Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019235.1 Corchorus olitorius cultivar O-4 contig19268, 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: 61389
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:1504 original size:21 final size:21

Alignment explanation


    Indices: 1478--1524  Score: 67
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       1468 TTTTGTTCCC

                                 
       1478 TTTTTCCATTTGCTTTCCTAT
          1 TTTTTCCATTTGCTTTCCTAT

                  **    *        
       1499 TTTTTCTTTTTGTTTTCCTAT
          1 TTTTTCCATTTGCTTTCCTAT

                 
       1520 TTTTT
          1 TTTTT

       1525 TTCAAGTGCA


Statistics
Matches: 23,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  21   23  1.00

ACGTcount: A:0.06, C:0.17, G:0.04, T:0.72


Consensus pattern (21 bp):   
TTTTTCCATTTGCTTTCCTAT

Found at i:3080 original size:29 final size:30

Alignment explanation


    Indices: 3029--3087  Score: 86
    Period size: 29  Copynumber: 2.0  Consensus size: 30

       3019 TATTTGTCGG

                                          
       3029 AATTTTATTAAATATATAAATATAAATAAA
          1 AATTTTATTAAATATATAAATATAAATAAA

                  *                        
       3059 AATTTTTTTGAAATA-A-AAATATAAATAAA
          1 AATTTTATT-AAATATATAAATATAAATAAA

       3088 CTTAATTATT


Statistics
Matches: 27,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  29   13  0.48
  30    9  0.33
  31    5  0.19

ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39


Consensus pattern (30 bp):   
AATTTTATTAAATATATAAATATAAATAAA

Found at i:12911 original size:4 final size:4

Alignment explanation


    Indices: 12902--12935  Score: 50
    Period size: 4  Copynumber: 8.2  Consensus size: 4

      12892 TAATTTGTAA

                                        *             
      12902 TTTG TTTG TTTG TTTG TTTG TTTA TTTGG TTTG T
          1 TTTG TTTG TTTG TTTG TTTG TTTG TTT-G TTTG T

      12936 AGGTAGGTAT


Statistics
Matches: 27,  Mismatches: 2, Indels: 2
        0.87            0.06        0.06

Matches are distributed among these distances:
   4   24  0.89
   5    3  0.11

ACGTcount: A:0.03, C:0.00, G:0.24, T:0.74


Consensus pattern (4 bp):   
TTTG

Found at i:15069 original size:11 final size:11

Alignment explanation


    Indices: 15055--15080  Score: 52
    Period size: 11  Copynumber: 2.4  Consensus size: 11

      15045 GACTACTATT

                       
      15055 ATTCTACTTTC
          1 ATTCTACTTTC

                       
      15066 ATTCTACTTTC
          1 ATTCTACTTTC

                
      15077 ATTC
          1 ATTC

      15081 ATAGAAAATT


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:0.19, C:0.27, G:0.00, T:0.54


Consensus pattern (11 bp):   
ATTCTACTTTC

Found at i:36049 original size:31 final size:31

Alignment explanation


    Indices: 35991--36101  Score: 123
    Period size: 31  Copynumber: 3.5  Consensus size: 31

      35981 TCCTTTTGTG

                   *   *                 ** 
      35991 CACGTGGTATGTCACGTGTCACTTTTTTGAAA
          1 CACGTGGCATGCCACGTGTCAC-TTTTTGGTA

               *                           
      36023 CACATGGCATGCCACGTGTCACTTTTTGGTA
          1 CACGTGGCATGCCACGTGTCACTTTTTGGTA

                   **  *   *    *          
      36054 CACGTGGTGTGTCACATGTCGCTTTTTGGTA
          1 CACGTGGCATGCCACGTGTCACTTTTTGGTA

                             
      36085 CACGTGGCATGCCACGT
          1 CACGTGGCATGCCACGT

      36102 TGGACACCGT


Statistics
Matches: 64,  Mismatches: 15, Indels: 1
        0.80            0.19        0.01

Matches are distributed among these distances:
  31   45  0.70
  32   19  0.30

ACGTcount: A:0.18, C:0.23, G:0.25, T:0.33


Consensus pattern (31 bp):   
CACGTGGCATGCCACGTGTCACTTTTTGGTA

Found at i:58121 original size:13 final size:15

Alignment explanation


    Indices: 58103--58134  Score: 50
    Period size: 14  Copynumber: 2.3  Consensus size: 15

      58093 TCAACTTTCC

                           
      58103 TTTTTC-GATTTTT-
          1 TTTTTCTGATTTTTA

                           
      58116 TTTTTCTGATTTTTA
          1 TTTTTCTGATTTTTA

                
      58131 TTTT
          1 TTTT

      58135 GTTGGTCCGT


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  13    6  0.35
  14    7  0.41
  15    4  0.24

ACGTcount: A:0.09, C:0.06, G:0.06, T:0.78


Consensus pattern (15 bp):   
TTTTTCTGATTTTTA
Done.