Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010595.1 Kokia drynarioides strain JFW-HI SEQ_125523, 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: 12112
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35


Found at i:76 original size:17 final size:18

Alignment explanation


    Indices: 49--85  Score: 51
    Period size: 17  Copynumber: 2.1  Consensus size: 18

         39 AAATTTTAAA

                               
         49 AATATTATTTTATC-ATTT
          1 AATATTATTTT-TCTATTT

                              
         67 AATA-TATTTTTCTATTT
          1 AATATTATTTTTCTATTT

              
         84 AA
          1 AA

         86 ATGAGGATTT


Statistics
Matches: 18,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  16    2  0.11
  17   12  0.67
  18    4  0.22

ACGTcount: A:0.35, C:0.05, G:0.00, T:0.59


Consensus pattern (18 bp):   
AATATTATTTTTCTATTT

Found at i:3752 original size:31 final size:31

Alignment explanation


    Indices: 3716--3777  Score: 81
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       3706 ATAATCATTG

                        *                   
       3716 AATTATTCGAAAGTTTTCATTTAAT-TCACTA
          1 AATTATTCGAAAATTTTCATTT-ATGTCACTA

                   *         *             
       3747 AATTATTTGAAAATTTTTATTTATGTCACTA
          1 AATTATTCGAAAATTTTCATTTATGTCACTA

       3778 GTTTGTCAAG


Statistics
Matches: 27,  Mismatches: 3, Indels: 2
        0.84            0.09        0.06

Matches are distributed among these distances:
  30    2  0.07
  31   25  0.93

ACGTcount: A:0.35, C:0.10, G:0.06, T:0.48


Consensus pattern (31 bp):   
AATTATTCGAAAATTTTCATTTATGTCACTA

Found at i:4680 original size:27 final size:25

Alignment explanation


    Indices: 4616--4710  Score: 81
    Period size: 27  Copynumber: 3.9  Consensus size: 25

       4606 TTTGTAATTT

                                *    
       4616 ATAAAATTTTAA---AATAATAATG
          1 ATAAAATTTTAATTTAATAAAAATG

                    ** *               
       4638 ATAAAATTACATTTTAATATTAAAATG
          1 ATAAAATTTTAATTTAATA--AAAATG

                                     
       4665 ATAAAATTTTAATTTAATAAAAAT-
          1 ATAAAATTTTAATTTAATAAAAATG

                 * *    *         
       4689 ATAAACTATTAAATTAATAAAA
          1 ATAAAATTTTAATTTAATAAAA

       4711 TTATATTTTT


Statistics
Matches: 58,  Mismatches: 10, Indels: 8
        0.76            0.13        0.11

Matches are distributed among these distances:
  22    9  0.16
  24   19  0.33
  25    9  0.16
  27   21  0.36

ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38


Consensus pattern (25 bp):   
ATAAAATTTTAATTTAATAAAAATG

Found at i:4692 original size:24 final size:24

Alignment explanation


    Indices: 4615--4715  Score: 73
    Period size: 24  Copynumber: 4.2  Consensus size: 24

       4605 TTTTGTAATT

                                 *  
       4615 TATAAAATTTTAA---AATAATAA
          1 TATAAAATTTTAATTTAATAAAAA

                      ** *             
       4636 TGATAAAATTACATTTTAATATTAAAA
          1 T-ATAAAATTTTAATTTAATA--AAAA

                                     
       4663 TGATAAAATTTTAATTTAATAAAAA
          1 T-ATAAAATTTTAATTTAATAAAAA

                  * *    *         *
       4688 TATAAACTATTAAATTAATAAAAT
          1 TATAAAATTTTAATTTAATAAAAA

                
       4712 TATA
          1 TATA

       4716 TTTTTACCGT


Statistics
Matches: 63,  Mismatches: 11, Indels: 9
        0.76            0.13        0.11

Matches are distributed among these distances:
  21    1  0.02
  22    9  0.14
  24   23  0.37
  25    9  0.14
  27   21  0.33

ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40


Consensus pattern (24 bp):   
TATAAAATTTTAATTTAATAAAAA

Found at i:8647 original size:2 final size:2

Alignment explanation


    Indices: 8640--8677  Score: 58
    Period size: 2  Copynumber: 19.0  Consensus size: 2

       8630 AATTGCTATT

                                                *     *             
       8640 AC AC AC AC AC AC AC AC AC AC AC AC GC AC GC AC AC AC AC
          1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC

       8678 CTGTAGTATG


Statistics
Matches: 32,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
   2   32  1.00

ACGTcount: A:0.45, C:0.50, G:0.05, T:0.00


Consensus pattern (2 bp):   
AC

Found at i:11589 original size:26 final size:24

Alignment explanation


    Indices: 11550--11597  Score: 62
    Period size: 26  Copynumber: 1.9  Consensus size: 24

      11540 GAAAGTTTGA

                                     
      11550 TTTTTCATTAAAATATT-AGGTTAT
          1 TTTTTCATTAAAAT-TTAAGGTTAT

                                    
      11574 TTTTTCCATATAAAATTTAAGGTT
          1 TTTTT-CAT-TAAAATTTAAGGTT

      11598 TTGCTTATCG


Statistics
Matches: 21,  Mismatches: 0, Indels: 4
        0.84            0.00        0.16

Matches are distributed among these distances:
  24    5  0.24
  25    5  0.24
  26   11  0.52

ACGTcount: A:0.33, C:0.06, G:0.08, T:0.52


Consensus pattern (24 bp):   
TTTTTCATTAAAATTTAAGGTTAT
Done.