Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010084.1 Corchorus olitorius cultivar O-4 contig10116, 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: 20090
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35


Found at i:7386 original size:58 final size:58

Alignment explanation


    Indices: 7296--7412  Score: 234
    Period size: 58  Copynumber: 2.0  Consensus size: 58

       7286 CGCCATCAAA

                                                                      
       7296 TATTGCACCATTTTAGTGTGAAAAAGGAATCTTTTTGGAATATTCCAACACCAAAAAT
          1 TATTGCACCATTTTAGTGTGAAAAAGGAATCTTTTTGGAATATTCCAACACCAAAAAT

                                                                      
       7354 TATTGCACCATTTTAGTGTGAAAAAGGAATCTTTTTGGAATATTCCAACACCAAAAAT
          1 TATTGCACCATTTTAGTGTGAAAAAGGAATCTTTTTGGAATATTCCAACACCAAAAAT

             
       7412 T
          1 T

       7413 TTCCTTCTCC


Statistics
Matches: 59,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  58   59  1.00

ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33


Consensus pattern (58 bp):   
TATTGCACCATTTTAGTGTGAAAAAGGAATCTTTTTGGAATATTCCAACACCAAAAAT

Found at i:8231 original size:13 final size:13

Alignment explanation


    Indices: 8204--8246  Score: 50
    Period size: 13  Copynumber: 3.3  Consensus size: 13

       8194 TTTTAACCCC

                    * *  
       8204 AAAATTAAGTCTT
          1 AAAATTAATTATT

                         
       8217 AAAATTAATTATT
          1 AAAATTAATTATT

                *       *
       8230 AAAAATAATTATG
          1 AAAATTAATTATT

                
       8243 AAAA
          1 AAAA

       8247 AACATATTCA


Statistics
Matches: 26,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  13   26  1.00

ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35


Consensus pattern (13 bp):   
AAAATTAATTATT

Found at i:10140 original size:48 final size:48

Alignment explanation


    Indices: 10079--10172  Score: 154
    Period size: 48  Copynumber: 2.0  Consensus size: 48

      10069 ACCAAAGCCC

                                  *     *                   
      10079 ACCGAGCGACCCATATACATATTGGACATCAATCCGAAACCAAAAACT
          1 ACCGAGCGACCCATATACATATCGGACACCAATCCGAAACCAAAAACT

                                                           
      10127 ACCGAGCTG-CCCATATACATATCGGACACCAATCCGAAACCAAAAA
          1 ACCGAGC-GACCCATATACATATCGGACACCAATCCGAAACCAAAAA

      10173 ACCTAGTCTT


Statistics
Matches: 43,  Mismatches: 2, Indels: 2
        0.91            0.04        0.04

Matches are distributed among these distances:
  48   42  0.98
  49    1  0.02

ACGTcount: A:0.41, C:0.31, G:0.13, T:0.15


Consensus pattern (48 bp):   
ACCGAGCGACCCATATACATATCGGACACCAATCCGAAACCAAAAACT

Found at i:19595 original size:61 final size:59

Alignment explanation


    Indices: 19526--19663  Score: 159
    Period size: 60  Copynumber: 2.3  Consensus size: 59

      19516 CAATATTTGC

                                                 *        *  *           
      19526 GAAAATGCTTAAATAAGGATCCAAAGGAAAAAAAATGTTCAAATCATGGCTCAAAGGTTGA
          1 GAAAATGCTTAAATAAGGATCCAAA-GAAAAAAAATGCTCAAAT-AAGGATCAAAGGTTGA

                              * *  *              *           *       *
      19587 GAAAATGCTTAAATAAGGGTGCAGAGAAAAAAAATGCTGAAATAAGGATCCAAGGTTGC
          1 GAAAATGCTTAAATAAGGATCCAAAGAAAAAAAATGCTCAAATAAGGATCAAAGGTTGA

                      *       
      19646 GAAAATTGCTCAAATAAG
          1 GAAAA-TGCTTAAATAAG

      19664 TCCTTACCGT


Statistics
Matches: 66,  Mismatches: 10, Indels: 3
        0.84            0.13        0.04

Matches are distributed among these distances:
  59   17  0.26
  60   27  0.41
  61   22  0.33

ACGTcount: A:0.47, C:0.11, G:0.22, T:0.20


Consensus pattern (59 bp):   
GAAAATGCTTAAATAAGGATCCAAAGAAAAAAAATGCTCAAATAAGGATCAAAGGTTGA

Found at i:19787 original size:2 final size:2

Alignment explanation


    Indices: 19780--19816  Score: 74
    Period size: 2  Copynumber: 18.5  Consensus size: 2

      19770 TAACATTTAA

                                                                   
      19780 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

      19817 AATCAAATAT


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   35  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Done.