Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012920.1 Kokia drynarioides strain JFW-HI SEQ_127936, 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, 845

Length: 1409
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.36


Found at i:380 original size:17 final size:17

Alignment explanation


    Indices: 355--429  Score: 80
    Period size: 17  Copynumber: 4.4  Consensus size: 17

        345 GGACTTTTAA

                *        **  
        355 TTAAGTTTTAAATCCAT
          1 TTAAATTTTAAATAAAT

                       *     
        372 TTAAATTTTAATTAAAT
          1 TTAAATTTTAAATAAAT

                         *    
        389 TTAAA-TTTAAAGCAAAT
          1 TTAAATTTTAAA-TAAAT

                    *        
        406 TTAAATTTAAAATAAAT
          1 TTAAATTTTAAATAAAT

                   
        423 TTAAATT
          1 TTAAATT

        430 AAAAAATAAA


Statistics
Matches: 48,  Mismatches: 8, Indels: 4
        0.80            0.13        0.07

Matches are distributed among these distances:
  16    5  0.10
  17   38  0.79
  18    5  0.10

ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45


Consensus pattern (17 bp):   
TTAAATTTTAAATAAAT

Found at i:384 original size:6 final size:6

Alignment explanation


    Indices: 370--429  Score: 63
    Period size: 6  Copynumber: 10.5  Consensus size: 6

        360 TTTTAAATCC

                       *                         **                
        370 ATTTAA ATTTTA A-TTAA ATTTAA ATTTAA A-GCAA ATTTAA ATTTAA
          1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA

              *              
        416 A-ATAA ATTTAA ATT
          1 ATTTAA ATTTAA ATT

        430 AAAAAATAAA


Statistics
Matches: 43,  Mismatches: 8, Indels: 6
        0.75            0.14        0.11

Matches are distributed among these distances:
   5   11  0.26
   6   32  0.74

ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45


Consensus pattern (6 bp):   
ATTTAA

Found at i:388 original size:11 final size:11

Alignment explanation


    Indices: 372--432  Score: 61
    Period size: 11  Copynumber: 5.5  Consensus size: 11

        362 TTAAATCCAT

                    *  
        372 TTAAATTTTAA
          1 TTAAATTTAAA

                       
        383 TTAAATTTAAA
          1 TTAAATTTAAA

                   **   
        394 TTTAAA-GCAAA
          1 -TTAAATTTAAA

                        
        405 TTTAAATTTAAA
          1 -TTAAATTTAAA

            *          
        417 ATAAATTTAAA
          1 TTAAATTTAAA

                 
        428 TTAAA
          1 TTAAA

        433 AAATAAATTT


Statistics
Matches: 41,  Mismatches: 7, Indels: 4
        0.79            0.13        0.08

Matches are distributed among these distances:
  11   33  0.80
  12    8  0.20

ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43


Consensus pattern (11 bp):   
TTAAATTTAAA

Found at i:434 original size:17 final size:17

Alignment explanation


    Indices: 370--442  Score: 92
    Period size: 17  Copynumber: 4.2  Consensus size: 17

        360 TTTTAAATCC

                      *  *   
        370 ATTTAAATTTTAATTAA
          1 ATTTAAATTTAAAATAA

                         **  
        387 ATTTAAATTTAAAGCAA
          1 ATTTAAATTTAAAATAA

                             
        404 ATTTAAATTTAAAATAA
          1 ATTTAAATTTAAAATAA

                      *       
        421 ATTTAAATTAAAAAATAA
          1 ATTTAAATT-TAAAATAA

                
        439 ATTT
          1 ATTT

        443 GAATCAATTT


Statistics
Matches: 49,  Mismatches: 6, Indels: 1
        0.88            0.11        0.02

Matches are distributed among these distances:
  17   38  0.78
  18   11  0.22

ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42


Consensus pattern (17 bp):   
ATTTAAATTTAAAATAA

Found at i:1220 original size:208 final size:206

Alignment explanation


    Indices: 797--1332  Score: 578
    Period size: 208  Copynumber: 2.6  Consensus size: 206

        787 GGTTTCATTG

                  *                           *    ***   *      **        *  
        797 ACTTGGCCTTCTTCTCAGTATCTCATCAGGAAGACGACCATATCACTTGTTTTGATCCACTTTTC
          1 ACTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCATTTGTTTCAATCCACTTCTC

              ** *      *     * **      **     * *    *                      
        862 TGCGCTTCATCAAGAAGATGGTTTTGGTTTACTTCCCCGTATTTCATCAAGAAGCTAATTCATTT
         66 TGTACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATATCATCAAGAAGCTAA-TCATTT

                 **                               *                        * 
        927 TATTATTTCGACCTGCTTCTCAACATCTCATCAGGAAGTTGGGGTTCGAAGATTCGCTCGAATTG
        130 TATTACATCGACCTGCTTCTCAACATCTCATCAGGAAGCTGGGGTTCGAAGATTCGCTCGAATCG

                       *
        992 AGAAGGGGTTTG
        195 AGAAGGGGTTTC

             *                      *             *             * *  *       
       1004 ATTTGGTCTTCTTCTCAGTATCTCTTCAGGAAGATGACTGCGTCATTTGTTTTAGT-TAGCTTCT
          1 ACTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCATTTGTTTCAATCCA-CTTCT

                 *                                      *                    
       1068 CTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCCA-TATCTCATCAAGAAGCTAA-CATT
         65 CTGTACCTCATCAGGAAGACGAATTTGGTCCACTTCT-CAGTATATCATCAAGAAGCTAATCATT

                                     ****                             *      
       1131 TTATTCTCACATCGACCTGCTTCTCGGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTC-A
        129 TTA-T-T-ACATCGACCTGCTTCTCAACATCTCATCAGGAAGCTGGGGTTCGAAGATTCGCTCGA

                    *         
       1195 CATCGAG-CGTGGGTTTC
        191 -ATCGAGAAG-GGGTTTC

                                                        *                   *
       1212 ACTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCACTTCTT
          1 ACTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCATTTGTTTCAATCCACTTCTC

                                                             *      
       1277 TGTACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATATCATCAGGAAGCT
         66 TGTACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATATCATCAAGAAGCT

       1333 GGGGTTCGAA


Statistics
Matches: 272,  Mismatches: 48, Indels: 17
        0.81            0.14        0.05

Matches are distributed among these distances:
 205    7  0.03
 206    2  0.01
 207   98  0.36
 208  164  0.60
 209    1  0.00

ACGTcount: A:0.22, C:0.23, G:0.19, T:0.35


Consensus pattern (206 bp):   
ACTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCATTTGTTTCAATCCACTTCTC
TGTACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATATCATCAAGAAGCTAATCATTTT
ATTACATCGACCTGCTTCTCAACATCTCATCAGGAAGCTGGGGTTCGAAGATTCGCTCGAATCGA
GAAGGGGTTTC
Done.