Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014655.1 Kokia drynarioides strain JFW-HI SEQ_129694, 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: 16665
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:4380 original size:13 final size:14

Alignment explanation


    Indices: 4358--4387  Score: 53
    Period size: 13  Copynumber: 2.2  Consensus size: 14

       4348 TAAAAATTGA

                          
       4358 AAAAATAATATTAT
          1 AAAAATAATATTAT

                          
       4372 AAAAA-AATATTAT
          1 AAAAATAATATTAT

               
       4385 AAA
          1 AAA

       4388 TTTAATATAC


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13   11  0.69
  14    5  0.31

ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30


Consensus pattern (14 bp):   
AAAAATAATATTAT

Found at i:8980 original size:16 final size:17

Alignment explanation


    Indices: 8959--9026  Score: 84
    Period size: 16  Copynumber: 3.9  Consensus size: 17

       8949 ATAACAACAT

                             
       8959 CAAAACAGTAAAAAAA-
          1 CAAAACAGTAAAAAAAC

                   *         
       8975 CAAAACAATAAAAAAAC
          1 CAAAACAGTAAAAAAAC

                 *              
       8992 CAAAATAGTAAAACAGCAAC
          1 CAAAACAGTAAAA-A--AAC

                           
       9012 CAAAACAGTAAAAAA
          1 CAAAACAGTAAAAAA

       9027 GAACTAAAAC


Statistics
Matches: 44,  Mismatches: 4, Indels: 7
        0.80            0.07        0.13

Matches are distributed among these distances:
  16   15  0.34
  17   12  0.27
  18    1  0.02
  19    1  0.02
  20   15  0.34

ACGTcount: A:0.71, C:0.16, G:0.06, T:0.07


Consensus pattern (17 bp):   
CAAAACAGTAAAAAAAC

Found at i:14382 original size:27 final size:27

Alignment explanation


    Indices: 14352--14410  Score: 73
    Period size: 27  Copynumber: 2.2  Consensus size: 27

      14342 CAGAAATATA

                    *    *             
      14352 GCTCATTCTAACCTAGAACAAATTATT
          1 GCTCATTCGAACCCAGAACAAATTATT

                      *       * *      
      14379 GCTCATTCGAGCCCAGAATAGATTATT
          1 GCTCATTCGAACCCAGAACAAATTATT

                 
      14406 GCTCA
          1 GCTCA

      14411 CACATGAGCC


Statistics
Matches: 27,  Mismatches: 5, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  27   27  1.00

ACGTcount: A:0.32, C:0.24, G:0.14, T:0.31


Consensus pattern (27 bp):   
GCTCATTCGAACCCAGAACAAATTATT

Found at i:14576 original size:28 final size:28

Alignment explanation


    Indices: 14544--14618  Score: 87
    Period size: 28  Copynumber: 2.7  Consensus size: 28

      14534 ATATAGAGTT

                    *   *        *   *  
      14544 ATGCTCTTTCGAACCAGAACATAAAGTA
          1 ATGCTCTTCCGAGCCAGAACACAAAATA

                          *    *        
      14572 ATGCTCTTCCGAGCTAGAATACAAAATA
          1 ATGCTCTTCCGAGCCAGAACACAAAATA

                    *          
      14600 ATGCTCTTGCGAGCCAGAA
          1 ATGCTCTTCCGAGCCAGAA

      14619 AACAGAATGT


Statistics
Matches: 39,  Mismatches: 8, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  28   39  1.00

ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24


Consensus pattern (28 bp):   
ATGCTCTTCCGAGCCAGAACACAAAATA
Done.