Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009122.1 Kokia drynarioides strain JFW-HI SEQ_123825, 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: 8308
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.38


Found at i:522 original size:22 final size:22

Alignment explanation


    Indices: 468--519  Score: 74
    Period size: 22  Copynumber: 2.5  Consensus size: 22

        458 TATTTTATAT

                                  
        468 AATTT-ATAATTTTTTATGTTA
          1 AATTTGATAATTTTTTATGTTA

                                   
        489 AATTTGATAATTTTTTA-GTTTA
          1 AATTTGATAATTTTTTATG-TTA

                      
        511 AA-TTGATAA
          1 AATTTGATAA

        520 ATTAATACAA


Statistics
Matches: 29,  Mismatches: 0, Indels: 4
        0.88            0.00        0.12

Matches are distributed among these distances:
  21   13  0.45
  22   16  0.55

ACGTcount: A:0.37, C:0.00, G:0.08, T:0.56


Consensus pattern (22 bp):   
AATTTGATAATTTTTTATGTTA

Found at i:633 original size:72 final size:71

Alignment explanation


    Indices: 490--622  Score: 178
    Period size: 72  Copynumber: 1.9  Consensus size: 71

        480 TTTATGTTAA

                                     *     *                      *  *       
        490 ATTTGATAATTTTTTAGTTTAAATTGATAAATTAATACAAAGTAAAATCTAAATTTTGATTTGAT
          1 ATTTGATAATTTTTTAGTTTAAATTAATAAAGTAATACAAAGTAAAATCTAAATATTAATTTGAT

                  
        555 AAAAAT
         66 AAAAAT

                                   *                    ***                
        561 ATTTGATAATATTTTTAGTTTAATTTAATAAAGTAATACAAA-TGGTATCTAAATATTAATTT
          1 ATTTGATAAT-TTTTTAGTTTAAATTAATAAAGTAATACAAAGTAAAATCTAAATATTAATTT

        623 ATTTAAAAAT


Statistics
Matches: 53,  Mismatches: 8, Indels: 2
        0.84            0.13        0.03

Matches are distributed among these distances:
  71   25  0.47
  72   28  0.53

ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45


Consensus pattern (71 bp):   
ATTTGATAATTTTTTAGTTTAAATTAATAAAGTAATACAAAGTAAAATCTAAATATTAATTTGAT
AAAAAT

Found at i:4477 original size:109 final size:109

Alignment explanation


    Indices: 4286--4566  Score: 386
    Period size: 109  Copynumber: 2.6  Consensus size: 109

       4276 ACAAACCATA

                                         *                       *    *      
       4286 GCGATGGTTGAGATCCTACATATGTTGCGAATTCTCGATAGCTTGTGTGAGCAGCATCATGAGTC
          1 GCGATGGTTGAGATCCTACATATGTTGCGGATTCTCGATAGCTTGTGTGAGCAACATCGTGAGTC

             *        *                    *             
       4351 GGTGAATACTGAATGGATACTATGTTCTGATGACA-CACACCGTC
         66 GATGAATACTAAATGGATACTATGTTCTGATAACATC-CACCGTC

                                                    *                        
       4395 GCGATGGTTGAGATCCTACATATGTTGCGGATTCTCGATACCTTGTGTGAGCAACATCGTGA-TC
          1 GCGATGGTTGAGATCCTACATATGTTGCGGATTCTCGATAGCTTGTGTGAGCAACATCGTGAGTC

                                                     *   
       4459 TGATGAATACTAAATGGATACTATGTTCTGATAACATCCACTGTC
         66 -GATGAATACTAAATGGATACTATGTTCTGATAACATCCACCGTC

             *     *            *     **        * *           *            
       4504 GTGATGGCTGAGATCCTACACATGTTATGGATTCTCAACAGCTTGTGTGAACAACATCGTGAG
          1 GCGATGGTTGAGATCCTACATATGTTGCGGATTCTCGATAGCTTGTGTGAGCAACATCGTGAG

       4567 CAGGTGATAT


Statistics
Matches: 152,  Mismatches: 17, Indels: 5
        0.87            0.10        0.03

Matches are distributed among these distances:
 108    2  0.01
 109  149  0.98
 110    1  0.01

ACGTcount: A:0.26, C:0.19, G:0.24, T:0.30


Consensus pattern (109 bp):   
GCGATGGTTGAGATCCTACATATGTTGCGGATTCTCGATAGCTTGTGTGAGCAACATCGTGAGTC
GATGAATACTAAATGGATACTATGTTCTGATAACATCCACCGTC
Done.