Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012613.1 Corchorus olitorius cultivar O-4 contig12646, 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: 20557
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31


Found at i:421 original size:19 final size:18

Alignment explanation


    Indices: 399--434  Score: 54
    Period size: 18  Copynumber: 2.0  Consensus size: 18

        389 AGGGTAATTA

                    *         
        399 AAAAAAAATTGTTTTCAT
          1 AAAAAAAAGTGTTTTCAT

                 *            
        417 AAAAAGAAGTGTTTTCAT
          1 AAAAAAAAGTGTTTTCAT

        435 GATAGAGGAG


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  18   16  1.00

ACGTcount: A:0.47, C:0.06, G:0.11, T:0.36


Consensus pattern (18 bp):   
AAAAAAAAGTGTTTTCAT

Found at i:1307 original size:19 final size:18

Alignment explanation


    Indices: 1283--1318  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       1273 TGAAGATTTA

                               
       1283 TTGAAGACAATTTGAAGAT
          1 TTGAAGACAA-TTGAAGAT

                    *        
       1302 TTGAAGACCATTGAAGA
          1 TTGAAGACAATTGAAGA

       1319 ATAATTTCAA


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

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28


Consensus pattern (18 bp):   
TTGAAGACAATTGAAGAT

Found at i:10389 original size:16 final size:16

Alignment explanation


    Indices: 10368--10400  Score: 66
    Period size: 16  Copynumber: 2.1  Consensus size: 16

      10358 GAAAAAATTA

                            
      10368 TGGCATATATTAAGAT
          1 TGGCATATATTAAGAT

                            
      10384 TGGCATATATTAAGAT
          1 TGGCATATATTAAGAT

             
      10400 T
          1 T

      10401 ATGATGCATG


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:0.36, C:0.06, G:0.18, T:0.39


Consensus pattern (16 bp):   
TGGCATATATTAAGAT

Found at i:10992 original size:21 final size:21

Alignment explanation


    Indices: 10963--11012  Score: 64
    Period size: 21  Copynumber: 2.4  Consensus size: 21

      10953 GGAATGATGA

                *       **       
      10963 TGGCTCGGGCATGGCCGGTGG
          1 TGGCACGGGCATAACCGGTGG

                      *          
      10984 TGGCACGGGCTTAACCGGTGG
          1 TGGCACGGGCATAACCGGTGG

                    
      11005 TGGCACGG
          1 TGGCACGG

      11013 TGAATGGGCG


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:0.10, C:0.24, G:0.48, T:0.18


Consensus pattern (21 bp):   
TGGCACGGGCATAACCGGTGG

Found at i:15149 original size:16 final size:15

Alignment explanation


    Indices: 15111--15152  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

      15101 ACAGAGATTG

                   *       
      15111 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                           
      15126 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
      15141 ACTAGAAAACAA
          1 AC-AGAAAACAA

      15153 AGCAGAGTAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA

Found at i:15928 original size:11 final size:11

Alignment explanation


    Indices: 15912--15937  Score: 52
    Period size: 11  Copynumber: 2.4  Consensus size: 11

      15902 CCTTTGCCTA

                       
      15912 AAAACTAGAAG
          1 AAAACTAGAAG

                       
      15923 AAAACTAGAAG
          1 AAAACTAGAAG

                
      15934 AAAA
          1 AAAA

      15938 GAAATTATCT


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

Matches are distributed among these distances:
  11   15  1.00

ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08


Consensus pattern (11 bp):   
AAAACTAGAAG
Done.