Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020136.1 Corchorus olitorius cultivar O-4 contig20169, 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: 13832
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34


Found at i:4250 original size:15 final size:15

Alignment explanation


    Indices: 4232--4269  Score: 58
    Period size: 15  Copynumber: 2.5  Consensus size: 15

       4222 CTTTAAAAAA

                           
       4232 CTTTCCTTCCCTTCC
          1 CTTTCCTTCCCTTCC

                 *  *      
       4247 CTTTCTTTTCCTTCC
          1 CTTTCCTTCCCTTCC

                    
       4262 CTTTCCTT
          1 CTTTCCTT

       4270 TAATTACTTG


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  15   20  1.00

ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55


Consensus pattern (15 bp):   
CTTTCCTTCCCTTCC

Found at i:4256 original size:20 final size:20

Alignment explanation


    Indices: 4233--4270  Score: 67
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       4223 TTTAAAAAAC

                                
       4233 TTTCCTTCCCTTCCCTTTCT
          1 TTTCCTTCCCTTCCCTTTCT

                        *     
       4253 TTTCCTTCCCTTTCCTTT
          1 TTTCCTTCCCTTCCCTTT

       4271 AATTACTTGA


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  20   17  1.00

ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58


Consensus pattern (20 bp):   
TTTCCTTCCCTTCCCTTTCT

Found at i:4809 original size:51 final size:51

Alignment explanation


    Indices: 4743--4861  Score: 211
    Period size: 51  Copynumber: 2.3  Consensus size: 51

       4733 AACTATTGGC

                                                      **        
       4743 TACTTAAAAGGCCAAATATATACTATATATTATTTTTAGTGATTATGGAAAT
          1 TACTT-AAAGGCCAAATATATACTATATATTATTTTTAGTGACAATGGAAAT

                                                               
       4795 TACTTAAAGGCCAAATATATACTATATATTATTTTTAGTGACAATGGAAAT
          1 TACTTAAAGGCCAAATATATACTATATATTATTTTTAGTGACAATGGAAAT

                            
       4846 TACTTAAAGGCCAAAT
          1 TACTTAAAGGCCAAAT

       4862 TGAGGATTAA


Statistics
Matches: 65,  Mismatches: 2, Indels: 1
        0.96            0.03        0.01

Matches are distributed among these distances:
  51   60  0.92
  52    5  0.08

ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37


Consensus pattern (51 bp):   
TACTTAAAGGCCAAATATATACTATATATTATTTTTAGTGACAATGGAAAT

Found at i:7011 original size:22 final size:24

Alignment explanation


    Indices: 6984--7027  Score: 65
    Period size: 24  Copynumber: 1.9  Consensus size: 24

       6974 GTGATGAACA

                            *       
       6984 AGAGAAAA-AA-CACGGAGCTTTG
          1 AGAGAAAATAAGCACGAAGCTTTG

                                  
       7006 AGAGAAAATAAGCACGAAGCTT
          1 AGAGAAAATAAGCACGAAGCTT

       7028 GGTTTTTTAC


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  22    8  0.42
  23    2  0.11
  24    9  0.47

ACGTcount: A:0.48, C:0.14, G:0.25, T:0.14


Consensus pattern (24 bp):   
AGAGAAAATAAGCACGAAGCTTTG

Found at i:9335 original size:21 final size:21

Alignment explanation


    Indices: 9310--9349  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       9300 AAATTAGGTT

                        *        
       9310 TAATTGGATGAGTAAAAGACC
          1 TAATTGGATGAGGAAAAGACC

                 *             
       9331 TAATTTGATGAGGAAAAGA
          1 TAATTGGATGAGGAAAAGA

       9350 ACCCTAGTTG


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

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.45, C:0.05, G:0.25, T:0.25


Consensus pattern (21 bp):   
TAATTGGATGAGGAAAAGACC

Found at i:12720 original size:16 final size:16

Alignment explanation


    Indices: 12699--12732  Score: 59
    Period size: 16  Copynumber: 2.1  Consensus size: 16

      12689 AAGTCAAAAA

                            
      12699 AAAAAAAAAAACAAGG
          1 AAAAAAAAAAACAAGG

                    *       
      12715 AAAAAAAATAACAAGG
          1 AAAAAAAAAAACAAGG

              
      12731 AA
          1 AA

      12733 GAAATGATTG


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   17  1.00

ACGTcount: A:0.79, C:0.06, G:0.12, T:0.03


Consensus pattern (16 bp):   
AAAAAAAAAAACAAGG
Done.