Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006863.1 Kokia drynarioides strain JFW-HI SEQ_121462, 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: 6922
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34


Found at i:3068 original size:54 final size:55

Alignment explanation


    Indices: 2998--3146  Score: 178
    Period size: 54  Copynumber: 2.7  Consensus size: 55

       2988 GTCAATTTTT

                  *    *                                           
       2998 AAAGACGAAATTATATTATCATATTTGAAAAATAAATTGATC-GGTCGATCTTTA
          1 AAAGACAAAATGATATTATCATATTTGAAAAATAAATTGATCAGGTCGATCTTTA

                                            *             *           
       3052 AAAGACAAAATGATATTATCATATTT-ATAAAGTAAATTGATCATATGTCGATCTTTA
          1 AAAGACAAAATGATATTATCATATTTGA-AAAATAAATTGATC--AGGTCGATCTTTA

                * *             *      *           
       3109 AAAGTCTAAATGATATTATCGTA-TTGCAAAATAAATTG
          1 AAAGACAAAATGATATTATCATATTTGAAAAATAAATTG

       3147 GCCGGTCTTT


Statistics
Matches: 81,  Mismatches: 9, Indels: 8
        0.83            0.09        0.08

Matches are distributed among these distances:
  53    1  0.01
  54   37  0.46
  56   12  0.15
  57   31  0.38

ACGTcount: A:0.44, C:0.09, G:0.12, T:0.36


Consensus pattern (55 bp):   
AAAGACAAAATGATATTATCATATTTGAAAAATAAATTGATCAGGTCGATCTTTA

Found at i:3078 original size:27 final size:26

Alignment explanation


    Indices: 3048--3133  Score: 64
    Period size: 27  Copynumber: 3.1  Consensus size: 26

       3038 TCGGTCGATC

                                       
       3048 TTTAAAAGACAAAATGATATTATCATA
          1 TTTAAAAG-CAAAATGATATTATCATA

                     *   *         *     *
       3075 TTTATAAAGTAAATTGATCATATGTCGATC
          1 TTTA-AAAGCAAAATGAT-AT-TATC-ATA

                      *             *  
       3105 TTTAAAAGTCTAAATGATATTATCGTA
          1 TTTAAAAG-CAAAATGATATTATCATA

              
       3132 TT
          1 TT

       3134 GCAAAATAAA


Statistics
Matches: 44,  Mismatches: 10, Indels: 10
        0.69            0.16        0.16

Matches are distributed among these distances:
  27   14  0.32
  28    9  0.20
  29    9  0.20
  30   12  0.27

ACGTcount: A:0.42, C:0.08, G:0.10, T:0.40


Consensus pattern (26 bp):   
TTTAAAAGCAAAATGATATTATCATA

Found at i:6874 original size:167 final size:158

Alignment explanation


    Indices: 6532--6922  Score: 613
    Period size: 167  Copynumber: 2.4  Consensus size: 158

       6522 TTTTATTAGA

                                                   *           *             
       6532 TAATAATAATAATAATTAACTTGC-AAAAATATAACAACCTGACCACTAAACAAAATAGAAAAAA
          1 TAATAATAATAATAATTAACTTGCAAAAAATATAACAACTTGACCACTAAATAAAATAG-----A

                                                                             
       6596 AAAAAAAAAAAAGAAACACTAACAATTTAGGCCATACTCAACATGACACAAAGGAAATTTTATTT
         61 AAAAAAAAAAAAGAAACACTAACAATTTAGGCCATACTCAACATGACACAAAGGAAATTTTATTT

                      *                      
       6661 AATAGAGCGGGCTAATTTTTGTCATCAAATGGT
        126 AATAGAGCGGACTAATTTTTGTCATCAAATGGT

                                                                             
       6694 TAATAATAATAATAATTAACTTGCAAAAAATATAACAACTTGACCACTAAATAAAATAGAAAAAA
          1 TAATAATAATAATAATTAACTTGCAAAAAATATAACAACTTGACCACTAAATAAAATAGAAAAAA

                                                             *               
       6759 AAAAAAAGAAACACTAACAATTTAGGCCATACTCAACATGACACAAAGGGAATTTTATTTAATGG
         66 AAAAAAAGAAACACTAACAATTTAGGCCATACTCAACATGACACAAAGGAAATTTTATTTAAT--

                                                 
       6824 AGAAAACTTGGCGGACTAATTTTTGTCATCAAATGGT
        129 AG---A----GCGGACTAATTTTTGTCATCAAATGGT

                                                                          
       6861 TAATAATAATAATAATTAACTTGCAAAAAATATAACAACTTGACCACTAAATAAAATAGAAA
          1 TAATAATAATAATAATTAACTTGCAAAAAATATAACAACTTGACCACTAAATAAAATAGAAA


Statistics
Matches: 215,  Mismatches: 4, Indels: 15
        0.92            0.02        0.06

Matches are distributed among these distances:
 158   68  0.32
 160    2  0.01
 162   24  0.11
 163   33  0.15
 167   88  0.41

ACGTcount: A:0.51, C:0.13, G:0.10, T:0.25


Consensus pattern (158 bp):   
TAATAATAATAATAATTAACTTGCAAAAAATATAACAACTTGACCACTAAATAAAATAGAAAAAA
AAAAAAAGAAACACTAACAATTTAGGCCATACTCAACATGACACAAAGGAAATTTTATTTAATAG
AGCGGACTAATTTTTGTCATCAAATGGT
Done.