Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022463.1 Corchorus olitorius cultivar O-4 contig22496, 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: 14519
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33


Found at i:2102 original size:28 final size:27

Alignment explanation


    Indices: 2061--2115  Score: 85
    Period size: 26  Copynumber: 2.0  Consensus size: 27

       2051 ACTGAGACTA

                                         
       2061 GACTCGAAACTGACTCGAAAAAACAAACT
          1 GACTCGAAACTGACTC--AAAAACAAACT

                                       
       2090 GACTC-AAACTGACTCAAAAACAAACT
          1 GACTCGAAACTGACTCAAAAACAAACT

       2116 CAAATTAAAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 3
        0.90            0.00        0.10

Matches are distributed among these distances:
  26   11  0.42
  28   10  0.38
  29    5  0.19

ACGTcount: A:0.49, C:0.25, G:0.11, T:0.15


Consensus pattern (27 bp):   
GACTCGAAACTGACTCAAAAACAAACT

Found at i:3364 original size:18 final size:18

Alignment explanation


    Indices: 3341--3378  Score: 58
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       3331 TTTTTTGTTT

                   *          
       3341 TTTTTTTTAAGTCAGTAA
          1 TTTTTTTAAAGTCAGTAA

                        *     
       3359 TTTTTTTAAAGTTAGTAA
          1 TTTTTTTAAAGTCAGTAA

              
       3377 TT
          1 TT

       3379 CTATATGGCA


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.29, C:0.03, G:0.11, T:0.58


Consensus pattern (18 bp):   
TTTTTTTAAAGTCAGTAA

Found at i:9065 original size:13 final size:13

Alignment explanation


    Indices: 9047--9071  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       9037 AACACAACTC

                         
       9047 CAAACCCAAACCG
          1 CAAACCCAAACCG

                        
       9060 CAAACCCAAACC
          1 CAAACCCAAACC

       9072 TTAAGTACTT


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.48, C:0.48, G:0.04, T:0.00


Consensus pattern (13 bp):   
CAAACCCAAACCG

Found at i:9993 original size:15 final size:16

Alignment explanation


    Indices: 9973--10005  Score: 50
    Period size: 17  Copynumber: 2.1  Consensus size: 16

       9963 TGGATCATGT

                            
       9973 TTAAG-AATAGGATAA
          1 TTAAGAAATAGGATAA

                             
       9988 TTAAGAAAATAGGATAA
          1 TTAAG-AAATAGGATAA

             
      10005 T
          1 T

      10006 GGATATATGT


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  15    5  0.31
  17   11  0.69

ACGTcount: A:0.55, C:0.00, G:0.18, T:0.27


Consensus pattern (16 bp):   
TTAAGAAATAGGATAA

Found at i:14077 original size:19 final size:20

Alignment explanation


    Indices: 14053--14108  Score: 60
    Period size: 21  Copynumber: 2.8  Consensus size: 20

      14043 GTTTAGCAAT

                                
      14053 TGTACAGATGAGATTA-CAC
          1 TGTACAGATGAGATTAGCAC

                  *  *        * *
      14072 TGTACATATTAGATTAGGTAT
          1 TGTACAGATGAGATTA-GCAC

                            
      14093 TGTACAGATGAGATTA
          1 TGTACAGATGAGATTA

      14109 TTAGAGCAGC


Statistics
Matches: 29,  Mismatches: 6, Indels: 2
        0.78            0.16        0.05

Matches are distributed among these distances:
  19   14  0.48
  21   15  0.52

ACGTcount: A:0.36, C:0.09, G:0.21, T:0.34


Consensus pattern (20 bp):   
TGTACAGATGAGATTAGCAC
Done.