Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009116.1 Kokia drynarioides strain JFW-HI SEQ_123818, 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: 14424
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33


Found at i:6899 original size:25 final size:25

Alignment explanation


    Indices: 6870--6959  Score: 72
    Period size: 25  Copynumber: 3.3  Consensus size: 25

       6860 AGTACATAAG

                                     
       6870 CATTTAACACAACACATATTAATCA
          1 CATTTAACACAACACATATTAATCA

                                    *   *    
       6895 CATTTAATCACATTAGTCACATAAATATTTCAA
          1 CATTTAA-CACA--A--CACAT-ATTA-ATC-A

                  *    *             
       6928 CATTTATCACATCACATATTAATCA
          1 CATTTAACACAACACATATTAATCA

                   
       6953 CATTTAA
          1 CATTTAA

       6960 TCTAATAATC


Statistics
Matches: 50,  Mismatches: 7, Indels: 16
        0.68            0.10        0.22

Matches are distributed among these distances:
  25   14  0.28
  26    6  0.12
  27    3  0.06
  28    6  0.12
  30    5  0.10
  31    3  0.06
  32    6  0.12
  33    7  0.14

ACGTcount: A:0.43, C:0.21, G:0.01, T:0.34


Consensus pattern (25 bp):   
CATTTAACACAACACATATTAATCA

Found at i:6915 original size:58 final size:58

Alignment explanation


    Indices: 6836--6982  Score: 156
    Period size: 58  Copynumber: 2.6  Consensus size: 58

       6826 CATTCTTTTA

                      *             * *                                
       6836 CACA-TTAATTACAATAATCACATGAGTACAT-AAGCATTTAACACAACACATATTAAT
          1 CACATTTAATCACAATAATCACATAAATACATCAA-CATTTAACACAACACATATTAAT

                          *  *           **          *    *           
       6893 CACATTTAATCACATTAGTCACATAAATATTTCAACATTTATCACATCACATATTAAT
          1 CACATTTAATCACAATAATCACATAAATACATCAACATTTAACACAACACATATTAAT

                        *               *    
       6951 CACATTTAATC-TAATAATCACATTAAACACAT
          1 CACATTTAATCACAATAATCACA-TAAATACAT

       6983 GTATACATAT


Statistics
Matches: 72,  Mismatches: 15, Indels: 5
        0.78            0.16        0.05

Matches are distributed among these distances:
  57   12  0.17
  58   58  0.81
  59    2  0.03

ACGTcount: A:0.45, C:0.20, G:0.03, T:0.32


Consensus pattern (58 bp):   
CACATTTAATCACAATAATCACATAAATACATCAACATTTAACACAACACATATTAAT

Found at i:7433 original size:36 final size:36

Alignment explanation


    Indices: 7385--7524  Score: 165
    Period size: 36  Copynumber: 3.9  Consensus size: 36

       7375 TTCATTACCA

                 *                   *     *    
       7385 CATGGAATGAATAACATACCCACATTTTTACGGTCT
          1 CATGGCATGAATAACATACCCACATATTTACTGTCT

                   *                        *    
       7421 CATGGCAGGAATAACATACCCACATATTTACTATCAT
          1 CATGGCATGAATAACATACCCACATATTTACTGTC-T

                 *            **   *           *
       7458 C-TGGTATGAATAACATATTCACGTATTTACTGTCA
          1 CATGGCATGAATAACATACCCACATATTTACTGTCT

                                     *      
       7493 CATGGCATGAATAACATACCCACATGTTTACT
          1 CATGGCATGAATAACATACCCACATATTTACT

       7525 TTCATAACAG


Statistics
Matches: 85,  Mismatches: 17, Indels: 4
        0.80            0.16        0.04

Matches are distributed among these distances:
  35    1  0.01
  36   82  0.96
  37    2  0.02

ACGTcount: A:0.34, C:0.22, G:0.13, T:0.31


Consensus pattern (36 bp):   
CATGGCATGAATAACATACCCACATATTTACTGTCT

Found at i:7497 original size:72 final size:72

Alignment explanation


    Indices: 7391--7529  Score: 197
    Period size: 72  Copynumber: 1.9  Consensus size: 72

       7381 ACCACATGGA

                               *         *                                   
       7391 ATGAATAACATACCCACATTTTTACGGTCTCATGGCAGGAATAACATACCCACATATTTACTATC
          1 ATGAATAACATACCCACATATTTACGGTCACATGGCAGGAATAACATACCCACATATTTACTATC

                   
       7456 ATCTGGT
         66 ATCTGGT

                        **   *       *           *                 *      *  
       7463 ATGAATAACATATTCACGTATTTACTGTCACATGGCATGAATAACATACCCACATGTTTACTTTC
          1 ATGAATAACATACCCACATATTTACGGTCACATGGCAGGAATAACATACCCACATATTTACTATC

              
       7528 AT
         66 AT

       7530 AACAGTCATC


Statistics
Matches: 58,  Mismatches: 9, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  72   58  1.00

ACGTcount: A:0.34, C:0.22, G:0.12, T:0.32


Consensus pattern (72 bp):   
ATGAATAACATACCCACATATTTACGGTCACATGGCAGGAATAACATACCCACATATTTACTATC
ATCTGGT

Found at i:10915 original size:41 final size:41

Alignment explanation


    Indices: 10858--10939  Score: 146
    Period size: 41  Copynumber: 2.0  Consensus size: 41

      10848 GAATATCAAA

                       *                             
      10858 TTGATTAAAAGTTTATGAGAATGTTCTTACATAATTAAAAT
          1 TTGATTAAAAGCTTATGAGAATGTTCTTACATAATTAAAAT

                                          *          
      10899 TTGATTAAAAGCTTATGAGAATGTTCTTACGTAATTAAAAT
          1 TTGATTAAAAGCTTATGAGAATGTTCTTACATAATTAAAAT

      10940 AAGTAATTTT


Statistics
Matches: 39,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  41   39  1.00

ACGTcount: A:0.40, C:0.06, G:0.13, T:0.40


Consensus pattern (41 bp):   
TTGATTAAAAGCTTATGAGAATGTTCTTACATAATTAAAAT

Found at i:14348 original size:21 final size:22

Alignment explanation


    Indices: 14300--14348  Score: 52
    Period size: 22  Copynumber: 2.3  Consensus size: 22

      14290 ATACTGCACA

                                  
      14300 AATA-AAATAATTAAAACTGTC
          1 AATACAAATAATTAAAACTGTC

                                    
      14321 AGA-ACAAAT-ATTATAAACTGT-
          1 A-ATACAAATAATTA-AAACTGTC

                   
      14342 AATACAA
          1 AATACAA

      14349 TATGTCAGAG


Statistics
Matches: 24,  Mismatches: 0, Indels: 8
        0.75            0.00        0.25

Matches are distributed among these distances:
  20    1  0.04
  21   11  0.46
  22   12  0.50

ACGTcount: A:0.57, C:0.10, G:0.06, T:0.27


Consensus pattern (22 bp):   
AATACAAATAATTAAAACTGTC
Done.