Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011242.1 Corchorus olitorius cultivar O-4 contig11275, 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: 11311
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32


Found at i:3803 original size:19 final size:19

Alignment explanation


    Indices: 3779--3819  Score: 82
    Period size: 19  Copynumber: 2.2  Consensus size: 19

       3769 ACCCAATATT

                               
       3779 TCTGTCATGTCCAGTTAAG
          1 TCTGTCATGTCCAGTTAAG

                               
       3798 TCTGTCATGTCCAGTTAAG
          1 TCTGTCATGTCCAGTTAAG

               
       3817 TCT
          1 TCT

       3820 CCCATAAACC


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   22  1.00

ACGTcount: A:0.20, C:0.22, G:0.20, T:0.39


Consensus pattern (19 bp):   
TCTGTCATGTCCAGTTAAG

Found at i:4232 original size:12 final size:13

Alignment explanation


    Indices: 4215--4243  Score: 51
    Period size: 13  Copynumber: 2.3  Consensus size: 13

       4205 TATGTGCACC

                         
       4215 TTTTC-TTTCTTT
          1 TTTTCTTTTCTTT

                         
       4227 TTTTCTTTTCTTT
          1 TTTTCTTTTCTTT

                
       4240 TTTT
          1 TTTT

       4244 TTTAGAAAAA


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

Matches are distributed among these distances:
  12    5  0.31
  13   11  0.69

ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86


Consensus pattern (13 bp):   
TTTTCTTTTCTTT

Found at i:4236 original size:17 final size:16

Alignment explanation


    Indices: 4214--4246  Score: 57
    Period size: 17  Copynumber: 2.0  Consensus size: 16

       4204 ATATGTGCAC

                             
       4214 CTTTTCTTTCTTTTTTT
          1 CTTTTCTTT-TTTTTTT

                            
       4231 CTTTTCTTTTTTTTTT
          1 CTTTTCTTTTTTTTTT

       4247 AGAAAAAACC


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

Matches are distributed among these distances:
  16    7  0.44
  17    9  0.56

ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85


Consensus pattern (16 bp):   
CTTTTCTTTTTTTTTT

Found at i:5642 original size:13 final size:13

Alignment explanation


    Indices: 5624--5651  Score: 56
    Period size: 13  Copynumber: 2.2  Consensus size: 13

       5614 TACCAACTTG

                         
       5624 AACGCAAAAGCTT
          1 AACGCAAAAGCTT

                         
       5637 AACGCAAAAGCTT
          1 AACGCAAAAGCTT

              
       5650 AA
          1 AA

       5652 GACCTAGTTT


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

Matches are distributed among these distances:
  13   15  1.00

ACGTcount: A:0.50, C:0.21, G:0.14, T:0.14


Consensus pattern (13 bp):   
AACGCAAAAGCTT

Found at i:6100 original size:111 final size:111

Alignment explanation


    Indices: 5980--6196  Score: 391
    Period size: 111  Copynumber: 2.0  Consensus size: 111

       5970 TGAAAAACAG

                                                                      *      
       5980 TTTTTTATCTCCAAACGCAATGTCAAACCTTTGATTTCTTGGGTCTT-TCAAGTATATGTGTCAT
          1 TTTTTTATCTCCAAACGCAATGTCAAACCTTTGATTTCTTGGGTCTTAT-AAGTATATATGTCAT

                                            *              
       6044 TCTTACAGCCCATCCCTTATGATATGGGATGCGACACTAACAGCTTT
         65 TCTTACAGCCCATCCCTTATGATATGGGATGCAACACTAACAGCTTT

                                                                             
       6091 TTTTTTATCTCCAAACGCAATGTCAAACCTTTGATTTCTTGGGTCTTATAAGTATATATGTCATT
          1 TTTTTTATCTCCAAACGCAATGTCAAACCTTTGATTTCTTGGGTCTTATAAGTATATATGTCATT

                                  *                  
       6156 CTTACAGCCCATCCCTTATGATGTGGGATGCAACACTAACA
         66 CTTACAGCCCATCCCTTATGATATGGGATGCAACACTAACA

       6197 TGTGAATTCC


Statistics
Matches: 102,  Mismatches: 3, Indels: 2
        0.95            0.03        0.02

Matches are distributed among these distances:
 111  101  0.99
 112    1  0.01

ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37


Consensus pattern (111 bp):   
TTTTTTATCTCCAAACGCAATGTCAAACCTTTGATTTCTTGGGTCTTATAAGTATATATGTCATT
CTTACAGCCCATCCCTTATGATATGGGATGCAACACTAACAGCTTT
Done.