Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004441.1 Kokia drynarioides strain JFW-HI SEQ_117836, 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: 4555
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37


Found at i:96 original size:24 final size:24

Alignment explanation


    Indices: 42--96  Score: 74
    Period size: 24  Copynumber: 2.3  Consensus size: 24

         32 TCTTTTAGTT

                                   *
         42 AAACTCTATTTATTTGTTTCAATT
          1 AAACTCTATTTATTTGTTTCAATC

              *    *           *    
         66 AAGCTCTGTTTATTTGTTTTAATC
          1 AAACTCTATTTATTTGTTTCAATC

                   
         90 AAACTCT
          1 AAACTCT

         97 TATTAGTCTA


Statistics
Matches: 26,  Mismatches: 5, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  24   26  1.00

ACGTcount: A:0.27, C:0.15, G:0.07, T:0.51


Consensus pattern (24 bp):   
AAACTCTATTTATTTGTTTCAATC

Found at i:1662 original size:14 final size:15

Alignment explanation


    Indices: 1643--1672  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       1633 GAAGGGAGAC

                           
       1643 TTTGTTT-TTTCTTT
          1 TTTGTTTGTTTCTTT

                           
       1657 TTTGTTTGTTTCTTT
          1 TTTGTTTGTTTCTTT

             
       1672 T
          1 T

       1673 ATTAGATCTT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    7  0.47
  15    8  0.53

ACGTcount: A:0.00, C:0.07, G:0.10, T:0.83


Consensus pattern (15 bp):   
TTTGTTTGTTTCTTT

Found at i:3148 original size:74 final size:74

Alignment explanation


    Indices: 3023--3166  Score: 218
    Period size: 74  Copynumber: 1.9  Consensus size: 74

       3013 AAATCATCAA

                     *                                                       
       3023 CAATTGTTTTCATTTTCATGTTTTTTTTTTTTCTCTAAGTACCCATTTGCATTAAATAAAAAAAA
          1 CAATTGTTTACATTTTCATG-TTTTTTTTTTTCTCTAAGTACCCATTTGCATTAAATAAAAAAAA

                      
       3088 CAAAAATCTT
         65 CAAAAATCTT

                                              * *                       *    
       3098 CAATTGTTTACATTTTCAATG-TTTTTTTTTTCTTTGAGTACCCATTTGCATTAAATAAATAAAA
          1 CAATTGTTTACATTTTC-ATGTTTTTTTTTTTCTCTAAGTACCCATTTGCATTAAATAAAAAAAA

            *    
       3162 GAAAA
         65 CAAAA

       3167 CTTATAGGGT


Statistics
Matches: 63,  Mismatches: 5, Indels: 3
        0.89            0.07        0.04

Matches are distributed among these distances:
  74   44  0.70
  75   16  0.25
  76    3  0.05

ACGTcount: A:0.34, C:0.13, G:0.07, T:0.46


Consensus pattern (74 bp):   
CAATTGTTTACATTTTCATGTTTTTTTTTTTCTCTAAGTACCCATTTGCATTAAATAAAAAAAAC
AAAAATCTT
Done.