Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013838.1 Corchorus olitorius cultivar O-4 contig13871, 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: 9396
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31


Found at i:8 original size:2 final size:2

Alignment explanation


    Indices: 2--32  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

          1 G

                                                          
          2 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

         33 TGTGCATTAT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:1336 original size:37 final size:39

Alignment explanation


    Indices: 1248--1361  Score: 171
    Period size: 38  Copynumber: 2.9  Consensus size: 39

       1238 ATATTTTTAA

                                                   
       1248 TTAAGTAATTCCAAAAGAAGATTTTGG-AAAATAAAAGT
          1 TTAAGTAATTCCAAAAGAAGATTTTGGAAAAATAAAAGT

               *                                   
       1286 TTAGGTAATTCCAAAAGAAG-TTTTGGAAAAATAAAAGT
          1 TTAAGTAATTCCAAAAGAAGATTTTGGAAAAATAAAAGT

                    *                              
       1324 TTAAG-AAATCCAAAAGAAGATTTTGGAAATTAATAAAA
          1 TTAAGTAATTCCAAAAGAAGATTTTGGAAA--AATAAAA

       1362 TTGATTAAGG


Statistics
Matches: 69,  Mismatches: 3, Indels: 6
        0.88            0.04        0.08

Matches are distributed among these distances:
  37   19  0.28
  38   43  0.62
  40    7  0.10

ACGTcount: A:0.51, C:0.05, G:0.16, T:0.28


Consensus pattern (39 bp):   
TTAAGTAATTCCAAAAGAAGATTTTGGAAAAATAAAAGT

Found at i:6008 original size:18 final size:17

Alignment explanation


    Indices: 5985--6022  Score: 67
    Period size: 18  Copynumber: 2.2  Consensus size: 17

       5975 CCCAAATTAC

                              
       5985 TTATGGAAATTAGGGAAA
          1 TTATGGAAATTA-GGAAA

                             
       6003 TTATGGAAATTAGGAAA
          1 TTATGGAAATTAGGAAA

               
       6020 TTA
          1 TTA

       6023 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:6020 original size:8 final size:9

Alignment explanation


    Indices: 5989--6022  Score: 52
    Period size: 9  Copynumber: 3.9  Consensus size: 9

       5979 AATTACTTAT

                     
       5989 GGAAATTAG
          1 GGAAATTAG

                    *
       5998 GGAAATTAT
          1 GGAAATTAG

                     
       6007 GGAAATTA-
          1 GGAAATTAG

                    
       6015 GGAAATTA
          1 GGAAATTA

       6023 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:7376 original size:49 final size:47

Alignment explanation


    Indices: 7299--7439  Score: 160
    Period size: 49  Copynumber: 2.9  Consensus size: 47

       7289 CAAGCAATCC

                *      *                                    
       7299 TTTACTTTTCACTGCACTTTTTCTCAATTTTTACTACAAAATTGAACT
          1 TTTAATTTTCATTGCACTTTTTCTCAATTTTTA-TACAAAATTGAACT

                     *                          *          *  
       7347 TTT-ATTTTTACTTGCATCTTTTTCTCAATTTTTAAGACAAAATTGATCT
          1 TTTAATTTTCA-TTGCA-CTTTTTCTCAATTTTT-ATACAAAATTGAACT

                        *         *                      
       7396 TTTAATTTTCATCGCACTTTTTATCAATTTTT-TGACAAAATTGA
          1 TTTAATTTTCATTGCACTTTTTCTCAATTTTTAT-ACAAAATTGA

       7440 TTGGCACGCT


Statistics
Matches: 79,  Mismatches: 9, Indels: 11
        0.80            0.09        0.11

Matches are distributed among these distances:
  47   15  0.19
  48   22  0.28
  49   35  0.44
  50    7  0.09

ACGTcount: A:0.28, C:0.16, G:0.06, T:0.50


Consensus pattern (47 bp):   
TTTAATTTTCATTGCACTTTTTCTCAATTTTTATACAAAATTGAACT

Found at i:8294 original size:17 final size:17

Alignment explanation


    Indices: 8260--8304  Score: 58
    Period size: 17  Copynumber: 2.8  Consensus size: 17

       8250 TGCTAGGGTG

                             
       8260 AATGGTGC-AA-ACAAC
          1 AATGGTGCGAACACAAC

                         *   
       8275 AATGGTGCGAACATAAC
          1 AATGGTGCGAACACAAC

                   *     
       8292 AATGGTGTGAACA
          1 AATGGTGCGAACA

       8305 ATAATGGAAA


Statistics
Matches: 26,  Mismatches: 2, Indels: 2
        0.87            0.07        0.07

Matches are distributed among these distances:
  15    8  0.31
  16    2  0.08
  17   16  0.62

ACGTcount: A:0.42, C:0.16, G:0.24, T:0.18


Consensus pattern (17 bp):   
AATGGTGCGAACACAAC
Done.