Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006334.1 Kokia drynarioides strain JFW-HI SEQ_120909, 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: 5641
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37


Found at i:1633 original size:31 final size:31

Alignment explanation


    Indices: 1596--1654  Score: 109
    Period size: 31  Copynumber: 1.9  Consensus size: 31

       1586 AACAACCTGG

                      *                    
       1596 TGACTTAAATGAAAACTTTTGAATAGTTTAA
          1 TGACTTAAATAAAAACTTTTGAATAGTTTAA

                                        
       1627 TGACTTAAATAAAAACTTTTGAATAGTT
          1 TGACTTAAATAAAAACTTTTGAATAGTT

       1655 CAATAACTAT


Statistics
Matches: 27,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  31   27  1.00

ACGTcount: A:0.42, C:0.07, G:0.12, T:0.39


Consensus pattern (31 bp):   
TGACTTAAATAAAAACTTTTGAATAGTTTAA

Found at i:3372 original size:17 final size:18

Alignment explanation


    Indices: 3318--3375  Score: 66
    Period size: 17  Copynumber: 3.3  Consensus size: 18

       3308 GGGGATTTGC

                 *            
       3318 AATTTCTTTTTATAATT-
          1 AATTTATTTTTATAATTA

                  *   *     * 
       3335 AATTTAATTTAATAATGA
          1 AATTTATTTTTATAATTA

                              
       3353 AATTTATTTTTA-AATTA
          1 AATTTATTTTTATAATTA

                  
       3370 AATTTA
          1 AATTTA

       3376 AGTAAATAAA


Statistics
Matches: 33,  Mismatches: 7, Indels: 2
        0.79            0.17        0.05

Matches are distributed among these distances:
  17   23  0.70
  18   10  0.30

ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55


Consensus pattern (18 bp):   
AATTTATTTTTATAATTA

Found at i:3384 original size:35 final size:35

Alignment explanation


    Indices: 3318--3384  Score: 91
    Period size: 35  Copynumber: 1.9  Consensus size: 35

       3308 GGGGATTTGC

                 *                  * *        
       3318 AATTTCTTTTTATAATTAATTTAATTTAATAATGA
          1 AATTTATTTTTATAATTAATTTAAGTAAATAATGA

                                             
       3353 AATTTATTTTTA-AATTAAATTTAAGTAAATAA
          1 AATTTATTTTTATAATT-AATTTAAGTAAATAA

       3385 ATATTTATTC


Statistics
Matches: 28,  Mismatches: 3, Indels: 2
        0.85            0.09        0.06

Matches are distributed among these distances:
  34    4  0.14
  35   24  0.86

ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51


Consensus pattern (35 bp):   
AATTTATTTTTATAATTAATTTAAGTAAATAATGA

Found at i:4251 original size:30 final size:31

Alignment explanation


    Indices: 4217--4283  Score: 84
    Period size: 31  Copynumber: 2.2  Consensus size: 31

       4207 TGATACTATG

                                *      *    
       4217 AATTTTAATT-TGGTGT-AATTATACACATGA
          1 AATTTTAATTATGGT-TCAAATATACAAATGA

                                    *      
       4247 AATTTTAATTATGGTTCAAATATATAAATGA
          1 AATTTTAATTATGGTTCAAATATACAAATGA

                  
       4278 AATTTT
          1 AATTTT

       4284 GATTGCGATT


Statistics
Matches: 32,  Mismatches: 3, Indels: 3
        0.84            0.08        0.08

Matches are distributed among these distances:
  30   11  0.34
  31   21  0.66

ACGTcount: A:0.40, C:0.04, G:0.10, T:0.45


Consensus pattern (31 bp):   
AATTTTAATTATGGTTCAAATATACAAATGA

Found at i:4296 original size:31 final size:31

Alignment explanation


    Indices: 4243--4301  Score: 73
    Period size: 31  Copynumber: 1.9  Consensus size: 31

       4233 AATTATACAC

                           * *             
       4243 ATGAAATTTTAATTATGGTTCAAATATATAA
          1 ATGAAATTTTAATTACGATTCAAATATATAA

                      *   *        *    
       4274 ATGAAATTTTGATTGCGATTCAACTATA
          1 ATGAAATTTTAATTACGATTCAAATATA

       4302 CACATTTAAA


Statistics
Matches: 23,  Mismatches: 5, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  31   23  1.00

ACGTcount: A:0.41, C:0.07, G:0.12, T:0.41


Consensus pattern (31 bp):   
ATGAAATTTTAATTACGATTCAAATATATAA
Done.