Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006880.1 Kokia drynarioides strain JFW-HI SEQ_121481, 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: 24127
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:504 original size:16 final size:17

Alignment explanation


    Indices: 483--516  Score: 52
    Period size: 16  Copynumber: 2.1  Consensus size: 17

        473 ATAGAATATT

                   *         
        483 ATTTTATTAATT-TAAA
          1 ATTTTATAAATTATAAA

                             
        499 ATTTTATAAATTATAAA
          1 ATTTTATAAATTATAAA

             
        516 A
          1 A

        517 AATAATTTAC


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  16   11  0.69
  17    5  0.31

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (17 bp):   
ATTTTATAAATTATAAA

Found at i:3034 original size:105 final size:105

Alignment explanation


    Indices: 2881--3192  Score: 428
    Period size: 105  Copynumber: 3.0  Consensus size: 105

       2871 ATATTTTCAT

                 *   *   *                   *    ***            *           
       2881 GTATAATATGTTGATTGATGCACATTGCAAGGAGGGGACAATTTCTGAAGCTGTAGATATTGTTG
          1 GTATAGTATATTGGTTGATGCACATTGCAAGGAAGGGATGGTTTCTGAAGCTGAAGATATTGTTG

                               *                    
       2946 ACACAATGAGAAAGCAAGGGATTGAGCCTAATGTTGTCAC
         66 ACACAATGAGAAAGCAAGGCATTGAGCCTAATGTTGTCAC

                                 *                     *        *  *         
       2986 GTATAGTATATTGGTTGATGCGCATTGCAAGGAAGGGATGGTTCCTGAAGCTAAACATATTGTTG
          1 GTATAGTATATTGGTTGATGCACATTGCAAGGAAGGGATGGTTTCTGAAGCTGAAGATATTGTTG

             *       *                              
       3051 AGACAATGATAAAGCAAGGCATTGAGCCTAATGTTGTCAC
         66 ACACAATGAGAAAGCAAGGCATTGAGCCTAATGTTGTCAC

                           *       *                     *                   
       3091 GTATAGTATATTGGTCGATGCACTTTGCAA-GAAGGGGATGGTTTTTGAAGCTGAAGATATTGTT
          1 GTATAGTATATTGGTTGATGCACATTGCAAGGAA-GGGATGGTTTCTGAAGCTGAAGATATTGTT

                          *               *       
       3155 GACACAATGAGAAATCAAGGCATTGAGCCTGATGTTGT
         65 GACACAATGAGAAAGCAAGGCATTGAGCCTAATGTTGT

       3193 TACCTATAAC


Statistics
Matches: 180,  Mismatches: 26, Indels: 2
        0.87            0.12        0.01

Matches are distributed among these distances:
 104    3  0.02
 105  177  0.98

ACGTcount: A:0.31, C:0.12, G:0.27, T:0.29


Consensus pattern (105 bp):   
GTATAGTATATTGGTTGATGCACATTGCAAGGAAGGGATGGTTTCTGAAGCTGAAGATATTGTTG
ACACAATGAGAAAGCAAGGCATTGAGCCTAATGTTGTCAC

Found at i:6377 original size:28 final size:28

Alignment explanation


    Indices: 6337--6405  Score: 111
    Period size: 28  Copynumber: 2.5  Consensus size: 28

       6327 CAAACTACAG

                                        
       6337 TAAGTGGCGAGCTTCCATAAATGAACAA
          1 TAAGTGGCGAGCTTCCATAAATGAACAA

                          *            *
       6365 TAAGTGGCGAGCTTTCATAAATGAACAG
          1 TAAGTGGCGAGCTTCCATAAATGAACAA

                   *     
       6393 TAAGTGGTGAGCT
          1 TAAGTGGCGAGCT

       6406 CATTATTTTT


Statistics
Matches: 38,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  28   38  1.00

ACGTcount: A:0.35, C:0.14, G:0.26, T:0.25


Consensus pattern (28 bp):   
TAAGTGGCGAGCTTCCATAAATGAACAA

Found at i:18409 original size:85 final size:85

Alignment explanation


    Indices: 18285--18466  Score: 244
    Period size: 85  Copynumber: 2.1  Consensus size: 85

      18275 TTTTTCAAAC

                                         *           *                       
      18285 TGTCTCTTCTAACTCAATACTTACGTTATTATCCTATGATTTCTCCATCTTTTGAGA-TGTTGCT
          1 TGTC-CTTCTAACTCAATACTTACGTTATCATCCTATGATTCCTCCATCTTTTGAGACT-TTG-T

                  *                
      18349 -TCACTTCACCTTTCCATTAGCA
         63 ATCACTGCACCTTTCCATTAGCA

             *                    **                                         
      18371 TTTCCTTCTAACTCAATACTCTTTG-TATCATCCTATGATTCCTCCATCTTTTGAGACTTTGTAT
          1 TGTCCTTCTAACTCAATACT-TACGTTATCATCCTATGATTCCTCCATCTTTTGAGACTTTGTAT

                                 
      18435 CACTGCACCTTTCCATTAGCA
         65 CACTGCACCTTTCCATTAGCA

                  *    
      18456 TGTCCTACTAA
          1 TGTCCTTCTAA

      18467 TACATCACAA


Statistics
Matches: 85,  Mismatches: 8, Indels: 7
        0.85            0.08        0.07

Matches are distributed among these distances:
  84    1  0.01
  85   78  0.92
  86    6  0.07

ACGTcount: A:0.21, C:0.27, G:0.09, T:0.43


Consensus pattern (85 bp):   
TGTCCTTCTAACTCAATACTTACGTTATCATCCTATGATTCCTCCATCTTTTGAGACTTTGTATC
ACTGCACCTTTCCATTAGCA
Done.