Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012078.1 Kokia drynarioides strain JFW-HI SEQ_127076, 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: 33524
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32

Warning! 50 characters in sequence are not A, C, G, or T


Found at i:64 original size:10 final size:10

Alignment explanation


    Indices: 28--71  Score: 52
    Period size: 10  Copynumber: 4.4  Consensus size: 10

         18 TATGCATAGG

                 *    
         28 TAAATGAAAA
          1 TAAATAAAAA

                    * 
         38 TAAATAAATA
          1 TAAATAAAAA

             **       
         48 TGTATAAAAA
          1 TAAATAAAAA

                      
         58 TAAATAAAAA
          1 TAAATAAAAA

                
         68 TAAA
          1 TAAA

         72 AATTTTATTT


Statistics
Matches: 27,  Mismatches: 7, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
  10   27  1.00

ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25


Consensus pattern (10 bp):   
TAAATAAAAA

Found at i:1319 original size:31 final size:30

Alignment explanation


    Indices: 1284--1358  Score: 96
    Period size: 31  Copynumber: 2.5  Consensus size: 30

       1274 TTACTATAAT

                       *       * *         
       1284 ATTTGATACTTGAACTTGATATTTTTTCTTA
          1 ATTTGATACTTAAACTTGACACTTTTT-TTA

                 *                        
       1315 ATTTGGTACTTAAACTTGACACTTTTTTTA
          1 ATTTGATACTTAAACTTGACACTTTTTTTA

             *            
       1345 AGTTGATACTTAAA
          1 ATTTGATACTTAAA

       1359 TTTTTTGGGG


Statistics
Matches: 38,  Mismatches: 6, Indels: 1
        0.84            0.13        0.02

Matches are distributed among these distances:
  30   15  0.39
  31   23  0.61

ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49


Consensus pattern (30 bp):   
ATTTGATACTTAAACTTGACACTTTTTTTA

Found at i:16726 original size:27 final size:27

Alignment explanation


    Indices: 16696--16748  Score: 70
    Period size: 27  Copynumber: 2.0  Consensus size: 27

      16686 TAGAGGGAAG

                               *       
      16696 AAAAAAAGAAATTGAAAGAGAAAAGAA
          1 AAAAAAAGAAATTGAAAGAAAAAAGAA

                 *    *    *          
      16723 AAAAACAGAACTTGAGAGAAAAAAGA
          1 AAAAAAAGAAATTGAAAGAAAAAAGA

      16749 GAGAAGAGTT


Statistics
Matches: 22,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  27   22  1.00

ACGTcount: A:0.70, C:0.04, G:0.19, T:0.08


Consensus pattern (27 bp):   
AAAAAAAGAAATTGAAAGAAAAAAGAA

Found at i:26368 original size:36 final size:36

Alignment explanation


    Indices: 26328--26399  Score: 144
    Period size: 36  Copynumber: 2.0  Consensus size: 36

      26318 ACCATCGGTT

                                                
      26328 GAAGAAGCTTCGATTCTGGAGTTAAAGCCATTGCGA
          1 GAAGAAGCTTCGATTCTGGAGTTAAAGCCATTGCGA

                                                
      26364 GAAGAAGCTTCGATTCTGGAGTTAAAGCCATTGCGA
          1 GAAGAAGCTTCGATTCTGGAGTTAAAGCCATTGCGA

      26400 ACACAAATGA


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  36   36  1.00

ACGTcount: A:0.31, C:0.17, G:0.28, T:0.25


Consensus pattern (36 bp):   
GAAGAAGCTTCGATTCTGGAGTTAAAGCCATTGCGA

Found at i:29209 original size:24 final size:24

Alignment explanation


    Indices: 29182--29227  Score: 58
    Period size: 24  Copynumber: 1.9  Consensus size: 24

      29172 CTTTGCAAAT

                *                    
      29182 TTTTCTGTTAATTT-TTGTCTTTCA
          1 TTTTATGTTAATTTGTT-TCTTTCA

                  *               
      29206 TTTTATTTTAATTTGTTTCTTT
          1 TTTTATGTTAATTTGTTTCTTT

      29228 AGTTTCTACA


Statistics
Matches: 19,  Mismatches: 2, Indels: 2
        0.83            0.09        0.09

Matches are distributed among these distances:
  24   17  0.89
  25    2  0.11

ACGTcount: A:0.13, C:0.09, G:0.07, T:0.72


Consensus pattern (24 bp):   
TTTTATGTTAATTTGTTTCTTTCA

Found at i:31009 original size:15 final size:15

Alignment explanation


    Indices: 30988--31037  Score: 59
    Period size: 15  Copynumber: 3.3  Consensus size: 15

      30978 GAGGGTGTTG

                           
      30988 AAGAAGAAG-AGAAA
          1 AAGAAGAAGAAGAAA

                    *       
      31002 AGAGAAGATGAAGAAA
          1 A-AGAAGAAGAAGAAA

                            
      31018 AAGAAG-AGAAGGAAA
          1 AAGAAGAAGAA-GAAA

                 
      31033 AAGAA
          1 AAGAA

      31038 CAACAACAAG


Statistics
Matches: 31,  Mismatches: 2, Indels: 5
        0.82            0.05        0.13

Matches are distributed among these distances:
  14    4  0.13
  15   21  0.68
  16    6  0.19

ACGTcount: A:0.68, C:0.00, G:0.30, T:0.02


Consensus pattern (15 bp):   
AAGAAGAAGAAGAAA

Found at i:31014 original size:18 final size:17

Alignment explanation


    Indices: 30987--31021  Score: 52
    Period size: 18  Copynumber: 2.0  Consensus size: 17

      30977 TGAGGGTGTT

                              
      30987 GAAGAAGAAGAGAAAAGA
          1 GAAGAAGAAGA-AAAAGA

                 *           
      31005 GAAGATGAAGAAAAAGA
          1 GAAGAAGAAGAAAAAGA

      31022 AGAGAAGGAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  17    6  0.38
  18   10  0.62

ACGTcount: A:0.66, C:0.00, G:0.31, T:0.03


Consensus pattern (17 bp):   
GAAGAAGAAGAAAAAGA
Done.