Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017166.1 Corchorus olitorius cultivar O-4 contig17199, 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: 11197
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35


Found at i:2607 original size:4 final size:4

Alignment explanation


    Indices: 2598--2625  Score: 56
    Period size: 4  Copynumber: 7.0  Consensus size: 4

       2588 TCATGTAATC

                                              
       2598 ATAA ATAA ATAA ATAA ATAA ATAA ATAA
          1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA

       2626 TGTTCTAATT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   24  1.00

ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25


Consensus pattern (4 bp):   
ATAA

Found at i:2899 original size:57 final size:57

Alignment explanation


    Indices: 2835--2945  Score: 186
    Period size: 57  Copynumber: 1.9  Consensus size: 57

       2825 GTATCTAATA

                                    *                                
       2835 TGATATGTACAGTGTTTAATCTCATAACTCCACTACAAACGAAGCCAATCACACCGC
          1 TGATATGTACAGTGTTTAATCTCACAACTCCACTACAAACGAAGCCAATCACACCGC

                                            *        *  *         
       2892 TGATATGTACAGTGTTTAATCTCACAACTCCAGTACAAACGGAGTCAATCACAC
          1 TGATATGTACAGTGTTTAATCTCACAACTCCACTACAAACGAAGCCAATCACAC

       2946 TGCTCTACTA


Statistics
Matches: 50,  Mismatches: 4, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  57   50  1.00

ACGTcount: A:0.35, C:0.26, G:0.14, T:0.25


Consensus pattern (57 bp):   
TGATATGTACAGTGTTTAATCTCACAACTCCACTACAAACGAAGCCAATCACACCGC

Found at i:3162 original size:4 final size:4

Alignment explanation


    Indices: 3153--3177  Score: 50
    Period size: 4  Copynumber: 6.2  Consensus size: 4

       3143 TTCTCAAGAA

                                           
       3153 AAAT AAAT AAAT AAAT AAAT AAAT A
          1 AAAT AAAT AAAT AAAT AAAT AAAT A

       3178 TTTCTAAATG


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   21  1.00

ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24


Consensus pattern (4 bp):   
AAAT

Found at i:4668 original size:24 final size:25

Alignment explanation


    Indices: 4641--4705  Score: 78
    Period size: 24  Copynumber: 2.6  Consensus size: 25

       4631 ATTGGGTTAG

                *                    
       4641 TCTTGAATTTTTTTAATGT-TTAAT
          1 TCTTAAATTTTTTTAATGTCTTAAT

                      *              
       4665 TCTTAAATTTATTTAATGTCTTAAT
          1 TCTTAAATTTTTTTAATGTCTTAAT

             *  *           
       4690 TATTCAATTTATTTTA
          1 TCTTAAATTT-TTTTA

       4706 CAATCCACTA


Statistics
Matches: 34,  Mismatches: 5, Indels: 2
        0.83            0.12        0.05

Matches are distributed among these distances:
  24   17  0.50
  25   13  0.38
  26    4  0.12

ACGTcount: A:0.29, C:0.06, G:0.05, T:0.60


Consensus pattern (25 bp):   
TCTTAAATTTTTTTAATGTCTTAAT

Found at i:4698 original size:25 final size:24

Alignment explanation


    Indices: 4646--4703  Score: 80
    Period size: 25  Copynumber: 2.4  Consensus size: 24

       4636 GTTAGTCTTG

                 *              *   
       4646 AATTTTTTTAATGTTTAATTCTTA
          1 AATTTATTTAATGTTTAATTATTA

                                    *
       4670 AATTTATTTAATGTCTTAATTATTC
          1 AATTTATTTAATGT-TTAATTATTA

                     
       4695 AATTTATTT
          1 AATTTATTT

       4704 TACAATCCAC


Statistics
Matches: 30,  Mismatches: 3, Indels: 1
        0.88            0.09        0.03

Matches are distributed among these distances:
  24   13  0.43
  25   17  0.57

ACGTcount: A:0.31, C:0.05, G:0.03, T:0.60


Consensus pattern (24 bp):   
AATTTATTTAATGTTTAATTATTA
Done.