Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020145.1 Corchorus olitorius cultivar O-4 contig20178, 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: 7974
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34


Found at i:405 original size:12 final size:12

Alignment explanation


    Indices: 373--429  Score: 64
    Period size: 13  Copynumber: 4.8  Consensus size: 12

        363 TCCGTTGAGG

                        
        373 AAATG-TTTTAT
          1 AAATGTTTTTAT

              *          
        384 AACTGCTTTTTAT
          1 AAATG-TTTTTAT

                        
        397 AAATG-TTTTAT
          1 AAATGTTTTTAT

                      *  
        408 AAAATGTTTTGAT
          1 -AAATGTTTTTAT

                     
        421 AAATGTTTT
          1 AAATGTTTT

        430 GGGTGCATAA


Statistics
Matches: 39,  Mismatches: 3, Indels: 7
        0.80            0.06        0.14

Matches are distributed among these distances:
  11   10  0.26
  12   14  0.36
  13   15  0.38

ACGTcount: A:0.33, C:0.04, G:0.11, T:0.53


Consensus pattern (12 bp):   
AAATGTTTTTAT

Found at i:405 original size:24 final size:24

Alignment explanation


    Indices: 373--429  Score: 80
    Period size: 24  Copynumber: 2.4  Consensus size: 24

        363 TCCGTTGAGG

                          *       *  
        373 AAATGTTTTAT-AACTGCTTTTTAT
          1 AAATGTTTTATAAAATG-TTTTGAT

                                    
        397 AAATGTTTTATAAAATGTTTTGAT
          1 AAATGTTTTATAAAATGTTTTGAT

                     
        421 AAATGTTTT
          1 AAATGTTTT

        430 GGGTGCATAA


Statistics
Matches: 30,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  24   26  0.87
  25    4  0.13

ACGTcount: A:0.33, C:0.04, G:0.11, T:0.53


Consensus pattern (24 bp):   
AAATGTTTTATAAAATGTTTTGAT

Found at i:430 original size:12 final size:11

Alignment explanation


    Indices: 373--429  Score: 69
    Period size: 12  Copynumber: 4.8  Consensus size: 11

        363 TCCGTTGAGG

                       
        373 AAATGTTTTAT
          1 AAATGTTTTAT

              *          
        384 AACTGCTTTTTAT
          1 AAATG--TTTTAT

                       
        397 AAATGTTTTAT
          1 AAATGTTTTAT

                         
        408 AAAATGTTTTGAT
          1 -AAATGTTTT-AT

                     
        421 AAATGTTTT
          1 AAATGTTTT

        430 GGGTGCATAA


Statistics
Matches: 40,  Mismatches: 2, Indels: 7
        0.82            0.04        0.14

Matches are distributed among these distances:
  11   10  0.25
  12   18  0.45
  13   12  0.30

ACGTcount: A:0.33, C:0.04, G:0.11, T:0.53


Consensus pattern (11 bp):   
AAATGTTTTAT

Found at i:4685 original size:3 final size:3

Alignment explanation


    Indices: 4679--4739  Score: 122
    Period size: 3  Copynumber: 20.3  Consensus size: 3

       4669 CTACTACTAC

                                                                           
       4679 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT

                             
       4727 TAT TAT TAT TAT T
          1 TAT TAT TAT TAT T

       4740 TTACTTCAAA


Statistics
Matches: 58,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   58  1.00

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (3 bp):   
TAT

Found at i:4955 original size:21 final size:20

Alignment explanation


    Indices: 4902--4955  Score: 58
    Period size: 21  Copynumber: 2.7  Consensus size: 20

       4892 AGGCTACTTC

                         *      
       4902 AAAAA-CTTATAAACTTAAA
          1 AAAAATCTTATAAGCTTAAA

                                * 
       4921 AAAAATC-TACTAAGCTTACTA
          1 AAAAATCTTA-TAAGCTTA-AA

                          
       4942 AAAAATCTTATAAG
          1 AAAAATCTTATAAG

       4956 GTTATTTATC


Statistics
Matches: 29,  Mismatches: 2, Indels: 6
        0.78            0.05        0.16

Matches are distributed among these distances:
  19    7  0.24
  20    8  0.28
  21   12  0.41
  22    2  0.07

ACGTcount: A:0.56, C:0.13, G:0.04, T:0.28


Consensus pattern (20 bp):   
AAAAATCTTATAAGCTTAAA

Found at i:5102 original size:22 final size:22

Alignment explanation


    Indices: 5054--5104  Score: 56
    Period size: 20  Copynumber: 2.5  Consensus size: 22

       5044 GCTTATAATA

                          *       
       5054 TTAC-TAAAAGGCTTATAACGT
          1 TTACTTAAAAGGCTGATAACGT

                                   
       5075 TT--TTAAAAGGCTGATATA-GT
          1 TTACTTAAAAGGCTGATA-ACGT

                      
       5095 TTACTTAAAA
          1 TTACTTAAAA

       5105 CCTTATTTGT


Statistics
Matches: 25,  Mismatches: 1, Indels: 7
        0.76            0.03        0.21

Matches are distributed among these distances:
  20   16  0.64
  21    3  0.12
  22    6  0.24

ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37


Consensus pattern (22 bp):   
TTACTTAAAAGGCTGATAACGT
Done.