Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011985.1 Kokia drynarioides strain JFW-HI SEQ_126983, 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: 2830
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.32

Warning! 50 characters in sequence are not A, C, G, or T


Found at i:1100 original size:23 final size:23

Alignment explanation


    Indices: 1070--1123  Score: 99
    Period size: 23  Copynumber: 2.3  Consensus size: 23

       1060 ATGCTAGCAC

                                   
       1070 GCTTACTGTTTCGCACTTCGTGT
          1 GCTTACTGTTTCGCACTTCGTGT

                                   
       1093 GCTTACTGTTTCGCACTTCGTGT
          1 GCTTACTGTTTCGCACTTCGTGT

              *     
       1116 GCCTACTG
          1 GCTTACTG

       1124 ATTTGCGCTA


Statistics
Matches: 30,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  23   30  1.00

ACGTcount: A:0.09, C:0.28, G:0.22, T:0.41


Consensus pattern (23 bp):   
GCTTACTGTTTCGCACTTCGTGT

Found at i:1182 original size:36 final size:36

Alignment explanation


    Indices: 1112--1183  Score: 92
    Period size: 36  Copynumber: 2.0  Consensus size: 36

       1102 TTCGCACTTC

                              *                 
       1112 GTGTGCCTACTGATTTGCGCTATGTGCGCCTACTGT
          1 GTGTGCCTACTGATTTGCACTATGTGCGCCTACTGT

                                  *    *  *      
       1148 GTGTGCCTACTGGA-TTGCACTGTGTGTGCTTACTGT
          1 GTGTGCCTACT-GATTTGCACTATGTGCGCCTACTGT

       1184 TAAGTACTTC


Statistics
Matches: 31,  Mismatches: 4, Indels: 2
        0.84            0.11        0.05

Matches are distributed among these distances:
  36   29  0.94
  37    2  0.06

ACGTcount: A:0.11, C:0.22, G:0.29, T:0.38


Consensus pattern (36 bp):   
GTGTGCCTACTGATTTGCACTATGTGCGCCTACTGT

Found at i:1421 original size:23 final size:23

Alignment explanation


    Indices: 1391--1438  Score: 96
    Period size: 23  Copynumber: 2.1  Consensus size: 23

       1381 ATGCTAGCAC

                                   
       1391 GCTTACTGTTTCGCACTTCGTGT
          1 GCTTACTGTTTCGCACTTCGTGT

                                   
       1414 GCTTACTGTTTCGCACTTCGTGT
          1 GCTTACTGTTTCGCACTTCGTGT

              
       1437 GC
          1 GC

       1439 CCACTGATTT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  23   25  1.00

ACGTcount: A:0.08, C:0.27, G:0.23, T:0.42


Consensus pattern (23 bp):   
GCTTACTGTTTCGCACTTCGTGT

Found at i:1444 original size:23 final size:23

Alignment explanation


    Indices: 1395--1444  Score: 82
    Period size: 23  Copynumber: 2.2  Consensus size: 23

       1385 TAGCACGCTT

                                 **
       1395 ACTGTTTCGCACTTCGTGTGCTT
          1 ACTGTTTCGCACTTCGTGTGCCC

                                   
       1418 ACTGTTTCGCACTTCGTGTGCCC
          1 ACTGTTTCGCACTTCGTGTGCCC

                
       1441 ACTG
          1 ACTG

       1445 ATTTGCGCTA


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  23   25  1.00

ACGTcount: A:0.10, C:0.30, G:0.22, T:0.38


Consensus pattern (23 bp):   
ACTGTTTCGCACTTCGTGTGCCC

Found at i:1497 original size:23 final size:23

Alignment explanation


    Indices: 1460--1512  Score: 90
    Period size: 23  Copynumber: 2.3  Consensus size: 23

       1450 CGCTATATGC

                                   
       1460 GCCTACT-GATTGCACTGTGTGT
          1 GCCTACTGGATTGCACTGTGTGT

                                   
       1482 GCCTACTGGATTGCACTGTGTGT
          1 GCCTACTGGATTGCACTGTGTGT

              *     
       1505 GCTTACTG
          1 GCCTACTG

       1513 TTTCCCCAGC


Statistics
Matches: 29,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
  22    7  0.24
  23   22  0.76

ACGTcount: A:0.13, C:0.23, G:0.28, T:0.36


Consensus pattern (23 bp):   
GCCTACTGGATTGCACTGTGTGT

Found at i:1512 original size:45 final size:46

Alignment explanation


    Indices: 1410--1512  Score: 104
    Period size: 45  Copynumber: 2.3  Consensus size: 46

       1400 TTCGCACTTC

                        *                            *    
       1410 GTGTGCTTACTGTTTCGCACTTCGTGTGCCCACTGATTTGCGCTAT
          1 GTGTGCTTACTGATTCGCACTTCGTGTGCCCACTGATTTGCACTAT

            *  *  *                        *              * 
       1456 ATGCGCCTACTGATT-GCACTGT-GTGTGCCTACTGGA-TTGCACTGT
          1 GTGTGCTTACTGATTCGCACT-TCGTGTGCCCACT-GATTTGCACTAT

                        
       1501 GTGTGCTTACTG
          1 GTGTGCTTACTG

       1513 TTTCCCCAGC


Statistics
Matches: 45,  Mismatches: 10, Indels: 5
        0.75            0.17        0.08

Matches are distributed among these distances:
  45   31  0.69
  46   14  0.31

ACGTcount: A:0.13, C:0.24, G:0.26, T:0.37


Consensus pattern (46 bp):   
GTGTGCTTACTGATTCGCACTTCGTGTGCCCACTGATTTGCACTAT
Done.