Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002989.1 Kokia drynarioides strain JFW-HI SEQ_115477, 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: 11268
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.34

Warning! 65 characters in sequence are not A, C, G, or T


Found at i:8 original size:3 final size:3

Alignment explanation


    Indices: 1--36  Score: 72
    Period size: 3  Copynumber: 12.0  Consensus size: 3

                                                           
          1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
          1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT

         37 GTTTATTCCC


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   33  1.00

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (3 bp):   
ATT

Found at i:79 original size:4 final size:4

Alignment explanation


    Indices: 65--105  Score: 57
    Period size: 4  Copynumber: 10.0  Consensus size: 4

         55 GCATATGTAT

                                                               
         65 TTTA TTTTA TTTA TTTA TTTA TTTA TTT- TGTTA TTTA TTTA
          1 TTTA -TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA

        106 CTCAATTTAT


Statistics
Matches: 34,  Mismatches: 0, Indels: 5
        0.87            0.00        0.13

Matches are distributed among these distances:
   3    1  0.03
   4   28  0.82
   5    5  0.15

ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76


Consensus pattern (4 bp):   
TTTA

Found at i:151 original size:36 final size:37

Alignment explanation


    Indices: 111--184  Score: 98
    Period size: 38  Copynumber: 2.0  Consensus size: 37

        101 ATTTACTCAA

                               **       *         
        111 TTTATTATTT-TA-CTGTATTTTATGTATATATTATTT
          1 TTTATTATTTATACCTGTAAATTATGTACATATT-TTT

                                                 
        147 TTTATTATTTATACCTGTAAATTATGTACATATTTTT
          1 TTTATTATTTATACCTGTAAATTATGTACATATTTTT

             
        184 T
          1 T

        185 GCATAATATT


Statistics
Matches: 33,  Mismatches: 3, Indels: 3
        0.85            0.08        0.08

Matches are distributed among these distances:
  36   10  0.30
  37    6  0.18
  38   17  0.52

ACGTcount: A:0.27, C:0.05, G:0.05, T:0.62


Consensus pattern (37 bp):   
TTTATTATTTATACCTGTAAATTATGTACATATTTTT

Found at i:4811 original size:195 final size:195

Alignment explanation


    Indices: 4423--4869  Score: 530
    Period size: 195  Copynumber: 2.3  Consensus size: 195

       4413 TACCTATACC

                                *                            *               
       4423 CGATGCTGCTCACACGAGCTATCAAGGACTCGCAACATATGCGGTACCTTAGCCA-CGATACAGT
          1 CGATGCTGCTCACACGAGCTGTCAAGGACTCGCAACATATGCGGTACCTCAGCCATCGATACAGT

            * *        *    *             *              *  *  **            
       4487 GTTTATCTATATAACGGTCTCCTAACGATGTTGCTCACACGAGCTGTCGAGTGTATGCACTTATG
         66 ATCTATCTATACAACGCTCTCCTAACGATGCTGCTCACACGAGCTATCAAGAATATGCACTTATG

                 *           *      *      *                    *   **       
       4552 CATAAGTCCCAGCCATCGTAGTGCCTGTAATTCATTCTAGGATTCATATCTCTTTTTTCGACTCA
        131 CATAAATCCCAGCCATCATAGTGCATGTAATCCATTCTAGGATTCATATCTCATTTCCCGACTCA

                                   *  *              *                       
       4617 CGATGCTGCTCACACGAGCTGTCGAGAACTCGCAACATATGTGGTACCTCAGCCATCGATAC-GA
          1 CGATGCTGCTCACACGAGCTGTCAAGGACTCGCAACATATGCGGTACCTCAGCCATCGATACAG-

                 *                      *                                    
       4681 TATCTGTGC-ATACAACTGCTC-CCTAATGATGCTGCTCACACGAGCTATCAAGAATATGCACTT
         65 TATCTAT-CTATACAAC-GCTCTCCTAACGATGCTGCTCACACGAGCTATCAAGAATATGCACTT

                       *                                        *            
       4744 ATGCATAAATCTCAGCCATCATAAG-GCATGTAATCCATTCTTA-GATTC-TTTGCTCATTTCCC
        128 ATGCATAAATCCCAGCCATCAT-AGTGCATGTAATCCATTC-TAGGATTCATAT-CTCATTTCCC

                  
       4806 GACTCA
        190 GACTCA

             *             *  *                *                      
       4812 CAATGCTGCTCACACAAGTTGTCAAGGACTCGCAATATATGCGGTACCTCAGCCATCG
          1 CGATGCTGCTCACACGAGCTGTCAAGGACTCGCAACATATGCGGTACCTCAGCCATCG

       4870 CATCGGTTTC


Statistics
Matches: 214,  Mismatches: 32, Indels: 13
        0.83            0.12        0.05

Matches are distributed among these distances:
 194   53  0.25
 195  153  0.71
 196    8  0.04

ACGTcount: A:0.26, C:0.27, G:0.18, T:0.28


Consensus pattern (195 bp):   
CGATGCTGCTCACACGAGCTGTCAAGGACTCGCAACATATGCGGTACCTCAGCCATCGATACAGT
ATCTATCTATACAACGCTCTCCTAACGATGCTGCTCACACGAGCTATCAAGAATATGCACTTATG
CATAAATCCCAGCCATCATAGTGCATGTAATCCATTCTAGGATTCATATCTCATTTCCCGACTCA
Done.