Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004756.1 Kokia drynarioides strain JFW-HI SEQ_118351, 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: 5293
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37


Found at i:552 original size:15 final size:16

Alignment explanation


    Indices: 534--563  Score: 53
    Period size: 15  Copynumber: 1.9  Consensus size: 16

        524 TTTCCCTATT

                            
        534 TTCTATTT-CTTTTAA
          1 TTCTATTTCCTTTTAA

                           
        549 TTCTATTTCCTTTTA
          1 TTCTATTTCCTTTTA

        564 TTTTTAATTC


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    8  0.57
  16    6  0.43

ACGTcount: A:0.17, C:0.17, G:0.00, T:0.67


Consensus pattern (16 bp):   
TTCTATTTCCTTTTAA

Found at i:567 original size:21 final size:20

Alignment explanation


    Indices: 533--588  Score: 67
    Period size: 22  Copynumber: 2.6  Consensus size: 20

        523 ATTTCCCTAT

                     *           
        533 TTTCTATTTCTTTTAATTCTA
          1 TTTCT-TTTATTTTAATTCTA

                                 *
        554 TTTCCTTTTATTTTTAATTCTG
          1 TTT-CTTTTA-TTTTAATTCTA

                         
        576 TTTCTTTTATTTT
          1 TTTCTTTTATTTT

        589 TCCTTAGATC


Statistics
Matches: 31,  Mismatches: 2, Indels: 5
        0.82            0.05        0.13

Matches are distributed among these distances:
  20    4  0.13
  21   12  0.39
  22   15  0.48

ACGTcount: A:0.14, C:0.12, G:0.02, T:0.71


Consensus pattern (20 bp):   
TTTCTTTTATTTTAATTCTA

Found at i:589 original size:21 final size:22

Alignment explanation


    Indices: 543--589  Score: 78
    Period size: 22  Copynumber: 2.2  Consensus size: 22

        533 TTTCTATTTC

                                  
        543 TTTTAATTCTATTTCCTTTTAT
          1 TTTTAATTCTATTTCCTTTTAT

                      *           
        565 TTTTAATTCTGTTT-CTTTTAT
          1 TTTTAATTCTATTTCCTTTTAT

                
        586 TTTT
          1 TTTT

        590 CCTTAGATCG


Statistics
Matches: 24,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  21   11  0.46
  22   13  0.54

ACGTcount: A:0.15, C:0.11, G:0.02, T:0.72


Consensus pattern (22 bp):   
TTTTAATTCTATTTCCTTTTAT

Found at i:1443 original size:27 final size:26

Alignment explanation


    Indices: 1393--1444  Score: 68
    Period size: 27  Copynumber: 2.0  Consensus size: 26

       1383 TAGGATTTTA

                    *        *        
       1393 AATTAATTTTAAATATTGTATAAGAT
          1 AATTAATTGTAAATATTCTATAAGAT

                                *     
       1419 AATTAATATGTAAATATTCTTTAAGA
          1 AATTAAT-TGTAAATATTCTATAAGA

       1445 CTTTGTTTAA


Statistics
Matches: 22,  Mismatches: 3, Indels: 1
        0.85            0.12        0.04

Matches are distributed among these distances:
  26    7  0.32
  27   15  0.68

ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44


Consensus pattern (26 bp):   
AATTAATTGTAAATATTCTATAAGAT

Found at i:1850 original size:20 final size:21

Alignment explanation


    Indices: 1827--1867  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       1817 TTTTTGTCAG

                       *         
       1827 TTTGAT-TTTATTTAGTTAAA
          1 TTTGATATTTAATTAGTTAAA

                           *     
       1847 TTTGATATTTAATTATTTAAA
          1 TTTGATATTTAATTAGTTAAA

       1868 AAAGAGTCAA


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  20    6  0.33
  21   12  0.67

ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59


Consensus pattern (21 bp):   
TTTGATATTTAATTAGTTAAA

Done.