Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008173.1 Kokia drynarioides strain JFW-HI SEQ_122832, 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: 18096
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34


Found at i:3215 original size:21 final size:22

Alignment explanation


    Indices: 3191--3231  Score: 57
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       3181 TTTTAGATGT

                                  
       3191 TAATTATGAT-ATTTTTATGCG
          1 TAATTATGATAATTTTTATGCG

                 * *            
       3212 TAATTTTTATAATTTTTATG
          1 TAATTATGATAATTTTTATG

       3232 GCTTTAAATT


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  21    8  0.47
  22    9  0.53

ACGTcount: A:0.29, C:0.02, G:0.10, T:0.59


Consensus pattern (22 bp):   
TAATTATGATAATTTTTATGCG

Found at i:11613 original size:82 final size:84

Alignment explanation


    Indices: 11427--11619  Score: 216
    Period size: 81  Copynumber: 2.3  Consensus size: 84

      11417 CGAGCCGTTC

                *   *                                                *      *
      11427 AACAAATTTTATTCTATATTTGGATTTTGATTCCAAATAATAATTAAGTAAATAAATTTGTACCG
          1 AACAGATTATATTCTATATTTGGATTTTGATTCCAAATAATAATTAAGTAAATAAATATGTACCA

                 *             
      11492 GGATTTATTTCCGCCATTT
         66 GGATTAATTTCCGCCATTT

                    *     *              *                    *           ** 
      11511 AACAGATTCTATTCCA-ATTT-GATTTTGTTTCCAAATAA-AA-TAAGTTGAATAAATATGTTTC
          1 AACAGATTATATTCTATATTTGGATTTTGATTCCAAATAATAATTAAG-TAAATAAATATGTACC

                       *         
      11572 AGGATTAATTTTCGCGCA-TT
         65 AGGATTAATTTCCGC-CATTT

              *                         
      11592 AATAGATTATATTCTATATTTGGATTTT
          1 AACAGATTATATTCTATATTTGGATTTT

      11620 ATAATAATTA


Statistics
Matches: 91,  Mismatches: 14, Indels: 9
        0.80            0.12        0.08

Matches are distributed among these distances:
  80    4  0.04
  81   41  0.45
  82   23  0.25
  83   10  0.11
  84   13  0.14

ACGTcount: A:0.34, C:0.11, G:0.11, T:0.44


Consensus pattern (84 bp):   
AACAGATTATATTCTATATTTGGATTTTGATTCCAAATAATAATTAAGTAAATAAATATGTACCA
GGATTAATTTCCGCCATTT

Found at i:14847 original size:17 final size:17

Alignment explanation


    Indices: 14825--14858  Score: 68
    Period size: 17  Copynumber: 2.0  Consensus size: 17

      14815 GACTTGATTC

                             
      14825 TATCAAATTGATTTAAA
          1 TATCAAATTGATTTAAA

                             
      14842 TATCAAATTGATTTAAA
          1 TATCAAATTGATTTAAA

      14859 GGCTCCTTTA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41


Consensus pattern (17 bp):   
TATCAAATTGATTTAAA

Found at i:17560 original size:18 final size:19

Alignment explanation


    Indices: 17537--17573  Score: 58
    Period size: 19  Copynumber: 2.0  Consensus size: 19

      17527 CGGTATTTTA

                               
      17537 TGAAAA-ATATCGATACCT
          1 TGAAAATATATCGATACCT

                   *           
      17555 TGAAAATGTATCGATACCT
          1 TGAAAATATATCGATACCT

      17574 GAGTTTTAGA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  18    6  0.35
  19   11  0.65

ACGTcount: A:0.41, C:0.16, G:0.14, T:0.30


Consensus pattern (19 bp):   
TGAAAATATATCGATACCT
Done.