Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000962.1 Kokia drynarioides strain JFW-HI SEQ_112138, 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: 24041
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32


Found at i:1016 original size:15 final size:15

Alignment explanation


    Indices: 974--1010  Score: 56
    Period size: 16  Copynumber: 2.4  Consensus size: 15

        964 TTAATGCTAT

                     *      
        974 TTAATAATACTATTTA
          1 TTAATAATAATA-TTA

                           
        990 TTAATAATAATATTA
          1 TTAATAATAATATTA

                  
       1005 TTAATA
          1 TTAATA

       1011 TCAATAAGTA


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  15    9  0.45
  16   11  0.55

ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49


Consensus pattern (15 bp):   
TTAATAATAATATTA

Found at i:1698 original size:17 final size:17

Alignment explanation


    Indices: 1672--1767  Score: 86
    Period size: 17  Copynumber: 5.6  Consensus size: 17

       1662 CTTTTTAATT

                 *      *    
       1672 AATTTTAATTTACAGTA
          1 AATTTAAATTTAAAGTA

                             
       1689 AATTTAAATTTAAAGTA
          1 AATTTAAATTTAAAGTA

                      **      
       1706 AATTTAAACTCAAAAGTA
          1 AATTTAAA-TTTAAAGTA

                            * 
       1724 AATTTAAATTTAGAA-CA
          1 AATTTAAATTTA-AAGTA

                *   *      * 
       1741 AATTCAAACTTAAAGCA
          1 AATTTAAATTTAAAGTA

                *     
       1758 AATTAAAATT
          1 AATTTAAATT

       1768 AAAATTTAGA


Statistics
Matches: 65,  Mismatches: 11, Indels: 6
        0.79            0.13        0.07

Matches are distributed among these distances:
  16    2  0.03
  17   46  0.71
  18   17  0.26

ACGTcount: A:0.52, C:0.07, G:0.05, T:0.35


Consensus pattern (17 bp):   
AATTTAAATTTAAAGTA

Found at i:1723 original size:18 final size:17

Alignment explanation


    Indices: 1685--1732  Score: 69
    Period size: 18  Copynumber: 2.8  Consensus size: 17

       1675 TTTAATTTAC

                         **  
       1685 AGTAAATTTAAATTTAA
          1 AGTAAATTTAAATCAAA

                              
       1702 AGTAAATTTAAACTCAAA
          1 AGTAAATTTAAA-TCAAA

                         
       1720 AGTAAATTTAAAT
          1 AGTAAATTTAAAT

       1733 TTAGAACAAA


Statistics
Matches: 28,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  17   13  0.46
  18   15  0.54

ACGTcount: A:0.54, C:0.04, G:0.06, T:0.35


Consensus pattern (17 bp):   
AGTAAATTTAAATCAAA

Found at i:1744 original size:35 final size:34

Alignment explanation


    Indices: 1685--1767  Score: 96
    Period size: 35  Copynumber: 2.4  Consensus size: 34

       1675 TTTAATTTAC

                               *     *         
       1685 AGTAAATTTAAATTTAAAGTAAATTTAAACTCAAA
          1 AGTAAATTTAAATTTAAAGCAAATTCAAACT-AAA

                                            *  
       1720 AGTAAATTTAAATTTAGAA-CAAATTCAAACTTAA
          1 AGTAAATTTAAATTTA-AAGCAAATTCAAACTAAA

              *     *     
       1754 AGCAAATTAAAATT
          1 AGTAAATTTAAATT

       1768 AAAATTTAGA


Statistics
Matches: 42,  Mismatches: 5, Indels: 3
        0.84            0.10        0.06

Matches are distributed among these distances:
  34   14  0.33
  35   26  0.62
  36    2  0.05

ACGTcount: A:0.54, C:0.07, G:0.06, T:0.33


Consensus pattern (34 bp):   
AGTAAATTTAAATTTAAAGCAAATTCAAACTAAA

Found at i:4161 original size:14 final size:12

Alignment explanation


    Indices: 4140--4187  Score: 51
    Period size: 13  Copynumber: 3.8  Consensus size: 12

       4130 TAAGGAATAC

                *       
       4140 TTTTAAAAAGTG
          1 TTTTGAAAAGTG

                         
       4152 TTTTGGAAAAGTG
          1 TTTT-GAAAAGTG

                         *
       4165 ATTTTGAAAAGTAT
          1 -TTTTGAAAAGT-G

                     
       4179 TTTTGAAAA
          1 TTTTGAAAA

       4188 ATTTGGTTTA


Statistics
Matches: 31,  Mismatches: 2, Indels: 5
        0.82            0.05        0.13

Matches are distributed among these distances:
  12    4  0.13
  13   23  0.74
  14    4  0.13

ACGTcount: A:0.40, C:0.00, G:0.19, T:0.42


Consensus pattern (12 bp):   
TTTTGAAAAGTG

Found at i:7858 original size:26 final size:26

Alignment explanation


    Indices: 7807--7858  Score: 79
    Period size: 26  Copynumber: 2.0  Consensus size: 26

       7797 AAACATATAT

                               *      
       7807 AAAACATTAACAAATATTCTTATAAA
          1 AAAACATTAACAAATATTCCTATAAA

                                       
       7833 AAAACATTAACAAATATTTCCT-TAAA
          1 AAAACATTAACAAATA-TTCCTATAAA

       7859 TAATAAAGTC


Statistics
Matches: 24,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  26   20  0.83
  27    4  0.17

ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31


Consensus pattern (26 bp):   
AAAACATTAACAAATATTCCTATAAA

Found at i:18497 original size:5 final size:6

Alignment explanation


    Indices: 18482--18507  Score: 52
    Period size: 6  Copynumber: 4.3  Consensus size: 6

      18472 AAACATCGTA

                                          
      18482 AAAAAG AAAAAG AAAAAG AAAAAG AA
          1 AAAAAG AAAAAG AAAAAG AAAAAG AA

      18508 TATATACTGC


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   20  1.00

ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00


Consensus pattern (6 bp):   
AAAAAG

Done.