Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000073.1 Kokia drynarioides strain JFW-HI SEQ_110687, 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: 6363
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28


Found at i:119 original size:50 final size:50

Alignment explanation


    Indices: 33--170  Score: 172
    Period size: 50  Copynumber: 2.7  Consensus size: 50

         23 TGCATGACTT

                                                                 
         33 GATTTAATGATGCAAACTTTAACTAACATGAGAGTTACATAATGCATGAT-AG
          1 GATTT-ATGATGCAAA-TTTAACTAACATGAGAGTTACATAATGCATG-TCAG

                         *                       *            *
         85 GATTTATGATGCATATTTAACTAACATGTA-AGTTACTTAATGCATGTCAT
          1 GATTTATGATGCAAATTTAACTAACATG-AGAGTTACATAATGCATGTCAG

            *              *                    
        135 TATTTATGATGCAAACTTAACTAATCATGAGAGTTA
          1 GATTTATGATGCAAATTTAACTAA-CATGAGAGTTA

        171 ATGGATGTCA


Statistics
Matches: 76,  Mismatches: 6, Indels: 9
        0.84            0.07        0.10

Matches are distributed among these distances:
  49    1  0.01
  50   51  0.67
  51   19  0.25
  52    5  0.07

ACGTcount: A:0.38, C:0.12, G:0.15, T:0.36


Consensus pattern (50 bp):   
GATTTATGATGCAAATTTAACTAACATGAGAGTTACATAATGCATGTCAG

Found at i:835 original size:216 final size:217

Alignment explanation


    Indices: 531--927  Score: 550
    Period size: 216  Copynumber: 1.8  Consensus size: 217

        521 GCTCACATCA

                *          *       *             *      *            *       
        531 ATTTTCGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCTGAACTTGTCAAATTTTTACG
          1 ATTTACGTGAGAATTATTTCTCTATTGGTTCTTGGACAAACTTCCGAACTTGTCAAACTTTTACG

              * *           *             *                     *          * 
        596 AGTTCTGTTATAACTTTGGTTCCTTA-ATGTATTCAAGA-CATCCATTCCTTTGAGAAATTTTTC
         66 AGATATGTTATAACTTCGGTTCCTTACA-GAATTCAAGATCATCCATTCCTTCGAGAAATTTTCC

            *                                                                
        659 GAACATTCCATGCACAAGAAATCGCATCA-TTTGGTCTAAATAGTTTGTCATTTTTGTAAACAAT
        130 AAACATTCCATGCACAAGAAATCGCAT-AGTTTGGTCTAAATAGTTTGTCATTTTTGTAAACAAT

                                    
        723 TTTTTTTCTTTGAATTAAAAACGT
        194 TTTTTTTCTTTGAATTAAAAACGT

                                                                             
        747 ATTTACGTGAGAATTATTTCTCTATTGGTT-TTGAGACAAACTTCCGAACTTGTCAAACTTTTAC
          1 ATTTACGTGAGAATTATTTCTCTATTGGTTCTTG-GACAAACTTCCGAACTTGTCAAACTTTTAC

                   *                          *     *               *        
        811 GAGATATTTTATAACTTCGGTTCCTTACAGAATTTAAGATGATCCATTCCTTCGAGCAATTTTCC
         65 GAGATATGTTATAACTTCGGTTCCTTACAGAATTCAAGATCATCCATTCCTTCGAGAAATTTTCC

                         * **               *                   
        876 AAACATTCCATGCTCGGGAAATCGCATAGTTTTGTCTAAATAGTTTGTCATT
        130 AAACATTCCATGCACAAGAAATCGCATAGTTTGGTCTAAATAGTTTGTCATT

        928 CTTGACCTTA


Statistics
Matches: 156,  Mismatches: 21, Indels: 7
        0.85            0.11        0.04

Matches are distributed among these distances:
 215    3  0.02
 216   86  0.55
 217   67  0.43

ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41


Consensus pattern (217 bp):   
ATTTACGTGAGAATTATTTCTCTATTGGTTCTTGGACAAACTTCCGAACTTGTCAAACTTTTACG
AGATATGTTATAACTTCGGTTCCTTACAGAATTCAAGATCATCCATTCCTTCGAGAAATTTTCCA
AACATTCCATGCACAAGAAATCGCATAGTTTGGTCTAAATAGTTTGTCATTTTTGTAAACAATTT
TTTTTCTTTGAATTAAAAACGT

Found at i:3393 original size:13 final size:14

Alignment explanation


    Indices: 3372--3410  Score: 53
    Period size: 13  Copynumber: 2.8  Consensus size: 14

       3362 AAGATCAAAG

                *         
       3372 AAAGTGAAAAGA-A
          1 AAAGAGAAAAGATA

                          
       3385 AAAGAGAAAAGATA
          1 AAAGAGAAAAGATA

                        
       3399 AAAGATGAAAAG
          1 AAAGA-GAAAAG

       3411 GAAGAAAAAG


Statistics
Matches: 23,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  13   11  0.48
  14    6  0.26
  15    6  0.26

ACGTcount: A:0.69, C:0.00, G:0.23, T:0.08


Consensus pattern (14 bp):   
AAAGAGAAAAGATA
Done.