Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013726.1 Kokia drynarioides strain JFW-HI SEQ_128754, 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: 2963
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.34


Found at i:959 original size:20 final size:20

Alignment explanation


    Indices: 934--981  Score: 96
    Period size: 20  Copynumber: 2.4  Consensus size: 20

        924 TCATAGAATA

                                
        934 ACTAAAGTGAAGTTTAAAAT
          1 ACTAAAGTGAAGTTTAAAAT

                                
        954 ACTAAAGTGAAGTTTAAAAT
          1 ACTAAAGTGAAGTTTAAAAT

                    
        974 ACTAAAGT
          1 ACTAAAGT

        982 TGTGACTAAT


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   28  1.00

ACGTcount: A:0.50, C:0.06, G:0.15, T:0.29


Consensus pattern (20 bp):   
ACTAAAGTGAAGTTTAAAAT

Found at i:1406 original size:22 final size:22

Alignment explanation


    Indices: 1378--1469  Score: 65
    Period size: 21  Copynumber: 4.4  Consensus size: 22

       1368 TATATGTATA

                                  
       1378 ATATTATATTCAATTTATTTAT
          1 ATATTATATTCAATTTATTTAT

                       *        * 
       1400 ATATTATA-TCTATTT-TTTTT
          1 ATATTATATTCAATTTATTTAT

                           *        
       1420 ATA-TATATTCTAA-ATATTTGAT
          1 ATATTATATTC-AATTTATTT-AT

                               *   
       1442 ATATT-T-TT-ATATTTATATAT
          1 ATATTATATTCA-ATTTATTTAT

                     
       1462 -TATTATAT
          1 ATATTATAT

       1470 ATATTTTTAT


Statistics
Matches: 54,  Mismatches: 7, Indels: 19
        0.68            0.09        0.24

Matches are distributed among these distances:
  19    9  0.17
  20   14  0.26
  21   17  0.31
  22   13  0.24
  23    1  0.02

ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61


Consensus pattern (22 bp):   
ATATTATATTCAATTTATTTAT

Found at i:1474 original size:20 final size:20

Alignment explanation


    Indices: 1393--1475  Score: 59
    Period size: 20  Copynumber: 4.2  Consensus size: 20

       1383 ATATTCAATT

                             *  
       1393 TATTTATATATTA-TATCTA
          1 TATTTATATATTATTATATA

              *   *          *  * 
       1412 TTTTTTTTATATATATTCTAAA
          1 -TATTTATATAT-TATTATATA

                                 
       1434 TATTTGATATA-T-TT-T-TA
          1 TATTT-ATATATTATTATATA

                                
       1451 TATTTATATATTATTATATA
          1 TATTTATATATTATTATATA

                 
       1471 TATTT
          1 TATTT

       1476 TTATTTCTAT


Statistics
Matches: 48,  Mismatches: 8, Indels: 14
        0.69            0.11        0.20

Matches are distributed among these distances:
  16    5  0.10
  17    7  0.15
  18    3  0.06
  19    3  0.06
  20   17  0.35
  21    6  0.12
  22    7  0.15

ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63


Consensus pattern (20 bp):   
TATTTATATATTATTATATA
Done.