAG

       1608 ATGAGAGTAG


Statistics
Matches: 46,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  23   46  1.00

ACGTcount: A:0.39, C:0.00, G:0.22, T:0.39


Consensus pattern (23 bp):   
TAATTGAATATTGATGATTGAAG

Found at i:1925 original size:15 final size:15

Alignment explanation


    Indices: 1905--1934  Score: 60
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       1895 GGGAAATGGC

                           
       1905 CCAGTGACATCTGAT
          1 CCAGTGACATCTGAT

                           
       1920 CCAGTGACATCTGAT
          1 CCAGTGACATCTGAT

       1935 AACGTATCTC


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   15  1.00

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


Consensus pattern (15 bp):   
CCAGTGACATCTGAT

Found at i:2166 original size:16 final size:16

Alignment explanation


    Indices: 2145--2177  Score: 66
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       2135 TTCTTTGCGG

                            
       2145 ATTAATATCGTATATA
          1 ATTAATATCGTATATA

                            
       2161 ATTAATATCGTATATA
          1 ATTAATATCGTATATA

             
       2177 A
          1 A

       2178 AGGGCTTTTC


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   17  1.00

ACGTcount: A:0.45, C:0.06, G:0.06, T:0.42


Consensus pattern (16 bp):   
ATTAATATCGTATATA
Done.