Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012158.1 Kokia drynarioides strain JFW-HI SEQ_127159, 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: 10757
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36


Found at i:1467 original size:19 final size:21

Alignment explanation


    Indices: 1429--1467  Score: 55
    Period size: 20  Copynumber: 2.0  Consensus size: 21

       1419 TTTTCTCCGC

                      *          
       1429 AAAACTTTTATTTCCCTTTCG
          1 AAAACTTTTACTTCCCTTTCG

                                
       1450 AAAA-TTTTACTT-CCTTTC
          1 AAAACTTTTACTTCCCTTTC

       1468 AAACCCCCAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  19    6  0.35
  20    7  0.41
  21    4  0.24

ACGTcount: A:0.26, C:0.23, G:0.03, T:0.49


Consensus pattern (21 bp):   
AAAACTTTTACTTCCCTTTCG

Found at i:5935 original size:19 final size:19

Alignment explanation


    Indices: 5913--5952  Score: 64
    Period size: 19  Copynumber: 2.2  Consensus size: 19

       5903 AATTTAATGA

                               
       5913 TTTTTA-ATTTTTAAATTT
          1 TTTTTATATTTTTAAATTT

                         *     
       5931 TTTTTATATTTTTGAATTT
          1 TTTTTATATTTTTAAATTT

               
       5950 TTT
          1 TTT

       5953 AAAATTTAAA


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  18    6  0.30
  19   14  0.70

ACGTcount: A:0.23, C:0.00, G:0.03, T:0.75


Consensus pattern (19 bp):   
TTTTTATATTTTTAAATTT

Found at i:5943 original size:27 final size:27

Alignment explanation


    Indices: 5866--5951  Score: 75
    Period size: 27  Copynumber: 3.1  Consensus size: 27

       5856 TTCAAAAATA

                   *                      
       5866 TTAAATATATATTTATATTTTTATAACTTT
          1 TTAAATAAAT-TTTATATTTTT-TAA-TTT

                        *               
       5896 TTAAATAAATTTAATGA-TTTTTAATTT
          1 TTAAATAAATTTTAT-ATTTTTTAATTT

                  ***            *     
       5923 TTAAATTTTTTTTATATTTTTGAATTT
          1 TTAAATAAATTTTATATTTTTTAATTT

              
       5950 TT
          1 TT

       5952 TAAAATTTAA


Statistics
Matches: 47,  Mismatches: 7, Indels: 7
        0.77            0.11        0.11

Matches are distributed among these distances:
  26    1  0.02
  27   25  0.53
  28    3  0.06
  29    8  0.17
  30   10  0.21

ACGTcount: A:0.34, C:0.01, G:0.02, T:0.63


Consensus pattern (27 bp):   
TTAAATAAATTTTATATTTTTTAATTT

Found at i:8017 original size:3 final size:3

Alignment explanation


    Indices: 8002--8031  Score: 51
    Period size: 3  Copynumber: 10.0  Consensus size: 3

       7992 AATTTTTTGT

                      *                            
       8002 TTC TTC TTA TTC TTC TTC TTC TTC TTC TTC
          1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC

       8032 ACAGCTGGGT


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   3   25  1.00

ACGTcount: A:0.03, C:0.30, G:0.00, T:0.67


Consensus pattern (3 bp):   
TTC

Found at i:10122 original size:23 final size:23

Alignment explanation


    Indices: 10052--10166  Score: 121
    Period size: 23  Copynumber: 5.0  Consensus size: 23

      10042 AAGAGAGTAT

                  *                
      10052 CAAAGTACTAA-CAGAGAGCACA
          1 CAAAGTGCTAATCAGAGAGCACA

                                       
      10074 -AAAGTGCTGGGCAA-CAGAGAGCACA
          1 CAAAGTGCT----AATCAGAGAGCACA

              *                 *   
      10099 CACAGTGCTAAAT-AGAGAGTACA
          1 CAAAGTGCT-AATCAGAGAGCACA

                  *                
      10122 CAAAGTACTAATCAGAGAGCACA
          1 CAAAGTGCTAATCAGAGAGCACA

                                  
      10145 CAAAGTGCTAATCAGAGAGCAC
          1 CAAAGTGCTAATCAGAGAGCAC

      10167 TGCTAATAAT


Statistics
Matches: 78,  Mismatches: 8, Indels: 13
        0.79            0.08        0.13

Matches are distributed among these distances:
  21    7  0.09
  22    3  0.04
  23   48  0.62
  25   13  0.17
  26    7  0.09

ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12


Consensus pattern (23 bp):   
CAAAGTGCTAATCAGAGAGCACA
Done.