Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011569.1 Kokia drynarioides strain JFW-HI SEQ_126558, 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: 12534
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35


Found at i:10274 original size:3 final size:3

Alignment explanation


    Indices: 10266--10296  Score: 53
    Period size: 3  Copynumber: 10.3  Consensus size: 3

      10256 AAGGGCCCAA

                         *                           
      10266 ATT ATT ATT AGT ATT ATT ATT ATT ATT ATT A
          1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A

      10297 GGGTTTCATG


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   3   26  1.00

ACGTcount: A:0.35, C:0.00, G:0.03, T:0.61


Consensus pattern (3 bp):   
ATT

Found at i:10505 original size:15 final size:15

Alignment explanation


    Indices: 10493--10522  Score: 60
    Period size: 15  Copynumber: 2.0  Consensus size: 15

      10483 ACAAAAAAGG

                           
      10493 TAAGAAGAAAAAACA
          1 TAAGAAGAAAAAACA

                           
      10508 TAAGAAGAAAAAACA
          1 TAAGAAGAAAAAACA

      10523 ACAACAAGCA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.73, C:0.07, G:0.13, T:0.07


Consensus pattern (15 bp):   
TAAGAAGAAAAAACA

Found at i:11051 original size:151 final size:146

Alignment explanation


    Indices: 10735--11090  Score: 457
    Period size: 151  Copynumber: 2.4  Consensus size: 146

      10725 TTTGGTTTTT

                     *                                   *    *      *       
      10735 TTTTTTTAAATAATTTCAAAATAAAAGTTTGGATTTTTAAGTAAAATAGTCATTTTCTTTAAAAA
          1 TTTTTTTAACT-ATTTCAAAATAAAAGTTT-GATTTTTAAGTAAAGTAGTGATTTTCATTAAAAA

                                                                             
      10800 AGAGAAAGTTTATATTTTAAAAAATAAAAATATGTTTTTTAGTTATTATAAAGAAAAAGTTTAAA
         64 AGAGAAAGTTTATATTTTAAAAAATAAAAATATGTTTTTTAGTTATTATAAAGAAAAAG-TTAAA

                        *      
      10865 ATTTTAAACAAAGTTTTGA
        128 ATTTTAAACAAAATTTTGA

                                                                             
      10884 TTTTTTTAAACTATTTCAAAATAAAAGTTTGAATTTTTAAGTAAAGTAGTGATTTTCATTAAAAA
          1 TTTTTTT-AACTATTTCAAAATAAAAGTTTG-ATTTTTAAGTAAAGTAGTGATTTTCATTAAAAA

                 *               *                 *             *           
      10949 AGAAATAAAGTTTATATTTTTTAAAAATAAAAATTTTATTTTTTTTAGTTATTTTAAA-AAAAA-
         64 AG--AGAAAGTTTATA-TTTTAAAAAATAAAAA---TATGTTTTTTAGTTATTATAAAGAAAAAG

                 *                  
      11012 TT-AATTTTTAAACAAAATTTTGA
        123 TTAAAATTTTAAACAAAATTTTGA

                             *         *         *                  
      11035 TTTATTTTAACTATTTCGAAATAAAAATTTTGATTTTGAAGTAAAGTAGTGATTTT
          1 TTT-TTTTAACTATTTCAAAAT-AAAAGTTTGATTTTTAAGTAAAGTAGTGATTTT

      11091 GTTTTAATCA


Statistics
Matches: 184,  Mismatches: 13, Indels: 18
        0.86            0.06        0.08

Matches are distributed among these distances:
 148    1  0.01
 149   57  0.31
 150    3  0.02
 151   69  0.38
 152   29  0.16
 154    5  0.03
 155   20  0.11

ACGTcount: A:0.44, C:0.03, G:0.09, T:0.45


Consensus pattern (146 bp):   
TTTTTTTAACTATTTCAAAATAAAAGTTTGATTTTTAAGTAAAGTAGTGATTTTCATTAAAAAAG
AGAAAGTTTATATTTTAAAAAATAAAAATATGTTTTTTAGTTATTATAAAGAAAAAGTTAAAATT
TTAAACAAAATTTTGA

Found at i:11801 original size:19 final size:19

Alignment explanation


    Indices: 11779--11823  Score: 56
    Period size: 19  Copynumber: 2.4  Consensus size: 19

      11769 TTATATTTGG

                                
      11779 ATTTAATATTTAAGATAT-T
          1 ATTTAATATTTAA-ATATGT

                 *         *   
      11798 ATTTATTATTTAAATTTGT
          1 ATTTAATATTTAAATATGT

                   
      11817 ATTTAAT
          1 ATTTAAT

      11824 TTATATTTAT


Statistics
Matches: 22,  Mismatches: 3, Indels: 2
        0.81            0.11        0.07

Matches are distributed among these distances:
  18    3  0.14
  19   19  0.86

ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58


Consensus pattern (19 bp):   
ATTTAATATTTAAATATGT
Done.