Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021925.1 Corchorus olitorius cultivar O-4 contig21958, 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: 18379
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33


Found at i:4595 original size:2 final size:2

Alignment explanation


    Indices: 4590--4617  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

       4580 TATATACTTT

                                                     
       4590 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       4618 AACAAAAACA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:12224 original size:21 final size:22

Alignment explanation


    Indices: 12198--12245  Score: 62
    Period size: 22  Copynumber: 2.2  Consensus size: 22

      12188 CAAACAGGTT

                                  
      12198 TCTTTT-CTCAGATCTATATGA
          1 TCTTTTGCTCAGATCTATATGA

                     *      * *   
      12219 TCTTTTGCTTAGATCTTTCTGA
          1 TCTTTTGCTCAGATCTATATGA

                 
      12241 TCTTT
          1 TCTTT

      12246 CACTTCAATT


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  21    6  0.26
  22   17  0.74

ACGTcount: A:0.17, C:0.19, G:0.10, T:0.54


Consensus pattern (22 bp):   
TCTTTTGCTCAGATCTATATGA

Found at i:13422 original size:22 final size:22

Alignment explanation


    Indices: 13396--13447  Score: 61
    Period size: 22  Copynumber: 2.4  Consensus size: 22

      13386 TTCCTATGCT

                               *   
      13396 TTTTGATAATC-TCTCTATGAGA
          1 TTTTGATAATCTTC-CTATAAGA

                 *               *
      13418 TTTTGTTAATCTTCCTATAAGT
          1 TTTTGATAATCTTCCTATAAGA

                    
      13440 TTTTGATA
          1 TTTTGATA

      13448 TTATAGTACA


Statistics
Matches: 25,  Mismatches: 4, Indels: 2
        0.81            0.13        0.06

Matches are distributed among these distances:
  22   23  0.92
  23    2  0.08

ACGTcount: A:0.25, C:0.12, G:0.12, T:0.52


Consensus pattern (22 bp):   
TTTTGATAATCTTCCTATAAGA

Found at i:15578 original size:18 final size:17

Alignment explanation


    Indices: 15555--15592  Score: 67
    Period size: 18  Copynumber: 2.2  Consensus size: 17

      15545 CCCAAATTAC

                              
      15555 TTATGGAAATTAGGGAAA
          1 TTATGGAAATTA-GGAAA

                             
      15573 TTATGGAAATTAGGAAA
          1 TTATGGAAATTAGGAAA

               
      15590 TTA
          1 TTA

      15593 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:15590 original size:8 final size:9

Alignment explanation


    Indices: 15559--15592  Score: 52
    Period size: 9  Copynumber: 3.9  Consensus size: 9

      15549 AATTACTTAT

                     
      15559 GGAAATTAG
          1 GGAAATTAG

                    *
      15568 GGAAATTAT
          1 GGAAATTAG

                     
      15577 GGAAATTA-
          1 GGAAATTAG

                    
      15585 GGAAATTA
          1 GGAAATTA

      15593 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:16919 original size:49 final size:49

Alignment explanation


    Indices: 16844--16972  Score: 183
    Period size: 49  Copynumber: 2.7  Consensus size: 49

      16834 CAAGCAATCC

                                              **             
      16844 TTTACTTTTTAC-TGCACTTTTTCTCAATTTTTACTACAAAATTGAACT
          1 TTTACTTTTTACTTGCACTTTTTCTCAATTTTTAAGACAAAATTGAACT

                           *                               *  
      16892 TTTA-TTTTTACTTGTATCTTTTTCTCAATTTTTAAGACAAAATTGATCT
          1 TTTACTTTTTACTTGCA-CTTTTTCTCAATTTTTAAGACAAAATTGAACT

                                   *         
      16941 TTTACTTTTTA-TTGCACTTTTTATCAATTTTT
          1 TTTACTTTTTACTTGCACTTTTTCTCAATTTTT

      16973 GGATAAAATT


Statistics
Matches: 72,  Mismatches: 6, Indels: 6
        0.86            0.07        0.07

Matches are distributed among these distances:
  47    7  0.10
  48   22  0.31
  49   37  0.51
  50    6  0.08

ACGTcount: A:0.25, C:0.15, G:0.05, T:0.56


Consensus pattern (49 bp):   
TTTACTTTTTACTTGCACTTTTTCTCAATTTTTAAGACAAAATTGAACT

Found at i:17823 original size:15 final size:15

Alignment explanation


    Indices: 17803--17836  Score: 50
    Period size: 15  Copynumber: 2.3  Consensus size: 15

      17793 TGCTAGGGTG

                           
      17803 AATGGTGCGAACAAC
          1 AATGGTGCGAACAAC

                   *      *
      17818 AATGGTGTGAACAAT
          1 AATGGTGCGAACAAC

                
      17833 AATG
          1 AATG

      17837 AAAACGGTGC


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.41, C:0.12, G:0.26, T:0.21


Consensus pattern (15 bp):   
AATGGTGCGAACAAC
Done.