Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008301.1 Kokia drynarioides strain JFW-HI SEQ_122966, 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: 3772
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.37


Found at i:1194 original size:29 final size:28

Alignment explanation


    Indices: 1139--1194  Score: 76
    Period size: 28  Copynumber: 2.0  Consensus size: 28

       1129 ATTATTTATA

                         *        *     
       1139 AAAATGATCTAAATTAAACATATATATC
          1 AAAATGATCTAAAATAAACATAAATATC

                    *                   
       1167 AAAATGATTTAAAATAAACAGTAAATAT
          1 AAAATGATCTAAAATAAACA-TAAATAT

       1195 TTTAAATGAT


Statistics
Matches: 24,  Mismatches: 3, Indels: 1
        0.86            0.11        0.04

Matches are distributed among these distances:
  28   18  0.75
  29    6  0.25

ACGTcount: A:0.57, C:0.07, G:0.05, T:0.30


Consensus pattern (28 bp):   
AAAATGATCTAAAATAAACATAAATATC

Found at i:1647 original size:42 final size:42

Alignment explanation


    Indices: 1582--1695  Score: 115
    Period size: 48  Copynumber: 2.6  Consensus size: 42

       1572 CTCAATACTT

                               *                        
       1582 TTTTTTATTTGATAAAAC-CATGATCAT-CACTTAAAAAATATA
          1 TTTTTTATTTGA-AAAACAGATGATCATACACTTAAAAAA-ATA

                                               *           
       1624 TTTTTTATTTGAAAAACAGATGATGGTCATAAACATTTAAAAAAATA
          1 TTTTTTATTTGAAAAACAGATGA---TCAT--ACACTTAAAAAAATA

                             *       
       1671 TCTTTTTATTTGAAAAAGAGATGAT
          1 T-TTTTTATTTGAAAAACAGATGAT

       1696 GATTATGATT


Statistics
Matches: 61,  Mismatches: 3, Indels: 13
        0.79            0.04        0.17

Matches are distributed among these distances:
  41    5  0.08
  42   16  0.26
  45    5  0.08
  47    4  0.07
  48   31  0.51

ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39


Consensus pattern (42 bp):   
TTTTTTATTTGAAAAACAGATGATCATACACTTAAAAAAATA

Found at i:3045 original size:20 final size:20

Alignment explanation


    Indices: 3020--3058  Score: 69
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       3010 TAGGGGCACC

                    *           
       3020 CTGCTGTTTCCTGCTACTGT
          1 CTGCTGTTGCCTGCTACTGT

                               
       3040 CTGCTGTTGCCTGCTACTG
          1 CTGCTGTTGCCTGCTACTG

       3059 CTTGTTGCTG


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  20   18  1.00

ACGTcount: A:0.05, C:0.31, G:0.23, T:0.41


Consensus pattern (20 bp):   
CTGCTGTTGCCTGCTACTGT

Found at i:3066 original size:17 final size:17

Alignment explanation


    Indices: 3020--3075  Score: 53
    Period size: 20  Copynumber: 3.2  Consensus size: 17

       3010 TAGGGGCACC

                     *       
       3020 CTGC-TGTTTCCTGCTA
          1 CTGCTTGTTGCCTGCTA

                                
       3036 CTGTCTGCTGTTGCCTGCTA
          1 CTG-CT--TGTTGCCTGCTA

                              
       3056 CTGCTTGTTG-CTGGCTA
          1 CTGCTTGTTGCCT-GCTA

               
       3073 CTG
          1 CTG

       3076 ACACCCGATT


Statistics
Matches: 34,  Mismatches: 1, Indels: 9
        0.77            0.02        0.20

Matches are distributed among these distances:
  16    5  0.15
  17   13  0.38
  19    2  0.06
  20   14  0.41

ACGTcount: A:0.05, C:0.29, G:0.25, T:0.41


Consensus pattern (17 bp):   
CTGCTTGTTGCCTGCTA

Found at i:3722 original size:207 final size:207

Alignment explanation


    Indices: 3348--3772  Score: 681
    Period size: 207  Copynumber: 2.1  Consensus size: 207

       3338 TGTTTGTGTT

                                                          *                  
       3348 TGATTTTTATTTAAATGTTATTTAAATTTAAATTTTATCTATATAATTTGATCTTGTTAGTCTAA
          1 TGATTTTTATTTAAATGTTATTTAAATTTAAATTTTATCTATATAACTTGATCTTGTTAGTCTAA

               *                                                             
       3413 ACCCTTAAAATTTAACATTAATTTATTTGAAATAAAAAAAATAACGATTCATAAAATTACAATAG
         66 ACCATTAAAATTTAACATTAATTTATTTGAAATAAAAAAAATAACGATTCATAAAATTACAATAG

             *  *                       * *                                  
       3478 TGCTCAAATGGTCCCCAAAATTAAAACAGATTATTAAATAAAAATTAAAACTTTATTTTGATACA
        131 TACTAAAATGGTCCCCAAAATTAAAACAAAATATTAAATAAAAATTAAAACTTTATTTTGATACA

                        
       3543 AAGTTTTAAGGC
        196 AAGTTTTAAGGC

                                                      *                   *  
       3555 TGATTTTTATTTAAATGTTATTTAAATTTAAATTTTATCTATTTAACTTGATCTTAGTTAGTGTA
          1 TGATTTTTATTTAAATGTTATTTAAATTTAAATTTTATCTATATAACTTGATCTT-GTTAGTCTA

               *   *                                   * *         *    *    
       3620 AACGATTGAAATTTAACATTAATTTATTTGAAATAAAAAAAATTATGATTCATAATATTATAATA
         65 AACCATTAAAATTTAACATTAATTTATTTGAAATAAAAAAAATAACGATTCATAAAATTACAATA

               *                                                             
       3685 GTATTAAAATGGTCCCCAAAATTAAAA-AAAATATTAAATAAAAATTAAAACTTTATTTTGATAC
        130 GTACTAAAATGGTCCCCAAAATTAAAACAAAATATTAAATAAAAATTAAAACTTTATTTTGATAC

                     *  *
       3749 AAAGTTTTAGGGT
        195 AAAGTTTTAAGGC

                       
       3762 TGATTTTTATT
          1 TGATTTTTATT


Statistics
Matches: 200,  Mismatches: 17, Indels: 2
        0.91            0.08        0.01

Matches are distributed among these distances:
 207  110  0.55
 208   90  0.45

ACGTcount: A:0.43, C:0.08, G:0.08, T:0.42


Consensus pattern (207 bp):   
TGATTTTTATTTAAATGTTATTTAAATTTAAATTTTATCTATATAACTTGATCTTGTTAGTCTAA
ACCATTAAAATTTAACATTAATTTATTTGAAATAAAAAAAATAACGATTCATAAAATTACAATAG
TACTAAAATGGTCCCCAAAATTAAAACAAAATATTAAATAAAAATTAAAACTTTATTTTGATACA
AAGTTTTAAGGC
Done.