Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006652.1 Kokia drynarioides strain JFW-HI SEQ_121243, 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: 8877
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:1122 original size:17 final size:15

Alignment explanation


    Indices: 1085--1129  Score: 63
    Period size: 15  Copynumber: 2.9  Consensus size: 15

       1075 TGAATAACGA

                          *
       1085 AAAATAAATAAAAAT
          1 AAAATAAATAAAAAC

                             
       1100 AAAATAAATAAAACACC
          1 AAAATAAATAAAA-A-C

                         
       1117 AAAATAAATAAAA
          1 AAAATAAATAAAA

       1130 TATAAAAAAA


Statistics
Matches: 27,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  15   13  0.48
  16    1  0.04
  17   13  0.48

ACGTcount: A:0.78, C:0.07, G:0.00, T:0.16


Consensus pattern (15 bp):   
AAAATAAATAAAAAC

Found at i:1137 original size:17 final size:16

Alignment explanation


    Indices: 1084--1137  Score: 65
    Period size: 17  Copynumber: 3.3  Consensus size: 16

       1074 GTGAATAACG

                            
       1084 AAAAATAAATAAAAAT
          1 AAAAATAAATAAAAAT

                            *
       1100 -AAAATAAATAAAACAC
          1 AAAAATAAATAAAA-AT

            *                
       1116 CAAAATAAATAAAATAT
          1 AAAAATAAATAAAA-AT

                 
       1133 AAAAA
          1 AAAAA

       1138 AAGCAAAGGA


Statistics
Matches: 32,  Mismatches: 4, Indels: 3
        0.82            0.10        0.08

Matches are distributed among these distances:
  15   13  0.41
  16    1  0.03
  17   18  0.56

ACGTcount: A:0.78, C:0.06, G:0.00, T:0.17


Consensus pattern (16 bp):   
AAAAATAAATAAAAAT

Found at i:6740 original size:16 final size:16

Alignment explanation


    Indices: 6721--6788  Score: 59
    Period size: 16  Copynumber: 4.2  Consensus size: 16

       6711 GTGAATAACG

                            
       6721 AAAAATAAATAAAAAC
          1 AAAAATAAATAAAAAC

                *            
       6737 AAAACT-AATAAAACAC
          1 AAAAATAAATAAAA-AC

            *          *    
       6753 CAAAATAAATAGAAA-
          1 AAAAATAAATAAAAAC

              *               
       6768 AACAATGAAATATAAAAC
          1 AAAAAT-AAATA-AAAAC

               
       6786 AAA
          1 AAA

       6789 TACAAAAAAA


Statistics
Matches: 39,  Mismatches: 8, Indels: 8
        0.71            0.15        0.15

Matches are distributed among these distances:
  15   11  0.28
  16   17  0.44
  17    9  0.23
  18    2  0.05

ACGTcount: A:0.74, C:0.10, G:0.03, T:0.13


Consensus pattern (16 bp):   
AAAAATAAATAAAAAC
Done.