Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014909.1 Kokia drynarioides strain JFW-HI SEQ_129952, 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: 5016
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.35


Found at i:636 original size:2 final size:2

Alignment explanation


    Indices: 629--657  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

        619 CTGTCAAATC

                                                       
        629 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

        658 ATTATAGCAA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:1184 original size:17 final size:17

Alignment explanation


    Indices: 1162--1215  Score: 62
    Period size: 17  Copynumber: 3.4  Consensus size: 17

       1152 ATGCATAAAT

                             
       1162 TTTGATTCAATGAGTAA
          1 TTTGATTCAATGAGTAA

                  *          
       1179 TTTGATGC-AT-A--AA
          1 TTTGATTCAATGAGTAA

                              
       1192 TTTTGATTCAATGAGTAA
          1 -TTTGATTCAATGAGTAA

                  
       1210 TTTGAT
          1 TTTGAT

       1216 ACATAAATTT


Statistics
Matches: 30,  Mismatches: 2, Indels: 10
        0.71            0.05        0.24

Matches are distributed among these distances:
  13    2  0.07
  14    7  0.23
  15    3  0.10
  16    3  0.10
  17   13  0.43
  18    2  0.07

ACGTcount: A:0.33, C:0.06, G:0.17, T:0.44


Consensus pattern (17 bp):   
TTTGATTCAATGAGTAA

Found at i:1187 original size:31 final size:31

Alignment explanation


    Indices: 1152--1226  Score: 141
    Period size: 31  Copynumber: 2.4  Consensus size: 31

       1142 CTTTAACATT

                                           
       1152 ATGCATAAATTTTGATTCAATGAGTAATTTG
          1 ATGCATAAATTTTGATTCAATGAGTAATTTG

                                           
       1183 ATGCATAAATTTTGATTCAATGAGTAATTTG
          1 ATGCATAAATTTTGATTCAATGAGTAATTTG

              *          
       1214 ATACATAAATTTT
          1 ATGCATAAATTTT

       1227 AATTTGATGT


Statistics
Matches: 43,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  31   43  1.00

ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43


Consensus pattern (31 bp):   
ATGCATAAATTTTGATTCAATGAGTAATTTG

Found at i:1896 original size:22 final size:19

Alignment explanation


    Indices: 1845--1896  Score: 61
    Period size: 18  Copynumber: 2.6  Consensus size: 19

       1835 TGATTTTATG

                               
       1845 TTTAATTATTT-ATTAAAT
          1 TTTAATTATTTAATTAAAT

                *                
       1863 TTTATTTATTTAATTTAACAT
          1 TTTAATTATTTAA-TTAA-AT

                         
       1884 TTTAATATATTTA
          1 TTTAAT-TATTTA

       1897 CTCATGAACA


Statistics
Matches: 28,  Mismatches: 2, Indels: 4
        0.82            0.06        0.12

Matches are distributed among these distances:
  18   10  0.36
  19    1  0.04
  20    4  0.14
  21    7  0.25
  22    6  0.21

ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62


Consensus pattern (19 bp):   
TTTAATTATTTAATTAAAT
Done.