Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012219.1 Kokia drynarioides strain JFW-HI SEQ_127220, 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: 1668
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35


Found at i:651 original size:7 final size:7

Alignment explanation


    Indices: 639--672  Score: 52
    Period size: 7  Copynumber: 5.0  Consensus size: 7

        629 GTTCTCTTTT

                   
        639 TTATTAA
          1 TTATTAA

                   
        646 TTATTAA
          1 TTATTAA

               *   
        653 TTAATAA
          1 TTATTAA

                   
        660 TTATT-A
          1 TTATTAA

                   
        666 TTATTAA
          1 TTATTAA

        673 AACATTTATT


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
   6    6  0.25
   7   18  0.75

ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56


Consensus pattern (7 bp):   
TTATTAA

Found at i:1290 original size:15 final size:15

Alignment explanation


    Indices: 1270--1338  Score: 93
    Period size: 15  Copynumber: 4.6  Consensus size: 15

       1260 TTTCGGGCAC

                     *     
       1270 TTTGTAATTAGGCCA
          1 TTTGTAATTGGGCCA

                  *        
       1285 TTTGTATTTGGGCCA
          1 TTTGTAATTGGGCCA

             *     *       
       1300 TCTGTAACTGGGCCA
          1 TTTGTAATTGGGCCA

                 *         
       1315 TTTGTTATTGGGCCA
          1 TTTGTAATTGGGCCA

                     
       1330 TTTGTAATT
          1 TTTGTAATT

       1339 TGGACTTTTG


Statistics
Matches: 45,  Mismatches: 9, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  15   45  1.00

ACGTcount: A:0.19, C:0.14, G:0.23, T:0.43


Consensus pattern (15 bp):   
TTTGTAATTGGGCCA

Found at i:1400 original size:17 final size:17

Alignment explanation


    Indices: 1378--1440  Score: 99
    Period size: 17  Copynumber: 3.7  Consensus size: 17

       1368 TGGACTTTTC

                     *    *  
       1378 TAAATTTAATTTTATAA
          1 TAAATTTAAATTTAAAA

                             
       1395 TAAATTTAAATTTAAAA
          1 TAAATTTAAATTTAAAA

                             
       1412 TAAATTTAAATTTAAAA
          1 TAAATTTAAATTTAAAA

                *       
       1429 TAAACTTAAATT
          1 TAAATTTAAATT

       1441 CAATTTCCAA


Statistics
Matches: 43,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  17   43  1.00

ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44


Consensus pattern (17 bp):   
TAAATTTAAATTTAAAA

Found at i:1404 original size:6 final size:6

Alignment explanation


    Indices: 1378--1440  Score: 53
    Period size: 6  Copynumber: 11.0  Consensus size: 6

       1368 TGGACTTTTC

                      *                              *              
       1378 TAAATT TAATTT TATAA-- TAAATT TAAATT TAAA-A TAAATT TAAATT
          1 TAAATT TAAATT TA-AATT TAAATT TAAATT TAAATT TAAATT TAAATT

                 *     *        
       1424 TAAA-A TAAACT TAAATT
          1 TAAATT TAAATT TAAATT

       1441 CAATTTCCAA


Statistics
Matches: 45,  Mismatches: 7, Indels: 10
        0.73            0.11        0.16

Matches are distributed among these distances:
   4    2  0.04
   5   10  0.22
   6   32  0.71
   7    1  0.02

ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44


Consensus pattern (6 bp):   
TAAATT
Done.