Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019608.1 Corchorus olitorius cultivar O-4 contig19641, 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: 10765
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.30


Found at i:832 original size:22 final size:22

Alignment explanation


    Indices: 807--849  Score: 52
    Period size: 21  Copynumber: 2.0  Consensus size: 22

        797 CCATGCCATT

                         *         
        807 ACGATGATGAAATGTGC-AACGG
          1 ACGA-GATGAAATATGCTAACGG

                 *               
        829 ACGAGGTGAAATATGCTAACG
          1 ACGAGATGAAATATGCTAACG

        850 CAAAACGGAA


Statistics
Matches: 18,  Mismatches: 2, Indels: 2
        0.82            0.09        0.09

Matches are distributed among these distances:
  21   10  0.56
  22    8  0.44

ACGTcount: A:0.37, C:0.14, G:0.30, T:0.19


Consensus pattern (22 bp):   
ACGAGATGAAATATGCTAACGG

Found at i:3538 original size:23 final size:22

Alignment explanation


    Indices: 3475--3547  Score: 74
    Period size: 23  Copynumber: 3.1  Consensus size: 22

       3465 AACATGTGTC

                                    
       3475 TTTTTTACTTAGAATATTTTAATT
          1 TTTTTTACTTAGAA-ATTTTAA-T

                   * **             
       3499 TTTTTTGCCAAACGAAATTTTAAT
          1 TTTTTT-ACTTA-GAAATTTTAAT

                                   
       3523 TTTTTTACTTATGAAATTTTAAT
          1 TTTTTTACTTA-GAAATTTTAAT

              
       3546 TT
          1 TT

       3548 AAATTAAAAA


Statistics
Matches: 40,  Mismatches: 7, Indels: 5
        0.77            0.13        0.10

Matches are distributed among these distances:
  23   15  0.38
  24   13  0.32
  25    9  0.22
  26    3  0.08

ACGTcount: A:0.30, C:0.07, G:0.05, T:0.58


Consensus pattern (22 bp):   
TTTTTTACTTAGAAATTTTAAT

Found at i:7898 original size:1 final size:1

Alignment explanation


    Indices: 7892--7924  Score: 57
    Period size: 1  Copynumber: 33.0  Consensus size: 1

       7882 AGGACTTTCC

                                *            
       7892 TTTTTTTTTTTTTTTTTTTTATTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

       7925 CTGCAATTCC


Statistics
Matches: 30,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   1   30  1.00

ACGTcount: A:0.03, C:0.00, G:0.00, T:0.97


Consensus pattern (1 bp):   
T

Found at i:8998 original size:21 final size:21

Alignment explanation


    Indices: 8974--9038  Score: 58
    Period size: 21  Copynumber: 3.0  Consensus size: 21

       8964 TGAATGATGT

                                 
       8974 CACGGGCATGGCCGGTGGTGG
          1 CACGGGCATGGCCGGTGGTGG

                   * ** *       *
       8995 CACGGGCTTAACTGGTGGTGA
          1 CACGGGCATGGCCGGTGGTGG

                   *         *    
       9016 CACGGTGAATGGCCGGTTGTGG
          1 CACGG-GCATGGCCGGTGGTGG

             
       9038 C
          1 C

       9039 TTGGTAGTGG


Statistics
Matches: 31,  Mismatches: 12, Indels: 1
        0.70            0.27        0.02

Matches are distributed among these distances:
  21   21  0.68
  22   10  0.32

ACGTcount: A:0.14, C:0.22, G:0.45, T:0.20


Consensus pattern (21 bp):   
CACGGGCATGGCCGGTGGTGG
Done.