Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010270.1 Corchorus olitorius cultivar O-4 contig10302, 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: 6534
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38


Found at i:130 original size:33 final size:33

Alignment explanation


    Indices: 88--164  Score: 154
    Period size: 33  Copynumber: 2.3  Consensus size: 33

         78 GATGGCAGCC

                                             
         88 CATGGTTTTGAAAGCAATATTTGGATTACGAAA
          1 CATGGTTTTGAAAGCAATATTTGGATTACGAAA

                                             
        121 CATGGTTTTGAAAGCAATATTTGGATTACGAAA
          1 CATGGTTTTGAAAGCAATATTTGGATTACGAAA

                       
        154 CATGGTTTTGA
          1 CATGGTTTTGA

        165 TATCACTGAT


Statistics
Matches: 44,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  33   44  1.00

ACGTcount: A:0.34, C:0.09, G:0.22, T:0.35


Consensus pattern (33 bp):   
CATGGTTTTGAAAGCAATATTTGGATTACGAAA

Found at i:1052 original size:35 final size:35

Alignment explanation


    Indices: 986--1052  Score: 82
    Period size: 35  Copynumber: 1.9  Consensus size: 35

        976 TAGATATTAC

                                 * *           
        986 GTTAAACATCTTATTATGATATTTATGATATAATT
          1 GTTAAACATCTTATTATGATAATAATGATATAATT

                              *        *     
       1021 GTTAAA-ATACTTATTATTATAATAATTATATA
          1 GTTAAACAT-CTTATTATGATAATAATGATATA

       1053 TAAGTAGTAG


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

Matches are distributed among these distances:
  34    2  0.07
  35   25  0.93

ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48


Consensus pattern (35 bp):   
GTTAAACATCTTATTATGATAATAATGATATAATT

Found at i:2037 original size:20 final size:19

Alignment explanation


    Indices: 2012--2049  Score: 58
    Period size: 19  Copynumber: 1.9  Consensus size: 19

       2002 GAATTTATTA

                                
       2012 ATAACCTTATAATTGTTTTG
          1 ATAACC-TATAATTGTTTTG

                   *          
       2032 ATAACCTCTAATTGTTTT
          1 ATAACCTATAATTGTTTT

       2050 TAGTAATCAT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  19   11  0.65
  20    6  0.35

ACGTcount: A:0.29, C:0.13, G:0.08, T:0.50


Consensus pattern (19 bp):   
ATAACCTATAATTGTTTTG

Found at i:5430 original size:2 final size:2

Alignment explanation


    Indices: 5425--5459  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

       5415 ATATATATAT

                                                                
       5425 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A

       5460 TAGCATATAG


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00


Consensus pattern (2 bp):   
AG

Found at i:5911 original size:3 final size:3

Alignment explanation


    Indices: 5905--6026  Score: 217
    Period size: 3  Copynumber: 40.7  Consensus size: 3

       5895 TTTGAAGTGA

                                                                           
       5905 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT

                                                             *             
       5953 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ATT AAT AAT AAT
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT

                 *            *               
       6001 AAT ATT AAT AAT AAC AAT AAT AAT AA
          1 AAT AAT AAT AAT AAT AAT AAT AAT AA

       6027 ATTTGGGAGT


Statistics
Matches: 113,  Mismatches: 6, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   3  113  1.00

ACGTcount: A:0.66, C:0.01, G:0.00, T:0.34


Consensus pattern (3 bp):   
AAT

Done.