Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008374.1 Kokia drynarioides strain JFW-HI SEQ_123041, 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: 10609
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37


Found at i:3110 original size:24 final size:24

Alignment explanation


    Indices: 3064--3109  Score: 67
    Period size: 23  Copynumber: 2.0  Consensus size: 24

       3054 CTCCTATTTA

                            *       
       3064 GTATCTAAATTTTGATCTATTTTG
          1 GTATCTAAATTTTGATATATTTTG

                *                  
       3088 GTATTTAAA-TTTGATATATTTT
          1 GTATCTAAATTTTGATATATTTT

       3110 TTTAATTTGG


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  23   12  0.60
  24    8  0.40

ACGTcount: A:0.28, C:0.04, G:0.11, T:0.57


Consensus pattern (24 bp):   
GTATCTAAATTTTGATATATTTTG

Found at i:3119 original size:31 final size:31

Alignment explanation


    Indices: 3084--3143  Score: 102
    Period size: 31  Copynumber: 1.9  Consensus size: 31

       3074 TTTGATCTAT

                   *            *          
       3084 TTTGGTATTTAAATTTGATATATTTTTTTAA
          1 TTTGGTACTTAAATTTGATAAATTTTTTTAA

                                         
       3115 TTTGGTACTTAAATTTGATAAATTTTTTT
          1 TTTGGTACTTAAATTTGATAAATTTTTTT

       3144 TTAAGTTGGT


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  31   27  1.00

ACGTcount: A:0.28, C:0.02, G:0.10, T:0.60


Consensus pattern (31 bp):   
TTTGGTACTTAAATTTGATAAATTTTTTTAA

Found at i:3153 original size:33 final size:31

Alignment explanation


    Indices: 3085--3160  Score: 98
    Period size: 33  Copynumber: 2.4  Consensus size: 31

       3075 TTGATCTATT

                  *                       *
       3085 TTGGTATTTAAATTTGATATATTTTTTTAAT
          1 TTGGTACTTAAATTTGATATATTTTTTTAAG

                                  *          
       3116 TTGGTACTTAAATTTGATAAATTTTTTTTTAAG
          1 TTGGTACTTAAATTTGAT--ATATTTTTTTAAG

                 *      
       3149 TTGGTGCTTAAA
          1 TTGGTACTTAAA

       3161 ATTTTTGTGA


Statistics
Matches: 39,  Mismatches: 4, Indels: 2
        0.87            0.09        0.04

Matches are distributed among these distances:
  31   17  0.44
  33   22  0.56

ACGTcount: A:0.29, C:0.03, G:0.13, T:0.55


Consensus pattern (31 bp):   
TTGGTACTTAAATTTGATATATTTTTTTAAG

Found at i:3210 original size:31 final size:29

Alignment explanation


    Indices: 3173--3249  Score: 77
    Period size: 29  Copynumber: 2.6  Consensus size: 29

       3163 TTTTGTGATA

                                            
       3173 CAATTTGGTACCTGAACTTGATTTTTTTCCTT
          1 CAATTTGGTACCTGAACTT--TTTTTTT-CTT

                   *                   *  
       3205 -AATTTGTTACCT-AATCTTTTTTTTTGTT
          1 CAATTTGGTACCTGAA-CTTTTTTTTTCTT

             *               
       3233 CGATTTGGTACCTGAAC
          1 CAATTTGGTACCTGAAC

       3250 ATGTACCACG


Statistics
Matches: 38,  Mismatches: 4, Indels: 9
        0.75            0.08        0.18

Matches are distributed among these distances:
  28    2  0.05
  29   18  0.47
  30    4  0.11
  31   14  0.37

ACGTcount: A:0.19, C:0.17, G:0.13, T:0.51


Consensus pattern (29 bp):   
CAATTTGGTACCTGAACTTTTTTTTTCTT
Done.