Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003010.1 Kokia drynarioides strain JFW-HI SEQ_115516, 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: 4436
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30


Found at i:3252 original size:100 final size:101

Alignment explanation


    Indices: 3034--3288  Score: 289
    Period size: 100  Copynumber: 2.5  Consensus size: 101

       3024 TGAAACGAAG

                 *       *           * *  *      *                    *  *   
       3034 TGAAGTTACAACACCAAATCCTATATCTCTTAAGTTGTAGTGGATCGGATTAAAACTATAGTAGC
          1 TGAAGCTACAACATCAAATCCTATACCCCTGAAGTTGCAGTGGATCGGATTAAAACTACAGAAGC

                                *     *         
       3099 AAATCTTTATCTCTCTAAAGTTGTAGTAAAGCAAGA
         66 AAATCTTTATCTCTCTAAAGATGTAGCAAAGCAAGA

                                *                              *  *          
       3135 TGAAGCTACAACATCAAATCGTATACCCCTGAAGTTGCAGTGGATCGGATTGAAGCTACAGAAGC
          1 TGAAGCTACAACATCAAATCCTATACCCCTGAAGTTGCAGTGGATCGGATTAAAACTACAGAAGC

                                        ***      
       3200 AAATC-TTATCTC-CTAGAAGATGTAGCGGGGCAAGA
         66 AAATCTTTATCTCTCTA-AAGATGTAGCAAAGCAAGA

                     *               *  *       *        *        
       3235 TGAAGCTACGACATCAAATCCTATATCCTTGAAGTTACAGTGGATTGGACTTAA
          1 TGAAGCTACAACATCAAATCCTATACCCCTGAAGTTGCAGTGGATCGGA-TTAA

       3289 GTTAAAGTAA


Statistics
Matches: 129,  Mismatches: 23, Indels: 4
        0.83            0.15        0.03

Matches are distributed among these distances:
  99    3  0.02
 100   64  0.50
 101   62  0.48

ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27


Consensus pattern (101 bp):   
TGAAGCTACAACATCAAATCCTATACCCCTGAAGTTGCAGTGGATCGGATTAAAACTACAGAAGC
AAATCTTTATCTCTCTAAAGATGTAGCAAAGCAAGA

Found at i:3349 original size:97 final size:100

Alignment explanation


    Indices: 3034--3367  Score: 288
    Period size: 100  Copynumber: 3.4  Consensus size: 100

       3024 TGAAACGAAG

                 *       *                       **             *  *   *  *  
       3034 TGAAGTTACAACACCAAATCCTATATCTCTT-AAGTTGTAGTGGATCGGATTAAAACTATAGTAG
          1 TGAAGCTACAACATCAAATCCTATATC-CTTGAAGTTACAGTGGATCGGATTGAAGCTACAGAAG

                                 **  *  ***       
       3098 CAAATCTTTATCTCTCTA-AAGTTGTAGTAAAGCAAGA
         65 CAAATC-TTATCTC-CTAGAAAATGCAGCGGAGCAAGA

                                *    *  *       *                            
       3135 TGAAGCTACAACATCAAATCGTATACCCCTGAAGTTGCAGTGGATCGGATTGAAGCTACAGAAGC
          1 TGAAGCTACAACATCAAATCCTATATCCTTGAAGTTACAGTGGATCGGATTGAAGCTACAGAAGC

                              *   *     *      
       3200 AAATCTTATCTCCTAGAAGATGTAGCGGGGCAAGA
         66 AAATCTTATCTCCTAGAAAATGCAGCGGAGCAAGA

                     *                                   *             *     
       3235 TGAAGCTACGACATCAAATCCTATATCCTTGAAGTTACAGTGGATTGGACTT-AAG-T-TA-AAG
          1 TGAAGCTACAACATCAAATCCTATATCCTTGAAGTTACAGTGGATCGGA-TTGAAGCTACAGAAG

            *                          *         
       3296 TAAATCTTATCTACCT-GAAAATGCAGTGGAGCAAGA
         65 CAAATCTTATCT-CCTAGAAAATGCAGCGGAGCAAGA

                        **           * *         
       3332 T-AAGGCTACAATGTCAAATCCTATCTTCTTGAAGTT
          1 TGAA-GCTACAACATCAAATCCTATATCCTTGAAGTT

       3368 GCAGAGAAGC


Statistics
Matches: 196,  Mismatches: 32, Indels: 14
        0.81            0.13        0.06

Matches are distributed among these distances:
  96    2  0.01
  97   58  0.30
  98    4  0.02
  99    4  0.02
 100   69  0.35
 101   59  0.30

ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28


Consensus pattern (100 bp):   
TGAAGCTACAACATCAAATCCTATATCCTTGAAGTTACAGTGGATCGGATTGAAGCTACAGAAGC
AAATCTTATCTCCTAGAAAATGCAGCGGAGCAAGA

Found at i:4030 original size:20 final size:20

Alignment explanation


    Indices: 3993--4030  Score: 58
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       3983 GTACTTGCAA

                        **      
       3993 ACAAAAAACAAAGGAAAAGG
          1 ACAAAAAACAAAAAAAAAGG

                              
       4013 ACAAAAAACAAAAAAAAA
          1 ACAAAAAACAAAAAAAAA

       4031 ATACAGAAAG


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  20   16  1.00

ACGTcount: A:0.79, C:0.11, G:0.11, T:0.00


Consensus pattern (20 bp):   
ACAAAAAACAAAAAAAAAGG
Done.