Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000047.1 Kokia drynarioides strain JFW-HI SEQ_91433, 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, 705

Length: 1176
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37


Found at i:583 original size:19 final size:19

Alignment explanation


    Indices: 561--615  Score: 58
    Period size: 20  Copynumber: 2.9  Consensus size: 19

        551 TTTTTAATTT

                            * *
        561 TTTTAAAATATTTTTTCTC
          1 TTTTAAAATATTTTTTATA

                 *              
        580 TTTTCGAAATATTTTTTATA
          1 TTTT-AAAATATTTTTTATA

                *            
        600 TTTTCAAAT-TTTTTTA
          1 TTTTAAAATATTTTTTA

        616 AAATTATATT


Statistics
Matches: 31,  Mismatches: 4, Indels: 3
        0.82            0.11        0.08

Matches are distributed among these distances:
  18    7  0.23
  19    8  0.26
  20   16  0.52

ACGTcount: A:0.27, C:0.07, G:0.02, T:0.64


Consensus pattern (19 bp):   
TTTTAAAATATTTTTTATA

Found at i:649 original size:57 final size:57

Alignment explanation


    Indices: 588--700  Score: 156
    Period size: 57  Copynumber: 2.0  Consensus size: 57

        578 TCTTTTCGAA

                                   *  **    *  *                      
        588 ATATTTTTTATA-TTTTCAAATTTTTTTAAAATTATATTTTCGAAATATTTTTTACAT
          1 ATATTTTTTATATTTTTCAAA-TATTAAAAAAATACATTTTCGAAATATTTTTTACAT

                             *                                      
        645 ATATTTTTTATATTTTTGAAATATTAAAAAAATACATTTTCGAAATATTTTTTACA
          1 ATATTTTTTATATTTTTCAAATATTAAAAAAATACATTTTCGAAATATTTTTTACA

        701 AATTAAAAAT


Statistics
Matches: 49,  Mismatches: 6, Indels: 2
        0.86            0.11        0.04

Matches are distributed among these distances:
  57   42  0.86
  58    7  0.14

ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55


Consensus pattern (57 bp):   
ATATTTTTTATATTTTTCAAATATTAAAAAAATACATTTTCGAAATATTTTTTACAT

Found at i:706 original size:35 final size:36

Alignment explanation


    Indices: 654--740  Score: 106
    Period size: 36  Copynumber: 2.4  Consensus size: 36

        644 TATATTTTTT

                                                
        654 ATATTTTTGAAATATTAAAAA-AATACATTTTCGAA
          1 ATATTTTTGAAATATTAAAAATAATACATTTTCGAA

                    *              **  *     *   
        689 ATATTTTTTACAA-ATTAAAAATCTTATATTTTTGAA
          1 ATATTTTTGA-AATATTAAAAATAATACATTTTCGAA

                            
        725 ATATTTTTGAAATATT
          1 ATATTTTTGAAATATT

        741 TTTTTACAAA


Statistics
Matches: 43,  Mismatches: 6, Indels: 5
        0.80            0.11        0.09

Matches are distributed among these distances:
  35   19  0.44
  36   24  0.56

ACGTcount: A:0.44, C:0.05, G:0.05, T:0.47


Consensus pattern (36 bp):   
ATATTTTTGAAATATTAAAAATAATACATTTTCGAA

Found at i:744 original size:12 final size:11

Alignment explanation


    Indices: 714--743  Score: 60
    Period size: 11  Copynumber: 2.7  Consensus size: 11

        704 TAAAAATCTT

                       
        714 ATATTTTTGAA
          1 ATATTTTTGAA

                       
        725 ATATTTTTGAA
          1 ATATTTTTGAA

                    
        736 ATATTTTT
          1 ATATTTTT

        744 TTACAAATGA


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   19  1.00

ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60


Consensus pattern (11 bp):   
ATATTTTTGAA
Done.