Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004367.1 Kokia drynarioides strain JFW-HI SEQ_117723, 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: 2354
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36


Found at i:1174 original size:15 final size:14

Alignment explanation


    Indices: 1150--1179  Score: 51
    Period size: 15  Copynumber: 2.1  Consensus size: 14

       1140 AAATAAATAT

                          
       1150 AAGTATTTATTTAA
          1 AAGTATTTATTTAA

                           
       1164 AAGTGATTTATTTAA
          1 AAGT-ATTTATTTAA

             
       1179 A
          1 A

       1180 TATAATGTTG


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    4  0.27
  15   11  0.73

ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47


Consensus pattern (14 bp):   
AAGTATTTATTTAA

Found at i:1281 original size:14 final size:14

Alignment explanation


    Indices: 1262--1309  Score: 53
    Period size: 14  Copynumber: 3.5  Consensus size: 14

       1252 AAATTATTTA

                    *     
       1262 TTTATATATATATT
          1 TTTATATAAATATT

                          
       1276 TTTATATAAATA-T
          1 TTTATATAAATATT

             *   *        
       1289 TATATTTAAATATT
          1 TTTATATAAATATT

             *     
       1303 TATATAT
          1 TTTATAT

       1310 TTATATGTAT


Statistics
Matches: 29,  Mismatches: 4, Indels: 2
        0.83            0.11        0.06

Matches are distributed among these distances:
  13   11  0.38
  14   18  0.62

ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58


Consensus pattern (14 bp):   
TTTATATAAATATT

Found at i:1313 original size:8 final size:8

Alignment explanation


    Indices: 1255--1315  Score: 54
    Period size: 8  Copynumber: 7.8  Consensus size: 8

       1245 TAAACAAAAA

                *   
       1255 TTATTTAT
          1 TTATATAT

                    
       1263 TTATATA-
          1 TTATATAT

                  * 
       1270 -TATATTT
          1 TTATATAT

                   *
       1277 TTATATAA
          1 TTATATAT

            *        
       1285 ATATTATAT
          1 TTA-TATAT

               *    
       1294 TTAAATAT
          1 TTATATAT

                    
       1302 TTATATAT
          1 TTATATAT

                  
       1310 TTATAT
          1 TTATAT

       1316 GTATTCACTA


Statistics
Matches: 41,  Mismatches: 9, Indels: 6
        0.73            0.16        0.11

Matches are distributed among these distances:
   6    5  0.12
   8   30  0.73
   9    6  0.15

ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61


Consensus pattern (8 bp):   
TTATATAT
Done.