Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001229.1 Corchorus olitorius cultivar O-4 contig01229, 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, 632

Length: 1054
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38


Found at i:506 original size:6 final size:6

Alignment explanation


    Indices: 495--524  Score: 51
    Period size: 6  Copynumber: 4.8  Consensus size: 6

        485 CAATAAAATA

                                              
        495 TATATC TATATC TATATC TATATAC TATAT
          1 TATATC TATATC TATATC TATAT-C TATAT

        525 AAGTCTAAAC


Statistics
Matches: 23,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   6   17  0.74
   7    6  0.26

ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50


Consensus pattern (6 bp):   
TATATC

Found at i:800 original size:42 final size:40

Alignment explanation


    Indices: 741--824  Score: 132
    Period size: 42  Copynumber: 2.0  Consensus size: 40

        731 TTTAATTCCG

                              *                     
        741 ATGTAATATATATAATAATTAAAATACTTACATTAATTAA
          1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA

                                  *                   
        781 ATGTAATAATACTATAATAACTGAAATACTTACATTAATTAA
          1 ATGTAAT-ATA-TATAATAACTAAAATACTTACATTAATTAA

              
        823 AT
          1 AT

        825 TCATAGGTTT


Statistics
Matches: 40,  Mismatches: 2, Indels: 2
        0.91            0.05        0.05

Matches are distributed among these distances:
  40    7  0.17
  41    3  0.08
  42   30  0.75

ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38


Consensus pattern (40 bp):   
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA

Found at i:819 original size:21 final size:21

Alignment explanation


    Indices: 753--824  Score: 58
    Period size: 21  Copynumber: 3.4  Consensus size: 21

        743 GTAATATATA

                  * *            
        753 TAATAATTAAAATACTTACAT
          1 TAATAAATGAAATACTTACAT

                      *     *     
        774 TAATTAAATGTAATA-ATAC-T
          1 TAA-TAAATGAAATACTTACAT

                   *              
        794 ATAATAACTGAAATACTTACAT
          1 -TAATAAATGAAATACTTACAT

                     
        816 TAATTAAAT
          1 TAA-TAAAT

        825 TCATAGGTTT


Statistics
Matches: 38,  Mismatches: 8, Indels: 9
        0.69            0.15        0.16

Matches are distributed among these distances:
  20   10  0.26
  21   15  0.39
  22   13  0.34

ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38


Consensus pattern (21 bp):   
TAATAAATGAAATACTTACAT
Done.