Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012446.1 Kokia drynarioides strain JFW-HI SEQ_127450, 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: 12675
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34


Found at i:535 original size:19 final size:19

Alignment explanation


    Indices: 498--535  Score: 58
    Period size: 19  Copynumber: 2.0  Consensus size: 19

        488 AAAACTAATA

                         **    
        498 ACAAATTTGATTATGGTGG
          1 ACAAATTTGATTACAGTGG

                               
        517 ACAAATTTGATTACAGTGG
          1 ACAAATTTGATTACAGTGG

        536 GTGACAGTGG


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  19   17  1.00

ACGTcount: A:0.34, C:0.08, G:0.24, T:0.34


Consensus pattern (19 bp):   
ACAAATTTGATTACAGTGG

Found at i:1338 original size:31 final size:31

Alignment explanation


    Indices: 1300--1395  Score: 90
    Period size: 31  Copynumber: 3.2  Consensus size: 31

       1290 TTAATATAAC

                                           
       1300 ATTTGGTATTTGAATTTGATATTTTTTTTTA
          1 ATTTGGTATTTGAATTTGATATTTTTTTTTA

                     * *               *  * 
       1331 ATTTGGTATCTAAACTTT--T-TTTTTATTCA
          1 ATTTGGTATTTGAA-TTTGATATTTTTTTTTA

                    *          *       **  
       1360 ATTTGGTACTTGAATTTGACATTTTTTCCTA
          1 ATTTGGTATTTGAATTTGATATTTTTTTTTA

                 
       1391 ATTTG
          1 ATTTG

       1396 ATACCTAAAT


Statistics
Matches: 49,  Mismatches: 12, Indels: 8
        0.71            0.17        0.12

Matches are distributed among these distances:
  28    3  0.06
  29   19  0.39
  30    1  0.02
  31   23  0.47
  32    3  0.06

ACGTcount: A:0.23, C:0.07, G:0.11, T:0.58


Consensus pattern (31 bp):   
ATTTGGTATTTGAATTTGATATTTTTTTTTA

Found at i:3960 original size:24 final size:21

Alignment explanation


    Indices: 3907--3997  Score: 64
    Period size: 22  Copynumber: 4.2  Consensus size: 21

       3897 TTGCTACTAT

                 *                
       3907 TTTTGTTGT-TTTTGTTT-TTG
          1 TTTTGGTGTATTTT-TTTGTTG

                *                  
       3927 TTTTAGTGTTATTTTTTCTGTTG
          1 TTTTGGTG-TATTTTTT-TGTTG

                        *         
       3950 TTTTGGTTGT-TGTTTTTGTTG
          1 TTTTGG-TGTATTTTTTTGTTG

                                    
       3971 -TTTGGATGCTATTTTTTTGTGTG
          1 TTTTGG-TG-TATTTTTTTGT-TG

                
       3994 TTTT
          1 TTTT

       3998 TACTATTGTT


Statistics
Matches: 56,  Mismatches: 6, Indels: 14
        0.74            0.08        0.18

Matches are distributed among these distances:
  20   13  0.23
  21    9  0.16
  22   18  0.32
  23   11  0.20
  24    5  0.09

ACGTcount: A:0.04, C:0.02, G:0.22, T:0.71


Consensus pattern (21 bp):   
TTTTGGTGTATTTTTTTGTTG
Done.