Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006078.1 Kokia drynarioides strain JFW-HI SEQ_120566, 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: 15207
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33


Found at i:362 original size:28 final size:27

Alignment explanation


    Indices: 287--362  Score: 80
    Period size: 28  Copynumber: 2.7  Consensus size: 27

        277 TCCTATACCT

                               *        
        287 AATAATTGAGGAGGTTGGCAACTCATTC
          1 AATAA-TGAGGAGGTTGGCCACTCATTC

                   *       *       **   
        315 AATAAGTCAGGAGGTGGGCCACTTGTTC
          1 AATAA-TGAGGAGGTTGGCCACTCATTC

                                
        343 AATAATAGAGGAGGTTGGCC
          1 AATAAT-GAGGAGGTTGGCC

        363 GTGTGGGCCT


Statistics
Matches: 39,  Mismatches: 8, Indels: 2
        0.80            0.16        0.04

Matches are distributed among these distances:
  27    1  0.03
  28   38  0.97

ACGTcount: A:0.30, C:0.14, G:0.30, T:0.25


Consensus pattern (27 bp):   
AATAATGAGGAGGTTGGCCACTCATTC

Found at i:3145 original size:35 final size:36

Alignment explanation


    Indices: 3014--3227  Score: 148
    Period size: 37  Copynumber: 5.9  Consensus size: 36

       3004 TTGTTAGGAA

                   *           *     *       *   
       3014 GAAATCGGGCTATGTGCCTGGCAGGTTTCGTGCAGGT
          1 GAAATCGAGCT-TGTGCCTAGCAGGCTTCGTGCTGGT

                               *     *   *    **  
       3051 GAAATC-AGGCTGTGTGCCAAGCAGACTTTGTGCCAGT
          1 GAAATCGA-GCT-TGTGCCTAGCAGGCTTCGTGCTGGT

                 * *         *     *             
       3088 GAAATTGGGCTATGTGCTTAGCAAGCTTCGTGCTGGT
          1 GAAATCGAGCT-TGTGCCTAGCAGGCTTCGTGCTGGT

                                        *   *** 
       3125 GAAATCGAG-TTGTGCCTAGCAGGCTTCATGCCAAT
          1 GAAATCGAGCTTGTGCCTAGCAGGCTTCGTGCTGGT

                  *             *                 
       3160 GAAATCAAGCTGTGTGCCTAACAGGCTTCGTG-TCGGT
          1 GAAATCGAGCT-TGTGCCTAGCAGGCTTCGTGCT-GGT

              *          *                  
       3197 G-TATCGAGCTTTATGCCTAGCAGGCTTCGTG
          1 GAAATCGAGC-TTGTGCCTAGCAGGCTTCGTG

       3228 TCGGTGTATC


Statistics
Matches: 134,  Mismatches: 37, Indels: 13
        0.73            0.20        0.07

Matches are distributed among these distances:
  35   27  0.20
  36   26  0.19
  37   81  0.60

ACGTcount: A:0.21, C:0.21, G:0.31, T:0.28


Consensus pattern (36 bp):   
GAAATCGAGCTTGTGCCTAGCAGGCTTCGTGCTGGT

Found at i:3221 original size:36 final size:36

Alignment explanation


    Indices: 3174--3269  Score: 149
    Period size: 36  Copynumber: 2.6  Consensus size: 36

       3164 TCAAGCTGTG

                  *                              
       3174 TGCCTAACAGGCTTCGTGTCGGTGTATC-GAGCTTTA
          1 TGCCTAGCAGGCTTCGTGTCGGTGTATCGGA-CTTTA

                                                
       3210 TGCCTAGCAGGCTTCGTGTCGGTGTATCGGACTTTA
          1 TGCCTAGCAGGCTTCGTGTCGGTGTATCGGACTTTA

                           *        
       3246 TGCCTAGCAGGCCTTTGTGTCGGT
          1 TGCCTAGCAGG-CTTCGTGTCGGT

       3270 AATTTGCATA


Statistics
Matches: 56,  Mismatches: 2, Indels: 3
        0.92            0.03        0.05

Matches are distributed among these distances:
  36   43  0.77
  37   13  0.23

ACGTcount: A:0.14, C:0.23, G:0.30, T:0.33


Consensus pattern (36 bp):   
TGCCTAGCAGGCTTCGTGTCGGTGTATCGGACTTTA

Found at i:4360 original size:35 final size:35

Alignment explanation


    Indices: 4313--4384  Score: 126
    Period size: 35  Copynumber: 2.1  Consensus size: 35

       4303 CTCGAAATAC

                                               
       4313 TTGTAATAGTTCATGTATGTTTTAATGAGATTGTT
          1 TTGTAATAGTTCATGTATGTTTTAATGAGATTGTT

                   *                *          
       4348 TTGTAATTGTTCATGTATGTTTTAGTGAGATTGTT
          1 TTGTAATAGTTCATGTATGTTTTAATGAGATTGTT

              
       4383 TT
          1 TT

       4385 AAGTGAATGT


Statistics
Matches: 35,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  35   35  1.00

ACGTcount: A:0.22, C:0.03, G:0.21, T:0.54


Consensus pattern (35 bp):   
TTGTAATAGTTCATGTATGTTTTAATGAGATTGTT

Found at i:11315 original size:15 final size:17

Alignment explanation


    Indices: 11281--11318  Score: 53
    Period size: 15  Copynumber: 2.4  Consensus size: 17

      11271 AGCAAAAAAT

                             
      11281 TAATTTCATCATTTTAA
          1 TAATTTCATCATTTTAA

                           * 
      11298 TAATTT-AT-ATTTTTA
          1 TAATTTCATCATTTTAA

                  
      11313 TAATTT
          1 TAATTT

      11319 TTAAAAGATT


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  15   12  0.60
  16    2  0.10
  17    6  0.30

ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61


Consensus pattern (17 bp):   
TAATTTCATCATTTTAA

Found at i:11413 original size:16 final size:16

Alignment explanation


    Indices: 11380--11424  Score: 58
    Period size: 16  Copynumber: 2.9  Consensus size: 16

      11370 TATCATTACT

                             
      11380 AATT-TAAAATTTTATA
          1 AATTATAAAA-TTTATA

                         *  
      11396 AATTATAAAATTTCTA
          1 AATTATAAAATTTATA

                          
      11412 AATTA-AAAATTTA
          1 AATTATAAAATTTA

      11425 CCATTTTAAA


Statistics
Matches: 26,  Mismatches: 2, Indels: 3
        0.84            0.06        0.10

Matches are distributed among these distances:
  15    7  0.27
  16   14  0.54
  17    5  0.19

ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44


Consensus pattern (16 bp):   
AATTATAAAATTTATA
Done.