Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003288.1 Kokia drynarioides strain JFW-HI SEQ_115960, 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: 3676
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.33


Found at i:3287 original size:22 final size:22

Alignment explanation


    Indices: 3259--3430  Score: 101
    Period size: 22  Copynumber: 7.9  Consensus size: 22

       3249 AGCGCACTTA

                      *           
       3259 CTGTTCAGCAGTGTGTGTGCTT
          1 CTGTTCAGCACTGTGTGTGCTT

                                  *
       3281 CTGTTCAGCACTGTGTGTGCCTA
          1 CTGTTCAGCACTGTGTGTG-CTT

                                    
       3304 CTGAATT--GCACTGTGTGTGC-T
          1 CTG--TTCAGCACTGTGTGTGCTT

              *      *   * ***    
       3325 -TATT-A-CGCT-AGCACGCTT
          1 CTGTTCAGCACTGTGTGTGCTT

                  *                
       3343 ACTGTTTAGCACTGTGTGTGCTT
          1 -CTGTTCAGCACTGTGTGTGCTT

            *                     *
       3366 TTGTTCAGCACTGTGTGTGCCTA
          1 CTGTTCAGCACTGTGTGTG-CTT

                         *          
       3389 CTGAATT--GCACAGTGTGTGCTT
          1 CTG--TTCAGCACTGTGTGTGCTT

                          *     
       3411 CTGTTCAGCACTGTATGTGC
          1 CTGTTCAGCACTGTGTGTGC

       3431 CTACTGAATT


Statistics
Matches: 112,  Mismatches: 23, Indels: 30
        0.68            0.14        0.18

Matches are distributed among these distances:
  17    3  0.03
  18    6  0.05
  20    6  0.05
  21    1  0.01
  22   55  0.49
  23   37  0.33
  25    4  0.04

ACGTcount: A:0.15, C:0.22, G:0.26, T:0.38


Consensus pattern (22 bp):   
CTGTTCAGCACTGTGTGTGCTT

Found at i:3398 original size:85 final size:85

Alignment explanation


    Indices: 3255--3410  Score: 276
    Period size: 85  Copynumber: 1.8  Consensus size: 85

       3245 CGCAAGCGCA

                          *                                             *    
       3255 CTTACTGTTCAGCAGTGTGTGTGCTTCTGTTCAGCACTGTGTGTGCCTACTGAATTGCACTGTGT
          1 CTTACTGTTCAGCACTGTGTGTGCTTCTGTTCAGCACTGTGTGTGCCTACTGAATTGCACAGTGT

                                
       3320 GTGCTTATTACGCTAGCACG
         66 GTGCTTATTACGCTAGCACG

                     *                *                                      
       3340 CTTACTGTTTAGCACTGTGTGTGCTTTTGTTCAGCACTGTGTGTGCCTACTGAATTGCACAGTGT
          1 CTTACTGTTCAGCACTGTGTGTGCTTCTGTTCAGCACTGTGTGTGCCTACTGAATTGCACAGTGT

                  
       3405 GTGCTT
         66 GTGCTT

       3411 CTGTTCAGCA


Statistics
Matches: 67,  Mismatches: 4, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  85   67  1.00

ACGTcount: A:0.15, C:0.21, G:0.26, T:0.38


Consensus pattern (85 bp):   
CTTACTGTTCAGCACTGTGTGTGCTTCTGTTCAGCACTGTGTGTGCCTACTGAATTGCACAGTGT
GTGCTTATTACGCTAGCACG

Found at i:3404 original size:23 final size:23

Alignment explanation


    Indices: 3373--3459  Score: 65
    Period size: 23  Copynumber: 3.8  Consensus size: 23

       3363 CTTTTGTTCA

                *                  
       3373 GCACTGTGTGTGCCTACTGAATT
          1 GCACAGTGTGTGCCTACTGAATT

                           *       
       3396 GCACAGTGTGTG-CTTCTG--TT
          1 GCACAGTGTGTGCCTACTGAATT

                  *  *               
       3416 CAGCACTGTATGTGCCTACTGAATT
          1 --GCACAGTGTGTGCCTACTGAATT

            *        *          
       3441 ACACTA-TGCGTGCCTACTG
          1 GCAC-AGTGTGTGCCTACTG

       3460 TTTCCCCAGC


Statistics
Matches: 49,  Mismatches: 9, Indels: 12
        0.70            0.13        0.17

Matches are distributed among these distances:
  20    2  0.04
  22   15  0.31
  23   30  0.61
  25    2  0.04

ACGTcount: A:0.18, C:0.24, G:0.24, T:0.33


Consensus pattern (23 bp):   
GCACAGTGTGTGCCTACTGAATT

Found at i:3430 original size:45 final size:45

Alignment explanation


    Indices: 3270--3445  Score: 186
    Period size: 45  Copynumber: 4.0  Consensus size: 45

       3260 TGTTCAGCAG

                                     *                   
       3270 TGTGTGTGCTTCTGTTCAGCACTGTGTGTGCCTACTGAATTGCAC
          1 TGTGTGTGCTTCTGTTCAGCACTGTATGTGCCTACTGAATTGCAC

                         *      *    *   *  *      *       
       3315 TGTGTGTGC-T-TATT-A-CGCTAGCA--CGCTTACTG-TTTAGCAC
          1 TGTGTGTGCTTCTGTTCAGCACT-GTATGTGCCTACTGAATT-GCAC

                       *             *                   
       3355 TGTGTGTGCTTTTGTTCAGCACTGTGTGTGCCTACTGAATTGCAC
          1 TGTGTGTGCTTCTGTTCAGCACTGTATGTGCCTACTGAATTGCAC

            *                                        *   
       3400 AGTGTGTGCTTCTGTTCAGCACTGTATGTGCCTACTGAATTACAC
          1 TGTGTGTGCTTCTGTTCAGCACTGTATGTGCCTACTGAATTGCAC

             
       3445 T
          1 T

       3446 ATGCGTGCCT


Statistics
Matches: 103,  Mismatches: 19, Indels: 18
        0.74            0.14        0.13

Matches are distributed among these distances:
  39    2  0.02
  40   20  0.19
  41    4  0.04
  42    5  0.05
  43    5  0.05
  44    4  0.04
  45   61  0.59
  46    2  0.02

ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38


Consensus pattern (45 bp):   
TGTGTGTGCTTCTGTTCAGCACTGTATGTGCCTACTGAATTGCAC
Done.