Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003594.1 Kokia drynarioides strain JFW-HI SEQ_116471, 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, 926

Length: 1544
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36


Found at i:277 original size:5 final size:5

Alignment explanation


    Indices: 267--293  Score: 54
    Period size: 5  Copynumber: 5.4  Consensus size: 5

        257 ATTTTTTAAC

                                            
        267 TCGAT TCGAT TCGAT TCGAT TCGAT TC
          1 TCGAT TCGAT TCGAT TCGAT TCGAT TC

        294 AAAAAAATTC


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   22  1.00

ACGTcount: A:0.19, C:0.22, G:0.19, T:0.41


Consensus pattern (5 bp):   
TCGAT

Found at i:1040 original size:32 final size:31

Alignment explanation


    Indices: 1002--1126  Score: 116
    Period size: 31  Copynumber: 4.1  Consensus size: 31

        992 AGACCCCAAA

                           *                 
       1002 AAGTTTAAGTACCAACTTA-AAAAATATGTGTC
          1 AAGTTTAAGTACCAAATTAGAAAAA-A-GTGTC

                                *          
       1034 AAGTTTAAGTACCAAATTAGGAAAAAGTGTC
          1 AAGTTTAAGTACCAAATTAGAAAAAAGTGTC

                    *                      **
       1065 AAGTTTAAATACCAAATTAGATCAAAAA---AA
          1 AAGTTTAAGTACCAAATTAGA--AAAAAGTGTC

                   *                  *    
       1095 AAGTTTAGGTACCAAATTA-AAAAAAATGTC
          1 AAGTTTAAGTACCAAATTAGAAAAAAGTGTC

              
       1125 AA
          1 AA

       1127 ATTCAGATAT


Statistics
Matches: 77,  Mismatches: 10, Indels: 14
        0.76            0.10        0.14

Matches are distributed among these distances:
  27    5  0.06
  29    1  0.01
  30   19  0.25
  31   24  0.31
  32   19  0.25
  33    9  0.12

ACGTcount: A:0.50, C:0.10, G:0.13, T:0.26


Consensus pattern (31 bp):   
AAGTTTAAGTACCAAATTAGAAAAAAGTGTC

Found at i:1067 original size:31 final size:33

Alignment explanation


    Indices: 1002--1085  Score: 120
    Period size: 31  Copynumber: 2.6  Consensus size: 33

        992 AGACCCCAAA

                           *                 
       1002 AAGTTTAAGTACCAACTTA-AAAAATATGTGTC
          1 AAGTTTAAGTACCAAATTAGAAAAATATGTGTC

                                *            
       1034 AAGTTTAAGTACCAAATTAGGAAAA-A-GTGTC
          1 AAGTTTAAGTACCAAATTAGAAAAATATGTGTC

                    *            
       1065 AAGTTTAAATACCAAATTAGA
          1 AAGTTTAAGTACCAAATTAGA

       1086 TCAAAAAAAA


Statistics
Matches: 47,  Mismatches: 4, Indels: 3
        0.87            0.07        0.06

Matches are distributed among these distances:
  31   24  0.51
  32   19  0.40
  33    4  0.09

ACGTcount: A:0.46, C:0.11, G:0.14, T:0.29


Consensus pattern (33 bp):   
AAGTTTAAGTACCAAATTAGAAAAATATGTGTC
Done.