Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004393.1 Kokia drynarioides strain JFW-HI SEQ_117769, 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: 3403
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36


Found at i:423 original size:6 final size:6

Alignment explanation


    Indices: 414--464  Score: 63
    Period size: 6  Copynumber: 8.8  Consensus size: 6

        404 AATTTTGAAG

                                                               *    
        414 TTAAAT TTAAAT TTAAGA- TT-AAT TTAAAT TTAAAT TTAAA- TCAAAT
          1 TTAAAT TTAAAT TTAA-AT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT

                 
        460 TTAAA
          1 TTAAA

        465 ATAAATTAAA


Statistics
Matches: 39,  Mismatches: 2, Indels: 8
        0.80            0.04        0.16

Matches are distributed among these distances:
   4    1  0.03
   5    7  0.18
   6   30  0.77
   7    1  0.03

ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45


Consensus pattern (6 bp):   
TTAAAT

Found at i:452 original size:17 final size:16

Alignment explanation


    Indices: 417--474  Score: 62
    Period size: 17  Copynumber: 3.5  Consensus size: 16

        407 TTTGAAGTTA

                             
        417 AATTTAAATTTAAGATT
          1 AATTTAAATTTAA-ATT

                             
        434 AATTTAAATTTAAATTT
          1 AATTTAAATTTAAA-TT

              * *         * 
        451 AAATCAAATTTAAAAT
          1 AATTTAAATTTAAATT

              *     
        467 AAATTAAA
          1 AATTTAAA

        475 AAAAGGCCCA


Statistics
Matches: 36,  Mismatches: 4, Indels: 3
        0.84            0.09        0.07

Matches are distributed among these distances:
  16    9  0.25
  17   27  0.75

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


Consensus pattern (16 bp):   
AATTTAAATTTAAATT

Found at i:460 original size:23 final size:23

Alignment explanation


    Indices: 414--464  Score: 77
    Period size: 23  Copynumber: 2.2  Consensus size: 23

        404 AATTTTGAAG

                               *   
        414 TTAAATTTAAATTTAAGATTAAT
          1 TTAAATTTAAATTTAAGATAAAT

                                    
        437 TTAAATTTAAATTTAA-ATCAAAT
          1 TTAAATTTAAATTTAAGAT-AAAT

                 
        460 TTAAA
          1 TTAAA

        465 ATAAATTAAA


Statistics
Matches: 26,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  22    2  0.08
  23   24  0.92

ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45


Consensus pattern (23 bp):   
TTAAATTTAAATTTAAGATAAAT

Found at i:470 original size:11 final size:11

Alignment explanation


    Indices: 421--475  Score: 51
    Period size: 11  Copynumber: 5.0  Consensus size: 11

        411 AAGTTAAATT

                     * 
        421 TAAATTTAAGA
          1 TAAATTTAAAA

             *         *
        432 TTAATTTAAATT
          1 TAAATTTAAA-A

                       
        444 TAAATTT-AAA
          1 TAAATTTAAAA

                        
        454 TCAAATTTAAAA
          1 T-AAATTTAAAA

                       
        466 TAAA-TTAAAA
          1 TAAATTTAAAA

        476 AAAGGCCCAG


Statistics
Matches: 36,  Mismatches: 5, Indels: 7
        0.75            0.10        0.15

Matches are distributed among these distances:
  10    7  0.19
  11   19  0.53
  12   10  0.28

ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40


Consensus pattern (11 bp):   
TAAATTTAAAA

Found at i:1150 original size:12 final size:12

Alignment explanation


    Indices: 1135--1160  Score: 52
    Period size: 12  Copynumber: 2.2  Consensus size: 12

       1125 ATACGCTTAA

                        
       1135 AAATATTAAAAC
          1 AAATATTAAAAC

                        
       1147 AAATATTAAAAC
          1 AAATATTAAAAC

              
       1159 AA
          1 AA

       1161 CAAACAAATT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   14  1.00

ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23


Consensus pattern (12 bp):   
AAATATTAAAAC

Found at i:1198 original size:41 final size:41

Alignment explanation


    Indices: 1137--1216  Score: 124
    Period size: 41  Copynumber: 2.0  Consensus size: 41

       1127 ACGCTTAAAA

                           *                         
       1137 ATATTAAAACAAATATTAAAACAACAAACAAATTAAAAACG
          1 ATATTAAAACAAATAGTAAAACAACAAACAAATTAAAAACG

                        * *                   *    
       1178 ATATTAAAACAATTCGTAAAACAACAAACAAATTGAAAA
          1 ATATTAAAACAAATAGTAAAACAACAAACAAATTAAAAA

       1217 TACAATAAGC


Statistics
Matches: 35,  Mismatches: 4, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  41   35  1.00

ACGTcount: A:0.64, C:0.12, G:0.04, T:0.20


Consensus pattern (41 bp):   
ATATTAAAACAAATAGTAAAACAACAAACAAATTAAAAACG
Done.