Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009186.1 Kokia drynarioides strain JFW-HI SEQ_123891, 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: 11325
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.36


Found at i:356 original size:21 final size:22

Alignment explanation


    Indices: 332--374  Score: 61
    Period size: 22  Copynumber: 2.0  Consensus size: 22

        322 ATAATTGGCA

                      *           
        332 TTATTT-TAATTATTTTTTATT
          1 TTATTTGTAACTATTTTTTATT

                    *             
        353 TTATTTGTTACTATTTTTTATT
          1 TTATTTGTAACTATTTTTTATT

        375 ATTTACTATA


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  21    6  0.32
  22   13  0.68

ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74


Consensus pattern (22 bp):   
TTATTTGTAACTATTTTTTATT

Found at i:373 original size:17 final size:17

Alignment explanation


    Indices: 351--404  Score: 58
    Period size: 17  Copynumber: 3.2  Consensus size: 17

        341 TTATTTTTTA

                             
        351 TTTTATTTGTTACTATT
          1 TTTTATTTGTTACTATT

                               
        368 TTTTATTAT-TTACTATAT
          1 TTTTATT-TGTTACTAT-T

              *   *          
        386 TTCTATATGTTA-TATT
          1 TTTTATTTGTTACTATT

               
        402 TTT
          1 TTT

        405 ATGCTATTAT


Statistics
Matches: 31,  Mismatches: 3, Indels: 7
        0.76            0.07        0.17

Matches are distributed among these distances:
  16    3  0.10
  17   18  0.58
  18   10  0.32

ACGTcount: A:0.22, C:0.06, G:0.04, T:0.69


Consensus pattern (17 bp):   
TTTTATTTGTTACTATT

Found at i:4400 original size:20 final size:20

Alignment explanation


    Indices: 4375--4432  Score: 55
    Period size: 20  Copynumber: 2.8  Consensus size: 20

       4365 CGGCCACAAG

                                 
       4375 TAAAAAAATAAATAAATT-TA
          1 TAAAAAAATAAA-AAATTATA

                  **  *         
       4395 TAAAAACTTAGAAAATTATA
          1 TAAAAAAATAAAAAATTATA

                              
       4415 TAAAAAAACTTAAAAAAT
          1 TAAAAAAA--TAAAAAAT

       4433 CATTAAAATT


Statistics
Matches: 29,  Mismatches: 6, Indels: 4
        0.74            0.15        0.10

Matches are distributed among these distances:
  19    5  0.17
  20   17  0.59
  22    7  0.24

ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28


Consensus pattern (20 bp):   
TAAAAAAATAAAAAATTATA

Found at i:4424 original size:22 final size:21

Alignment explanation


    Indices: 4396--4440  Score: 63
    Period size: 22  Copynumber: 2.1  Consensus size: 21

       4386 ATAAATTTAT

                     *     *      
       4396 AAAAACTTAGAAAATTATATAA
          1 AAAAACTTAAAAAATCAT-TAA

                                 
       4418 AAAAACTTAAAAAATCATTAA
          1 AAAAACTTAAAAAATCATTAA

              
       4439 AA
          1 AA

       4441 TTAAAAAAAA


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  21    5  0.24
  22   16  0.76

ACGTcount: A:0.67, C:0.07, G:0.02, T:0.24


Consensus pattern (21 bp):   
AAAAACTTAAAAAATCATTAA

Found at i:4592 original size:16 final size:16

Alignment explanation


    Indices: 4572--4605  Score: 50
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       4562 AAAAGAAAAG

                             
       4572 AAAAAAACGTAAAAATT
          1 AAAAAAA-GTAAAAATT

                   *        
       4589 AAAAAAATTAAAAATT
          1 AAAAAAAGTAAAAATT

             
       4605 A
          1 A

       4606 TTCTATTTAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  16    9  0.56
  17    7  0.44

ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21


Consensus pattern (16 bp):   
AAAAAAAGTAAAAATT
Done.