Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008818.1 Kokia drynarioides strain JFW-HI SEQ_123502, 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: 10189
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.32


Found at i:336 original size:34 final size:34

Alignment explanation


    Indices: 265--354  Score: 92
    Period size: 34  Copynumber: 2.6  Consensus size: 34

        255 TCGATCGTGA

                   *      *       *         * 
        265 GCCCAGCTCTAGTTGGATAAACTAACGATGTTGT
          1 GCCCAGCACTAGTTAGATAAACCAACGATGTTCT

                   *               *           
        299 GCCCAGCGCTAGTTAGATAAACCGACGAATG-TCT
          1 GCCCAGCACTAGTTAGATAAACCAACG-ATGTTCT

                 *          *     
        333 GCCCAACACTAGTTAGTTAAAC
          1 GCCCAGCACTAGTTAGATAAAC

        355 TGACAATATA


Statistics
Matches: 47,  Mismatches: 8, Indels: 2
        0.82            0.14        0.04

Matches are distributed among these distances:
  34   44  0.94
  35    3  0.06

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


Consensus pattern (34 bp):   
GCCCAGCACTAGTTAGATAAACCAACGATGTTCT

Found at i:442 original size:34 final size:34

Alignment explanation


    Indices: 402--503  Score: 91
    Period size: 34  Copynumber: 3.0  Consensus size: 34

        392 AATCGACGAT

                                               
        402 GTTGTGCCCAGTGCTAGTCAGATAAACCGACGAAA
          1 GTTGTGCCCAGTGCTAGTCAGAT-AACCGACGAAA

                   *             *      *  *    
        437 G-TGTGCACAGCT-CTAGTCAAATTAACTGAAGAAA
          1 GTTGTGCCCAG-TGCTAGTCAGA-TAACCGACGAAA

                *   *  *       *             
        471 GTTGAGCCTAGCGCTAGTCGGATAACCGACGAA
          1 GTTGTGCCCAGTGCTAGTCAGATAACCGACGAA

        504 TCATAGTCAT


Statistics
Matches: 51,  Mismatches: 12, Indels: 9
        0.71            0.17        0.12

Matches are distributed among these distances:
  34   35  0.69
  35   16  0.31

ACGTcount: A:0.32, C:0.22, G:0.25, T:0.21


Consensus pattern (34 bp):   
GTTGTGCCCAGTGCTAGTCAGATAACCGACGAAA

Found at i:1915 original size:21 final size:23

Alignment explanation


    Indices: 1882--1929  Score: 57
    Period size: 22  Copynumber: 2.2  Consensus size: 23

       1872 CTTCTAACTA

                *                   
       1882 CTAATTAATATTTTAAAC-TT-CT
          1 CTAAATAATA-TTTAAACATTGCT

                                   
       1904 CTAAATAA-ATTTAAACATTGCT
          1 CTAAATAATATTTAAACATTGCT

                
       1926 CTAA
          1 CTAA

       1930 TAGATTAGAT


Statistics
Matches: 23,  Mismatches: 1, Indels: 4
        0.82            0.04        0.14

Matches are distributed among these distances:
  20    7  0.30
  21    3  0.13
  22   13  0.57

ACGTcount: A:0.42, C:0.15, G:0.02, T:0.42


Consensus pattern (23 bp):   
CTAAATAATATTTAAACATTGCT

Found at i:4440 original size:23 final size:23

Alignment explanation


    Indices: 4421--4470  Score: 73
    Period size: 23  Copynumber: 2.2  Consensus size: 23

       4411 TCCATTTACA

                                   
       4421 CATAAATCACATTAATATTTAAG
          1 CATAAATCACATTAATATTTAAG

                   * *      *      
       4444 CATAAATTATATTAATCTTTAAG
          1 CATAAATCACATTAATATTTAAG

                
       4467 CATA
          1 CATA

       4471 TAGCGCATGA


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


Consensus pattern (23 bp):   
CATAAATCACATTAATATTTAAG

Found at i:7894 original size:23 final size:23

Alignment explanation


    Indices: 7827--7887  Score: 104
    Period size: 23  Copynumber: 2.7  Consensus size: 23

       7817 CCAATTTACA

                       *           
       7827 CATAAATCACAATAATATTTAAG
          1 CATAAATCACATTAATATTTAAG

            *                      
       7850 TATAAATCACATTAATATTTAAG
          1 CATAAATCACATTAATATTTAAG

                           
       7873 CATAAATCACATTAA
          1 CATAAATCACATTAA

       7888 CCTTTAATCA


Statistics
Matches: 35,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  23   35  1.00

ACGTcount: A:0.51, C:0.13, G:0.03, T:0.33


Consensus pattern (23 bp):   
CATAAATCACATTAATATTTAAG

Found at i:7899 original size:23 final size:23

Alignment explanation


    Indices: 7827--7899  Score: 94
    Period size: 23  Copynumber: 3.2  Consensus size: 23

       7817 CCAATTTACA

                       *            
       7827 CATAAATCACAATAATATTTAAGT
          1 CATAAATCACATTAATATTTAA-T

                                  *
       7851 -ATAAATCACATTAATATTTAAG
          1 CATAAATCACATTAATATTTAAT

                           **      
       7873 CATAAATCACATTAACCTTTAAT
          1 CATAAATCACATTAATATTTAAT

                
       7896 CATA
          1 CATA

       7900 TAACGCATGA


Statistics
Matches: 43,  Mismatches: 5, Indels: 3
        0.84            0.10        0.06

Matches are distributed among these distances:
  23   43  1.00

ACGTcount: A:0.48, C:0.15, G:0.03, T:0.34


Consensus pattern (23 bp):   
CATAAATCACATTAATATTTAAT
Done.