Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007438.1 Kokia drynarioides strain JFW-HI SEQ_122059, 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, 989

Length: 1649
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.35


Found at i:1307 original size:27 final size:27

Alignment explanation


    Indices: 1275--1328  Score: 74
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       1265 TGACACCCAG

                               *        
       1275 TGGAGGAACA-CGAAGTGGTGGCACCAA
          1 TGGAGGAACATC-AAGTGGCGGCACCAA

                    *                  
       1302 TGGAGGAATATCAAGTGGCGGCACCAA
          1 TGGAGGAACATCAAGTGGCGGCACCAA

       1329 GGGGTGTTTT


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  27   23  0.96
  28    1  0.04

ACGTcount: A:0.33, C:0.19, G:0.35, T:0.13


Consensus pattern (27 bp):   
TGGAGGAACATCAAGTGGCGGCACCAA

Found at i:1513 original size:11 final size:11

Alignment explanation


    Indices: 1497--1542  Score: 51
    Period size: 11  Copynumber: 4.3  Consensus size: 11

       1487 GGGGACCAAC

                  *   *
       1497 GAAAAATGAAG
          1 GAAAAAAGAAA

                       
       1508 GAAAAAAGAAA
          1 GAAAAAAGAAA

                       
       1519 GAAAAAAG--A
          1 GAAAAAAGAAA

                        
       1528 GAAAGAAAGAAA
          1 GAAA-AAAGAAA

               
       1540 GAA
          1 GAA

       1543 GGAAGAAGGA


Statistics
Matches: 30,  Mismatches: 2, Indels: 5
        0.81            0.05        0.14

Matches are distributed among these distances:
   9    5  0.17
  10    4  0.13
  11   17  0.57
  12    4  0.13

ACGTcount: A:0.74, C:0.00, G:0.24, T:0.02


Consensus pattern (11 bp):   
GAAAAAAGAAA

Found at i:1548 original size:21 final size:20

Alignment explanation


    Indices: 1504--1548  Score: 56
    Period size: 21  Copynumber: 2.2  Consensus size: 20

       1494 AACGAAAAAT

                                
       1504 GAAG-GAAAAAAGAAAGAAA
          1 GAAGAGAAAAAAGAAAGAAA

            *                   *
       1523 AAAGAGAAAGAAAGAAAGAAG
          1 GAAGAGAAA-AAAGAAAGAAA

                 
       1544 GAAGA
          1 GAAGA

       1549 AGGAAGAAGG


Statistics
Matches: 21,  Mismatches: 3, Indels: 2
        0.81            0.12        0.08

Matches are distributed among these distances:
  19    3  0.14
  20    4  0.19
  21   14  0.67

ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00


Consensus pattern (20 bp):   
GAAGAGAAAAAAGAAAGAAA

Found at i:1550 original size:7 final size:7

Alignment explanation


    Indices: 1538--1566  Score: 51
    Period size: 7  Copynumber: 4.3  Consensus size: 7

       1528 GAAAGAAAGA

                   
       1538 AAGAAGG
          1 AAGAAGG

                   
       1545 AAGAAGG
          1 AAGAAGG

                   
       1552 AAGAAGG
          1 AAGAAGG

                   
       1559 -AGAAGG
          1 AAGAAGG

              
       1565 AA
          1 AA

       1567 AAAAAAAAAT


Statistics
Matches: 21,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
   6    6  0.29
   7   15  0.71

ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00


Consensus pattern (7 bp):   
AAGAAGG
Done.