Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004545.1 Kokia drynarioides strain JFW-HI SEQ_118008, 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: 2519
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.37


Found at i:1130 original size:27 final size:27

Alignment explanation


    Indices: 1100--1187  Score: 124
    Period size: 27  Copynumber: 3.3  Consensus size: 27

       1090 CCTCCCTATG

                                     * 
       1100 TTCCTCCTTATCTCCCTCTGAAACAAC
          1 TTCCTCCTTATCTCCCTCTGAAACAGC

                          *     *      
       1127 TTCCTCCTTATCTCTCTCTGGAACAGC
          1 TTCCTCCTTATCTCCCTCTGAAACAGC

                   *                    
       1154 TTCCTCCCTATCTCCCTCT-AGAACAGC
          1 TTCCTCCTTATCTCCCTCTGA-AACAGC

                   
       1181 TTCCTCC
          1 TTCCTCC

       1188 CCTCCCTCTC


Statistics
Matches: 54,  Mismatches: 6, Indels: 2
        0.87            0.10        0.03

Matches are distributed among these distances:
  27   54  1.00

ACGTcount: A:0.17, C:0.42, G:0.07, T:0.34


Consensus pattern (27 bp):   
TTCCTCCTTATCTCCCTCTGAAACAGC

Found at i:1188 original size:27 final size:27

Alignment explanation


    Indices: 1056--1188  Score: 121
    Period size: 27  Copynumber: 5.0  Consensus size: 27

       1046 ATCACTATCA

                         *    *      * 
       1056 CTATCTCCCTCTAAAACAACTTCCTTC
          1 CTATCTCCCTCTAGAACAGCTTCCTCC

                        ***  *         
       1083 CTATCTCCCTC-CCTA-TG-TTCCTCC
          1 CTATCTCCCTCTAGAACAGCTTCCTCC

            *                  *        
       1107 TTATCTCCCTCT-GAAACAACTTCCTCC
          1 CTATCTCCCTCTAG-AACAGCTTCCTCC

            *      *    *              
       1134 TTATCTCTCTCTGGAACAGCTTCCTCC
          1 CTATCTCCCTCTAGAACAGCTTCCTCC

                                       
       1161 CTATCTCCCTCTAGAACAGCTTCCTCC
          1 CTATCTCCCTCTAGAACAGCTTCCTCC

             
       1188 C
          1 C

       1189 CTCCCTCTCG


Statistics
Matches: 85,  Mismatches: 16, Indels: 10
        0.77            0.14        0.09

Matches are distributed among these distances:
  24   16  0.19
  25    1  0.01
  26    1  0.01
  27   66  0.78
  28    1  0.01

ACGTcount: A:0.18, C:0.43, G:0.05, T:0.34


Consensus pattern (27 bp):   
CTATCTCCCTCTAGAACAGCTTCCTCC

Found at i:1205 original size:24 final size:25

Alignment explanation


    Indices: 1110--1207  Score: 83
    Period size: 27  Copynumber: 3.8  Consensus size: 25

       1100 TTCCTCCTTA

                            *          *
       1110 TCTCCCTCT-GAAACAACTTCCTCCTTA
          1 TCTCCCTCTAG-AACAGCTTCCTCC--C

                *    *               
       1137 TCTCTCTCTGGAACAGCTTCCTCCC
          1 TCTCCCTCTAGAACAGCTTCCTCCC

                                       
       1162 TATCTCCCTCTAGAACAGCTTCCTCCC
          1 --TCTCCCTCTAGAACAGCTTCCTCCC

                     *   *      
       1189 -CTCCCTCTCGAAAAGCTTC
          1 TCTCCCTCTAGAACAGCTTC

       1208 ACCACCACAC


Statistics
Matches: 61,  Mismatches: 7, Indels: 9
        0.79            0.09        0.12

Matches are distributed among these distances:
  24   17  0.28
  27   43  0.70
  28    1  0.02

ACGTcount: A:0.18, C:0.43, G:0.08, T:0.31


Consensus pattern (25 bp):   
TCTCCCTCTAGAACAGCTTCCTCCC
Done.