Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001925.1 Kokia drynarioides strain JFW-HI SEQ_113725, 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: 2687
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32


Found at i:1243 original size:80 final size:80

Alignment explanation


    Indices: 1102--1251  Score: 219
    Period size: 80  Copynumber: 1.9  Consensus size: 80

       1092 ACTAATTTCA

                       *        **              *                            
       1102 TTTTAACTCTTGTAAGGAAGTTAATGAGTCATGTCTCTTCATTAGGATCTAATGTAATTGAAAAG
          1 TTTTAACTCTTATAAGGAAGCCAATGAGTCATGTCTATTCATTAGGATCTAATGTAATTGAAAAG

                           
       1167 GCATGACAATTTTGT
         66 GCATGACAATTTTGT

                          *                                   *    **      * 
       1182 TTTTAACTCTTATAGGGAAGCCAATGAGTCATGTCTATTCATTAGGATCTGATGTGGTTGAAATG
          1 TTTTAACTCTTATAAGGAAGCCAATGAGTCATGTCTATTCATTAGGATCTAATGTAATTGAAAAG

                 
       1247 GCATG
         66 GCATG

       1252 GCATTTCTCC


Statistics
Matches: 61,  Mismatches: 9, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  80   61  1.00

ACGTcount: A:0.29, C:0.12, G:0.21, T:0.37


Consensus pattern (80 bp):   
TTTTAACTCTTATAAGGAAGCCAATGAGTCATGTCTATTCATTAGGATCTAATGTAATTGAAAAG
GCATGACAATTTTGT

Found at i:1297 original size:80 final size:78

Alignment explanation


    Indices: 1213--1371  Score: 219
    Period size: 80  Copynumber: 2.0  Consensus size: 78

       1203 CAATGAGTCA

                                    * *     * *                      *       
       1213 TGTCTATTCATTAGGATCTGATGTGGTTGAAATGGCATGGCATTTCTCCTTAAATGATGACTTAT
          1 TGTCTATTCATTAGGATCTGATGTAGATGAAAAGACATGGCATTTCTCCTT-AATGAAGACTTA-

                *          
       1278 TGTATCCTTAATGTG
         64 TGTAACCTTAATGTG

                 *           *                 *                             
       1293 TGTCTCTTCATTAGGATTTGATGTAGATGAAAAGATATGGCATTTCTCCTTAATGAAGACTTATG
          1 TGTCTATTCATTAGGATCTGATGTAGATGAAAAGACATGGCATTTCTCCTTAATGAAGACTTATG

                         
       1358 TAACCTTAATGTG
         66 TAACCTTAATGTG

             
       1371 T
          1 T

       1372 TTATTGGTTG


Statistics
Matches: 70,  Mismatches: 9, Indels: 2
        0.86            0.11        0.02

Matches are distributed among these distances:
  78   15  0.21
  79   11  0.16
  80   44  0.63

ACGTcount: A:0.26, C:0.13, G:0.20, T:0.40


Consensus pattern (78 bp):   
TGTCTATTCATTAGGATCTGATGTAGATGAAAAGACATGGCATTTCTCCTTAATGAAGACTTATG
TAACCTTAATGTG

Found at i:1838 original size:48 final size:48

Alignment explanation


    Indices: 1786--1927  Score: 203
    Period size: 48  Copynumber: 2.9  Consensus size: 48

       1776 CAAGGCATTT

                        *              **     *         *   
       1786 AACAAAGATGCAGTTAACAAACAAAACGTTTAATAATGCAAATTCCTA
          1 AACAAAGATGCATTTAACAAACAAAACACTTAATGATGCAAATTACTA

                                     *            *      *  
       1834 AACAAAGATGCATTTAACAAACAAATCACTTAATGATGTAAATTATTA
          1 AACAAAGATGCATTTAACAAACAAAACACTTAATGATGCAAATTACTA

                                                          
       1882 AACAAAGATGCATTTAACAAACAAAACACTTAATGATGCATAATTA
          1 AACAAAGATGCATTTAACAAACAAAACACTTAATGATGCA-AATTA

       1928 AACAACTTTA


Statistics
Matches: 83,  Mismatches: 10, Indels: 1
        0.88            0.11        0.01

Matches are distributed among these distances:
  48   78  0.94
  49    5  0.06

ACGTcount: A:0.51, C:0.15, G:0.09, T:0.25


Consensus pattern (48 bp):   
AACAAAGATGCATTTAACAAACAAAACACTTAATGATGCAAATTACTA
Done.