Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010971.1 Kokia drynarioides strain JFW-HI SEQ_125940, 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: 2500
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.36


Found at i:643 original size:46 final size:46

Alignment explanation


    Indices: 562--666  Score: 131
    Period size: 46  Copynumber: 2.3  Consensus size: 46

        552 GAACTTTATT

                     *   *                *          *    
        562 TTAAATTTATAATCATTTTAATTTTGAAAATAAATTTAAACTTAAA
          1 TTAAATTTAAAATAATTTTAATTTTGAAAACAAATTTAAACCTAAA

                                       *            *      
        608 TTAAATTTAAAATAAATTTTAATTTT-TAAACAAATTTAATCCTAAA
          1 TTAAATTTAAAAT-AATTTTAATTTTGAAAACAAATTTAAACCTAAA

            *            
        654 ATAAATTTAAAAT
          1 TTAAATTTAAAAT

        667 GAGTTTGGGC


Statistics
Matches: 51,  Mismatches: 7, Indels: 2
        0.85            0.12        0.03

Matches are distributed among these distances:
  46   40  0.78
  47   11  0.22

ACGTcount: A:0.50, C:0.05, G:0.01, T:0.44


Consensus pattern (46 bp):   
TTAAATTTAAAATAATTTTAATTTTGAAAACAAATTTAAACCTAAA

Found at i:662 original size:17 final size:17

Alignment explanation


    Indices: 615--663  Score: 53
    Period size: 17  Copynumber: 2.8  Consensus size: 17

        605 AAATTAAATT

                            **
        615 TAAAATAAATTTTAATTT
          1 TAAAATAAA-TTTAATCC

             *   *           
        633 TTAAACAAATTTAATCC
          1 TAAAATAAATTTAATCC

                          
        650 TAAAATAAATTTAA
          1 TAAAATAAATTTAA

        664 AATGAGTTTG


Statistics
Matches: 25,  Mismatches: 6, Indels: 1
        0.78            0.19        0.03

Matches are distributed among these distances:
  17   18  0.72
  18    7  0.28

ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41


Consensus pattern (17 bp):   
TAAAATAAATTTAATCC

Found at i:994 original size:2 final size:2

Alignment explanation


    Indices: 987--1011  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

        977 AAATCGAATG

                                                 
        987 TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA T

       1012 GAAAAATATG


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:1454 original size:158 final size:157

Alignment explanation


    Indices: 1157--1617  Score: 566
    Period size: 158  Copynumber: 2.9  Consensus size: 157

       1147 TACAGTTCAA

                         *                                                   
       1157 GGTGTTGGTCTTGGATGTCCTACCGATGGA-TAAGGTCCTGCATTTGTTATGGATTCTCCACAGC
          1 GGTGTTGGTCTTGAATGTCCTACCGAT-GACTAAGGTCCTGCATTTGTTATGGATTCTCCACAGC

                                       *   *                     **          
       1221 TCGTGTGAGCAGCATCGTGTAGCCTAATATCCCGACCCACAGCTCGTGTGAGCAAACCAATTTCA
         65 TCGTGTGAGCAGCATCGTGTAGCCTAACATCTCGACCCACAGCTCGTGTGAGCGGACC-ATTTCA

                 *                       
       1286 TAGCTTGTGTGAGCATTACAGGTTATATG
        129 TAGCTCGTGTGAGCATTACAGGTTATATG

                         *                 *            *   *         * *    
       1315 GGTGTTGGTCTTGTATGTCCTACCGATGACTGAGGTCCTGCATTGGTTGTGGATTCTCTATAGCT
          1 GGTGTTGGTCTTGAATGTCCTACCGATGACTAAGGTCCTGCATTTGTTATGGATTCTCCACAGCT

             *                             *           *                *   *
       1380 CATGTGAGCAGCATCGTGTAGCCTAACATCTAGACCCACAGCTTGTGTGAGCGGACTCATCTCAC
         66 CGTGTGAGCAGCATCGTGTAGCCTAACATCTCGACCCACAGCTCGTGTGAGCGGAC-CATTTCAT

                                        
       1445 AGCTCGTGTGAGCATTACAGGTTATATG
        130 AGCTCGTGTGAGCATTACAGGTTATATG

             ****      **           *   *        *        *   *              
       1473 GCCACTGGTCTCAAATGTCCTACCAATGGCTAAGGT-TTGACATTTATTACGGATTCTCCACAGC
          1 GGTGTTGGTCTTGAATGTCCTACCGATGACTAAGGTCCTG-CATTTGTTATGGATTCTCCACAGC

                            *       **                              *        
       1537 TCGTGTGAGCAGCATCATGTAGCCCCACATCTCGACCCACAGCTCGTGTGAGCAGGTCCATTTCA
         65 TCGTGTGAGCAGCATCGTGTAGCCTAACATCTCGACCCACAGCTCGTGTGAGC-GGACCATTTCA

                  *         
       1602 TAGCTCCTGTGAGCAT
        129 TAGCTCGTGTGAGCAT

       1618 ATATGGTTAC


Statistics
Matches: 256,  Mismatches: 43, Indels: 8
        0.83            0.14        0.03

Matches are distributed among these distances:
 157    4  0.02
 158  248  0.97
 159    4  0.02

ACGTcount: A:0.22, C:0.24, G:0.25, T:0.30


Consensus pattern (157 bp):   
GGTGTTGGTCTTGAATGTCCTACCGATGACTAAGGTCCTGCATTTGTTATGGATTCTCCACAGCT
CGTGTGAGCAGCATCGTGTAGCCTAACATCTCGACCCACAGCTCGTGTGAGCGGACCATTTCATA
GCTCGTGTGAGCATTACAGGTTATATG

Done.