Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012840.1 Kokia drynarioides strain JFW-HI SEQ_127853, 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: 7366
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33

Warning! 50 characters in sequence are not A, C, G, or T


Found at i:299 original size:39 final size:39

Alignment explanation


    Indices: 253--370  Score: 152
    Period size: 39  Copynumber: 3.0  Consensus size: 39

        243 CACCATCAAC

                                                   
        253 CAATCTCTTACCCCGAGCTTGGGGTAGATTGCAACCATT
          1 CAATCTCTTACCCCGAGCTTGGGGTAGATTGCAACCATT

                                *                  
        292 CAATCTCTTACCCCGAGCTTAGGGTAGA-T-C-ACCATT
          1 CAATCTCTTACCCCGAGCTTGGGGTAGATTGCAACCATT

                      *          *     *              
        328 AGCCAATCTCCTACCCCGAGCCTGGGGCAGATTGCAACCATT
          1 ---CAATCTCTTACCCCGAGCTTGGGGTAGATTGCAACCATT

             
        370 C
          1 C

        371 GGTCTTTTAC


Statistics
Matches: 68,  Mismatches: 5, Indels: 12
        0.80            0.06        0.14

Matches are distributed among these distances:
  36    6  0.09
  37    1  0.01
  38    1  0.01
  39   52  0.76
  40    1  0.01
  41    1  0.01
  42    6  0.09

ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25


Consensus pattern (39 bp):   
CAATCTCTTACCCCGAGCTTGGGGTAGATTGCAACCATT

Found at i:370 original size:78 final size:78

Alignment explanation


    Indices: 241--434  Score: 246
    Period size: 78  Copynumber: 2.5  Consensus size: 78

        231 GTGAAGTTAC

                      *                   *     *                            
        241 ATCACCATCAACCAATCTCTTACCCCGAGCTTGGGGTAGATTGCAACCATTCAATCTCTTACCCC
          1 ATCACCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCATTCAATCTCTTACCCC

            *     *    *  
        306 GAG-CTTAGGGTAG
         66 AAGCCTGA-GGCAG

                    *          *                                **   *     * 
        319 ATCACCATTAGCCAATCTCCTACCCCGAGCCTGGGGCAGATTGCAACCATTCGGTCTTTTACCTC
          1 ATCACCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCATTCAATCTCTTACCCC

                         
        384 AAGCCTGAGGCAG
         66 AAGCCTGAGGCAG

                 *                  *             
        397 ATCACTATCAGCCAATCTCTTACCTCGAGCCTGGGGCA
          1 ATCACCATCAGCCAATCTCTTACCCCGAGCCTGGGGCA

        435 AATCATCATC


Statistics
Matches: 99,  Mismatches: 16, Indels: 2
        0.85            0.14        0.02

Matches are distributed among these distances:
  78   96  0.97
  79    3  0.03

ACGTcount: A:0.24, C:0.32, G:0.19, T:0.24


Consensus pattern (78 bp):   
ATCACCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCATTCAATCTCTTACCCC
AAGCCTGAGGCAG

Found at i:420 original size:39 final size:39

Alignment explanation


    Indices: 377--459  Score: 105
    Period size: 39  Copynumber: 2.1  Consensus size: 39

        367 ATTCGGTCTT

                               *           *        
        377 TTACCTCAAGCCTGAGGCAGATCA-CTATCAGCCAATCTC
          1 TTACCTCAAGCCTGAGGCAAATCATC-ATCAACCAATCTC

                   *      *                        
        416 TTACCTCGAGCCTGGGGCAAATCATCATCAACCAATCTC
          1 TTACCTCAAGCCTGAGGCAAATCATCATCAACCAATCTC

            *    
        455 CTACC
          1 TTACC

        460 CCGAGTCTGG


Statistics
Matches: 38,  Mismatches: 5, Indels: 2
        0.84            0.11        0.04

Matches are distributed among these distances:
  39   37  0.97
  40    1  0.03

ACGTcount: A:0.28, C:0.35, G:0.14, T:0.23


Consensus pattern (39 bp):   
TTACCTCAAGCCTGAGGCAAATCATCATCAACCAATCTC
Done.