Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012171.1 Kokia drynarioides strain JFW-HI SEQ_127172, 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: 17165
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35


Found at i:1987 original size:53 final size:53

Alignment explanation


    Indices: 1921--2169  Score: 365
    Period size: 53  Copynumber: 4.7  Consensus size: 53

       1911 TTGTTCCAAA

                    *                   *                *       
       1921 GATTAAAGATCCGATGACTCTATGTCATAGTGAGTTATATGAATCTTATCACG
          1 GATTAAAGGTCCGATGACTCTATGTCATCGTGAGTTATATGAATCCTATCACG

                                 *                             * 
       1974 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCATG
          1 GATTAAAGGTCCGATGACTCTATGTCATCGTGAGTTATATGAATCCTATCACG

                               * *                           *   
       2027 GATTAAAGGTCCGATGACTATGTGTCATCGTGAGTTATATGAATCCTATTACG
          1 GATTAAAGGTCCGATGACTCTATGTCATCGTGAGTTATATGAATCCTATCACG

                  *    *       *                 *     *       * 
       2080 GATTAAGGGTCTGATGACTTTATGTCATCGTGAGTTACATGAAGCC-ATCATG
          1 GATTAAAGGTCCGATGACTCTATGTCATCGTGAGTTATATGAATCCTATCACG

                                                  
       2132 GATTAAAGGTCCGATGACTCTATGTCATCGTGAGTTAT
          1 GATTAAAGGTCCGATGACTCTATGTCATCGTGAGTTAT

       2170 CAAATGCGAA


Statistics
Matches: 176,  Mismatches: 20, Indels: 1
        0.89            0.10        0.01

Matches are distributed among these distances:
  52   38  0.22
  53  138  0.78

ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34


Consensus pattern (53 bp):   
GATTAAAGGTCCGATGACTCTATGTCATCGTGAGTTATATGAATCCTATCACG

Found at i:5161 original size:29 final size:28

Alignment explanation


    Indices: 5107--5161  Score: 65
    Period size: 29  Copynumber: 1.9  Consensus size: 28

       5097 GGGTTTATTC

                          *   *         
       5107 TTTCTTGTGTTATTTAATTTTATCATGT
          1 TTTCTTGTGTTATTCAATATTATCATGT

                        *         *    
       5135 TTTCTATGTGTTCTTCAATATTGTCAT
          1 TTTCT-TGTGTTATTCAATATTATCAT

       5162 CAATAATGGT


Statistics
Matches: 22,  Mismatches: 4, Indels: 1
        0.81            0.15        0.04

Matches are distributed among these distances:
  28    5  0.23
  29   17  0.77

ACGTcount: A:0.18, C:0.11, G:0.11, T:0.60


Consensus pattern (28 bp):   
TTTCTTGTGTTATTCAATATTATCATGT

Found at i:6741 original size:25 final size:25

Alignment explanation


    Indices: 6712--6761  Score: 91
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       6702 CAACTTATAA

                       *             
       6712 CTTCTGAACTTTTTCAATTTCTCTT
          1 CTTCTGAACTTCTTCAATTTCTCTT

                                     
       6737 CTTCTGAACTTCTTCAATTTCTCTT
          1 CTTCTGAACTTCTTCAATTTCTCTT

       6762 GCTACAACTT


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  25   24  1.00

ACGTcount: A:0.16, C:0.26, G:0.04, T:0.54


Consensus pattern (25 bp):   
CTTCTGAACTTCTTCAATTTCTCTT

Found at i:9145 original size:16 final size:16

Alignment explanation


    Indices: 9124--9156  Score: 66
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       9114 CACAATTTTA

                            
       9124 GGCATAGAAATCATTC
          1 GGCATAGAAATCATTC

                            
       9140 GGCATAGAAATCATTC
          1 GGCATAGAAATCATTC

             
       9156 G
          1 G

       9157 TTGAAGAAAC


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   17  1.00

ACGTcount: A:0.36, C:0.18, G:0.21, T:0.24


Consensus pattern (16 bp):   
GGCATAGAAATCATTC
Done.