Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003175.1 Kokia drynarioides strain JFW-HI SEQ_115777, 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: 7539
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34

Warning! 57 characters in sequence are not A, C, G, or T


Found at i:2944 original size:30 final size:29

Alignment explanation


    Indices: 2849--2984  Score: 87
    Period size: 30  Copynumber: 4.5  Consensus size: 29

       2839 AATAAAGGGA

                 *                         
       2849 AATTTTAAAACAAATAAAAAT-AAAGGATTT
          1 AATTTGAAAA-AAA-AAAAATAAAAGGATTT

            *                         **  **
       2879 GA-TTGAACAAAAAAACAAAATAAAAACATAA
          1 AATTTG-A-AAAAAAA-AAAATAAAAGGATTT

                 *                        
       2910 AATTTTAAAAAGAAAAAAATAAAAGGATTT
          1 AATTTGAAAAA-AAAAAAATAAAAGGATTT

                      *** *               
       2940 AATTTGAAAATCGAGAAATAAAAGGGATTT
          1 AATTTGAAAAAAAAAAAATAAAA-GGATTT

                *          
       2970 AATTAGAAAAAAAAA
          1 AATTTGAAAAAAAAA

       2985 CTGAATAAAT


Statistics
Matches: 77,  Mismatches: 22, Indels: 14
        0.68            0.19        0.12

Matches are distributed among these distances:
  29   12  0.16
  30   50  0.65
  31   13  0.17
  32    2  0.03

ACGTcount: A:0.63, C:0.04, G:0.10, T:0.23


Consensus pattern (29 bp):   
AATTTGAAAAAAAAAAAATAAAAGGATTT

Found at i:2949 original size:29 final size:29

Alignment explanation


    Indices: 2917--2984  Score: 75
    Period size: 29  Copynumber: 2.3  Consensus size: 29

       2907 TAAAATTTTA

                                        * 
       2917 AAAAGAAAAAAATAAAA-GGATTTAATTTG
          1 AAAA-AAAAAAATAAAAGGGATTTAATTAG

                 ** *                     
       2946 AAAATCGAGAAATAAAAGGGATTTAATTAG
          1 AAAA-AAAAAAATAAAAGGGATTTAATTAG

                     
       2976 AAAAAAAAA
          1 AAAAAAAAA

       2985 CTGAATAAAT


Statistics
Matches: 30,  Mismatches: 8, Indels: 2
        0.75            0.20        0.05

Matches are distributed among these distances:
  29   15  0.50
  30   15  0.50

ACGTcount: A:0.63, C:0.01, G:0.15, T:0.21


Consensus pattern (29 bp):   
AAAAAAAAAAATAAAAGGGATTTAATTAG

Found at i:4216 original size:17 final size:16

Alignment explanation


    Indices: 4194--4240  Score: 58
    Period size: 17  Copynumber: 2.8  Consensus size: 16

       4184 TTGGTTTGAG

                          *  
       4194 TTTGGGTCTTGGGTGTT
          1 TTTGGGT-TTGGGTATT

                             
       4211 TTTGGGTTATGGGTATT
          1 TTTGGGTT-TGGGTATT

            *            
       4228 ATTGGGTTTGGGT
          1 TTTGGGTTTGGGT

       4241 TGTAAAAGGG


Statistics
Matches: 27,  Mismatches: 2, Indels: 3
        0.84            0.06        0.09

Matches are distributed among these distances:
  16    6  0.22
  17   21  0.78

ACGTcount: A:0.06, C:0.02, G:0.40, T:0.51


Consensus pattern (16 bp):   
TTTGGGTTTGGGTATT

Found at i:5473 original size:20 final size:21

Alignment explanation


    Indices: 5448--5488  Score: 75
    Period size: 20  Copynumber: 2.0  Consensus size: 21

       5438 TTCAGCATAC

                                 
       5448 TTACCTCCCTATCTAG-AATT
          1 TTACCTCCCTATCTAGTAATT

                                 
       5468 TTACCTCCCTATCTAGTAATT
          1 TTACCTCCCTATCTAGTAATT

       5489 CCCTAGAGAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  20   16  0.80
  21    4  0.20

ACGTcount: A:0.24, C:0.29, G:0.05, T:0.41


Consensus pattern (21 bp):   
TTACCTCCCTATCTAGTAATT

Found at i:7517 original size:19 final size:19

Alignment explanation


    Indices: 7463--7520  Score: 53
    Period size: 19  Copynumber: 2.9  Consensus size: 19

       7453 TATCTAGTTG

                     *           
       7463 TTTATTTTGACATTTAATTTA
          1 TTTA-TTTGTCATTT-ATTTA

              *    * **        
       7484 TTGATTTTTTGTTTATTTA
          1 TTTATTTGTCATTTATTTA

                              
       7503 TTTATTTGTCATTTATTT
          1 TTTATTTGTCATTTATTT

       7521 TCATGCCTAA


Statistics
Matches: 28,  Mismatches: 9, Indels: 2
        0.72            0.23        0.05

Matches are distributed among these distances:
  19   19  0.68
  20    6  0.21
  21    3  0.11

ACGTcount: A:0.21, C:0.03, G:0.07, T:0.69


Consensus pattern (19 bp):   
TTTATTTGTCATTTATTTA
Done.