Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004341.1 Kokia drynarioides strain JFW-HI SEQ_117676, 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: 2522
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34


Found at i:1185 original size:35 final size:35

Alignment explanation


    Indices: 1070--1244  Score: 143
    Period size: 35  Copynumber: 5.1  Consensus size: 35

       1060 ATCTACCGTT

                                     *          
       1070 CAAGAATTTCAATTCATTCATATATTATAAACAAT-
          1 CAAGAATTT-AATTCATTCATATATCATAAACAATA

               *  *                  **         
       1105 CAATAACTTAATTCATTCATATATCGCAAACAATCA
          1 CAAGAATTTAATTCATTCATATATCATAAACAAT-A

                 *        *              *     
       1141 CAA-ATTTTAATTCTTTCATATATCATAATCAATA
          1 CAAGAATTTAATTCATTCATATATCATAAACAATA

            *           *                        
       1175 AAAGAATTTAATCCATTCATATAT--TAATAGCAA-A
          1 CAAGAATTTAATTCATTCATATATCATAA-A-CAATA

                 *                              
       1209 -AAGATTTTCAATTCATTCATATAT--TAAACAAT-
          1 CAAGAATTT-AATTCATTCATATATCATAAACAATA

                
       1241 CAAG
          1 CAAG

       1245 GAAGTAAAAC


Statistics
Matches: 114,  Mismatches: 18, Indels: 18
        0.76            0.12        0.12

Matches are distributed among these distances:
  32    3  0.03
  33   14  0.12
  34   43  0.38
  35   51  0.45
  36    3  0.03

ACGTcount: A:0.45, C:0.15, G:0.03, T:0.36


Consensus pattern (35 bp):   
CAAGAATTTAATTCATTCATATATCATAAACAATA

Found at i:1228 original size:69 final size:69

Alignment explanation


    Indices: 1070--1240  Score: 167
    Period size: 69  Copynumber: 2.5  Consensus size: 69

       1060 ATCTACCGTT

                 *                   *         *  *        *                 
       1070 CAAGAATTTCAATTCATTCATATATTATAAACAATCAATAACTTAATTCATTCATATATCGCAAA
          1 CAAGATTTTCAATTCATTCATATATCATAAACAATAAAGAACTTAATCCATTCATATATC-CAAA

                  
       1135 CAATCA
         65 CAA-CA

                           *              *           *                  *   
       1141 CAA-ATTTT-AATTCTTTCATATATCATAATCAATAAAAGAATTTAATCCATTCATATAT-TAAT
          1 CAAGATTTTCAATTCATTCATATATCATAAACAAT-AAAGAACTTAATCCATTCATATATCCAA-

                   
       1203 AGCAA-A
         64 A-CAACA

                                               
       1209 -AAGATTTTCAATTCATTCATATAT--TAAACAAT
          1 CAAGATTTTCAATTCATTCATATATCATAAACAAT

       1241 CAAGGAAGTA


Statistics
Matches: 84,  Mismatches: 11, Indels: 14
        0.77            0.10        0.13

Matches are distributed among these distances:
  67    9  0.11
  68    8  0.10
  69   37  0.44
  70   27  0.32
  71    3  0.04

ACGTcount: A:0.45, C:0.15, G:0.03, T:0.37


Consensus pattern (69 bp):   
CAAGATTTTCAATTCATTCATATATCATAAACAATAAAGAACTTAATCCATTCATATATCCAAAC
AACA

Found at i:2469 original size:126 final size:127

Alignment explanation


    Indices: 2244--2492  Score: 329
    Period size: 126  Copynumber: 2.0  Consensus size: 127

       2234 TACATACAGG

                   *               *                              *          
       2244 TGCAAACGAGCTACCATATGGTTGAGGATCCACAACCCCTAGCAGATAAAAGCTGTCAGAAAAAG
          1 TGCAAACAAGCTACCATATGGTTCAGGATCCACAACCCCTAGCAGATAAAAGCTATCAGAAAAAG

             *         *              **                *                 
       2309 TTGTGAATACTCCGTATAAAAGTCGCTGTTGGAATCTAC-TAAGTTATGAATACACAAAGGA
         66 TCGTGAATACTACGTATAAAAGTCGCAATTGGAATCTACTTAAGCTATGAATACACAAAGGA

                           *                    *   *   *      *    *   *    
       2370 TGCAAACAAGCTACCGTATGGTTCAGGATCCACAACTCCTCGCATATAAAATCTATTAGAGAAAG
          1 TGCAAACAAGCTACCATATGGTTCAGGATCCACAACCCCTAGCAGATAAAAGCTATCAGAAAAAG

                        *       *  *                                  
       2435 TCGTGAATACTATGTATAAAGGTTGCAATTGGAATCTACTTAAGCTATGAATACACAA
         66 TCGTGAATACTACGTATAAAAGTCGCAATTGGAATCTACTTAAGCTATGAATACACAA

       2493 CGGTAAAACA


Statistics
Matches: 104,  Mismatches: 18, Indels: 1
        0.85            0.15        0.01

Matches are distributed among these distances:
 126   87  0.84
 127   17  0.16

ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25


Consensus pattern (127 bp):   
TGCAAACAAGCTACCATATGGTTCAGGATCCACAACCCCTAGCAGATAAAAGCTATCAGAAAAAG
TCGTGAATACTACGTATAAAAGTCGCAATTGGAATCTACTTAAGCTATGAATACACAAAGGA
Done.