Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013781.1 Kokia drynarioides strain JFW-HI SEQ_128809, 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: 9204
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.34


Found at i:2103 original size:56 final size:55

Alignment explanation


    Indices: 2007--2117  Score: 132
    Period size: 56  Copynumber: 2.0  Consensus size: 55

       1997 GTATATCAAT

                    **       *   *            **                    
       2007 ATGACAATTGATTTAAATATATAAACAATAAATTTGAAAGAAAAAAATATTCCAAC
          1 ATGACAATCAATTTAAACATAAAAACAATAAATTCAAAAG-AAAAAATATTCCAAC

                                         *            **           
       2063 ATGACAATCAATTTAAACATAAAAACAATCAATTCAAAAGAAGTAATATTCCAAC
          1 ATGACAATCAATTTAAACATAAAAACAATAAATTCAAAAGAAAAAATATTCCAAC

       2118 GTAACAACCG


Statistics
Matches: 46,  Mismatches: 9, Indels: 1
        0.82            0.16        0.02

Matches are distributed among these distances:
  55   13  0.28
  56   33  0.72

ACGTcount: A:0.55, C:0.13, G:0.06, T:0.26


Consensus pattern (55 bp):   
ATGACAATCAATTTAAACATAAAAACAATAAATTCAAAAGAAAAAATATTCCAAC

Found at i:2966 original size:21 final size:20

Alignment explanation


    Indices: 2920--2966  Score: 58
    Period size: 21  Copynumber: 2.3  Consensus size: 20

       2910 AATATTTATT

                       *        
       2920 TAATATTTTAATTAAAATAA
          1 TAATATTTTAAGTAAAATAA

                            *    
       2940 TAATATTTATAAGTAATATAA
          1 TAATATTT-TAAGTAAAATAA

             *    
       2961 TTATAT
          1 TAATAT

       2967 ATAAAAAGAA


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  20    8  0.35
  21   15  0.65

ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47


Consensus pattern (20 bp):   
TAATATTTTAAGTAAAATAA

Found at i:3399 original size:17 final size:18

Alignment explanation


    Indices: 3377--3417  Score: 57
    Period size: 17  Copynumber: 2.3  Consensus size: 18

       3367 TATTAATGGC

                  *           
       3377 ATAAAATATAAAAAATGA
          1 ATAAAAAATAAAAAATGA

                          *   
       3395 A-AAAAAATAAAAATTGA
          1 ATAAAAAATAAAAAATGA

                  
       3412 ATAAAA
          1 ATAAAA

       3418 GGCAAAAATA


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  17   15  0.75
  18    5  0.25

ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20


Consensus pattern (18 bp):   
ATAAAAAATAAAAAATGA

Found at i:3451 original size:4 final size:4

Alignment explanation


    Indices: 3436--3588  Score: 82
    Period size: 4  Copynumber: 36.8  Consensus size: 4

       3426 TATAAATGGC

                  *                 *                                     
       3436 ATAA AAAA ATAA ATAAA ATAC ATAA A-AA ATAA ATAA ATAA GATTAA ATAA
          1 ATAA ATAA ATAA AT-AA ATAA ATAA ATAA ATAA ATAA ATAA -A-TAA ATAA

              **   *                                 *    *            
       3486 AGGCA AGAA TATAA ATAA CATAA A-AA ATGAAA ACAA AAAA ATAA ATAA
          1 A-TAA ATAA -ATAA ATAA -ATAA ATAA AT--AA ATAA ATAA ATAA ATAA

                                      *         *                      *  
       3534 A-ACA ATAA ATAA ATAA A-AA TTAA AT-A CTAA ATAAA ATAA TATAA ACAA
          1 ATA-A ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT-AA ATAA -ATAA ATAA

                    
       3582 ATAA ATA
          1 ATAA ATA

       3589 GGACCAAATT


Statistics
Matches: 116,  Mismatches: 17, Indels: 32
        0.70            0.10        0.19

Matches are distributed among these distances:
   3   11  0.09
   4   75  0.65
   5   24  0.21
   6    6  0.05

ACGTcount: A:0.72, C:0.05, G:0.03, T:0.20


Consensus pattern (4 bp):   
ATAA

Found at i:3498 original size:69 final size:74

Alignment explanation


    Indices: 3399--3559  Score: 197
    Period size: 69  Copynumber: 2.2  Consensus size: 74

       3389 AAATGAAAAA

                       *                      **            *    *      *    
       3399 AAATAAAAATTGAATAAAAGGCAAAAATATAAATGGCAT-AAAAA-AATA-AATAAAATACATAA
          1 AAATAAAAATTAAAT-AAAGGCAAAAATATAAATAACATAAAAAAGAAAACAAAAAAATAAATAA

                      
       3461 AA-AATAAAT
         65 AACAATAAAT

                   *               *                                         
       3470 AAAT-AAGATTAAATAAAGGCAAGAATATAAATAACATAAAAAATGAAAACAAAAAAATAAATAA
          1 AAATAAAAATTAAATAAAGGCAAAAATATAAATAACATAAAAAA-GAAAACAAAAAAATAAATAA

                      
       3534 AACAATAAAT
         65 AACAATAAAT

                            
       3544 AAATAAAAATTAAATA
          1 AAATAAAAATTAAATA

       3560 CTAAATAAAA


Statistics
Matches: 75,  Mismatches: 9, Indels: 8
        0.82            0.10        0.09

Matches are distributed among these distances:
  69   20  0.27
  70   13  0.17
  71    4  0.05
  72    3  0.04
  73   14  0.19
  74   11  0.15
  75   10  0.13

ACGTcount: A:0.70, C:0.04, G:0.06, T:0.19


Consensus pattern (74 bp):   
AAATAAAAATTAAATAAAGGCAAAAATATAAATAACATAAAAAAGAAAACAAAAAAATAAATAAA
ACAATAAAT

Found at i:3723 original size:5 final size:5

Alignment explanation


    Indices: 3713--3751  Score: 60
    Period size: 5  Copynumber: 7.8  Consensus size: 5

       3703 CTTAGAAACA

                                 *     *                  
       3713 AAAAT AAAAT AAAAT AAACT AAATT AAAAT AAAAT AAAA
          1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA

       3752 ATTATAGGGA


Statistics
Matches: 31,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
   5   31  1.00

ACGTcount: A:0.77, C:0.03, G:0.00, T:0.21


Consensus pattern (5 bp):   
AAAAT

Done.