Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000478.1 Kokia drynarioides strain JFW-HI SEQ_111353, 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: 1754
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.37


Found at i:234 original size:18 final size:18

Alignment explanation


    Indices: 194--240  Score: 60
    Period size: 18  Copynumber: 2.6  Consensus size: 18

        184 CATTAGTCCA

                          **  
        194 AATTACAAAT-AAATTAC
          1 AATTACAAATAAAAAAAC

                               
        211 ACATTACAAATAAAAAAAC
          1 A-ATTACAAATAAAAAAAC

                       
        230 AATTACAAATA
          1 AATTACAAATA

        241 GCCCAATACC


Statistics
Matches: 26,  Mismatches: 2, Indels: 3
        0.84            0.06        0.10

Matches are distributed among these distances:
  17    1  0.04
  18   19  0.73
  19    6  0.23

ACGTcount: A:0.64, C:0.13, G:0.00, T:0.23


Consensus pattern (18 bp):   
AATTACAAATAAAAAAAC

Found at i:1404 original size:25 final size:22

Alignment explanation


    Indices: 1354--1404  Score: 66
    Period size: 25  Copynumber: 2.2  Consensus size: 22

       1344 CATTTTTATT

                                 *
       1354 TTTGTTTTAATTTATCCTTTAT
          1 TTTGTTTTAATTTATCCTTTAA

                                     
       1376 TTTGTTTTCTAATTTATGCCTTTAA
          1 TTTG-TTT-TAATTTAT-CCTTTAA

                
       1401 TTTG
          1 TTTG

       1405 CTTATAGTTT


Statistics
Matches: 25,  Mismatches: 1, Indels: 3
        0.86            0.03        0.10

Matches are distributed among these distances:
  22    4  0.16
  23    3  0.12
  24    8  0.32
  25   10  0.40

ACGTcount: A:0.18, C:0.10, G:0.08, T:0.65


Consensus pattern (22 bp):   
TTTGTTTTAATTTATCCTTTAA

Found at i:1551 original size:25 final size:26

Alignment explanation


    Indices: 1518--1568  Score: 77
    Period size: 25  Copynumber: 2.0  Consensus size: 26

       1508 TATTGTTTGT

                     *                
       1518 TTTTATTTTGTTCTGTT-ATTTTTTA
          1 TTTTATTTTATTCTGTTCATTTTTTA

                        *             
       1543 TTTTATTTTATTTTGTTCATTTTTTA
          1 TTTTATTTTATTCTGTTCATTTTTTA

       1569 GTACTTTTAT


Statistics
Matches: 23,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  25   15  0.65
  26    8  0.35

ACGTcount: A:0.14, C:0.04, G:0.06, T:0.76


Consensus pattern (26 bp):   
TTTTATTTTATTCTGTTCATTTTTTA

Found at i:1577 original size:30 final size:30

Alignment explanation


    Indices: 1518--1580  Score: 76
    Period size: 30  Copynumber: 2.1  Consensus size: 30

       1508 TATTGTTTGT

                                 **       
       1518 TTTTATTTTGTTCTGTTATTTTTTATTTTA
          1 TTTTATTTTGTTCTGTTATTTAGTATTTTA

                                            
       1548 TTTTATTTTGTTCAT-TT-TTTAGTACTTTTA
          1 TTTTATTTTGTTC-TGTTATTTAGTA-TTTTA

               
       1578 TTT
          1 TTT

       1581 CATGCTATTT


Statistics
Matches: 29,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
  29    5  0.17
  30   23  0.79
  31    1  0.03

ACGTcount: A:0.14, C:0.05, G:0.06, T:0.75


Consensus pattern (30 bp):   
TTTTATTTTGTTCTGTTATTTAGTATTTTA
Done.