Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019463.1 Corchorus olitorius cultivar O-4 contig19496, 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: 7887
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.27


Found at i:3147 original size:18 final size:17

Alignment explanation


    Indices: 3124--3161  Score: 67
    Period size: 18  Copynumber: 2.2  Consensus size: 17

       3114 CCCAAATTAC

                              
       3124 TTATGGAAATTAGGGAAA
          1 TTATGGAAATTA-GGAAA

                             
       3142 TTATGGAAATTAGGAAA
          1 TTATGGAAATTAGGAAA

               
       3159 TTA
          1 TTA

       3162 AATGAATTAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  17    8  0.40
  18   12  0.60

ACGTcount: A:0.45, C:0.00, G:0.24, T:0.32


Consensus pattern (17 bp):   
TTATGGAAATTAGGAAA

Found at i:3159 original size:8 final size:9

Alignment explanation


    Indices: 3128--3161  Score: 52
    Period size: 9  Copynumber: 3.9  Consensus size: 9

       3118 AATTACTTAT

                     
       3128 GGAAATTAG
          1 GGAAATTAG

                    *
       3137 GGAAATTAT
          1 GGAAATTAG

                     
       3146 GGAAATTA-
          1 GGAAATTAG

                    
       3154 GGAAATTA
          1 GGAAATTA

       3162 AATGAATTAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
   8    8  0.33
   9   16  0.67

ACGTcount: A:0.47, C:0.00, G:0.26, T:0.26


Consensus pattern (9 bp):   
GGAAATTAG

Found at i:4514 original size:49 final size:47

Alignment explanation


    Indices: 4444--4578  Score: 168
    Period size: 49  Copynumber: 2.8  Consensus size: 47

       4434 ATCCTTTACT

                                                            
       4444 TTTTAC-TGCACTTTTTCTCAATTTTTACTACAAAATTGAACTTTTAA
          1 TTTTACTTGCACTTTTTCTCAATTTTTA-TACAAAATTGAACTTTTAA

                                          *          *       
       4491 TTTTACTTGCATCTTTTTCTCAATTTTTAAGACAAAATTGATCTTTTAA
          1 TTTTACTTGCA-CTTTTTCTCAATTTTT-ATACAAAATTGAACTTTTAA

                    *         *                      
       4540 TTTT-CATCGCACTTTTTATCAATTTTT-TGACAAAATTGA
          1 TTTTAC-TTGCACTTTTTCTCAATTTTTAT-ACAAAATTGA

       4579 TTGGCACGCT


Statistics
Matches: 78,  Mismatches: 5, Indels: 10
        0.84            0.05        0.11

Matches are distributed among these distances:
  47   16  0.21
  48   20  0.26
  49   41  0.53
  50    1  0.01

ACGTcount: A:0.29, C:0.16, G:0.06, T:0.50


Consensus pattern (47 bp):   
TTTTACTTGCACTTTTTCTCAATTTTTATACAAAATTGAACTTTTAA

Found at i:5432 original size:12 final size:15

Alignment explanation


    Indices: 5394--5428  Score: 70
    Period size: 15  Copynumber: 2.3  Consensus size: 15

       5384 TGCTAGGGTG

                           
       5394 AATGGTGCAAACAAC
          1 AATGGTGCAAACAAC

                           
       5409 AATGGTGCAAACAAC
          1 AATGGTGCAAACAAC

                 
       5424 AATGG
          1 AATGG

       5429 AAACGGTGCA


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   20  1.00

ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14


Consensus pattern (15 bp):   
AATGGTGCAAACAAC
Done.