Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012962.1 Kokia drynarioides strain JFW-HI SEQ_127980, 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: 3151
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31


Found at i:1333 original size:26 final size:26

Alignment explanation


    Indices: 1297--1348  Score: 104
    Period size: 26  Copynumber: 2.0  Consensus size: 26

       1287 CATGTATCGT

                                      
       1297 TTGATGCTAGAGCAATATGCTGGGGA
          1 TTGATGCTAGAGCAATATGCTGGGGA

                                      
       1323 TTGATGCTAGAGCAATATGCTGGGGA
          1 TTGATGCTAGAGCAATATGCTGGGGA

       1349 AGAGGTATGT


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  26   26  1.00

ACGTcount: A:0.27, C:0.12, G:0.35, T:0.27


Consensus pattern (26 bp):   
TTGATGCTAGAGCAATATGCTGGGGA

Found at i:1457 original size:43 final size:43

Alignment explanation


    Indices: 1374--1458  Score: 109
    Period size: 43  Copynumber: 2.0  Consensus size: 43

       1364 GTTAACATGT

                             *    *           *        
       1374 TAAATTATATTACTTGACTCGTGTTAATATGTTTGAATGTTAG
          1 TAAATTATATTACTTGAATCGTATTAATATGTTTAAATGTTAG

                           *    *                      
       1417 TAAATTATATTACTTTAATCTTATTAATAT-TTTAACATGTTA
          1 TAAATTATATTACTTGAATCGTATTAATATGTTTAA-ATGTTA

       1459 TTAATTGTGC


Statistics
Matches: 36,  Mismatches: 5, Indels: 2
        0.84            0.12        0.05

Matches are distributed among these distances:
  42    4  0.11
  43   32  0.89

ACGTcount: A:0.34, C:0.07, G:0.09, T:0.49


Consensus pattern (43 bp):   
TAAATTATATTACTTGAATCGTATTAATATGTTTAAATGTTAG

Found at i:2088 original size:45 final size:45

Alignment explanation


    Indices: 2026--2148  Score: 169
    Period size: 45  Copynumber: 2.7  Consensus size: 45

       2016 GCATAGCTCA

                                                       * 
       2026 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATGC
          1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC

                                   *                     
       2071 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATAC
          1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC

                  **               *           
       2116 T-ATAGGGAAGGATATCAAG-CTGAGTTTGACGAG
          1 TCA-AGCCAAGGATATC-AGCCTCAGTTTGACGAG

       2149 GCATCGCGAT


Statistics
Matches: 70,  Mismatches: 6, Indels: 4
        0.88            0.08        0.05

Matches are distributed among these distances:
  44    1  0.01
  45   67  0.96
  46    2  0.03

ACGTcount: A:0.32, C:0.25, G:0.24, T:0.20


Consensus pattern (45 bp):   
TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC

Found at i:2190 original size:21 final size:21

Alignment explanation


    Indices: 2157--2199  Score: 59
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       2147 AGGCATCGCG

                    *            
       2157 ATACACTATTCCTCCCGTGCA
          1 ATACACTACTCCTCCCGTGCA

                *          *     
       2178 ATACTCTACTCCTCCGGTGCA
          1 ATACACTACTCCTCCCGTGCA

             
       2199 A
          1 A

       2200 ATGGACCCTA


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  21   19  1.00

ACGTcount: A:0.23, C:0.37, G:0.12, T:0.28


Consensus pattern (21 bp):   
ATACACTACTCCTCCCGTGCA
Done.