Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022096.1 Corchorus olitorius cultivar O-4 contig22129, 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: 24738
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35


Found at i:4194 original size:2 final size:2

Alignment explanation


    Indices: 4187--4214  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

       4177 TACTTTTATT

                                                     
       4187 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

       4215 AGCAAGGGAA


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:14625 original size:28 final size:28

Alignment explanation


    Indices: 14563--14637  Score: 80
    Period size: 28  Copynumber: 2.7  Consensus size: 28

      14553 TATGGGCATA

                              *    *    
      14563 AAATTACCGTTTTACCCTAAGAATGAAT
          1 AAATTACCGTTTTACCCTTAGAAAGAAT

             *                        * 
      14591 ACATTACCGTTTTACCCTTAGAAAG-TT
          1 AAATTACCGTTTTACCCTTAGAAAGAAT

                    *      *    
      14618 AAATTTACAGTTTTAACCTT
          1 AAA-TTACCGTTTTACCCTT

      14638 GTACTTTGAA


Statistics
Matches: 39,  Mismatches: 7, Indels: 2
        0.81            0.15        0.04

Matches are distributed among these distances:
  27    3  0.08
  28   36  0.92

ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37


Consensus pattern (28 bp):   
AAATTACCGTTTTACCCTTAGAAAGAAT

Found at i:15148 original size:13 final size:12

Alignment explanation


    Indices: 15130--15174  Score: 54
    Period size: 14  Copynumber: 3.5  Consensus size: 12

      15120 ATTTTATTAC

                         
      15130 TGTTTTATTAAAT
          1 TGTTTTA-TAAAT

                        
      15143 TGTTTTATAAAT
          1 TGTTTTATAAAT

            *             
      15155 GGTTTTAAATAAAT
          1 TGTTTT--ATAAAT

                  
      15169 TGTTTT
          1 TGTTTT

      15175 GGGTGCATGA


Statistics
Matches: 28,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  12   10  0.36
  13    7  0.25
  14   11  0.39

ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58


Consensus pattern (12 bp):   
TGTTTTATAAAT

Found at i:17513 original size:18 final size:17

Alignment explanation


    Indices: 17486--17521  Score: 63
    Period size: 18  Copynumber: 2.1  Consensus size: 17

      17476 TTTCTCTTCA

                             
      17486 TCTATTTTTCTTCTAGT
          1 TCTATTTTTCTTCTAGT

                              
      17503 TCTAGTTTTTCTTCTAGT
          1 TCTA-TTTTTCTTCTAGT

             
      17521 T
          1 T

      17522 TTTAGGCTAG


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  17    4  0.22
  18   14  0.78

ACGTcount: A:0.11, C:0.17, G:0.08, T:0.64


Consensus pattern (17 bp):   
TCTATTTTTCTTCTAGT

Found at i:21011 original size:16 final size:17

Alignment explanation


    Indices: 20982--21014  Score: 50
    Period size: 16  Copynumber: 2.0  Consensus size: 17

      20972 AATATTAATT

                     *       
      20982 AATAGTTATTATATATA
          1 AATAGTTATCATATATA

                             
      20999 AATA-TTATCATATATA
          1 AATAGTTATCATATATA

      21015 TAAATATTTT


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  16   11  0.73
  17    4  0.27

ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45


Consensus pattern (17 bp):   
AATAGTTATCATATATA
Done.