Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016718.1 Corchorus olitorius cultivar O-4 contig16751, 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: 7929
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37


Found at i:49 original size:21 final size:24

Alignment explanation


    Indices: 7--54  Score: 66
    Period size: 24  Copynumber: 2.1  Consensus size: 24

          1 CTTCTA

                                    
          7 TTTTTTTATATCTTTGGATTGTTG
          1 TTTTTTTATATCTTTGGATTGTTG

                   *                
         31 TTTTTTTCTAT-TTT-G-TTGTTG
          1 TTTTTTTATATCTTTGGATTGTTG

               
         52 TTT
          1 TTT

         55 CATTTTTTTT


Statistics
Matches: 23,  Mismatches: 1, Indels: 3
        0.85            0.04        0.11

Matches are distributed among these distances:
  21    9  0.39
  22    1  0.04
  23    3  0.13
  24   10  0.43

ACGTcount: A:0.08, C:0.04, G:0.15, T:0.73


Consensus pattern (24 bp):   
TTTTTTTATATCTTTGGATTGTTG

Found at i:2852 original size:2 final size:2

Alignment explanation


    Indices: 2841--2872  Score: 57
    Period size: 2  Copynumber: 16.5  Consensus size: 2

       2831 ATAGAAGCTT

                                                             
       2841 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       2873 CATACCTTGA


Statistics
Matches: 29,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   28  0.97

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


Consensus pattern (2 bp):   
TA

Found at i:3336 original size:14 final size:15

Alignment explanation


    Indices: 3315--3350  Score: 51
    Period size: 13  Copynumber: 2.6  Consensus size: 15

       3305 TCAATCCTAA

                           
       3315 TTTT-AAAAAGCAC-
          1 TTTTCAAAAAGCACT

                           
       3328 TTTTC-AAAAGCACT
          1 TTTTCAAAAAGCACT

                     
       3342 TTTTCAAAA
          1 TTTTCAAAA

       3351 TCAAGTCTTT


Statistics
Matches: 20,  Mismatches: 0, Indels: 4
        0.83            0.00        0.17

Matches are distributed among these distances:
  13   12  0.60
  14    5  0.25
  15    3  0.15

ACGTcount: A:0.42, C:0.17, G:0.06, T:0.36


Consensus pattern (15 bp):   
TTTTCAAAAAGCACT

Found at i:5414 original size:14 final size:14

Alignment explanation


    Indices: 5395--5422  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

       5385 AGAAATTAAA

                          
       5395 CGACTTGATGAGTG
          1 CGACTTGATGAGTG

                          
       5409 CGACTTGATGAGTG
          1 CGACTTGATGAGTG

       5423 GTAATTTGTC


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.21, C:0.14, G:0.36, T:0.29


Consensus pattern (14 bp):   
CGACTTGATGAGTG

Found at i:6876 original size:13 final size:13

Alignment explanation


    Indices: 6858--6900  Score: 59
    Period size: 13  Copynumber: 3.2  Consensus size: 13

       6848 TAATGAATAA

                         
       6858 AATAAAATAAAAT
          1 AATAAAATAAAAT

                          
       6871 AATAAAATAAATAT
          1 AATAAAATAAA-AT

                 *    *  
       6885 AATAATATAATAT
          1 AATAAAATAAAAT

               
       6898 AAT
          1 AAT

       6901 TTTTATATGA


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

Matches are distributed among these distances:
  13   16  0.59
  14   11  0.41

ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30


Consensus pattern (13 bp):   
AATAAAATAAAAT

Found at i:6888 original size:17 final size:17

Alignment explanation


    Indices: 6848--6896  Score: 62
    Period size: 17  Copynumber: 2.8  Consensus size: 17

       6838 ATATTGTCCT

                               
       6848 TAATGAATAAAATAAAATA
          1 TAAT-AATAAAAT-AAATA

            *                
       6867 AAATAATAAAATAAATA
          1 TAATAATAAAATAAATA

                    *    
       6884 TAATAATATAATA
          1 TAATAATAAAATA

       6897 TAATTTTTAT


Statistics
Matches: 27,  Mismatches: 3, Indels: 2
        0.84            0.09        0.06

Matches are distributed among these distances:
  17   16  0.59
  18    8  0.30
  19    3  0.11

ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29


Consensus pattern (17 bp):   
TAATAATAAAATAAATA
Done.