Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000640.1 Kokia drynarioides strain JFW-HI SEQ_111610, 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: 1705
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:460 original size:29 final size:28

Alignment explanation


    Indices: 428--623  Score: 126
    Period size: 29  Copynumber: 6.6  Consensus size: 28

        418 AAAAAGGTAA

                                       * 
        428 TTTTGAGAGTTTCGAGGTCAAAATGGAGT
          1 TTTTG-GAGTTTCGAGGTCAAAATGGAAT

                   ** *  *  *            
        457 TTTTGGACATCCGGGGGCAAAATGGTAAT
          1 TTTTGGAGTTTCGAGGTCAAAATGG-AAT

                  *      *               *
        486 TTTTGAAAGTTTCTAGGTCAAAAATGGAAA
          1 TTTTG-GAGTTTCGAGGTC-AAAATGGAAT

            *                  *          
        516 ATTTGGA-TGTTCGAGGGTAAAAATGGAAT
          1 TTTTGGAGT-TTCGA-GGTCAAAATGGAAT

                         * *    *          
        545 TTTTGGAAGTTTTAGGGGTAAAAAATGGAAT
          1 TTTTGG-AG-TTTCGAGGT-CAAAATGGAAT

                           *   *          
        576 TTTTGGA-TGTTCGGGGGTAAAAATGGAAT
          1 TTTTGGAGT-TTC-GAGGTCAAAATGGAAT

                               
        605 TTTTGGGAGTTTCGAGGTC
          1 TTTT-GGAGTTTCGAGGTC

        624 TCCAGGATAA


Statistics
Matches: 129,  Mismatches: 25, Indels: 26
        0.72            0.14        0.14

Matches are distributed among these distances:
  28   17  0.13
  29   52  0.40
  30   31  0.24
  31   28  0.22
  32    1  0.01

ACGTcount: A:0.30, C:0.06, G:0.30, T:0.34


Consensus pattern (28 bp):   
TTTTGGAGTTTCGAGGTCAAAATGGAAT

Found at i:460 original size:57 final size:59

Alignment explanation


    Indices: 380--514  Score: 148
    Period size: 57  Copynumber: 2.3  Consensus size: 59

        370 TTTGGGAAAA

                *   *      *              *      *                 *   
        380 TTCGGGGTTAAAAATTGAATTTTTAGACATTAGAGGGTAAAAAGGTAA-TTTTGAGAGT
          1 TTCGAGGTCAAAAATGGAATTTTTAGACATCAGAGGGCAAAAAGGTAATTTTTGAAAGT

                              *     *      * *        *                
        438 TTCGAGGTC-AAAATGGAGTTTTTGGACATCCGGGGGCAAAATGGTAATTTTTGAAAGT
          1 TTCGAGGTCAAAAATGGAATTTTTAGACATCAGAGGGCAAAAAGGTAATTTTTGAAAGT

               *               
        496 TTCTAGGTCAAAAATGGAA
          1 TTCGAGGTCAAAAATGGAA

        515 AATTTGGATG


Statistics
Matches: 62,  Mismatches: 13, Indels: 3
        0.79            0.17        0.04

Matches are distributed among these distances:
  57   30  0.48
  58   24  0.39
  59    8  0.13

ACGTcount: A:0.34, C:0.07, G:0.27, T:0.32


Consensus pattern (59 bp):   
TTCGAGGTCAAAAATGGAATTTTTAGACATCAGAGGGCAAAAAGGTAATTTTTGAAAGT

Found at i:511 original size:31 final size:30

Alignment explanation


    Indices: 475--617  Score: 141
    Period size: 29  Copynumber: 4.8  Consensus size: 30

        465 ATCCGGGGGC

                            *               
        475 AAAATGGTAATTTTTGAAAGTTTCTA-GGTCA
          1 AAAATGG-AATTTTTGGAAGTTTCTAGGGT-A

                     **      *     *      
        506 AAAATGGAAAATTTGGATG-TTCGAGGGTA
          1 AAAATGGAATTTTTGGAAGTTTCTAGGGTA

                                            
        535 AAAATGGAATTTTTGGAAGTTT-TAGGGGTAA
          1 AAAATGGAATTTTTGGAAGTTTCTA-GGGT-A

                             *     **     
        566 AAAATGGAATTTTTGGATG-TTCGGGGGTA
          1 AAAATGGAATTTTTGGAAGTTTCTAGGGTA

                            *      
        595 AAAATGGAATTTTTGGGAGTTTC
          1 AAAATGGAATTTTTGGAAGTTTC

        618 GAGGTCTCCA


Statistics
Matches: 92,  Mismatches: 14, Indels: 13
        0.77            0.12        0.11

Matches are distributed among these distances:
  29   40  0.43
  30   26  0.28
  31   26  0.28

ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35


Consensus pattern (30 bp):   
AAAATGGAATTTTTGGAAGTTTCTAGGGTA

Found at i:581 original size:60 final size:59

Alignment explanation


    Indices: 475--622  Score: 199
    Period size: 60  Copynumber: 2.5  Consensus size: 59

        465 ATCCGGGGGC

                            *            *                              
        475 AAAATGGTAATTTTTGAAAGTTTCTAGGTCAAAAATGGAAAATTTGGATGTTCGAGGGTA
          1 AAAATGG-AATTTTTGGAAGTTTCTAGGTAAAAAATGGAAAATTTGGATGTTCGAGGGTA

                                                     **            *     
        535 AAAATGGAATTTTTGGAAGTTT-TAGGGGTAAAAAATGGAATTTTTGGATGTTCGGGGGTA
          1 AAAATGGAATTTTTGGAAGTTTCTA--GGTAAAAAATGGAAAATTTGGATGTTCGAGGGTA

                            *      *    
        595 AAAATGGAATTTTTGGGAGTTTCGAGGT
          1 AAAATGGAATTTTTGGAAGTTTCTAGGT

        623 CTCCAGGATA


Statistics
Matches: 78,  Mismatches: 7, Indels: 7
        0.85            0.08        0.08

Matches are distributed among these distances:
  58    2  0.03
  59   17  0.22
  60   58  0.74
  61    1  0.01

ACGTcount: A:0.33, C:0.03, G:0.29, T:0.34


Consensus pattern (59 bp):   
AAAATGGAATTTTTGGAAGTTTCTAGGTAAAAAATGGAAAATTTGGATGTTCGAGGGTA
Done.