Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005724.1 Kokia drynarioides strain JFW-HI SEQ_119956, 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: 16580
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34


Found at i:6348 original size:15 final size:16

Alignment explanation


    Indices: 6328--6357  Score: 53
    Period size: 15  Copynumber: 1.9  Consensus size: 16

       6318 ATTTATCAAA

                            
       6328 AAAAATAAT-ATTTTT
          1 AAAAATAATCATTTTT

                           
       6343 AAAAATAATCATTTT
          1 AAAAATAATCATTTT

       6358 AACAATCTAT


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    9  0.64
  16    5  0.36

ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43


Consensus pattern (16 bp):   
AAAAATAATCATTTTT

Found at i:11337 original size:11 final size:11

Alignment explanation


    Indices: 11313--11349  Score: 56
    Period size: 11  Copynumber: 3.2  Consensus size: 11

      11303 TTCCATGTCA

                         
      11313 TTGATATATATTT
          1 TTGATAT-T-TTT

                       
      11326 TTGATATTTTT
          1 TTGATATTTTT

                       
      11337 TTGATATTTTT
          1 TTGATATTTTT

              
      11348 TT
          1 TT

      11350 TATCCTGAAC


Statistics
Matches: 24,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  11   16  0.67
  12    1  0.04
  13    7  0.29

ACGTcount: A:0.22, C:0.00, G:0.08, T:0.70


Consensus pattern (11 bp):   
TTGATATTTTT

Found at i:15279 original size:15 final size:15

Alignment explanation


    Indices: 15259--15290  Score: 55
    Period size: 15  Copynumber: 2.1  Consensus size: 15

      15249 TTGTTGATAA

                   *       
      15259 TAATAGCGTCAAAAG
          1 TAATAGCATCAAAAG

                           
      15274 TAATAGCATCAAAAG
          1 TAATAGCATCAAAAG

              
      15289 TA
          1 TA

      15291 TAATAGTAGT


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.50, C:0.12, G:0.16, T:0.22


Consensus pattern (15 bp):   
TAATAGCATCAAAAG

Found at i:15296 original size:17 final size:16

Alignment explanation


    Indices: 15258--15296  Score: 53
    Period size: 15  Copynumber: 2.4  Consensus size: 16

      15248 TTTGTTGATA

                    *       
      15258 ATAATAGCGTCAAAAG
          1 ATAATAGCATCAAAAG

                            
      15274 -TAATAGCATCAAAAG
          1 ATAATAGCATCAAAAG

                    
      15289 TATAATAG
          1 -ATAATAG

      15297 TAGTGCAAAA


Statistics
Matches: 20,  Mismatches: 1, Indels: 3
        0.83            0.04        0.12

Matches are distributed among these distances:
  15   14  0.70
  17    6  0.30

ACGTcount: A:0.51, C:0.10, G:0.15, T:0.23


Consensus pattern (16 bp):   
ATAATAGCATCAAAAG

Found at i:15872 original size:11 final size:11

Alignment explanation


    Indices: 15847--15894  Score: 53
    Period size: 11  Copynumber: 4.4  Consensus size: 11

      15837 GGCCTTTTTT

                  *   *
      15847 AATTTATTTTT
          1 AATTTAATTTA

                 *     
      15858 AATTTGATTTA
          1 AATTTAATTTA

                        
      15869 AA-TTAATATTA
          1 AATTTAAT-TTA

                       
      15880 AATTTAATTTA
          1 AATTTAATTTA

                
      15891 AATT
          1 AATT

      15895 AAAAAGTCCA


Statistics
Matches: 31,  Mismatches: 4, Indels: 4
        0.79            0.10        0.10

Matches are distributed among these distances:
  10    4  0.13
  11   22  0.71
  12    5  0.16

ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56


Consensus pattern (11 bp):   
AATTTAATTTA
Done.