Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000081.1 Kokia drynarioides strain JFW-HI SEQ_110704, 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: 1993
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42


Found at i:362 original size:21 final size:20

Alignment explanation


    Indices: 336--400  Score: 78
    Period size: 21  Copynumber: 3.1  Consensus size: 20

        326 TTATCCCTTG

                      *           
        336 AATAATTATTATATAATTTTCT
          1 AATAATT-TTTTATAATTTT-T

                                 
        358 -ATAATTTTGTTATAATTTTT
          1 AATAATTTT-TTATAATTTTT

                                 
        378 AATAATTTTTTTATAATTTTT
          1 AATAA-TTTTTTATAATTTTT

              
        399 AA
          1 AA

        401 AAATCAATTA


Statistics
Matches: 39,  Mismatches: 1, Indels: 7
        0.83            0.02        0.15

Matches are distributed among these distances:
  20    3  0.08
  21   32  0.82
  22    4  0.10

ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60


Consensus pattern (20 bp):   
AATAATTTTTTATAATTTTT

Found at i:393 original size:32 final size:32

Alignment explanation


    Indices: 337--397  Score: 88
    Period size: 32  Copynumber: 1.9  Consensus size: 32

        327 TATCCCTTGA

                                            
        337 ATAATTATTATATAATTTTCTATAATTTTGTT
          1 ATAATTATTATATAATTTTCTATAATTTTGTT

                  *             *         
        369 ATAATTTTTA-ATAATTTTTTTATAATTTT
          1 ATAATTATTATATAA-TTTTCTATAATTTT

        398 TAAAAATCAA


Statistics
Matches: 26,  Mismatches: 2, Indels: 2
        0.87            0.07        0.07

Matches are distributed among these distances:
  31    4  0.15
  32   22  0.85

ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62


Consensus pattern (32 bp):   
ATAATTATTATATAATTTTCTATAATTTTGTT

Found at i:398 original size:11 final size:11

Alignment explanation


    Indices: 337--398  Score: 65
    Period size: 11  Copynumber: 5.8  Consensus size: 11

        327 TATCCCTTGA

                  *  * 
        337 ATAATTATTAT
          1 ATAATTTTTTT

                     * 
        348 ATAA-TTTTCT
          1 ATAATTTTTTT

                    *  
        358 ATAATTTTGTT
          1 ATAATTTTTTT

                      *
        369 ATAA-TTTTTA
          1 ATAATTTTTTT

                       
        379 ATAATTTTTTT
          1 ATAATTTTTTT

                     
        390 ATAATTTTT
          1 ATAATTTTT

        399 AAAAATCAAT


Statistics
Matches: 42,  Mismatches: 7, Indels: 4
        0.79            0.13        0.08

Matches are distributed among these distances:
  10   16  0.38
  11   26  0.62

ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63


Consensus pattern (11 bp):   
ATAATTTTTTT

Found at i:1204 original size:17 final size:17

Alignment explanation


    Indices: 1179--1213  Score: 52
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       1169 TTTACATATT

                *            
       1179 TTAAGTTACTTACTTGG
          1 TTAAATTACTTACTTGG

                        *    
       1196 TTAAATTACTTAGTTGG
          1 TTAAATTACTTACTTGG

             
       1213 T
          1 T

       1214 CGCCCATATT


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

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.26, C:0.09, G:0.17, T:0.49


Consensus pattern (17 bp):   
TTAAATTACTTACTTGG
Done.