Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020503.1 Corchorus olitorius cultivar O-4 contig20536, 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: 4179
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:554 original size:16 final size:15

Alignment explanation


    Indices: 516--557  Score: 75
    Period size: 15  Copynumber: 2.7  Consensus size: 15

        506 ACAGAGATTG

                           
        516 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                           
        531 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
        546 ACTAGAAAACAA
          1 AC-AGAAAACAA

        558 AGCAAAGTAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15   17  0.65
  16    9  0.35

ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA

Found at i:3362 original size:14 final size:15

Alignment explanation


    Indices: 3343--3372  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       3333 CAATCAAAGC

                           
       3343 AATAAT-CAAGGAAA
          1 AATAATGCAAGGAAA

                           
       3357 AATAATGCAAGGAAA
          1 AATAATGCAAGGAAA

             
       3372 A
          1 A

       3373 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:3750 original size:21 final size:21

Alignment explanation


    Indices: 3726--3777  Score: 77
    Period size: 21  Copynumber: 2.5  Consensus size: 21

       3716 GGCACTGAAT

                *             *  
       3726 GGTGATGGCACGGGCATAGCC
          1 GGTGGTGGCACGGGCATAACC

                           *     
       3747 GGTGGTGGCACGGGCTTAACC
          1 GGTGGTGGCACGGGCATAACC

                      
       3768 GGTGGTGGCA
          1 GGTGGTGGCA

       3778 TGGTGAATGG


Statistics
Matches: 28,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  21   28  1.00

ACGTcount: A:0.15, C:0.21, G:0.46, T:0.17


Consensus pattern (21 bp):   
GGTGGTGGCACGGGCATAACC

Done.