Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009680.1 Kokia drynarioides strain JFW-HI SEQ_124398, 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: 9379
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34


Found at i:1297 original size:3 final size:3

Alignment explanation


    Indices: 1289--1326  Score: 76
    Period size: 3  Copynumber: 12.7  Consensus size: 3

       1279 ATTTAAAGCC

                                                              
       1289 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA

       1327 GGGCCACATT


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   35  1.00

ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32


Consensus pattern (3 bp):   
AAT

Found at i:2197 original size:25 final size:26

Alignment explanation


    Indices: 2158--2211  Score: 92
    Period size: 25  Copynumber: 2.1  Consensus size: 26

       2148 TTTTTTAAGG

                                       
       2158 TTTAAAAGCTTTTTTTTTAAAAGAACC
          1 TTTAAAAGC-TTTTTTTTAAAAGAACC

                                      
       2185 TTTAAAAGC-TTTTTTTAAAAGAACC
          1 TTTAAAAGCTTTTTTTTAAAAGAACC

              
       2210 TT
          1 TT

       2212 CCATCAGAGC


Statistics
Matches: 27,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
  25   18  0.67
  27    9  0.33

ACGTcount: A:0.37, C:0.11, G:0.07, T:0.44


Consensus pattern (26 bp):   
TTTAAAAGCTTTTTTTTAAAAGAACC

Found at i:8054 original size:20 final size:19

Alignment explanation


    Indices: 8025--8063  Score: 69
    Period size: 20  Copynumber: 2.0  Consensus size: 19

       8015 TTTTCTAGAT

                               
       8025 GTTTGAAATTGTGTGATGA
          1 GTTTGAAATTGTGTGATGA

                                
       8044 GTTTCGAAATTGTGTGATGA
          1 GTTT-GAAATTGTGTGATGA

       8064 AATTAGAAAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  19    4  0.21
  20   15  0.79

ACGTcount: A:0.26, C:0.03, G:0.31, T:0.41


Consensus pattern (19 bp):   
GTTTGAAATTGTGTGATGA

Found at i:8072 original size:20 final size:20

Alignment explanation


    Indices: 8029--8072  Score: 61
    Period size: 20  Copynumber: 2.2  Consensus size: 20

       8019 CTAGATGTTT

                           **  *
       8029 GAAATTGTGTGATGAGTTTC
          1 GAAATTGTGTGATGAAATTA

                                
       8049 GAAATTGTGTGATGAAATTA
          1 GAAATTGTGTGATGAAATTA

                
       8069 GAAA
          1 GAAA

       8073 ATATTCTGCT


Statistics
Matches: 21,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  20   21  1.00

ACGTcount: A:0.36, C:0.02, G:0.27, T:0.34


Consensus pattern (20 bp):   
GAAATTGTGTGATGAAATTA

Found at i:9021 original size:15 final size:16

Alignment explanation


    Indices: 9001--9035  Score: 54
    Period size: 15  Copynumber: 2.2  Consensus size: 16

       8991 ATAAACTGTC

                    *       
       9001 GAAACCATGTC-TTTT
          1 GAAACCATCTCTTTTT

                            
       9016 GAAACCATCTCTTTTT
          1 GAAACCATCTCTTTTT

                
       9032 GAAA
          1 GAAA

       9036 ACGACGTGTT


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  15   10  0.56
  16    8  0.44

ACGTcount: A:0.31, C:0.20, G:0.11, T:0.37


Consensus pattern (16 bp):   
GAAACCATCTCTTTTT

Done.