Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004361.1 Kokia drynarioides strain JFW-HI SEQ_117714, 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, 821

Length: 1369
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35


Found at i:399 original size:47 final size:47

Alignment explanation


    Indices: 349--516  Score: 176
    Period size: 51  Copynumber: 3.4  Consensus size: 47

        339 GAAAGGGTTC

                  *                                        
        349 GATGACAAACTGTCATCGTAAATGAATCCTATATGGATTAAAGGT-T
          1 GATGACTAACTGTCATCGTAAATGAATCCTATATGGATTAAAGGTCT

                      *   *  *                 *          *     
        395 CGATGACTAAGTGTTATTGTGAGTGAATGAATCCTTTATGGATTAATGGTCT
          1 -GATGACTAACTGTCATCGT-A---AATGAATCCTATATGGATTAAAGGTCT

                                              *                
        447 GATGACTAACTGTCATCGTGAGTAAATGAATCCTGTATGGATTAAAGGTCT
          1 GATGACTAACTGTCATC----GTAAATGAATCCTATATGGATTAAAGGTCT

                     *         
        498 GATGACTAAGTGTCATCGT
          1 GATGACTAACTGTCATCGT

        517 GAGTTTATAG


Statistics
Matches: 100,  Mismatches: 12, Indels: 18
        0.77            0.09        0.14

Matches are distributed among these distances:
  47   17  0.17
  48    1  0.01
  51   78  0.78
  52    1  0.01
  54    1  0.01
  55    2  0.02

ACGTcount: A:0.31, C:0.12, G:0.23, T:0.33


Consensus pattern (47 bp):   
GATGACTAACTGTCATCGTAAATGAATCCTATATGGATTAAAGGTCT

Found at i:436 original size:51 final size:51

Alignment explanation


    Indices: 366--539  Score: 233
    Period size: 51  Copynumber: 3.4  Consensus size: 51

        356 AACTGTCATC

                                                        *  *    
        366 GTAAATGAATCCTATATGGATTAAAGGT-TCGATGACTAAGTGTTATTGTGA
          1 GTAAATGAATCCTATATGGATTAAAGGTCT-GATGACTAAGTGTCATCGTGA

              *          *          *              *           
        417 GTGAATGAATCCTTTATGGATTAATGGTCTGATGACTAACTGTCATCGTGA
          1 GTAAATGAATCCTATATGGATTAAAGGTCTGATGACTAAGTGTCATCGTGA

                         *                                     
        468 GTAAATGAATCCTGTATGGATTAAAGGTCTGATGACTAAGTGTCATCGTGA
          1 GTAAATGAATCCTATATGGATTAAAGGTCTGATGACTAAGTGTCATCGTGA

              **     *           
        519 GTTTATAGATTCCTATATGGA
          1 GTAAAT-GAATCCTATATGGA

        540 ACGAGAGGTT


Statistics
Matches: 107,  Mismatches: 14, Indels: 3
        0.86            0.11        0.02

Matches are distributed among these distances:
  51   94  0.88
  52   13  0.12

ACGTcount: A:0.30, C:0.11, G:0.24, T:0.35


Consensus pattern (51 bp):   
GTAAATGAATCCTATATGGATTAAAGGTCTGATGACTAAGTGTCATCGTGA

Found at i:1335 original size:21 final size:21

Alignment explanation


    Indices: 1291--1349  Score: 57
    Period size: 21  Copynumber: 2.8  Consensus size: 21

       1281 TAGATGCATG

                     *       *   
       1291 ACATGTATCTGTAGAAATTAT
          1 ACATGTATCGGTAGAAACTAT

                                  
       1312 ACATGTATCGGTAG-AACTAGT
          1 ACATGTATCGGTAGAAACTA-T

               *   *  *      
       1333 ACAGGTACCGATAGAAA
          1 ACATGTATCGGTAGAAA

       1350 TCTGCACTGT


Statistics
Matches: 31,  Mismatches: 5, Indels: 3
        0.79            0.13        0.08

Matches are distributed among these distances:
  20    4  0.13
  21   25  0.81
  22    2  0.06

ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27


Consensus pattern (21 bp):   
ACATGTATCGGTAGAAACTAT
Done.