Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024809.1 Corchorus olitorius cultivar O-4 contig24842, 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: 2514
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32


Found at i:40 original size:30 final size:29

Alignment explanation


    Indices: 4--127  Score: 97
    Period size: 29  Copynumber: 4.2  Consensus size: 29

          1 TTA

                                           
          4 TTGCATATAC-GGGGCAGTTTTGGTCAGTTT
          1 TTGCATATACGGGGGCA-TTTTGGTCA-TTT

                    *                    
         34 TTGCATATCCGGGGGCATTTTGGTCATTT
          1 TTGCATATACGGGGGCATTTTGGTCATTT

              ** *  * *         *      * 
         63 TTATACATTCAGGGGCATTTCGGTCATCT
          1 TTGCATATACGGGGGCATTTTGGTCATTT

            * *  *  * *      *           
         92 GTACACATTCTGGGGCAGTTTGGTCATTT
          1 TTGCATATACGGGGGCATTTTGGTCATTT

                   
        121 TTGCATA
          1 TTGCATA

        128 CACTAGGTTC


Statistics
Matches: 76,  Mismatches: 17, Indels: 3
        0.79            0.18        0.03

Matches are distributed among these distances:
  29   52  0.68
  30   18  0.24
  31    6  0.08

ACGTcount: A:0.18, C:0.17, G:0.26, T:0.40


Consensus pattern (29 bp):   
TTGCATATACGGGGGCATTTTGGTCATTT

Found at i:77 original size:29 final size:29

Alignment explanation


    Indices: 14--122  Score: 103
    Period size: 29  Copynumber: 3.7  Consensus size: 29

          4 TTGCATATAC

                            *      *       *
         14 GGGGCAGTTTTGGTCAGTTTT-TGCATATCCG
          1 GGGGCA-TTTTGGTCATTTTTATACAT-T-CA

                                         
         45 GGGGCATTTTGGTCATTTTTATACATTCA
          1 GGGGCATTTTGGTCATTTTTATACATTCA

                     *      * *  *      *
         74 GGGGCATTTCGGTCATCTGTACACATTCT
          1 GGGGCATTTTGGTCATTTTTATACATTCA

                  *             
        103 GGGGCAGTTTGGTCATTTTT
          1 GGGGCATTTTGGTCATTTTT

        123 GCATACACTA


Statistics
Matches: 65,  Mismatches: 12, Indels: 4
        0.80            0.15        0.05

Matches are distributed among these distances:
  29   41  0.63
  30   14  0.22
  31   10  0.15

ACGTcount: A:0.16, C:0.17, G:0.28, T:0.40


Consensus pattern (29 bp):   
GGGGCATTTTGGTCATTTTTATACATTCA

Found at i:761 original size:15 final size:16

Alignment explanation


    Indices: 741--782  Score: 68
    Period size: 15  Copynumber: 2.7  Consensus size: 16

        731 GCAGAGGTTG

                            
        741 AAAGAAAACAATTA-A
          1 AAAGAAAACAATTATA

                            
        756 AAAGAAAACAATTATA
          1 AAAGAAAACAATTATA

             *         
        772 ATAGAAAACAA
          1 AAAGAAAACAA

        783 AACAAAGTAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   14  0.56
  16   11  0.44

ACGTcount: A:0.71, C:0.07, G:0.07, T:0.14


Consensus pattern (16 bp):   
AAAGAAAACAATTATA

Done.