Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008558.1 Kokia drynarioides strain JFW-HI SEQ_123236, 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: 10734
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:1165 original size:16 final size:17

Alignment explanation


    Indices: 1125--1177  Score: 58
    Period size: 16  Copynumber: 3.2  Consensus size: 17

       1115 AATTAAAACA

                              
       1125 TTTAGAATTATATTTAA-
          1 TTTAGAATTA-ATTTAAT

                             
       1142 -TTAGAATTAATTTAAT
          1 TTTAGAATTAATTTAAT

                     *        
       1158 TTTA-AATTCATGTTAAT
          1 TTTAGAATTAAT-TTAAT

               
       1175 TTT
          1 TTT

       1178 TTTGGTTTTT


Statistics
Matches: 32,  Mismatches: 1, Indels: 6
        0.82            0.03        0.15

Matches are distributed among these distances:
  15    6  0.19
  16   15  0.47
  17   11  0.34

ACGTcount: A:0.38, C:0.02, G:0.06, T:0.55


Consensus pattern (17 bp):   
TTTAGAATTAATTTAAT

Found at i:1561 original size:88 final size:87

Alignment explanation


    Indices: 1430--1602  Score: 204
    Period size: 88  Copynumber: 2.0  Consensus size: 87

       1420 TCTTGAATTG

                               *                          *    *             
       1430 GATTTATTTTATTTTAGCCTTAAGATTTAGATTTTAGGGTTTAACAGATTTTATTAAATATTAGT
          1 GATTTATTTTATTTTAGCCCTAAGATTTAGATTTTAGGGTTTAACACATTTAATTAAATATTAGT

                      *            
       1495 TT-GAAATTTTGGTTATGGATCA
         66 TTAG-AATTTAGGTTATGGATCA

                                    *     **      **     **          *  *    
       1517 GATTTATTTTATTTTTAGCCCTAATATTTATTTTTTAGTTTTTAATTCATTTAATTATATTTTAG
          1 GATTTATTTTA-TTTTAGCCCTAAGATTTAGATTTTAGGGTTTAACACATTTAATTAAATATTAG

                                 
       1582 TTTAGAATTTAGGTTATGGAT
         65 TTTAGAATTTAGGTTATGGAT

       1603 ATTCATTGCA


Statistics
Matches: 71,  Mismatches: 13, Indels: 3
        0.82            0.15        0.03

Matches are distributed among these distances:
  87   11  0.15
  88   59  0.83
  89    1  0.01

ACGTcount: A:0.28, C:0.05, G:0.13, T:0.54


Consensus pattern (87 bp):   
GATTTATTTTATTTTAGCCCTAAGATTTAGATTTTAGGGTTTAACACATTTAATTAAATATTAGT
TTAGAATTTAGGTTATGGATCA

Found at i:4468 original size:3 final size:3

Alignment explanation


    Indices: 4460--4515  Score: 64
    Period size: 3  Copynumber: 18.7  Consensus size: 3

       4450 TGGGTATTAT

                                                                          
       4460 AGA AGA AGA AGA AGCA AG- AGA AGA AGA GAGA A-A AGA AG- AGA AGGA
          1 AGA AGA AGA AGA AG-A AGA AGA AGA AGA -AGA AGA AGA AGA AGA A-GA

                          
       4505 AGA AGA AGA AG
          1 AGA AGA AGA AG

       4516 GAATTGCCCT


Statistics
Matches: 47,  Mismatches: 0, Indels: 12
        0.80            0.00        0.20

Matches are distributed among these distances:
   2    6  0.13
   3   32  0.68
   4    9  0.19

ACGTcount: A:0.62, C:0.02, G:0.36, T:0.00


Consensus pattern (3 bp):   
AGA

Found at i:6372 original size:18 final size:18

Alignment explanation


    Indices: 6340--6375  Score: 54
    Period size: 18  Copynumber: 2.0  Consensus size: 18

       6330 TTACAGTTGT

                     **       
       6340 AAAAGGGAGTTAGATCTG
          1 AAAAGGGAGGAAGATCTG

                              
       6358 AAAAGGGAGGAAGATCTG
          1 AAAAGGGAGGAAGATCTG

       6376 GAAATTACCA


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  18   16  1.00

ACGTcount: A:0.42, C:0.06, G:0.36, T:0.17


Consensus pattern (18 bp):   
AAAAGGGAGGAAGATCTG

Found at i:9482 original size:29 final size:29

Alignment explanation


    Indices: 9440--9497  Score: 116
    Period size: 29  Copynumber: 2.0  Consensus size: 29

       9430 AATGTATACC

                                         
       9440 ATTAGAATCGACAAGCTCTCCAAAATAAG
          1 ATTAGAATCGACAAGCTCTCCAAAATAAG

                                         
       9469 ATTAGAATCGACAAGCTCTCCAAAATAAG
          1 ATTAGAATCGACAAGCTCTCCAAAATAAG

       9498 GACAACTTAT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  29   29  1.00

ACGTcount: A:0.45, C:0.21, G:0.14, T:0.21


Consensus pattern (29 bp):   
ATTAGAATCGACAAGCTCTCCAAAATAAG
Done.