Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019553.1 Corchorus olitorius cultivar O-4 contig19586, 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: 13277
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30


Found at i:1914 original size:22 final size:22

Alignment explanation


    Indices: 1889--1934  Score: 83
    Period size: 22  Copynumber: 2.1  Consensus size: 22

       1879 ACAAATTCTG

                                  
       1889 TTTTTATTTTATTCTTTTGCAA
          1 TTTTTATTTTATTCTTTTGCAA

                 *                
       1911 TTTTTTTTTTATTCTTTTGCAA
          1 TTTTTATTTTATTCTTTTGCAA

              
       1933 TT
          1 TT

       1935 CTGAACAGCT


Statistics
Matches: 23,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  22   23  1.00

ACGTcount: A:0.15, C:0.09, G:0.04, T:0.72


Consensus pattern (22 bp):   
TTTTTATTTTATTCTTTTGCAA

Found at i:4155 original size:72 final size:72

Alignment explanation


    Indices: 4044--4199  Score: 156
    Period size: 72  Copynumber: 2.2  Consensus size: 72

       4034 AAAGAAGAGC

                   *        *                        *                       
       4044 AATTACCAATTTCAGGTGGAATAGGTCCACCCAAATGGTTTTC-AGAGAGATCCAATGAAATGAG
          1 AATTACCGATTTCAGGCGGAATAGGTCCACCCAAATGG-TTCCAAGAGAGATCCAATGAAATGAG

                    
       4108 TGCTCCCA
         65 TGCTCCCA

                               *    *     **                  *  * *    *    
       4116 AATTACCGATTTCAGGCGGGATAGTTCCA-TTAAACTGGTTCCAAGAGAGGTCTAGTGAAGTGAG
          1 AATTACCGATTTCAGGCGGAATAGGTCCACCCAAA-TGGTTCCAAGAGAGATCCAATGAAATGAG

                  * 
       4180 TGCTCCTA
         65 TGCTCCCA

                         
       4188 AACTT-CCGATTT
          1 AA-TTACCGATTT

       4200 GAGATGCAAT


Statistics
Matches: 69,  Mismatches: 12, Indels: 6
        0.79            0.14        0.07

Matches are distributed among these distances:
  71    6  0.09
  72   61  0.88
  73    2  0.03

ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28


Consensus pattern (72 bp):   
AATTACCGATTTCAGGCGGAATAGGTCCACCCAAATGGTTCCAAGAGAGATCCAATGAAATGAGT
GCTCCCA

Found at i:10460 original size:42 final size:43

Alignment explanation


    Indices: 10413--10495  Score: 125
    Period size: 42  Copynumber: 2.0  Consensus size: 43

      10403 CGTGTTTGAC

                                          *             
      10413 TTATCGTGTCTCGTGT-CTGAATCGTGTC-GGACACGATTAAGA
          1 TTATCGTGTCTCGTGTCCT-AATCGTGTCAAGACACGATTAAGA

                     *                               
      10455 TTATCGTGTTTCGTGTCCTAATCGTGTCAAGACACGATTAA
          1 TTATCGTGTCTCGTGTCCTAATCGTGTCAAGACACGATTAA

      10496 CACGTTTAAG


Statistics
Matches: 37,  Mismatches: 2, Indels: 3
        0.88            0.05        0.07

Matches are distributed among these distances:
  42   24  0.65
  43   13  0.35

ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35


Consensus pattern (43 bp):   
TTATCGTGTCTCGTGTCCTAATCGTGTCAAGACACGATTAAGA

Found at i:10508 original size:20 final size:21

Alignment explanation


    Indices: 10483--10525  Score: 61
    Period size: 20  Copynumber: 2.1  Consensus size: 21

      10473 TAATCGTGTC

                     *           
      10483 AAGACACGATTAACACG-TTT
          1 AAGACACGAGTAACACGCTTT

                       *         
      10503 AAGACACGAGTGACACGCTTT
          1 AAGACACGAGTAACACGCTTT

              
      10524 AA
          1 AA

      10526 TTAACGGGTT


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  20   15  0.75
  21    5  0.25

ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21


Consensus pattern (21 bp):   
AAGACACGAGTAACACGCTTT

Found at i:11005 original size:12 final size:12

Alignment explanation


    Indices: 10988--11019  Score: 55
    Period size: 12  Copynumber: 2.7  Consensus size: 12

      10978 TACCCTATGT

                        
      10988 AAACACGACACG
          1 AAACACGACACG

                        
      11000 AAACACGACACG
          1 AAACACGACACG

            *       
      11012 GAACACGA
          1 AAACACGA

      11020 ATTGCCAGGT


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  12   19  1.00

ACGTcount: A:0.50, C:0.31, G:0.19, T:0.00


Consensus pattern (12 bp):   
AAACACGACACG

Found at i:11654 original size:3 final size:3

Alignment explanation


    Indices: 11646--11673  Score: 56
    Period size: 3  Copynumber: 9.3  Consensus size: 3

      11636 GAGAAGCAAA

                                                 
      11646 AGG AGG AGG AGG AGG AGG AGG AGG AGG A
          1 AGG AGG AGG AGG AGG AGG AGG AGG AGG A

      11674 TGTGGCGGAG


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   25  1.00

ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00


Consensus pattern (3 bp):   
AGG

Done.