Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009180.1 Kokia drynarioides strain JFW-HI SEQ_123885, 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: 8645
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:1862 original size:265 final size:265

Alignment explanation


    Indices: 1389--1918  Score: 1006
    Period size: 265  Copynumber: 2.0  Consensus size: 265

       1379 CACCTAGAGC

                                                                             
       1389 ATTAATCAATGACCAAGGCACTCATTTTCATTGCAATCAAGTTGCGACAGCATTAGAGCATTATG
          1 ATTAATCAATGACCAAGGCACTCATTTTCATTGCAATCAAGTTGCGACAGCATTAGAGCATTATG

                                          *       *                          
       1454 GTGTTAAACATCGAATGACAACCACATATCTTCCACAAGCGAATAGCCAAATTGAAGTATCTAAT
         66 GTGTTAAACATCGAATGACAACCACATATCATCCACAAACGAATAGCCAAATTGAAGTATCTAAT

                                                                             
       1519 CAACAAATTAAAAATATCCTTAAAAGGTGGTAAATCCATCCAGACGTGATTAGTCTTCAAGGCTC
        131 CAACAAATTAAAAATATCCTTAAAAGGTGGTAAATCCATCCAGACGTGATTAGTCTTCAAGGCTC

                                                                *            
       1584 AATGATGCATTGTGAGCGATTCGCAAAGCGTAGAAAATACCATTAGGAATGTTGTGGTATAAGCT
        196 AATGATGCATTGTGAGCGATTCGCAAAGCGTAGAAAATACCATTAGGAATGTCGTGGTATAAGCT

                 
       1649 TGTTT
        261 TGTTT

                        *                                                    
       1654 ATTAATCAATGATCAAGGCACTCATTTTCATTGCAATCAAGTTGCGACAGCATTAGAGCATTATG
          1 ATTAATCAATGACCAAGGCACTCATTTTCATTGCAATCAAGTTGCGACAGCATTAGAGCATTATG

                                                                             
       1719 GTGTTAAACATCGAATGACAACCACATATCATCCACAAACGAATAGCCAAATTGAAGTATCTAAT
         66 GTGTTAAACATCGAATGACAACCACATATCATCCACAAACGAATAGCCAAATTGAAGTATCTAAT

                                                               *             
       1784 CAACAAATTAAAAATATCCTTAAAAGGTGGTAAATCCATCCAGACGTGATTGGTCTTCAAGGCTC
        131 CAACAAATTAAAAATATCCTTAAAAGGTGGTAAATCCATCCAGACGTGATTAGTCTTCAAGGCTC

                                   *                                         
       1849 AATGATGCATTGTGAGCGATTCGTAAAGCGTAGAAAATACCATTAGGAATGTCGTGGTATAAGCT
        196 AATGATGCATTGTGAGCGATTCGCAAAGCGTAGAAAATACCATTAGGAATGTCGTGGTATAAGCT

                 
       1914 TGTTT
        261 TGTTT

       1919 TTGGTAAATC


Statistics
Matches: 259,  Mismatches: 6, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
 265  259  1.00

ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28


Consensus pattern (265 bp):   
ATTAATCAATGACCAAGGCACTCATTTTCATTGCAATCAAGTTGCGACAGCATTAGAGCATTATG
GTGTTAAACATCGAATGACAACCACATATCATCCACAAACGAATAGCCAAATTGAAGTATCTAAT
CAACAAATTAAAAATATCCTTAAAAGGTGGTAAATCCATCCAGACGTGATTAGTCTTCAAGGCTC
AATGATGCATTGTGAGCGATTCGCAAAGCGTAGAAAATACCATTAGGAATGTCGTGGTATAAGCT
TGTTT

Found at i:4213 original size:15 final size:15

Alignment explanation


    Indices: 4190--4232  Score: 50
    Period size: 15  Copynumber: 2.8  Consensus size: 15

       4180 ATCGAGGAGG

                       *    
       4190 AGAAGGAAGAGGAGAA
          1 AGAA-GAAGAGAAGAA

                     *     
       4206 AGAAGAAGAAAAGAA
          1 AGAAGAAGAGAAGAA

                 *      
       4221 AGAAGGAGAGAA
          1 AGAAGAAGAGAA

       4233 AGAGGAAGTT


Statistics
Matches: 23,  Mismatches: 4, Indels: 1
        0.82            0.14        0.04

Matches are distributed among these distances:
  15   19  0.83
  16    4  0.17

ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00


Consensus pattern (15 bp):   
AGAAGAAGAGAAGAA
Done.