Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012529.1 Kokia drynarioides strain JFW-HI SEQ_127536, 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: 14656
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32

Warning! 10 characters in sequence are not A, C, G, or T


Found at i:4369 original size:169 final size:165

Alignment explanation


    Indices: 4096--4503  Score: 401
    Period size: 168  Copynumber: 2.4  Consensus size: 165

       4086 CTGGTGTTTA

                            *  *   *      *    *     *                       
       4096 TAAGCAACCAAACAGATAACCAATGTAATTCAAAACACTAATATACATCTTTTTCATTT-TCTTT
          1 TAAGCAACCAAACAGACAAACAAGGTAATTAAAAAGACTAACATACATCTTTTTC-TTTCTCTTT

                *    *      *         *                                      
       4160 GAATAAAAATAAATTAGGAAACCAAAGTTAAACCAAAAACCCTTCGA-ATGCATAAG-AAAGTTG
         65 GAATGAAAACAAATTAAGAAACCAAAATTAAACCAAAAACCCTTCGATA-GCATAAGAAAAGTT-

            *****       ***                 *        
       4223 TTTTTTTCTTGTTTTGATTTCCCAGAATTTCCCGGGCTTTC
        128 CAAAATT-TT-TCCCGATTTCCCA-AATTTCCAGGGCTTTC

                                          *                   *              
       4264 TAAGCAACCAAACAGACAAACAAGGTAATTTAAAAGACTAACATACTATCCTTTTCTTTCTCTTT
          1 TAAGCAACCAAACAGACAAACAAGGTAATTAAAAAGACTAACATAC-ATCTTTTTCTTTCTCTTT

                       **        *                       *         *         
       4329 GAATGAAAACACCTTAAGAAAGCAAAATT-AACCGAAAAACCCTTTGATAGCATATGAAAAGTTC
         65 GAATGAAAACAAATTAAGAAACCAAAATTAAACC-AAAAACCCTTCGATAGCATAAGAAAAGTTC

                               *  *         *    
       4393 AAAATTTTTCCCGATTTCCTAATTTTCCAGGGGTTTC
        129 AAAATTTTTCCCGATTTCCCAAATTTCCAGGGCTTTC

            *                                      *                  *      
       4430 AAAGCAACCAAACAGACAAACAAGGTAAGTTAAAAGAGATTAACATACCATCTTTTTCCTTCTCT
          1 TAAGCAACCAAACAGACAAACAAGGTAA-TTAAAA-AGACTAACATA-CATCTTTTTCTTTCTCT

                     
       4495 TTGAATGAA
         63 TTGAATGAA

       4504 GAATAAACCT


Statistics
Matches: 199,  Mismatches: 33, Indels: 16
        0.80            0.13        0.06

Matches are distributed among these distances:
 166   40  0.20
 167   14  0.07
 168   82  0.41
 169   56  0.28
 170    7  0.04

ACGTcount: A:0.39, C:0.19, G:0.11, T:0.30


Consensus pattern (165 bp):   
TAAGCAACCAAACAGACAAACAAGGTAATTAAAAAGACTAACATACATCTTTTTCTTTCTCTTTG
AATGAAAACAAATTAAGAAACCAAAATTAAACCAAAAACCCTTCGATAGCATAAGAAAAGTTCAA
AATTTTTCCCGATTTCCCAAATTTCCAGGGCTTTC

Found at i:5055 original size:23 final size:25

Alignment explanation


    Indices: 5010--5055  Score: 69
    Period size: 23  Copynumber: 1.9  Consensus size: 25

       5000 AAATATAGTT

                          *          
       5010 AAATATAATATATTTAAATTAAACA
          1 AAATATAATATATTAAAATTAAACA

                                   
       5035 AAATATAAT-T-TTAAAATTAAA
          1 AAATATAATATATTAAAATTAAA

       5056 AAATACAATA


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  23   10  0.50
  24    1  0.05
  25    9  0.45

ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37


Consensus pattern (25 bp):   
AAATATAATATATTAAAATTAAACA
Done.