Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017429.1 Corchorus olitorius cultivar O-4 contig17462, 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: 5767
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31


Found at i:318 original size:12 final size:13

Alignment explanation


    Indices: 292--348  Score: 50
    Period size: 12  Copynumber: 4.7  Consensus size: 13

        282 TTATGCACCC

                     *   
        292 AAAACATTTGT-T
          1 AAAACATTTATAT

                         
        304 AAAACATTT-TAT
          1 AAAACATTTATAT

               *         
        316 AAAGCATTTATAT
          1 AAAACATTTATAT

               *   *     
        329 AAAGCA-GT-TAT
          1 AAAACATTTATAT

                     
        340 AAAACATTT
          1 AAAACATTT

        349 CCTCAACGGG


Statistics
Matches: 38,  Mismatches: 4, Indels: 6
        0.79            0.08        0.12

Matches are distributed among these distances:
  11    9  0.24
  12   20  0.53
  13    9  0.24

ACGTcount: A:0.47, C:0.09, G:0.07, T:0.37


Consensus pattern (13 bp):   
AAAACATTTATAT

Found at i:331 original size:13 final size:13

Alignment explanation


    Indices: 303--348  Score: 53
    Period size: 13  Copynumber: 3.8  Consensus size: 13

        293 AAACATTTGT

                *        
        303 TAAAACATTT-TA
          1 TAAAGCATTTATA

                         
        315 TAAAGCATTTATA
          1 TAAAGCATTTATA

                   *     
        328 TAAAGCAGTTATA
          1 TAAAGCATTTATA

                      
        341 -AAA-CATTT
          1 TAAAGCATTT

        349 CCTCAACGGG


Statistics
Matches: 30,  Mismatches: 3, Indels: 3
        0.83            0.08        0.08

Matches are distributed among these distances:
  11    4  0.13
  12   12  0.40
  13   14  0.47

ACGTcount: A:0.48, C:0.09, G:0.07, T:0.37


Consensus pattern (13 bp):   
TAAAGCATTTATA

Found at i:516 original size:13 final size:13

Alignment explanation


    Indices: 488--526  Score: 51
    Period size: 13  Copynumber: 2.8  Consensus size: 13

        478 CAAACACAAG

                           
        488 AAAATCATTAAAATC
          1 AAAATCA-T-AAATC

                         
        503 AAAATCATAAATC
          1 AAAATCATAAATC

               *       
        516 AAAGTCATAAA
          1 AAAATCATAAA

        527 CCAGAGTAAA


Statistics
Matches: 23,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  13   15  0.65
  14    1  0.04
  15    7  0.30

ACGTcount: A:0.62, C:0.13, G:0.03, T:0.23


Consensus pattern (13 bp):   
AAAATCATAAATC

Found at i:701 original size:20 final size:19

Alignment explanation


    Indices: 672--715  Score: 54
    Period size: 20  Copynumber: 2.3  Consensus size: 19

        662 GTCTTATAGG

                       *        
        672 GTTTAATACAAGTTTC-AGA
          1 GTTTAATAC-ACTTTCTAGA

                                
        691 GTTTGAATACACTTTCTAGA
          1 GTTT-AATACACTTTCTAGA

                 
        711 GTTTA
          1 GTTTA

        716 TTTAATCATT


Statistics
Matches: 22,  Mismatches: 1, Indels: 4
        0.81            0.04        0.15

Matches are distributed among these distances:
  19   10  0.45
  20   12  0.55

ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41


Consensus pattern (19 bp):   
GTTTAATACACTTTCTAGA
Done.