Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000873.1 Kokia drynarioides strain JFW-HI SEQ_111991, 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: 5004
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37


Found at i:1143 original size:23 final size:23

Alignment explanation


    Indices: 1092--1143  Score: 61
    Period size: 24  Copynumber: 2.2  Consensus size: 23

       1082 AGCATTATTC

                       *           
       1092 GTGAACATGTTTAATTATATGTT
          1 GTGAACATGTTCAATTATATGTT

                          *          
       1115 GATGAACATGTTCATTTA-ATGTTT
          1 G-TGAACATGTTCAATTATATG-TT

                 
       1139 GTGAA
          1 GTGAA

       1144 TATTAAACTA


Statistics
Matches: 25,  Mismatches: 2, Indels: 4
        0.81            0.06        0.13

Matches are distributed among these distances:
  23    8  0.32
  24   17  0.68

ACGTcount: A:0.31, C:0.06, G:0.19, T:0.44


Consensus pattern (23 bp):   
GTGAACATGTTCAATTATATGTT

Found at i:1186 original size:28 final size:27

Alignment explanation


    Indices: 1153--1206  Score: 81
    Period size: 28  Copynumber: 2.0  Consensus size: 27

       1143 ATATTAAACT

                     *      *           
       1153 AACGAACATGAACACATAATTTTAAATA
          1 AACGAACATAAACA-AAAATTTTAAATA

                                      
       1181 AACGAACATAAACAAAAATTTTAAAT
          1 AACGAACATAAACAAAAATTTTAAAT

       1207 TCTTAACGAA


Statistics
Matches: 24,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  27   11  0.46
  28   13  0.54

ACGTcount: A:0.57, C:0.13, G:0.06, T:0.24


Consensus pattern (27 bp):   
AACGAACATAAACAAAAATTTTAAATA

Found at i:3998 original size:29 final size:30

Alignment explanation


    Indices: 3955--4032  Score: 95
    Period size: 29  Copynumber: 2.6  Consensus size: 30

       3945 GAAATAAATC

                    *                      
       3955 AAATCAAAATCTCATGTACACAATTGCACA-
          1 AAATCAAAGT-TCATGTACACAATTGCACAT

                             *             
       3985 AAATCAAAGTTCATGTATACAATTGCACATT
          1 AAATCAAAGTTCATGTACACAATTGCACA-T

               *  *          
       4016 AAACCATAGTTCATGTA
          1 AAATCAAAGTTCATGTA

       4033 TAATTTTGGT


Statistics
Matches: 42,  Mismatches: 4, Indels: 3
        0.86            0.08        0.06

Matches are distributed among these distances:
  29   18  0.43
  30    9  0.21
  31   15  0.36

ACGTcount: A:0.44, C:0.19, G:0.09, T:0.28


Consensus pattern (30 bp):   
AAATCAAAGTTCATGTACACAATTGCACAT

Done.