Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018240.1 Corchorus olitorius cultivar O-4 contig18273, 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: 3172
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29


Found at i:321 original size:28 final size:29

Alignment explanation


    Indices: 250--324  Score: 98
    Period size: 29  Copynumber: 2.6  Consensus size: 29

        240 AAATGAACTT

                   *                     
        250 AAAATGATCAAAATGCCCCTGAATATGTA
          1 AAAATGACCAAAATGCCCCTGAATATGTA

            *         *             *    
        279 GAAATGACCATAATGCCCCTGAATGTG-A
          1 AAAATGACCAAAATGCCCCTGAATATGTA

                 *            
        307 AAAATTACCAAAATGCCC
          1 AAAATGACCAAAATGCCC

        325 TTAGGTGATC


Statistics
Matches: 39,  Mismatches: 7, Indels: 1
        0.83            0.15        0.02

Matches are distributed among these distances:
  28   16  0.41
  29   23  0.59

ACGTcount: A:0.43, C:0.21, G:0.15, T:0.21


Consensus pattern (29 bp):   
AAAATGACCAAAATGCCCCTGAATATGTA

Found at i:370 original size:14 final size:14

Alignment explanation


    Indices: 351--380  Score: 60
    Period size: 14  Copynumber: 2.1  Consensus size: 14

        341 CCAATTAAGC

                          
        351 AACAAATTGATTTA
          1 AACAAATTGATTTA

                          
        365 AACAAATTGATTTA
          1 AACAAATTGATTTA

              
        379 AA
          1 AA

        381 TAAAGGATAT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   16  1.00

ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33


Consensus pattern (14 bp):   
AACAAATTGATTTA

Found at i:765 original size:17 final size:17

Alignment explanation


    Indices: 738--770  Score: 50
    Period size: 16  Copynumber: 1.9  Consensus size: 17

        728 AGTGCAAATT

                              
        738 AAAATAGAAAAAATAAAG
          1 AAAATAG-AAAAATAAAG

                            
        756 AAAA-AGAAAAATAAA
          1 AAAATAGAAAAATAAA

        771 ACGCAATCTC


Statistics
Matches: 15,  Mismatches: 0, Indels: 2
        0.88            0.00        0.12

Matches are distributed among these distances:
  16    9  0.60
  17    2  0.13
  18    4  0.27

ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09


Consensus pattern (17 bp):   
AAAATAGAAAAATAAAG

Found at i:1003 original size:12 final size:13

Alignment explanation


    Indices: 981--1010  Score: 53
    Period size: 12  Copynumber: 2.4  Consensus size: 13

        971 ACTAGTAATT

                         
        981 AAAATCAATCAAG
          1 AAAATCAATCAAG

                         
        994 AAAA-CAATCAAG
          1 AAAATCAATCAAG

                 
       1006 AAAAT
          1 AAAAT

       1011 TAAAGAAAAC


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  12   12  0.75
  13    4  0.25

ACGTcount: A:0.67, C:0.13, G:0.07, T:0.13


Consensus pattern (13 bp):   
AAAATCAATCAAG
Done.