Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012436.1 Corchorus olitorius cultivar O-4 contig12469, 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, 846

Length: 1411
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:106 original size:41 final size:41

Alignment explanation


    Indices: 7--251  Score: 264
    Period size: 41  Copynumber: 5.8  Consensus size: 41

          1 ATNTAA

                  *                                  *  
          7 ATGCCTTTGTGTTATATATGTGTTTGAGGACTTTTGTAATAGAG
          1 ATGCCTCTGTGTTATATATGTGTTTGAGGAC-TTTG--ATATAG

                                       *              
         51 ATGCC-CATGTGTTATATATGTGTTTGGGGACTTTGATATAG
          1 ATGCCTC-TGTGTTATATATGTGTTTGAGGACTTTGATATAG

                                                    *  
         92 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAAAG
          1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTG--ATATAG

            **   *                    *      *       
        135 GCGCCCCTGTG-T-TATATGTGTTTGGGGACTTGGATATAG
          1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGATATAG

            *                                          
        174 GTGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGA-ATAG
          1 ATGCCTCTGTGTTATATATGTGTTTGAGGAC-TTT-GATATAG

                   *                    *       
        216 AATTGCCCCTGTGTTATATATGTGTTTGGGGACTTT
          1 -A-TGCCTCTGTGTTATATATGTGTTTGAGGACTTT

        252 TTGGTTATTG


Statistics
Matches: 173,  Mismatches: 18, Indels: 21
        0.82            0.08        0.10

Matches are distributed among these distances:
  39   14  0.08
  40    1  0.01
  41   72  0.42
  42    8  0.05
  43   22  0.13
  44   56  0.32

ACGTcount: A:0.20, C:0.11, G:0.27, T:0.42


Consensus pattern (41 bp):   
ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTGATATAG

Found at i:181 original size:82 final size:85

Alignment explanation


    Indices: 7--250  Score: 370
    Period size: 82  Copynumber: 2.9  Consensus size: 85

          1 ATNTAA

                  *                                  *        *              
          7 ATGCCTTTGTGTTATATATGTGTTTGAGGACTTTTGTAATAGAGATGCCCATGTGTTATATATGT
          1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGTAATAAAGATGCCCCTGTGTTATATATGT

                        *       
         72 GTTTGGGGACTTTGATATAG
         66 GTTTGGGGACTTGGATATAG

                                                        **                   
         92 ATGCCTCTGTGTTATATATGTGTTTGAGGAC-TTTGTAATAAAGGCGCCCCTGTG-T-TATATGT
          1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGTAATAAAGATGCCCCTGTGTTATATATGT

                                
        154 GTTTGGGGACTTGGATATAG
         66 GTTTGGGGACTTGGATATAG

            *                                   *        *                   
        174 GTGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAGAA-TTGCCCCTGTGTTATATATG
          1 ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGTAATA-AAGATGCCCCTGTGTTATATATG

                         
        238 TGTTTGGGGACTT
         65 TGTTTGGGGACTT

        251 TTTGGTTATT


Statistics
Matches: 145,  Mismatches: 10, Indels: 8
        0.89            0.06        0.05

Matches are distributed among these distances:
  82   56  0.39
  83   18  0.12
  84   22  0.15
  85   49  0.34

ACGTcount: A:0.20, C:0.11, G:0.27, T:0.42


Consensus pattern (85 bp):   
ATGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGTAATAAAGATGCCCCTGTGTTATATATGT
GTTTGGGGACTTGGATATAG

Found at i:1377 original size:2 final size:2

Alignment explanation


    Indices: 1370--1411  Score: 84
    Period size: 2  Copynumber: 21.0  Consensus size: 2

       1360 CATCTGTCCC

                                                                          
       1370 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT


Statistics
Matches: 40,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   40  1.00

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


Consensus pattern (2 bp):   
AT

Done.