Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010393.1 Kokia drynarioides strain JFW-HI SEQ_125272, 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: 5366
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.34

Warning! 16 characters in sequence are not A, C, G, or T


Found at i:490 original size:16 final size:17

Alignment explanation


    Indices: 465--509  Score: 56
    Period size: 16  Copynumber: 2.6  Consensus size: 17

        455 ATTTTATTAT

                 *           
        465 TATTAATATTACT-AAA
          1 TATTATTATTACTAAAA

                       *     
        481 TATTATTATTATTAAAA
          1 TATTATTATTACTAAAA

                        
        498 TAGTTATTATTA
          1 TA-TTATTATTA

        510 ATATTATTAA


Statistics
Matches: 25,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  16   11  0.44
  17    5  0.20
  18    9  0.36

ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51


Consensus pattern (17 bp):   
TATTATTATTACTAAAA

Found at i:1172 original size:6 final size:6

Alignment explanation


    Indices: 1157--1220  Score: 58
    Period size: 6  Copynumber: 10.5  Consensus size: 6

       1147 GTTTTAAATC

                        *                          **                
       1157 AATTTA AATTTT AA-TTA AATTTA AATTTAA AGAGATA AATTTA AATTTA
          1 AATTTA AATTTA AATTTA AATTTA AATTT-A A-ATTTA AATTTA AATTTA

              **             
       1206 AAAATA AATTTA AAT
          1 AATTTA AATTTA AAT

       1221 CAATTTAAAC


Statistics
Matches: 45,  Mismatches: 10, Indels: 6
        0.74            0.16        0.10

Matches are distributed among these distances:
   5    4  0.09
   6   35  0.78
   7    4  0.09
   8    2  0.04

ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42


Consensus pattern (6 bp):   
AATTTA

Found at i:1197 original size:20 final size:18

Alignment explanation


    Indices: 1152--1220  Score: 86
    Period size: 20  Copynumber: 3.8  Consensus size: 18

       1142 ATTAGGTTTT

                *            *
       1152 AAATCAATTTAAATTT-T
          1 AAATAAATTTAAATTTAA

              *               
       1169 AATTAAATTTAAATTTAA
          1 AAATAAATTTAAATTTAA

                                
       1187 AGAGATAAATTTAAATTTAA
          1 A-A-ATAAATTTAAATTTAA

                          
       1207 AAATAAATTTAAAT
          1 AAATAAATTTAAAT

       1221 CAATTTAAAC


Statistics
Matches: 45,  Mismatches: 4, Indels: 5
        0.83            0.07        0.09

Matches are distributed among these distances:
  17   14  0.31
  18   13  0.29
  19    2  0.04
  20   16  0.36

ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41


Consensus pattern (18 bp):   
AAATAAATTTAAATTTAA

Found at i:3548 original size:36 final size:36

Alignment explanation


    Indices: 3436--3531  Score: 183
    Period size: 36  Copynumber: 2.7  Consensus size: 36

       3426 ATATAATCAG

                                                
       3436 TCACATGGCATGAAAAACATACCCACATATTTACTA
          1 TCACATGGCATGAAAAACATACCCACATATTTACTA

                                                
       3472 TCACATGGCATGAAAAACATACCCACATATTTACTA
          1 TCACATGGCATGAAAAACATACCCACATATTTACTA

                          *         
       3508 TCACATGGCATGAATAACATACCC
          1 TCACATGGCATGAAAAACATACCC

       3532 TCACATTCAC


Statistics
Matches: 59,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  36   59  1.00

ACGTcount: A:0.41, C:0.26, G:0.09, T:0.24


Consensus pattern (36 bp):   
TCACATGGCATGAAAAACATACCCACATATTTACTA
Done.