Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007238.1 Kokia drynarioides strain JFW-HI SEQ_121853, 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: 5510
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33


Found at i:1341 original size:39 final size:40

Alignment explanation


    Indices: 1281--1391  Score: 109
    Period size: 39  Copynumber: 2.7  Consensus size: 40

       1271 TAAAAACTAC

                                                     
       1281 TTAAA-TATTTAGATTAATTTAAATTTTATGCATCATCATA
          1 TTAAATTATTTA-ATTAATTTAAATTTTATGCATCATCATA

                                  * *  * **     *  *
       1321 TTAAATTATTTAATT-ATTTAACTATTGTTTATCATTATG
          1 TTAAATTATTTAATTAATTTAAATTTTATGCATCATCATA

                                            
       1360 TTAAATTATTTAAATATAATTTATAATTTTAT
          1 TTAAATTATTT-AAT-TAATTTA-AATTTTAT

       1392 TTAAATTTAA


Statistics
Matches: 56,  Mismatches: 10, Indels: 7
        0.77            0.14        0.10

Matches are distributed among these distances:
  39   28  0.50
  40   11  0.20
  41    7  0.12
  42    5  0.09
  43    5  0.09

ACGTcount: A:0.39, C:0.05, G:0.04, T:0.53


Consensus pattern (40 bp):   
TTAAATTATTTAATTAATTTAAATTTTATGCATCATCATA

Found at i:1383 original size:31 final size:29

Alignment explanation


    Indices: 1325--1383  Score: 73
    Period size: 31  Copynumber: 2.0  Consensus size: 29

       1315 ATCATATTAA

                             *   **      
       1325 ATTATTTAATTATTTAACTATTGTTTATC
          1 ATTATTTAATTATTTAAATATAATTTATC

                                          
       1354 ATTATGTTAAATTATTTAAATATAATTTAT
          1 ATTAT-TT-AATTATTTAAATATAATTTAT

       1384 AATTTTATTT


Statistics
Matches: 25,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  29    5  0.20
  30    2  0.08
  31   18  0.72

ACGTcount: A:0.37, C:0.03, G:0.03, T:0.56


Consensus pattern (29 bp):   
ATTATTTAATTATTTAAATATAATTTATC

Found at i:1410 original size:23 final size:23

Alignment explanation


    Indices: 1365--1412  Score: 62
    Period size: 23  Copynumber: 2.1  Consensus size: 23

       1355 TTATGTTAAA

                            *      
       1365 TTATTTAAATATAATTTATAATT
          1 TTATTTAAATATAATTCATAATT

                      *             
       1388 TTATTTAAATTTAAATTCA-AATT
          1 TTATTTAAATAT-AATTCATAATT

              
       1411 TT
          1 TT

       1413 TGTAATATTC


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  23   17  0.77
  24    5  0.23

ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56


Consensus pattern (23 bp):   
TTATTTAAATATAATTCATAATT
Done.