Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012824.1 Kokia drynarioides strain JFW-HI SEQ_127837, 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: 2543
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.36


Found at i:2144 original size:12 final size:12

Alignment explanation


    Indices: 2129--2214  Score: 66
    Period size: 12  Copynumber: 7.2  Consensus size: 12

       2119 TTGGTTACTG

                 *      
       2129 TTTTGGTGTTGT
          1 TTTTGCTGTTGT

                *     **
       2141 TTTTACTGTTAC
          1 TTTTGCTGTTGT

                    * * 
       2153 TTTTGCTGCTAT
          1 TTTTGCTGTTGT

                 *      
       2165 TTTTGTTGTTGT
          1 TTTTGCTGTTGT

                 *      
       2177 TTTTGTTGTTG-
          1 TTTTGCTGTTGT

                      * 
       2188 TTTTGCTGTTAT
          1 TTTTGCTGTTGT

                *  *    
       2200 TTTTACTATTGT
          1 TTTTGCTGTTGT

               
       2212 TTT
          1 TTT

       2215 GGTTGTTATT


Statistics
Matches: 58,  Mismatches: 15, Indels: 2
        0.77            0.20        0.03

Matches are distributed among these distances:
  11    9  0.16
  12   49  0.84

ACGTcount: A:0.07, C:0.07, G:0.19, T:0.67


Consensus pattern (12 bp):   
TTTTGCTGTTGT

Found at i:2169 original size:36 final size:35

Alignment explanation


    Indices: 2129--2203  Score: 96
    Period size: 36  Copynumber: 2.1  Consensus size: 35

       2119 TTGGTTACTG

                                                
       2129 TTTTGGTGTTGTTTTTACTGTTACTTTTGCTGCTAT
          1 TTTTGGTGTTGTTTTTACTGTT-CTTTTGCTGCTAT

                 *          **    *        *   
       2165 TTTTGTTGTTGTTTTTGTTGTTGTTTTGCTGTTAT
          1 TTTTGGTGTTGTTTTTACTGTTCTTTTGCTGCTAT

                
       2200 TTTT
          1 TTTT

       2204 ACTATTGTTT


Statistics
Matches: 34,  Mismatches: 5, Indels: 1
        0.85            0.12        0.03

Matches are distributed among these distances:
  35   15  0.44
  36   19  0.56

ACGTcount: A:0.05, C:0.07, G:0.20, T:0.68


Consensus pattern (35 bp):   
TTTTGGTGTTGTTTTTACTGTTCTTTTGCTGCTAT

Found at i:2191 original size:23 final size:23

Alignment explanation


    Indices: 2165--2233  Score: 75
    Period size: 23  Copynumber: 3.0  Consensus size: 23

       2155 TTGCTGCTAT

                      *            
       2165 TTTTGTTGTTGTTTTTGTTGTTG
          1 TTTTGTTGTTATTTTTGTTGTTG

                 *          ** *   
       2188 TTTTGCTGTTATTTTTACTATTG
          1 TTTTGTTGTTATTTTTGTTGTTG

                            *      
       2211 TTTTGGTTGTTATTTTGGTTGTT
          1 TTTT-GTTGTTATTTTTGTTGTT

       2234 TGGATGTTAT


Statistics
Matches: 35,  Mismatches: 10, Indels: 1
        0.76            0.22        0.02

Matches are distributed among these distances:
  23   22  0.63
  24   13  0.37

ACGTcount: A:0.06, C:0.03, G:0.22, T:0.70


Consensus pattern (23 bp):   
TTTTGTTGTTATTTTTGTTGTTG

Found at i:2201 original size:35 final size:35

Alignment explanation


    Indices: 2129--2227  Score: 108
    Period size: 35  Copynumber: 2.8  Consensus size: 35

       2119 TTGGTTACTG

                 *          **                  
       2129 TTTTGGTGTTGTTTTTACTGTTACTTTTGCTGCTAT
          1 TTTTGCTGTTGTTTTTGTTGTTA-TTTTGCTGCTAT

                 *                *        *   
       2165 TTTTGTTGTTGTTTTTGTTGTTGTTTTGCTGTTAT
          1 TTTTGCTGTTGTTTTTGTTGTTATTTTGCTGCTAT

                *  *       *            
       2200 TTTTACTATTGTTTTGGTTGTTATTTTG
          1 TTTTGCTGTTGTTTTTGTTGTTATTTTG

       2228 GTTGTTTGGA


Statistics
Matches: 53,  Mismatches: 10, Indels: 1
        0.83            0.16        0.02

Matches are distributed among these distances:
  35   34  0.64
  36   19  0.36

ACGTcount: A:0.07, C:0.06, G:0.20, T:0.67


Consensus pattern (35 bp):   
TTTTGCTGTTGTTTTTGTTGTTATTTTGCTGCTAT

Found at i:2226 original size:12 final size:12

Alignment explanation


    Indices: 2147--2233  Score: 59
    Period size: 12  Copynumber: 7.3  Consensus size: 12

       2137 TTGTTTTTAC

                 *     *
       2147 TGTTACTTTTGC
          1 TGTTATTTTTGT

              *         
       2159 TGCTATTTTTGT
          1 TGTTATTTTTGT

                *       
       2171 TGTTGTTTTTGT
          1 TGTTATTTTTGT

                 *     *
       2183 TGTT-GTTTTGC
          1 TGTTATTTTTGT

                      **
       2194 TGTTATTTTTAC
          1 TGTTATTTTTGT

             *  *    *  
       2206 TATTGTTTTGGT
          1 TGTTATTTTTGT

                     *  
       2218 TGTTATTTTGGT
          1 TGTTATTTTTGT

                
       2230 TGTT
          1 TGTT

       2234 TGGATGTTAT


Statistics
Matches: 58,  Mismatches: 16, Indels: 2
        0.76            0.21        0.03

Matches are distributed among these distances:
  11    9  0.16
  12   49  0.84

ACGTcount: A:0.07, C:0.06, G:0.21, T:0.67


Consensus pattern (12 bp):   
TGTTATTTTTGT

Found at i:2402 original size:10 final size:10

Alignment explanation


    Indices: 2360--2402  Score: 56
    Period size: 10  Copynumber: 4.6  Consensus size: 10

       2350 AATCTAAAAT

                      
       2360 TTTTTTAATA
          1 TTTTTTAATA

             *        
       2370 TCTTTTAA-A
          1 TTTTTTAATA

                      
       2379 TTTTTT--TA
          1 TTTTTTAATA

                      
       2387 TTTTTTAATA
          1 TTTTTTAATA

                  
       2397 TTTTTT
          1 TTTTTT

       2403 TTAATGTTTT


Statistics
Matches: 28,  Mismatches: 2, Indels: 6
        0.78            0.06        0.17

Matches are distributed among these distances:
   8    7  0.25
   9    6  0.21
  10   15  0.54

ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74


Consensus pattern (10 bp):   
TTTTTTAATA
Done.