Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010974.1 Kokia drynarioides strain JFW-HI SEQ_125943, 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: 3318
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35


Found at i:478 original size:30 final size:31

Alignment explanation


    Indices: 410--488  Score: 106
    Period size: 30  Copynumber: 2.6  Consensus size: 31

        400 TCTTTGGTCC

                       *        *          
        410 AAGTTGGTACTCAAACTTGATACTTTTTCTT
          1 AAGTTGGTACTTAAACTTGACACTTTTTCTT

             **                         *  
        441 ATTTTGGTACTTAAACTTGACA-TTTTTTTT
          1 AAGTTGGTACTTAAACTTGACACTTTTTCTT

                              
        471 AAGTTGGTACTTAAACTT
          1 AAGTTGGTACTTAAACTT

        489 TTTAGGGTCC


Statistics
Matches: 41,  Mismatches: 7, Indels: 1
        0.84            0.14        0.02

Matches are distributed among these distances:
  30   23  0.56
  31   18  0.44

ACGTcount: A:0.27, C:0.13, G:0.13, T:0.48


Consensus pattern (31 bp):   
AAGTTGGTACTTAAACTTGACACTTTTTCTT

Found at i:526 original size:89 final size:91

Alignment explanation


    Indices: 351--518  Score: 216
    Period size: 90  Copynumber: 1.9  Consensus size: 91

        341 TAATATAATA

                                                         *      **           
        351 TTTGGTAACTAAACTTGACATTTTTTTTTTAAATTGGTACCTAAATTTTTCTTTGGTCCAAGTTG
          1 TTTGGTAACTAAACTTGACA-TTTTTTTTTAAATTGGTACCTAAACTTTTCTAGGGTCCAAGTTG

                        *              
        416 GTACTCAAACTTGATACTTTTTCTTAT
         65 GTACTCAAACTTCATACTTTTTCTTAT

                                            *       *                    *   
        443 TTTGGT-ACTTAAACTTGACA-TTTTTTTTAAGTTGGTACTTAAACTTTT-TAGGGTCCAATTTG
          1 TTTGGTAAC-TAAACTTGACATTTTTTTTTAAATTGGTACCTAAACTTTTCTAGGGTCCAAGTTG

                 **       
        505 GTACTTGAACTTCA
         65 GTACTCAAACTTCA

        519 CCTTTTTTTT


Statistics
Matches: 66,  Mismatches: 9, Indels: 5
        0.82            0.11        0.06

Matches are distributed among these distances:
  89   22  0.33
  90   25  0.38
  91    2  0.03
  92   17  0.26

ACGTcount: A:0.25, C:0.14, G:0.14, T:0.48


Consensus pattern (91 bp):   
TTTGGTAACTAAACTTGACATTTTTTTTTAAATTGGTACCTAAACTTTTCTAGGGTCCAAGTTGG
TACTCAAACTTCATACTTTTTCTTAT

Found at i:530 original size:92 final size:90

Alignment explanation


    Indices: 350--542  Score: 201
    Period size: 92  Copynumber: 2.1  Consensus size: 90

        340 TTAATATAAT

                                                          *      **          
        350 ATTTGGTAACTAAACTTGACATTTTTTTTTTAAATTGGTACCTAAATTTTTCTTTGGTCCAAGTT
          1 ATTTGGT-ACTAAACTTGACA-TTTTTTTTTAAATTGGTACCTAAACTTTTCTAGGGTCCAAGTT

                         *          *  
        415 GGTACTCAAACTTGATACTTTTTCTTA
         64 GGTACTCAAACTTCATACTTTTTCCTA

            *                               *       *                    *   
        442 TTTTGGTACTTAAACTTGACA-TTTTTTTTAAGTTGGTACTTAAACTTTT-TAGGGTCCAATTTG
          1 ATTTGGTAC-TAAACTTGACATTTTTTTTTAAATTGGTACCTAAACTTTTCTAGGGTCCAAGTTG

                 **           **         
        505 GTACTTGAACTTCACCTTTTTTTTTCCTA
         65 GTACTCAAACTTCA---TACTTTTTCCTA

                     
        534 ATTTGGTAC
          1 ATTTGGTAC

        543 CTAATTTTTT


Statistics
Matches: 83,  Mismatches: 14, Indels: 8
        0.79            0.13        0.08

Matches are distributed among these distances:
  89   22  0.27
  90   25  0.30
  91    2  0.02
  92   34  0.41

ACGTcount: A:0.24, C:0.15, G:0.13, T:0.49


Consensus pattern (90 bp):   
ATTTGGTACTAAACTTGACATTTTTTTTTAAATTGGTACCTAAACTTTTCTAGGGTCCAAGTTGG
TACTCAAACTTCATACTTTTTCCTA

Found at i:820 original size:60 final size:59

Alignment explanation


    Indices: 693--833  Score: 151
    Period size: 60  Copynumber: 2.4  Consensus size: 59

        683 ATAAATTTTG

                       *   *        * *         *           *    *    *
        693 GTACCAAATTGAATCTAAAAAAAGTTTAGTAGCAAATTAAGAAAAAATGTCAAGTTCAG
          1 GTACCAAATTGGATCAAAAAAAAGCTAAGTAGCAAAGTAAGAAAAAATATCAACTTCAA

                           *                *                            
        752 GTACCAAATTGGATCCAAAAAAAGCTAAGATATCAAAGTAAGAAAAAATATCAACTTCAAA
          1 GTACCAAATTGGATCAAAAAAAAGCTAAG-TAGCAAAGTAAGAAAAAATATCAACTTC-AA

               *                   
        813 G-ATCAAATTGGAT-AAAAAAAA
          1 GTACCAAATTGGATCAAAAAAAA

        834 TTTAGATATC


Statistics
Matches: 69,  Mismatches: 11, Indels: 4
        0.82            0.13        0.05

Matches are distributed among these distances:
  59   32  0.46
  60   35  0.51
  61    2  0.03

ACGTcount: A:0.53, C:0.11, G:0.13, T:0.22


Consensus pattern (59 bp):   
GTACCAAATTGGATCAAAAAAAAGCTAAGTAGCAAAGTAAGAAAAAATATCAACTTCAA
Done.