Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012732.1 Kokia drynarioides strain JFW-HI SEQ_127743, 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: 14655
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35


Found at i:84 original size:30 final size:29

Alignment explanation


    Indices: 1--86  Score: 93
    Period size: 29  Copynumber: 2.9  Consensus size: 29

                       *       *      *  
          1 CCCAAAACTTTTTAAAATTCCATTTTTAC
          1 CCCAAAACTTTCTAAAATTTCATTTTGAC

               *     *                    
         30 CCCCAAAC-CTCTAAAATTTCCATTTTGAC
          1 CCCAAAACTTTCTAAAATTT-CATTTTGAC

                        *               
         59 CCCAAAACTTTCAAAAATTGTCATTTTG
          1 CCCAAAACTTTCTAAAATT-TCATTTTG

         87 CCCTCGAATG


Statistics
Matches: 46,  Mismatches: 8, Indels: 5
        0.78            0.14        0.08

Matches are distributed among these distances:
  28    8  0.17
  29   22  0.48
  30   15  0.33
  31    1  0.02

ACGTcount: A:0.34, C:0.27, G:0.03, T:0.36


Consensus pattern (29 bp):   
CCCAAAACTTTCTAAAATTTCATTTTGAC

Found at i:174 original size:29 final size:29

Alignment explanation


    Indices: 14--174  Score: 78
    Period size: 29  Copynumber: 5.5  Consensus size: 29

          4 AAAACTTTTT

                                   *     
         14 AAAATTCCATTTTTACCCCCAAACCTCTA
          1 AAAATTCCATTTTTACCCCCAAATCTCTA

               *         *         *  *   
         43 AAATTTCCATTTTGA-CCCCAAAACTTTCA
          1 AAAATTCCATTTTTACCCCCAAATCTCT-A

                   *       *   * *   *  * 
         72 AAAATTGTCA-TTTTGCCCTCGAATGTCCA
          1 AAAATT-CCATTTTTACCCCCAAATCTCTA

                *             ** *        *
        101 AAAACTCCATTTTTCGACTTCGAAA-CTCTC
          1 AAAATTCCATTTTT--ACCCCCAAATCTCTA

               *      *              *    
        131 AAATTTACC-CTTTTACCCCCAAATATCTA
          1 AAAATT-CCATTTTTACCCCCAAATCTCTA

                           
        160 AAAATTCCATTTTTA
          1 AAAATTCCATTTTTA

        175 ACCATGAATT


Statistics
Matches: 88,  Mismatches: 35, Indels: 18
        0.62            0.25        0.13

Matches are distributed among these distances:
  28   20  0.23
  29   45  0.51
  30   18  0.20
  31    5  0.06

ACGTcount: A:0.33, C:0.28, G:0.04, T:0.35


Consensus pattern (29 bp):   
AAAATTCCATTTTTACCCCCAAATCTCTA

Found at i:596 original size:97 final size:96

Alignment explanation


    Indices: 463--645  Score: 246
    Period size: 97  Copynumber: 1.9  Consensus size: 96

        453 AAAACTTTAA

                                                    *                       *
        463 AATCGAGGCAATATTCTTTTATTTCGAGTTTCGAAAATTTGCACCTTAACTTACTAGGTGCAATT
          1 AATCGAGGCAATATTCTTTTATTTCGAGTTTCGAAAATTTACACCTTAACTTACTAGGTGCAA-C

            *    *                          
        528 TTTTCTTCAAATCGAAATAATCGAATACCCTT
         65 CTTTCCTCAAATCGAAATAATCGAATACCCTT

                        *                                *                   
        560 AATCGAGGCAATGTT-TTCTTATCTTCGA--TTCTGAAAATTTACGCCTTAACTTACTAGGTGCA
          1 AATCGAGGCAATATTCTT-TTAT-TTCGAGTTTC-GAAAATTTACACCTTAACTTACTAGGTGCA

                             *      
        622 ACCTTTCCTCAAATCGAGATAATC
         63 ACCTTTCCTCAAATCGAAATAATC

        646 CTTTTCCCAA


Statistics
Matches: 76,  Mismatches: 7, Indels: 7
        0.84            0.08        0.08

Matches are distributed among these distances:
  96   24  0.32
  97   47  0.62
  98    5  0.07

ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37


Consensus pattern (96 bp):   
AATCGAGGCAATATTCTTTTATTTCGAGTTTCGAAAATTTACACCTTAACTTACTAGGTGCAACC
TTTCCTCAAATCGAAATAATCGAATACCCTT

Found at i:9226 original size:60 final size:57

Alignment explanation


    Indices: 9136--9247  Score: 179
    Period size: 60  Copynumber: 1.9  Consensus size: 57

       9126 CCGATGACAA

                             *              *                        
       9136 TGTTGAATCCAAAAACTTCAACTTGAATGAGATGAGCAATGATGAATCCGACAGCAG
          1 TGTTGAATCCAAAAACTCCAACTTGAATGAGAAGAGCAATGATGAATCCGACAGCAG

                                                                   
       9193 TGTTGAATCCAGTGAAAACTCCAACTTGAATGAGAAGAGCAATGATGAATCCGAC
          1 TGTTGAATCCA---AAAACTCCAACTTGAATGAGAAGAGCAATGATGAATCCGAC

       9248 GACGGTTTTT


Statistics
Matches: 50,  Mismatches: 2, Indels: 3
        0.91            0.04        0.05

Matches are distributed among these distances:
  57   11  0.22
  60   39  0.78

ACGTcount: A:0.38, C:0.18, G:0.21, T:0.22


Consensus pattern (57 bp):   
TGTTGAATCCAAAAACTCCAACTTGAATGAGAAGAGCAATGATGAATCCGACAGCAG
Done.