Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006011.1 Kokia drynarioides strain JFW-HI SEQ_120449, 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: 14776
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35


Found at i:1354 original size:20 final size:21

Alignment explanation


    Indices: 1301--1354  Score: 58
    Period size: 20  Copynumber: 2.6  Consensus size: 21

       1291 TCACTGCTCA

                *          *     
       1301 AAATAAATCAAATATTAAATT
          1 AAATTAATCAAATATCAAATT

                    *             
       1322 AAA-TAATTAAA-ATACAAATT
          1 AAATTAATCAAATAT-CAAATT

                         
       1342 AAATTAATCAAAT
          1 AAATTAATCAAAT

       1355 TTAATTTAAT


Statistics
Matches: 26,  Mismatches: 4, Indels: 5
        0.74            0.11        0.14

Matches are distributed among these distances:
  19    2  0.08
  20   14  0.54
  21   10  0.38

ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31


Consensus pattern (21 bp):   
AAATTAATCAAATATCAAATT

Found at i:4653 original size:16 final size:17

Alignment explanation


    Indices: 4632--4668  Score: 51
    Period size: 16  Copynumber: 2.2  Consensus size: 17

       4622 TTCAAAAACA

                              
       4632 TTTTATTT-AATAA-TAT
          1 TTTTATTTCAA-AAGTAT

                             
       4648 TTTTATTTCAAAAGTAT
          1 TTTTATTTCAAAAGTAT

                
       4665 TTTT
          1 TTTT

       4669 TTATCTAAAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  16   10  0.53
  17    9  0.47

ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62


Consensus pattern (17 bp):   
TTTTATTTCAAAAGTAT

Found at i:10940 original size:24 final size:24

Alignment explanation


    Indices: 10908--10953  Score: 74
    Period size: 24  Copynumber: 1.9  Consensus size: 24

      10898 TATCAATCCT

                                    
      10908 CAATTCAATCCGAAAATGAGTTAA
          1 CAATTCAATCCGAAAATGAGTTAA

                         * *      
      10932 CAATTCAATCCGATACTGAGTT
          1 CAATTCAATCCGAAAATGAGTT

      10954 GAGCAATTAA


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  24   20  1.00

ACGTcount: A:0.39, C:0.20, G:0.13, T:0.28


Consensus pattern (24 bp):   
CAATTCAATCCGAAAATGAGTTAA

Found at i:13539 original size:2 final size:2

Alignment explanation


    Indices: 13532--13578  Score: 78
    Period size: 2  Copynumber: 24.0  Consensus size: 2

      13522 AAGTACCCAA

                                                                     *    
      13532 AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT TT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                    
      13573 AT AT AT
          1 AT AT AT

      13579 GTATTGATGT


Statistics
Matches: 42,  Mismatches: 2, Indels: 2
        0.91            0.04        0.04

Matches are distributed among these distances:
   1    1  0.02
   2   41  0.98

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (2 bp):   
AT

Done.