Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007815.1 Kokia drynarioides strain JFW-HI SEQ_122451, 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: 2137
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38


Found at i:385 original size:29 final size:28

Alignment explanation


    Indices: 346--448  Score: 93
    Period size: 29  Copynumber: 3.5  Consensus size: 28

        336 ACTTTTTCCT

                                         
        346 AATTTGGTACCTAAACTTTTTTTGGATCC
          1 AATTTGGTACCTAAACTTTTTTT-GATCC

                 *      *        *         
        375 AATTTTGTACCTGAACTTGGCATTTT--TCC
          1 AATTTGGTACCTAAACTT---TTTTTGATCC

                           *            * 
        404 TAATTTGGTACCTAAGCTTTTTTTAGATTC
          1 -AATTTGGTACCTAAACTTTTTTT-GATCC

                           
        434 AATTTGGTACCTAAA
          1 AATTTGGTACCTAAA

        449 ATTATTAAAT


Statistics
Matches: 58,  Mismatches: 9, Indels: 14
        0.72            0.11        0.17

Matches are distributed among these distances:
  27    4  0.07
  29   33  0.57
  30   17  0.29
  32    4  0.07

ACGTcount: A:0.25, C:0.17, G:0.14, T:0.45


Consensus pattern (28 bp):   
AATTTGGTACCTAAACTTTTTTTGATCC

Found at i:413 original size:59 final size:59

Alignment explanation


    Indices: 263--445  Score: 253
    Period size: 59  Copynumber: 3.1  Consensus size: 59

        253 ATAACACTTG

                       *                       *      *       *   *    
        263 GTACCTGAACTCGACACTTTTTCCTAATTTGGTACTTAAACTCTTTTTGACCCAGTTTT
          1 GTACCTGAACTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTTGATCCAATTTT

                                                                        
        322 -TACCTGAACTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTTGGATCCAATTTT
          1 GTACCTGAACTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTT-GATCCAATTTT

                         *                         *            *      *
        381 GTACCTGAACTTGGCA-TTTTTCCTAATTTGGTACCTAAGCTTTTTTTAGATTCAATTTG
          1 GTACCTGAACTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTT-GATCCAATTTT

                  
        440 GTACCT
          1 GTACCT

        446 AAAATTATTA


Statistics
Matches: 112,  Mismatches: 10, Indels: 4
        0.89            0.08        0.03

Matches are distributed among these distances:
  58   44  0.39
  59   54  0.48
  60   14  0.12

ACGTcount: A:0.22, C:0.21, G:0.13, T:0.44


Consensus pattern (59 bp):   
GTACCTGAACTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTTGATCCAATTTT

Found at i:726 original size:31 final size:29

Alignment explanation


    Indices: 651--726  Score: 80
    Period size: 31  Copynumber: 2.6  Consensus size: 29

        641 ATCCCAAAAT

                         *               
        651 GTTTAAGTACCAACTTAAAAAAGAGTCAA
          1 GTTTAAGTACCAAATTAAAAAAGAGTCAA

            *    *    *              *     
        680 TTTTAGGTACAAAATTAGGAAAAAGTGTCAA
          1 GTTTAAGTACCAAATTA--AAAAAGAGTCAA

                *           
        711 GTTTGAGTACCAAATT
          1 GTTTAAGTACCAAATT

        727 GGACCAAAAA


Statistics
Matches: 36,  Mismatches: 9, Indels: 2
        0.77            0.19        0.04

Matches are distributed among these distances:
  29   13  0.36
  31   23  0.64

ACGTcount: A:0.43, C:0.11, G:0.17, T:0.29


Consensus pattern (29 bp):   
GTTTAAGTACCAAATTAAAAAAGAGTCAA
Done.