Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008516.1 Kokia drynarioides strain JFW-HI SEQ_123192, 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: 11043
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32


Found at i:4279 original size:15 final size:15

Alignment explanation


    Indices: 4259--4300  Score: 57
    Period size: 15  Copynumber: 2.8  Consensus size: 15

       4249 CCATATACGA

                          *
       4259 ATATATATATACTAT
          1 ATATATATATACTAC

                       *   
       4274 ATATATATATATTAC
          1 ATATATATATACTAC

               *        
       4289 ATACATATATAC
          1 ATATATATATAC

       4301 ATACCTATTT


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  15   23  1.00

ACGTcount: A:0.48, C:0.10, G:0.00, T:0.43


Consensus pattern (15 bp):   
ATATATATATACTAC

Found at i:4706 original size:24 final size:24

Alignment explanation


    Indices: 4666--4712  Score: 69
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       4656 ATTTAGCAGT

                             *      
       4666 ATAATATATTTATCATTTATTAGC
          1 ATAATATATTTATCATTGATTAGC

                                    
       4690 ATAATATATTT-TACATTGATTAG
          1 ATAATATATTTAT-CATTGATTAG

       4713 AATTAGGCTT


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  23    1  0.05
  24   20  0.95

ACGTcount: A:0.38, C:0.06, G:0.06, T:0.49


Consensus pattern (24 bp):   
ATAATATATTTATCATTGATTAGC

Found at i:7782 original size:24 final size:24

Alignment explanation


    Indices: 7745--7804  Score: 77
    Period size: 24  Copynumber: 2.5  Consensus size: 24

       7735 TTTCTAGAAG

                 *   *               
       7745 ATTTAGTAGTATAATATA-TTTAGC
          1 ATTTATTAGAATAATATATTTTA-C

                                    
       7769 ATTTATTAGAATAATATATTTTAC
          1 ATTTATTAGAATAATATATTTTAC

               *        
       7793 ATTGATTAGAAT
          1 ATTTATTAGAAT

       7805 TAGGCTTTTT


Statistics
Matches: 32,  Mismatches: 3, Indels: 2
        0.86            0.08        0.05

Matches are distributed among these distances:
  24   28  0.88
  25    4  0.12

ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47


Consensus pattern (24 bp):   
ATTTATTAGAATAATATATTTTAC

Found at i:10829 original size:40 final size:40

Alignment explanation


    Indices: 10716--10911  Score: 128
    Period size: 40  Copynumber: 4.9  Consensus size: 40

      10706 TTTCTAATCA

                    *          *        *            
      10716 ATTCACCGGCTCATAGCCTACTAAGCCGTAGCTTGAATTTT
          1 ATTCACCGACTCATAGCCTGCTAAGCCGAAGCTTGAA-TTT

             *   ** *  **       *    *               
      10757 AAT-AATGGCTTGTAGCCTGATAAGTC-ATAGCTTGAATTT
          1 ATTCACCGACTCATAGCCTGCTAAGCCGA-AGCTTGAATTT

                        *   *  **                   
      10796 ATTCACCGACTCGTAGTCTTTTAAGCCGAAGCTTGAATTT
          1 ATTCACCGACTCATAGCCTGCTAAGCCGAAGCTTGAATTT

                 *  *                *               
      10836 ATTCATCGGCTCATAGCCTGCTAAGTCGAAGCTTGAATTCT
          1 ATTCACCGACTCATAGCCTGCTAAGCCGAAGCTTGAATT-T

                 ***    *   **                  
      10877 A-TCAATAACTCGTAGGTTGCTAAGCCGAAGCTTGA
          1 ATTCACCGACTCATAGCCTGCTAAGCCGAAGCTTGA

      10912 CTTCTTTTCA


Statistics
Matches: 118,  Mismatches: 33, Indels: 9
        0.74            0.21        0.06

Matches are distributed among these distances:
  39    5  0.04
  40  108  0.92
  41    5  0.04

ACGTcount: A:0.27, C:0.21, G:0.19, T:0.32


Consensus pattern (40 bp):   
ATTCACCGACTCATAGCCTGCTAAGCCGAAGCTTGAATTT

Found at i:10888 original size:80 final size:80

Alignment explanation


    Indices: 10736--10911  Score: 189
    Period size: 80  Copynumber: 2.2  Consensus size: 80

      10726 TCATAGCCTA

                    *                      **                                
      10736 CTAAGCCGTAGCTTGAATTTTAATAATGGCTTGTAGCCTGATAAGTCATAGCTTGAATTTATTCA
          1 CTAAGCCGAAGCTTGAATTTTAATAATGGCTCATAGCCTGATAAGTCATAGCTTGAATTTATTCA

            * *            *
      10801 CCGACTCGTA-GTCTT
         66 ACAACTCGTAGGT-TG

            *                     * *                *                       
      10816 TTAAGCCGAAGCTTGAA-TTTATTCATCGGCTCATAGCCTGCTAAGTCGA-AGCTTGAATTCTA-
          1 CTAAGCCGAAGCTTGAATTTTAATAAT-GGCTCATAGCCTGATAAGTC-ATAGCTTGAATT-TAT

                *             
      10878 TCAATAACTCGTAGGTTG
         63 TCAACAACTCGTAGGTTG

                            
      10896 CTAAGCCGAAGCTTGA
          1 CTAAGCCGAAGCTTGA

      10912 CTTCTTTTCA


Statistics
Matches: 80,  Mismatches: 12, Indels: 8
        0.80            0.12        0.08

Matches are distributed among these distances:
  79    7  0.09
  80   68  0.85
  81    5  0.06

ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33


Consensus pattern (80 bp):   
CTAAGCCGAAGCTTGAATTTTAATAATGGCTCATAGCCTGATAAGTCATAGCTTGAATTTATTCA
ACAACTCGTAGGTTG

Found at i:11008 original size:2 final size:2

Alignment explanation


    Indices: 11001--11043  Score: 86
    Period size: 2  Copynumber: 21.5  Consensus size: 2

      10991 AAATCTAAAG

                                                                          
      11001 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

             
      11043 A
          1 A


Statistics
Matches: 41,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   41  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Done.