Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014136.1 Corchorus olitorius cultivar O-4 contig14169, 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: 20284
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31


Found at i:6102 original size:33 final size:33

Alignment explanation


    Indices: 6065--6169  Score: 113
    Period size: 33  Copynumber: 3.2  Consensus size: 33

       6055 ATTACCATCC

                           *                  
       6065 AAAACAGAATTTA-TTTCATCACAAACAACACCT
          1 AAAACAG-ATTTAGTGTCATCACAAACAACACCT

                                           * 
       6098 AAAACAGATTTAGTGTCATCACAAACAACACTT
          1 AAAACAGATTTAGTGTCATCACAAACAACACCT

               *** *      *       *       *  
       6131 AAATTTGGTTTAGTATCATCACTAACAACATCT
          1 AAAACAGATTTAGTGTCATCACAAACAACACCT

                  
       6164 AAAACA
          1 AAAACA

       6170 CCCTTTGCAA


Statistics
Matches: 58,  Mismatches: 13, Indels: 2
        0.79            0.18        0.03

Matches are distributed among these distances:
  32    5  0.09
  33   53  0.91

ACGTcount: A:0.46, C:0.21, G:0.07, T:0.27


Consensus pattern (33 bp):   
AAAACAGATTTAGTGTCATCACAAACAACACCT

Found at i:7748 original size:25 final size:24

Alignment explanation


    Indices: 7711--7758  Score: 71
    Period size: 26  Copynumber: 2.0  Consensus size: 24

       7701 CTAGAAAATT

                                      
       7711 TGAAAAACTTTGATTGATGAGATGAA
          1 TGAAAAACTTTGA-TGAT-AGATGAA

                                   
       7737 TGAAAAAC-TTGATGATAGATGA
          1 TGAAAAACTTTGATGATAGATGA

       7759 GTAGAAGGAT


Statistics
Matches: 22,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  23    6  0.27
  24    4  0.18
  25    4  0.18
  26    8  0.36

ACGTcount: A:0.44, C:0.04, G:0.23, T:0.29


Consensus pattern (24 bp):   
TGAAAAACTTTGATGATAGATGAA

Found at i:18626 original size:48 final size:47

Alignment explanation


    Indices: 18554--18698  Score: 184
    Period size: 49  Copynumber: 3.0  Consensus size: 47

      18544 TGTGCCAATC

                               *         *                  
      18554 AATTTTGTATAAAAATTGATAAAAA-GTGTAATGAAAAGTAAATGATT
          1 AATTTTGTATAAAAATTGAGAAAAAGGTGCAATGAAAAGTAAA-GATT

                                                   *         
      18601 AATTTTGTCATAAAAATTGAGAAAAAGGTGCAATGAAAATTAAAGATTT
          1 AATTTTGT-ATAAAAATTGAGAAAAAGGTGCAATGAAAAGTAAAGA-TT

              *      *                       *               
      18650 AACTTTGTTGTAAAAATTGAGAAAAAGGTGCAAGGAAAAGTAAAAGATT
          1 AATTTTG-TATAAAAATTGAGAAAAAGGTGCAATGAAAAGT-AAAGATT

      18699 GCTTTGAGTG


Statistics
Matches: 86,  Mismatches: 7, Indels: 8
        0.85            0.07        0.08

Matches are distributed among these distances:
  47    8  0.09
  48   18  0.21
  49   54  0.63
  50    6  0.07

ACGTcount: A:0.50, C:0.03, G:0.18, T:0.30


Consensus pattern (47 bp):   
AATTTTGTATAAAAATTGAGAAAAAGGTGCAATGAAAAGTAAAGATT

Found at i:19807 original size:22 final size:22

Alignment explanation


    Indices: 19781--19834  Score: 54
    Period size: 28  Copynumber: 2.2  Consensus size: 22

      19771 ATACAATTAC

                                  
      19781 ACCAAATGATAATCAATTCCAT
          1 ACCAAATGATAATCAATTCCAT

                                        
      19803 ACCAATTACAAATGATAATCAATTCCAT
          1 A-C-----CAAATGATAATCAATTCCAT

                
      19831 ACCA
          1 ACCA

      19835 TTGAAACCAC


Statistics
Matches: 26,  Mismatches: 0, Indels: 12
        0.68            0.00        0.32

Matches are distributed among these distances:
  22    3  0.12
  23    1  0.04
  27    1  0.04
  28   21  0.81

ACGTcount: A:0.46, C:0.24, G:0.04, T:0.26


Consensus pattern (22 bp):   
ACCAAATGATAATCAATTCCAT
Done.