Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006936.1 Kokia drynarioides strain JFW-HI SEQ_121539, 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: 8172
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35


Found at i:2630 original size:31 final size:29

Alignment explanation


    Indices: 2562--2633  Score: 81
    Period size: 31  Copynumber: 2.4  Consensus size: 29

       2552 TTGTCTCGGT

                          *           *  
       2562 ATTTTAGTCACTTATGTTTGAAATGTTAC
          1 ATTTTAGTCACTTACGTTTGAAATGTAAC

            *                     * *      
       2591 GTTTTAGTCACTTACGTTATCGTATTGTAAC
          1 ATTTTAGTCACTTACGTT-T-GAAATGTAAC

                        
       2622 ATTTTAGTCACT
          1 ATTTTAGTCACT

       2634 AAACGTTAAT


Statistics
Matches: 35,  Mismatches: 6, Indels: 2
        0.81            0.14        0.05

Matches are distributed among these distances:
  29   16  0.46
  30    1  0.03
  31   18  0.51

ACGTcount: A:0.25, C:0.14, G:0.14, T:0.47


Consensus pattern (29 bp):   
ATTTTAGTCACTTACGTTTGAAATGTAAC

Found at i:5853 original size:29 final size:33

Alignment explanation


    Indices: 5807--5873  Score: 81
    Period size: 29  Copynumber: 2.2  Consensus size: 33

       5797 CCAAAAACTG

                         *                   
       5807 TTGTTGTTTTATTGTTA-T-TTTT-T-ACTATT
          1 TTGTTGTTTTATTCTTATTGTTTTCTCACTATT

                                              
       5836 TTGTTGTTATT-TTCTTATTGTTTTCTCACTATT
          1 TTGTTGTT-TTATTCTTATTGTTTTCTCACTATT

                 
       5869 TTGTT
          1 TTGTT

       5874 ACCATTTCAC


Statistics
Matches: 32,  Mismatches: 1, Indels: 6
        0.82            0.03        0.15

Matches are distributed among these distances:
  29   13  0.41
  30    3  0.09
  31    4  0.12
  32    1  0.03
  33   11  0.34

ACGTcount: A:0.12, C:0.07, G:0.10, T:0.70


Consensus pattern (33 bp):   
TTGTTGTTTTATTCTTATTGTTTTCTCACTATT

Found at i:7934 original size:35 final size:35

Alignment explanation


    Indices: 7883--7956  Score: 123
    Period size: 34  Copynumber: 2.1  Consensus size: 35

       7873 TGAAGTAAGG

                       *                        
       7883 AAGGTTAGAATTTTTTTTTTTAAGGATTAAATAGTA
          1 AAGGTTAGAA-ATTTTTTTTTAAGGATTAAATAGTA

                                               
       7919 AAGG-TAGAAATTTTTTTTTAAGGATTAAATAGTA
          1 AAGGTTAGAAATTTTTTTTTAAGGATTAAATAGTA

                
       7953 AAGG
          1 AAGG

       7957 AGAGAAAATA


Statistics
Matches: 37,  Mismatches: 1, Indels: 2
        0.93            0.03        0.05

Matches are distributed among these distances:
  34   28  0.76
  35    5  0.14
  36    4  0.11

ACGTcount: A:0.39, C:0.00, G:0.19, T:0.42


Consensus pattern (35 bp):   
AAGGTTAGAAATTTTTTTTTAAGGATTAAATAGTA

Found at i:7963 original size:35 final size:34

Alignment explanation


    Indices: 7895--7963  Score: 120
    Period size: 34  Copynumber: 2.0  Consensus size: 34

       7885 GGTTAGAATT

                                        *     
       7895 TTTTTTTTTAAGGATTAAATAGTAAAGGTAGAAA
          1 TTTTTTTTTAAGGATTAAATAGTAAAGGGAGAAA

                                               
       7929 TTTTTTTTTAAGGATTAAATAGTAAAGGAGAGAAA
          1 TTTTTTTTTAAGGATTAAATAGTAAAGG-GAGAAA

       7964 ATATGGGGGA


Statistics
Matches: 33,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
  34   28  0.85
  35    5  0.15

ACGTcount: A:0.42, C:0.00, G:0.19, T:0.39


Consensus pattern (34 bp):   
TTTTTTTTTAAGGATTAAATAGTAAAGGGAGAAA
Done.