Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004188.1 Kokia drynarioides strain JFW-HI SEQ_117421, 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:0.32, C:0.16, G:0.18, T:0.34


Found at i:988 original size:14 final size:14

Alignment explanation


    Indices: 969--1020  Score: 52
    Period size: 14  Copynumber: 3.4  Consensus size: 14

        959 ACATATTAAA

                          
        969 CATCTAAATAAAAC
          1 CATCTAAATAAAAC

                               
        983 CATCTATCACATATTAAA-
          1 CATCTA--A-ATA--AAAC

                          
       1001 CATCTAAATAAAAC
          1 CATCTAAATAAAAC

                  
       1015 CATCTA
          1 CATCTA

       1021 TCGTACGTTA


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

Matches are distributed among these distances:
  13    3  0.09
  14   12  0.38
  15    3  0.09
  16    2  0.06
  17    3  0.09
  18    6  0.19
  19    3  0.09

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


Consensus pattern (14 bp):   
CATCTAAATAAAAC

Found at i:1000 original size:32 final size:32

Alignment explanation


    Indices: 959--1022  Score: 128
    Period size: 32  Copynumber: 2.0  Consensus size: 32

        949 AACAAATGAA

                                            
        959 ACATATTAAACATCTAAATAAAACCATCTATC
          1 ACATATTAAACATCTAAATAAAACCATCTATC

                                            
        991 ACATATTAAACATCTAAATAAAACCATCTATC
          1 ACATATTAAACATCTAAATAAAACCATCTATC

       1023 GTACGTTAAC


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


Consensus pattern (32 bp):   
ACATATTAAACATCTAAATAAAACCATCTATC

Found at i:1006 original size:18 final size:16

Alignment explanation


    Indices: 958--1007  Score: 52
    Period size: 14  Copynumber: 3.1  Consensus size: 16

        948 CAACAAATGA

                            
        958 AACATATTAAACATCT
          1 AACATATTAAACATCT

                             
        974 AA-ATA--AAACCATCT
          1 AACATATTAAA-CATCT

                              
        988 ATCACATATTAAACATCT
          1 A--ACATATTAAACATCT

              
       1006 AA
          1 AA

       1008 ATAAAACCAT


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

Matches are distributed among these distances:
  13    3  0.11
  14    6  0.21
  15    3  0.11
  16    4  0.14
  17    3  0.11
  18    6  0.21
  19    3  0.11

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


Consensus pattern (16 bp):   
AACATATTAAACATCT

Found at i:1085 original size:23 final size:23

Alignment explanation


    Indices: 1055--1099  Score: 72
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       1045 TCAAATTATA

                                   
       1055 CATTGTATCTAAAAAAAACCATC
          1 CATTGTATCTAAAAAAAACCATC

                      *  *        
       1078 CATTGTATCTCAATAAAACCAT
          1 CATTGTATCTAAAAAAAACCAT

       1100 TCATCTATCT


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


Consensus pattern (23 bp):   
CATTGTATCTAAAAAAAACCATC
Done.