Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002317.1 Kokia drynarioides strain JFW-HI SEQ_114362, 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, 967

Length: 1612
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36


Found at i:656 original size:16 final size:18

Alignment explanation


    Indices: 617--650  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

        607 TAAGTTTATA

                              
        617 ATATTT-TATATTATGTT
          1 ATATTTATATATTATGTT

              *              
        634 ATTTTTATATATTATGT
          1 ATATTTATATATTATGT

        651 AATTTAGAAC


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  17    5  0.33
  18   10  0.67

ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65


Consensus pattern (18 bp):   
ATATTTATATATTATGTT

Found at i:1424 original size:15 final size:15

Alignment explanation


    Indices: 1382--1426  Score: 56
    Period size: 15  Copynumber: 3.0  Consensus size: 15

       1372 TCCACAATAT

                           
       1382 AATTACATGATATAA
          1 AATTACATGATATAA

                *    *      
       1397 ATATGA-ATAATATAA
          1 A-ATTACATGATATAA

                           
       1412 AATTACATGATATAA
          1 AATTACATGATATAA

       1427 TAGAAAAAAT


Statistics
Matches: 24,  Mismatches: 4, Indels: 4
        0.75            0.12        0.12

Matches are distributed among these distances:
  14    3  0.12
  15   18  0.75
  16    3  0.12

ACGTcount: A:0.56, C:0.04, G:0.07, T:0.33


Consensus pattern (15 bp):   
AATTACATGATATAA

Found at i:1581 original size:27 final size:28

Alignment explanation


    Indices: 1534--1591  Score: 75
    Period size: 27  Copynumber: 2.1  Consensus size: 28

       1524 AAAAATAACT

                                      *  
       1534 TATATATATTTATAATATAATATATGTGA
          1 TATATATATTTAT-ATATAATATATGGGA

                                         
       1563 TATATATAATTTAT-T-TAATATATGGGA
          1 TATATAT-ATTTATATATAATATATGGGA

              
       1590 TA
          1 TA

       1592 GATTTCTTGT


Statistics
Matches: 27,  Mismatches: 1, Indels: 4
        0.84            0.03        0.12

Matches are distributed among these distances:
  27   13  0.48
  28    1  0.04
  29    7  0.26
  30    6  0.22

ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48


Consensus pattern (28 bp):   
TATATATATTTATATATAATATATGGGA

Found at i:1583 original size:18 final size:17

Alignment explanation


    Indices: 1537--1585  Score: 57
    Period size: 16  Copynumber: 2.9  Consensus size: 17

       1527 AATAACTTAT

                             
       1537 ATATATTTATA-ATATA
          1 ATATATTTATATATATA

                    *         
       1553 ATATATGTGATATATATA
          1 ATATAT-TTATATATATA

              *             
       1571 ATTTATTTA-ATATAT
          1 ATATATTTATATATAT

       1586 GGGATAGATT


Statistics
Matches: 28,  Mismatches: 3, Indels: 4
        0.80            0.09        0.11

Matches are distributed among these distances:
  16   12  0.43
  17    6  0.21
  18   10  0.36

ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51


Consensus pattern (17 bp):   
ATATATTTATATATATA
Done.