Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008787.1 Kokia drynarioides strain JFW-HI SEQ_123470, 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: 6621
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36


Found at i:966 original size:3 final size:3

Alignment explanation


    Indices: 958--983  Score: 52
    Period size: 3  Copynumber: 8.7  Consensus size: 3

        948 TTTGAAATTA

                                              
        958 TAC TAC TAC TAC TAC TAC TAC TAC TA
          1 TAC TAC TAC TAC TAC TAC TAC TAC TA

        984 AAAAAAAAAA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   23  1.00

ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35


Consensus pattern (3 bp):   
TAC

Found at i:1625 original size:22 final size:22

Alignment explanation


    Indices: 1582--1627  Score: 67
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       1572 TGTAATGATT

                                   
       1582 ATGAAACGACACGGCGAGAGGTG
          1 ATGAAACGA-ACGGCGAGAGGTG

                                   
       1605 ATGAAACG-ACGGCAGAGAGGTG
          1 ATGAAACGAACGGC-GAGAGGTG

             
       1627 A
          1 A

       1628 AGAGGAAGTG


Statistics
Matches: 22,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  21    5  0.23
  22    9  0.41
  23    8  0.36

ACGTcount: A:0.37, C:0.15, G:0.39, T:0.09


Consensus pattern (22 bp):   
ATGAAACGAACGGCGAGAGGTG

Found at i:4043 original size:34 final size:34

Alignment explanation


    Indices: 3995--4061  Score: 116
    Period size: 34  Copynumber: 2.0  Consensus size: 34

       3985 AACATCTGGG

                *          *                  
       3995 TAAGGTAAAAGGTAATAAATTAAAAATATTTGGA
          1 TAAGATAAAAGGTAAAAAATTAAAAATATTTGGA

                                             
       4029 TAAGATAAAAGGTAAAAAATTAAAAATATTTGG
          1 TAAGATAAAAGGTAAAAAATTAAAAATATTTGG

       4062 GTTTAGTTTA


Statistics
Matches: 31,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  34   31  1.00

ACGTcount: A:0.55, C:0.00, G:0.16, T:0.28


Consensus pattern (34 bp):   
TAAGATAAAAGGTAAAAAATTAAAAATATTTGGA

Found at i:5493 original size:14 final size:16

Alignment explanation


    Indices: 5458--5497  Score: 52
    Period size: 14  Copynumber: 2.8  Consensus size: 16

       5448 TTTGAAATAT

                            
       5458 TTAAAATCTAAATTAA
          1 TTAAAATCTAAATTAA

                            
       5474 TT-AAATCT-AATT-A
          1 TTAAAATCTAAATTAA

                        
       5487 TTAAAAT-TAAA
          1 TTAAAATCTAAA

       5498 AGTTGATACC


Statistics
Matches: 22,  Mismatches: 0, Indels: 6
        0.79            0.00        0.21

Matches are distributed among these distances:
  13    4  0.18
  14   10  0.45
  15    6  0.27
  16    2  0.09

ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40


Consensus pattern (16 bp):   
TTAAAATCTAAATTAA

Found at i:5843 original size:22 final size:20

Alignment explanation


    Indices: 5808--5852  Score: 54
    Period size: 21  Copynumber: 2.1  Consensus size: 20

       5798 AATTTTTTAA

                              *  
       5808 TTTTTAATTTTTTATAGATTT
          1 TTTTTAATTTTTTAT-GAATT

                 *               
       5829 TTTTTTATATTTTTATGAATT
          1 TTTTTAAT-TTTTTATGAATT

               
       5850 TTT
          1 TTT

       5853 AATTAATTAT


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  21   14  0.67
  22    7  0.33

ACGTcount: A:0.22, C:0.00, G:0.04, T:0.73


Consensus pattern (20 bp):   
TTTTTAATTTTTTATGAATT
Done.