Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010802.1 Kokia drynarioides strain JFW-HI SEQ_125769, 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, 658

Length: 1097
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.34

Warning! 50 characters in sequence are not A, C, G, or T


Found at i:436 original size:12 final size:12

Alignment explanation


    Indices: 419--446  Score: 56
    Period size: 12  Copynumber: 2.3  Consensus size: 12

        409 TTATTTAACA

                        
        419 TTAATATAAAAT
          1 TTAATATAAAAT

                        
        431 TTAATATAAAAT
          1 TTAATATAAAAT

                
        443 TTAA
          1 TTAA

        447 ATTTATTATT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   16  1.00

ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43


Consensus pattern (12 bp):   
TTAATATAAAAT

Found at i:485 original size:10 final size:10

Alignment explanation


    Indices: 470--535  Score: 55
    Period size: 10  Copynumber: 6.4  Consensus size: 10

        460 TGAAAATATT

                      
        470 TATTTTTATA
          1 TATTTTTATA

                      
        480 TATTTTTA-A
          1 TATTTTTATA

            *           
        489 AATTTATTATTA
          1 TATTT-TTA-TA

                       
        501 TATTTTT-TAA
          1 TATTTTTAT-A

            *         *
        511 AATTATTTATG
          1 TATT-TTTATA

                      
        522 TATTTTTATA
          1 TATTTTTATA

                
        532 TATT
          1 TATT

        536 CGTTTAAGTT


Statistics
Matches: 44,  Mismatches: 6, Indels: 12
        0.71            0.10        0.19

Matches are distributed among these distances:
   9    6  0.14
  10   24  0.55
  11    8  0.18
  12    6  0.14

ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65


Consensus pattern (10 bp):   
TATTTTTATA

Found at i:493 original size:23 final size:22

Alignment explanation


    Indices: 437--528  Score: 87
    Period size: 23  Copynumber: 4.0  Consensus size: 22

        427 AAATTTAATA

                     **            
        437 TAAAATTTAAATTTATTATTTTT
          1 TAAAATTTATTTTTA-TATTTTT

                                      
        460 TGAAAATATTTATTTTTATATATTTT
          1 T--AAA-ATTTATTTTTATAT-TTTT

                       *          
        486 TAAAATTTATTATTATATTTTT
          1 TAAAATTTATTTTTATATTTTT

                        * *       
        508 TAAAA-TTATTTATGTATTTTT
          1 TAAAATTTATTTTTATATTTTT

        529 ATATATTCGT


Statistics
Matches: 59,  Mismatches: 6, Indels: 10
        0.79            0.08        0.13

Matches are distributed among these distances:
  21   13  0.22
  22    9  0.15
  23   14  0.24
  24    3  0.05
  25    6  0.10
  26   14  0.24

ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62


Consensus pattern (22 bp):   
TAAAATTTATTTTTATATTTTT

Found at i:504 original size:21 final size:20

Alignment explanation


    Indices: 471--528  Score: 73
    Period size: 22  Copynumber: 2.8  Consensus size: 20

        461 GAAAATATTT

                                
        471 ATTTTTATATA-TTTTTAAA
          1 ATTTTTATATATTTTTTAAA

                                  
        490 ATTTATTATTATATTTTTTAAA
          1 ATTT-TTA-TATATTTTTTAAA

                     *       
        512 ATTATTTATGTATTTTT
          1 ATT-TTTATATATTTTT

        529 ATATATTCGT


Statistics
Matches: 34,  Mismatches: 1, Indels: 6
        0.83            0.02        0.15

Matches are distributed among these distances:
  19    4  0.12
  20    3  0.09
  21   12  0.35
  22   14  0.41
  23    1  0.03

ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66


Consensus pattern (20 bp):   
ATTTTTATATATTTTTTAAA
Done.