Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005428.1 Kokia drynarioides strain JFW-HI SEQ_119457, 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: 14449
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:4719 original size:15 final size:15

Alignment explanation


    Indices: 4699--4746  Score: 53
    Period size: 15  Copynumber: 3.2  Consensus size: 15

       4689 TTTAACTGTC

                           
       4699 ATTTTGGGTTCTGAA
          1 ATTTTGGGTTCTGAA

                        *  *
       4714 ATTTTGGGCTTCAG-C
          1 ATTTTGGG-TTCTGAA

                        *  
       4729 ATTTTGGGTTCTAAA
          1 ATTTTGGGTTCTGAA

               
       4744 ATT
          1 ATT

       4747 CGCATTTAAC


Statistics
Matches: 26,  Mismatches: 5, Indels: 4
        0.74            0.14        0.11

Matches are distributed among these distances:
  14    3  0.12
  15   19  0.73
  16    4  0.15

ACGTcount: A:0.21, C:0.10, G:0.23, T:0.46


Consensus pattern (15 bp):   
ATTTTGGGTTCTGAA

Found at i:5158 original size:13 final size:13

Alignment explanation


    Indices: 5138--5167  Score: 53
    Period size: 13  Copynumber: 2.4  Consensus size: 13

       5128 TTTATTTATA

                         
       5138 AAAT-CAAATAAT
          1 AAATACAAATAAT

                         
       5150 AAATACAAATAAT
          1 AAATACAAATAAT

                 
       5163 AAATA
          1 AAATA

       5168 TATAATTATT


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

Matches are distributed among these distances:
  12    4  0.24
  13   13  0.76

ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23


Consensus pattern (13 bp):   
AAATACAAATAAT

Found at i:6614 original size:12 final size:12

Alignment explanation


    Indices: 6599--6663  Score: 50
    Period size: 12  Copynumber: 5.8  Consensus size: 12

       6589 AATAAAATAA

                        
       6599 CAACAAAAACAG
          1 CAACAAAAACAG

                *       
       6611 CAACCAAAACAG
          1 CAACAAAAACAG

             *         *
       6623 -TA-AAAAACAA
          1 CAACAAAAACAG

              *         
       6633 CATC-AAAACAG
          1 CAACAAAAACAG

                         
       6644 CAATC-AAAACAG
          1 CAA-CAAAAACAG

                     
       6656 CAA-AAAAA
          1 CAACAAAAA

       6664 GCACTAAAAC


Statistics
Matches: 41,  Mismatches: 8, Indels: 9
        0.71            0.14        0.16

Matches are distributed among these distances:
  10    6  0.15
  11   13  0.32
  12   22  0.54

ACGTcount: A:0.66, C:0.23, G:0.06, T:0.05


Consensus pattern (12 bp):   
CAACAAAAACAG

Found at i:6645 original size:33 final size:31

Alignment explanation


    Indices: 6586--6662  Score: 100
    Period size: 33  Copynumber: 2.4  Consensus size: 31

       6576 CAGCAAAAAT

                *                           
       6586 AACAATAAAATAACAACAAAAACAGCAACCAA
          1 AACAGTAAAA-AACAACAAAAACAGCAACCAA

                                         *   
       6618 AACAGTAAAAAACAACATCAAAACAGCAATCAA
          1 AACAGTAAAAAACAACA--AAAACAGCAACCAA

                 *      
       6651 AACAGCAAAAAA
          1 AACAGTAAAAAA

       6663 AGCACTAAAA


Statistics
Matches: 40,  Mismatches: 3, Indels: 3
        0.87            0.07        0.07

Matches are distributed among these distances:
  31    7  0.17
  32    9  0.22
  33   24  0.60

ACGTcount: A:0.68, C:0.21, G:0.05, T:0.06


Consensus pattern (31 bp):   
AACAGTAAAAAACAACAAAAACAGCAACCAA
Done.