Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001119.1 Kokia drynarioides strain JFW-HI SEQ_112401, 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, 709

Length: 1183
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.38


Found at i:177 original size:15 final size:15

Alignment explanation


    Indices: 141--169  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

        131 TGCTTATAAT

                           
        141 ATAATTTTTATAAAA
          1 ATAATTTTTATAAAA

                           
        156 ATAATTTTT-TAAAA
          1 ATAATTTTTATAAAA

        170 TTGAATTTAA


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  14    5  0.36
  15    9  0.64

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (15 bp):   
ATAATTTTTATAAAA

Found at i:461 original size:15 final size:16

Alignment explanation


    Indices: 443--472  Score: 53
    Period size: 15  Copynumber: 1.9  Consensus size: 16

        433 CTTTAAAATT

                            
        443 TATTAAAAT-ATAAAC
          1 TATTAAAATAATAAAC

                           
        458 TATTAAAATAATAAA
          1 TATTAAAATAATAAA

        473 ATTACATTTT


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    9  0.64
  16    5  0.36

ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33


Consensus pattern (16 bp):   
TATTAAAATAATAAAC

Found at i:1108 original size:19 final size:21

Alignment explanation


    Indices: 1084--1128  Score: 67
    Period size: 19  Copynumber: 2.2  Consensus size: 21

       1074 ATTTTTATCC

                                 
       1084 TAAAAAAATT-AAATTC-AAA
          1 TAAAAAAATTAAAATTCAAAA

                  *              
       1103 TAAAAATATTAAAATTCAAAA
          1 TAAAAAAATTAAAATTCAAAA

                 
       1124 TAAAA
          1 TAAAA

       1129 TTATTGATGT


Statistics
Matches: 23,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  19    9  0.39
  20    6  0.26
  21    8  0.35

ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27


Consensus pattern (21 bp):   
TAAAAAAATTAAAATTCAAAA

Found at i:1117 original size:20 final size:20

Alignment explanation


    Indices: 1084--1133  Score: 66
    Period size: 21  Copynumber: 2.5  Consensus size: 20

       1074 ATTTTTATCC

                  *             
       1084 TAAAAAAATTAAATTC-AAA
          1 TAAAAATATTAAATTCAAAA

                                 
       1103 TAAAAATATTAAAATTCAAAA
          1 TAAAAATATT-AAATTCAAAA

                 *    
       1124 TAAAATTATT
          1 TAAAAATATT

       1134 GATGTGACAT


Statistics
Matches: 27,  Mismatches: 2, Indels: 2
        0.87            0.06        0.06

Matches are distributed among these distances:
  19    9  0.33
  20    6  0.22
  21   12  0.44

ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32


Consensus pattern (20 bp):   
TAAAAATATTAAATTCAAAA

Done.