Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006405.1 Kokia drynarioides strain JFW-HI SEQ_120982, 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: 12853
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:1644 original size:27 final size:27

Alignment explanation


    Indices: 1577--1647  Score: 81
    Period size: 27  Copynumber: 2.6  Consensus size: 27

       1567 CACGACAAGT

                            *    *     
       1577 AAGAATAACCTTTGTGATGAAGTCTGA
          1 AAGAATAACCTTTGTGGTGAACTCTGA

                   ***                 
       1604 AAGAATAGTTTTTGTGGTGAACTCT-A
          1 AAGAATAACCTTTGTGGTGAACTCTGA

                              
       1630 AAGGAATAACCTTTGTGG
          1 AA-GAATAACCTTTGTGG

       1648 CGAATTATGA


Statistics
Matches: 35,  Mismatches: 8, Indels: 2
        0.78            0.18        0.04

Matches are distributed among these distances:
  26    3  0.09
  27   32  0.91

ACGTcount: A:0.34, C:0.10, G:0.24, T:0.32


Consensus pattern (27 bp):   
AAGAATAACCTTTGTGGTGAACTCTGA

Found at i:1672 original size:54 final size:54

Alignment explanation


    Indices: 1579--1684  Score: 133
    Period size: 54  Copynumber: 2.0  Consensus size: 54

       1569 CGACAAGTAA

                           *     *                        *       
       1579 GAATAACCTTTGTGATGAAGTCTGAAAGAATAGTTTTTGTGGTGAACTCTAAAG
          1 GAATAACCTTTGTGACGAAGTATGAAAGAATAGTTTTTGTGGTGAAATCTAAAG

                          *    *     * *                         
       1633 GAATAACCTTTGTGGCGAATTATGATATAATA-TTCTTTGTGGTGAAATCTAA
          1 GAATAACCTTTGTGACGAAGTATGAAAGAATAGTT-TTTGTGGTGAAATCTAA

       1685 GTGTATTGCC


Statistics
Matches: 44,  Mismatches: 7, Indels: 2
        0.83            0.13        0.04

Matches are distributed among these distances:
  53    2  0.05
  54   42  0.95

ACGTcount: A:0.33, C:0.09, G:0.22, T:0.36


Consensus pattern (54 bp):   
GAATAACCTTTGTGACGAAGTATGAAAGAATAGTTTTTGTGGTGAAATCTAAAG

Found at i:4198 original size:52 final size:52

Alignment explanation


    Indices: 4136--4280  Score: 211
    Period size: 52  Copynumber: 2.8  Consensus size: 52

       4126 TTGTTCCGTT

                 *     *              *                          
       4136 AAGGAATCATACACTCACGATGACACTTAGTCATCGGACCTCATAAT-TCATA
          1 AAGGATTCATATACTCACGATGACACATAGTCATCGGACCTCATAATCT-ATA

            *                                                *  
       4188 GAGGATTCATATACTCACGATGACACATAGTCATCGGACCTCATAATCTGTA
          1 AAGGATTCATATACTCACGATGACACATAGTCATCGGACCTCATAATCTATA

                                     *   *           
       4240 AAGGATTCATATACTCACGATGACAGATATTCATCGGACCT
          1 AAGGATTCATATACTCACGATGACACATAGTCATCGGACCT

       4281 TTTCTCATTT


Statistics
Matches: 84,  Mismatches: 8, Indels: 2
        0.89            0.09        0.02

Matches are distributed among these distances:
  52   83  0.99
  53    1  0.01

ACGTcount: A:0.34, C:0.23, G:0.16, T:0.26


Consensus pattern (52 bp):   
AAGGATTCATATACTCACGATGACACATAGTCATCGGACCTCATAATCTATA
Done.