Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005354.1 Kokia drynarioides strain JFW-HI SEQ_119332, 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: 13387
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.35


Found at i:883 original size:24 final size:26

Alignment explanation


    Indices: 847--894  Score: 66
    Period size: 24  Copynumber: 1.9  Consensus size: 26

        837 AGAGAAATGT

                                      
        847 AAATGTGATATATGA-A-ATTATGAA
          1 AAATGTGATATATGAGAGATTATGAA

                                     
        871 AAATGATGA-ATATGAGAGATTATG
          1 AAATG-TGATATATGAGAGATTATG

        895 CCCATGTAGA


Statistics
Matches: 21,  Mismatches: 0, Indels: 4
        0.84            0.00        0.16

Matches are distributed among these distances:
  24   11  0.52
  25    4  0.19
  26    6  0.29

ACGTcount: A:0.48, C:0.00, G:0.21, T:0.31


Consensus pattern (26 bp):   
AAATGTGATATATGAGAGATTATGAA

Found at i:1004 original size:23 final size:23

Alignment explanation


    Indices: 978--1050  Score: 76
    Period size: 23  Copynumber: 3.2  Consensus size: 23

        968 AGCACGTTTC

                                   
        978 GTGCCCTCTATTCAGCACTATGT
          1 GTGCCCTCTATTCAGCACTATGT

                   * *         *   
       1001 GTGCCCTTTGTTCAGCACTGTGT
          1 GTGCCCTCTATTCAGCACTATGT

                 *      *      * * 
       1024 GTG-CTTCTATTTAGCACTTTTT
          1 GTGCCCTCTATTCAGCACTATGT

                 
       1046 GTGCC
          1 GTGCC

       1051 TACTGTTGCC


Statistics
Matches: 40,  Mismatches: 9, Indels: 2
        0.78            0.18        0.04

Matches are distributed among these distances:
  22   16  0.40
  23   24  0.60

ACGTcount: A:0.12, C:0.26, G:0.21, T:0.41


Consensus pattern (23 bp):   
GTGCCCTCTATTCAGCACTATGT

Found at i:2545 original size:20 final size:21

Alignment explanation


    Indices: 2520--2582  Score: 87
    Period size: 20  Copynumber: 3.1  Consensus size: 21

       2510 AATTAGAAAA

                       *         
       2520 TGACATTTTA-TATGTCATGT
          1 TGACATTTTAGCATGTCATGT

                                 
       2540 TGACA-TTTAGCATGTCATGT
          1 TGACATTTTAGCATGTCATGT

                               * 
       2560 TGACA-TTTAGCATGTCATAT
          1 TGACATTTTAGCATGTCATGT

               
       2580 TGA
          1 TGA

       2583 TGTACAAAAA


Statistics
Matches: 40,  Mismatches: 2, Indels: 2
        0.91            0.05        0.05

Matches are distributed among these distances:
  19    4  0.10
  20   36  0.90

ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43


Consensus pattern (21 bp):   
TGACATTTTAGCATGTCATGT

Found at i:5595 original size:21 final size:21

Alignment explanation


    Indices: 5544--5596  Score: 61
    Period size: 21  Copynumber: 2.4  Consensus size: 21

       5534 AAAGATAAAT

                                   
       5544 TAAATATTTCAATACATGTGGCA
          1 TAAA-ATTT-AATACATGTGGCA

               *               **
       5567 TAATATTTAATACATGTGGGG
          1 TAAAATTTAATACATGTGGCA

                     
       5588 TAAAATTTA
          1 TAAAATTTA

       5597 TTAGTATTAA


Statistics
Matches: 26,  Mismatches: 4, Indels: 2
        0.81            0.12        0.06

Matches are distributed among these distances:
  21   19  0.73
  22    4  0.15
  23    3  0.12

ACGTcount: A:0.40, C:0.08, G:0.15, T:0.38


Consensus pattern (21 bp):   
TAAAATTTAATACATGTGGCA

Found at i:8252 original size:2 final size:2

Alignment explanation


    Indices: 8245--8291  Score: 76
    Period size: 2  Copynumber: 23.5  Consensus size: 2

       8235 TTGATAAAAC

                                                             *  *         
       8245 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TG TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                   
       8287 TA TA T
          1 TA TA T

       8292 GTGTGTGTGT


Statistics
Matches: 43,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   2   43  1.00

ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51


Consensus pattern (2 bp):   
TA

Done.