Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004435.1 Kokia drynarioides strain JFW-HI SEQ_117828, 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: 9368
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33


Found at i:302 original size:21 final size:21

Alignment explanation


    Indices: 276--320  Score: 54
    Period size: 21  Copynumber: 2.1  Consensus size: 21

        266 AAATGCCTTG

                   **            
        276 CGTGGCATGACACACAATGTC
          1 CGTGGCACAACACACAATGTC

                  *      *       
        297 CGTGGCGCAACACCCAATGTC
          1 CGTGGCACAACACACAATGTC

               
        318 CGT
          1 CGT

        321 ATTGCAACAC


Statistics
Matches: 20,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.24, C:0.33, G:0.24, T:0.18


Consensus pattern (21 bp):   
CGTGGCACAACACACAATGTC

Found at i:327 original size:21 final size:21

Alignment explanation


    Indices: 285--334  Score: 64
    Period size: 21  Copynumber: 2.4  Consensus size: 21

        275 GCGTGGCATG

                           *     
        285 ACACACAATGTCCGTGGCGCA
          1 ACACACAATGTCCGTAGCGCA

                *           **   
        306 ACACCCAATGTCCGTATTGCA
          1 ACACACAATGTCCGTAGCGCA

                    
        327 ACACACAA
          1 ACACACAA

        335 CCTTGTGTTA


Statistics
Matches: 24,  Mismatches: 5, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  21   24  1.00

ACGTcount: A:0.34, C:0.34, G:0.16, T:0.16


Consensus pattern (21 bp):   
ACACACAATGTCCGTAGCGCA

Found at i:383 original size:21 final size:21

Alignment explanation


    Indices: 331--389  Score: 73
    Period size: 21  Copynumber: 2.8  Consensus size: 21

        321 ATTGCAACAC

                         *       
        331 ACAACCTTGTGTTAAGCCACA
          1 ACAACCTTGTGTTGAGCCACA

               *  *              
        352 ACAGCCCTGTGTTGAGCCACA
          1 ACAACCTTGTGTTGAGCCACA

                *      *     
        373 ACAAACTTGTGGTGAGC
          1 ACAACCTTGTGTTGAGC

        390 TATAGCCTGA


Statistics
Matches: 31,  Mismatches: 7, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  21   31  1.00

ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22


Consensus pattern (21 bp):   
ACAACCTTGTGTTGAGCCACA

Found at i:1587 original size:16 final size:17

Alignment explanation


    Indices: 1566--1600  Score: 54
    Period size: 16  Copynumber: 2.1  Consensus size: 17

       1556 AATTAAAATA

                  *          
       1566 AATTAATTAA-TTTCTC
          1 AATTAAATAATTTTCTC

                             
       1582 AATTAAATAATTTTCTC
          1 AATTAAATAATTTTCTC

              
       1599 AA
          1 AA

       1601 CCCGATTATA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  16    9  0.53
  17    8  0.47

ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46


Consensus pattern (17 bp):   
AATTAAATAATTTTCTC

Found at i:2550 original size:19 final size:21

Alignment explanation


    Indices: 2526--2565  Score: 57
    Period size: 19  Copynumber: 2.0  Consensus size: 21

       2516 TCGAAACAAT

                       *         
       2526 AATGTGA-AATTA-AAAATGA
          1 AATGTGATAATAATAAAATGA

                                 
       2545 AATGTGATAATAATAAAATGA
          1 AATGTGATAATAATAAAATGA

       2566 GGTCCCCAAC


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  19    7  0.39
  20    4  0.22
  21    7  0.39

ACGTcount: A:0.57, C:0.00, G:0.15, T:0.28


Consensus pattern (21 bp):   
AATGTGATAATAATAAAATGA

Found at i:7096 original size:28 final size:28

Alignment explanation


    Indices: 7056--7109  Score: 99
    Period size: 28  Copynumber: 1.9  Consensus size: 28

       7046 ATTGCCTTAT

                *                       
       7056 GCTCTAATTCAACTGGCAAGTGACATTC
          1 GCTCCAATTCAACTGGCAAGTGACATTC

                                      
       7084 GCTCCAATTCAACTGGCAAGTGACAT
          1 GCTCCAATTCAACTGGCAAGTGACAT

       7110 GCTTTCCAAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  28   25  1.00

ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26


Consensus pattern (28 bp):   
GCTCCAATTCAACTGGCAAGTGACATTC

Done.