Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019558.1 Corchorus olitorius cultivar O-4 contig19591, 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: 6695
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28


Found at i:1968 original size:15 final size:16

Alignment explanation


    Indices: 1948--1987  Score: 64
    Period size: 15  Copynumber: 2.6  Consensus size: 16

       1938 AGGGGTTGAA

                            
       1948 AGAAAACAATTAAAC-
          1 AGAAAACAATTAAACT

                            
       1963 AGAAAACAATTAAACT
          1 AGAAAACAATTAAACT

              *      
       1979 AGGAAACAA
          1 AGAAAACAA

       1988 AAGAAAGCAA


Statistics
Matches: 23,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  15   15  0.65
  16    8  0.35

ACGTcount: A:0.65, C:0.12, G:0.10, T:0.12


Consensus pattern (16 bp):   
AGAAAACAATTAAACT

Found at i:3384 original size:29 final size:30

Alignment explanation


    Indices: 3346--3405  Score: 86
    Period size: 29  Copynumber: 2.0  Consensus size: 30

       3336 AATGCTTTCC

                *      *                  
       3346 TCTTGAAATAATTCTTCAAT-GTCTTCAAA
          1 TCTTCAAATAAGTCTTCAATAGTCTTCAAA

                                           
       3375 TCTTCAAATAAGTCTTCAATGAGTCTTCAAA
          1 TCTTCAAATAAGTCTTCAAT-AGTCTTCAAA

       3406 CACGAACTTC


Statistics
Matches: 27,  Mismatches: 2, Indels: 2
        0.87            0.06        0.06

Matches are distributed among these distances:
  29   18  0.67
  31    9  0.33

ACGTcount: A:0.35, C:0.18, G:0.08, T:0.38


Consensus pattern (30 bp):   
TCTTCAAATAAGTCTTCAATAGTCTTCAAA

Found at i:5452 original size:23 final size:23

Alignment explanation


    Indices: 5325--5485  Score: 173
    Period size: 23  Copynumber: 7.0  Consensus size: 23

       5315 AAGAGAAATA

                     *             
       5325 AGCAAAACAGCAACATTTTGAAC
          1 AGCAAAACAACAACATTTTGAAC

             *           *         
       5348 AACAAAACAACAAAATTTTGAAC
          1 AGCAAAACAACAACATTTTGAAC

              *    * *              
       5371 AGAAAAATAGCAA-ATTTTTGAAC
          1 AGCAAAACAACAACA-TTTTGAAC

                  *      *         
       5394 AGCAAAGCAACAATATTTTGAAC
          1 AGCAAAACAACAACATTTTGAAC

                        *          
       5417 AGCAAAACAACAGCATTTTGAAC
          1 AGCAAAACAACAACATTTTGAAC

                        *       * *
       5440 AGCAAAACAACAGCATTTT-CAT
          1 AGCAAAACAACAACATTTTGAAC

                     *         *   
       5462 AGCAAAACAGCAACATTTTCAAC
          1 AGCAAAACAACAACATTTTGAAC

             
       5485 A
          1 A

       5486 AAGAAAACAA


Statistics
Matches: 115,  Mismatches: 20, Indels: 6
        0.82            0.14        0.04

Matches are distributed among these distances:
  22   19  0.17
  23   95  0.83
  24    1  0.01

ACGTcount: A:0.50, C:0.19, G:0.11, T:0.20


Consensus pattern (23 bp):   
AGCAAAACAACAACATTTTGAAC

Found at i:5458 original size:46 final size:46

Alignment explanation


    Indices: 5325--5485  Score: 191
    Period size: 46  Copynumber: 3.5  Consensus size: 46

       5315 AAGAGAAATA

                                    *                     
       5325 AGCAAAACAGCAACATTTTGAACAACAAAACAACAAAATTTTGAAC
          1 AGCAAAACAGCAACATTTTGAACAGCAAAACAACAAAATTTTGAAC

              *    *                      *      *         
       5371 AGAAAAATAGCAA-ATTTTTGAACAGCAAAGCAACAATATTTTGAAC
          1 AGCAAAACAGCAACA-TTTTGAACAGCAAAACAACAAAATTTTGAAC

                     *  *                      **      * *
       5417 AGCAAAACAACAGCATTTTGAACAGCAAAACAACAGCATTTT-CAT
          1 AGCAAAACAGCAACATTTTGAACAGCAAAACAACAAAATTTTGAAC

                               *    
       5462 AGCAAAACAGCAACATTTTCAACA
          1 AGCAAAACAGCAACATTTTGAACA

       5486 AAGAAAACAA


Statistics
Matches: 96,  Mismatches: 17, Indels: 5
        0.81            0.14        0.04

Matches are distributed among these distances:
  45   23  0.24
  46   72  0.75
  47    1  0.01

ACGTcount: A:0.50, C:0.19, G:0.11, T:0.20


Consensus pattern (46 bp):   
AGCAAAACAGCAACATTTTGAACAGCAAAACAACAAAATTTTGAAC

Done.