Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007786.1 Kokia drynarioides strain JFW-HI SEQ_122420, 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: 16550
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33


Found at i:5745 original size:20 final size:21

Alignment explanation


    Indices: 5703--5745  Score: 61
    Period size: 20  Copynumber: 2.1  Consensus size: 21

       5693 GTTTCAAGTA

                              *  
       5703 TTAGGTTTTGGATTTAGAGTT
          1 TTAGGTTTTGGATTTAGAATT

                           *     
       5724 TTAGG-TTTGGATTTTGAATT
          1 TTAGGTTTTGGATTTAGAATT

              
       5744 TT
          1 TT

       5746 GGATTTCAAG


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  20   15  0.75
  21    5  0.25

ACGTcount: A:0.19, C:0.00, G:0.26, T:0.56


Consensus pattern (21 bp):   
TTAGGTTTTGGATTTAGAATT

Found at i:6605 original size:17 final size:18

Alignment explanation


    Indices: 6572--6605  Score: 52
    Period size: 17  Copynumber: 1.9  Consensus size: 18

       6562 TTTAAATGTA

                        *     
       6572 AATTTTAATTTTTTTTAT
          1 AATTTTAATTTTATTTAT

                             
       6590 AATTTT-ATTTTATTTA
          1 AATTTTAATTTTATTTA

       6606 ATTCTTTTTA


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  17    9  0.60
  18    6  0.40

ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71


Consensus pattern (18 bp):   
AATTTTAATTTTATTTAT

Found at i:6622 original size:97 final size:98

Alignment explanation


    Indices: 6455--6648  Score: 363
    Period size: 97  Copynumber: 2.0  Consensus size: 98

       6445 AAAAAATTAC

                                                                 *   *       
       6455 ATATTATTTTTTAAATGTAAATTTTAATTTTTTTTTATAATTTTATTTTATTTGATTTTTTTTAA
          1 ATATTATTTTTTAAATGTAAATTTTAATTTTTTTTTATAATTTTATTTTATTTAATTCTTTTTAA

                                             
       6520 TAATACAAAAATAAAATCGATGCATTTAATAGA
         66 TAATACAAAAATAAAATCGATGCATTTAATAGA

                                                                             
       6553 ATATTATTTTTTAAATGTAAATTTTAA-TTTTTTTTATAATTTTATTTTATTTAATTCTTTTTAA
          1 ATATTATTTTTTAAATGTAAATTTTAATTTTTTTTTATAATTTTATTTTATTTAATTCTTTTTAA

                                            
       6617 TAATACAAAAATAAAATCGATGCATTTAATAG
         66 TAATACAAAAATAAAATCGATGCATTTAATAG

       6649 TAAACGGACT


Statistics
Matches: 94,  Mismatches: 2, Indels: 1
        0.97            0.02        0.01

Matches are distributed among these distances:
  97   67  0.71
  98   27  0.29

ACGTcount: A:0.38, C:0.04, G:0.05, T:0.54


Consensus pattern (98 bp):   
ATATTATTTTTTAAATGTAAATTTTAATTTTTTTTTATAATTTTATTTTATTTAATTCTTTTTAA
TAATACAAAAATAAAATCGATGCATTTAATAGA

Found at i:7465 original size:2 final size:2

Alignment explanation


    Indices: 7458--7483  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       7448 TGTATGAAAA

                                                  
       7458 AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT

       7484 TGTTAATATC


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:10348 original size:52 final size:51

Alignment explanation


    Indices: 10270--10372  Score: 197
    Period size: 52  Copynumber: 2.0  Consensus size: 51

      10260 CTCAAACCTC

                                                                
      10270 CATTAATCATATGTTAATATTCGTAATTTATGAACAAAAACTAAAATTAAAG
          1 CATTAATCATATGTTAATATTCGTAATTTATGAAC-AAAACTAAAATTAAAG

                                                               
      10322 CATTAATCATATGTTAATATTCGTAATTTATGAACAAAACTAAAATTAAAG
          1 CATTAATCATATGTTAATATTCGTAATTTATGAACAAAACTAAAATTAAAG

      10373 AAAATCAGCT


Statistics
Matches: 51,  Mismatches: 0, Indels: 1
        0.98            0.00        0.02

Matches are distributed among these distances:
  51   16  0.31
  52   35  0.69

ACGTcount: A:0.48, C:0.10, G:0.08, T:0.35


Consensus pattern (51 bp):   
CATTAATCATATGTTAATATTCGTAATTTATGAACAAAACTAAAATTAAAG

Found at i:16255 original size:2 final size:2

Alignment explanation


    Indices: 16248--16283  Score: 72
    Period size: 2  Copynumber: 18.0  Consensus size: 2

      16238 CCCTCAGCCC

                                                                 
      16248 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      16284 TCCAAACAGT


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   34  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.