Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008696.1 Kokia drynarioides strain JFW-HI SEQ_123378, 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: 20973
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35


Found at i:3263 original size:32 final size:33

Alignment explanation


    Indices: 3199--3263  Score: 87
    Period size: 32  Copynumber: 2.0  Consensus size: 33

       3189 GTCTGCTTAG

                   * *                 *     
       3199 TATTGCTTATCAAAATCACTTTTGAGATAAAAA
          1 TATTGCTAAGCAAAATCACTTTTGAGACAAAAA

                             *               
       3232 TATTGCTAAGCAAAAT-TCTTTTGAGACAAAAA
          1 TATTGCTAAGCAAAATCACTTTTGAGACAAAAA

       3264 ATGCTTTGGA


Statistics
Matches: 28,  Mismatches: 4, Indels: 1
        0.85            0.12        0.03

Matches are distributed among these distances:
  32   14  0.50
  33   14  0.50

ACGTcount: A:0.43, C:0.12, G:0.11, T:0.34


Consensus pattern (33 bp):   
TATTGCTAAGCAAAATCACTTTTGAGACAAAAA

Found at i:3264 original size:33 final size:33

Alignment explanation


    Indices: 3199--3265  Score: 82
    Period size: 33  Copynumber: 2.0  Consensus size: 33

       3189 GTCTGCTTAG

                   * *                 *     
       3199 TATTGCTTATCAAAATCACTTTTGAGATAAAAA
          1 TATTGCTAAGCAAAATCACTTTTGAGAAAAAAA

                             *                
       3232 TATTGCTAAGCAAAAT-TCTTTTGAGACAAAAAA
          1 TATTGCTAAGCAAAATCACTTTTGAGA-AAAAAA

             
       3265 T
          1 T

       3266 GCTTTGGAAA


Statistics
Matches: 29,  Mismatches: 4, Indels: 2
        0.83            0.11        0.06

Matches are distributed among these distances:
  32    9  0.31
  33   20  0.69

ACGTcount: A:0.43, C:0.12, G:0.10, T:0.34


Consensus pattern (33 bp):   
TATTGCTAAGCAAAATCACTTTTGAGAAAAAAA

Found at i:15648 original size:32 final size:31

Alignment explanation


    Indices: 15607--15666  Score: 84
    Period size: 32  Copynumber: 1.9  Consensus size: 31

      15597 CATATCGTAA

                      *   *                
      15607 TTTTACATTATAATTATTTTGTAATATAGGG
          1 TTTTACATTACAATCATTTTGTAATATAGGG

                        *                
      15638 TTTTCACATTACGATCATTTTGTAATATA
          1 TTTT-ACATTACAATCATTTTGTAATATA

      15667 AGGTATAATT


Statistics
Matches: 25,  Mismatches: 3, Indels: 1
        0.86            0.10        0.03

Matches are distributed among these distances:
  31    4  0.16
  32   21  0.84

ACGTcount: A:0.32, C:0.08, G:0.10, T:0.50


Consensus pattern (31 bp):   
TTTTACATTACAATCATTTTGTAATATAGGG

Found at i:20262 original size:6 final size:6

Alignment explanation


    Indices: 20251--20278  Score: 56
    Period size: 6  Copynumber: 4.7  Consensus size: 6

      20241 GTACCTATAA

                                            
      20251 ATAAAT ATAAAT ATAAAT ATAAAT ATAA
          1 ATAAAT ATAAAT ATAAAT ATAAAT ATAA

      20279 TAATACAATA


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   22  1.00

ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32


Consensus pattern (6 bp):   
ATAAAT

Done.