Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009168.1 Kokia drynarioides strain JFW-HI SEQ_123873, 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: 7322
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33


Found at i:166 original size:46 final size:46

Alignment explanation


    Indices: 99--203  Score: 156
    Period size: 46  Copynumber: 2.3  Consensus size: 46

         89 AAATGAAATA

                   *      * *         *                   
         99 TGGGTTTCTGAAATTTGAATTTTTTTTAAAATCAAACCTAAAAACT
          1 TGGGTTTTTGAAATCTAAATTTTTTTAAAAATCAAACCTAAAAACT

                                                 *  *     
        145 TGGGTTTTTGAAATCTAAATTTTTTTAAAAATCAAACTTAGAAACT
          1 TGGGTTTTTGAAATCTAAATTTTTTTAAAAATCAAACCTAAAAACT

                         
        191 TGGGTTTTTGAAA
          1 TGGGTTTTTGAAA

        204 CCTGTTCTTT


Statistics
Matches: 53,  Mismatches: 6, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  46   53  1.00

ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42


Consensus pattern (46 bp):   
TGGGTTTTTGAAATCTAAATTTTTTTAAAAATCAAACCTAAAAACT

Found at i:4416 original size:125 final size:125

Alignment explanation


    Indices: 4189--4438  Score: 392
    Period size: 125  Copynumber: 2.0  Consensus size: 125

       4179 AGTAGGTTAG

                                     *             *                         
       4189 TGATCTGTTGGTTTCATACCTAGCAGATTAAACTATTTTTCACACTTGAAGAACTTGAAATCAAA
          1 TGATCTGTTGGTTTCATACCTAGCAAATTAAACTATTTTGCACACTTGAAGAACTTGAAATCAAA

                              *                      *   *              
       4254 TATTTTCCTTATGTTTTCGTAGGATTTAGCTTAGATTTCTTGTTTGAATAAATTGTGTAA
         66 TATTTTCCTTATGTTTTCATAGGATTTAGCTTAGATTTCTTATTTAAATAAATTGTGTAA

                *                        *                      *           *
       4314 TGATTTGTTGGTTTCATACCTAGCAAATTGAACTATTTTGCACACTTGAAGAGCTTGAAATCAAG
          1 TGATCTGTTGGTTTCATACCTAGCAAATTAAACTATTTTGCACACTTGAAGAACTTGAAATCAAA

                  **                     *                              
       4379 TATTTTTGTTATGTTTTCATAGGATTTAGTTTAGATTTCTTATTTAAATAAATTGTGTAA
         66 TATTTTCCTTATGTTTTCATAGGATTTAGCTTAGATTTCTTATTTAAATAAATTGTGTAA

       4439 CCTATGTGTT


Statistics
Matches: 113,  Mismatches: 12, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
 125  113  1.00

ACGTcount: A:0.29, C:0.11, G:0.16, T:0.44


Consensus pattern (125 bp):   
TGATCTGTTGGTTTCATACCTAGCAAATTAAACTATTTTGCACACTTGAAGAACTTGAAATCAAA
TATTTTCCTTATGTTTTCATAGGATTTAGCTTAGATTTCTTATTTAAATAAATTGTGTAA

Found at i:5500 original size:14 final size:14

Alignment explanation


    Indices: 5481--5507  Score: 54
    Period size: 14  Copynumber: 1.9  Consensus size: 14

       5471 ACTTTACTTT

                          
       5481 ATTTTATTTTTATC
          1 ATTTTATTTTTATC

                         
       5495 ATTTTATTTTTAT
          1 ATTTTATTTTTAT

       5508 GCTTTCAAAC


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   13  1.00

ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74


Consensus pattern (14 bp):   
ATTTTATTTTTATC

Found at i:6188 original size:20 final size:20

Alignment explanation


    Indices: 6160--6197  Score: 58
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       6150 ATACCATTAC

                      *         
       6160 TTAGATTTTAGTTTTCAATT
          1 TTAGATTTTACTTTTCAATT

                *             
       6180 TTAGGTTTTACTTTTCAA
          1 TTAGATTTTACTTTTCAA

       6198 GTTGTGAAAT


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  20   16  1.00

ACGTcount: A:0.24, C:0.08, G:0.11, T:0.58


Consensus pattern (20 bp):   
TTAGATTTTACTTTTCAATT
Done.