Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002670.1 Kokia drynarioides strain JFW-HI SEQ_114924, 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: 19398
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32

Warning! 3 characters in sequence are not A, C, G, or T


Found at i:7266 original size:57 final size:56

Alignment explanation


    Indices: 7205--7315  Score: 127
    Period size: 57  Copynumber: 2.0  Consensus size: 56

       7195 ATACTACTCT

                                            *    *                     
       7205 AATATA-AACATTAAAAT-AATATTAAGATGACTATATAAAAAATTTTAATAAATAAAA
          1 AATATATAA-ATTAAAATAAATATTAAGAT-AATATAAAAAAAATTTTAA-AAATAAAA

                        ***           *                           
       7262 AATATATAAATTTTTATAAATATTAATATAATATAAAAAAAATTTTAAAAATAA
          1 AATATATAAATTAAAATAAATATTAAGATAATATAAAAAAAATTTTAAAAATAA

       7316 TATGGATGGG


Statistics
Matches: 46,  Mismatches: 6, Indels: 5
        0.81            0.11        0.09

Matches are distributed among these distances:
  56    6  0.13
  57   28  0.61
  58   12  0.26

ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35


Consensus pattern (56 bp):   
AATATATAAATTAAAATAAATATTAAGATAATATAAAAAAAATTTTAAAAATAAAA

Found at i:16082 original size:29 final size:29

Alignment explanation


    Indices: 16038--16115  Score: 120
    Period size: 29  Copynumber: 2.7  Consensus size: 29

      16028 GCTCTCTATG

                     * *          *      
      16038 TCAAGCTCCCTACTTTCTTCTTTCAACCT
          1 TCAAGCTCCATCCTTTCTTCTTACAACCT

                                         
      16067 TCAAGCTCCATCCTTTCTTCTTACAACCT
          1 TCAAGCTCCATCCTTTCTTCTTACAACCT

                     *          
      16096 TCAAGCTCCTTCCTTTCTTC
          1 TCAAGCTCCATCCTTTCTTC

      16116 AATCTTCAAG


Statistics
Matches: 45,  Mismatches: 4, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  29   45  1.00

ACGTcount: A:0.17, C:0.38, G:0.04, T:0.41


Consensus pattern (29 bp):   
TCAAGCTCCATCCTTTCTTCTTACAACCT

Found at i:16106 original size:25 final size:24

Alignment explanation


    Indices: 16050--16129  Score: 79
    Period size: 25  Copynumber: 3.0  Consensus size: 24

      16040 AAGCTCCCTA

                                         
      16050 CTTTCTTCTTTCAACCTTCAAGCTCCATC
          1 CTTTCTTC-TTCAACCTTCAAG---C-TC

                                     
      16079 CTTTCTTCTTACAACCTTCAAGCTC
          1 CTTTCTTCTT-CAACCTTCAAGCTC

               *          *          
      16104 CTTCCTTTCTTCAATCTTCAAGCTC
          1 CTTTC-TTCTTCAACCTTCAAGCTC

             
      16129 C
          1 C

      16130 CGATTCCTTC


Statistics
Matches: 47,  Mismatches: 2, Indels: 8
        0.82            0.04        0.14

Matches are distributed among these distances:
  25   20  0.43
  26    6  0.13
  28    2  0.04
  29   19  0.40

ACGTcount: A:0.17, C:0.38, G:0.04, T:0.41


Consensus pattern (24 bp):   
CTTTCTTCTTCAACCTTCAAGCTC

Found at i:18559 original size:24 final size:24

Alignment explanation


    Indices: 18529--18611  Score: 112
    Period size: 24  Copynumber: 3.5  Consensus size: 24

      18519 TACCTCACAC

                                    
      18529 GAGCCCAGAATGGTTAGCTCTTAT
          1 GAGCCCAGAATGGTTAGCTCTTAT

              *    *          *    *
      18553 GATCCCAAAATGGTTAGCGCTTAC
          1 GAGCCCAGAATGGTTAGCTCTTAT

                 *           *      
      18577 GAGCCTAGAATGGTTAGTTCTTAT
          1 GAGCCCAGAATGGTTAGCTCTTAT

                       
      18601 GAGCCCAGAAT
          1 GAGCCCAGAAT

      18612 CAGAATAATG


Statistics
Matches: 48,  Mismatches: 11, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  24   48  1.00

ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28


Consensus pattern (24 bp):   
GAGCCCAGAATGGTTAGCTCTTAT

Found at i:18640 original size:27 final size:27

Alignment explanation


    Indices: 18605--18669  Score: 112
    Period size: 27  Copynumber: 2.4  Consensus size: 27

      18595 TCTTATGAGC

                           *        *  
      18605 CCAGAATCAGAATAATGCTCTTTCGAG
          1 CCAGAATCAGAATAACGCTCTTTCAAG

                                       
      18632 CCAGAATCAGAATAACGCTCTTTCAAG
          1 CCAGAATCAGAATAACGCTCTTTCAAG

                       
      18659 CCAGAATCAGA
          1 CCAGAATCAGA

      18670 TTACTCTTCA


Statistics
Matches: 36,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  27   36  1.00

ACGTcount: A:0.37, C:0.25, G:0.17, T:0.22


Consensus pattern (27 bp):   
CCAGAATCAGAATAACGCTCTTTCAAG

Done.