Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010870.1 Kokia drynarioides strain JFW-HI SEQ_125838, 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: 4803
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34


Found at i:346 original size:21 final size:21

Alignment explanation


    Indices: 318--412  Score: 94
    Period size: 21  Copynumber: 4.8  Consensus size: 21

        308 TGTGCCTAGT

                                 
        318 AGGCTTTGTGCCGGTGTTTTC
          1 AGGCTTTGTGCCGGTGTTTTC

             *        *           
        339 AAGCTTTGTGAC--TAG---T-
          1 AGGCTTTGTGCCGGT-GTTTTC

                       *    *    
        355 AGGCTTTGTGCAGGTGATTTC
          1 AGGCTTTGTGCCGGTGTTTTC

                                 
        376 AGGCTTTGTGCCGGTGTTTTC
          1 AGGCTTTGTGCCGGTGTTTTC

                   *        
        397 AGGCTTTATGCCGGTG
          1 AGGCTTTGTGCCGGTG

        413 ATTCAATAAC


Statistics
Matches: 59,  Mismatches: 8, Indels: 14
        0.73            0.10        0.17

Matches are distributed among these distances:
  16    9  0.15
  17    2  0.03
  18    1  0.02
  19    1  0.02
  20    2  0.03
  21   44  0.75

ACGTcount: A:0.12, C:0.17, G:0.33, T:0.39


Consensus pattern (21 bp):   
AGGCTTTGTGCCGGTGTTTTC

Found at i:354 original size:37 final size:37

Alignment explanation


    Indices: 299--385  Score: 138
    Period size: 37  Copynumber: 2.4  Consensus size: 37

        289 CTTACACAAA

                         *                *    * 
        299 TTCAGGCTTTGTGCCTAGTAGGCTTTGTGCCGGTGTT
          1 TTCAGGCTTTGTGACTAGTAGGCTTTGTGCAGGTGAT

                *                                
        336 TTCAAGCTTTGTGACTAGTAGGCTTTGTGCAGGTGAT
          1 TTCAGGCTTTGTGACTAGTAGGCTTTGTGCAGGTGAT

                         
        373 TTCAGGCTTTGTG
          1 TTCAGGCTTTGTG

        386 CCGGTGTTTT


Statistics
Matches: 45,  Mismatches: 5, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  37   45  1.00

ACGTcount: A:0.13, C:0.16, G:0.31, T:0.40


Consensus pattern (37 bp):   
TTCAGGCTTTGTGACTAGTAGGCTTTGTGCAGGTGAT

Found at i:3983 original size:25 final size:25

Alignment explanation


    Indices: 3955--4090  Score: 111
    Period size: 25  Copynumber: 5.6  Consensus size: 25

       3945 ACTTAACAGT

                                      
       3955 AAGCACACA-AGTGCTAGGAAAACAA
          1 AAGCACACACAGTGCT-GGAAAACAA

                              **    *
       3980 AAGCACACACAGTGCTGGGTAACAG
          1 AAGCACACACAGTGCTGGAAAACAA

                       *            *
       4005 AAGCACACACAATGCT-G--AACAG
          1 AAGCACACACAGTGCTGGAAAACAA

                           *   **    *
       4027 AAGCACAC-CTAGTGTTGGGTAACAG
          1 AAGCACACAC-AGTGCTGGAAAACAA

                              **    *
       4052 AAGCACACACAGTGCTGGGTAACAG
          1 AAGCACACACAGTGCTGGAAAACAA

                          
       4077 AAGCACACACAGTG
          1 AAGCACACACAGTG

       4091 TTGAACAGAA


Statistics
Matches: 98,  Mismatches: 7, Indels: 12
        0.84            0.06        0.10

Matches are distributed among these distances:
  21    1  0.01
  22   17  0.17
  23    1  0.01
  24    1  0.01
  25   71  0.72
  26    7  0.07

ACGTcount: A:0.40, C:0.24, G:0.24, T:0.12


Consensus pattern (25 bp):   
AAGCACACACAGTGCTGGAAAACAA

Found at i:4046 original size:47 final size:49

Alignment explanation


    Indices: 3948--4093  Score: 174
    Period size: 47  Copynumber: 3.0  Consensus size: 49

       3938 CCGAAGTACT

                              *        *    *              *    
       3948 TAACAGTAAGCACACA-AGTGCTAGGAAAACAAAAGCACACACAGTGCTGGG
          1 TAACAG-AAGCACACACAATGCT-GG-TAACAGAAGCACACACAGTGTTGGG

                                                              
       3999 TAACAGAAGCACACACAATGCT-G-AACAGAAGCACAC-CTAGTGTTGGG
          1 TAACAGAAGCACACACAATGCTGGTAACAGAAGCACACAC-AGTGTTGGG

                             *                              
       4046 TAACAGAAGCACACACAGTGCTGGGTAACAGAAGCACACACAGTGTTG
          1 TAACAGAAGCACACACAATGCT-GGTAACAGAAGCACACACAGTGTTG

       4094 AACAGAAGCG


Statistics
Matches: 85,  Mismatches: 4, Indels: 13
        0.83            0.04        0.13

Matches are distributed among these distances:
  46    1  0.01
  47   41  0.48
  49    2  0.02
  50   29  0.34
  51   12  0.14

ACGTcount: A:0.40, C:0.23, G:0.24, T:0.14


Consensus pattern (49 bp):   
TAACAGAAGCACACACAATGCTGGTAACAGAAGCACACACAGTGTTGGG

Done.