Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001333.1 Kokia drynarioides strain JFW-HI SEQ_112776, 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: 2952
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.32


Found at i:1851 original size:304 final size:299

Alignment explanation


    Indices: 1307--1870  Score: 898
    Period size: 304  Copynumber: 1.9  Consensus size: 299

       1297 AACAAGTCTC

                                                                           * 
       1307 GATTTATAATTTGGAAAATGAAAATGGAGTCGCCAATAAATTTTTTAAAACAGGTGTAATTGGGT
          1 GATTTATAATTTGGAAAATGAAAATGGAGTCGCCAATAAATTTTTTAAAACAGGTGTAATTGGAT

               *                                                           * 
       1372 CACCTTTCGAGATTTTTTTAAAAATCATTAAAATAATTTTGGTATTTGAAACCATAAAACGAGTT
         66 CACATTTCGAGATTTTTTTAAAAATCATTAAAATAATTTTGGTATTTGAAACCATAAAACGAGCT

            *                             *          *   *       *           
       1437 TGAGAGTCGGTTACGAATAAGGAATGATTAGCACCCTTACATGCTTAAAATTGGTACCTAATCGA
        131 CGAGAGTCGGTTACGAATAAGGAATGATTAACACCCTTACACGCTCAAAATTGATACCTAATCGA

                              *                *                             
       1502 TTATTCAAAATCTTATTTGTTGAAAACTAAAAATTTGAGAAAAATTTAAATCGCAATCCTTAAAT
        196 TTATTCAAAATCTTATTTATTGAAAACTAAAAATTCGAGAAAAATTTAAATCGCAATCCTTAAAT

                                                   
       1567 ACATGTGTCGAAACCATTTTTTTTGAAAAAAAAAGTTTT
        261 ACATGTGTCGAAACCATTTTTTTTGAAAAAAAAAGTTTT

                    *                                             *          
       1606 GATTTATATTTTGGAAAATGAAAATGGAGTCGCCACCAATAAATTTTTTTAAAATAGGTGTAATT
          1 GATTTATAATTTGGAAAATGAAAATGGAGTCG---CCAATAAA-TTTTTTAAAACAGGTGTAATT

                  *                                       * *               *
       1671 GGATCATATTTCGAGATTTTTTTAAAAAATCATTAAAATAATTTTGTTCTTTGAAACCATAAAAT
         62 GGATCACATTTCGAGATTTTTTT-AAAAATCATTAAAATAATTTTGGTATTTGAAACCATAAAAC

                                                                             
       1736 GAGCTCGAGAGTCGGTTAC-ACATAAGGAATGATTAACACCCTTACACG-TCCAAAATTGATACC
        126 GAGCTCGAGAGTCGGTTACGA-ATAAGGAATGATTAACACCCTTACACGCT-CAAAATTGATACC

                                                                         *   
       1799 TAATCGATTATTCAAAATCTTATTTATTGAAAACTAAAAATTCGAGAAAAATTTAAATCGCGATC
        189 TAATCGATTATTCAAAATCTTATTTATTGAAAACTAAAAATTCGAGAAAAATTTAAATCGCAATC

                   
       1864 CTTAAAT
        254 CTTAAAT

       1871 GTATGAACGT


Statistics
Matches: 241,  Mismatches: 17, Indels: 9
        0.90            0.06        0.03

Matches are distributed among these distances:
 299   31  0.13
 302    8  0.03
 303   42  0.17
 304  160  0.66

ACGTcount: A:0.39, C:0.12, G:0.14, T:0.34


Consensus pattern (299 bp):   
GATTTATAATTTGGAAAATGAAAATGGAGTCGCCAATAAATTTTTTAAAACAGGTGTAATTGGAT
CACATTTCGAGATTTTTTTAAAAATCATTAAAATAATTTTGGTATTTGAAACCATAAAACGAGCT
CGAGAGTCGGTTACGAATAAGGAATGATTAACACCCTTACACGCTCAAAATTGATACCTAATCGA
TTATTCAAAATCTTATTTATTGAAAACTAAAAATTCGAGAAAAATTTAAATCGCAATCCTTAAAT
ACATGTGTCGAAACCATTTTTTTTGAAAAAAAAAGTTTT

Found at i:2255 original size:18 final size:17

Alignment explanation


    Indices: 2208--2256  Score: 53
    Period size: 18  Copynumber: 2.7  Consensus size: 17

       2198 ATTTACAGGT

                              
       2208 ATAAATAATAAAAAAACA
          1 ATAAATAAT-AAAAAACA

               *          *   
       2226 ATATATACATAAAATACA
          1 ATAAATA-ATAAAAAACA

                         
       2244 ATAAGATAATAAA
          1 ATAA-ATAATAAA

       2257 TTGAGTAAAT


Statistics
Matches: 26,  Mismatches: 3, Indels: 4
        0.79            0.09        0.12

Matches are distributed among these distances:
  18   21  0.81
  19    5  0.19

ACGTcount: A:0.69, C:0.06, G:0.02, T:0.22


Consensus pattern (17 bp):   
ATAAATAATAAAAAACA

Found at i:2365 original size:3 final size:3

Alignment explanation


    Indices: 2359--2396  Score: 76
    Period size: 3  Copynumber: 12.7  Consensus size: 3

       2349 AATAATAATA

                                                              
       2359 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
          1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT

       2397 AATAATAATA


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   35  1.00

ACGTcount: A:0.34, C:0.00, G:0.32, T:0.34


Consensus pattern (3 bp):   
ATG

Found at i:2528 original size:30 final size:30

Alignment explanation


    Indices: 2492--2637  Score: 168
    Period size: 30  Copynumber: 4.9  Consensus size: 30

       2482 ATTAAAACTA

                                          
       2492 GGTCAAATTTGAATTTTTGGAAAGTTTGGG
          1 GGTCAAATTTGAATTTTTGGAAAGTTTGGG

                     *            *   *   
       2522 GGTCAAATTAGAATTTTTGGAAGGTTCGGG
          1 GGTCAAATTTGAATTTTTGGAAAGTTTGGG

                   *  *  *    *        *  
       2552 GGTCAAAATTAAAATTTTAGAAAGTTTAGG
          1 GGTCAAATTTGAATTTTTGGAAAGTTTGGG

                                         *
       2582 GGTCAAATTTGAATTTTTGGAAAGTTT-GA
          1 GGTCAAATTTGAATTTTTGGAAAGTTTGGG

             *       **        *       
       2611 GTTCAAATTCAAATTTTTGTAAAGTTT
          1 GGTCAAATTTGAATTTTTGGAAAGTTT

       2638 AAGAGTTAAA


Statistics
Matches: 96,  Mismatches: 20, Indels: 1
        0.82            0.17        0.01

Matches are distributed among these distances:
  29   24  0.25
  30   72  0.75

ACGTcount: A:0.32, C:0.05, G:0.24, T:0.39


Consensus pattern (30 bp):   
GGTCAAATTTGAATTTTTGGAAAGTTTGGG

Done.