Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004765.1 Kokia drynarioides strain JFW-HI SEQ_118368, 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: 30463
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34


Found at i:4094 original size:99 final size:99

Alignment explanation


    Indices: 3923--4116  Score: 316
    Period size: 99  Copynumber: 2.0  Consensus size: 99

       3913 AGTATGTCCC

                                           *       *                         
       3923 TATTGTGTGTATGATAAATCAATTCATAATTGTTGTTTTGTATTACCGAAAAATAAATTGACGTG
          1 TATTGTGTGTATGATAAATCAATTCATAATTATTGTTTTATATTACCGAAAAATAAATTGACGTG

             *                                
       3988 GGTAGATTGAGTGTAGTTAGGTGAGATTAATTTT
         66 GATAGATTGAGTGTAGTTAGGTGAGATTAATTTT

                                              *           *   *          *   
       4022 TATTGTGTGTATGATAAATCAATTCATAATTATTTTTTTATATTACTGAAGAATAAATTGATGTG
          1 TATTGTGTGTATGATAAATCAATTCATAATTATTGTTTTATATTACCGAAAAATAAATTGACGTG

                                     *    
       4087 GATAGATTGAGTGTAGTTAGGTGAGGTTAA
         66 GATAGATTGAGTGTAGTTAGGTGAGATTAA

       4117 GAGAATTAGT


Statistics
Matches: 87,  Mismatches: 8, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  99   87  1.00

ACGTcount: A:0.32, C:0.04, G:0.22, T:0.42


Consensus pattern (99 bp):   
TATTGTGTGTATGATAAATCAATTCATAATTATTGTTTTATATTACCGAAAAATAAATTGACGTG
GATAGATTGAGTGTAGTTAGGTGAGATTAATTTT

Found at i:5052 original size:17 final size:17

Alignment explanation


    Indices: 5017--5050  Score: 50
    Period size: 17  Copynumber: 1.9  Consensus size: 17

       5007 TTATGTTTAT

                     *       
       5017 TATTTAAAATTTTAAAA
          1 TATTTAAAAGTTTAAAA

                             
       5034 TATTTAAAGAGTTTAAA
          1 TATTTAAA-AGTTTAAA

       5051 TAGATAATTT


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

Matches are distributed among these distances:
  17    8  0.53
  18    7  0.47

ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44


Consensus pattern (17 bp):   
TATTTAAAAGTTTAAAA

Found at i:16525 original size:3 final size:3

Alignment explanation


    Indices: 16517--16553  Score: 65
    Period size: 3  Copynumber: 12.3  Consensus size: 3

      16507 AATTTGCCCT

                                            *                
      16517 TTA TTA TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA T
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T

      16554 AGGTTATGTT


Statistics
Matches: 32,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   3   32  1.00

ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65


Consensus pattern (3 bp):   
TTA

Found at i:16667 original size:2 final size:2

Alignment explanation


    Indices: 16614--16653  Score: 71
    Period size: 2  Copynumber: 19.5  Consensus size: 2

      16604 ATTTATTTCA

                                                                       
      16614 AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

      16654 CTTATTAATA


Statistics
Matches: 37,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   2   35  0.95
   3    2  0.05

ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47


Consensus pattern (2 bp):   
AT

Found at i:20155 original size:2 final size:2

Alignment explanation


    Indices: 20148--20177  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

      20138 AAAGGCCTCA

                                                        
      20148 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      20178 TAAAAAGTTG


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:29969 original size:19 final size:20

Alignment explanation


    Indices: 29945--29983  Score: 53
    Period size: 19  Copynumber: 2.0  Consensus size: 20

      29935 TAATAAGTTT

                  *             
      29945 AAATATTAAT-TATATAAAA
          1 AAATATAAATGTATATAAAA

                        *       
      29964 AAATATAAATGTGTATAAAA
          1 AAATATAAATGTATATAAAA

      29984 TTAATTTAAG


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

Matches are distributed among these distances:
  19    9  0.53
  20    8  0.47

ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33


Consensus pattern (20 bp):   
AAATATAAATGTATATAAAA

Found at i:30198 original size:35 final size:35

Alignment explanation


    Indices: 30157--30226  Score: 122
    Period size: 35  Copynumber: 2.0  Consensus size: 35

      30147 AATGAAGTAG

                                   *           
      30157 AGATCTATTTCTAATAACTATTAGAGTTAAAGGTA
          1 AGATCTATTTCTAATAACTATTAAAGTTAAAGGTA

                                        *      
      30192 AGATCTATTTCTAATAACTATTAAAGTTCAAGGTA
          1 AGATCTATTTCTAATAACTATTAAAGTTAAAGGTA

      30227 TACCAAACCT


Statistics
Matches: 33,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  35   33  1.00

ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37


Consensus pattern (35 bp):   
AGATCTATTTCTAATAACTATTAAAGTTAAAGGTA
Done.