Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009511.1 Kokia drynarioides strain JFW-HI SEQ_124222, 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: 9150
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31


Found at i:3496 original size:37 final size:37

Alignment explanation


    Indices: 3439--3563  Score: 169
    Period size: 37  Copynumber: 3.4  Consensus size: 37

       3429 TACTGACACA

                  *                        *     
       3439 AAGCCTGCTAGGCATGTAGCCCGAATACACCGGCACG
          1 AAGCCTACTAGGCATGTAGCCCGAATACACCAGCACG

              *                                  
       3476 AAACCTACTAGGCATGTAGCCCGAATACACCAGCACG
          1 AAGCCTACTAGGCATGTAGCCCGAATACACCAGCACG

                *         **     *   *     *     
       3513 AAGCTTACTAGGCACATAGCCTGAAAACACCTGCACG
          1 AAGCCTACTAGGCATGTAGCCCGAATACACCAGCACG

                          
       3550 AAGCCTACTAGGCA
          1 AAGCCTACTAGGCA

       3564 CATAGTCTGA


Statistics
Matches: 77,  Mismatches: 11, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  37   77  1.00

ACGTcount: A:0.33, C:0.31, G:0.22, T:0.14


Consensus pattern (37 bp):   
AAGCCTACTAGGCATGTAGCCCGAATACACCAGCACG

Found at i:5954 original size:23 final size:23

Alignment explanation


    Indices: 5927--5984  Score: 116
    Period size: 23  Copynumber: 2.5  Consensus size: 23

       5917 TCGTCCATCA

                                   
       5927 TTGCTGACTAGACCTTCTAGAAG
          1 TTGCTGACTAGACCTTCTAGAAG

                                   
       5950 TTGCTGACTAGACCTTCTAGAAG
          1 TTGCTGACTAGACCTTCTAGAAG

                        
       5973 TTGCTGACTAGA
          1 TTGCTGACTAGA

       5985 TGCCACGTCA


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  23   35  1.00

ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31


Consensus pattern (23 bp):   
TTGCTGACTAGACCTTCTAGAAG

Found at i:6731 original size:12 final size:12

Alignment explanation


    Indices: 6716--6755  Score: 55
    Period size: 12  Copynumber: 3.3  Consensus size: 12

       6706 TAAGCAACCA

                        
       6716 TTTTTCTTCTTC
          1 TTTTTCTTCTTC

                   *    
       6728 TTTTTCTCCTT-
          1 TTTTTCTTCTTC

                         
       6739 TTTTTCTTTCTTC
          1 TTTTTC-TTCTTC

                
       6752 TTTT
          1 TTTT

       6756 CGAACCTTTT


Statistics
Matches: 24,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  11    6  0.25
  12   14  0.58
  13    4  0.17

ACGTcount: A:0.00, C:0.23, G:0.00, T:0.78


Consensus pattern (12 bp):   
TTTTTCTTCTTC
Done.