Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009355.1 Kokia drynarioides strain JFW-HI SEQ_124062, 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: 15359
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33


Found at i:2963 original size:21 final size:21

Alignment explanation


    Indices: 2937--2992  Score: 85
    Period size: 21  Copynumber: 2.7  Consensus size: 21

       2927 AATAGTGCAG

                                 
       2937 ACTTCTATCGATACAAGTGAC
          1 ACTTCTATCGATACAAGTGAC

             *     *             
       2958 AGTTCTACCGATACAAGTGAC
          1 ACTTCTATCGATACAAGTGAC

            *             
       2979 TCTTCTATCGATAC
          1 ACTTCTATCGATAC

       2993 TAGAAACTCT


Statistics
Matches: 30,  Mismatches: 5, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  21   30  1.00

ACGTcount: A:0.30, C:0.25, G:0.14, T:0.30


Consensus pattern (21 bp):   
ACTTCTATCGATACAAGTGAC

Found at i:8966 original size:26 final size:23

Alignment explanation


    Indices: 8915--8986  Score: 67
    Period size: 26  Copynumber: 3.0  Consensus size: 23

       8905 ATTAAATAAA

                      *       *     
       8915 AAATAAAAGAGATAACAATAAAAT
          1 AAATAAAA-AAATAACAACAAAAT

                                   *  
       8939 AACATGAAAATAAATAACAACAAGAT
          1 AA-AT-AAAA-AAATAACAACAAAAT

                                   
       8965 AAATAAAAAAATAA-AA-AAAAT
          1 AAATAAAAAAATAACAACAAAAT

             
       8986 A
          1 A

       8987 CTAAAATAAA


Statistics
Matches: 41,  Mismatches: 5, Indels: 7
        0.77            0.09        0.13

Matches are distributed among these distances:
  21    5  0.12
  22    2  0.05
  23    6  0.15
  24    6  0.15
  25    4  0.10
  26   18  0.44

ACGTcount: A:0.74, C:0.06, G:0.06, T:0.15


Consensus pattern (23 bp):   
AAATAAAAAAATAACAACAAAAT

Found at i:9005 original size:29 final size:27

Alignment explanation


    Indices: 8963--9022  Score: 66
    Period size: 29  Copynumber: 2.1  Consensus size: 27

       8953 TAACAACAAG

                 *                       
       8963 ATAAATAAAAAAATAAAAAAAATACTAAA
          1 ATAAACAAAAAAATAAAAAAAATA--AAA

                     *     *   *       
       8992 ATAAACAAACAAATATAAACAATAAAA
          1 ATAAACAAAAAAATAAAAAAAATAAAA

                
       9019 ATAA
          1 ATAA

       9023 TTGAGATTAA


Statistics
Matches: 27,  Mismatches: 4, Indels: 2
        0.82            0.12        0.06

Matches are distributed among these distances:
  27    7  0.26
  29   20  0.74

ACGTcount: A:0.77, C:0.07, G:0.00, T:0.17


Consensus pattern (27 bp):   
ATAAACAAAAAAATAAAAAAAATAAAA

Found at i:9072 original size:15 final size:15

Alignment explanation


    Indices: 9038--9079  Score: 50
    Period size: 15  Copynumber: 2.8  Consensus size: 15

       9028 ATTAAGCATG

                      *    
       9038 AAAATAAAT-GACAA
          1 AAAATAAATAAACAA

                            
       9052 ATAAATAAATAAACAA
          1 A-AAATAAATAAACAA

                 *      
       9068 AAAATCAATAAA
          1 AAAATAAATAAA

       9080 TTAAATATAA


Statistics
Matches: 24,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  14    1  0.04
  15   18  0.75
  16    5  0.21

ACGTcount: A:0.74, C:0.07, G:0.02, T:0.17


Consensus pattern (15 bp):   
AAAATAAATAAACAA

Found at i:9089 original size:26 final size:26

Alignment explanation


    Indices: 9056--9127  Score: 69
    Period size: 24  Copynumber: 2.8  Consensus size: 26

       9046 TGACAAATAA

                             *         
       9056 ATAAATA-AACAAAAAATCAA-TAAAT
          1 ATAAATATAA-AAAAAAACAACTAAAT

                         *            
       9081 -TAAATATAAAAATAAACAACTAAAT
          1 ATAAATATAAAAAAAAACAACTAAAT

                             *    
       9106 ATAAATAATAATAAAAAGACAA
          1 ATAAAT-ATAA-AAAAAAACAA

       9128 ACTTCGATGA


Statistics
Matches: 38,  Mismatches: 4, Indels: 7
        0.78            0.08        0.14

Matches are distributed among these distances:
  24   14  0.37
  25    7  0.18
  26    5  0.13
  27    4  0.11
  28    8  0.21

ACGTcount: A:0.71, C:0.07, G:0.01, T:0.21


Consensus pattern (26 bp):   
ATAAATATAAAAAAAAACAACTAAAT

Found at i:9569 original size:20 final size:21

Alignment explanation


    Indices: 9534--9572  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       9524 AAGGTAGCTA

                                 
       9534 TTAGGTTTTTCCATTTTTATT
          1 TTAGGTTTTTCCATTTTTATT

                       *       
       9555 TTAGGTTTTT-TATTTTTA
          1 TTAGGTTTTTCCATTTTTA

       9573 GGCTTTGTAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  20    7  0.41
  21   10  0.59

ACGTcount: A:0.15, C:0.05, G:0.10, T:0.69


Consensus pattern (21 bp):   
TTAGGTTTTTCCATTTTTATT

Found at i:10141 original size:2 final size:2

Alignment explanation


    Indices: 10134--10164  Score: 55
    Period size: 2  Copynumber: 16.0  Consensus size: 2

      10124 ACTTAGGATG

                                                           
      10134 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      10165 AAATAATCAA


Statistics
Matches: 28,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   1    1  0.04
   2   27  0.96

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Done.