Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007678.1 Kokia drynarioides strain JFW-HI SEQ_122309, 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: 19071
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31


Found at i:458 original size:26 final size:26

Alignment explanation


    Indices: 407--458  Score: 79
    Period size: 26  Copynumber: 2.0  Consensus size: 26

        397 AAACATATAT

                               *      
        407 AAAACATTAACAAATATTCTTATAAA
          1 AAAACATTAACAAATATTCCTATAAA

                                       
        433 AAAACATTAACAAATATTTCCT-TAAA
          1 AAAACATTAACAAATA-TTCCTATAAA

        459 TAATAAAGTC


Statistics
Matches: 24,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  26   20  0.83
  27    4  0.17

ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31


Consensus pattern (26 bp):   
AAAACATTAACAAATATTCCTATAAA

Found at i:11097 original size:5 final size:6

Alignment explanation


    Indices: 11082--11107  Score: 52
    Period size: 6  Copynumber: 4.3  Consensus size: 6

      11072 AAACATCGTA

                                          
      11082 AAAAAG AAAAAG AAAAAG AAAAAG AA
          1 AAAAAG AAAAAG AAAAAG AAAAAG AA

      11108 TATATACTGC


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   20  1.00

ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00


Consensus pattern (6 bp):   
AAAAAG

Found at i:16814 original size:31 final size:32

Alignment explanation


    Indices: 16733--16810  Score: 90
    Period size: 32  Copynumber: 2.5  Consensus size: 32

      16723 TTTTTTGGTC

                         *                  
      16733 CAAA-TTGGTACCCAAACTTGACACTTTTTTT
          1 CAAAGTTGGTACCTAAACTTGACACTTTTTTT

             ** *                           
      16764 CTGATTTGGTACCTAAACTTGACAC-TTTTTT
          1 CAAAGTTGGTACCTAAACTTGACACTTTTTTT

                        *    
      16795 -AAAGTTGGTACTTAAA
          1 CAAAGTTGGTACCTAAA

      16811 ACTTTTTGAG


Statistics
Matches: 39,  Mismatches: 7, Indels: 3
        0.80            0.14        0.06

Matches are distributed among these distances:
  30   12  0.31
  31    8  0.21
  32   19  0.49

ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40


Consensus pattern (32 bp):   
CAAAGTTGGTACCTAAACTTGACACTTTTTTT

Found at i:17375 original size:7 final size:7

Alignment explanation


    Indices: 17363--17389  Score: 54
    Period size: 7  Copynumber: 3.9  Consensus size: 7

      17353 CTATGTTATT

                   
      17363 ATGAATG
          1 ATGAATG

                   
      17370 ATGAATG
          1 ATGAATG

                   
      17377 ATGAATG
          1 ATGAATG

                  
      17384 ATGAAT
          1 ATGAAT

      17390 TAAACAGTGG


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   20  1.00

ACGTcount: A:0.44, C:0.00, G:0.26, T:0.30


Consensus pattern (7 bp):   
ATGAATG

Found at i:17666 original size:20 final size:20

Alignment explanation


    Indices: 17624--17667  Score: 54
    Period size: 20  Copynumber: 2.2  Consensus size: 20

      17614 GGTCTGATTT

                *             * 
      17624 TTTTGGATTTTTTAAATTGA
          1 TTTTCGATTTTTTAAATTAA

                                 
      17644 TTTTCGATTTTTTATAA-TAA
          1 TTTTCGATTTTTTA-AATTAA

                
      17664 TTTT
          1 TTTT

      17668 AAGTATTTGA


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  20   19  0.90
  21    2  0.10

ACGTcount: A:0.25, C:0.02, G:0.09, T:0.64


Consensus pattern (20 bp):   
TTTTCGATTTTTTAAATTAA
Done.