Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015968.1 Corchorus olitorius cultivar O-4 contig16001, 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: 6682
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27


Found at i:1391 original size:18 final size:17

Alignment explanation


    Indices: 1368--1405  Score: 67
    Period size: 18  Copynumber: 2.2  Consensus size: 17

       1358 CCCAAATTAC

                              
       1368 TTATGGAAATTAGGGAAA
          1 TTATGGAAATTA-GGAAA

                             
       1386 TTATGGAAATTAGGAAA
          1 TTATGGAAATTAGGAAA

               
       1403 TTA
          1 TTA

       1406 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:1403 original size:8 final size:9

Alignment explanation


    Indices: 1372--1405  Score: 52
    Period size: 9  Copynumber: 3.9  Consensus size: 9

       1362 AATTACTTAT

                     
       1372 GGAAATTAG
          1 GGAAATTAG

                    *
       1381 GGAAATTAT
          1 GGAAATTAG

                     
       1390 GGAAATTA-
          1 GGAAATTAG

                    
       1398 GGAAATTA
          1 GGAAATTA

       1406 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:2779 original size:46 final size:46

Alignment explanation


    Indices: 2683--2821  Score: 156
    Period size: 47  Copynumber: 3.0  Consensus size: 46

       2673 CAAGCAATCC

                *      *                      *          *  
       2683 TTTACTTTTCACTGCACTTTTTCTCAATTTTTACTACAAAATTGAACT
          1 TTTAATTTTCATTGCACTTTTTCTCAATTTTT--GACAAAATTGATCT

                     *                                      
       2731 TTT-ATTTTTACTTGCATCTTTTTCTCAA-TTTTGACAAAATTGATCT
          1 TTTAATTTTCA-TTGCA-CTTTTTCTCAATTTTTGACAAAATTGATCT

                        *         *                      
       2777 TTTAATTTTCATCGCACTTTTTATCAATTTTTTGACAAAATTGAT
          1 TTTAATTTTCATTGCACTTTTTCTCAA-TTTTTGACAAAATTGAT

       2822 TGGCACGCTC


Statistics
Matches: 78,  Mismatches: 8, Indels: 11
        0.80            0.08        0.11

Matches are distributed among these distances:
  45   10  0.13
  46   19  0.24
  47   27  0.35
  48   11  0.14
  49   11  0.14

ACGTcount: A:0.27, C:0.17, G:0.06, T:0.51


Consensus pattern (46 bp):   
TTTAATTTTCATTGCACTTTTTCTCAATTTTTGACAAAATTGATCT

Found at i:3686 original size:15 final size:15

Alignment explanation


    Indices: 3645--3688  Score: 70
    Period size: 15  Copynumber: 2.9  Consensus size: 15

       3635 TGCTAGGGTG

                    *      
       3645 AATGGTGCAAACAAC
          1 AATGGTGCGAACAAC

                           
       3660 AATGGTGCGAACAAC
          1 AATGGTGCGAACAAC

                   *      
       3675 AATGGTGTGAACAA
          1 AATGGTGCGAACAA

       3689 TAACGGAAAC


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  15   27  1.00

ACGTcount: A:0.43, C:0.16, G:0.25, T:0.16


Consensus pattern (15 bp):   
AATGGTGCGAACAAC
Done.