Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000313.1 Kokia drynarioides strain JFW-HI SEQ_111074, 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: 7001
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.31


Found at i:1248 original size:30 final size:29

Alignment explanation


    Indices: 1189--1250  Score: 81
    Period size: 30  Copynumber: 2.1  Consensus size: 29

       1179 TTAAAAAATT

                             *      *    
       1189 ATTAACCAATCTCTAATTGAATTAGATCA
          1 ATTAACCAATCTCTAATCGAATTAAATCA

                                           
       1218 ATTAACCAATCGAT-TAATCGAATTAAATCA
          1 ATTAACCAATC--TCTAATCGAATTAAATCA

               
       1248 ATT
          1 ATT

       1251 CGGTTGATTA


Statistics
Matches: 29,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  29   11  0.38
  30   17  0.59
  31    1  0.03

ACGTcount: A:0.44, C:0.16, G:0.06, T:0.34


Consensus pattern (29 bp):   
ATTAACCAATCTCTAATCGAATTAAATCA

Found at i:1368 original size:6 final size:6

Alignment explanation


    Indices: 1357--1381  Score: 50
    Period size: 6  Copynumber: 4.2  Consensus size: 6

       1347 ACATCAATAT

                                         
       1357 TCTATA TCTATA TCTATA TCTATA T
          1 TCTATA TCTATA TCTATA TCTATA T

       1382 ATACATAAAT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   19  1.00

ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52


Consensus pattern (6 bp):   
TCTATA

Found at i:1640 original size:2 final size:2

Alignment explanation


    Indices: 1633--1659  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       1623 AGGCATGCTT

                                                    
       1633 TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA T

       1660 GATACAACTC


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:6274 original size:12 final size:12

Alignment explanation


    Indices: 6257--6289  Score: 57
    Period size: 12  Copynumber: 2.8  Consensus size: 12

       6247 AGAGCCAGAT

                        
       6257 TCATCTTCATCC
          1 TCATCTTCATCC

                    *   
       6269 TCATCTTCGTCC
          1 TCATCTTCATCC

                     
       6281 TCATCTTCA
          1 TCATCTTCA

       6290 AACTTCTCCT


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  12   19  1.00

ACGTcount: A:0.15, C:0.39, G:0.03, T:0.42


Consensus pattern (12 bp):   
TCATCTTCATCC
Done.