Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020339.1 Corchorus olitorius cultivar O-4 contig20372, 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: 8496
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31


Found at i:1397 original size:17 final size:18

Alignment explanation


    Indices: 1364--1399  Score: 56
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       1354 CTCCTCTTGC

                     *        
       1364 ATGAAAACACTTCTTTTT
          1 ATGAAAACAATTCTTTTT

                              
       1382 ATGAAAACAATT-TTTTT
          1 ATGAAAACAATTCTTTTT

             
       1399 A
          1 A

       1400 ACTACTTTTT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  17    6  0.35
  18   11  0.65

ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44


Consensus pattern (18 bp):   
ATGAAAACAATTCTTTTT

Found at i:1718 original size:16 final size:16

Alignment explanation


    Indices: 1697--1729  Score: 57
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       1687 GAAAAAATTA

                            
       1697 TGGCATATATTAAGAT
          1 TGGCATATATTAAGAT

                    *       
       1713 TGGCATATGTTAAGAT
          1 TGGCATATATTAAGAT

             
       1729 T
          1 T

       1730 ATGATGCATG


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.33, C:0.06, G:0.21, T:0.39


Consensus pattern (16 bp):   
TGGCATATATTAAGAT

Found at i:2322 original size:21 final size:21

Alignment explanation


    Indices: 2296--2345  Score: 64
    Period size: 21  Copynumber: 2.4  Consensus size: 21

       2286 GGAATGGCGA

                        **       
       2296 TGGCACGGGCATGGCCGGTGG
          1 TGGCACGGGCATAACCGGTGG

                      *          
       2317 TGGCACGGGCTTAACCGGTGG
          1 TGGCACGGGCATAACCGGTGG

            *       
       2338 CGGCACGG
          1 TGGCACGG

       2346 TGAATGGGTG


Statistics
Matches: 25,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  21   25  1.00

ACGTcount: A:0.12, C:0.26, G:0.48, T:0.14


Consensus pattern (21 bp):   
TGGCACGGGCATAACCGGTGG

Found at i:8465 original size:2 final size:2

Alignment explanation


    Indices: 8458--8496  Score: 78
    Period size: 2  Copynumber: 19.5  Consensus size: 2

       8448 ATCAGAGCCA

                                                                      
       8458 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   37  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Done.