Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018378.1 Corchorus olitorius cultivar O-4 contig18411, 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: 5505
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30


Found at i:1040 original size:27 final size:27

Alignment explanation


    Indices: 1010--1089  Score: 99
    Period size: 27  Copynumber: 3.0  Consensus size: 27

       1000 AACCTAGGGA

                                       
       1010 ACTAACTTTGAATGGGAAACTGACTTG
          1 ACTAACTTTGAATGGGAAACTGACTTG

                *                       
       1037 ACTAGCTTTGAAT-GGAGAACTGACTTG
          1 ACTAACTTTGAATGGGA-AACTGACTTG

               *    *     *  *        
       1064 ACTGACTTGGAATGAGAGACTGACTT
          1 ACTAACTTTGAATGGGAAACTGACTT

       1090 TGAATGATCC


Statistics
Matches: 45,  Mismatches: 6, Indels: 4
        0.82            0.11        0.07

Matches are distributed among these distances:
  26    3  0.07
  27   40  0.89
  28    2  0.04

ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29


Consensus pattern (27 bp):   
ACTAACTTTGAATGGGAAACTGACTTG

Found at i:2869 original size:84 final size:84

Alignment explanation


    Indices: 2728--2893  Score: 242
    Period size: 84  Copynumber: 2.0  Consensus size: 84

       2718 GCGACTATTT

                  *                                      *                   
       2728 TGTGGATCTAGTGGCACTAAAGAACCATGAGTGACCAGAGAATCAGAACAATTTTCCTGTCGAAG
          1 TGTGGAGCTAGTGGCACTAAAGAACCATGAGTGACCAGAGAATCAAAACAATTTTCCTGTCGAAG

                               
       2793 TAATGGCACTGAAGAGGTC
         66 TAATGGCACTGAAGAGGTC

                                     *       **              *          *   *
       2812 TGTGGAGCTAGTGGCACTAAAGAACGATGAGTGGTCAGAGAATCAAAACGATTTTCCTGTGGAAT
          1 TGTGGAGCTAGTGGCACTAAAGAACCATGAGTGACCAGAGAATCAAAACAATTTTCCTGTCGAAG

              *        *     
       2877 TAGTGGCACTGTAGAGG
         66 TAATGGCACTGAAGAGG

       2894 AAGCATTAGT


Statistics
Matches: 72,  Mismatches: 10, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  84   72  1.00

ACGTcount: A:0.32, C:0.16, G:0.29, T:0.23


Consensus pattern (84 bp):   
TGTGGAGCTAGTGGCACTAAAGAACCATGAGTGACCAGAGAATCAAAACAATTTTCCTGTCGAAG
TAATGGCACTGAAGAGGTC

Found at i:5438 original size:13 final size:14

Alignment explanation


    Indices: 5421--5466  Score: 62
    Period size: 13  Copynumber: 3.5  Consensus size: 14

       5411 ATATAGTAGT

                          
       5421 AAGATAGTAAGAT-
          1 AAGATAGTAAGATA

                     *    
       5434 AAGATAGTATGATA
          1 AAGATAGTAAGATA

                          
       5448 AAGATA--AAGATA
          1 AAGATAGTAAGATA

                   
       5460 AAGATAG
          1 AAGATAG

       5467 AGATATATAT


Statistics
Matches: 29,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
  12   11  0.38
  13   12  0.41
  14    6  0.21

ACGTcount: A:0.57, C:0.00, G:0.22, T:0.22


Consensus pattern (14 bp):   
AAGATAGTAAGATA

Found at i:5476 original size:2 final size:2

Alignment explanation


    Indices: 5469--5504  Score: 72
    Period size: 2  Copynumber: 18.0  Consensus size: 2

       5459 AAAGATAGAG

                                                                 
       5469 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       5505 G


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   34  1.00

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


Consensus pattern (2 bp):   
AT

Done.