Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006919.1 Kokia drynarioides strain JFW-HI SEQ_121522, 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, 965

Length: 1609
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32


Found at i:539 original size:23 final size:23

Alignment explanation


    Indices: 511--555  Score: 72
    Period size: 23  Copynumber: 2.0  Consensus size: 23

        501 AGATAGATGA

                                   
        511 ATGGTTTTATTGAGATACAATGG
          1 ATGGTTTTATTGAGATACAATGG

                    *  *          
        534 ATGGTTTTTTTTAGATACAATG
          1 ATGGTTTTATTGAGATACAATG

        556 TATAATTTGA


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  23   20  1.00

ACGTcount: A:0.29, C:0.04, G:0.22, T:0.44


Consensus pattern (23 bp):   
ATGGTTTTATTGAGATACAATGG

Found at i:609 original size:14 final size:14

Alignment explanation


    Indices: 590--641  Score: 52
    Period size: 14  Copynumber: 3.4  Consensus size: 14

        580 TAACGTACGA

                          
        590 TAGATGGTTTTATT
          1 TAGATGGTTTTATT

                             
        604 TAGAT-GTTTAATATGT
          1 TAGATGGTTT--TAT-T

                            
        620 GATAGATGGTTTTATT
          1 --TAGATGGTTTTATT

                  
        636 TAGATG
          1 TAGATG

        642 TTTAATATGT


Statistics
Matches: 32,  Mismatches: 0, Indels: 12
        0.73            0.00        0.27

Matches are distributed among these distances:
  13    4  0.12
  14   11  0.34
  15    3  0.09
  16    2  0.06
  17    3  0.09
  18    5  0.16
  19    4  0.12

ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50


Consensus pattern (14 bp):   
TAGATGGTTTTATT

Found at i:624 original size:32 final size:32

Alignment explanation


    Indices: 588--651  Score: 128
    Period size: 32  Copynumber: 2.0  Consensus size: 32

        578 GTTAACGTAC

                                            
        588 GATAGATGGTTTTATTTAGATGTTTAATATGT
          1 GATAGATGGTTTTATTTAGATGTTTAATATGT

                                            
        620 GATAGATGGTTTTATTTAGATGTTTAATATGT
          1 GATAGATGGTTTTATTTAGATGTTTAATATGT

        652 TTAATTTGTT


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  32   32  1.00

ACGTcount: A:0.28, C:0.00, G:0.22, T:0.50


Consensus pattern (32 bp):   
GATAGATGGTTTTATTTAGATGTTTAATATGT

Found at i:627 original size:18 final size:16

Alignment explanation


    Indices: 603--652  Score: 52
    Period size: 14  Copynumber: 3.1  Consensus size: 16

        593 ATGGTTTTAT

                            
        603 TTAGATGTTTAATATG
          1 TTAGATGTTTAATATG

                               
        619 TGATAGATGGTTT--TAT-
          1 T--TAGAT-GTTTAATATG

                            
        635 TTAGATGTTTAATATG
          1 TTAGATGTTTAATATG

              
        651 TT
          1 TT

        653 TAATTTGTTG


Statistics
Matches: 28,  Mismatches: 0, Indels: 12
        0.70            0.00        0.30

Matches are distributed among these distances:
  13    4  0.14
  14    5  0.18
  15    3  0.11
  16    4  0.14
  17    3  0.11
  18    5  0.18
  19    4  0.14

ACGTcount: A:0.28, C:0.00, G:0.20, T:0.52


Consensus pattern (16 bp):   
TTAGATGTTTAATATG
Done.