Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000947.1 Kokia drynarioides strain JFW-HI SEQ_112117, 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: 15874
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34


Found at i:29 original size:23 final size:23

Alignment explanation


    Indices: 1--153  Score: 150
    Period size: 23  Copynumber: 6.6  Consensus size: 23

                                   
          1 TGTGCTCTCTGTTTAGCACTTTG
          1 TGTGCTCTCTGTTTAGCACTTTG

                       *            
         24 TGTGCTCTCTGATTAGCA-TTGTG
          1 TGTGCTCTCTGTTTAGCACTT-TG

                    *  *           
         47 TGTGCTCTTTGATTAGCACTTTG
          1 TGTGCTCTCTGTTTAGCACTTTG

               *             **    
         70 TGTACTCTCTGTTTAGCGTTTTG
          1 TGTGCTCTCTGTTTAGCACTTTG

                            *        *
         93 TGTGCTCTCTGTTGCCCAGCAC-TTA
          1 TGTGCTCTCTGTT---TAGCACTTTG

                            *    * 
        118 TGTGCTCTCTGTTTAGTACTTCG
          1 TGTGCTCTCTGTTTAGCACTTTG

               *          
        141 -GTACTCTCTGTTT
          1 TGTGCTCTCTGTTT

        154 GTTTTGTTTA


Statistics
Matches: 107,  Mismatches: 17, Indels: 13
        0.78            0.12        0.09

Matches are distributed among these distances:
  22   18  0.17
  23   69  0.64
  24    2  0.02
  25   15  0.14
  26    3  0.03

ACGTcount: A:0.10, C:0.22, G:0.22, T:0.46


Consensus pattern (23 bp):   
TGTGCTCTCTGTTTAGCACTTTG

Found at i:1541 original size:113 final size:113

Alignment explanation


    Indices: 1394--1634  Score: 455
    Period size: 113  Copynumber: 2.1  Consensus size: 113

       1384 TTAGTATATC

                 *                                                           
       1394 TACATACCCACATATCAACATCAACCAAAGTGATGGCCATGCCTTGTATCCAACCATGAAACGAG
          1 TACATGCCCACATATCAACATCAACCAAAGTGATGGCCATGCCTTGTATCCAACCATGAAACGAG

                    *       *                               
       1459 GCTCATGAGGAAAAACCCAACAAATTTGTTTGGTAAAGGAAATTGCAA
         66 GCTCATGAAGAAAAACACAACAAATTTGTTTGGTAAAGGAAATTGCAA

                                                                             
       1507 TACATGCCCACATATCAACATCAACCAAAGTGATGGCCATGCCTTGTATCCAACCATGAAACGAG
          1 TACATGCCCACATATCAACATCAACCAAAGTGATGGCCATGCCTTGTATCCAACCATGAAACGAG

                                                            
       1572 GCTCATGAAGAAAAACACAACAAATTTGTTTGGTAAAGGAAATTGCAA
         66 GCTCATGAAGAAAAACACAACAAATTTGTTTGGTAAAGGAAATTGCAA

                           
       1620 TACATGCCCACATAT
          1 TACATGCCCACATAT

       1635 TTAGTTAGTT


Statistics
Matches: 125,  Mismatches: 3, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
 113  125  1.00

ACGTcount: A:0.39, C:0.23, G:0.16, T:0.22


Consensus pattern (113 bp):   
TACATGCCCACATATCAACATCAACCAAAGTGATGGCCATGCCTTGTATCCAACCATGAAACGAG
GCTCATGAAGAAAAACACAACAAATTTGTTTGGTAAAGGAAATTGCAA

Found at i:2655 original size:15 final size:15

Alignment explanation


    Indices: 2637--2678  Score: 75
    Period size: 15  Copynumber: 2.8  Consensus size: 15

       2627 AATCATATTT

                  *        
       2637 AATACAAAAACATGA
          1 AATACACAAACATGA

                           
       2652 AATACACAAACATGA
          1 AATACACAAACATGA

                        
       2667 AATACACAAACA
          1 AATACACAAACA

       2679 CTCCTTGTAG


Statistics
Matches: 26,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  15   26  1.00

ACGTcount: A:0.64, C:0.19, G:0.05, T:0.12


Consensus pattern (15 bp):   
AATACACAAACATGA

Found at i:13231 original size:23 final size:24

Alignment explanation


    Indices: 13177--13231  Score: 67
    Period size: 24  Copynumber: 2.3  Consensus size: 24

      13167 ATCTTTCAGT

                *                  *
      13177 TAAATTCTGTTTAATTGTTTTAAT
          1 TAAACTCTGTTTAATTGTTTTAAG

                         *       *  
      13201 TAAACTCTGTTTATTTG-TTTGAG
          1 TAAACTCTGTTTAATTGTTTTAAG

                    
      13224 TAAACTCT
          1 TAAACTCT

      13232 CATTAATCTA


Statistics
Matches: 27,  Mismatches: 4, Indels: 1
        0.84            0.12        0.03

Matches are distributed among these distances:
  23   12  0.44
  24   15  0.56

ACGTcount: A:0.27, C:0.09, G:0.11, T:0.53


Consensus pattern (24 bp):   
TAAACTCTGTTTAATTGTTTTAAG
Done.