Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013378.1 Kokia drynarioides strain JFW-HI SEQ_128401, 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: 3770
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38


Found at i:375 original size:2 final size:2

Alignment explanation


    Indices: 370--420  Score: 102
    Period size: 2  Copynumber: 25.5  Consensus size: 2

        360 ATTTTTTTCC

                                                                          
        370 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                         
        412 TA TA TA TA T
          1 TA TA TA TA T

        421 CACCTTGGGT


Statistics
Matches: 49,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   49  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:1427 original size:123 final size:123

Alignment explanation


    Indices: 1208--1454  Score: 476
    Period size: 123  Copynumber: 2.0  Consensus size: 123

       1198 AAACGATATT

                                                                             
       1208 TATTTTGAACCTGATGAAATTAAAATCAATATAATTTTAATCAATATTTTATCGAATCGAAAAAC
          1 TATTTTGAACCTGATGAAATTAAAATCAATATAATTTTAATCAATATTTTATCGAATCGAAAAAC

                                                *                     
       1273 TTTATATTATTATATAAAATAAAAGTACAATTTTTTTATTGGGGGTACTAAGATAGCA
         66 TTTATATTATTATATAAAATAAAAGTACAATTTTTTAATTGGGGGTACTAAGATAGCA

                                                                             
       1331 TATTTTGAACCTGATGAAATTAAAATCAATATAATTTTAATCAATATTTTATCGAATCGAAAAAC
          1 TATTTTGAACCTGATGAAATTAAAATCAATATAATTTTAATCAATATTTTATCGAATCGAAAAAC

                                                                *     
       1396 TTTATATTATTATATAAAATAAAAGTACAATTTTTTAATTGGGGGTACTAAGGTAGCA
         66 TTTATATTATTATATAAAATAAAAGTACAATTTTTTAATTGGGGGTACTAAGATAGCA

             
       1454 T
          1 T

       1455 TGAAGTACCT


Statistics
Matches: 122,  Mismatches: 2, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
 123  122  1.00

ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39


Consensus pattern (123 bp):   
TATTTTGAACCTGATGAAATTAAAATCAATATAATTTTAATCAATATTTTATCGAATCGAAAAAC
TTTATATTATTATATAAAATAAAAGTACAATTTTTTAATTGGGGGTACTAAGATAGCA

Found at i:1997 original size:17 final size:18

Alignment explanation


    Indices: 1975--2008  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       1965 AATTATTTTT

                              
       1975 AAAAAT-TTTAATAAATA
          1 AAAAATATTTAATAAATA

                       *     
       1992 AAAAATATTTATTAAAT
          1 AAAAATATTTAATAAAT

       2009 TGTATTTGTA


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  17    6  0.40
  18    9  0.60

ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38


Consensus pattern (18 bp):   
AAAAATATTTAATAAATA

Found at i:2585 original size:19 final size:19

Alignment explanation


    Indices: 2548--2585  Score: 76
    Period size: 19  Copynumber: 2.0  Consensus size: 19

       2538 AAAATTGACT

                               
       2548 TAATCCTTTAAAATTATAA
          1 TAATCCTTTAAAATTATAA

                               
       2567 TAATCCTTTAAAATTATAA
          1 TAATCCTTTAAAATTATAA

       2586 AGATATAAAC


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   19  1.00

ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42


Consensus pattern (19 bp):   
TAATCCTTTAAAATTATAA

Found at i:2783 original size:21 final size:22

Alignment explanation


    Indices: 2759--2799  Score: 57
    Period size: 21  Copynumber: 1.9  Consensus size: 22

       2749 AATAAATAGT

                                  
       2759 ATAAATATTTA-AATATTATAC
          1 ATAAATATTTATAATATTATAC

                  *      *      
       2780 ATAAATGTTTATATTATTAT
          1 ATAAATATTTATAATATTAT

       2800 GACTGTAACT


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  21   10  0.59
  22    7  0.41

ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49


Consensus pattern (22 bp):   
ATAAATATTTATAATATTATAC
Done.