Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024822.1 Corchorus olitorius cultivar O-4 contig24855, 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: 24838
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29


Found at i:239 original size:24 final size:23

Alignment explanation


    Indices: 207--252  Score: 83
    Period size: 24  Copynumber: 2.0  Consensus size: 23

        197 ACGTTTGCAC

                                    
        207 AAATATCTAAGAATTTGAATTAAA
          1 AAATATCTAAGAATTT-AATTAAA

                                  
        231 AAATATCTAAGAATTTAATTAA
          1 AAATATCTAAGAATTTAATTAA

        253 TGTAAGTATT


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  23    6  0.27
  24   16  0.73

ACGTcount: A:0.54, C:0.04, G:0.07, T:0.35


Consensus pattern (23 bp):   
AAATATCTAAGAATTTAATTAAA

Found at i:289 original size:39 final size:40

Alignment explanation


    Indices: 243--323  Score: 128
    Period size: 39  Copynumber: 2.0  Consensus size: 40

        233 ATATCTAAGA

                                   *                
        243 ATTTAATTAATGTAAGTATTTCAGTTATTA-TAATATTAC
          1 ATTTAATTAATGTAAGTATTTCAATTATTATTAATATTAC

                                 *          *       
        282 ATTTAATTAATGTAAGTATTTTAATTATTATTTATATTAC
          1 ATTTAATTAATGTAAGTATTTCAATTATTATTAATATTAC

              
        322 AT
          1 AT

        324 AGGAATTAAA


Statistics
Matches: 38,  Mismatches: 3, Indels: 1
        0.90            0.07        0.02

Matches are distributed among these distances:
  39   28  0.74
  40   10  0.26

ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52


Consensus pattern (40 bp):   
ATTTAATTAATGTAAGTATTTCAATTATTATTAATATTAC

Found at i:3488 original size:2 final size:2

Alignment explanation


    Indices: 3483--3512  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

       3473 TTAAAAAACA

                                                        
       3483 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

       3513 TGTTTTAATT


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:4380 original size:17 final size:16

Alignment explanation


    Indices: 4326--4376  Score: 66
    Period size: 17  Copynumber: 3.1  Consensus size: 16

       4316 ATCACCCCCC

                   *         
       4326 AGATCACTAGTGATCTA
          1 AGATCACCAGTGATC-A

                             
       4343 AGATCACCAGTGATGCA
          1 AGATCACCAGTGAT-CA

                    *       
       4360 AGATCACCGGTGATCA
          1 AGATCACCAGTGATCA

             
       4376 A
          1 A

       4377 AGATTACATG


Statistics
Matches: 31,  Mismatches: 2, Indels: 3
        0.86            0.06        0.08

Matches are distributed among these distances:
  16    3  0.10
  17   27  0.87
  18    1  0.03

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


Consensus pattern (16 bp):   
AGATCACCAGTGATCA

Found at i:16847 original size:3 final size:3

Alignment explanation


    Indices: 16839--16863  Score: 50
    Period size: 3  Copynumber: 8.3  Consensus size: 3

      16829 CTATAGTTAA

                                             
      16839 TAT TAT TAT TAT TAT TAT TAT TAT T
          1 TAT TAT TAT TAT TAT TAT TAT TAT T

      16864 CATTTTACTC


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

Matches are distributed among these distances:
   3   22  1.00

ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68


Consensus pattern (3 bp):   
TAT

Done.