Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008535.1 Kokia drynarioides strain JFW-HI SEQ_123212, 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: 12756
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37


Found at i:3845 original size:119 final size:118

Alignment explanation


    Indices: 3713--3950  Score: 449
    Period size: 119  Copynumber: 2.0  Consensus size: 118

       3703 TTCTAAATAA

                                      *                                      
       3713 TAATAATAATAAATCTAATCAATCTTTATTTAGAAAAATAATTCAAAAATTCATTAGGAATTTTT
          1 TAATAATAATAAATCTAATCAATCTTCATTTAGAAAAATAATTCAAAAATTCATTAGGAATTTTT

                    *                                             
       3778 TAAAATTAGTTTTTTTTAAACAATTTCATTATAGGTTATCATATTTGTTCTTTT
         66 TAAAATTAATTTTTTTT-AACAATTTCATTATAGGTTATCATATTTGTTCTTTT

                                                                             
       3832 TAATAATAATAAATCTAATCAATCTTCATTTAGAAAAATAATTCAAAAATTCATTAGGAATTTTT
          1 TAATAATAATAAATCTAATCAATCTTCATTTAGAAAAATAATTCAAAAATTCATTAGGAATTTTT

                                                                 
       3897 TAAAATTAATTTTTTTTAACAATTTCATTATAGGTTATCATATTTGTTCTTTT
         66 TAAAATTAATTTTTTTTAACAATTTCATTATAGGTTATCATATTTGTTCTTTT

             
       3950 T
          1 T

       3951 GACATGATGC


Statistics
Matches: 117,  Mismatches: 2, Indels: 1
        0.98            0.02        0.01

Matches are distributed among these distances:
 118   37  0.32
 119   80  0.68

ACGTcount: A:0.39, C:0.08, G:0.05, T:0.47


Consensus pattern (118 bp):   
TAATAATAATAAATCTAATCAATCTTCATTTAGAAAAATAATTCAAAAATTCATTAGGAATTTTT
TAAAATTAATTTTTTTTAACAATTTCATTATAGGTTATCATATTTGTTCTTTT

Found at i:4167 original size:22 final size:22

Alignment explanation


    Indices: 4142--4183  Score: 59
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       4132 GATTAGAAAT

                                   
       4142 TTAACTGA-ATAATTAAAAACAA
          1 TTAACT-ATATAATTAAAAACAA

                          *     
       4164 TTAACTATATAATTTAAAAC
          1 TTAACTATATAATTAAAAAC

       4184 TTGGGATAAA


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

Matches are distributed among these distances:
  21    1  0.06
  22   17  0.94

ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33


Consensus pattern (22 bp):   
TTAACTATATAATTAAAAACAA

Found at i:9709 original size:17 final size:17

Alignment explanation


    Indices: 9687--9720  Score: 68
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       9677 AAGTCATTTA

                             
       9687 AGATTAAGTTATTCAAG
          1 AGATTAAGTTATTCAAG

                             
       9704 AGATTAAGTTATTCAAG
          1 AGATTAAGTTATTCAAG

       9721 CTTAATCATT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.41, C:0.06, G:0.18, T:0.35


Consensus pattern (17 bp):   
AGATTAAGTTATTCAAG
Done.