Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009058.1 Kokia drynarioides strain JFW-HI SEQ_123758, 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: 22858
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35


Found at i:115 original size:2 final size:2

Alignment explanation


    Indices: 110--134  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

        100 ATATATTTCC

                                                 
        110 TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA T

        135 GCATTTGAAA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:4274 original size:23 final size:22

Alignment explanation


    Indices: 4230--4278  Score: 55
    Period size: 23  Copynumber: 2.2  Consensus size: 22

       4220 AAATTCTTGT

                       *     *     
       4230 TAAAATAAAATTAAGTGGTAAAA
          1 TAAAATAAAATAAAGTGCT-AAA

                                   
       4253 TAAAATAAAAGTAAAGT-CTAAA
          1 TAAAATAAAA-TAAAGTGCTAAA

                
       4275 TAAA
          1 TAAA

       4279 CTAGACTTCT


Statistics
Matches: 23,  Mismatches: 2, Indels: 3
        0.82            0.07        0.11

Matches are distributed among these distances:
  22    7  0.30
  23   11  0.48
  24    5  0.22

ACGTcount: A:0.63, C:0.02, G:0.10, T:0.24


Consensus pattern (22 bp):   
TAAAATAAAATAAAGTGCTAAA

Found at i:8605 original size:41 final size:41

Alignment explanation


    Indices: 8546--8641  Score: 174
    Period size: 41  Copynumber: 2.3  Consensus size: 41

       8536 TTGTTCGTAG

                       *                             
       8546 AGAATTCTTGTCAAGGTGGAGATTGTTAGAATTGGGTGAAT
          1 AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTGGGTGAAT

             *                                       
       8587 ATAATTCTTGTTAAGGTGGAGATTGTTAGAATTGGGTGAAT
          1 AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTGGGTGAAT

                          
       8628 AGAATTCTTGTTAA
          1 AGAATTCTTGTTAA

       8642 AATAAAATTC


Statistics
Matches: 52,  Mismatches: 3, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  41   52  1.00

ACGTcount: A:0.30, C:0.04, G:0.28, T:0.38


Consensus pattern (41 bp):   
AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTGGGTGAAT

Found at i:9885 original size:25 final size:26

Alignment explanation


    Indices: 9856--9918  Score: 76
    Period size: 27  Copynumber: 2.5  Consensus size: 26

       9846 AAATCATAAT

                                      
       9856 TTAATAATTATTA-TTTAAAAAAAAA
          1 TTAATAATTATTATTTTAAAAAAAAA

                     *        *       *
       9881 TTAATAATTTTATATTTTTAAAAAAAT
          1 TTAATAATTAT-TATTTTAAAAAAAAA

                        
       9908 TTAA-AATTATT
          1 TTAATAATTATT

       9919 TGCTGATATG


Statistics
Matches: 32,  Mismatches: 4, Indels: 4
        0.80            0.10        0.10

Matches are distributed among these distances:
  25   11  0.34
  26    7  0.22
  27   14  0.44

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (26 bp):   
TTAATAATTATTATTTTAAAAAAAAA

Found at i:11572 original size:15 final size:16

Alignment explanation


    Indices: 11552--11598  Score: 55
    Period size: 15  Copynumber: 3.1  Consensus size: 16

      11542 ATTGAAAAGT

                            
      11552 TTTAATTTAATTAA-A
          1 TTTAATTTAATTAATA

                     *      
      11567 TTTAATTT-TTTAATA
          1 TTTAATTTAATTAATA

            *               
      11582 ATTAATTTAATT-ATA
          1 TTTAATTTAATTAATA

              
      11597 TT
          1 TT

      11599 ATTTTTATTT


Statistics
Matches: 26,  Mismatches: 4, Indels: 4
        0.76            0.12        0.12

Matches are distributed among these distances:
  14    4  0.15
  15   20  0.77
  16    2  0.08

ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60


Consensus pattern (16 bp):   
TTTAATTTAATTAATA

Found at i:17253 original size:20 final size:19

Alignment explanation


    Indices: 17228--17267  Score: 53
    Period size: 19  Copynumber: 2.1  Consensus size: 19

      17218 CATGTCAATG

                      *         
      17228 ACATATGTTATGAAAAATAT
          1 ACATAT-TTAAGAAAAATAT

                       *       
      17248 ACATATTTAAGTAAAATAT
          1 ACATATTTAAGAAAAATAT

             
      17267 A
          1 A

      17268 TTGAAGTTGT


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  19   12  0.67
  20    6  0.33

ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35


Consensus pattern (19 bp):   
ACATATTTAAGAAAAATAT

Found at i:17723 original size:18 final size:18

Alignment explanation


    Indices: 17702--17744  Score: 70
    Period size: 17  Copynumber: 2.4  Consensus size: 18

      17692 GGAAAAAATA

                              
      17702 GTTAAAAGAATATGAAAG
          1 GTTAAAAGAATATGAAAG

                          *   
      17720 GTT-AAAGAATATGGAAG
          1 GTTAAAAGAATATGAAAG

                    
      17737 GTTAAAAG
          1 GTTAAAAG

      17745 TCAAGGGAGA


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

Matches are distributed among these distances:
  17   16  0.70
  18    7  0.30

ACGTcount: A:0.51, C:0.00, G:0.26, T:0.23


Consensus pattern (18 bp):   
GTTAAAAGAATATGAAAG

Done.