Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005747.1 Kokia drynarioides strain JFW-HI SEQ_119994, 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: 1979
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.32


Found at i:1351 original size:13 final size:13

Alignment explanation


    Indices: 1317--1345  Score: 58
    Period size: 13  Copynumber: 2.2  Consensus size: 13

       1307 TTGATCTTTC

                         
       1317 CATATCATATAAA
          1 CATATCATATAAA

                         
       1330 CATATCATATAAA
          1 CATATCATATAAA

               
       1343 CAT
          1 CAT

       1346 CACATACCTT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   16  1.00

ACGTcount: A:0.52, C:0.17, G:0.00, T:0.31


Consensus pattern (13 bp):   
CATATCATATAAA

Found at i:1473 original size:41 final size:40

Alignment explanation


    Indices: 1409--1581  Score: 178
    Period size: 37  Copynumber: 4.5  Consensus size: 40

       1399 CGACATGAAA

                      *       *                      
       1409 CCTGCTAGGCTCAAAGCCTGATAATATACACCGGCACGAAG
          1 CCTGCTAGGCACAAAGCCCGATAA-ATACACCGGCACGAAG

             *          *                           
       1450 CTTGCTAGGCACTAAGCCCGATAAATACACCGGCACGAAG
          1 CCTGCTAGGCACAAAGCCCGATAAATACACCGGCACGAAG

               *                           *  **    
       1490 CCTACTAGGCACAAAGCCC---AAATACACCAGCTTGAAG
          1 CCTGCTAGGCACAAAGCCCGATAAATACACCGGCACGAAG

                         *        *         *       
       1527 CCTGCTAGGCACACAG-CC--TGAATACACCGACACGAAG
          1 CCTGCTAGGCACAAAGCCCGATAAATACACCGGCACGAAG

               *         *    
       1564 CCTACTAGGCACACAGCC
          1 CCTGCTAGGCACAAAGCC

       1582 TGAATACTAT


Statistics
Matches: 112,  Mismatches: 18, Indels: 7
        0.82            0.13        0.05

Matches are distributed among these distances:
  36    2  0.02
  37   57  0.51
  38    1  0.01
  40   32  0.29
  41   20  0.18

ACGTcount: A:0.33, C:0.33, G:0.20, T:0.14


Consensus pattern (40 bp):   
CCTGCTAGGCACAAAGCCCGATAAATACACCGGCACGAAG

Found at i:1901 original size:5 final size:5

Alignment explanation


    Indices: 1891--1916  Score: 52
    Period size: 5  Copynumber: 5.2  Consensus size: 5

       1881 TATTCCAATA

                                           
       1891 GTGAT GTGAT GTGAT GTGAT GTGAT G
          1 GTGAT GTGAT GTGAT GTGAT GTGAT G

       1917 AGAGGTCCCC


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   21  1.00

ACGTcount: A:0.19, C:0.00, G:0.42, T:0.38


Consensus pattern (5 bp):   
GTGAT

Done.