Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004629.1 Kokia drynarioides strain JFW-HI SEQ_118150, 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, 639

Length: 1065
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.35


Found at i:126 original size:21 final size:22

Alignment explanation


    Indices: 100--251  Score: 128
    Period size: 23  Copynumber: 6.5  Consensus size: 22

         90 ATATGAAACA

                     *            
        100 AACAGAGAGTAC-CAAAGTACT
          1 AACAGAGAGCACACAAAGTACT

                          *       
        121 AACAGAGAGCACA-TAAGTACT
          1 AACAGAGAGCACACAAAGTACT

                               *   *  
        142 GGGCAACAGAGAGCACACACAGTGCT
          1 ----AACAGAGAGCACACAAAGTACT

                      *       *    
        168 AAACAGAGAGTACACAAAATACT
          1 -AACAGAGAGCACACAAAGTACT

                                *  
        191 AATCAGAGAGCACACAAAGTGCT
          1 AA-CAGAGAGCACACAAAGTACT

                                    * 
        214 AATCAGAGAGCACACACAATGCTAAT
          1 AA-CAGAGAGCACACA-AA-G-TACT

                        
        240 AACAGAGAGCAC
          1 AACAGAGAGCAC

        252 GAGACGTGCT


Statistics
Matches: 106,  Mismatches: 15, Indels: 16
        0.77            0.11        0.12

Matches are distributed among these distances:
  21   18  0.17
  22    2  0.02
  23   51  0.48
  24    2  0.02
  25   24  0.23
  26    9  0.08

ACGTcount: A:0.46, C:0.22, G:0.20, T:0.12


Consensus pattern (22 bp):   
AACAGAGAGCACACAAAGTACT

Found at i:172 original size:23 final size:23

Alignment explanation


    Indices: 146--269  Score: 133
    Period size: 23  Copynumber: 5.3  Consensus size: 23

        136 AGTACTGGGC

                                   
        146 AACAGAGAGCACACACAGTGCTA
          1 AACAGAGAGCACACACAGTGCTA

                     *     * * *   
        169 AACAGAGAGTACACAAAATACTA
          1 AACAGAGAGCACACACAGTGCTA

             *             *       
        192 ATCAGAGAGCACACAAAGTGCTA
          1 AACAGAGAGCACACACAGTGCTA

             *               *      
        215 ATCAGAGAGCACACACAATGCTAA
          1 AACAGAGAGCACACACAGTGCT-A

                           *         
        239 TAACAGAGAGCACGAGAC-GTGCTA
          1 -AACAGAGAGCAC-ACACAGTGCTA

                   
        263 AACAGAG
          1 AACAGAG

        270 CGCGCGCTAG


Statistics
Matches: 85,  Mismatches: 13, Indels: 6
        0.82            0.12        0.06

Matches are distributed among these distances:
  23   65  0.76
  24    2  0.02
  25   15  0.18
  26    3  0.04

ACGTcount: A:0.46, C:0.22, G:0.21, T:0.11


Consensus pattern (23 bp):   
AACAGAGAGCACACACAGTGCTA

Found at i:198 original size:46 final size:47

Alignment explanation


    Indices: 147--269  Score: 160
    Period size: 46  Copynumber: 2.6  Consensus size: 47

        137 GTACTGGGCA

                                           *               
        147 ACAGAGAGCACACACAGTGCTAAACAGAGAGTACACAAAATACTAAT
          1 ACAGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAATACTAAT

                          *        *             *   *     
        194 -CAGAGAGCACACAAAGTGCTAATCAGAGAGCACACACAATGCTAAT
          1 ACAGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAATACTAAT

                          *                
        240 AACAGAGAGCACGAGAC-GTGCTAAACAGAG
          1 -ACAGAGAGCAC-ACACAGTGCTAAACAGAG

        270 CGCGCGCTAG


Statistics
Matches: 65,  Mismatches: 8, Indels: 5
        0.83            0.10        0.06

Matches are distributed among these distances:
  46   41  0.63
  48   22  0.34
  49    2  0.03

ACGTcount: A:0.46, C:0.22, G:0.21, T:0.11


Consensus pattern (47 bp):   
ACAGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAATACTAAT

Found at i:221 original size:69 final size:67

Alignment explanation


    Indices: 99--248  Score: 178
    Period size: 69  Copynumber: 2.1  Consensus size: 67

         89 TATATGAAAC

                             *                 *                            *
         99 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTACTGGGCAACAGAGAGCACACACAG
          1 AAACAGAGAGTACCAAAATACTAACAGAGAGCACAAAAGTACT--G-AACAGAGAGCACACACAA

                 
        164 TGCT-
         63 TGCTA

                                                       *                     
        168 AAACAGAGAGTACACAAAATACTAATCAGAGAGCACACAAAGTGCT-AATCAGAGAGCACACACA
          1 AAACAGAGAGTAC-CAAAATACTAA-CAGAGAGCACA-AAAGTACTGAA-CAGAGAGCACACACA

                  
        232 ATGCTA
         62 ATGCTA

                       
        238 ATAACAGAGAG
          1 A-AACAGAGAG

        249 CACGAGACGT


Statistics
Matches: 71,  Mismatches: 4, Indels: 10
        0.84            0.05        0.12

Matches are distributed among these distances:
  68    2  0.03
  69   32  0.45
  70   11  0.15
  71   20  0.28
  72    6  0.08

ACGTcount: A:0.47, C:0.21, G:0.21, T:0.12


Consensus pattern (67 bp):   
AAACAGAGAGTACCAAAATACTAACAGAGAGCACAAAAGTACTGAACAGAGAGCACACACAATGC
TA

Done.