Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010013.1 Kokia drynarioides strain JFW-HI SEQ_124774, 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: 25204
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33


Found at i:3256 original size:2 final size:2

Alignment explanation


    Indices: 3249--3273  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       3239 CCCTTACCCT

                                                 
       3249 AC AC AC AC AC AC AC AC AC AC AC AC A
          1 AC AC AC AC AC AC AC AC AC AC AC AC A

       3274 TACCTATTGA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00


Consensus pattern (2 bp):   
AC

Found at i:5660 original size:2 final size:2

Alignment explanation


    Indices: 5653--5681  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

       5643 AAATGTAATT

                                                       
       5653 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       5682 TAATTCTCAG


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:15529 original size:10 final size:10

Alignment explanation


    Indices: 15514--15538  Score: 50
    Period size: 10  Copynumber: 2.5  Consensus size: 10

      15504 AGAGAGGGAG

                      
      15514 AAAAAAGAAA
          1 AAAAAAGAAA

                      
      15524 AAAAAAGAAA
          1 AAAAAAGAAA

                 
      15534 AAAAA
          1 AAAAA

      15539 GATCCTGGAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   15  1.00

ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00


Consensus pattern (10 bp):   
AAAAAAGAAA

Found at i:23340 original size:17 final size:17

Alignment explanation


    Indices: 23305--23343  Score: 53
    Period size: 17  Copynumber: 2.4  Consensus size: 17

      23295 TGTAACTCAC

                             
      23305 TAAAA-AAAATATTAAT
          1 TAAAATAAAATATTAAT

                     *     * 
      23321 TAAAATAAATTATTAGT
          1 TAAAATAAAATATTAAT

                  
      23338 TAAAAT
          1 TAAAAT

      23344 TTTTATTATA


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  16    5  0.25
  17   15  0.75

ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36


Consensus pattern (17 bp):   
TAAAATAAAATATTAAT

Found at i:23438 original size:146 final size:146

Alignment explanation


    Indices: 23265--23557  Score: 514
    Period size: 146  Copynumber: 2.0  Consensus size: 146

      23255 TTTATTAGCC

                        *                                                    
      23265 GTGTTTATTGTTTAAGCTTTGACTTGTTATTGTAACTCACTAAAAAAAATATTAATTAAAATAAA
          1 GTGTTTATTGTTCAAGCTTTGACTTGTTATTGTAACTCACTAAAAAAAATATTAATTAAAATAAA

                               *                 ***                         
      23330 TTATTAGTTAAAATTTTTATTATAAAATCTTTAAAAATTTTTTATTATAATTTAAATCATAAAAC
         66 TTATTAGTTAAAATTTTTAGTATAAAATCTTTAAAAAAAATTTATTATAATTTAAATCATAAAAC

                     *      
      23395 TTTATTAAATTTTTTT
        131 TTTATTAAAATTTTTT

                          *       *                                          
      23411 GTGTTTATTGTTCAGGCTTTGATTTGTTATTGTAACTCACTAAAAAAAATATTAATTAAAATAAA
          1 GTGTTTATTGTTCAAGCTTTGACTTGTTATTGTAACTCACTAAAAAAAATATTAATTAAAATAAA

                                                                             
      23476 TTATTAGTTAAAATTTTTAGTATAAAATCTTTAAAAAAAATTTATTATAATTTAAATCATAAAAC
         66 TTATTAGTTAAAATTTTTAGTATAAAATCTTTAAAAAAAATTTATTATAATTTAAATCATAAAAC

                            
      23541 TTTATTAAAATTTTTT
        131 TTTATTAAAATTTTTT

             
      23557 G
          1 G

      23558 GTTATTCAAT


Statistics
Matches: 139,  Mismatches: 8, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
 146  139  1.00

ACGTcount: A:0.41, C:0.05, G:0.06, T:0.47


Consensus pattern (146 bp):   
GTGTTTATTGTTCAAGCTTTGACTTGTTATTGTAACTCACTAAAAAAAATATTAATTAAAATAAA
TTATTAGTTAAAATTTTTAGTATAAAATCTTTAAAAAAAATTTATTATAATTTAAATCATAAAAC
TTTATTAAAATTTTTT

Found at i:23486 original size:17 final size:17

Alignment explanation


    Indices: 23451--23489  Score: 53
    Period size: 17  Copynumber: 2.4  Consensus size: 17

      23441 TGTAACTCAC

                             
      23451 TAAAA-AAAATATTAAT
          1 TAAAATAAAATATTAAT

                     *     * 
      23467 TAAAATAAATTATTAGT
          1 TAAAATAAAATATTAAT

                  
      23484 TAAAAT
          1 TAAAAT

      23490 TTTTAGTATA


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  16    5  0.25
  17   15  0.75

ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36


Consensus pattern (17 bp):   
TAAAATAAAATATTAAT

Done.