Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023735.1 Corchorus olitorius cultivar O-4 contig23768, 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: 15051
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:1062 original size:14 final size:15

Alignment explanation


    Indices: 1043--1072  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       1033 CAATCAAAGC

                           
       1043 AATAAT-CAAGGAAA
          1 AATAATGCAAGGAAA

                           
       1057 AATAATGCAAGGAAA
          1 AATAATGCAAGGAAA

             
       1072 A
          1 A

       1073 TTAAAGAGAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    6  0.40
  15    9  0.60

ACGTcount: A:0.63, C:0.07, G:0.17, T:0.13


Consensus pattern (15 bp):   
AATAATGCAAGGAAA

Found at i:3971 original size:25 final size:27

Alignment explanation


    Indices: 3936--3997  Score: 92
    Period size: 25  Copynumber: 2.3  Consensus size: 27

       3926 ACAAGAAAAA

                             *         
       3936 ATTTTTTTAATGACGCAGAAT-TTTTT
          1 ATTTTTTTAATGACGCAAAATATTTTT

                                        
       3962 -TTTTTTTAATGACGCAAAATAATTTTT
          1 ATTTTTTTAATGACGCAAAAT-ATTTTT

                     
       3989 ATTTTTTTA
          1 ATTTTTTTA

       3998 GAAAAAACGG


Statistics
Matches: 32,  Mismatches: 1, Indels: 4
        0.86            0.03        0.11

Matches are distributed among these distances:
  25   19  0.59
  27    5  0.16
  28    8  0.25

ACGTcount: A:0.29, C:0.06, G:0.08, T:0.56


Consensus pattern (27 bp):   
ATTTTTTTAATGACGCAAAATATTTTT

Found at i:3986 original size:28 final size:25

Alignment explanation


    Indices: 3936--3997  Score: 79
    Period size: 28  Copynumber: 2.4  Consensus size: 25

       3926 ACAAGAAAAA

                                     
       3936 ATTTTTTTAATGACGCAGAATTTTT
          1 ATTTTTTTAATGACGCAGAATTTTT

            *                   *       
       3961 TTTTTTTTAATGACGCAAAATAATTTTT
          1 ATTTTTTTAATGACGC---AGAATTTTT

                     
       3989 ATTTTTTTA
          1 ATTTTTTTA

       3998 GAAAAAACGG


Statistics
Matches: 31,  Mismatches: 3, Indels: 3
        0.84            0.08        0.08

Matches are distributed among these distances:
  25   15  0.48
  28   16  0.52

ACGTcount: A:0.29, C:0.06, G:0.08, T:0.56


Consensus pattern (25 bp):   
ATTTTTTTAATGACGCAGAATTTTT

Found at i:4385 original size:16 final size:15

Alignment explanation


    Indices: 4347--4388  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       4337 ACAGAGATTG

                   *       
       4347 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                           
       4362 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
       4377 ACTAGAAAACAA
          1 AC-AGAAAACAA

       4389 ACCAAAGTAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA

Found at i:7518 original size:26 final size:26

Alignment explanation


    Indices: 7479--7539  Score: 95
    Period size: 26  Copynumber: 2.3  Consensus size: 26

       7469 GTACTTGAAG

                                *      
       7479 TGACCAAAATGCCCCTGGACGCGCAAA
          1 TGACC-AAATGCCCCTGGACACGCAAA

                                *     
       7506 TGACCAAATGCCCCTGGACATGCAAA
          1 TGACCAAATGCCCCTGGACACGCAAA

                    
       7532 TGACCAAA
          1 TGACCAAA

       7540 ATAAGAAGTA


Statistics
Matches: 32,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  26   27  0.84
  27    5  0.16

ACGTcount: A:0.36, C:0.31, G:0.20, T:0.13


Consensus pattern (26 bp):   
TGACCAAATGCCCCTGGACACGCAAA

Found at i:8550 original size:12 final size:12

Alignment explanation


    Indices: 8533--8563  Score: 53
    Period size: 12  Copynumber: 2.5  Consensus size: 12

       8523 ACCCTTGCCT

                        
       8533 AAAAACTAGAAG
          1 AAAAACTAGAAG

                        
       8545 AAAAACTAGAAG
          1 AAAAACTAGAAG

                   
       8557 AATAAAC
          1 AA-AAAC

       8564 CTAAAAGTAA


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  12   14  0.78
  13    4  0.22

ACGTcount: A:0.68, C:0.10, G:0.13, T:0.10


Consensus pattern (12 bp):   
AAAAACTAGAAG
Done.