Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018273.1 Corchorus olitorius cultivar O-4 contig18306, 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: 4831
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32


Found at i:1214 original size:2 final size:2

Alignment explanation


    Indices: 1207--1262  Score: 57
    Period size: 2  Copynumber: 30.0  Consensus size: 2

       1197 CATTTATACA

                                                *                 *   *   
       1207 AT AT AT AT AT AT AT AT AT AT AT AT GT AT -T A- AT AT TT AG A-
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                                      
       1246 AT -T AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT

       1263 TAATACTAAA


Statistics
Matches: 45,  Mismatches: 5, Indels: 8
        0.78            0.09        0.14

Matches are distributed among these distances:
   1    4  0.09
   2   41  0.91

ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:1822 original size:12 final size:13

Alignment explanation


    Indices: 1793--1825  Score: 59
    Period size: 13  Copynumber: 2.6  Consensus size: 13

       1783 AACCCATTCG

                         
       1793 ATCCAATTTTTCT
          1 ATCCAATTTTTCT

                         
       1806 ATCCAATTTTTCT
          1 ATCCAATTTTTCT

                    
       1819 -TCCAATT
          1 ATCCAATT

       1826 ACAACTCTGC


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  12    7  0.35
  13   13  0.65

ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52


Consensus pattern (13 bp):   
ATCCAATTTTTCT

Found at i:2552 original size:45 final size:45

Alignment explanation


    Indices: 2501--2592  Score: 157
    Period size: 45  Copynumber: 2.0  Consensus size: 45

       2491 ATTGCATGCA

                                               *         
       2501 ACACATTACATAAAGGCACGTGTCCCTAAATAAATGACATTCACT
          1 ACACATTACATAAAGGCACGTGTCCCTAAATAAATCACATTCACT

                                         *       *       
       2546 ACACATTACATAAAGGCACGTGTCCCTAATTAAATCATATTCACT
          1 ACACATTACATAAAGGCACGTGTCCCTAAATAAATCACATTCACT

              
       2591 AC
          1 AC

       2593 GTACTAAAAG


Statistics
Matches: 44,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  45   44  1.00

ACGTcount: A:0.39, C:0.25, G:0.10, T:0.26


Consensus pattern (45 bp):   
ACACATTACATAAAGGCACGTGTCCCTAAATAAATCACATTCACT

Found at i:3298 original size:22 final size:24

Alignment explanation


    Indices: 3263--3316  Score: 60
    Period size: 22  Copynumber: 2.3  Consensus size: 24

       3253 ATAAATGTTG

                            *      *
       3263 CTGATAA-TCTTCT-CTTTTATCT
          1 CTGATAATTCTTCTCCATTTATCA

                                    
       3285 CTGATAATTC-TCTCCATTTATCA
          1 CTGATAATTCTTCTCCATTTATCA

                     
       3308 CTTGATAAT
          1 C-TGATAAT

       3317 ATCTAGCCAG


Statistics
Matches: 27,  Mismatches: 2, Indels: 4
        0.82            0.06        0.12

Matches are distributed among these distances:
  22   10  0.37
  23   10  0.37
  24    7  0.26

ACGTcount: A:0.24, C:0.22, G:0.06, T:0.48


Consensus pattern (24 bp):   
CTGATAATTCTTCTCCATTTATCA

Found at i:4130 original size:11 final size:11

Alignment explanation


    Indices: 4114--4145  Score: 55
    Period size: 11  Copynumber: 2.9  Consensus size: 11

       4104 AATATGTGCT

                       
       4114 ATAACAAAATC
          1 ATAACAAAATC

                       
       4125 ATAACAAAATC
          1 ATAACAAAATC

                 *    
       4136 ATAACCAAAT
          1 ATAACAAAAT

       4146 ACACTCTCCT


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  11   20  1.00

ACGTcount: A:0.62, C:0.19, G:0.00, T:0.19


Consensus pattern (11 bp):   
ATAACAAAATC
Done.