Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005619.1 Kokia drynarioides strain JFW-HI SEQ_119775, 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, 873

Length: 1455
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33


Found at i:173 original size:30 final size:29

Alignment explanation


    Indices: 139--287  Score: 135
    Period size: 30  Copynumber: 5.1  Consensus size: 29

        129 TTGTACTTTT

                          *   *           
        139 AATTACATTTTTGAGCCCGAAACTTTCAAA
          1 AATTACATTTTT-ACCCCAAAACTTTCAAA

                             *           
        169 AATTACA-TTTTACCCCTAAAC-TTCAAA
          1 AATTACATTTTTACCCCAAAACTTTCAAA

              **                        *  
        196 AAAAATCATTTTTGACCCCAAAAC-TTCTAA
          1 AATTA-CATTTTT-ACCCCAAAACTTTCAAA

                              *            
        226 AATTCACATTTTTACCCCTAAA-TTTCCAAA
          1 AATT-ACATTTTTACCCCAAAACTTT-CAAA

                *            *            
        256 AATTCCATTTTTAACCCTAAAACTTTCAAA
          1 AATTACATTTTT-ACCCCAAAACTTTCAAA

              
        286 AA
          1 AA

        288 AAAAAAAGGG


Statistics
Matches: 98,  Mismatches: 13, Indels: 16
        0.77            0.10        0.13

Matches are distributed among these distances:
  27    9  0.09
  28   10  0.10
  29   25  0.26
  30   50  0.51
  31    4  0.04

ACGTcount: A:0.40, C:0.23, G:0.03, T:0.34


Consensus pattern (29 bp):   
AATTACATTTTTACCCCAAAACTTTCAAA

Found at i:199 original size:29 final size:29

Alignment explanation


    Indices: 139--288  Score: 128
    Period size: 29  Copynumber: 5.1  Consensus size: 29

        129 TTGTACTTTT

                          *   *            
        139 AATTACATTTTTGAGCCCGAAACTTTC-AAA
          1 AATTACATTTTT-ACCCCTAAAC-TTCAAAA

                                         
        169 AATTACA-TTTTACCCCTAAACTTCAAAA
          1 AATTACATTTTTACCCCTAAACTTCAAAA

               *               *        *  
        197 AA-AATCATTTTTGACCCCAAAACTTC-TAA
          1 AATTA-CATTTTT-ACCCCTAAACTTCAAAA

                                  *   *   
        226 AATTCACATTTTTACCCCTAAATTTCCAAA
          1 AATT-ACATTTTTACCCCTAAACTTCAAAA

                *        *                 
        256 AATTCCATTTTTAACCCTAAAACTTTCAAAA
          1 AATTACATTTTTACCCCT-AAAC-TTCAAAA

              
        287 AA
          1 AA

        289 AAAAAAGGGA


Statistics
Matches: 98,  Mismatches: 13, Indels: 17
        0.77            0.10        0.13

Matches are distributed among these distances:
  27    4  0.04
  28   15  0.15
  29   35  0.36
  30   35  0.36
  31    9  0.09

ACGTcount: A:0.41, C:0.23, G:0.03, T:0.33


Consensus pattern (29 bp):   
AATTACATTTTTACCCCTAAACTTCAAAA

Found at i:278 original size:59 final size:57

Alignment explanation


    Indices: 144--287  Score: 155
    Period size: 59  Copynumber: 2.5  Consensus size: 57

        134 CTTTTAATTA

                   * *   *                                            
        144 CATTTTTGAGCCCGAAACTTTCAAAAATTACATTTTACCCCTAAACTTCAAAAAAAAT
          1 CATTTTTAACCCCAAAAC-TTCAAAAATTACATTTTACCCCTAAACTTCAAAAAAAAT

                   *             *                        *    *     * 
        202 CATTTTTGACCCCAAAACTTCTAAAATTCACATTTTTACCCCTAAATTTC-CAAAAATT
          1 CATTTTTAACCCCAAAACTTCAAAAATT-ACA-TTTTACCCCTAAACTTCAAAAAAAAT

                         *              
        260 CCATTTTTAACCCTAAAACTTTCAAAAA
          1 -CATTTTTAACCCCAAAAC-TTCAAAAA

        288 AAAAAAAGGG


Statistics
Matches: 73,  Mismatches: 9, Indels: 6
        0.83            0.10        0.07

Matches are distributed among these distances:
  57    9  0.12
  58   25  0.34
  59   32  0.44
  60    7  0.10

ACGTcount: A:0.40, C:0.24, G:0.03, T:0.33


Consensus pattern (57 bp):   
CATTTTTAACCCCAAAACTTCAAAAATTACATTTTACCCCTAAACTTCAAAAAAAAT

Found at i:1304 original size:19 final size:19

Alignment explanation


    Indices: 1280--1319  Score: 71
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       1270 GAAATGAGTG

                               
       1280 ATTAAAAGATGAATAATTA
          1 ATTAAAAGATGAATAATTA

                          *    
       1299 ATTAAAAGATGAATGATTA
          1 ATTAAAAGATGAATAATTA

              
       1318 AT
          1 AT

       1320 GACACTTGTA


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  19   20  1.00

ACGTcount: A:0.55, C:0.00, G:0.12, T:0.33


Consensus pattern (19 bp):   
ATTAAAAGATGAATAATTA
Done.