Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003102.1 Kokia drynarioides strain JFW-HI SEQ_115670, 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: 28628
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35


Found at i:215 original size:17 final size:18

Alignment explanation


    Indices: 177--217  Score: 57
    Period size: 18  Copynumber: 2.3  Consensus size: 18

        167 CTTTACTTTT

                       *   *  
        177 ATTTTATTTTACCAGTGA
          1 ATTTTATTTTAACAGAGA

                              
        195 ATTTTATTTTAACA-AGA
          1 ATTTTATTTTAACAGAGA

                  
        212 ATTTTA
          1 ATTTTA

        218 GTCACCTAAT


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  17    8  0.38
  18   13  0.62

ACGTcount: A:0.34, C:0.07, G:0.07, T:0.51


Consensus pattern (18 bp):   
ATTTTATTTTAACAGAGA

Found at i:787 original size:17 final size:18

Alignment explanation


    Indices: 761--795  Score: 54
    Period size: 17  Copynumber: 2.0  Consensus size: 18

        751 GTTCATAATA

                 *            
        761 ATAAACAAATT-TGAATT
          1 ATAAAAAAATTGTGAATT

                              
        778 ATAAAAAAATTGTGAATT
          1 ATAAAAAAATTGTGAATT

        796 TAGTTACCGG


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  17   10  0.62
  18    6  0.38

ACGTcount: A:0.54, C:0.03, G:0.09, T:0.34


Consensus pattern (18 bp):   
ATAAAAAAATTGTGAATT

Found at i:1194 original size:6 final size:6

Alignment explanation


    Indices: 1186--1289  Score: 82
    Period size: 6  Copynumber: 16.8  Consensus size: 6

       1176 AGACTGAGCC

                 *      *                          *     *         
       1186 TGAAGC TGAAGC TGAAGA TGAAGA TGAAGA TGAAAA TGAGGA TGAAGA
          1 TGAAGA TGAAGA TGAAGA TGAAGA TGAAGA TGAAGA TGAAGA TGAAGA

              *      **     **                           *      *     
       1234 TGGAGA TGGGGA TGGGGA TGAAGA TGAGGATGA TGAAGA AGAAGA CGAAGA
          1 TGAAGA TGAAGA TGAAGA TGAAGA TGA--A-GA TGAAGA TGAAGA TGAAGA

                 
       1285 TGAAG
          1 TGAAG

       1290 CCGACGCCGA


Statistics
Matches: 83,  Mismatches: 12, Indels: 6
        0.82            0.12        0.06

Matches are distributed among these distances:
   6   76  0.92
   7    1  0.01
   8    1  0.01
   9    5  0.06

ACGTcount: A:0.42, C:0.03, G:0.39, T:0.15


Consensus pattern (6 bp):   
TGAAGA

Found at i:3575 original size:31 final size:31

Alignment explanation


    Indices: 3540--3619  Score: 117
    Period size: 31  Copynumber: 2.6  Consensus size: 31

       3530 TATTTTTCAT

                         *        *         
       3540 TTGCTTCAATTTCTATGCTTATGCC-CCATTA
          1 TTGCTTCAATTTCCATGCTTATACCTCC-TTA

                             *             
       3571 TTGCTTCAATTTCCATGATTATACCTCCTTA
          1 TTGCTTCAATTTCCATGCTTATACCTCCTTA

                              
       3602 TTGCTTCAATTTCCATGC
          1 TTGCTTCAATTTCCATGC

       3620 CTTACTATAA


Statistics
Matches: 44,  Mismatches: 4, Indels: 2
        0.88            0.08        0.04

Matches are distributed among these distances:
  31   42  0.95
  32    2  0.05

ACGTcount: A:0.20, C:0.26, G:0.09, T:0.45


Consensus pattern (31 bp):   
TTGCTTCAATTTCCATGCTTATACCTCCTTA

Found at i:12074 original size:13 final size:13

Alignment explanation


    Indices: 12058--12083  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

      12048 CTTCAGCCTC

                         
      12058 TGTTTTTTTTTAT
          1 TGTTTTTTTTTAT

                         
      12071 TGTTTTTTTTTAT
          1 TGTTTTTTTTTAT

      12084 ATATATATAT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.08, C:0.00, G:0.08, T:0.85


Consensus pattern (13 bp):   
TGTTTTTTTTTAT
Done.