Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008117.1 Kokia drynarioides strain JFW-HI SEQ_122775, 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: 4360
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.38


Found at i:128 original size:19 final size:19

Alignment explanation


    Indices: 104--150  Score: 58
    Period size: 19  Copynumber: 2.5  Consensus size: 19

         94 AAAAAAAAGG

                   *          *
        104 TTAATTTTATGAGGTGGAC
          1 TTAATTTAATGAGGTGGAA

                  *     *      
        123 TTAATTAAATGATGTGGAA
          1 TTAATTTAATGAGGTGGAA

                     
        142 TTAATTTAA
          1 TTAATTTAA

        151 GATATGACGT


Statistics
Matches: 23,  Mismatches: 5, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  19   23  1.00

ACGTcount: A:0.36, C:0.02, G:0.19, T:0.43


Consensus pattern (19 bp):   
TTAATTTAATGAGGTGGAA

Found at i:2375 original size:17 final size:18

Alignment explanation


    Indices: 2350--2383  Score: 52
    Period size: 17  Copynumber: 1.9  Consensus size: 18

       2340 ATAACGTTTA

                *             
       2350 TATATATTTTTT-GTAAG
          1 TATAAATTTTTTAGTAAG

                             
       2367 TATAAATTTTTTAGTAA
          1 TATAAATTTTTTAGTAA

       2384 AAGAGCCAAA


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

Matches are distributed among these distances:
  17   11  0.73
  18    4  0.27

ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56


Consensus pattern (18 bp):   
TATAAATTTTTTAGTAAG

Found at i:3169 original size:86 final size:89

Alignment explanation


    Indices: 3042--3271  Score: 274
    Period size: 90  Copynumber: 2.6  Consensus size: 89

       3032 TAATGTTCAA

                                          *                         *       *
       3042 AGGGTCTTTTTGATGTA-TTTGACAA-TTCGAGTACCCAATTGAGTGC-AAAAAAATCGAGG-GT
          1 AGGGTCTTTTTGATGTATTTTGA-AAGTTCAAGTACCCAATTGAGTGCAAAAAAAAGC-AGGAGC

                          *      *    
       3103 TTAATTG-T-TTTTTGAAAAAGTTTG
         64 TTAATTGCTCTTTTCGAAAAAATTTG

                *          *                             *                   
       3127 AGGGCCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTTCAAAATAAAAGCAGGAGCT
          1 AGGGTCTTTTTGATGTATTTTGAAAGTTCAAGTACCCAATTGAGTGCAAAA-AAAAGCAGGAGCT

                                     
       3192 TAATTGCTCTTTTCGAAAAAATTTG
         65 TAATTGCTCTTTTCGAAAAAATTTG

              *                               **   *      *        
       3217 AGAGTCTTTTTGATGTATTTTGAAAGTTCAAGTATTCAAGTGAGTGAAAAAAAAA
          1 AGGGTCTTTTTGATGTATTTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAA

       3272 AAAAATGGAG


Statistics
Matches: 122,  Mismatches: 16, Indels: 10
        0.82            0.11        0.07

Matches are distributed among these distances:
  85   17  0.14
  86   24  0.20
  87    6  0.05
  88   13  0.11
  89    5  0.04
  90   57  0.47

ACGTcount: A:0.34, C:0.10, G:0.20, T:0.35


Consensus pattern (89 bp):   
AGGGTCTTTTTGATGTATTTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAAGCAGGAGCTT
AATTGCTCTTTTCGAAAAAATTTG

Found at i:3302 original size:90 final size:88

Alignment explanation


    Indices: 3103--3302  Score: 222
    Period size: 90  Copynumber: 2.2  Consensus size: 88

       3093 AATCGAGGGT

                                       *                                    *
       3103 TTAATTG-TTTTTTGAAAAAGTTTGAGGGCCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAAT
          1 TTAATTGCTTTTTT-AAAAAGTTTGAGAGCCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAAG

                 **    *    **      
       3167 TGAGTTCAAAATAAAAGCAGGAGC
         65 TGAGTAAAAAAAAAAAAAAGGAGC

                           *     *        *          *                  **   
       3191 TTAATTGCTCTTTTCGAAAAAATTTGAGAGTCTTTTTGATGTATTTTGAAAGTTCAAGTATTCAA
          1 TTAATTGCT-TTTT-TAAAAAGTTTGAGAGCCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAA

                                        
       3256 GTGAGTGAAAAAAAAAAAAAATGGAGAC
         64 GTGAGT-AAAAAAAAAAAAAA-GGAG-C

                               
       3284 TTAATTGCTTTTTTAAAAA
          1 TTAATTGCTTTTTTAAAAA

       3303 AATTTGAAGA


Statistics
Matches: 92,  Mismatches: 14, Indels: 9
        0.80            0.12        0.08

Matches are distributed among these distances:
  88    7  0.08
  89    1  0.01
  90   52  0.57
  91   14  0.15
  92    8  0.09
  93   10  0.11

ACGTcount: A:0.36, C:0.09, G:0.18, T:0.36


Consensus pattern (88 bp):   
TTAATTGCTTTTTTAAAAAGTTTGAGAGCCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAAGT
GAGTAAAAAAAAAAAAAAGGAGC
Done.