Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014867.1 Kokia drynarioides strain JFW-HI SEQ_129910, 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: 23398
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35


Found at i:10228 original size:22 final size:22

Alignment explanation


    Indices: 10211--10252  Score: 59
    Period size: 22  Copynumber: 2.0  Consensus size: 22

      10201 CAAAAAAGTC

                *                 
      10211 AAAATTCA-AAATTCAAAAATA
          1 AAAAATCAGAAATTCAAAAATA

                       *         
      10232 AAAAATCAGAACTTCAAAAAT
          1 AAAAATCAGAAATTCAAAAAT

      10253 TGCCTAAATA


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  21    7  0.39
  22   11  0.61

ACGTcount: A:0.64, C:0.12, G:0.02, T:0.21


Consensus pattern (22 bp):   
AAAAATCAGAAATTCAAAAATA

Found at i:10228 original size:29 final size:29

Alignment explanation


    Indices: 10195--10250  Score: 78
    Period size: 29  Copynumber: 1.9  Consensus size: 29

      10185 AAAACGAATC

                                          
      10195 CAAAAACAAAAAAGTCA-AAATTCAAAATT
          1 CAAAAACAAAAAA-TCAGAAATTCAAAATT

                  *            *       
      10224 CAAAAATAAAAAATCAGAACTTCAAAA
          1 CAAAAACAAAAAATCAGAAATTCAAAA

      10251 ATTGCCTAAA


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  28    3  0.12
  29   21  0.88

ACGTcount: A:0.66, C:0.14, G:0.04, T:0.16


Consensus pattern (29 bp):   
CAAAAACAAAAAATCAGAAATTCAAAATT

Found at i:10913 original size:26 final size:25

Alignment explanation


    Indices: 10849--10913  Score: 67
    Period size: 26  Copynumber: 2.6  Consensus size: 25

      10839 GTACCTTAAT

                *                    
      10849 TTGACTTTGATTTTCAATTTAGTAC
          1 TTGAATTTGATTTTCAATTTAGTAC

            *   *   **           *    
      10874 ATGAGTTTTTTTTTCTAATTTGGTAC
          1 TTGAATTTGATTTTC-AATTTAGTAC

                          
      10900 TTGAATTTGATTTT
          1 TTGAATTTGATTTT

      10914 AGGTTTCAAA


Statistics
Matches: 30,  Mismatches: 9, Indels: 1
        0.75            0.22        0.03

Matches are distributed among these distances:
  25   11  0.37
  26   19  0.63

ACGTcount: A:0.22, C:0.08, G:0.14, T:0.57


Consensus pattern (25 bp):   
TTGAATTTGATTTTCAATTTAGTAC

Found at i:11950 original size:22 final size:22

Alignment explanation


    Indices: 11908--11980  Score: 57
    Period size: 24  Copynumber: 3.3  Consensus size: 22

      11898 ATTAAAATAG

                                     
      11908 ATATATAAAATT-TTAACAAATAAA
          1 ATATATAAAATTATT---AAATAAA

                                    
      11932 ATATATAAAATTATTAAATATTAA
          1 ATATATAAAATTATTAAATA--AA

                         *        
      11956 AT-TA-AAAA-TAATAAA-AAA
          1 ATATATAAAATTATTAAATAAA

                   
      11974 ATATATA
          1 ATATATA

      11981 TATTTAAAAA


Statistics
Matches: 43,  Mismatches: 1, Indels: 14
        0.74            0.02        0.24

Matches are distributed among these distances:
  18    4  0.09
  19    2  0.05
  20    2  0.05
  21    6  0.14
  22    9  0.21
  23    2  0.05
  24   16  0.37
  25    2  0.05

ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34


Consensus pattern (22 bp):   
ATATATAAAATTATTAAATAAA

Found at i:17614 original size:2 final size:2

Alignment explanation


    Indices: 17602--17635  Score: 59
    Period size: 2  Copynumber: 17.0  Consensus size: 2

      17592 GTTGATTTAA

                  *                                           
      17602 CT CT TT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
          1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT

      17636 TATATTTATA


Statistics
Matches: 30,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   2   30  1.00

ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53


Consensus pattern (2 bp):   
CT

Done.