Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014986.1 Kokia drynarioides strain JFW-HI SEQ_130030, 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: 14926
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32

Warning! 200 characters in sequence are not A, C, G, or T


Found at i:1331 original size:19 final size:20

Alignment explanation


    Indices: 1309--1347  Score: 62
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       1299 TCAAAGATTG

                                
       1309 ATATTTA-ATTTAAGTTCGA
          1 ATATTTATATTTAAGTTCGA

                    *           
       1328 ATATTTATTTTTAAGTTCGA
          1 ATATTTATATTTAAGTTCGA

       1348 GTTGATTATG


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  19    7  0.39
  20   11  0.61

ACGTcount: A:0.33, C:0.05, G:0.10, T:0.51


Consensus pattern (20 bp):   
ATATTTATATTTAAGTTCGA

Found at i:8222 original size:20 final size:21

Alignment explanation


    Indices: 8156--8224  Score: 95
    Period size: 21  Copynumber: 3.3  Consensus size: 21

       8146 TCACTTCGTT

                                 
       8156 TCTTTTTGTCCAAGTTACTTC
          1 TCTTTTTGTCCAAGTTACTTC

                            *    
       8177 TCTTTTTGTCCAAGTTGCTTC
          1 TCTTTTTGTCCAAGTTACTTC

                      *  * *     
       8198 TCTTTTTGTCTAACTCACTTC
          1 TCTTTTTGTCCAAGTTACTTC

                   
       8219 -CTTTTT
          1 TCTTTTT

       8225 TCTTTGTGAG


Statistics
Matches: 43,  Mismatches: 5, Indels: 1
        0.88            0.10        0.02

Matches are distributed among these distances:
  20    6  0.14
  21   37  0.86

ACGTcount: A:0.12, C:0.25, G:0.09, T:0.55


Consensus pattern (21 bp):   
TCTTTTTGTCCAAGTTACTTC

Found at i:10563 original size:18 final size:18

Alignment explanation


    Indices: 10530--10605  Score: 104
    Period size: 18  Copynumber: 4.4  Consensus size: 18

      10520 AAGGTTTTCT

                              
      10530 TATTGATGATA-T--CGA
          1 TATTGATGATAGTGACGA

                              
      10545 TATTGATGATAGTGACGA
          1 TATTGATGATAGTGACGA

                    *        *
      10563 TATTGATGCTAGTGACGC
          1 TATTGATGATAGTGACGA

                             *
      10581 TATTGATGATAGTGACGC
          1 TATTGATGATAGTGACGA

                   
      10599 TATTGAT
          1 TATTGAT

      10606 CGTGACCTTG


Statistics
Matches: 55,  Mismatches: 3, Indels: 3
        0.90            0.05        0.05

Matches are distributed among these distances:
  15   11  0.20
  16    1  0.02
  18   43  0.78

ACGTcount: A:0.29, C:0.09, G:0.25, T:0.37


Consensus pattern (18 bp):   
TATTGATGATAGTGACGA

Found at i:12194 original size:20 final size:22

Alignment explanation


    Indices: 12154--12194  Score: 59
    Period size: 22  Copynumber: 2.0  Consensus size: 22

      12144 TTAAAAAGTA

                      *           
      12154 ATAGTGTAAAGACTGATTGACT
          1 ATAGTGTAAACACTGATTGACT

                                 
      12176 ATAGTGTAAACA-T-ATTGAC
          1 ATAGTGTAAACACTGATTGAC

      12195 AGTACAGTGA


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  20    6  0.33
  21    1  0.06
  22   11  0.61

ACGTcount: A:0.39, C:0.10, G:0.20, T:0.32


Consensus pattern (22 bp):   
ATAGTGTAAACACTGATTGACT

Found at i:12224 original size:170 final size:170

Alignment explanation


    Indices: 11942--12251  Score: 593
    Period size: 170  Copynumber: 1.8  Consensus size: 170

      11932 TACCAGGCAC

                                                                             
      11942 GAGTTATTGTTGATATTGTTTGGATTATCGGGTTAAAAAGTAATAGTGTAAAGACTGATTGACTA
          1 GAGTTATTGTTGATATTGTTTGGATTATCGGGTTAAAAAGTAATAGTGTAAAGACTGATTGACTA

                      *                                                      
      12007 AAGTGTAAACTTATTGACAGTACAGTGATCAAATTATACATTACTAATAGTTGAGTGATCAAATT
         66 AAGTGTAAACATATTGACAGTACAGTGATCAAATTATACATTACTAATAGTTGAGTGATCAAATT

                                                    
      12072 GTAAACTTATTTACAGTAGCTTTAGTAGGATTTGAGGCTT
        131 GTAAACTTATTTACAGTAGCTTTAGTAGGATTTGAGGCTT

                                                                             
      12112 GAGTTATTGTTGATATTGTTTGGATTATCGGGTTAAAAAGTAATAGTGTAAAGACTGATTGACTA
          1 GAGTTATTGTTGATATTGTTTGGATTATCGGGTTAAAAAGTAATAGTGTAAAGACTGATTGACTA

            *                                                                
      12177 TAGTGTAAACATATTGACAGTACAGTGATCAAATTATACATTACTAATAGTTGAGTGATCAAATT
         66 AAGTGTAAACATATTGACAGTACAGTGATCAAATTATACATTACTAATAGTTGAGTGATCAAATT

                 *    
      12242 GTAAATTTAT
        131 GTAAACTTAT

      12252 CAGTCCCCAC


Statistics
Matches: 137,  Mismatches: 3, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
 170  137  1.00

ACGTcount: A:0.35, C:0.08, G:0.20, T:0.37


Consensus pattern (170 bp):   
GAGTTATTGTTGATATTGTTTGGATTATCGGGTTAAAAAGTAATAGTGTAAAGACTGATTGACTA
AAGTGTAAACATATTGACAGTACAGTGATCAAATTATACATTACTAATAGTTGAGTGATCAAATT
GTAAACTTATTTACAGTAGCTTTAGTAGGATTTGAGGCTT

Found at i:14912 original size:22 final size:23

Alignment explanation


    Indices: 14861--14926  Score: 89
    Period size: 23  Copynumber: 2.9  Consensus size: 23

      14851 TGCTGGGAAA

                 *       *         
      14861 CAGTAAGCACACACAGTGCAATC
          1 CAGTAGGCACACATAGTGCAATC

                                   
      14884 CAGTAGGCACACATAGTGCAAT-
          1 CAGTAGGCACACATAGTGCAATC

                    *       *    
      14906 CAGTAGGCGCACATAGCGCAA
          1 CAGTAGGCACACATAGTGCAA


Statistics
Matches: 39,  Mismatches: 4, Indels: 1
        0.89            0.09        0.02

Matches are distributed among these distances:
  22   19  0.49
  23   20  0.51

ACGTcount: A:0.36, C:0.27, G:0.23, T:0.14


Consensus pattern (23 bp):   
CAGTAGGCACACATAGTGCAATC
Done.