Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003304.1 Kokia drynarioides strain JFW-HI SEQ_115984, 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: 9336
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.35


Found at i:5261 original size:17 final size:17

Alignment explanation


    Indices: 5241--5273  Score: 50
    Period size: 17  Copynumber: 1.9  Consensus size: 17

       5231 AAATAAGCTT

                              
       5241 AAAA-ATTAAAGAAAATG
          1 AAAACATTAAA-AAAATG

                            
       5258 AAAACATTAAAAAAAT
          1 AAAACATTAAAAAAAT

       5274 AAATTTAAAA


Statistics
Matches: 15,  Mismatches: 0, Indels: 2
        0.88            0.00        0.12

Matches are distributed among these distances:
  17    9  0.60
  18    6  0.40

ACGTcount: A:0.73, C:0.03, G:0.06, T:0.18


Consensus pattern (17 bp):   
AAAACATTAAAAAAATG

Found at i:6618 original size:18 final size:17

Alignment explanation


    Indices: 6595--6628  Score: 50
    Period size: 18  Copynumber: 1.9  Consensus size: 17

       6585 AACATTATTT

                  *           
       6595 AATAATTTTTATTCTTAC
          1 AATAATATTT-TTCTTAC

                            
       6613 AATAATATTTTTCTTA
          1 AATAATATTTTTCTTA

       6629 TTTATAGATA


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  17    6  0.40
  18    9  0.60

ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56


Consensus pattern (17 bp):   
AATAATATTTTTCTTAC

Found at i:7740 original size:9 final size:9

Alignment explanation


    Indices: 7726--7754  Score: 51
    Period size: 9  Copynumber: 3.3  Consensus size: 9

       7716 TTCAAACTAC

                     
       7726 ATAAAATAA
          1 ATAAAATAA

                     
       7735 ATAAAATAA
          1 ATAAAATAA

                     
       7744 AT-AAATAA
          1 ATAAAATAA

               
       7752 ATA
          1 ATA

       7755 TTTTATTTGT


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
   8    8  0.42
   9   11  0.58

ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24


Consensus pattern (9 bp):   
ATAAAATAA

Found at i:9146 original size:21 final size:20

Alignment explanation


    Indices: 9104--9143  Score: 62
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       9094 AGACAAAAAC

                  *   *         
       9104 AAAAAATTATGTATCAAATT
          1 AAAAAAATATATATCAAATT

                                
       9124 AAAAAAATATATATCAAATT
          1 AAAAAAATATATATCAAATT

       9144 TAAGTACCAA


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  20   18  1.00

ACGTcount: A:0.60, C:0.05, G:0.03, T:0.33


Consensus pattern (20 bp):   
AAAAAAATATATATCAAATT
Done.