Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015756.1 Corchorus olitorius cultivar O-4 contig15789, 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: 1938
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32


Found at i:10 original size:2 final size:2

Alignment explanation


    Indices: 4--52  Score: 89
    Period size: 2  Copynumber: 24.0  Consensus size: 2

          1 TAC

                                                                           
          4 TA TA TA TA GTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                    
         47 TA TA TA
          1 TA TA TA

         53 AAATATAGGA


Statistics
Matches: 46,  Mismatches: 0, Indels: 2
        0.96            0.00        0.04

Matches are distributed among these distances:
   2   44  0.96
   3    2  0.04

ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49


Consensus pattern (2 bp):   
TA

Found at i:215 original size:43 final size:43

Alignment explanation


    Indices: 175--504  Score: 386
    Period size: 43  Copynumber: 7.6  Consensus size: 43

        165 GAAATGCCTT

                                                       
        175 TGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCC
          1 TGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCC

                               *                  * *     * 
        218 TGTGTTATATATGTGTTTGGGGACTTTGATATTTGATATAAATGCCTC
          1 TGTGTTATATATGTGTTTGAGGACTTTG-TA----ATAGAGATGCCCC

                                                        
        266 TGTGTTATATATGTGTTTGAGGACTTTGTAATAGA-ATTGCCCC
          1 TGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGA-TGCCCC

                               *             *  *    * 
        309 TGTGTTATATATGTGTTTGGGGAC-TTG-AATATAGGTGCCTC
          1 TGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCC

                              *              *  *      
        350 TGTGTTATATATGTGTTTAAGGACTTTGTAATAAAGGTGCCCC
          1 TGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCC

                               *        *             * 
        393 TGTGTTATATATGTGTTTGGGGAC-TTGGATATAG-G-TGCCTC
          1 TGTGTTATATATGTGTTTGAGGACTTTGTA-ATAGAGATGCCCC

                                         *               
        434 TGTGTTATATATGTGTTTGAGGACTTTTGGAATAGA-ATTGCCCC
          1 TGTGTTATATATGTGTTTGAGGAC-TTTGTAATAGAGA-TGCCCC

                               *       
        478 TGTGTTATATATGTGTTTGGGGACTTT
          1 TGTGTTATATATGTGTTTGAGGACTTT

        505 TTGGTTATTG


Statistics
Matches: 249,  Mismatches: 23, Indels: 30
        0.82            0.08        0.10

Matches are distributed among these distances:
  41   60  0.24
  42   16  0.06
  43  104  0.42
  44   30  0.12
  47    2  0.01
  48   37  0.15

ACGTcount: A:0.22, C:0.10, G:0.26, T:0.42


Consensus pattern (43 bp):   
TGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCC

Found at i:359 original size:84 final size:84

Alignment explanation


    Indices: 169--503  Score: 503
    Period size: 84  Copynumber: 3.9  Consensus size: 84

        159 TAAGGAGAAA

                 *                                                           
        169 TGCCTTTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGA-TGCCCCTGTGTTATATATGTG
          1 TGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGA-ATTGCCCCTGTGTTATATATGTG

                                     **
        233 TTTGGGGACTTTGATATTTGATATAAA
         65 TTTGGGGAC-TTG--A----ATATAGG

                                                                             
        260 TGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAATTGCCCCTGTGTTATATATGTGT
          1 TGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAATTGCCCCTGTGTTATATATGTGT

                               
        325 TTGGGGACTTGAATATAGG
         66 TTGGGGACTTGAATATAGG

                                    *                  *                     
        344 TGCCTCTGTGTTATATATGTGTTTAAGGACTTTGTAATA-AAGGTGCCCCTGTGTTATATATGTG
          1 TGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAA-TTGCCCCTGTGTTATATATGTG

                        *       
        408 TTTGGGGACTTGGATATAGG
         65 TTTGGGGACTTGAATATAGG

                                               *                             
        428 TGCCTCTGTGTTATATATGTGTTTGAGGACTTTTGGAATAGAATTGCCCCTGTGTTATATATGTG
          1 TGCCTCTGTGTTATATATGTGTTTGAGGAC-TTTGTAATAGAATTGCCCCTGTGTTATATATGTG

                       
        493 TTTGGGGACTT
         65 TTTGGGGACTT

        504 TTTGGTTATT


Statistics
Matches: 231,  Mismatches: 9, Indels: 14
        0.91            0.04        0.06

Matches are distributed among these distances:
  83    2  0.01
  84  112  0.48
  85   40  0.17
  86    2  0.01
  88    1  0.00
  90    4  0.02
  91   70  0.30

ACGTcount: A:0.21, C:0.10, G:0.26, T:0.42


Consensus pattern (84 bp):   
TGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAATTGCCCCTGTGTTATATATGTGT
TTGGGGACTTGAATATAGG
Done.