Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012218.1 Kokia drynarioides strain JFW-HI SEQ_127219, 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: 10535
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33


Found at i:1169 original size:19 final size:18

Alignment explanation


    Indices: 1147--1182  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       1137 TCAAAAAGTT

                               
       1147 GAGAAAAAAAGAAAAATAC
          1 GAGAAAAAAA-AAAAATAC

                    *        
       1166 GAGAAAAATAAAAAATA
          1 GAGAAAAAAAAAAAATA

       1183 AAAAAATATT


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.75, C:0.03, G:0.14, T:0.08


Consensus pattern (18 bp):   
GAGAAAAAAAAAAAATAC

Found at i:3740 original size:19 final size:17

Alignment explanation


    Indices: 3716--3750  Score: 52
    Period size: 19  Copynumber: 1.9  Consensus size: 17

       3706 TTAAATAATT

                               
       3716 ATTATTTTATTTTATTGTG
          1 ATTATTTT-TTTT-TTGTG

                            
       3735 ATTATTTTTTTTTTGT
          1 ATTATTTTTTTTTTGT

       3751 CACCACGTAC


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

Matches are distributed among these distances:
  17    4  0.25
  18    4  0.25
  19    8  0.50

ACGTcount: A:0.17, C:0.00, G:0.09, T:0.74


Consensus pattern (17 bp):   
ATTATTTTTTTTTTGTG

Found at i:6829 original size:16 final size:16

Alignment explanation


    Indices: 6808--6879  Score: 108
    Period size: 16  Copynumber: 4.5  Consensus size: 16

       6798 CGTTTGGTTC

                            
       6808 GCTGTAATGGAATAGA
          1 GCTGTAATGGAATAGA

                     *      
       6824 GCTGTAATGAAATAGA
          1 GCTGTAATGGAATAGA

            *        *      
       6840 ACTGTAATGTAATAGA
          1 GCTGTAATGGAATAGA

                           *
       6856 GCTGTAATGGAATAGG
          1 GCTGTAATGGAATAGA

                    
       6872 GCTGTAAT
          1 GCTGTAAT

       6880 CATTATTTCA


Statistics
Matches: 50,  Mismatches: 6, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  16   50  1.00

ACGTcount: A:0.38, C:0.07, G:0.28, T:0.28


Consensus pattern (16 bp):   
GCTGTAATGGAATAGA

Found at i:6922 original size:46 final size:44

Alignment explanation


    Indices: 6861--6954  Score: 118
    Period size: 44  Copynumber: 2.1  Consensus size: 44

       6851 ATAGAGCTGT

                      *          *                         
       6861 AATGGAATAGGGCTGTAATCATTATTTCAGT-TGTTTGGTTGAATGA
          1 AATGGAATAGAGCTGTAAT-AATA-TTC-GTGTGTTTGGTTGAATGA

                                      *                *
       6907 AATGGAATAGAGCTGTAATAATATTCTTGTGTTTGGTTGAATGG
          1 AATGGAATAGAGCTGTAATAATATTCGTGTGTTTGGTTGAATGA

                
       6951 AATG
          1 AATG

       6955 ATGCTTGCAA


Statistics
Matches: 43,  Mismatches: 4, Indels: 4
        0.84            0.08        0.08

Matches are distributed among these distances:
  43    1  0.02
  44   21  0.49
  45    3  0.07
  46   18  0.42

ACGTcount: A:0.30, C:0.05, G:0.27, T:0.38


Consensus pattern (44 bp):   
AATGGAATAGAGCTGTAATAATATTCGTGTGTTTGGTTGAATGA

Found at i:7122 original size:55 final size:55

Alignment explanation


    Indices: 7056--7222  Score: 180
    Period size: 55  Copynumber: 3.0  Consensus size: 55

       7046 TTGTTAAATT

                  *                                   *      *      
       7056 TTAATAAGATTATTATTAAATATAATTAAATAAAAATAAATATTTTAATCATATT-
          1 TTAATATGATTATTATTAAATATAATT-AATAAAAATAAATAATTTAATAATATTC

                                                     *                 
       7111 TTAACT-TGATTATTATTAAATATAATTTAATAAAATAGTATATAATTTAATAATATTC
          1 TTAA-TATGATTATTATTAAATATAA-TTAATAAAA-A-TAAATAATTTAATAATATTC

                   *                               *     *          
       7169 TTAATATAATTATTATTAAAATATGAATTAATAAAAAT-CATAATAT-ATAATATT
          1 TTAATATGATTATTATT-AAATAT-AATTAATAAAAATAAATAATTTAATAATATT

       7223 AGAAAAATAA


Statistics
Matches: 97,  Mismatches: 7, Indels: 16
        0.81            0.06        0.13

Matches are distributed among these distances:
  55   37  0.38
  56   10  0.10
  57   18  0.19
  58   15  0.15
  59   15  0.15
  60    2  0.02

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


Consensus pattern (55 bp):   
TTAATATGATTATTATTAAATATAATTAATAAAAATAAATAATTTAATAATATTC
Done.