Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004655.1 Kokia drynarioides strain JFW-HI SEQ_118192, 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: 1859
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35


Found at i:280 original size:134 final size:133

Alignment explanation


    Indices: 27--281  Score: 350
    Period size: 134  Copynumber: 1.9  Consensus size: 133

         17 GGTTTCATTG

                     *                            **            **           
         27 ACTTGACCTTCTTCTCAATATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCTC
          1 ACTTGACCTGCTTCTCAATATCTCATCAGGAAGATGACAACATCACTTGTTTCAATCCACTTCTC

                                *       *        *           *               
         92 TATGTTTCATCAGGAAGACGGATTTGATTCACTTCTCCGTATCTCATCAGGAAGCTAACTACTTT
         66 TATGTTTCATCAGGAAGACGAATTTGATCCACTTCTCAGTATCTCATCAAGAAGCTAACTACTTT

               
        157 ATT
        131 ATT

                              *                          *             *     
        160 ACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGATGACAACATCGCTTGTTTCAATCCGCTTCT
          1 ACTT-GACCTGCTTCTCAATATCTCATCAGGAAGATGACAACATCACTTGTTTCAATCCACTTCT

              *                         *                  *          
        225 CTGT-TTCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCGTCAAGAAGCT
         65 CTATGTT-TCATCAGGAAGACGAATTTGATCCACTTCTCAGTATCTCATCAAGAAGCT

        282 GGGATTCAAA


Statistics
Matches: 105,  Mismatches: 15, Indels: 3
        0.85            0.12        0.02

Matches are distributed among these distances:
 133    6  0.06
 134   99  0.94

ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34


Consensus pattern (133 bp):   
ACTTGACCTGCTTCTCAATATCTCATCAGGAAGATGACAACATCACTTGTTTCAATCCACTTCTC
TATGTTTCATCAGGAAGACGAATTTGATCCACTTCTCAGTATCTCATCAAGAAGCTAACTACTTT
ATT

Found at i:1274 original size:20 final size:20

Alignment explanation


    Indices: 1249--1294  Score: 65
    Period size: 20  Copynumber: 2.3  Consensus size: 20

       1239 TTAGGATGCC

                      *         
       1249 ATGCTCAGAATGAGTAAAAA
          1 ATGCTCAGAACGAGTAAAAA

                  **            
       1269 ATGCTCCTAACGAGTAAAAA
          1 ATGCTCAGAACGAGTAAAAA

                  
       1289 ATGCTC
          1 ATGCTC

       1295 CTAACTATAT


Statistics
Matches: 23,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  20   23  1.00

ACGTcount: A:0.43, C:0.17, G:0.17, T:0.22


Consensus pattern (20 bp):   
ATGCTCAGAACGAGTAAAAA

Found at i:1295 original size:20 final size:20

Alignment explanation


    Indices: 1260--1299  Score: 80
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       1250 TGCTCAGAAT

                                
       1260 GAGTAAAAAATGCTCCTAAC
          1 GAGTAAAAAATGCTCCTAAC

                                
       1280 GAGTAAAAAATGCTCCTAAC
          1 GAGTAAAAAATGCTCCTAAC

       1300 TATATGTATG


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.45, C:0.20, G:0.15, T:0.20


Consensus pattern (20 bp):   
GAGTAAAAAATGCTCCTAAC
Done.