Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009858.1 Kokia drynarioides strain JFW-HI SEQ_124590, 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: 8038
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.32

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:4786 original size:74 final size:73

Alignment explanation


    Indices: 4628--4813  Score: 212
    Period size: 74  Copynumber: 2.5  Consensus size: 73

       4618 TGTGCCATAT

                *       *                 *     *                   **       
       4628 AAATAAGAAACAATGAGTTACACAGGTTGGGCACACTGGCGTGTGCTAGACCGTGTGGGAATTCT
          1 AAATCAGAAACAGTGAGTTACACAGGTTGGACACACGGGCGTGTGCTAGACCGTGTCAGAATTCT

                    
       4693 ATTCAGTG
         66 ATTCAGTG

                  *                 *  *                                     
       4701 AAATCAAAAACAGTGAGTTACACGGGGCTGGACACACGGGCGTGTGCTAGACCGTG-CAGATATT
          1 AAATCAGAAACAGTGAGTTACAC-AGGTTGGACACACGGGCGTGTGCTAGACCGTGTCAGA-ATT

            * *  **   
       4765 TTGTTTTGTG
         64 CTATTCAGTG

            *   *                                  
       4775 GAATTAGAAACAGTGAGTTACACAGGTTGGACACACGGG
          1 AAATCAGAAACAGTGAGTTACACAGGTTGGACACACGGG

       4814 TGTAGGTATG


Statistics
Matches: 93,  Mismatches: 18, Indels: 4
        0.81            0.16        0.03

Matches are distributed among these distances:
  73   36  0.39
  74   57  0.61

ACGTcount: A:0.30, C:0.17, G:0.30, T:0.24


Consensus pattern (73 bp):   
AAATCAGAAACAGTGAGTTACACAGGTTGGACACACGGGCGTGTGCTAGACCGTGTCAGAATTCT
ATTCAGTG

Found at i:5144 original size:39 final size:38

Alignment explanation


    Indices: 5101--5233  Score: 167
    Period size: 39  Copynumber: 3.4  Consensus size: 38

       5091 ACTGATTAGC

                            * **          *       
       5101 AGTGACACTGTAAACATTATGATGCTATACCGAACTAG
          1 AGTGACACTGTAAACACTGCGATGCTATACTGAACTAG

                                    *            * 
       5139 TAGTGACACTGTAAACACTGCGATCCTATACTGAACTGG
          1 -AGTGACACTGTAAACACTGCGATGCTATACTGAACTAG

                                 *                 
       5178 CAGTGACACTGTAAACACTGCAATGCTATACTGAACTAG
          1 -AGTGACACTGTAAACACTGCGATGCTATACTGAACTAG

            *                
       5217 CGATGACACTGTAAACA
          1 AG-TGACACTGTAAACA

       5234 TCGCAAGACT


Statistics
Matches: 82,  Mismatches: 11, Indels: 2
        0.86            0.12        0.02

Matches are distributed among these distances:
  38    1  0.01
  39   81  0.99

ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24


Consensus pattern (38 bp):   
AGTGACACTGTAAACACTGCGATGCTATACTGAACTAG

Found at i:5246 original size:39 final size:38

Alignment explanation


    Indices: 5097--5272  Score: 162
    Period size: 39  Copynumber: 4.5  Consensus size: 38

       5087 CCCTACTGAT

                                  *    *       *    
       5097 TAGCAGTGACACTGTAAACATTATG-ATGCTATACCGAAC
          1 TAGCAGTGACACTGTAAACA--CTGCAAGCTATACTGAAC

               *                      **           
       5136 TAGTAGTGACACTGTAAACACTGCGATCCTATACTGAAC
          1 TAGCAGTGACACTGTAAACACTGC-AAGCTATACTGAAC

             *                                     
       5175 TGGCAGTGACACTGTAAACACTGCAATGCTATACTGAAC
          1 TAGCAGTGACACTGTAAACACTGCAA-GCTATACTGAAC

                                               *      
       5214 TAGC-GATGACACTGTAAACA-TCGCAAGACTATATTGCAA-
          1 TAGCAG-TGACACTGTAAACACT-GCAAG-CTATACTG-AAC

               *       *        
       5253 TAGTAGTGACATTGTAAACA
          1 TAGCAGTGACACTGTAAACA

       5273 TTACTAAAGC


Statistics
Matches: 117,  Mismatches: 12, Indels: 16
        0.81            0.08        0.11

Matches are distributed among these distances:
  37    2  0.02
  38    4  0.03
  39  108  0.92
  40    3  0.03

ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25


Consensus pattern (38 bp):   
TAGCAGTGACACTGTAAACACTGCAAGCTATACTGAAC

Found at i:5246 original size:78 final size:78

Alignment explanation


    Indices: 5097--5272  Score: 187
    Period size: 78  Copynumber: 2.3  Consensus size: 78

       5087 CCCTACTGAT

                                *  **                 *                    * 
       5097 TAGCAGTGACACTGTAAACATTATGATGCTATACCGAACTAGTAGTGACACTGTAAACACTGCGA
          1 TAGCAGTGACACTGTAAACACTACAATGCTATACCGAACTAGGAGTGACACTGTAAACACTGCAA

            **           
       5162 TCCTATACTG-AA
         66 GACTATACTGCAA

              *                    *           *                             
       5174 CTGGCAGTGACACTGTAAACACTGCAATGCTATACTGAACTAGCGA-TGACACTGTAAACA-TCG
          1 -TAGCAGTGACACTGTAAACACTACAATGCTATACCGAACTAG-GAGTGACACTGTAAACACT-G

                      *     
       5237 CAAGACTATATTGCAA
         63 CAAGACTATACTGCAA

               *       *        
       5253 TAGTAGTGACATTGTAAACA
          1 TAGCAGTGACACTGTAAACA

       5273 TTACTAAAGC


Statistics
Matches: 81,  Mismatches: 14, Indels: 6
        0.80            0.14        0.06

Matches are distributed among these distances:
  77    1  0.01
  78   77  0.95
  79    3  0.04

ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25


Consensus pattern (78 bp):   
TAGCAGTGACACTGTAAACACTACAATGCTATACCGAACTAGGAGTGACACTGTAAACACTGCAA
GACTATACTGCAA
Done.