Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019574.1 Corchorus olitorius cultivar O-4 contig19607, 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: 7718
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35


Found at i:9 original size:2 final size:2

Alignment explanation


    Indices: 3--39  Score: 74
    Period size: 2  Copynumber: 18.5  Consensus size: 2

          1 AC

                                                                   
          3 TA TA TA 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 TA TA TA T

         40 GGGTATAATA


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   35  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:113 original size:54 final size:54

Alignment explanation


    Indices: 31--134  Score: 199
    Period size: 54  Copynumber: 1.9  Consensus size: 54

         21 TATATATATA

                                                *                 
         31 TATATATATGGGTATAATACTTTAAATTTGCAGGCTGACCCAAGATTAGACATT
          1 TATATATATGGGTATAATACTTTAAATTTGCAGGCTCACCCAAGATTAGACATT

                                                              
         85 TATATATATGGGTATAATACTTTAAATTTGCAGGCTCACCCAAGATTAGA
          1 TATATATATGGGTATAATACTTTAAATTTGCAGGCTCACCCAAGATTAGA

        135 ACAGTAATTA


Statistics
Matches: 49,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  54   49  1.00

ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35


Consensus pattern (54 bp):   
TATATATATGGGTATAATACTTTAAATTTGCAGGCTCACCCAAGATTAGACATT

Found at i:855 original size:20 final size:21

Alignment explanation


    Indices: 825--865  Score: 75
    Period size: 20  Copynumber: 2.0  Consensus size: 21

        815 TGAAAACGAA

                                 
        825 CAGAGAGAAGAAGAGAGGAGG
          1 CAGAGAGAAGAAGAGAGGAGG

                                 
        846 CAGA-AGAAGAAGAGAGGAGG
          1 CAGAGAGAAGAAGAGAGGAGG

        866 TGGAAGAATA


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

Matches are distributed among these distances:
  20   16  0.80
  21    4  0.20

ACGTcount: A:0.49, C:0.05, G:0.46, T:0.00


Consensus pattern (21 bp):   
CAGAGAGAAGAAGAGAGGAGG

Found at i:2687 original size:23 final size:22

Alignment explanation


    Indices: 2661--2703  Score: 59
    Period size: 23  Copynumber: 1.9  Consensus size: 22

       2651 CCTGTTCCCT

                 *                 
       2661 TTCTCTTTCTTTTTCTTTTTTCG
          1 TTCTCATTCTTTTT-TTTTTTCG

                *               
       2684 TTCTGATTCTTTTTTTTTTT
          1 TTCTCATTCTTTTTTTTTTT

       2704 GGTTGAAATT


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  22    6  0.33
  23   12  0.67

ACGTcount: A:0.02, C:0.16, G:0.05, T:0.77


Consensus pattern (22 bp):   
TTCTCATTCTTTTTTTTTTTCG

Found at i:3577 original size:15 final size:16

Alignment explanation


    Indices: 3553--3592  Score: 55
    Period size: 15  Copynumber: 2.6  Consensus size: 16

       3543 AGAGGTTGAA

                 *          
       3553 AGAAAGCAATTAAAC-
          1 AGAAAACAATTAAACT

                        *   
       3568 AGAAAACAATTATACT
          1 AGAAAACAATTAAACT

                     
       3584 AGAAAACAA
          1 AGAAAACAA

       3593 AACAAAGTAA


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  15   13  0.59
  16    9  0.41

ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15


Consensus pattern (16 bp):   
AGAAAACAATTAAACT

Found at i:4377 original size:11 final size:12

Alignment explanation


    Indices: 4351--4377  Score: 54
    Period size: 12  Copynumber: 2.2  Consensus size: 12

       4341 ACCCTTGCCT

                        
       4351 AAAACTAGAAGA
          1 AAAACTAGAAGA

                        
       4363 AAAACTAGAAGA
          1 AAAACTAGAAGA

               
       4375 AAA
          1 AAA

       4378 GAAATTATCT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   15  1.00

ACGTcount: A:0.70, C:0.07, G:0.15, T:0.07


Consensus pattern (12 bp):   
AAAACTAGAAGA
Done.