Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001397.1 Kokia drynarioides strain JFW-HI SEQ_112885, 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: 7798
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35


Found at i:2894 original size:161 final size:163

Alignment explanation


    Indices: 2672--3091  Score: 469
    Period size: 161  Copynumber: 2.6  Consensus size: 163

       2662 AAGTTACTAT

                      *                             *   *         *          
       2672 TTTATCTTAGACCGAATAATTTATTATCATTTAACCAATGCAGACAAGCTTCATGTATTATAGTT
          1 TTTATCTTAGGCCGAATAATTTATTATCATTTAACCAATGGAGAAAAGCTTCATATATTATAGTT

                                        **  *            * *                 
       2737 TCTACAAATGAAACAATTGGCTTACTAGTGTTGC-TGATTGTAGCTTTATGCTACTAACACT-AA
         66 TCTACAAATGAAACAATTGGCTTACTAGACTTACTTGATTGTAGCCTCATGCTACTAACA-TGAA

                      *      *                  
       2800 TAATCGTAGGTAC-GGGTTGAATAA-ATTATTATT-
        130 -AATCGTA-GAACAGGGCTGAATAATATTATTATTG

                               *                            *                
       2833 TATT-TCTTAGGCCGAATAGTTTATTATCATTTAACCAATGGAGAAAAACTTCATATATTATA-T
          1 T-TTATCTTAGGCCGAATAATTTATTATCATTTAACCAATGGAGAAAAGCTTCATATATTATAGT

                           *  *                    *          *     *        
       2896 TTCCTACAAATGAAATAACTGGCTTACT-GACTTACTTGGTTGTAGCCTCGTGCTATTAACATGA
         65 TT-CTACAAATGAAACAATTGGCTTACTAGACTTACTTGATTGTAGCCTCATGCTACTAACATGA

             **                                    
       2960 AGGTCGTAGAACAATGGGCTGAATAAGTTATTATTATTG
        129 AAATCGTAGAAC-A-GGGCTGAATAA--TATTATTATTG

                               *   *               *                   *     
       2999 TTTATCTTAGGCCGAATAACTTAGTATCATTTAACCAATAGAGAAAAGCTTCATATATTGTAGTT
          1 TTTATCTTAGGCCGAATAATTTATTATCATTTAACCAATGGAGAAAAGCTTCATATATTATAGTT

                 *              *       
       3064 TCTACGAATGAAACAATTGGTTTACTAG
         66 TCTACAAATGAAACAATTGGCTTACTAG

       3092 CTCAATTGTT


Statistics
Matches: 215,  Mismatches: 30, Indels: 22
        0.81            0.11        0.08

Matches are distributed among these distances:
 159    3  0.01
 160   13  0.06
 161   98  0.46
 162   12  0.06
 165   11  0.05
 166   74  0.34
 167    4  0.02

ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37


Consensus pattern (163 bp):   
TTTATCTTAGGCCGAATAATTTATTATCATTTAACCAATGGAGAAAAGCTTCATATATTATAGTT
TCTACAAATGAAACAATTGGCTTACTAGACTTACTTGATTGTAGCCTCATGCTACTAACATGAAA
ATCGTAGAACAGGGCTGAATAATATTATTATTG

Found at i:4949 original size:7 final size:7

Alignment explanation


    Indices: 4937--4961  Score: 50
    Period size: 7  Copynumber: 3.6  Consensus size: 7

       4927 TATAATTAAA

                   
       4937 AAAAAAT
          1 AAAAAAT

                   
       4944 AAAAAAT
          1 AAAAAAT

                   
       4951 AAAAAAT
          1 AAAAAAT

                
       4958 AAAA
          1 AAAA

       4962 TGGATGACTC


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   18  1.00

ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12


Consensus pattern (7 bp):   
AAAAAAT
Done.