Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008819.1 Kokia drynarioides strain JFW-HI SEQ_123503, 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: 15282
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34


Found at i:1994 original size:23 final size:23

Alignment explanation


    Indices: 1938--1987  Score: 73
    Period size: 23  Copynumber: 2.2  Consensus size: 23

       1928 TCATGCGCTA

                      *            
       1938 TATGCTTAAAGATTAATATAATT
          1 TATGCTTAAATATTAATATAATT

                             * *   
       1961 TATGCTTAAATATTAATGTGATT
          1 TATGCTTAAATATTAATATAATT

                
       1984 TATG
          1 TATG

       1988 TGTAAATGGA


Statistics
Matches: 24,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  23   24  1.00

ACGTcount: A:0.38, C:0.04, G:0.12, T:0.46


Consensus pattern (23 bp):   
TATGCTTAAATATTAATATAATT

Found at i:4517 original size:21 final size:23

Alignment explanation


    Indices: 4478--4526  Score: 59
    Period size: 22  Copynumber: 2.2  Consensus size: 23

       4468 TATCTAATCT

                                   
       4478 ATTAGAGCAATGTTTAAAT-TTA
          1 ATTAGAGCAATGTTTAAATATTA

            *                       
       4500 TTTAGAG-AA-GTTTAAAATATTA
          1 ATTAGAGCAATGTTT-AAATATTA

                 
       4522 ATTAG
          1 ATTAG

       4527 TAGTTAGAAG


Statistics
Matches: 23,  Mismatches: 2, Indels: 4
        0.79            0.07        0.14

Matches are distributed among these distances:
  20    4  0.17
  21    6  0.26
  22   13  0.57

ACGTcount: A:0.43, C:0.02, G:0.14, T:0.41


Consensus pattern (23 bp):   
ATTAGAGCAATGTTTAAATATTA

Found at i:6004 original size:34 final size:34

Alignment explanation


    Indices: 5905--6004  Score: 87
    Period size: 34  Copynumber: 2.9  Consensus size: 34

       5895 ATGACTATGA

                          *       *  *   *     
       5905 TTCGTCGG-TTATCCGACTAGCGCTAGGCTCAACT
          1 TTCGTCGGTTTATCTGACTAGCACTGGGCAC-ACT

               *  *   *  *             *       
       5939 TTCTTCAGTTAATTTGACTAG-AGCTGTGCACACT
          1 TTCGTCGGTTTATCTGACTAGCA-CTGGGCACACT

                                            
       5973 TTCGTCGGTTTATCTGACTAGCACTGGGCACA
          1 TTCGTCGGTTTATCTGACTAGCACTGGGCACA

       6005 ACATCGTCGA


Statistics
Matches: 49,  Mismatches: 14, Indels: 6
        0.71            0.20        0.09

Matches are distributed among these distances:
  34   34  0.69
  35   15  0.31

ACGTcount: A:0.20, C:0.25, G:0.22, T:0.33


Consensus pattern (34 bp):   
TTCGTCGGTTTATCTGACTAGCACTGGGCACACT

Found at i:6126 original size:34 final size:34

Alignment explanation


    Indices: 6050--6143  Score: 100
    Period size: 34  Copynumber: 2.8  Consensus size: 34

       6040 TATTTATATT

                     *        * *      *      
       6050 GTCAGTTTAACTAACTAGTGTTGGGCAGACATTC
          1 GTCAGTTTATCTAACTAGAGCTGGGCAAACATTC

               *              *                
       6084 GTCGGTTTATCTAACTAGCGCTGGGCACAACA-TC
          1 GTCAGTTTATCTAACTAGAGCTGGGCA-AACATTC

              *        *              
       6118 GTTAGTTTATCCAACTAGAGCTGGGC
          1 GTCAGTTTATCTAACTAGAGCTGGGC

       6144 TCACGATCGA


Statistics
Matches: 50,  Mismatches: 9, Indels: 2
        0.82            0.15        0.03

Matches are distributed among these distances:
  34   47  0.94
  35    3  0.06

ACGTcount: A:0.24, C:0.21, G:0.24, T:0.30


Consensus pattern (34 bp):   
GTCAGTTTATCTAACTAGAGCTGGGCAAACATTC

Found at i:6779 original size:7 final size:7

Alignment explanation


    Indices: 6767--6801  Score: 70
    Period size: 7  Copynumber: 5.0  Consensus size: 7

       6757 TAAATCAAAT

                   
       6767 GTGTTGA
          1 GTGTTGA

                   
       6774 GTGTTGA
          1 GTGTTGA

                   
       6781 GTGTTGA
          1 GTGTTGA

                   
       6788 GTGTTGA
          1 GTGTTGA

                   
       6795 GTGTTGA
          1 GTGTTGA

       6802 ATATTTAAAT


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   28  1.00

ACGTcount: A:0.14, C:0.00, G:0.43, T:0.43


Consensus pattern (7 bp):   
GTGTTGA

Found at i:8281 original size:12 final size:11

Alignment explanation


    Indices: 8253--8304  Score: 50
    Period size: 12  Copynumber: 4.4  Consensus size: 11

       8243 CAAAATTTTC

                       
       8253 TTTCTTTTCTT
          1 TTTCTTTTCTT

             *          
       8264 TCTCTTTCTCTT
          1 TTTCTTT-TCTT

                         
       8276 TTTCTTATTACTT
          1 TTTCTT-TT-CTT

                *       
       8289 TGTTTTTTTCTT
          1 T-TTCTTTTCTT

                
       8301 TTTC
          1 TTTC

       8305 AAATGATTGA


Statistics
Matches: 33,  Mismatches: 4, Indels: 8
        0.73            0.09        0.18

Matches are distributed among these distances:
  11    8  0.24
  12   14  0.42
  13    7  0.21
  14    4  0.12

ACGTcount: A:0.04, C:0.19, G:0.02, T:0.75


Consensus pattern (11 bp):   
TTTCTTTTCTT
Done.